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>
6 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
7 ;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
8 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
10 ;;; This file is part of GNU Guix.
12 ;;; GNU Guix is free software; you can redistribute it and/or modify it
13 ;;; under the terms of the GNU General Public License as published by
14 ;;; the Free Software Foundation; either version 3 of the License, or (at
15 ;;; your option) any later version.
17 ;;; GNU Guix is distributed in the hope that it will be useful, but
18 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
19 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
20 ;;; GNU General Public License for more details.
22 ;;; You should have received a copy of the GNU General Public License
23 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
25 (define-module (gnu packages bioconductor)
26 #:use-module ((guix licenses) #:prefix license:)
27 #:use-module (guix packages)
28 #:use-module (guix download)
29 #:use-module (guix git-download)
30 #:use-module (guix build-system r)
31 #:use-module (gnu packages)
32 #:use-module (gnu packages base)
33 #:use-module (gnu packages bioinformatics)
34 #:use-module (gnu packages cran)
35 #:use-module (gnu packages compression)
36 #:use-module (gnu packages gcc)
37 #:use-module (gnu packages graph)
38 #:use-module (gnu packages graphviz)
39 #:use-module (gnu packages haskell-xyz)
40 #:use-module (gnu packages image)
41 #:use-module (gnu packages maths)
42 #:use-module (gnu packages netpbm)
43 #:use-module (gnu packages perl)
44 #:use-module (gnu packages pkg-config)
45 #:use-module (gnu packages statistics)
46 #:use-module (gnu packages web)
47 #:use-module (gnu packages xml)
48 #:use-module (srfi srfi-1))
53 (define-public r-reactome-db
55 (name "r-reactome-db")
60 (uri (bioconductor-uri "reactome.db" version 'annotation))
63 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
64 (properties `((upstream-name . "reactome.db")))
65 (build-system r-build-system)
67 `(("r-annotationdbi" ,r-annotationdbi)))
68 (home-page "https://bioconductor.org/packages/reactome.db/")
69 (synopsis "Annotation maps for reactome")
71 "This package provides a set of annotation maps for the REACTOME
72 database, assembled using data from REACTOME.")
73 (license license:cc-by4.0)))
75 (define-public r-bsgenome-celegans-ucsc-ce6
77 (name "r-bsgenome-celegans-ucsc-ce6")
81 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
85 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
87 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
88 (build-system r-build-system)
90 `(("r-bsgenome" ,r-bsgenome)))
92 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
93 (synopsis "Full genome sequences for Worm")
95 "This package provides full genome sequences for Caenorhabditis
96 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
98 (license license:artistic2.0)))
100 (define-public r-bsgenome-celegans-ucsc-ce10
102 (name "r-bsgenome-celegans-ucsc-ce10")
106 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
107 version 'annotation))
110 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
112 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
113 (build-system r-build-system)
115 `(("r-bsgenome" ,r-bsgenome)))
117 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
118 (synopsis "Full genome sequences for Worm")
120 "This package provides full genome sequences for Caenorhabditis
121 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
123 (license license:artistic2.0)))
125 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
127 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
131 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
132 version 'annotation))
135 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
137 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
138 (build-system r-build-system)
140 `(("r-bsgenome" ,r-bsgenome)))
142 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
143 (synopsis "Full genome sequences for Fly")
145 "This package provides full genome sequences for Drosophila
146 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
148 (license license:artistic2.0)))
150 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
152 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
156 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
157 version 'annotation))
160 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
162 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
163 (build-system r-build-system)
165 `(("r-bsgenome" ,r-bsgenome)))
167 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
168 (synopsis "Full genome sequences for Fly")
170 "This package provides full genome sequences for Drosophila
171 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
172 Biostrings objects.")
173 (license license:artistic2.0)))
175 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
177 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
181 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
182 version 'annotation))
185 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
187 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
188 (build-system r-build-system)
190 `(("r-bsgenome" ,r-bsgenome)
191 ("r-bsgenome-dmelanogaster-ucsc-dm3"
192 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
193 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
194 (synopsis "Full masked genome sequences for Fly")
196 "This package provides full masked genome sequences for Drosophila
197 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
198 Biostrings objects. The sequences are the same as in
199 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
200 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
201 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
202 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
203 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
204 (license license:artistic2.0)))
206 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
208 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
212 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
213 version 'annotation))
216 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
218 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
219 (build-system r-build-system)
221 `(("r-bsgenome" ,r-bsgenome)))
223 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
224 (synopsis "Full genome sequences for Homo sapiens")
226 "This package provides full genome sequences for Homo sapiens from
227 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
228 (license license:artistic2.0)))
230 (define-public r-bsgenome-hsapiens-ncbi-grch38
232 (name "r-bsgenome-hsapiens-ncbi-grch38")
237 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
238 version 'annotation))
241 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
242 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
243 (build-system r-build-system)
244 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
246 "https://bioconductor.org/packages/release/data/annotation/html/\
247 BSgenome.Hsapiens.NCBI.GRCh38.html")
248 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
250 "This package provides full genome sequences for Homo sapiens (Human) as
251 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
252 (license license:artistic2.0)))
254 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
256 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
260 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
261 version 'annotation))
264 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
266 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
267 (build-system r-build-system)
269 `(("r-bsgenome" ,r-bsgenome)
270 ("r-bsgenome-hsapiens-ucsc-hg19"
271 ,r-bsgenome-hsapiens-ucsc-hg19)))
272 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
273 (synopsis "Full masked genome sequences for Homo sapiens")
275 "This package provides full genome sequences for Homo sapiens (Human) as
276 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
277 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
278 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
279 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
280 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
281 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
283 (license license:artistic2.0)))
285 (define-public r-bsgenome-mmusculus-ucsc-mm9
287 (name "r-bsgenome-mmusculus-ucsc-mm9")
291 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
292 version 'annotation))
295 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
297 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
298 (build-system r-build-system)
300 `(("r-bsgenome" ,r-bsgenome)))
302 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
303 (synopsis "Full genome sequences for Mouse")
305 "This package provides full genome sequences for Mus musculus (Mouse) as
306 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
307 (license license:artistic2.0)))
309 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
311 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
315 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
316 version 'annotation))
319 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
321 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
322 (build-system r-build-system)
324 `(("r-bsgenome" ,r-bsgenome)
325 ("r-bsgenome-mmusculus-ucsc-mm9"
326 ,r-bsgenome-mmusculus-ucsc-mm9)))
327 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
328 (synopsis "Full masked genome sequences for Mouse")
330 "This package provides full genome sequences for Mus musculus (Mouse) as
331 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
332 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
333 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
334 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
335 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
336 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
338 (license license:artistic2.0)))
340 (define-public r-bsgenome-mmusculus-ucsc-mm10
342 (name "r-bsgenome-mmusculus-ucsc-mm10")
346 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
347 version 'annotation))
350 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
353 (build-system r-build-system)
355 `(("r-bsgenome" ,r-bsgenome)))
357 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
358 (synopsis "Full genome sequences for Mouse")
360 "This package provides full genome sequences for Mus
361 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
362 in Biostrings objects.")
363 (license license:artistic2.0)))
365 (define-public r-org-ce-eg-db
367 (name "r-org-ce-eg-db")
371 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
374 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
376 `((upstream-name . "org.Ce.eg.db")))
377 (build-system r-build-system)
379 `(("r-annotationdbi" ,r-annotationdbi)))
380 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
381 (synopsis "Genome wide annotation for Worm")
383 "This package provides mappings from Entrez gene identifiers to various
384 annotations for the genome of the model worm Caenorhabditis elegans.")
385 (license license:artistic2.0)))
387 (define-public r-org-dm-eg-db
389 (name "r-org-dm-eg-db")
393 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
396 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
398 `((upstream-name . "org.Dm.eg.db")))
399 (build-system r-build-system)
401 `(("r-annotationdbi" ,r-annotationdbi)))
402 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
403 (synopsis "Genome wide annotation for Fly")
405 "This package provides mappings from Entrez gene identifiers to various
406 annotations for the genome of the model fruit fly Drosophila melanogaster.")
407 (license license:artistic2.0)))
409 (define-public r-org-dr-eg-db
411 (name "r-org-dr-eg-db")
415 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
418 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
420 `((upstream-name . "org.Dr.eg.db")))
421 (build-system r-build-system)
423 `(("r-annotationdbi" ,r-annotationdbi)))
424 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
425 (synopsis "Annotation for Zebrafish")
427 "This package provides genome wide annotations for Zebrafish, primarily
428 based on mapping using Entrez Gene identifiers.")
429 (license license:artistic2.0)))
431 (define-public r-org-hs-eg-db
433 (name "r-org-hs-eg-db")
437 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
440 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
442 `((upstream-name . "org.Hs.eg.db")))
443 (build-system r-build-system)
445 `(("r-annotationdbi" ,r-annotationdbi)))
446 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
447 (synopsis "Genome wide annotation for Human")
449 "This package contains genome-wide annotations for Human, primarily based
450 on mapping using Entrez Gene identifiers.")
451 (license license:artistic2.0)))
453 (define-public r-org-mm-eg-db
455 (name "r-org-mm-eg-db")
459 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
462 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
464 `((upstream-name . "org.Mm.eg.db")))
465 (build-system r-build-system)
467 `(("r-annotationdbi" ,r-annotationdbi)))
468 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
469 (synopsis "Genome wide annotation for Mouse")
471 "This package provides mappings from Entrez gene identifiers to various
472 annotations for the genome of the model mouse Mus musculus.")
473 (license license:artistic2.0)))
475 (define-public r-bsgenome-hsapiens-ucsc-hg19
477 (name "r-bsgenome-hsapiens-ucsc-hg19")
481 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
482 version 'annotation))
485 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
487 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
488 (build-system r-build-system)
490 `(("r-bsgenome" ,r-bsgenome)))
492 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
493 (synopsis "Full genome sequences for Homo sapiens")
495 "This package provides full genome sequences for Homo sapiens as provided
496 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
497 (license license:artistic2.0)))
499 (define-public r-bsgenome-hsapiens-ucsc-hg38
501 (name "r-bsgenome-hsapiens-ucsc-hg38")
505 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
506 version 'annotation))
509 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
511 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
512 (build-system r-build-system)
514 `(("r-bsgenome" ,r-bsgenome)))
516 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
517 (synopsis "Full genome sequences for Homo sapiens")
519 "This package provides full genome sequences for Homo sapiens (Human)
520 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
521 (license license:artistic2.0)))
523 (define-public r-ensdb-hsapiens-v75
525 (name "r-ensdb-hsapiens-v75")
530 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
533 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
535 `((upstream-name . "EnsDb.Hsapiens.v75")))
536 (build-system r-build-system)
538 `(("r-ensembldb" ,r-ensembldb)))
539 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
540 (synopsis "Ensembl based annotation package")
542 "This package exposes an annotation database generated from Ensembl.")
543 (license license:artistic2.0)))
545 (define-public r-genelendatabase
547 (name "r-genelendatabase")
552 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
555 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
557 `((upstream-name . "geneLenDataBase")))
558 (build-system r-build-system)
560 `(("r-rtracklayer" ,r-rtracklayer)
561 ("r-genomicfeatures" ,r-genomicfeatures)))
562 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
563 (synopsis "Lengths of mRNA transcripts for a number of genomes")
565 "This package provides the lengths of mRNA transcripts for a number of
566 genomes and gene ID formats, largely based on the UCSC table browser.")
567 (license license:lgpl2.0+)))
569 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
571 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
575 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
576 version 'annotation))
579 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
581 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
582 (build-system r-build-system)
584 `(("r-genomicfeatures" ,r-genomicfeatures)))
586 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
587 (synopsis "Annotation package for human genome in TxDb format")
589 "This package provides an annotation database of Homo sapiens genome
590 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
591 track. The database is exposed as a @code{TxDb} object.")
592 (license license:artistic2.0)))
594 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
596 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
600 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
601 version 'annotation))
604 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
606 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
607 (build-system r-build-system)
609 `(("r-genomicfeatures" ,r-genomicfeatures)))
611 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
612 (synopsis "Annotation package for human genome in TxDb format")
614 "This package provides an annotation database of Homo sapiens genome
615 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
616 track. The database is exposed as a @code{TxDb} object.")
617 (license license:artistic2.0)))
619 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
621 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
625 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
626 version 'annotation))
629 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
631 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
632 (build-system r-build-system)
634 `(("r-genomicfeatures" ,r-genomicfeatures)
635 ("r-annotationdbi" ,r-annotationdbi)))
637 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
638 (synopsis "Annotation package for mouse genome in TxDb format")
640 "This package provides an annotation database of Mouse genome data. It
641 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
642 database is exposed as a @code{TxDb} object.")
643 (license license:artistic2.0)))
645 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
647 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
651 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
652 version 'annotation))
655 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
657 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
658 (build-system r-build-system)
660 `(("r-bsgenome" ,r-bsgenome)
661 ("r-genomicfeatures" ,r-genomicfeatures)
662 ("r-annotationdbi" ,r-annotationdbi)))
664 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
665 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
667 "This package loads a TxDb object, which is an R interface to
668 prefabricated databases contained in this package. This package provides
669 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
670 based on the knownGene track.")
671 (license license:artistic2.0)))
673 (define-public r-txdb-celegans-ucsc-ce6-ensgene
675 (name "r-txdb-celegans-ucsc-ce6-ensgene")
680 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
681 version 'annotation))
684 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
686 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
687 (build-system r-build-system)
689 `(("r-annotationdbi" ,r-annotationdbi)
690 ("r-genomicfeatures" ,r-genomicfeatures)))
691 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
692 (synopsis "Annotation package for C elegans TxDb objects")
694 "This package exposes a C elegans annotation database generated from UCSC
695 by exposing these as TxDb objects.")
696 (license license:artistic2.0)))
698 (define-public r-fdb-infiniummethylation-hg19
700 (name "r-fdb-infiniummethylation-hg19")
704 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
705 version 'annotation))
708 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
710 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
711 (build-system r-build-system)
713 `(("r-biostrings" ,r-biostrings)
714 ("r-genomicfeatures" ,r-genomicfeatures)
715 ("r-annotationdbi" ,r-annotationdbi)
716 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
717 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
718 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
719 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
721 "This is an annotation package for Illumina Infinium DNA methylation
722 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
724 (license license:artistic2.0)))
726 (define-public r-illuminahumanmethylationepicmanifest
728 (name "r-illuminahumanmethylationepicmanifest")
732 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
733 version 'annotation))
736 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
738 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
739 (build-system r-build-system)
741 `(("r-minfi" ,r-minfi)))
742 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
743 (synopsis "Manifest for Illumina's EPIC methylation arrays")
745 "This is a manifest package for Illumina's EPIC methylation arrays.")
746 (license license:artistic2.0)))
748 (define-public r-ideoviz
754 (uri (bioconductor-uri "IdeoViz" version))
757 "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50"))))
758 (build-system r-build-system)
760 `(("r-biobase" ,r-biobase)
761 ("r-iranges" ,r-iranges)
762 ("r-genomicranges" ,r-genomicranges)
763 ("r-rcolorbrewer" ,r-rcolorbrewer)
764 ("r-rtracklayer" ,r-rtracklayer)
765 ("r-genomeinfodb" ,r-genomeinfodb)))
766 (home-page "https://bioconductor.org/packages/IdeoViz/")
767 (synopsis "Plots data along a chromosomal ideogram")
768 (description "This package provides functions to plot data associated with
769 arbitrary genomic intervals along chromosomal ideogram.")
770 (license license:gpl2)))
772 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
773 ;; from Bioconductor.
774 (define-public r-deconstructsigs
776 (name "r-deconstructsigs")
780 (uri (cran-uri "deconstructSigs" version))
783 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
785 `((upstream-name . "deconstructSigs")))
786 (build-system r-build-system)
788 `(("r-bsgenome" ,r-bsgenome)
789 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
790 ("r-genomeinfodb" ,r-genomeinfodb)
791 ("r-reshape2" ,r-reshape2)))
792 (home-page "https://github.com/raerose01/deconstructSigs")
793 (synopsis "Identifies signatures present in a tumor sample")
794 (description "This package takes sample information in the form of the
795 fraction of mutations in each of 96 trinucleotide contexts and identifies
796 the weighted combination of published signatures that, when summed, most
797 closely reconstructs the mutational profile.")
798 (license license:gpl2+)))
800 ;; This is a CRAN package, but it depends on Bioconductor packages.
808 (uri (cran-uri "NMF" version))
811 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
812 (properties `((upstream-name . "NMF")))
813 (build-system r-build-system)
815 `(("r-cluster" ,r-cluster)
816 ("r-biobase" ,r-biobase)
817 ("r-biocmanager" ,r-biocmanager)
818 ("r-bigmemory" ,r-bigmemory) ; suggested
819 ("r-synchronicity" ,r-synchronicity) ; suggested
820 ("r-colorspace" ,r-colorspace)
821 ("r-digest" ,r-digest)
822 ("r-doparallel" ,r-doparallel)
823 ("r-foreach" ,r-foreach)
824 ("r-ggplot2" ,r-ggplot2)
825 ("r-gridbase" ,r-gridbase)
826 ("r-pkgmaker" ,r-pkgmaker)
827 ("r-rcolorbrewer" ,r-rcolorbrewer)
828 ("r-registry" ,r-registry)
829 ("r-reshape2" ,r-reshape2)
830 ("r-rngtools" ,r-rngtools)
831 ("r-stringr" ,r-stringr)))
833 `(("r-knitr" ,r-knitr)))
834 (home-page "http://renozao.github.io/NMF")
835 (synopsis "Algorithms and framework for nonnegative matrix factorization")
837 "This package provides a framework to perform Non-negative Matrix
838 Factorization (NMF). The package implements a set of already published
839 algorithms and seeding methods, and provides a framework to test, develop and
840 plug new or custom algorithms. Most of the built-in algorithms have been
841 optimized in C++, and the main interface function provides an easy way of
842 performing parallel computations on multicore machines.")
843 (license license:gpl2+)))
845 (define-public r-do-db
851 (uri (bioconductor-uri "DO.db" version 'annotation))
854 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
856 `((upstream-name . "DO.db")))
857 (build-system r-build-system)
859 `(("r-annotationdbi" ,r-annotationdbi)))
860 (home-page "https://www.bioconductor.org/packages/DO.db/")
861 (synopsis "Annotation maps describing the entire Disease Ontology")
863 "This package provides a set of annotation maps describing the entire
865 (license license:artistic2.0)))
867 (define-public r-pasilla
874 "http://bioconductor.org/packages/release/data/experiment"
875 "/src/contrib/pasilla_" version ".tar.gz"))
878 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
879 (build-system r-build-system)
881 `(("r-biocstyle" ,r-biocstyle)
882 ("r-dexseq" ,r-dexseq)
884 ("r-rmarkdown" ,r-rmarkdown)))
885 (home-page "https://www.bioconductor.org/packages/pasilla/")
886 (synopsis "Data package with per-exon and per-gene read counts")
887 (description "This package provides per-exon and per-gene read counts
888 computed for selected genes from RNA-seq data that were presented in the
889 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
890 by Brooks et al., Genome Research 2011.")
891 (license license:lgpl2.1+)))
893 (define-public r-pfam-db
900 (uri (bioconductor-uri "PFAM.db" version 'annotation))
903 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
904 (properties `((upstream-name . "PFAM.db")))
905 (build-system r-build-system)
907 `(("r-annotationdbi" ,r-annotationdbi)))
908 (home-page "https://bioconductor.org/packages/PFAM.db")
909 (synopsis "Set of protein ID mappings for PFAM")
911 "This package provides a set of protein ID mappings for PFAM, assembled
912 using data from public repositories.")
913 (license license:artistic2.0)))
915 (define-public r-phastcons100way-ucsc-hg19
917 (name "r-phastcons100way-ucsc-hg19")
922 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
923 version 'annotation))
926 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
928 `((upstream-name . "phastCons100way.UCSC.hg19")))
929 (build-system r-build-system)
931 `(("r-bsgenome" ,r-bsgenome)
932 ("r-genomeinfodb" ,r-genomeinfodb)
933 ("r-genomicranges" ,r-genomicranges)
934 ("r-genomicscores" ,r-genomicscores)
935 ("r-iranges" ,r-iranges)
936 ("r-s4vectors" ,r-s4vectors)))
937 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
938 (synopsis "UCSC phastCons conservation scores for hg19")
940 "This package provides UCSC phastCons conservation scores for the human
941 genome (hg19) calculated from multiple alignments with other 99 vertebrate
943 (license license:artistic2.0)))
948 (define-public r-abadata
954 (uri (bioconductor-uri "ABAData" version 'experiment))
957 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
959 `((upstream-name . "ABAData")))
960 (build-system r-build-system)
962 `(("r-annotationdbi" ,r-annotationdbi)))
963 (home-page "https://www.bioconductor.org/packages/ABAData/")
964 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
966 "This package provides the data for the gene expression enrichment
967 analysis conducted in the package ABAEnrichment. The package includes three
968 datasets which are derived from the Allen Brain Atlas:
971 @item Gene expression data from Human Brain (adults) averaged across donors,
972 @item Gene expression data from the Developing Human Brain pooled into five
973 age categories and averaged across donors, and
974 @item a developmental effect score based on the Developing Human Brain
978 All datasets are restricted to protein coding genes.")
979 (license license:gpl2+)))
981 (define-public r-arrmdata
987 (uri (bioconductor-uri "ARRmData" version 'experiment))
990 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
992 `((upstream-name . "ARRmData")))
993 (build-system r-build-system)
994 (home-page "https://www.bioconductor.org/packages/ARRmData/")
995 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
997 "This package provides raw beta values from 36 samples across 3 groups
998 from Illumina 450k methylation arrays.")
999 (license license:artistic2.0)))
1001 (define-public r-hsmmsinglecell
1003 (name "r-hsmmsinglecell")
1007 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1010 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1012 `((upstream-name . "HSMMSingleCell")))
1013 (build-system r-build-system)
1014 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1015 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1017 "Skeletal myoblasts undergo a well-characterized sequence of
1018 morphological and transcriptional changes during differentiation. In this
1019 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1020 under high mitogen conditions (GM) and then differentiated by switching to
1021 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1022 hundred cells taken over a time-course of serum-induced differentiation.
1023 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1024 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1025 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1026 which were then sequenced to a depth of ~4 million reads per library,
1027 resulting in a complete gene expression profile for each cell.")
1028 (license license:artistic2.0)))
1030 (define-public r-all
1036 (uri (bioconductor-uri "ALL" version 'experiment))
1039 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1040 (properties `((upstream-name . "ALL")))
1041 (build-system r-build-system)
1043 `(("r-biobase" ,r-biobase)))
1044 (home-page "https://bioconductor.org/packages/ALL")
1045 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1047 "The data consist of microarrays from 128 different individuals with
1048 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1049 are available. The data have been normalized (using rma) and it is the
1050 jointly normalized data that are available here. The data are presented in
1051 the form of an @code{exprSet} object.")
1052 (license license:artistic2.0)))
1054 (define-public r-affydata
1061 (uri (bioconductor-uri "affydata" version 'experiment))
1064 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1065 (properties `((upstream-name . "affydata")))
1066 (build-system r-build-system)
1068 `(("r-affy" ,r-affy)))
1069 (home-page "https://bioconductor.org/packages/affydata/")
1070 (synopsis "Affymetrix data for demonstration purposes")
1072 "This package provides example datasets that represent 'real world
1073 examples' of Affymetrix data, unlike the artificial examples included in the
1074 package @code{affy}.")
1075 (license license:gpl2+)))
1077 (define-public r-coverageview
1079 (name "r-coverageview")
1083 (uri (bioconductor-uri "CoverageView" version))
1086 "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj"))))
1087 (build-system r-build-system)
1089 `(("r-s4vectors" ,r-s4vectors)
1090 ("r-iranges" ,r-iranges)
1091 ("r-genomicranges" ,r-genomicranges)
1092 ("r-genomicalignments" ,r-genomicalignments)
1093 ("r-rtracklayer" ,r-rtracklayer)
1094 ("r-rsamtools" ,r-rsamtools)))
1095 (home-page "https://bioconductor.org/packages/CoverageView/")
1096 (synopsis "Coverage visualization package for R")
1097 (description "This package provides a framework for the visualization of
1098 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1099 be also used for genome-wide nucleosome positioning experiments or other
1100 experiment types where it is important to have a framework in order to inspect
1101 how the coverage distributed across the genome.")
1102 (license license:artistic2.0)))
1104 (define-public r-cummerbund
1106 (name "r-cummerbund")
1110 (uri (bioconductor-uri "cummeRbund" version))
1113 "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc"))))
1114 (build-system r-build-system)
1116 `(("r-biobase" ,r-biobase)
1117 ("r-biocgenerics" ,r-biocgenerics)
1118 ("r-fastcluster", r-fastcluster)
1119 ("r-ggplot2" ,r-ggplot2)
1122 ("r-reshape2" ,r-reshape2)
1123 ("r-rsqlite" ,r-rsqlite)
1124 ("r-rtracklayer" ,r-rtracklayer)
1125 ("r-s4vectors" ,r-s4vectors)))
1126 (home-page "https://bioconductor.org/packages/cummeRbund/")
1127 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1128 (description "This package allows for persistent storage, access,
1129 exploration, and manipulation of Cufflinks high-throughput sequencing
1130 data. In addition, provides numerous plotting functions for commonly
1131 used visualizations.")
1132 (license license:artistic2.0)))
1134 (define-public r-curatedtcgadata
1136 (name "r-curatedtcgadata")
1141 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1144 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1146 `((upstream-name . "curatedTCGAData")))
1147 (build-system r-build-system)
1149 `(("r-annotationhub" ,r-annotationhub)
1150 ("r-experimenthub" ,r-experimenthub)
1151 ("r-hdf5array" ,r-hdf5array)
1152 ("r-multiassayexperiment" ,r-multiassayexperiment)
1153 ("r-s4vectors" ,r-s4vectors)
1154 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1155 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1156 (synopsis "Curated data from The Cancer Genome Atlas")
1158 "This package provides publicly available data from The Cancer Genome
1159 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1160 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1161 number, mutation, microRNA, protein, and others) with clinical / pathological
1162 data. It also links assay barcodes with patient identifiers, enabling
1163 harmonized subsetting of rows (features) and columns (patients / samples)
1164 across the entire multi-'omics experiment.")
1165 (license license:artistic2.0)))
1170 (define-public r-biocversion
1172 (name "r-biocversion")
1177 (uri (bioconductor-uri "BiocVersion" version))
1180 "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz"))))
1181 (properties `((upstream-name . "BiocVersion")))
1182 (build-system r-build-system)
1183 (home-page "https://bioconductor.org/packages/BiocVersion/")
1184 (synopsis "Set the appropriate version of Bioconductor packages")
1186 "This package provides repository information for the appropriate version
1188 (license license:artistic2.0)))
1190 (define-public r-biocgenerics
1192 (name "r-biocgenerics")
1196 (uri (bioconductor-uri "BiocGenerics" version))
1199 "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk"))))
1201 `((upstream-name . "BiocGenerics")))
1202 (build-system r-build-system)
1203 (home-page "https://bioconductor.org/packages/BiocGenerics")
1204 (synopsis "S4 generic functions for Bioconductor")
1206 "This package provides S4 generic functions needed by many Bioconductor
1208 (license license:artistic2.0)))
1210 (define-public r-affycomp
1217 (uri (bioconductor-uri "affycomp" version))
1220 "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0"))))
1221 (properties `((upstream-name . "affycomp")))
1222 (build-system r-build-system)
1223 (propagated-inputs `(("r-biobase" ,r-biobase)))
1224 (home-page "https://bioconductor.org/packages/affycomp/")
1225 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1227 "The package contains functions that can be used to compare expression
1228 measures for Affymetrix Oligonucleotide Arrays.")
1229 (license license:gpl2+)))
1231 (define-public r-affycompatible
1233 (name "r-affycompatible")
1238 (uri (bioconductor-uri "AffyCompatible" version))
1241 "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd"))))
1243 `((upstream-name . "AffyCompatible")))
1244 (build-system r-build-system)
1246 `(("r-biostrings" ,r-biostrings)
1247 ("r-rcurl" ,r-rcurl)
1249 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1250 (synopsis "Work with Affymetrix GeneChip files")
1252 "This package provides an interface to Affymetrix chip annotation and
1253 sample attribute files. The package allows an easy way for users to download
1254 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1255 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1256 Command Console} (AGCC)-compatible sample annotation files.")
1257 (license license:artistic2.0)))
1259 (define-public r-affycontam
1261 (name "r-affycontam")
1266 (uri (bioconductor-uri "affyContam" version))
1269 "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i"))))
1270 (properties `((upstream-name . "affyContam")))
1271 (build-system r-build-system)
1273 `(("r-affy" ,r-affy)
1274 ("r-affydata" ,r-affydata)
1275 ("r-biobase" ,r-biobase)))
1276 (home-page "https://bioconductor.org/packages/affyContam/")
1277 (synopsis "Structured corruption of Affymetrix CEL file data")
1279 "Microarray quality assessment is a major concern of microarray analysts.
1280 This package provides some simple approaches to in silico creation of quality
1281 problems in CEL-level data to help evaluate performance of quality metrics.")
1282 (license license:artistic2.0)))
1284 (define-public r-affycoretools
1286 (name "r-affycoretools")
1291 (uri (bioconductor-uri "affycoretools" version))
1294 "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s"))))
1295 (properties `((upstream-name . "affycoretools")))
1296 (build-system r-build-system)
1298 `(("r-affy" ,r-affy)
1299 ("r-annotationdbi" ,r-annotationdbi)
1300 ("r-biobase" ,r-biobase)
1301 ("r-biocgenerics" ,r-biocgenerics)
1303 ("r-edger" ,r-edger)
1304 ("r-gcrma" ,r-gcrma)
1305 ("r-glimma" ,r-glimma)
1306 ("r-ggplot2" ,r-ggplot2)
1307 ("r-gostats" ,r-gostats)
1308 ("r-gplots" ,r-gplots)
1309 ("r-hwriter" ,r-hwriter)
1310 ("r-lattice" ,r-lattice)
1311 ("r-limma" ,r-limma)
1312 ("r-oligoclasses" ,r-oligoclasses)
1313 ("r-reportingtools" ,r-reportingtools)
1314 ("r-rsqlite" ,r-rsqlite)
1315 ("r-s4vectors" ,r-s4vectors)
1316 ("r-xtable" ,r-xtable)))
1318 `(("r-knitr" ,r-knitr)))
1319 (home-page "https://bioconductor.org/packages/affycoretools/")
1320 (synopsis "Functions for analyses with Affymetrix GeneChips")
1322 "This package provides various wrapper functions that have been written
1323 to streamline the more common analyses that a Biostatistician might see.")
1324 (license license:artistic2.0)))
1326 (define-public r-affxparser
1328 (name "r-affxparser")
1333 (uri (bioconductor-uri "affxparser" version))
1336 "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq"))))
1337 (properties `((upstream-name . "affxparser")))
1338 (build-system r-build-system)
1339 (home-page "https://github.com/HenrikBengtsson/affxparser")
1340 (synopsis "Affymetrix File Parsing SDK")
1342 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1343 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1344 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1345 are supported. Currently, there are methods for reading @dfn{chip definition
1346 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1347 either in full or in part. For example, probe signals from a few probesets
1348 can be extracted very quickly from a set of CEL files into a convenient list
1350 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1352 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1354 (define-public r-annotate
1361 (uri (bioconductor-uri "annotate" version))
1364 "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w"))))
1365 (build-system r-build-system)
1367 `(("r-annotationdbi" ,r-annotationdbi)
1368 ("r-biobase" ,r-biobase)
1369 ("r-biocgenerics" ,r-biocgenerics)
1371 ("r-rcurl" ,r-rcurl)
1373 ("r-xtable" ,r-xtable)))
1375 "https://bioconductor.org/packages/annotate")
1376 (synopsis "Annotation for microarrays")
1377 (description "This package provides R environments for the annotation of
1379 (license license:artistic2.0)))
1381 (define-public r-hpar
1388 (uri (bioconductor-uri "hpar" version))
1391 "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9"))))
1392 (build-system r-build-system)
1394 `(("r-knitr" ,r-knitr)))
1395 (home-page "https://bioconductor.org/packages/hpar/")
1396 (synopsis "Human Protein Atlas in R")
1397 (description "This package provides a simple interface to and data from
1398 the Human Protein Atlas project.")
1399 (license license:artistic2.0)))
1401 (define-public r-regioner
1408 (uri (bioconductor-uri "regioneR" version))
1411 "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
1412 (properties `((upstream-name . "regioneR")))
1413 (build-system r-build-system)
1415 `(("r-biostrings" ,r-biostrings)
1416 ("r-bsgenome" ,r-bsgenome)
1417 ("r-genomeinfodb" ,r-genomeinfodb)
1418 ("r-genomicranges" ,r-genomicranges)
1419 ("r-iranges" ,r-iranges)
1420 ("r-memoise" ,r-memoise)
1421 ("r-rtracklayer" ,r-rtracklayer)
1422 ("r-s4vectors" ,r-s4vectors)))
1424 `(("r-knitr" ,r-knitr)))
1425 (home-page "https://bioconductor.org/packages/regioneR/")
1426 (synopsis "Association analysis of genomic regions")
1427 (description "This package offers a statistical framework based on
1428 customizable permutation tests to assess the association between genomic
1429 region sets and other genomic features.")
1430 (license license:artistic2.0)))
1432 (define-public r-reportingtools
1434 (name "r-reportingtools")
1439 (uri (bioconductor-uri "ReportingTools" version))
1442 "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx"))))
1444 `((upstream-name . "ReportingTools")))
1445 (build-system r-build-system)
1447 `(("r-annotate" ,r-annotate)
1448 ("r-annotationdbi" ,r-annotationdbi)
1449 ("r-biobase" ,r-biobase)
1450 ("r-biocgenerics" ,r-biocgenerics)
1451 ("r-category" ,r-category)
1452 ("r-deseq2" ,r-deseq2)
1453 ("r-edger" ,r-edger)
1454 ("r-ggbio" ,r-ggbio)
1455 ("r-ggplot2" ,r-ggplot2)
1456 ("r-gostats" ,r-gostats)
1457 ("r-gseabase" ,r-gseabase)
1458 ("r-hwriter" ,r-hwriter)
1459 ("r-iranges" ,r-iranges)
1460 ("r-knitr" ,r-knitr)
1461 ("r-lattice" ,r-lattice)
1462 ("r-limma" ,r-limma)
1463 ("r-pfam-db" ,r-pfam-db)
1464 ("r-r-utils" ,r-r-utils)
1467 `(("r-knitr" ,r-knitr)))
1468 (home-page "https://bioconductor.org/packages/ReportingTools/")
1469 (synopsis "Tools for making reports in various formats")
1471 "The ReportingTools package enables users to easily display reports of
1472 analysis results generated from sources such as microarray and sequencing
1473 data. The package allows users to create HTML pages that may be viewed on a
1474 web browser, or in other formats. Users can generate tables with sortable and
1475 filterable columns, make and display plots, and link table entries to other
1476 data sources such as NCBI or larger plots within the HTML page. Using the
1477 package, users can also produce a table of contents page to link various
1478 reports together for a particular project that can be viewed in a web
1480 (license license:artistic2.0)))
1482 (define-public r-geneplotter
1484 (name "r-geneplotter")
1489 (uri (bioconductor-uri "geneplotter" version))
1492 "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5"))))
1493 (build-system r-build-system)
1495 `(("r-annotate" ,r-annotate)
1496 ("r-annotationdbi" ,r-annotationdbi)
1497 ("r-biobase" ,r-biobase)
1498 ("r-biocgenerics" ,r-biocgenerics)
1499 ("r-lattice" ,r-lattice)
1500 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1501 (home-page "https://bioconductor.org/packages/geneplotter")
1502 (synopsis "Graphics functions for genomic data")
1504 "This package provides functions for plotting genomic data.")
1505 (license license:artistic2.0)))
1507 (define-public r-oligoclasses
1509 (name "r-oligoclasses")
1514 (uri (bioconductor-uri "oligoClasses" version))
1517 "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
1518 (properties `((upstream-name . "oligoClasses")))
1519 (build-system r-build-system)
1521 `(("r-affyio" ,r-affyio)
1522 ("r-biobase" ,r-biobase)
1523 ("r-biocgenerics" ,r-biocgenerics)
1524 ("r-biocmanager" ,r-biocmanager)
1525 ("r-biostrings" ,r-biostrings)
1528 ("r-foreach" ,r-foreach)
1529 ("r-genomicranges" ,r-genomicranges)
1530 ("r-iranges" ,r-iranges)
1531 ("r-rsqlite" ,r-rsqlite)
1532 ("r-s4vectors" ,r-s4vectors)
1533 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1534 (home-page "https://bioconductor.org/packages/oligoClasses/")
1535 (synopsis "Classes for high-throughput arrays")
1537 "This package contains class definitions, validity checks, and
1538 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1540 (license license:gpl2+)))
1542 (define-public r-oligo
1549 (uri (bioconductor-uri "oligo" version))
1552 "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
1553 (properties `((upstream-name . "oligo")))
1554 (build-system r-build-system)
1555 (inputs `(("zlib" ,zlib)))
1557 `(("r-affxparser" ,r-affxparser)
1558 ("r-affyio" ,r-affyio)
1559 ("r-biobase" ,r-biobase)
1560 ("r-biocgenerics" ,r-biocgenerics)
1561 ("r-biostrings" ,r-biostrings)
1564 ("r-oligoclasses" ,r-oligoclasses)
1565 ("r-preprocesscore" ,r-preprocesscore)
1566 ("r-rsqlite" ,r-rsqlite)
1567 ("r-zlibbioc" ,r-zlibbioc)))
1569 `(("r-knitr" ,r-knitr)))
1570 (home-page "https://bioconductor.org/packages/oligo/")
1571 (synopsis "Preprocessing tools for oligonucleotide arrays")
1573 "This package provides a package to analyze oligonucleotide
1574 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1575 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1576 (license license:lgpl2.0+)))
1578 (define-public r-qvalue
1585 (uri (bioconductor-uri "qvalue" version))
1588 "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f"))))
1589 (build-system r-build-system)
1591 `(("r-ggplot2" ,r-ggplot2)
1592 ("r-reshape2" ,r-reshape2)))
1594 `(("r-knitr" ,r-knitr)))
1595 (home-page "https://github.com/StoreyLab/qvalue")
1596 (synopsis "Q-value estimation for false discovery rate control")
1598 "This package takes a list of p-values resulting from the simultaneous
1599 testing of many hypotheses and estimates their q-values and local @dfn{false
1600 discovery rate} (FDR) values. The q-value of a test measures the proportion
1601 of false positives incurred when that particular test is called significant.
1602 The local FDR measures the posterior probability the null hypothesis is true
1603 given the test's p-value. Various plots are automatically generated, allowing
1604 one to make sensible significance cut-offs. The software can be applied to
1605 problems in genomics, brain imaging, astrophysics, and data mining.")
1606 ;; Any version of the LGPL.
1607 (license license:lgpl3+)))
1609 (define-public r-diffbind
1616 (uri (bioconductor-uri "DiffBind" version))
1619 "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5"))))
1620 (properties `((upstream-name . "DiffBind")))
1621 (build-system r-build-system)
1625 `(("r-amap" ,r-amap)
1626 ("r-biocparallel" ,r-biocparallel)
1627 ("r-deseq2" ,r-deseq2)
1628 ("r-dplyr" ,r-dplyr)
1629 ("r-edger" ,r-edger)
1630 ("r-genomicalignments" ,r-genomicalignments)
1631 ("r-genomicranges" ,r-genomicranges)
1632 ("r-ggplot2" ,r-ggplot2)
1633 ("r-ggrepel" ,r-ggrepel)
1634 ("r-gplots" ,r-gplots)
1635 ("r-iranges" ,r-iranges)
1636 ("r-lattice" ,r-lattice)
1637 ("r-limma" ,r-limma)
1638 ("r-locfit" ,r-locfit)
1639 ("r-rcolorbrewer" , r-rcolorbrewer)
1641 ("r-rhtslib" ,r-rhtslib)
1642 ("r-rsamtools" ,r-rsamtools)
1643 ("r-s4vectors" ,r-s4vectors)
1644 ("r-summarizedexperiment" ,r-summarizedexperiment)
1645 ("r-systempiper" ,r-systempiper)))
1646 (home-page "https://bioconductor.org/packages/DiffBind")
1647 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1649 "This package computes differentially bound sites from multiple
1650 ChIP-seq experiments using affinity (quantitative) data. Also enables
1651 occupancy (overlap) analysis and plotting functions.")
1652 (license license:artistic2.0)))
1654 (define-public r-ripseeker
1656 (name "r-ripseeker")
1661 (uri (bioconductor-uri "RIPSeeker" version))
1664 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1665 (properties `((upstream-name . "RIPSeeker")))
1666 (build-system r-build-system)
1668 `(("r-s4vectors" ,r-s4vectors)
1669 ("r-iranges" ,r-iranges)
1670 ("r-genomicranges" ,r-genomicranges)
1671 ("r-summarizedexperiment" ,r-summarizedexperiment)
1672 ("r-rsamtools" ,r-rsamtools)
1673 ("r-genomicalignments" ,r-genomicalignments)
1674 ("r-rtracklayer" ,r-rtracklayer)))
1675 (home-page "https://bioconductor.org/packages/RIPSeeker")
1677 "Identifying protein-associated transcripts from RIP-seq experiments")
1679 "This package infers and discriminates RIP peaks from RIP-seq alignments
1680 using two-state HMM with negative binomial emission probability. While
1681 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1682 a suite of bioinformatics tools integrated within this self-contained software
1683 package comprehensively addressing issues ranging from post-alignments
1684 processing to visualization and annotation.")
1685 (license license:gpl2)))
1687 (define-public r-multtest
1694 (uri (bioconductor-uri "multtest" version))
1697 "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2"))))
1698 (build-system r-build-system)
1700 `(("r-survival" ,r-survival)
1701 ("r-biocgenerics" ,r-biocgenerics)
1702 ("r-biobase" ,r-biobase)
1703 ("r-mass" ,r-mass)))
1704 (home-page "https://bioconductor.org/packages/multtest")
1705 (synopsis "Resampling-based multiple hypothesis testing")
1707 "This package can do non-parametric bootstrap and permutation
1708 resampling-based multiple testing procedures (including empirical Bayes
1709 methods) for controlling the family-wise error rate (FWER), generalized
1710 family-wise error rate (gFWER), tail probability of the proportion of
1711 false positives (TPPFP), and false discovery rate (FDR). Several choices
1712 of bootstrap-based null distribution are implemented (centered, centered
1713 and scaled, quantile-transformed). Single-step and step-wise methods are
1714 available. Tests based on a variety of T- and F-statistics (including
1715 T-statistics based on regression parameters from linear and survival models
1716 as well as those based on correlation parameters) are included. When probing
1717 hypotheses with T-statistics, users may also select a potentially faster null
1718 distribution which is multivariate normal with mean zero and variance
1719 covariance matrix derived from the vector influence function. Results are
1720 reported in terms of adjusted P-values, confidence regions and test statistic
1721 cutoffs. The procedures are directly applicable to identifying differentially
1722 expressed genes in DNA microarray experiments.")
1723 (license license:lgpl3)))
1725 (define-public r-graph
1731 (uri (bioconductor-uri "graph" version))
1734 "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g"))))
1735 (build-system r-build-system)
1737 `(("r-biocgenerics" ,r-biocgenerics)))
1738 (home-page "https://bioconductor.org/packages/graph")
1739 (synopsis "Handle graph data structures in R")
1741 "This package implements some simple graph handling capabilities for R.")
1742 (license license:artistic2.0)))
1744 ;; This is a CRAN package, but it depends on a Bioconductor package.
1745 (define-public r-ggm
1752 (uri (cran-uri "ggm" version))
1755 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1756 (properties `((upstream-name . "ggm")))
1757 (build-system r-build-system)
1759 `(("r-graph" ,r-graph)
1760 ("r-igraph" ,r-igraph)))
1761 (home-page "https://cran.r-project.org/package=ggm")
1762 (synopsis "Functions for graphical Markov models")
1764 "This package provides functions and datasets for maximum likelihood
1765 fitting of some classes of graphical Markov models.")
1766 (license license:gpl2+)))
1768 ;; This is a CRAN package, but it depends on a Bioconductor package.
1769 (define-public r-codedepends
1771 (name "r-codedepends")
1776 (uri (cran-uri "CodeDepends" version))
1779 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1780 (properties `((upstream-name . "CodeDepends")))
1781 (build-system r-build-system)
1783 `(("r-codetools" ,r-codetools)
1784 ("r-graph" ,r-graph)
1786 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1787 (synopsis "Analysis of R code for reproducible research and code comprehension")
1789 "This package provides tools for analyzing R expressions or blocks of
1790 code and determining the dependencies between them. It focuses on R scripts,
1791 but can be used on the bodies of functions. There are many facilities
1792 including the ability to summarize or get a high-level view of code,
1793 determining dependencies between variables, code improvement suggestions.")
1794 ;; Any version of the GPL
1795 (license (list license:gpl2+ license:gpl3+))))
1797 (define-public r-chippeakanno
1799 (name "r-chippeakanno")
1804 (uri (bioconductor-uri "ChIPpeakAnno" version))
1807 "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
1808 (properties `((upstream-name . "ChIPpeakAnno")))
1809 (build-system r-build-system)
1811 `(("r-annotationdbi" ,r-annotationdbi)
1812 ("r-biobase" ,r-biobase)
1813 ("r-biocgenerics" ,r-biocgenerics)
1814 ("r-biocmanager" ,r-biocmanager)
1815 ("r-biomart" ,r-biomart)
1816 ("r-biostrings" ,r-biostrings)
1817 ("r-bsgenome" ,r-bsgenome)
1819 ("r-delayedarray" ,r-delayedarray)
1820 ("r-ensembldb" ,r-ensembldb)
1821 ("r-genomeinfodb" ,r-genomeinfodb)
1822 ("r-genomicalignments" ,r-genomicalignments)
1823 ("r-genomicfeatures" ,r-genomicfeatures)
1824 ("r-genomicranges" ,r-genomicranges)
1825 ("r-go-db" ,r-go-db)
1826 ("r-graph" ,r-graph)
1828 ("r-iranges" ,r-iranges)
1829 ("r-limma" ,r-limma)
1830 ("r-matrixstats" ,r-matrixstats)
1831 ("r-multtest" ,r-multtest)
1833 ("r-regioner" ,r-regioner)
1834 ("r-rsamtools" ,r-rsamtools)
1835 ("r-rtracklayer" ,r-rtracklayer)
1836 ("r-s4vectors" ,r-s4vectors)
1837 ("r-seqinr" ,r-seqinr)
1838 ("r-summarizedexperiment" ,r-summarizedexperiment)
1839 ("r-venndiagram" ,r-venndiagram)))
1841 `(("r-knitr" ,r-knitr)))
1842 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1843 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1845 "The package includes functions to retrieve the sequences around the peak,
1846 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1847 custom features such as most conserved elements and other transcription factor
1848 binding sites supplied by users. Starting 2.0.5, new functions have been added
1849 for finding the peaks with bi-directional promoters with summary statistics
1850 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1851 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1852 enrichedGO (addGeneIDs).")
1853 (license license:gpl2+)))
1855 (define-public r-marray
1861 (uri (bioconductor-uri "marray" version))
1863 (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
1864 (build-system r-build-system)
1866 `(("r-limma" ,r-limma)))
1867 (home-page "https://bioconductor.org/packages/marray")
1868 (synopsis "Exploratory analysis for two-color spotted microarray data")
1869 (description "This package contains class definitions for two-color spotted
1870 microarray data. It also includes functions for data input, diagnostic plots,
1871 normalization and quality checking.")
1872 (license license:lgpl2.0+)))
1874 (define-public r-cghbase
1880 (uri (bioconductor-uri "CGHbase" version))
1882 (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
1883 (properties `((upstream-name . "CGHbase")))
1884 (build-system r-build-system)
1886 `(("r-biobase" ,r-biobase)
1887 ("r-marray" ,r-marray)))
1888 (home-page "https://bioconductor.org/packages/CGHbase")
1889 (synopsis "Base functions and classes for arrayCGH data analysis")
1890 (description "This package contains functions and classes that are needed by
1891 the @code{arrayCGH} packages.")
1892 (license license:gpl2+)))
1894 (define-public r-cghcall
1900 (uri (bioconductor-uri "CGHcall" version))
1902 (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
1903 (properties `((upstream-name . "CGHcall")))
1904 (build-system r-build-system)
1906 `(("r-biobase" ,r-biobase)
1907 ("r-cghbase" ,r-cghbase)
1908 ("r-impute" ,r-impute)
1909 ("r-dnacopy" ,r-dnacopy)
1910 ("r-snowfall" ,r-snowfall)))
1911 (home-page "https://bioconductor.org/packages/CGHcall")
1912 (synopsis "Base functions and classes for arrayCGH data analysis")
1913 (description "This package contains functions and classes that are needed by
1914 @code{arrayCGH} packages.")
1915 (license license:gpl2+)))
1917 (define-public r-qdnaseq
1923 (uri (bioconductor-uri "QDNAseq" version))
1925 (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
1926 (properties `((upstream-name . "QDNAseq")))
1927 (build-system r-build-system)
1929 `(("r-biobase" ,r-biobase)
1930 ("r-cghbase" ,r-cghbase)
1931 ("r-cghcall" ,r-cghcall)
1932 ("r-dnacopy" ,r-dnacopy)
1933 ("r-future" ,r-future)
1934 ("r-future-apply" ,r-future-apply)
1935 ("r-genomicranges" ,r-genomicranges)
1936 ("r-iranges" ,r-iranges)
1937 ("r-matrixstats" ,r-matrixstats)
1938 ("r-r-utils" ,r-r-utils)
1939 ("r-rsamtools" ,r-rsamtools)))
1940 (home-page "https://bioconductor.org/packages/QDNAseq")
1941 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1942 (description "The genome is divided into non-overlapping fixed-sized bins,
1943 number of sequence reads in each counted, adjusted with a simultaneous
1944 two-dimensional loess correction for sequence mappability and GC content, and
1945 filtered to remove spurious regions in the genome. Downstream steps of
1946 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1948 (license license:gpl2+)))
1950 (define-public r-bayseq
1957 (uri (bioconductor-uri "baySeq" version))
1960 "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
1961 (properties `((upstream-name . "baySeq")))
1962 (build-system r-build-system)
1964 `(("r-abind" ,r-abind)
1965 ("r-edger" ,r-edger)
1966 ("r-genomicranges" ,r-genomicranges)))
1967 (home-page "https://bioconductor.org/packages/baySeq/")
1968 (synopsis "Bayesian analysis of differential expression patterns in count data")
1970 "This package identifies differential expression in high-throughput count
1971 data, such as that derived from next-generation sequencing machines,
1972 calculating estimated posterior likelihoods of differential expression (or
1973 more complex hypotheses) via empirical Bayesian methods.")
1974 (license license:gpl3)))
1976 (define-public r-chipcomp
1983 (uri (bioconductor-uri "ChIPComp" version))
1986 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
1987 (properties `((upstream-name . "ChIPComp")))
1988 (build-system r-build-system)
1990 `(("r-biocgenerics" ,r-biocgenerics)
1991 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1992 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1993 ("r-genomeinfodb" ,r-genomeinfodb)
1994 ("r-genomicranges" ,r-genomicranges)
1995 ("r-iranges" ,r-iranges)
1996 ("r-limma" ,r-limma)
1997 ("r-rsamtools" ,r-rsamtools)
1998 ("r-rtracklayer" ,r-rtracklayer)
1999 ("r-s4vectors" ,r-s4vectors)))
2000 (home-page "https://bioconductor.org/packages/ChIPComp")
2001 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2003 "ChIPComp implements a statistical method for quantitative comparison of
2004 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2005 sites across multiple conditions considering matching control in ChIP-seq
2007 ;; Any version of the GPL.
2008 (license license:gpl3+)))
2010 (define-public r-riboprofiling
2012 (name "r-riboprofiling")
2017 (uri (bioconductor-uri "RiboProfiling" version))
2020 "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
2021 (properties `((upstream-name . "RiboProfiling")))
2022 (build-system r-build-system)
2024 `(("r-biocgenerics" ,r-biocgenerics)
2025 ("r-biostrings" ,r-biostrings)
2026 ("r-data-table" ,r-data-table)
2027 ("r-genomeinfodb" ,r-genomeinfodb)
2028 ("r-genomicalignments" ,r-genomicalignments)
2029 ("r-genomicfeatures" ,r-genomicfeatures)
2030 ("r-genomicranges" ,r-genomicranges)
2031 ("r-ggbio" ,r-ggbio)
2032 ("r-ggplot2" ,r-ggplot2)
2033 ("r-iranges" ,r-iranges)
2035 ("r-reshape2" ,r-reshape2)
2036 ("r-rsamtools" ,r-rsamtools)
2037 ("r-rtracklayer" ,r-rtracklayer)
2038 ("r-s4vectors" ,r-s4vectors)
2039 ("r-sqldf" ,r-sqldf)))
2041 `(("r-knitr" ,r-knitr)))
2042 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2043 (synopsis "Ribosome profiling data analysis")
2044 (description "Starting with a BAM file, this package provides the
2045 necessary functions for quality assessment, read start position recalibration,
2046 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2047 of count data: pairs, log fold-change, codon frequency and coverage
2048 assessment, principal component analysis on codon coverage.")
2049 (license license:gpl3)))
2051 (define-public r-riboseqr
2058 (uri (bioconductor-uri "riboSeqR" version))
2061 "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
2062 (properties `((upstream-name . "riboSeqR")))
2063 (build-system r-build-system)
2065 `(("r-abind" ,r-abind)
2066 ("r-bayseq" ,r-bayseq)
2067 ("r-genomeinfodb" ,r-genomeinfodb)
2068 ("r-genomicranges" ,r-genomicranges)
2069 ("r-iranges" ,r-iranges)
2070 ("r-rsamtools" ,r-rsamtools)
2071 ("r-seqlogo" ,r-seqlogo)))
2072 (home-page "https://bioconductor.org/packages/riboSeqR/")
2073 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2075 "This package provides plotting functions, frameshift detection and
2076 parsing of genetic sequencing data from ribosome profiling experiments.")
2077 (license license:gpl3)))
2079 (define-public r-interactionset
2081 (name "r-interactionset")
2086 (uri (bioconductor-uri "InteractionSet" version))
2089 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
2091 `((upstream-name . "InteractionSet")))
2092 (build-system r-build-system)
2094 `(("r-biocgenerics" ,r-biocgenerics)
2095 ("r-genomeinfodb" ,r-genomeinfodb)
2096 ("r-genomicranges" ,r-genomicranges)
2097 ("r-iranges" ,r-iranges)
2098 ("r-matrix" ,r-matrix)
2100 ("r-s4vectors" ,r-s4vectors)
2101 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2103 `(("r-knitr" ,r-knitr)))
2104 (home-page "https://bioconductor.org/packages/InteractionSet")
2105 (synopsis "Base classes for storing genomic interaction data")
2107 "This package provides the @code{GInteractions},
2108 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2109 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2111 (license license:gpl3)))
2113 (define-public r-genomicinteractions
2115 (name "r-genomicinteractions")
2120 (uri (bioconductor-uri "GenomicInteractions" version))
2123 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
2125 `((upstream-name . "GenomicInteractions")))
2126 (build-system r-build-system)
2128 `(("r-biobase" ,r-biobase)
2129 ("r-biocgenerics" ,r-biocgenerics)
2130 ("r-data-table" ,r-data-table)
2131 ("r-dplyr" ,r-dplyr)
2132 ("r-genomeinfodb" ,r-genomeinfodb)
2133 ("r-genomicranges" ,r-genomicranges)
2134 ("r-ggplot2" ,r-ggplot2)
2135 ("r-gridextra" ,r-gridextra)
2137 ("r-igraph" ,r-igraph)
2138 ("r-interactionset" ,r-interactionset)
2139 ("r-iranges" ,r-iranges)
2140 ("r-rsamtools" ,r-rsamtools)
2141 ("r-rtracklayer" ,r-rtracklayer)
2142 ("r-s4vectors" ,r-s4vectors)
2143 ("r-stringr" ,r-stringr)))
2145 `(("r-knitr" ,r-knitr)))
2146 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2147 (synopsis "R package for handling genomic interaction data")
2149 "This R package provides tools for handling genomic interaction data,
2150 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2151 information and producing various plots and statistics.")
2152 (license license:gpl3)))
2154 (define-public r-ctc
2161 (uri (bioconductor-uri "ctc" version))
2164 "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
2165 (build-system r-build-system)
2166 (propagated-inputs `(("r-amap" ,r-amap)))
2167 (home-page "https://bioconductor.org/packages/ctc/")
2168 (synopsis "Cluster and tree conversion")
2170 "This package provides tools for exporting and importing classification
2171 trees and clusters to other programs.")
2172 (license license:gpl2)))
2174 (define-public r-goseq
2181 (uri (bioconductor-uri "goseq" version))
2184 "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
2185 (build-system r-build-system)
2187 `(("r-annotationdbi" ,r-annotationdbi)
2188 ("r-biasedurn" ,r-biasedurn)
2189 ("r-biocgenerics" ,r-biocgenerics)
2190 ("r-genelendatabase" ,r-genelendatabase)
2191 ("r-go-db" ,r-go-db)
2192 ("r-mgcv" ,r-mgcv)))
2193 (home-page "https://bioconductor.org/packages/goseq/")
2194 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2196 "This package provides tools to detect Gene Ontology and/or other user
2197 defined categories which are over/under represented in RNA-seq data.")
2198 (license license:lgpl2.0+)))
2200 (define-public r-glimma
2207 (uri (bioconductor-uri "Glimma" version))
2210 "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
2211 (properties `((upstream-name . "Glimma")))
2212 (build-system r-build-system)
2214 `(("r-edger" ,r-edger)
2215 ("r-jsonlite" ,r-jsonlite)
2216 ("r-s4vectors" ,r-s4vectors)))
2218 `(("r-knitr" ,r-knitr)))
2219 (home-page "https://github.com/Shians/Glimma")
2220 (synopsis "Interactive HTML graphics")
2222 "This package generates interactive visualisations for analysis of
2223 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2224 HTML page. The interactions are built on top of the popular static
2225 representations of analysis results in order to provide additional
2227 (license license:lgpl3)))
2229 (define-public r-rots
2236 (uri (bioconductor-uri "ROTS" version))
2239 "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
2240 (properties `((upstream-name . "ROTS")))
2241 (build-system r-build-system)
2243 `(("r-biobase" ,r-biobase)
2244 ("r-rcpp" ,r-rcpp)))
2245 (home-page "https://bioconductor.org/packages/ROTS/")
2246 (synopsis "Reproducibility-Optimized Test Statistic")
2248 "This package provides tools for calculating the
2249 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2251 (license license:gpl2+)))
2253 (define-public r-plgem
2260 (uri (bioconductor-uri "plgem" version))
2263 "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
2264 (build-system r-build-system)
2266 `(("r-biobase" ,r-biobase)
2267 ("r-mass" ,r-mass)))
2268 (home-page "http://www.genopolis.it")
2269 (synopsis "Detect differential expression in microarray and proteomics datasets")
2271 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2272 model the variance-versus-mean dependence that exists in a variety of
2273 genome-wide datasets, including microarray and proteomics data. The use of
2274 PLGEM has been shown to improve the detection of differentially expressed
2275 genes or proteins in these datasets.")
2276 (license license:gpl2)))
2278 (define-public r-inspect
2285 (uri (bioconductor-uri "INSPEcT" version))
2288 "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z"))))
2289 (properties `((upstream-name . "INSPEcT")))
2290 (build-system r-build-system)
2292 `(("r-biobase" ,r-biobase)
2293 ("r-biocgenerics" ,r-biocgenerics)
2294 ("r-biocparallel" ,r-biocparallel)
2295 ("r-deseq2" ,r-deseq2)
2296 ("r-desolve" ,r-desolve)
2297 ("r-gdata" ,r-gdata)
2298 ("r-genomeinfodb" ,r-genomeinfodb)
2299 ("r-genomicalignments" ,r-genomicalignments)
2300 ("r-genomicfeatures" ,r-genomicfeatures)
2301 ("r-genomicranges" ,r-genomicranges)
2302 ("r-iranges" ,r-iranges)
2303 ("r-kernsmooth" ,r-kernsmooth)
2304 ("r-plgem" ,r-plgem)
2306 ("r-rootsolve" ,r-rootsolve)
2307 ("r-rsamtools" ,r-rsamtools)
2308 ("r-rtracklayer" ,r-rtracklayer)
2309 ("r-s4vectors" ,r-s4vectors)
2310 ("r-shiny" ,r-shiny)
2311 ("r-summarizedexperiment" ,r-summarizedexperiment)
2312 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2313 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2315 `(("r-knitr" ,r-knitr)))
2316 (home-page "https://bioconductor.org/packages/INSPEcT")
2317 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2319 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2320 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2321 order to evaluate synthesis, processing and degradation rates and assess via
2322 modeling the rates that determines changes in mature mRNA levels.")
2323 (license license:gpl2)))
2325 (define-public r-dnabarcodes
2327 (name "r-dnabarcodes")
2332 (uri (bioconductor-uri "DNABarcodes" version))
2335 "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7"))))
2336 (properties `((upstream-name . "DNABarcodes")))
2337 (build-system r-build-system)
2340 ("r-matrix" ,r-matrix)
2341 ("r-rcpp" ,r-rcpp)))
2343 `(("r-knitr" ,r-knitr)))
2344 (home-page "https://bioconductor.org/packages/DNABarcodes")
2345 (synopsis "Create and analyze DNA barcodes")
2347 "This package offers tools to create DNA barcode sets capable of
2348 correcting insertion, deletion, and substitution errors. Existing barcodes
2349 can be analyzed regarding their minimal, maximal and average distances between
2350 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2351 demultiplexed, i.e. assigned to their original reference barcode.")
2352 (license license:gpl2)))
2354 (define-public r-ruvseq
2361 (uri (bioconductor-uri "RUVSeq" version))
2364 "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x"))))
2365 (properties `((upstream-name . "RUVSeq")))
2366 (build-system r-build-system)
2368 `(("r-biobase" ,r-biobase)
2369 ("r-edaseq" ,r-edaseq)
2370 ("r-edger" ,r-edger)
2371 ("r-mass" ,r-mass)))
2373 `(("r-knitr" ,r-knitr)))
2374 (home-page "https://github.com/drisso/RUVSeq")
2375 (synopsis "Remove unwanted variation from RNA-Seq data")
2377 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2378 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2380 (license license:artistic2.0)))
2382 (define-public r-biocneighbors
2384 (name "r-biocneighbors")
2389 (uri (bioconductor-uri "BiocNeighbors" version))
2392 "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy"))))
2393 (properties `((upstream-name . "BiocNeighbors")))
2394 (build-system r-build-system)
2396 `(("r-biocparallel" ,r-biocparallel)
2397 ("r-matrix" ,r-matrix)
2399 ("r-rcppannoy" ,r-rcppannoy)
2400 ("r-rcpphnsw" ,r-rcpphnsw)
2401 ("r-s4vectors" ,r-s4vectors)))
2403 `(("r-knitr" ,r-knitr)))
2404 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2405 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2407 "This package implements exact and approximate methods for nearest
2408 neighbor detection, in a framework that allows them to be easily switched
2409 within Bioconductor packages or workflows. The exact algorithm is implemented
2410 using pre-clustering with the k-means algorithm. Functions are also provided
2411 to search for all neighbors within a given distance. Parallelization is
2412 achieved for all methods using the BiocParallel framework.")
2413 (license license:gpl3)))
2415 (define-public r-biocsingular
2417 (name "r-biocsingular")
2422 (uri (bioconductor-uri "BiocSingular" version))
2425 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
2426 (properties `((upstream-name . "BiocSingular")))
2427 (build-system r-build-system)
2429 `(("r-beachmat" ,r-beachmat)
2430 ("r-biocgenerics" ,r-biocgenerics)
2431 ("r-biocparallel" ,r-biocparallel)
2432 ("r-delayedarray" ,r-delayedarray)
2433 ("r-irlba" ,r-irlba)
2434 ("r-matrix" ,r-matrix)
2437 ("r-s4vectors" ,r-s4vectors)))
2439 `(("r-knitr" ,r-knitr)))
2440 (home-page "https://github.com/LTLA/BiocSingular")
2441 (synopsis "Singular value decomposition for Bioconductor packages")
2443 "This package implements exact and approximate methods for singular value
2444 decomposition and principal components analysis, in a framework that allows
2445 them to be easily switched within Bioconductor packages or workflows. Where
2446 possible, parallelization is achieved using the BiocParallel framework.")
2447 (license license:gpl3)))
2449 (define-public r-destiny
2456 (uri (bioconductor-uri "destiny" version))
2459 "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n"))))
2460 (build-system r-build-system)
2462 `(("r-biobase" ,r-biobase)
2463 ("r-biocgenerics" ,r-biocgenerics)
2464 ("r-ggplot-multistats" ,r-ggplot-multistats)
2465 ("r-ggplot2" ,r-ggplot2)
2466 ("r-ggthemes" ,r-ggthemes)
2467 ("r-irlba" ,r-irlba)
2468 ("r-knn-covertree" ,r-knn-covertree)
2469 ("r-matrix" ,r-matrix)
2470 ("r-nbconvertr" ,r-nbconvertr)
2471 ("r-pcamethods" ,r-pcamethods)
2472 ("r-proxy" ,r-proxy)
2474 ("r-rcppeigen" ,r-rcppeigen)
2475 ("r-rcpphnsw" ,r-rcpphnsw)
2476 ("r-rspectra" ,r-rspectra)
2477 ("r-scales" ,r-scales)
2478 ("r-scatterplot3d" ,r-scatterplot3d)
2479 ("r-singlecellexperiment" ,r-singlecellexperiment)
2480 ("r-smoother" ,r-smoother)
2481 ("r-summarizedexperiment" ,r-summarizedexperiment)
2482 ("r-tidyr" ,r-tidyr)
2483 ("r-tidyselect" ,r-tidyselect)
2486 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2487 (home-page "https://bioconductor.org/packages/destiny/")
2488 (synopsis "Create and plot diffusion maps")
2489 (description "This package provides tools to create and plot diffusion
2491 ;; Any version of the GPL
2492 (license license:gpl3+)))
2494 (define-public r-savr
2501 (uri (bioconductor-uri "savR" version))
2504 "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a"))))
2505 (properties `((upstream-name . "savR")))
2506 (build-system r-build-system)
2508 `(("r-ggplot2" ,r-ggplot2)
2509 ("r-gridextra" ,r-gridextra)
2510 ("r-reshape2" ,r-reshape2)
2511 ("r-scales" ,r-scales)
2513 (home-page "https://github.com/bcalder/savR")
2514 (synopsis "Parse and analyze Illumina SAV files")
2516 "This package provides tools to parse Illumina Sequence Analysis
2517 Viewer (SAV) files, access data, and generate QC plots.")
2518 (license license:agpl3+)))
2520 (define-public r-chipexoqual
2522 (name "r-chipexoqual")
2527 (uri (bioconductor-uri "ChIPexoQual" version))
2530 "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp"))))
2531 (properties `((upstream-name . "ChIPexoQual")))
2532 (build-system r-build-system)
2534 `(("r-biocparallel" ,r-biocparallel)
2535 ("r-biovizbase" ,r-biovizbase)
2536 ("r-broom" ,r-broom)
2537 ("r-data-table" ,r-data-table)
2538 ("r-dplyr" ,r-dplyr)
2539 ("r-genomeinfodb" ,r-genomeinfodb)
2540 ("r-genomicalignments" ,r-genomicalignments)
2541 ("r-genomicranges" ,r-genomicranges)
2542 ("r-ggplot2" ,r-ggplot2)
2543 ("r-hexbin" ,r-hexbin)
2544 ("r-iranges" ,r-iranges)
2545 ("r-rcolorbrewer" ,r-rcolorbrewer)
2546 ("r-rmarkdown" ,r-rmarkdown)
2547 ("r-rsamtools" ,r-rsamtools)
2548 ("r-s4vectors" ,r-s4vectors)
2549 ("r-scales" ,r-scales)
2550 ("r-viridis" ,r-viridis)))
2552 `(("r-knitr" ,r-knitr)))
2553 (home-page "https://github.com/keleslab/ChIPexoQual")
2554 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2556 "This package provides a quality control pipeline for ChIP-exo/nexus
2558 (license license:gpl2+)))
2560 (define-public r-copynumber
2562 (name "r-copynumber")
2566 (uri (bioconductor-uri "copynumber" version))
2569 "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my"))))
2570 (build-system r-build-system)
2572 `(("r-s4vectors" ,r-s4vectors)
2573 ("r-iranges" ,r-iranges)
2574 ("r-genomicranges" ,r-genomicranges)
2575 ("r-biocgenerics" ,r-biocgenerics)))
2576 (home-page "https://bioconductor.org/packages/copynumber")
2577 (synopsis "Segmentation of single- and multi-track copy number data")
2579 "This package segments single- and multi-track copy number data by a
2580 penalized least squares regression method.")
2581 (license license:artistic2.0)))
2583 (define-public r-dnacopy
2590 (uri (bioconductor-uri "DNAcopy" version))
2593 "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza"))))
2594 (properties `((upstream-name . "DNAcopy")))
2595 (build-system r-build-system)
2596 (native-inputs `(("gfortran" ,gfortran)))
2597 (home-page "https://bioconductor.org/packages/DNAcopy")
2598 (synopsis "DNA copy number data analysis")
2600 "This package implements the @dfn{circular binary segmentation} (CBS)
2601 algorithm to segment DNA copy number data and identify genomic regions with
2602 abnormal copy number.")
2603 (license license:gpl2+)))
2605 ;; This is a CRAN package, but it uncharacteristically depends on a
2606 ;; Bioconductor package.
2607 (define-public r-htscluster
2609 (name "r-htscluster")
2614 (uri (cran-uri "HTSCluster" version))
2617 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2618 (properties `((upstream-name . "HTSCluster")))
2619 (build-system r-build-system)
2621 `(("r-capushe" ,r-capushe)
2622 ("r-edger" ,r-edger)
2623 ("r-plotrix" ,r-plotrix)))
2624 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2625 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2627 "This package provides a Poisson mixture model is implemented to cluster
2628 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2629 estimation is performed using either the EM or CEM algorithm, and the slope
2630 heuristics are used for model selection (i.e., to choose the number of
2632 (license license:gpl3+)))
2634 (define-public r-deds
2641 (uri (bioconductor-uri "DEDS" version))
2644 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2645 (properties `((upstream-name . "DEDS")))
2646 (build-system r-build-system)
2647 (home-page "https://bioconductor.org/packages/DEDS/")
2648 (synopsis "Differential expression via distance summary for microarray data")
2650 "This library contains functions that calculate various statistics of
2651 differential expression for microarray data, including t statistics, fold
2652 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2653 also implements a new methodology called DEDS (Differential Expression via
2654 Distance Summary), which selects differentially expressed genes by integrating
2655 and summarizing a set of statistics using a weighted distance approach.")
2656 ;; Any version of the LGPL.
2657 (license license:lgpl3+)))
2659 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2661 (define-public r-nbpseq
2668 (uri (cran-uri "NBPSeq" version))
2671 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2672 (properties `((upstream-name . "NBPSeq")))
2673 (build-system r-build-system)
2675 `(("r-qvalue" ,r-qvalue)))
2676 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2677 (synopsis "Negative binomial models for RNA-Seq data")
2679 "This package provides negative binomial models for two-group comparisons
2680 and regression inferences from RNA-sequencing data.")
2681 (license license:gpl2)))
2683 (define-public r-ebseq
2690 (uri (bioconductor-uri "EBSeq" version))
2693 "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f"))))
2694 (properties `((upstream-name . "EBSeq")))
2695 (build-system r-build-system)
2697 `(("r-blockmodeling" ,r-blockmodeling)
2698 ("r-gplots" ,r-gplots)
2699 ("r-testthat" ,r-testthat)))
2700 (home-page "https://bioconductor.org/packages/EBSeq")
2701 (synopsis "Differential expression analysis of RNA-seq data")
2703 "This package provides tools for differential expression analysis at both
2704 gene and isoform level using RNA-seq data")
2705 (license license:artistic2.0)))
2707 (define-public r-karyoploter
2709 (name "r-karyoploter")
2713 (uri (bioconductor-uri "karyoploteR" version))
2716 "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
2717 (build-system r-build-system)
2719 `(("r-annotationdbi" ,r-annotationdbi)
2720 ("r-bamsignals" ,r-bamsignals)
2721 ("r-bezier" ,r-bezier)
2722 ("r-biovizbase" ,r-biovizbase)
2723 ("r-digest" ,r-digest)
2724 ("r-genomeinfodb" ,r-genomeinfodb)
2725 ("r-genomicfeatures" ,r-genomicfeatures)
2726 ("r-genomicranges" ,r-genomicranges)
2727 ("r-iranges" ,r-iranges)
2728 ("r-memoise" ,r-memoise)
2729 ("r-regioner" ,r-regioner)
2730 ("r-rsamtools" ,r-rsamtools)
2731 ("r-rtracklayer" ,r-rtracklayer)
2732 ("r-s4vectors" ,r-s4vectors)
2733 ("r-variantannotation" ,r-variantannotation)))
2735 `(("r-knitr" ,r-knitr)))
2736 (home-page "https://bioconductor.org/packages/karyoploteR/")
2737 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2738 (description "This package creates karyotype plots of arbitrary genomes and
2739 offers a complete set of functions to plot arbitrary data on them. It mimicks
2740 many R base graphics functions coupling them with a coordinate change function
2741 automatically mapping the chromosome and data coordinates into the plot
2743 (license license:artistic2.0)))
2745 (define-public r-lpsymphony
2747 (name "r-lpsymphony")
2752 (uri (bioconductor-uri "lpsymphony" version))
2755 "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4"))))
2756 (build-system r-build-system)
2760 `(("pkg-config" ,pkg-config)
2761 ("r-knitr" ,r-knitr)))
2762 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2763 (synopsis "Symphony integer linear programming solver in R")
2765 "This package was derived from Rsymphony. The package provides an R
2766 interface to SYMPHONY, a linear programming solver written in C++. The main
2767 difference between this package and Rsymphony is that it includes the solver
2768 source code, while Rsymphony expects to find header and library files on the
2769 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2770 to install interface to SYMPHONY.")
2771 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2772 ;; lpsimphony is released under the same terms.
2773 (license license:epl1.0)))
2775 (define-public r-ihw
2782 (uri (bioconductor-uri "IHW" version))
2785 "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j"))))
2786 (properties `((upstream-name . "IHW")))
2787 (build-system r-build-system)
2789 `(("r-biocgenerics" ,r-biocgenerics)
2790 ("r-fdrtool" ,r-fdrtool)
2791 ("r-lpsymphony" ,r-lpsymphony)
2792 ("r-slam" ,r-slam)))
2794 `(("r-knitr" ,r-knitr)))
2795 (home-page "https://bioconductor.org/packages/IHW")
2796 (synopsis "Independent hypothesis weighting")
2798 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2799 procedure that increases power compared to the method of Benjamini and
2800 Hochberg by assigning data-driven weights to each hypothesis. The input to
2801 IHW is a two-column table of p-values and covariates. The covariate can be
2802 any continuous-valued or categorical variable that is thought to be
2803 informative on the statistical properties of each hypothesis test, while it is
2804 independent of the p-value under the null hypothesis.")
2805 (license license:artistic2.0)))
2807 (define-public r-icobra
2814 (uri (bioconductor-uri "iCOBRA" version))
2817 "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1"))))
2818 (properties `((upstream-name . "iCOBRA")))
2819 (build-system r-build-system)
2821 `(("r-dplyr" ,r-dplyr)
2823 ("r-ggplot2" ,r-ggplot2)
2824 ("r-limma" ,r-limma)
2825 ("r-reshape2" ,r-reshape2)
2827 ("r-scales" ,r-scales)
2828 ("r-shiny" ,r-shiny)
2829 ("r-shinybs" ,r-shinybs)
2830 ("r-shinydashboard" ,r-shinydashboard)
2831 ("r-upsetr" ,r-upsetr)))
2833 `(("r-knitr" ,r-knitr)))
2834 (home-page "https://bioconductor.org/packages/iCOBRA")
2835 (synopsis "Comparison and visualization of ranking and assignment methods")
2837 "This package provides functions for calculation and visualization of
2838 performance metrics for evaluation of ranking and binary
2839 classification (assignment) methods. It also contains a Shiny application for
2840 interactive exploration of results.")
2841 (license license:gpl2+)))
2843 (define-public r-mast
2850 (uri (bioconductor-uri "MAST" version))
2853 "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr"))))
2854 (properties `((upstream-name . "MAST")))
2855 (build-system r-build-system)
2857 `(("r-abind" ,r-abind)
2858 ("r-biobase" ,r-biobase)
2859 ("r-biocgenerics" ,r-biocgenerics)
2860 ("r-data-table" ,r-data-table)
2861 ("r-ggplot2" ,r-ggplot2)
2863 ("r-progress" ,r-progress)
2864 ("r-reshape2" ,r-reshape2)
2865 ("r-s4vectors" ,r-s4vectors)
2866 ("r-singlecellexperiment" ,r-singlecellexperiment)
2867 ("r-stringr" ,r-stringr)
2868 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2870 `(("r-knitr" ,r-knitr)))
2871 (home-page "https://github.com/RGLab/MAST/")
2872 (synopsis "Model-based analysis of single cell transcriptomics")
2874 "This package provides methods and models for handling zero-inflated
2875 single cell assay data.")
2876 (license license:gpl2+)))
2878 (define-public r-monocle
2885 (uri (bioconductor-uri "monocle" version))
2888 "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd"))))
2889 (build-system r-build-system)
2891 `(("r-biobase" ,r-biobase)
2892 ("r-biocgenerics" ,r-biocgenerics)
2893 ("r-biocviews" ,r-biocviews)
2894 ("r-cluster" ,r-cluster)
2895 ("r-combinat" ,r-combinat)
2896 ("r-ddrtree" ,r-ddrtree)
2897 ("r-densityclust" ,r-densityclust)
2898 ("r-dplyr" ,r-dplyr)
2899 ("r-fastica" ,r-fastica)
2900 ("r-ggplot2" ,r-ggplot2)
2901 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2902 ("r-igraph" ,r-igraph)
2903 ("r-irlba" ,r-irlba)
2904 ("r-limma" ,r-limma)
2906 ("r-matrix" ,r-matrix)
2907 ("r-matrixstats" ,r-matrixstats)
2908 ("r-pheatmap" ,r-pheatmap)
2910 ("r-proxy" ,r-proxy)
2911 ("r-qlcmatrix" ,r-qlcmatrix)
2914 ("r-reshape2" ,r-reshape2)
2915 ("r-rtsne" ,r-rtsne)
2917 ("r-stringr" ,r-stringr)
2918 ("r-tibble" ,r-tibble)
2920 ("r-viridis" ,r-viridis)))
2922 `(("r-knitr" ,r-knitr)))
2923 (home-page "https://bioconductor.org/packages/monocle")
2924 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2926 "Monocle performs differential expression and time-series analysis for
2927 single-cell expression experiments. It orders individual cells according to
2928 progress through a biological process, without knowing ahead of time which
2929 genes define progress through that process. Monocle also performs
2930 differential expression analysis, clustering, visualization, and other useful
2931 tasks on single cell expression data. It is designed to work with RNA-Seq and
2932 qPCR data, but could be used with other types as well.")
2933 (license license:artistic2.0)))
2935 (define-public r-monocle3
2943 (url "https://github.com/cole-trapnell-lab/monocle3")
2945 (file-name (git-file-name name version))
2948 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2949 (build-system r-build-system)
2951 `(("r-biobase" ,r-biobase)
2952 ("r-biocgenerics" ,r-biocgenerics)
2953 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2954 ("r-dplyr" ,r-dplyr)
2955 ("r-ggplot2" ,r-ggplot2)
2956 ("r-ggrepel" ,r-ggrepel)
2958 ("r-htmlwidgets" ,r-htmlwidgets)
2959 ("r-igraph" ,r-igraph)
2960 ("r-irlba" ,r-irlba)
2961 ("r-limma" ,r-limma)
2962 ("r-lmtest" ,r-lmtest)
2964 ("r-matrix" ,r-matrix)
2965 ("r-matrix-utils" ,r-matrix-utils)
2966 ("r-pbapply" ,r-pbapply)
2967 ("r-pbmcapply" ,r-pbmcapply)
2968 ("r-pheatmap" ,r-pheatmap)
2969 ("r-plotly" ,r-plotly)
2971 ("r-proxy" ,r-proxy)
2973 ("r-purrr" ,r-purrr)
2976 ("r-rcppparallel" ,r-rcppparallel)
2977 ("r-reshape2" ,r-reshape2)
2978 ("r-reticulate" ,r-reticulate)
2979 ("r-rhpcblasctl" ,r-rhpcblasctl)
2980 ("r-rtsne" ,r-rtsne)
2981 ("r-shiny" ,r-shiny)
2983 ("r-spdep" ,r-spdep)
2984 ("r-speedglm" ,r-speedglm)
2985 ("r-stringr" ,r-stringr)
2986 ("r-singlecellexperiment" ,r-singlecellexperiment)
2987 ("r-tibble" ,r-tibble)
2988 ("r-tidyr" ,r-tidyr)
2990 ("r-viridis" ,r-viridis)))
2991 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2992 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2994 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2995 (license license:expat)))
2997 (define-public r-noiseq
3004 (uri (bioconductor-uri "NOISeq" version))
3007 "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33"))))
3008 (properties `((upstream-name . "NOISeq")))
3009 (build-system r-build-system)
3011 `(("r-biobase" ,r-biobase)
3012 ("r-matrix" ,r-matrix)))
3013 (home-page "https://bioconductor.org/packages/NOISeq")
3014 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3016 "This package provides tools to support the analysis of RNA-seq
3017 expression data or other similar kind of data. It provides exploratory plots
3018 to evaluate saturation, count distribution, expression per chromosome, type of
3019 detected features, features length, etc. It also supports the analysis of
3020 differential expression between two experimental conditions with no parametric
3022 (license license:artistic2.0)))
3024 (define-public r-scdd
3031 (uri (bioconductor-uri "scDD" version))
3034 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
3035 (properties `((upstream-name . "scDD")))
3036 (build-system r-build-system)
3039 ("r-biocparallel" ,r-biocparallel)
3040 ("r-ebseq" ,r-ebseq)
3041 ("r-fields" ,r-fields)
3042 ("r-ggplot2" ,r-ggplot2)
3043 ("r-mclust" ,r-mclust)
3044 ("r-outliers" ,r-outliers)
3045 ("r-s4vectors" ,r-s4vectors)
3046 ("r-scran" ,r-scran)
3047 ("r-singlecellexperiment" ,r-singlecellexperiment)
3048 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3050 `(("r-knitr" ,r-knitr)))
3051 (home-page "https://github.com/kdkorthauer/scDD")
3052 (synopsis "Mixture modeling of single-cell RNA-seq data")
3054 "This package implements a method to analyze single-cell RNA-seq data
3055 utilizing flexible Dirichlet Process mixture models. Genes with differential
3056 distributions of expression are classified into several interesting patterns
3057 of differences between two conditions. The package also includes functions
3058 for simulating data with these patterns from negative binomial
3060 (license license:gpl2)))
3062 (define-public r-scone
3069 (uri (bioconductor-uri "scone" version))
3072 "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g"))))
3073 (build-system r-build-system)
3075 `(("r-aroma-light" ,r-aroma-light)
3076 ("r-biocparallel" ,r-biocparallel)
3078 ("r-class" ,r-class)
3079 ("r-cluster" ,r-cluster)
3080 ("r-compositions" ,r-compositions)
3081 ("r-diptest" ,r-diptest)
3082 ("r-edger" ,r-edger)
3084 ("r-gplots" ,r-gplots)
3085 ("r-hexbin" ,r-hexbin)
3086 ("r-limma" ,r-limma)
3087 ("r-matrixstats" ,r-matrixstats)
3088 ("r-mixtools" ,r-mixtools)
3089 ("r-rarpack" ,r-rarpack)
3090 ("r-rcolorbrewer" ,r-rcolorbrewer)
3091 ("r-rhdf5" ,r-rhdf5)
3092 ("r-ruvseq" ,r-ruvseq)
3093 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3095 `(("r-knitr" ,r-knitr)))
3096 (home-page "https://bioconductor.org/packages/scone")
3097 (synopsis "Single cell overview of normalized expression data")
3099 "SCONE is an R package for comparing and ranking the performance of
3100 different normalization schemes for single-cell RNA-seq and other
3101 high-throughput analyses.")
3102 (license license:artistic2.0)))
3104 (define-public r-geoquery
3111 (uri (bioconductor-uri "GEOquery" version))
3114 "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m"))))
3115 (properties `((upstream-name . "GEOquery")))
3116 (build-system r-build-system)
3118 `(("r-biobase" ,r-biobase)
3119 ("r-dplyr" ,r-dplyr)
3121 ("r-limma" ,r-limma)
3122 ("r-magrittr" ,r-magrittr)
3123 ("r-readr" ,r-readr)
3124 ("r-tidyr" ,r-tidyr)
3125 ("r-xml2" ,r-xml2)))
3127 `(("r-knitr" ,r-knitr)))
3128 (home-page "https://github.com/seandavi/GEOquery/")
3129 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3131 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3132 microarray data. Given the rich and varied nature of this resource, it is
3133 only natural to want to apply BioConductor tools to these data. GEOquery is
3134 the bridge between GEO and BioConductor.")
3135 (license license:gpl2)))
3137 (define-public r-illuminaio
3139 (name "r-illuminaio")
3144 (uri (bioconductor-uri "illuminaio" version))
3147 "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c"))))
3148 (build-system r-build-system)
3150 `(("r-base64" ,r-base64)))
3151 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3152 (synopsis "Parse Illumina microarray output files")
3154 "This package provides tools for parsing Illumina's microarray output
3155 files, including IDAT.")
3156 (license license:gpl2)))
3158 (define-public r-siggenes
3165 (uri (bioconductor-uri "siggenes" version))
3168 "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy"))))
3169 (build-system r-build-system)
3171 `(("r-biobase" ,r-biobase)
3172 ("r-multtest" ,r-multtest)
3173 ("r-scrime" ,r-scrime)))
3174 (home-page "https://bioconductor.org/packages/siggenes/")
3176 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3178 "This package provides tools for the identification of differentially
3179 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3180 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3181 Bayes Analyses of Microarrays} (EBAM).")
3182 (license license:lgpl2.0+)))
3184 (define-public r-bumphunter
3186 (name "r-bumphunter")
3191 (uri (bioconductor-uri "bumphunter" version))
3194 "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq"))))
3195 (build-system r-build-system)
3197 `(("r-annotationdbi" ,r-annotationdbi)
3198 ("r-biocgenerics" ,r-biocgenerics)
3199 ("r-dorng" ,r-dorng)
3200 ("r-foreach" ,r-foreach)
3201 ("r-genomeinfodb" ,r-genomeinfodb)
3202 ("r-genomicfeatures" ,r-genomicfeatures)
3203 ("r-genomicranges" ,r-genomicranges)
3204 ("r-iranges" ,r-iranges)
3205 ("r-iterators" ,r-iterators)
3206 ("r-limma" ,r-limma)
3207 ("r-locfit" ,r-locfit)
3208 ("r-matrixstats" ,r-matrixstats)
3209 ("r-s4vectors" ,r-s4vectors)))
3210 (home-page "https://github.com/ririzarr/bumphunter")
3211 (synopsis "Find bumps in genomic data")
3213 "This package provides tools for finding bumps in genomic data in order
3214 to identify differentially methylated regions in epigenetic epidemiology
3216 (license license:artistic2.0)))
3218 (define-public r-minfi
3225 (uri (bioconductor-uri "minfi" version))
3228 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
3229 (build-system r-build-system)
3231 `(("r-beanplot" ,r-beanplot)
3232 ("r-biobase" ,r-biobase)
3233 ("r-biocgenerics" ,r-biocgenerics)
3234 ("r-biocparallel" ,r-biocparallel)
3235 ("r-biostrings" ,r-biostrings)
3236 ("r-bumphunter" ,r-bumphunter)
3237 ("r-data-table" ,r-data-table)
3238 ("r-delayedarray" ,r-delayedarray)
3239 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3240 ("r-genefilter" ,r-genefilter)
3241 ("r-genomeinfodb" ,r-genomeinfodb)
3242 ("r-genomicranges" ,r-genomicranges)
3243 ("r-geoquery" ,r-geoquery)
3244 ("r-hdf5array" ,r-hdf5array)
3245 ("r-illuminaio" ,r-illuminaio)
3246 ("r-iranges" ,r-iranges)
3247 ("r-lattice" ,r-lattice)
3248 ("r-limma" ,r-limma)
3250 ("r-mclust" ,r-mclust)
3252 ("r-nor1mix" ,r-nor1mix)
3253 ("r-preprocesscore" ,r-preprocesscore)
3254 ("r-quadprog" ,r-quadprog)
3255 ("r-rcolorbrewer" ,r-rcolorbrewer)
3256 ("r-reshape" ,r-reshape)
3257 ("r-s4vectors" ,r-s4vectors)
3258 ("r-siggenes" ,r-siggenes)
3259 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3261 `(("r-knitr" ,r-knitr)))
3262 (home-page "https://github.com/hansenlab/minfi")
3263 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3265 "This package provides tools to analyze and visualize Illumina Infinium
3266 methylation arrays.")
3267 (license license:artistic2.0)))
3269 (define-public r-methylumi
3271 (name "r-methylumi")
3276 (uri (bioconductor-uri "methylumi" version))
3279 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
3280 (build-system r-build-system)
3282 `(("r-annotate" ,r-annotate)
3283 ("r-annotationdbi" ,r-annotationdbi)
3284 ("r-biobase" ,r-biobase)
3285 ("r-biocgenerics" ,r-biocgenerics)
3286 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3287 ("r-genefilter" ,r-genefilter)
3288 ("r-genomeinfodb" ,r-genomeinfodb)
3289 ("r-genomicranges" ,r-genomicranges)
3290 ("r-ggplot2" ,r-ggplot2)
3291 ("r-illuminaio" ,r-illuminaio)
3292 ("r-iranges" ,r-iranges)
3293 ("r-lattice" ,r-lattice)
3294 ("r-matrixstats" ,r-matrixstats)
3295 ("r-minfi" ,r-minfi)
3296 ("r-reshape2" ,r-reshape2)
3297 ("r-s4vectors" ,r-s4vectors)
3298 ("r-scales" ,r-scales)
3299 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3301 `(("r-knitr" ,r-knitr)))
3302 (home-page "https://bioconductor.org/packages/methylumi")
3303 (synopsis "Handle Illumina methylation data")
3305 "This package provides classes for holding and manipulating Illumina
3306 methylation data. Based on eSet, it can contain MIAME information, sample
3307 information, feature information, and multiple matrices of data. An
3308 \"intelligent\" import function, methylumiR can read the Illumina text files
3309 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3310 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3311 background correction, and quality control features for GoldenGate, Infinium,
3312 and Infinium HD arrays are also included.")
3313 (license license:gpl2)))
3315 (define-public r-lumi
3322 (uri (bioconductor-uri "lumi" version))
3325 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
3326 (build-system r-build-system)
3328 `(("r-affy" ,r-affy)
3329 ("r-annotate" ,r-annotate)
3330 ("r-annotationdbi" ,r-annotationdbi)
3331 ("r-biobase" ,r-biobase)
3333 ("r-genomicfeatures" ,r-genomicfeatures)
3334 ("r-genomicranges" ,r-genomicranges)
3335 ("r-kernsmooth" ,r-kernsmooth)
3336 ("r-lattice" ,r-lattice)
3338 ("r-methylumi" ,r-methylumi)
3340 ("r-nleqslv" ,r-nleqslv)
3341 ("r-preprocesscore" ,r-preprocesscore)
3342 ("r-rsqlite" ,r-rsqlite)))
3343 (home-page "https://bioconductor.org/packages/lumi")
3344 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3346 "The lumi package provides an integrated solution for the Illumina
3347 microarray data analysis. It includes functions of Illumina
3348 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3349 variance stabilization, normalization and gene annotation at the probe level.
3350 It also includes the functions of processing Illumina methylation microarrays,
3351 especially Illumina Infinium methylation microarrays.")
3352 (license license:lgpl2.0+)))
3354 (define-public r-linnorm
3361 (uri (bioconductor-uri "Linnorm" version))
3364 "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp"))))
3365 (properties `((upstream-name . "Linnorm")))
3366 (build-system r-build-system)
3368 `(("r-amap" ,r-amap)
3369 ("r-apcluster" ,r-apcluster)
3370 ("r-ellipse" ,r-ellipse)
3371 ("r-fastcluster" ,r-fastcluster)
3373 ("r-ggdendro" ,r-ggdendro)
3374 ("r-ggplot2" ,r-ggplot2)
3375 ("r-gmodels" ,r-gmodels)
3376 ("r-igraph" ,r-igraph)
3377 ("r-limma" ,r-limma)
3379 ("r-mclust" ,r-mclust)
3381 ("r-rcpparmadillo" ,r-rcpparmadillo)
3382 ("r-rtsne" ,r-rtsne)
3383 ("r-statmod" ,r-statmod)
3384 ("r-vegan" ,r-vegan)
3387 `(("r-knitr" ,r-knitr)))
3388 (home-page "http://www.jjwanglab.org/Linnorm/")
3389 (synopsis "Linear model and normality based transformation method")
3391 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3392 count data or any large scale count data. It transforms such datasets for
3393 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3394 the following pipelines are implemented:
3397 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3398 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3399 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3400 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3401 @item Differential expression analysis or differential peak detection using
3402 limma (@code{Linnorm.limma})
3403 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3404 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3405 @item Stable gene selection for scRNA-seq data; for users without or who do
3406 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3407 @item Data imputation (@code{Linnorm.DataImput}).
3410 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3411 @code{RnaXSim} function is included for simulating RNA-seq data for the
3412 evaluation of DEG analysis methods.")
3413 (license license:expat)))
3415 (define-public r-ioniser
3422 (uri (bioconductor-uri "IONiseR" version))
3425 "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w"))))
3426 (properties `((upstream-name . "IONiseR")))
3427 (build-system r-build-system)
3429 `(("r-biocgenerics" ,r-biocgenerics)
3430 ("r-biocparallel" ,r-biocparallel)
3431 ("r-biostrings" ,r-biostrings)
3432 ("r-bit64" ,r-bit64)
3433 ("r-dplyr" ,r-dplyr)
3434 ("r-ggplot2" ,r-ggplot2)
3435 ("r-magrittr" ,r-magrittr)
3436 ("r-rhdf5" ,r-rhdf5)
3437 ("r-shortread" ,r-shortread)
3438 ("r-stringr" ,r-stringr)
3439 ("r-tibble" ,r-tibble)
3440 ("r-tidyr" ,r-tidyr)
3441 ("r-xvector" ,r-xvector)))
3443 `(("r-knitr" ,r-knitr)))
3444 (home-page "https://bioconductor.org/packages/IONiseR/")
3445 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3447 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3448 MinION data. It extracts summary statistics from a set of fast5 files and can
3449 be used either before or after base calling. In addition to standard
3450 summaries of the read-types produced, it provides a number of plots for
3451 visualising metrics relative to experiment run time or spatially over the
3452 surface of a flowcell.")
3453 (license license:expat)))
3455 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3456 (define-public r-gkmsvm
3463 (uri (cran-uri "gkmSVM" version))
3466 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3467 (properties `((upstream-name . "gkmSVM")))
3468 (build-system r-build-system)
3470 `(("r-kernlab" ,r-kernlab)
3473 ("r-seqinr" ,r-seqinr)))
3474 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3475 (synopsis "Gapped-kmer support vector machine")
3477 "This R package provides tools for training gapped-kmer SVM classifiers
3478 for DNA and protein sequences. This package supports several sequence
3479 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3480 (license license:gpl2+)))
3482 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3483 (define-public r-mutoss
3490 (uri (cran-uri "mutoss" version))
3493 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3494 (properties `((upstream-name . "mutoss")))
3495 (build-system r-build-system)
3497 `(("r-multcomp" ,r-multcomp)
3498 ("r-multtest" ,r-multtest)
3499 ("r-mvtnorm" ,r-mvtnorm)
3500 ("r-plotrix" ,r-plotrix)))
3501 (home-page "https://github.com/kornl/mutoss/")
3502 (synopsis "Unified multiple testing procedures")
3504 "This package is designed to ease the application and comparison of
3505 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3506 are standardized and usable by the accompanying mutossGUI package.")
3507 ;; Any version of the GPL.
3508 (license (list license:gpl2+ license:gpl3+))))
3510 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3511 ;; from Bioconductor, so we put it here.
3512 (define-public r-metap
3519 (uri (cran-uri "metap" version))
3522 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3523 (build-system r-build-system)
3525 `(("r-lattice" ,r-lattice)
3526 ("r-mutoss" ,r-mutoss)
3527 ("r-rdpack" ,r-rdpack)
3528 ("r-tfisher" ,r-tfisher)))
3529 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3530 (synopsis "Meta-analysis of significance values")
3532 "The canonical way to perform meta-analysis involves using effect sizes.
3533 When they are not available this package provides a number of methods for
3534 meta-analysis of significance values including the methods of Edgington,
3535 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3536 published results; and a routine for graphical display.")
3537 (license license:gpl2)))
3539 (define-public r-triform
3546 (uri (bioconductor-uri "triform" version))
3549 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3550 (build-system r-build-system)
3552 `(("r-biocgenerics" ,r-biocgenerics)
3553 ("r-iranges" ,r-iranges)
3554 ("r-yaml" ,r-yaml)))
3555 (home-page "https://bioconductor.org/packages/triform/")
3556 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3558 "The Triform algorithm uses model-free statistics to identify peak-like
3559 distributions of TF ChIP sequencing reads, taking advantage of an improved
3560 peak definition in combination with known profile characteristics.")
3561 (license license:gpl2)))
3563 (define-public r-varianttools
3565 (name "r-varianttools")
3570 (uri (bioconductor-uri "VariantTools" version))
3573 "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx"))))
3574 (properties `((upstream-name . "VariantTools")))
3575 (build-system r-build-system)
3577 `(("r-biobase" ,r-biobase)
3578 ("r-biocgenerics" ,r-biocgenerics)
3579 ("r-biocparallel" ,r-biocparallel)
3580 ("r-biostrings" ,r-biostrings)
3581 ("r-bsgenome" ,r-bsgenome)
3582 ("r-genomeinfodb" ,r-genomeinfodb)
3583 ("r-genomicfeatures" ,r-genomicfeatures)
3584 ("r-genomicranges" ,r-genomicranges)
3585 ("r-iranges" ,r-iranges)
3586 ("r-matrix" ,r-matrix)
3587 ("r-rsamtools" ,r-rsamtools)
3588 ("r-rtracklayer" ,r-rtracklayer)
3589 ("r-s4vectors" ,r-s4vectors)
3590 ("r-variantannotation" ,r-variantannotation)))
3591 (home-page "https://bioconductor.org/packages/VariantTools/")
3592 (synopsis "Tools for exploratory analysis of variant calls")
3594 "Explore, diagnose, and compare variant calls using filters. The
3595 VariantTools package supports a workflow for loading data, calling single
3596 sample variants and tumor-specific somatic mutations or other sample-specific
3597 variant types (e.g., RNA editing). Most of the functions operate on
3598 alignments (BAM files) or datasets of called variants. The user is expected
3599 to have already aligned the reads with a separate tool, e.g., GSNAP via
3601 (license license:artistic2.0)))
3603 (define-public r-heatplus
3610 (uri (bioconductor-uri "Heatplus" version))
3613 "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw"))))
3614 (properties `((upstream-name . "Heatplus")))
3615 (build-system r-build-system)
3617 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3618 (home-page "https://github.com/alexploner/Heatplus")
3619 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3621 "This package provides tools to display a rectangular heatmap (intensity
3622 plot) of a data matrix. By default, both samples (columns) and features (row)
3623 of the matrix are sorted according to a hierarchical clustering, and the
3624 corresponding dendrogram is plotted. Optionally, panels with additional
3625 information about samples and features can be added to the plot.")
3626 (license license:gpl2+)))
3628 (define-public r-gosemsim
3635 (uri (bioconductor-uri "GOSemSim" version))
3638 "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
3639 (properties `((upstream-name . "GOSemSim")))
3640 (build-system r-build-system)
3642 `(("r-annotationdbi" ,r-annotationdbi)
3643 ("r-go-db" ,r-go-db)
3644 ("r-rcpp" ,r-rcpp)))
3646 `(("r-knitr" ,r-knitr)))
3647 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3648 (synopsis "GO-terms semantic similarity measures")
3650 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3651 quantitative ways to compute similarities between genes and gene groups, and
3652 have became important basis for many bioinformatics analysis approaches.
3653 GOSemSim is an R package for semantic similarity computation among GO terms,
3654 sets of GO terms, gene products and gene clusters.")
3655 (license license:artistic2.0)))
3657 (define-public r-anota
3664 (uri (bioconductor-uri "anota" version))
3667 "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm"))))
3668 (build-system r-build-system)
3670 `(("r-multtest" ,r-multtest)
3671 ("r-qvalue" ,r-qvalue)))
3672 (home-page "https://bioconductor.org/packages/anota/")
3673 (synopsis "Analysis of translational activity")
3675 "Genome wide studies of translational control is emerging as a tool to
3676 study various biological conditions. The output from such analysis is both
3677 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3678 involved in translation (the actively translating mRNA level) for each mRNA.
3679 The standard analysis of such data strives towards identifying differential
3680 translational between two or more sample classes - i.e. differences in
3681 actively translated mRNA levels that are independent of underlying differences
3682 in cytosolic mRNA levels. This package allows for such analysis using partial
3683 variances and the random variance model. As 10s of thousands of mRNAs are
3684 analyzed in parallel the library performs a number of tests to assure that
3685 the data set is suitable for such analysis.")
3686 (license license:gpl3)))
3688 (define-public r-sigpathway
3690 (name "r-sigpathway")
3695 (uri (bioconductor-uri "sigPathway" version))
3698 "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5"))))
3699 (properties `((upstream-name . "sigPathway")))
3700 (build-system r-build-system)
3701 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3702 (synopsis "Pathway analysis")
3704 "This package is used to conduct pathway analysis by calculating the NT_k
3705 and NE_k statistics in a statistical framework for determining whether a
3706 specified group of genes for a pathway has a coordinated association with a
3707 phenotype of interest.")
3708 (license license:gpl2)))
3710 (define-public r-fgsea
3717 (uri (bioconductor-uri "fgsea" version))
3720 "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc"))))
3721 (build-system r-build-system)
3724 ("r-biocparallel" ,r-biocparallel)
3725 ("r-data-table" ,r-data-table)
3726 ("r-fastmatch" ,r-fastmatch)
3727 ("r-ggplot2" ,r-ggplot2)
3728 ("r-gridextra" ,r-gridextra)
3729 ("r-matrix" ,r-matrix)
3730 ("r-rcpp" ,r-rcpp)))
3732 `(("r-knitr" ,r-knitr)))
3733 (home-page "https://github.com/ctlab/fgsea/")
3734 (synopsis "Fast gene set enrichment analysis")
3736 "The package implements an algorithm for fast gene set enrichment
3737 analysis. Using the fast algorithm makes more permutations and gets
3738 more fine grained p-values, which allows using accurate standard approaches
3739 to multiple hypothesis correction.")
3740 (license license:expat)))
3742 (define-public r-dose
3749 (uri (bioconductor-uri "DOSE" version))
3752 "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8"))))
3753 (properties `((upstream-name . "DOSE")))
3754 (build-system r-build-system)
3756 `(("r-annotationdbi" ,r-annotationdbi)
3757 ("r-biocparallel" ,r-biocparallel)
3758 ("r-do-db" ,r-do-db)
3759 ("r-fgsea" ,r-fgsea)
3760 ("r-ggplot2" ,r-ggplot2)
3761 ("r-gosemsim" ,r-gosemsim)
3762 ("r-qvalue" ,r-qvalue)
3763 ("r-reshape2" ,r-reshape2)))
3765 `(("r-knitr" ,r-knitr)))
3766 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3767 (synopsis "Disease ontology semantic and enrichment analysis")
3769 "This package implements five methods proposed by Resnik, Schlicker,
3770 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3771 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3772 including hypergeometric model and gene set enrichment analysis are also
3773 implemented for discovering disease associations of high-throughput biological
3775 (license license:artistic2.0)))
3777 (define-public r-enrichplot
3779 (name "r-enrichplot")
3784 (uri (bioconductor-uri "enrichplot" version))
3787 "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7"))))
3788 (build-system r-build-system)
3790 `(("r-annotationdbi" ,r-annotationdbi)
3791 ("r-cowplot" ,r-cowplot)
3793 ("r-europepmc" ,r-europepmc)
3794 ("r-ggplot2" ,r-ggplot2)
3795 ("r-ggplotify" ,r-ggplotify)
3796 ("r-ggraph" ,r-ggraph)
3797 ("r-ggridges" ,r-ggridges)
3798 ("r-gosemsim" ,r-gosemsim)
3799 ("r-gridextra" ,r-gridextra)
3800 ("r-igraph" ,r-igraph)
3802 ("r-purrr" ,r-purrr)
3803 ("r-rcolorbrewer" ,r-rcolorbrewer)
3804 ("r-reshape2" ,r-reshape2)
3805 ("r-scatterpie" ,r-scatterpie)))
3807 `(("r-knitr" ,r-knitr)))
3808 (home-page "https://github.com/GuangchuangYu/enrichplot")
3809 (synopsis "Visualization of functional enrichment result")
3811 "The enrichplot package implements several visualization methods for
3812 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3813 All the visualization methods are developed based on ggplot2 graphics.")
3814 (license license:artistic2.0)))
3816 (define-public r-clusterprofiler
3818 (name "r-clusterprofiler")
3823 (uri (bioconductor-uri "clusterProfiler" version))
3826 "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
3828 `((upstream-name . "clusterProfiler")))
3829 (build-system r-build-system)
3831 `(("r-annotationdbi" ,r-annotationdbi)
3833 ("r-downloader" ,r-downloader)
3834 ("r-dplyr" ,r-dplyr)
3835 ("r-enrichplot" ,r-enrichplot)
3836 ("r-go-db" ,r-go-db)
3837 ("r-gosemsim" ,r-gosemsim)
3838 ("r-magrittr" ,r-magrittr)
3840 ("r-qvalue" ,r-qvalue)
3841 ("r-rlang" ,r-rlang)
3842 ("r-rvcheck" ,r-rvcheck)
3843 ("r-tidyr" ,r-tidyr)))
3845 `(("r-knitr" ,r-knitr)))
3846 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3847 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3849 "This package implements methods to analyze and visualize functional
3850 profiles (GO and KEGG) of gene and gene clusters.")
3851 (license license:artistic2.0)))
3853 (define-public r-mlinterfaces
3855 (name "r-mlinterfaces")
3860 (uri (bioconductor-uri "MLInterfaces" version))
3863 "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq"))))
3864 (properties `((upstream-name . "MLInterfaces")))
3865 (build-system r-build-system)
3867 `(("r-annotate" ,r-annotate)
3868 ("r-biobase" ,r-biobase)
3869 ("r-biocgenerics" ,r-biocgenerics)
3870 ("r-cluster" ,r-cluster)
3873 ("r-gdata" ,r-gdata)
3874 ("r-genefilter" ,r-genefilter)
3875 ("r-ggvis" ,r-ggvis)
3876 ("r-hwriter" ,r-hwriter)
3878 ("r-mlbench" ,r-mlbench)
3880 ("r-rcolorbrewer" ,r-rcolorbrewer)
3882 ("r-rpart" ,r-rpart)
3883 ("r-sfsmisc" ,r-sfsmisc)
3884 ("r-shiny" ,r-shiny)
3885 ("r-threejs" ,r-threejs)))
3886 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3887 (synopsis "Interfaces to R machine learning procedures")
3889 "This package provides uniform interfaces to machine learning code for
3890 data in R and Bioconductor containers.")
3891 ;; Any version of the LGPL.
3892 (license license:lgpl2.1+)))
3894 (define-public r-annaffy
3901 (uri (bioconductor-uri "annaffy" version))
3904 "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
3905 (build-system r-build-system)
3908 (modify-phases %standard-phases
3909 (add-after 'unpack 'remove-reference-to-non-free-data
3911 (substitute* "DESCRIPTION"
3915 `(("r-annotationdbi" ,r-annotationdbi)
3916 ("r-biobase" ,r-biobase)
3918 ("r-go-db" ,r-go-db)))
3919 (home-page "https://bioconductor.org/packages/annaffy/")
3920 (synopsis "Annotation tools for Affymetrix biological metadata")
3922 "This package provides functions for handling data from Bioconductor
3923 Affymetrix annotation data packages. It produces compact HTML and text
3924 reports including experimental data and URL links to many online databases.
3925 It allows searching of biological metadata using various criteria.")
3926 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3927 ;; the LGPL 2.1 is included.
3928 (license license:lgpl2.1+)))
3930 (define-public r-a4core
3937 (uri (bioconductor-uri "a4Core" version))
3940 "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp"))))
3941 (properties `((upstream-name . "a4Core")))
3942 (build-system r-build-system)
3944 `(("r-biobase" ,r-biobase)
3945 ("r-glmnet" ,r-glmnet)))
3946 (home-page "https://bioconductor.org/packages/a4Core")
3947 (synopsis "Automated Affymetrix array analysis core package")
3949 "This is the core package for the automated analysis of Affymetrix
3951 (license license:gpl3)))
3953 (define-public r-a4classif
3955 (name "r-a4classif")
3960 (uri (bioconductor-uri "a4Classif" version))
3963 "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr"))))
3964 (properties `((upstream-name . "a4Classif")))
3965 (build-system r-build-system)
3967 `(("r-a4core" ,r-a4core)
3968 ("r-a4preproc" ,r-a4preproc)
3969 ("r-glmnet" ,r-glmnet)
3970 ("r-mlinterfaces" ,r-mlinterfaces)
3973 ("r-varselrf" ,r-varselrf)))
3974 (home-page "https://bioconductor.org/packages/a4Classif/")
3975 (synopsis "Automated Affymetrix array analysis classification package")
3977 "This is the classification package for the automated analysis of
3978 Affymetrix arrays.")
3979 (license license:gpl3)))
3981 (define-public r-a4preproc
3983 (name "r-a4preproc")
3988 (uri (bioconductor-uri "a4Preproc" version))
3991 "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8"))))
3992 (properties `((upstream-name . "a4Preproc")))
3993 (build-system r-build-system)
3995 `(("r-annotationdbi" ,r-annotationdbi)))
3996 (home-page "https://bioconductor.org/packages/a4Preproc/")
3997 (synopsis "Automated Affymetrix array analysis preprocessing package")
3999 "This is a package for the automated analysis of Affymetrix arrays. It
4000 is used for preprocessing the arrays.")
4001 (license license:gpl3)))
4003 (define-public r-a4reporting
4005 (name "r-a4reporting")
4010 (uri (bioconductor-uri "a4Reporting" version))
4013 "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f"))))
4014 (properties `((upstream-name . "a4Reporting")))
4015 (build-system r-build-system)
4017 `(("r-annaffy" ,r-annaffy)
4018 ("r-xtable" ,r-xtable)))
4019 (home-page "https://bioconductor.org/packages/a4Reporting/")
4020 (synopsis "Automated Affymetrix array analysis reporting package")
4022 "This is a package for the automated analysis of Affymetrix arrays. It
4023 provides reporting features.")
4024 (license license:gpl3)))
4026 (define-public r-a4base
4033 (uri (bioconductor-uri "a4Base" version))
4036 "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02"))))
4037 (properties `((upstream-name . "a4Base")))
4038 (build-system r-build-system)
4040 `(("r-a4core" ,r-a4core)
4041 ("r-a4preproc" ,r-a4preproc)
4042 ("r-annaffy" ,r-annaffy)
4043 ("r-annotationdbi" ,r-annotationdbi)
4044 ("r-biobase" ,r-biobase)
4045 ("r-genefilter" ,r-genefilter)
4046 ("r-glmnet" ,r-glmnet)
4047 ("r-gplots" ,r-gplots)
4048 ("r-limma" ,r-limma)
4050 ("r-multtest" ,r-multtest)))
4051 (home-page "https://bioconductor.org/packages/a4Base/")
4052 (synopsis "Automated Affymetrix array analysis base package")
4054 "This package provides basic features for the automated analysis of
4055 Affymetrix arrays.")
4056 (license license:gpl3)))
4065 (uri (bioconductor-uri "a4" version))
4068 "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7"))))
4069 (build-system r-build-system)
4071 `(("r-a4base" ,r-a4base)
4072 ("r-a4classif" ,r-a4classif)
4073 ("r-a4core" ,r-a4core)
4074 ("r-a4preproc" ,r-a4preproc)
4075 ("r-a4reporting" ,r-a4reporting)))
4076 (home-page "https://bioconductor.org/packages/a4/")
4077 (synopsis "Automated Affymetrix array analysis umbrella package")
4079 "This package provides a software suite for the automated analysis of
4080 Affymetrix arrays.")
4081 (license license:gpl3)))
4083 (define-public r-abseqr
4090 (uri (bioconductor-uri "abseqR" version))
4093 "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5"))))
4094 (properties `((upstream-name . "abseqR")))
4095 (build-system r-build-system)
4097 `(("pandoc" ,pandoc)
4098 ("pandoc-citeproc" ,pandoc-citeproc)))
4100 `(("r-biocparallel" ,r-biocparallel)
4101 ("r-biocstyle" ,r-biocstyle)
4102 ("r-circlize" ,r-circlize)
4103 ("r-flexdashboard" ,r-flexdashboard)
4104 ("r-ggcorrplot" ,r-ggcorrplot)
4105 ("r-ggdendro" ,r-ggdendro)
4106 ("r-ggplot2" ,r-ggplot2)
4107 ("r-gridextra" ,r-gridextra)
4108 ("r-knitr" ,r-knitr)
4109 ("r-plotly" ,r-plotly)
4112 ("r-rcolorbrewer" ,r-rcolorbrewer)
4113 ("r-reshape2" ,r-reshape2)
4114 ("r-rmarkdown" ,r-rmarkdown)
4115 ("r-stringr" ,r-stringr)
4116 ("r-vegan" ,r-vegan)
4117 ("r-venndiagram" ,r-venndiagram)))
4119 `(("r-knitr" ,r-knitr)))
4120 (home-page "https://github.com/malhamdoosh/abseqR")
4121 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4123 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4124 sequencing datasets generated from antibody libraries and abseqR is one of its
4125 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4126 capabilities and allows them to generate interactive HTML reports for the
4127 convenience of viewing and sharing with other researchers. Additionally,
4128 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4129 further downstream analysis on its output.")
4130 (license license:gpl3)))
4132 (define-public r-bacon
4139 (uri (bioconductor-uri "bacon" version))
4142 "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl"))))
4143 (build-system r-build-system)
4145 `(("r-biocparallel" ,r-biocparallel)
4146 ("r-ellipse" ,r-ellipse)
4147 ("r-ggplot2" ,r-ggplot2)))
4149 `(("r-knitr" ,r-knitr)))
4150 (home-page "https://bioconductor.org/packages/bacon/")
4151 (synopsis "Controlling bias and inflation in association studies")
4153 "Bacon can be used to remove inflation and bias often observed in
4154 epigenome- and transcriptome-wide association studies. To this end bacon
4155 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4156 fitting a three-component normal mixture on z-scores.")
4157 (license license:gpl2+)))
4159 (define-public r-rgadem
4166 (uri (bioconductor-uri "rGADEM" version))
4169 "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8"))))
4170 (properties `((upstream-name . "rGADEM")))
4171 (build-system r-build-system)
4173 `(("r-biostrings" ,r-biostrings)
4174 ("r-bsgenome" ,r-bsgenome)
4175 ("r-genomicranges" ,r-genomicranges)
4176 ("r-iranges" ,r-iranges)
4177 ("r-seqlogo" ,r-seqlogo)))
4178 (home-page "https://bioconductor.org/packages/rGADEM/")
4179 (synopsis "De novo sequence motif discovery")
4181 "rGADEM is an efficient de novo motif discovery tool for large-scale
4182 genomic sequence data.")
4183 (license license:artistic2.0)))
4185 (define-public r-motiv
4192 (uri (bioconductor-uri "MotIV" version))
4195 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4196 (properties `((upstream-name . "MotIV")))
4197 (build-system r-build-system)
4201 `(("r-biocgenerics" ,r-biocgenerics)
4202 ("r-biostrings" ,r-biostrings)
4203 ("r-genomicranges" ,r-genomicranges)
4204 ("r-iranges" ,r-iranges)
4205 ("r-lattice" ,r-lattice)
4206 ("r-rgadem" ,r-rgadem)
4207 ("r-s4vectors" ,r-s4vectors)))
4208 (home-page "https://bioconductor.org/packages/MotIV/")
4209 (synopsis "Motif identification and validation")
4211 "This package is used for the identification and validation of sequence
4212 motifs. It makes use of STAMP for comparing a set of motifs to a given
4213 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4214 distributions, modules and filter motifs.")
4215 (license license:gpl2)))
4217 (define-public r-motifdb
4223 (uri (bioconductor-uri "MotifDb" version))
4225 (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm"))))
4226 (properties `((upstream-name . "MotifDb")))
4227 (build-system r-build-system)
4229 `(("r-biocgenerics" ,r-biocgenerics)
4230 ("r-biostrings" ,r-biostrings)
4231 ("r-genomicranges" ,r-genomicranges)
4232 ("r-iranges" ,r-iranges)
4233 ("r-rtracklayer" ,r-rtracklayer)
4234 ("r-s4vectors" ,r-s4vectors)
4235 ("r-splitstackshape" ,r-splitstackshape)))
4237 `(("r-knitr" ,r-knitr)))
4238 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4239 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4240 (description "This package provides more than 2000 annotated position
4241 frequency matrices from nine public sources, for multiple organisms.")
4242 (license license:artistic2.0)))
4244 (define-public r-motifbreakr
4246 (name "r-motifbreakr")
4250 (uri (bioconductor-uri "motifbreakR" version))
4252 (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm"))))
4253 (properties `((upstream-name . "motifbreakR")))
4254 (build-system r-build-system)
4256 `(("r-biocgenerics" ,r-biocgenerics)
4257 ("r-biocparallel" ,r-biocparallel)
4258 ("r-biostrings" ,r-biostrings)
4259 ("r-bsgenome" ,r-bsgenome)
4260 ("r-genomeinfodb" ,r-genomeinfodb)
4261 ("r-genomicranges" ,r-genomicranges)
4262 ("r-grimport" ,r-grimport)
4264 ("r-iranges" ,r-iranges)
4265 ("r-matrixstats" ,r-matrixstats)
4266 ("r-motifdb" ,r-motifdb)
4267 ("r-motifstack" ,r-motifstack)
4268 ("r-rtracklayer" ,r-rtracklayer)
4269 ("r-s4vectors" ,r-s4vectors)
4270 ("r-stringr" ,r-stringr)
4271 ("r-summarizedexperiment" ,r-summarizedexperiment)
4272 ("r-tfmpvalue" ,r-tfmpvalue)
4273 ("r-variantannotation" ,r-variantannotation)))
4275 `(("r-knitr" ,r-knitr)))
4276 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4277 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4278 (description "This package allows biologists to judge in the first place
4279 whether the sequence surrounding the polymorphism is a good match, and in
4280 the second place how much information is gained or lost in one allele of
4281 the polymorphism relative to another. This package gives a choice of
4282 algorithms for interrogation of genomes with motifs from public sources:
4284 @item a weighted-sum probability matrix;
4285 @item log-probabilities;
4286 @item weighted by relative entropy.
4289 This package can predict effects for novel or previously described variants in
4290 public databases, making it suitable for tasks beyond the scope of its original
4291 design. Lastly, it can be used to interrogate any genome curated within
4293 (license license:gpl2+)))
4295 (define-public r-motifstack
4297 (name "r-motifstack")
4302 (uri (bioconductor-uri "motifStack" version))
4305 "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
4306 (properties `((upstream-name . "motifStack")))
4307 (build-system r-build-system)
4309 `(("r-ade4" ,r-ade4)
4310 ("r-biostrings" ,r-biostrings)
4311 ("r-ggplot2" ,r-ggplot2)
4312 ("r-grimport2" ,r-grimport2)
4313 ("r-htmlwidgets" ,r-htmlwidgets)
4314 ("r-motiv" ,r-motiv)
4315 ("r-scales" ,r-scales)
4318 `(("r-knitr" ,r-knitr)))
4319 (home-page "https://bioconductor.org/packages/motifStack/")
4320 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4322 "The motifStack package is designed for graphic representation of
4323 multiple motifs with different similarity scores. It works with both DNA/RNA
4324 sequence motifs and amino acid sequence motifs. In addition, it provides the
4325 flexibility for users to customize the graphic parameters such as the font
4326 type and symbol colors.")
4327 (license license:gpl2+)))
4329 (define-public r-genomicscores
4331 (name "r-genomicscores")
4336 (uri (bioconductor-uri "GenomicScores" version))
4339 "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb"))))
4340 (properties `((upstream-name . "GenomicScores")))
4341 (build-system r-build-system)
4343 `(("r-annotationhub" ,r-annotationhub)
4344 ("r-biobase" ,r-biobase)
4345 ("r-biocgenerics" ,r-biocgenerics)
4346 ("r-biostrings" ,r-biostrings)
4347 ("r-delayedarray" ,r-delayedarray)
4348 ("r-genomeinfodb" ,r-genomeinfodb)
4349 ("r-genomicranges" ,r-genomicranges)
4350 ("r-hdf5array" ,r-hdf5array)
4351 ("r-iranges" ,r-iranges)
4352 ("r-rhdf5" ,r-rhdf5)
4353 ("r-s4vectors" ,r-s4vectors)
4356 `(("r-knitr" ,r-knitr)))
4357 (home-page "https://github.com/rcastelo/GenomicScores/")
4358 (synopsis "Work with genome-wide position-specific scores")
4360 "This package provides infrastructure to store and access genome-wide
4361 position-specific scores within R and Bioconductor.")
4362 (license license:artistic2.0)))
4364 (define-public r-atacseqqc
4366 (name "r-atacseqqc")
4371 (uri (bioconductor-uri "ATACseqQC" version))
4374 "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
4375 (properties `((upstream-name . "ATACseqQC")))
4376 (build-system r-build-system)
4378 `(("r-biocgenerics" ,r-biocgenerics)
4379 ("r-biostrings" ,r-biostrings)
4380 ("r-bsgenome" ,r-bsgenome)
4381 ("r-chippeakanno" ,r-chippeakanno)
4382 ("r-edger" ,r-edger)
4383 ("r-genomeinfodb" ,r-genomeinfodb)
4384 ("r-genomicalignments" ,r-genomicalignments)
4385 ("r-genomicranges" ,r-genomicranges)
4386 ("r-genomicscores" ,r-genomicscores)
4387 ("r-iranges" ,r-iranges)
4388 ("r-kernsmooth" ,r-kernsmooth)
4389 ("r-limma" ,r-limma)
4390 ("r-motifstack" ,r-motifstack)
4391 ("r-preseqr" ,r-preseqr)
4392 ("r-randomforest" ,r-randomforest)
4393 ("r-rsamtools" ,r-rsamtools)
4394 ("r-rtracklayer" ,r-rtracklayer)
4395 ("r-s4vectors" ,r-s4vectors)))
4397 `(("r-knitr" ,r-knitr)))
4398 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4399 (synopsis "ATAC-seq quality control")
4401 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4402 sequencing, is a rapid and sensitive method for chromatin accessibility
4403 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4404 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4405 assess whether their ATAC-seq experiment is successful. It includes
4406 diagnostic plots of fragment size distribution, proportion of mitochondria
4407 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4409 (license license:gpl2+)))
4411 (define-public r-gofuncr
4418 (uri (bioconductor-uri "GOfuncR" version))
4421 "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1"))))
4422 (properties `((upstream-name . "GOfuncR")))
4423 (build-system r-build-system)
4425 `(("r-annotationdbi" ,r-annotationdbi)
4426 ("r-genomicranges" ,r-genomicranges)
4427 ("r-gtools" ,r-gtools)
4428 ("r-iranges" ,r-iranges)
4429 ("r-mapplots" ,r-mapplots)
4431 ("r-vioplot" ,r-vioplot)))
4433 `(("r-knitr" ,r-knitr)))
4434 (home-page "https://bioconductor.org/packages/GOfuncR/")
4435 (synopsis "Gene ontology enrichment using FUNC")
4437 "GOfuncR performs a gene ontology enrichment analysis based on the
4438 ontology enrichment software FUNC. GO-annotations are obtained from
4439 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4440 included in the package and updated regularly. GOfuncR provides the standard
4441 candidate vs background enrichment analysis using the hypergeometric test, as
4442 well as three additional tests:
4445 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4446 @item a binomial test that is used when genes are associated with two counts,
4448 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4449 associated with four counts.
4452 To correct for multiple testing and interdependency of the tests, family-wise
4453 error rates are computed based on random permutations of the gene-associated
4454 variables. GOfuncR also provides tools for exploring the ontology graph and
4455 the annotations, and options to take gene-length or spatial clustering of
4456 genes into account. It is also possible to provide custom gene coordinates,
4457 annotations and ontologies.")
4458 (license license:gpl2+)))
4460 (define-public r-abaenrichment
4462 (name "r-abaenrichment")
4467 (uri (bioconductor-uri "ABAEnrichment" version))
4470 "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw"))))
4471 (properties `((upstream-name . "ABAEnrichment")))
4472 (build-system r-build-system)
4474 `(("r-abadata" ,r-abadata)
4475 ("r-data-table" ,r-data-table)
4476 ("r-gofuncr" ,r-gofuncr)
4477 ("r-gplots" ,r-gplots)
4478 ("r-gtools" ,r-gtools)
4479 ("r-rcpp" ,r-rcpp)))
4481 `(("r-knitr" ,r-knitr)))
4482 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4483 (synopsis "Gene expression enrichment in human brain regions")
4485 "The package ABAEnrichment is designed to test for enrichment of user
4486 defined candidate genes in the set of expressed genes in different human brain
4487 regions. The core function @code{aba_enrich} integrates the expression of the
4488 candidate gene set (averaged across donors) and the structural information of
4489 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4490 (license license:gpl2+)))
4492 (define-public r-annotationfuncs
4494 (name "r-annotationfuncs")
4499 (uri (bioconductor-uri "AnnotationFuncs" version))
4502 "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d"))))
4504 `((upstream-name . "AnnotationFuncs")))
4505 (build-system r-build-system)
4507 `(("r-annotationdbi" ,r-annotationdbi)
4509 (home-page "https://www.iysik.com/r/annotationfuncs")
4510 (synopsis "Annotation translation functions")
4512 "This package provides functions for handling translating between
4513 different identifieres using the Biocore Data Team data-packages (e.g.
4514 @code{org.Bt.eg.db}).")
4515 (license license:gpl2)))
4517 (define-public r-annotationtools
4519 (name "r-annotationtools")
4524 (uri (bioconductor-uri "annotationTools" version))
4527 "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk"))))
4529 `((upstream-name . "annotationTools")))
4530 (build-system r-build-system)
4531 (propagated-inputs `(("r-biobase" ,r-biobase)))
4532 (home-page "https://bioconductor.org/packages/annotationTools/")
4533 (synopsis "Annotate microarrays and perform gene expression analyses")
4535 "This package provides functions to annotate microarrays, find orthologs,
4536 and integrate heterogeneous gene expression profiles using annotation and
4537 other molecular biology information available as flat file database (plain
4539 ;; Any version of the GPL.
4540 (license (list license:gpl2+))))
4542 (define-public r-allelicimbalance
4544 (name "r-allelicimbalance")
4549 (uri (bioconductor-uri "AllelicImbalance" version))
4552 "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr"))))
4554 `((upstream-name . "AllelicImbalance")))
4555 (build-system r-build-system)
4557 `(("r-annotationdbi" ,r-annotationdbi)
4558 ("r-biocgenerics" ,r-biocgenerics)
4559 ("r-biostrings" ,r-biostrings)
4560 ("r-bsgenome" ,r-bsgenome)
4561 ("r-genomeinfodb" ,r-genomeinfodb)
4562 ("r-genomicalignments" ,r-genomicalignments)
4563 ("r-genomicfeatures" ,r-genomicfeatures)
4564 ("r-genomicranges" ,r-genomicranges)
4565 ("r-gridextra" ,r-gridextra)
4567 ("r-iranges" ,r-iranges)
4568 ("r-lattice" ,r-lattice)
4569 ("r-latticeextra" ,r-latticeextra)
4571 ("r-rsamtools" ,r-rsamtools)
4572 ("r-s4vectors" ,r-s4vectors)
4573 ("r-seqinr" ,r-seqinr)
4574 ("r-summarizedexperiment" ,r-summarizedexperiment)
4575 ("r-variantannotation" ,r-variantannotation)))
4577 `(("r-knitr" ,r-knitr)))
4578 (home-page "https://github.com/pappewaio/AllelicImbalance")
4579 (synopsis "Investigate allele-specific expression")
4581 "This package provides a framework for allele-specific expression
4582 investigation using RNA-seq data.")
4583 (license license:gpl3)))
4585 (define-public r-aucell
4592 (uri (bioconductor-uri "AUCell" version))
4595 "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns"))))
4596 (properties `((upstream-name . "AUCell")))
4597 (build-system r-build-system)
4599 `(("r-biocgenerics" ,r-biocgenerics)
4600 ("r-data-table" ,r-data-table)
4601 ("r-gseabase" ,r-gseabase)
4602 ("r-mixtools" ,r-mixtools)
4603 ("r-r-utils" ,r-r-utils)
4604 ("r-s4vectors" ,r-s4vectors)
4605 ("r-shiny" ,r-shiny)
4606 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4608 `(("r-knitr" ,r-knitr)))
4609 (home-page "https://bioconductor.org/packages/AUCell/")
4610 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4612 "AUCell identifies cells with active gene sets (e.g. signatures,
4613 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4614 Under the Curve} (AUC) to calculate whether a critical subset of the input
4615 gene set is enriched within the expressed genes for each cell. The
4616 distribution of AUC scores across all the cells allows exploring the relative
4617 expression of the signature. Since the scoring method is ranking-based,
4618 AUCell is independent of the gene expression units and the normalization
4619 procedure. In addition, since the cells are evaluated individually, it can
4620 easily be applied to bigger datasets, subsetting the expression matrix if
4622 (license license:gpl3)))
4624 (define-public r-ebimage
4631 (uri (bioconductor-uri "EBImage" version))
4634 "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v"))))
4635 (properties `((upstream-name . "EBImage")))
4636 (build-system r-build-system)
4638 `(("r-abind" ,r-abind)
4639 ("r-biocgenerics" ,r-biocgenerics)
4640 ("r-fftwtools" ,r-fftwtools)
4641 ("r-htmltools" ,r-htmltools)
4642 ("r-htmlwidgets" ,r-htmlwidgets)
4644 ("r-locfit" ,r-locfit)
4646 ("r-rcurl" ,r-rcurl)
4647 ("r-tiff" ,r-tiff)))
4649 `(("r-knitr" ,r-knitr))) ; for vignettes
4650 (home-page "https://github.com/aoles/EBImage")
4651 (synopsis "Image processing and analysis toolbox for R")
4653 "EBImage provides general purpose functionality for image processing and
4654 analysis. In the context of (high-throughput) microscopy-based cellular
4655 assays, EBImage offers tools to segment cells and extract quantitative
4656 cellular descriptors. This allows the automation of such tasks using the R
4657 programming language and facilitates the use of other tools in the R
4658 environment for signal processing, statistical modeling, machine learning and
4659 visualization with image data.")
4660 ;; Any version of the LGPL.
4661 (license license:lgpl2.1+)))
4663 (define-public r-yamss
4670 (uri (bioconductor-uri "yamss" version))
4673 "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c"))))
4674 (build-system r-build-system)
4676 `(("r-biocgenerics" ,r-biocgenerics)
4677 ("r-data-table" ,r-data-table)
4678 ("r-ebimage" ,r-ebimage)
4679 ("r-iranges" ,r-iranges)
4680 ("r-limma" ,r-limma)
4681 ("r-matrix" ,r-matrix)
4683 ("r-s4vectors" ,r-s4vectors)
4684 ("r-summarizedexperiment"
4685 ,r-summarizedexperiment)))
4687 `(("r-knitr" ,r-knitr)))
4688 (home-page "https://github.com/hansenlab/yamss")
4689 (synopsis "Tools for high-throughput metabolomics")
4691 "This package provides tools to analyze and visualize high-throughput
4692 metabolomics data acquired using chromatography-mass spectrometry. These tools
4693 preprocess data in a way that enables reliable and powerful differential
4695 (license license:artistic2.0)))
4697 (define-public r-gtrellis
4704 (uri (bioconductor-uri "gtrellis" version))
4707 "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1"))))
4708 (build-system r-build-system)
4710 `(("r-circlize" ,r-circlize)
4711 ("r-genomicranges" ,r-genomicranges)
4712 ("r-getoptlong" ,r-getoptlong)
4713 ("r-iranges" ,r-iranges)))
4715 `(("r-knitr" ,r-knitr)))
4716 (home-page "https://github.com/jokergoo/gtrellis")
4717 (synopsis "Genome level Trellis layout")
4719 "Genome level Trellis graph visualizes genomic data conditioned by
4720 genomic categories (e.g. chromosomes). For each genomic category, multiple
4721 dimensional data which are represented as tracks describe different features
4722 from different aspects. This package provides high flexibility to arrange
4723 genomic categories and to add self-defined graphics in the plot.")
4724 (license license:expat)))
4726 (define-public r-somaticsignatures
4728 (name "r-somaticsignatures")
4733 (uri (bioconductor-uri "SomaticSignatures" version))
4736 "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1"))))
4738 `((upstream-name . "SomaticSignatures")))
4739 (build-system r-build-system)
4741 `(("r-biobase" ,r-biobase)
4742 ("r-biostrings" ,r-biostrings)
4743 ("r-genomeinfodb" ,r-genomeinfodb)
4744 ("r-genomicranges" ,r-genomicranges)
4745 ("r-ggbio" ,r-ggbio)
4746 ("r-ggplot2" ,r-ggplot2)
4747 ("r-iranges" ,r-iranges)
4749 ("r-pcamethods" ,r-pcamethods)
4750 ("r-proxy" ,r-proxy)
4751 ("r-reshape2" ,r-reshape2)
4752 ("r-s4vectors" ,r-s4vectors)
4753 ("r-variantannotation" ,r-variantannotation)))
4755 `(("r-knitr" ,r-knitr)))
4756 (home-page "https://github.com/juliangehring/SomaticSignatures")
4757 (synopsis "Somatic signatures")
4759 "This package identifies mutational signatures of @dfn{single nucleotide
4760 variants} (SNVs). It provides a infrastructure related to the methodology
4761 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4762 decomposition algorithms.")
4763 (license license:expat)))
4765 (define-public r-yapsa
4772 (uri (bioconductor-uri "YAPSA" version))
4775 "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
4776 (properties `((upstream-name . "YAPSA")))
4777 (build-system r-build-system)
4779 `(("r-biostrings" ,r-biostrings)
4780 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4781 ("r-circlize" ,r-circlize)
4782 ("r-complexheatmap" ,r-complexheatmap)
4783 ("r-corrplot" ,r-corrplot)
4784 ("r-dendextend" ,r-dendextend)
4785 ("r-doparallel" ,r-doparallel)
4786 ("r-dplyr" ,r-dplyr)
4787 ("r-genomeinfodb" ,r-genomeinfodb)
4788 ("r-genomicranges" ,r-genomicranges)
4789 ("r-getoptlong" ,r-getoptlong)
4790 ("r-ggbeeswarm" ,r-ggbeeswarm)
4791 ("r-ggplot2" ,r-ggplot2)
4792 ("r-gridextra" ,r-gridextra)
4793 ("r-gtrellis" ,r-gtrellis)
4794 ("r-keggrest" ,r-keggrest)
4796 ("r-magrittr" ,r-magrittr)
4797 ("r-pmcmr" ,r-pmcmr)
4798 ("r-pracma" ,r-pracma)
4799 ("r-reshape2" ,r-reshape2)
4800 ("r-somaticsignatures" ,r-somaticsignatures)
4801 ("r-variantannotation" ,r-variantannotation)))
4803 `(("r-knitr" ,r-knitr)))
4804 (home-page "https://bioconductor.org/packages/YAPSA/")
4805 (synopsis "Yet another package for signature analysis")
4807 "This package provides functions and routines useful in the analysis of
4808 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4809 functions to perform a signature analysis with known signatures and a
4810 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4812 (license license:gpl3)))
4814 (define-public r-gcrma
4821 (uri (bioconductor-uri "gcrma" version))
4824 "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g"))))
4825 (build-system r-build-system)
4827 `(("r-affy" ,r-affy)
4828 ("r-affyio" ,r-affyio)
4829 ("r-biobase" ,r-biobase)
4830 ("r-biocmanager" ,r-biocmanager)
4831 ("r-biostrings" ,r-biostrings)
4832 ("r-xvector" ,r-xvector)))
4833 (home-page "https://bioconductor.org/packages/gcrma/")
4834 (synopsis "Background adjustment using sequence information")
4836 "Gcrma adjusts for background intensities in Affymetrix array data which
4837 include optical noise and @dfn{non-specific binding} (NSB). The main function
4838 @code{gcrma} converts background adjusted probe intensities to expression
4839 measures using the same normalization and summarization methods as a
4840 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4841 to estimate probe affinity to NSB. The sequence information is summarized in
4842 a more complex way than the simple GC content. Instead, the base types (A, T,
4843 G or C) at each position along the probe determine the affinity of each probe.
4844 The parameters of the position-specific base contributions to the probe
4845 affinity is estimated in an NSB experiment in which only NSB but no
4846 gene-specific bidning is expected.")
4847 ;; Any version of the LGPL
4848 (license license:lgpl2.1+)))
4850 (define-public r-simpleaffy
4852 (name "r-simpleaffy")
4857 (uri (bioconductor-uri "simpleaffy" version))
4860 "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7"))))
4861 (build-system r-build-system)
4863 `(("r-affy" ,r-affy)
4864 ("r-biobase" ,r-biobase)
4865 ("r-biocgenerics" ,r-biocgenerics)
4866 ("r-gcrma" ,r-gcrma)
4867 ("r-genefilter" ,r-genefilter)))
4868 (home-page "https://bioconductor.org/packages/simpleaffy/")
4869 (synopsis "Very simple high level analysis of Affymetrix data")
4871 "This package provides high level functions for reading Affy @file{.CEL}
4872 files, phenotypic data, and then computing simple things with it, such as
4873 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4874 library. It also has some basic scatter plot functions and mechanisms for
4875 generating high resolution journal figures.")
4876 (license license:gpl2+)))
4878 (define-public r-yaqcaffy
4885 (uri (bioconductor-uri "yaqcaffy" version))
4888 "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0"))))
4889 (build-system r-build-system)
4891 `(("r-simpleaffy" ,r-simpleaffy)))
4892 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4893 (synopsis "Affymetrix quality control and reproducibility analysis")
4895 "This is a package that can be used for quality control of Affymetrix
4896 GeneChip expression data and reproducibility analysis of human whole genome
4897 chips with the MAQC reference datasets.")
4898 (license license:artistic2.0)))
4900 (define-public r-quantro
4907 (uri (bioconductor-uri "quantro" version))
4910 "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
4911 (build-system r-build-system)
4913 `(("r-biobase" ,r-biobase)
4914 ("r-doparallel" ,r-doparallel)
4915 ("r-foreach" ,r-foreach)
4916 ("r-ggplot2" ,r-ggplot2)
4917 ("r-iterators" ,r-iterators)
4918 ("r-minfi" ,r-minfi)
4919 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4921 `(("r-knitr" ,r-knitr)))
4922 (home-page "https://bioconductor.org/packages/quantro/")
4923 (synopsis "Test for when to use quantile normalization")
4925 "This package provides a data-driven test for the assumptions of quantile
4926 normalization using raw data such as objects that inherit eSets (e.g.
4927 ExpressionSet, MethylSet). Group level information about each sample (such as
4928 Tumor / Normal status) must also be provided because the test assesses if
4929 there are global differences in the distributions between the user-defined
4931 (license license:gpl3+)))
4933 (define-public r-yarn
4940 (uri (bioconductor-uri "yarn" version))
4943 "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
4944 (build-system r-build-system)
4946 `(("r-biobase" ,r-biobase)
4947 ("r-biomart" ,r-biomart)
4948 ("r-downloader" ,r-downloader)
4949 ("r-edger" ,r-edger)
4950 ("r-gplots" ,r-gplots)
4951 ("r-limma" ,r-limma)
4952 ("r-matrixstats" ,r-matrixstats)
4953 ("r-preprocesscore" ,r-preprocesscore)
4954 ("r-quantro" ,r-quantro)
4955 ("r-rcolorbrewer" ,r-rcolorbrewer)
4956 ("r-readr" ,r-readr)))
4958 `(("r-knitr" ,r-knitr)))
4959 (home-page "https://bioconductor.org/packages/yarn/")
4960 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4962 "Expedite large RNA-Seq analyses using a combination of previously
4963 developed tools. YARN is meant to make it easier for the user in performing
4964 basic mis-annotation quality control, filtering, and condition-aware
4965 normalization. YARN leverages many Bioconductor tools and statistical
4966 techniques to account for the large heterogeneity and sparsity found in very
4967 large RNA-seq experiments.")
4968 (license license:artistic2.0)))
4970 (define-public r-roar
4977 (uri (bioconductor-uri "roar" version))
4980 "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f"))))
4981 (build-system r-build-system)
4983 `(("r-biocgenerics" ,r-biocgenerics)
4984 ("r-genomeinfodb" ,r-genomeinfodb)
4985 ("r-genomicalignments" ,r-genomicalignments)
4986 ("r-genomicranges" ,r-genomicranges)
4987 ("r-iranges" ,r-iranges)
4988 ("r-rtracklayer" ,r-rtracklayer)
4989 ("r-s4vectors" ,r-s4vectors)
4990 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4991 (home-page "https://github.com/vodkatad/roar/")
4992 (synopsis "Identify differential APA usage from RNA-seq alignments")
4994 "This package provides tools for identifying preferential usage of APA
4995 sites, comparing two biological conditions, starting from known alternative
4996 sites and alignments obtained from standard RNA-seq experiments.")
4997 (license license:gpl3)))
4999 (define-public r-xbseq
5006 (uri (bioconductor-uri "XBSeq" version))
5009 "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0"))))
5010 (properties `((upstream-name . "XBSeq")))
5011 (build-system r-build-system)
5013 `(("r-biobase" ,r-biobase)
5014 ("r-deseq2" ,r-deseq2)
5015 ("r-dplyr" ,r-dplyr)
5016 ("r-ggplot2" ,r-ggplot2)
5017 ("r-locfit" ,r-locfit)
5018 ("r-magrittr" ,r-magrittr)
5019 ("r-matrixstats" ,r-matrixstats)
5020 ("r-pracma" ,r-pracma)
5021 ("r-roar" ,r-roar)))
5023 `(("r-knitr" ,r-knitr)))
5024 (home-page "https://github.com/Liuy12/XBSeq")
5025 (synopsis "Test for differential expression for RNA-seq data")
5027 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5028 expression} (DE), where a statistical model was established based on the
5029 assumption that observed signals are the convolution of true expression
5030 signals and sequencing noises. The mapped reads in non-exonic regions are
5031 considered as sequencing noises, which follows a Poisson distribution. Given
5032 measurable observed signal and background noise from RNA-seq data, true
5033 expression signals, assuming governed by the negative binomial distribution,
5034 can be delineated and thus the accurate detection of differential expressed
5036 (license license:gpl3+)))
5038 (define-public r-massspecwavelet
5040 (name "r-massspecwavelet")
5045 (uri (bioconductor-uri "MassSpecWavelet" version))
5048 "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq"))))
5050 `((upstream-name . "MassSpecWavelet")))
5051 (build-system r-build-system)
5053 `(("r-waveslim" ,r-waveslim)))
5054 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5055 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5057 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5058 data mainly through the use of wavelet transforms. It supports peak detection
5059 based on @dfn{Continuous Wavelet Transform} (CWT).")
5060 (license license:lgpl2.0+)))
5062 (define-public r-xcms
5069 (uri (bioconductor-uri "xcms" version))
5072 "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn"))))
5073 (build-system r-build-system)
5075 `(("r-biobase" ,r-biobase)
5076 ("r-biocgenerics" ,r-biocgenerics)
5077 ("r-biocparallel" ,r-biocparallel)
5078 ("r-iranges" ,r-iranges)
5079 ("r-lattice" ,r-lattice)
5080 ("r-massspecwavelet" ,r-massspecwavelet)
5081 ("r-msnbase" ,r-msnbase)
5084 ("r-protgenerics" ,r-protgenerics)
5086 ("r-rcolorbrewer" ,r-rcolorbrewer)
5087 ("r-robustbase" ,r-robustbase)
5088 ("r-s4vectors" ,r-s4vectors)
5089 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5091 `(("r-knitr" ,r-knitr)))
5092 (home-page "https://bioconductor.org/packages/xcms/")
5093 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5095 "This package provides a framework for processing and visualization of
5096 chromatographically separated and single-spectra mass spectral data. It
5097 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5098 data for high-throughput, untargeted analyte profiling.")
5099 (license license:gpl2+)))
5101 (define-public r-wrench
5108 (uri (bioconductor-uri "Wrench" version))
5111 "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6"))))
5112 (properties `((upstream-name . "Wrench")))
5113 (build-system r-build-system)
5115 `(("r-limma" ,r-limma)
5116 ("r-locfit" ,r-locfit)
5117 ("r-matrixstats" ,r-matrixstats)))
5119 `(("r-knitr" ,r-knitr)))
5120 (home-page "https://github.com/HCBravoLab/Wrench")
5121 (synopsis "Wrench normalization for sparse count data")
5123 "Wrench is a package for normalization sparse genomic count data, like
5124 that arising from 16s metagenomic surveys.")
5125 (license license:artistic2.0)))
5127 (define-public r-wiggleplotr
5129 (name "r-wiggleplotr")
5134 (uri (bioconductor-uri "wiggleplotr" version))
5137 "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
5138 (build-system r-build-system)
5140 `(("r-assertthat" ,r-assertthat)
5141 ("r-cowplot" ,r-cowplot)
5142 ("r-dplyr" ,r-dplyr)
5143 ("r-genomeinfodb" ,r-genomeinfodb)
5144 ("r-genomicranges" ,r-genomicranges)
5145 ("r-ggplot2" ,r-ggplot2)
5146 ("r-iranges" ,r-iranges)
5147 ("r-purrr" ,r-purrr)
5148 ("r-rtracklayer" ,r-rtracklayer)
5149 ("r-s4vectors" ,r-s4vectors)))
5151 `(("r-knitr" ,r-knitr)))
5152 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5153 (synopsis "Make read coverage plots from BigWig files")
5155 "This package provides tools to visualize read coverage from sequencing
5156 experiments together with genomic annotations (genes, transcripts, peaks).
5157 Introns of long transcripts can be rescaled to a fixed length for better
5158 visualization of exonic read coverage.")
5159 (license license:asl2.0)))
5161 (define-public r-widgettools
5163 (name "r-widgettools")
5168 (uri (bioconductor-uri "widgetTools" version))
5171 "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx"))))
5172 (properties `((upstream-name . "widgetTools")))
5173 (build-system r-build-system)
5174 (home-page "https://bioconductor.org/packages/widgetTools/")
5175 (synopsis "Tools for creating interactive tcltk widgets")
5177 "This package contains tools to support the construction of tcltk
5179 ;; Any version of the LGPL.
5180 (license license:lgpl3+)))
5182 (define-public r-webbioc
5189 (uri (bioconductor-uri "webbioc" version))
5192 "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f"))))
5193 (build-system r-build-system)
5195 `(("netpbm" ,netpbm)
5198 `(("r-affy" ,r-affy)
5199 ("r-annaffy" ,r-annaffy)
5200 ("r-biobase" ,r-biobase)
5201 ("r-biocmanager" ,r-biocmanager)
5202 ("r-gcrma" ,r-gcrma)
5203 ("r-multtest" ,r-multtest)
5204 ("r-qvalue" ,r-qvalue)
5206 (home-page "https://www.bioconductor.org/")
5207 (synopsis "Bioconductor web interface")
5209 "This package provides an integrated web interface for doing microarray
5210 analysis using several of the Bioconductor packages. It is intended to be
5211 deployed as a centralized bioinformatics resource for use by many users.
5212 Currently only Affymetrix oligonucleotide analysis is supported.")
5213 (license license:gpl2+)))
5215 (define-public r-zfpkm
5222 (uri (bioconductor-uri "zFPKM" version))
5225 "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys"))))
5226 (properties `((upstream-name . "zFPKM")))
5227 (build-system r-build-system)
5229 `(("r-checkmate" ,r-checkmate)
5230 ("r-dplyr" ,r-dplyr)
5231 ("r-ggplot2" ,r-ggplot2)
5232 ("r-summarizedexperiment" ,r-summarizedexperiment)
5233 ("r-tidyr" ,r-tidyr)))
5235 `(("r-knitr" ,r-knitr)))
5236 (home-page "https://github.com/ronammar/zFPKM/")
5237 (synopsis "Functions to facilitate zFPKM transformations")
5239 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5240 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5242 (license license:gpl3)))
5244 (define-public r-rbowtie2
5251 (uri (bioconductor-uri "Rbowtie2" version))
5254 "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
5255 (properties `((upstream-name . "Rbowtie2")))
5256 (build-system r-build-system)
5260 `(("r-knitr" ,r-knitr)))
5261 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5262 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5264 "This package provides an R wrapper of the popular @code{bowtie2}
5265 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5266 rapid adapter trimming, identification, and read merging.")
5267 (license license:gpl3+)))
5269 (define-public r-progeny
5276 (uri (bioconductor-uri "progeny" version))
5279 "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh"))))
5280 (build-system r-build-system)
5282 `(("r-biobase" ,r-biobase)
5283 ("r-dplyr" ,r-dplyr)
5284 ("r-ggplot2" ,r-ggplot2)
5285 ("r-ggrepel" ,r-ggrepel)
5286 ("r-gridextra" ,r-gridextra)
5287 ("r-tidyr" ,r-tidyr)))
5289 `(("r-knitr" ,r-knitr)))
5290 (home-page "https://github.com/saezlab/progeny")
5291 (synopsis "Pathway responsive gene activity inference")
5293 "This package provides a function to infer pathway activity from gene
5294 expression. It contains the linear model inferred in the publication
5295 \"Perturbation-response genes reveal signaling footprints in cancer gene
5297 (license license:asl2.0)))
5299 (define-public r-arrmnormalization
5301 (name "r-arrmnormalization")
5306 (uri (bioconductor-uri "ARRmNormalization" version))
5309 "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv"))))
5311 `((upstream-name . "ARRmNormalization")))
5312 (build-system r-build-system)
5313 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5314 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5315 (synopsis "Adaptive robust regression normalization for methylation data")
5317 "This is a package to perform the @dfn{Adaptive Robust Regression
5318 method} (ARRm) for the normalization of methylation data from the Illumina
5319 Infinium HumanMethylation 450k assay.")
5320 (license license:artistic2.0)))
5322 (define-public r-biocfilecache
5324 (name "r-biocfilecache")
5329 (uri (bioconductor-uri "BiocFileCache" version))
5332 "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
5333 (properties `((upstream-name . "BiocFileCache")))
5334 (build-system r-build-system)
5336 `(("r-curl" ,r-curl)
5338 ("r-dbplyr" ,r-dbplyr)
5339 ("r-dplyr" ,r-dplyr)
5341 ("r-rappdirs" ,r-rappdirs)
5342 ("r-rsqlite" ,r-rsqlite)))
5344 `(("r-knitr" ,r-knitr)))
5345 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5346 (synopsis "Manage files across sessions")
5348 "This package creates a persistent on-disk cache of files that the user
5349 can add, update, and retrieve. It is useful for managing resources (such as
5350 custom Txdb objects) that are costly or difficult to create, web resources,
5351 and data files used across sessions.")
5352 (license license:artistic2.0)))
5354 (define-public r-iclusterplus
5356 (name "r-iclusterplus")
5361 (uri (bioconductor-uri "iClusterPlus" version))
5364 "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w"))))
5365 (properties `((upstream-name . "iClusterPlus")))
5366 (build-system r-build-system)
5367 (native-inputs `(("gfortran" ,gfortran)))
5368 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5369 (synopsis "Integrative clustering of multi-type genomic data")
5371 "iClusterPlus is developed for integrative clustering analysis of
5372 multi-type genomic data and is an enhanced version of iCluster proposed and
5373 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5374 from the experiments where biological samples (e.g. tumor samples) are
5375 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5376 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5377 on. In the iClusterPlus model, binary observations such as somatic mutation
5378 are modeled as Binomial processes; categorical observations such as copy
5379 number states are realizations of Multinomial random variables; counts are
5380 modeled as Poisson random processes; and continuous measures are modeled by
5381 Gaussian distributions.")
5382 (license license:gpl2+)))
5384 (define-public r-rbowtie
5391 (uri (bioconductor-uri "Rbowtie" version))
5394 "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
5395 (properties `((upstream-name . "Rbowtie")))
5396 (build-system r-build-system)
5400 `(("r-knitr" ,r-knitr)))
5401 (home-page "https://bioconductor.org/packages/Rbowtie/")
5402 (synopsis "R bowtie wrapper")
5404 "This package provides an R wrapper around the popular bowtie short read
5405 aligner and around SpliceMap, a de novo splice junction discovery and
5407 (license license:artistic2.0)))
5409 (define-public r-sgseq
5416 (uri (bioconductor-uri "SGSeq" version))
5419 "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c"))))
5420 (properties `((upstream-name . "SGSeq")))
5421 (build-system r-build-system)
5423 `(("r-annotationdbi" ,r-annotationdbi)
5424 ("r-biocgenerics" ,r-biocgenerics)
5425 ("r-biostrings" ,r-biostrings)
5426 ("r-genomeinfodb" ,r-genomeinfodb)
5427 ("r-genomicalignments" ,r-genomicalignments)
5428 ("r-genomicfeatures" ,r-genomicfeatures)
5429 ("r-genomicranges" ,r-genomicranges)
5430 ("r-igraph" ,r-igraph)
5431 ("r-iranges" ,r-iranges)
5432 ("r-rsamtools" ,r-rsamtools)
5433 ("r-rtracklayer" ,r-rtracklayer)
5434 ("r-runit" ,r-runit)
5435 ("r-s4vectors" ,r-s4vectors)
5436 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5438 `(("r-knitr" ,r-knitr)))
5439 (home-page "https://bioconductor.org/packages/SGSeq/")
5440 (synopsis "Splice event prediction and quantification from RNA-seq data")
5442 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5443 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5444 represented as a splice graph, which can be obtained from existing annotation
5445 or predicted from the mapped sequence reads. Splice events are identified
5446 from the graph and are quantified locally using structurally compatible reads
5447 at the start or end of each splice variant. The software includes functions
5448 for splice event prediction, quantification, visualization and
5450 (license license:artistic2.0)))
5452 (define-public r-rhisat2
5459 (uri (bioconductor-uri "Rhisat2" version))
5462 "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a"))))
5463 (properties `((upstream-name . "Rhisat2")))
5464 (build-system r-build-system)
5467 (modify-phases %standard-phases
5468 (add-after 'unpack 'make-reproducible
5470 (substitute* "src/Makefile"
5471 (("`hostname`") "guix")
5473 ;; Avoid shelling out to "which".
5474 (("^CC =.*") (which "gcc"))
5475 (("^CPP =.*") (which "g++")))
5478 `(("r-genomicfeatures" ,r-genomicfeatures)
5479 ("r-genomicranges" ,r-genomicranges)
5480 ("r-sgseq" ,r-sgseq)))
5482 `(("r-knitr" ,r-knitr)))
5483 (home-page "https://github.com/fmicompbio/Rhisat2")
5484 (synopsis "R Wrapper for HISAT2 sequence aligner")
5486 "This package provides an R interface to the HISAT2 spliced short-read
5487 aligner by Kim et al. (2015). The package contains wrapper functions to
5488 create a genome index and to perform the read alignment to the generated
5490 (license license:gpl3)))
5492 (define-public r-quasr
5499 (uri (bioconductor-uri "QuasR" version))
5502 "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8"))))
5503 (properties `((upstream-name . "QuasR")))
5504 (build-system r-build-system)
5508 `(("r-annotationdbi" ,r-annotationdbi)
5509 ("r-biobase" ,r-biobase)
5510 ("r-biocgenerics" ,r-biocgenerics)
5511 ("r-biocmanager" ,r-biocmanager)
5512 ("r-biocparallel" ,r-biocparallel)
5513 ("r-biostrings" ,r-biostrings)
5514 ("r-bsgenome" ,r-bsgenome)
5515 ("r-genomeinfodb" ,r-genomeinfodb)
5516 ("r-genomicalignments" ,r-genomicalignments)
5517 ("r-genomicfeatures" ,r-genomicfeatures)
5518 ("r-genomicfiles" ,r-genomicfiles)
5519 ("r-genomicranges" ,r-genomicranges)
5520 ("r-iranges" ,r-iranges)
5521 ("r-rbowtie" ,r-rbowtie)
5522 ("r-rhisat2" ,r-rhisat2)
5523 ("r-rhtslib" ,r-rhtslib)
5524 ("r-rsamtools" ,r-rsamtools)
5525 ("r-rtracklayer" ,r-rtracklayer)
5526 ("r-s4vectors" ,r-s4vectors)
5527 ("r-shortread" ,r-shortread)))
5529 `(("r-knitr" ,r-knitr)))
5530 (home-page "https://bioconductor.org/packages/QuasR/")
5531 (synopsis "Quantify and annotate short reads in R")
5533 "This package provides a framework for the quantification and analysis of
5534 short genomic reads. It covers a complete workflow starting from raw sequence
5535 reads, over creation of alignments and quality control plots, to the
5536 quantification of genomic regions of interest.")
5537 (license license:gpl2)))
5539 (define-public r-rqc
5546 (uri (bioconductor-uri "Rqc" version))
5549 "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3"))))
5550 (properties `((upstream-name . "Rqc")))
5551 (build-system r-build-system)
5553 `(("r-biocgenerics" ,r-biocgenerics)
5554 ("r-biocparallel" ,r-biocparallel)
5555 ("r-biocstyle" ,r-biocstyle)
5556 ("r-biostrings" ,r-biostrings)
5557 ("r-biovizbase" ,r-biovizbase)
5558 ("r-genomicalignments" ,r-genomicalignments)
5559 ("r-genomicfiles" ,r-genomicfiles)
5560 ("r-ggplot2" ,r-ggplot2)
5561 ("r-iranges" ,r-iranges)
5562 ("r-knitr" ,r-knitr)
5563 ("r-markdown" ,r-markdown)
5566 ("r-reshape2" ,r-reshape2)
5567 ("r-rsamtools" ,r-rsamtools)
5568 ("r-s4vectors" ,r-s4vectors)
5569 ("r-shiny" ,r-shiny)
5570 ("r-shortread" ,r-shortread)))
5572 `(("r-knitr" ,r-knitr)))
5573 (home-page "https://github.com/labbcb/Rqc")
5574 (synopsis "Quality control tool for high-throughput sequencing data")
5576 "Rqc is an optimized tool designed for quality control and assessment of
5577 high-throughput sequencing data. It performs parallel processing of entire
5578 files and produces a report which contains a set of high-resolution
5580 (license license:gpl2+)))
5582 (define-public r-birewire
5589 (uri (bioconductor-uri "BiRewire" version))
5592 "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g"))))
5593 (properties `((upstream-name . "BiRewire")))
5594 (build-system r-build-system)
5596 `(("r-igraph" ,r-igraph)
5597 ("r-matrix" ,r-matrix)
5599 ("r-tsne" ,r-tsne)))
5600 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5601 (synopsis "Tools for randomization of bipartite graphs")
5603 "This package provides functions for bipartite network rewiring through N
5604 consecutive switching steps and for the computation of the minimal number of
5605 switching steps to be performed in order to maximise the dissimilarity with
5606 respect to the original network. It includes functions for the analysis of
5607 the introduced randomness across the switching steps and several other
5608 routines to analyse the resulting networks and their natural projections.")
5609 (license license:gpl3)))
5611 (define-public r-birta
5618 (uri (bioconductor-uri "birta" version))
5621 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5622 (build-system r-build-system)
5624 `(("r-biobase" ,r-biobase)
5625 ("r-limma" ,r-limma)
5626 ("r-mass" ,r-mass)))
5627 (home-page "https://bioconductor.org/packages/birta")
5628 (synopsis "Bayesian inference of regulation of transcriptional activity")
5630 "Expression levels of mRNA molecules are regulated by different
5631 processes, comprising inhibition or activation by transcription factors and
5632 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5633 Inference of Regulation of Transcriptional Activity) uses the regulatory
5634 networks of transcription factors and miRNAs together with mRNA and miRNA
5635 expression data to predict switches in regulatory activity between two
5636 conditions. A Bayesian network is used to model the regulatory structure and
5637 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5638 (license license:gpl2+)))
5640 (define-public r-multidataset
5642 (name "r-multidataset")
5647 (uri (bioconductor-uri "MultiDataSet" version))
5650 "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39"))))
5651 (properties `((upstream-name . "MultiDataSet")))
5652 (build-system r-build-system)
5654 `(("r-biobase" ,r-biobase)
5655 ("r-biocgenerics" ,r-biocgenerics)
5656 ("r-genomicranges" ,r-genomicranges)
5657 ("r-ggplot2" ,r-ggplot2)
5658 ("r-ggrepel" ,r-ggrepel)
5659 ("r-iranges" ,r-iranges)
5660 ("r-limma" ,r-limma)
5661 ("r-qqman" ,r-qqman)
5662 ("r-s4vectors" ,r-s4vectors)
5663 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5665 `(("r-knitr" ,r-knitr)))
5666 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5667 (synopsis "Implementation of MultiDataSet and ResultSet")
5669 "This package provides an implementation of the BRGE's (Bioinformatic
5670 Research Group in Epidemiology from Center for Research in Environmental
5671 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5672 integrating multi omics data sets and ResultSet is a container for omics
5673 results. This package contains base classes for MEAL and rexposome
5675 (license license:expat)))
5677 (define-public r-ropls
5684 (uri (bioconductor-uri "ropls" version))
5687 "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx"))))
5688 (build-system r-build-system)
5690 `(("r-biobase" ,r-biobase)
5691 ("r-multidataset" ,r-multidataset)))
5693 `(("r-knitr" ,r-knitr))) ; for vignettes
5694 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5695 (synopsis "Multivariate analysis and feature selection of omics data")
5697 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5698 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5699 regression, classification, and feature selection of omics data where the
5700 number of variables exceeds the number of samples and with multicollinearity
5701 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5702 separately model the variation correlated (predictive) to the factor of
5703 interest and the uncorrelated (orthogonal) variation. While performing
5704 similarly to PLS, OPLS facilitates interpretation.
5706 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5707 analysis and feature selection of omics data. In addition to scores, loadings
5708 and weights plots, the package provides metrics and graphics to determine the
5709 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5710 validity of the model by permutation testing, detect outliers, and perform
5711 feature selection (e.g. with Variable Importance in Projection or regression
5713 (license license:cecill)))
5715 (define-public r-biosigner
5717 (name "r-biosigner")
5722 (uri (bioconductor-uri "biosigner" version))
5725 "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06"))))
5726 (build-system r-build-system)
5728 `(("r-biobase" ,r-biobase)
5729 ("r-e1071" ,r-e1071)
5730 ("r-multidataset" ,r-multidataset)
5731 ("r-randomforest" ,r-randomforest)
5732 ("r-ropls" ,r-ropls)))
5734 `(("r-knitr" ,r-knitr)))
5735 (home-page "https://bioconductor.org/packages/biosigner/")
5736 (synopsis "Signature discovery from omics data")
5738 "Feature selection is critical in omics data analysis to extract
5739 restricted and meaningful molecular signatures from complex and high-dimension
5740 data, and to build robust classifiers. This package implements a method to
5741 assess the relevance of the variables for the prediction performances of the
5742 classifier. The approach can be run in parallel with the PLS-DA, Random
5743 Forest, and SVM binary classifiers. The signatures and the corresponding
5744 'restricted' models are returned, enabling future predictions on new
5746 (license license:cecill)))
5748 (define-public r-annotatr
5755 (uri (bioconductor-uri "annotatr" version))
5758 "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl"))))
5759 (build-system r-build-system)
5761 `(("r-annotationdbi" ,r-annotationdbi)
5762 ("r-annotationhub" ,r-annotationhub)
5763 ("r-dplyr" ,r-dplyr)
5764 ("r-genomeinfodb" ,r-genomeinfodb)
5765 ("r-genomicfeatures" ,r-genomicfeatures)
5766 ("r-genomicranges" ,r-genomicranges)
5767 ("r-ggplot2" ,r-ggplot2)
5768 ("r-iranges" ,r-iranges)
5769 ("r-readr" ,r-readr)
5770 ("r-regioner" ,r-regioner)
5771 ("r-reshape2" ,r-reshape2)
5772 ("r-rtracklayer" ,r-rtracklayer)
5773 ("r-s4vectors" ,r-s4vectors)))
5775 `(("r-knitr" ,r-knitr)))
5776 (home-page "https://bioconductor.org/packages/annotatr/")
5777 (synopsis "Annotation of genomic regions to genomic annotations")
5779 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5780 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5781 to investigate the intersecting genomic annotations. Such annotations include
5782 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5783 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5784 enhancers. The annotatr package provides an easy way to summarize and
5785 visualize the intersection of genomic sites/regions with genomic
5787 (license license:gpl3)))
5789 (define-public r-rsubread
5796 (uri (bioconductor-uri "Rsubread" version))
5799 "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
5800 (properties `((upstream-name . "Rsubread")))
5801 (build-system r-build-system)
5802 (inputs `(("zlib" ,zlib)))
5804 `(("r-matrix" ,r-matrix)))
5805 (home-page "https://bioconductor.org/packages/Rsubread/")
5806 (synopsis "Subread sequence alignment and counting for R")
5808 "This package provides tools for alignment, quantification and analysis
5809 of second and third generation sequencing data. It includes functionality for
5810 read mapping, read counting, SNP calling, structural variant detection and
5811 gene fusion discovery. It can be applied to all major sequencing techologies
5812 and to both short and long sequence reads.")
5813 (license license:gpl3)))
5815 (define-public r-flowutils
5817 (name "r-flowutils")
5822 (uri (bioconductor-uri "flowUtils" version))
5825 "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4"))))
5826 (properties `((upstream-name . "flowUtils")))
5827 (build-system r-build-system)
5829 `(("r-biobase" ,r-biobase)
5830 ("r-corpcor" ,r-corpcor)
5831 ("r-flowcore" ,r-flowcore)
5832 ("r-graph" ,r-graph)
5833 ("r-runit" ,r-runit)
5835 (home-page "https://github.com/jspidlen/flowUtils")
5836 (synopsis "Utilities for flow cytometry")
5838 "This package provides utilities for flow cytometry data.")
5839 (license license:artistic2.0)))
5841 (define-public r-consensusclusterplus
5843 (name "r-consensusclusterplus")
5848 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5851 "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq"))))
5853 `((upstream-name . "ConsensusClusterPlus")))
5854 (build-system r-build-system)
5857 ("r-biobase" ,r-biobase)
5858 ("r-cluster" ,r-cluster)))
5859 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5860 (synopsis "Clustering algorithm")
5862 "This package provides an implementation of an algorithm for determining
5863 cluster count and membership by stability evidence in unsupervised analysis.")
5864 (license license:gpl2)))
5866 (define-public r-cytolib
5873 (uri (bioconductor-uri "cytolib" version))
5876 "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj"))))
5877 (properties `((upstream-name . "cytolib")))
5878 (build-system r-build-system)
5882 `(("r-knitr" ,r-knitr)))
5886 ("r-rcpparmadillo" ,r-rcpparmadillo)
5887 ("r-rcppparallel" ,r-rcppparallel)
5888 ("r-rhdf5lib" ,r-rhdf5lib)
5889 ("r-rprotobuflib" ,r-rprotobuflib)))
5890 (home-page "https://bioconductor.org/packages/cytolib/")
5891 (synopsis "C++ infrastructure for working with gated cytometry")
5893 "This package provides the core data structure and API to represent and
5894 interact with gated cytometry data.")
5895 (license license:artistic2.0)))
5897 (define-public r-flowcore
5904 (uri (bioconductor-uri "flowCore" version))
5907 "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p"))))
5908 (properties `((upstream-name . "flowCore")))
5909 (build-system r-build-system)
5912 ("r-biobase" ,r-biobase)
5913 ("r-biocgenerics" ,r-biocgenerics)
5914 ("r-cytolib" ,r-cytolib)
5915 ("r-matrixstats" ,r-matrixstats)
5917 ("r-rcpparmadillo" ,r-rcpparmadillo)
5918 ("r-rprotobuflib" ,r-rprotobuflib)))
5920 `(("r-knitr" ,r-knitr)))
5921 (home-page "https://bioconductor.org/packages/flowCore")
5922 (synopsis "Basic structures for flow cytometry data")
5924 "This package provides S4 data structures and basic functions to deal
5925 with flow cytometry data.")
5926 (license license:artistic2.0)))
5928 (define-public r-flowmeans
5930 (name "r-flowmeans")
5935 (uri (bioconductor-uri "flowMeans" version))
5938 "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7"))))
5939 (properties `((upstream-name . "flowMeans")))
5940 (build-system r-build-system)
5942 `(("r-biobase" ,r-biobase)
5943 ("r-feature" ,r-feature)
5944 ("r-flowcore" ,r-flowcore)
5945 ("r-rrcov" ,r-rrcov)))
5946 (home-page "https://bioconductor.org/packages/flowMeans")
5947 (synopsis "Non-parametric flow cytometry data gating")
5949 "This package provides tools to identify cell populations in Flow
5950 Cytometry data using non-parametric clustering and segmented-regression-based
5951 change point detection.")
5952 (license license:artistic2.0)))
5954 (define-public r-ncdfflow
5961 (uri (bioconductor-uri "ncdfFlow" version))
5964 "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f"))))
5965 (properties `((upstream-name . "ncdfFlow")))
5966 (build-system r-build-system)
5971 ("r-biobase" ,r-biobase)
5972 ("r-biocgenerics" ,r-biocgenerics)
5973 ("r-flowcore" ,r-flowcore)
5975 ("r-rcpparmadillo" ,r-rcpparmadillo)
5976 ("r-rhdf5lib" ,r-rhdf5lib)
5977 ("r-zlibbioc" ,r-zlibbioc)))
5979 `(("r-knitr" ,r-knitr)))
5980 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5981 (synopsis "HDF5 based storage for flow cytometry data")
5983 "This package provides HDF5 storage based methods and functions for
5984 manipulation of flow cytometry data.")
5985 (license license:artistic2.0)))
5987 (define-public r-ggcyto
5994 (uri (bioconductor-uri "ggcyto" version))
5997 "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
5998 (properties `((upstream-name . "ggcyto")))
5999 (build-system r-build-system)
6001 `(("r-data-table" ,r-data-table)
6002 ("r-flowcore" ,r-flowcore)
6003 ("r-flowworkspace" ,r-flowworkspace)
6004 ("r-ggplot2" ,r-ggplot2)
6005 ("r-gridextra" ,r-gridextra)
6006 ("r-hexbin" ,r-hexbin)
6007 ("r-ncdfflow" ,r-ncdfflow)
6009 ("r-rcolorbrewer" ,r-rcolorbrewer)
6010 ("r-rlang" ,r-rlang)
6011 ("r-scales" ,r-scales)))
6013 `(("r-knitr" ,r-knitr)))
6014 (home-page "https://github.com/RGLab/ggcyto/issues")
6015 (synopsis "Visualize Cytometry data with ggplot")
6017 "With the dedicated fortify method implemented for @code{flowSet},
6018 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6019 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6020 and some custom layers also make it easy to add gates and population
6021 statistics to the plot.")
6022 (license license:artistic2.0)))
6024 (define-public r-flowviz
6031 (uri (bioconductor-uri "flowViz" version))
6034 "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq"))))
6035 (properties `((upstream-name . "flowViz")))
6036 (build-system r-build-system)
6038 `(("r-biobase" ,r-biobase)
6039 ("r-flowcore" ,r-flowcore)
6040 ("r-hexbin" ,r-hexbin)
6041 ("r-idpmisc" ,r-idpmisc)
6042 ("r-kernsmooth" ,r-kernsmooth)
6043 ("r-lattice" ,r-lattice)
6044 ("r-latticeextra" ,r-latticeextra)
6046 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6048 `(("r-knitr" ,r-knitr)))
6049 (home-page "https://bioconductor.org/packages/flowViz/")
6050 (synopsis "Visualization for flow cytometry")
6052 "This package provides visualization tools for flow cytometry data.")
6053 (license license:artistic2.0)))
6055 (define-public r-flowclust
6057 (name "r-flowclust")
6062 (uri (bioconductor-uri "flowClust" version))
6065 "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b"))))
6066 (properties `((upstream-name . "flowClust")))
6067 (build-system r-build-system)
6070 (list "--configure-args=--enable-bundled-gsl=no")))
6072 `(("r-biobase" ,r-biobase)
6073 ("r-biocgenerics" ,r-biocgenerics)
6075 ("r-corpcor" ,r-corpcor)
6076 ("r-ellipse" ,r-ellipse)
6077 ("r-flowcore" ,r-flowcore)
6078 ("r-flowviz" ,r-flowviz)
6079 ("r-graph" ,r-graph)
6080 ("r-mnormt" ,r-mnormt)))
6084 `(("pkg-config" ,pkg-config)
6085 ("r-knitr" ,r-knitr)))
6086 (home-page "https://bioconductor.org/packages/flowClust")
6087 (synopsis "Clustering for flow cytometry")
6089 "This package provides robust model-based clustering using a t-mixture
6090 model with Box-Cox transformation.")
6091 (license license:artistic2.0)))
6093 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6094 ;; make it use our protobuf package instead.
6095 (define-public r-rprotobuflib
6097 (name "r-rprotobuflib")
6102 (uri (bioconductor-uri "RProtoBufLib" version))
6105 "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
6106 (properties `((upstream-name . "RProtoBufLib")))
6107 (build-system r-build-system)
6110 (modify-phases %standard-phases
6111 (add-after 'unpack 'unpack-bundled-sources
6113 (with-directory-excursion "src"
6114 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6117 `(("r-knitr" ,r-knitr)))
6118 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6119 (synopsis "C++ headers and static libraries of Protocol buffers")
6121 "This package provides the headers and static library of Protocol buffers
6122 for other R packages to compile and link against.")
6123 (license license:bsd-3)))
6125 (define-public r-flowworkspace
6127 (name "r-flowworkspace")
6132 (uri (bioconductor-uri "flowWorkspace" version))
6135 "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
6136 (properties `((upstream-name . "flowWorkspace")))
6137 (build-system r-build-system)
6140 ("r-biobase" ,r-biobase)
6141 ("r-biocgenerics" ,r-biocgenerics)
6142 ("r-cytolib" ,r-cytolib)
6143 ("r-data-table" ,r-data-table)
6144 ("r-digest" ,r-digest)
6145 ("r-dplyr" ,r-dplyr)
6146 ("r-flowcore" ,r-flowcore)
6147 ("r-ggplot2" ,r-ggplot2)
6148 ("r-graph" ,r-graph)
6149 ("r-lattice" ,r-lattice)
6150 ("r-latticeextra" ,r-latticeextra)
6151 ("r-matrixstats" ,r-matrixstats)
6152 ("r-ncdfflow" ,r-ncdfflow)
6155 ("r-rcpparmadillo" ,r-rcpparmadillo)
6156 ("r-rcppparallel" ,r-rcppparallel)
6157 ("r-rgraphviz" ,r-rgraphviz)
6158 ("r-rhdf5lib" ,r-rhdf5lib)
6159 ("r-rprotobuflib" ,r-rprotobuflib)
6160 ("r-scales" ,r-scales)
6161 ("r-stringr" ,r-stringr)
6164 `(("r-knitr" ,r-knitr)))
6165 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6166 (synopsis "Infrastructure for working with cytometry data")
6168 "This package is designed to facilitate comparison of automated gating
6169 methods against manual gating done in flowJo. This package allows you to
6170 import basic flowJo workspaces into BioConductor and replicate the gating from
6171 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6172 samples, compensation, and transformation are performed so that the output
6173 matches the flowJo analysis.")
6174 (license license:artistic2.0)))
6176 (define-public r-flowstats
6178 (name "r-flowstats")
6183 (uri (bioconductor-uri "flowStats" version))
6186 "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
6187 (properties `((upstream-name . "flowStats")))
6188 (build-system r-build-system)
6190 `(("r-biobase" ,r-biobase)
6191 ("r-biocgenerics" ,r-biocgenerics)
6192 ("r-cluster" ,r-cluster)
6194 ("r-flowcore" ,r-flowcore)
6195 ("r-flowviz" ,r-flowviz)
6196 ("r-flowworkspace" ,r-flowworkspace)
6197 ("r-kernsmooth" ,r-kernsmooth)
6199 ("r-lattice" ,r-lattice)
6201 ("r-ncdfflow" ,r-ncdfflow)
6202 ("r-rcolorbrewer" ,r-rcolorbrewer)
6203 ("r-rrcov" ,r-rrcov)))
6204 (home-page "http://www.github.com/RGLab/flowStats")
6205 (synopsis "Statistical methods for the analysis of flow cytometry data")
6207 "This package provides methods and functionality to analyze flow data
6208 that is beyond the basic infrastructure provided by the @code{flowCore}
6210 (license license:artistic2.0)))
6212 (define-public r-opencyto
6219 (uri (bioconductor-uri "openCyto" version))
6222 "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
6223 (properties `((upstream-name . "openCyto")))
6224 (build-system r-build-system)
6226 `(("r-biobase" ,r-biobase)
6227 ("r-biocgenerics" ,r-biocgenerics)
6229 ("r-data-table" ,r-data-table)
6230 ("r-flowclust" ,r-flowclust)
6231 ("r-flowcore" ,r-flowcore)
6232 ("r-flowstats" ,r-flowstats)
6233 ("r-flowviz" ,r-flowviz)
6234 ("r-flowworkspace" ,r-flowworkspace)
6235 ("r-graph" ,r-graph)
6236 ("r-gtools" ,r-gtools)
6238 ("r-lattice" ,r-lattice)
6240 ("r-ncdfflow" ,r-ncdfflow)
6242 ("r-r-utils" ,r-r-utils)
6244 ("r-rcolorbrewer" ,r-rcolorbrewer)
6246 ("r-rrcov" ,r-rrcov)))
6248 `(("r-knitr" ,r-knitr)))
6249 (home-page "https://bioconductor.org/packages/openCyto")
6250 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6252 "This package is designed to facilitate the automated gating methods in a
6253 sequential way to mimic the manual gating strategy.")
6254 (license license:artistic2.0)))
6256 (define-public r-cytoml
6263 (uri (bioconductor-uri "CytoML" version))
6266 "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
6267 (properties `((upstream-name . "CytoML")))
6268 (build-system r-build-system)
6270 `(("libxml2" ,libxml2)))
6272 `(("r-base64enc" ,r-base64enc)
6274 ("r-biobase" ,r-biobase)
6275 ("r-corpcor" ,r-corpcor)
6276 ("r-cytolib" ,r-cytolib)
6277 ("r-data-table" ,r-data-table)
6278 ("r-dplyr" ,r-dplyr)
6279 ("r-flowcore" ,r-flowcore)
6280 ("r-flowworkspace" ,r-flowworkspace)
6281 ("r-ggcyto" ,r-ggcyto)
6282 ("r-graph" ,r-graph)
6283 ("r-jsonlite" ,r-jsonlite)
6284 ("r-lattice" ,r-lattice)
6285 ("r-opencyto" ,r-opencyto)
6289 ("r-rcpparmadillo" ,r-rcpparmadillo)
6290 ("r-rcppparallel" ,r-rcppparallel)
6291 ("r-rgraphviz" ,r-rgraphviz)
6292 ("r-rhdf5lib" ,r-rhdf5lib)
6293 ("r-rprotobuflib" ,r-rprotobuflib)
6294 ("r-runit" ,r-runit)
6295 ("r-tibble" ,r-tibble)
6298 ("r-yaml" ,r-yaml)))
6300 `(("r-knitr" ,r-knitr)))
6301 (home-page "https://github.com/RGLab/CytoML")
6302 (synopsis "GatingML interface for cross platform cytometry data sharing")
6304 "This package provides an interface to implementations of the GatingML2.0
6305 standard to exchange gated cytometry data with other software platforms.")
6306 (license license:artistic2.0)))
6308 (define-public r-flowsom
6315 (uri (bioconductor-uri "FlowSOM" version))
6318 "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
6319 (properties `((upstream-name . "FlowSOM")))
6320 (build-system r-build-system)
6322 `(("r-biocgenerics" ,r-biocgenerics)
6323 ("r-consensusclusterplus" ,r-consensusclusterplus)
6324 ("r-cytoml" ,r-cytoml)
6325 ("r-flowcore" ,r-flowcore)
6326 ("r-flowworkspace" ,r-flowworkspace)
6327 ("r-igraph" ,r-igraph)
6328 ("r-rcolorbrewer" ,r-rcolorbrewer)
6331 (home-page "https://bioconductor.org/packages/FlowSOM/")
6332 (synopsis "Visualize and interpret cytometry data")
6334 "FlowSOM offers visualization options for cytometry data, by using
6335 self-organizing map clustering and minimal spanning trees.")
6336 (license license:gpl2+)))
6338 (define-public r-mixomics
6345 (uri (bioconductor-uri "mixOmics" version))
6348 "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
6349 (properties `((upstream-name . "mixOmics")))
6350 (build-system r-build-system)
6352 `(("r-corpcor" ,r-corpcor)
6353 ("r-dplyr" ,r-dplyr)
6354 ("r-ellipse" ,r-ellipse)
6355 ("r-ggplot2" ,r-ggplot2)
6356 ("r-gridextra" ,r-gridextra)
6357 ("r-igraph" ,r-igraph)
6358 ("r-lattice" ,r-lattice)
6360 ("r-matrixstats" ,r-matrixstats)
6361 ("r-rarpack" ,r-rarpack)
6362 ("r-rcolorbrewer" ,r-rcolorbrewer)
6363 ("r-reshape2" ,r-reshape2)
6364 ("r-tidyr" ,r-tidyr)))
6366 `(("r-knitr" ,r-knitr)))
6367 (home-page "http://www.mixOmics.org")
6368 (synopsis "Multivariate methods for exploration of biological datasets")
6370 "mixOmics offers a wide range of multivariate methods for the exploration
6371 and integration of biological datasets with a particular focus on variable
6372 selection. The package proposes several sparse multivariate models we have
6373 developed to identify the key variables that are highly correlated, and/or
6374 explain the biological outcome of interest. The data that can be analysed
6375 with mixOmics may come from high throughput sequencing technologies, such as
6376 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6377 also beyond the realm of omics (e.g. spectral imaging). The methods
6378 implemented in mixOmics can also handle missing values without having to
6379 delete entire rows with missing data.")
6380 (license license:gpl2+)))
6382 (define-public r-depecher
6389 (uri (bioconductor-uri "DepecheR" version))
6392 "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
6393 (properties `((upstream-name . "DepecheR")))
6394 (build-system r-build-system)
6396 `(("r-beanplot" ,r-beanplot)
6397 ("r-dosnow" ,r-dosnow)
6398 ("r-dplyr" ,r-dplyr)
6400 ("r-foreach" ,r-foreach)
6401 ("r-ggplot2" ,r-ggplot2)
6402 ("r-gplots" ,r-gplots)
6404 ("r-matrixstats" ,r-matrixstats)
6405 ("r-mixomics" ,r-mixomics)
6406 ("r-moments" ,r-moments)
6408 ("r-rcppeigen" ,r-rcppeigen)
6409 ("r-reshape2" ,r-reshape2)
6410 ("r-robustbase" ,r-robustbase)
6411 ("r-viridis" ,r-viridis)))
6413 `(("r-knitr" ,r-knitr)))
6414 (home-page "https://bioconductor.org/packages/DepecheR/")
6415 (synopsis "Identify traits of clusters in high-dimensional entities")
6417 "The purpose of this package is to identify traits in a dataset that can
6418 separate groups. This is done on two levels. First, clustering is performed,
6419 using an implementation of sparse K-means. Secondly, the generated clusters
6420 are used to predict outcomes of groups of individuals based on their
6421 distribution of observations in the different clusters. As certain clusters
6422 with separating information will be identified, and these clusters are defined
6423 by a sparse number of variables, this method can reduce the complexity of
6424 data, to only emphasize the data that actually matters.")
6425 (license license:expat)))
6427 (define-public r-rcistarget
6429 (name "r-rcistarget")
6434 (uri (bioconductor-uri "RcisTarget" version))
6437 "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
6438 (properties `((upstream-name . "RcisTarget")))
6439 (build-system r-build-system)
6441 `(("r-aucell" ,r-aucell)
6442 ("r-biocgenerics" ,r-biocgenerics)
6443 ("r-data-table" ,r-data-table)
6444 ("r-feather" ,r-feather)
6445 ("r-gseabase" ,r-gseabase)
6446 ("r-r-utils" ,r-r-utils)
6447 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6449 `(("r-knitr" ,r-knitr)))
6450 (home-page "https://aertslab.org/#scenic")
6451 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6453 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6454 over-represented on a gene list. In a first step, RcisTarget selects DNA
6455 motifs that are significantly over-represented in the surroundings of the
6456 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6457 achieved by using a database that contains genome-wide cross-species rankings
6458 for each motif. The motifs that are then annotated to TFs and those that have
6459 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6460 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6461 genes in the gene-set that are ranked above the leading edge).")
6462 (license license:gpl3)))
6464 (define-public r-cicero
6471 (uri (bioconductor-uri "cicero" version))
6474 "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
6475 (build-system r-build-system)
6477 `(("r-assertthat" ,r-assertthat)
6478 ("r-biobase" ,r-biobase)
6479 ("r-biocgenerics" ,r-biocgenerics)
6480 ("r-data-table" ,r-data-table)
6481 ("r-dplyr" ,r-dplyr)
6483 ("r-genomicranges" ,r-genomicranges)
6484 ("r-ggplot2" ,r-ggplot2)
6485 ("r-glasso" ,r-glasso)
6487 ("r-igraph" ,r-igraph)
6488 ("r-iranges" ,r-iranges)
6489 ("r-matrix" ,r-matrix)
6490 ("r-monocle" ,r-monocle)
6492 ("r-reshape2" ,r-reshape2)
6493 ("r-s4vectors" ,r-s4vectors)
6494 ("r-stringi" ,r-stringi)
6495 ("r-stringr" ,r-stringr)
6496 ("r-tibble" ,r-tibble)
6497 ("r-tidyr" ,r-tidyr)
6498 ("r-vgam" ,r-vgam)))
6500 `(("r-knitr" ,r-knitr)))
6501 (home-page "https://bioconductor.org/packages/cicero/")
6502 (synopsis "Predict cis-co-accessibility from single-cell data")
6504 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6505 accessibility data. It also extends the monocle package for use in chromatin
6506 accessibility data.")
6507 (license license:expat)))
6509 ;; This is the latest commit on the "monocle3" branch.
6510 (define-public r-cicero-monocle3
6511 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6513 (package (inherit r-cicero)
6514 (name "r-cicero-monocle3")
6515 (version (git-version "1.3.2" revision commit))
6520 (url "https://github.com/cole-trapnell-lab/cicero-release")
6522 (file-name (git-file-name name version))
6525 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6527 `(("r-monocle3" ,r-monocle3)
6528 ,@(alist-delete "r-monocle"
6529 (package-propagated-inputs r-cicero)))))))
6531 (define-public r-cistopic
6532 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6536 (version (git-version "0.2.1" revision commit))
6541 (url "https://github.com/aertslab/cisTopic")
6543 (file-name (git-file-name name version))
6546 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6547 (build-system r-build-system)
6549 `(("r-aucell" ,r-aucell)
6550 ("r-data-table" ,r-data-table)
6551 ("r-dplyr" ,r-dplyr)
6552 ("r-dosnow" ,r-dosnow)
6554 ("r-feather" ,r-feather)
6555 ("r-fitdistrplus" ,r-fitdistrplus)
6556 ("r-genomicranges" ,r-genomicranges)
6557 ("r-ggplot2" ,r-ggplot2)
6559 ("r-matrix" ,r-matrix)
6561 ("r-rcistarget" ,r-rcistarget)
6562 ("r-rtracklayer" ,r-rtracklayer)
6563 ("r-s4vectors" ,r-s4vectors)))
6564 (home-page "https://github.com/aertslab/cisTopic")
6565 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6567 "The sparse nature of single cell epigenomics data can be overruled using
6568 probabilistic modelling methods such as @dfn{Latent Dirichlet
6569 Allocation} (LDA). This package allows the probabilistic modelling of
6570 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6571 includes functionalities to identify cell states based on the contribution of
6572 cisTopics and explore the nature and regulatory proteins driving them.")
6573 (license license:gpl3))))
6575 (define-public r-genie3
6582 (uri (bioconductor-uri "GENIE3" version))
6585 "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
6586 (properties `((upstream-name . "GENIE3")))
6587 (build-system r-build-system)
6588 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6590 `(("r-knitr" ,r-knitr)))
6591 (home-page "https://bioconductor.org/packages/GENIE3")
6592 (synopsis "Gene network inference with ensemble of trees")
6594 "This package implements the GENIE3 algorithm for inferring gene
6595 regulatory networks from expression data.")
6596 (license license:gpl2+)))
6598 (define-public r-roc
6605 (uri (bioconductor-uri "ROC" version))
6608 "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
6609 (properties `((upstream-name . "ROC")))
6610 (build-system r-build-system)
6612 `(("r-knitr" ,r-knitr)))
6613 (home-page "https://www.bioconductor.org/packages/ROC/")
6614 (synopsis "Utilities for ROC curves")
6616 "This package provides utilities for @dfn{Receiver Operating
6617 Characteristic} (ROC) curves, with a focus on micro arrays.")
6618 (license license:artistic2.0)))
6620 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6622 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6627 (uri (bioconductor-uri
6628 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6629 version 'annotation))
6632 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6635 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6636 (build-system r-build-system)
6637 (propagated-inputs `(("r-minfi" ,r-minfi)))
6639 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6640 (synopsis "Annotation for Illumina's 450k methylation arrays")
6642 "This package provides manifests and annotation for Illumina's 450k array
6644 (license license:artistic2.0)))
6646 (define-public r-watermelon
6648 (name "r-watermelon")
6653 (uri (bioconductor-uri "wateRmelon" version))
6656 "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
6657 (properties `((upstream-name . "wateRmelon")))
6658 (build-system r-build-system)
6660 `(("r-biobase" ,r-biobase)
6661 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6662 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6663 ("r-illuminaio" ,r-illuminaio)
6664 ("r-limma" ,r-limma)
6666 ("r-matrixstats" ,r-matrixstats)
6667 ("r-methylumi" ,r-methylumi)
6669 (home-page "https://bioconductor.org/packages/wateRmelon/")
6670 (synopsis "Illumina 450 methylation array normalization and metrics")
6672 "The standard index of DNA methylation (beta) is computed from methylated
6673 and unmethylated signal intensities. Betas calculated from raw signal
6674 intensities perform well, but using 11 methylomic datasets we demonstrate that
6675 quantile normalization methods produce marked improvement. The commonly used
6676 procedure of normalizing betas is inferior to the separate normalization of M
6677 and U, and it is also advantageous to normalize Type I and Type II assays
6678 separately. This package provides 15 flavours of betas and three performance
6679 metrics, with methods for objects produced by the @code{methylumi} and
6680 @code{minfi} packages.")
6681 (license license:gpl3)))
6683 (define-public r-gdsfmt
6690 (uri (bioconductor-uri "gdsfmt" version))
6693 "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
6694 (modules '((guix build utils)))
6695 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6696 ;; them and link with system libraries instead.
6699 (for-each delete-file-recursively
6703 (substitute* "src/Makevars"
6704 (("all: \\$\\(SHLIB\\)") "all:")
6705 (("\\$\\(SHLIB\\): liblzma.a") "")
6706 (("(ZLIB|LZ4)/.*") "")
6707 (("CoreArray/dVLIntGDS.cpp.*")
6708 "CoreArray/dVLIntGDS.cpp")
6709 (("CoreArray/dVLIntGDS.o.*")
6710 "CoreArray/dVLIntGDS.o")
6711 (("PKG_LIBS = ./liblzma.a")
6712 "PKG_LIBS = -llz4"))
6713 (substitute* "src/CoreArray/dStream.h"
6714 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6715 (string-append "include <" header ">")))
6717 (properties `((upstream-name . "gdsfmt")))
6718 (build-system r-build-system)
6724 `(("r-knitr" ,r-knitr)))
6725 (home-page "http://corearray.sourceforge.net/")
6727 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6729 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6730 Data Structure} (GDS) data files, which are portable across platforms with
6731 hierarchical structure to store multiple scalable array-oriented data sets
6732 with metadata information. It is suited for large-scale datasets, especially
6733 for data which are much larger than the available random-access memory. The
6734 @code{gdsfmt} package offers efficient operations specifically designed for
6735 integers of less than 8 bits, since a diploid genotype, like
6736 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6737 byte. Data compression and decompression are available with relatively
6738 efficient random access. It is also allowed to read a GDS file in parallel
6739 with multiple R processes supported by the package @code{parallel}.")
6740 (license license:lgpl3)))
6742 (define-public r-bigmelon
6749 (uri (bioconductor-uri "bigmelon" version))
6752 "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
6753 (properties `((upstream-name . "bigmelon")))
6754 (build-system r-build-system)
6756 `(("r-biobase" ,r-biobase)
6757 ("r-biocgenerics" ,r-biocgenerics)
6758 ("r-gdsfmt" ,r-gdsfmt)
6759 ("r-geoquery" ,r-geoquery)
6760 ("r-methylumi" ,r-methylumi)
6761 ("r-minfi" ,r-minfi)
6762 ("r-watermelon" ,r-watermelon)))
6763 (home-page "https://bioconductor.org/packages/bigmelon/")
6764 (synopsis "Illumina methylation array analysis for large experiments")
6766 "This package provides methods for working with Illumina arrays using the
6767 @code{gdsfmt} package.")
6768 (license license:gpl3)))
6770 (define-public r-seqbias
6777 (uri (bioconductor-uri "seqbias" version))
6780 "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
6781 (properties `((upstream-name . "seqbias")))
6782 (build-system r-build-system)
6784 `(("r-biostrings" ,r-biostrings)
6785 ("r-genomicranges" ,r-genomicranges)
6786 ("r-rhtslib" ,r-rhtslib)))
6788 `(("zlib" ,zlib))) ; This comes from rhtslib.
6789 (home-page "https://bioconductor.org/packages/seqbias/")
6790 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6792 "This package implements a model of per-position sequencing bias in
6793 high-throughput sequencing data using a simple Bayesian network, the structure
6794 and parameters of which are trained on a set of aligned reads and a reference
6796 (license license:lgpl3)))
6798 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6800 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6804 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6805 version 'annotation))
6808 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6809 (build-system r-build-system)
6810 ;; As this package provides little more than a very large data file it
6811 ;; doesn't make sense to build substitutes.
6812 (arguments `(#:substitutable? #f))
6814 `(("r-biocgenerics" ,r-biocgenerics)
6815 ("r-s4vectors" ,r-s4vectors)
6816 ("r-iranges" ,r-iranges)
6817 ("r-genomeinfodb" ,r-genomeinfodb)
6818 ("r-genomicranges" ,r-genomicranges)
6819 ("r-bsgenome" ,r-bsgenome)
6820 ("r-biostrings" ,r-biostrings)))
6822 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6823 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6824 (description "This package provides SNP locations and alleles for Homo
6825 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6826 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6827 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6828 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6829 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6830 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6831 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6832 correct position but this injection will exclude chrM (i.e. nothing will be
6833 injected in that sequence).")
6834 (license license:artistic2.0)))
6836 (define-public r-reqon
6843 (uri (bioconductor-uri "ReQON" version))
6846 "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
6847 (properties `((upstream-name . "ReQON")))
6848 (build-system r-build-system)
6850 `(("r-rjava" ,r-rjava)
6851 ("r-rsamtools" ,r-rsamtools)
6852 ("r-seqbias" ,r-seqbias)))
6853 (home-page "https://bioconductor.org/packages/ReQON/")
6854 (synopsis "Recalibrating quality of nucleotides")
6856 "This package provides an implementation of an algorithm for
6857 recalibrating the base quality scores for aligned sequencing data in BAM
6859 (license license:gpl2)))
6861 (define-public r-wavcluster
6863 (name "r-wavcluster")
6868 (uri (bioconductor-uri "wavClusteR" version))
6871 "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
6872 (properties `((upstream-name . "wavClusteR")))
6873 (build-system r-build-system)
6875 `(("r-biocgenerics" ,r-biocgenerics)
6876 ("r-biostrings" ,r-biostrings)
6877 ("r-foreach" ,r-foreach)
6878 ("r-genomicfeatures" ,r-genomicfeatures)
6879 ("r-genomicranges" ,r-genomicranges)
6880 ("r-ggplot2" ,r-ggplot2)
6881 ("r-hmisc" ,r-hmisc)
6882 ("r-iranges" ,r-iranges)
6883 ("r-mclust" ,r-mclust)
6884 ("r-rsamtools" ,r-rsamtools)
6885 ("r-rtracklayer" ,r-rtracklayer)
6886 ("r-s4vectors" ,r-s4vectors)
6887 ("r-seqinr" ,r-seqinr)
6888 ("r-stringr" ,r-stringr)
6889 ("r-wmtsa" ,r-wmtsa)))
6891 `(("r-knitr" ,r-knitr)))
6892 (home-page "https://bioconductor.org/packages/wavClusteR/")
6893 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6895 "This package provides an integrated pipeline for the analysis of
6896 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6897 sequencing errors, SNPs and additional non-experimental sources by a non-
6898 parametric mixture model. The protein binding sites (clusters) are then
6899 resolved at high resolution and cluster statistics are estimated using a
6900 rigorous Bayesian framework. Post-processing of the results, data export for
6901 UCSC genome browser visualization and motif search analysis are provided. In
6902 addition, the package integrates RNA-Seq data to estimate the False
6903 Discovery Rate of cluster detection. Key functions support parallel multicore
6904 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6905 be applied to the analysis of other NGS data obtained from experimental
6906 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6907 (license license:gpl2)))
6909 (define-public r-timeseriesexperiment
6911 (name "r-timeseriesexperiment")
6916 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6919 "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
6921 `((upstream-name . "TimeSeriesExperiment")))
6922 (build-system r-build-system)
6924 `(("r-deseq2" ,r-deseq2)
6925 ("r-dplyr" ,r-dplyr)
6926 ("r-dynamictreecut" ,r-dynamictreecut)
6927 ("r-edger" ,r-edger)
6928 ("r-ggplot2" ,r-ggplot2)
6929 ("r-hmisc" ,r-hmisc)
6930 ("r-limma" ,r-limma)
6931 ("r-magrittr" ,r-magrittr)
6932 ("r-proxy" ,r-proxy)
6933 ("r-s4vectors" ,r-s4vectors)
6934 ("r-summarizedexperiment" ,r-summarizedexperiment)
6935 ("r-tibble" ,r-tibble)
6936 ("r-tidyr" ,r-tidyr)
6937 ("r-vegan" ,r-vegan)
6938 ("r-viridis" ,r-viridis)))
6940 `(("r-knitr" ,r-knitr)))
6941 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6942 (synopsis "Analysis for short time-series data")
6944 "This package is a visualization and analysis toolbox for short time
6945 course data which includes dimensionality reduction, clustering, two-sample
6946 differential expression testing and gene ranking techniques. The package also
6947 provides methods for retrieving enriched pathways.")
6948 (license license:lgpl3+)))
6950 (define-public r-variantfiltering
6952 (name "r-variantfiltering")
6957 (uri (bioconductor-uri "VariantFiltering" version))
6960 "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
6962 `((upstream-name . "VariantFiltering")))
6963 (build-system r-build-system)
6965 `(("r-annotationdbi" ,r-annotationdbi)
6966 ("r-biobase" ,r-biobase)
6967 ("r-biocgenerics" ,r-biocgenerics)
6968 ("r-biocparallel" ,r-biocparallel)
6969 ("r-biostrings" ,r-biostrings)
6970 ("r-bsgenome" ,r-bsgenome)
6972 ("r-genomeinfodb" ,r-genomeinfodb)
6973 ("r-genomicfeatures" ,r-genomicfeatures)
6974 ("r-genomicranges" ,r-genomicranges)
6975 ("r-genomicscores" ,r-genomicscores)
6976 ("r-graph" ,r-graph)
6978 ("r-iranges" ,r-iranges)
6980 ("r-rsamtools" ,r-rsamtools)
6981 ("r-s4vectors" ,r-s4vectors)
6982 ("r-shiny" ,r-shiny)
6983 ("r-shinyjs" ,r-shinyjs)
6984 ("r-shinythemes" ,r-shinythemes)
6985 ("r-shinytree" ,r-shinytree)
6986 ("r-summarizedexperiment" ,r-summarizedexperiment)
6987 ("r-variantannotation" ,r-variantannotation)
6988 ("r-xvector" ,r-xvector)))
6989 (home-page "https://github.com/rcastelo/VariantFiltering")
6990 (synopsis "Filtering of coding and non-coding genetic variants")
6992 "Filter genetic variants using different criteria such as inheritance
6993 model, amino acid change consequence, minor allele frequencies across human
6994 populations, splice site strength, conservation, etc.")
6995 (license license:artistic2.0)))
6997 (define-public r-genomegraphs
6999 (name "r-genomegraphs")
7004 (uri (bioconductor-uri "GenomeGraphs" version))
7007 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7008 (properties `((upstream-name . "GenomeGraphs")))
7009 (build-system r-build-system)
7011 `(("r-biomart" ,r-biomart)))
7012 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7013 (synopsis "Plotting genomic information from Ensembl")
7015 "Genomic data analyses requires integrated visualization of known genomic
7016 information and new experimental data. GenomeGraphs uses the biomaRt package
7017 to perform live annotation queries to Ensembl and translates this to e.g.
7018 gene/transcript structures in viewports of the grid graphics package. This
7019 results in genomic information plotted together with your data. Another
7020 strength of GenomeGraphs is to plot different data types such as array CGH,
7021 gene expression, sequencing and other data, together in one plot using the
7022 same genome coordinate system.")
7023 (license license:artistic2.0)))
7025 (define-public r-wavetiling
7027 (name "r-wavetiling")
7032 (uri (bioconductor-uri "waveTiling" version))
7035 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7036 (properties `((upstream-name . "waveTiling")))
7037 (build-system r-build-system)
7039 `(("r-affy" ,r-affy)
7040 ("r-biobase" ,r-biobase)
7041 ("r-biostrings" ,r-biostrings)
7042 ("r-genomegraphs" ,r-genomegraphs)
7043 ("r-genomicranges" ,r-genomicranges)
7044 ("r-iranges" ,r-iranges)
7045 ("r-oligo" ,r-oligo)
7046 ("r-oligoclasses" ,r-oligoclasses)
7047 ("r-preprocesscore" ,r-preprocesscore)
7048 ("r-waveslim" ,r-waveslim)))
7049 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7050 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7052 "This package is designed to conduct transcriptome analysis for tiling
7053 arrays based on fast wavelet-based functional models.")
7054 (license license:gpl2+)))
7056 (define-public r-variancepartition
7058 (name "r-variancepartition")
7063 (uri (bioconductor-uri "variancePartition" version))
7066 "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
7068 `((upstream-name . "variancePartition")))
7069 (build-system r-build-system)
7071 `(("r-biobase" ,r-biobase)
7072 ("r-biocparallel" ,r-biocparallel)
7073 ("r-colorramps" ,r-colorramps)
7074 ("r-doparallel" ,r-doparallel)
7075 ("r-foreach" ,r-foreach)
7076 ("r-ggplot2" ,r-ggplot2)
7077 ("r-gplots" ,r-gplots)
7078 ("r-iterators" ,r-iterators)
7079 ("r-limma" ,r-limma)
7081 ("r-lmertest" ,r-lmertest)
7083 ("r-pbkrtest" ,r-pbkrtest)
7084 ("r-progress" ,r-progress)
7085 ("r-reshape2" ,r-reshape2)
7086 ("r-scales" ,r-scales)))
7088 `(("r-knitr" ,r-knitr)))
7089 (home-page "https://bioconductor.org/packages/variancePartition/")
7090 (synopsis "Analyze variation in gene expression experiments")
7092 "This is a package providing tools to quantify and interpret multiple
7093 sources of biological and technical variation in gene expression experiments.
7094 It uses a linear mixed model to quantify variation in gene expression
7095 attributable to individual, tissue, time point, or technical variables. The
7096 package includes dream differential expression analysis for repeated
7098 (license license:gpl2+)))
7100 (define-public r-htqpcr
7107 (uri (bioconductor-uri "HTqPCR" version))
7110 "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
7111 (properties `((upstream-name . "HTqPCR")))
7112 (build-system r-build-system)
7114 `(("r-affy" ,r-affy)
7115 ("r-biobase" ,r-biobase)
7116 ("r-gplots" ,r-gplots)
7117 ("r-limma" ,r-limma)
7118 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7119 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7120 "groups/bertone/software/HTqPCR.pdf"))
7121 (synopsis "Automated analysis of high-throughput qPCR data")
7123 "Analysis of Ct values from high throughput quantitative real-time
7124 PCR (qPCR) assays across multiple conditions or replicates. The input data
7125 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7126 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7127 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7128 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7129 loading, quality assessment, normalization, visualization and parametric or
7130 non-parametric testing for statistical significance in Ct values between
7131 features (e.g. genes, microRNAs).")
7132 (license license:artistic2.0)))
7134 (define-public r-unifiedwmwqpcr
7136 (name "r-unifiedwmwqpcr")
7141 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7144 "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
7146 `((upstream-name . "unifiedWMWqPCR")))
7147 (build-system r-build-system)
7149 `(("r-biocgenerics" ,r-biocgenerics)
7150 ("r-htqpcr" ,r-htqpcr)))
7151 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7152 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7154 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7155 data. This modified test allows for testing differential expression in qPCR
7157 (license license:gpl2+)))
7159 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7161 (define-public r-activedriverwgs
7163 (name "r-activedriverwgs")
7168 (uri (cran-uri "ActiveDriverWGS" version))
7171 "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
7173 `((upstream-name . "ActiveDriverWGS")))
7174 (build-system r-build-system)
7176 `(("r-biostrings" ,r-biostrings)
7177 ("r-bsgenome" ,r-bsgenome)
7178 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7179 ("r-genomeinfodb" ,r-genomeinfodb)
7180 ("r-genomicranges" ,r-genomicranges)
7181 ("r-iranges" ,r-iranges)
7182 ("r-s4vectors" ,r-s4vectors)))
7184 `(("r-knitr" ,r-knitr)))
7185 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7186 (synopsis "Driver discovery tool for cancer whole genomes")
7188 "This package provides a method for finding an enrichment of cancer
7189 simple somatic mutations (SNVs and Indels) in functional elements across the
7190 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7191 using whole genome sequencing data.")
7192 (license license:gpl3)))
7194 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7196 (define-public r-activepathways
7198 (name "r-activepathways")
7203 (uri (cran-uri "ActivePathways" version))
7206 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7208 `((upstream-name . "ActivePathways")))
7209 (build-system r-build-system)
7211 `(("r-data-table" ,r-data-table)
7212 ("r-ggplot2" ,r-ggplot2)))
7214 `(("r-knitr" ,r-knitr)))
7215 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7216 (synopsis "Multivariate pathway enrichment analysis")
7218 "This package represents an integrative method of analyzing multi omics
7219 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7220 uses a statistical data fusion approach, rationalizes contributing evidence
7221 and highlights associated genes, improving systems-level understanding of
7222 cellular organization in health and disease.")
7223 (license license:gpl3)))
7225 (define-public r-bgmix
7232 (uri (bioconductor-uri "BGmix" version))
7235 "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
7236 (properties `((upstream-name . "BGmix")))
7237 (build-system r-build-system)
7239 `(("r-kernsmooth" ,r-kernsmooth)))
7240 (home-page "https://bioconductor.org/packages/BGmix/")
7241 (synopsis "Bayesian models for differential gene expression")
7243 "This package provides fully Bayesian mixture models for differential
7245 (license license:gpl2)))
7247 (define-public r-bgx
7254 (uri (bioconductor-uri "bgx" version))
7257 "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
7258 (properties `((upstream-name . "bgx")))
7259 (build-system r-build-system)
7261 `(("r-affy" ,r-affy)
7262 ("r-biobase" ,r-biobase)
7263 ("r-gcrma" ,r-gcrma)
7264 ("r-rcpp" ,r-rcpp)))
7265 (home-page "https://bioconductor.org/packages/bgx/")
7266 (synopsis "Bayesian gene expression")
7268 "This package provides tools for Bayesian integrated analysis of
7269 Affymetrix GeneChips.")
7270 (license license:gpl2)))
7272 (define-public r-bhc
7279 (uri (bioconductor-uri "BHC" version))
7282 "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
7283 (properties `((upstream-name . "BHC")))
7284 (build-system r-build-system)
7285 (home-page "https://bioconductor.org/packages/BHC/")
7286 (synopsis "Bayesian hierarchical clustering")
7288 "The method implemented in this package performs bottom-up hierarchical
7289 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7290 in the data and Bayesian model selection to decide at each step which clusters
7291 to merge. This avoids several limitations of traditional methods, for example
7292 how many clusters there should be and how to choose a principled distance
7293 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7294 categories) or time-series data. This version also includes a randomised
7295 algorithm which is more efficient for larger data sets.")
7296 (license license:gpl3)))
7298 (define-public r-bicare
7305 (uri (bioconductor-uri "BicARE" version))
7308 "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
7309 (properties `((upstream-name . "BicARE")))
7310 (build-system r-build-system)
7312 `(("r-biobase" ,r-biobase)
7313 ("r-gseabase" ,r-gseabase)
7314 ("r-multtest" ,r-multtest)))
7315 (home-page "http://bioinfo.curie.fr")
7316 (synopsis "Biclustering analysis and results exploration")
7318 "This is a package for biclustering analysis and exploration of
7320 (license license:gpl2)))
7322 (define-public r-bifet
7329 (uri (bioconductor-uri "BiFET" version))
7332 "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
7333 (properties `((upstream-name . "BiFET")))
7334 (build-system r-build-system)
7336 `(("r-genomicranges" ,r-genomicranges)
7337 ("r-poibin" ,r-poibin)))
7339 `(("r-knitr" ,r-knitr)))
7340 (home-page "https://bioconductor.org/packages/BiFET")
7341 (synopsis "Bias-free footprint enrichment test")
7343 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7344 over-represented in target regions compared to background regions after
7345 correcting for the bias arising from the imbalance in read counts and GC
7346 contents between the target and background regions. For a given TF k, BiFET
7347 tests the null hypothesis that the target regions have the same probability of
7348 having footprints for the TF k as the background regions while correcting for
7349 the read count and GC content bias.")
7350 (license license:gpl3)))
7352 (define-public r-rsbml
7359 (uri (bioconductor-uri "rsbml" version))
7362 "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
7363 (properties `((upstream-name . "rsbml")))
7364 (build-system r-build-system)
7366 `(("libsbml" ,libsbml)
7369 `(("r-biocgenerics" ,r-biocgenerics)
7370 ("r-graph" ,r-graph)))
7372 `(("pkg-config" ,pkg-config)))
7373 (home-page "http://www.sbml.org")
7374 (synopsis "R support for SBML")
7376 "This package provides an R interface to libsbml for SBML parsing,
7377 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7378 (license license:artistic2.0)))
7380 (define-public r-hypergraph
7382 (name "r-hypergraph")
7387 (uri (bioconductor-uri "hypergraph" version))
7390 "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
7391 (properties `((upstream-name . "hypergraph")))
7392 (build-system r-build-system)
7394 `(("r-graph" ,r-graph)))
7395 (home-page "https://bioconductor.org/packages/hypergraph")
7396 (synopsis "Hypergraph data structures")
7398 "This package implements some simple capabilities for representing and
7399 manipulating hypergraphs.")
7400 (license license:artistic2.0)))
7402 (define-public r-hyperdraw
7404 (name "r-hyperdraw")
7409 (uri (bioconductor-uri "hyperdraw" version))
7412 "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
7413 (properties `((upstream-name . "hyperdraw")))
7414 (build-system r-build-system)
7415 (inputs `(("graphviz" ,graphviz)))
7417 `(("r-graph" ,r-graph)
7418 ("r-hypergraph" ,r-hypergraph)
7419 ("r-rgraphviz" ,r-rgraphviz)))
7420 (home-page "https://bioconductor.org/packages/hyperdraw")
7421 (synopsis "Visualizing hypergraphs")
7423 "This package provides functions for visualizing hypergraphs.")
7424 (license license:gpl2+)))
7426 (define-public r-biggr
7433 (uri (bioconductor-uri "BiGGR" version))
7436 "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
7437 (properties `((upstream-name . "BiGGR")))
7438 (build-system r-build-system)
7440 `(("r-hyperdraw" ,r-hyperdraw)
7441 ("r-hypergraph" ,r-hypergraph)
7443 ("r-limsolve" ,r-limsolve)
7444 ("r-rsbml" ,r-rsbml)
7445 ("r-stringr" ,r-stringr)))
7446 (home-page "https://bioconductor.org/packages/BiGGR/")
7447 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7449 "This package provides an interface to simulate metabolic reconstruction
7450 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7451 reconstruction databases. The package facilitates @dfn{flux balance
7452 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7453 networks and estimated fluxes can be visualized with hypergraphs.")
7454 (license license:gpl3+)))
7456 (define-public r-bigmemoryextras
7458 (name "r-bigmemoryextras")
7463 (uri (bioconductor-uri "bigmemoryExtras" version))
7466 "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
7468 `((upstream-name . "bigmemoryExtras")))
7469 (build-system r-build-system)
7471 `(("r-bigmemory" ,r-bigmemory)))
7473 `(("r-knitr" ,r-knitr)))
7474 (home-page "https://github.com/phaverty/bigmemoryExtras")
7475 (synopsis "Extension of the bigmemory package")
7477 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7478 safety and convenience features to the @code{filebacked.big.matrix} class from
7479 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7480 monitoring and gracefully restoring the connection to on-disk data and it also
7481 protects against accidental data modification with a filesystem-based
7482 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7483 classes as @code{assayData} matrices within the @code{Biobase} package's
7484 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7485 related to attaching to, and indexing into, file-backed matrices with
7486 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7487 a file-backed matrix with factor properties.")
7488 (license license:artistic2.0)))
7490 (define-public r-bigpint
7497 (uri (bioconductor-uri "bigPint" version))
7500 "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
7501 (properties `((upstream-name . "bigPint")))
7502 (build-system r-build-system)
7504 `(("r-delayedarray" ,r-delayedarray)
7505 ("r-dplyr" ,r-dplyr)
7506 ("r-ggally" ,r-ggally)
7507 ("r-ggplot2" ,r-ggplot2)
7508 ("r-gridextra" ,r-gridextra)
7509 ("r-hexbin" ,r-hexbin)
7510 ("r-hmisc" ,r-hmisc)
7511 ("r-htmlwidgets" ,r-htmlwidgets)
7512 ("r-plotly" ,r-plotly)
7514 ("r-rcolorbrewer" ,r-rcolorbrewer)
7515 ("r-reshape" ,r-reshape)
7516 ("r-shiny" ,r-shiny)
7517 ("r-shinycssloaders" ,r-shinycssloaders)
7518 ("r-shinydashboard" ,r-shinydashboard)
7519 ("r-stringr" ,r-stringr)
7520 ("r-summarizedexperiment" ,r-summarizedexperiment)
7521 ("r-tidyr" ,r-tidyr)))
7523 `(("r-knitr" ,r-knitr)))
7524 (home-page "https://github.com/lindsayrutter/bigPint")
7525 (synopsis "Big multivariate data plotted interactively")
7527 "This package provides methods for visualizing large multivariate
7528 datasets using static and interactive scatterplot matrices, parallel
7529 coordinate plots, volcano plots, and litre plots. It includes examples for
7530 visualizing RNA-sequencing datasets and differentially expressed genes.")
7531 (license license:gpl3)))
7533 (define-public r-chemminer
7535 (name "r-chemminer")
7540 (uri (bioconductor-uri "ChemmineR" version))
7543 "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
7544 (properties `((upstream-name . "ChemmineR")))
7545 (build-system r-build-system)
7547 `(("r-base64enc" ,r-base64enc)
7549 ("r-biocgenerics" ,r-biocgenerics)
7551 ("r-digest" ,r-digest)
7553 ("r-ggplot2" ,r-ggplot2)
7554 ("r-gridextra" ,r-gridextra)
7557 ("r-rcurl" ,r-rcurl)
7558 ("r-rjson" ,r-rjson)
7559 ("r-rsvg" ,r-rsvg)))
7561 `(("r-knitr" ,r-knitr)))
7562 (home-page "https://github.com/girke-lab/ChemmineR")
7563 (synopsis "Cheminformatics toolkit for R")
7565 "ChemmineR is a cheminformatics package for analyzing drug-like small
7566 molecule data in R. It contains functions for efficient processing of large
7567 numbers of molecules, physicochemical/structural property predictions,
7568 structural similarity searching, classification and clustering of compound
7569 libraries with a wide spectrum of algorithms. In addition, it offers
7570 visualization functions for compound clustering results and chemical
7572 (license license:artistic2.0)))
7574 (define-public r-bioassayr
7576 (name "r-bioassayr")
7581 (uri (bioconductor-uri "bioassayR" version))
7584 "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
7585 (properties `((upstream-name . "bioassayR")))
7586 (build-system r-build-system)
7588 `(("r-biocgenerics" ,r-biocgenerics)
7589 ("r-chemminer" ,r-chemminer)
7591 ("r-matrix" ,r-matrix)
7592 ("r-rjson" ,r-rjson)
7593 ("r-rsqlite" ,r-rsqlite)
7596 `(("r-knitr" ,r-knitr)))
7597 (home-page "https://github.com/TylerBackman/bioassayR")
7598 (synopsis "Cross-target analysis of small molecule bioactivity")
7600 "bioassayR is a computational tool that enables simultaneous analysis of
7601 thousands of bioassay experiments performed over a diverse set of compounds
7602 and biological targets. Unique features include support for large-scale
7603 cross-target analyses of both public and custom bioassays, generation of
7604 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7605 preloaded database that provides access to a substantial portion of publicly
7606 available bioactivity data.")
7607 (license license:artistic2.0)))
7609 (define-public r-biobroom
7616 (uri (bioconductor-uri "biobroom" version))
7619 "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
7620 (properties `((upstream-name . "biobroom")))
7621 (build-system r-build-system)
7623 `(("r-biobase" ,r-biobase)
7624 ("r-broom" ,r-broom)
7625 ("r-dplyr" ,r-dplyr)
7626 ("r-tidyr" ,r-tidyr)))
7628 `(("r-knitr" ,r-knitr)))
7629 (home-page "https://github.com/StoreyLab/biobroom")
7630 (synopsis "Turn Bioconductor objects into tidy data frames")
7632 "This package contains methods for converting standard objects
7633 constructed by bioinformatics packages, especially those in Bioconductor, and
7634 converting them to @code{tidy} data. It thus serves as a complement to the
7635 @code{broom} package, and follows the same tidy, augment, glance division of
7636 tidying methods. Tidying data makes it easy to recombine, reshape and
7637 visualize bioinformatics analyses.")
7638 ;; Any version of the LGPL.
7639 (license license:lgpl3+)))
7641 (define-public r-graphite
7648 (uri (bioconductor-uri "graphite" version))
7651 "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
7652 (properties `((upstream-name . "graphite")))
7653 (build-system r-build-system)
7655 `(("r-annotationdbi" ,r-annotationdbi)
7656 ("r-checkmate" ,r-checkmate)
7657 ("r-graph" ,r-graph)
7659 ("r-rappdirs" ,r-rappdirs)))
7660 (home-page "https://bioconductor.org/packages/graphite/")
7661 (synopsis "Networks from pathway databases")
7663 "Graphite provides networks derived from eight public pathway databases,
7664 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7666 (license license:agpl3+)))
7668 (define-public r-reactomepa
7670 (name "r-reactomepa")
7675 (uri (bioconductor-uri "ReactomePA" version))
7678 "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
7679 (properties `((upstream-name . "ReactomePA")))
7680 (build-system r-build-system)
7682 `(("r-annotationdbi" ,r-annotationdbi)
7684 ("r-enrichplot" ,r-enrichplot)
7685 ("r-ggplot2" ,r-ggplot2)
7686 ("r-ggraph" ,r-ggraph)
7687 ("r-graphite" ,r-graphite)
7688 ("r-igraph" ,r-igraph)
7689 ("r-reactome-db" ,r-reactome-db)))
7691 `(("r-knitr" ,r-knitr)))
7692 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7693 (synopsis "Reactome pathway analysis")
7695 "This package provides functions for pathway analysis based on the
7696 REACTOME pathway database. It implements enrichment analysis, gene set
7697 enrichment analysis and several functions for visualization.")
7698 (license license:gpl2)))
7700 (define-public r-ebarrays
7707 (uri (bioconductor-uri "EBarrays" version))
7710 "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
7711 (properties `((upstream-name . "EBarrays")))
7712 (build-system r-build-system)
7714 `(("r-biobase" ,r-biobase)
7715 ("r-cluster" ,r-cluster)
7716 ("r-lattice" ,r-lattice)))
7717 (home-page "https://bioconductor.org/packages/EBarrays/")
7718 (synopsis "Gene clustering and differential expression identification")
7720 "EBarrays provides tools for the analysis of replicated/unreplicated
7722 (license license:gpl2+)))
7724 (define-public r-bioccasestudies
7726 (name "r-bioccasestudies")
7731 (uri (bioconductor-uri "BiocCaseStudies" version))
7734 "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
7736 `((upstream-name . "BiocCaseStudies")))
7737 (build-system r-build-system)
7738 (propagated-inputs `(("r-biobase" ,r-biobase)))
7739 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7740 (synopsis "Support for the case studies monograph")
7742 "This package provides software and data to support the case studies
7744 (license license:artistic2.0)))
7746 (define-public r-biocgraph
7748 (name "r-biocgraph")
7753 (uri (bioconductor-uri "biocGraph" version))
7756 "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
7757 (properties `((upstream-name . "biocGraph")))
7758 (build-system r-build-system)
7760 `(("r-biocgenerics" ,r-biocgenerics)
7761 ("r-geneplotter" ,r-geneplotter)
7762 ("r-graph" ,r-graph)
7763 ("r-rgraphviz" ,r-rgraphviz)))
7764 (home-page "https://bioconductor.org/packages/biocGraph/")
7765 (synopsis "Graph examples and use cases in Bioinformatics")
7767 "This package provides examples and code that make use of the
7768 different graph related packages produced by Bioconductor.")
7769 (license license:artistic2.0)))
7771 (define-public r-experimenthub
7773 (name "r-experimenthub")
7778 (uri (bioconductor-uri "ExperimentHub" version))
7781 "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
7782 (properties `((upstream-name . "ExperimentHub")))
7783 (build-system r-build-system)
7785 `(("r-annotationhub" ,r-annotationhub)
7786 ("r-biocfilecache" ,r-biocfilecache)
7787 ("r-biocgenerics" ,r-biocgenerics)
7788 ("r-biocmanager" ,r-biocmanager)
7790 ("r-rappdirs" ,r-rappdirs)
7791 ("r-s4vectors" ,r-s4vectors)))
7793 `(("r-knitr" ,r-knitr)))
7794 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7795 (synopsis "Client to access ExperimentHub resources")
7797 "This package provides a client for the Bioconductor ExperimentHub web
7798 resource. ExperimentHub provides a central location where curated data from
7799 experiments, publications or training courses can be accessed. Each resource
7800 has associated metadata, tags and date of modification. The client creates
7801 and manages a local cache of files retrieved enabling quick and reproducible
7803 (license license:artistic2.0)))
7805 (define-public r-multiassayexperiment
7807 (name "r-multiassayexperiment")
7812 (uri (bioconductor-uri "MultiAssayExperiment" version))
7815 "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
7817 `((upstream-name . "MultiAssayExperiment")))
7818 (build-system r-build-system)
7820 `(("r-biobase" ,r-biobase)
7821 ("r-biocgenerics" ,r-biocgenerics)
7822 ("r-genomicranges" ,r-genomicranges)
7823 ("r-iranges" ,r-iranges)
7824 ("r-s4vectors" ,r-s4vectors)
7825 ("r-summarizedexperiment" ,r-summarizedexperiment)
7826 ("r-tidyr" ,r-tidyr)))
7828 `(("r-knitr" ,r-knitr)))
7829 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7830 (synopsis "Integration of multi-omics experiments in Bioconductor")
7832 "MultiAssayExperiment harmonizes data management of multiple assays
7833 performed on an overlapping set of specimens. It provides a familiar
7834 Bioconductor user experience by extending concepts from
7835 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7836 classes for individual assays, and allowing subsetting by genomic ranges or
7838 (license license:artistic2.0)))
7840 (define-public r-bioconcotk
7842 (name "r-bioconcotk")
7847 (uri (bioconductor-uri "BiocOncoTK" version))
7850 "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
7851 (properties `((upstream-name . "BiocOncoTK")))
7852 (build-system r-build-system)
7854 `(("r-bigrquery" ,r-bigrquery)
7856 ("r-complexheatmap" ,r-complexheatmap)
7857 ("r-curatedtcgadata" ,r-curatedtcgadata)
7859 ("r-dplyr" ,r-dplyr)
7861 ("r-genomicfeatures" ,r-genomicfeatures)
7862 ("r-genomicranges" ,r-genomicranges)
7863 ("r-ggplot2" ,r-ggplot2)
7864 ("r-ggpubr" ,r-ggpubr)
7865 ("r-graph" ,r-graph)
7867 ("r-iranges" ,r-iranges)
7868 ("r-magrittr" ,r-magrittr)
7870 ("r-rgraphviz" ,r-rgraphviz)
7871 ("r-rjson" ,r-rjson)
7872 ("r-s4vectors" ,r-s4vectors)
7873 ("r-scales" ,r-scales)
7874 ("r-shiny" ,r-shiny)
7875 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7877 `(("r-knitr" ,r-knitr)))
7878 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7879 (synopsis "Bioconductor components for general cancer genomics")
7881 "The purpose of this package is to provide a central interface to various
7882 tools for genome-scale analysis of cancer studies.")
7883 (license license:artistic2.0)))
7885 (define-public r-biocor
7892 (uri (bioconductor-uri "BioCor" version))
7895 "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
7896 (properties `((upstream-name . "BioCor")))
7897 (build-system r-build-system)
7899 `(("r-biocparallel" ,r-biocparallel)
7900 ("r-gseabase" ,r-gseabase)
7901 ("r-matrix" ,r-matrix)))
7903 `(("r-knitr" ,r-knitr)))
7904 (home-page "https://llrs.github.io/BioCor/")
7905 (synopsis "Functional similarities")
7907 "This package provides tools to calculate functional similarities based
7908 on the pathways described on KEGG and REACTOME or in gene sets. These
7909 similarities can be calculated for pathways or gene sets, genes, or clusters
7910 and combined with other similarities. They can be used to improve networks,
7911 gene selection, testing relationships, and so on.")
7912 (license license:expat)))
7914 (define-public r-biocpkgtools
7916 (name "r-biocpkgtools")
7921 (uri (bioconductor-uri "BiocPkgTools" version))
7924 "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
7925 (properties `((upstream-name . "BiocPkgTools")))
7926 (build-system r-build-system)
7928 `(("r-biocfilecache" ,r-biocfilecache)
7929 ("r-biocmanager" ,r-biocmanager)
7930 ("r-biocviews" ,r-biocviews)
7931 ("r-dplyr" ,r-dplyr)
7934 ("r-graph" ,r-graph)
7935 ("r-htmltools" ,r-htmltools)
7936 ("r-htmlwidgets" ,r-htmlwidgets)
7938 ("r-igraph" ,r-igraph)
7939 ("r-jsonlite" ,r-jsonlite)
7940 ("r-magrittr" ,r-magrittr)
7941 ("r-rappdirs" ,r-rappdirs)
7943 ("r-readr" ,r-readr)
7945 ("r-rlang" ,r-rlang)
7946 ("r-rvest" ,r-rvest)
7947 ("r-stringr" ,r-stringr)
7948 ("r-tibble" ,r-tibble)
7949 ("r-tidyr" ,r-tidyr)
7950 ("r-tidyselect" ,r-tidyselect)
7951 ("r-xml2" ,r-xml2)))
7953 `(("r-knitr" ,r-knitr)))
7954 (home-page "https://github.com/seandavi/BiocPkgTools")
7955 (synopsis "Collection of tools for learning about Bioconductor packages")
7957 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7958 and build status. This package is a simple collection of functions to access
7959 that metadata from R. The goal is to expose metadata for data mining and
7960 value-added functionality such as package searching, text mining, and
7961 analytics on packages.")
7962 (license license:expat)))
7964 (define-public r-biocset
7971 (uri (bioconductor-uri "BiocSet" version))
7974 "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
7975 (properties `((upstream-name . "BiocSet")))
7976 (build-system r-build-system)
7978 `(("r-annotationdbi" ,r-annotationdbi)
7979 ("r-dplyr" ,r-dplyr)
7980 ("r-keggrest" ,r-keggrest)
7982 ("r-rlang" ,r-rlang)
7983 ("r-rtracklayer" ,r-rtracklayer)
7984 ("r-tibble" ,r-tibble)))
7986 `(("r-knitr" ,r-knitr)))
7988 "https://bioconductor.org/packages/BiocSet")
7990 "Representing Different Biological Sets")
7992 "BiocSet displays different biological sets in a triple tibble format.
7993 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7994 The user has the ability to activate one of these three tibbles to perform
7995 common functions from the @code{dplyr} package. Mapping functionality and
7996 accessing web references for elements/sets are also available in BiocSet.")
7997 (license license:artistic2.0)))
7999 (define-public r-biocworkflowtools
8001 (name "r-biocworkflowtools")
8006 (uri (bioconductor-uri "BiocWorkflowTools" version))
8009 "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
8011 `((upstream-name . "BiocWorkflowTools")))
8012 (build-system r-build-system)
8014 `(("r-biocstyle" ,r-biocstyle)
8015 ("r-bookdown" ,r-bookdown)
8016 ("r-git2r" ,r-git2r)
8018 ("r-knitr" ,r-knitr)
8019 ("r-rmarkdown" ,r-rmarkdown)
8020 ("r-rstudioapi" ,r-rstudioapi)
8021 ("r-stringr" ,r-stringr)
8022 ("r-usethis" ,r-usethis)))
8024 `(("r-knitr" ,r-knitr)))
8025 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8026 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8028 "This package provides functions to ease the transition between
8029 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8030 (license license:expat)))
8032 (define-public r-biodist
8039 (uri (bioconductor-uri "bioDist" version))
8042 "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
8043 (properties `((upstream-name . "bioDist")))
8044 (build-system r-build-system)
8046 `(("r-biobase" ,r-biobase)
8047 ("r-kernsmooth" ,r-kernsmooth)))
8048 (home-page "https://bioconductor.org/packages/bioDist/")
8049 (synopsis "Different distance measures")
8051 "This package provides a collection of software tools for calculating
8052 distance measures.")
8053 (license license:artistic2.0)))
8055 (define-public r-pcatools
8062 (uri (bioconductor-uri "PCAtools" version))
8065 "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
8066 (properties `((upstream-name . "PCAtools")))
8067 (build-system r-build-system)
8069 `(("r-beachmat" ,r-beachmat)
8071 ("r-biocparallel" ,r-biocparallel)
8072 ("r-biocsingular" ,r-biocsingular)
8073 ("r-cowplot" ,r-cowplot)
8074 ("r-delayedarray" ,r-delayedarray)
8075 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8076 ("r-dqrng" ,r-dqrng)
8077 ("r-ggplot2" ,r-ggplot2)
8078 ("r-ggrepel" ,r-ggrepel)
8079 ("r-lattice" ,r-lattice)
8080 ("r-matrix" ,r-matrix)
8082 ("r-reshape2" ,r-reshape2)))
8083 (native-inputs `(("r-knitr" ,r-knitr)))
8084 (home-page "https://github.com/kevinblighe/PCAtools")
8085 (synopsis "PCAtools: everything Principal Components Analysis")
8087 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8088 structure of the data without the need to build any model to represent it.
8089 This \"summary\" of the data is arrived at through a process of reduction that
8090 can transform the large number of variables into a lesser number that are
8091 uncorrelated (i.e. the 'principal components'), while at the same time being
8092 capable of easy interpretation on the original data. PCAtools provides
8093 functions for data exploration via PCA, and allows the user to generate
8094 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8095 can also identify an optimal number of principal components via different
8096 metrics, such as the elbow method and Horn's parallel analysis, which has
8097 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8098 dimensional mass cytometry data.")
8099 (license license:gpl3)))
8101 (define-public r-rgreat
8108 (uri (bioconductor-uri "rGREAT" version))
8111 "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
8112 (properties `((upstream-name . "rGREAT")))
8113 (build-system r-build-system)
8115 `(("r-genomicranges" ,r-genomicranges)
8116 ("r-getoptlong" ,r-getoptlong)
8117 ("r-iranges" ,r-iranges)
8118 ("r-rcurl" ,r-rcurl)
8119 ("r-rjson" ,r-rjson)))
8120 (native-inputs `(("r-knitr" ,r-knitr)))
8121 (home-page "https://github.com/jokergoo/rGREAT")
8122 (synopsis "Client for GREAT analysis")
8124 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8125 Tool) analysis automatic by constructing a HTTP POST request according to
8126 user's input and automatically retrieving results from GREAT web server.")
8127 (license license:expat)))
8129 (define-public r-m3c
8136 (uri (bioconductor-uri "M3C" version))
8139 "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
8140 (properties `((upstream-name . "M3C")))
8141 (build-system r-build-system)
8143 `(("r-cluster" ,r-cluster)
8144 ("r-corpcor" ,r-corpcor)
8145 ("r-doparallel" ,r-doparallel)
8146 ("r-dosnow" ,r-dosnow)
8147 ("r-foreach" ,r-foreach)
8148 ("r-ggplot2" ,r-ggplot2)
8149 ("r-matrix" ,r-matrix)
8150 ("r-matrixcalc" ,r-matrixcalc)
8151 ("r-rtsne" ,r-rtsne)
8152 ("r-umap" ,r-umap)))
8153 (native-inputs `(("r-knitr" ,r-knitr)))
8154 (home-page "https://bioconductor.org/packages/M3C")
8155 (synopsis "Monte Carlo reference-based consensus clustering")
8157 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8158 simulation to eliminate overestimation of @code{K} and can reject the null
8159 hypothesis @code{K=1}.")
8160 (license license:agpl3+)))
8162 (define-public r-icens
8169 (uri (bioconductor-uri "Icens" version))
8172 "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
8173 (properties `((upstream-name . "Icens")))
8174 (build-system r-build-system)
8176 `(("r-survival" ,r-survival)))
8177 (home-page "https://bioconductor.org/packages/Icens")
8178 (synopsis "NPMLE for censored and truncated data")
8180 "This package provides many functions for computing the
8181 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8183 (license license:artistic2.0)))
8185 ;; This is a CRAN package but it depends on r-icens, which is published on
8187 (define-public r-interval
8194 (uri (cran-uri "interval" version))
8197 "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
8198 (properties `((upstream-name . "interval")))
8199 (build-system r-build-system)
8201 `(("r-icens" ,r-icens)
8202 ("r-mlecens" ,r-mlecens)
8204 ("r-survival" ,r-survival)))
8205 (home-page "https://cran.r-project.org/web/packages/interval/")
8206 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8208 "This package provides functions to fit nonparametric survival curves,
8209 plot them, and perform logrank or Wilcoxon type tests.")
8210 (license license:gpl2+)))
8212 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8213 ;; Bioconductor package.
8214 (define-public r-fhtest
8221 (uri (cran-uri "FHtest" version))
8224 "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))
8225 (properties `((upstream-name . "FHtest")))
8226 (build-system r-build-system)
8228 `(("r-interval" ,r-interval)
8229 ("r-kmsurv" ,r-kmsurv)
8232 ("r-survival" ,r-survival)))
8233 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8234 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8236 "This package provides functions to compare two or more survival curves
8240 @item The Fleming-Harrington test for right-censored data based on
8241 permutations and on counting processes.
8242 @item An extension of the Fleming-Harrington test for interval-censored data
8243 based on a permutation distribution and on a score vector distribution.
8246 (license license:gpl2+)))
8248 (define-public r-fourcseq
8255 (uri (bioconductor-uri "FourCSeq" version))
8257 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
8258 (properties `((upstream-name . "FourCSeq")))
8259 (build-system r-build-system)
8261 `(("r-biobase" ,r-biobase)
8262 ("r-biostrings" ,r-biostrings)
8263 ("r-deseq2" ,r-deseq2)
8265 ("r-genomicalignments" ,r-genomicalignments)
8266 ("r-genomicranges" ,r-genomicranges)
8267 ("r-ggbio" ,r-ggbio)
8268 ("r-ggplot2" ,r-ggplot2)
8269 ("r-gtools" ,r-gtools)
8271 ("r-matrix" ,r-matrix)
8272 ("r-reshape2" ,r-reshape2)
8273 ("r-rsamtools" ,r-rsamtools)
8274 ("r-rtracklayer" ,r-rtracklayer)
8275 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8277 `(("r-knitr" ,r-knitr)))
8279 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8280 (synopsis "Analysis of multiplexed 4C sequencing data")
8282 "This package is an R package dedicated to the analysis of (multiplexed)
8283 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8284 interactions between DNA elements and identify differential interactions
8285 between conditions. The statistical analysis in R starts with individual bam
8286 files for each sample as inputs. To obtain these files, the package contains
8287 a Python script to demultiplex libraries and trim off primer sequences. With
8288 a standard alignment software the required bam files can be then be
8290 (license license:gpl3+)))
8292 (define-public r-preprocesscore
8294 (name "r-preprocesscore")
8299 (uri (bioconductor-uri "preprocessCore" version))
8302 "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
8304 `((upstream-name . "preprocessCore")))
8305 (build-system r-build-system)
8306 (home-page "https://github.com/bmbolstad/preprocessCore")
8307 (synopsis "Collection of pre-processing functions")
8309 "This package provides a library of core pre-processing and normalization
8311 (license license:lgpl2.0+)))
8313 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
8314 ;; Bioconductor package.
8315 (define-public r-wgcna
8322 (uri (cran-uri "WGCNA" version))
8325 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
8326 (properties `((upstream-name . "WGCNA")))
8327 (build-system r-build-system)
8329 `(("r-annotationdbi" ,r-annotationdbi)
8330 ("r-doparallel" ,r-doparallel)
8331 ("r-dynamictreecut" ,r-dynamictreecut)
8332 ("r-fastcluster" ,r-fastcluster)
8333 ("r-foreach" ,r-foreach)
8334 ("r-go-db" ,r-go-db)
8335 ("r-hmisc" ,r-hmisc)
8336 ("r-impute" ,r-impute)
8338 ("r-survival" ,r-survival)
8339 ("r-matrixstats" ,r-matrixstats)
8340 ("r-preprocesscore" ,r-preprocesscore)))
8342 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8343 (synopsis "Weighted correlation network analysis")
8345 "This package provides functions necessary to perform Weighted
8346 Correlation Network Analysis on high-dimensional data. It includes functions
8347 for rudimentary data cleaning, construction and summarization of correlation
8348 networks, module identification and functions for relating both variables and
8349 modules to sample traits. It also includes a number of utility functions for
8350 data manipulation and visualization.")
8351 (license license:gpl2+)))
8353 (define-public r-rgraphviz
8355 (name "r-rgraphviz")
8360 (uri (bioconductor-uri "Rgraphviz" version))
8363 "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
8364 (properties `((upstream-name . "Rgraphviz")))
8365 (build-system r-build-system)
8368 (modify-phases %standard-phases
8369 (add-after 'unpack 'make-reproducible
8371 ;; The replacement value is taken from src/graphviz/builddate.h
8372 (substitute* "src/graphviz/configure"
8373 (("VERSION_DATE=.*")
8374 "VERSION_DATE=20200427.2341\n"))
8376 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8377 ;; graphviz. It does not build with the latest version of graphviz, so
8378 ;; we do not add graphviz to the inputs.
8379 (inputs `(("zlib" ,zlib)))
8381 `(("r-graph" ,r-graph)))
8383 `(("pkg-config" ,pkg-config)))
8384 (home-page "https://bioconductor.org/packages/Rgraphviz")
8385 (synopsis "Plotting capabilities for R graph objects")
8387 "This package interfaces R with the graphviz library for plotting R graph
8388 objects from the @code{graph} package.")
8389 (license license:epl1.0)))
8391 (define-public r-fithic
8397 (uri (bioconductor-uri "FitHiC" version))
8400 "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
8401 (properties `((upstream-name . "FitHiC")))
8402 (build-system r-build-system)
8404 `(("r-data-table" ,r-data-table)
8405 ("r-fdrtool" ,r-fdrtool)
8406 ("r-rcpp" ,r-rcpp)))
8408 `(("r-knitr" ,r-knitr)))
8409 (home-page "https://bioconductor.org/packages/FitHiC")
8410 (synopsis "Confidence estimation for intra-chromosomal contact maps")
8412 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
8413 intra-chromosomal contact maps produced by genome-wide genome architecture
8414 assays such as Hi-C.")
8415 (license license:gpl2+)))
8417 (define-public r-hitc
8423 (uri (bioconductor-uri "HiTC" version))
8426 "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
8427 (properties `((upstream-name . "HiTC")))
8428 (build-system r-build-system)
8430 `(("r-biostrings" ,r-biostrings)
8431 ("r-genomeinfodb" ,r-genomeinfodb)
8432 ("r-genomicranges" ,r-genomicranges)
8433 ("r-iranges" ,r-iranges)
8434 ("r-matrix" ,r-matrix)
8435 ("r-rcolorbrewer" ,r-rcolorbrewer)
8436 ("r-rtracklayer" ,r-rtracklayer)))
8437 (home-page "https://bioconductor.org/packages/HiTC")
8438 (synopsis "High throughput chromosome conformation capture analysis")
8440 "The HiTC package was developed to explore high-throughput \"C\" data
8441 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
8442 quality controls, normalization, visualization, and further analysis are also
8444 (license license:artistic2.0)))
8446 (define-public r-hdf5array
8448 (name "r-hdf5array")
8453 (uri (bioconductor-uri "HDF5Array" version))
8456 "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
8457 (properties `((upstream-name . "HDF5Array")))
8458 (build-system r-build-system)
8462 `(("r-biocgenerics" ,r-biocgenerics)
8463 ("r-delayedarray" ,r-delayedarray)
8464 ("r-iranges" ,r-iranges)
8465 ("r-matrix" ,r-matrix)
8466 ("r-rhdf5" ,r-rhdf5)
8467 ("r-rhdf5lib" ,r-rhdf5lib)
8468 ("r-s4vectors" ,r-s4vectors)))
8469 (home-page "https://bioconductor.org/packages/HDF5Array")
8470 (synopsis "HDF5 back end for DelayedArray objects")
8471 (description "This package provides an array-like container for convenient
8472 access and manipulation of HDF5 datasets. It supports delayed operations and
8474 (license license:artistic2.0)))
8476 (define-public r-rhdf5lib
8483 (uri (bioconductor-uri "Rhdf5lib" version))
8486 "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
8487 (modules '((guix build utils)))
8490 ;; Delete bundled binaries
8491 (delete-file-recursively "src/wininclude/")
8492 (delete-file-recursively "src/winlib-4.9.3/")
8493 (delete-file-recursively "src/winlib-8.3.0/")
8494 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
8496 (properties `((upstream-name . "Rhdf5lib")))
8497 (build-system r-build-system)
8500 (modify-phases %standard-phases
8501 (add-after 'unpack 'do-not-use-bundled-hdf5
8502 (lambda* (#:key inputs #:allow-other-keys)
8503 (for-each delete-file '("configure" "configure.ac"))
8504 ;; Do not make other packages link with the proprietary libsz.
8505 (substitute* "R/zzz.R"
8506 ((" \"%s/libsz.a\"") ""))
8507 (with-directory-excursion "src"
8508 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
8509 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
8511 ;; Remove timestamp and host system information to make
8512 ;; the build reproducible.
8513 (substitute* "hdf5/src/libhdf5.settings.in"
8514 (("Configured on: @CONFIG_DATE@")
8515 "Configured on: Guix")
8516 (("Uname information:.*")
8517 "Uname information: Linux\n")
8518 ;; Remove unnecessary store reference.
8520 "C Compiler: GCC\n"))
8521 (rename-file "Makevars.in" "Makevars")
8522 (substitute* "Makevars"
8523 (("@ZLIB_LIB@") "-lz")
8524 (("@ZLIB_INCLUDE@") "")
8525 (("HDF5_CXX_LIB=.*")
8526 (string-append "HDF5_CXX_LIB="
8527 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
8529 (string-append "HDF5_LIB="
8530 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
8531 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
8532 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
8533 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
8534 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
8536 (string-append "HDF5_HL_LIB="
8537 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
8538 (("HDF5_HL_CXX_LIB=.*")
8539 (string-append "HDF5_HL_CXX_LIB="
8540 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
8541 ;; szip is non-free software
8542 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
8543 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
8548 `(("hdf5" ,hdf5-1.10)))
8550 `(("hdf5-source" ,(package-source hdf5-1.10))
8551 ("r-knitr" ,r-knitr)))
8552 (home-page "https://bioconductor.org/packages/Rhdf5lib")
8553 (synopsis "HDF5 library as an R package")
8554 (description "This package provides C and C++ HDF5 libraries for use in R
8556 (license license:artistic2.0)))
8558 (define-public r-beachmat
8565 (uri (bioconductor-uri "beachmat" version))
8568 "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
8569 (build-system r-build-system)
8571 `(("r-biocgenerics" ,r-biocgenerics)
8572 ("r-delayedarray" ,r-delayedarray)
8573 ("r-matrix" ,r-matrix)))
8575 `(("r-knitr" ,r-knitr)))
8576 (home-page "https://bioconductor.org/packages/beachmat")
8577 (synopsis "Compiling Bioconductor to handle each matrix type")
8578 (description "This package provides a consistent C++ class interface for a
8579 variety of commonly used matrix types, including sparse and HDF5-backed
8581 (license license:gpl3)))
8583 (define-public r-singlecellexperiment
8585 (name "r-singlecellexperiment")
8590 (uri (bioconductor-uri "SingleCellExperiment" version))
8593 "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
8595 `((upstream-name . "SingleCellExperiment")))
8596 (build-system r-build-system)
8598 `(("r-biocgenerics" ,r-biocgenerics)
8599 ("r-s4vectors" ,r-s4vectors)
8600 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8602 `(("r-knitr" ,r-knitr)))
8603 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
8604 (synopsis "S4 classes for single cell data")
8605 (description "This package defines an S4 class for storing data from
8606 single-cell experiments. This includes specialized methods to store and
8607 retrieve spike-in information, dimensionality reduction coordinates and size
8608 factors for each cell, along with the usual metadata for genes and
8610 (license license:gpl3)))
8612 (define-public r-scater
8618 (uri (bioconductor-uri "scater" version))
8621 "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
8622 (build-system r-build-system)
8624 `(("r-beachmat" ,r-beachmat)
8625 ("r-biocgenerics" ,r-biocgenerics)
8626 ("r-biocneighbors" ,r-biocneighbors)
8627 ("r-biocparallel" ,r-biocparallel)
8628 ("r-biocsingular" ,r-biocsingular)
8629 ("r-delayedarray" ,r-delayedarray)
8630 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8631 ("r-ggbeeswarm" ,r-ggbeeswarm)
8632 ("r-ggplot2" ,r-ggplot2)
8633 ("r-matrix" ,r-matrix)
8635 ("r-rlang" ,r-rlang)
8636 ("r-s4vectors" ,r-s4vectors)
8637 ("r-singlecellexperiment" ,r-singlecellexperiment)
8638 ("r-summarizedexperiment" ,r-summarizedexperiment)
8639 ("r-viridis" ,r-viridis)))
8641 `(("r-knitr" ,r-knitr)))
8642 (home-page "https://github.com/davismcc/scater")
8643 (synopsis "Single-cell analysis toolkit for gene expression data in R")
8644 (description "This package provides a collection of tools for doing
8645 various analyses of single-cell RNA-seq gene expression data, with a focus on
8647 (license license:gpl2+)))
8649 (define-public r-scran
8656 (uri (bioconductor-uri "scran" version))
8659 "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
8660 (build-system r-build-system)
8662 `(("r-beachmat" ,r-beachmat)
8664 ("r-biocgenerics" ,r-biocgenerics)
8665 ("r-biocneighbors" ,r-biocneighbors)
8666 ("r-biocparallel" ,r-biocparallel)
8667 ("r-biocsingular" ,r-biocsingular)
8668 ("r-delayedarray" ,r-delayedarray)
8669 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8670 ("r-dqrng" ,r-dqrng)
8671 ("r-edger" ,r-edger)
8672 ("r-igraph" ,r-igraph)
8673 ("r-iranges" ,r-iranges)
8674 ("r-limma" ,r-limma)
8675 ("r-matrix" ,r-matrix)
8677 ("r-s4vectors" ,r-s4vectors)
8678 ("r-scater" ,r-scater)
8679 ("r-singlecellexperiment" ,r-singlecellexperiment)
8680 ("r-statmod" ,r-statmod)
8681 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8683 `(("r-knitr" ,r-knitr)))
8684 (home-page "https://bioconductor.org/packages/scran")
8685 (synopsis "Methods for single-cell RNA-Seq data analysis")
8686 (description "This package implements a variety of low-level analyses of
8687 single-cell RNA-seq data. Methods are provided for normalization of
8688 cell-specific biases, assignment of cell cycle phase, and detection of highly
8689 variable and significantly correlated genes.")
8690 (license license:gpl3)))
8692 (define-public r-delayedmatrixstats
8694 (name "r-delayedmatrixstats")
8699 (uri (bioconductor-uri "DelayedMatrixStats" version))
8702 "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
8704 `((upstream-name . "DelayedMatrixStats")))
8705 (build-system r-build-system)
8707 `(("r-biocparallel" ,r-biocparallel)
8708 ("r-delayedarray" ,r-delayedarray)
8709 ("r-hdf5array" ,r-hdf5array)
8710 ("r-iranges" ,r-iranges)
8711 ("r-matrix" ,r-matrix)
8712 ("r-matrixstats" ,r-matrixstats)
8713 ("r-s4vectors" ,r-s4vectors)))
8715 `(("r-knitr" ,r-knitr)))
8716 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
8717 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
8719 "This package provides a port of the @code{matrixStats} API for use with
8720 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
8721 contains high-performing functions operating on rows and columns of
8722 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
8723 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
8724 are optimized per data type and for subsetted calculations such that both
8725 memory usage and processing time is minimized.")
8726 (license license:expat)))