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, 2020 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-org-eck12-eg-db
55 (name "r-org-eck12-eg-db")
60 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
62 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
64 `((upstream-name . "org.EcK12.eg.db")))
65 (build-system r-build-system)
67 `(("r-annotationdbi" ,r-annotationdbi)))
68 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
69 (synopsis "Genome wide annotation for E coli strain K12")
71 "This package provides genome wide annotation for E coli strain K12,
72 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
73 National Center for Biotechnology Information (NCBI)’s database for
74 gene-specific information. Entrez Gene maintains records from genomes which
75 have been completely sequenced, which have an active research community to
76 submit gene-specific information, or which are scheduled for intense sequence
78 (license license:artistic2.0)))
80 (define-public r-reactome-db
82 (name "r-reactome-db")
87 (uri (bioconductor-uri "reactome.db" version 'annotation))
90 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
91 (properties `((upstream-name . "reactome.db")))
92 (build-system r-build-system)
94 `(("r-annotationdbi" ,r-annotationdbi)))
95 (home-page "https://bioconductor.org/packages/reactome.db/")
96 (synopsis "Annotation maps for reactome")
98 "This package provides a set of annotation maps for the REACTOME
99 database, assembled using data from REACTOME.")
100 (license license:cc-by4.0)))
102 (define-public r-bsgenome-celegans-ucsc-ce6
104 (name "r-bsgenome-celegans-ucsc-ce6")
108 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
109 version 'annotation))
112 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
114 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
115 (build-system r-build-system)
117 `(("r-bsgenome" ,r-bsgenome)))
119 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
120 (synopsis "Full genome sequences for Worm")
122 "This package provides full genome sequences for Caenorhabditis
123 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
125 (license license:artistic2.0)))
127 (define-public r-bsgenome-celegans-ucsc-ce10
129 (name "r-bsgenome-celegans-ucsc-ce10")
133 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
134 version 'annotation))
137 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
139 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
140 (build-system r-build-system)
142 `(("r-bsgenome" ,r-bsgenome)))
144 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
145 (synopsis "Full genome sequences for Worm")
147 "This package provides full genome sequences for Caenorhabditis
148 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
150 (license license:artistic2.0)))
152 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
154 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
158 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
159 version 'annotation))
162 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
164 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
165 (build-system r-build-system)
167 `(("r-bsgenome" ,r-bsgenome)))
169 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
170 (synopsis "Full genome sequences for Fly")
172 "This package provides full genome sequences for Drosophila
173 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
175 (license license:artistic2.0)))
177 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
179 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
183 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
184 version 'annotation))
187 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
189 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
190 (build-system r-build-system)
192 `(("r-bsgenome" ,r-bsgenome)))
194 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
195 (synopsis "Full genome sequences for Fly")
197 "This package provides full genome sequences for Drosophila
198 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
199 Biostrings objects.")
200 (license license:artistic2.0)))
202 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
204 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
208 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
209 version 'annotation))
212 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
214 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
215 (build-system r-build-system)
217 `(("r-bsgenome" ,r-bsgenome)
218 ("r-bsgenome-dmelanogaster-ucsc-dm3"
219 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
220 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
221 (synopsis "Full masked genome sequences for Fly")
223 "This package provides full masked genome sequences for Drosophila
224 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
225 Biostrings objects. The sequences are the same as in
226 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
227 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
228 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
229 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
230 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
231 (license license:artistic2.0)))
233 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
235 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
239 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
240 version 'annotation))
243 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
245 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
246 (build-system r-build-system)
248 `(("r-bsgenome" ,r-bsgenome)))
250 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
251 (synopsis "Full genome sequences for Homo sapiens")
253 "This package provides full genome sequences for Homo sapiens from
254 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
255 (license license:artistic2.0)))
257 (define-public r-bsgenome-hsapiens-ncbi-grch38
259 (name "r-bsgenome-hsapiens-ncbi-grch38")
264 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
265 version 'annotation))
268 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
269 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
270 (build-system r-build-system)
271 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
273 "https://bioconductor.org/packages/release/data/annotation/html/\
274 BSgenome.Hsapiens.NCBI.GRCh38.html")
275 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
277 "This package provides full genome sequences for Homo sapiens (Human) as
278 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
279 (license license:artistic2.0)))
281 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
283 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
287 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
288 version 'annotation))
291 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
293 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
294 (build-system r-build-system)
296 `(("r-bsgenome" ,r-bsgenome)
297 ("r-bsgenome-hsapiens-ucsc-hg19"
298 ,r-bsgenome-hsapiens-ucsc-hg19)))
299 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
300 (synopsis "Full masked genome sequences for Homo sapiens")
302 "This package provides full genome sequences for Homo sapiens (Human) as
303 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
304 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
305 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
306 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
307 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
308 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
310 (license license:artistic2.0)))
312 (define-public r-bsgenome-mmusculus-ucsc-mm9
314 (name "r-bsgenome-mmusculus-ucsc-mm9")
318 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
319 version 'annotation))
322 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
324 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
325 (build-system r-build-system)
327 `(("r-bsgenome" ,r-bsgenome)))
329 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
330 (synopsis "Full genome sequences for Mouse")
332 "This package provides full genome sequences for Mus musculus (Mouse) as
333 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
334 (license license:artistic2.0)))
336 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
338 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
342 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
343 version 'annotation))
346 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
348 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
349 (build-system r-build-system)
351 `(("r-bsgenome" ,r-bsgenome)
352 ("r-bsgenome-mmusculus-ucsc-mm9"
353 ,r-bsgenome-mmusculus-ucsc-mm9)))
354 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
355 (synopsis "Full masked genome sequences for Mouse")
357 "This package provides full genome sequences for Mus musculus (Mouse) as
358 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
359 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
360 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
361 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
362 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
363 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
365 (license license:artistic2.0)))
367 (define-public r-bsgenome-mmusculus-ucsc-mm10
369 (name "r-bsgenome-mmusculus-ucsc-mm10")
373 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
374 version 'annotation))
377 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
379 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
380 (build-system r-build-system)
382 `(("r-bsgenome" ,r-bsgenome)))
384 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
385 (synopsis "Full genome sequences for Mouse")
387 "This package provides full genome sequences for Mus
388 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
389 in Biostrings objects.")
390 (license license:artistic2.0)))
392 (define-public r-org-ce-eg-db
394 (name "r-org-ce-eg-db")
398 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
401 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
403 `((upstream-name . "org.Ce.eg.db")))
404 (build-system r-build-system)
406 `(("r-annotationdbi" ,r-annotationdbi)))
407 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
408 (synopsis "Genome wide annotation for Worm")
410 "This package provides mappings from Entrez gene identifiers to various
411 annotations for the genome of the model worm Caenorhabditis elegans.")
412 (license license:artistic2.0)))
414 (define-public r-org-dm-eg-db
416 (name "r-org-dm-eg-db")
420 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
423 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
425 `((upstream-name . "org.Dm.eg.db")))
426 (build-system r-build-system)
428 `(("r-annotationdbi" ,r-annotationdbi)))
429 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
430 (synopsis "Genome wide annotation for Fly")
432 "This package provides mappings from Entrez gene identifiers to various
433 annotations for the genome of the model fruit fly Drosophila melanogaster.")
434 (license license:artistic2.0)))
436 (define-public r-org-dr-eg-db
438 (name "r-org-dr-eg-db")
442 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
445 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
447 `((upstream-name . "org.Dr.eg.db")))
448 (build-system r-build-system)
450 `(("r-annotationdbi" ,r-annotationdbi)))
451 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
452 (synopsis "Annotation for Zebrafish")
454 "This package provides genome wide annotations for Zebrafish, primarily
455 based on mapping using Entrez Gene identifiers.")
456 (license license:artistic2.0)))
458 (define-public r-org-hs-eg-db
460 (name "r-org-hs-eg-db")
464 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
467 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
469 `((upstream-name . "org.Hs.eg.db")))
470 (build-system r-build-system)
472 `(("r-annotationdbi" ,r-annotationdbi)))
473 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
474 (synopsis "Genome wide annotation for Human")
476 "This package contains genome-wide annotations for Human, primarily based
477 on mapping using Entrez Gene identifiers.")
478 (license license:artistic2.0)))
480 (define-public r-org-mm-eg-db
482 (name "r-org-mm-eg-db")
486 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
489 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
491 `((upstream-name . "org.Mm.eg.db")))
492 (build-system r-build-system)
494 `(("r-annotationdbi" ,r-annotationdbi)))
495 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
496 (synopsis "Genome wide annotation for Mouse")
498 "This package provides mappings from Entrez gene identifiers to various
499 annotations for the genome of the model mouse Mus musculus.")
500 (license license:artistic2.0)))
502 (define-public r-bsgenome-hsapiens-ucsc-hg19
504 (name "r-bsgenome-hsapiens-ucsc-hg19")
508 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
509 version 'annotation))
512 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
514 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
515 (build-system r-build-system)
517 `(("r-bsgenome" ,r-bsgenome)))
519 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
520 (synopsis "Full genome sequences for Homo sapiens")
522 "This package provides full genome sequences for Homo sapiens as provided
523 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
524 (license license:artistic2.0)))
526 (define-public r-bsgenome-hsapiens-ucsc-hg38
528 (name "r-bsgenome-hsapiens-ucsc-hg38")
532 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
533 version 'annotation))
536 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
538 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
539 (build-system r-build-system)
541 `(("r-bsgenome" ,r-bsgenome)))
543 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
544 (synopsis "Full genome sequences for Homo sapiens")
546 "This package provides full genome sequences for Homo sapiens (Human)
547 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
548 (license license:artistic2.0)))
550 (define-public r-ensdb-hsapiens-v75
552 (name "r-ensdb-hsapiens-v75")
557 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
560 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
562 `((upstream-name . "EnsDb.Hsapiens.v75")))
563 (build-system r-build-system)
565 `(("r-ensembldb" ,r-ensembldb)))
566 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
567 (synopsis "Ensembl based annotation package")
569 "This package exposes an annotation database generated from Ensembl.")
570 (license license:artistic2.0)))
572 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
574 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
578 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
579 version 'annotation))
582 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
584 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
585 (build-system r-build-system)
587 `(("r-genomicfeatures" ,r-genomicfeatures)))
589 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
590 (synopsis "Annotation package for human genome in TxDb format")
592 "This package provides an annotation database of Homo sapiens genome
593 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
594 track. The database is exposed as a @code{TxDb} object.")
595 (license license:artistic2.0)))
597 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
599 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
603 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
604 version 'annotation))
607 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
609 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
610 (build-system r-build-system)
612 `(("r-genomicfeatures" ,r-genomicfeatures)))
614 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
615 (synopsis "Annotation package for human genome in TxDb format")
617 "This package provides an annotation database of Homo sapiens genome
618 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
619 track. The database is exposed as a @code{TxDb} object.")
620 (license license:artistic2.0)))
622 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
624 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
628 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
629 version 'annotation))
632 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
634 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
635 (build-system r-build-system)
637 `(("r-genomicfeatures" ,r-genomicfeatures)
638 ("r-annotationdbi" ,r-annotationdbi)))
640 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
641 (synopsis "Annotation package for mouse genome in TxDb format")
643 "This package provides an annotation database of Mouse genome data. It
644 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
645 database is exposed as a @code{TxDb} object.")
646 (license license:artistic2.0)))
648 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
650 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
654 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
655 version 'annotation))
658 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
660 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
661 (build-system r-build-system)
663 `(("r-bsgenome" ,r-bsgenome)
664 ("r-genomicfeatures" ,r-genomicfeatures)
665 ("r-annotationdbi" ,r-annotationdbi)))
667 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
668 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
670 "This package loads a TxDb object, which is an R interface to
671 prefabricated databases contained in this package. This package provides
672 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
673 based on the knownGene track.")
674 (license license:artistic2.0)))
676 (define-public r-txdb-celegans-ucsc-ce6-ensgene
678 (name "r-txdb-celegans-ucsc-ce6-ensgene")
683 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
684 version 'annotation))
687 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
689 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
690 (build-system r-build-system)
692 `(("r-annotationdbi" ,r-annotationdbi)
693 ("r-genomicfeatures" ,r-genomicfeatures)))
694 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
695 (synopsis "Annotation package for C elegans TxDb objects")
697 "This package exposes a C elegans annotation database generated from UCSC
698 by exposing these as TxDb objects.")
699 (license license:artistic2.0)))
701 (define-public r-fdb-infiniummethylation-hg19
703 (name "r-fdb-infiniummethylation-hg19")
707 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
708 version 'annotation))
711 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
713 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
714 (build-system r-build-system)
716 `(("r-biostrings" ,r-biostrings)
717 ("r-genomicfeatures" ,r-genomicfeatures)
718 ("r-annotationdbi" ,r-annotationdbi)
719 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
720 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
721 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
722 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
724 "This is an annotation package for Illumina Infinium DNA methylation
725 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
727 (license license:artistic2.0)))
729 (define-public r-illuminahumanmethylationepicmanifest
731 (name "r-illuminahumanmethylationepicmanifest")
735 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
736 version 'annotation))
739 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
741 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
742 (build-system r-build-system)
744 `(("r-minfi" ,r-minfi)))
745 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
746 (synopsis "Manifest for Illumina's EPIC methylation arrays")
748 "This is a manifest package for Illumina's EPIC methylation arrays.")
749 (license license:artistic2.0)))
751 (define-public r-do-db
757 (uri (bioconductor-uri "DO.db" version 'annotation))
760 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
762 `((upstream-name . "DO.db")))
763 (build-system r-build-system)
765 `(("r-annotationdbi" ,r-annotationdbi)))
766 (home-page "https://www.bioconductor.org/packages/DO.db/")
767 (synopsis "Annotation maps describing the entire Disease Ontology")
769 "This package provides a set of annotation maps describing the entire
771 (license license:artistic2.0)))
773 (define-public r-pfam-db
780 (uri (bioconductor-uri "PFAM.db" version 'annotation))
783 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
784 (properties `((upstream-name . "PFAM.db")))
785 (build-system r-build-system)
787 `(("r-annotationdbi" ,r-annotationdbi)))
788 (home-page "https://bioconductor.org/packages/PFAM.db")
789 (synopsis "Set of protein ID mappings for PFAM")
791 "This package provides a set of protein ID mappings for PFAM, assembled
792 using data from public repositories.")
793 (license license:artistic2.0)))
795 (define-public r-phastcons100way-ucsc-hg19
797 (name "r-phastcons100way-ucsc-hg19")
802 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
803 version 'annotation))
806 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
808 `((upstream-name . "phastCons100way.UCSC.hg19")))
809 (build-system r-build-system)
811 `(("r-bsgenome" ,r-bsgenome)
812 ("r-genomeinfodb" ,r-genomeinfodb)
813 ("r-genomicranges" ,r-genomicranges)
814 ("r-genomicscores" ,r-genomicscores)
815 ("r-iranges" ,r-iranges)
816 ("r-s4vectors" ,r-s4vectors)))
817 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
818 (synopsis "UCSC phastCons conservation scores for hg19")
820 "This package provides UCSC phastCons conservation scores for the human
821 genome (hg19) calculated from multiple alignments with other 99 vertebrate
823 (license license:artistic2.0)))
828 (define-public r-abadata
834 (uri (bioconductor-uri "ABAData" version 'experiment))
837 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
839 `((upstream-name . "ABAData")))
840 (build-system r-build-system)
842 `(("r-annotationdbi" ,r-annotationdbi)))
843 (home-page "https://www.bioconductor.org/packages/ABAData/")
844 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
846 "This package provides the data for the gene expression enrichment
847 analysis conducted in the package ABAEnrichment. The package includes three
848 datasets which are derived from the Allen Brain Atlas:
851 @item Gene expression data from Human Brain (adults) averaged across donors,
852 @item Gene expression data from the Developing Human Brain pooled into five
853 age categories and averaged across donors, and
854 @item a developmental effect score based on the Developing Human Brain
858 All datasets are restricted to protein coding genes.")
859 (license license:gpl2+)))
861 (define-public r-arrmdata
867 (uri (bioconductor-uri "ARRmData" version 'experiment))
870 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
872 `((upstream-name . "ARRmData")))
873 (build-system r-build-system)
874 (home-page "https://www.bioconductor.org/packages/ARRmData/")
875 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
877 "This package provides raw beta values from 36 samples across 3 groups
878 from Illumina 450k methylation arrays.")
879 (license license:artistic2.0)))
881 (define-public r-genelendatabase
883 (name "r-genelendatabase")
888 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
891 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
893 `((upstream-name . "geneLenDataBase")))
894 (build-system r-build-system)
896 `(("r-rtracklayer" ,r-rtracklayer)
897 ("r-genomicfeatures" ,r-genomicfeatures)))
898 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
899 (synopsis "Lengths of mRNA transcripts for a number of genomes")
901 "This package provides the lengths of mRNA transcripts for a number of
902 genomes and gene ID formats, largely based on the UCSC table browser.")
903 (license license:lgpl2.0+)))
905 (define-public r-pasilla
912 "http://bioconductor.org/packages/release/data/experiment"
913 "/src/contrib/pasilla_" version ".tar.gz"))
916 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
917 (build-system r-build-system)
919 `(("r-biocstyle" ,r-biocstyle)
920 ("r-dexseq" ,r-dexseq)
922 ("r-rmarkdown" ,r-rmarkdown)))
923 (home-page "https://www.bioconductor.org/packages/pasilla/")
924 (synopsis "Data package with per-exon and per-gene read counts")
925 (description "This package provides per-exon and per-gene read counts
926 computed for selected genes from RNA-seq data that were presented in the
927 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
928 by Brooks et al., Genome Research 2011.")
929 (license license:lgpl2.1+)))
931 (define-public r-hsmmsinglecell
933 (name "r-hsmmsinglecell")
937 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
940 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
942 `((upstream-name . "HSMMSingleCell")))
943 (build-system r-build-system)
944 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
945 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
947 "Skeletal myoblasts undergo a well-characterized sequence of
948 morphological and transcriptional changes during differentiation. In this
949 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
950 under high mitogen conditions (GM) and then differentiated by switching to
951 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
952 hundred cells taken over a time-course of serum-induced differentiation.
953 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
954 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
955 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
956 which were then sequenced to a depth of ~4 million reads per library,
957 resulting in a complete gene expression profile for each cell.")
958 (license license:artistic2.0)))
966 (uri (bioconductor-uri "ALL" version 'experiment))
969 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
970 (properties `((upstream-name . "ALL")))
971 (build-system r-build-system)
973 `(("r-biobase" ,r-biobase)))
974 (home-page "https://bioconductor.org/packages/ALL")
975 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
977 "The data consist of microarrays from 128 different individuals with
978 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
979 are available. The data have been normalized (using rma) and it is the
980 jointly normalized data that are available here. The data are presented in
981 the form of an @code{exprSet} object.")
982 (license license:artistic2.0)))
984 (define-public r-affydata
991 (uri (bioconductor-uri "affydata" version 'experiment))
994 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
995 (properties `((upstream-name . "affydata")))
996 (build-system r-build-system)
998 `(("r-affy" ,r-affy)))
999 (home-page "https://bioconductor.org/packages/affydata/")
1000 (synopsis "Affymetrix data for demonstration purposes")
1002 "This package provides example datasets that represent 'real world
1003 examples' of Affymetrix data, unlike the artificial examples included in the
1004 package @code{affy}.")
1005 (license license:gpl2+)))
1007 (define-public r-gagedata
1014 (uri (bioconductor-uri "gageData" version 'experiment))
1016 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
1017 (properties `((upstream-name . "gageData")))
1018 (build-system r-build-system)
1019 (home-page "https://bioconductor.org/packages/gageData")
1020 (synopsis "Auxillary data for gage package")
1022 "This is a supportive data package for the software package @code{gage}.
1023 However, the data supplied here are also useful for gene set or pathway
1024 analysis or microarray data analysis in general. In this package, we provide
1025 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1026 BMP6 (originally published as an demo dataset for GAGE, also registered as
1027 GSE13604 in GEO). This package also includes commonly used gene set data based
1028 on KEGG pathways and GO terms for major research species, including human,
1029 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1030 yeast are also included.")
1031 (license license:gpl2+)))
1033 (define-public r-curatedtcgadata
1035 (name "r-curatedtcgadata")
1040 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1043 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1045 `((upstream-name . "curatedTCGAData")))
1046 (build-system r-build-system)
1048 `(("r-annotationhub" ,r-annotationhub)
1049 ("r-experimenthub" ,r-experimenthub)
1050 ("r-hdf5array" ,r-hdf5array)
1051 ("r-multiassayexperiment" ,r-multiassayexperiment)
1052 ("r-s4vectors" ,r-s4vectors)
1053 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1054 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1055 (synopsis "Curated data from The Cancer Genome Atlas")
1057 "This package provides publicly available data from The Cancer Genome
1058 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1059 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1060 number, mutation, microRNA, protein, and others) with clinical / pathological
1061 data. It also links assay barcodes with patient identifiers, enabling
1062 harmonized subsetting of rows (features) and columns (patients / samples)
1063 across the entire multi-'omics experiment.")
1064 (license license:artistic2.0)))
1069 (define-public r-biocversion
1071 (name "r-biocversion")
1076 (uri (bioconductor-uri "BiocVersion" version))
1079 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
1080 (properties `((upstream-name . "BiocVersion")))
1081 (build-system r-build-system)
1082 (home-page "https://bioconductor.org/packages/BiocVersion/")
1083 (synopsis "Set the appropriate version of Bioconductor packages")
1085 "This package provides repository information for the appropriate version
1087 (license license:artistic2.0)))
1089 (define-public r-biocgenerics
1091 (name "r-biocgenerics")
1095 (uri (bioconductor-uri "BiocGenerics" version))
1098 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
1100 `((upstream-name . "BiocGenerics")))
1101 (build-system r-build-system)
1102 (home-page "https://bioconductor.org/packages/BiocGenerics")
1103 (synopsis "S4 generic functions for Bioconductor")
1105 "This package provides S4 generic functions needed by many Bioconductor
1107 (license license:artistic2.0)))
1109 (define-public r-coverageview
1111 (name "r-coverageview")
1115 (uri (bioconductor-uri "CoverageView" version))
1118 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
1119 (build-system r-build-system)
1121 `(("r-s4vectors" ,r-s4vectors)
1122 ("r-iranges" ,r-iranges)
1123 ("r-genomicranges" ,r-genomicranges)
1124 ("r-genomicalignments" ,r-genomicalignments)
1125 ("r-rtracklayer" ,r-rtracklayer)
1126 ("r-rsamtools" ,r-rsamtools)))
1127 (home-page "https://bioconductor.org/packages/CoverageView/")
1128 (synopsis "Coverage visualization package for R")
1129 (description "This package provides a framework for the visualization of
1130 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1131 be also used for genome-wide nucleosome positioning experiments or other
1132 experiment types where it is important to have a framework in order to inspect
1133 how the coverage distributed across the genome.")
1134 (license license:artistic2.0)))
1136 (define-public r-cummerbund
1138 (name "r-cummerbund")
1142 (uri (bioconductor-uri "cummeRbund" version))
1145 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
1146 (build-system r-build-system)
1148 `(("r-biobase" ,r-biobase)
1149 ("r-biocgenerics" ,r-biocgenerics)
1150 ("r-fastcluster" ,r-fastcluster)
1151 ("r-ggplot2" ,r-ggplot2)
1154 ("r-reshape2" ,r-reshape2)
1155 ("r-rsqlite" ,r-rsqlite)
1156 ("r-rtracklayer" ,r-rtracklayer)
1157 ("r-s4vectors" ,r-s4vectors)))
1158 (home-page "https://bioconductor.org/packages/cummeRbund/")
1159 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1160 (description "This package allows for persistent storage, access,
1161 exploration, and manipulation of Cufflinks high-throughput sequencing
1162 data. In addition, provides numerous plotting functions for commonly
1163 used visualizations.")
1164 (license license:artistic2.0)))
1166 (define-public r-bluster
1172 (uri (bioconductor-uri "bluster" version))
1175 "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
1176 (properties `((upstream-name . "bluster")))
1177 (build-system r-build-system)
1179 `(("r-biocneighbors" ,r-biocneighbors)
1180 ("r-biocparallel" ,r-biocparallel)
1181 ("r-igraph" ,r-igraph)
1182 ("r-matrix" ,r-matrix)
1184 ("r-s4vectors" ,r-s4vectors)))
1186 `(("r-knitr" ,r-knitr)))
1187 (home-page "https://bioconductor.org/packages/bluster")
1188 (synopsis "Clustering algorithms for Bioconductor")
1189 (description"This package wraps common clustering algorithms in an easily
1190 extended S4 framework. Backends are implemented for hierarchical, k-means
1191 and graph-based clustering. Several utilities are also provided to compare
1192 and evaluate clustering results.")
1193 (license license:gpl3)))
1195 (define-public r-ideoviz
1201 (uri (bioconductor-uri "IdeoViz" version))
1204 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
1205 (build-system r-build-system)
1207 `(("r-biobase" ,r-biobase)
1208 ("r-iranges" ,r-iranges)
1209 ("r-genomicranges" ,r-genomicranges)
1210 ("r-rcolorbrewer" ,r-rcolorbrewer)
1211 ("r-rtracklayer" ,r-rtracklayer)
1212 ("r-genomeinfodb" ,r-genomeinfodb)))
1213 (home-page "https://bioconductor.org/packages/IdeoViz/")
1214 (synopsis "Plots data along a chromosomal ideogram")
1215 (description "This package provides functions to plot data associated with
1216 arbitrary genomic intervals along chromosomal ideogram.")
1217 (license license:gpl2)))
1219 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
1220 ;; from Bioconductor.
1221 (define-public r-deconstructsigs
1223 (name "r-deconstructsigs")
1227 (uri (cran-uri "deconstructSigs" version))
1230 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
1232 `((upstream-name . "deconstructSigs")))
1233 (build-system r-build-system)
1235 `(("r-bsgenome" ,r-bsgenome)
1236 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1237 ("r-genomeinfodb" ,r-genomeinfodb)
1238 ("r-reshape2" ,r-reshape2)))
1239 (home-page "https://github.com/raerose01/deconstructSigs")
1240 (synopsis "Identifies signatures present in a tumor sample")
1241 (description "This package takes sample information in the form of the
1242 fraction of mutations in each of 96 trinucleotide contexts and identifies
1243 the weighted combination of published signatures that, when summed, most
1244 closely reconstructs the mutational profile.")
1245 (license license:gpl2+)))
1247 ;; This is a CRAN package, but it depends on Bioconductor packages.
1248 (define-public r-nmf
1255 (uri (cran-uri "NMF" version))
1258 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
1259 (properties `((upstream-name . "NMF")))
1260 (build-system r-build-system)
1262 `(("r-cluster" ,r-cluster)
1263 ("r-biobase" ,r-biobase)
1264 ("r-biocmanager" ,r-biocmanager)
1265 ("r-bigmemory" ,r-bigmemory) ; suggested
1266 ("r-synchronicity" ,r-synchronicity) ; suggested
1267 ("r-colorspace" ,r-colorspace)
1268 ("r-digest" ,r-digest)
1269 ("r-doparallel" ,r-doparallel)
1270 ("r-foreach" ,r-foreach)
1271 ("r-ggplot2" ,r-ggplot2)
1272 ("r-gridbase" ,r-gridbase)
1273 ("r-pkgmaker" ,r-pkgmaker)
1274 ("r-rcolorbrewer" ,r-rcolorbrewer)
1275 ("r-registry" ,r-registry)
1276 ("r-reshape2" ,r-reshape2)
1277 ("r-rngtools" ,r-rngtools)
1278 ("r-stringr" ,r-stringr)))
1280 `(("r-knitr" ,r-knitr)))
1281 (home-page "http://renozao.github.io/NMF")
1282 (synopsis "Algorithms and framework for nonnegative matrix factorization")
1284 "This package provides a framework to perform Non-negative Matrix
1285 Factorization (NMF). The package implements a set of already published
1286 algorithms and seeding methods, and provides a framework to test, develop and
1287 plug new or custom algorithms. Most of the built-in algorithms have been
1288 optimized in C++, and the main interface function provides an easy way of
1289 performing parallel computations on multicore machines.")
1290 (license license:gpl2+)))
1292 (define-public r-affycomp
1299 (uri (bioconductor-uri "affycomp" version))
1302 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
1303 (properties `((upstream-name . "affycomp")))
1304 (build-system r-build-system)
1305 (propagated-inputs `(("r-biobase" ,r-biobase)))
1306 (home-page "https://bioconductor.org/packages/affycomp/")
1307 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1309 "The package contains functions that can be used to compare expression
1310 measures for Affymetrix Oligonucleotide Arrays.")
1311 (license license:gpl2+)))
1313 (define-public r-affycompatible
1315 (name "r-affycompatible")
1320 (uri (bioconductor-uri "AffyCompatible" version))
1323 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
1325 `((upstream-name . "AffyCompatible")))
1326 (build-system r-build-system)
1328 `(("r-biostrings" ,r-biostrings)
1329 ("r-rcurl" ,r-rcurl)
1331 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1332 (synopsis "Work with Affymetrix GeneChip files")
1334 "This package provides an interface to Affymetrix chip annotation and
1335 sample attribute files. The package allows an easy way for users to download
1336 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1337 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1338 Command Console} (AGCC)-compatible sample annotation files.")
1339 (license license:artistic2.0)))
1341 (define-public r-affycontam
1343 (name "r-affycontam")
1348 (uri (bioconductor-uri "affyContam" version))
1351 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
1352 (properties `((upstream-name . "affyContam")))
1353 (build-system r-build-system)
1355 `(("r-affy" ,r-affy)
1356 ("r-affydata" ,r-affydata)
1357 ("r-biobase" ,r-biobase)))
1358 (home-page "https://bioconductor.org/packages/affyContam/")
1359 (synopsis "Structured corruption of Affymetrix CEL file data")
1361 "Microarray quality assessment is a major concern of microarray analysts.
1362 This package provides some simple approaches to in silico creation of quality
1363 problems in CEL-level data to help evaluate performance of quality metrics.")
1364 (license license:artistic2.0)))
1366 (define-public r-affycoretools
1368 (name "r-affycoretools")
1373 (uri (bioconductor-uri "affycoretools" version))
1376 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
1377 (properties `((upstream-name . "affycoretools")))
1378 (build-system r-build-system)
1380 `(("r-affy" ,r-affy)
1381 ("r-annotationdbi" ,r-annotationdbi)
1382 ("r-biobase" ,r-biobase)
1383 ("r-biocgenerics" ,r-biocgenerics)
1385 ("r-edger" ,r-edger)
1386 ("r-gcrma" ,r-gcrma)
1387 ("r-glimma" ,r-glimma)
1388 ("r-ggplot2" ,r-ggplot2)
1389 ("r-gostats" ,r-gostats)
1390 ("r-gplots" ,r-gplots)
1391 ("r-hwriter" ,r-hwriter)
1392 ("r-lattice" ,r-lattice)
1393 ("r-limma" ,r-limma)
1394 ("r-oligoclasses" ,r-oligoclasses)
1395 ("r-reportingtools" ,r-reportingtools)
1396 ("r-rsqlite" ,r-rsqlite)
1397 ("r-s4vectors" ,r-s4vectors)
1398 ("r-xtable" ,r-xtable)))
1400 `(("r-knitr" ,r-knitr)))
1401 (home-page "https://bioconductor.org/packages/affycoretools/")
1402 (synopsis "Functions for analyses with Affymetrix GeneChips")
1404 "This package provides various wrapper functions that have been written
1405 to streamline the more common analyses that a Biostatistician might see.")
1406 (license license:artistic2.0)))
1408 (define-public r-affxparser
1410 (name "r-affxparser")
1415 (uri (bioconductor-uri "affxparser" version))
1418 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
1419 (properties `((upstream-name . "affxparser")))
1420 (build-system r-build-system)
1421 (home-page "https://github.com/HenrikBengtsson/affxparser")
1422 (synopsis "Affymetrix File Parsing SDK")
1424 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1425 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1426 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1427 are supported. Currently, there are methods for reading @dfn{chip definition
1428 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1429 either in full or in part. For example, probe signals from a few probesets
1430 can be extracted very quickly from a set of CEL files into a convenient list
1432 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1434 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1436 (define-public r-annotate
1443 (uri (bioconductor-uri "annotate" version))
1446 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
1447 (build-system r-build-system)
1449 `(("r-annotationdbi" ,r-annotationdbi)
1450 ("r-biobase" ,r-biobase)
1451 ("r-biocgenerics" ,r-biocgenerics)
1455 ("r-xtable" ,r-xtable)))
1457 "https://bioconductor.org/packages/annotate")
1458 (synopsis "Annotation for microarrays")
1459 (description "This package provides R environments for the annotation of
1461 (license license:artistic2.0)))
1463 (define-public r-hpar
1470 (uri (bioconductor-uri "hpar" version))
1473 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
1474 (build-system r-build-system)
1476 `(("r-knitr" ,r-knitr)))
1477 (home-page "https://bioconductor.org/packages/hpar/")
1478 (synopsis "Human Protein Atlas in R")
1479 (description "This package provides a simple interface to and data from
1480 the Human Protein Atlas project.")
1481 (license license:artistic2.0)))
1483 (define-public r-regioner
1490 (uri (bioconductor-uri "regioneR" version))
1493 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
1494 (properties `((upstream-name . "regioneR")))
1495 (build-system r-build-system)
1497 `(("r-biostrings" ,r-biostrings)
1498 ("r-bsgenome" ,r-bsgenome)
1499 ("r-genomeinfodb" ,r-genomeinfodb)
1500 ("r-genomicranges" ,r-genomicranges)
1501 ("r-iranges" ,r-iranges)
1502 ("r-memoise" ,r-memoise)
1503 ("r-rtracklayer" ,r-rtracklayer)
1504 ("r-s4vectors" ,r-s4vectors)))
1506 `(("r-knitr" ,r-knitr)))
1507 (home-page "https://bioconductor.org/packages/regioneR/")
1508 (synopsis "Association analysis of genomic regions")
1509 (description "This package offers a statistical framework based on
1510 customizable permutation tests to assess the association between genomic
1511 region sets and other genomic features.")
1512 (license license:artistic2.0)))
1514 (define-public r-reportingtools
1516 (name "r-reportingtools")
1521 (uri (bioconductor-uri "ReportingTools" version))
1524 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
1526 `((upstream-name . "ReportingTools")))
1527 (build-system r-build-system)
1529 `(("r-annotate" ,r-annotate)
1530 ("r-annotationdbi" ,r-annotationdbi)
1531 ("r-biobase" ,r-biobase)
1532 ("r-biocgenerics" ,r-biocgenerics)
1533 ("r-category" ,r-category)
1534 ("r-deseq2" ,r-deseq2)
1535 ("r-edger" ,r-edger)
1536 ("r-ggbio" ,r-ggbio)
1537 ("r-ggplot2" ,r-ggplot2)
1538 ("r-gostats" ,r-gostats)
1539 ("r-gseabase" ,r-gseabase)
1540 ("r-hwriter" ,r-hwriter)
1541 ("r-iranges" ,r-iranges)
1542 ("r-knitr" ,r-knitr)
1543 ("r-lattice" ,r-lattice)
1544 ("r-limma" ,r-limma)
1545 ("r-pfam-db" ,r-pfam-db)
1546 ("r-r-utils" ,r-r-utils)
1549 `(("r-knitr" ,r-knitr)))
1550 (home-page "https://bioconductor.org/packages/ReportingTools/")
1551 (synopsis "Tools for making reports in various formats")
1553 "The ReportingTools package enables users to easily display reports of
1554 analysis results generated from sources such as microarray and sequencing
1555 data. The package allows users to create HTML pages that may be viewed on a
1556 web browser, or in other formats. Users can generate tables with sortable and
1557 filterable columns, make and display plots, and link table entries to other
1558 data sources such as NCBI or larger plots within the HTML page. Using the
1559 package, users can also produce a table of contents page to link various
1560 reports together for a particular project that can be viewed in a web
1562 (license license:artistic2.0)))
1564 (define-public r-geneplotter
1566 (name "r-geneplotter")
1571 (uri (bioconductor-uri "geneplotter" version))
1574 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
1575 (build-system r-build-system)
1577 `(("r-annotate" ,r-annotate)
1578 ("r-annotationdbi" ,r-annotationdbi)
1579 ("r-biobase" ,r-biobase)
1580 ("r-biocgenerics" ,r-biocgenerics)
1581 ("r-lattice" ,r-lattice)
1582 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1583 (home-page "https://bioconductor.org/packages/geneplotter")
1584 (synopsis "Graphics functions for genomic data")
1586 "This package provides functions for plotting genomic data.")
1587 (license license:artistic2.0)))
1589 (define-public r-oligoclasses
1591 (name "r-oligoclasses")
1596 (uri (bioconductor-uri "oligoClasses" version))
1599 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
1600 (properties `((upstream-name . "oligoClasses")))
1601 (build-system r-build-system)
1603 `(("r-affyio" ,r-affyio)
1604 ("r-biobase" ,r-biobase)
1605 ("r-biocgenerics" ,r-biocgenerics)
1606 ("r-biocmanager" ,r-biocmanager)
1607 ("r-biostrings" ,r-biostrings)
1610 ("r-foreach" ,r-foreach)
1611 ("r-genomicranges" ,r-genomicranges)
1612 ("r-iranges" ,r-iranges)
1613 ("r-rsqlite" ,r-rsqlite)
1614 ("r-s4vectors" ,r-s4vectors)
1615 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1616 (home-page "https://bioconductor.org/packages/oligoClasses/")
1617 (synopsis "Classes for high-throughput arrays")
1619 "This package contains class definitions, validity checks, and
1620 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1622 (license license:gpl2+)))
1624 (define-public r-oligo
1631 (uri (bioconductor-uri "oligo" version))
1634 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
1635 (properties `((upstream-name . "oligo")))
1636 (build-system r-build-system)
1637 (inputs `(("zlib" ,zlib)))
1639 `(("r-affxparser" ,r-affxparser)
1640 ("r-affyio" ,r-affyio)
1641 ("r-biobase" ,r-biobase)
1642 ("r-biocgenerics" ,r-biocgenerics)
1643 ("r-biostrings" ,r-biostrings)
1646 ("r-oligoclasses" ,r-oligoclasses)
1647 ("r-preprocesscore" ,r-preprocesscore)
1648 ("r-rsqlite" ,r-rsqlite)
1649 ("r-zlibbioc" ,r-zlibbioc)))
1651 `(("r-knitr" ,r-knitr)))
1652 (home-page "https://bioconductor.org/packages/oligo/")
1653 (synopsis "Preprocessing tools for oligonucleotide arrays")
1655 "This package provides a package to analyze oligonucleotide
1656 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1657 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1658 (license license:lgpl2.0+)))
1660 (define-public r-qvalue
1667 (uri (bioconductor-uri "qvalue" version))
1670 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
1671 (build-system r-build-system)
1673 `(("r-ggplot2" ,r-ggplot2)
1674 ("r-reshape2" ,r-reshape2)))
1676 `(("r-knitr" ,r-knitr)))
1677 (home-page "https://github.com/StoreyLab/qvalue")
1678 (synopsis "Q-value estimation for false discovery rate control")
1680 "This package takes a list of p-values resulting from the simultaneous
1681 testing of many hypotheses and estimates their q-values and local @dfn{false
1682 discovery rate} (FDR) values. The q-value of a test measures the proportion
1683 of false positives incurred when that particular test is called significant.
1684 The local FDR measures the posterior probability the null hypothesis is true
1685 given the test's p-value. Various plots are automatically generated, allowing
1686 one to make sensible significance cut-offs. The software can be applied to
1687 problems in genomics, brain imaging, astrophysics, and data mining.")
1688 ;; Any version of the LGPL.
1689 (license license:lgpl3+)))
1691 (define r-rcppnumerical
1693 (name "r-rcppnumerical")
1697 (uri (cran-uri "RcppNumerical" version))
1700 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
1701 (properties `((upstream-name . "RcppNumerical")))
1702 (build-system r-build-system)
1704 `(("r-rcpp" ,r-rcpp)
1705 ("r-rcppeigen" ,r-rcppeigen)))
1707 `(("r-knitr" ,r-knitr)))
1708 (home-page "https://github.com/yixuan/RcppNumerical")
1709 (synopsis "Rcpp integration for numerical computing libraries")
1710 (description "This package provides a collection of open source libraries
1711 for numerical computing (numerical integration, optimization, etc.) and their
1712 integration with @code{Rcpp}.")
1713 (license license:gpl2+)))
1715 (define-public r-apeglm
1721 (uri (bioconductor-uri "apeglm" version))
1724 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
1725 (properties `((upstream-name . "apeglm")))
1726 (build-system r-build-system)
1728 `(("r-emdbook" ,r-emdbook)
1729 ("r-genomicranges" ,r-genomicranges)
1731 ("r-rcppeigen" ,r-rcppeigen)
1732 ("r-rcppnumerical" ,r-rcppnumerical)
1733 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1734 (native-inputs `(("r-knitr" ,r-knitr)))
1735 (home-page "https://bioconductor.org/packages/apeglm")
1736 (synopsis "Approximate posterior estimation for GLM coefficients")
1737 (description "This package provides Bayesian shrinkage estimators for
1738 effect sizes for a variety of GLM models, using approximation of the
1739 posterior for individual coefficients.")
1740 (license license:gpl2)))
1742 (define-public r-greylistchip
1744 (name "r-greylistchip")
1748 (uri (bioconductor-uri "GreyListChIP" version))
1751 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
1752 (properties `((upstream-name . "GreyListChIP")))
1753 (build-system r-build-system)
1755 `(("r-bsgenome" ,r-bsgenome)
1756 ("r-genomeinfodb" ,r-genomeinfodb)
1757 ("r-genomicalignments" ,r-genomicalignments)
1758 ("r-genomicranges" ,r-genomicranges)
1760 ("r-rsamtools" ,r-rsamtools)
1761 ("r-rtracklayer" ,r-rtracklayer)
1762 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1763 (home-page "https://bioconductor.org/packages/GreyListChIP")
1764 (synopsis "Greylist artefact regions based on ChIP inputs")
1765 (description "This package identifies regions of ChIP experiments with high
1766 signal in the input, that lead to spurious peaks during peak calling.")
1767 (license license:artistic2.0)))
1769 (define-public r-diffbind
1776 (uri (bioconductor-uri "DiffBind" version))
1779 "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a"))))
1780 (properties `((upstream-name . "DiffBind")))
1781 (build-system r-build-system)
1783 `(("r-amap" ,r-amap)
1784 ("r-apeglm" ,r-apeglm)
1786 ("r-biocparallel" ,r-biocparallel)
1787 ("r-deseq2" ,r-deseq2)
1788 ("r-dplyr" ,r-dplyr)
1789 ("r-genomicalignments" ,r-genomicalignments)
1790 ("r-genomicranges" ,r-genomicranges)
1791 ("r-ggplot2" ,r-ggplot2)
1792 ("r-ggrepel" ,r-ggrepel)
1793 ("r-gplots" ,r-gplots)
1794 ("r-greylistchip" ,r-greylistchip)
1795 ("r-iranges" ,r-iranges)
1796 ("r-lattice" ,r-lattice)
1797 ("r-limma" ,r-limma)
1798 ("r-locfit" ,r-locfit)
1799 ("r-rcolorbrewer" , r-rcolorbrewer)
1801 ("r-rhtslib" ,r-rhtslib)
1802 ("r-rsamtools" ,r-rsamtools)
1803 ("r-s4vectors" ,r-s4vectors)
1804 ("r-summarizedexperiment" ,r-summarizedexperiment)
1805 ("r-systempiper" ,r-systempiper)))
1806 (home-page "https://bioconductor.org/packages/DiffBind")
1807 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1809 "This package computes differentially bound sites from multiple
1810 ChIP-seq experiments using affinity (quantitative) data. Also enables
1811 occupancy (overlap) analysis and plotting functions.")
1812 (license license:artistic2.0)))
1814 (define-public r-ripseeker
1816 (name "r-ripseeker")
1821 (uri (bioconductor-uri "RIPSeeker" version))
1824 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1825 (properties `((upstream-name . "RIPSeeker")))
1826 (build-system r-build-system)
1828 `(("r-s4vectors" ,r-s4vectors)
1829 ("r-iranges" ,r-iranges)
1830 ("r-genomicranges" ,r-genomicranges)
1831 ("r-summarizedexperiment" ,r-summarizedexperiment)
1832 ("r-rsamtools" ,r-rsamtools)
1833 ("r-genomicalignments" ,r-genomicalignments)
1834 ("r-rtracklayer" ,r-rtracklayer)))
1835 (home-page "https://bioconductor.org/packages/RIPSeeker")
1837 "Identifying protein-associated transcripts from RIP-seq experiments")
1839 "This package infers and discriminates RIP peaks from RIP-seq alignments
1840 using two-state HMM with negative binomial emission probability. While
1841 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1842 a suite of bioinformatics tools integrated within this self-contained software
1843 package comprehensively addressing issues ranging from post-alignments
1844 processing to visualization and annotation.")
1845 (license license:gpl2)))
1847 (define-public r-multtest
1854 (uri (bioconductor-uri "multtest" version))
1857 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
1858 (build-system r-build-system)
1860 `(("r-survival" ,r-survival)
1861 ("r-biocgenerics" ,r-biocgenerics)
1862 ("r-biobase" ,r-biobase)
1863 ("r-mass" ,r-mass)))
1864 (home-page "https://bioconductor.org/packages/multtest")
1865 (synopsis "Resampling-based multiple hypothesis testing")
1867 "This package can do non-parametric bootstrap and permutation
1868 resampling-based multiple testing procedures (including empirical Bayes
1869 methods) for controlling the family-wise error rate (FWER), generalized
1870 family-wise error rate (gFWER), tail probability of the proportion of
1871 false positives (TPPFP), and false discovery rate (FDR). Several choices
1872 of bootstrap-based null distribution are implemented (centered, centered
1873 and scaled, quantile-transformed). Single-step and step-wise methods are
1874 available. Tests based on a variety of T- and F-statistics (including
1875 T-statistics based on regression parameters from linear and survival models
1876 as well as those based on correlation parameters) are included. When probing
1877 hypotheses with T-statistics, users may also select a potentially faster null
1878 distribution which is multivariate normal with mean zero and variance
1879 covariance matrix derived from the vector influence function. Results are
1880 reported in terms of adjusted P-values, confidence regions and test statistic
1881 cutoffs. The procedures are directly applicable to identifying differentially
1882 expressed genes in DNA microarray experiments.")
1883 (license license:lgpl3)))
1885 (define-public r-graph
1891 (uri (bioconductor-uri "graph" version))
1894 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
1895 (build-system r-build-system)
1897 `(("r-biocgenerics" ,r-biocgenerics)))
1898 (home-page "https://bioconductor.org/packages/graph")
1899 (synopsis "Handle graph data structures in R")
1901 "This package implements some simple graph handling capabilities for R.")
1902 (license license:artistic2.0)))
1904 ;; This is a CRAN package, but it depends on a Bioconductor package.
1905 (define-public r-ggm
1912 (uri (cran-uri "ggm" version))
1915 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1916 (properties `((upstream-name . "ggm")))
1917 (build-system r-build-system)
1919 `(("r-graph" ,r-graph)
1920 ("r-igraph" ,r-igraph)))
1921 (home-page "https://cran.r-project.org/package=ggm")
1922 (synopsis "Functions for graphical Markov models")
1924 "This package provides functions and datasets for maximum likelihood
1925 fitting of some classes of graphical Markov models.")
1926 (license license:gpl2+)))
1928 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
1929 (define-public r-perfmeas
1936 (uri (cran-uri "PerfMeas" version))
1939 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
1940 (properties `((upstream-name . "PerfMeas")))
1941 (build-system r-build-system)
1943 `(("r-graph" ,r-graph)
1944 ("r-limma" ,r-limma)
1945 ("r-rbgl" ,r-rbgl)))
1946 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
1947 (synopsis "Performance measures for ranking and classification tasks")
1949 "This package implements different performance measures for
1950 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
1951 a given recall, F-score for single and multiple classes are available.")
1952 (license license:gpl2+)))
1954 ;; This is a CRAN package, but it depends on a Bioconductor package.
1955 (define-public r-codedepends
1957 (name "r-codedepends")
1962 (uri (cran-uri "CodeDepends" version))
1965 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1966 (properties `((upstream-name . "CodeDepends")))
1967 (build-system r-build-system)
1969 `(("r-codetools" ,r-codetools)
1970 ("r-graph" ,r-graph)
1972 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1973 (synopsis "Analysis of R code for reproducible research and code comprehension")
1975 "This package provides tools for analyzing R expressions or blocks of
1976 code and determining the dependencies between them. It focuses on R scripts,
1977 but can be used on the bodies of functions. There are many facilities
1978 including the ability to summarize or get a high-level view of code,
1979 determining dependencies between variables, code improvement suggestions.")
1980 ;; Any version of the GPL
1981 (license (list license:gpl2+ license:gpl3+))))
1983 (define-public r-chippeakanno
1985 (name "r-chippeakanno")
1990 (uri (bioconductor-uri "ChIPpeakAnno" version))
1993 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
1994 (properties `((upstream-name . "ChIPpeakAnno")))
1995 (build-system r-build-system)
1997 `(("r-annotationdbi" ,r-annotationdbi)
1998 ("r-biocgenerics" ,r-biocgenerics)
1999 ("r-biomart" ,r-biomart)
2000 ("r-biostrings" ,r-biostrings)
2002 ("r-ensembldb" ,r-ensembldb)
2003 ("r-genomeinfodb" ,r-genomeinfodb)
2004 ("r-genomicalignments" ,r-genomicalignments)
2005 ("r-genomicfeatures" ,r-genomicfeatures)
2006 ("r-genomicranges" ,r-genomicranges)
2007 ("r-ggplot2" ,r-ggplot2)
2008 ("r-graph" ,r-graph)
2009 ("r-iranges" ,r-iranges)
2010 ("r-keggrest" ,r-keggrest)
2011 ("r-matrixstats" ,r-matrixstats)
2012 ("r-multtest" ,r-multtest)
2014 ("r-regioner" ,r-regioner)
2015 ("r-rsamtools" ,r-rsamtools)
2016 ("r-rtracklayer" ,r-rtracklayer)
2017 ("r-s4vectors" ,r-s4vectors)
2018 ("r-summarizedexperiment" ,r-summarizedexperiment)
2019 ("r-venndiagram" ,r-venndiagram)))
2021 `(("r-knitr" ,r-knitr)))
2022 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2023 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2025 "The package includes functions to retrieve the sequences around the peak,
2026 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2027 custom features such as most conserved elements and other transcription factor
2028 binding sites supplied by users. Starting 2.0.5, new functions have been added
2029 for finding the peaks with bi-directional promoters with summary statistics
2030 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2031 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2032 enrichedGO (addGeneIDs).")
2033 (license license:gpl2+)))
2035 (define-public r-matrixgenerics
2037 (name "r-matrixgenerics")
2041 (uri (bioconductor-uri "MatrixGenerics" version))
2044 "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc"))))
2046 `((upstream-name . "MatrixGenerics")))
2047 (build-system r-build-system)
2049 `(("r-matrixstats" ,r-matrixstats)))
2050 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2051 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2053 "This package provides S4 generic functions modeled after the
2054 @code{matrixStats} API for alternative matrix implementations. Packages with
2055 alternative matrix implementation can depend on this package and implement the
2056 generic functions that are defined here for a useful set of row and column
2057 summary statistics. Other package developers can import this package and
2058 handle a different matrix implementations without worrying about
2059 incompatibilities.")
2060 (license license:artistic2.0)))
2062 (define-public r-marray
2068 (uri (bioconductor-uri "marray" version))
2070 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
2071 (build-system r-build-system)
2073 `(("r-limma" ,r-limma)))
2074 (home-page "https://bioconductor.org/packages/marray")
2075 (synopsis "Exploratory analysis for two-color spotted microarray data")
2076 (description "This package contains class definitions for two-color spotted
2077 microarray data. It also includes functions for data input, diagnostic plots,
2078 normalization and quality checking.")
2079 (license license:lgpl2.0+)))
2081 (define-public r-cghbase
2087 (uri (bioconductor-uri "CGHbase" version))
2089 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
2090 (properties `((upstream-name . "CGHbase")))
2091 (build-system r-build-system)
2093 `(("r-biobase" ,r-biobase)
2094 ("r-marray" ,r-marray)))
2095 (home-page "https://bioconductor.org/packages/CGHbase")
2096 (synopsis "Base functions and classes for arrayCGH data analysis")
2097 (description "This package contains functions and classes that are needed by
2098 the @code{arrayCGH} packages.")
2099 (license license:gpl2+)))
2101 (define-public r-cghcall
2107 (uri (bioconductor-uri "CGHcall" version))
2109 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
2110 (properties `((upstream-name . "CGHcall")))
2111 (build-system r-build-system)
2113 `(("r-biobase" ,r-biobase)
2114 ("r-cghbase" ,r-cghbase)
2115 ("r-impute" ,r-impute)
2116 ("r-dnacopy" ,r-dnacopy)
2117 ("r-snowfall" ,r-snowfall)))
2118 (home-page "https://bioconductor.org/packages/CGHcall")
2119 (synopsis "Base functions and classes for arrayCGH data analysis")
2120 (description "This package contains functions and classes that are needed by
2121 @code{arrayCGH} packages.")
2122 (license license:gpl2+)))
2124 (define-public r-qdnaseq
2130 (uri (bioconductor-uri "QDNAseq" version))
2132 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
2133 (properties `((upstream-name . "QDNAseq")))
2134 (build-system r-build-system)
2136 `(("r-biobase" ,r-biobase)
2137 ("r-cghbase" ,r-cghbase)
2138 ("r-cghcall" ,r-cghcall)
2139 ("r-dnacopy" ,r-dnacopy)
2140 ("r-future" ,r-future)
2141 ("r-future-apply" ,r-future-apply)
2142 ("r-genomicranges" ,r-genomicranges)
2143 ("r-iranges" ,r-iranges)
2144 ("r-matrixstats" ,r-matrixstats)
2145 ("r-r-utils" ,r-r-utils)
2146 ("r-rsamtools" ,r-rsamtools)))
2147 (home-page "https://bioconductor.org/packages/QDNAseq")
2148 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2149 (description "The genome is divided into non-overlapping fixed-sized bins,
2150 number of sequence reads in each counted, adjusted with a simultaneous
2151 two-dimensional loess correction for sequence mappability and GC content, and
2152 filtered to remove spurious regions in the genome. Downstream steps of
2153 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2155 (license license:gpl2+)))
2157 (define-public r-bayseq
2164 (uri (bioconductor-uri "baySeq" version))
2167 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
2168 (properties `((upstream-name . "baySeq")))
2169 (build-system r-build-system)
2171 `(("r-abind" ,r-abind)
2172 ("r-edger" ,r-edger)
2173 ("r-genomicranges" ,r-genomicranges)))
2174 (home-page "https://bioconductor.org/packages/baySeq/")
2175 (synopsis "Bayesian analysis of differential expression patterns in count data")
2177 "This package identifies differential expression in high-throughput count
2178 data, such as that derived from next-generation sequencing machines,
2179 calculating estimated posterior likelihoods of differential expression (or
2180 more complex hypotheses) via empirical Bayesian methods.")
2181 (license license:gpl3)))
2183 (define-public r-chipcomp
2190 (uri (bioconductor-uri "ChIPComp" version))
2193 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
2194 (properties `((upstream-name . "ChIPComp")))
2195 (build-system r-build-system)
2197 `(("r-biocgenerics" ,r-biocgenerics)
2198 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2199 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2200 ("r-genomeinfodb" ,r-genomeinfodb)
2201 ("r-genomicranges" ,r-genomicranges)
2202 ("r-iranges" ,r-iranges)
2203 ("r-limma" ,r-limma)
2204 ("r-rsamtools" ,r-rsamtools)
2205 ("r-rtracklayer" ,r-rtracklayer)
2206 ("r-s4vectors" ,r-s4vectors)))
2207 (home-page "https://bioconductor.org/packages/ChIPComp")
2208 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2210 "ChIPComp implements a statistical method for quantitative comparison of
2211 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2212 sites across multiple conditions considering matching control in ChIP-seq
2214 ;; Any version of the GPL.
2215 (license license:gpl3+)))
2217 (define-public r-riboprofiling
2219 (name "r-riboprofiling")
2224 (uri (bioconductor-uri "RiboProfiling" version))
2227 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
2228 (properties `((upstream-name . "RiboProfiling")))
2229 (build-system r-build-system)
2231 `(("r-biocgenerics" ,r-biocgenerics)
2232 ("r-biostrings" ,r-biostrings)
2233 ("r-data-table" ,r-data-table)
2234 ("r-genomeinfodb" ,r-genomeinfodb)
2235 ("r-genomicalignments" ,r-genomicalignments)
2236 ("r-genomicfeatures" ,r-genomicfeatures)
2237 ("r-genomicranges" ,r-genomicranges)
2238 ("r-ggbio" ,r-ggbio)
2239 ("r-ggplot2" ,r-ggplot2)
2240 ("r-iranges" ,r-iranges)
2242 ("r-reshape2" ,r-reshape2)
2243 ("r-rsamtools" ,r-rsamtools)
2244 ("r-rtracklayer" ,r-rtracklayer)
2245 ("r-s4vectors" ,r-s4vectors)
2246 ("r-sqldf" ,r-sqldf)))
2248 `(("r-knitr" ,r-knitr)))
2249 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2250 (synopsis "Ribosome profiling data analysis")
2251 (description "Starting with a BAM file, this package provides the
2252 necessary functions for quality assessment, read start position recalibration,
2253 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2254 of count data: pairs, log fold-change, codon frequency and coverage
2255 assessment, principal component analysis on codon coverage.")
2256 (license license:gpl3)))
2258 (define-public r-riboseqr
2265 (uri (bioconductor-uri "riboSeqR" version))
2268 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
2269 (properties `((upstream-name . "riboSeqR")))
2270 (build-system r-build-system)
2272 `(("r-abind" ,r-abind)
2273 ("r-bayseq" ,r-bayseq)
2274 ("r-genomeinfodb" ,r-genomeinfodb)
2275 ("r-genomicranges" ,r-genomicranges)
2276 ("r-iranges" ,r-iranges)
2277 ("r-rsamtools" ,r-rsamtools)
2278 ("r-seqlogo" ,r-seqlogo)))
2279 (home-page "https://bioconductor.org/packages/riboSeqR/")
2280 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2282 "This package provides plotting functions, frameshift detection and
2283 parsing of genetic sequencing data from ribosome profiling experiments.")
2284 (license license:gpl3)))
2286 (define-public r-interactionset
2288 (name "r-interactionset")
2293 (uri (bioconductor-uri "InteractionSet" version))
2296 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
2298 `((upstream-name . "InteractionSet")))
2299 (build-system r-build-system)
2301 `(("r-biocgenerics" ,r-biocgenerics)
2302 ("r-genomeinfodb" ,r-genomeinfodb)
2303 ("r-genomicranges" ,r-genomicranges)
2304 ("r-iranges" ,r-iranges)
2305 ("r-matrix" ,r-matrix)
2307 ("r-s4vectors" ,r-s4vectors)
2308 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2310 `(("r-knitr" ,r-knitr)))
2311 (home-page "https://bioconductor.org/packages/InteractionSet")
2312 (synopsis "Base classes for storing genomic interaction data")
2314 "This package provides the @code{GInteractions},
2315 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2316 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2318 (license license:gpl3)))
2320 (define-public r-genomicinteractions
2322 (name "r-genomicinteractions")
2327 (uri (bioconductor-uri "GenomicInteractions" version))
2330 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
2332 `((upstream-name . "GenomicInteractions")))
2333 (build-system r-build-system)
2335 `(("r-biobase" ,r-biobase)
2336 ("r-biocgenerics" ,r-biocgenerics)
2337 ("r-data-table" ,r-data-table)
2338 ("r-dplyr" ,r-dplyr)
2339 ("r-genomeinfodb" ,r-genomeinfodb)
2340 ("r-genomicranges" ,r-genomicranges)
2341 ("r-ggplot2" ,r-ggplot2)
2342 ("r-gridextra" ,r-gridextra)
2344 ("r-igraph" ,r-igraph)
2345 ("r-interactionset" ,r-interactionset)
2346 ("r-iranges" ,r-iranges)
2347 ("r-rsamtools" ,r-rsamtools)
2348 ("r-rtracklayer" ,r-rtracklayer)
2349 ("r-s4vectors" ,r-s4vectors)
2350 ("r-stringr" ,r-stringr)))
2352 `(("r-knitr" ,r-knitr)))
2353 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2354 (synopsis "R package for handling genomic interaction data")
2356 "This R package provides tools for handling genomic interaction data,
2357 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2358 information and producing various plots and statistics.")
2359 (license license:gpl3)))
2361 (define-public r-ctc
2368 (uri (bioconductor-uri "ctc" version))
2371 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
2372 (build-system r-build-system)
2373 (propagated-inputs `(("r-amap" ,r-amap)))
2374 (home-page "https://bioconductor.org/packages/ctc/")
2375 (synopsis "Cluster and tree conversion")
2377 "This package provides tools for exporting and importing classification
2378 trees and clusters to other programs.")
2379 (license license:gpl2)))
2381 (define-public r-goseq
2388 (uri (bioconductor-uri "goseq" version))
2391 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
2392 (build-system r-build-system)
2394 `(("r-annotationdbi" ,r-annotationdbi)
2395 ("r-biasedurn" ,r-biasedurn)
2396 ("r-biocgenerics" ,r-biocgenerics)
2397 ("r-genelendatabase" ,r-genelendatabase)
2398 ("r-go-db" ,r-go-db)
2399 ("r-mgcv" ,r-mgcv)))
2400 (home-page "https://bioconductor.org/packages/goseq/")
2401 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2403 "This package provides tools to detect Gene Ontology and/or other user
2404 defined categories which are over/under represented in RNA-seq data.")
2405 (license license:lgpl2.0+)))
2407 (define-public r-glimma
2414 (uri (bioconductor-uri "Glimma" version))
2417 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
2418 (properties `((upstream-name . "Glimma")))
2419 (build-system r-build-system)
2421 `(("r-deseq2" ,r-deseq2)
2422 ("r-edger" ,r-edger)
2423 ("r-htmlwidgets" ,r-htmlwidgets)
2424 ("r-jsonlite" ,r-jsonlite)
2425 ("r-limma" ,r-limma)
2426 ("r-s4vectors" ,r-s4vectors)
2427 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2429 `(("r-knitr" ,r-knitr)))
2430 (home-page "https://github.com/Shians/Glimma")
2431 (synopsis "Interactive HTML graphics")
2433 "This package generates interactive visualisations for analysis of
2434 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2435 HTML page. The interactions are built on top of the popular static
2436 representations of analysis results in order to provide additional
2438 (license license:lgpl3)))
2440 (define-public r-rots
2447 (uri (bioconductor-uri "ROTS" version))
2450 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
2451 (properties `((upstream-name . "ROTS")))
2452 (build-system r-build-system)
2454 `(("r-biobase" ,r-biobase)
2455 ("r-rcpp" ,r-rcpp)))
2456 (home-page "https://bioconductor.org/packages/ROTS/")
2457 (synopsis "Reproducibility-Optimized Test Statistic")
2459 "This package provides tools for calculating the
2460 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2462 (license license:gpl2+)))
2464 (define-public r-plgem
2471 (uri (bioconductor-uri "plgem" version))
2474 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
2475 (build-system r-build-system)
2477 `(("r-biobase" ,r-biobase)
2478 ("r-mass" ,r-mass)))
2479 (home-page "http://www.genopolis.it")
2480 (synopsis "Detect differential expression in microarray and proteomics datasets")
2482 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2483 model the variance-versus-mean dependence that exists in a variety of
2484 genome-wide datasets, including microarray and proteomics data. The use of
2485 PLGEM has been shown to improve the detection of differentially expressed
2486 genes or proteins in these datasets.")
2487 (license license:gpl2)))
2489 (define-public r-inspect
2496 (uri (bioconductor-uri "INSPEcT" version))
2499 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
2500 (properties `((upstream-name . "INSPEcT")))
2501 (build-system r-build-system)
2503 `(("r-biobase" ,r-biobase)
2504 ("r-biocgenerics" ,r-biocgenerics)
2505 ("r-biocparallel" ,r-biocparallel)
2506 ("r-deseq2" ,r-deseq2)
2507 ("r-desolve" ,r-desolve)
2508 ("r-gdata" ,r-gdata)
2509 ("r-genomeinfodb" ,r-genomeinfodb)
2510 ("r-genomicalignments" ,r-genomicalignments)
2511 ("r-genomicfeatures" ,r-genomicfeatures)
2512 ("r-genomicranges" ,r-genomicranges)
2513 ("r-iranges" ,r-iranges)
2514 ("r-kernsmooth" ,r-kernsmooth)
2515 ("r-plgem" ,r-plgem)
2517 ("r-rootsolve" ,r-rootsolve)
2518 ("r-rsamtools" ,r-rsamtools)
2519 ("r-rtracklayer" ,r-rtracklayer)
2520 ("r-s4vectors" ,r-s4vectors)
2521 ("r-shiny" ,r-shiny)
2522 ("r-summarizedexperiment" ,r-summarizedexperiment)
2523 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2524 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2526 `(("r-knitr" ,r-knitr)))
2527 (home-page "https://bioconductor.org/packages/INSPEcT")
2528 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2530 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2531 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2532 order to evaluate synthesis, processing and degradation rates and assess via
2533 modeling the rates that determines changes in mature mRNA levels.")
2534 (license license:gpl2)))
2536 (define-public r-dnabarcodes
2538 (name "r-dnabarcodes")
2543 (uri (bioconductor-uri "DNABarcodes" version))
2546 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
2547 (properties `((upstream-name . "DNABarcodes")))
2548 (build-system r-build-system)
2551 ("r-matrix" ,r-matrix)
2552 ("r-rcpp" ,r-rcpp)))
2554 `(("r-knitr" ,r-knitr)))
2555 (home-page "https://bioconductor.org/packages/DNABarcodes")
2556 (synopsis "Create and analyze DNA barcodes")
2558 "This package offers tools to create DNA barcode sets capable of
2559 correcting insertion, deletion, and substitution errors. Existing barcodes
2560 can be analyzed regarding their minimal, maximal and average distances between
2561 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2562 demultiplexed, i.e. assigned to their original reference barcode.")
2563 (license license:gpl2)))
2565 (define-public r-ruvseq
2572 (uri (bioconductor-uri "RUVSeq" version))
2575 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
2576 (properties `((upstream-name . "RUVSeq")))
2577 (build-system r-build-system)
2579 `(("r-biobase" ,r-biobase)
2580 ("r-edaseq" ,r-edaseq)
2581 ("r-edger" ,r-edger)
2582 ("r-mass" ,r-mass)))
2584 `(("r-knitr" ,r-knitr)))
2585 (home-page "https://github.com/drisso/RUVSeq")
2586 (synopsis "Remove unwanted variation from RNA-Seq data")
2588 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2589 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2591 (license license:artistic2.0)))
2593 (define-public r-biocneighbors
2595 (name "r-biocneighbors")
2600 (uri (bioconductor-uri "BiocNeighbors" version))
2603 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
2604 (properties `((upstream-name . "BiocNeighbors")))
2605 (build-system r-build-system)
2607 `(("r-biocparallel" ,r-biocparallel)
2608 ("r-matrix" ,r-matrix)
2610 ("r-rcpphnsw" ,r-rcpphnsw)
2611 ("r-s4vectors" ,r-s4vectors)))
2613 `(("r-knitr" ,r-knitr)))
2614 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2615 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2617 "This package implements exact and approximate methods for nearest
2618 neighbor detection, in a framework that allows them to be easily switched
2619 within Bioconductor packages or workflows. The exact algorithm is implemented
2620 using pre-clustering with the k-means algorithm. Functions are also provided
2621 to search for all neighbors within a given distance. Parallelization is
2622 achieved for all methods using the BiocParallel framework.")
2623 (license license:gpl3)))
2625 (define-public r-biocsingular
2627 (name "r-biocsingular")
2632 (uri (bioconductor-uri "BiocSingular" version))
2635 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
2636 (properties `((upstream-name . "BiocSingular")))
2637 (build-system r-build-system)
2639 `(("r-beachmat" ,r-beachmat)
2640 ("r-biocgenerics" ,r-biocgenerics)
2641 ("r-biocparallel" ,r-biocparallel)
2642 ("r-delayedarray" ,r-delayedarray)
2643 ("r-irlba" ,r-irlba)
2644 ("r-matrix" ,r-matrix)
2647 ("r-s4vectors" ,r-s4vectors)))
2649 `(("r-knitr" ,r-knitr)))
2650 (home-page "https://github.com/LTLA/BiocSingular")
2651 (synopsis "Singular value decomposition for Bioconductor packages")
2653 "This package implements exact and approximate methods for singular value
2654 decomposition and principal components analysis, in a framework that allows
2655 them to be easily switched within Bioconductor packages or workflows. Where
2656 possible, parallelization is achieved using the BiocParallel framework.")
2657 (license license:gpl3)))
2659 (define-public r-destiny
2666 (uri (bioconductor-uri "destiny" version))
2669 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
2670 (build-system r-build-system)
2672 `(("r-biobase" ,r-biobase)
2673 ("r-biocgenerics" ,r-biocgenerics)
2674 ("r-ggplot-multistats" ,r-ggplot-multistats)
2675 ("r-ggplot2" ,r-ggplot2)
2676 ("r-ggthemes" ,r-ggthemes)
2677 ("r-irlba" ,r-irlba)
2678 ("r-knn-covertree" ,r-knn-covertree)
2679 ("r-matrix" ,r-matrix)
2680 ("r-pcamethods" ,r-pcamethods)
2681 ("r-proxy" ,r-proxy)
2683 ("r-rcppeigen" ,r-rcppeigen)
2684 ("r-rcpphnsw" ,r-rcpphnsw)
2685 ("r-rspectra" ,r-rspectra)
2686 ("r-scales" ,r-scales)
2687 ("r-scatterplot3d" ,r-scatterplot3d)
2688 ("r-singlecellexperiment" ,r-singlecellexperiment)
2689 ("r-smoother" ,r-smoother)
2690 ("r-summarizedexperiment" ,r-summarizedexperiment)
2691 ("r-tidyr" ,r-tidyr)
2692 ("r-tidyselect" ,r-tidyselect)
2695 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2696 (home-page "https://bioconductor.org/packages/destiny/")
2697 (synopsis "Create and plot diffusion maps")
2698 (description "This package provides tools to create and plot diffusion
2700 ;; Any version of the GPL
2701 (license license:gpl3+)))
2703 (define-public r-savr
2710 (uri (bioconductor-uri "savR" version))
2713 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
2714 (properties `((upstream-name . "savR")))
2715 (build-system r-build-system)
2717 `(("r-ggplot2" ,r-ggplot2)
2718 ("r-gridextra" ,r-gridextra)
2719 ("r-reshape2" ,r-reshape2)
2720 ("r-scales" ,r-scales)
2722 (home-page "https://github.com/bcalder/savR")
2723 (synopsis "Parse and analyze Illumina SAV files")
2725 "This package provides tools to parse Illumina Sequence Analysis
2726 Viewer (SAV) files, access data, and generate QC plots.")
2727 (license license:agpl3+)))
2729 (define-public r-chipexoqual
2731 (name "r-chipexoqual")
2736 (uri (bioconductor-uri "ChIPexoQual" version))
2739 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
2740 (properties `((upstream-name . "ChIPexoQual")))
2741 (build-system r-build-system)
2743 `(("r-biocparallel" ,r-biocparallel)
2744 ("r-biovizbase" ,r-biovizbase)
2745 ("r-broom" ,r-broom)
2746 ("r-data-table" ,r-data-table)
2747 ("r-dplyr" ,r-dplyr)
2748 ("r-genomeinfodb" ,r-genomeinfodb)
2749 ("r-genomicalignments" ,r-genomicalignments)
2750 ("r-genomicranges" ,r-genomicranges)
2751 ("r-ggplot2" ,r-ggplot2)
2752 ("r-hexbin" ,r-hexbin)
2753 ("r-iranges" ,r-iranges)
2754 ("r-rcolorbrewer" ,r-rcolorbrewer)
2755 ("r-rmarkdown" ,r-rmarkdown)
2756 ("r-rsamtools" ,r-rsamtools)
2757 ("r-s4vectors" ,r-s4vectors)
2758 ("r-scales" ,r-scales)
2759 ("r-viridis" ,r-viridis)))
2761 `(("r-knitr" ,r-knitr)))
2762 (home-page "https://github.com/keleslab/ChIPexoQual")
2763 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2765 "This package provides a quality control pipeline for ChIP-exo/nexus
2767 (license license:gpl2+)))
2769 (define-public r-copynumber
2771 (name "r-copynumber")
2775 (uri (bioconductor-uri "copynumber" version))
2778 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
2779 (build-system r-build-system)
2781 `(("r-s4vectors" ,r-s4vectors)
2782 ("r-iranges" ,r-iranges)
2783 ("r-genomicranges" ,r-genomicranges)
2784 ("r-biocgenerics" ,r-biocgenerics)))
2785 (home-page "https://bioconductor.org/packages/copynumber")
2786 (synopsis "Segmentation of single- and multi-track copy number data")
2788 "This package segments single- and multi-track copy number data by a
2789 penalized least squares regression method.")
2790 (license license:artistic2.0)))
2792 (define-public r-dnacopy
2799 (uri (bioconductor-uri "DNAcopy" version))
2802 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
2803 (properties `((upstream-name . "DNAcopy")))
2804 (build-system r-build-system)
2805 (native-inputs `(("gfortran" ,gfortran)))
2806 (home-page "https://bioconductor.org/packages/DNAcopy")
2807 (synopsis "DNA copy number data analysis")
2809 "This package implements the @dfn{circular binary segmentation} (CBS)
2810 algorithm to segment DNA copy number data and identify genomic regions with
2811 abnormal copy number.")
2812 (license license:gpl2+)))
2814 ;; This is a CRAN package, but it uncharacteristically depends on a
2815 ;; Bioconductor package.
2816 (define-public r-htscluster
2818 (name "r-htscluster")
2823 (uri (cran-uri "HTSCluster" version))
2826 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2827 (properties `((upstream-name . "HTSCluster")))
2828 (build-system r-build-system)
2830 `(("r-capushe" ,r-capushe)
2831 ("r-edger" ,r-edger)
2832 ("r-plotrix" ,r-plotrix)))
2833 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2834 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2836 "This package provides a Poisson mixture model is implemented to cluster
2837 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2838 estimation is performed using either the EM or CEM algorithm, and the slope
2839 heuristics are used for model selection (i.e., to choose the number of
2841 (license license:gpl3+)))
2843 (define-public r-deds
2850 (uri (bioconductor-uri "DEDS" version))
2853 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2854 (properties `((upstream-name . "DEDS")))
2855 (build-system r-build-system)
2856 (home-page "https://bioconductor.org/packages/DEDS/")
2857 (synopsis "Differential expression via distance summary for microarray data")
2859 "This library contains functions that calculate various statistics of
2860 differential expression for microarray data, including t statistics, fold
2861 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2862 also implements a new methodology called DEDS (Differential Expression via
2863 Distance Summary), which selects differentially expressed genes by integrating
2864 and summarizing a set of statistics using a weighted distance approach.")
2865 ;; Any version of the LGPL.
2866 (license license:lgpl3+)))
2868 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2870 (define-public r-nbpseq
2877 (uri (cran-uri "NBPSeq" version))
2880 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2881 (properties `((upstream-name . "NBPSeq")))
2882 (build-system r-build-system)
2884 `(("r-qvalue" ,r-qvalue)))
2885 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2886 (synopsis "Negative binomial models for RNA-Seq data")
2888 "This package provides negative binomial models for two-group comparisons
2889 and regression inferences from RNA-sequencing data.")
2890 (license license:gpl2)))
2892 (define-public r-ebseq
2899 (uri (bioconductor-uri "EBSeq" version))
2902 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
2903 (properties `((upstream-name . "EBSeq")))
2904 (build-system r-build-system)
2906 `(("r-blockmodeling" ,r-blockmodeling)
2907 ("r-gplots" ,r-gplots)
2908 ("r-testthat" ,r-testthat)))
2909 (home-page "https://bioconductor.org/packages/EBSeq")
2910 (synopsis "Differential expression analysis of RNA-seq data")
2912 "This package provides tools for differential expression analysis at both
2913 gene and isoform level using RNA-seq data")
2914 (license license:artistic2.0)))
2916 (define-public r-karyoploter
2918 (name "r-karyoploter")
2922 (uri (bioconductor-uri "karyoploteR" version))
2925 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
2926 (build-system r-build-system)
2928 `(("r-annotationdbi" ,r-annotationdbi)
2929 ("r-bamsignals" ,r-bamsignals)
2930 ("r-bezier" ,r-bezier)
2931 ("r-biovizbase" ,r-biovizbase)
2932 ("r-digest" ,r-digest)
2933 ("r-genomeinfodb" ,r-genomeinfodb)
2934 ("r-genomicfeatures" ,r-genomicfeatures)
2935 ("r-genomicranges" ,r-genomicranges)
2936 ("r-iranges" ,r-iranges)
2937 ("r-memoise" ,r-memoise)
2938 ("r-regioner" ,r-regioner)
2939 ("r-rsamtools" ,r-rsamtools)
2940 ("r-rtracklayer" ,r-rtracklayer)
2941 ("r-s4vectors" ,r-s4vectors)
2942 ("r-variantannotation" ,r-variantannotation)))
2944 `(("r-knitr" ,r-knitr)))
2945 (home-page "https://bioconductor.org/packages/karyoploteR/")
2946 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2947 (description "This package creates karyotype plots of arbitrary genomes and
2948 offers a complete set of functions to plot arbitrary data on them. It mimics
2949 many R base graphics functions coupling them with a coordinate change function
2950 automatically mapping the chromosome and data coordinates into the plot
2952 (license license:artistic2.0)))
2954 (define-public r-lpsymphony
2956 (name "r-lpsymphony")
2961 (uri (bioconductor-uri "lpsymphony" version))
2964 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
2965 (build-system r-build-system)
2969 `(("pkg-config" ,pkg-config)
2970 ("r-knitr" ,r-knitr)))
2971 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2972 (synopsis "Symphony integer linear programming solver in R")
2974 "This package was derived from Rsymphony. The package provides an R
2975 interface to SYMPHONY, a linear programming solver written in C++. The main
2976 difference between this package and Rsymphony is that it includes the solver
2977 source code, while Rsymphony expects to find header and library files on the
2978 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2979 to install interface to SYMPHONY.")
2980 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2981 ;; lpsimphony is released under the same terms.
2982 (license license:epl1.0)))
2984 (define-public r-ihw
2991 (uri (bioconductor-uri "IHW" version))
2994 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
2995 (properties `((upstream-name . "IHW")))
2996 (build-system r-build-system)
2998 `(("r-biocgenerics" ,r-biocgenerics)
2999 ("r-fdrtool" ,r-fdrtool)
3000 ("r-lpsymphony" ,r-lpsymphony)
3001 ("r-slam" ,r-slam)))
3003 `(("r-knitr" ,r-knitr)))
3004 (home-page "https://bioconductor.org/packages/IHW")
3005 (synopsis "Independent hypothesis weighting")
3007 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3008 procedure that increases power compared to the method of Benjamini and
3009 Hochberg by assigning data-driven weights to each hypothesis. The input to
3010 IHW is a two-column table of p-values and covariates. The covariate can be
3011 any continuous-valued or categorical variable that is thought to be
3012 informative on the statistical properties of each hypothesis test, while it is
3013 independent of the p-value under the null hypothesis.")
3014 (license license:artistic2.0)))
3016 (define-public r-icobra
3023 (uri (bioconductor-uri "iCOBRA" version))
3026 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3027 (properties `((upstream-name . "iCOBRA")))
3028 (build-system r-build-system)
3030 `(("r-dplyr" ,r-dplyr)
3032 ("r-ggplot2" ,r-ggplot2)
3033 ("r-limma" ,r-limma)
3034 ("r-reshape2" ,r-reshape2)
3036 ("r-scales" ,r-scales)
3037 ("r-shiny" ,r-shiny)
3038 ("r-shinybs" ,r-shinybs)
3039 ("r-shinydashboard" ,r-shinydashboard)
3040 ("r-upsetr" ,r-upsetr)))
3042 `(("r-knitr" ,r-knitr)))
3043 (home-page "https://bioconductor.org/packages/iCOBRA")
3044 (synopsis "Comparison and visualization of ranking and assignment methods")
3046 "This package provides functions for calculation and visualization of
3047 performance metrics for evaluation of ranking and binary
3048 classification (assignment) methods. It also contains a Shiny application for
3049 interactive exploration of results.")
3050 (license license:gpl2+)))
3052 (define-public r-mast
3059 (uri (bioconductor-uri "MAST" version))
3062 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
3063 (properties `((upstream-name . "MAST")))
3064 (build-system r-build-system)
3066 `(("r-abind" ,r-abind)
3067 ("r-biobase" ,r-biobase)
3068 ("r-biocgenerics" ,r-biocgenerics)
3069 ("r-data-table" ,r-data-table)
3070 ("r-ggplot2" ,r-ggplot2)
3072 ("r-progress" ,r-progress)
3073 ("r-reshape2" ,r-reshape2)
3074 ("r-s4vectors" ,r-s4vectors)
3075 ("r-singlecellexperiment" ,r-singlecellexperiment)
3076 ("r-stringr" ,r-stringr)
3077 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3079 `(("r-knitr" ,r-knitr)))
3080 (home-page "https://github.com/RGLab/MAST/")
3081 (synopsis "Model-based analysis of single cell transcriptomics")
3083 "This package provides methods and models for handling zero-inflated
3084 single cell assay data.")
3085 (license license:gpl2+)))
3087 (define-public r-monocle
3094 (uri (bioconductor-uri "monocle" version))
3097 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
3098 (build-system r-build-system)
3100 `(("r-biobase" ,r-biobase)
3101 ("r-biocgenerics" ,r-biocgenerics)
3102 ("r-biocviews" ,r-biocviews)
3103 ("r-cluster" ,r-cluster)
3104 ("r-combinat" ,r-combinat)
3105 ("r-ddrtree" ,r-ddrtree)
3106 ("r-densityclust" ,r-densityclust)
3107 ("r-dplyr" ,r-dplyr)
3108 ("r-fastica" ,r-fastica)
3109 ("r-ggplot2" ,r-ggplot2)
3110 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3111 ("r-igraph" ,r-igraph)
3112 ("r-irlba" ,r-irlba)
3113 ("r-limma" ,r-limma)
3115 ("r-matrix" ,r-matrix)
3116 ("r-matrixstats" ,r-matrixstats)
3117 ("r-pheatmap" ,r-pheatmap)
3119 ("r-proxy" ,r-proxy)
3120 ("r-qlcmatrix" ,r-qlcmatrix)
3123 ("r-reshape2" ,r-reshape2)
3124 ("r-rtsne" ,r-rtsne)
3126 ("r-stringr" ,r-stringr)
3127 ("r-tibble" ,r-tibble)
3129 ("r-viridis" ,r-viridis)))
3131 `(("r-knitr" ,r-knitr)))
3132 (home-page "https://bioconductor.org/packages/monocle")
3133 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3135 "Monocle performs differential expression and time-series analysis for
3136 single-cell expression experiments. It orders individual cells according to
3137 progress through a biological process, without knowing ahead of time which
3138 genes define progress through that process. Monocle also performs
3139 differential expression analysis, clustering, visualization, and other useful
3140 tasks on single cell expression data. It is designed to work with RNA-Seq and
3141 qPCR data, but could be used with other types as well.")
3142 (license license:artistic2.0)))
3144 (define-public r-monocle3
3152 (url "https://github.com/cole-trapnell-lab/monocle3")
3154 (file-name (git-file-name name version))
3157 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3158 (build-system r-build-system)
3160 `(("r-biobase" ,r-biobase)
3161 ("r-biocgenerics" ,r-biocgenerics)
3162 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3163 ("r-dplyr" ,r-dplyr)
3164 ("r-ggplot2" ,r-ggplot2)
3165 ("r-ggrepel" ,r-ggrepel)
3167 ("r-htmlwidgets" ,r-htmlwidgets)
3168 ("r-igraph" ,r-igraph)
3169 ("r-irlba" ,r-irlba)
3170 ("r-limma" ,r-limma)
3171 ("r-lmtest" ,r-lmtest)
3173 ("r-matrix" ,r-matrix)
3174 ("r-matrix-utils" ,r-matrix-utils)
3175 ("r-pbapply" ,r-pbapply)
3176 ("r-pbmcapply" ,r-pbmcapply)
3177 ("r-pheatmap" ,r-pheatmap)
3178 ("r-plotly" ,r-plotly)
3180 ("r-proxy" ,r-proxy)
3182 ("r-purrr" ,r-purrr)
3185 ("r-rcppparallel" ,r-rcppparallel)
3186 ("r-reshape2" ,r-reshape2)
3187 ("r-reticulate" ,r-reticulate)
3188 ("r-rhpcblasctl" ,r-rhpcblasctl)
3189 ("r-rtsne" ,r-rtsne)
3190 ("r-shiny" ,r-shiny)
3192 ("r-spdep" ,r-spdep)
3193 ("r-speedglm" ,r-speedglm)
3194 ("r-stringr" ,r-stringr)
3195 ("r-singlecellexperiment" ,r-singlecellexperiment)
3196 ("r-tibble" ,r-tibble)
3197 ("r-tidyr" ,r-tidyr)
3199 ("r-viridis" ,r-viridis)))
3200 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3201 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3203 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3204 (license license:expat)))
3206 (define-public r-noiseq
3213 (uri (bioconductor-uri "NOISeq" version))
3216 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
3217 (properties `((upstream-name . "NOISeq")))
3218 (build-system r-build-system)
3220 `(("r-biobase" ,r-biobase)
3221 ("r-matrix" ,r-matrix)))
3222 (home-page "https://bioconductor.org/packages/NOISeq")
3223 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3225 "This package provides tools to support the analysis of RNA-seq
3226 expression data or other similar kind of data. It provides exploratory plots
3227 to evaluate saturation, count distribution, expression per chromosome, type of
3228 detected features, features length, etc. It also supports the analysis of
3229 differential expression between two experimental conditions with no parametric
3231 (license license:artistic2.0)))
3233 (define-public r-scdd
3240 (uri (bioconductor-uri "scDD" version))
3243 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
3244 (properties `((upstream-name . "scDD")))
3245 (build-system r-build-system)
3248 ("r-biocparallel" ,r-biocparallel)
3249 ("r-ebseq" ,r-ebseq)
3250 ("r-fields" ,r-fields)
3251 ("r-ggplot2" ,r-ggplot2)
3252 ("r-mclust" ,r-mclust)
3253 ("r-outliers" ,r-outliers)
3254 ("r-s4vectors" ,r-s4vectors)
3255 ("r-scran" ,r-scran)
3256 ("r-singlecellexperiment" ,r-singlecellexperiment)
3257 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3259 `(("r-knitr" ,r-knitr)))
3260 (home-page "https://github.com/kdkorthauer/scDD")
3261 (synopsis "Mixture modeling of single-cell RNA-seq data")
3263 "This package implements a method to analyze single-cell RNA-seq data
3264 utilizing flexible Dirichlet Process mixture models. Genes with differential
3265 distributions of expression are classified into several interesting patterns
3266 of differences between two conditions. The package also includes functions
3267 for simulating data with these patterns from negative binomial
3269 (license license:gpl2)))
3271 (define-public r-scone
3278 (uri (bioconductor-uri "scone" version))
3281 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
3282 (build-system r-build-system)
3284 `(("r-aroma-light" ,r-aroma-light)
3285 ("r-biocparallel" ,r-biocparallel)
3287 ("r-class" ,r-class)
3288 ("r-cluster" ,r-cluster)
3289 ("r-compositions" ,r-compositions)
3290 ("r-diptest" ,r-diptest)
3291 ("r-edger" ,r-edger)
3293 ("r-gplots" ,r-gplots)
3294 ("r-hexbin" ,r-hexbin)
3295 ("r-limma" ,r-limma)
3296 ("r-matrixstats" ,r-matrixstats)
3297 ("r-mixtools" ,r-mixtools)
3298 ("r-rarpack" ,r-rarpack)
3299 ("r-rcolorbrewer" ,r-rcolorbrewer)
3300 ("r-rhdf5" ,r-rhdf5)
3301 ("r-ruvseq" ,r-ruvseq)
3302 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3304 `(("r-knitr" ,r-knitr)))
3305 (home-page "https://bioconductor.org/packages/scone")
3306 (synopsis "Single cell overview of normalized expression data")
3308 "SCONE is an R package for comparing and ranking the performance of
3309 different normalization schemes for single-cell RNA-seq and other
3310 high-throughput analyses.")
3311 (license license:artistic2.0)))
3313 (define-public r-geoquery
3320 (uri (bioconductor-uri "GEOquery" version))
3323 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
3324 (properties `((upstream-name . "GEOquery")))
3325 (build-system r-build-system)
3327 `(("r-biobase" ,r-biobase)
3328 ("r-dplyr" ,r-dplyr)
3330 ("r-limma" ,r-limma)
3331 ("r-magrittr" ,r-magrittr)
3332 ("r-readr" ,r-readr)
3333 ("r-tidyr" ,r-tidyr)
3334 ("r-xml2" ,r-xml2)))
3336 `(("r-knitr" ,r-knitr)))
3337 (home-page "https://github.com/seandavi/GEOquery/")
3338 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3340 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3341 microarray data. Given the rich and varied nature of this resource, it is
3342 only natural to want to apply BioConductor tools to these data. GEOquery is
3343 the bridge between GEO and BioConductor.")
3344 (license license:gpl2)))
3346 (define-public r-illuminaio
3348 (name "r-illuminaio")
3353 (uri (bioconductor-uri "illuminaio" version))
3356 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
3357 (build-system r-build-system)
3359 `(("r-base64" ,r-base64)))
3360 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3361 (synopsis "Parse Illumina microarray output files")
3363 "This package provides tools for parsing Illumina's microarray output
3364 files, including IDAT.")
3365 (license license:gpl2)))
3367 (define-public r-siggenes
3374 (uri (bioconductor-uri "siggenes" version))
3377 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
3378 (build-system r-build-system)
3380 `(("r-biobase" ,r-biobase)
3381 ("r-multtest" ,r-multtest)
3382 ("r-scrime" ,r-scrime)))
3383 (home-page "https://bioconductor.org/packages/siggenes/")
3385 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3387 "This package provides tools for the identification of differentially
3388 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3389 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3390 Bayes Analyses of Microarrays} (EBAM).")
3391 (license license:lgpl2.0+)))
3393 (define-public r-bumphunter
3395 (name "r-bumphunter")
3400 (uri (bioconductor-uri "bumphunter" version))
3403 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
3404 (build-system r-build-system)
3406 `(("r-annotationdbi" ,r-annotationdbi)
3407 ("r-biocgenerics" ,r-biocgenerics)
3408 ("r-dorng" ,r-dorng)
3409 ("r-foreach" ,r-foreach)
3410 ("r-genomeinfodb" ,r-genomeinfodb)
3411 ("r-genomicfeatures" ,r-genomicfeatures)
3412 ("r-genomicranges" ,r-genomicranges)
3413 ("r-iranges" ,r-iranges)
3414 ("r-iterators" ,r-iterators)
3415 ("r-limma" ,r-limma)
3416 ("r-locfit" ,r-locfit)
3417 ("r-matrixstats" ,r-matrixstats)
3418 ("r-s4vectors" ,r-s4vectors)))
3419 (home-page "https://github.com/ririzarr/bumphunter")
3420 (synopsis "Find bumps in genomic data")
3422 "This package provides tools for finding bumps in genomic data in order
3423 to identify differentially methylated regions in epigenetic epidemiology
3425 (license license:artistic2.0)))
3427 (define-public r-minfi
3434 (uri (bioconductor-uri "minfi" version))
3437 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
3438 (build-system r-build-system)
3440 `(("r-beanplot" ,r-beanplot)
3441 ("r-biobase" ,r-biobase)
3442 ("r-biocgenerics" ,r-biocgenerics)
3443 ("r-biocparallel" ,r-biocparallel)
3444 ("r-biostrings" ,r-biostrings)
3445 ("r-bumphunter" ,r-bumphunter)
3446 ("r-data-table" ,r-data-table)
3447 ("r-delayedarray" ,r-delayedarray)
3448 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3449 ("r-genefilter" ,r-genefilter)
3450 ("r-genomeinfodb" ,r-genomeinfodb)
3451 ("r-genomicranges" ,r-genomicranges)
3452 ("r-geoquery" ,r-geoquery)
3453 ("r-hdf5array" ,r-hdf5array)
3454 ("r-illuminaio" ,r-illuminaio)
3455 ("r-iranges" ,r-iranges)
3456 ("r-lattice" ,r-lattice)
3457 ("r-limma" ,r-limma)
3459 ("r-mclust" ,r-mclust)
3461 ("r-nor1mix" ,r-nor1mix)
3462 ("r-preprocesscore" ,r-preprocesscore)
3463 ("r-quadprog" ,r-quadprog)
3464 ("r-rcolorbrewer" ,r-rcolorbrewer)
3465 ("r-reshape" ,r-reshape)
3466 ("r-s4vectors" ,r-s4vectors)
3467 ("r-siggenes" ,r-siggenes)
3468 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3470 `(("r-knitr" ,r-knitr)))
3471 (home-page "https://github.com/hansenlab/minfi")
3472 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3474 "This package provides tools to analyze and visualize Illumina Infinium
3475 methylation arrays.")
3476 (license license:artistic2.0)))
3478 (define-public r-methylumi
3480 (name "r-methylumi")
3485 (uri (bioconductor-uri "methylumi" version))
3488 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
3489 (build-system r-build-system)
3491 `(("r-annotate" ,r-annotate)
3492 ("r-annotationdbi" ,r-annotationdbi)
3493 ("r-biobase" ,r-biobase)
3494 ("r-biocgenerics" ,r-biocgenerics)
3495 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3496 ("r-genefilter" ,r-genefilter)
3497 ("r-genomeinfodb" ,r-genomeinfodb)
3498 ("r-genomicranges" ,r-genomicranges)
3499 ("r-ggplot2" ,r-ggplot2)
3500 ("r-illuminaio" ,r-illuminaio)
3501 ("r-iranges" ,r-iranges)
3502 ("r-lattice" ,r-lattice)
3503 ("r-matrixstats" ,r-matrixstats)
3504 ("r-minfi" ,r-minfi)
3505 ("r-reshape2" ,r-reshape2)
3506 ("r-s4vectors" ,r-s4vectors)
3507 ("r-scales" ,r-scales)
3508 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3510 `(("r-knitr" ,r-knitr)))
3511 (home-page "https://bioconductor.org/packages/methylumi")
3512 (synopsis "Handle Illumina methylation data")
3514 "This package provides classes for holding and manipulating Illumina
3515 methylation data. Based on eSet, it can contain MIAME information, sample
3516 information, feature information, and multiple matrices of data. An
3517 \"intelligent\" import function, methylumiR can read the Illumina text files
3518 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3519 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3520 background correction, and quality control features for GoldenGate, Infinium,
3521 and Infinium HD arrays are also included.")
3522 (license license:gpl2)))
3524 (define-public r-lumi
3531 (uri (bioconductor-uri "lumi" version))
3534 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
3535 (build-system r-build-system)
3537 `(("r-affy" ,r-affy)
3538 ("r-annotate" ,r-annotate)
3539 ("r-annotationdbi" ,r-annotationdbi)
3540 ("r-biobase" ,r-biobase)
3542 ("r-genomicfeatures" ,r-genomicfeatures)
3543 ("r-genomicranges" ,r-genomicranges)
3544 ("r-kernsmooth" ,r-kernsmooth)
3545 ("r-lattice" ,r-lattice)
3547 ("r-methylumi" ,r-methylumi)
3549 ("r-nleqslv" ,r-nleqslv)
3550 ("r-preprocesscore" ,r-preprocesscore)
3551 ("r-rsqlite" ,r-rsqlite)))
3552 (home-page "https://bioconductor.org/packages/lumi")
3553 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3555 "The lumi package provides an integrated solution for the Illumina
3556 microarray data analysis. It includes functions of Illumina
3557 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3558 variance stabilization, normalization and gene annotation at the probe level.
3559 It also includes the functions of processing Illumina methylation microarrays,
3560 especially Illumina Infinium methylation microarrays.")
3561 (license license:lgpl2.0+)))
3563 (define-public r-linnorm
3570 (uri (bioconductor-uri "Linnorm" version))
3573 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
3574 (properties `((upstream-name . "Linnorm")))
3575 (build-system r-build-system)
3577 `(("r-amap" ,r-amap)
3578 ("r-apcluster" ,r-apcluster)
3579 ("r-ellipse" ,r-ellipse)
3580 ("r-fastcluster" ,r-fastcluster)
3582 ("r-ggdendro" ,r-ggdendro)
3583 ("r-ggplot2" ,r-ggplot2)
3584 ("r-gmodels" ,r-gmodels)
3585 ("r-igraph" ,r-igraph)
3586 ("r-limma" ,r-limma)
3588 ("r-mclust" ,r-mclust)
3590 ("r-rcpparmadillo" ,r-rcpparmadillo)
3591 ("r-rtsne" ,r-rtsne)
3592 ("r-statmod" ,r-statmod)
3593 ("r-vegan" ,r-vegan)
3596 `(("r-knitr" ,r-knitr)))
3597 (home-page "http://www.jjwanglab.org/Linnorm/")
3598 (synopsis "Linear model and normality based transformation method")
3600 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3601 count data or any large scale count data. It transforms such datasets for
3602 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3603 the following pipelines are implemented:
3606 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3607 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3608 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3609 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3610 @item Differential expression analysis or differential peak detection using
3611 limma (@code{Linnorm.limma})
3612 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3613 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3614 @item Stable gene selection for scRNA-seq data; for users without or who do
3615 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3616 @item Data imputation (@code{Linnorm.DataImput}).
3619 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3620 @code{RnaXSim} function is included for simulating RNA-seq data for the
3621 evaluation of DEG analysis methods.")
3622 (license license:expat)))
3624 (define-public r-ioniser
3631 (uri (bioconductor-uri "IONiseR" version))
3634 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
3635 (properties `((upstream-name . "IONiseR")))
3636 (build-system r-build-system)
3638 `(("r-biocgenerics" ,r-biocgenerics)
3639 ("r-biocparallel" ,r-biocparallel)
3640 ("r-biostrings" ,r-biostrings)
3641 ("r-bit64" ,r-bit64)
3642 ("r-dplyr" ,r-dplyr)
3643 ("r-ggplot2" ,r-ggplot2)
3644 ("r-magrittr" ,r-magrittr)
3645 ("r-rhdf5" ,r-rhdf5)
3646 ("r-shortread" ,r-shortread)
3647 ("r-stringr" ,r-stringr)
3648 ("r-tibble" ,r-tibble)
3649 ("r-tidyr" ,r-tidyr)
3650 ("r-xvector" ,r-xvector)))
3652 `(("r-knitr" ,r-knitr)))
3653 (home-page "https://bioconductor.org/packages/IONiseR/")
3654 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3656 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3657 MinION data. It extracts summary statistics from a set of fast5 files and can
3658 be used either before or after base calling. In addition to standard
3659 summaries of the read-types produced, it provides a number of plots for
3660 visualising metrics relative to experiment run time or spatially over the
3661 surface of a flowcell.")
3662 (license license:expat)))
3664 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3665 (define-public r-gkmsvm
3672 (uri (cran-uri "gkmSVM" version))
3675 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3676 (properties `((upstream-name . "gkmSVM")))
3677 (build-system r-build-system)
3679 `(("r-kernlab" ,r-kernlab)
3682 ("r-seqinr" ,r-seqinr)))
3683 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3684 (synopsis "Gapped-kmer support vector machine")
3686 "This R package provides tools for training gapped-kmer SVM classifiers
3687 for DNA and protein sequences. This package supports several sequence
3688 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3689 (license license:gpl2+)))
3691 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3692 (define-public r-mutoss
3699 (uri (cran-uri "mutoss" version))
3702 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3703 (properties `((upstream-name . "mutoss")))
3704 (build-system r-build-system)
3706 `(("r-multcomp" ,r-multcomp)
3707 ("r-multtest" ,r-multtest)
3708 ("r-mvtnorm" ,r-mvtnorm)
3709 ("r-plotrix" ,r-plotrix)))
3710 (home-page "https://github.com/kornl/mutoss/")
3711 (synopsis "Unified multiple testing procedures")
3713 "This package is designed to ease the application and comparison of
3714 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3715 are standardized and usable by the accompanying mutossGUI package.")
3716 ;; Any version of the GPL.
3717 (license (list license:gpl2+ license:gpl3+))))
3719 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3720 ;; from Bioconductor, so we put it here.
3721 (define-public r-metap
3728 (uri (cran-uri "metap" version))
3731 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3732 (build-system r-build-system)
3734 `(("r-lattice" ,r-lattice)
3735 ("r-mutoss" ,r-mutoss)
3736 ("r-rdpack" ,r-rdpack)
3737 ("r-tfisher" ,r-tfisher)))
3738 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3739 (synopsis "Meta-analysis of significance values")
3741 "The canonical way to perform meta-analysis involves using effect sizes.
3742 When they are not available this package provides a number of methods for
3743 meta-analysis of significance values including the methods of Edgington,
3744 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3745 published results; and a routine for graphical display.")
3746 (license license:gpl2)))
3748 (define-public r-triform
3755 (uri (bioconductor-uri "triform" version))
3758 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3759 (build-system r-build-system)
3761 `(("r-biocgenerics" ,r-biocgenerics)
3762 ("r-iranges" ,r-iranges)
3763 ("r-yaml" ,r-yaml)))
3764 (home-page "https://bioconductor.org/packages/triform/")
3765 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3767 "The Triform algorithm uses model-free statistics to identify peak-like
3768 distributions of TF ChIP sequencing reads, taking advantage of an improved
3769 peak definition in combination with known profile characteristics.")
3770 (license license:gpl2)))
3772 (define-public r-varianttools
3774 (name "r-varianttools")
3779 (uri (bioconductor-uri "VariantTools" version))
3782 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
3783 (properties `((upstream-name . "VariantTools")))
3784 (build-system r-build-system)
3786 `(("r-biobase" ,r-biobase)
3787 ("r-biocgenerics" ,r-biocgenerics)
3788 ("r-biocparallel" ,r-biocparallel)
3789 ("r-biostrings" ,r-biostrings)
3790 ("r-bsgenome" ,r-bsgenome)
3791 ("r-genomeinfodb" ,r-genomeinfodb)
3792 ("r-genomicfeatures" ,r-genomicfeatures)
3793 ("r-genomicranges" ,r-genomicranges)
3794 ("r-iranges" ,r-iranges)
3795 ("r-matrix" ,r-matrix)
3796 ("r-rsamtools" ,r-rsamtools)
3797 ("r-rtracklayer" ,r-rtracklayer)
3798 ("r-s4vectors" ,r-s4vectors)
3799 ("r-variantannotation" ,r-variantannotation)))
3800 (home-page "https://bioconductor.org/packages/VariantTools/")
3801 (synopsis "Tools for exploratory analysis of variant calls")
3803 "Explore, diagnose, and compare variant calls using filters. The
3804 VariantTools package supports a workflow for loading data, calling single
3805 sample variants and tumor-specific somatic mutations or other sample-specific
3806 variant types (e.g., RNA editing). Most of the functions operate on
3807 alignments (BAM files) or datasets of called variants. The user is expected
3808 to have already aligned the reads with a separate tool, e.g., GSNAP via
3810 (license license:artistic2.0)))
3812 (define-public r-heatplus
3819 (uri (bioconductor-uri "Heatplus" version))
3822 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
3823 (properties `((upstream-name . "Heatplus")))
3824 (build-system r-build-system)
3826 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3827 (home-page "https://github.com/alexploner/Heatplus")
3828 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3830 "This package provides tools to display a rectangular heatmap (intensity
3831 plot) of a data matrix. By default, both samples (columns) and features (row)
3832 of the matrix are sorted according to a hierarchical clustering, and the
3833 corresponding dendrogram is plotted. Optionally, panels with additional
3834 information about samples and features can be added to the plot.")
3835 (license license:gpl2+)))
3837 (define-public r-gosemsim
3844 (uri (bioconductor-uri "GOSemSim" version))
3847 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
3848 (properties `((upstream-name . "GOSemSim")))
3849 (build-system r-build-system)
3851 `(("r-annotationdbi" ,r-annotationdbi)
3852 ("r-go-db" ,r-go-db)
3853 ("r-rcpp" ,r-rcpp)))
3855 `(("r-knitr" ,r-knitr)))
3856 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3857 (synopsis "GO-terms semantic similarity measures")
3859 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3860 quantitative ways to compute similarities between genes and gene groups, and
3861 have became important basis for many bioinformatics analysis approaches.
3862 GOSemSim is an R package for semantic similarity computation among GO terms,
3863 sets of GO terms, gene products and gene clusters.")
3864 (license license:artistic2.0)))
3866 (define-public r-anota
3873 (uri (bioconductor-uri "anota" version))
3876 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
3877 (build-system r-build-system)
3879 `(("r-multtest" ,r-multtest)
3880 ("r-qvalue" ,r-qvalue)))
3881 (home-page "https://bioconductor.org/packages/anota/")
3882 (synopsis "Analysis of translational activity")
3884 "Genome wide studies of translational control is emerging as a tool to
3885 study various biological conditions. The output from such analysis is both
3886 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
3887 involved in translation (the actively translating mRNA level) for each mRNA.
3888 The standard analysis of such data strives towards identifying differential
3889 translational between two or more sample classes - i.e. differences in
3890 actively translated mRNA levels that are independent of underlying differences
3891 in cytosolic mRNA levels. This package allows for such analysis using partial
3892 variances and the random variance model. As 10s of thousands of mRNAs are
3893 analyzed in parallel the library performs a number of tests to assure that
3894 the data set is suitable for such analysis.")
3895 (license license:gpl3)))
3897 (define-public r-sigpathway
3899 (name "r-sigpathway")
3904 (uri (bioconductor-uri "sigPathway" version))
3907 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
3908 (properties `((upstream-name . "sigPathway")))
3909 (build-system r-build-system)
3910 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3911 (synopsis "Pathway analysis")
3913 "This package is used to conduct pathway analysis by calculating the NT_k
3914 and NE_k statistics in a statistical framework for determining whether a
3915 specified group of genes for a pathway has a coordinated association with a
3916 phenotype of interest.")
3917 (license license:gpl2)))
3919 (define-public r-fgsea
3926 (uri (bioconductor-uri "fgsea" version))
3929 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
3930 (build-system r-build-system)
3933 ("r-biocparallel" ,r-biocparallel)
3934 ("r-data-table" ,r-data-table)
3935 ("r-fastmatch" ,r-fastmatch)
3936 ("r-ggplot2" ,r-ggplot2)
3937 ("r-gridextra" ,r-gridextra)
3938 ("r-matrix" ,r-matrix)
3939 ("r-rcpp" ,r-rcpp)))
3941 `(("r-knitr" ,r-knitr)))
3942 (home-page "https://github.com/ctlab/fgsea/")
3943 (synopsis "Fast gene set enrichment analysis")
3945 "The package implements an algorithm for fast gene set enrichment
3946 analysis. Using the fast algorithm makes more permutations and gets
3947 more fine grained p-values, which allows using accurate standard approaches
3948 to multiple hypothesis correction.")
3949 (license license:expat)))
3951 (define-public r-dose
3958 (uri (bioconductor-uri "DOSE" version))
3961 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
3962 (properties `((upstream-name . "DOSE")))
3963 (build-system r-build-system)
3965 `(("r-annotationdbi" ,r-annotationdbi)
3966 ("r-biocparallel" ,r-biocparallel)
3967 ("r-do-db" ,r-do-db)
3968 ("r-fgsea" ,r-fgsea)
3969 ("r-ggplot2" ,r-ggplot2)
3970 ("r-gosemsim" ,r-gosemsim)
3971 ("r-qvalue" ,r-qvalue)
3972 ("r-reshape2" ,r-reshape2)))
3974 `(("r-knitr" ,r-knitr)))
3975 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3976 (synopsis "Disease ontology semantic and enrichment analysis")
3978 "This package implements five methods proposed by Resnik, Schlicker,
3979 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3980 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3981 including hypergeometric model and gene set enrichment analysis are also
3982 implemented for discovering disease associations of high-throughput biological
3984 (license license:artistic2.0)))
3986 (define-public r-enrichplot
3988 (name "r-enrichplot")
3993 (uri (bioconductor-uri "enrichplot" version))
3996 "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd"))))
3997 (build-system r-build-system)
3999 `(("r-cowplot" ,r-cowplot)
4001 ("r-ggplot2" ,r-ggplot2)
4002 ("r-ggraph" ,r-ggraph)
4003 ("r-gosemsim" ,r-gosemsim)
4004 ("r-igraph" ,r-igraph)
4005 ("r-magrittr" ,r-magrittr)
4007 ("r-purrr" ,r-purrr)
4008 ("r-rcolorbrewer" ,r-rcolorbrewer)
4009 ("r-reshape2" ,r-reshape2)
4010 ("r-scatterpie" ,r-scatterpie)
4011 ("r-shadowtext" ,r-shadowtext)))
4013 `(("r-knitr" ,r-knitr)))
4014 (home-page "https://github.com/GuangchuangYu/enrichplot")
4015 (synopsis "Visualization of functional enrichment result")
4017 "The enrichplot package implements several visualization methods for
4018 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4019 All the visualization methods are developed based on ggplot2 graphics.")
4020 (license license:artistic2.0)))
4022 (define-public r-clusterprofiler
4024 (name "r-clusterprofiler")
4029 (uri (bioconductor-uri "clusterProfiler" version))
4032 "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9"))))
4034 `((upstream-name . "clusterProfiler")))
4035 (build-system r-build-system)
4037 `(("r-annotationdbi" ,r-annotationdbi)
4039 ("r-downloader" ,r-downloader)
4040 ("r-dplyr" ,r-dplyr)
4041 ("r-enrichplot" ,r-enrichplot)
4042 ("r-go-db" ,r-go-db)
4043 ("r-gosemsim" ,r-gosemsim)
4044 ("r-magrittr" ,r-magrittr)
4046 ("r-qvalue" ,r-qvalue)
4047 ("r-rlang" ,r-rlang)
4048 ("r-rvcheck" ,r-rvcheck)
4049 ("r-tidyr" ,r-tidyr)))
4051 `(("r-knitr" ,r-knitr)))
4052 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4053 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4055 "This package implements methods to analyze and visualize functional
4056 profiles (GO and KEGG) of gene and gene clusters.")
4057 (license license:artistic2.0)))
4059 (define-public r-mlinterfaces
4061 (name "r-mlinterfaces")
4066 (uri (bioconductor-uri "MLInterfaces" version))
4069 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4070 (properties `((upstream-name . "MLInterfaces")))
4071 (build-system r-build-system)
4073 `(("r-annotate" ,r-annotate)
4074 ("r-biobase" ,r-biobase)
4075 ("r-biocgenerics" ,r-biocgenerics)
4076 ("r-cluster" ,r-cluster)
4079 ("r-gdata" ,r-gdata)
4080 ("r-genefilter" ,r-genefilter)
4081 ("r-ggvis" ,r-ggvis)
4082 ("r-hwriter" ,r-hwriter)
4084 ("r-mlbench" ,r-mlbench)
4086 ("r-rcolorbrewer" ,r-rcolorbrewer)
4088 ("r-rpart" ,r-rpart)
4089 ("r-sfsmisc" ,r-sfsmisc)
4090 ("r-shiny" ,r-shiny)
4091 ("r-threejs" ,r-threejs)))
4092 (home-page "https://bioconductor.org/packages/MLInterfaces/")
4093 (synopsis "Interfaces to R machine learning procedures")
4095 "This package provides uniform interfaces to machine learning code for
4096 data in R and Bioconductor containers.")
4097 ;; Any version of the LGPL.
4098 (license license:lgpl2.1+)))
4100 (define-public r-annaffy
4107 (uri (bioconductor-uri "annaffy" version))
4110 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
4111 (build-system r-build-system)
4114 (modify-phases %standard-phases
4115 (add-after 'unpack 'remove-reference-to-non-free-data
4117 (substitute* "DESCRIPTION"
4121 `(("r-annotationdbi" ,r-annotationdbi)
4122 ("r-biobase" ,r-biobase)
4124 ("r-go-db" ,r-go-db)))
4125 (home-page "https://bioconductor.org/packages/annaffy/")
4126 (synopsis "Annotation tools for Affymetrix biological metadata")
4128 "This package provides functions for handling data from Bioconductor
4129 Affymetrix annotation data packages. It produces compact HTML and text
4130 reports including experimental data and URL links to many online databases.
4131 It allows searching of biological metadata using various criteria.")
4132 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4133 ;; the LGPL 2.1 is included.
4134 (license license:lgpl2.1+)))
4136 (define-public r-a4core
4143 (uri (bioconductor-uri "a4Core" version))
4146 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
4147 (properties `((upstream-name . "a4Core")))
4148 (build-system r-build-system)
4150 `(("r-biobase" ,r-biobase)
4151 ("r-glmnet" ,r-glmnet)))
4153 `(("r-knitr" ,r-knitr)))
4154 (home-page "https://bioconductor.org/packages/a4Core")
4155 (synopsis "Automated Affymetrix array analysis core package")
4157 "This is the core package for the automated analysis of Affymetrix
4159 (license license:gpl3)))
4161 (define-public r-a4classif
4163 (name "r-a4classif")
4168 (uri (bioconductor-uri "a4Classif" version))
4171 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
4172 (properties `((upstream-name . "a4Classif")))
4173 (build-system r-build-system)
4175 `(("r-a4core" ,r-a4core)
4176 ("r-a4preproc" ,r-a4preproc)
4177 ("r-biobase" ,r-biobase)
4178 ("r-glmnet" ,r-glmnet)
4181 ("r-varselrf" ,r-varselrf)))
4183 `(("r-knitr" ,r-knitr)))
4184 (home-page "https://bioconductor.org/packages/a4Classif/")
4185 (synopsis "Automated Affymetrix array analysis classification package")
4187 "This is the classification package for the automated analysis of
4188 Affymetrix arrays.")
4189 (license license:gpl3)))
4191 (define-public r-a4preproc
4193 (name "r-a4preproc")
4198 (uri (bioconductor-uri "a4Preproc" version))
4201 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
4202 (properties `((upstream-name . "a4Preproc")))
4203 (build-system r-build-system)
4205 `(("r-biobase" ,r-biobase)
4206 ("r-biocgenerics" ,r-biocgenerics)))
4208 `(("r-knitr" ,r-knitr)))
4209 (home-page "https://bioconductor.org/packages/a4Preproc/")
4210 (synopsis "Automated Affymetrix array analysis preprocessing package")
4212 "This is a package for the automated analysis of Affymetrix arrays. It
4213 is used for preprocessing the arrays.")
4214 (license license:gpl3)))
4216 (define-public r-a4reporting
4218 (name "r-a4reporting")
4223 (uri (bioconductor-uri "a4Reporting" version))
4226 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
4227 (properties `((upstream-name . "a4Reporting")))
4228 (build-system r-build-system)
4230 `(("r-xtable" ,r-xtable)))
4232 `(("r-knitr" ,r-knitr)))
4233 (home-page "https://bioconductor.org/packages/a4Reporting/")
4234 (synopsis "Automated Affymetrix array analysis reporting package")
4236 "This is a package for the automated analysis of Affymetrix arrays. It
4237 provides reporting features.")
4238 (license license:gpl3)))
4240 (define-public r-a4base
4247 (uri (bioconductor-uri "a4Base" version))
4250 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
4251 (properties `((upstream-name . "a4Base")))
4252 (build-system r-build-system)
4254 `(("r-a4core" ,r-a4core)
4255 ("r-a4preproc" ,r-a4preproc)
4256 ("r-annaffy" ,r-annaffy)
4257 ("r-biobase" ,r-biobase)
4258 ("r-genefilter" ,r-genefilter)
4259 ("r-glmnet" ,r-glmnet)
4260 ("r-gplots" ,r-gplots)
4261 ("r-limma" ,r-limma)
4263 ("r-multtest" ,r-multtest)))
4264 (home-page "https://bioconductor.org/packages/a4Base/")
4265 (synopsis "Automated Affymetrix array analysis base package")
4267 "This package provides basic features for the automated analysis of
4268 Affymetrix arrays.")
4269 (license license:gpl3)))
4278 (uri (bioconductor-uri "a4" version))
4281 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
4282 (build-system r-build-system)
4284 `(("r-a4base" ,r-a4base)
4285 ("r-a4classif" ,r-a4classif)
4286 ("r-a4core" ,r-a4core)
4287 ("r-a4preproc" ,r-a4preproc)
4288 ("r-a4reporting" ,r-a4reporting)))
4289 (home-page "https://bioconductor.org/packages/a4/")
4290 (synopsis "Automated Affymetrix array analysis umbrella package")
4292 "This package provides a software suite for the automated analysis of
4293 Affymetrix arrays.")
4294 (license license:gpl3)))
4296 (define-public r-abseqr
4303 (uri (bioconductor-uri "abseqR" version))
4306 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
4307 (properties `((upstream-name . "abseqR")))
4308 (build-system r-build-system)
4310 `(("pandoc" ,pandoc)))
4312 `(("r-biocparallel" ,r-biocparallel)
4313 ("r-biocstyle" ,r-biocstyle)
4314 ("r-circlize" ,r-circlize)
4315 ("r-flexdashboard" ,r-flexdashboard)
4316 ("r-ggcorrplot" ,r-ggcorrplot)
4317 ("r-ggdendro" ,r-ggdendro)
4318 ("r-ggplot2" ,r-ggplot2)
4319 ("r-gridextra" ,r-gridextra)
4320 ("r-knitr" ,r-knitr)
4321 ("r-plotly" ,r-plotly)
4324 ("r-rcolorbrewer" ,r-rcolorbrewer)
4325 ("r-reshape2" ,r-reshape2)
4326 ("r-rmarkdown" ,r-rmarkdown)
4327 ("r-stringr" ,r-stringr)
4328 ("r-vegan" ,r-vegan)
4329 ("r-venndiagram" ,r-venndiagram)))
4331 `(("r-knitr" ,r-knitr)))
4332 (home-page "https://github.com/malhamdoosh/abseqR")
4333 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4335 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4336 sequencing datasets generated from antibody libraries and abseqR is one of its
4337 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4338 capabilities and allows them to generate interactive HTML reports for the
4339 convenience of viewing and sharing with other researchers. Additionally,
4340 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4341 further downstream analysis on its output.")
4342 (license license:gpl3)))
4344 (define-public r-bacon
4351 (uri (bioconductor-uri "bacon" version))
4354 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
4355 (build-system r-build-system)
4357 `(("r-biocparallel" ,r-biocparallel)
4358 ("r-ellipse" ,r-ellipse)
4359 ("r-ggplot2" ,r-ggplot2)))
4361 `(("r-knitr" ,r-knitr)))
4362 (home-page "https://bioconductor.org/packages/bacon/")
4363 (synopsis "Controlling bias and inflation in association studies")
4365 "Bacon can be used to remove inflation and bias often observed in
4366 epigenome- and transcriptome-wide association studies. To this end bacon
4367 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4368 fitting a three-component normal mixture on z-scores.")
4369 (license license:gpl2+)))
4371 (define-public r-rgadem
4378 (uri (bioconductor-uri "rGADEM" version))
4381 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
4382 (properties `((upstream-name . "rGADEM")))
4383 (build-system r-build-system)
4385 `(("r-biostrings" ,r-biostrings)
4386 ("r-bsgenome" ,r-bsgenome)
4387 ("r-genomicranges" ,r-genomicranges)
4388 ("r-iranges" ,r-iranges)
4389 ("r-seqlogo" ,r-seqlogo)))
4390 (home-page "https://bioconductor.org/packages/rGADEM/")
4391 (synopsis "De novo sequence motif discovery")
4393 "rGADEM is an efficient de novo motif discovery tool for large-scale
4394 genomic sequence data.")
4395 (license license:artistic2.0)))
4397 (define-public r-motiv
4404 (uri (bioconductor-uri "MotIV" version))
4407 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4408 (properties `((upstream-name . "MotIV")))
4409 (build-system r-build-system)
4413 `(("r-biocgenerics" ,r-biocgenerics)
4414 ("r-biostrings" ,r-biostrings)
4415 ("r-genomicranges" ,r-genomicranges)
4416 ("r-iranges" ,r-iranges)
4417 ("r-lattice" ,r-lattice)
4418 ("r-rgadem" ,r-rgadem)
4419 ("r-s4vectors" ,r-s4vectors)))
4420 (home-page "https://bioconductor.org/packages/MotIV/")
4421 (synopsis "Motif identification and validation")
4423 "This package is used for the identification and validation of sequence
4424 motifs. It makes use of STAMP for comparing a set of motifs to a given
4425 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4426 distributions, modules and filter motifs.")
4427 (license license:gpl2)))
4429 (define-public r-motifdb
4435 (uri (bioconductor-uri "MotifDb" version))
4437 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
4438 (properties `((upstream-name . "MotifDb")))
4439 (build-system r-build-system)
4441 `(("r-biocgenerics" ,r-biocgenerics)
4442 ("r-biostrings" ,r-biostrings)
4443 ("r-genomicranges" ,r-genomicranges)
4444 ("r-iranges" ,r-iranges)
4445 ("r-rtracklayer" ,r-rtracklayer)
4446 ("r-s4vectors" ,r-s4vectors)
4447 ("r-splitstackshape" ,r-splitstackshape)))
4449 `(("r-knitr" ,r-knitr)))
4450 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4451 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4452 (description "This package provides more than 2000 annotated position
4453 frequency matrices from nine public sources, for multiple organisms.")
4454 (license license:artistic2.0)))
4456 (define-public r-motifbreakr
4458 (name "r-motifbreakr")
4462 (uri (bioconductor-uri "motifbreakR" version))
4464 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
4465 (properties `((upstream-name . "motifbreakR")))
4466 (build-system r-build-system)
4468 `(("r-biocgenerics" ,r-biocgenerics)
4469 ("r-biocparallel" ,r-biocparallel)
4470 ("r-biostrings" ,r-biostrings)
4471 ("r-bsgenome" ,r-bsgenome)
4472 ("r-genomeinfodb" ,r-genomeinfodb)
4473 ("r-genomicranges" ,r-genomicranges)
4474 ("r-grimport" ,r-grimport)
4476 ("r-iranges" ,r-iranges)
4477 ("r-matrixstats" ,r-matrixstats)
4478 ("r-motifdb" ,r-motifdb)
4479 ("r-motifstack" ,r-motifstack)
4480 ("r-rtracklayer" ,r-rtracklayer)
4481 ("r-s4vectors" ,r-s4vectors)
4482 ("r-stringr" ,r-stringr)
4483 ("r-summarizedexperiment" ,r-summarizedexperiment)
4484 ("r-tfmpvalue" ,r-tfmpvalue)
4485 ("r-variantannotation" ,r-variantannotation)))
4487 `(("r-knitr" ,r-knitr)))
4488 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4489 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4490 (description "This package allows biologists to judge in the first place
4491 whether the sequence surrounding the polymorphism is a good match, and in
4492 the second place how much information is gained or lost in one allele of
4493 the polymorphism relative to another. This package gives a choice of
4494 algorithms for interrogation of genomes with motifs from public sources:
4496 @item a weighted-sum probability matrix;
4497 @item log-probabilities;
4498 @item weighted by relative entropy.
4501 This package can predict effects for novel or previously described variants in
4502 public databases, making it suitable for tasks beyond the scope of its original
4503 design. Lastly, it can be used to interrogate any genome curated within
4505 (license license:gpl2+)))
4507 (define-public r-motifstack
4509 (name "r-motifstack")
4514 (uri (bioconductor-uri "motifStack" version))
4517 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
4518 (properties `((upstream-name . "motifStack")))
4519 (build-system r-build-system)
4521 `(("r-ade4" ,r-ade4)
4522 ("r-biostrings" ,r-biostrings)
4523 ("r-ggplot2" ,r-ggplot2)
4524 ("r-htmlwidgets" ,r-htmlwidgets)
4527 `(("r-knitr" ,r-knitr)))
4528 (home-page "https://bioconductor.org/packages/motifStack/")
4529 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4531 "The motifStack package is designed for graphic representation of
4532 multiple motifs with different similarity scores. It works with both DNA/RNA
4533 sequence motifs and amino acid sequence motifs. In addition, it provides the
4534 flexibility for users to customize the graphic parameters such as the font
4535 type and symbol colors.")
4536 (license license:gpl2+)))
4538 (define-public r-genomicscores
4540 (name "r-genomicscores")
4545 (uri (bioconductor-uri "GenomicScores" version))
4548 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
4549 (properties `((upstream-name . "GenomicScores")))
4550 (build-system r-build-system)
4552 `(("r-annotationhub" ,r-annotationhub)
4553 ("r-biobase" ,r-biobase)
4554 ("r-biocfilecache" ,r-biocfilecache)
4555 ("r-biocgenerics" ,r-biocgenerics)
4556 ("r-biocmanager" ,r-biocmanager)
4557 ("r-biostrings" ,r-biostrings)
4558 ("r-delayedarray" ,r-delayedarray)
4559 ("r-genomeinfodb" ,r-genomeinfodb)
4560 ("r-genomicranges" ,r-genomicranges)
4561 ("r-hdf5array" ,r-hdf5array)
4562 ("r-iranges" ,r-iranges)
4563 ("r-rhdf5" ,r-rhdf5)
4564 ("r-s4vectors" ,r-s4vectors)
4567 `(("r-knitr" ,r-knitr)))
4568 (home-page "https://github.com/rcastelo/GenomicScores/")
4569 (synopsis "Work with genome-wide position-specific scores")
4571 "This package provides infrastructure to store and access genome-wide
4572 position-specific scores within R and Bioconductor.")
4573 (license license:artistic2.0)))
4575 (define-public r-atacseqqc
4577 (name "r-atacseqqc")
4582 (uri (bioconductor-uri "ATACseqQC" version))
4585 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
4586 (properties `((upstream-name . "ATACseqQC")))
4587 (build-system r-build-system)
4589 `(("r-biocgenerics" ,r-biocgenerics)
4590 ("r-biostrings" ,r-biostrings)
4591 ("r-bsgenome" ,r-bsgenome)
4592 ("r-chippeakanno" ,r-chippeakanno)
4593 ("r-edger" ,r-edger)
4594 ("r-genomeinfodb" ,r-genomeinfodb)
4595 ("r-genomicalignments" ,r-genomicalignments)
4596 ("r-genomicranges" ,r-genomicranges)
4597 ("r-genomicscores" ,r-genomicscores)
4598 ("r-iranges" ,r-iranges)
4599 ("r-kernsmooth" ,r-kernsmooth)
4600 ("r-limma" ,r-limma)
4601 ("r-motifstack" ,r-motifstack)
4602 ("r-preseqr" ,r-preseqr)
4603 ("r-randomforest" ,r-randomforest)
4604 ("r-rsamtools" ,r-rsamtools)
4605 ("r-rtracklayer" ,r-rtracklayer)
4606 ("r-s4vectors" ,r-s4vectors)))
4608 `(("r-knitr" ,r-knitr)))
4609 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4610 (synopsis "ATAC-seq quality control")
4612 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4613 sequencing, is a rapid and sensitive method for chromatin accessibility
4614 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4615 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4616 assess whether their ATAC-seq experiment is successful. It includes
4617 diagnostic plots of fragment size distribution, proportion of mitochondria
4618 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4620 (license license:gpl2+)))
4622 (define-public r-gofuncr
4629 (uri (bioconductor-uri "GOfuncR" version))
4632 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
4633 (properties `((upstream-name . "GOfuncR")))
4634 (build-system r-build-system)
4636 `(("r-annotationdbi" ,r-annotationdbi)
4637 ("r-genomicranges" ,r-genomicranges)
4638 ("r-gtools" ,r-gtools)
4639 ("r-iranges" ,r-iranges)
4640 ("r-mapplots" ,r-mapplots)
4642 ("r-vioplot" ,r-vioplot)))
4644 `(("r-knitr" ,r-knitr)))
4645 (home-page "https://bioconductor.org/packages/GOfuncR/")
4646 (synopsis "Gene ontology enrichment using FUNC")
4648 "GOfuncR performs a gene ontology enrichment analysis based on the
4649 ontology enrichment software FUNC. GO-annotations are obtained from
4650 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4651 included in the package and updated regularly. GOfuncR provides the standard
4652 candidate vs background enrichment analysis using the hypergeometric test, as
4653 well as three additional tests:
4656 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4657 @item a binomial test that is used when genes are associated with two counts,
4659 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4660 associated with four counts.
4663 To correct for multiple testing and interdependency of the tests, family-wise
4664 error rates are computed based on random permutations of the gene-associated
4665 variables. GOfuncR also provides tools for exploring the ontology graph and
4666 the annotations, and options to take gene-length or spatial clustering of
4667 genes into account. It is also possible to provide custom gene coordinates,
4668 annotations and ontologies.")
4669 (license license:gpl2+)))
4671 (define-public r-abaenrichment
4673 (name "r-abaenrichment")
4678 (uri (bioconductor-uri "ABAEnrichment" version))
4681 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
4682 (properties `((upstream-name . "ABAEnrichment")))
4683 (build-system r-build-system)
4685 `(("r-abadata" ,r-abadata)
4686 ("r-data-table" ,r-data-table)
4687 ("r-gofuncr" ,r-gofuncr)
4688 ("r-gplots" ,r-gplots)
4689 ("r-gtools" ,r-gtools)
4690 ("r-rcpp" ,r-rcpp)))
4692 `(("r-knitr" ,r-knitr)))
4693 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4694 (synopsis "Gene expression enrichment in human brain regions")
4696 "The package ABAEnrichment is designed to test for enrichment of user
4697 defined candidate genes in the set of expressed genes in different human brain
4698 regions. The core function @code{aba_enrich} integrates the expression of the
4699 candidate gene set (averaged across donors) and the structural information of
4700 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4701 (license license:gpl2+)))
4703 (define-public r-annotationfuncs
4705 (name "r-annotationfuncs")
4710 (uri (bioconductor-uri "AnnotationFuncs" version))
4713 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
4715 `((upstream-name . "AnnotationFuncs")))
4716 (build-system r-build-system)
4718 `(("r-annotationdbi" ,r-annotationdbi)
4720 (home-page "https://www.iysik.com/r/annotationfuncs")
4721 (synopsis "Annotation translation functions")
4723 "This package provides functions for handling translating between
4724 different identifieres using the Biocore Data Team data-packages (e.g.
4725 @code{org.Bt.eg.db}).")
4726 (license license:gpl2)))
4728 (define-public r-annotationtools
4730 (name "r-annotationtools")
4735 (uri (bioconductor-uri "annotationTools" version))
4738 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
4740 `((upstream-name . "annotationTools")))
4741 (build-system r-build-system)
4742 (propagated-inputs `(("r-biobase" ,r-biobase)))
4743 (home-page "https://bioconductor.org/packages/annotationTools/")
4744 (synopsis "Annotate microarrays and perform gene expression analyses")
4746 "This package provides functions to annotate microarrays, find orthologs,
4747 and integrate heterogeneous gene expression profiles using annotation and
4748 other molecular biology information available as flat file database (plain
4750 ;; Any version of the GPL.
4751 (license (list license:gpl2+))))
4753 (define-public r-allelicimbalance
4755 (name "r-allelicimbalance")
4760 (uri (bioconductor-uri "AllelicImbalance" version))
4763 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
4765 `((upstream-name . "AllelicImbalance")))
4766 (build-system r-build-system)
4768 `(("r-annotationdbi" ,r-annotationdbi)
4769 ("r-biocgenerics" ,r-biocgenerics)
4770 ("r-biostrings" ,r-biostrings)
4771 ("r-bsgenome" ,r-bsgenome)
4772 ("r-genomeinfodb" ,r-genomeinfodb)
4773 ("r-genomicalignments" ,r-genomicalignments)
4774 ("r-genomicfeatures" ,r-genomicfeatures)
4775 ("r-genomicranges" ,r-genomicranges)
4776 ("r-gridextra" ,r-gridextra)
4778 ("r-iranges" ,r-iranges)
4779 ("r-lattice" ,r-lattice)
4780 ("r-latticeextra" ,r-latticeextra)
4782 ("r-rsamtools" ,r-rsamtools)
4783 ("r-s4vectors" ,r-s4vectors)
4784 ("r-seqinr" ,r-seqinr)
4785 ("r-summarizedexperiment" ,r-summarizedexperiment)
4786 ("r-variantannotation" ,r-variantannotation)))
4788 `(("r-knitr" ,r-knitr)))
4789 (home-page "https://github.com/pappewaio/AllelicImbalance")
4790 (synopsis "Investigate allele-specific expression")
4792 "This package provides a framework for allele-specific expression
4793 investigation using RNA-seq data.")
4794 (license license:gpl3)))
4796 (define-public r-aucell
4803 (uri (bioconductor-uri "AUCell" version))
4806 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
4807 (properties `((upstream-name . "AUCell")))
4808 (build-system r-build-system)
4810 `(("r-biocgenerics" ,r-biocgenerics)
4811 ("r-data-table" ,r-data-table)
4812 ("r-gseabase" ,r-gseabase)
4813 ("r-mixtools" ,r-mixtools)
4814 ("r-r-utils" ,r-r-utils)
4815 ("r-s4vectors" ,r-s4vectors)
4816 ("r-shiny" ,r-shiny)
4817 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4819 `(("r-knitr" ,r-knitr)))
4820 (home-page "https://bioconductor.org/packages/AUCell/")
4821 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4823 "AUCell identifies cells with active gene sets (e.g. signatures,
4824 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4825 Under the Curve} (AUC) to calculate whether a critical subset of the input
4826 gene set is enriched within the expressed genes for each cell. The
4827 distribution of AUC scores across all the cells allows exploring the relative
4828 expression of the signature. Since the scoring method is ranking-based,
4829 AUCell is independent of the gene expression units and the normalization
4830 procedure. In addition, since the cells are evaluated individually, it can
4831 easily be applied to bigger datasets, subsetting the expression matrix if
4833 (license license:gpl3)))
4835 (define-public r-ebimage
4842 (uri (bioconductor-uri "EBImage" version))
4845 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
4846 (properties `((upstream-name . "EBImage")))
4847 (build-system r-build-system)
4849 `(("r-abind" ,r-abind)
4850 ("r-biocgenerics" ,r-biocgenerics)
4851 ("r-fftwtools" ,r-fftwtools)
4852 ("r-htmltools" ,r-htmltools)
4853 ("r-htmlwidgets" ,r-htmlwidgets)
4855 ("r-locfit" ,r-locfit)
4857 ("r-rcurl" ,r-rcurl)
4858 ("r-tiff" ,r-tiff)))
4860 `(("r-knitr" ,r-knitr))) ; for vignettes
4861 (home-page "https://github.com/aoles/EBImage")
4862 (synopsis "Image processing and analysis toolbox for R")
4864 "EBImage provides general purpose functionality for image processing and
4865 analysis. In the context of (high-throughput) microscopy-based cellular
4866 assays, EBImage offers tools to segment cells and extract quantitative
4867 cellular descriptors. This allows the automation of such tasks using the R
4868 programming language and facilitates the use of other tools in the R
4869 environment for signal processing, statistical modeling, machine learning and
4870 visualization with image data.")
4871 ;; Any version of the LGPL.
4872 (license license:lgpl2.1+)))
4874 (define-public r-yamss
4881 (uri (bioconductor-uri "yamss" version))
4884 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
4885 (build-system r-build-system)
4887 `(("r-biocgenerics" ,r-biocgenerics)
4888 ("r-data-table" ,r-data-table)
4889 ("r-ebimage" ,r-ebimage)
4890 ("r-iranges" ,r-iranges)
4891 ("r-limma" ,r-limma)
4892 ("r-matrix" ,r-matrix)
4894 ("r-s4vectors" ,r-s4vectors)
4895 ("r-summarizedexperiment"
4896 ,r-summarizedexperiment)))
4898 `(("r-knitr" ,r-knitr)))
4899 (home-page "https://github.com/hansenlab/yamss")
4900 (synopsis "Tools for high-throughput metabolomics")
4902 "This package provides tools to analyze and visualize high-throughput
4903 metabolomics data acquired using chromatography-mass spectrometry. These tools
4904 preprocess data in a way that enables reliable and powerful differential
4906 (license license:artistic2.0)))
4908 (define-public r-gtrellis
4915 (uri (bioconductor-uri "gtrellis" version))
4918 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
4919 (build-system r-build-system)
4921 `(("r-circlize" ,r-circlize)
4922 ("r-genomicranges" ,r-genomicranges)
4923 ("r-getoptlong" ,r-getoptlong)
4924 ("r-iranges" ,r-iranges)))
4926 `(("r-knitr" ,r-knitr)))
4927 (home-page "https://github.com/jokergoo/gtrellis")
4928 (synopsis "Genome level Trellis layout")
4930 "Genome level Trellis graph visualizes genomic data conditioned by
4931 genomic categories (e.g. chromosomes). For each genomic category, multiple
4932 dimensional data which are represented as tracks describe different features
4933 from different aspects. This package provides high flexibility to arrange
4934 genomic categories and to add self-defined graphics in the plot.")
4935 (license license:expat)))
4937 (define-public r-somaticsignatures
4939 (name "r-somaticsignatures")
4944 (uri (bioconductor-uri "SomaticSignatures" version))
4947 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
4949 `((upstream-name . "SomaticSignatures")))
4950 (build-system r-build-system)
4952 `(("r-biobase" ,r-biobase)
4953 ("r-biostrings" ,r-biostrings)
4954 ("r-genomeinfodb" ,r-genomeinfodb)
4955 ("r-genomicranges" ,r-genomicranges)
4956 ("r-ggbio" ,r-ggbio)
4957 ("r-ggplot2" ,r-ggplot2)
4958 ("r-iranges" ,r-iranges)
4960 ("r-pcamethods" ,r-pcamethods)
4961 ("r-proxy" ,r-proxy)
4962 ("r-reshape2" ,r-reshape2)
4963 ("r-s4vectors" ,r-s4vectors)
4964 ("r-variantannotation" ,r-variantannotation)))
4966 `(("r-knitr" ,r-knitr)))
4967 (home-page "https://github.com/juliangehring/SomaticSignatures")
4968 (synopsis "Somatic signatures")
4970 "This package identifies mutational signatures of @dfn{single nucleotide
4971 variants} (SNVs). It provides a infrastructure related to the methodology
4972 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4973 decomposition algorithms.")
4974 (license license:expat)))
4976 (define-public r-yapsa
4983 (uri (bioconductor-uri "YAPSA" version))
4986 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
4987 (properties `((upstream-name . "YAPSA")))
4988 (build-system r-build-system)
4990 `(("r-biostrings" ,r-biostrings)
4991 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4992 ("r-circlize" ,r-circlize)
4993 ("r-complexheatmap" ,r-complexheatmap)
4994 ("r-corrplot" ,r-corrplot)
4995 ("r-dendextend" ,r-dendextend)
4996 ("r-doparallel" ,r-doparallel)
4997 ("r-dplyr" ,r-dplyr)
4998 ("r-genomeinfodb" ,r-genomeinfodb)
4999 ("r-genomicranges" ,r-genomicranges)
5000 ("r-getoptlong" ,r-getoptlong)
5001 ("r-ggbeeswarm" ,r-ggbeeswarm)
5002 ("r-ggplot2" ,r-ggplot2)
5003 ("r-gridextra" ,r-gridextra)
5004 ("r-gtrellis" ,r-gtrellis)
5005 ("r-keggrest" ,r-keggrest)
5006 ("r-limsolve" ,r-limsolve)
5007 ("r-magrittr" ,r-magrittr)
5008 ("r-pmcmr" ,r-pmcmr)
5009 ("r-pracma" ,r-pracma)
5010 ("r-reshape2" ,r-reshape2)
5011 ("r-somaticsignatures" ,r-somaticsignatures)
5012 ("r-variantannotation" ,r-variantannotation)))
5014 `(("r-knitr" ,r-knitr)))
5015 (home-page "https://bioconductor.org/packages/YAPSA/")
5016 (synopsis "Yet another package for signature analysis")
5018 "This package provides functions and routines useful in the analysis of
5019 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5020 functions to perform a signature analysis with known signatures and a
5021 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5023 (license license:gpl3)))
5025 (define-public r-gcrma
5032 (uri (bioconductor-uri "gcrma" version))
5035 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5036 (build-system r-build-system)
5038 `(("r-affy" ,r-affy)
5039 ("r-affyio" ,r-affyio)
5040 ("r-biobase" ,r-biobase)
5041 ("r-biocmanager" ,r-biocmanager)
5042 ("r-biostrings" ,r-biostrings)
5043 ("r-xvector" ,r-xvector)))
5044 (home-page "https://bioconductor.org/packages/gcrma/")
5045 (synopsis "Background adjustment using sequence information")
5047 "Gcrma adjusts for background intensities in Affymetrix array data which
5048 include optical noise and @dfn{non-specific binding} (NSB). The main function
5049 @code{gcrma} converts background adjusted probe intensities to expression
5050 measures using the same normalization and summarization methods as a
5051 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5052 to estimate probe affinity to NSB. The sequence information is summarized in
5053 a more complex way than the simple GC content. Instead, the base types (A, T,
5054 G or C) at each position along the probe determine the affinity of each probe.
5055 The parameters of the position-specific base contributions to the probe
5056 affinity is estimated in an NSB experiment in which only NSB but no
5057 gene-specific binding is expected.")
5058 ;; Any version of the LGPL
5059 (license license:lgpl2.1+)))
5061 (define-public r-simpleaffy
5063 (name "r-simpleaffy")
5068 (uri (bioconductor-uri "simpleaffy" version))
5071 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5072 (build-system r-build-system)
5074 `(("r-affy" ,r-affy)
5075 ("r-biobase" ,r-biobase)
5076 ("r-biocgenerics" ,r-biocgenerics)
5077 ("r-gcrma" ,r-gcrma)
5078 ("r-genefilter" ,r-genefilter)))
5079 (home-page "https://bioconductor.org/packages/simpleaffy/")
5080 (synopsis "Very simple high level analysis of Affymetrix data")
5082 "This package provides high level functions for reading Affy @file{.CEL}
5083 files, phenotypic data, and then computing simple things with it, such as
5084 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5085 library. It also has some basic scatter plot functions and mechanisms for
5086 generating high resolution journal figures.")
5087 (license license:gpl2+)))
5089 (define-public r-yaqcaffy
5096 (uri (bioconductor-uri "yaqcaffy" version))
5099 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
5100 (build-system r-build-system)
5102 `(("r-simpleaffy" ,r-simpleaffy)))
5103 (home-page "https://bioconductor.org/packages/yaqcaffy/")
5104 (synopsis "Affymetrix quality control and reproducibility analysis")
5106 "This is a package that can be used for quality control of Affymetrix
5107 GeneChip expression data and reproducibility analysis of human whole genome
5108 chips with the MAQC reference datasets.")
5109 (license license:artistic2.0)))
5111 (define-public r-quantro
5118 (uri (bioconductor-uri "quantro" version))
5121 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
5122 (build-system r-build-system)
5124 `(("r-biobase" ,r-biobase)
5125 ("r-doparallel" ,r-doparallel)
5126 ("r-foreach" ,r-foreach)
5127 ("r-ggplot2" ,r-ggplot2)
5128 ("r-iterators" ,r-iterators)
5129 ("r-minfi" ,r-minfi)
5130 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5132 `(("r-knitr" ,r-knitr)))
5133 (home-page "https://bioconductor.org/packages/quantro/")
5134 (synopsis "Test for when to use quantile normalization")
5136 "This package provides a data-driven test for the assumptions of quantile
5137 normalization using raw data such as objects that inherit eSets (e.g.
5138 ExpressionSet, MethylSet). Group level information about each sample (such as
5139 Tumor / Normal status) must also be provided because the test assesses if
5140 there are global differences in the distributions between the user-defined
5142 (license license:gpl3+)))
5144 (define-public r-yarn
5151 (uri (bioconductor-uri "yarn" version))
5154 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
5155 (build-system r-build-system)
5157 `(("r-biobase" ,r-biobase)
5158 ("r-biomart" ,r-biomart)
5159 ("r-downloader" ,r-downloader)
5160 ("r-edger" ,r-edger)
5161 ("r-gplots" ,r-gplots)
5162 ("r-limma" ,r-limma)
5163 ("r-matrixstats" ,r-matrixstats)
5164 ("r-preprocesscore" ,r-preprocesscore)
5165 ("r-quantro" ,r-quantro)
5166 ("r-rcolorbrewer" ,r-rcolorbrewer)
5167 ("r-readr" ,r-readr)))
5169 `(("r-knitr" ,r-knitr)))
5170 (home-page "https://bioconductor.org/packages/yarn/")
5171 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5173 "Expedite large RNA-Seq analyses using a combination of previously
5174 developed tools. YARN is meant to make it easier for the user in performing
5175 basic mis-annotation quality control, filtering, and condition-aware
5176 normalization. YARN leverages many Bioconductor tools and statistical
5177 techniques to account for the large heterogeneity and sparsity found in very
5178 large RNA-seq experiments.")
5179 (license license:artistic2.0)))
5181 (define-public r-roar
5188 (uri (bioconductor-uri "roar" version))
5191 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
5192 (build-system r-build-system)
5194 `(("r-biocgenerics" ,r-biocgenerics)
5195 ("r-genomeinfodb" ,r-genomeinfodb)
5196 ("r-genomicalignments" ,r-genomicalignments)
5197 ("r-genomicranges" ,r-genomicranges)
5198 ("r-iranges" ,r-iranges)
5199 ("r-rtracklayer" ,r-rtracklayer)
5200 ("r-s4vectors" ,r-s4vectors)
5201 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5202 (home-page "https://github.com/vodkatad/roar/")
5203 (synopsis "Identify differential APA usage from RNA-seq alignments")
5205 "This package provides tools for identifying preferential usage of APA
5206 sites, comparing two biological conditions, starting from known alternative
5207 sites and alignments obtained from standard RNA-seq experiments.")
5208 (license license:gpl3)))
5210 (define-public r-xbseq
5217 (uri (bioconductor-uri "XBSeq" version))
5220 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
5221 (properties `((upstream-name . "XBSeq")))
5222 (build-system r-build-system)
5224 `(("r-biobase" ,r-biobase)
5225 ("r-deseq2" ,r-deseq2)
5226 ("r-dplyr" ,r-dplyr)
5227 ("r-ggplot2" ,r-ggplot2)
5228 ("r-locfit" ,r-locfit)
5229 ("r-magrittr" ,r-magrittr)
5230 ("r-matrixstats" ,r-matrixstats)
5231 ("r-pracma" ,r-pracma)
5232 ("r-roar" ,r-roar)))
5234 `(("r-knitr" ,r-knitr)))
5235 (home-page "https://github.com/Liuy12/XBSeq")
5236 (synopsis "Test for differential expression for RNA-seq data")
5238 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5239 expression} (DE), where a statistical model was established based on the
5240 assumption that observed signals are the convolution of true expression
5241 signals and sequencing noises. The mapped reads in non-exonic regions are
5242 considered as sequencing noises, which follows a Poisson distribution. Given
5243 measurable observed signal and background noise from RNA-seq data, true
5244 expression signals, assuming governed by the negative binomial distribution,
5245 can be delineated and thus the accurate detection of differential expressed
5247 (license license:gpl3+)))
5249 (define-public r-massspecwavelet
5251 (name "r-massspecwavelet")
5256 (uri (bioconductor-uri "MassSpecWavelet" version))
5259 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
5261 `((upstream-name . "MassSpecWavelet")))
5262 (build-system r-build-system)
5264 `(("r-waveslim" ,r-waveslim)))
5265 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5266 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5268 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5269 data mainly through the use of wavelet transforms. It supports peak detection
5270 based on @dfn{Continuous Wavelet Transform} (CWT).")
5271 (license license:lgpl2.0+)))
5273 (define-public r-xcms
5280 (uri (bioconductor-uri "xcms" version))
5283 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
5284 (build-system r-build-system)
5286 `(("r-biobase" ,r-biobase)
5287 ("r-biocgenerics" ,r-biocgenerics)
5288 ("r-biocparallel" ,r-biocparallel)
5289 ("r-iranges" ,r-iranges)
5290 ("r-lattice" ,r-lattice)
5291 ("r-massspecwavelet" ,r-massspecwavelet)
5292 ("r-mscoreutils" ,r-mscoreutils)
5293 ("r-msnbase" ,r-msnbase)
5296 ("r-protgenerics" ,r-protgenerics)
5298 ("r-rcolorbrewer" ,r-rcolorbrewer)
5299 ("r-robustbase" ,r-robustbase)
5300 ("r-s4vectors" ,r-s4vectors)
5301 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5303 `(("r-knitr" ,r-knitr)))
5304 (home-page "https://bioconductor.org/packages/xcms/")
5305 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5307 "This package provides a framework for processing and visualization of
5308 chromatographically separated and single-spectra mass spectral data. It
5309 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5310 data for high-throughput, untargeted analyte profiling.")
5311 (license license:gpl2+)))
5313 (define-public r-wrench
5320 (uri (bioconductor-uri "Wrench" version))
5323 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
5324 (properties `((upstream-name . "Wrench")))
5325 (build-system r-build-system)
5327 `(("r-limma" ,r-limma)
5328 ("r-locfit" ,r-locfit)
5329 ("r-matrixstats" ,r-matrixstats)))
5331 `(("r-knitr" ,r-knitr)))
5332 (home-page "https://github.com/HCBravoLab/Wrench")
5333 (synopsis "Wrench normalization for sparse count data")
5335 "Wrench is a package for normalization sparse genomic count data, like
5336 that arising from 16s metagenomic surveys.")
5337 (license license:artistic2.0)))
5339 (define-public r-wiggleplotr
5341 (name "r-wiggleplotr")
5346 (uri (bioconductor-uri "wiggleplotr" version))
5349 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
5350 (build-system r-build-system)
5352 `(("r-assertthat" ,r-assertthat)
5353 ("r-cowplot" ,r-cowplot)
5354 ("r-dplyr" ,r-dplyr)
5355 ("r-genomeinfodb" ,r-genomeinfodb)
5356 ("r-genomicranges" ,r-genomicranges)
5357 ("r-ggplot2" ,r-ggplot2)
5358 ("r-iranges" ,r-iranges)
5359 ("r-purrr" ,r-purrr)
5360 ("r-rtracklayer" ,r-rtracklayer)
5361 ("r-s4vectors" ,r-s4vectors)))
5363 `(("r-knitr" ,r-knitr)))
5364 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5365 (synopsis "Make read coverage plots from BigWig files")
5367 "This package provides tools to visualize read coverage from sequencing
5368 experiments together with genomic annotations (genes, transcripts, peaks).
5369 Introns of long transcripts can be rescaled to a fixed length for better
5370 visualization of exonic read coverage.")
5371 (license license:asl2.0)))
5373 (define-public r-widgettools
5375 (name "r-widgettools")
5380 (uri (bioconductor-uri "widgetTools" version))
5383 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
5384 (properties `((upstream-name . "widgetTools")))
5385 (build-system r-build-system)
5386 (home-page "https://bioconductor.org/packages/widgetTools/")
5387 (synopsis "Tools for creating interactive tcltk widgets")
5389 "This package contains tools to support the construction of tcltk
5391 ;; Any version of the LGPL.
5392 (license license:lgpl3+)))
5394 (define-public r-webbioc
5401 (uri (bioconductor-uri "webbioc" version))
5404 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
5405 (build-system r-build-system)
5407 `(("netpbm" ,netpbm)
5410 `(("r-affy" ,r-affy)
5411 ("r-annaffy" ,r-annaffy)
5412 ("r-biobase" ,r-biobase)
5413 ("r-biocmanager" ,r-biocmanager)
5414 ("r-gcrma" ,r-gcrma)
5415 ("r-multtest" ,r-multtest)
5416 ("r-qvalue" ,r-qvalue)
5418 (home-page "https://www.bioconductor.org/")
5419 (synopsis "Bioconductor web interface")
5421 "This package provides an integrated web interface for doing microarray
5422 analysis using several of the Bioconductor packages. It is intended to be
5423 deployed as a centralized bioinformatics resource for use by many users.
5424 Currently only Affymetrix oligonucleotide analysis is supported.")
5425 (license license:gpl2+)))
5427 (define-public r-zfpkm
5434 (uri (bioconductor-uri "zFPKM" version))
5437 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
5438 (properties `((upstream-name . "zFPKM")))
5439 (build-system r-build-system)
5441 `(("r-checkmate" ,r-checkmate)
5442 ("r-dplyr" ,r-dplyr)
5443 ("r-ggplot2" ,r-ggplot2)
5444 ("r-summarizedexperiment" ,r-summarizedexperiment)
5445 ("r-tidyr" ,r-tidyr)))
5447 `(("r-knitr" ,r-knitr)))
5448 (home-page "https://github.com/ronammar/zFPKM/")
5449 (synopsis "Functions to facilitate zFPKM transformations")
5451 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5452 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5454 (license license:gpl3)))
5456 (define-public r-rbowtie2
5463 (uri (bioconductor-uri "Rbowtie2" version))
5466 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
5467 (properties `((upstream-name . "Rbowtie2")))
5468 (build-system r-build-system)
5472 `(("r-knitr" ,r-knitr)))
5473 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5474 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5476 "This package provides an R wrapper of the popular @code{bowtie2}
5477 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5478 rapid adapter trimming, identification, and read merging.")
5479 (license license:gpl3+)))
5481 (define-public r-progeny
5488 (uri (bioconductor-uri "progeny" version))
5491 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
5492 (build-system r-build-system)
5494 `(("r-biobase" ,r-biobase)
5495 ("r-dplyr" ,r-dplyr)
5496 ("r-ggplot2" ,r-ggplot2)
5497 ("r-ggrepel" ,r-ggrepel)
5498 ("r-gridextra" ,r-gridextra)
5499 ("r-tidyr" ,r-tidyr)))
5501 `(("r-knitr" ,r-knitr)))
5502 (home-page "https://github.com/saezlab/progeny")
5503 (synopsis "Pathway responsive gene activity inference")
5505 "This package provides a function to infer pathway activity from gene
5506 expression. It contains the linear model inferred in the publication
5507 \"Perturbation-response genes reveal signaling footprints in cancer gene
5509 (license license:asl2.0)))
5511 (define-public r-arrmnormalization
5513 (name "r-arrmnormalization")
5518 (uri (bioconductor-uri "ARRmNormalization" version))
5521 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
5523 `((upstream-name . "ARRmNormalization")))
5524 (build-system r-build-system)
5525 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5526 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5527 (synopsis "Adaptive robust regression normalization for methylation data")
5529 "This is a package to perform the @dfn{Adaptive Robust Regression
5530 method} (ARRm) for the normalization of methylation data from the Illumina
5531 Infinium HumanMethylation 450k assay.")
5532 (license license:artistic2.0)))
5534 (define-public r-biocfilecache
5536 (name "r-biocfilecache")
5541 (uri (bioconductor-uri "BiocFileCache" version))
5544 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
5545 (properties `((upstream-name . "BiocFileCache")))
5546 (build-system r-build-system)
5548 `(("r-curl" ,r-curl)
5550 ("r-dbplyr" ,r-dbplyr)
5551 ("r-dplyr" ,r-dplyr)
5553 ("r-rappdirs" ,r-rappdirs)
5554 ("r-rsqlite" ,r-rsqlite)))
5556 `(("r-knitr" ,r-knitr)))
5557 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5558 (synopsis "Manage files across sessions")
5560 "This package creates a persistent on-disk cache of files that the user
5561 can add, update, and retrieve. It is useful for managing resources (such as
5562 custom Txdb objects) that are costly or difficult to create, web resources,
5563 and data files used across sessions.")
5564 (license license:artistic2.0)))
5566 (define-public r-iclusterplus
5568 (name "r-iclusterplus")
5573 (uri (bioconductor-uri "iClusterPlus" version))
5576 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
5577 (properties `((upstream-name . "iClusterPlus")))
5578 (build-system r-build-system)
5579 (native-inputs `(("gfortran" ,gfortran)))
5580 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5581 (synopsis "Integrative clustering of multi-type genomic data")
5583 "iClusterPlus is developed for integrative clustering analysis of
5584 multi-type genomic data and is an enhanced version of iCluster proposed and
5585 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5586 from the experiments where biological samples (e.g. tumor samples) are
5587 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5588 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5589 on. In the iClusterPlus model, binary observations such as somatic mutation
5590 are modeled as Binomial processes; categorical observations such as copy
5591 number states are realizations of Multinomial random variables; counts are
5592 modeled as Poisson random processes; and continuous measures are modeled by
5593 Gaussian distributions.")
5594 (license license:gpl2+)))
5596 (define-public r-rbowtie
5603 (uri (bioconductor-uri "Rbowtie" version))
5606 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
5607 (properties `((upstream-name . "Rbowtie")))
5608 (build-system r-build-system)
5612 `(("r-knitr" ,r-knitr)))
5613 (home-page "https://bioconductor.org/packages/Rbowtie/")
5614 (synopsis "R bowtie wrapper")
5616 "This package provides an R wrapper around the popular bowtie short read
5617 aligner and around SpliceMap, a de novo splice junction discovery and
5619 (license license:artistic2.0)))
5621 (define-public r-sgseq
5628 (uri (bioconductor-uri "SGSeq" version))
5631 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
5632 (properties `((upstream-name . "SGSeq")))
5633 (build-system r-build-system)
5635 `(("r-annotationdbi" ,r-annotationdbi)
5636 ("r-biocgenerics" ,r-biocgenerics)
5637 ("r-biostrings" ,r-biostrings)
5638 ("r-genomeinfodb" ,r-genomeinfodb)
5639 ("r-genomicalignments" ,r-genomicalignments)
5640 ("r-genomicfeatures" ,r-genomicfeatures)
5641 ("r-genomicranges" ,r-genomicranges)
5642 ("r-igraph" ,r-igraph)
5643 ("r-iranges" ,r-iranges)
5644 ("r-rsamtools" ,r-rsamtools)
5645 ("r-rtracklayer" ,r-rtracklayer)
5646 ("r-runit" ,r-runit)
5647 ("r-s4vectors" ,r-s4vectors)
5648 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5650 `(("r-knitr" ,r-knitr)))
5651 (home-page "https://bioconductor.org/packages/SGSeq/")
5652 (synopsis "Splice event prediction and quantification from RNA-seq data")
5654 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5655 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5656 represented as a splice graph, which can be obtained from existing annotation
5657 or predicted from the mapped sequence reads. Splice events are identified
5658 from the graph and are quantified locally using structurally compatible reads
5659 at the start or end of each splice variant. The software includes functions
5660 for splice event prediction, quantification, visualization and
5662 (license license:artistic2.0)))
5664 (define-public r-rhisat2
5671 (uri (bioconductor-uri "Rhisat2" version))
5674 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
5675 (properties `((upstream-name . "Rhisat2")))
5676 (build-system r-build-system)
5679 (modify-phases %standard-phases
5680 (add-after 'unpack 'make-reproducible
5682 (substitute* "src/Makefile"
5683 (("`hostname`") "guix")
5685 ;; Avoid shelling out to "which".
5686 (("^CC =.*") (which "gcc"))
5687 (("^CPP =.*") (which "g++")))
5690 `(("r-genomicfeatures" ,r-genomicfeatures)
5691 ("r-genomicranges" ,r-genomicranges)
5692 ("r-sgseq" ,r-sgseq)))
5694 `(("r-knitr" ,r-knitr)))
5695 (home-page "https://github.com/fmicompbio/Rhisat2")
5696 (synopsis "R Wrapper for HISAT2 sequence aligner")
5698 "This package provides an R interface to the HISAT2 spliced short-read
5699 aligner by Kim et al. (2015). The package contains wrapper functions to
5700 create a genome index and to perform the read alignment to the generated
5702 (license license:gpl3)))
5704 (define-public r-quasr
5711 (uri (bioconductor-uri "QuasR" version))
5714 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
5715 (properties `((upstream-name . "QuasR")))
5716 (build-system r-build-system)
5718 `(("r-annotationdbi" ,r-annotationdbi)
5719 ("r-biobase" ,r-biobase)
5720 ("r-biocgenerics" ,r-biocgenerics)
5721 ("r-biocmanager" ,r-biocmanager)
5722 ("r-biocparallel" ,r-biocparallel)
5723 ("r-biostrings" ,r-biostrings)
5724 ("r-bsgenome" ,r-bsgenome)
5725 ("r-genomeinfodb" ,r-genomeinfodb)
5726 ("r-genomicalignments" ,r-genomicalignments)
5727 ("r-genomicfeatures" ,r-genomicfeatures)
5728 ("r-genomicfiles" ,r-genomicfiles)
5729 ("r-genomicranges" ,r-genomicranges)
5730 ("r-iranges" ,r-iranges)
5731 ("r-rbowtie" ,r-rbowtie)
5732 ("r-rhisat2" ,r-rhisat2)
5733 ("r-rhtslib" ,r-rhtslib)
5734 ("r-rsamtools" ,r-rsamtools)
5735 ("r-rtracklayer" ,r-rtracklayer)
5736 ("r-s4vectors" ,r-s4vectors)
5737 ("r-shortread" ,r-shortread)))
5739 `(("r-knitr" ,r-knitr)))
5740 (home-page "https://bioconductor.org/packages/QuasR/")
5741 (synopsis "Quantify and annotate short reads in R")
5743 "This package provides a framework for the quantification and analysis of
5744 short genomic reads. It covers a complete workflow starting from raw sequence
5745 reads, over creation of alignments and quality control plots, to the
5746 quantification of genomic regions of interest.")
5747 (license license:gpl2)))
5749 (define-public r-rqc
5756 (uri (bioconductor-uri "Rqc" version))
5759 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
5760 (properties `((upstream-name . "Rqc")))
5761 (build-system r-build-system)
5763 `(("r-biocgenerics" ,r-biocgenerics)
5764 ("r-biocparallel" ,r-biocparallel)
5765 ("r-biocstyle" ,r-biocstyle)
5766 ("r-biostrings" ,r-biostrings)
5767 ("r-biovizbase" ,r-biovizbase)
5768 ("r-genomicalignments" ,r-genomicalignments)
5769 ("r-genomicfiles" ,r-genomicfiles)
5770 ("r-ggplot2" ,r-ggplot2)
5771 ("r-iranges" ,r-iranges)
5772 ("r-knitr" ,r-knitr)
5773 ("r-markdown" ,r-markdown)
5776 ("r-reshape2" ,r-reshape2)
5777 ("r-rsamtools" ,r-rsamtools)
5778 ("r-s4vectors" ,r-s4vectors)
5779 ("r-shiny" ,r-shiny)
5780 ("r-shortread" ,r-shortread)))
5782 `(("r-knitr" ,r-knitr)))
5783 (home-page "https://github.com/labbcb/Rqc")
5784 (synopsis "Quality control tool for high-throughput sequencing data")
5786 "Rqc is an optimized tool designed for quality control and assessment of
5787 high-throughput sequencing data. It performs parallel processing of entire
5788 files and produces a report which contains a set of high-resolution
5790 (license license:gpl2+)))
5792 (define-public r-birewire
5799 (uri (bioconductor-uri "BiRewire" version))
5802 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
5803 (properties `((upstream-name . "BiRewire")))
5804 (build-system r-build-system)
5806 `(("r-igraph" ,r-igraph)
5807 ("r-matrix" ,r-matrix)
5809 ("r-tsne" ,r-tsne)))
5810 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5811 (synopsis "Tools for randomization of bipartite graphs")
5813 "This package provides functions for bipartite network rewiring through N
5814 consecutive switching steps and for the computation of the minimal number of
5815 switching steps to be performed in order to maximise the dissimilarity with
5816 respect to the original network. It includes functions for the analysis of
5817 the introduced randomness across the switching steps and several other
5818 routines to analyse the resulting networks and their natural projections.")
5819 (license license:gpl3)))
5821 (define-public r-birta
5828 (uri (bioconductor-uri "birta" version))
5831 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5832 (build-system r-build-system)
5834 `(("r-biobase" ,r-biobase)
5835 ("r-limma" ,r-limma)
5836 ("r-mass" ,r-mass)))
5837 (home-page "https://bioconductor.org/packages/birta")
5838 (synopsis "Bayesian inference of regulation of transcriptional activity")
5840 "Expression levels of mRNA molecules are regulated by different
5841 processes, comprising inhibition or activation by transcription factors and
5842 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5843 Inference of Regulation of Transcriptional Activity) uses the regulatory
5844 networks of transcription factors and miRNAs together with mRNA and miRNA
5845 expression data to predict switches in regulatory activity between two
5846 conditions. A Bayesian network is used to model the regulatory structure and
5847 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5848 (license license:gpl2+)))
5850 (define-public r-multidataset
5852 (name "r-multidataset")
5857 (uri (bioconductor-uri "MultiDataSet" version))
5860 "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w"))))
5861 (properties `((upstream-name . "MultiDataSet")))
5862 (build-system r-build-system)
5864 `(("r-biobase" ,r-biobase)
5865 ("r-biocgenerics" ,r-biocgenerics)
5866 ("r-genomicranges" ,r-genomicranges)
5867 ("r-ggplot2" ,r-ggplot2)
5868 ("r-ggrepel" ,r-ggrepel)
5869 ("r-iranges" ,r-iranges)
5870 ("r-limma" ,r-limma)
5871 ("r-qqman" ,r-qqman)
5872 ("r-s4vectors" ,r-s4vectors)
5873 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5875 `(("r-knitr" ,r-knitr)))
5876 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5877 (synopsis "Implementation of MultiDataSet and ResultSet")
5879 "This package provides an implementation of the BRGE's (Bioinformatic
5880 Research Group in Epidemiology from Center for Research in Environmental
5881 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5882 integrating multi omics data sets and ResultSet is a container for omics
5883 results. This package contains base classes for MEAL and rexposome
5885 (license license:expat)))
5887 (define-public r-ropls
5894 (uri (bioconductor-uri "ropls" version))
5897 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
5898 (build-system r-build-system)
5900 `(("r-biobase" ,r-biobase)
5901 ("r-multidataset" ,r-multidataset)))
5903 `(("r-knitr" ,r-knitr))) ; for vignettes
5904 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5905 (synopsis "Multivariate analysis and feature selection of omics data")
5907 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5908 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5909 regression, classification, and feature selection of omics data where the
5910 number of variables exceeds the number of samples and with multicollinearity
5911 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5912 separately model the variation correlated (predictive) to the factor of
5913 interest and the uncorrelated (orthogonal) variation. While performing
5914 similarly to PLS, OPLS facilitates interpretation.
5916 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5917 analysis and feature selection of omics data. In addition to scores, loadings
5918 and weights plots, the package provides metrics and graphics to determine the
5919 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5920 validity of the model by permutation testing, detect outliers, and perform
5921 feature selection (e.g. with Variable Importance in Projection or regression
5923 (license license:cecill)))
5925 (define-public r-biosigner
5927 (name "r-biosigner")
5932 (uri (bioconductor-uri "biosigner" version))
5935 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
5936 (build-system r-build-system)
5938 `(("r-biobase" ,r-biobase)
5939 ("r-e1071" ,r-e1071)
5940 ("r-multidataset" ,r-multidataset)
5941 ("r-randomforest" ,r-randomforest)
5942 ("r-ropls" ,r-ropls)))
5944 `(("r-knitr" ,r-knitr)))
5945 (home-page "https://bioconductor.org/packages/biosigner/")
5946 (synopsis "Signature discovery from omics data")
5948 "Feature selection is critical in omics data analysis to extract
5949 restricted and meaningful molecular signatures from complex and high-dimension
5950 data, and to build robust classifiers. This package implements a method to
5951 assess the relevance of the variables for the prediction performances of the
5952 classifier. The approach can be run in parallel with the PLS-DA, Random
5953 Forest, and SVM binary classifiers. The signatures and the corresponding
5954 'restricted' models are returned, enabling future predictions on new
5956 (license license:cecill)))
5958 (define-public r-annotatr
5965 (uri (bioconductor-uri "annotatr" version))
5968 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
5969 (build-system r-build-system)
5971 `(("r-annotationdbi" ,r-annotationdbi)
5972 ("r-annotationhub" ,r-annotationhub)
5973 ("r-dplyr" ,r-dplyr)
5974 ("r-genomeinfodb" ,r-genomeinfodb)
5975 ("r-genomicfeatures" ,r-genomicfeatures)
5976 ("r-genomicranges" ,r-genomicranges)
5977 ("r-ggplot2" ,r-ggplot2)
5978 ("r-iranges" ,r-iranges)
5979 ("r-readr" ,r-readr)
5980 ("r-regioner" ,r-regioner)
5981 ("r-reshape2" ,r-reshape2)
5982 ("r-rtracklayer" ,r-rtracklayer)
5983 ("r-s4vectors" ,r-s4vectors)))
5985 `(("r-knitr" ,r-knitr)))
5986 (home-page "https://bioconductor.org/packages/annotatr/")
5987 (synopsis "Annotation of genomic regions to genomic annotations")
5989 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5990 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5991 to investigate the intersecting genomic annotations. Such annotations include
5992 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5993 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5994 enhancers. The annotatr package provides an easy way to summarize and
5995 visualize the intersection of genomic sites/regions with genomic
5997 (license license:gpl3)))
5999 (define-public r-rsubread
6006 (uri (bioconductor-uri "Rsubread" version))
6009 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
6010 (properties `((upstream-name . "Rsubread")))
6011 (build-system r-build-system)
6012 (inputs `(("zlib" ,zlib)))
6014 `(("r-matrix" ,r-matrix)))
6015 (home-page "https://bioconductor.org/packages/Rsubread/")
6016 (synopsis "Subread sequence alignment and counting for R")
6018 "This package provides tools for alignment, quantification and analysis
6019 of second and third generation sequencing data. It includes functionality for
6020 read mapping, read counting, SNP calling, structural variant detection and
6021 gene fusion discovery. It can be applied to all major sequencing techologies
6022 and to both short and long sequence reads.")
6023 (license license:gpl3)))
6025 (define-public r-flowutils
6027 (name "r-flowutils")
6032 (uri (bioconductor-uri "flowUtils" version))
6035 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6036 (properties `((upstream-name . "flowUtils")))
6037 (build-system r-build-system)
6039 `(("r-biobase" ,r-biobase)
6040 ("r-corpcor" ,r-corpcor)
6041 ("r-flowcore" ,r-flowcore)
6042 ("r-graph" ,r-graph)
6043 ("r-runit" ,r-runit)
6045 (home-page "https://github.com/jspidlen/flowUtils")
6046 (synopsis "Utilities for flow cytometry")
6048 "This package provides utilities for flow cytometry data.")
6049 (license license:artistic2.0)))
6051 (define-public r-consensusclusterplus
6053 (name "r-consensusclusterplus")
6058 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6061 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6063 `((upstream-name . "ConsensusClusterPlus")))
6064 (build-system r-build-system)
6067 ("r-biobase" ,r-biobase)
6068 ("r-cluster" ,r-cluster)))
6069 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6070 (synopsis "Clustering algorithm")
6072 "This package provides an implementation of an algorithm for determining
6073 cluster count and membership by stability evidence in unsupervised analysis.")
6074 (license license:gpl2)))
6076 (define-public r-cytolib
6083 (uri (bioconductor-uri "cytolib" version))
6086 "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw"))))
6087 (properties `((upstream-name . "cytolib")))
6088 (build-system r-build-system)
6091 (modify-phases %standard-phases
6092 (add-after 'unpack 'fix-linking
6094 (substitute* "src/Makevars.in"
6095 ;; This is to avoid having a plain directory on the list of
6096 ;; libraries to link.
6097 (("\\(RHDF5_LIBS\\)" match)
6098 (string-append match "/libhdf5.a")))
6101 `(("r-knitr" ,r-knitr)
6102 ("pkg-config" ,pkg-config)))
6106 ("r-rcpparmadillo" ,r-rcpparmadillo)
6107 ("r-rcppparallel" ,r-rcppparallel)
6108 ("r-rhdf5lib" ,r-rhdf5lib)
6109 ("r-rprotobuflib" ,r-rprotobuflib)))
6110 (home-page "https://bioconductor.org/packages/cytolib/")
6111 (synopsis "C++ infrastructure for working with gated cytometry")
6113 "This package provides the core data structure and API to represent and
6114 interact with gated cytometry data.")
6115 (license license:artistic2.0)))
6117 (define-public r-flowcore
6124 (uri (bioconductor-uri "flowCore" version))
6127 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
6128 (properties `((upstream-name . "flowCore")))
6129 (build-system r-build-system)
6132 ("r-biobase" ,r-biobase)
6133 ("r-biocgenerics" ,r-biocgenerics)
6134 ("r-cytolib" ,r-cytolib)
6135 ("r-matrixstats" ,r-matrixstats)
6137 ("r-rcpparmadillo" ,r-rcpparmadillo)
6138 ("r-rprotobuflib" ,r-rprotobuflib)
6139 ("r-s4vectors" ,r-s4vectors)))
6141 `(("r-knitr" ,r-knitr)))
6142 (home-page "https://bioconductor.org/packages/flowCore")
6143 (synopsis "Basic structures for flow cytometry data")
6145 "This package provides S4 data structures and basic functions to deal
6146 with flow cytometry data.")
6147 (license license:artistic2.0)))
6149 (define-public r-flowmeans
6151 (name "r-flowmeans")
6156 (uri (bioconductor-uri "flowMeans" version))
6159 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
6160 (properties `((upstream-name . "flowMeans")))
6161 (build-system r-build-system)
6163 `(("r-biobase" ,r-biobase)
6164 ("r-feature" ,r-feature)
6165 ("r-flowcore" ,r-flowcore)
6166 ("r-rrcov" ,r-rrcov)))
6167 (home-page "https://bioconductor.org/packages/flowMeans")
6168 (synopsis "Non-parametric flow cytometry data gating")
6170 "This package provides tools to identify cell populations in Flow
6171 Cytometry data using non-parametric clustering and segmented-regression-based
6172 change point detection.")
6173 (license license:artistic2.0)))
6175 (define-public r-ncdfflow
6182 (uri (bioconductor-uri "ncdfFlow" version))
6185 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
6186 (properties `((upstream-name . "ncdfFlow")))
6187 (build-system r-build-system)
6190 (modify-phases %standard-phases
6191 (add-after 'unpack 'fix-linking
6193 (substitute* "src/Makevars"
6194 ;; This is to avoid having a plain directory on the list of
6195 ;; libraries to link.
6196 (("\\(RHDF5_LIBS\\)" match)
6197 (string-append match "/libhdf5.a")))
6201 ("r-biobase" ,r-biobase)
6202 ("r-biocgenerics" ,r-biocgenerics)
6203 ("r-flowcore" ,r-flowcore)
6205 ("r-rcpparmadillo" ,r-rcpparmadillo)
6206 ("r-rhdf5lib" ,r-rhdf5lib)
6207 ("r-zlibbioc" ,r-zlibbioc)))
6209 `(("r-knitr" ,r-knitr)))
6210 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6211 (synopsis "HDF5 based storage for flow cytometry data")
6213 "This package provides HDF5 storage based methods and functions for
6214 manipulation of flow cytometry data.")
6215 (license license:artistic2.0)))
6217 (define-public r-ggcyto
6224 (uri (bioconductor-uri "ggcyto" version))
6227 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
6228 (properties `((upstream-name . "ggcyto")))
6229 (build-system r-build-system)
6231 `(("r-data-table" ,r-data-table)
6232 ("r-flowcore" ,r-flowcore)
6233 ("r-flowworkspace" ,r-flowworkspace)
6234 ("r-ggplot2" ,r-ggplot2)
6235 ("r-gridextra" ,r-gridextra)
6236 ("r-hexbin" ,r-hexbin)
6237 ("r-ncdfflow" ,r-ncdfflow)
6239 ("r-rcolorbrewer" ,r-rcolorbrewer)
6240 ("r-rlang" ,r-rlang)
6241 ("r-scales" ,r-scales)))
6243 `(("r-knitr" ,r-knitr)))
6244 (home-page "https://github.com/RGLab/ggcyto/issues")
6245 (synopsis "Visualize Cytometry data with ggplot")
6247 "With the dedicated fortify method implemented for @code{flowSet},
6248 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6249 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6250 and some custom layers also make it easy to add gates and population
6251 statistics to the plot.")
6252 (license license:artistic2.0)))
6254 (define-public r-flowviz
6261 (uri (bioconductor-uri "flowViz" version))
6264 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
6265 (properties `((upstream-name . "flowViz")))
6266 (build-system r-build-system)
6268 `(("r-biobase" ,r-biobase)
6269 ("r-flowcore" ,r-flowcore)
6270 ("r-hexbin" ,r-hexbin)
6271 ("r-idpmisc" ,r-idpmisc)
6272 ("r-kernsmooth" ,r-kernsmooth)
6273 ("r-lattice" ,r-lattice)
6274 ("r-latticeextra" ,r-latticeextra)
6276 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6278 `(("r-knitr" ,r-knitr)))
6279 (home-page "https://bioconductor.org/packages/flowViz/")
6280 (synopsis "Visualization for flow cytometry")
6282 "This package provides visualization tools for flow cytometry data.")
6283 (license license:artistic2.0)))
6285 (define-public r-flowclust
6287 (name "r-flowclust")
6292 (uri (bioconductor-uri "flowClust" version))
6295 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
6296 (properties `((upstream-name . "flowClust")))
6297 (build-system r-build-system)
6300 (list "--configure-args=--enable-bundled-gsl=no")))
6302 `(("r-biobase" ,r-biobase)
6303 ("r-biocgenerics" ,r-biocgenerics)
6305 ("r-corpcor" ,r-corpcor)
6306 ("r-ellipse" ,r-ellipse)
6307 ("r-flowcore" ,r-flowcore)
6308 ("r-flowviz" ,r-flowviz)
6309 ("r-graph" ,r-graph)
6310 ("r-mnormt" ,r-mnormt)))
6314 `(("pkg-config" ,pkg-config)
6315 ("r-knitr" ,r-knitr)))
6316 (home-page "https://bioconductor.org/packages/flowClust")
6317 (synopsis "Clustering for flow cytometry")
6319 "This package provides robust model-based clustering using a t-mixture
6320 model with Box-Cox transformation.")
6321 (license license:artistic2.0)))
6323 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6324 ;; make it use our protobuf package instead.
6325 (define-public r-rprotobuflib
6327 (name "r-rprotobuflib")
6332 (uri (bioconductor-uri "RProtoBufLib" version))
6335 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
6336 (properties `((upstream-name . "RProtoBufLib")))
6337 (build-system r-build-system)
6340 (modify-phases %standard-phases
6341 (add-after 'unpack 'unpack-bundled-sources
6343 (with-directory-excursion "src"
6344 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6347 `(("r-knitr" ,r-knitr)))
6348 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6349 (synopsis "C++ headers and static libraries of Protocol buffers")
6351 "This package provides the headers and static library of Protocol buffers
6352 for other R packages to compile and link against.")
6353 (license license:bsd-3)))
6355 (define-public r-flowworkspace
6357 (name "r-flowworkspace")
6362 (uri (bioconductor-uri "flowWorkspace" version))
6365 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
6366 (properties `((upstream-name . "flowWorkspace")))
6367 (build-system r-build-system)
6370 (modify-phases %standard-phases
6371 (add-after 'unpack 'fix-linking
6373 (substitute* "src/Makevars"
6374 ;; This is to avoid having a plain directory on the list of
6375 ;; libraries to link.
6376 (("\\{h5lib\\}" match)
6377 (string-append match "/libhdf5.a")))
6380 `(("r-aws-s3" ,r-aws-s3)
6381 ("r-aws-signature" ,r-aws-signature)
6383 ("r-biobase" ,r-biobase)
6384 ("r-biocgenerics" ,r-biocgenerics)
6385 ("r-cytolib" ,r-cytolib)
6386 ("r-data-table" ,r-data-table)
6387 ("r-digest" ,r-digest)
6388 ("r-dplyr" ,r-dplyr)
6389 ("r-flowcore" ,r-flowcore)
6390 ("r-ggplot2" ,r-ggplot2)
6391 ("r-graph" ,r-graph)
6392 ("r-lattice" ,r-lattice)
6393 ("r-latticeextra" ,r-latticeextra)
6394 ("r-matrixstats" ,r-matrixstats)
6395 ("r-ncdfflow" ,r-ncdfflow)
6398 ("r-rcpparmadillo" ,r-rcpparmadillo)
6399 ("r-rcppparallel" ,r-rcppparallel)
6400 ("r-rgraphviz" ,r-rgraphviz)
6401 ("r-rhdf5lib" ,r-rhdf5lib)
6402 ("r-rprotobuflib" ,r-rprotobuflib)
6403 ("r-scales" ,r-scales)
6406 `(("r-knitr" ,r-knitr)))
6407 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6408 (synopsis "Infrastructure for working with cytometry data")
6410 "This package is designed to facilitate comparison of automated gating
6411 methods against manual gating done in flowJo. This package allows you to
6412 import basic flowJo workspaces into BioConductor and replicate the gating from
6413 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6414 samples, compensation, and transformation are performed so that the output
6415 matches the flowJo analysis.")
6416 (license license:artistic2.0)))
6418 (define-public r-flowstats
6420 (name "r-flowstats")
6425 (uri (bioconductor-uri "flowStats" version))
6428 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
6429 (properties `((upstream-name . "flowStats")))
6430 (build-system r-build-system)
6432 `(("r-biobase" ,r-biobase)
6433 ("r-biocgenerics" ,r-biocgenerics)
6434 ("r-cluster" ,r-cluster)
6436 ("r-flowcore" ,r-flowcore)
6437 ("r-flowviz" ,r-flowviz)
6438 ("r-flowworkspace" ,r-flowworkspace)
6439 ("r-kernsmooth" ,r-kernsmooth)
6441 ("r-lattice" ,r-lattice)
6443 ("r-ncdfflow" ,r-ncdfflow)
6444 ("r-rcolorbrewer" ,r-rcolorbrewer)
6445 ("r-rrcov" ,r-rrcov)))
6446 (home-page "http://www.github.com/RGLab/flowStats")
6447 (synopsis "Statistical methods for the analysis of flow cytometry data")
6449 "This package provides methods and functionality to analyze flow data
6450 that is beyond the basic infrastructure provided by the @code{flowCore}
6452 (license license:artistic2.0)))
6454 (define-public r-opencyto
6461 (uri (bioconductor-uri "openCyto" version))
6464 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
6465 (properties `((upstream-name . "openCyto")))
6466 (build-system r-build-system)
6468 `(("r-biobase" ,r-biobase)
6469 ("r-biocgenerics" ,r-biocgenerics)
6471 ("r-data-table" ,r-data-table)
6472 ("r-flowclust" ,r-flowclust)
6473 ("r-flowcore" ,r-flowcore)
6474 ("r-flowstats" ,r-flowstats)
6475 ("r-flowviz" ,r-flowviz)
6476 ("r-flowworkspace" ,r-flowworkspace)
6477 ("r-graph" ,r-graph)
6478 ("r-gtools" ,r-gtools)
6480 ("r-lattice" ,r-lattice)
6482 ("r-ncdfflow" ,r-ncdfflow)
6484 ("r-r-utils" ,r-r-utils)
6486 ("r-rcolorbrewer" ,r-rcolorbrewer)
6488 ("r-rrcov" ,r-rrcov)))
6490 `(("r-knitr" ,r-knitr)))
6491 (home-page "https://bioconductor.org/packages/openCyto")
6492 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6494 "This package is designed to facilitate the automated gating methods in a
6495 sequential way to mimic the manual gating strategy.")
6496 (license license:artistic2.0)))
6498 (define-public r-cytoml
6505 (uri (bioconductor-uri "CytoML" version))
6508 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
6509 (properties `((upstream-name . "CytoML")))
6510 (build-system r-build-system)
6513 (modify-phases %standard-phases
6514 (add-after 'unpack 'fix-linking
6516 (substitute* "src/Makevars.in"
6517 ;; This is to avoid having a plain directory on the list of
6518 ;; libraries to link.
6519 (("\\{h5lib\\}" match)
6520 (string-append match "/libhdf5.a")))
6523 `(("libxml2" ,libxml2)))
6525 `(("r-base64enc" ,r-base64enc)
6527 ("r-biobase" ,r-biobase)
6528 ("r-corpcor" ,r-corpcor)
6529 ("r-cytolib" ,r-cytolib)
6530 ("r-data-table" ,r-data-table)
6531 ("r-dplyr" ,r-dplyr)
6532 ("r-flowcore" ,r-flowcore)
6533 ("r-flowworkspace" ,r-flowworkspace)
6534 ("r-ggcyto" ,r-ggcyto)
6535 ("r-graph" ,r-graph)
6536 ("r-jsonlite" ,r-jsonlite)
6537 ("r-lattice" ,r-lattice)
6538 ("r-opencyto" ,r-opencyto)
6542 ("r-rcpparmadillo" ,r-rcpparmadillo)
6543 ("r-rcppparallel" ,r-rcppparallel)
6544 ("r-rgraphviz" ,r-rgraphviz)
6545 ("r-rhdf5lib" ,r-rhdf5lib)
6546 ("r-rprotobuflib" ,r-rprotobuflib)
6547 ("r-runit" ,r-runit)
6548 ("r-tibble" ,r-tibble)
6551 ("r-yaml" ,r-yaml)))
6553 `(("r-knitr" ,r-knitr)))
6554 (home-page "https://github.com/RGLab/CytoML")
6555 (synopsis "GatingML interface for cross platform cytometry data sharing")
6557 "This package provides an interface to implementations of the GatingML2.0
6558 standard to exchange gated cytometry data with other software platforms.")
6559 (license license:artistic2.0)))
6561 (define-public r-flowsom
6568 (uri (bioconductor-uri "FlowSOM" version))
6571 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
6572 (properties `((upstream-name . "FlowSOM")))
6573 (build-system r-build-system)
6575 `(("r-biocgenerics" ,r-biocgenerics)
6576 ("r-consensusclusterplus" ,r-consensusclusterplus)
6577 ("r-cytoml" ,r-cytoml)
6578 ("r-flowcore" ,r-flowcore)
6579 ("r-flowworkspace" ,r-flowworkspace)
6580 ("r-igraph" ,r-igraph)
6581 ("r-rcolorbrewer" ,r-rcolorbrewer)
6584 (home-page "https://bioconductor.org/packages/FlowSOM/")
6585 (synopsis "Visualize and interpret cytometry data")
6587 "FlowSOM offers visualization options for cytometry data, by using
6588 self-organizing map clustering and minimal spanning trees.")
6589 (license license:gpl2+)))
6591 (define-public r-mixomics
6598 (uri (bioconductor-uri "mixOmics" version))
6601 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
6602 (properties `((upstream-name . "mixOmics")))
6603 (build-system r-build-system)
6605 `(("r-corpcor" ,r-corpcor)
6606 ("r-dplyr" ,r-dplyr)
6607 ("r-ellipse" ,r-ellipse)
6608 ("r-ggrepel" ,r-ggrepel)
6609 ("r-ggplot2" ,r-ggplot2)
6610 ("r-gridextra" ,r-gridextra)
6611 ("r-igraph" ,r-igraph)
6612 ("r-lattice" ,r-lattice)
6614 ("r-matrixstats" ,r-matrixstats)
6615 ("r-rarpack" ,r-rarpack)
6616 ("r-rcolorbrewer" ,r-rcolorbrewer)
6617 ("r-reshape2" ,r-reshape2)
6618 ("r-tidyr" ,r-tidyr)))
6620 `(("r-knitr" ,r-knitr)))
6621 (home-page "http://www.mixOmics.org")
6622 (synopsis "Multivariate methods for exploration of biological datasets")
6624 "mixOmics offers a wide range of multivariate methods for the exploration
6625 and integration of biological datasets with a particular focus on variable
6626 selection. The package proposes several sparse multivariate models we have
6627 developed to identify the key variables that are highly correlated, and/or
6628 explain the biological outcome of interest. The data that can be analysed
6629 with mixOmics may come from high throughput sequencing technologies, such as
6630 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6631 also beyond the realm of omics (e.g. spectral imaging). The methods
6632 implemented in mixOmics can also handle missing values without having to
6633 delete entire rows with missing data.")
6634 (license license:gpl2+)))
6636 (define-public r-depecher
6637 (package ;Source/Weave error
6643 (uri (bioconductor-uri "DepecheR" version))
6646 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
6647 (properties `((upstream-name . "DepecheR")))
6648 (build-system r-build-system)
6650 `(("r-beanplot" ,r-beanplot)
6651 ("r-dosnow" ,r-dosnow)
6652 ("r-dplyr" ,r-dplyr)
6654 ("r-foreach" ,r-foreach)
6655 ("r-ggplot2" ,r-ggplot2)
6656 ("r-gmodels" ,r-gmodels)
6657 ("r-gplots" ,r-gplots)
6659 ("r-matrixstats" ,r-matrixstats)
6660 ("r-mixomics" ,r-mixomics)
6661 ("r-moments" ,r-moments)
6663 ("r-rcppeigen" ,r-rcppeigen)
6664 ("r-reshape2" ,r-reshape2)
6665 ("r-robustbase" ,r-robustbase)
6666 ("r-viridis" ,r-viridis)))
6668 `(("r-knitr" ,r-knitr)))
6669 (home-page "https://bioconductor.org/packages/DepecheR/")
6670 (synopsis "Identify traits of clusters in high-dimensional entities")
6672 "The purpose of this package is to identify traits in a dataset that can
6673 separate groups. This is done on two levels. First, clustering is performed,
6674 using an implementation of sparse K-means. Secondly, the generated clusters
6675 are used to predict outcomes of groups of individuals based on their
6676 distribution of observations in the different clusters. As certain clusters
6677 with separating information will be identified, and these clusters are defined
6678 by a sparse number of variables, this method can reduce the complexity of
6679 data, to only emphasize the data that actually matters.")
6680 (license license:expat)))
6682 (define-public r-rcistarget
6684 (name "r-rcistarget")
6689 (uri (bioconductor-uri "RcisTarget" version))
6692 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
6693 (properties `((upstream-name . "RcisTarget")))
6694 (build-system r-build-system)
6696 `(("r-aucell" ,r-aucell)
6697 ("r-biocgenerics" ,r-biocgenerics)
6698 ("r-data-table" ,r-data-table)
6699 ("r-feather" ,r-feather)
6700 ("r-gseabase" ,r-gseabase)
6701 ("r-r-utils" ,r-r-utils)
6702 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6704 `(("r-knitr" ,r-knitr)))
6705 (home-page "https://aertslab.org/#scenic")
6706 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6708 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6709 over-represented on a gene list. In a first step, RcisTarget selects DNA
6710 motifs that are significantly over-represented in the surroundings of the
6711 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6712 achieved by using a database that contains genome-wide cross-species rankings
6713 for each motif. The motifs that are then annotated to TFs and those that have
6714 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6715 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6716 genes in the gene-set that are ranked above the leading edge).")
6717 (license license:gpl3)))
6719 (define-public r-cicero
6726 (uri (bioconductor-uri "cicero" version))
6729 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
6730 (build-system r-build-system)
6732 `(("r-assertthat" ,r-assertthat)
6733 ("r-biobase" ,r-biobase)
6734 ("r-biocgenerics" ,r-biocgenerics)
6735 ("r-data-table" ,r-data-table)
6736 ("r-dplyr" ,r-dplyr)
6738 ("r-genomicranges" ,r-genomicranges)
6739 ("r-ggplot2" ,r-ggplot2)
6740 ("r-glasso" ,r-glasso)
6742 ("r-igraph" ,r-igraph)
6743 ("r-iranges" ,r-iranges)
6744 ("r-matrix" ,r-matrix)
6745 ("r-monocle" ,r-monocle)
6747 ("r-reshape2" ,r-reshape2)
6748 ("r-s4vectors" ,r-s4vectors)
6749 ("r-stringi" ,r-stringi)
6750 ("r-stringr" ,r-stringr)
6751 ("r-tibble" ,r-tibble)
6752 ("r-tidyr" ,r-tidyr)
6753 ("r-vgam" ,r-vgam)))
6755 `(("r-knitr" ,r-knitr)))
6756 (home-page "https://bioconductor.org/packages/cicero/")
6757 (synopsis "Predict cis-co-accessibility from single-cell data")
6759 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6760 accessibility data. It also extends the monocle package for use in chromatin
6761 accessibility data.")
6762 (license license:expat)))
6764 ;; This is the latest commit on the "monocle3" branch.
6765 (define-public r-cicero-monocle3
6766 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6768 (package (inherit r-cicero)
6769 (name "r-cicero-monocle3")
6770 (version (git-version "1.3.2" revision commit))
6775 (url "https://github.com/cole-trapnell-lab/cicero-release")
6777 (file-name (git-file-name name version))
6780 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6782 `(("r-monocle3" ,r-monocle3)
6783 ,@(alist-delete "r-monocle"
6784 (package-propagated-inputs r-cicero)))))))
6786 (define-public r-cistopic
6787 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6791 (version (git-version "0.2.1" revision commit))
6796 (url "https://github.com/aertslab/cisTopic")
6798 (file-name (git-file-name name version))
6801 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6802 (build-system r-build-system)
6804 `(("r-aucell" ,r-aucell)
6805 ("r-data-table" ,r-data-table)
6806 ("r-dplyr" ,r-dplyr)
6807 ("r-dosnow" ,r-dosnow)
6809 ("r-feather" ,r-feather)
6810 ("r-fitdistrplus" ,r-fitdistrplus)
6811 ("r-genomicranges" ,r-genomicranges)
6812 ("r-ggplot2" ,r-ggplot2)
6814 ("r-matrix" ,r-matrix)
6816 ("r-rcistarget" ,r-rcistarget)
6817 ("r-rtracklayer" ,r-rtracklayer)
6818 ("r-s4vectors" ,r-s4vectors)))
6819 (home-page "https://github.com/aertslab/cisTopic")
6820 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6822 "The sparse nature of single cell epigenomics data can be overruled using
6823 probabilistic modelling methods such as @dfn{Latent Dirichlet
6824 Allocation} (LDA). This package allows the probabilistic modelling of
6825 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6826 includes functionalities to identify cell states based on the contribution of
6827 cisTopics and explore the nature and regulatory proteins driving them.")
6828 (license license:gpl3))))
6830 (define-public r-genie3
6837 (uri (bioconductor-uri "GENIE3" version))
6840 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
6841 (properties `((upstream-name . "GENIE3")))
6842 (build-system r-build-system)
6843 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6845 `(("r-knitr" ,r-knitr)))
6846 (home-page "https://bioconductor.org/packages/GENIE3")
6847 (synopsis "Gene network inference with ensemble of trees")
6849 "This package implements the GENIE3 algorithm for inferring gene
6850 regulatory networks from expression data.")
6851 (license license:gpl2+)))
6853 (define-public r-roc
6860 (uri (bioconductor-uri "ROC" version))
6863 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
6864 (properties `((upstream-name . "ROC")))
6865 (build-system r-build-system)
6867 `(("r-knitr" ,r-knitr)))
6868 (home-page "https://www.bioconductor.org/packages/ROC/")
6869 (synopsis "Utilities for ROC curves")
6871 "This package provides utilities for @dfn{Receiver Operating
6872 Characteristic} (ROC) curves, with a focus on micro arrays.")
6873 (license license:artistic2.0)))
6875 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6877 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6882 (uri (bioconductor-uri
6883 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6884 version 'annotation))
6887 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6890 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6891 (build-system r-build-system)
6892 (propagated-inputs `(("r-minfi" ,r-minfi)))
6894 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6895 (synopsis "Annotation for Illumina's 450k methylation arrays")
6897 "This package provides manifests and annotation for Illumina's 450k array
6899 (license license:artistic2.0)))
6901 (define-public r-watermelon
6903 (name "r-watermelon")
6908 (uri (bioconductor-uri "wateRmelon" version))
6911 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
6912 (properties `((upstream-name . "wateRmelon")))
6913 (build-system r-build-system)
6915 `(("r-biobase" ,r-biobase)
6916 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6917 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6918 ("r-illuminaio" ,r-illuminaio)
6919 ("r-limma" ,r-limma)
6921 ("r-matrixstats" ,r-matrixstats)
6922 ("r-methylumi" ,r-methylumi)
6924 (home-page "https://bioconductor.org/packages/wateRmelon/")
6925 (synopsis "Illumina 450 methylation array normalization and metrics")
6927 "The standard index of DNA methylation (beta) is computed from methylated
6928 and unmethylated signal intensities. Betas calculated from raw signal
6929 intensities perform well, but using 11 methylomic datasets we demonstrate that
6930 quantile normalization methods produce marked improvement. The commonly used
6931 procedure of normalizing betas is inferior to the separate normalization of M
6932 and U, and it is also advantageous to normalize Type I and Type II assays
6933 separately. This package provides 15 flavours of betas and three performance
6934 metrics, with methods for objects produced by the @code{methylumi} and
6935 @code{minfi} packages.")
6936 (license license:gpl3)))
6938 (define-public r-gdsfmt
6945 (uri (bioconductor-uri "gdsfmt" version))
6948 "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a"))
6949 (modules '((guix build utils)))
6950 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6951 ;; them and link with system libraries instead.
6954 (for-each delete-file-recursively
6958 (substitute* "src/Makevars"
6959 (("all: \\$\\(SHLIB\\)") "all:")
6960 (("\\$\\(SHLIB\\): liblzma.a") "")
6961 (("(ZLIB|LZ4)/.*") "")
6962 (("CoreArray/dVLIntGDS.cpp.*")
6963 "CoreArray/dVLIntGDS.cpp")
6964 (("CoreArray/dVLIntGDS.o.*")
6965 "CoreArray/dVLIntGDS.o")
6966 (("PKG_LIBS = ./liblzma.a")
6967 "PKG_LIBS = -llz4"))
6968 (substitute* "src/CoreArray/dStream.h"
6969 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6970 (string-append "include <" header ">")))
6972 (properties `((upstream-name . "gdsfmt")))
6973 (build-system r-build-system)
6979 `(("r-knitr" ,r-knitr)))
6980 (home-page "http://corearray.sourceforge.net/")
6982 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6984 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6985 Data Structure} (GDS) data files, which are portable across platforms with
6986 hierarchical structure to store multiple scalable array-oriented data sets
6987 with metadata information. It is suited for large-scale datasets, especially
6988 for data which are much larger than the available random-access memory. The
6989 @code{gdsfmt} package offers efficient operations specifically designed for
6990 integers of less than 8 bits, since a diploid genotype, like
6991 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6992 byte. Data compression and decompression are available with relatively
6993 efficient random access. It is also allowed to read a GDS file in parallel
6994 with multiple R processes supported by the package @code{parallel}.")
6995 (license license:lgpl3)))
6997 (define-public r-bigmelon
7004 (uri (bioconductor-uri "bigmelon" version))
7007 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7008 (properties `((upstream-name . "bigmelon")))
7009 (build-system r-build-system)
7011 `(("r-biobase" ,r-biobase)
7012 ("r-biocgenerics" ,r-biocgenerics)
7013 ("r-gdsfmt" ,r-gdsfmt)
7014 ("r-geoquery" ,r-geoquery)
7015 ("r-methylumi" ,r-methylumi)
7016 ("r-minfi" ,r-minfi)
7017 ("r-watermelon" ,r-watermelon)))
7018 (home-page "https://bioconductor.org/packages/bigmelon/")
7019 (synopsis "Illumina methylation array analysis for large experiments")
7021 "This package provides methods for working with Illumina arrays using the
7022 @code{gdsfmt} package.")
7023 (license license:gpl3)))
7025 (define-public r-seqbias
7032 (uri (bioconductor-uri "seqbias" version))
7035 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
7036 (properties `((upstream-name . "seqbias")))
7037 (build-system r-build-system)
7039 `(("r-biostrings" ,r-biostrings)
7040 ("r-genomicranges" ,r-genomicranges)
7041 ("r-rhtslib" ,r-rhtslib)))
7042 (home-page "https://bioconductor.org/packages/seqbias/")
7043 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
7045 "This package implements a model of per-position sequencing bias in
7046 high-throughput sequencing data using a simple Bayesian network, the structure
7047 and parameters of which are trained on a set of aligned reads and a reference
7049 (license license:lgpl3)))
7051 (define-public r-snplocs-hsapiens-dbsnp144-grch37
7053 (name "r-snplocs-hsapiens-dbsnp144-grch37")
7057 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
7058 version 'annotation))
7061 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
7062 (build-system r-build-system)
7063 ;; As this package provides little more than a very large data file it
7064 ;; doesn't make sense to build substitutes.
7065 (arguments `(#:substitutable? #f))
7067 `(("r-biocgenerics" ,r-biocgenerics)
7068 ("r-s4vectors" ,r-s4vectors)
7069 ("r-iranges" ,r-iranges)
7070 ("r-genomeinfodb" ,r-genomeinfodb)
7071 ("r-genomicranges" ,r-genomicranges)
7072 ("r-bsgenome" ,r-bsgenome)
7073 ("r-biostrings" ,r-biostrings)))
7075 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
7076 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
7077 (description "This package provides SNP locations and alleles for Homo
7078 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
7079 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
7080 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
7081 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
7082 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
7083 the mitochondrion chromosome. Therefore, the SNPs in this package can be
7084 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
7085 correct position but this injection will exclude chrM (i.e. nothing will be
7086 injected in that sequence).")
7087 (license license:artistic2.0)))
7089 (define-public r-reqon
7096 (uri (bioconductor-uri "ReQON" version))
7099 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
7100 (properties `((upstream-name . "ReQON")))
7101 (build-system r-build-system)
7103 `(("r-rjava" ,r-rjava)
7104 ("r-rsamtools" ,r-rsamtools)
7105 ("r-seqbias" ,r-seqbias)))
7106 (home-page "https://bioconductor.org/packages/ReQON/")
7107 (synopsis "Recalibrating quality of nucleotides")
7109 "This package provides an implementation of an algorithm for
7110 recalibrating the base quality scores for aligned sequencing data in BAM
7112 (license license:gpl2)))
7114 (define-public r-wavcluster
7116 (name "r-wavcluster")
7121 (uri (bioconductor-uri "wavClusteR" version))
7124 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
7125 (properties `((upstream-name . "wavClusteR")))
7126 (build-system r-build-system)
7128 `(("r-biocgenerics" ,r-biocgenerics)
7129 ("r-biostrings" ,r-biostrings)
7130 ("r-foreach" ,r-foreach)
7131 ("r-genomicfeatures" ,r-genomicfeatures)
7132 ("r-genomicranges" ,r-genomicranges)
7133 ("r-ggplot2" ,r-ggplot2)
7134 ("r-hmisc" ,r-hmisc)
7135 ("r-iranges" ,r-iranges)
7136 ("r-mclust" ,r-mclust)
7137 ("r-rsamtools" ,r-rsamtools)
7138 ("r-rtracklayer" ,r-rtracklayer)
7139 ("r-s4vectors" ,r-s4vectors)
7140 ("r-seqinr" ,r-seqinr)
7141 ("r-stringr" ,r-stringr)))
7143 `(("r-knitr" ,r-knitr)))
7144 (home-page "https://bioconductor.org/packages/wavClusteR/")
7145 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
7147 "This package provides an integrated pipeline for the analysis of
7148 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7149 sequencing errors, SNPs and additional non-experimental sources by a non-
7150 parametric mixture model. The protein binding sites (clusters) are then
7151 resolved at high resolution and cluster statistics are estimated using a
7152 rigorous Bayesian framework. Post-processing of the results, data export for
7153 UCSC genome browser visualization and motif search analysis are provided. In
7154 addition, the package integrates RNA-Seq data to estimate the False
7155 Discovery Rate of cluster detection. Key functions support parallel multicore
7156 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7157 be applied to the analysis of other NGS data obtained from experimental
7158 procedures that induce nucleotide substitutions (e.g. BisSeq).")
7159 (license license:gpl2)))
7161 (define-public r-timeseriesexperiment
7163 (name "r-timeseriesexperiment")
7168 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7171 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
7173 `((upstream-name . "TimeSeriesExperiment")))
7174 (build-system r-build-system)
7176 `(("r-deseq2" ,r-deseq2)
7177 ("r-dplyr" ,r-dplyr)
7178 ("r-dynamictreecut" ,r-dynamictreecut)
7179 ("r-edger" ,r-edger)
7180 ("r-ggplot2" ,r-ggplot2)
7181 ("r-hmisc" ,r-hmisc)
7182 ("r-limma" ,r-limma)
7183 ("r-magrittr" ,r-magrittr)
7184 ("r-proxy" ,r-proxy)
7185 ("r-s4vectors" ,r-s4vectors)
7186 ("r-summarizedexperiment" ,r-summarizedexperiment)
7187 ("r-tibble" ,r-tibble)
7188 ("r-tidyr" ,r-tidyr)
7189 ("r-vegan" ,r-vegan)
7190 ("r-viridis" ,r-viridis)))
7192 `(("r-knitr" ,r-knitr)))
7193 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7194 (synopsis "Analysis for short time-series data")
7196 "This package is a visualization and analysis toolbox for short time
7197 course data which includes dimensionality reduction, clustering, two-sample
7198 differential expression testing and gene ranking techniques. The package also
7199 provides methods for retrieving enriched pathways.")
7200 (license license:lgpl3+)))
7202 (define-public r-variantfiltering
7204 (name "r-variantfiltering")
7209 (uri (bioconductor-uri "VariantFiltering" version))
7212 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
7214 `((upstream-name . "VariantFiltering")))
7215 (build-system r-build-system)
7217 `(("r-annotationdbi" ,r-annotationdbi)
7218 ("r-biobase" ,r-biobase)
7219 ("r-biocgenerics" ,r-biocgenerics)
7220 ("r-biocparallel" ,r-biocparallel)
7221 ("r-biostrings" ,r-biostrings)
7222 ("r-bsgenome" ,r-bsgenome)
7224 ("r-genomeinfodb" ,r-genomeinfodb)
7225 ("r-genomicfeatures" ,r-genomicfeatures)
7226 ("r-genomicranges" ,r-genomicranges)
7227 ("r-genomicscores" ,r-genomicscores)
7228 ("r-graph" ,r-graph)
7230 ("r-iranges" ,r-iranges)
7232 ("r-rsamtools" ,r-rsamtools)
7233 ("r-s4vectors" ,r-s4vectors)
7234 ("r-shiny" ,r-shiny)
7235 ("r-shinyjs" ,r-shinyjs)
7236 ("r-shinythemes" ,r-shinythemes)
7237 ("r-shinytree" ,r-shinytree)
7238 ("r-summarizedexperiment" ,r-summarizedexperiment)
7239 ("r-variantannotation" ,r-variantannotation)
7240 ("r-xvector" ,r-xvector)))
7241 (home-page "https://github.com/rcastelo/VariantFiltering")
7242 (synopsis "Filtering of coding and non-coding genetic variants")
7244 "Filter genetic variants using different criteria such as inheritance
7245 model, amino acid change consequence, minor allele frequencies across human
7246 populations, splice site strength, conservation, etc.")
7247 (license license:artistic2.0)))
7249 (define-public r-genomegraphs
7251 (name "r-genomegraphs")
7256 (uri (bioconductor-uri "GenomeGraphs" version))
7259 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7260 (properties `((upstream-name . "GenomeGraphs")))
7261 (build-system r-build-system)
7263 `(("r-biomart" ,r-biomart)))
7264 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7265 (synopsis "Plotting genomic information from Ensembl")
7267 "Genomic data analyses requires integrated visualization of known genomic
7268 information and new experimental data. GenomeGraphs uses the biomaRt package
7269 to perform live annotation queries to Ensembl and translates this to e.g.
7270 gene/transcript structures in viewports of the grid graphics package. This
7271 results in genomic information plotted together with your data. Another
7272 strength of GenomeGraphs is to plot different data types such as array CGH,
7273 gene expression, sequencing and other data, together in one plot using the
7274 same genome coordinate system.")
7275 (license license:artistic2.0)))
7277 (define-public r-wavetiling
7279 (name "r-wavetiling")
7284 (uri (bioconductor-uri "waveTiling" version))
7287 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7288 (properties `((upstream-name . "waveTiling")))
7289 (build-system r-build-system)
7291 `(("r-affy" ,r-affy)
7292 ("r-biobase" ,r-biobase)
7293 ("r-biostrings" ,r-biostrings)
7294 ("r-genomegraphs" ,r-genomegraphs)
7295 ("r-genomicranges" ,r-genomicranges)
7296 ("r-iranges" ,r-iranges)
7297 ("r-oligo" ,r-oligo)
7298 ("r-oligoclasses" ,r-oligoclasses)
7299 ("r-preprocesscore" ,r-preprocesscore)
7300 ("r-waveslim" ,r-waveslim)))
7301 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7302 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7304 "This package is designed to conduct transcriptome analysis for tiling
7305 arrays based on fast wavelet-based functional models.")
7306 (license license:gpl2+)))
7308 (define-public r-variancepartition
7310 (name "r-variancepartition")
7315 (uri (bioconductor-uri "variancePartition" version))
7318 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
7320 `((upstream-name . "variancePartition")))
7321 (build-system r-build-system)
7323 `(("r-biobase" ,r-biobase)
7324 ("r-biocparallel" ,r-biocparallel)
7325 ("r-colorramps" ,r-colorramps)
7326 ("r-doparallel" ,r-doparallel)
7327 ("r-foreach" ,r-foreach)
7328 ("r-ggplot2" ,r-ggplot2)
7329 ("r-gplots" ,r-gplots)
7330 ("r-iterators" ,r-iterators)
7331 ("r-limma" ,r-limma)
7333 ("r-lmertest" ,r-lmertest)
7335 ("r-pbkrtest" ,r-pbkrtest)
7336 ("r-progress" ,r-progress)
7337 ("r-reshape2" ,r-reshape2)
7338 ("r-scales" ,r-scales)))
7340 `(("r-knitr" ,r-knitr)))
7341 (home-page "https://bioconductor.org/packages/variancePartition/")
7342 (synopsis "Analyze variation in gene expression experiments")
7344 "This is a package providing tools to quantify and interpret multiple
7345 sources of biological and technical variation in gene expression experiments.
7346 It uses a linear mixed model to quantify variation in gene expression
7347 attributable to individual, tissue, time point, or technical variables. The
7348 package includes dream differential expression analysis for repeated
7350 (license license:gpl2+)))
7352 (define-public r-htqpcr
7359 (uri (bioconductor-uri "HTqPCR" version))
7362 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
7363 (properties `((upstream-name . "HTqPCR")))
7364 (build-system r-build-system)
7366 `(("r-affy" ,r-affy)
7367 ("r-biobase" ,r-biobase)
7368 ("r-gplots" ,r-gplots)
7369 ("r-limma" ,r-limma)
7370 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7371 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7372 "groups/bertone/software/HTqPCR.pdf"))
7373 (synopsis "Automated analysis of high-throughput qPCR data")
7375 "Analysis of Ct values from high throughput quantitative real-time
7376 PCR (qPCR) assays across multiple conditions or replicates. The input data
7377 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7378 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7379 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7380 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7381 loading, quality assessment, normalization, visualization and parametric or
7382 non-parametric testing for statistical significance in Ct values between
7383 features (e.g. genes, microRNAs).")
7384 (license license:artistic2.0)))
7386 (define-public r-unifiedwmwqpcr
7388 (name "r-unifiedwmwqpcr")
7393 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7396 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
7398 `((upstream-name . "unifiedWMWqPCR")))
7399 (build-system r-build-system)
7401 `(("r-biocgenerics" ,r-biocgenerics)
7402 ("r-htqpcr" ,r-htqpcr)))
7403 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7404 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7406 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7407 data. This modified test allows for testing differential expression in qPCR
7409 (license license:gpl2+)))
7411 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7413 (define-public r-activedriverwgs
7415 (name "r-activedriverwgs")
7420 (uri (cran-uri "ActiveDriverWGS" version))
7423 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
7425 `((upstream-name . "ActiveDriverWGS")))
7426 (build-system r-build-system)
7428 `(("r-biostrings" ,r-biostrings)
7429 ("r-bsgenome" ,r-bsgenome)
7430 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7431 ("r-genomeinfodb" ,r-genomeinfodb)
7432 ("r-genomicranges" ,r-genomicranges)
7433 ("r-iranges" ,r-iranges)
7434 ("r-s4vectors" ,r-s4vectors)))
7436 `(("r-knitr" ,r-knitr)))
7437 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7438 (synopsis "Driver discovery tool for cancer whole genomes")
7440 "This package provides a method for finding an enrichment of cancer
7441 simple somatic mutations (SNVs and Indels) in functional elements across the
7442 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7443 using whole genome sequencing data.")
7444 (license license:gpl3)))
7446 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7448 (define-public r-activepathways
7450 (name "r-activepathways")
7455 (uri (cran-uri "ActivePathways" version))
7458 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7460 `((upstream-name . "ActivePathways")))
7461 (build-system r-build-system)
7463 `(("r-data-table" ,r-data-table)
7464 ("r-ggplot2" ,r-ggplot2)))
7466 `(("r-knitr" ,r-knitr)))
7467 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7468 (synopsis "Multivariate pathway enrichment analysis")
7470 "This package represents an integrative method of analyzing multi omics
7471 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7472 uses a statistical data fusion approach, rationalizes contributing evidence
7473 and highlights associated genes, improving systems-level understanding of
7474 cellular organization in health and disease.")
7475 (license license:gpl3)))
7477 (define-public r-bgmix
7484 (uri (bioconductor-uri "BGmix" version))
7487 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
7488 (properties `((upstream-name . "BGmix")))
7489 (build-system r-build-system)
7491 `(("r-kernsmooth" ,r-kernsmooth)))
7492 (home-page "https://bioconductor.org/packages/BGmix/")
7493 (synopsis "Bayesian models for differential gene expression")
7495 "This package provides fully Bayesian mixture models for differential
7497 (license license:gpl2)))
7499 (define-public r-bgx
7506 (uri (bioconductor-uri "bgx" version))
7509 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
7510 (properties `((upstream-name . "bgx")))
7511 (build-system r-build-system)
7513 `(("r-affy" ,r-affy)
7514 ("r-biobase" ,r-biobase)
7515 ("r-gcrma" ,r-gcrma)
7516 ("r-rcpp" ,r-rcpp)))
7517 (home-page "https://bioconductor.org/packages/bgx/")
7518 (synopsis "Bayesian gene expression")
7520 "This package provides tools for Bayesian integrated analysis of
7521 Affymetrix GeneChips.")
7522 (license license:gpl2)))
7524 (define-public r-bhc
7531 (uri (bioconductor-uri "BHC" version))
7534 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
7535 (properties `((upstream-name . "BHC")))
7536 (build-system r-build-system)
7537 (home-page "https://bioconductor.org/packages/BHC/")
7538 (synopsis "Bayesian hierarchical clustering")
7540 "The method implemented in this package performs bottom-up hierarchical
7541 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7542 in the data and Bayesian model selection to decide at each step which clusters
7543 to merge. This avoids several limitations of traditional methods, for example
7544 how many clusters there should be and how to choose a principled distance
7545 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7546 categories) or time-series data. This version also includes a randomised
7547 algorithm which is more efficient for larger data sets.")
7548 (license license:gpl3)))
7550 (define-public r-bicare
7557 (uri (bioconductor-uri "BicARE" version))
7560 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
7561 (properties `((upstream-name . "BicARE")))
7562 (build-system r-build-system)
7564 `(("r-biobase" ,r-biobase)
7565 ("r-gseabase" ,r-gseabase)
7566 ("r-multtest" ,r-multtest)))
7567 (home-page "http://bioinfo.curie.fr")
7568 (synopsis "Biclustering analysis and results exploration")
7570 "This is a package for biclustering analysis and exploration of
7572 (license license:gpl2)))
7574 (define-public r-bifet
7581 (uri (bioconductor-uri "BiFET" version))
7584 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
7585 (properties `((upstream-name . "BiFET")))
7586 (build-system r-build-system)
7588 `(("r-genomicranges" ,r-genomicranges)
7589 ("r-poibin" ,r-poibin)))
7591 `(("r-knitr" ,r-knitr)))
7592 (home-page "https://bioconductor.org/packages/BiFET")
7593 (synopsis "Bias-free footprint enrichment test")
7595 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7596 over-represented in target regions compared to background regions after
7597 correcting for the bias arising from the imbalance in read counts and GC
7598 contents between the target and background regions. For a given TF k, BiFET
7599 tests the null hypothesis that the target regions have the same probability of
7600 having footprints for the TF k as the background regions while correcting for
7601 the read count and GC content bias.")
7602 (license license:gpl3)))
7604 (define-public r-rsbml
7611 (uri (bioconductor-uri "rsbml" version))
7614 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
7615 (properties `((upstream-name . "rsbml")))
7616 (build-system r-build-system)
7618 `(("libsbml" ,libsbml)
7621 `(("r-biocgenerics" ,r-biocgenerics)
7622 ("r-graph" ,r-graph)))
7624 `(("pkg-config" ,pkg-config)))
7625 (home-page "http://www.sbml.org")
7626 (synopsis "R support for SBML")
7628 "This package provides an R interface to libsbml for SBML parsing,
7629 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7630 (license license:artistic2.0)))
7632 (define-public r-hypergraph
7634 (name "r-hypergraph")
7639 (uri (bioconductor-uri "hypergraph" version))
7642 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
7643 (properties `((upstream-name . "hypergraph")))
7644 (build-system r-build-system)
7646 `(("r-graph" ,r-graph)))
7647 (home-page "https://bioconductor.org/packages/hypergraph")
7648 (synopsis "Hypergraph data structures")
7650 "This package implements some simple capabilities for representing and
7651 manipulating hypergraphs.")
7652 (license license:artistic2.0)))
7654 (define-public r-hyperdraw
7656 (name "r-hyperdraw")
7661 (uri (bioconductor-uri "hyperdraw" version))
7664 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
7665 (properties `((upstream-name . "hyperdraw")))
7666 (build-system r-build-system)
7667 (inputs `(("graphviz" ,graphviz)))
7669 `(("r-graph" ,r-graph)
7670 ("r-hypergraph" ,r-hypergraph)
7671 ("r-rgraphviz" ,r-rgraphviz)))
7672 (home-page "https://bioconductor.org/packages/hyperdraw")
7673 (synopsis "Visualizing hypergraphs")
7675 "This package provides functions for visualizing hypergraphs.")
7676 (license license:gpl2+)))
7678 (define-public r-biggr
7685 (uri (bioconductor-uri "BiGGR" version))
7688 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
7689 (properties `((upstream-name . "BiGGR")))
7690 (build-system r-build-system)
7692 `(("r-hyperdraw" ,r-hyperdraw)
7693 ("r-hypergraph" ,r-hypergraph)
7695 ("r-limsolve" ,r-limsolve)
7696 ("r-rsbml" ,r-rsbml)
7697 ("r-stringr" ,r-stringr)))
7698 (home-page "https://bioconductor.org/packages/BiGGR/")
7699 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7701 "This package provides an interface to simulate metabolic reconstruction
7702 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7703 reconstruction databases. The package facilitates @dfn{flux balance
7704 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7705 networks and estimated fluxes can be visualized with hypergraphs.")
7706 (license license:gpl3+)))
7708 (define-public r-bigmemoryextras
7710 (name "r-bigmemoryextras")
7715 (uri (bioconductor-uri "bigmemoryExtras" version))
7718 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
7720 `((upstream-name . "bigmemoryExtras")))
7721 (build-system r-build-system)
7723 `(("r-bigmemory" ,r-bigmemory)))
7725 `(("r-knitr" ,r-knitr)))
7726 (home-page "https://github.com/phaverty/bigmemoryExtras")
7727 (synopsis "Extension of the bigmemory package")
7729 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7730 safety and convenience features to the @code{filebacked.big.matrix} class from
7731 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7732 monitoring and gracefully restoring the connection to on-disk data and it also
7733 protects against accidental data modification with a file-system-based
7734 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7735 classes as @code{assayData} matrices within the @code{Biobase} package's
7736 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7737 related to attaching to, and indexing into, file-backed matrices with
7738 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7739 a file-backed matrix with factor properties.")
7740 (license license:artistic2.0)))
7742 (define-public r-bigpint
7749 (uri (bioconductor-uri "bigPint" version))
7752 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
7753 (properties `((upstream-name . "bigPint")))
7754 (build-system r-build-system)
7756 `(("r-delayedarray" ,r-delayedarray)
7757 ("r-dplyr" ,r-dplyr)
7758 ("r-ggally" ,r-ggally)
7759 ("r-ggplot2" ,r-ggplot2)
7760 ("r-gridextra" ,r-gridextra)
7761 ("r-hexbin" ,r-hexbin)
7762 ("r-hmisc" ,r-hmisc)
7763 ("r-htmlwidgets" ,r-htmlwidgets)
7764 ("r-plotly" ,r-plotly)
7766 ("r-rcolorbrewer" ,r-rcolorbrewer)
7767 ("r-reshape" ,r-reshape)
7768 ("r-shiny" ,r-shiny)
7769 ("r-shinycssloaders" ,r-shinycssloaders)
7770 ("r-shinydashboard" ,r-shinydashboard)
7771 ("r-stringr" ,r-stringr)
7772 ("r-summarizedexperiment" ,r-summarizedexperiment)
7773 ("r-tidyr" ,r-tidyr)))
7775 `(("r-knitr" ,r-knitr)))
7776 (home-page "https://github.com/lindsayrutter/bigPint")
7777 (synopsis "Big multivariate data plotted interactively")
7779 "This package provides methods for visualizing large multivariate
7780 datasets using static and interactive scatterplot matrices, parallel
7781 coordinate plots, volcano plots, and litre plots. It includes examples for
7782 visualizing RNA-sequencing datasets and differentially expressed genes.")
7783 (license license:gpl3)))
7785 (define-public r-chemminer
7787 (name "r-chemminer")
7792 (uri (bioconductor-uri "ChemmineR" version))
7795 "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19"))))
7796 (properties `((upstream-name . "ChemmineR")))
7797 (build-system r-build-system)
7799 `(("r-base64enc" ,r-base64enc)
7801 ("r-biocgenerics" ,r-biocgenerics)
7803 ("r-digest" ,r-digest)
7805 ("r-ggplot2" ,r-ggplot2)
7806 ("r-gridextra" ,r-gridextra)
7809 ("r-rcurl" ,r-rcurl)
7810 ("r-rjson" ,r-rjson)
7811 ("r-rsvg" ,r-rsvg)))
7813 `(("r-knitr" ,r-knitr)))
7814 (home-page "https://github.com/girke-lab/ChemmineR")
7815 (synopsis "Cheminformatics toolkit for R")
7817 "ChemmineR is a cheminformatics package for analyzing drug-like small
7818 molecule data in R. It contains functions for efficient processing of large
7819 numbers of molecules, physicochemical/structural property predictions,
7820 structural similarity searching, classification and clustering of compound
7821 libraries with a wide spectrum of algorithms. In addition, it offers
7822 visualization functions for compound clustering results and chemical
7824 (license license:artistic2.0)))
7826 (define-public r-bioassayr
7828 (name "r-bioassayr")
7833 (uri (bioconductor-uri "bioassayR" version))
7836 "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f"))))
7837 (properties `((upstream-name . "bioassayR")))
7838 (build-system r-build-system)
7840 `(("r-biocgenerics" ,r-biocgenerics)
7841 ("r-chemminer" ,r-chemminer)
7843 ("r-matrix" ,r-matrix)
7844 ("r-rjson" ,r-rjson)
7845 ("r-rsqlite" ,r-rsqlite)
7848 `(("r-knitr" ,r-knitr)))
7849 (home-page "https://github.com/TylerBackman/bioassayR")
7850 (synopsis "Cross-target analysis of small molecule bioactivity")
7852 "bioassayR is a computational tool that enables simultaneous analysis of
7853 thousands of bioassay experiments performed over a diverse set of compounds
7854 and biological targets. Unique features include support for large-scale
7855 cross-target analyses of both public and custom bioassays, generation of
7856 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7857 preloaded database that provides access to a substantial portion of publicly
7858 available bioactivity data.")
7859 (license license:artistic2.0)))
7861 (define-public r-biobroom
7868 (uri (bioconductor-uri "biobroom" version))
7871 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
7872 (properties `((upstream-name . "biobroom")))
7873 (build-system r-build-system)
7875 `(("r-biobase" ,r-biobase)
7876 ("r-broom" ,r-broom)
7877 ("r-dplyr" ,r-dplyr)
7878 ("r-tidyr" ,r-tidyr)))
7880 `(("r-knitr" ,r-knitr)))
7881 (home-page "https://github.com/StoreyLab/biobroom")
7882 (synopsis "Turn Bioconductor objects into tidy data frames")
7884 "This package contains methods for converting standard objects
7885 constructed by bioinformatics packages, especially those in Bioconductor, and
7886 converting them to @code{tidy} data. It thus serves as a complement to the
7887 @code{broom} package, and follows the same tidy, augment, glance division of
7888 tidying methods. Tidying data makes it easy to recombine, reshape and
7889 visualize bioinformatics analyses.")
7890 ;; Any version of the LGPL.
7891 (license license:lgpl3+)))
7893 (define-public r-graphite
7900 (uri (bioconductor-uri "graphite" version))
7903 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
7904 (properties `((upstream-name . "graphite")))
7905 (build-system r-build-system)
7907 `(("r-annotationdbi" ,r-annotationdbi)
7908 ("r-checkmate" ,r-checkmate)
7909 ("r-graph" ,r-graph)
7911 ("r-rappdirs" ,r-rappdirs)))
7912 (home-page "https://bioconductor.org/packages/graphite/")
7913 (synopsis "Networks from pathway databases")
7915 "Graphite provides networks derived from eight public pathway databases,
7916 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7918 (license license:agpl3+)))
7920 (define-public r-reactomepa
7922 (name "r-reactomepa")
7927 (uri (bioconductor-uri "ReactomePA" version))
7930 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
7931 (properties `((upstream-name . "ReactomePA")))
7932 (build-system r-build-system)
7934 `(("r-annotationdbi" ,r-annotationdbi)
7936 ("r-enrichplot" ,r-enrichplot)
7937 ("r-ggplot2" ,r-ggplot2)
7938 ("r-ggraph" ,r-ggraph)
7939 ("r-graphite" ,r-graphite)
7940 ("r-igraph" ,r-igraph)
7941 ("r-reactome-db" ,r-reactome-db)))
7943 `(("r-knitr" ,r-knitr)))
7944 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7945 (synopsis "Reactome pathway analysis")
7947 "This package provides functions for pathway analysis based on the
7948 REACTOME pathway database. It implements enrichment analysis, gene set
7949 enrichment analysis and several functions for visualization.")
7950 (license license:gpl2)))
7952 (define-public r-ebarrays
7959 (uri (bioconductor-uri "EBarrays" version))
7962 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
7963 (properties `((upstream-name . "EBarrays")))
7964 (build-system r-build-system)
7966 `(("r-biobase" ,r-biobase)
7967 ("r-cluster" ,r-cluster)
7968 ("r-lattice" ,r-lattice)))
7969 (home-page "https://bioconductor.org/packages/EBarrays/")
7970 (synopsis "Gene clustering and differential expression identification")
7972 "EBarrays provides tools for the analysis of replicated/unreplicated
7974 (license license:gpl2+)))
7976 (define-public r-bioccasestudies
7978 (name "r-bioccasestudies")
7983 (uri (bioconductor-uri "BiocCaseStudies" version))
7986 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
7988 `((upstream-name . "BiocCaseStudies")))
7989 (build-system r-build-system)
7990 (propagated-inputs `(("r-biobase" ,r-biobase)))
7991 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7992 (synopsis "Support for the case studies monograph")
7994 "This package provides software and data to support the case studies
7996 (license license:artistic2.0)))
7998 (define-public r-biocgraph
8000 (name "r-biocgraph")
8005 (uri (bioconductor-uri "biocGraph" version))
8008 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
8009 (properties `((upstream-name . "biocGraph")))
8010 (build-system r-build-system)
8012 `(("r-biocgenerics" ,r-biocgenerics)
8013 ("r-geneplotter" ,r-geneplotter)
8014 ("r-graph" ,r-graph)
8015 ("r-rgraphviz" ,r-rgraphviz)))
8016 (home-page "https://bioconductor.org/packages/biocGraph/")
8017 (synopsis "Graph examples and use cases in Bioinformatics")
8019 "This package provides examples and code that make use of the
8020 different graph related packages produced by Bioconductor.")
8021 (license license:artistic2.0)))
8023 (define-public r-experimenthub
8025 (name "r-experimenthub")
8030 (uri (bioconductor-uri "ExperimentHub" version))
8033 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
8034 (properties `((upstream-name . "ExperimentHub")))
8035 (build-system r-build-system)
8037 `(("r-annotationhub" ,r-annotationhub)
8038 ("r-biocfilecache" ,r-biocfilecache)
8039 ("r-biocgenerics" ,r-biocgenerics)
8040 ("r-biocmanager" ,r-biocmanager)
8042 ("r-rappdirs" ,r-rappdirs)
8043 ("r-s4vectors" ,r-s4vectors)))
8045 `(("r-knitr" ,r-knitr)))
8046 (home-page "https://bioconductor.org/packages/ExperimentHub/")
8047 (synopsis "Client to access ExperimentHub resources")
8049 "This package provides a client for the Bioconductor ExperimentHub web
8050 resource. ExperimentHub provides a central location where curated data from
8051 experiments, publications or training courses can be accessed. Each resource
8052 has associated metadata, tags and date of modification. The client creates
8053 and manages a local cache of files retrieved enabling quick and reproducible
8055 (license license:artistic2.0)))
8057 (define-public r-multiassayexperiment
8059 (name "r-multiassayexperiment")
8064 (uri (bioconductor-uri "MultiAssayExperiment" version))
8067 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
8069 `((upstream-name . "MultiAssayExperiment")))
8070 (build-system r-build-system)
8072 `(("r-biobase" ,r-biobase)
8073 ("r-biocgenerics" ,r-biocgenerics)
8074 ("r-genomicranges" ,r-genomicranges)
8075 ("r-iranges" ,r-iranges)
8076 ("r-s4vectors" ,r-s4vectors)
8077 ("r-summarizedexperiment" ,r-summarizedexperiment)
8078 ("r-tidyr" ,r-tidyr)))
8080 `(("r-knitr" ,r-knitr)))
8081 (home-page "https://waldronlab.io/MultiAssayExperiment/")
8082 (synopsis "Integration of multi-omics experiments in Bioconductor")
8084 "MultiAssayExperiment harmonizes data management of multiple assays
8085 performed on an overlapping set of specimens. It provides a familiar
8086 Bioconductor user experience by extending concepts from
8087 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
8088 classes for individual assays, and allowing subsetting by genomic ranges or
8090 (license license:artistic2.0)))
8092 (define-public r-bioconcotk
8094 (name "r-bioconcotk")
8099 (uri (bioconductor-uri "BiocOncoTK" version))
8102 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
8103 (properties `((upstream-name . "BiocOncoTK")))
8104 (build-system r-build-system)
8106 `(("r-bigrquery" ,r-bigrquery)
8108 ("r-complexheatmap" ,r-complexheatmap)
8109 ("r-curatedtcgadata" ,r-curatedtcgadata)
8111 ("r-dplyr" ,r-dplyr)
8113 ("r-genomicfeatures" ,r-genomicfeatures)
8114 ("r-genomicranges" ,r-genomicranges)
8115 ("r-ggplot2" ,r-ggplot2)
8116 ("r-ggpubr" ,r-ggpubr)
8117 ("r-graph" ,r-graph)
8119 ("r-iranges" ,r-iranges)
8120 ("r-magrittr" ,r-magrittr)
8122 ("r-rgraphviz" ,r-rgraphviz)
8123 ("r-rjson" ,r-rjson)
8124 ("r-s4vectors" ,r-s4vectors)
8125 ("r-scales" ,r-scales)
8126 ("r-shiny" ,r-shiny)
8127 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8129 `(("r-knitr" ,r-knitr)))
8130 (home-page "https://bioconductor.org/packages/BiocOncoTK")
8131 (synopsis "Bioconductor components for general cancer genomics")
8133 "The purpose of this package is to provide a central interface to various
8134 tools for genome-scale analysis of cancer studies.")
8135 (license license:artistic2.0)))
8137 (define-public r-biocor
8144 (uri (bioconductor-uri "BioCor" version))
8147 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
8148 (properties `((upstream-name . "BioCor")))
8149 (build-system r-build-system)
8151 `(("r-biocparallel" ,r-biocparallel)
8152 ("r-gseabase" ,r-gseabase)
8153 ("r-matrix" ,r-matrix)))
8155 `(("r-knitr" ,r-knitr)))
8156 (home-page "https://llrs.github.io/BioCor/")
8157 (synopsis "Functional similarities")
8159 "This package provides tools to calculate functional similarities based
8160 on the pathways described on KEGG and REACTOME or in gene sets. These
8161 similarities can be calculated for pathways or gene sets, genes, or clusters
8162 and combined with other similarities. They can be used to improve networks,
8163 gene selection, testing relationships, and so on.")
8164 (license license:expat)))
8166 (define-public r-biocpkgtools
8168 (name "r-biocpkgtools")
8173 (uri (bioconductor-uri "BiocPkgTools" version))
8176 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
8177 (properties `((upstream-name . "BiocPkgTools")))
8178 (build-system r-build-system)
8180 `(("r-biocfilecache" ,r-biocfilecache)
8181 ("r-biocmanager" ,r-biocmanager)
8182 ("r-biocviews" ,r-biocviews)
8183 ("r-dplyr" ,r-dplyr)
8186 ("r-graph" ,r-graph)
8187 ("r-htmltools" ,r-htmltools)
8188 ("r-htmlwidgets" ,r-htmlwidgets)
8190 ("r-igraph" ,r-igraph)
8191 ("r-jsonlite" ,r-jsonlite)
8192 ("r-magrittr" ,r-magrittr)
8193 ("r-rappdirs" ,r-rappdirs)
8195 ("r-readr" ,r-readr)
8197 ("r-rlang" ,r-rlang)
8198 ("r-rvest" ,r-rvest)
8199 ("r-stringr" ,r-stringr)
8200 ("r-tibble" ,r-tibble)
8201 ("r-tidyr" ,r-tidyr)
8202 ("r-tidyselect" ,r-tidyselect)
8203 ("r-xml2" ,r-xml2)))
8205 `(("r-knitr" ,r-knitr)))
8206 (home-page "https://github.com/seandavi/BiocPkgTools")
8207 (synopsis "Collection of tools for learning about Bioconductor packages")
8209 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8210 and build status. This package is a simple collection of functions to access
8211 that metadata from R. The goal is to expose metadata for data mining and
8212 value-added functionality such as package searching, text mining, and
8213 analytics on packages.")
8214 (license license:expat)))
8216 (define-public r-biocset
8223 (uri (bioconductor-uri "BiocSet" version))
8226 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
8227 (properties `((upstream-name . "BiocSet")))
8228 (build-system r-build-system)
8230 `(("r-annotationdbi" ,r-annotationdbi)
8231 ("r-biocio" ,r-biocio)
8232 ("r-dplyr" ,r-dplyr)
8233 ("r-keggrest" ,r-keggrest)
8234 ("r-ontologyindex" ,r-ontologyindex)
8236 ("r-rlang" ,r-rlang)
8237 ("r-s4vectors" ,r-s4vectors)
8238 ("r-tibble" ,r-tibble)
8239 ("r-tidyr" ,r-tidyr)))
8241 `(("r-knitr" ,r-knitr)))
8243 "https://bioconductor.org/packages/BiocSet")
8245 "Representing Different Biological Sets")
8247 "BiocSet displays different biological sets in a triple tibble format.
8248 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
8249 The user has the ability to activate one of these three tibbles to perform
8250 common functions from the @code{dplyr} package. Mapping functionality and
8251 accessing web references for elements/sets are also available in BiocSet.")
8252 (license license:artistic2.0)))
8254 (define-public r-biocworkflowtools
8256 (name "r-biocworkflowtools")
8261 (uri (bioconductor-uri "BiocWorkflowTools" version))
8264 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
8266 `((upstream-name . "BiocWorkflowTools")))
8267 (build-system r-build-system)
8269 `(("r-biocstyle" ,r-biocstyle)
8270 ("r-bookdown" ,r-bookdown)
8271 ("r-git2r" ,r-git2r)
8273 ("r-knitr" ,r-knitr)
8274 ("r-rmarkdown" ,r-rmarkdown)
8275 ("r-rstudioapi" ,r-rstudioapi)
8276 ("r-stringr" ,r-stringr)
8277 ("r-usethis" ,r-usethis)))
8279 `(("r-knitr" ,r-knitr)))
8280 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8281 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8283 "This package provides functions to ease the transition between
8284 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8285 (license license:expat)))
8287 (define-public r-biodist
8294 (uri (bioconductor-uri "bioDist" version))
8297 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
8298 (properties `((upstream-name . "bioDist")))
8299 (build-system r-build-system)
8301 `(("r-biobase" ,r-biobase)
8302 ("r-kernsmooth" ,r-kernsmooth)))
8303 (home-page "https://bioconductor.org/packages/bioDist/")
8304 (synopsis "Different distance measures")
8306 "This package provides a collection of software tools for calculating
8307 distance measures.")
8308 (license license:artistic2.0)))
8310 (define-public r-pcatools
8317 (uri (bioconductor-uri "PCAtools" version))
8320 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
8321 (properties `((upstream-name . "PCAtools")))
8322 (build-system r-build-system)
8324 `(("r-beachmat" ,r-beachmat)
8326 ("r-biocparallel" ,r-biocparallel)
8327 ("r-biocsingular" ,r-biocsingular)
8328 ("r-cowplot" ,r-cowplot)
8329 ("r-delayedarray" ,r-delayedarray)
8330 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8331 ("r-dqrng" ,r-dqrng)
8332 ("r-ggplot2" ,r-ggplot2)
8333 ("r-ggrepel" ,r-ggrepel)
8334 ("r-lattice" ,r-lattice)
8335 ("r-matrix" ,r-matrix)
8337 ("r-reshape2" ,r-reshape2)))
8338 (native-inputs `(("r-knitr" ,r-knitr)))
8339 (home-page "https://github.com/kevinblighe/PCAtools")
8340 (synopsis "PCAtools: everything Principal Components Analysis")
8342 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8343 structure of the data without the need to build any model to represent it.
8344 This \"summary\" of the data is arrived at through a process of reduction that
8345 can transform the large number of variables into a lesser number that are
8346 uncorrelated (i.e. the 'principal components'), while at the same time being
8347 capable of easy interpretation on the original data. PCAtools provides
8348 functions for data exploration via PCA, and allows the user to generate
8349 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8350 can also identify an optimal number of principal components via different
8351 metrics, such as the elbow method and Horn's parallel analysis, which has
8352 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8353 dimensional mass cytometry data.")
8354 (license license:gpl3)))
8356 (define-public r-rgreat
8363 (uri (bioconductor-uri "rGREAT" version))
8366 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
8367 (properties `((upstream-name . "rGREAT")))
8368 (build-system r-build-system)
8370 `(("r-genomicranges" ,r-genomicranges)
8371 ("r-getoptlong" ,r-getoptlong)
8372 ("r-iranges" ,r-iranges)
8373 ("r-rcurl" ,r-rcurl)
8374 ("r-rjson" ,r-rjson)))
8375 (native-inputs `(("r-knitr" ,r-knitr)))
8376 (home-page "https://github.com/jokergoo/rGREAT")
8377 (synopsis "Client for GREAT analysis")
8379 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8380 Tool) analysis automatic by constructing a HTTP POST request according to
8381 user's input and automatically retrieving results from GREAT web server.")
8382 (license license:expat)))
8384 (define-public r-m3c
8391 (uri (bioconductor-uri "M3C" version))
8394 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
8395 (properties `((upstream-name . "M3C")))
8396 (build-system r-build-system)
8398 `(("r-cluster" ,r-cluster)
8399 ("r-corpcor" ,r-corpcor)
8400 ("r-doparallel" ,r-doparallel)
8401 ("r-dosnow" ,r-dosnow)
8402 ("r-foreach" ,r-foreach)
8403 ("r-ggplot2" ,r-ggplot2)
8404 ("r-matrix" ,r-matrix)
8405 ("r-matrixcalc" ,r-matrixcalc)
8406 ("r-rtsne" ,r-rtsne)
8407 ("r-umap" ,r-umap)))
8408 (native-inputs `(("r-knitr" ,r-knitr)))
8409 (home-page "https://bioconductor.org/packages/M3C")
8410 (synopsis "Monte Carlo reference-based consensus clustering")
8412 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8413 simulation to eliminate overestimation of @code{K} and can reject the null
8414 hypothesis @code{K=1}.")
8415 (license license:agpl3+)))
8417 (define-public r-icens
8424 (uri (bioconductor-uri "Icens" version))
8427 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
8428 (properties `((upstream-name . "Icens")))
8429 (build-system r-build-system)
8431 `(("r-survival" ,r-survival)))
8432 (home-page "https://bioconductor.org/packages/Icens")
8433 (synopsis "NPMLE for censored and truncated data")
8435 "This package provides many functions for computing the
8436 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8438 (license license:artistic2.0)))
8440 ;; This is a CRAN package but it depends on r-icens, which is published on
8442 (define-public r-interval
8449 (uri (cran-uri "interval" version))
8452 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
8453 (properties `((upstream-name . "interval")))
8454 (build-system r-build-system)
8456 `(("r-icens" ,r-icens)
8457 ("r-mlecens" ,r-mlecens)
8459 ("r-survival" ,r-survival)))
8460 (home-page "https://cran.r-project.org/web/packages/interval/")
8461 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8463 "This package provides functions to fit nonparametric survival curves,
8464 plot them, and perform logrank or Wilcoxon type tests.")
8465 (license license:gpl2+)))
8467 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8468 ;; Bioconductor package.
8469 (define-public r-fhtest
8476 (uri (cran-uri "FHtest" version))
8479 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
8480 (properties `((upstream-name . "FHtest")))
8481 (build-system r-build-system)
8483 `(("r-interval" ,r-interval)
8484 ("r-kmsurv" ,r-kmsurv)
8487 ("r-survival" ,r-survival)))
8488 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8489 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8491 "This package provides functions to compare two or more survival curves
8495 @item The Fleming-Harrington test for right-censored data based on
8496 permutations and on counting processes.
8497 @item An extension of the Fleming-Harrington test for interval-censored data
8498 based on a permutation distribution and on a score vector distribution.
8501 (license license:gpl2+)))
8503 (define-public r-fourcseq
8510 (uri (bioconductor-uri "FourCSeq" version))
8512 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
8513 (properties `((upstream-name . "FourCSeq")))
8514 (build-system r-build-system)
8516 `(("r-biobase" ,r-biobase)
8517 ("r-biostrings" ,r-biostrings)
8518 ("r-deseq2" ,r-deseq2)
8520 ("r-genomicalignments" ,r-genomicalignments)
8521 ("r-genomicranges" ,r-genomicranges)
8522 ("r-ggbio" ,r-ggbio)
8523 ("r-ggplot2" ,r-ggplot2)
8524 ("r-gtools" ,r-gtools)
8526 ("r-matrix" ,r-matrix)
8527 ("r-reshape2" ,r-reshape2)
8528 ("r-rsamtools" ,r-rsamtools)
8529 ("r-rtracklayer" ,r-rtracklayer)
8530 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8532 `(("r-knitr" ,r-knitr)))
8534 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8535 (synopsis "Analysis of multiplexed 4C sequencing data")
8537 "This package is an R package dedicated to the analysis of (multiplexed)
8538 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8539 interactions between DNA elements and identify differential interactions
8540 between conditions. The statistical analysis in R starts with individual bam
8541 files for each sample as inputs. To obtain these files, the package contains
8542 a Python script to demultiplex libraries and trim off primer sequences. With
8543 a standard alignment software the required bam files can be then be
8545 (license license:gpl3+)))
8547 (define-public r-preprocesscore
8549 (name "r-preprocesscore")
8554 (uri (bioconductor-uri "preprocessCore" version))
8557 "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38"))))
8559 `((upstream-name . "preprocessCore")))
8560 (build-system r-build-system)
8561 (home-page "https://github.com/bmbolstad/preprocessCore")
8562 (synopsis "Collection of pre-processing functions")
8564 "This package provides a library of core pre-processing and normalization
8566 (license license:lgpl2.0+)))
8568 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
8569 ;; Bioconductor package.
8570 (define-public r-wgcna
8577 (uri (cran-uri "WGCNA" version))
8580 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
8581 (properties `((upstream-name . "WGCNA")))
8582 (build-system r-build-system)
8584 `(("r-annotationdbi" ,r-annotationdbi)
8585 ("r-doparallel" ,r-doparallel)
8586 ("r-dynamictreecut" ,r-dynamictreecut)
8587 ("r-fastcluster" ,r-fastcluster)
8588 ("r-foreach" ,r-foreach)
8589 ("r-go-db" ,r-go-db)
8590 ("r-hmisc" ,r-hmisc)
8591 ("r-impute" ,r-impute)
8593 ("r-survival" ,r-survival)
8594 ("r-matrixstats" ,r-matrixstats)
8595 ("r-preprocesscore" ,r-preprocesscore)))
8597 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8598 (synopsis "Weighted correlation network analysis")
8600 "This package provides functions necessary to perform Weighted
8601 Correlation Network Analysis on high-dimensional data. It includes functions
8602 for rudimentary data cleaning, construction and summarization of correlation
8603 networks, module identification and functions for relating both variables and
8604 modules to sample traits. It also includes a number of utility functions for
8605 data manipulation and visualization.")
8606 (license license:gpl2+)))
8608 (define-public r-rgraphviz
8610 (name "r-rgraphviz")
8615 (uri (bioconductor-uri "Rgraphviz" version))
8618 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
8619 (properties `((upstream-name . "Rgraphviz")))
8620 (build-system r-build-system)
8623 (modify-phases %standard-phases
8624 (add-after 'unpack 'make-reproducible
8626 ;; The replacement value is taken from src/graphviz/builddate.h
8627 (substitute* "src/graphviz/configure"
8628 (("VERSION_DATE=.*")
8629 "VERSION_DATE=20200427.2341\n"))
8631 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8632 ;; graphviz. It does not build with the latest version of graphviz, so
8633 ;; we do not add graphviz to the inputs.
8634 (inputs `(("zlib" ,zlib)))
8636 `(("r-graph" ,r-graph)))
8638 `(("pkg-config" ,pkg-config)))
8639 (home-page "https://bioconductor.org/packages/Rgraphviz")
8640 (synopsis "Plotting capabilities for R graph objects")
8642 "This package interfaces R with the graphviz library for plotting R graph
8643 objects from the @code{graph} package.")
8644 (license license:epl1.0)))
8646 (define-public r-fithic
8652 (uri (bioconductor-uri "FitHiC" version))
8655 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
8656 (properties `((upstream-name . "FitHiC")))
8657 (build-system r-build-system)
8659 `(("r-data-table" ,r-data-table)
8660 ("r-fdrtool" ,r-fdrtool)
8661 ("r-rcpp" ,r-rcpp)))
8663 `(("r-knitr" ,r-knitr)))
8664 (home-page "https://bioconductor.org/packages/FitHiC")
8665 (synopsis "Confidence estimation for intra-chromosomal contact maps")
8667 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
8668 intra-chromosomal contact maps produced by genome-wide genome architecture
8669 assays such as Hi-C.")
8670 (license license:gpl2+)))
8672 (define-public r-hitc
8678 (uri (bioconductor-uri "HiTC" version))
8681 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
8682 (properties `((upstream-name . "HiTC")))
8683 (build-system r-build-system)
8685 `(("r-biostrings" ,r-biostrings)
8686 ("r-genomeinfodb" ,r-genomeinfodb)
8687 ("r-genomicranges" ,r-genomicranges)
8688 ("r-iranges" ,r-iranges)
8689 ("r-matrix" ,r-matrix)
8690 ("r-rcolorbrewer" ,r-rcolorbrewer)
8691 ("r-rtracklayer" ,r-rtracklayer)))
8692 (home-page "https://bioconductor.org/packages/HiTC")
8693 (synopsis "High throughput chromosome conformation capture analysis")
8695 "The HiTC package was developed to explore high-throughput \"C\" data
8696 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
8697 quality controls, normalization, visualization, and further analysis are also
8699 (license license:artistic2.0)))
8701 (define-public r-hdf5array
8703 (name "r-hdf5array")
8708 (uri (bioconductor-uri "HDF5Array" version))
8711 "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28"))))
8712 (properties `((upstream-name . "HDF5Array")))
8713 (build-system r-build-system)
8716 (modify-phases %standard-phases
8717 (add-after 'unpack 'fix-linking
8719 (substitute* "src/Makevars"
8720 ;; This is to avoid having a plain directory on the list of
8721 ;; libraries to link.
8722 (("\\(RHDF5LIB_LIBS\\)" match)
8723 (string-append match "/libhdf5.a")))
8728 `(("r-biocgenerics" ,r-biocgenerics)
8729 ("r-delayedarray" ,r-delayedarray)
8730 ("r-iranges" ,r-iranges)
8731 ("r-matrix" ,r-matrix)
8732 ("r-rhdf5" ,r-rhdf5)
8733 ("r-rhdf5lib" ,r-rhdf5lib)
8734 ("r-s4vectors" ,r-s4vectors)))
8735 (home-page "https://bioconductor.org/packages/HDF5Array")
8736 (synopsis "HDF5 back end for DelayedArray objects")
8737 (description "This package provides an array-like container for convenient
8738 access and manipulation of HDF5 datasets. It supports delayed operations and
8740 (license license:artistic2.0)))
8742 (define-public r-rhdf5lib
8749 (uri (bioconductor-uri "Rhdf5lib" version))
8752 "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2"))
8753 (modules '((guix build utils)))
8756 ;; Delete bundled binaries
8757 (delete-file-recursively "src/wininclude/")
8758 (delete-file-recursively "src/winlib-4.9.3/")
8759 (delete-file-recursively "src/winlib-8.3.0/")
8760 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
8762 (properties `((upstream-name . "Rhdf5lib")))
8763 (build-system r-build-system)
8766 (modify-phases %standard-phases
8767 (add-after 'unpack 'do-not-use-bundled-hdf5
8768 (lambda* (#:key inputs #:allow-other-keys)
8769 (for-each delete-file '("configure" "configure.ac"))
8770 ;; Do not make other packages link with the proprietary libsz.
8771 (substitute* "R/zzz.R"
8772 ((" \"%s/libsz.a\"") ""))
8773 (with-directory-excursion "src"
8774 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
8775 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
8777 ;; Remove timestamp and host system information to make
8778 ;; the build reproducible.
8779 (substitute* "hdf5/src/libhdf5.settings.in"
8780 (("Configured on: @CONFIG_DATE@")
8781 "Configured on: Guix")
8782 (("Uname information:.*")
8783 "Uname information: Linux\n")
8784 ;; Remove unnecessary store reference.
8786 "C Compiler: GCC\n"))
8787 (rename-file "hdf5/src/libhdf5.settings.in"
8788 "hdf5/src/libhdf5.settings")
8789 (rename-file "Makevars.in" "Makevars")
8790 (substitute* "Makevars"
8791 (("@ZLIB_LIB@") "-lz")
8792 (("@ZLIB_INCLUDE@") "")
8793 (("HDF5_CXX_LIB=.*")
8794 (string-append "HDF5_CXX_LIB="
8795 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
8797 (string-append "HDF5_LIB="
8798 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
8799 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
8800 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
8801 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
8802 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
8804 (string-append "HDF5_HL_LIB="
8805 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
8806 (("HDF5_HL_CXX_LIB=.*")
8807 (string-append "HDF5_HL_CXX_LIB="
8808 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
8809 ;; szip is non-free software
8810 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
8811 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
8816 `(("hdf5" ,hdf5-1.10)))
8818 `(("hdf5-source" ,(package-source hdf5-1.10))
8819 ("r-knitr" ,r-knitr)))
8820 (home-page "https://bioconductor.org/packages/Rhdf5lib")
8821 (synopsis "HDF5 library as an R package")
8822 (description "This package provides C and C++ HDF5 libraries for use in R
8824 (license license:artistic2.0)))
8826 (define-public r-beachmat
8833 (uri (bioconductor-uri "beachmat" version))
8836 "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7"))))
8837 (build-system r-build-system)
8839 `(("r-biocgenerics" ,r-biocgenerics)
8840 ("r-delayedarray" ,r-delayedarray)
8841 ("r-matrix" ,r-matrix)))
8843 `(("r-knitr" ,r-knitr)))
8844 (home-page "https://bioconductor.org/packages/beachmat")
8845 (synopsis "Compiling Bioconductor to handle each matrix type")
8846 (description "This package provides a consistent C++ class interface for a
8847 variety of commonly used matrix types, including sparse and HDF5-backed
8849 (license license:gpl3)))
8851 (define-public r-singlecellexperiment
8853 (name "r-singlecellexperiment")
8858 (uri (bioconductor-uri "SingleCellExperiment" version))
8861 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
8863 `((upstream-name . "SingleCellExperiment")))
8864 (build-system r-build-system)
8866 `(("r-biocgenerics" ,r-biocgenerics)
8867 ("r-s4vectors" ,r-s4vectors)
8868 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8870 `(("r-knitr" ,r-knitr)))
8871 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
8872 (synopsis "S4 classes for single cell data")
8873 (description "This package defines an S4 class for storing data from
8874 single-cell experiments. This includes specialized methods to store and
8875 retrieve spike-in information, dimensionality reduction coordinates and size
8876 factors for each cell, along with the usual metadata for genes and
8878 (license license:gpl3)))
8880 (define-public r-scuttle
8887 (uri (bioconductor-uri "scuttle" version))
8890 "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m"))))
8891 (properties `((upstream-name . "scuttle")))
8892 (build-system r-build-system)
8894 `(("r-beachmat" ,r-beachmat)
8895 ("r-biocgenerics" ,r-biocgenerics)
8896 ("r-biocparallel" ,r-biocparallel)
8897 ("r-delayedarray" ,r-delayedarray)
8898 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8899 ("r-genomicranges" ,r-genomicranges)
8900 ("r-matrix" ,r-matrix)
8902 ("r-s4vectors" ,r-s4vectors)
8903 ("r-singlecellexperiment" ,r-singlecellexperiment)
8904 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8905 (native-inputs `(("r-knitr" ,r-knitr)))
8906 (home-page "https://bioconductor.org/packages/scuttle")
8907 (synopsis "Single-cell RNA-Seq analysis utilities")
8909 "This package provides basic utility functions for performing single-cell
8910 analyses, focusing on simple normalization, quality control and data
8911 transformations. It also provides some helper functions to assist development
8912 of other packages.")
8913 (license license:gpl3)))
8915 (define-public r-scater
8921 (uri (bioconductor-uri "scater" version))
8924 "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535"))))
8925 (build-system r-build-system)
8927 `(("r-biocgenerics" ,r-biocgenerics)
8928 ("r-biocneighbors" ,r-biocneighbors)
8929 ("r-biocparallel" ,r-biocparallel)
8930 ("r-biocsingular" ,r-biocsingular)
8931 ("r-delayedarray" ,r-delayedarray)
8932 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8933 ("r-ggbeeswarm" ,r-ggbeeswarm)
8934 ("r-ggplot2" ,r-ggplot2)
8935 ("r-gridextra" ,r-gridextra)
8936 ("r-matrix" ,r-matrix)
8937 ("r-rlang" ,r-rlang)
8938 ("r-s4vectors" ,r-s4vectors)
8939 ("r-scuttle" ,r-scuttle)
8940 ("r-singlecellexperiment" ,r-singlecellexperiment)
8941 ("r-summarizedexperiment" ,r-summarizedexperiment)
8942 ("r-viridis" ,r-viridis)))
8944 `(("r-knitr" ,r-knitr)))
8945 (home-page "https://github.com/davismcc/scater")
8946 (synopsis "Single-cell analysis toolkit for gene expression data in R")
8947 (description "This package provides a collection of tools for doing
8948 various analyses of single-cell RNA-seq gene expression data, with a focus on
8950 (license license:gpl2+)))
8952 (define-public r-scran
8959 (uri (bioconductor-uri "scran" version))
8962 "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww"))))
8963 (build-system r-build-system)
8965 `(("r-beachmat" ,r-beachmat)
8967 ("r-biocgenerics" ,r-biocgenerics)
8968 ("r-biocneighbors" ,r-biocneighbors)
8969 ("r-biocparallel" ,r-biocparallel)
8970 ("r-biocsingular" ,r-biocsingular)
8971 ("r-bluster" ,r-bluster)
8972 ("r-delayedarray" ,r-delayedarray)
8973 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8974 ("r-dqrng" ,r-dqrng)
8975 ("r-edger" ,r-edger)
8976 ("r-igraph" ,r-igraph)
8977 ("r-limma" ,r-limma)
8978 ("r-matrix" ,r-matrix)
8980 ("r-s4vectors" ,r-s4vectors)
8981 ("r-scuttle" ,r-scuttle)
8982 ("r-singlecellexperiment" ,r-singlecellexperiment)
8983 ("r-statmod" ,r-statmod)
8984 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8986 `(("r-knitr" ,r-knitr)))
8987 (home-page "https://bioconductor.org/packages/scran")
8988 (synopsis "Methods for single-cell RNA-Seq data analysis")
8989 (description "This package implements a variety of low-level analyses of
8990 single-cell RNA-seq data. Methods are provided for normalization of
8991 cell-specific biases, assignment of cell cycle phase, and detection of highly
8992 variable and significantly correlated genes.")
8993 (license license:gpl3)))
8995 (define-public r-sparsematrixstats
8997 (name "r-sparsematrixstats")
9002 (uri (bioconductor-uri "sparseMatrixStats" version))
9005 "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh"))))
9007 `((upstream-name . "sparseMatrixStats")))
9008 (build-system r-build-system)
9010 `(("r-matrix" ,r-matrix)
9011 ("r-matrixgenerics" ,r-matrixgenerics)
9012 ("r-matrixstats" ,r-matrixstats)
9013 ("r-rcpp" ,r-rcpp)))
9014 (native-inputs `(("r-knitr" ,r-knitr)))
9015 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
9016 (synopsis "Summary statistics for rows and columns of sparse matrices")
9018 "This package provides high performance functions for row and column
9019 operations on sparse matrices. Currently, the optimizations are limited to
9020 data in the column sparse format.")
9021 (license license:expat)))
9023 (define-public r-delayedmatrixstats
9025 (name "r-delayedmatrixstats")
9030 (uri (bioconductor-uri "DelayedMatrixStats" version))
9033 "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0"))))
9035 `((upstream-name . "DelayedMatrixStats")))
9036 (build-system r-build-system)
9038 `(("r-biocparallel" ,r-biocparallel)
9039 ("r-delayedarray" ,r-delayedarray)
9040 ("r-hdf5array" ,r-hdf5array)
9041 ("r-iranges" ,r-iranges)
9042 ("r-matrix" ,r-matrix)
9043 ("r-matrixgenerics" ,r-matrixgenerics)
9044 ("r-matrixstats" ,r-matrixstats)
9045 ("r-s4vectors" ,r-s4vectors)
9046 ("r-sparsematrixstats" ,r-sparsematrixstats)))
9048 `(("r-knitr" ,r-knitr)))
9049 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
9050 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
9052 "This package provides a port of the @code{matrixStats} API for use with
9053 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
9054 contains high-performing functions operating on rows and columns of
9055 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
9056 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
9057 are optimized per data type and for subsetted calculations such that both
9058 memory usage and processing time is minimized.")
9059 (license license:expat)))
9061 (define-public r-mscoreutils
9063 (name "r-mscoreutils")
9068 (uri (bioconductor-uri "MsCoreUtils" version))
9071 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
9072 (properties `((upstream-name . "MsCoreUtils")))
9073 (build-system r-build-system)
9075 `(("r-mass" ,r-mass)
9077 ("r-s4vectors" ,r-s4vectors)))
9079 `(("r-knitr" ,r-knitr)))
9080 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
9081 (synopsis "Core utils for mass spectrometry data")
9083 "This package defines low-level functions for mass spectrometry data and
9084 is independent of any high-level data structures. These functions include
9085 mass spectra processing functions (noise estimation, smoothing, binning),
9086 quantitative aggregation functions (median polish, robust summarisation,
9087 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
9088 well as misc helper functions, that are used across high-level data structure
9089 within the R for Mass Spectrometry packages.")
9090 (license license:artistic2.0)))
9092 (define-public r-biocio
9099 (uri (bioconductor-uri "BiocIO" version))
9102 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
9103 (properties `((upstream-name . "BiocIO")))
9104 (build-system r-build-system)
9106 `(("r-biocgenerics" ,r-biocgenerics)
9107 ("r-genomicranges" ,r-genomicranges)
9108 ("r-rcurl" ,r-rcurl)
9109 ("r-s4vectors" ,r-s4vectors)))
9111 `(("r-knitr" ,r-knitr)))
9112 (home-page "https://bioconductor.org/packages/BiocIO")
9113 (synopsis "Standard input and output for Bioconductor packages")
9115 "This package implements `import()` and `export()` standard generics for
9116 importing and exporting biological data formats. `import()` supports
9117 whole-file as well as chunk-wise iterative import. The `import()` interface
9118 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
9119 row or element-like components of the file resource), `select()` (on
9120 column-like components of the file resource) and `collect()`. The `import()`
9121 interface optionally provides transparent access to remote (e.g. via https)
9122 as well as local access. Developers can register a file extension, e.g.,
9123 `.loom` for dispatch from character-based URIs to specific `import()` /
9124 `export()` methods based on classes representing file types, e.g.,
9126 (license license:artistic2.0)))
9128 (define-public r-msmseda
9135 (uri (bioconductor-uri "msmsEDA" version))
9138 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
9139 (properties `((upstream-name . "msmsEDA")))
9140 (build-system r-build-system)
9142 `(("r-gplots" ,r-gplots)
9144 ("r-msnbase" ,r-msnbase)
9145 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9147 "https://bioconductor.org/packages/msmsEDA")
9148 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
9150 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
9151 experiments, and visualize de influence of the involved factors.")
9152 (license license:gpl2)))
9154 (define-public r-msmstests
9156 (name "r-msmstests")
9161 (uri (bioconductor-uri "msmsTests" version))
9164 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
9165 (properties `((upstream-name . "msmsTests")))
9166 (build-system r-build-system)
9168 `(("r-edger" ,r-edger)
9169 ("r-msmseda" ,r-msmseda)
9170 ("r-msnbase" ,r-msnbase)
9171 ("r-qvalue" ,r-qvalue)))
9173 "https://bioconductor.org/packages/msmsTests")
9174 (synopsis "Differential LC-MS/MS expression tests")
9176 "This packages provides statistical tests for label-free LC-MS/MS data
9177 by spectral counts, to discover differentially expressed proteins between two
9178 biological conditions. Three tests are available: Poisson GLM regression,
9179 quasi-likelihood GLM regression, and the negative binomial of the edgeR
9180 package.The three models admit blocking factors to control for nuissance
9181 variables.To assure a good level of reproducibility a post-test filter is
9182 available, where we may set the minimum effect size considered biologicaly
9183 relevant, and the minimum expression of the most abundant condition.")
9184 (license license:gpl2)))
9186 (define-public r-catalyst
9193 (uri (bioconductor-uri "CATALYST" version))
9196 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
9197 (properties `((upstream-name . "CATALYST")))
9198 (build-system r-build-system)
9200 `(("r-circlize" ,r-circlize)
9201 ("r-complexheatmap" ,r-complexheatmap)
9202 ("r-consensusclusterplus" ,r-consensusclusterplus)
9203 ("r-cowplot" ,r-cowplot)
9204 ("r-data-table" ,r-data-table)
9205 ("r-dplyr" ,r-dplyr)
9207 ("r-flowcore" ,r-flowcore)
9208 ("r-flowsom" ,r-flowsom)
9209 ("r-ggplot2" ,r-ggplot2)
9210 ("r-ggrepel" ,r-ggrepel)
9211 ("r-ggridges" ,r-ggridges)
9212 ("r-gridextra" ,r-gridextra)
9213 ("r-magrittr" ,r-magrittr)
9214 ("r-matrix" ,r-matrix)
9215 ("r-matrixstats" ,r-matrixstats)
9217 ("r-purrr" ,r-purrr)
9218 ("r-rcolorbrewer" ,r-rcolorbrewer)
9219 ("r-reshape2" ,r-reshape2)
9220 ("r-rtsne" ,r-rtsne)
9221 ("r-s4vectors" ,r-s4vectors)
9222 ("r-scales" ,r-scales)
9223 ("r-scater" ,r-scater)
9224 ("r-singlecellexperiment" ,r-singlecellexperiment)
9225 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9227 `(("r-knitr" ,r-knitr)))
9229 "https://github.com/HelenaLC/CATALYST")
9230 (synopsis "Cytometry data analysis tools")
9232 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
9233 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
9234 reporters to label antibodies, thereby substantially decreasing spectral
9235 overlap and allowing for examination of over 50 parameters at the single cell
9236 level. While spectral overlap is significantly less pronounced in CyTOF than
9237 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
9238 and oxide formation can impede data interpretability. We designed
9239 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
9240 preprocessing of cytometry data, including i) normalization using bead
9241 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
9242 (license license:gpl2+)))
9244 (define-public r-gwascat
9251 (uri (bioconductor-uri "gwascat" version))
9254 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
9255 (build-system r-build-system)
9257 `(("r-annotationdbi" ,r-annotationdbi)
9258 ("r-biocfilecache" ,r-biocfilecache)
9259 ("r-biostrings" ,r-biostrings)
9260 ("r-genomeinfodb" ,r-genomeinfodb)
9261 ("r-genomicfeatures" ,r-genomicfeatures)
9262 ("r-genomicranges" ,r-genomicranges)
9263 ("r-iranges" ,r-iranges)
9264 ("r-readr" ,r-readr)
9265 ("r-s4vectors" ,r-s4vectors)
9266 ("r-snpstats" ,r-snpstats)
9267 ("r-variantannotation" ,r-variantannotation)))
9269 `(("r-knitr" ,r-knitr)))
9270 (home-page "https://bioconductor.org/packages/gwascat")
9271 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
9273 "This package provides tools for representing and modeling data in the
9274 EMBL-EBI GWAS catalog.")
9275 (license license:artistic2.0)))
9277 (define-public r-kegggraph
9279 (name "r-kegggraph")
9284 (uri (bioconductor-uri "KEGGgraph" version))
9286 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
9287 (properties `((upstream-name . "KEGGgraph")))
9288 (build-system r-build-system)
9290 `(("r-graph" ,r-graph)
9291 ("r-rcurl" ,r-rcurl)
9293 (home-page "https://bioconductor.org/packages/KEGGgraph")
9294 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
9296 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
9297 object as well as a collection of tools to analyze, dissect and visualize these
9298 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
9299 maintaining all essential pathway attributes. The package offers
9300 functionalities including parsing, graph operation, visualization and etc.")
9301 (license license:gpl2+)))
9303 (define-public r-pathview
9310 (uri (bioconductor-uri "pathview" version))
9312 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
9313 (properties `((upstream-name . "pathview")))
9314 (build-system r-build-system)
9316 `(("r-annotationdbi" ,r-annotationdbi)
9317 ("r-graph" ,r-graph)
9318 ("r-kegggraph" ,r-kegggraph)
9319 ("r-keggrest" ,r-keggrest)
9320 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
9322 ("r-rgraphviz" ,r-rgraphviz)
9324 (home-page "https://pathview.uncc.edu/")
9325 (synopsis "Tool set for pathway based data integration and visualization")
9327 "@code{r-pathview} is a tool set for pathway based data integration and
9328 visualization. It maps and renders a wide variety of biological data on
9329 relevant pathway graphs. All users need is to supply their data and specify
9330 the target pathway. This package automatically downloads the pathway graph
9331 data, parses the data file, maps user data to the pathway, and render pathway
9332 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
9333 integrates with pathway and gene set (enrichment) analysis tools for
9334 large-scale and fully automated analysis.")
9335 (license license:gpl3+)))
9337 (define-public r-sushi
9343 (uri (bioconductor-uri "Sushi" version))
9346 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
9347 (properties `((upstream-name . "Sushi")))
9348 (build-system r-build-system)
9350 `(("r-biomart" ,r-biomart)
9352 (home-page "https://bioconductor.org/packages/Sushi")
9353 (synopsis "Tools for visualizing genomics data")
9355 "This package provides flexible, quantitative, and integrative genomic
9356 visualizations for publication-quality multi-panel figures.")
9357 (license license:gpl2+)))