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-reactome-db
55 (name "r-reactome-db")
60 (uri (bioconductor-uri "reactome.db" version 'annotation))
63 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
64 (properties `((upstream-name . "reactome.db")))
65 (build-system r-build-system)
67 `(("r-annotationdbi" ,r-annotationdbi)))
68 (home-page "https://bioconductor.org/packages/reactome.db/")
69 (synopsis "Annotation maps for reactome")
71 "This package provides a set of annotation maps for the REACTOME
72 database, assembled using data from REACTOME.")
73 (license license:cc-by4.0)))
75 (define-public r-bsgenome-celegans-ucsc-ce6
77 (name "r-bsgenome-celegans-ucsc-ce6")
81 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
85 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
87 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
88 (build-system r-build-system)
90 `(("r-bsgenome" ,r-bsgenome)))
92 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
93 (synopsis "Full genome sequences for Worm")
95 "This package provides full genome sequences for Caenorhabditis
96 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
98 (license license:artistic2.0)))
100 (define-public r-bsgenome-celegans-ucsc-ce10
102 (name "r-bsgenome-celegans-ucsc-ce10")
106 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
107 version 'annotation))
110 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
112 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
113 (build-system r-build-system)
115 `(("r-bsgenome" ,r-bsgenome)))
117 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
118 (synopsis "Full genome sequences for Worm")
120 "This package provides full genome sequences for Caenorhabditis
121 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
123 (license license:artistic2.0)))
125 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
127 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
131 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
132 version 'annotation))
135 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
137 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
138 (build-system r-build-system)
140 `(("r-bsgenome" ,r-bsgenome)))
142 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
143 (synopsis "Full genome sequences for Fly")
145 "This package provides full genome sequences for Drosophila
146 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
148 (license license:artistic2.0)))
150 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
152 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
156 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
157 version 'annotation))
160 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
162 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
163 (build-system r-build-system)
165 `(("r-bsgenome" ,r-bsgenome)))
167 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
168 (synopsis "Full genome sequences for Fly")
170 "This package provides full genome sequences for Drosophila
171 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
172 Biostrings objects.")
173 (license license:artistic2.0)))
175 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
177 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
181 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
182 version 'annotation))
185 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
187 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
188 (build-system r-build-system)
190 `(("r-bsgenome" ,r-bsgenome)
191 ("r-bsgenome-dmelanogaster-ucsc-dm3"
192 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
193 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
194 (synopsis "Full masked genome sequences for Fly")
196 "This package provides full masked genome sequences for Drosophila
197 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
198 Biostrings objects. The sequences are the same as in
199 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
200 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
201 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
202 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
203 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
204 (license license:artistic2.0)))
206 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
208 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
212 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
213 version 'annotation))
216 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
218 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
219 (build-system r-build-system)
221 `(("r-bsgenome" ,r-bsgenome)))
223 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
224 (synopsis "Full genome sequences for Homo sapiens")
226 "This package provides full genome sequences for Homo sapiens from
227 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
228 (license license:artistic2.0)))
230 (define-public r-bsgenome-hsapiens-ncbi-grch38
232 (name "r-bsgenome-hsapiens-ncbi-grch38")
237 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
238 version 'annotation))
241 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
242 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
243 (build-system r-build-system)
244 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
246 "https://bioconductor.org/packages/release/data/annotation/html/\
247 BSgenome.Hsapiens.NCBI.GRCh38.html")
248 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
250 "This package provides full genome sequences for Homo sapiens (Human) as
251 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
252 (license license:artistic2.0)))
254 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
256 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
260 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
261 version 'annotation))
264 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
266 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
267 (build-system r-build-system)
269 `(("r-bsgenome" ,r-bsgenome)
270 ("r-bsgenome-hsapiens-ucsc-hg19"
271 ,r-bsgenome-hsapiens-ucsc-hg19)))
272 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
273 (synopsis "Full masked genome sequences for Homo sapiens")
275 "This package provides full genome sequences for Homo sapiens (Human) as
276 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
277 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
278 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
279 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
280 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
281 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
283 (license license:artistic2.0)))
285 (define-public r-bsgenome-mmusculus-ucsc-mm9
287 (name "r-bsgenome-mmusculus-ucsc-mm9")
291 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
292 version 'annotation))
295 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
297 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
298 (build-system r-build-system)
300 `(("r-bsgenome" ,r-bsgenome)))
302 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
303 (synopsis "Full genome sequences for Mouse")
305 "This package provides full genome sequences for Mus musculus (Mouse) as
306 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
307 (license license:artistic2.0)))
309 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
311 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
315 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
316 version 'annotation))
319 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
321 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
322 (build-system r-build-system)
324 `(("r-bsgenome" ,r-bsgenome)
325 ("r-bsgenome-mmusculus-ucsc-mm9"
326 ,r-bsgenome-mmusculus-ucsc-mm9)))
327 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
328 (synopsis "Full masked genome sequences for Mouse")
330 "This package provides full genome sequences for Mus musculus (Mouse) as
331 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
332 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
333 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
334 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
335 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
336 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
338 (license license:artistic2.0)))
340 (define-public r-bsgenome-mmusculus-ucsc-mm10
342 (name "r-bsgenome-mmusculus-ucsc-mm10")
346 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
347 version 'annotation))
350 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
353 (build-system r-build-system)
355 `(("r-bsgenome" ,r-bsgenome)))
357 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
358 (synopsis "Full genome sequences for Mouse")
360 "This package provides full genome sequences for Mus
361 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
362 in Biostrings objects.")
363 (license license:artistic2.0)))
365 (define-public r-org-ce-eg-db
367 (name "r-org-ce-eg-db")
371 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
374 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
376 `((upstream-name . "org.Ce.eg.db")))
377 (build-system r-build-system)
379 `(("r-annotationdbi" ,r-annotationdbi)))
380 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
381 (synopsis "Genome wide annotation for Worm")
383 "This package provides mappings from Entrez gene identifiers to various
384 annotations for the genome of the model worm Caenorhabditis elegans.")
385 (license license:artistic2.0)))
387 (define-public r-org-dm-eg-db
389 (name "r-org-dm-eg-db")
393 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
396 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
398 `((upstream-name . "org.Dm.eg.db")))
399 (build-system r-build-system)
401 `(("r-annotationdbi" ,r-annotationdbi)))
402 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
403 (synopsis "Genome wide annotation for Fly")
405 "This package provides mappings from Entrez gene identifiers to various
406 annotations for the genome of the model fruit fly Drosophila melanogaster.")
407 (license license:artistic2.0)))
409 (define-public r-org-dr-eg-db
411 (name "r-org-dr-eg-db")
415 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
418 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
420 `((upstream-name . "org.Dr.eg.db")))
421 (build-system r-build-system)
423 `(("r-annotationdbi" ,r-annotationdbi)))
424 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
425 (synopsis "Annotation for Zebrafish")
427 "This package provides genome wide annotations for Zebrafish, primarily
428 based on mapping using Entrez Gene identifiers.")
429 (license license:artistic2.0)))
431 (define-public r-org-hs-eg-db
433 (name "r-org-hs-eg-db")
437 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
440 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
442 `((upstream-name . "org.Hs.eg.db")))
443 (build-system r-build-system)
445 `(("r-annotationdbi" ,r-annotationdbi)))
446 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
447 (synopsis "Genome wide annotation for Human")
449 "This package contains genome-wide annotations for Human, primarily based
450 on mapping using Entrez Gene identifiers.")
451 (license license:artistic2.0)))
453 (define-public r-org-mm-eg-db
455 (name "r-org-mm-eg-db")
459 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
462 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
464 `((upstream-name . "org.Mm.eg.db")))
465 (build-system r-build-system)
467 `(("r-annotationdbi" ,r-annotationdbi)))
468 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
469 (synopsis "Genome wide annotation for Mouse")
471 "This package provides mappings from Entrez gene identifiers to various
472 annotations for the genome of the model mouse Mus musculus.")
473 (license license:artistic2.0)))
475 (define-public r-bsgenome-hsapiens-ucsc-hg19
477 (name "r-bsgenome-hsapiens-ucsc-hg19")
481 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
482 version 'annotation))
485 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
487 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
488 (build-system r-build-system)
490 `(("r-bsgenome" ,r-bsgenome)))
492 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
493 (synopsis "Full genome sequences for Homo sapiens")
495 "This package provides full genome sequences for Homo sapiens as provided
496 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
497 (license license:artistic2.0)))
499 (define-public r-bsgenome-hsapiens-ucsc-hg38
501 (name "r-bsgenome-hsapiens-ucsc-hg38")
505 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
506 version 'annotation))
509 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
511 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
512 (build-system r-build-system)
514 `(("r-bsgenome" ,r-bsgenome)))
516 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
517 (synopsis "Full genome sequences for Homo sapiens")
519 "This package provides full genome sequences for Homo sapiens (Human)
520 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
521 (license license:artistic2.0)))
523 (define-public r-ensdb-hsapiens-v75
525 (name "r-ensdb-hsapiens-v75")
530 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
533 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
535 `((upstream-name . "EnsDb.Hsapiens.v75")))
536 (build-system r-build-system)
538 `(("r-ensembldb" ,r-ensembldb)))
539 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
540 (synopsis "Ensembl based annotation package")
542 "This package exposes an annotation database generated from Ensembl.")
543 (license license:artistic2.0)))
545 (define-public r-genelendatabase
547 (name "r-genelendatabase")
552 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
555 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
557 `((upstream-name . "geneLenDataBase")))
558 (build-system r-build-system)
560 `(("r-rtracklayer" ,r-rtracklayer)
561 ("r-genomicfeatures" ,r-genomicfeatures)))
562 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
563 (synopsis "Lengths of mRNA transcripts for a number of genomes")
565 "This package provides the lengths of mRNA transcripts for a number of
566 genomes and gene ID formats, largely based on the UCSC table browser.")
567 (license license:lgpl2.0+)))
569 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
571 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
575 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
576 version 'annotation))
579 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
581 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
582 (build-system r-build-system)
584 `(("r-genomicfeatures" ,r-genomicfeatures)))
586 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
587 (synopsis "Annotation package for human genome in TxDb format")
589 "This package provides an annotation database of Homo sapiens genome
590 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
591 track. The database is exposed as a @code{TxDb} object.")
592 (license license:artistic2.0)))
594 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
596 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
600 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
601 version 'annotation))
604 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
606 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
607 (build-system r-build-system)
609 `(("r-genomicfeatures" ,r-genomicfeatures)))
611 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
612 (synopsis "Annotation package for human genome in TxDb format")
614 "This package provides an annotation database of Homo sapiens genome
615 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
616 track. The database is exposed as a @code{TxDb} object.")
617 (license license:artistic2.0)))
619 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
621 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
625 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
626 version 'annotation))
629 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
631 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
632 (build-system r-build-system)
634 `(("r-genomicfeatures" ,r-genomicfeatures)
635 ("r-annotationdbi" ,r-annotationdbi)))
637 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
638 (synopsis "Annotation package for mouse genome in TxDb format")
640 "This package provides an annotation database of Mouse genome data. It
641 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
642 database is exposed as a @code{TxDb} object.")
643 (license license:artistic2.0)))
645 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
647 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
651 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
652 version 'annotation))
655 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
657 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
658 (build-system r-build-system)
660 `(("r-bsgenome" ,r-bsgenome)
661 ("r-genomicfeatures" ,r-genomicfeatures)
662 ("r-annotationdbi" ,r-annotationdbi)))
664 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
665 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
667 "This package loads a TxDb object, which is an R interface to
668 prefabricated databases contained in this package. This package provides
669 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
670 based on the knownGene track.")
671 (license license:artistic2.0)))
673 (define-public r-txdb-celegans-ucsc-ce6-ensgene
675 (name "r-txdb-celegans-ucsc-ce6-ensgene")
680 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
681 version 'annotation))
684 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
686 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
687 (build-system r-build-system)
689 `(("r-annotationdbi" ,r-annotationdbi)
690 ("r-genomicfeatures" ,r-genomicfeatures)))
691 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
692 (synopsis "Annotation package for C elegans TxDb objects")
694 "This package exposes a C elegans annotation database generated from UCSC
695 by exposing these as TxDb objects.")
696 (license license:artistic2.0)))
698 (define-public r-fdb-infiniummethylation-hg19
700 (name "r-fdb-infiniummethylation-hg19")
704 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
705 version 'annotation))
708 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
710 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
711 (build-system r-build-system)
713 `(("r-biostrings" ,r-biostrings)
714 ("r-genomicfeatures" ,r-genomicfeatures)
715 ("r-annotationdbi" ,r-annotationdbi)
716 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
717 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
718 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
719 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
721 "This is an annotation package for Illumina Infinium DNA methylation
722 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
724 (license license:artistic2.0)))
726 (define-public r-illuminahumanmethylationepicmanifest
728 (name "r-illuminahumanmethylationepicmanifest")
732 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
733 version 'annotation))
736 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
738 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
739 (build-system r-build-system)
741 `(("r-minfi" ,r-minfi)))
742 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
743 (synopsis "Manifest for Illumina's EPIC methylation arrays")
745 "This is a manifest package for Illumina's EPIC methylation arrays.")
746 (license license:artistic2.0)))
748 (define-public r-ideoviz
754 (uri (bioconductor-uri "IdeoViz" version))
757 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
758 (build-system r-build-system)
760 `(("r-biobase" ,r-biobase)
761 ("r-iranges" ,r-iranges)
762 ("r-genomicranges" ,r-genomicranges)
763 ("r-rcolorbrewer" ,r-rcolorbrewer)
764 ("r-rtracklayer" ,r-rtracklayer)
765 ("r-genomeinfodb" ,r-genomeinfodb)))
766 (home-page "https://bioconductor.org/packages/IdeoViz/")
767 (synopsis "Plots data along a chromosomal ideogram")
768 (description "This package provides functions to plot data associated with
769 arbitrary genomic intervals along chromosomal ideogram.")
770 (license license:gpl2)))
772 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
773 ;; from Bioconductor.
774 (define-public r-deconstructsigs
776 (name "r-deconstructsigs")
780 (uri (cran-uri "deconstructSigs" version))
783 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
785 `((upstream-name . "deconstructSigs")))
786 (build-system r-build-system)
788 `(("r-bsgenome" ,r-bsgenome)
789 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
790 ("r-genomeinfodb" ,r-genomeinfodb)
791 ("r-reshape2" ,r-reshape2)))
792 (home-page "https://github.com/raerose01/deconstructSigs")
793 (synopsis "Identifies signatures present in a tumor sample")
794 (description "This package takes sample information in the form of the
795 fraction of mutations in each of 96 trinucleotide contexts and identifies
796 the weighted combination of published signatures that, when summed, most
797 closely reconstructs the mutational profile.")
798 (license license:gpl2+)))
800 ;; This is a CRAN package, but it depends on Bioconductor packages.
808 (uri (cran-uri "NMF" version))
811 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
812 (properties `((upstream-name . "NMF")))
813 (build-system r-build-system)
815 `(("r-cluster" ,r-cluster)
816 ("r-biobase" ,r-biobase)
817 ("r-biocmanager" ,r-biocmanager)
818 ("r-bigmemory" ,r-bigmemory) ; suggested
819 ("r-synchronicity" ,r-synchronicity) ; suggested
820 ("r-colorspace" ,r-colorspace)
821 ("r-digest" ,r-digest)
822 ("r-doparallel" ,r-doparallel)
823 ("r-foreach" ,r-foreach)
824 ("r-ggplot2" ,r-ggplot2)
825 ("r-gridbase" ,r-gridbase)
826 ("r-pkgmaker" ,r-pkgmaker)
827 ("r-rcolorbrewer" ,r-rcolorbrewer)
828 ("r-registry" ,r-registry)
829 ("r-reshape2" ,r-reshape2)
830 ("r-rngtools" ,r-rngtools)
831 ("r-stringr" ,r-stringr)))
833 `(("r-knitr" ,r-knitr)))
834 (home-page "http://renozao.github.io/NMF")
835 (synopsis "Algorithms and framework for nonnegative matrix factorization")
837 "This package provides a framework to perform Non-negative Matrix
838 Factorization (NMF). The package implements a set of already published
839 algorithms and seeding methods, and provides a framework to test, develop and
840 plug new or custom algorithms. Most of the built-in algorithms have been
841 optimized in C++, and the main interface function provides an easy way of
842 performing parallel computations on multicore machines.")
843 (license license:gpl2+)))
845 (define-public r-do-db
851 (uri (bioconductor-uri "DO.db" version 'annotation))
854 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
856 `((upstream-name . "DO.db")))
857 (build-system r-build-system)
859 `(("r-annotationdbi" ,r-annotationdbi)))
860 (home-page "https://www.bioconductor.org/packages/DO.db/")
861 (synopsis "Annotation maps describing the entire Disease Ontology")
863 "This package provides a set of annotation maps describing the entire
865 (license license:artistic2.0)))
867 (define-public r-pasilla
874 "http://bioconductor.org/packages/release/data/experiment"
875 "/src/contrib/pasilla_" version ".tar.gz"))
878 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
879 (build-system r-build-system)
881 `(("r-biocstyle" ,r-biocstyle)
882 ("r-dexseq" ,r-dexseq)
884 ("r-rmarkdown" ,r-rmarkdown)))
885 (home-page "https://www.bioconductor.org/packages/pasilla/")
886 (synopsis "Data package with per-exon and per-gene read counts")
887 (description "This package provides per-exon and per-gene read counts
888 computed for selected genes from RNA-seq data that were presented in the
889 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
890 by Brooks et al., Genome Research 2011.")
891 (license license:lgpl2.1+)))
893 (define-public r-pfam-db
900 (uri (bioconductor-uri "PFAM.db" version 'annotation))
903 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
904 (properties `((upstream-name . "PFAM.db")))
905 (build-system r-build-system)
907 `(("r-annotationdbi" ,r-annotationdbi)))
908 (home-page "https://bioconductor.org/packages/PFAM.db")
909 (synopsis "Set of protein ID mappings for PFAM")
911 "This package provides a set of protein ID mappings for PFAM, assembled
912 using data from public repositories.")
913 (license license:artistic2.0)))
915 (define-public r-phastcons100way-ucsc-hg19
917 (name "r-phastcons100way-ucsc-hg19")
922 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
923 version 'annotation))
926 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
928 `((upstream-name . "phastCons100way.UCSC.hg19")))
929 (build-system r-build-system)
931 `(("r-bsgenome" ,r-bsgenome)
932 ("r-genomeinfodb" ,r-genomeinfodb)
933 ("r-genomicranges" ,r-genomicranges)
934 ("r-genomicscores" ,r-genomicscores)
935 ("r-iranges" ,r-iranges)
936 ("r-s4vectors" ,r-s4vectors)))
937 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
938 (synopsis "UCSC phastCons conservation scores for hg19")
940 "This package provides UCSC phastCons conservation scores for the human
941 genome (hg19) calculated from multiple alignments with other 99 vertebrate
943 (license license:artistic2.0)))
948 (define-public r-abadata
954 (uri (bioconductor-uri "ABAData" version 'experiment))
957 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
959 `((upstream-name . "ABAData")))
960 (build-system r-build-system)
962 `(("r-annotationdbi" ,r-annotationdbi)))
963 (home-page "https://www.bioconductor.org/packages/ABAData/")
964 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
966 "This package provides the data for the gene expression enrichment
967 analysis conducted in the package ABAEnrichment. The package includes three
968 datasets which are derived from the Allen Brain Atlas:
971 @item Gene expression data from Human Brain (adults) averaged across donors,
972 @item Gene expression data from the Developing Human Brain pooled into five
973 age categories and averaged across donors, and
974 @item a developmental effect score based on the Developing Human Brain
978 All datasets are restricted to protein coding genes.")
979 (license license:gpl2+)))
981 (define-public r-arrmdata
987 (uri (bioconductor-uri "ARRmData" version 'experiment))
990 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
992 `((upstream-name . "ARRmData")))
993 (build-system r-build-system)
994 (home-page "https://www.bioconductor.org/packages/ARRmData/")
995 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
997 "This package provides raw beta values from 36 samples across 3 groups
998 from Illumina 450k methylation arrays.")
999 (license license:artistic2.0)))
1001 (define-public r-hsmmsinglecell
1003 (name "r-hsmmsinglecell")
1007 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1010 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1012 `((upstream-name . "HSMMSingleCell")))
1013 (build-system r-build-system)
1014 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1015 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1017 "Skeletal myoblasts undergo a well-characterized sequence of
1018 morphological and transcriptional changes during differentiation. In this
1019 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1020 under high mitogen conditions (GM) and then differentiated by switching to
1021 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1022 hundred cells taken over a time-course of serum-induced differentiation.
1023 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1024 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1025 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1026 which were then sequenced to a depth of ~4 million reads per library,
1027 resulting in a complete gene expression profile for each cell.")
1028 (license license:artistic2.0)))
1030 (define-public r-all
1036 (uri (bioconductor-uri "ALL" version 'experiment))
1039 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1040 (properties `((upstream-name . "ALL")))
1041 (build-system r-build-system)
1043 `(("r-biobase" ,r-biobase)))
1044 (home-page "https://bioconductor.org/packages/ALL")
1045 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1047 "The data consist of microarrays from 128 different individuals with
1048 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1049 are available. The data have been normalized (using rma) and it is the
1050 jointly normalized data that are available here. The data are presented in
1051 the form of an @code{exprSet} object.")
1052 (license license:artistic2.0)))
1054 (define-public r-affydata
1061 (uri (bioconductor-uri "affydata" version 'experiment))
1064 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1065 (properties `((upstream-name . "affydata")))
1066 (build-system r-build-system)
1068 `(("r-affy" ,r-affy)))
1069 (home-page "https://bioconductor.org/packages/affydata/")
1070 (synopsis "Affymetrix data for demonstration purposes")
1072 "This package provides example datasets that represent 'real world
1073 examples' of Affymetrix data, unlike the artificial examples included in the
1074 package @code{affy}.")
1075 (license license:gpl2+)))
1077 (define-public r-coverageview
1079 (name "r-coverageview")
1083 (uri (bioconductor-uri "CoverageView" version))
1086 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
1087 (build-system r-build-system)
1089 `(("r-s4vectors" ,r-s4vectors)
1090 ("r-iranges" ,r-iranges)
1091 ("r-genomicranges" ,r-genomicranges)
1092 ("r-genomicalignments" ,r-genomicalignments)
1093 ("r-rtracklayer" ,r-rtracklayer)
1094 ("r-rsamtools" ,r-rsamtools)))
1095 (home-page "https://bioconductor.org/packages/CoverageView/")
1096 (synopsis "Coverage visualization package for R")
1097 (description "This package provides a framework for the visualization of
1098 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1099 be also used for genome-wide nucleosome positioning experiments or other
1100 experiment types where it is important to have a framework in order to inspect
1101 how the coverage distributed across the genome.")
1102 (license license:artistic2.0)))
1104 (define-public r-cummerbund
1106 (name "r-cummerbund")
1110 (uri (bioconductor-uri "cummeRbund" version))
1113 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
1114 (build-system r-build-system)
1116 `(("r-biobase" ,r-biobase)
1117 ("r-biocgenerics" ,r-biocgenerics)
1118 ("r-fastcluster" ,r-fastcluster)
1119 ("r-ggplot2" ,r-ggplot2)
1122 ("r-reshape2" ,r-reshape2)
1123 ("r-rsqlite" ,r-rsqlite)
1124 ("r-rtracklayer" ,r-rtracklayer)
1125 ("r-s4vectors" ,r-s4vectors)))
1126 (home-page "https://bioconductor.org/packages/cummeRbund/")
1127 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1128 (description "This package allows for persistent storage, access,
1129 exploration, and manipulation of Cufflinks high-throughput sequencing
1130 data. In addition, provides numerous plotting functions for commonly
1131 used visualizations.")
1132 (license license:artistic2.0)))
1134 (define-public r-curatedtcgadata
1136 (name "r-curatedtcgadata")
1141 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1144 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1146 `((upstream-name . "curatedTCGAData")))
1147 (build-system r-build-system)
1149 `(("r-annotationhub" ,r-annotationhub)
1150 ("r-experimenthub" ,r-experimenthub)
1151 ("r-hdf5array" ,r-hdf5array)
1152 ("r-multiassayexperiment" ,r-multiassayexperiment)
1153 ("r-s4vectors" ,r-s4vectors)
1154 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1155 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1156 (synopsis "Curated data from The Cancer Genome Atlas")
1158 "This package provides publicly available data from The Cancer Genome
1159 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1160 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1161 number, mutation, microRNA, protein, and others) with clinical / pathological
1162 data. It also links assay barcodes with patient identifiers, enabling
1163 harmonized subsetting of rows (features) and columns (patients / samples)
1164 across the entire multi-'omics experiment.")
1165 (license license:artistic2.0)))
1170 (define-public r-biocversion
1172 (name "r-biocversion")
1177 (uri (bioconductor-uri "BiocVersion" version))
1180 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
1181 (properties `((upstream-name . "BiocVersion")))
1182 (build-system r-build-system)
1183 (home-page "https://bioconductor.org/packages/BiocVersion/")
1184 (synopsis "Set the appropriate version of Bioconductor packages")
1186 "This package provides repository information for the appropriate version
1188 (license license:artistic2.0)))
1190 (define-public r-biocgenerics
1192 (name "r-biocgenerics")
1196 (uri (bioconductor-uri "BiocGenerics" version))
1199 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
1201 `((upstream-name . "BiocGenerics")))
1202 (build-system r-build-system)
1203 (home-page "https://bioconductor.org/packages/BiocGenerics")
1204 (synopsis "S4 generic functions for Bioconductor")
1206 "This package provides S4 generic functions needed by many Bioconductor
1208 (license license:artistic2.0)))
1210 (define-public r-affycomp
1217 (uri (bioconductor-uri "affycomp" version))
1220 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
1221 (properties `((upstream-name . "affycomp")))
1222 (build-system r-build-system)
1223 (propagated-inputs `(("r-biobase" ,r-biobase)))
1224 (home-page "https://bioconductor.org/packages/affycomp/")
1225 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1227 "The package contains functions that can be used to compare expression
1228 measures for Affymetrix Oligonucleotide Arrays.")
1229 (license license:gpl2+)))
1231 (define-public r-affycompatible
1233 (name "r-affycompatible")
1238 (uri (bioconductor-uri "AffyCompatible" version))
1241 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
1243 `((upstream-name . "AffyCompatible")))
1244 (build-system r-build-system)
1246 `(("r-biostrings" ,r-biostrings)
1247 ("r-rcurl" ,r-rcurl)
1249 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1250 (synopsis "Work with Affymetrix GeneChip files")
1252 "This package provides an interface to Affymetrix chip annotation and
1253 sample attribute files. The package allows an easy way for users to download
1254 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1255 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1256 Command Console} (AGCC)-compatible sample annotation files.")
1257 (license license:artistic2.0)))
1259 (define-public r-affycontam
1261 (name "r-affycontam")
1266 (uri (bioconductor-uri "affyContam" version))
1269 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
1270 (properties `((upstream-name . "affyContam")))
1271 (build-system r-build-system)
1273 `(("r-affy" ,r-affy)
1274 ("r-affydata" ,r-affydata)
1275 ("r-biobase" ,r-biobase)))
1276 (home-page "https://bioconductor.org/packages/affyContam/")
1277 (synopsis "Structured corruption of Affymetrix CEL file data")
1279 "Microarray quality assessment is a major concern of microarray analysts.
1280 This package provides some simple approaches to in silico creation of quality
1281 problems in CEL-level data to help evaluate performance of quality metrics.")
1282 (license license:artistic2.0)))
1284 (define-public r-affycoretools
1286 (name "r-affycoretools")
1291 (uri (bioconductor-uri "affycoretools" version))
1294 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
1295 (properties `((upstream-name . "affycoretools")))
1296 (build-system r-build-system)
1298 `(("r-affy" ,r-affy)
1299 ("r-annotationdbi" ,r-annotationdbi)
1300 ("r-biobase" ,r-biobase)
1301 ("r-biocgenerics" ,r-biocgenerics)
1303 ("r-edger" ,r-edger)
1304 ("r-gcrma" ,r-gcrma)
1305 ("r-glimma" ,r-glimma)
1306 ("r-ggplot2" ,r-ggplot2)
1307 ("r-gostats" ,r-gostats)
1308 ("r-gplots" ,r-gplots)
1309 ("r-hwriter" ,r-hwriter)
1310 ("r-lattice" ,r-lattice)
1311 ("r-limma" ,r-limma)
1312 ("r-oligoclasses" ,r-oligoclasses)
1313 ("r-reportingtools" ,r-reportingtools)
1314 ("r-rsqlite" ,r-rsqlite)
1315 ("r-s4vectors" ,r-s4vectors)
1316 ("r-xtable" ,r-xtable)))
1318 `(("r-knitr" ,r-knitr)))
1319 (home-page "https://bioconductor.org/packages/affycoretools/")
1320 (synopsis "Functions for analyses with Affymetrix GeneChips")
1322 "This package provides various wrapper functions that have been written
1323 to streamline the more common analyses that a Biostatistician might see.")
1324 (license license:artistic2.0)))
1326 (define-public r-affxparser
1328 (name "r-affxparser")
1333 (uri (bioconductor-uri "affxparser" version))
1336 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
1337 (properties `((upstream-name . "affxparser")))
1338 (build-system r-build-system)
1339 (home-page "https://github.com/HenrikBengtsson/affxparser")
1340 (synopsis "Affymetrix File Parsing SDK")
1342 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1343 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1344 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1345 are supported. Currently, there are methods for reading @dfn{chip definition
1346 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1347 either in full or in part. For example, probe signals from a few probesets
1348 can be extracted very quickly from a set of CEL files into a convenient list
1350 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1352 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1354 (define-public r-annotate
1361 (uri (bioconductor-uri "annotate" version))
1364 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
1365 (build-system r-build-system)
1367 `(("r-annotationdbi" ,r-annotationdbi)
1368 ("r-biobase" ,r-biobase)
1369 ("r-biocgenerics" ,r-biocgenerics)
1373 ("r-xtable" ,r-xtable)))
1375 "https://bioconductor.org/packages/annotate")
1376 (synopsis "Annotation for microarrays")
1377 (description "This package provides R environments for the annotation of
1379 (license license:artistic2.0)))
1381 (define-public r-hpar
1388 (uri (bioconductor-uri "hpar" version))
1391 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
1392 (build-system r-build-system)
1394 `(("r-knitr" ,r-knitr)))
1395 (home-page "https://bioconductor.org/packages/hpar/")
1396 (synopsis "Human Protein Atlas in R")
1397 (description "This package provides a simple interface to and data from
1398 the Human Protein Atlas project.")
1399 (license license:artistic2.0)))
1401 (define-public r-regioner
1408 (uri (bioconductor-uri "regioneR" version))
1411 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
1412 (properties `((upstream-name . "regioneR")))
1413 (build-system r-build-system)
1415 `(("r-biostrings" ,r-biostrings)
1416 ("r-bsgenome" ,r-bsgenome)
1417 ("r-genomeinfodb" ,r-genomeinfodb)
1418 ("r-genomicranges" ,r-genomicranges)
1419 ("r-iranges" ,r-iranges)
1420 ("r-memoise" ,r-memoise)
1421 ("r-rtracklayer" ,r-rtracklayer)
1422 ("r-s4vectors" ,r-s4vectors)))
1424 `(("r-knitr" ,r-knitr)))
1425 (home-page "https://bioconductor.org/packages/regioneR/")
1426 (synopsis "Association analysis of genomic regions")
1427 (description "This package offers a statistical framework based on
1428 customizable permutation tests to assess the association between genomic
1429 region sets and other genomic features.")
1430 (license license:artistic2.0)))
1432 (define-public r-reportingtools
1434 (name "r-reportingtools")
1439 (uri (bioconductor-uri "ReportingTools" version))
1442 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
1444 `((upstream-name . "ReportingTools")))
1445 (build-system r-build-system)
1447 `(("r-annotate" ,r-annotate)
1448 ("r-annotationdbi" ,r-annotationdbi)
1449 ("r-biobase" ,r-biobase)
1450 ("r-biocgenerics" ,r-biocgenerics)
1451 ("r-category" ,r-category)
1452 ("r-deseq2" ,r-deseq2)
1453 ("r-edger" ,r-edger)
1454 ("r-ggbio" ,r-ggbio)
1455 ("r-ggplot2" ,r-ggplot2)
1456 ("r-gostats" ,r-gostats)
1457 ("r-gseabase" ,r-gseabase)
1458 ("r-hwriter" ,r-hwriter)
1459 ("r-iranges" ,r-iranges)
1460 ("r-knitr" ,r-knitr)
1461 ("r-lattice" ,r-lattice)
1462 ("r-limma" ,r-limma)
1463 ("r-pfam-db" ,r-pfam-db)
1464 ("r-r-utils" ,r-r-utils)
1467 `(("r-knitr" ,r-knitr)))
1468 (home-page "https://bioconductor.org/packages/ReportingTools/")
1469 (synopsis "Tools for making reports in various formats")
1471 "The ReportingTools package enables users to easily display reports of
1472 analysis results generated from sources such as microarray and sequencing
1473 data. The package allows users to create HTML pages that may be viewed on a
1474 web browser, or in other formats. Users can generate tables with sortable and
1475 filterable columns, make and display plots, and link table entries to other
1476 data sources such as NCBI or larger plots within the HTML page. Using the
1477 package, users can also produce a table of contents page to link various
1478 reports together for a particular project that can be viewed in a web
1480 (license license:artistic2.0)))
1482 (define-public r-geneplotter
1484 (name "r-geneplotter")
1489 (uri (bioconductor-uri "geneplotter" version))
1492 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
1493 (build-system r-build-system)
1495 `(("r-annotate" ,r-annotate)
1496 ("r-annotationdbi" ,r-annotationdbi)
1497 ("r-biobase" ,r-biobase)
1498 ("r-biocgenerics" ,r-biocgenerics)
1499 ("r-lattice" ,r-lattice)
1500 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1501 (home-page "https://bioconductor.org/packages/geneplotter")
1502 (synopsis "Graphics functions for genomic data")
1504 "This package provides functions for plotting genomic data.")
1505 (license license:artistic2.0)))
1507 (define-public r-oligoclasses
1509 (name "r-oligoclasses")
1514 (uri (bioconductor-uri "oligoClasses" version))
1517 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
1518 (properties `((upstream-name . "oligoClasses")))
1519 (build-system r-build-system)
1521 `(("r-affyio" ,r-affyio)
1522 ("r-biobase" ,r-biobase)
1523 ("r-biocgenerics" ,r-biocgenerics)
1524 ("r-biocmanager" ,r-biocmanager)
1525 ("r-biostrings" ,r-biostrings)
1528 ("r-foreach" ,r-foreach)
1529 ("r-genomicranges" ,r-genomicranges)
1530 ("r-iranges" ,r-iranges)
1531 ("r-rsqlite" ,r-rsqlite)
1532 ("r-s4vectors" ,r-s4vectors)
1533 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1534 (home-page "https://bioconductor.org/packages/oligoClasses/")
1535 (synopsis "Classes for high-throughput arrays")
1537 "This package contains class definitions, validity checks, and
1538 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1540 (license license:gpl2+)))
1542 (define-public r-oligo
1549 (uri (bioconductor-uri "oligo" version))
1552 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
1553 (properties `((upstream-name . "oligo")))
1554 (build-system r-build-system)
1555 (inputs `(("zlib" ,zlib)))
1557 `(("r-affxparser" ,r-affxparser)
1558 ("r-affyio" ,r-affyio)
1559 ("r-biobase" ,r-biobase)
1560 ("r-biocgenerics" ,r-biocgenerics)
1561 ("r-biostrings" ,r-biostrings)
1564 ("r-oligoclasses" ,r-oligoclasses)
1565 ("r-preprocesscore" ,r-preprocesscore)
1566 ("r-rsqlite" ,r-rsqlite)
1567 ("r-zlibbioc" ,r-zlibbioc)))
1569 `(("r-knitr" ,r-knitr)))
1570 (home-page "https://bioconductor.org/packages/oligo/")
1571 (synopsis "Preprocessing tools for oligonucleotide arrays")
1573 "This package provides a package to analyze oligonucleotide
1574 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1575 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1576 (license license:lgpl2.0+)))
1578 (define-public r-qvalue
1585 (uri (bioconductor-uri "qvalue" version))
1588 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
1589 (build-system r-build-system)
1591 `(("r-ggplot2" ,r-ggplot2)
1592 ("r-reshape2" ,r-reshape2)))
1594 `(("r-knitr" ,r-knitr)))
1595 (home-page "https://github.com/StoreyLab/qvalue")
1596 (synopsis "Q-value estimation for false discovery rate control")
1598 "This package takes a list of p-values resulting from the simultaneous
1599 testing of many hypotheses and estimates their q-values and local @dfn{false
1600 discovery rate} (FDR) values. The q-value of a test measures the proportion
1601 of false positives incurred when that particular test is called significant.
1602 The local FDR measures the posterior probability the null hypothesis is true
1603 given the test's p-value. Various plots are automatically generated, allowing
1604 one to make sensible significance cut-offs. The software can be applied to
1605 problems in genomics, brain imaging, astrophysics, and data mining.")
1606 ;; Any version of the LGPL.
1607 (license license:lgpl3+)))
1609 (define r-rcppnumerical
1611 (name "r-rcppnumerical")
1615 (uri (cran-uri "RcppNumerical" version))
1618 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
1619 (properties `((upstream-name . "RcppNumerical")))
1620 (build-system r-build-system)
1622 `(("r-rcpp" ,r-rcpp)
1623 ("r-rcppeigen" ,r-rcppeigen)))
1625 `(("r-knitr" ,r-knitr)))
1626 (home-page "https://github.com/yixuan/RcppNumerical")
1627 (synopsis "Rcpp integration for numerical computing libraries")
1628 (description "This package provides a collection of open source libraries
1629 for numerical computing (numerical integration, optimization, etc.) and their
1630 integration with @code{Rcpp}.")
1631 (license license:gpl2+)))
1633 (define-public r-apeglm
1639 (uri (bioconductor-uri "apeglm" version))
1642 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
1643 (properties `((upstream-name . "apeglm")))
1644 (build-system r-build-system)
1646 `(("r-emdbook" ,r-emdbook)
1647 ("r-genomicranges" ,r-genomicranges)
1649 ("r-rcppeigen" ,r-rcppeigen)
1650 ("r-rcppnumerical" ,r-rcppnumerical)
1651 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1652 (native-inputs `(("r-knitr" ,r-knitr)))
1653 (home-page "https://bioconductor.org/packages/apeglm")
1654 (synopsis "Approximate posterior estimation for GLM coefficients")
1655 (description "This package provides Bayesian shrinkage estimators for
1656 effect sizes for a variety of GLM models, using approximation of the
1657 posterior for individual coefficients.")
1658 (license license:gpl2)))
1660 (define-public r-greylistchip
1662 (name "r-greylistchip")
1666 (uri (bioconductor-uri "GreyListChIP" version))
1669 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
1670 (properties `((upstream-name . "GreyListChIP")))
1671 (build-system r-build-system)
1673 `(("r-bsgenome" ,r-bsgenome)
1674 ("r-genomeinfodb" ,r-genomeinfodb)
1675 ("r-genomicalignments" ,r-genomicalignments)
1676 ("r-genomicranges" ,r-genomicranges)
1678 ("r-rsamtools" ,r-rsamtools)
1679 ("r-rtracklayer" ,r-rtracklayer)
1680 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1681 (home-page "https://bioconductor.org/packages/GreyListChIP")
1682 (synopsis "Greylist artefact regions based on ChIP inputs")
1683 (description "This package identifies regions of ChIP experiments with high
1684 signal in the input, that lead to spurious peaks during peak calling.")
1685 (license license:artistic2.0)))
1687 (define-public r-diffbind
1694 (uri (bioconductor-uri "DiffBind" version))
1697 "0irhqsi6rrkrkc7dhwmfpqfd0mnigs17027czcx8vgbrbra4lcvd"))))
1698 (properties `((upstream-name . "DiffBind")))
1699 (build-system r-build-system)
1703 `(("r-amap" ,r-amap)
1704 ("r-apeglm" ,r-apeglm)
1706 ("r-biocparallel" ,r-biocparallel)
1707 ("r-deseq2" ,r-deseq2)
1708 ("r-dplyr" ,r-dplyr)
1709 ("r-genomicalignments" ,r-genomicalignments)
1710 ("r-genomicranges" ,r-genomicranges)
1711 ("r-ggplot2" ,r-ggplot2)
1712 ("r-ggrepel" ,r-ggrepel)
1713 ("r-gplots" ,r-gplots)
1714 ("r-greylistchip" ,r-greylistchip)
1715 ("r-iranges" ,r-iranges)
1716 ("r-lattice" ,r-lattice)
1717 ("r-limma" ,r-limma)
1718 ("r-locfit" ,r-locfit)
1719 ("r-rcolorbrewer" , r-rcolorbrewer)
1721 ("r-rhtslib" ,r-rhtslib)
1722 ("r-rsamtools" ,r-rsamtools)
1723 ("r-s4vectors" ,r-s4vectors)
1724 ("r-summarizedexperiment" ,r-summarizedexperiment)
1725 ("r-systempiper" ,r-systempiper)))
1726 (home-page "https://bioconductor.org/packages/DiffBind")
1727 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1729 "This package computes differentially bound sites from multiple
1730 ChIP-seq experiments using affinity (quantitative) data. Also enables
1731 occupancy (overlap) analysis and plotting functions.")
1732 (license license:artistic2.0)))
1734 (define-public r-ripseeker
1736 (name "r-ripseeker")
1741 (uri (bioconductor-uri "RIPSeeker" version))
1744 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1745 (properties `((upstream-name . "RIPSeeker")))
1746 (build-system r-build-system)
1748 `(("r-s4vectors" ,r-s4vectors)
1749 ("r-iranges" ,r-iranges)
1750 ("r-genomicranges" ,r-genomicranges)
1751 ("r-summarizedexperiment" ,r-summarizedexperiment)
1752 ("r-rsamtools" ,r-rsamtools)
1753 ("r-genomicalignments" ,r-genomicalignments)
1754 ("r-rtracklayer" ,r-rtracklayer)))
1755 (home-page "https://bioconductor.org/packages/RIPSeeker")
1757 "Identifying protein-associated transcripts from RIP-seq experiments")
1759 "This package infers and discriminates RIP peaks from RIP-seq alignments
1760 using two-state HMM with negative binomial emission probability. While
1761 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1762 a suite of bioinformatics tools integrated within this self-contained software
1763 package comprehensively addressing issues ranging from post-alignments
1764 processing to visualization and annotation.")
1765 (license license:gpl2)))
1767 (define-public r-multtest
1774 (uri (bioconductor-uri "multtest" version))
1777 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
1778 (build-system r-build-system)
1780 `(("r-survival" ,r-survival)
1781 ("r-biocgenerics" ,r-biocgenerics)
1782 ("r-biobase" ,r-biobase)
1783 ("r-mass" ,r-mass)))
1784 (home-page "https://bioconductor.org/packages/multtest")
1785 (synopsis "Resampling-based multiple hypothesis testing")
1787 "This package can do non-parametric bootstrap and permutation
1788 resampling-based multiple testing procedures (including empirical Bayes
1789 methods) for controlling the family-wise error rate (FWER), generalized
1790 family-wise error rate (gFWER), tail probability of the proportion of
1791 false positives (TPPFP), and false discovery rate (FDR). Several choices
1792 of bootstrap-based null distribution are implemented (centered, centered
1793 and scaled, quantile-transformed). Single-step and step-wise methods are
1794 available. Tests based on a variety of T- and F-statistics (including
1795 T-statistics based on regression parameters from linear and survival models
1796 as well as those based on correlation parameters) are included. When probing
1797 hypotheses with T-statistics, users may also select a potentially faster null
1798 distribution which is multivariate normal with mean zero and variance
1799 covariance matrix derived from the vector influence function. Results are
1800 reported in terms of adjusted P-values, confidence regions and test statistic
1801 cutoffs. The procedures are directly applicable to identifying differentially
1802 expressed genes in DNA microarray experiments.")
1803 (license license:lgpl3)))
1805 (define-public r-graph
1811 (uri (bioconductor-uri "graph" version))
1814 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
1815 (build-system r-build-system)
1817 `(("r-biocgenerics" ,r-biocgenerics)))
1818 (home-page "https://bioconductor.org/packages/graph")
1819 (synopsis "Handle graph data structures in R")
1821 "This package implements some simple graph handling capabilities for R.")
1822 (license license:artistic2.0)))
1824 ;; This is a CRAN package, but it depends on a Bioconductor package.
1825 (define-public r-ggm
1832 (uri (cran-uri "ggm" version))
1835 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1836 (properties `((upstream-name . "ggm")))
1837 (build-system r-build-system)
1839 `(("r-graph" ,r-graph)
1840 ("r-igraph" ,r-igraph)))
1841 (home-page "https://cran.r-project.org/package=ggm")
1842 (synopsis "Functions for graphical Markov models")
1844 "This package provides functions and datasets for maximum likelihood
1845 fitting of some classes of graphical Markov models.")
1846 (license license:gpl2+)))
1848 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
1849 (define-public r-perfmeas
1856 (uri (cran-uri "PerfMeas" version))
1859 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
1860 (properties `((upstream-name . "PerfMeas")))
1861 (build-system r-build-system)
1863 `(("r-graph" ,r-graph)
1864 ("r-limma" ,r-limma)
1865 ("r-rbgl" ,r-rbgl)))
1866 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
1867 (synopsis "Performance measures for ranking and classification tasks")
1869 "This package implements different performance measures for
1870 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
1871 a given recall, F-score for single and multiple classes are available.")
1872 (license license:gpl2+)))
1874 ;; This is a CRAN package, but it depends on a Bioconductor package.
1875 (define-public r-codedepends
1877 (name "r-codedepends")
1882 (uri (cran-uri "CodeDepends" version))
1885 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1886 (properties `((upstream-name . "CodeDepends")))
1887 (build-system r-build-system)
1889 `(("r-codetools" ,r-codetools)
1890 ("r-graph" ,r-graph)
1892 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1893 (synopsis "Analysis of R code for reproducible research and code comprehension")
1895 "This package provides tools for analyzing R expressions or blocks of
1896 code and determining the dependencies between them. It focuses on R scripts,
1897 but can be used on the bodies of functions. There are many facilities
1898 including the ability to summarize or get a high-level view of code,
1899 determining dependencies between variables, code improvement suggestions.")
1900 ;; Any version of the GPL
1901 (license (list license:gpl2+ license:gpl3+))))
1903 (define-public r-chippeakanno
1905 (name "r-chippeakanno")
1910 (uri (bioconductor-uri "ChIPpeakAnno" version))
1913 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
1914 (properties `((upstream-name . "ChIPpeakAnno")))
1915 (build-system r-build-system)
1917 `(("r-annotationdbi" ,r-annotationdbi)
1918 ("r-biocgenerics" ,r-biocgenerics)
1919 ("r-biomart" ,r-biomart)
1920 ("r-biostrings" ,r-biostrings)
1922 ("r-ensembldb" ,r-ensembldb)
1923 ("r-genomeinfodb" ,r-genomeinfodb)
1924 ("r-genomicalignments" ,r-genomicalignments)
1925 ("r-genomicfeatures" ,r-genomicfeatures)
1926 ("r-genomicranges" ,r-genomicranges)
1927 ("r-ggplot2" ,r-ggplot2)
1928 ("r-graph" ,r-graph)
1929 ("r-iranges" ,r-iranges)
1930 ("r-keggrest" ,r-keggrest)
1931 ("r-matrixstats" ,r-matrixstats)
1932 ("r-multtest" ,r-multtest)
1934 ("r-regioner" ,r-regioner)
1935 ("r-rsamtools" ,r-rsamtools)
1936 ("r-rtracklayer" ,r-rtracklayer)
1937 ("r-s4vectors" ,r-s4vectors)
1938 ("r-summarizedexperiment" ,r-summarizedexperiment)
1939 ("r-venndiagram" ,r-venndiagram)))
1941 `(("r-knitr" ,r-knitr)))
1942 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1943 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1945 "The package includes functions to retrieve the sequences around the peak,
1946 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1947 custom features such as most conserved elements and other transcription factor
1948 binding sites supplied by users. Starting 2.0.5, new functions have been added
1949 for finding the peaks with bi-directional promoters with summary statistics
1950 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1951 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1952 enrichedGO (addGeneIDs).")
1953 (license license:gpl2+)))
1955 (define-public r-marray
1961 (uri (bioconductor-uri "marray" version))
1963 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
1964 (build-system r-build-system)
1966 `(("r-limma" ,r-limma)))
1967 (home-page "https://bioconductor.org/packages/marray")
1968 (synopsis "Exploratory analysis for two-color spotted microarray data")
1969 (description "This package contains class definitions for two-color spotted
1970 microarray data. It also includes functions for data input, diagnostic plots,
1971 normalization and quality checking.")
1972 (license license:lgpl2.0+)))
1974 (define-public r-cghbase
1980 (uri (bioconductor-uri "CGHbase" version))
1982 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
1983 (properties `((upstream-name . "CGHbase")))
1984 (build-system r-build-system)
1986 `(("r-biobase" ,r-biobase)
1987 ("r-marray" ,r-marray)))
1988 (home-page "https://bioconductor.org/packages/CGHbase")
1989 (synopsis "Base functions and classes for arrayCGH data analysis")
1990 (description "This package contains functions and classes that are needed by
1991 the @code{arrayCGH} packages.")
1992 (license license:gpl2+)))
1994 (define-public r-cghcall
2000 (uri (bioconductor-uri "CGHcall" version))
2002 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
2003 (properties `((upstream-name . "CGHcall")))
2004 (build-system r-build-system)
2006 `(("r-biobase" ,r-biobase)
2007 ("r-cghbase" ,r-cghbase)
2008 ("r-impute" ,r-impute)
2009 ("r-dnacopy" ,r-dnacopy)
2010 ("r-snowfall" ,r-snowfall)))
2011 (home-page "https://bioconductor.org/packages/CGHcall")
2012 (synopsis "Base functions and classes for arrayCGH data analysis")
2013 (description "This package contains functions and classes that are needed by
2014 @code{arrayCGH} packages.")
2015 (license license:gpl2+)))
2017 (define-public r-qdnaseq
2023 (uri (bioconductor-uri "QDNAseq" version))
2025 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
2026 (properties `((upstream-name . "QDNAseq")))
2027 (build-system r-build-system)
2029 `(("r-biobase" ,r-biobase)
2030 ("r-cghbase" ,r-cghbase)
2031 ("r-cghcall" ,r-cghcall)
2032 ("r-dnacopy" ,r-dnacopy)
2033 ("r-future" ,r-future)
2034 ("r-future-apply" ,r-future-apply)
2035 ("r-genomicranges" ,r-genomicranges)
2036 ("r-iranges" ,r-iranges)
2037 ("r-matrixstats" ,r-matrixstats)
2038 ("r-r-utils" ,r-r-utils)
2039 ("r-rsamtools" ,r-rsamtools)))
2040 (home-page "https://bioconductor.org/packages/QDNAseq")
2041 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2042 (description "The genome is divided into non-overlapping fixed-sized bins,
2043 number of sequence reads in each counted, adjusted with a simultaneous
2044 two-dimensional loess correction for sequence mappability and GC content, and
2045 filtered to remove spurious regions in the genome. Downstream steps of
2046 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2048 (license license:gpl2+)))
2050 (define-public r-bayseq
2057 (uri (bioconductor-uri "baySeq" version))
2060 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
2061 (properties `((upstream-name . "baySeq")))
2062 (build-system r-build-system)
2064 `(("r-abind" ,r-abind)
2065 ("r-edger" ,r-edger)
2066 ("r-genomicranges" ,r-genomicranges)))
2067 (home-page "https://bioconductor.org/packages/baySeq/")
2068 (synopsis "Bayesian analysis of differential expression patterns in count data")
2070 "This package identifies differential expression in high-throughput count
2071 data, such as that derived from next-generation sequencing machines,
2072 calculating estimated posterior likelihoods of differential expression (or
2073 more complex hypotheses) via empirical Bayesian methods.")
2074 (license license:gpl3)))
2076 (define-public r-chipcomp
2083 (uri (bioconductor-uri "ChIPComp" version))
2086 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
2087 (properties `((upstream-name . "ChIPComp")))
2088 (build-system r-build-system)
2090 `(("r-biocgenerics" ,r-biocgenerics)
2091 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2092 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2093 ("r-genomeinfodb" ,r-genomeinfodb)
2094 ("r-genomicranges" ,r-genomicranges)
2095 ("r-iranges" ,r-iranges)
2096 ("r-limma" ,r-limma)
2097 ("r-rsamtools" ,r-rsamtools)
2098 ("r-rtracklayer" ,r-rtracklayer)
2099 ("r-s4vectors" ,r-s4vectors)))
2100 (home-page "https://bioconductor.org/packages/ChIPComp")
2101 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2103 "ChIPComp implements a statistical method for quantitative comparison of
2104 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2105 sites across multiple conditions considering matching control in ChIP-seq
2107 ;; Any version of the GPL.
2108 (license license:gpl3+)))
2110 (define-public r-riboprofiling
2112 (name "r-riboprofiling")
2117 (uri (bioconductor-uri "RiboProfiling" version))
2120 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
2121 (properties `((upstream-name . "RiboProfiling")))
2122 (build-system r-build-system)
2124 `(("r-biocgenerics" ,r-biocgenerics)
2125 ("r-biostrings" ,r-biostrings)
2126 ("r-data-table" ,r-data-table)
2127 ("r-genomeinfodb" ,r-genomeinfodb)
2128 ("r-genomicalignments" ,r-genomicalignments)
2129 ("r-genomicfeatures" ,r-genomicfeatures)
2130 ("r-genomicranges" ,r-genomicranges)
2131 ("r-ggbio" ,r-ggbio)
2132 ("r-ggplot2" ,r-ggplot2)
2133 ("r-iranges" ,r-iranges)
2135 ("r-reshape2" ,r-reshape2)
2136 ("r-rsamtools" ,r-rsamtools)
2137 ("r-rtracklayer" ,r-rtracklayer)
2138 ("r-s4vectors" ,r-s4vectors)
2139 ("r-sqldf" ,r-sqldf)))
2141 `(("r-knitr" ,r-knitr)))
2142 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2143 (synopsis "Ribosome profiling data analysis")
2144 (description "Starting with a BAM file, this package provides the
2145 necessary functions for quality assessment, read start position recalibration,
2146 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2147 of count data: pairs, log fold-change, codon frequency and coverage
2148 assessment, principal component analysis on codon coverage.")
2149 (license license:gpl3)))
2151 (define-public r-riboseqr
2158 (uri (bioconductor-uri "riboSeqR" version))
2161 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
2162 (properties `((upstream-name . "riboSeqR")))
2163 (build-system r-build-system)
2165 `(("r-abind" ,r-abind)
2166 ("r-bayseq" ,r-bayseq)
2167 ("r-genomeinfodb" ,r-genomeinfodb)
2168 ("r-genomicranges" ,r-genomicranges)
2169 ("r-iranges" ,r-iranges)
2170 ("r-rsamtools" ,r-rsamtools)
2171 ("r-seqlogo" ,r-seqlogo)))
2172 (home-page "https://bioconductor.org/packages/riboSeqR/")
2173 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2175 "This package provides plotting functions, frameshift detection and
2176 parsing of genetic sequencing data from ribosome profiling experiments.")
2177 (license license:gpl3)))
2179 (define-public r-interactionset
2181 (name "r-interactionset")
2186 (uri (bioconductor-uri "InteractionSet" version))
2189 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
2191 `((upstream-name . "InteractionSet")))
2192 (build-system r-build-system)
2194 `(("r-biocgenerics" ,r-biocgenerics)
2195 ("r-genomeinfodb" ,r-genomeinfodb)
2196 ("r-genomicranges" ,r-genomicranges)
2197 ("r-iranges" ,r-iranges)
2198 ("r-matrix" ,r-matrix)
2200 ("r-s4vectors" ,r-s4vectors)
2201 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2203 `(("r-knitr" ,r-knitr)))
2204 (home-page "https://bioconductor.org/packages/InteractionSet")
2205 (synopsis "Base classes for storing genomic interaction data")
2207 "This package provides the @code{GInteractions},
2208 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2209 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2211 (license license:gpl3)))
2213 (define-public r-genomicinteractions
2215 (name "r-genomicinteractions")
2220 (uri (bioconductor-uri "GenomicInteractions" version))
2223 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
2225 `((upstream-name . "GenomicInteractions")))
2226 (build-system r-build-system)
2228 `(("r-biobase" ,r-biobase)
2229 ("r-biocgenerics" ,r-biocgenerics)
2230 ("r-data-table" ,r-data-table)
2231 ("r-dplyr" ,r-dplyr)
2232 ("r-genomeinfodb" ,r-genomeinfodb)
2233 ("r-genomicranges" ,r-genomicranges)
2234 ("r-ggplot2" ,r-ggplot2)
2235 ("r-gridextra" ,r-gridextra)
2237 ("r-igraph" ,r-igraph)
2238 ("r-interactionset" ,r-interactionset)
2239 ("r-iranges" ,r-iranges)
2240 ("r-rsamtools" ,r-rsamtools)
2241 ("r-rtracklayer" ,r-rtracklayer)
2242 ("r-s4vectors" ,r-s4vectors)
2243 ("r-stringr" ,r-stringr)))
2245 `(("r-knitr" ,r-knitr)))
2246 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2247 (synopsis "R package for handling genomic interaction data")
2249 "This R package provides tools for handling genomic interaction data,
2250 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2251 information and producing various plots and statistics.")
2252 (license license:gpl3)))
2254 (define-public r-ctc
2261 (uri (bioconductor-uri "ctc" version))
2264 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
2265 (build-system r-build-system)
2266 (propagated-inputs `(("r-amap" ,r-amap)))
2267 (home-page "https://bioconductor.org/packages/ctc/")
2268 (synopsis "Cluster and tree conversion")
2270 "This package provides tools for exporting and importing classification
2271 trees and clusters to other programs.")
2272 (license license:gpl2)))
2274 (define-public r-goseq
2281 (uri (bioconductor-uri "goseq" version))
2284 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
2285 (build-system r-build-system)
2287 `(("r-annotationdbi" ,r-annotationdbi)
2288 ("r-biasedurn" ,r-biasedurn)
2289 ("r-biocgenerics" ,r-biocgenerics)
2290 ("r-genelendatabase" ,r-genelendatabase)
2291 ("r-go-db" ,r-go-db)
2292 ("r-mgcv" ,r-mgcv)))
2293 (home-page "https://bioconductor.org/packages/goseq/")
2294 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2296 "This package provides tools to detect Gene Ontology and/or other user
2297 defined categories which are over/under represented in RNA-seq data.")
2298 (license license:lgpl2.0+)))
2300 (define-public r-glimma
2307 (uri (bioconductor-uri "Glimma" version))
2310 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
2311 (properties `((upstream-name . "Glimma")))
2312 (build-system r-build-system)
2314 `(("r-deseq2" ,r-deseq2)
2315 ("r-edger" ,r-edger)
2316 ("r-htmlwidgets" ,r-htmlwidgets)
2317 ("r-jsonlite" ,r-jsonlite)
2318 ("r-limma" ,r-limma)
2319 ("r-s4vectors" ,r-s4vectors)
2320 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2322 `(("r-knitr" ,r-knitr)))
2323 (home-page "https://github.com/Shians/Glimma")
2324 (synopsis "Interactive HTML graphics")
2326 "This package generates interactive visualisations for analysis of
2327 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2328 HTML page. The interactions are built on top of the popular static
2329 representations of analysis results in order to provide additional
2331 (license license:lgpl3)))
2333 (define-public r-rots
2340 (uri (bioconductor-uri "ROTS" version))
2343 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
2344 (properties `((upstream-name . "ROTS")))
2345 (build-system r-build-system)
2347 `(("r-biobase" ,r-biobase)
2348 ("r-rcpp" ,r-rcpp)))
2349 (home-page "https://bioconductor.org/packages/ROTS/")
2350 (synopsis "Reproducibility-Optimized Test Statistic")
2352 "This package provides tools for calculating the
2353 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2355 (license license:gpl2+)))
2357 (define-public r-plgem
2364 (uri (bioconductor-uri "plgem" version))
2367 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
2368 (build-system r-build-system)
2370 `(("r-biobase" ,r-biobase)
2371 ("r-mass" ,r-mass)))
2372 (home-page "http://www.genopolis.it")
2373 (synopsis "Detect differential expression in microarray and proteomics datasets")
2375 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2376 model the variance-versus-mean dependence that exists in a variety of
2377 genome-wide datasets, including microarray and proteomics data. The use of
2378 PLGEM has been shown to improve the detection of differentially expressed
2379 genes or proteins in these datasets.")
2380 (license license:gpl2)))
2382 (define-public r-inspect
2389 (uri (bioconductor-uri "INSPEcT" version))
2392 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
2393 (properties `((upstream-name . "INSPEcT")))
2394 (build-system r-build-system)
2396 `(("r-biobase" ,r-biobase)
2397 ("r-biocgenerics" ,r-biocgenerics)
2398 ("r-biocparallel" ,r-biocparallel)
2399 ("r-deseq2" ,r-deseq2)
2400 ("r-desolve" ,r-desolve)
2401 ("r-gdata" ,r-gdata)
2402 ("r-genomeinfodb" ,r-genomeinfodb)
2403 ("r-genomicalignments" ,r-genomicalignments)
2404 ("r-genomicfeatures" ,r-genomicfeatures)
2405 ("r-genomicranges" ,r-genomicranges)
2406 ("r-iranges" ,r-iranges)
2407 ("r-kernsmooth" ,r-kernsmooth)
2408 ("r-plgem" ,r-plgem)
2410 ("r-rootsolve" ,r-rootsolve)
2411 ("r-rsamtools" ,r-rsamtools)
2412 ("r-rtracklayer" ,r-rtracklayer)
2413 ("r-s4vectors" ,r-s4vectors)
2414 ("r-shiny" ,r-shiny)
2415 ("r-summarizedexperiment" ,r-summarizedexperiment)
2416 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2417 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2419 `(("r-knitr" ,r-knitr)))
2420 (home-page "https://bioconductor.org/packages/INSPEcT")
2421 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2423 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2424 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2425 order to evaluate synthesis, processing and degradation rates and assess via
2426 modeling the rates that determines changes in mature mRNA levels.")
2427 (license license:gpl2)))
2429 (define-public r-dnabarcodes
2431 (name "r-dnabarcodes")
2436 (uri (bioconductor-uri "DNABarcodes" version))
2439 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
2440 (properties `((upstream-name . "DNABarcodes")))
2441 (build-system r-build-system)
2444 ("r-matrix" ,r-matrix)
2445 ("r-rcpp" ,r-rcpp)))
2447 `(("r-knitr" ,r-knitr)))
2448 (home-page "https://bioconductor.org/packages/DNABarcodes")
2449 (synopsis "Create and analyze DNA barcodes")
2451 "This package offers tools to create DNA barcode sets capable of
2452 correcting insertion, deletion, and substitution errors. Existing barcodes
2453 can be analyzed regarding their minimal, maximal and average distances between
2454 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2455 demultiplexed, i.e. assigned to their original reference barcode.")
2456 (license license:gpl2)))
2458 (define-public r-ruvseq
2465 (uri (bioconductor-uri "RUVSeq" version))
2468 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
2469 (properties `((upstream-name . "RUVSeq")))
2470 (build-system r-build-system)
2472 `(("r-biobase" ,r-biobase)
2473 ("r-edaseq" ,r-edaseq)
2474 ("r-edger" ,r-edger)
2475 ("r-mass" ,r-mass)))
2477 `(("r-knitr" ,r-knitr)))
2478 (home-page "https://github.com/drisso/RUVSeq")
2479 (synopsis "Remove unwanted variation from RNA-Seq data")
2481 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2482 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2484 (license license:artistic2.0)))
2486 (define-public r-biocneighbors
2488 (name "r-biocneighbors")
2493 (uri (bioconductor-uri "BiocNeighbors" version))
2496 "0hip1sgi3zkrf8g9bw12alaszivja3difalnybr5s7gvh8qd5sf4"))))
2497 (properties `((upstream-name . "BiocNeighbors")))
2498 (build-system r-build-system)
2500 `(("r-biocparallel" ,r-biocparallel)
2501 ("r-matrix" ,r-matrix)
2503 ("r-rcppannoy" ,r-rcppannoy)
2504 ("r-rcpphnsw" ,r-rcpphnsw)
2505 ("r-s4vectors" ,r-s4vectors)))
2507 `(("r-knitr" ,r-knitr)))
2508 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2509 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2511 "This package implements exact and approximate methods for nearest
2512 neighbor detection, in a framework that allows them to be easily switched
2513 within Bioconductor packages or workflows. The exact algorithm is implemented
2514 using pre-clustering with the k-means algorithm. Functions are also provided
2515 to search for all neighbors within a given distance. Parallelization is
2516 achieved for all methods using the BiocParallel framework.")
2517 (license license:gpl3)))
2519 (define-public r-biocsingular
2521 (name "r-biocsingular")
2526 (uri (bioconductor-uri "BiocSingular" version))
2529 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
2530 (properties `((upstream-name . "BiocSingular")))
2531 (build-system r-build-system)
2533 `(("r-beachmat" ,r-beachmat)
2534 ("r-biocgenerics" ,r-biocgenerics)
2535 ("r-biocparallel" ,r-biocparallel)
2536 ("r-delayedarray" ,r-delayedarray)
2537 ("r-irlba" ,r-irlba)
2538 ("r-matrix" ,r-matrix)
2541 ("r-s4vectors" ,r-s4vectors)))
2543 `(("r-knitr" ,r-knitr)))
2544 (home-page "https://github.com/LTLA/BiocSingular")
2545 (synopsis "Singular value decomposition for Bioconductor packages")
2547 "This package implements exact and approximate methods for singular value
2548 decomposition and principal components analysis, in a framework that allows
2549 them to be easily switched within Bioconductor packages or workflows. Where
2550 possible, parallelization is achieved using the BiocParallel framework.")
2551 (license license:gpl3)))
2553 (define-public r-destiny
2560 (uri (bioconductor-uri "destiny" version))
2563 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
2564 (build-system r-build-system)
2566 `(("r-biobase" ,r-biobase)
2567 ("r-biocgenerics" ,r-biocgenerics)
2568 ("r-ggplot-multistats" ,r-ggplot-multistats)
2569 ("r-ggplot2" ,r-ggplot2)
2570 ("r-ggthemes" ,r-ggthemes)
2571 ("r-irlba" ,r-irlba)
2572 ("r-knn-covertree" ,r-knn-covertree)
2573 ("r-matrix" ,r-matrix)
2574 ("r-pcamethods" ,r-pcamethods)
2575 ("r-proxy" ,r-proxy)
2577 ("r-rcppeigen" ,r-rcppeigen)
2578 ("r-rcpphnsw" ,r-rcpphnsw)
2579 ("r-rspectra" ,r-rspectra)
2580 ("r-scales" ,r-scales)
2581 ("r-scatterplot3d" ,r-scatterplot3d)
2582 ("r-singlecellexperiment" ,r-singlecellexperiment)
2583 ("r-smoother" ,r-smoother)
2584 ("r-summarizedexperiment" ,r-summarizedexperiment)
2585 ("r-tidyr" ,r-tidyr)
2586 ("r-tidyselect" ,r-tidyselect)
2589 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2590 (home-page "https://bioconductor.org/packages/destiny/")
2591 (synopsis "Create and plot diffusion maps")
2592 (description "This package provides tools to create and plot diffusion
2594 ;; Any version of the GPL
2595 (license license:gpl3+)))
2597 (define-public r-savr
2604 (uri (bioconductor-uri "savR" version))
2607 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
2608 (properties `((upstream-name . "savR")))
2609 (build-system r-build-system)
2611 `(("r-ggplot2" ,r-ggplot2)
2612 ("r-gridextra" ,r-gridextra)
2613 ("r-reshape2" ,r-reshape2)
2614 ("r-scales" ,r-scales)
2616 (home-page "https://github.com/bcalder/savR")
2617 (synopsis "Parse and analyze Illumina SAV files")
2619 "This package provides tools to parse Illumina Sequence Analysis
2620 Viewer (SAV) files, access data, and generate QC plots.")
2621 (license license:agpl3+)))
2623 (define-public r-chipexoqual
2625 (name "r-chipexoqual")
2630 (uri (bioconductor-uri "ChIPexoQual" version))
2633 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
2634 (properties `((upstream-name . "ChIPexoQual")))
2635 (build-system r-build-system)
2637 `(("r-biocparallel" ,r-biocparallel)
2638 ("r-biovizbase" ,r-biovizbase)
2639 ("r-broom" ,r-broom)
2640 ("r-data-table" ,r-data-table)
2641 ("r-dplyr" ,r-dplyr)
2642 ("r-genomeinfodb" ,r-genomeinfodb)
2643 ("r-genomicalignments" ,r-genomicalignments)
2644 ("r-genomicranges" ,r-genomicranges)
2645 ("r-ggplot2" ,r-ggplot2)
2646 ("r-hexbin" ,r-hexbin)
2647 ("r-iranges" ,r-iranges)
2648 ("r-rcolorbrewer" ,r-rcolorbrewer)
2649 ("r-rmarkdown" ,r-rmarkdown)
2650 ("r-rsamtools" ,r-rsamtools)
2651 ("r-s4vectors" ,r-s4vectors)
2652 ("r-scales" ,r-scales)
2653 ("r-viridis" ,r-viridis)))
2655 `(("r-knitr" ,r-knitr)))
2656 (home-page "https://github.com/keleslab/ChIPexoQual")
2657 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2659 "This package provides a quality control pipeline for ChIP-exo/nexus
2661 (license license:gpl2+)))
2663 (define-public r-copynumber
2665 (name "r-copynumber")
2669 (uri (bioconductor-uri "copynumber" version))
2672 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
2673 (build-system r-build-system)
2675 `(("r-s4vectors" ,r-s4vectors)
2676 ("r-iranges" ,r-iranges)
2677 ("r-genomicranges" ,r-genomicranges)
2678 ("r-biocgenerics" ,r-biocgenerics)))
2679 (home-page "https://bioconductor.org/packages/copynumber")
2680 (synopsis "Segmentation of single- and multi-track copy number data")
2682 "This package segments single- and multi-track copy number data by a
2683 penalized least squares regression method.")
2684 (license license:artistic2.0)))
2686 (define-public r-dnacopy
2693 (uri (bioconductor-uri "DNAcopy" version))
2696 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
2697 (properties `((upstream-name . "DNAcopy")))
2698 (build-system r-build-system)
2699 (native-inputs `(("gfortran" ,gfortran)))
2700 (home-page "https://bioconductor.org/packages/DNAcopy")
2701 (synopsis "DNA copy number data analysis")
2703 "This package implements the @dfn{circular binary segmentation} (CBS)
2704 algorithm to segment DNA copy number data and identify genomic regions with
2705 abnormal copy number.")
2706 (license license:gpl2+)))
2708 ;; This is a CRAN package, but it uncharacteristically depends on a
2709 ;; Bioconductor package.
2710 (define-public r-htscluster
2712 (name "r-htscluster")
2717 (uri (cran-uri "HTSCluster" version))
2720 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2721 (properties `((upstream-name . "HTSCluster")))
2722 (build-system r-build-system)
2724 `(("r-capushe" ,r-capushe)
2725 ("r-edger" ,r-edger)
2726 ("r-plotrix" ,r-plotrix)))
2727 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2728 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2730 "This package provides a Poisson mixture model is implemented to cluster
2731 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2732 estimation is performed using either the EM or CEM algorithm, and the slope
2733 heuristics are used for model selection (i.e., to choose the number of
2735 (license license:gpl3+)))
2737 (define-public r-deds
2744 (uri (bioconductor-uri "DEDS" version))
2747 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2748 (properties `((upstream-name . "DEDS")))
2749 (build-system r-build-system)
2750 (home-page "https://bioconductor.org/packages/DEDS/")
2751 (synopsis "Differential expression via distance summary for microarray data")
2753 "This library contains functions that calculate various statistics of
2754 differential expression for microarray data, including t statistics, fold
2755 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2756 also implements a new methodology called DEDS (Differential Expression via
2757 Distance Summary), which selects differentially expressed genes by integrating
2758 and summarizing a set of statistics using a weighted distance approach.")
2759 ;; Any version of the LGPL.
2760 (license license:lgpl3+)))
2762 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2764 (define-public r-nbpseq
2771 (uri (cran-uri "NBPSeq" version))
2774 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2775 (properties `((upstream-name . "NBPSeq")))
2776 (build-system r-build-system)
2778 `(("r-qvalue" ,r-qvalue)))
2779 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2780 (synopsis "Negative binomial models for RNA-Seq data")
2782 "This package provides negative binomial models for two-group comparisons
2783 and regression inferences from RNA-sequencing data.")
2784 (license license:gpl2)))
2786 (define-public r-ebseq
2793 (uri (bioconductor-uri "EBSeq" version))
2796 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
2797 (properties `((upstream-name . "EBSeq")))
2798 (build-system r-build-system)
2800 `(("r-blockmodeling" ,r-blockmodeling)
2801 ("r-gplots" ,r-gplots)
2802 ("r-testthat" ,r-testthat)))
2803 (home-page "https://bioconductor.org/packages/EBSeq")
2804 (synopsis "Differential expression analysis of RNA-seq data")
2806 "This package provides tools for differential expression analysis at both
2807 gene and isoform level using RNA-seq data")
2808 (license license:artistic2.0)))
2810 (define-public r-karyoploter
2812 (name "r-karyoploter")
2816 (uri (bioconductor-uri "karyoploteR" version))
2819 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
2820 (build-system r-build-system)
2822 `(("r-annotationdbi" ,r-annotationdbi)
2823 ("r-bamsignals" ,r-bamsignals)
2824 ("r-bezier" ,r-bezier)
2825 ("r-biovizbase" ,r-biovizbase)
2826 ("r-digest" ,r-digest)
2827 ("r-genomeinfodb" ,r-genomeinfodb)
2828 ("r-genomicfeatures" ,r-genomicfeatures)
2829 ("r-genomicranges" ,r-genomicranges)
2830 ("r-iranges" ,r-iranges)
2831 ("r-memoise" ,r-memoise)
2832 ("r-regioner" ,r-regioner)
2833 ("r-rsamtools" ,r-rsamtools)
2834 ("r-rtracklayer" ,r-rtracklayer)
2835 ("r-s4vectors" ,r-s4vectors)
2836 ("r-variantannotation" ,r-variantannotation)))
2838 `(("r-knitr" ,r-knitr)))
2839 (home-page "https://bioconductor.org/packages/karyoploteR/")
2840 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2841 (description "This package creates karyotype plots of arbitrary genomes and
2842 offers a complete set of functions to plot arbitrary data on them. It mimics
2843 many R base graphics functions coupling them with a coordinate change function
2844 automatically mapping the chromosome and data coordinates into the plot
2846 (license license:artistic2.0)))
2848 (define-public r-lpsymphony
2850 (name "r-lpsymphony")
2855 (uri (bioconductor-uri "lpsymphony" version))
2858 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
2859 (build-system r-build-system)
2863 `(("pkg-config" ,pkg-config)
2864 ("r-knitr" ,r-knitr)))
2865 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2866 (synopsis "Symphony integer linear programming solver in R")
2868 "This package was derived from Rsymphony. The package provides an R
2869 interface to SYMPHONY, a linear programming solver written in C++. The main
2870 difference between this package and Rsymphony is that it includes the solver
2871 source code, while Rsymphony expects to find header and library files on the
2872 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2873 to install interface to SYMPHONY.")
2874 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2875 ;; lpsimphony is released under the same terms.
2876 (license license:epl1.0)))
2878 (define-public r-ihw
2885 (uri (bioconductor-uri "IHW" version))
2888 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
2889 (properties `((upstream-name . "IHW")))
2890 (build-system r-build-system)
2892 `(("r-biocgenerics" ,r-biocgenerics)
2893 ("r-fdrtool" ,r-fdrtool)
2894 ("r-lpsymphony" ,r-lpsymphony)
2895 ("r-slam" ,r-slam)))
2897 `(("r-knitr" ,r-knitr)))
2898 (home-page "https://bioconductor.org/packages/IHW")
2899 (synopsis "Independent hypothesis weighting")
2901 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2902 procedure that increases power compared to the method of Benjamini and
2903 Hochberg by assigning data-driven weights to each hypothesis. The input to
2904 IHW is a two-column table of p-values and covariates. The covariate can be
2905 any continuous-valued or categorical variable that is thought to be
2906 informative on the statistical properties of each hypothesis test, while it is
2907 independent of the p-value under the null hypothesis.")
2908 (license license:artistic2.0)))
2910 (define-public r-icobra
2917 (uri (bioconductor-uri "iCOBRA" version))
2920 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
2921 (properties `((upstream-name . "iCOBRA")))
2922 (build-system r-build-system)
2924 `(("r-dplyr" ,r-dplyr)
2926 ("r-ggplot2" ,r-ggplot2)
2927 ("r-limma" ,r-limma)
2928 ("r-reshape2" ,r-reshape2)
2930 ("r-scales" ,r-scales)
2931 ("r-shiny" ,r-shiny)
2932 ("r-shinybs" ,r-shinybs)
2933 ("r-shinydashboard" ,r-shinydashboard)
2934 ("r-upsetr" ,r-upsetr)))
2936 `(("r-knitr" ,r-knitr)))
2937 (home-page "https://bioconductor.org/packages/iCOBRA")
2938 (synopsis "Comparison and visualization of ranking and assignment methods")
2940 "This package provides functions for calculation and visualization of
2941 performance metrics for evaluation of ranking and binary
2942 classification (assignment) methods. It also contains a Shiny application for
2943 interactive exploration of results.")
2944 (license license:gpl2+)))
2946 (define-public r-mast
2953 (uri (bioconductor-uri "MAST" version))
2956 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
2957 (properties `((upstream-name . "MAST")))
2958 (build-system r-build-system)
2960 `(("r-abind" ,r-abind)
2961 ("r-biobase" ,r-biobase)
2962 ("r-biocgenerics" ,r-biocgenerics)
2963 ("r-data-table" ,r-data-table)
2964 ("r-ggplot2" ,r-ggplot2)
2966 ("r-progress" ,r-progress)
2967 ("r-reshape2" ,r-reshape2)
2968 ("r-s4vectors" ,r-s4vectors)
2969 ("r-singlecellexperiment" ,r-singlecellexperiment)
2970 ("r-stringr" ,r-stringr)
2971 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2973 `(("r-knitr" ,r-knitr)))
2974 (home-page "https://github.com/RGLab/MAST/")
2975 (synopsis "Model-based analysis of single cell transcriptomics")
2977 "This package provides methods and models for handling zero-inflated
2978 single cell assay data.")
2979 (license license:gpl2+)))
2981 (define-public r-monocle
2988 (uri (bioconductor-uri "monocle" version))
2991 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
2992 (build-system r-build-system)
2994 `(("r-biobase" ,r-biobase)
2995 ("r-biocgenerics" ,r-biocgenerics)
2996 ("r-biocviews" ,r-biocviews)
2997 ("r-cluster" ,r-cluster)
2998 ("r-combinat" ,r-combinat)
2999 ("r-ddrtree" ,r-ddrtree)
3000 ("r-densityclust" ,r-densityclust)
3001 ("r-dplyr" ,r-dplyr)
3002 ("r-fastica" ,r-fastica)
3003 ("r-ggplot2" ,r-ggplot2)
3004 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3005 ("r-igraph" ,r-igraph)
3006 ("r-irlba" ,r-irlba)
3007 ("r-limma" ,r-limma)
3009 ("r-matrix" ,r-matrix)
3010 ("r-matrixstats" ,r-matrixstats)
3011 ("r-pheatmap" ,r-pheatmap)
3013 ("r-proxy" ,r-proxy)
3014 ("r-qlcmatrix" ,r-qlcmatrix)
3017 ("r-reshape2" ,r-reshape2)
3018 ("r-rtsne" ,r-rtsne)
3020 ("r-stringr" ,r-stringr)
3021 ("r-tibble" ,r-tibble)
3023 ("r-viridis" ,r-viridis)))
3025 `(("r-knitr" ,r-knitr)))
3026 (home-page "https://bioconductor.org/packages/monocle")
3027 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3029 "Monocle performs differential expression and time-series analysis for
3030 single-cell expression experiments. It orders individual cells according to
3031 progress through a biological process, without knowing ahead of time which
3032 genes define progress through that process. Monocle also performs
3033 differential expression analysis, clustering, visualization, and other useful
3034 tasks on single cell expression data. It is designed to work with RNA-Seq and
3035 qPCR data, but could be used with other types as well.")
3036 (license license:artistic2.0)))
3038 (define-public r-monocle3
3046 (url "https://github.com/cole-trapnell-lab/monocle3")
3048 (file-name (git-file-name name version))
3051 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3052 (build-system r-build-system)
3054 `(("r-biobase" ,r-biobase)
3055 ("r-biocgenerics" ,r-biocgenerics)
3056 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3057 ("r-dplyr" ,r-dplyr)
3058 ("r-ggplot2" ,r-ggplot2)
3059 ("r-ggrepel" ,r-ggrepel)
3061 ("r-htmlwidgets" ,r-htmlwidgets)
3062 ("r-igraph" ,r-igraph)
3063 ("r-irlba" ,r-irlba)
3064 ("r-limma" ,r-limma)
3065 ("r-lmtest" ,r-lmtest)
3067 ("r-matrix" ,r-matrix)
3068 ("r-matrix-utils" ,r-matrix-utils)
3069 ("r-pbapply" ,r-pbapply)
3070 ("r-pbmcapply" ,r-pbmcapply)
3071 ("r-pheatmap" ,r-pheatmap)
3072 ("r-plotly" ,r-plotly)
3074 ("r-proxy" ,r-proxy)
3076 ("r-purrr" ,r-purrr)
3079 ("r-rcppparallel" ,r-rcppparallel)
3080 ("r-reshape2" ,r-reshape2)
3081 ("r-reticulate" ,r-reticulate)
3082 ("r-rhpcblasctl" ,r-rhpcblasctl)
3083 ("r-rtsne" ,r-rtsne)
3084 ("r-shiny" ,r-shiny)
3086 ("r-spdep" ,r-spdep)
3087 ("r-speedglm" ,r-speedglm)
3088 ("r-stringr" ,r-stringr)
3089 ("r-singlecellexperiment" ,r-singlecellexperiment)
3090 ("r-tibble" ,r-tibble)
3091 ("r-tidyr" ,r-tidyr)
3093 ("r-viridis" ,r-viridis)))
3094 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3095 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3097 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3098 (license license:expat)))
3100 (define-public r-noiseq
3107 (uri (bioconductor-uri "NOISeq" version))
3110 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
3111 (properties `((upstream-name . "NOISeq")))
3112 (build-system r-build-system)
3114 `(("r-biobase" ,r-biobase)
3115 ("r-matrix" ,r-matrix)))
3116 (home-page "https://bioconductor.org/packages/NOISeq")
3117 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3119 "This package provides tools to support the analysis of RNA-seq
3120 expression data or other similar kind of data. It provides exploratory plots
3121 to evaluate saturation, count distribution, expression per chromosome, type of
3122 detected features, features length, etc. It also supports the analysis of
3123 differential expression between two experimental conditions with no parametric
3125 (license license:artistic2.0)))
3127 (define-public r-scdd
3134 (uri (bioconductor-uri "scDD" version))
3137 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
3138 (properties `((upstream-name . "scDD")))
3139 (build-system r-build-system)
3142 ("r-biocparallel" ,r-biocparallel)
3143 ("r-ebseq" ,r-ebseq)
3144 ("r-fields" ,r-fields)
3145 ("r-ggplot2" ,r-ggplot2)
3146 ("r-mclust" ,r-mclust)
3147 ("r-outliers" ,r-outliers)
3148 ("r-s4vectors" ,r-s4vectors)
3149 ("r-scran" ,r-scran)
3150 ("r-singlecellexperiment" ,r-singlecellexperiment)
3151 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3153 `(("r-knitr" ,r-knitr)))
3154 (home-page "https://github.com/kdkorthauer/scDD")
3155 (synopsis "Mixture modeling of single-cell RNA-seq data")
3157 "This package implements a method to analyze single-cell RNA-seq data
3158 utilizing flexible Dirichlet Process mixture models. Genes with differential
3159 distributions of expression are classified into several interesting patterns
3160 of differences between two conditions. The package also includes functions
3161 for simulating data with these patterns from negative binomial
3163 (license license:gpl2)))
3165 (define-public r-scone
3172 (uri (bioconductor-uri "scone" version))
3175 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
3176 (build-system r-build-system)
3178 `(("r-aroma-light" ,r-aroma-light)
3179 ("r-biocparallel" ,r-biocparallel)
3181 ("r-class" ,r-class)
3182 ("r-cluster" ,r-cluster)
3183 ("r-compositions" ,r-compositions)
3184 ("r-diptest" ,r-diptest)
3185 ("r-edger" ,r-edger)
3187 ("r-gplots" ,r-gplots)
3188 ("r-hexbin" ,r-hexbin)
3189 ("r-limma" ,r-limma)
3190 ("r-matrixstats" ,r-matrixstats)
3191 ("r-mixtools" ,r-mixtools)
3192 ("r-rarpack" ,r-rarpack)
3193 ("r-rcolorbrewer" ,r-rcolorbrewer)
3194 ("r-rhdf5" ,r-rhdf5)
3195 ("r-ruvseq" ,r-ruvseq)
3196 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3198 `(("r-knitr" ,r-knitr)))
3199 (home-page "https://bioconductor.org/packages/scone")
3200 (synopsis "Single cell overview of normalized expression data")
3202 "SCONE is an R package for comparing and ranking the performance of
3203 different normalization schemes for single-cell RNA-seq and other
3204 high-throughput analyses.")
3205 (license license:artistic2.0)))
3207 (define-public r-geoquery
3214 (uri (bioconductor-uri "GEOquery" version))
3217 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
3218 (properties `((upstream-name . "GEOquery")))
3219 (build-system r-build-system)
3221 `(("r-biobase" ,r-biobase)
3222 ("r-dplyr" ,r-dplyr)
3224 ("r-limma" ,r-limma)
3225 ("r-magrittr" ,r-magrittr)
3226 ("r-readr" ,r-readr)
3227 ("r-tidyr" ,r-tidyr)
3228 ("r-xml2" ,r-xml2)))
3230 `(("r-knitr" ,r-knitr)))
3231 (home-page "https://github.com/seandavi/GEOquery/")
3232 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3234 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3235 microarray data. Given the rich and varied nature of this resource, it is
3236 only natural to want to apply BioConductor tools to these data. GEOquery is
3237 the bridge between GEO and BioConductor.")
3238 (license license:gpl2)))
3240 (define-public r-illuminaio
3242 (name "r-illuminaio")
3247 (uri (bioconductor-uri "illuminaio" version))
3250 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
3251 (build-system r-build-system)
3253 `(("r-base64" ,r-base64)))
3254 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3255 (synopsis "Parse Illumina microarray output files")
3257 "This package provides tools for parsing Illumina's microarray output
3258 files, including IDAT.")
3259 (license license:gpl2)))
3261 (define-public r-siggenes
3268 (uri (bioconductor-uri "siggenes" version))
3271 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
3272 (build-system r-build-system)
3274 `(("r-biobase" ,r-biobase)
3275 ("r-multtest" ,r-multtest)
3276 ("r-scrime" ,r-scrime)))
3277 (home-page "https://bioconductor.org/packages/siggenes/")
3279 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3281 "This package provides tools for the identification of differentially
3282 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3283 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3284 Bayes Analyses of Microarrays} (EBAM).")
3285 (license license:lgpl2.0+)))
3287 (define-public r-bumphunter
3289 (name "r-bumphunter")
3294 (uri (bioconductor-uri "bumphunter" version))
3297 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
3298 (build-system r-build-system)
3300 `(("r-annotationdbi" ,r-annotationdbi)
3301 ("r-biocgenerics" ,r-biocgenerics)
3302 ("r-dorng" ,r-dorng)
3303 ("r-foreach" ,r-foreach)
3304 ("r-genomeinfodb" ,r-genomeinfodb)
3305 ("r-genomicfeatures" ,r-genomicfeatures)
3306 ("r-genomicranges" ,r-genomicranges)
3307 ("r-iranges" ,r-iranges)
3308 ("r-iterators" ,r-iterators)
3309 ("r-limma" ,r-limma)
3310 ("r-locfit" ,r-locfit)
3311 ("r-matrixstats" ,r-matrixstats)
3312 ("r-s4vectors" ,r-s4vectors)))
3313 (home-page "https://github.com/ririzarr/bumphunter")
3314 (synopsis "Find bumps in genomic data")
3316 "This package provides tools for finding bumps in genomic data in order
3317 to identify differentially methylated regions in epigenetic epidemiology
3319 (license license:artistic2.0)))
3321 (define-public r-minfi
3328 (uri (bioconductor-uri "minfi" version))
3331 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
3332 (build-system r-build-system)
3334 `(("r-beanplot" ,r-beanplot)
3335 ("r-biobase" ,r-biobase)
3336 ("r-biocgenerics" ,r-biocgenerics)
3337 ("r-biocparallel" ,r-biocparallel)
3338 ("r-biostrings" ,r-biostrings)
3339 ("r-bumphunter" ,r-bumphunter)
3340 ("r-data-table" ,r-data-table)
3341 ("r-delayedarray" ,r-delayedarray)
3342 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3343 ("r-genefilter" ,r-genefilter)
3344 ("r-genomeinfodb" ,r-genomeinfodb)
3345 ("r-genomicranges" ,r-genomicranges)
3346 ("r-geoquery" ,r-geoquery)
3347 ("r-hdf5array" ,r-hdf5array)
3348 ("r-illuminaio" ,r-illuminaio)
3349 ("r-iranges" ,r-iranges)
3350 ("r-lattice" ,r-lattice)
3351 ("r-limma" ,r-limma)
3353 ("r-mclust" ,r-mclust)
3355 ("r-nor1mix" ,r-nor1mix)
3356 ("r-preprocesscore" ,r-preprocesscore)
3357 ("r-quadprog" ,r-quadprog)
3358 ("r-rcolorbrewer" ,r-rcolorbrewer)
3359 ("r-reshape" ,r-reshape)
3360 ("r-s4vectors" ,r-s4vectors)
3361 ("r-siggenes" ,r-siggenes)
3362 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3364 `(("r-knitr" ,r-knitr)))
3365 (home-page "https://github.com/hansenlab/minfi")
3366 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3368 "This package provides tools to analyze and visualize Illumina Infinium
3369 methylation arrays.")
3370 (license license:artistic2.0)))
3372 (define-public r-methylumi
3374 (name "r-methylumi")
3379 (uri (bioconductor-uri "methylumi" version))
3382 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
3383 (build-system r-build-system)
3385 `(("r-annotate" ,r-annotate)
3386 ("r-annotationdbi" ,r-annotationdbi)
3387 ("r-biobase" ,r-biobase)
3388 ("r-biocgenerics" ,r-biocgenerics)
3389 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3390 ("r-genefilter" ,r-genefilter)
3391 ("r-genomeinfodb" ,r-genomeinfodb)
3392 ("r-genomicranges" ,r-genomicranges)
3393 ("r-ggplot2" ,r-ggplot2)
3394 ("r-illuminaio" ,r-illuminaio)
3395 ("r-iranges" ,r-iranges)
3396 ("r-lattice" ,r-lattice)
3397 ("r-matrixstats" ,r-matrixstats)
3398 ("r-minfi" ,r-minfi)
3399 ("r-reshape2" ,r-reshape2)
3400 ("r-s4vectors" ,r-s4vectors)
3401 ("r-scales" ,r-scales)
3402 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3404 `(("r-knitr" ,r-knitr)))
3405 (home-page "https://bioconductor.org/packages/methylumi")
3406 (synopsis "Handle Illumina methylation data")
3408 "This package provides classes for holding and manipulating Illumina
3409 methylation data. Based on eSet, it can contain MIAME information, sample
3410 information, feature information, and multiple matrices of data. An
3411 \"intelligent\" import function, methylumiR can read the Illumina text files
3412 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3413 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3414 background correction, and quality control features for GoldenGate, Infinium,
3415 and Infinium HD arrays are also included.")
3416 (license license:gpl2)))
3418 (define-public r-lumi
3425 (uri (bioconductor-uri "lumi" version))
3428 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
3429 (build-system r-build-system)
3431 `(("r-affy" ,r-affy)
3432 ("r-annotate" ,r-annotate)
3433 ("r-annotationdbi" ,r-annotationdbi)
3434 ("r-biobase" ,r-biobase)
3436 ("r-genomicfeatures" ,r-genomicfeatures)
3437 ("r-genomicranges" ,r-genomicranges)
3438 ("r-kernsmooth" ,r-kernsmooth)
3439 ("r-lattice" ,r-lattice)
3441 ("r-methylumi" ,r-methylumi)
3443 ("r-nleqslv" ,r-nleqslv)
3444 ("r-preprocesscore" ,r-preprocesscore)
3445 ("r-rsqlite" ,r-rsqlite)))
3446 (home-page "https://bioconductor.org/packages/lumi")
3447 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3449 "The lumi package provides an integrated solution for the Illumina
3450 microarray data analysis. It includes functions of Illumina
3451 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3452 variance stabilization, normalization and gene annotation at the probe level.
3453 It also includes the functions of processing Illumina methylation microarrays,
3454 especially Illumina Infinium methylation microarrays.")
3455 (license license:lgpl2.0+)))
3457 (define-public r-linnorm
3464 (uri (bioconductor-uri "Linnorm" version))
3467 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
3468 (properties `((upstream-name . "Linnorm")))
3469 (build-system r-build-system)
3471 `(("r-amap" ,r-amap)
3472 ("r-apcluster" ,r-apcluster)
3473 ("r-ellipse" ,r-ellipse)
3474 ("r-fastcluster" ,r-fastcluster)
3476 ("r-ggdendro" ,r-ggdendro)
3477 ("r-ggplot2" ,r-ggplot2)
3478 ("r-gmodels" ,r-gmodels)
3479 ("r-igraph" ,r-igraph)
3480 ("r-limma" ,r-limma)
3482 ("r-mclust" ,r-mclust)
3484 ("r-rcpparmadillo" ,r-rcpparmadillo)
3485 ("r-rtsne" ,r-rtsne)
3486 ("r-statmod" ,r-statmod)
3487 ("r-vegan" ,r-vegan)
3490 `(("r-knitr" ,r-knitr)))
3491 (home-page "http://www.jjwanglab.org/Linnorm/")
3492 (synopsis "Linear model and normality based transformation method")
3494 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3495 count data or any large scale count data. It transforms such datasets for
3496 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3497 the following pipelines are implemented:
3500 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3501 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3502 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3503 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3504 @item Differential expression analysis or differential peak detection using
3505 limma (@code{Linnorm.limma})
3506 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3507 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3508 @item Stable gene selection for scRNA-seq data; for users without or who do
3509 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3510 @item Data imputation (@code{Linnorm.DataImput}).
3513 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3514 @code{RnaXSim} function is included for simulating RNA-seq data for the
3515 evaluation of DEG analysis methods.")
3516 (license license:expat)))
3518 (define-public r-ioniser
3525 (uri (bioconductor-uri "IONiseR" version))
3528 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
3529 (properties `((upstream-name . "IONiseR")))
3530 (build-system r-build-system)
3532 `(("r-biocgenerics" ,r-biocgenerics)
3533 ("r-biocparallel" ,r-biocparallel)
3534 ("r-biostrings" ,r-biostrings)
3535 ("r-bit64" ,r-bit64)
3536 ("r-dplyr" ,r-dplyr)
3537 ("r-ggplot2" ,r-ggplot2)
3538 ("r-magrittr" ,r-magrittr)
3539 ("r-rhdf5" ,r-rhdf5)
3540 ("r-shortread" ,r-shortread)
3541 ("r-stringr" ,r-stringr)
3542 ("r-tibble" ,r-tibble)
3543 ("r-tidyr" ,r-tidyr)
3544 ("r-xvector" ,r-xvector)))
3546 `(("r-knitr" ,r-knitr)))
3547 (home-page "https://bioconductor.org/packages/IONiseR/")
3548 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3550 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3551 MinION data. It extracts summary statistics from a set of fast5 files and can
3552 be used either before or after base calling. In addition to standard
3553 summaries of the read-types produced, it provides a number of plots for
3554 visualising metrics relative to experiment run time or spatially over the
3555 surface of a flowcell.")
3556 (license license:expat)))
3558 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3559 (define-public r-gkmsvm
3566 (uri (cran-uri "gkmSVM" version))
3569 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3570 (properties `((upstream-name . "gkmSVM")))
3571 (build-system r-build-system)
3573 `(("r-kernlab" ,r-kernlab)
3576 ("r-seqinr" ,r-seqinr)))
3577 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3578 (synopsis "Gapped-kmer support vector machine")
3580 "This R package provides tools for training gapped-kmer SVM classifiers
3581 for DNA and protein sequences. This package supports several sequence
3582 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3583 (license license:gpl2+)))
3585 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3586 (define-public r-mutoss
3593 (uri (cran-uri "mutoss" version))
3596 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3597 (properties `((upstream-name . "mutoss")))
3598 (build-system r-build-system)
3600 `(("r-multcomp" ,r-multcomp)
3601 ("r-multtest" ,r-multtest)
3602 ("r-mvtnorm" ,r-mvtnorm)
3603 ("r-plotrix" ,r-plotrix)))
3604 (home-page "https://github.com/kornl/mutoss/")
3605 (synopsis "Unified multiple testing procedures")
3607 "This package is designed to ease the application and comparison of
3608 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3609 are standardized and usable by the accompanying mutossGUI package.")
3610 ;; Any version of the GPL.
3611 (license (list license:gpl2+ license:gpl3+))))
3613 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3614 ;; from Bioconductor, so we put it here.
3615 (define-public r-metap
3622 (uri (cran-uri "metap" version))
3625 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3626 (build-system r-build-system)
3628 `(("r-lattice" ,r-lattice)
3629 ("r-mutoss" ,r-mutoss)
3630 ("r-rdpack" ,r-rdpack)
3631 ("r-tfisher" ,r-tfisher)))
3632 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3633 (synopsis "Meta-analysis of significance values")
3635 "The canonical way to perform meta-analysis involves using effect sizes.
3636 When they are not available this package provides a number of methods for
3637 meta-analysis of significance values including the methods of Edgington,
3638 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3639 published results; and a routine for graphical display.")
3640 (license license:gpl2)))
3642 (define-public r-triform
3649 (uri (bioconductor-uri "triform" version))
3652 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3653 (build-system r-build-system)
3655 `(("r-biocgenerics" ,r-biocgenerics)
3656 ("r-iranges" ,r-iranges)
3657 ("r-yaml" ,r-yaml)))
3658 (home-page "https://bioconductor.org/packages/triform/")
3659 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3661 "The Triform algorithm uses model-free statistics to identify peak-like
3662 distributions of TF ChIP sequencing reads, taking advantage of an improved
3663 peak definition in combination with known profile characteristics.")
3664 (license license:gpl2)))
3666 (define-public r-varianttools
3668 (name "r-varianttools")
3673 (uri (bioconductor-uri "VariantTools" version))
3676 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
3677 (properties `((upstream-name . "VariantTools")))
3678 (build-system r-build-system)
3680 `(("r-biobase" ,r-biobase)
3681 ("r-biocgenerics" ,r-biocgenerics)
3682 ("r-biocparallel" ,r-biocparallel)
3683 ("r-biostrings" ,r-biostrings)
3684 ("r-bsgenome" ,r-bsgenome)
3685 ("r-genomeinfodb" ,r-genomeinfodb)
3686 ("r-genomicfeatures" ,r-genomicfeatures)
3687 ("r-genomicranges" ,r-genomicranges)
3688 ("r-iranges" ,r-iranges)
3689 ("r-matrix" ,r-matrix)
3690 ("r-rsamtools" ,r-rsamtools)
3691 ("r-rtracklayer" ,r-rtracklayer)
3692 ("r-s4vectors" ,r-s4vectors)
3693 ("r-variantannotation" ,r-variantannotation)))
3694 (home-page "https://bioconductor.org/packages/VariantTools/")
3695 (synopsis "Tools for exploratory analysis of variant calls")
3697 "Explore, diagnose, and compare variant calls using filters. The
3698 VariantTools package supports a workflow for loading data, calling single
3699 sample variants and tumor-specific somatic mutations or other sample-specific
3700 variant types (e.g., RNA editing). Most of the functions operate on
3701 alignments (BAM files) or datasets of called variants. The user is expected
3702 to have already aligned the reads with a separate tool, e.g., GSNAP via
3704 (license license:artistic2.0)))
3706 (define-public r-heatplus
3713 (uri (bioconductor-uri "Heatplus" version))
3716 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
3717 (properties `((upstream-name . "Heatplus")))
3718 (build-system r-build-system)
3720 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3721 (home-page "https://github.com/alexploner/Heatplus")
3722 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3724 "This package provides tools to display a rectangular heatmap (intensity
3725 plot) of a data matrix. By default, both samples (columns) and features (row)
3726 of the matrix are sorted according to a hierarchical clustering, and the
3727 corresponding dendrogram is plotted. Optionally, panels with additional
3728 information about samples and features can be added to the plot.")
3729 (license license:gpl2+)))
3731 (define-public r-gosemsim
3738 (uri (bioconductor-uri "GOSemSim" version))
3741 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
3742 (properties `((upstream-name . "GOSemSim")))
3743 (build-system r-build-system)
3745 `(("r-annotationdbi" ,r-annotationdbi)
3746 ("r-go-db" ,r-go-db)
3747 ("r-rcpp" ,r-rcpp)))
3749 `(("r-knitr" ,r-knitr)))
3750 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3751 (synopsis "GO-terms semantic similarity measures")
3753 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3754 quantitative ways to compute similarities between genes and gene groups, and
3755 have became important basis for many bioinformatics analysis approaches.
3756 GOSemSim is an R package for semantic similarity computation among GO terms,
3757 sets of GO terms, gene products and gene clusters.")
3758 (license license:artistic2.0)))
3760 (define-public r-anota
3767 (uri (bioconductor-uri "anota" version))
3770 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
3771 (build-system r-build-system)
3773 `(("r-multtest" ,r-multtest)
3774 ("r-qvalue" ,r-qvalue)))
3775 (home-page "https://bioconductor.org/packages/anota/")
3776 (synopsis "Analysis of translational activity")
3778 "Genome wide studies of translational control is emerging as a tool to
3779 study various biological conditions. The output from such analysis is both
3780 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
3781 involved in translation (the actively translating mRNA level) for each mRNA.
3782 The standard analysis of such data strives towards identifying differential
3783 translational between two or more sample classes - i.e. differences in
3784 actively translated mRNA levels that are independent of underlying differences
3785 in cytosolic mRNA levels. This package allows for such analysis using partial
3786 variances and the random variance model. As 10s of thousands of mRNAs are
3787 analyzed in parallel the library performs a number of tests to assure that
3788 the data set is suitable for such analysis.")
3789 (license license:gpl3)))
3791 (define-public r-sigpathway
3793 (name "r-sigpathway")
3798 (uri (bioconductor-uri "sigPathway" version))
3801 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
3802 (properties `((upstream-name . "sigPathway")))
3803 (build-system r-build-system)
3804 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3805 (synopsis "Pathway analysis")
3807 "This package is used to conduct pathway analysis by calculating the NT_k
3808 and NE_k statistics in a statistical framework for determining whether a
3809 specified group of genes for a pathway has a coordinated association with a
3810 phenotype of interest.")
3811 (license license:gpl2)))
3813 (define-public r-fgsea
3820 (uri (bioconductor-uri "fgsea" version))
3823 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
3824 (build-system r-build-system)
3827 ("r-biocparallel" ,r-biocparallel)
3828 ("r-data-table" ,r-data-table)
3829 ("r-fastmatch" ,r-fastmatch)
3830 ("r-ggplot2" ,r-ggplot2)
3831 ("r-gridextra" ,r-gridextra)
3832 ("r-matrix" ,r-matrix)
3833 ("r-rcpp" ,r-rcpp)))
3835 `(("r-knitr" ,r-knitr)))
3836 (home-page "https://github.com/ctlab/fgsea/")
3837 (synopsis "Fast gene set enrichment analysis")
3839 "The package implements an algorithm for fast gene set enrichment
3840 analysis. Using the fast algorithm makes more permutations and gets
3841 more fine grained p-values, which allows using accurate standard approaches
3842 to multiple hypothesis correction.")
3843 (license license:expat)))
3845 (define-public r-dose
3852 (uri (bioconductor-uri "DOSE" version))
3855 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
3856 (properties `((upstream-name . "DOSE")))
3857 (build-system r-build-system)
3859 `(("r-annotationdbi" ,r-annotationdbi)
3860 ("r-biocparallel" ,r-biocparallel)
3861 ("r-do-db" ,r-do-db)
3862 ("r-fgsea" ,r-fgsea)
3863 ("r-ggplot2" ,r-ggplot2)
3864 ("r-gosemsim" ,r-gosemsim)
3865 ("r-qvalue" ,r-qvalue)
3866 ("r-reshape2" ,r-reshape2)))
3868 `(("r-knitr" ,r-knitr)))
3869 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3870 (synopsis "Disease ontology semantic and enrichment analysis")
3872 "This package implements five methods proposed by Resnik, Schlicker,
3873 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3874 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3875 including hypergeometric model and gene set enrichment analysis are also
3876 implemented for discovering disease associations of high-throughput biological
3878 (license license:artistic2.0)))
3880 (define-public r-enrichplot
3882 (name "r-enrichplot")
3887 (uri (bioconductor-uri "enrichplot" version))
3890 "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd"))))
3891 (build-system r-build-system)
3893 `(("r-cowplot" ,r-cowplot)
3895 ("r-ggplot2" ,r-ggplot2)
3896 ("r-ggraph" ,r-ggraph)
3897 ("r-gosemsim" ,r-gosemsim)
3898 ("r-igraph" ,r-igraph)
3899 ("r-magrittr" ,r-magrittr)
3901 ("r-purrr" ,r-purrr)
3902 ("r-rcolorbrewer" ,r-rcolorbrewer)
3903 ("r-reshape2" ,r-reshape2)
3904 ("r-scatterpie" ,r-scatterpie)
3905 ("r-shadowtext" ,r-shadowtext)))
3907 `(("r-knitr" ,r-knitr)))
3908 (home-page "https://github.com/GuangchuangYu/enrichplot")
3909 (synopsis "Visualization of functional enrichment result")
3911 "The enrichplot package implements several visualization methods for
3912 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3913 All the visualization methods are developed based on ggplot2 graphics.")
3914 (license license:artistic2.0)))
3916 (define-public r-clusterprofiler
3918 (name "r-clusterprofiler")
3923 (uri (bioconductor-uri "clusterProfiler" version))
3926 "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9"))))
3928 `((upstream-name . "clusterProfiler")))
3929 (build-system r-build-system)
3931 `(("r-annotationdbi" ,r-annotationdbi)
3933 ("r-downloader" ,r-downloader)
3934 ("r-dplyr" ,r-dplyr)
3935 ("r-enrichplot" ,r-enrichplot)
3936 ("r-go-db" ,r-go-db)
3937 ("r-gosemsim" ,r-gosemsim)
3938 ("r-magrittr" ,r-magrittr)
3940 ("r-qvalue" ,r-qvalue)
3941 ("r-rlang" ,r-rlang)
3942 ("r-rvcheck" ,r-rvcheck)
3943 ("r-tidyr" ,r-tidyr)))
3945 `(("r-knitr" ,r-knitr)))
3946 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3947 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3949 "This package implements methods to analyze and visualize functional
3950 profiles (GO and KEGG) of gene and gene clusters.")
3951 (license license:artistic2.0)))
3953 (define-public r-mlinterfaces
3955 (name "r-mlinterfaces")
3960 (uri (bioconductor-uri "MLInterfaces" version))
3963 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
3964 (properties `((upstream-name . "MLInterfaces")))
3965 (build-system r-build-system)
3967 `(("r-annotate" ,r-annotate)
3968 ("r-biobase" ,r-biobase)
3969 ("r-biocgenerics" ,r-biocgenerics)
3970 ("r-cluster" ,r-cluster)
3973 ("r-gdata" ,r-gdata)
3974 ("r-genefilter" ,r-genefilter)
3975 ("r-ggvis" ,r-ggvis)
3976 ("r-hwriter" ,r-hwriter)
3978 ("r-mlbench" ,r-mlbench)
3980 ("r-rcolorbrewer" ,r-rcolorbrewer)
3982 ("r-rpart" ,r-rpart)
3983 ("r-sfsmisc" ,r-sfsmisc)
3984 ("r-shiny" ,r-shiny)
3985 ("r-threejs" ,r-threejs)))
3986 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3987 (synopsis "Interfaces to R machine learning procedures")
3989 "This package provides uniform interfaces to machine learning code for
3990 data in R and Bioconductor containers.")
3991 ;; Any version of the LGPL.
3992 (license license:lgpl2.1+)))
3994 (define-public r-annaffy
4001 (uri (bioconductor-uri "annaffy" version))
4004 "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
4005 (build-system r-build-system)
4008 (modify-phases %standard-phases
4009 (add-after 'unpack 'remove-reference-to-non-free-data
4011 (substitute* "DESCRIPTION"
4015 `(("r-annotationdbi" ,r-annotationdbi)
4016 ("r-biobase" ,r-biobase)
4018 ("r-go-db" ,r-go-db)))
4019 (home-page "https://bioconductor.org/packages/annaffy/")
4020 (synopsis "Annotation tools for Affymetrix biological metadata")
4022 "This package provides functions for handling data from Bioconductor
4023 Affymetrix annotation data packages. It produces compact HTML and text
4024 reports including experimental data and URL links to many online databases.
4025 It allows searching of biological metadata using various criteria.")
4026 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4027 ;; the LGPL 2.1 is included.
4028 (license license:lgpl2.1+)))
4030 (define-public r-a4core
4037 (uri (bioconductor-uri "a4Core" version))
4040 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
4041 (properties `((upstream-name . "a4Core")))
4042 (build-system r-build-system)
4044 `(("r-biobase" ,r-biobase)
4045 ("r-glmnet" ,r-glmnet)))
4047 `(("r-knitr" ,r-knitr)))
4048 (home-page "https://bioconductor.org/packages/a4Core")
4049 (synopsis "Automated Affymetrix array analysis core package")
4051 "This is the core package for the automated analysis of Affymetrix
4053 (license license:gpl3)))
4055 (define-public r-a4classif
4057 (name "r-a4classif")
4062 (uri (bioconductor-uri "a4Classif" version))
4065 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
4066 (properties `((upstream-name . "a4Classif")))
4067 (build-system r-build-system)
4069 `(("r-a4core" ,r-a4core)
4070 ("r-a4preproc" ,r-a4preproc)
4071 ("r-biobase" ,r-biobase)
4072 ("r-glmnet" ,r-glmnet)
4075 ("r-varselrf" ,r-varselrf)))
4077 `(("r-knitr" ,r-knitr)))
4078 (home-page "https://bioconductor.org/packages/a4Classif/")
4079 (synopsis "Automated Affymetrix array analysis classification package")
4081 "This is the classification package for the automated analysis of
4082 Affymetrix arrays.")
4083 (license license:gpl3)))
4085 (define-public r-a4preproc
4087 (name "r-a4preproc")
4092 (uri (bioconductor-uri "a4Preproc" version))
4095 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
4096 (properties `((upstream-name . "a4Preproc")))
4097 (build-system r-build-system)
4099 `(("r-biobase" ,r-biobase)
4100 ("r-biocgenerics" ,r-biocgenerics)))
4102 `(("r-knitr" ,r-knitr)))
4103 (home-page "https://bioconductor.org/packages/a4Preproc/")
4104 (synopsis "Automated Affymetrix array analysis preprocessing package")
4106 "This is a package for the automated analysis of Affymetrix arrays. It
4107 is used for preprocessing the arrays.")
4108 (license license:gpl3)))
4110 (define-public r-a4reporting
4112 (name "r-a4reporting")
4117 (uri (bioconductor-uri "a4Reporting" version))
4120 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
4121 (properties `((upstream-name . "a4Reporting")))
4122 (build-system r-build-system)
4124 `(("r-xtable" ,r-xtable)))
4126 `(("r-knitr" ,r-knitr)))
4127 (home-page "https://bioconductor.org/packages/a4Reporting/")
4128 (synopsis "Automated Affymetrix array analysis reporting package")
4130 "This is a package for the automated analysis of Affymetrix arrays. It
4131 provides reporting features.")
4132 (license license:gpl3)))
4134 (define-public r-a4base
4141 (uri (bioconductor-uri "a4Base" version))
4144 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
4145 (properties `((upstream-name . "a4Base")))
4146 (build-system r-build-system)
4148 `(("r-a4core" ,r-a4core)
4149 ("r-a4preproc" ,r-a4preproc)
4150 ("r-annaffy" ,r-annaffy)
4151 ("r-biobase" ,r-biobase)
4152 ("r-genefilter" ,r-genefilter)
4153 ("r-glmnet" ,r-glmnet)
4154 ("r-gplots" ,r-gplots)
4155 ("r-limma" ,r-limma)
4157 ("r-multtest" ,r-multtest)))
4158 (home-page "https://bioconductor.org/packages/a4Base/")
4159 (synopsis "Automated Affymetrix array analysis base package")
4161 "This package provides basic features for the automated analysis of
4162 Affymetrix arrays.")
4163 (license license:gpl3)))
4172 (uri (bioconductor-uri "a4" version))
4175 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
4176 (build-system r-build-system)
4178 `(("r-a4base" ,r-a4base)
4179 ("r-a4classif" ,r-a4classif)
4180 ("r-a4core" ,r-a4core)
4181 ("r-a4preproc" ,r-a4preproc)
4182 ("r-a4reporting" ,r-a4reporting)))
4183 (home-page "https://bioconductor.org/packages/a4/")
4184 (synopsis "Automated Affymetrix array analysis umbrella package")
4186 "This package provides a software suite for the automated analysis of
4187 Affymetrix arrays.")
4188 (license license:gpl3)))
4190 (define-public r-abseqr
4197 (uri (bioconductor-uri "abseqR" version))
4200 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
4201 (properties `((upstream-name . "abseqR")))
4202 (build-system r-build-system)
4204 `(("pandoc" ,pandoc)))
4206 `(("r-biocparallel" ,r-biocparallel)
4207 ("r-biocstyle" ,r-biocstyle)
4208 ("r-circlize" ,r-circlize)
4209 ("r-flexdashboard" ,r-flexdashboard)
4210 ("r-ggcorrplot" ,r-ggcorrplot)
4211 ("r-ggdendro" ,r-ggdendro)
4212 ("r-ggplot2" ,r-ggplot2)
4213 ("r-gridextra" ,r-gridextra)
4214 ("r-knitr" ,r-knitr)
4215 ("r-plotly" ,r-plotly)
4218 ("r-rcolorbrewer" ,r-rcolorbrewer)
4219 ("r-reshape2" ,r-reshape2)
4220 ("r-rmarkdown" ,r-rmarkdown)
4221 ("r-stringr" ,r-stringr)
4222 ("r-vegan" ,r-vegan)
4223 ("r-venndiagram" ,r-venndiagram)))
4225 `(("r-knitr" ,r-knitr)))
4226 (home-page "https://github.com/malhamdoosh/abseqR")
4227 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4229 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4230 sequencing datasets generated from antibody libraries and abseqR is one of its
4231 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4232 capabilities and allows them to generate interactive HTML reports for the
4233 convenience of viewing and sharing with other researchers. Additionally,
4234 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4235 further downstream analysis on its output.")
4236 (license license:gpl3)))
4238 (define-public r-bacon
4245 (uri (bioconductor-uri "bacon" version))
4248 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
4249 (build-system r-build-system)
4251 `(("r-biocparallel" ,r-biocparallel)
4252 ("r-ellipse" ,r-ellipse)
4253 ("r-ggplot2" ,r-ggplot2)))
4255 `(("r-knitr" ,r-knitr)))
4256 (home-page "https://bioconductor.org/packages/bacon/")
4257 (synopsis "Controlling bias and inflation in association studies")
4259 "Bacon can be used to remove inflation and bias often observed in
4260 epigenome- and transcriptome-wide association studies. To this end bacon
4261 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4262 fitting a three-component normal mixture on z-scores.")
4263 (license license:gpl2+)))
4265 (define-public r-rgadem
4272 (uri (bioconductor-uri "rGADEM" version))
4275 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
4276 (properties `((upstream-name . "rGADEM")))
4277 (build-system r-build-system)
4279 `(("r-biostrings" ,r-biostrings)
4280 ("r-bsgenome" ,r-bsgenome)
4281 ("r-genomicranges" ,r-genomicranges)
4282 ("r-iranges" ,r-iranges)
4283 ("r-seqlogo" ,r-seqlogo)))
4284 (home-page "https://bioconductor.org/packages/rGADEM/")
4285 (synopsis "De novo sequence motif discovery")
4287 "rGADEM is an efficient de novo motif discovery tool for large-scale
4288 genomic sequence data.")
4289 (license license:artistic2.0)))
4291 (define-public r-motiv
4298 (uri (bioconductor-uri "MotIV" version))
4301 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4302 (properties `((upstream-name . "MotIV")))
4303 (build-system r-build-system)
4307 `(("r-biocgenerics" ,r-biocgenerics)
4308 ("r-biostrings" ,r-biostrings)
4309 ("r-genomicranges" ,r-genomicranges)
4310 ("r-iranges" ,r-iranges)
4311 ("r-lattice" ,r-lattice)
4312 ("r-rgadem" ,r-rgadem)
4313 ("r-s4vectors" ,r-s4vectors)))
4314 (home-page "https://bioconductor.org/packages/MotIV/")
4315 (synopsis "Motif identification and validation")
4317 "This package is used for the identification and validation of sequence
4318 motifs. It makes use of STAMP for comparing a set of motifs to a given
4319 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4320 distributions, modules and filter motifs.")
4321 (license license:gpl2)))
4323 (define-public r-motifdb
4329 (uri (bioconductor-uri "MotifDb" version))
4331 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
4332 (properties `((upstream-name . "MotifDb")))
4333 (build-system r-build-system)
4335 `(("r-biocgenerics" ,r-biocgenerics)
4336 ("r-biostrings" ,r-biostrings)
4337 ("r-genomicranges" ,r-genomicranges)
4338 ("r-iranges" ,r-iranges)
4339 ("r-rtracklayer" ,r-rtracklayer)
4340 ("r-s4vectors" ,r-s4vectors)
4341 ("r-splitstackshape" ,r-splitstackshape)))
4343 `(("r-knitr" ,r-knitr)))
4344 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4345 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4346 (description "This package provides more than 2000 annotated position
4347 frequency matrices from nine public sources, for multiple organisms.")
4348 (license license:artistic2.0)))
4350 (define-public r-motifbreakr
4352 (name "r-motifbreakr")
4356 (uri (bioconductor-uri "motifbreakR" version))
4358 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
4359 (properties `((upstream-name . "motifbreakR")))
4360 (build-system r-build-system)
4362 `(("r-biocgenerics" ,r-biocgenerics)
4363 ("r-biocparallel" ,r-biocparallel)
4364 ("r-biostrings" ,r-biostrings)
4365 ("r-bsgenome" ,r-bsgenome)
4366 ("r-genomeinfodb" ,r-genomeinfodb)
4367 ("r-genomicranges" ,r-genomicranges)
4368 ("r-grimport" ,r-grimport)
4370 ("r-iranges" ,r-iranges)
4371 ("r-matrixstats" ,r-matrixstats)
4372 ("r-motifdb" ,r-motifdb)
4373 ("r-motifstack" ,r-motifstack)
4374 ("r-rtracklayer" ,r-rtracklayer)
4375 ("r-s4vectors" ,r-s4vectors)
4376 ("r-stringr" ,r-stringr)
4377 ("r-summarizedexperiment" ,r-summarizedexperiment)
4378 ("r-tfmpvalue" ,r-tfmpvalue)
4379 ("r-variantannotation" ,r-variantannotation)))
4381 `(("r-knitr" ,r-knitr)))
4382 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4383 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4384 (description "This package allows biologists to judge in the first place
4385 whether the sequence surrounding the polymorphism is a good match, and in
4386 the second place how much information is gained or lost in one allele of
4387 the polymorphism relative to another. This package gives a choice of
4388 algorithms for interrogation of genomes with motifs from public sources:
4390 @item a weighted-sum probability matrix;
4391 @item log-probabilities;
4392 @item weighted by relative entropy.
4395 This package can predict effects for novel or previously described variants in
4396 public databases, making it suitable for tasks beyond the scope of its original
4397 design. Lastly, it can be used to interrogate any genome curated within
4399 (license license:gpl2+)))
4401 (define-public r-motifstack
4403 (name "r-motifstack")
4408 (uri (bioconductor-uri "motifStack" version))
4411 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
4412 (properties `((upstream-name . "motifStack")))
4413 (build-system r-build-system)
4415 `(("r-ade4" ,r-ade4)
4416 ("r-biostrings" ,r-biostrings)
4417 ("r-ggplot2" ,r-ggplot2)
4418 ("r-htmlwidgets" ,r-htmlwidgets)
4421 `(("r-knitr" ,r-knitr)))
4422 (home-page "https://bioconductor.org/packages/motifStack/")
4423 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4425 "The motifStack package is designed for graphic representation of
4426 multiple motifs with different similarity scores. It works with both DNA/RNA
4427 sequence motifs and amino acid sequence motifs. In addition, it provides the
4428 flexibility for users to customize the graphic parameters such as the font
4429 type and symbol colors.")
4430 (license license:gpl2+)))
4432 (define-public r-genomicscores
4434 (name "r-genomicscores")
4439 (uri (bioconductor-uri "GenomicScores" version))
4442 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
4443 (properties `((upstream-name . "GenomicScores")))
4444 (build-system r-build-system)
4446 `(("r-annotationhub" ,r-annotationhub)
4447 ("r-biobase" ,r-biobase)
4448 ("r-biocfilecache" ,r-biocfilecache)
4449 ("r-biocgenerics" ,r-biocgenerics)
4450 ("r-biocmanager" ,r-biocmanager)
4451 ("r-biostrings" ,r-biostrings)
4452 ("r-delayedarray" ,r-delayedarray)
4453 ("r-genomeinfodb" ,r-genomeinfodb)
4454 ("r-genomicranges" ,r-genomicranges)
4455 ("r-hdf5array" ,r-hdf5array)
4456 ("r-iranges" ,r-iranges)
4457 ("r-rhdf5" ,r-rhdf5)
4458 ("r-s4vectors" ,r-s4vectors)
4461 `(("r-knitr" ,r-knitr)))
4462 (home-page "https://github.com/rcastelo/GenomicScores/")
4463 (synopsis "Work with genome-wide position-specific scores")
4465 "This package provides infrastructure to store and access genome-wide
4466 position-specific scores within R and Bioconductor.")
4467 (license license:artistic2.0)))
4469 (define-public r-atacseqqc
4471 (name "r-atacseqqc")
4476 (uri (bioconductor-uri "ATACseqQC" version))
4479 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
4480 (properties `((upstream-name . "ATACseqQC")))
4481 (build-system r-build-system)
4483 `(("r-biocgenerics" ,r-biocgenerics)
4484 ("r-biostrings" ,r-biostrings)
4485 ("r-bsgenome" ,r-bsgenome)
4486 ("r-chippeakanno" ,r-chippeakanno)
4487 ("r-edger" ,r-edger)
4488 ("r-genomeinfodb" ,r-genomeinfodb)
4489 ("r-genomicalignments" ,r-genomicalignments)
4490 ("r-genomicranges" ,r-genomicranges)
4491 ("r-genomicscores" ,r-genomicscores)
4492 ("r-iranges" ,r-iranges)
4493 ("r-kernsmooth" ,r-kernsmooth)
4494 ("r-limma" ,r-limma)
4495 ("r-motifstack" ,r-motifstack)
4496 ("r-preseqr" ,r-preseqr)
4497 ("r-randomforest" ,r-randomforest)
4498 ("r-rsamtools" ,r-rsamtools)
4499 ("r-rtracklayer" ,r-rtracklayer)
4500 ("r-s4vectors" ,r-s4vectors)))
4502 `(("r-knitr" ,r-knitr)))
4503 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4504 (synopsis "ATAC-seq quality control")
4506 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4507 sequencing, is a rapid and sensitive method for chromatin accessibility
4508 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4509 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4510 assess whether their ATAC-seq experiment is successful. It includes
4511 diagnostic plots of fragment size distribution, proportion of mitochondria
4512 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4514 (license license:gpl2+)))
4516 (define-public r-gofuncr
4523 (uri (bioconductor-uri "GOfuncR" version))
4526 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
4527 (properties `((upstream-name . "GOfuncR")))
4528 (build-system r-build-system)
4530 `(("r-annotationdbi" ,r-annotationdbi)
4531 ("r-genomicranges" ,r-genomicranges)
4532 ("r-gtools" ,r-gtools)
4533 ("r-iranges" ,r-iranges)
4534 ("r-mapplots" ,r-mapplots)
4536 ("r-vioplot" ,r-vioplot)))
4538 `(("r-knitr" ,r-knitr)))
4539 (home-page "https://bioconductor.org/packages/GOfuncR/")
4540 (synopsis "Gene ontology enrichment using FUNC")
4542 "GOfuncR performs a gene ontology enrichment analysis based on the
4543 ontology enrichment software FUNC. GO-annotations are obtained from
4544 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4545 included in the package and updated regularly. GOfuncR provides the standard
4546 candidate vs background enrichment analysis using the hypergeometric test, as
4547 well as three additional tests:
4550 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4551 @item a binomial test that is used when genes are associated with two counts,
4553 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4554 associated with four counts.
4557 To correct for multiple testing and interdependency of the tests, family-wise
4558 error rates are computed based on random permutations of the gene-associated
4559 variables. GOfuncR also provides tools for exploring the ontology graph and
4560 the annotations, and options to take gene-length or spatial clustering of
4561 genes into account. It is also possible to provide custom gene coordinates,
4562 annotations and ontologies.")
4563 (license license:gpl2+)))
4565 (define-public r-abaenrichment
4567 (name "r-abaenrichment")
4572 (uri (bioconductor-uri "ABAEnrichment" version))
4575 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
4576 (properties `((upstream-name . "ABAEnrichment")))
4577 (build-system r-build-system)
4579 `(("r-abadata" ,r-abadata)
4580 ("r-data-table" ,r-data-table)
4581 ("r-gofuncr" ,r-gofuncr)
4582 ("r-gplots" ,r-gplots)
4583 ("r-gtools" ,r-gtools)
4584 ("r-rcpp" ,r-rcpp)))
4586 `(("r-knitr" ,r-knitr)))
4587 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4588 (synopsis "Gene expression enrichment in human brain regions")
4590 "The package ABAEnrichment is designed to test for enrichment of user
4591 defined candidate genes in the set of expressed genes in different human brain
4592 regions. The core function @code{aba_enrich} integrates the expression of the
4593 candidate gene set (averaged across donors) and the structural information of
4594 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4595 (license license:gpl2+)))
4597 (define-public r-annotationfuncs
4599 (name "r-annotationfuncs")
4604 (uri (bioconductor-uri "AnnotationFuncs" version))
4607 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
4609 `((upstream-name . "AnnotationFuncs")))
4610 (build-system r-build-system)
4612 `(("r-annotationdbi" ,r-annotationdbi)
4614 (home-page "https://www.iysik.com/r/annotationfuncs")
4615 (synopsis "Annotation translation functions")
4617 "This package provides functions for handling translating between
4618 different identifieres using the Biocore Data Team data-packages (e.g.
4619 @code{org.Bt.eg.db}).")
4620 (license license:gpl2)))
4622 (define-public r-annotationtools
4624 (name "r-annotationtools")
4629 (uri (bioconductor-uri "annotationTools" version))
4632 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
4634 `((upstream-name . "annotationTools")))
4635 (build-system r-build-system)
4636 (propagated-inputs `(("r-biobase" ,r-biobase)))
4637 (home-page "https://bioconductor.org/packages/annotationTools/")
4638 (synopsis "Annotate microarrays and perform gene expression analyses")
4640 "This package provides functions to annotate microarrays, find orthologs,
4641 and integrate heterogeneous gene expression profiles using annotation and
4642 other molecular biology information available as flat file database (plain
4644 ;; Any version of the GPL.
4645 (license (list license:gpl2+))))
4647 (define-public r-allelicimbalance
4649 (name "r-allelicimbalance")
4654 (uri (bioconductor-uri "AllelicImbalance" version))
4657 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
4659 `((upstream-name . "AllelicImbalance")))
4660 (build-system r-build-system)
4662 `(("r-annotationdbi" ,r-annotationdbi)
4663 ("r-biocgenerics" ,r-biocgenerics)
4664 ("r-biostrings" ,r-biostrings)
4665 ("r-bsgenome" ,r-bsgenome)
4666 ("r-genomeinfodb" ,r-genomeinfodb)
4667 ("r-genomicalignments" ,r-genomicalignments)
4668 ("r-genomicfeatures" ,r-genomicfeatures)
4669 ("r-genomicranges" ,r-genomicranges)
4670 ("r-gridextra" ,r-gridextra)
4672 ("r-iranges" ,r-iranges)
4673 ("r-lattice" ,r-lattice)
4674 ("r-latticeextra" ,r-latticeextra)
4676 ("r-rsamtools" ,r-rsamtools)
4677 ("r-s4vectors" ,r-s4vectors)
4678 ("r-seqinr" ,r-seqinr)
4679 ("r-summarizedexperiment" ,r-summarizedexperiment)
4680 ("r-variantannotation" ,r-variantannotation)))
4682 `(("r-knitr" ,r-knitr)))
4683 (home-page "https://github.com/pappewaio/AllelicImbalance")
4684 (synopsis "Investigate allele-specific expression")
4686 "This package provides a framework for allele-specific expression
4687 investigation using RNA-seq data.")
4688 (license license:gpl3)))
4690 (define-public r-aucell
4697 (uri (bioconductor-uri "AUCell" version))
4700 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
4701 (properties `((upstream-name . "AUCell")))
4702 (build-system r-build-system)
4704 `(("r-biocgenerics" ,r-biocgenerics)
4705 ("r-data-table" ,r-data-table)
4706 ("r-gseabase" ,r-gseabase)
4707 ("r-mixtools" ,r-mixtools)
4708 ("r-r-utils" ,r-r-utils)
4709 ("r-s4vectors" ,r-s4vectors)
4710 ("r-shiny" ,r-shiny)
4711 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4713 `(("r-knitr" ,r-knitr)))
4714 (home-page "https://bioconductor.org/packages/AUCell/")
4715 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4717 "AUCell identifies cells with active gene sets (e.g. signatures,
4718 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4719 Under the Curve} (AUC) to calculate whether a critical subset of the input
4720 gene set is enriched within the expressed genes for each cell. The
4721 distribution of AUC scores across all the cells allows exploring the relative
4722 expression of the signature. Since the scoring method is ranking-based,
4723 AUCell is independent of the gene expression units and the normalization
4724 procedure. In addition, since the cells are evaluated individually, it can
4725 easily be applied to bigger datasets, subsetting the expression matrix if
4727 (license license:gpl3)))
4729 (define-public r-ebimage
4736 (uri (bioconductor-uri "EBImage" version))
4739 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
4740 (properties `((upstream-name . "EBImage")))
4741 (build-system r-build-system)
4743 `(("r-abind" ,r-abind)
4744 ("r-biocgenerics" ,r-biocgenerics)
4745 ("r-fftwtools" ,r-fftwtools)
4746 ("r-htmltools" ,r-htmltools)
4747 ("r-htmlwidgets" ,r-htmlwidgets)
4749 ("r-locfit" ,r-locfit)
4751 ("r-rcurl" ,r-rcurl)
4752 ("r-tiff" ,r-tiff)))
4754 `(("r-knitr" ,r-knitr))) ; for vignettes
4755 (home-page "https://github.com/aoles/EBImage")
4756 (synopsis "Image processing and analysis toolbox for R")
4758 "EBImage provides general purpose functionality for image processing and
4759 analysis. In the context of (high-throughput) microscopy-based cellular
4760 assays, EBImage offers tools to segment cells and extract quantitative
4761 cellular descriptors. This allows the automation of such tasks using the R
4762 programming language and facilitates the use of other tools in the R
4763 environment for signal processing, statistical modeling, machine learning and
4764 visualization with image data.")
4765 ;; Any version of the LGPL.
4766 (license license:lgpl2.1+)))
4768 (define-public r-yamss
4775 (uri (bioconductor-uri "yamss" version))
4778 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
4779 (build-system r-build-system)
4781 `(("r-biocgenerics" ,r-biocgenerics)
4782 ("r-data-table" ,r-data-table)
4783 ("r-ebimage" ,r-ebimage)
4784 ("r-iranges" ,r-iranges)
4785 ("r-limma" ,r-limma)
4786 ("r-matrix" ,r-matrix)
4788 ("r-s4vectors" ,r-s4vectors)
4789 ("r-summarizedexperiment"
4790 ,r-summarizedexperiment)))
4792 `(("r-knitr" ,r-knitr)))
4793 (home-page "https://github.com/hansenlab/yamss")
4794 (synopsis "Tools for high-throughput metabolomics")
4796 "This package provides tools to analyze and visualize high-throughput
4797 metabolomics data acquired using chromatography-mass spectrometry. These tools
4798 preprocess data in a way that enables reliable and powerful differential
4800 (license license:artistic2.0)))
4802 (define-public r-gtrellis
4809 (uri (bioconductor-uri "gtrellis" version))
4812 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
4813 (build-system r-build-system)
4815 `(("r-circlize" ,r-circlize)
4816 ("r-genomicranges" ,r-genomicranges)
4817 ("r-getoptlong" ,r-getoptlong)
4818 ("r-iranges" ,r-iranges)))
4820 `(("r-knitr" ,r-knitr)))
4821 (home-page "https://github.com/jokergoo/gtrellis")
4822 (synopsis "Genome level Trellis layout")
4824 "Genome level Trellis graph visualizes genomic data conditioned by
4825 genomic categories (e.g. chromosomes). For each genomic category, multiple
4826 dimensional data which are represented as tracks describe different features
4827 from different aspects. This package provides high flexibility to arrange
4828 genomic categories and to add self-defined graphics in the plot.")
4829 (license license:expat)))
4831 (define-public r-somaticsignatures
4833 (name "r-somaticsignatures")
4838 (uri (bioconductor-uri "SomaticSignatures" version))
4841 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
4843 `((upstream-name . "SomaticSignatures")))
4844 (build-system r-build-system)
4846 `(("r-biobase" ,r-biobase)
4847 ("r-biostrings" ,r-biostrings)
4848 ("r-genomeinfodb" ,r-genomeinfodb)
4849 ("r-genomicranges" ,r-genomicranges)
4850 ("r-ggbio" ,r-ggbio)
4851 ("r-ggplot2" ,r-ggplot2)
4852 ("r-iranges" ,r-iranges)
4854 ("r-pcamethods" ,r-pcamethods)
4855 ("r-proxy" ,r-proxy)
4856 ("r-reshape2" ,r-reshape2)
4857 ("r-s4vectors" ,r-s4vectors)
4858 ("r-variantannotation" ,r-variantannotation)))
4860 `(("r-knitr" ,r-knitr)))
4861 (home-page "https://github.com/juliangehring/SomaticSignatures")
4862 (synopsis "Somatic signatures")
4864 "This package identifies mutational signatures of @dfn{single nucleotide
4865 variants} (SNVs). It provides a infrastructure related to the methodology
4866 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4867 decomposition algorithms.")
4868 (license license:expat)))
4870 (define-public r-yapsa
4877 (uri (bioconductor-uri "YAPSA" version))
4880 "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
4881 (properties `((upstream-name . "YAPSA")))
4882 (build-system r-build-system)
4884 `(("r-biostrings" ,r-biostrings)
4885 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4886 ("r-circlize" ,r-circlize)
4887 ("r-complexheatmap" ,r-complexheatmap)
4888 ("r-corrplot" ,r-corrplot)
4889 ("r-dendextend" ,r-dendextend)
4890 ("r-doparallel" ,r-doparallel)
4891 ("r-dplyr" ,r-dplyr)
4892 ("r-genomeinfodb" ,r-genomeinfodb)
4893 ("r-genomicranges" ,r-genomicranges)
4894 ("r-getoptlong" ,r-getoptlong)
4895 ("r-ggbeeswarm" ,r-ggbeeswarm)
4896 ("r-ggplot2" ,r-ggplot2)
4897 ("r-gridextra" ,r-gridextra)
4898 ("r-gtrellis" ,r-gtrellis)
4899 ("r-keggrest" ,r-keggrest)
4901 ("r-magrittr" ,r-magrittr)
4902 ("r-pmcmr" ,r-pmcmr)
4903 ("r-pracma" ,r-pracma)
4904 ("r-reshape2" ,r-reshape2)
4905 ("r-somaticsignatures" ,r-somaticsignatures)
4906 ("r-variantannotation" ,r-variantannotation)))
4908 `(("r-knitr" ,r-knitr)))
4909 (home-page "https://bioconductor.org/packages/YAPSA/")
4910 (synopsis "Yet another package for signature analysis")
4912 "This package provides functions and routines useful in the analysis of
4913 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4914 functions to perform a signature analysis with known signatures and a
4915 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4917 (license license:gpl3)))
4919 (define-public r-gcrma
4926 (uri (bioconductor-uri "gcrma" version))
4929 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
4930 (build-system r-build-system)
4932 `(("r-affy" ,r-affy)
4933 ("r-affyio" ,r-affyio)
4934 ("r-biobase" ,r-biobase)
4935 ("r-biocmanager" ,r-biocmanager)
4936 ("r-biostrings" ,r-biostrings)
4937 ("r-xvector" ,r-xvector)))
4938 (home-page "https://bioconductor.org/packages/gcrma/")
4939 (synopsis "Background adjustment using sequence information")
4941 "Gcrma adjusts for background intensities in Affymetrix array data which
4942 include optical noise and @dfn{non-specific binding} (NSB). The main function
4943 @code{gcrma} converts background adjusted probe intensities to expression
4944 measures using the same normalization and summarization methods as a
4945 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4946 to estimate probe affinity to NSB. The sequence information is summarized in
4947 a more complex way than the simple GC content. Instead, the base types (A, T,
4948 G or C) at each position along the probe determine the affinity of each probe.
4949 The parameters of the position-specific base contributions to the probe
4950 affinity is estimated in an NSB experiment in which only NSB but no
4951 gene-specific binding is expected.")
4952 ;; Any version of the LGPL
4953 (license license:lgpl2.1+)))
4955 (define-public r-simpleaffy
4957 (name "r-simpleaffy")
4962 (uri (bioconductor-uri "simpleaffy" version))
4965 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
4966 (build-system r-build-system)
4968 `(("r-affy" ,r-affy)
4969 ("r-biobase" ,r-biobase)
4970 ("r-biocgenerics" ,r-biocgenerics)
4971 ("r-gcrma" ,r-gcrma)
4972 ("r-genefilter" ,r-genefilter)))
4973 (home-page "https://bioconductor.org/packages/simpleaffy/")
4974 (synopsis "Very simple high level analysis of Affymetrix data")
4976 "This package provides high level functions for reading Affy @file{.CEL}
4977 files, phenotypic data, and then computing simple things with it, such as
4978 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4979 library. It also has some basic scatter plot functions and mechanisms for
4980 generating high resolution journal figures.")
4981 (license license:gpl2+)))
4983 (define-public r-yaqcaffy
4990 (uri (bioconductor-uri "yaqcaffy" version))
4993 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
4994 (build-system r-build-system)
4996 `(("r-simpleaffy" ,r-simpleaffy)))
4997 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4998 (synopsis "Affymetrix quality control and reproducibility analysis")
5000 "This is a package that can be used for quality control of Affymetrix
5001 GeneChip expression data and reproducibility analysis of human whole genome
5002 chips with the MAQC reference datasets.")
5003 (license license:artistic2.0)))
5005 (define-public r-quantro
5012 (uri (bioconductor-uri "quantro" version))
5015 "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
5016 (build-system r-build-system)
5018 `(("r-biobase" ,r-biobase)
5019 ("r-doparallel" ,r-doparallel)
5020 ("r-foreach" ,r-foreach)
5021 ("r-ggplot2" ,r-ggplot2)
5022 ("r-iterators" ,r-iterators)
5023 ("r-minfi" ,r-minfi)
5024 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5026 `(("r-knitr" ,r-knitr)))
5027 (home-page "https://bioconductor.org/packages/quantro/")
5028 (synopsis "Test for when to use quantile normalization")
5030 "This package provides a data-driven test for the assumptions of quantile
5031 normalization using raw data such as objects that inherit eSets (e.g.
5032 ExpressionSet, MethylSet). Group level information about each sample (such as
5033 Tumor / Normal status) must also be provided because the test assesses if
5034 there are global differences in the distributions between the user-defined
5036 (license license:gpl3+)))
5038 (define-public r-yarn
5045 (uri (bioconductor-uri "yarn" version))
5048 "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
5049 (build-system r-build-system)
5051 `(("r-biobase" ,r-biobase)
5052 ("r-biomart" ,r-biomart)
5053 ("r-downloader" ,r-downloader)
5054 ("r-edger" ,r-edger)
5055 ("r-gplots" ,r-gplots)
5056 ("r-limma" ,r-limma)
5057 ("r-matrixstats" ,r-matrixstats)
5058 ("r-preprocesscore" ,r-preprocesscore)
5059 ("r-quantro" ,r-quantro)
5060 ("r-rcolorbrewer" ,r-rcolorbrewer)
5061 ("r-readr" ,r-readr)))
5063 `(("r-knitr" ,r-knitr)))
5064 (home-page "https://bioconductor.org/packages/yarn/")
5065 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5067 "Expedite large RNA-Seq analyses using a combination of previously
5068 developed tools. YARN is meant to make it easier for the user in performing
5069 basic mis-annotation quality control, filtering, and condition-aware
5070 normalization. YARN leverages many Bioconductor tools and statistical
5071 techniques to account for the large heterogeneity and sparsity found in very
5072 large RNA-seq experiments.")
5073 (license license:artistic2.0)))
5075 (define-public r-roar
5082 (uri (bioconductor-uri "roar" version))
5085 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
5086 (build-system r-build-system)
5088 `(("r-biocgenerics" ,r-biocgenerics)
5089 ("r-genomeinfodb" ,r-genomeinfodb)
5090 ("r-genomicalignments" ,r-genomicalignments)
5091 ("r-genomicranges" ,r-genomicranges)
5092 ("r-iranges" ,r-iranges)
5093 ("r-rtracklayer" ,r-rtracklayer)
5094 ("r-s4vectors" ,r-s4vectors)
5095 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5096 (home-page "https://github.com/vodkatad/roar/")
5097 (synopsis "Identify differential APA usage from RNA-seq alignments")
5099 "This package provides tools for identifying preferential usage of APA
5100 sites, comparing two biological conditions, starting from known alternative
5101 sites and alignments obtained from standard RNA-seq experiments.")
5102 (license license:gpl3)))
5104 (define-public r-xbseq
5111 (uri (bioconductor-uri "XBSeq" version))
5114 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
5115 (properties `((upstream-name . "XBSeq")))
5116 (build-system r-build-system)
5118 `(("r-biobase" ,r-biobase)
5119 ("r-deseq2" ,r-deseq2)
5120 ("r-dplyr" ,r-dplyr)
5121 ("r-ggplot2" ,r-ggplot2)
5122 ("r-locfit" ,r-locfit)
5123 ("r-magrittr" ,r-magrittr)
5124 ("r-matrixstats" ,r-matrixstats)
5125 ("r-pracma" ,r-pracma)
5126 ("r-roar" ,r-roar)))
5128 `(("r-knitr" ,r-knitr)))
5129 (home-page "https://github.com/Liuy12/XBSeq")
5130 (synopsis "Test for differential expression for RNA-seq data")
5132 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5133 expression} (DE), where a statistical model was established based on the
5134 assumption that observed signals are the convolution of true expression
5135 signals and sequencing noises. The mapped reads in non-exonic regions are
5136 considered as sequencing noises, which follows a Poisson distribution. Given
5137 measurable observed signal and background noise from RNA-seq data, true
5138 expression signals, assuming governed by the negative binomial distribution,
5139 can be delineated and thus the accurate detection of differential expressed
5141 (license license:gpl3+)))
5143 (define-public r-massspecwavelet
5145 (name "r-massspecwavelet")
5150 (uri (bioconductor-uri "MassSpecWavelet" version))
5153 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
5155 `((upstream-name . "MassSpecWavelet")))
5156 (build-system r-build-system)
5158 `(("r-waveslim" ,r-waveslim)))
5159 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5160 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5162 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5163 data mainly through the use of wavelet transforms. It supports peak detection
5164 based on @dfn{Continuous Wavelet Transform} (CWT).")
5165 (license license:lgpl2.0+)))
5167 (define-public r-xcms
5174 (uri (bioconductor-uri "xcms" version))
5177 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
5178 (build-system r-build-system)
5180 `(("r-biobase" ,r-biobase)
5181 ("r-biocgenerics" ,r-biocgenerics)
5182 ("r-biocparallel" ,r-biocparallel)
5183 ("r-iranges" ,r-iranges)
5184 ("r-lattice" ,r-lattice)
5185 ("r-massspecwavelet" ,r-massspecwavelet)
5186 ("r-mscoreutils" ,r-mscoreutils)
5187 ("r-msnbase" ,r-msnbase)
5190 ("r-protgenerics" ,r-protgenerics)
5192 ("r-rcolorbrewer" ,r-rcolorbrewer)
5193 ("r-robustbase" ,r-robustbase)
5194 ("r-s4vectors" ,r-s4vectors)
5195 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5197 `(("r-knitr" ,r-knitr)))
5198 (home-page "https://bioconductor.org/packages/xcms/")
5199 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5201 "This package provides a framework for processing and visualization of
5202 chromatographically separated and single-spectra mass spectral data. It
5203 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5204 data for high-throughput, untargeted analyte profiling.")
5205 (license license:gpl2+)))
5207 (define-public r-wrench
5214 (uri (bioconductor-uri "Wrench" version))
5217 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
5218 (properties `((upstream-name . "Wrench")))
5219 (build-system r-build-system)
5221 `(("r-limma" ,r-limma)
5222 ("r-locfit" ,r-locfit)
5223 ("r-matrixstats" ,r-matrixstats)))
5225 `(("r-knitr" ,r-knitr)))
5226 (home-page "https://github.com/HCBravoLab/Wrench")
5227 (synopsis "Wrench normalization for sparse count data")
5229 "Wrench is a package for normalization sparse genomic count data, like
5230 that arising from 16s metagenomic surveys.")
5231 (license license:artistic2.0)))
5233 (define-public r-wiggleplotr
5235 (name "r-wiggleplotr")
5240 (uri (bioconductor-uri "wiggleplotr" version))
5243 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
5244 (build-system r-build-system)
5246 `(("r-assertthat" ,r-assertthat)
5247 ("r-cowplot" ,r-cowplot)
5248 ("r-dplyr" ,r-dplyr)
5249 ("r-genomeinfodb" ,r-genomeinfodb)
5250 ("r-genomicranges" ,r-genomicranges)
5251 ("r-ggplot2" ,r-ggplot2)
5252 ("r-iranges" ,r-iranges)
5253 ("r-purrr" ,r-purrr)
5254 ("r-rtracklayer" ,r-rtracklayer)
5255 ("r-s4vectors" ,r-s4vectors)))
5257 `(("r-knitr" ,r-knitr)))
5258 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5259 (synopsis "Make read coverage plots from BigWig files")
5261 "This package provides tools to visualize read coverage from sequencing
5262 experiments together with genomic annotations (genes, transcripts, peaks).
5263 Introns of long transcripts can be rescaled to a fixed length for better
5264 visualization of exonic read coverage.")
5265 (license license:asl2.0)))
5267 (define-public r-widgettools
5269 (name "r-widgettools")
5274 (uri (bioconductor-uri "widgetTools" version))
5277 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
5278 (properties `((upstream-name . "widgetTools")))
5279 (build-system r-build-system)
5280 (home-page "https://bioconductor.org/packages/widgetTools/")
5281 (synopsis "Tools for creating interactive tcltk widgets")
5283 "This package contains tools to support the construction of tcltk
5285 ;; Any version of the LGPL.
5286 (license license:lgpl3+)))
5288 (define-public r-webbioc
5295 (uri (bioconductor-uri "webbioc" version))
5298 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
5299 (build-system r-build-system)
5301 `(("netpbm" ,netpbm)
5304 `(("r-affy" ,r-affy)
5305 ("r-annaffy" ,r-annaffy)
5306 ("r-biobase" ,r-biobase)
5307 ("r-biocmanager" ,r-biocmanager)
5308 ("r-gcrma" ,r-gcrma)
5309 ("r-multtest" ,r-multtest)
5310 ("r-qvalue" ,r-qvalue)
5312 (home-page "https://www.bioconductor.org/")
5313 (synopsis "Bioconductor web interface")
5315 "This package provides an integrated web interface for doing microarray
5316 analysis using several of the Bioconductor packages. It is intended to be
5317 deployed as a centralized bioinformatics resource for use by many users.
5318 Currently only Affymetrix oligonucleotide analysis is supported.")
5319 (license license:gpl2+)))
5321 (define-public r-zfpkm
5328 (uri (bioconductor-uri "zFPKM" version))
5331 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
5332 (properties `((upstream-name . "zFPKM")))
5333 (build-system r-build-system)
5335 `(("r-checkmate" ,r-checkmate)
5336 ("r-dplyr" ,r-dplyr)
5337 ("r-ggplot2" ,r-ggplot2)
5338 ("r-summarizedexperiment" ,r-summarizedexperiment)
5339 ("r-tidyr" ,r-tidyr)))
5341 `(("r-knitr" ,r-knitr)))
5342 (home-page "https://github.com/ronammar/zFPKM/")
5343 (synopsis "Functions to facilitate zFPKM transformations")
5345 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5346 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5348 (license license:gpl3)))
5350 (define-public r-rbowtie2
5357 (uri (bioconductor-uri "Rbowtie2" version))
5360 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
5361 (properties `((upstream-name . "Rbowtie2")))
5362 (build-system r-build-system)
5366 `(("r-knitr" ,r-knitr)))
5367 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5368 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5370 "This package provides an R wrapper of the popular @code{bowtie2}
5371 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5372 rapid adapter trimming, identification, and read merging.")
5373 (license license:gpl3+)))
5375 (define-public r-progeny
5382 (uri (bioconductor-uri "progeny" version))
5385 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
5386 (build-system r-build-system)
5388 `(("r-biobase" ,r-biobase)
5389 ("r-dplyr" ,r-dplyr)
5390 ("r-ggplot2" ,r-ggplot2)
5391 ("r-ggrepel" ,r-ggrepel)
5392 ("r-gridextra" ,r-gridextra)
5393 ("r-tidyr" ,r-tidyr)))
5395 `(("r-knitr" ,r-knitr)))
5396 (home-page "https://github.com/saezlab/progeny")
5397 (synopsis "Pathway responsive gene activity inference")
5399 "This package provides a function to infer pathway activity from gene
5400 expression. It contains the linear model inferred in the publication
5401 \"Perturbation-response genes reveal signaling footprints in cancer gene
5403 (license license:asl2.0)))
5405 (define-public r-arrmnormalization
5407 (name "r-arrmnormalization")
5412 (uri (bioconductor-uri "ARRmNormalization" version))
5415 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
5417 `((upstream-name . "ARRmNormalization")))
5418 (build-system r-build-system)
5419 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5420 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5421 (synopsis "Adaptive robust regression normalization for methylation data")
5423 "This is a package to perform the @dfn{Adaptive Robust Regression
5424 method} (ARRm) for the normalization of methylation data from the Illumina
5425 Infinium HumanMethylation 450k assay.")
5426 (license license:artistic2.0)))
5428 (define-public r-biocfilecache
5430 (name "r-biocfilecache")
5435 (uri (bioconductor-uri "BiocFileCache" version))
5438 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
5439 (properties `((upstream-name . "BiocFileCache")))
5440 (build-system r-build-system)
5442 `(("r-curl" ,r-curl)
5444 ("r-dbplyr" ,r-dbplyr)
5445 ("r-dplyr" ,r-dplyr)
5447 ("r-rappdirs" ,r-rappdirs)
5448 ("r-rsqlite" ,r-rsqlite)))
5450 `(("r-knitr" ,r-knitr)))
5451 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5452 (synopsis "Manage files across sessions")
5454 "This package creates a persistent on-disk cache of files that the user
5455 can add, update, and retrieve. It is useful for managing resources (such as
5456 custom Txdb objects) that are costly or difficult to create, web resources,
5457 and data files used across sessions.")
5458 (license license:artistic2.0)))
5460 (define-public r-iclusterplus
5462 (name "r-iclusterplus")
5467 (uri (bioconductor-uri "iClusterPlus" version))
5470 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
5471 (properties `((upstream-name . "iClusterPlus")))
5472 (build-system r-build-system)
5473 (native-inputs `(("gfortran" ,gfortran)))
5474 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5475 (synopsis "Integrative clustering of multi-type genomic data")
5477 "iClusterPlus is developed for integrative clustering analysis of
5478 multi-type genomic data and is an enhanced version of iCluster proposed and
5479 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5480 from the experiments where biological samples (e.g. tumor samples) are
5481 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5482 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5483 on. In the iClusterPlus model, binary observations such as somatic mutation
5484 are modeled as Binomial processes; categorical observations such as copy
5485 number states are realizations of Multinomial random variables; counts are
5486 modeled as Poisson random processes; and continuous measures are modeled by
5487 Gaussian distributions.")
5488 (license license:gpl2+)))
5490 (define-public r-rbowtie
5497 (uri (bioconductor-uri "Rbowtie" version))
5500 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
5501 (properties `((upstream-name . "Rbowtie")))
5502 (build-system r-build-system)
5506 `(("r-knitr" ,r-knitr)))
5507 (home-page "https://bioconductor.org/packages/Rbowtie/")
5508 (synopsis "R bowtie wrapper")
5510 "This package provides an R wrapper around the popular bowtie short read
5511 aligner and around SpliceMap, a de novo splice junction discovery and
5513 (license license:artistic2.0)))
5515 (define-public r-sgseq
5522 (uri (bioconductor-uri "SGSeq" version))
5525 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
5526 (properties `((upstream-name . "SGSeq")))
5527 (build-system r-build-system)
5529 `(("r-annotationdbi" ,r-annotationdbi)
5530 ("r-biocgenerics" ,r-biocgenerics)
5531 ("r-biostrings" ,r-biostrings)
5532 ("r-genomeinfodb" ,r-genomeinfodb)
5533 ("r-genomicalignments" ,r-genomicalignments)
5534 ("r-genomicfeatures" ,r-genomicfeatures)
5535 ("r-genomicranges" ,r-genomicranges)
5536 ("r-igraph" ,r-igraph)
5537 ("r-iranges" ,r-iranges)
5538 ("r-rsamtools" ,r-rsamtools)
5539 ("r-rtracklayer" ,r-rtracklayer)
5540 ("r-runit" ,r-runit)
5541 ("r-s4vectors" ,r-s4vectors)
5542 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5544 `(("r-knitr" ,r-knitr)))
5545 (home-page "https://bioconductor.org/packages/SGSeq/")
5546 (synopsis "Splice event prediction and quantification from RNA-seq data")
5548 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5549 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5550 represented as a splice graph, which can be obtained from existing annotation
5551 or predicted from the mapped sequence reads. Splice events are identified
5552 from the graph and are quantified locally using structurally compatible reads
5553 at the start or end of each splice variant. The software includes functions
5554 for splice event prediction, quantification, visualization and
5556 (license license:artistic2.0)))
5558 (define-public r-rhisat2
5565 (uri (bioconductor-uri "Rhisat2" version))
5568 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
5569 (properties `((upstream-name . "Rhisat2")))
5570 (build-system r-build-system)
5573 (modify-phases %standard-phases
5574 (add-after 'unpack 'make-reproducible
5576 (substitute* "src/Makefile"
5577 (("`hostname`") "guix")
5579 ;; Avoid shelling out to "which".
5580 (("^CC =.*") (which "gcc"))
5581 (("^CPP =.*") (which "g++")))
5584 `(("r-genomicfeatures" ,r-genomicfeatures)
5585 ("r-genomicranges" ,r-genomicranges)
5586 ("r-sgseq" ,r-sgseq)))
5588 `(("r-knitr" ,r-knitr)))
5589 (home-page "https://github.com/fmicompbio/Rhisat2")
5590 (synopsis "R Wrapper for HISAT2 sequence aligner")
5592 "This package provides an R interface to the HISAT2 spliced short-read
5593 aligner by Kim et al. (2015). The package contains wrapper functions to
5594 create a genome index and to perform the read alignment to the generated
5596 (license license:gpl3)))
5598 (define-public r-quasr
5605 (uri (bioconductor-uri "QuasR" version))
5608 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
5609 (properties `((upstream-name . "QuasR")))
5610 (build-system r-build-system)
5614 `(("r-annotationdbi" ,r-annotationdbi)
5615 ("r-biobase" ,r-biobase)
5616 ("r-biocgenerics" ,r-biocgenerics)
5617 ("r-biocmanager" ,r-biocmanager)
5618 ("r-biocparallel" ,r-biocparallel)
5619 ("r-biostrings" ,r-biostrings)
5620 ("r-bsgenome" ,r-bsgenome)
5621 ("r-genomeinfodb" ,r-genomeinfodb)
5622 ("r-genomicalignments" ,r-genomicalignments)
5623 ("r-genomicfeatures" ,r-genomicfeatures)
5624 ("r-genomicfiles" ,r-genomicfiles)
5625 ("r-genomicranges" ,r-genomicranges)
5626 ("r-iranges" ,r-iranges)
5627 ("r-rbowtie" ,r-rbowtie)
5628 ("r-rhisat2" ,r-rhisat2)
5629 ("r-rhtslib" ,r-rhtslib)
5630 ("r-rsamtools" ,r-rsamtools)
5631 ("r-rtracklayer" ,r-rtracklayer)
5632 ("r-s4vectors" ,r-s4vectors)
5633 ("r-shortread" ,r-shortread)))
5635 `(("r-knitr" ,r-knitr)))
5636 (home-page "https://bioconductor.org/packages/QuasR/")
5637 (synopsis "Quantify and annotate short reads in R")
5639 "This package provides a framework for the quantification and analysis of
5640 short genomic reads. It covers a complete workflow starting from raw sequence
5641 reads, over creation of alignments and quality control plots, to the
5642 quantification of genomic regions of interest.")
5643 (license license:gpl2)))
5645 (define-public r-rqc
5652 (uri (bioconductor-uri "Rqc" version))
5655 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
5656 (properties `((upstream-name . "Rqc")))
5657 (build-system r-build-system)
5659 `(("r-biocgenerics" ,r-biocgenerics)
5660 ("r-biocparallel" ,r-biocparallel)
5661 ("r-biocstyle" ,r-biocstyle)
5662 ("r-biostrings" ,r-biostrings)
5663 ("r-biovizbase" ,r-biovizbase)
5664 ("r-genomicalignments" ,r-genomicalignments)
5665 ("r-genomicfiles" ,r-genomicfiles)
5666 ("r-ggplot2" ,r-ggplot2)
5667 ("r-iranges" ,r-iranges)
5668 ("r-knitr" ,r-knitr)
5669 ("r-markdown" ,r-markdown)
5672 ("r-reshape2" ,r-reshape2)
5673 ("r-rsamtools" ,r-rsamtools)
5674 ("r-s4vectors" ,r-s4vectors)
5675 ("r-shiny" ,r-shiny)
5676 ("r-shortread" ,r-shortread)))
5678 `(("r-knitr" ,r-knitr)))
5679 (home-page "https://github.com/labbcb/Rqc")
5680 (synopsis "Quality control tool for high-throughput sequencing data")
5682 "Rqc is an optimized tool designed for quality control and assessment of
5683 high-throughput sequencing data. It performs parallel processing of entire
5684 files and produces a report which contains a set of high-resolution
5686 (license license:gpl2+)))
5688 (define-public r-birewire
5695 (uri (bioconductor-uri "BiRewire" version))
5698 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
5699 (properties `((upstream-name . "BiRewire")))
5700 (build-system r-build-system)
5702 `(("r-igraph" ,r-igraph)
5703 ("r-matrix" ,r-matrix)
5705 ("r-tsne" ,r-tsne)))
5706 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5707 (synopsis "Tools for randomization of bipartite graphs")
5709 "This package provides functions for bipartite network rewiring through N
5710 consecutive switching steps and for the computation of the minimal number of
5711 switching steps to be performed in order to maximise the dissimilarity with
5712 respect to the original network. It includes functions for the analysis of
5713 the introduced randomness across the switching steps and several other
5714 routines to analyse the resulting networks and their natural projections.")
5715 (license license:gpl3)))
5717 (define-public r-birta
5724 (uri (bioconductor-uri "birta" version))
5727 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5728 (build-system r-build-system)
5730 `(("r-biobase" ,r-biobase)
5731 ("r-limma" ,r-limma)
5732 ("r-mass" ,r-mass)))
5733 (home-page "https://bioconductor.org/packages/birta")
5734 (synopsis "Bayesian inference of regulation of transcriptional activity")
5736 "Expression levels of mRNA molecules are regulated by different
5737 processes, comprising inhibition or activation by transcription factors and
5738 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5739 Inference of Regulation of Transcriptional Activity) uses the regulatory
5740 networks of transcription factors and miRNAs together with mRNA and miRNA
5741 expression data to predict switches in regulatory activity between two
5742 conditions. A Bayesian network is used to model the regulatory structure and
5743 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5744 (license license:gpl2+)))
5746 (define-public r-multidataset
5748 (name "r-multidataset")
5753 (uri (bioconductor-uri "MultiDataSet" version))
5756 "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w"))))
5757 (properties `((upstream-name . "MultiDataSet")))
5758 (build-system r-build-system)
5760 `(("r-biobase" ,r-biobase)
5761 ("r-biocgenerics" ,r-biocgenerics)
5762 ("r-genomicranges" ,r-genomicranges)
5763 ("r-ggplot2" ,r-ggplot2)
5764 ("r-ggrepel" ,r-ggrepel)
5765 ("r-iranges" ,r-iranges)
5766 ("r-limma" ,r-limma)
5767 ("r-qqman" ,r-qqman)
5768 ("r-s4vectors" ,r-s4vectors)
5769 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5771 `(("r-knitr" ,r-knitr)))
5772 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5773 (synopsis "Implementation of MultiDataSet and ResultSet")
5775 "This package provides an implementation of the BRGE's (Bioinformatic
5776 Research Group in Epidemiology from Center for Research in Environmental
5777 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5778 integrating multi omics data sets and ResultSet is a container for omics
5779 results. This package contains base classes for MEAL and rexposome
5781 (license license:expat)))
5783 (define-public r-ropls
5790 (uri (bioconductor-uri "ropls" version))
5793 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
5794 (build-system r-build-system)
5796 `(("r-biobase" ,r-biobase)
5797 ("r-multidataset" ,r-multidataset)))
5799 `(("r-knitr" ,r-knitr))) ; for vignettes
5800 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5801 (synopsis "Multivariate analysis and feature selection of omics data")
5803 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5804 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5805 regression, classification, and feature selection of omics data where the
5806 number of variables exceeds the number of samples and with multicollinearity
5807 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5808 separately model the variation correlated (predictive) to the factor of
5809 interest and the uncorrelated (orthogonal) variation. While performing
5810 similarly to PLS, OPLS facilitates interpretation.
5812 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5813 analysis and feature selection of omics data. In addition to scores, loadings
5814 and weights plots, the package provides metrics and graphics to determine the
5815 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5816 validity of the model by permutation testing, detect outliers, and perform
5817 feature selection (e.g. with Variable Importance in Projection or regression
5819 (license license:cecill)))
5821 (define-public r-biosigner
5823 (name "r-biosigner")
5828 (uri (bioconductor-uri "biosigner" version))
5831 "1rqfmn9lpaajij9p302dfwv57pm4hw7xn2p7lx7hvpb3psa719xm"))))
5832 (build-system r-build-system)
5834 `(("r-biobase" ,r-biobase)
5835 ("r-e1071" ,r-e1071)
5836 ("r-multidataset" ,r-multidataset)
5837 ("r-randomforest" ,r-randomforest)
5838 ("r-ropls" ,r-ropls)))
5840 `(("r-knitr" ,r-knitr)))
5841 (home-page "https://bioconductor.org/packages/biosigner/")
5842 (synopsis "Signature discovery from omics data")
5844 "Feature selection is critical in omics data analysis to extract
5845 restricted and meaningful molecular signatures from complex and high-dimension
5846 data, and to build robust classifiers. This package implements a method to
5847 assess the relevance of the variables for the prediction performances of the
5848 classifier. The approach can be run in parallel with the PLS-DA, Random
5849 Forest, and SVM binary classifiers. The signatures and the corresponding
5850 'restricted' models are returned, enabling future predictions on new
5852 (license license:cecill)))
5854 (define-public r-annotatr
5861 (uri (bioconductor-uri "annotatr" version))
5864 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
5865 (build-system r-build-system)
5867 `(("r-annotationdbi" ,r-annotationdbi)
5868 ("r-annotationhub" ,r-annotationhub)
5869 ("r-dplyr" ,r-dplyr)
5870 ("r-genomeinfodb" ,r-genomeinfodb)
5871 ("r-genomicfeatures" ,r-genomicfeatures)
5872 ("r-genomicranges" ,r-genomicranges)
5873 ("r-ggplot2" ,r-ggplot2)
5874 ("r-iranges" ,r-iranges)
5875 ("r-readr" ,r-readr)
5876 ("r-regioner" ,r-regioner)
5877 ("r-reshape2" ,r-reshape2)
5878 ("r-rtracklayer" ,r-rtracklayer)
5879 ("r-s4vectors" ,r-s4vectors)))
5881 `(("r-knitr" ,r-knitr)))
5882 (home-page "https://bioconductor.org/packages/annotatr/")
5883 (synopsis "Annotation of genomic regions to genomic annotations")
5885 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5886 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5887 to investigate the intersecting genomic annotations. Such annotations include
5888 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5889 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5890 enhancers. The annotatr package provides an easy way to summarize and
5891 visualize the intersection of genomic sites/regions with genomic
5893 (license license:gpl3)))
5895 (define-public r-rsubread
5902 (uri (bioconductor-uri "Rsubread" version))
5905 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
5906 (properties `((upstream-name . "Rsubread")))
5907 (build-system r-build-system)
5908 (inputs `(("zlib" ,zlib)))
5910 `(("r-matrix" ,r-matrix)))
5911 (home-page "https://bioconductor.org/packages/Rsubread/")
5912 (synopsis "Subread sequence alignment and counting for R")
5914 "This package provides tools for alignment, quantification and analysis
5915 of second and third generation sequencing data. It includes functionality for
5916 read mapping, read counting, SNP calling, structural variant detection and
5917 gene fusion discovery. It can be applied to all major sequencing techologies
5918 and to both short and long sequence reads.")
5919 (license license:gpl3)))
5921 (define-public r-flowutils
5923 (name "r-flowutils")
5928 (uri (bioconductor-uri "flowUtils" version))
5931 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
5932 (properties `((upstream-name . "flowUtils")))
5933 (build-system r-build-system)
5935 `(("r-biobase" ,r-biobase)
5936 ("r-corpcor" ,r-corpcor)
5937 ("r-flowcore" ,r-flowcore)
5938 ("r-graph" ,r-graph)
5939 ("r-runit" ,r-runit)
5941 (home-page "https://github.com/jspidlen/flowUtils")
5942 (synopsis "Utilities for flow cytometry")
5944 "This package provides utilities for flow cytometry data.")
5945 (license license:artistic2.0)))
5947 (define-public r-consensusclusterplus
5949 (name "r-consensusclusterplus")
5954 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5957 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
5959 `((upstream-name . "ConsensusClusterPlus")))
5960 (build-system r-build-system)
5963 ("r-biobase" ,r-biobase)
5964 ("r-cluster" ,r-cluster)))
5965 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5966 (synopsis "Clustering algorithm")
5968 "This package provides an implementation of an algorithm for determining
5969 cluster count and membership by stability evidence in unsupervised analysis.")
5970 (license license:gpl2)))
5972 (define-public r-cytolib
5979 (uri (bioconductor-uri "cytolib" version))
5982 "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw"))))
5983 (properties `((upstream-name . "cytolib")))
5984 (build-system r-build-system)
5988 `(("r-knitr" ,r-knitr)
5989 ("pkg-config" ,pkg-config)))
5993 ("r-rcpparmadillo" ,r-rcpparmadillo)
5994 ("r-rcppparallel" ,r-rcppparallel)
5995 ("r-rhdf5lib" ,r-rhdf5lib)
5996 ("r-rprotobuflib" ,r-rprotobuflib)))
5997 (home-page "https://bioconductor.org/packages/cytolib/")
5998 (synopsis "C++ infrastructure for working with gated cytometry")
6000 "This package provides the core data structure and API to represent and
6001 interact with gated cytometry data.")
6002 (license license:artistic2.0)))
6004 (define-public r-flowcore
6011 (uri (bioconductor-uri "flowCore" version))
6014 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
6015 (properties `((upstream-name . "flowCore")))
6016 (build-system r-build-system)
6019 ("r-biobase" ,r-biobase)
6020 ("r-biocgenerics" ,r-biocgenerics)
6021 ("r-cytolib" ,r-cytolib)
6022 ("r-matrixstats" ,r-matrixstats)
6024 ("r-rcpparmadillo" ,r-rcpparmadillo)
6025 ("r-rprotobuflib" ,r-rprotobuflib)
6026 ("r-s4vectors" ,r-s4vectors)))
6028 `(("r-knitr" ,r-knitr)))
6029 (home-page "https://bioconductor.org/packages/flowCore")
6030 (synopsis "Basic structures for flow cytometry data")
6032 "This package provides S4 data structures and basic functions to deal
6033 with flow cytometry data.")
6034 (license license:artistic2.0)))
6036 (define-public r-flowmeans
6038 (name "r-flowmeans")
6043 (uri (bioconductor-uri "flowMeans" version))
6046 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
6047 (properties `((upstream-name . "flowMeans")))
6048 (build-system r-build-system)
6050 `(("r-biobase" ,r-biobase)
6051 ("r-feature" ,r-feature)
6052 ("r-flowcore" ,r-flowcore)
6053 ("r-rrcov" ,r-rrcov)))
6054 (home-page "https://bioconductor.org/packages/flowMeans")
6055 (synopsis "Non-parametric flow cytometry data gating")
6057 "This package provides tools to identify cell populations in Flow
6058 Cytometry data using non-parametric clustering and segmented-regression-based
6059 change point detection.")
6060 (license license:artistic2.0)))
6062 (define-public r-ncdfflow
6069 (uri (bioconductor-uri "ncdfFlow" version))
6072 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
6073 (properties `((upstream-name . "ncdfFlow")))
6074 (build-system r-build-system)
6079 ("r-biobase" ,r-biobase)
6080 ("r-biocgenerics" ,r-biocgenerics)
6081 ("r-flowcore" ,r-flowcore)
6083 ("r-rcpparmadillo" ,r-rcpparmadillo)
6084 ("r-rhdf5lib" ,r-rhdf5lib)
6085 ("r-zlibbioc" ,r-zlibbioc)))
6087 `(("r-knitr" ,r-knitr)))
6088 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6089 (synopsis "HDF5 based storage for flow cytometry data")
6091 "This package provides HDF5 storage based methods and functions for
6092 manipulation of flow cytometry data.")
6093 (license license:artistic2.0)))
6095 (define-public r-ggcyto
6102 (uri (bioconductor-uri "ggcyto" version))
6105 "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
6106 (properties `((upstream-name . "ggcyto")))
6107 (build-system r-build-system)
6109 `(("r-data-table" ,r-data-table)
6110 ("r-flowcore" ,r-flowcore)
6111 ("r-flowworkspace" ,r-flowworkspace)
6112 ("r-ggplot2" ,r-ggplot2)
6113 ("r-gridextra" ,r-gridextra)
6114 ("r-hexbin" ,r-hexbin)
6115 ("r-ncdfflow" ,r-ncdfflow)
6117 ("r-rcolorbrewer" ,r-rcolorbrewer)
6118 ("r-rlang" ,r-rlang)
6119 ("r-scales" ,r-scales)))
6121 `(("r-knitr" ,r-knitr)))
6122 (home-page "https://github.com/RGLab/ggcyto/issues")
6123 (synopsis "Visualize Cytometry data with ggplot")
6125 "With the dedicated fortify method implemented for @code{flowSet},
6126 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6127 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6128 and some custom layers also make it easy to add gates and population
6129 statistics to the plot.")
6130 (license license:artistic2.0)))
6132 (define-public r-flowviz
6139 (uri (bioconductor-uri "flowViz" version))
6142 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
6143 (properties `((upstream-name . "flowViz")))
6144 (build-system r-build-system)
6146 `(("r-biobase" ,r-biobase)
6147 ("r-flowcore" ,r-flowcore)
6148 ("r-hexbin" ,r-hexbin)
6149 ("r-idpmisc" ,r-idpmisc)
6150 ("r-kernsmooth" ,r-kernsmooth)
6151 ("r-lattice" ,r-lattice)
6152 ("r-latticeextra" ,r-latticeextra)
6154 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6156 `(("r-knitr" ,r-knitr)))
6157 (home-page "https://bioconductor.org/packages/flowViz/")
6158 (synopsis "Visualization for flow cytometry")
6160 "This package provides visualization tools for flow cytometry data.")
6161 (license license:artistic2.0)))
6163 (define-public r-flowclust
6165 (name "r-flowclust")
6170 (uri (bioconductor-uri "flowClust" version))
6173 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
6174 (properties `((upstream-name . "flowClust")))
6175 (build-system r-build-system)
6178 (list "--configure-args=--enable-bundled-gsl=no")))
6180 `(("r-biobase" ,r-biobase)
6181 ("r-biocgenerics" ,r-biocgenerics)
6183 ("r-corpcor" ,r-corpcor)
6184 ("r-ellipse" ,r-ellipse)
6185 ("r-flowcore" ,r-flowcore)
6186 ("r-flowviz" ,r-flowviz)
6187 ("r-graph" ,r-graph)
6188 ("r-mnormt" ,r-mnormt)))
6192 `(("pkg-config" ,pkg-config)
6193 ("r-knitr" ,r-knitr)))
6194 (home-page "https://bioconductor.org/packages/flowClust")
6195 (synopsis "Clustering for flow cytometry")
6197 "This package provides robust model-based clustering using a t-mixture
6198 model with Box-Cox transformation.")
6199 (license license:artistic2.0)))
6201 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6202 ;; make it use our protobuf package instead.
6203 (define-public r-rprotobuflib
6205 (name "r-rprotobuflib")
6210 (uri (bioconductor-uri "RProtoBufLib" version))
6213 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
6214 (properties `((upstream-name . "RProtoBufLib")))
6215 (build-system r-build-system)
6218 (modify-phases %standard-phases
6219 (add-after 'unpack 'unpack-bundled-sources
6221 (with-directory-excursion "src"
6222 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6225 `(("r-knitr" ,r-knitr)))
6226 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6227 (synopsis "C++ headers and static libraries of Protocol buffers")
6229 "This package provides the headers and static library of Protocol buffers
6230 for other R packages to compile and link against.")
6231 (license license:bsd-3)))
6233 (define-public r-flowworkspace
6235 (name "r-flowworkspace")
6240 (uri (bioconductor-uri "flowWorkspace" version))
6243 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
6244 (properties `((upstream-name . "flowWorkspace")))
6245 (build-system r-build-system)
6249 `(("r-aws-s3" ,r-aws-s3)
6250 ("r-aws-signature" ,r-aws-signature)
6252 ("r-biobase" ,r-biobase)
6253 ("r-biocgenerics" ,r-biocgenerics)
6254 ("r-cytolib" ,r-cytolib)
6255 ("r-data-table" ,r-data-table)
6256 ("r-digest" ,r-digest)
6257 ("r-dplyr" ,r-dplyr)
6258 ("r-flowcore" ,r-flowcore)
6259 ("r-ggplot2" ,r-ggplot2)
6260 ("r-graph" ,r-graph)
6261 ("r-lattice" ,r-lattice)
6262 ("r-latticeextra" ,r-latticeextra)
6263 ("r-matrixstats" ,r-matrixstats)
6264 ("r-ncdfflow" ,r-ncdfflow)
6267 ("r-rcpparmadillo" ,r-rcpparmadillo)
6268 ("r-rcppparallel" ,r-rcppparallel)
6269 ("r-rgraphviz" ,r-rgraphviz)
6270 ("r-rhdf5lib" ,r-rhdf5lib)
6271 ("r-rprotobuflib" ,r-rprotobuflib)
6272 ("r-scales" ,r-scales)
6275 `(("r-knitr" ,r-knitr)))
6276 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6277 (synopsis "Infrastructure for working with cytometry data")
6279 "This package is designed to facilitate comparison of automated gating
6280 methods against manual gating done in flowJo. This package allows you to
6281 import basic flowJo workspaces into BioConductor and replicate the gating from
6282 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6283 samples, compensation, and transformation are performed so that the output
6284 matches the flowJo analysis.")
6285 (license license:artistic2.0)))
6287 (define-public r-flowstats
6289 (name "r-flowstats")
6294 (uri (bioconductor-uri "flowStats" version))
6297 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
6298 (properties `((upstream-name . "flowStats")))
6299 (build-system r-build-system)
6301 `(("r-biobase" ,r-biobase)
6302 ("r-biocgenerics" ,r-biocgenerics)
6303 ("r-cluster" ,r-cluster)
6305 ("r-flowcore" ,r-flowcore)
6306 ("r-flowviz" ,r-flowviz)
6307 ("r-flowworkspace" ,r-flowworkspace)
6308 ("r-kernsmooth" ,r-kernsmooth)
6310 ("r-lattice" ,r-lattice)
6312 ("r-ncdfflow" ,r-ncdfflow)
6313 ("r-rcolorbrewer" ,r-rcolorbrewer)
6314 ("r-rrcov" ,r-rrcov)))
6315 (home-page "http://www.github.com/RGLab/flowStats")
6316 (synopsis "Statistical methods for the analysis of flow cytometry data")
6318 "This package provides methods and functionality to analyze flow data
6319 that is beyond the basic infrastructure provided by the @code{flowCore}
6321 (license license:artistic2.0)))
6323 (define-public r-opencyto
6330 (uri (bioconductor-uri "openCyto" version))
6333 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
6334 (properties `((upstream-name . "openCyto")))
6335 (build-system r-build-system)
6337 `(("r-biobase" ,r-biobase)
6338 ("r-biocgenerics" ,r-biocgenerics)
6340 ("r-data-table" ,r-data-table)
6341 ("r-flowclust" ,r-flowclust)
6342 ("r-flowcore" ,r-flowcore)
6343 ("r-flowstats" ,r-flowstats)
6344 ("r-flowviz" ,r-flowviz)
6345 ("r-flowworkspace" ,r-flowworkspace)
6346 ("r-graph" ,r-graph)
6347 ("r-gtools" ,r-gtools)
6349 ("r-lattice" ,r-lattice)
6351 ("r-ncdfflow" ,r-ncdfflow)
6353 ("r-r-utils" ,r-r-utils)
6355 ("r-rcolorbrewer" ,r-rcolorbrewer)
6357 ("r-rrcov" ,r-rrcov)))
6359 `(("r-knitr" ,r-knitr)))
6360 (home-page "https://bioconductor.org/packages/openCyto")
6361 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6363 "This package is designed to facilitate the automated gating methods in a
6364 sequential way to mimic the manual gating strategy.")
6365 (license license:artistic2.0)))
6367 (define-public r-cytoml
6374 (uri (bioconductor-uri "CytoML" version))
6377 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
6378 (properties `((upstream-name . "CytoML")))
6379 (build-system r-build-system)
6381 `(("libxml2" ,libxml2)))
6383 `(("r-base64enc" ,r-base64enc)
6385 ("r-biobase" ,r-biobase)
6386 ("r-corpcor" ,r-corpcor)
6387 ("r-cytolib" ,r-cytolib)
6388 ("r-data-table" ,r-data-table)
6389 ("r-dplyr" ,r-dplyr)
6390 ("r-flowcore" ,r-flowcore)
6391 ("r-flowworkspace" ,r-flowworkspace)
6392 ("r-ggcyto" ,r-ggcyto)
6393 ("r-graph" ,r-graph)
6394 ("r-jsonlite" ,r-jsonlite)
6395 ("r-lattice" ,r-lattice)
6396 ("r-opencyto" ,r-opencyto)
6400 ("r-rcpparmadillo" ,r-rcpparmadillo)
6401 ("r-rcppparallel" ,r-rcppparallel)
6402 ("r-rgraphviz" ,r-rgraphviz)
6403 ("r-rhdf5lib" ,r-rhdf5lib)
6404 ("r-rprotobuflib" ,r-rprotobuflib)
6405 ("r-runit" ,r-runit)
6406 ("r-tibble" ,r-tibble)
6409 ("r-yaml" ,r-yaml)))
6411 `(("r-knitr" ,r-knitr)))
6412 (home-page "https://github.com/RGLab/CytoML")
6413 (synopsis "GatingML interface for cross platform cytometry data sharing")
6415 "This package provides an interface to implementations of the GatingML2.0
6416 standard to exchange gated cytometry data with other software platforms.")
6417 (license license:artistic2.0)))
6419 (define-public r-flowsom
6426 (uri (bioconductor-uri "FlowSOM" version))
6429 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
6430 (properties `((upstream-name . "FlowSOM")))
6431 (build-system r-build-system)
6433 `(("r-biocgenerics" ,r-biocgenerics)
6434 ("r-consensusclusterplus" ,r-consensusclusterplus)
6435 ("r-cytoml" ,r-cytoml)
6436 ("r-flowcore" ,r-flowcore)
6437 ("r-flowworkspace" ,r-flowworkspace)
6438 ("r-igraph" ,r-igraph)
6439 ("r-rcolorbrewer" ,r-rcolorbrewer)
6442 (home-page "https://bioconductor.org/packages/FlowSOM/")
6443 (synopsis "Visualize and interpret cytometry data")
6445 "FlowSOM offers visualization options for cytometry data, by using
6446 self-organizing map clustering and minimal spanning trees.")
6447 (license license:gpl2+)))
6449 (define-public r-mixomics
6456 (uri (bioconductor-uri "mixOmics" version))
6459 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
6460 (properties `((upstream-name . "mixOmics")))
6461 (build-system r-build-system)
6463 `(("r-corpcor" ,r-corpcor)
6464 ("r-dplyr" ,r-dplyr)
6465 ("r-ellipse" ,r-ellipse)
6466 ("r-ggrepel" ,r-ggrepel)
6467 ("r-ggplot2" ,r-ggplot2)
6468 ("r-gridextra" ,r-gridextra)
6469 ("r-igraph" ,r-igraph)
6470 ("r-lattice" ,r-lattice)
6472 ("r-matrixstats" ,r-matrixstats)
6473 ("r-rarpack" ,r-rarpack)
6474 ("r-rcolorbrewer" ,r-rcolorbrewer)
6475 ("r-reshape2" ,r-reshape2)
6476 ("r-tidyr" ,r-tidyr)))
6478 `(("r-knitr" ,r-knitr)))
6479 (home-page "http://www.mixOmics.org")
6480 (synopsis "Multivariate methods for exploration of biological datasets")
6482 "mixOmics offers a wide range of multivariate methods for the exploration
6483 and integration of biological datasets with a particular focus on variable
6484 selection. The package proposes several sparse multivariate models we have
6485 developed to identify the key variables that are highly correlated, and/or
6486 explain the biological outcome of interest. The data that can be analysed
6487 with mixOmics may come from high throughput sequencing technologies, such as
6488 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6489 also beyond the realm of omics (e.g. spectral imaging). The methods
6490 implemented in mixOmics can also handle missing values without having to
6491 delete entire rows with missing data.")
6492 (license license:gpl2+)))
6494 (define-public r-depecher
6495 (package ;Source/Weave error
6501 (uri (bioconductor-uri "DepecheR" version))
6504 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
6505 (properties `((upstream-name . "DepecheR")))
6506 (build-system r-build-system)
6508 `(("r-beanplot" ,r-beanplot)
6509 ("r-dosnow" ,r-dosnow)
6510 ("r-dplyr" ,r-dplyr)
6512 ("r-foreach" ,r-foreach)
6513 ("r-ggplot2" ,r-ggplot2)
6514 ("r-gmodels" ,r-gmodels)
6515 ("r-gplots" ,r-gplots)
6517 ("r-matrixstats" ,r-matrixstats)
6518 ("r-mixomics" ,r-mixomics)
6519 ("r-moments" ,r-moments)
6521 ("r-rcppeigen" ,r-rcppeigen)
6522 ("r-reshape2" ,r-reshape2)
6523 ("r-robustbase" ,r-robustbase)
6524 ("r-viridis" ,r-viridis)))
6526 `(("r-knitr" ,r-knitr)))
6527 (home-page "https://bioconductor.org/packages/DepecheR/")
6528 (synopsis "Identify traits of clusters in high-dimensional entities")
6530 "The purpose of this package is to identify traits in a dataset that can
6531 separate groups. This is done on two levels. First, clustering is performed,
6532 using an implementation of sparse K-means. Secondly, the generated clusters
6533 are used to predict outcomes of groups of individuals based on their
6534 distribution of observations in the different clusters. As certain clusters
6535 with separating information will be identified, and these clusters are defined
6536 by a sparse number of variables, this method can reduce the complexity of
6537 data, to only emphasize the data that actually matters.")
6538 (license license:expat)))
6540 (define-public r-rcistarget
6542 (name "r-rcistarget")
6547 (uri (bioconductor-uri "RcisTarget" version))
6550 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
6551 (properties `((upstream-name . "RcisTarget")))
6552 (build-system r-build-system)
6554 `(("r-aucell" ,r-aucell)
6555 ("r-biocgenerics" ,r-biocgenerics)
6556 ("r-data-table" ,r-data-table)
6557 ("r-feather" ,r-feather)
6558 ("r-gseabase" ,r-gseabase)
6559 ("r-r-utils" ,r-r-utils)
6560 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6562 `(("r-knitr" ,r-knitr)))
6563 (home-page "https://aertslab.org/#scenic")
6564 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6566 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6567 over-represented on a gene list. In a first step, RcisTarget selects DNA
6568 motifs that are significantly over-represented in the surroundings of the
6569 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6570 achieved by using a database that contains genome-wide cross-species rankings
6571 for each motif. The motifs that are then annotated to TFs and those that have
6572 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6573 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6574 genes in the gene-set that are ranked above the leading edge).")
6575 (license license:gpl3)))
6577 (define-public r-cicero
6584 (uri (bioconductor-uri "cicero" version))
6587 "0hrra9ngpzmd57dwm0058zy0g7ymsil4pmvi3sgppfzimgviqiwf"))))
6588 (build-system r-build-system)
6590 `(("r-assertthat" ,r-assertthat)
6591 ("r-biobase" ,r-biobase)
6592 ("r-biocgenerics" ,r-biocgenerics)
6593 ("r-data-table" ,r-data-table)
6594 ("r-dplyr" ,r-dplyr)
6596 ("r-genomicranges" ,r-genomicranges)
6597 ("r-ggplot2" ,r-ggplot2)
6598 ("r-glasso" ,r-glasso)
6600 ("r-igraph" ,r-igraph)
6601 ("r-iranges" ,r-iranges)
6602 ("r-matrix" ,r-matrix)
6603 ("r-monocle" ,r-monocle)
6605 ("r-reshape2" ,r-reshape2)
6606 ("r-s4vectors" ,r-s4vectors)
6607 ("r-stringi" ,r-stringi)
6608 ("r-stringr" ,r-stringr)
6609 ("r-tibble" ,r-tibble)
6610 ("r-tidyr" ,r-tidyr)
6611 ("r-vgam" ,r-vgam)))
6613 `(("r-knitr" ,r-knitr)))
6614 (home-page "https://bioconductor.org/packages/cicero/")
6615 (synopsis "Predict cis-co-accessibility from single-cell data")
6617 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6618 accessibility data. It also extends the monocle package for use in chromatin
6619 accessibility data.")
6620 (license license:expat)))
6622 ;; This is the latest commit on the "monocle3" branch.
6623 (define-public r-cicero-monocle3
6624 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6626 (package (inherit r-cicero)
6627 (name "r-cicero-monocle3")
6628 (version (git-version "1.3.2" revision commit))
6633 (url "https://github.com/cole-trapnell-lab/cicero-release")
6635 (file-name (git-file-name name version))
6638 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6640 `(("r-monocle3" ,r-monocle3)
6641 ,@(alist-delete "r-monocle"
6642 (package-propagated-inputs r-cicero)))))))
6644 (define-public r-cistopic
6645 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6649 (version (git-version "0.2.1" revision commit))
6654 (url "https://github.com/aertslab/cisTopic")
6656 (file-name (git-file-name name version))
6659 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6660 (build-system r-build-system)
6662 `(("r-aucell" ,r-aucell)
6663 ("r-data-table" ,r-data-table)
6664 ("r-dplyr" ,r-dplyr)
6665 ("r-dosnow" ,r-dosnow)
6667 ("r-feather" ,r-feather)
6668 ("r-fitdistrplus" ,r-fitdistrplus)
6669 ("r-genomicranges" ,r-genomicranges)
6670 ("r-ggplot2" ,r-ggplot2)
6672 ("r-matrix" ,r-matrix)
6674 ("r-rcistarget" ,r-rcistarget)
6675 ("r-rtracklayer" ,r-rtracklayer)
6676 ("r-s4vectors" ,r-s4vectors)))
6677 (home-page "https://github.com/aertslab/cisTopic")
6678 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6680 "The sparse nature of single cell epigenomics data can be overruled using
6681 probabilistic modelling methods such as @dfn{Latent Dirichlet
6682 Allocation} (LDA). This package allows the probabilistic modelling of
6683 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6684 includes functionalities to identify cell states based on the contribution of
6685 cisTopics and explore the nature and regulatory proteins driving them.")
6686 (license license:gpl3))))
6688 (define-public r-genie3
6695 (uri (bioconductor-uri "GENIE3" version))
6698 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
6699 (properties `((upstream-name . "GENIE3")))
6700 (build-system r-build-system)
6701 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6703 `(("r-knitr" ,r-knitr)))
6704 (home-page "https://bioconductor.org/packages/GENIE3")
6705 (synopsis "Gene network inference with ensemble of trees")
6707 "This package implements the GENIE3 algorithm for inferring gene
6708 regulatory networks from expression data.")
6709 (license license:gpl2+)))
6711 (define-public r-roc
6718 (uri (bioconductor-uri "ROC" version))
6721 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
6722 (properties `((upstream-name . "ROC")))
6723 (build-system r-build-system)
6725 `(("r-knitr" ,r-knitr)))
6726 (home-page "https://www.bioconductor.org/packages/ROC/")
6727 (synopsis "Utilities for ROC curves")
6729 "This package provides utilities for @dfn{Receiver Operating
6730 Characteristic} (ROC) curves, with a focus on micro arrays.")
6731 (license license:artistic2.0)))
6733 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6735 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6740 (uri (bioconductor-uri
6741 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6742 version 'annotation))
6745 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6748 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6749 (build-system r-build-system)
6750 (propagated-inputs `(("r-minfi" ,r-minfi)))
6752 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6753 (synopsis "Annotation for Illumina's 450k methylation arrays")
6755 "This package provides manifests and annotation for Illumina's 450k array
6757 (license license:artistic2.0)))
6759 (define-public r-watermelon
6761 (name "r-watermelon")
6766 (uri (bioconductor-uri "wateRmelon" version))
6769 "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
6770 (properties `((upstream-name . "wateRmelon")))
6771 (build-system r-build-system)
6773 `(("r-biobase" ,r-biobase)
6774 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6775 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6776 ("r-illuminaio" ,r-illuminaio)
6777 ("r-limma" ,r-limma)
6779 ("r-matrixstats" ,r-matrixstats)
6780 ("r-methylumi" ,r-methylumi)
6782 (home-page "https://bioconductor.org/packages/wateRmelon/")
6783 (synopsis "Illumina 450 methylation array normalization and metrics")
6785 "The standard index of DNA methylation (beta) is computed from methylated
6786 and unmethylated signal intensities. Betas calculated from raw signal
6787 intensities perform well, but using 11 methylomic datasets we demonstrate that
6788 quantile normalization methods produce marked improvement. The commonly used
6789 procedure of normalizing betas is inferior to the separate normalization of M
6790 and U, and it is also advantageous to normalize Type I and Type II assays
6791 separately. This package provides 15 flavours of betas and three performance
6792 metrics, with methods for objects produced by the @code{methylumi} and
6793 @code{minfi} packages.")
6794 (license license:gpl3)))
6796 (define-public r-gdsfmt
6803 (uri (bioconductor-uri "gdsfmt" version))
6806 "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a"))
6807 (modules '((guix build utils)))
6808 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6809 ;; them and link with system libraries instead.
6812 (for-each delete-file-recursively
6816 (substitute* "src/Makevars"
6817 (("all: \\$\\(SHLIB\\)") "all:")
6818 (("\\$\\(SHLIB\\): liblzma.a") "")
6819 (("(ZLIB|LZ4)/.*") "")
6820 (("CoreArray/dVLIntGDS.cpp.*")
6821 "CoreArray/dVLIntGDS.cpp")
6822 (("CoreArray/dVLIntGDS.o.*")
6823 "CoreArray/dVLIntGDS.o")
6824 (("PKG_LIBS = ./liblzma.a")
6825 "PKG_LIBS = -llz4"))
6826 (substitute* "src/CoreArray/dStream.h"
6827 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6828 (string-append "include <" header ">")))
6830 (properties `((upstream-name . "gdsfmt")))
6831 (build-system r-build-system)
6837 `(("r-knitr" ,r-knitr)))
6838 (home-page "http://corearray.sourceforge.net/")
6840 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6842 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6843 Data Structure} (GDS) data files, which are portable across platforms with
6844 hierarchical structure to store multiple scalable array-oriented data sets
6845 with metadata information. It is suited for large-scale datasets, especially
6846 for data which are much larger than the available random-access memory. The
6847 @code{gdsfmt} package offers efficient operations specifically designed for
6848 integers of less than 8 bits, since a diploid genotype, like
6849 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6850 byte. Data compression and decompression are available with relatively
6851 efficient random access. It is also allowed to read a GDS file in parallel
6852 with multiple R processes supported by the package @code{parallel}.")
6853 (license license:lgpl3)))
6855 (define-public r-bigmelon
6862 (uri (bioconductor-uri "bigmelon" version))
6865 "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
6866 (properties `((upstream-name . "bigmelon")))
6867 (build-system r-build-system)
6869 `(("r-biobase" ,r-biobase)
6870 ("r-biocgenerics" ,r-biocgenerics)
6871 ("r-gdsfmt" ,r-gdsfmt)
6872 ("r-geoquery" ,r-geoquery)
6873 ("r-methylumi" ,r-methylumi)
6874 ("r-minfi" ,r-minfi)
6875 ("r-watermelon" ,r-watermelon)))
6876 (home-page "https://bioconductor.org/packages/bigmelon/")
6877 (synopsis "Illumina methylation array analysis for large experiments")
6879 "This package provides methods for working with Illumina arrays using the
6880 @code{gdsfmt} package.")
6881 (license license:gpl3)))
6883 (define-public r-seqbias
6890 (uri (bioconductor-uri "seqbias" version))
6893 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
6894 (properties `((upstream-name . "seqbias")))
6895 (build-system r-build-system)
6897 `(("r-biostrings" ,r-biostrings)
6898 ("r-genomicranges" ,r-genomicranges)
6899 ("r-rhtslib" ,r-rhtslib)))
6901 `(("zlib" ,zlib))) ; This comes from rhtslib.
6902 (home-page "https://bioconductor.org/packages/seqbias/")
6903 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6905 "This package implements a model of per-position sequencing bias in
6906 high-throughput sequencing data using a simple Bayesian network, the structure
6907 and parameters of which are trained on a set of aligned reads and a reference
6909 (license license:lgpl3)))
6911 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6913 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6917 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6918 version 'annotation))
6921 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6922 (build-system r-build-system)
6923 ;; As this package provides little more than a very large data file it
6924 ;; doesn't make sense to build substitutes.
6925 (arguments `(#:substitutable? #f))
6927 `(("r-biocgenerics" ,r-biocgenerics)
6928 ("r-s4vectors" ,r-s4vectors)
6929 ("r-iranges" ,r-iranges)
6930 ("r-genomeinfodb" ,r-genomeinfodb)
6931 ("r-genomicranges" ,r-genomicranges)
6932 ("r-bsgenome" ,r-bsgenome)
6933 ("r-biostrings" ,r-biostrings)))
6935 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6936 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6937 (description "This package provides SNP locations and alleles for Homo
6938 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6939 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6940 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6941 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6942 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6943 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6944 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6945 correct position but this injection will exclude chrM (i.e. nothing will be
6946 injected in that sequence).")
6947 (license license:artistic2.0)))
6949 (define-public r-reqon
6956 (uri (bioconductor-uri "ReQON" version))
6959 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
6960 (properties `((upstream-name . "ReQON")))
6961 (build-system r-build-system)
6963 `(("r-rjava" ,r-rjava)
6964 ("r-rsamtools" ,r-rsamtools)
6965 ("r-seqbias" ,r-seqbias)))
6966 (home-page "https://bioconductor.org/packages/ReQON/")
6967 (synopsis "Recalibrating quality of nucleotides")
6969 "This package provides an implementation of an algorithm for
6970 recalibrating the base quality scores for aligned sequencing data in BAM
6972 (license license:gpl2)))
6974 (define-public r-wavcluster
6976 (name "r-wavcluster")
6981 (uri (bioconductor-uri "wavClusteR" version))
6984 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
6985 (properties `((upstream-name . "wavClusteR")))
6986 (build-system r-build-system)
6988 `(("r-biocgenerics" ,r-biocgenerics)
6989 ("r-biostrings" ,r-biostrings)
6990 ("r-foreach" ,r-foreach)
6991 ("r-genomicfeatures" ,r-genomicfeatures)
6992 ("r-genomicranges" ,r-genomicranges)
6993 ("r-ggplot2" ,r-ggplot2)
6994 ("r-hmisc" ,r-hmisc)
6995 ("r-iranges" ,r-iranges)
6996 ("r-mclust" ,r-mclust)
6997 ("r-rsamtools" ,r-rsamtools)
6998 ("r-rtracklayer" ,r-rtracklayer)
6999 ("r-s4vectors" ,r-s4vectors)
7000 ("r-seqinr" ,r-seqinr)
7001 ("r-stringr" ,r-stringr)))
7003 `(("r-knitr" ,r-knitr)))
7004 (home-page "https://bioconductor.org/packages/wavClusteR/")
7005 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
7007 "This package provides an integrated pipeline for the analysis of
7008 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7009 sequencing errors, SNPs and additional non-experimental sources by a non-
7010 parametric mixture model. The protein binding sites (clusters) are then
7011 resolved at high resolution and cluster statistics are estimated using a
7012 rigorous Bayesian framework. Post-processing of the results, data export for
7013 UCSC genome browser visualization and motif search analysis are provided. In
7014 addition, the package integrates RNA-Seq data to estimate the False
7015 Discovery Rate of cluster detection. Key functions support parallel multicore
7016 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7017 be applied to the analysis of other NGS data obtained from experimental
7018 procedures that induce nucleotide substitutions (e.g. BisSeq).")
7019 (license license:gpl2)))
7021 (define-public r-timeseriesexperiment
7023 (name "r-timeseriesexperiment")
7028 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7031 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
7033 `((upstream-name . "TimeSeriesExperiment")))
7034 (build-system r-build-system)
7036 `(("r-deseq2" ,r-deseq2)
7037 ("r-dplyr" ,r-dplyr)
7038 ("r-dynamictreecut" ,r-dynamictreecut)
7039 ("r-edger" ,r-edger)
7040 ("r-ggplot2" ,r-ggplot2)
7041 ("r-hmisc" ,r-hmisc)
7042 ("r-limma" ,r-limma)
7043 ("r-magrittr" ,r-magrittr)
7044 ("r-proxy" ,r-proxy)
7045 ("r-s4vectors" ,r-s4vectors)
7046 ("r-summarizedexperiment" ,r-summarizedexperiment)
7047 ("r-tibble" ,r-tibble)
7048 ("r-tidyr" ,r-tidyr)
7049 ("r-vegan" ,r-vegan)
7050 ("r-viridis" ,r-viridis)))
7052 `(("r-knitr" ,r-knitr)))
7053 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7054 (synopsis "Analysis for short time-series data")
7056 "This package is a visualization and analysis toolbox for short time
7057 course data which includes dimensionality reduction, clustering, two-sample
7058 differential expression testing and gene ranking techniques. The package also
7059 provides methods for retrieving enriched pathways.")
7060 (license license:lgpl3+)))
7062 (define-public r-variantfiltering
7064 (name "r-variantfiltering")
7069 (uri (bioconductor-uri "VariantFiltering" version))
7072 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
7074 `((upstream-name . "VariantFiltering")))
7075 (build-system r-build-system)
7077 `(("r-annotationdbi" ,r-annotationdbi)
7078 ("r-biobase" ,r-biobase)
7079 ("r-biocgenerics" ,r-biocgenerics)
7080 ("r-biocparallel" ,r-biocparallel)
7081 ("r-biostrings" ,r-biostrings)
7082 ("r-bsgenome" ,r-bsgenome)
7084 ("r-genomeinfodb" ,r-genomeinfodb)
7085 ("r-genomicfeatures" ,r-genomicfeatures)
7086 ("r-genomicranges" ,r-genomicranges)
7087 ("r-genomicscores" ,r-genomicscores)
7088 ("r-graph" ,r-graph)
7090 ("r-iranges" ,r-iranges)
7092 ("r-rsamtools" ,r-rsamtools)
7093 ("r-s4vectors" ,r-s4vectors)
7094 ("r-shiny" ,r-shiny)
7095 ("r-shinyjs" ,r-shinyjs)
7096 ("r-shinythemes" ,r-shinythemes)
7097 ("r-shinytree" ,r-shinytree)
7098 ("r-summarizedexperiment" ,r-summarizedexperiment)
7099 ("r-variantannotation" ,r-variantannotation)
7100 ("r-xvector" ,r-xvector)))
7101 (home-page "https://github.com/rcastelo/VariantFiltering")
7102 (synopsis "Filtering of coding and non-coding genetic variants")
7104 "Filter genetic variants using different criteria such as inheritance
7105 model, amino acid change consequence, minor allele frequencies across human
7106 populations, splice site strength, conservation, etc.")
7107 (license license:artistic2.0)))
7109 (define-public r-genomegraphs
7111 (name "r-genomegraphs")
7116 (uri (bioconductor-uri "GenomeGraphs" version))
7119 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7120 (properties `((upstream-name . "GenomeGraphs")))
7121 (build-system r-build-system)
7123 `(("r-biomart" ,r-biomart)))
7124 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7125 (synopsis "Plotting genomic information from Ensembl")
7127 "Genomic data analyses requires integrated visualization of known genomic
7128 information and new experimental data. GenomeGraphs uses the biomaRt package
7129 to perform live annotation queries to Ensembl and translates this to e.g.
7130 gene/transcript structures in viewports of the grid graphics package. This
7131 results in genomic information plotted together with your data. Another
7132 strength of GenomeGraphs is to plot different data types such as array CGH,
7133 gene expression, sequencing and other data, together in one plot using the
7134 same genome coordinate system.")
7135 (license license:artistic2.0)))
7137 (define-public r-wavetiling
7139 (name "r-wavetiling")
7144 (uri (bioconductor-uri "waveTiling" version))
7147 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7148 (properties `((upstream-name . "waveTiling")))
7149 (build-system r-build-system)
7151 `(("r-affy" ,r-affy)
7152 ("r-biobase" ,r-biobase)
7153 ("r-biostrings" ,r-biostrings)
7154 ("r-genomegraphs" ,r-genomegraphs)
7155 ("r-genomicranges" ,r-genomicranges)
7156 ("r-iranges" ,r-iranges)
7157 ("r-oligo" ,r-oligo)
7158 ("r-oligoclasses" ,r-oligoclasses)
7159 ("r-preprocesscore" ,r-preprocesscore)
7160 ("r-waveslim" ,r-waveslim)))
7161 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7162 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7164 "This package is designed to conduct transcriptome analysis for tiling
7165 arrays based on fast wavelet-based functional models.")
7166 (license license:gpl2+)))
7168 (define-public r-variancepartition
7170 (name "r-variancepartition")
7175 (uri (bioconductor-uri "variancePartition" version))
7178 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
7180 `((upstream-name . "variancePartition")))
7181 (build-system r-build-system)
7183 `(("r-biobase" ,r-biobase)
7184 ("r-biocparallel" ,r-biocparallel)
7185 ("r-colorramps" ,r-colorramps)
7186 ("r-doparallel" ,r-doparallel)
7187 ("r-foreach" ,r-foreach)
7188 ("r-ggplot2" ,r-ggplot2)
7189 ("r-gplots" ,r-gplots)
7190 ("r-iterators" ,r-iterators)
7191 ("r-limma" ,r-limma)
7193 ("r-lmertest" ,r-lmertest)
7195 ("r-pbkrtest" ,r-pbkrtest)
7196 ("r-progress" ,r-progress)
7197 ("r-reshape2" ,r-reshape2)
7198 ("r-scales" ,r-scales)))
7200 `(("r-knitr" ,r-knitr)))
7201 (home-page "https://bioconductor.org/packages/variancePartition/")
7202 (synopsis "Analyze variation in gene expression experiments")
7204 "This is a package providing tools to quantify and interpret multiple
7205 sources of biological and technical variation in gene expression experiments.
7206 It uses a linear mixed model to quantify variation in gene expression
7207 attributable to individual, tissue, time point, or technical variables. The
7208 package includes dream differential expression analysis for repeated
7210 (license license:gpl2+)))
7212 (define-public r-htqpcr
7219 (uri (bioconductor-uri "HTqPCR" version))
7222 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
7223 (properties `((upstream-name . "HTqPCR")))
7224 (build-system r-build-system)
7226 `(("r-affy" ,r-affy)
7227 ("r-biobase" ,r-biobase)
7228 ("r-gplots" ,r-gplots)
7229 ("r-limma" ,r-limma)
7230 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7231 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7232 "groups/bertone/software/HTqPCR.pdf"))
7233 (synopsis "Automated analysis of high-throughput qPCR data")
7235 "Analysis of Ct values from high throughput quantitative real-time
7236 PCR (qPCR) assays across multiple conditions or replicates. The input data
7237 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7238 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7239 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7240 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7241 loading, quality assessment, normalization, visualization and parametric or
7242 non-parametric testing for statistical significance in Ct values between
7243 features (e.g. genes, microRNAs).")
7244 (license license:artistic2.0)))
7246 (define-public r-unifiedwmwqpcr
7248 (name "r-unifiedwmwqpcr")
7253 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7256 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
7258 `((upstream-name . "unifiedWMWqPCR")))
7259 (build-system r-build-system)
7261 `(("r-biocgenerics" ,r-biocgenerics)
7262 ("r-htqpcr" ,r-htqpcr)))
7263 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7264 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7266 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7267 data. This modified test allows for testing differential expression in qPCR
7269 (license license:gpl2+)))
7271 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7273 (define-public r-activedriverwgs
7275 (name "r-activedriverwgs")
7280 (uri (cran-uri "ActiveDriverWGS" version))
7283 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
7285 `((upstream-name . "ActiveDriverWGS")))
7286 (build-system r-build-system)
7288 `(("r-biostrings" ,r-biostrings)
7289 ("r-bsgenome" ,r-bsgenome)
7290 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7291 ("r-genomeinfodb" ,r-genomeinfodb)
7292 ("r-genomicranges" ,r-genomicranges)
7293 ("r-iranges" ,r-iranges)
7294 ("r-s4vectors" ,r-s4vectors)))
7296 `(("r-knitr" ,r-knitr)))
7297 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7298 (synopsis "Driver discovery tool for cancer whole genomes")
7300 "This package provides a method for finding an enrichment of cancer
7301 simple somatic mutations (SNVs and Indels) in functional elements across the
7302 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7303 using whole genome sequencing data.")
7304 (license license:gpl3)))
7306 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7308 (define-public r-activepathways
7310 (name "r-activepathways")
7315 (uri (cran-uri "ActivePathways" version))
7318 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7320 `((upstream-name . "ActivePathways")))
7321 (build-system r-build-system)
7323 `(("r-data-table" ,r-data-table)
7324 ("r-ggplot2" ,r-ggplot2)))
7326 `(("r-knitr" ,r-knitr)))
7327 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7328 (synopsis "Multivariate pathway enrichment analysis")
7330 "This package represents an integrative method of analyzing multi omics
7331 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7332 uses a statistical data fusion approach, rationalizes contributing evidence
7333 and highlights associated genes, improving systems-level understanding of
7334 cellular organization in health and disease.")
7335 (license license:gpl3)))
7337 (define-public r-bgmix
7344 (uri (bioconductor-uri "BGmix" version))
7347 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
7348 (properties `((upstream-name . "BGmix")))
7349 (build-system r-build-system)
7351 `(("r-kernsmooth" ,r-kernsmooth)))
7352 (home-page "https://bioconductor.org/packages/BGmix/")
7353 (synopsis "Bayesian models for differential gene expression")
7355 "This package provides fully Bayesian mixture models for differential
7357 (license license:gpl2)))
7359 (define-public r-bgx
7366 (uri (bioconductor-uri "bgx" version))
7369 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
7370 (properties `((upstream-name . "bgx")))
7371 (build-system r-build-system)
7373 `(("r-affy" ,r-affy)
7374 ("r-biobase" ,r-biobase)
7375 ("r-gcrma" ,r-gcrma)
7376 ("r-rcpp" ,r-rcpp)))
7377 (home-page "https://bioconductor.org/packages/bgx/")
7378 (synopsis "Bayesian gene expression")
7380 "This package provides tools for Bayesian integrated analysis of
7381 Affymetrix GeneChips.")
7382 (license license:gpl2)))
7384 (define-public r-bhc
7391 (uri (bioconductor-uri "BHC" version))
7394 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
7395 (properties `((upstream-name . "BHC")))
7396 (build-system r-build-system)
7397 (home-page "https://bioconductor.org/packages/BHC/")
7398 (synopsis "Bayesian hierarchical clustering")
7400 "The method implemented in this package performs bottom-up hierarchical
7401 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7402 in the data and Bayesian model selection to decide at each step which clusters
7403 to merge. This avoids several limitations of traditional methods, for example
7404 how many clusters there should be and how to choose a principled distance
7405 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7406 categories) or time-series data. This version also includes a randomised
7407 algorithm which is more efficient for larger data sets.")
7408 (license license:gpl3)))
7410 (define-public r-bicare
7417 (uri (bioconductor-uri "BicARE" version))
7420 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
7421 (properties `((upstream-name . "BicARE")))
7422 (build-system r-build-system)
7424 `(("r-biobase" ,r-biobase)
7425 ("r-gseabase" ,r-gseabase)
7426 ("r-multtest" ,r-multtest)))
7427 (home-page "http://bioinfo.curie.fr")
7428 (synopsis "Biclustering analysis and results exploration")
7430 "This is a package for biclustering analysis and exploration of
7432 (license license:gpl2)))
7434 (define-public r-bifet
7441 (uri (bioconductor-uri "BiFET" version))
7444 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
7445 (properties `((upstream-name . "BiFET")))
7446 (build-system r-build-system)
7448 `(("r-genomicranges" ,r-genomicranges)
7449 ("r-poibin" ,r-poibin)))
7451 `(("r-knitr" ,r-knitr)))
7452 (home-page "https://bioconductor.org/packages/BiFET")
7453 (synopsis "Bias-free footprint enrichment test")
7455 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7456 over-represented in target regions compared to background regions after
7457 correcting for the bias arising from the imbalance in read counts and GC
7458 contents between the target and background regions. For a given TF k, BiFET
7459 tests the null hypothesis that the target regions have the same probability of
7460 having footprints for the TF k as the background regions while correcting for
7461 the read count and GC content bias.")
7462 (license license:gpl3)))
7464 (define-public r-rsbml
7471 (uri (bioconductor-uri "rsbml" version))
7474 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
7475 (properties `((upstream-name . "rsbml")))
7476 (build-system r-build-system)
7478 `(("libsbml" ,libsbml)
7481 `(("r-biocgenerics" ,r-biocgenerics)
7482 ("r-graph" ,r-graph)))
7484 `(("pkg-config" ,pkg-config)))
7485 (home-page "http://www.sbml.org")
7486 (synopsis "R support for SBML")
7488 "This package provides an R interface to libsbml for SBML parsing,
7489 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7490 (license license:artistic2.0)))
7492 (define-public r-hypergraph
7494 (name "r-hypergraph")
7499 (uri (bioconductor-uri "hypergraph" version))
7502 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
7503 (properties `((upstream-name . "hypergraph")))
7504 (build-system r-build-system)
7506 `(("r-graph" ,r-graph)))
7507 (home-page "https://bioconductor.org/packages/hypergraph")
7508 (synopsis "Hypergraph data structures")
7510 "This package implements some simple capabilities for representing and
7511 manipulating hypergraphs.")
7512 (license license:artistic2.0)))
7514 (define-public r-hyperdraw
7516 (name "r-hyperdraw")
7521 (uri (bioconductor-uri "hyperdraw" version))
7524 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
7525 (properties `((upstream-name . "hyperdraw")))
7526 (build-system r-build-system)
7527 (inputs `(("graphviz" ,graphviz)))
7529 `(("r-graph" ,r-graph)
7530 ("r-hypergraph" ,r-hypergraph)
7531 ("r-rgraphviz" ,r-rgraphviz)))
7532 (home-page "https://bioconductor.org/packages/hyperdraw")
7533 (synopsis "Visualizing hypergraphs")
7535 "This package provides functions for visualizing hypergraphs.")
7536 (license license:gpl2+)))
7538 (define-public r-biggr
7545 (uri (bioconductor-uri "BiGGR" version))
7548 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
7549 (properties `((upstream-name . "BiGGR")))
7550 (build-system r-build-system)
7552 `(("r-hyperdraw" ,r-hyperdraw)
7553 ("r-hypergraph" ,r-hypergraph)
7555 ("r-limsolve" ,r-limsolve)
7556 ("r-rsbml" ,r-rsbml)
7557 ("r-stringr" ,r-stringr)))
7558 (home-page "https://bioconductor.org/packages/BiGGR/")
7559 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7561 "This package provides an interface to simulate metabolic reconstruction
7562 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7563 reconstruction databases. The package facilitates @dfn{flux balance
7564 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7565 networks and estimated fluxes can be visualized with hypergraphs.")
7566 (license license:gpl3+)))
7568 (define-public r-bigmemoryextras
7570 (name "r-bigmemoryextras")
7575 (uri (bioconductor-uri "bigmemoryExtras" version))
7578 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
7580 `((upstream-name . "bigmemoryExtras")))
7581 (build-system r-build-system)
7583 `(("r-bigmemory" ,r-bigmemory)))
7585 `(("r-knitr" ,r-knitr)))
7586 (home-page "https://github.com/phaverty/bigmemoryExtras")
7587 (synopsis "Extension of the bigmemory package")
7589 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7590 safety and convenience features to the @code{filebacked.big.matrix} class from
7591 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7592 monitoring and gracefully restoring the connection to on-disk data and it also
7593 protects against accidental data modification with a file-system-based
7594 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7595 classes as @code{assayData} matrices within the @code{Biobase} package's
7596 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7597 related to attaching to, and indexing into, file-backed matrices with
7598 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7599 a file-backed matrix with factor properties.")
7600 (license license:artistic2.0)))
7602 (define-public r-bigpint
7609 (uri (bioconductor-uri "bigPint" version))
7612 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
7613 (properties `((upstream-name . "bigPint")))
7614 (build-system r-build-system)
7616 `(("r-delayedarray" ,r-delayedarray)
7617 ("r-dplyr" ,r-dplyr)
7618 ("r-ggally" ,r-ggally)
7619 ("r-ggplot2" ,r-ggplot2)
7620 ("r-gridextra" ,r-gridextra)
7621 ("r-hexbin" ,r-hexbin)
7622 ("r-hmisc" ,r-hmisc)
7623 ("r-htmlwidgets" ,r-htmlwidgets)
7624 ("r-plotly" ,r-plotly)
7626 ("r-rcolorbrewer" ,r-rcolorbrewer)
7627 ("r-reshape" ,r-reshape)
7628 ("r-shiny" ,r-shiny)
7629 ("r-shinycssloaders" ,r-shinycssloaders)
7630 ("r-shinydashboard" ,r-shinydashboard)
7631 ("r-stringr" ,r-stringr)
7632 ("r-summarizedexperiment" ,r-summarizedexperiment)
7633 ("r-tidyr" ,r-tidyr)))
7635 `(("r-knitr" ,r-knitr)))
7636 (home-page "https://github.com/lindsayrutter/bigPint")
7637 (synopsis "Big multivariate data plotted interactively")
7639 "This package provides methods for visualizing large multivariate
7640 datasets using static and interactive scatterplot matrices, parallel
7641 coordinate plots, volcano plots, and litre plots. It includes examples for
7642 visualizing RNA-sequencing datasets and differentially expressed genes.")
7643 (license license:gpl3)))
7645 (define-public r-chemminer
7647 (name "r-chemminer")
7652 (uri (bioconductor-uri "ChemmineR" version))
7655 "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19"))))
7656 (properties `((upstream-name . "ChemmineR")))
7657 (build-system r-build-system)
7659 `(("r-base64enc" ,r-base64enc)
7661 ("r-biocgenerics" ,r-biocgenerics)
7663 ("r-digest" ,r-digest)
7665 ("r-ggplot2" ,r-ggplot2)
7666 ("r-gridextra" ,r-gridextra)
7669 ("r-rcurl" ,r-rcurl)
7670 ("r-rjson" ,r-rjson)
7671 ("r-rsvg" ,r-rsvg)))
7673 `(("r-knitr" ,r-knitr)))
7674 (home-page "https://github.com/girke-lab/ChemmineR")
7675 (synopsis "Cheminformatics toolkit for R")
7677 "ChemmineR is a cheminformatics package for analyzing drug-like small
7678 molecule data in R. It contains functions for efficient processing of large
7679 numbers of molecules, physicochemical/structural property predictions,
7680 structural similarity searching, classification and clustering of compound
7681 libraries with a wide spectrum of algorithms. In addition, it offers
7682 visualization functions for compound clustering results and chemical
7684 (license license:artistic2.0)))
7686 (define-public r-bioassayr
7688 (name "r-bioassayr")
7693 (uri (bioconductor-uri "bioassayR" version))
7696 "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f"))))
7697 (properties `((upstream-name . "bioassayR")))
7698 (build-system r-build-system)
7700 `(("r-biocgenerics" ,r-biocgenerics)
7701 ("r-chemminer" ,r-chemminer)
7703 ("r-matrix" ,r-matrix)
7704 ("r-rjson" ,r-rjson)
7705 ("r-rsqlite" ,r-rsqlite)
7708 `(("r-knitr" ,r-knitr)))
7709 (home-page "https://github.com/TylerBackman/bioassayR")
7710 (synopsis "Cross-target analysis of small molecule bioactivity")
7712 "bioassayR is a computational tool that enables simultaneous analysis of
7713 thousands of bioassay experiments performed over a diverse set of compounds
7714 and biological targets. Unique features include support for large-scale
7715 cross-target analyses of both public and custom bioassays, generation of
7716 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7717 preloaded database that provides access to a substantial portion of publicly
7718 available bioactivity data.")
7719 (license license:artistic2.0)))
7721 (define-public r-biobroom
7728 (uri (bioconductor-uri "biobroom" version))
7731 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
7732 (properties `((upstream-name . "biobroom")))
7733 (build-system r-build-system)
7735 `(("r-biobase" ,r-biobase)
7736 ("r-broom" ,r-broom)
7737 ("r-dplyr" ,r-dplyr)
7738 ("r-tidyr" ,r-tidyr)))
7740 `(("r-knitr" ,r-knitr)))
7741 (home-page "https://github.com/StoreyLab/biobroom")
7742 (synopsis "Turn Bioconductor objects into tidy data frames")
7744 "This package contains methods for converting standard objects
7745 constructed by bioinformatics packages, especially those in Bioconductor, and
7746 converting them to @code{tidy} data. It thus serves as a complement to the
7747 @code{broom} package, and follows the same tidy, augment, glance division of
7748 tidying methods. Tidying data makes it easy to recombine, reshape and
7749 visualize bioinformatics analyses.")
7750 ;; Any version of the LGPL.
7751 (license license:lgpl3+)))
7753 (define-public r-graphite
7760 (uri (bioconductor-uri "graphite" version))
7763 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
7764 (properties `((upstream-name . "graphite")))
7765 (build-system r-build-system)
7767 `(("r-annotationdbi" ,r-annotationdbi)
7768 ("r-checkmate" ,r-checkmate)
7769 ("r-graph" ,r-graph)
7771 ("r-rappdirs" ,r-rappdirs)))
7772 (home-page "https://bioconductor.org/packages/graphite/")
7773 (synopsis "Networks from pathway databases")
7775 "Graphite provides networks derived from eight public pathway databases,
7776 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7778 (license license:agpl3+)))
7780 (define-public r-reactomepa
7782 (name "r-reactomepa")
7787 (uri (bioconductor-uri "ReactomePA" version))
7790 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
7791 (properties `((upstream-name . "ReactomePA")))
7792 (build-system r-build-system)
7794 `(("r-annotationdbi" ,r-annotationdbi)
7796 ("r-enrichplot" ,r-enrichplot)
7797 ("r-ggplot2" ,r-ggplot2)
7798 ("r-ggraph" ,r-ggraph)
7799 ("r-graphite" ,r-graphite)
7800 ("r-igraph" ,r-igraph)
7801 ("r-reactome-db" ,r-reactome-db)))
7803 `(("r-knitr" ,r-knitr)))
7804 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7805 (synopsis "Reactome pathway analysis")
7807 "This package provides functions for pathway analysis based on the
7808 REACTOME pathway database. It implements enrichment analysis, gene set
7809 enrichment analysis and several functions for visualization.")
7810 (license license:gpl2)))
7812 (define-public r-ebarrays
7819 (uri (bioconductor-uri "EBarrays" version))
7822 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
7823 (properties `((upstream-name . "EBarrays")))
7824 (build-system r-build-system)
7826 `(("r-biobase" ,r-biobase)
7827 ("r-cluster" ,r-cluster)
7828 ("r-lattice" ,r-lattice)))
7829 (home-page "https://bioconductor.org/packages/EBarrays/")
7830 (synopsis "Gene clustering and differential expression identification")
7832 "EBarrays provides tools for the analysis of replicated/unreplicated
7834 (license license:gpl2+)))
7836 (define-public r-bioccasestudies
7838 (name "r-bioccasestudies")
7843 (uri (bioconductor-uri "BiocCaseStudies" version))
7846 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
7848 `((upstream-name . "BiocCaseStudies")))
7849 (build-system r-build-system)
7850 (propagated-inputs `(("r-biobase" ,r-biobase)))
7851 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7852 (synopsis "Support for the case studies monograph")
7854 "This package provides software and data to support the case studies
7856 (license license:artistic2.0)))
7858 (define-public r-biocgraph
7860 (name "r-biocgraph")
7865 (uri (bioconductor-uri "biocGraph" version))
7868 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
7869 (properties `((upstream-name . "biocGraph")))
7870 (build-system r-build-system)
7872 `(("r-biocgenerics" ,r-biocgenerics)
7873 ("r-geneplotter" ,r-geneplotter)
7874 ("r-graph" ,r-graph)
7875 ("r-rgraphviz" ,r-rgraphviz)))
7876 (home-page "https://bioconductor.org/packages/biocGraph/")
7877 (synopsis "Graph examples and use cases in Bioinformatics")
7879 "This package provides examples and code that make use of the
7880 different graph related packages produced by Bioconductor.")
7881 (license license:artistic2.0)))
7883 (define-public r-experimenthub
7885 (name "r-experimenthub")
7890 (uri (bioconductor-uri "ExperimentHub" version))
7893 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
7894 (properties `((upstream-name . "ExperimentHub")))
7895 (build-system r-build-system)
7897 `(("r-annotationhub" ,r-annotationhub)
7898 ("r-biocfilecache" ,r-biocfilecache)
7899 ("r-biocgenerics" ,r-biocgenerics)
7900 ("r-biocmanager" ,r-biocmanager)
7902 ("r-rappdirs" ,r-rappdirs)
7903 ("r-s4vectors" ,r-s4vectors)))
7905 `(("r-knitr" ,r-knitr)))
7906 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7907 (synopsis "Client to access ExperimentHub resources")
7909 "This package provides a client for the Bioconductor ExperimentHub web
7910 resource. ExperimentHub provides a central location where curated data from
7911 experiments, publications or training courses can be accessed. Each resource
7912 has associated metadata, tags and date of modification. The client creates
7913 and manages a local cache of files retrieved enabling quick and reproducible
7915 (license license:artistic2.0)))
7917 (define-public r-multiassayexperiment
7919 (name "r-multiassayexperiment")
7924 (uri (bioconductor-uri "MultiAssayExperiment" version))
7927 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
7929 `((upstream-name . "MultiAssayExperiment")))
7930 (build-system r-build-system)
7932 `(("r-biobase" ,r-biobase)
7933 ("r-biocgenerics" ,r-biocgenerics)
7934 ("r-genomicranges" ,r-genomicranges)
7935 ("r-iranges" ,r-iranges)
7936 ("r-s4vectors" ,r-s4vectors)
7937 ("r-summarizedexperiment" ,r-summarizedexperiment)
7938 ("r-tidyr" ,r-tidyr)))
7940 `(("r-knitr" ,r-knitr)))
7941 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7942 (synopsis "Integration of multi-omics experiments in Bioconductor")
7944 "MultiAssayExperiment harmonizes data management of multiple assays
7945 performed on an overlapping set of specimens. It provides a familiar
7946 Bioconductor user experience by extending concepts from
7947 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7948 classes for individual assays, and allowing subsetting by genomic ranges or
7950 (license license:artistic2.0)))
7952 (define-public r-bioconcotk
7954 (name "r-bioconcotk")
7959 (uri (bioconductor-uri "BiocOncoTK" version))
7962 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
7963 (properties `((upstream-name . "BiocOncoTK")))
7964 (build-system r-build-system)
7966 `(("r-bigrquery" ,r-bigrquery)
7968 ("r-complexheatmap" ,r-complexheatmap)
7969 ("r-curatedtcgadata" ,r-curatedtcgadata)
7971 ("r-dplyr" ,r-dplyr)
7973 ("r-genomicfeatures" ,r-genomicfeatures)
7974 ("r-genomicranges" ,r-genomicranges)
7975 ("r-ggplot2" ,r-ggplot2)
7976 ("r-ggpubr" ,r-ggpubr)
7977 ("r-graph" ,r-graph)
7979 ("r-iranges" ,r-iranges)
7980 ("r-magrittr" ,r-magrittr)
7982 ("r-rgraphviz" ,r-rgraphviz)
7983 ("r-rjson" ,r-rjson)
7984 ("r-s4vectors" ,r-s4vectors)
7985 ("r-scales" ,r-scales)
7986 ("r-shiny" ,r-shiny)
7987 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7989 `(("r-knitr" ,r-knitr)))
7990 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7991 (synopsis "Bioconductor components for general cancer genomics")
7993 "The purpose of this package is to provide a central interface to various
7994 tools for genome-scale analysis of cancer studies.")
7995 (license license:artistic2.0)))
7997 (define-public r-biocor
8004 (uri (bioconductor-uri "BioCor" version))
8007 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
8008 (properties `((upstream-name . "BioCor")))
8009 (build-system r-build-system)
8011 `(("r-biocparallel" ,r-biocparallel)
8012 ("r-gseabase" ,r-gseabase)
8013 ("r-matrix" ,r-matrix)))
8015 `(("r-knitr" ,r-knitr)))
8016 (home-page "https://llrs.github.io/BioCor/")
8017 (synopsis "Functional similarities")
8019 "This package provides tools to calculate functional similarities based
8020 on the pathways described on KEGG and REACTOME or in gene sets. These
8021 similarities can be calculated for pathways or gene sets, genes, or clusters
8022 and combined with other similarities. They can be used to improve networks,
8023 gene selection, testing relationships, and so on.")
8024 (license license:expat)))
8026 (define-public r-biocpkgtools
8028 (name "r-biocpkgtools")
8033 (uri (bioconductor-uri "BiocPkgTools" version))
8036 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
8037 (properties `((upstream-name . "BiocPkgTools")))
8038 (build-system r-build-system)
8040 `(("r-biocfilecache" ,r-biocfilecache)
8041 ("r-biocmanager" ,r-biocmanager)
8042 ("r-biocviews" ,r-biocviews)
8043 ("r-dplyr" ,r-dplyr)
8046 ("r-graph" ,r-graph)
8047 ("r-htmltools" ,r-htmltools)
8048 ("r-htmlwidgets" ,r-htmlwidgets)
8050 ("r-igraph" ,r-igraph)
8051 ("r-jsonlite" ,r-jsonlite)
8052 ("r-magrittr" ,r-magrittr)
8053 ("r-rappdirs" ,r-rappdirs)
8055 ("r-readr" ,r-readr)
8057 ("r-rlang" ,r-rlang)
8058 ("r-rvest" ,r-rvest)
8059 ("r-stringr" ,r-stringr)
8060 ("r-tibble" ,r-tibble)
8061 ("r-tidyr" ,r-tidyr)
8062 ("r-tidyselect" ,r-tidyselect)
8063 ("r-xml2" ,r-xml2)))
8065 `(("r-knitr" ,r-knitr)))
8066 (home-page "https://github.com/seandavi/BiocPkgTools")
8067 (synopsis "Collection of tools for learning about Bioconductor packages")
8069 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8070 and build status. This package is a simple collection of functions to access
8071 that metadata from R. The goal is to expose metadata for data mining and
8072 value-added functionality such as package searching, text mining, and
8073 analytics on packages.")
8074 (license license:expat)))
8076 (define-public r-biocset
8083 (uri (bioconductor-uri "BiocSet" version))
8086 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
8087 (properties `((upstream-name . "BiocSet")))
8088 (build-system r-build-system)
8090 `(("r-annotationdbi" ,r-annotationdbi)
8091 ("r-biocio" ,r-biocio)
8092 ("r-dplyr" ,r-dplyr)
8093 ("r-keggrest" ,r-keggrest)
8094 ("r-ontologyindex" ,r-ontologyindex)
8096 ("r-rlang" ,r-rlang)
8097 ("r-s4vectors" ,r-s4vectors)
8098 ("r-tibble" ,r-tibble)
8099 ("r-tidyr" ,r-tidyr)))
8101 `(("r-knitr" ,r-knitr)))
8103 "https://bioconductor.org/packages/BiocSet")
8105 "Representing Different Biological Sets")
8107 "BiocSet displays different biological sets in a triple tibble format.
8108 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
8109 The user has the ability to activate one of these three tibbles to perform
8110 common functions from the @code{dplyr} package. Mapping functionality and
8111 accessing web references for elements/sets are also available in BiocSet.")
8112 (license license:artistic2.0)))
8114 (define-public r-biocworkflowtools
8116 (name "r-biocworkflowtools")
8121 (uri (bioconductor-uri "BiocWorkflowTools" version))
8124 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
8126 `((upstream-name . "BiocWorkflowTools")))
8127 (build-system r-build-system)
8129 `(("r-biocstyle" ,r-biocstyle)
8130 ("r-bookdown" ,r-bookdown)
8131 ("r-git2r" ,r-git2r)
8133 ("r-knitr" ,r-knitr)
8134 ("r-rmarkdown" ,r-rmarkdown)
8135 ("r-rstudioapi" ,r-rstudioapi)
8136 ("r-stringr" ,r-stringr)
8137 ("r-usethis" ,r-usethis)))
8139 `(("r-knitr" ,r-knitr)))
8140 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8141 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8143 "This package provides functions to ease the transition between
8144 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8145 (license license:expat)))
8147 (define-public r-biodist
8154 (uri (bioconductor-uri "bioDist" version))
8157 "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
8158 (properties `((upstream-name . "bioDist")))
8159 (build-system r-build-system)
8161 `(("r-biobase" ,r-biobase)
8162 ("r-kernsmooth" ,r-kernsmooth)))
8163 (home-page "https://bioconductor.org/packages/bioDist/")
8164 (synopsis "Different distance measures")
8166 "This package provides a collection of software tools for calculating
8167 distance measures.")
8168 (license license:artistic2.0)))
8170 (define-public r-pcatools
8177 (uri (bioconductor-uri "PCAtools" version))
8180 "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
8181 (properties `((upstream-name . "PCAtools")))
8182 (build-system r-build-system)
8184 `(("r-beachmat" ,r-beachmat)
8186 ("r-biocparallel" ,r-biocparallel)
8187 ("r-biocsingular" ,r-biocsingular)
8188 ("r-cowplot" ,r-cowplot)
8189 ("r-delayedarray" ,r-delayedarray)
8190 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8191 ("r-dqrng" ,r-dqrng)
8192 ("r-ggplot2" ,r-ggplot2)
8193 ("r-ggrepel" ,r-ggrepel)
8194 ("r-lattice" ,r-lattice)
8195 ("r-matrix" ,r-matrix)
8197 ("r-reshape2" ,r-reshape2)))
8198 (native-inputs `(("r-knitr" ,r-knitr)))
8199 (home-page "https://github.com/kevinblighe/PCAtools")
8200 (synopsis "PCAtools: everything Principal Components Analysis")
8202 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8203 structure of the data without the need to build any model to represent it.
8204 This \"summary\" of the data is arrived at through a process of reduction that
8205 can transform the large number of variables into a lesser number that are
8206 uncorrelated (i.e. the 'principal components'), while at the same time being
8207 capable of easy interpretation on the original data. PCAtools provides
8208 functions for data exploration via PCA, and allows the user to generate
8209 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8210 can also identify an optimal number of principal components via different
8211 metrics, such as the elbow method and Horn's parallel analysis, which has
8212 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8213 dimensional mass cytometry data.")
8214 (license license:gpl3)))
8216 (define-public r-rgreat
8223 (uri (bioconductor-uri "rGREAT" version))
8226 "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
8227 (properties `((upstream-name . "rGREAT")))
8228 (build-system r-build-system)
8230 `(("r-genomicranges" ,r-genomicranges)
8231 ("r-getoptlong" ,r-getoptlong)
8232 ("r-iranges" ,r-iranges)
8233 ("r-rcurl" ,r-rcurl)
8234 ("r-rjson" ,r-rjson)))
8235 (native-inputs `(("r-knitr" ,r-knitr)))
8236 (home-page "https://github.com/jokergoo/rGREAT")
8237 (synopsis "Client for GREAT analysis")
8239 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8240 Tool) analysis automatic by constructing a HTTP POST request according to
8241 user's input and automatically retrieving results from GREAT web server.")
8242 (license license:expat)))
8244 (define-public r-m3c
8251 (uri (bioconductor-uri "M3C" version))
8254 "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
8255 (properties `((upstream-name . "M3C")))
8256 (build-system r-build-system)
8258 `(("r-cluster" ,r-cluster)
8259 ("r-corpcor" ,r-corpcor)
8260 ("r-doparallel" ,r-doparallel)
8261 ("r-dosnow" ,r-dosnow)
8262 ("r-foreach" ,r-foreach)
8263 ("r-ggplot2" ,r-ggplot2)
8264 ("r-matrix" ,r-matrix)
8265 ("r-matrixcalc" ,r-matrixcalc)
8266 ("r-rtsne" ,r-rtsne)
8267 ("r-umap" ,r-umap)))
8268 (native-inputs `(("r-knitr" ,r-knitr)))
8269 (home-page "https://bioconductor.org/packages/M3C")
8270 (synopsis "Monte Carlo reference-based consensus clustering")
8272 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8273 simulation to eliminate overestimation of @code{K} and can reject the null
8274 hypothesis @code{K=1}.")
8275 (license license:agpl3+)))
8277 (define-public r-icens
8284 (uri (bioconductor-uri "Icens" version))
8287 "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
8288 (properties `((upstream-name . "Icens")))
8289 (build-system r-build-system)
8291 `(("r-survival" ,r-survival)))
8292 (home-page "https://bioconductor.org/packages/Icens")
8293 (synopsis "NPMLE for censored and truncated data")
8295 "This package provides many functions for computing the
8296 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8298 (license license:artistic2.0)))
8300 ;; This is a CRAN package but it depends on r-icens, which is published on
8302 (define-public r-interval
8309 (uri (cran-uri "interval" version))
8312 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
8313 (properties `((upstream-name . "interval")))
8314 (build-system r-build-system)
8316 `(("r-icens" ,r-icens)
8317 ("r-mlecens" ,r-mlecens)
8319 ("r-survival" ,r-survival)))
8320 (home-page "https://cran.r-project.org/web/packages/interval/")
8321 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8323 "This package provides functions to fit nonparametric survival curves,
8324 plot them, and perform logrank or Wilcoxon type tests.")
8325 (license license:gpl2+)))
8327 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8328 ;; Bioconductor package.
8329 (define-public r-fhtest
8336 (uri (cran-uri "FHtest" version))
8339 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
8340 (properties `((upstream-name . "FHtest")))
8341 (build-system r-build-system)
8343 `(("r-interval" ,r-interval)
8344 ("r-kmsurv" ,r-kmsurv)
8347 ("r-survival" ,r-survival)))
8348 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8349 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8351 "This package provides functions to compare two or more survival curves
8355 @item The Fleming-Harrington test for right-censored data based on
8356 permutations and on counting processes.
8357 @item An extension of the Fleming-Harrington test for interval-censored data
8358 based on a permutation distribution and on a score vector distribution.
8361 (license license:gpl2+)))
8363 (define-public r-fourcseq
8370 (uri (bioconductor-uri "FourCSeq" version))
8372 (base32 "14q1ijnqnbd9xs60sfvyqjfiypjrvhacpwp2v85yfhcxw870cx5b"))))
8373 (properties `((upstream-name . "FourCSeq")))
8374 (build-system r-build-system)
8376 `(("r-biobase" ,r-biobase)
8377 ("r-biostrings" ,r-biostrings)
8378 ("r-deseq2" ,r-deseq2)
8380 ("r-genomicalignments" ,r-genomicalignments)
8381 ("r-genomicranges" ,r-genomicranges)
8382 ("r-ggbio" ,r-ggbio)
8383 ("r-ggplot2" ,r-ggplot2)
8384 ("r-gtools" ,r-gtools)
8386 ("r-matrix" ,r-matrix)
8387 ("r-reshape2" ,r-reshape2)
8388 ("r-rsamtools" ,r-rsamtools)
8389 ("r-rtracklayer" ,r-rtracklayer)
8390 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8392 `(("r-knitr" ,r-knitr)))
8394 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8395 (synopsis "Analysis of multiplexed 4C sequencing data")
8397 "This package is an R package dedicated to the analysis of (multiplexed)
8398 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8399 interactions between DNA elements and identify differential interactions
8400 between conditions. The statistical analysis in R starts with individual bam
8401 files for each sample as inputs. To obtain these files, the package contains
8402 a Python script to demultiplex libraries and trim off primer sequences. With
8403 a standard alignment software the required bam files can be then be
8405 (license license:gpl3+)))
8407 (define-public r-preprocesscore
8409 (name "r-preprocesscore")
8414 (uri (bioconductor-uri "preprocessCore" version))
8417 "0q1406kswylc8zn5k3wyd34p34pfzbhi1ggkfsh30zcjp6adbwjl"))))
8419 `((upstream-name . "preprocessCore")))
8420 (build-system r-build-system)
8421 (home-page "https://github.com/bmbolstad/preprocessCore")
8422 (synopsis "Collection of pre-processing functions")
8424 "This package provides a library of core pre-processing and normalization
8426 (license license:lgpl2.0+)))
8428 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
8429 ;; Bioconductor package.
8430 (define-public r-wgcna
8437 (uri (cran-uri "WGCNA" version))
8440 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
8441 (properties `((upstream-name . "WGCNA")))
8442 (build-system r-build-system)
8444 `(("r-annotationdbi" ,r-annotationdbi)
8445 ("r-doparallel" ,r-doparallel)
8446 ("r-dynamictreecut" ,r-dynamictreecut)
8447 ("r-fastcluster" ,r-fastcluster)
8448 ("r-foreach" ,r-foreach)
8449 ("r-go-db" ,r-go-db)
8450 ("r-hmisc" ,r-hmisc)
8451 ("r-impute" ,r-impute)
8453 ("r-survival" ,r-survival)
8454 ("r-matrixstats" ,r-matrixstats)
8455 ("r-preprocesscore" ,r-preprocesscore)))
8457 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8458 (synopsis "Weighted correlation network analysis")
8460 "This package provides functions necessary to perform Weighted
8461 Correlation Network Analysis on high-dimensional data. It includes functions
8462 for rudimentary data cleaning, construction and summarization of correlation
8463 networks, module identification and functions for relating both variables and
8464 modules to sample traits. It also includes a number of utility functions for
8465 data manipulation and visualization.")
8466 (license license:gpl2+)))
8468 (define-public r-rgraphviz
8470 (name "r-rgraphviz")
8475 (uri (bioconductor-uri "Rgraphviz" version))
8478 "1calpvzgcz6v7s4x6bf35kj83sga95zjp7x87p5d3qnbv7q2wz5y"))))
8479 (properties `((upstream-name . "Rgraphviz")))
8480 (build-system r-build-system)
8483 (modify-phases %standard-phases
8484 (add-after 'unpack 'make-reproducible
8486 ;; The replacement value is taken from src/graphviz/builddate.h
8487 (substitute* "src/graphviz/configure"
8488 (("VERSION_DATE=.*")
8489 "VERSION_DATE=20200427.2341\n"))
8491 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8492 ;; graphviz. It does not build with the latest version of graphviz, so
8493 ;; we do not add graphviz to the inputs.
8494 (inputs `(("zlib" ,zlib)))
8496 `(("r-graph" ,r-graph)))
8498 `(("pkg-config" ,pkg-config)))
8499 (home-page "https://bioconductor.org/packages/Rgraphviz")
8500 (synopsis "Plotting capabilities for R graph objects")
8502 "This package interfaces R with the graphviz library for plotting R graph
8503 objects from the @code{graph} package.")
8504 (license license:epl1.0)))
8506 (define-public r-fithic
8512 (uri (bioconductor-uri "FitHiC" version))
8515 "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
8516 (properties `((upstream-name . "FitHiC")))
8517 (build-system r-build-system)
8519 `(("r-data-table" ,r-data-table)
8520 ("r-fdrtool" ,r-fdrtool)
8521 ("r-rcpp" ,r-rcpp)))
8523 `(("r-knitr" ,r-knitr)))
8524 (home-page "https://bioconductor.org/packages/FitHiC")
8525 (synopsis "Confidence estimation for intra-chromosomal contact maps")
8527 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
8528 intra-chromosomal contact maps produced by genome-wide genome architecture
8529 assays such as Hi-C.")
8530 (license license:gpl2+)))
8532 (define-public r-hitc
8538 (uri (bioconductor-uri "HiTC" version))
8541 "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
8542 (properties `((upstream-name . "HiTC")))
8543 (build-system r-build-system)
8545 `(("r-biostrings" ,r-biostrings)
8546 ("r-genomeinfodb" ,r-genomeinfodb)
8547 ("r-genomicranges" ,r-genomicranges)
8548 ("r-iranges" ,r-iranges)
8549 ("r-matrix" ,r-matrix)
8550 ("r-rcolorbrewer" ,r-rcolorbrewer)
8551 ("r-rtracklayer" ,r-rtracklayer)))
8552 (home-page "https://bioconductor.org/packages/HiTC")
8553 (synopsis "High throughput chromosome conformation capture analysis")
8555 "The HiTC package was developed to explore high-throughput \"C\" data
8556 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
8557 quality controls, normalization, visualization, and further analysis are also
8559 (license license:artistic2.0)))
8561 (define-public r-hdf5array
8563 (name "r-hdf5array")
8568 (uri (bioconductor-uri "HDF5Array" version))
8571 "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
8572 (properties `((upstream-name . "HDF5Array")))
8573 (build-system r-build-system)
8577 `(("r-biocgenerics" ,r-biocgenerics)
8578 ("r-delayedarray" ,r-delayedarray)
8579 ("r-iranges" ,r-iranges)
8580 ("r-matrix" ,r-matrix)
8581 ("r-rhdf5" ,r-rhdf5)
8582 ("r-rhdf5lib" ,r-rhdf5lib)
8583 ("r-s4vectors" ,r-s4vectors)))
8584 (home-page "https://bioconductor.org/packages/HDF5Array")
8585 (synopsis "HDF5 back end for DelayedArray objects")
8586 (description "This package provides an array-like container for convenient
8587 access and manipulation of HDF5 datasets. It supports delayed operations and
8589 (license license:artistic2.0)))
8591 (define-public r-rhdf5lib
8598 (uri (bioconductor-uri "Rhdf5lib" version))
8601 "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
8602 (modules '((guix build utils)))
8605 ;; Delete bundled binaries
8606 (delete-file-recursively "src/wininclude/")
8607 (delete-file-recursively "src/winlib-4.9.3/")
8608 (delete-file-recursively "src/winlib-8.3.0/")
8609 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
8611 (properties `((upstream-name . "Rhdf5lib")))
8612 (build-system r-build-system)
8615 (modify-phases %standard-phases
8616 (add-after 'unpack 'do-not-use-bundled-hdf5
8617 (lambda* (#:key inputs #:allow-other-keys)
8618 (for-each delete-file '("configure" "configure.ac"))
8619 ;; Do not make other packages link with the proprietary libsz.
8620 (substitute* "R/zzz.R"
8621 ((" \"%s/libsz.a\"") ""))
8622 (with-directory-excursion "src"
8623 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
8624 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
8626 ;; Remove timestamp and host system information to make
8627 ;; the build reproducible.
8628 (substitute* "hdf5/src/libhdf5.settings.in"
8629 (("Configured on: @CONFIG_DATE@")
8630 "Configured on: Guix")
8631 (("Uname information:.*")
8632 "Uname information: Linux\n")
8633 ;; Remove unnecessary store reference.
8635 "C Compiler: GCC\n"))
8636 (rename-file "Makevars.in" "Makevars")
8637 (substitute* "Makevars"
8638 (("@ZLIB_LIB@") "-lz")
8639 (("@ZLIB_INCLUDE@") "")
8640 (("HDF5_CXX_LIB=.*")
8641 (string-append "HDF5_CXX_LIB="
8642 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
8644 (string-append "HDF5_LIB="
8645 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
8646 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
8647 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
8648 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
8649 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
8651 (string-append "HDF5_HL_LIB="
8652 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
8653 (("HDF5_HL_CXX_LIB=.*")
8654 (string-append "HDF5_HL_CXX_LIB="
8655 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
8656 ;; szip is non-free software
8657 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
8658 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
8663 `(("hdf5" ,hdf5-1.10)))
8665 `(("hdf5-source" ,(package-source hdf5-1.10))
8666 ("r-knitr" ,r-knitr)))
8667 (home-page "https://bioconductor.org/packages/Rhdf5lib")
8668 (synopsis "HDF5 library as an R package")
8669 (description "This package provides C and C++ HDF5 libraries for use in R
8671 (license license:artistic2.0)))
8673 (define-public r-beachmat
8680 (uri (bioconductor-uri "beachmat" version))
8683 "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
8684 (build-system r-build-system)
8686 `(("r-biocgenerics" ,r-biocgenerics)
8687 ("r-delayedarray" ,r-delayedarray)
8688 ("r-matrix" ,r-matrix)))
8690 `(("r-knitr" ,r-knitr)))
8691 (home-page "https://bioconductor.org/packages/beachmat")
8692 (synopsis "Compiling Bioconductor to handle each matrix type")
8693 (description "This package provides a consistent C++ class interface for a
8694 variety of commonly used matrix types, including sparse and HDF5-backed
8696 (license license:gpl3)))
8698 (define-public r-singlecellexperiment
8700 (name "r-singlecellexperiment")
8705 (uri (bioconductor-uri "SingleCellExperiment" version))
8708 "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
8710 `((upstream-name . "SingleCellExperiment")))
8711 (build-system r-build-system)
8713 `(("r-biocgenerics" ,r-biocgenerics)
8714 ("r-s4vectors" ,r-s4vectors)
8715 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8717 `(("r-knitr" ,r-knitr)))
8718 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
8719 (synopsis "S4 classes for single cell data")
8720 (description "This package defines an S4 class for storing data from
8721 single-cell experiments. This includes specialized methods to store and
8722 retrieve spike-in information, dimensionality reduction coordinates and size
8723 factors for each cell, along with the usual metadata for genes and
8725 (license license:gpl3)))
8727 (define-public r-scater
8733 (uri (bioconductor-uri "scater" version))
8736 "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
8737 (build-system r-build-system)
8739 `(("r-beachmat" ,r-beachmat)
8740 ("r-biocgenerics" ,r-biocgenerics)
8741 ("r-biocneighbors" ,r-biocneighbors)
8742 ("r-biocparallel" ,r-biocparallel)
8743 ("r-biocsingular" ,r-biocsingular)
8744 ("r-delayedarray" ,r-delayedarray)
8745 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8746 ("r-ggbeeswarm" ,r-ggbeeswarm)
8747 ("r-ggplot2" ,r-ggplot2)
8748 ("r-matrix" ,r-matrix)
8750 ("r-rlang" ,r-rlang)
8751 ("r-s4vectors" ,r-s4vectors)
8752 ("r-singlecellexperiment" ,r-singlecellexperiment)
8753 ("r-summarizedexperiment" ,r-summarizedexperiment)
8754 ("r-viridis" ,r-viridis)))
8756 `(("r-knitr" ,r-knitr)))
8757 (home-page "https://github.com/davismcc/scater")
8758 (synopsis "Single-cell analysis toolkit for gene expression data in R")
8759 (description "This package provides a collection of tools for doing
8760 various analyses of single-cell RNA-seq gene expression data, with a focus on
8762 (license license:gpl2+)))
8764 (define-public r-scran
8771 (uri (bioconductor-uri "scran" version))
8774 "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
8775 (build-system r-build-system)
8777 `(("r-beachmat" ,r-beachmat)
8779 ("r-biocgenerics" ,r-biocgenerics)
8780 ("r-biocneighbors" ,r-biocneighbors)
8781 ("r-biocparallel" ,r-biocparallel)
8782 ("r-biocsingular" ,r-biocsingular)
8783 ("r-delayedarray" ,r-delayedarray)
8784 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8785 ("r-dqrng" ,r-dqrng)
8786 ("r-edger" ,r-edger)
8787 ("r-igraph" ,r-igraph)
8788 ("r-iranges" ,r-iranges)
8789 ("r-limma" ,r-limma)
8790 ("r-matrix" ,r-matrix)
8792 ("r-s4vectors" ,r-s4vectors)
8793 ("r-scater" ,r-scater)
8794 ("r-singlecellexperiment" ,r-singlecellexperiment)
8795 ("r-statmod" ,r-statmod)
8796 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8798 `(("r-knitr" ,r-knitr)))
8799 (home-page "https://bioconductor.org/packages/scran")
8800 (synopsis "Methods for single-cell RNA-Seq data analysis")
8801 (description "This package implements a variety of low-level analyses of
8802 single-cell RNA-seq data. Methods are provided for normalization of
8803 cell-specific biases, assignment of cell cycle phase, and detection of highly
8804 variable and significantly correlated genes.")
8805 (license license:gpl3)))
8807 (define-public r-delayedmatrixstats
8809 (name "r-delayedmatrixstats")
8814 (uri (bioconductor-uri "DelayedMatrixStats" version))
8817 "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
8819 `((upstream-name . "DelayedMatrixStats")))
8820 (build-system r-build-system)
8822 `(("r-biocparallel" ,r-biocparallel)
8823 ("r-delayedarray" ,r-delayedarray)
8824 ("r-hdf5array" ,r-hdf5array)
8825 ("r-iranges" ,r-iranges)
8826 ("r-matrix" ,r-matrix)
8827 ("r-matrixstats" ,r-matrixstats)
8828 ("r-s4vectors" ,r-s4vectors)))
8830 `(("r-knitr" ,r-knitr)))
8831 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
8832 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
8834 "This package provides a port of the @code{matrixStats} API for use with
8835 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
8836 contains high-performing functions operating on rows and columns of
8837 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
8838 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
8839 are optimized per data type and for subsetted calculations such that both
8840 memory usage and processing time is minimized.")
8841 (license license:expat)))
8843 (define-public r-mscoreutils
8845 (name "r-mscoreutils")
8850 (uri (bioconductor-uri "MsCoreUtils" version))
8853 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
8854 (properties `((upstream-name . "MsCoreUtils")))
8855 (build-system r-build-system)
8857 `(("r-mass" ,r-mass)
8859 ("r-s4vectors" ,r-s4vectors)))
8861 `(("r-knitr" ,r-knitr)))
8862 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
8863 (synopsis "Core utils for mass spectrometry data")
8865 "This package defines low-level functions for mass spectrometry data and
8866 is independent of any high-level data structures. These functions include
8867 mass spectra processing functions (noise estimation, smoothing, binning),
8868 quantitative aggregation functions (median polish, robust summarisation,
8869 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
8870 well as misc helper functions, that are used across high-level data structure
8871 within the R for Mass Spectrometry packages.")
8872 (license license:artistic2.0)))
8874 (define-public r-biocio
8881 (uri (bioconductor-uri "BiocIO" version))
8884 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
8885 (properties `((upstream-name . "BiocIO")))
8886 (build-system r-build-system)
8888 `(("r-biocgenerics" ,r-biocgenerics)
8889 ("r-genomicranges" ,r-genomicranges)
8890 ("r-rcurl" ,r-rcurl)
8891 ("r-s4vectors" ,r-s4vectors)))
8893 `(("r-knitr" ,r-knitr)))
8894 (home-page "https://bioconductor.org/packages/BiocIO")
8895 (synopsis "Standard input and output for Bioconductor packages")
8897 "This package implements `import()` and `export()` standard generics for
8898 importing and exporting biological data formats. `import()` supports
8899 whole-file as well as chunk-wise iterative import. The `import()` interface
8900 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
8901 row or element-like components of the file resource), `select()` (on
8902 column-like components of the file resource) and `collect()`. The `import()`
8903 interface optionally provides transparent access to remote (e.g. via https)
8904 as well as local access. Developers can register a file extension, e.g.,
8905 `.loom` for dispatch from character-based URIs to specific `import()` /
8906 `export()` methods based on classes representing file types, e.g.,
8908 (license license:artistic2.0)))