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, 2021 Simon Tournier <zimon.toutoune@gmail.com>
6 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
7 ;;; Copyright © 2020, 2021 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
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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.
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23 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
25 (define-module (gnu packages bioconductor)
26 #:use-module ((guix licenses) #:prefix license:)
27 #:use-module (guix packages)
28 #:use-module (guix download)
29 #:use-module (guix git-download)
30 #:use-module (guix build-system r)
31 #:use-module (gnu packages)
32 #:use-module (gnu packages base)
33 #:use-module (gnu packages bioinformatics)
34 #:use-module (gnu packages cran)
35 #:use-module (gnu packages compression)
36 #:use-module (gnu packages gcc)
37 #:use-module (gnu packages graph)
38 #:use-module (gnu packages graphviz)
39 #:use-module (gnu packages haskell-xyz)
40 #:use-module (gnu packages image)
41 #:use-module (gnu packages maths)
42 #:use-module (gnu packages netpbm)
43 #:use-module (gnu packages perl)
44 #:use-module (gnu packages pkg-config)
45 #:use-module (gnu packages statistics)
46 #:use-module (gnu packages web)
47 #:use-module (gnu packages xml)
48 #:use-module (srfi srfi-1))
53 (define-public r-org-eck12-eg-db
55 (name "r-org-eck12-eg-db")
60 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
62 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
64 `((upstream-name . "org.EcK12.eg.db")))
65 (build-system r-build-system)
67 `(("r-annotationdbi" ,r-annotationdbi)))
68 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
69 (synopsis "Genome wide annotation for E coli strain K12")
71 "This package provides genome wide annotation for E coli strain K12,
72 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
73 National Center for Biotechnology Information (NCBI)’s database for
74 gene-specific information. Entrez Gene maintains records from genomes which
75 have been completely sequenced, which have an active research community to
76 submit gene-specific information, or which are scheduled for intense sequence
78 (license license:artistic2.0)))
80 (define-public r-reactome-db
82 (name "r-reactome-db")
87 (uri (bioconductor-uri "reactome.db" version 'annotation))
90 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
91 (properties `((upstream-name . "reactome.db")))
92 (build-system r-build-system)
94 `(("r-annotationdbi" ,r-annotationdbi)))
95 (home-page "https://bioconductor.org/packages/reactome.db/")
96 (synopsis "Annotation maps for reactome")
98 "This package provides a set of annotation maps for the REACTOME
99 database, assembled using data from REACTOME.")
100 (license license:cc-by4.0)))
102 (define-public r-bsgenome-celegans-ucsc-ce6
104 (name "r-bsgenome-celegans-ucsc-ce6")
108 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
109 version 'annotation))
112 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
114 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
115 (build-system r-build-system)
117 `(("r-bsgenome" ,r-bsgenome)))
119 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
120 (synopsis "Full genome sequences for Worm")
122 "This package provides full genome sequences for Caenorhabditis
123 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
125 (license license:artistic2.0)))
127 (define-public r-bsgenome-celegans-ucsc-ce10
129 (name "r-bsgenome-celegans-ucsc-ce10")
133 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
134 version 'annotation))
137 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
139 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
140 (build-system r-build-system)
142 `(("r-bsgenome" ,r-bsgenome)))
144 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
145 (synopsis "Full genome sequences for Worm")
147 "This package provides full genome sequences for Caenorhabditis
148 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
150 (license license:artistic2.0)))
152 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
154 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
158 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
159 version 'annotation))
162 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
164 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
165 (build-system r-build-system)
167 `(("r-bsgenome" ,r-bsgenome)))
169 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
170 (synopsis "Full genome sequences for Fly")
172 "This package provides full genome sequences for Drosophila
173 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
175 (license license:artistic2.0)))
177 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
179 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
183 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
184 version 'annotation))
187 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
189 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
190 (build-system r-build-system)
192 `(("r-bsgenome" ,r-bsgenome)))
194 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
195 (synopsis "Full genome sequences for Fly")
197 "This package provides full genome sequences for Drosophila
198 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
199 Biostrings objects.")
200 (license license:artistic2.0)))
202 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
204 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
208 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
209 version 'annotation))
212 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
214 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
215 (build-system r-build-system)
217 `(("r-bsgenome" ,r-bsgenome)
218 ("r-bsgenome-dmelanogaster-ucsc-dm3"
219 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
220 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
221 (synopsis "Full masked genome sequences for Fly")
223 "This package provides full masked genome sequences for Drosophila
224 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
225 Biostrings objects. The sequences are the same as in
226 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
227 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
228 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
229 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
230 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
231 (license license:artistic2.0)))
233 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
235 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
239 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
240 version 'annotation))
243 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
245 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
246 (build-system r-build-system)
248 `(("r-bsgenome" ,r-bsgenome)))
250 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
251 (synopsis "Full genome sequences for Homo sapiens")
253 "This package provides full genome sequences for Homo sapiens from
254 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
255 (license license:artistic2.0)))
257 (define-public r-bsgenome-hsapiens-ncbi-grch38
259 (name "r-bsgenome-hsapiens-ncbi-grch38")
264 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
265 version 'annotation))
268 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
269 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
270 (build-system r-build-system)
271 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
273 "https://bioconductor.org/packages/release/data/annotation/html/\
274 BSgenome.Hsapiens.NCBI.GRCh38.html")
275 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
277 "This package provides full genome sequences for Homo sapiens (Human) as
278 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
279 (license license:artistic2.0)))
281 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
283 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
287 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
288 version 'annotation))
291 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
293 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
294 (build-system r-build-system)
296 `(("r-bsgenome" ,r-bsgenome)
297 ("r-bsgenome-hsapiens-ucsc-hg19"
298 ,r-bsgenome-hsapiens-ucsc-hg19)))
299 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
300 (synopsis "Full masked genome sequences for Homo sapiens")
302 "This package provides full genome sequences for Homo sapiens (Human) as
303 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
304 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
305 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
306 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
307 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
308 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
310 (license license:artistic2.0)))
312 (define-public r-bsgenome-mmusculus-ucsc-mm9
314 (name "r-bsgenome-mmusculus-ucsc-mm9")
318 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
319 version 'annotation))
322 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
324 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
325 (build-system r-build-system)
327 `(("r-bsgenome" ,r-bsgenome)))
329 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
330 (synopsis "Full genome sequences for Mouse")
332 "This package provides full genome sequences for Mus musculus (Mouse) as
333 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
334 (license license:artistic2.0)))
336 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
338 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
342 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
343 version 'annotation))
346 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
348 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
349 (build-system r-build-system)
351 `(("r-bsgenome" ,r-bsgenome)
352 ("r-bsgenome-mmusculus-ucsc-mm9"
353 ,r-bsgenome-mmusculus-ucsc-mm9)))
354 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
355 (synopsis "Full masked genome sequences for Mouse")
357 "This package provides full genome sequences for Mus musculus (Mouse) as
358 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
359 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
360 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
361 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
362 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
363 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
365 (license license:artistic2.0)))
367 (define-public r-bsgenome-mmusculus-ucsc-mm10
369 (name "r-bsgenome-mmusculus-ucsc-mm10")
373 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
374 version 'annotation))
377 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
379 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
380 (build-system r-build-system)
382 `(("r-bsgenome" ,r-bsgenome)))
384 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
385 (synopsis "Full genome sequences for Mouse")
387 "This package provides full genome sequences for Mus
388 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
389 in Biostrings objects.")
390 (license license:artistic2.0)))
392 (define-public r-homo-sapiens
394 (name "r-homo-sapiens")
398 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
401 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
403 `((upstream-name . "Homo.sapiens")))
404 (build-system r-build-system)
406 `(("r-genomicfeatures" ,r-genomicfeatures)
408 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
409 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
410 ("r-organismdbi" ,r-organismdbi)
411 ("r-annotationdbi" ,r-annotationdbi)))
412 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
413 (synopsis "Annotation package for the Homo.sapiens object")
415 "This package contains the Homo.sapiens object to access data from
416 several related annotation packages.")
417 (license license:artistic2.0)))
419 (define-public r-org-ce-eg-db
421 (name "r-org-ce-eg-db")
425 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
428 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
430 `((upstream-name . "org.Ce.eg.db")))
431 (build-system r-build-system)
433 `(("r-annotationdbi" ,r-annotationdbi)))
434 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
435 (synopsis "Genome wide annotation for Worm")
437 "This package provides mappings from Entrez gene identifiers to various
438 annotations for the genome of the model worm Caenorhabditis elegans.")
439 (license license:artistic2.0)))
441 (define-public r-org-dm-eg-db
443 (name "r-org-dm-eg-db")
447 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
450 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
452 `((upstream-name . "org.Dm.eg.db")))
453 (build-system r-build-system)
455 `(("r-annotationdbi" ,r-annotationdbi)))
456 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
457 (synopsis "Genome wide annotation for Fly")
459 "This package provides mappings from Entrez gene identifiers to various
460 annotations for the genome of the model fruit fly Drosophila melanogaster.")
461 (license license:artistic2.0)))
463 (define-public r-org-dr-eg-db
465 (name "r-org-dr-eg-db")
469 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
472 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
474 `((upstream-name . "org.Dr.eg.db")))
475 (build-system r-build-system)
477 `(("r-annotationdbi" ,r-annotationdbi)))
478 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
479 (synopsis "Annotation for Zebrafish")
481 "This package provides genome wide annotations for Zebrafish, primarily
482 based on mapping using Entrez Gene identifiers.")
483 (license license:artistic2.0)))
485 (define-public r-org-hs-eg-db
487 (name "r-org-hs-eg-db")
491 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
494 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
496 `((upstream-name . "org.Hs.eg.db")))
497 (build-system r-build-system)
499 `(("r-annotationdbi" ,r-annotationdbi)))
500 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
501 (synopsis "Genome wide annotation for Human")
503 "This package contains genome-wide annotations for Human, primarily based
504 on mapping using Entrez Gene identifiers.")
505 (license license:artistic2.0)))
507 (define-public r-org-mm-eg-db
509 (name "r-org-mm-eg-db")
513 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
516 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
518 `((upstream-name . "org.Mm.eg.db")))
519 (build-system r-build-system)
521 `(("r-annotationdbi" ,r-annotationdbi)))
522 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
523 (synopsis "Genome wide annotation for Mouse")
525 "This package provides mappings from Entrez gene identifiers to various
526 annotations for the genome of the model mouse Mus musculus.")
527 (license license:artistic2.0)))
529 (define-public r-bsgenome-hsapiens-ucsc-hg19
531 (name "r-bsgenome-hsapiens-ucsc-hg19")
535 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
536 version 'annotation))
539 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
541 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
542 (build-system r-build-system)
544 `(("r-bsgenome" ,r-bsgenome)))
546 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
547 (synopsis "Full genome sequences for Homo sapiens")
549 "This package provides full genome sequences for Homo sapiens as provided
550 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
551 (license license:artistic2.0)))
553 (define-public r-bsgenome-hsapiens-ucsc-hg38
555 (name "r-bsgenome-hsapiens-ucsc-hg38")
559 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
560 version 'annotation))
563 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
565 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
566 (build-system r-build-system)
568 `(("r-bsgenome" ,r-bsgenome)))
570 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
571 (synopsis "Full genome sequences for Homo sapiens")
573 "This package provides full genome sequences for Homo sapiens (Human)
574 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
575 (license license:artistic2.0)))
577 (define-public r-ensdb-hsapiens-v75
579 (name "r-ensdb-hsapiens-v75")
584 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
587 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
589 `((upstream-name . "EnsDb.Hsapiens.v75")))
590 (build-system r-build-system)
592 `(("r-ensembldb" ,r-ensembldb)))
593 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
594 (synopsis "Ensembl based annotation package")
596 "This package exposes an annotation database generated from Ensembl.")
597 (license license:artistic2.0)))
599 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
601 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
605 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
606 version 'annotation))
609 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
611 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
612 (build-system r-build-system)
614 `(("r-genomicfeatures" ,r-genomicfeatures)))
616 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
617 (synopsis "Annotation package for human genome in TxDb format")
619 "This package provides an annotation database of Homo sapiens genome
620 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
621 track. The database is exposed as a @code{TxDb} object.")
622 (license license:artistic2.0)))
624 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
626 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
630 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
631 version 'annotation))
634 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
636 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
637 (build-system r-build-system)
639 `(("r-genomicfeatures" ,r-genomicfeatures)))
641 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
642 (synopsis "Annotation package for human genome in TxDb format")
644 "This package provides an annotation database of Homo sapiens genome
645 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
646 track. The database is exposed as a @code{TxDb} object.")
647 (license license:artistic2.0)))
649 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
651 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
655 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
656 version 'annotation))
659 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
661 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
662 (build-system r-build-system)
664 `(("r-genomicfeatures" ,r-genomicfeatures)
665 ("r-annotationdbi" ,r-annotationdbi)))
667 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
668 (synopsis "Annotation package for mouse genome in TxDb format")
670 "This package provides an annotation database of Mouse genome data. It
671 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
672 database is exposed as a @code{TxDb} object.")
673 (license license:artistic2.0)))
675 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
677 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
681 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
682 version 'annotation))
685 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
687 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
688 (build-system r-build-system)
690 `(("r-bsgenome" ,r-bsgenome)
691 ("r-genomicfeatures" ,r-genomicfeatures)
692 ("r-annotationdbi" ,r-annotationdbi)))
694 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
695 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
697 "This package loads a TxDb object, which is an R interface to
698 prefabricated databases contained in this package. This package provides
699 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
700 based on the knownGene track.")
701 (license license:artistic2.0)))
703 (define-public r-txdb-celegans-ucsc-ce6-ensgene
705 (name "r-txdb-celegans-ucsc-ce6-ensgene")
710 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
711 version 'annotation))
714 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
716 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
717 (build-system r-build-system)
719 `(("r-annotationdbi" ,r-annotationdbi)
720 ("r-genomicfeatures" ,r-genomicfeatures)))
721 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
722 (synopsis "Annotation package for C elegans TxDb objects")
724 "This package exposes a C elegans annotation database generated from UCSC
725 by exposing these as TxDb objects.")
726 (license license:artistic2.0)))
728 (define-public r-fdb-infiniummethylation-hg19
730 (name "r-fdb-infiniummethylation-hg19")
734 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
735 version 'annotation))
738 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
740 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
741 (build-system r-build-system)
743 `(("r-biostrings" ,r-biostrings)
744 ("r-genomicfeatures" ,r-genomicfeatures)
745 ("r-annotationdbi" ,r-annotationdbi)
746 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
747 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
748 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
749 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
751 "This is an annotation package for Illumina Infinium DNA methylation
752 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
754 (license license:artistic2.0)))
756 (define-public r-illuminahumanmethylationepicmanifest
758 (name "r-illuminahumanmethylationepicmanifest")
762 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
763 version 'annotation))
766 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
768 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
769 (build-system r-build-system)
771 `(("r-minfi" ,r-minfi)))
772 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
773 (synopsis "Manifest for Illumina's EPIC methylation arrays")
775 "This is a manifest package for Illumina's EPIC methylation arrays.")
776 (license license:artistic2.0)))
778 (define-public r-do-db
784 (uri (bioconductor-uri "DO.db" version 'annotation))
787 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
789 `((upstream-name . "DO.db")))
790 (build-system r-build-system)
792 `(("r-annotationdbi" ,r-annotationdbi)))
793 (home-page "https://www.bioconductor.org/packages/DO.db/")
794 (synopsis "Annotation maps describing the entire Disease Ontology")
796 "This package provides a set of annotation maps describing the entire
798 (license license:artistic2.0)))
800 (define-public r-pfam-db
807 (uri (bioconductor-uri "PFAM.db" version 'annotation))
810 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
811 (properties `((upstream-name . "PFAM.db")))
812 (build-system r-build-system)
814 `(("r-annotationdbi" ,r-annotationdbi)))
815 (home-page "https://bioconductor.org/packages/PFAM.db")
816 (synopsis "Set of protein ID mappings for PFAM")
818 "This package provides a set of protein ID mappings for PFAM, assembled
819 using data from public repositories.")
820 (license license:artistic2.0)))
822 (define-public r-phastcons100way-ucsc-hg19
824 (name "r-phastcons100way-ucsc-hg19")
829 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
830 version 'annotation))
833 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
835 `((upstream-name . "phastCons100way.UCSC.hg19")))
836 (build-system r-build-system)
838 `(("r-bsgenome" ,r-bsgenome)
839 ("r-genomeinfodb" ,r-genomeinfodb)
840 ("r-genomicranges" ,r-genomicranges)
841 ("r-genomicscores" ,r-genomicscores)
842 ("r-iranges" ,r-iranges)
843 ("r-s4vectors" ,r-s4vectors)))
844 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
845 (synopsis "UCSC phastCons conservation scores for hg19")
847 "This package provides UCSC phastCons conservation scores for the human
848 genome (hg19) calculated from multiple alignments with other 99 vertebrate
850 (license license:artistic2.0)))
855 (define-public r-abadata
861 (uri (bioconductor-uri "ABAData" version 'experiment))
864 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
866 `((upstream-name . "ABAData")))
867 (build-system r-build-system)
869 `(("r-annotationdbi" ,r-annotationdbi)))
870 (home-page "https://www.bioconductor.org/packages/ABAData/")
871 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
873 "This package provides the data for the gene expression enrichment
874 analysis conducted in the package ABAEnrichment. The package includes three
875 datasets which are derived from the Allen Brain Atlas:
878 @item Gene expression data from Human Brain (adults) averaged across donors,
879 @item Gene expression data from the Developing Human Brain pooled into five
880 age categories and averaged across donors, and
881 @item a developmental effect score based on the Developing Human Brain
885 All datasets are restricted to protein coding genes.")
886 (license license:gpl2+)))
888 (define-public r-arrmdata
894 (uri (bioconductor-uri "ARRmData" version 'experiment))
897 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
899 `((upstream-name . "ARRmData")))
900 (build-system r-build-system)
901 (home-page "https://www.bioconductor.org/packages/ARRmData/")
902 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
904 "This package provides raw beta values from 36 samples across 3 groups
905 from Illumina 450k methylation arrays.")
906 (license license:artistic2.0)))
908 (define-public r-genelendatabase
910 (name "r-genelendatabase")
915 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
918 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
920 `((upstream-name . "geneLenDataBase")))
921 (build-system r-build-system)
923 `(("r-rtracklayer" ,r-rtracklayer)
924 ("r-genomicfeatures" ,r-genomicfeatures)))
925 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
926 (synopsis "Lengths of mRNA transcripts for a number of genomes")
928 "This package provides the lengths of mRNA transcripts for a number of
929 genomes and gene ID formats, largely based on the UCSC table browser.")
930 (license license:lgpl2.0+)))
932 (define-public r-pasilla
939 "http://bioconductor.org/packages/release/data/experiment"
940 "/src/contrib/pasilla_" version ".tar.gz"))
943 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
944 (build-system r-build-system)
946 `(("r-biocstyle" ,r-biocstyle)
947 ("r-dexseq" ,r-dexseq)
949 ("r-rmarkdown" ,r-rmarkdown)))
950 (home-page "https://www.bioconductor.org/packages/pasilla/")
951 (synopsis "Data package with per-exon and per-gene read counts")
952 (description "This package provides per-exon and per-gene read counts
953 computed for selected genes from RNA-seq data that were presented in the
954 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
955 by Brooks et al., Genome Research 2011.")
956 (license license:lgpl2.1+)))
958 (define-public r-hsmmsinglecell
960 (name "r-hsmmsinglecell")
964 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
967 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
969 `((upstream-name . "HSMMSingleCell")))
970 (build-system r-build-system)
971 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
972 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
974 "Skeletal myoblasts undergo a well-characterized sequence of
975 morphological and transcriptional changes during differentiation. In this
976 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
977 under high mitogen conditions (GM) and then differentiated by switching to
978 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
979 hundred cells taken over a time-course of serum-induced differentiation.
980 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
981 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
982 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
983 which were then sequenced to a depth of ~4 million reads per library,
984 resulting in a complete gene expression profile for each cell.")
985 (license license:artistic2.0)))
993 (uri (bioconductor-uri "ALL" version 'experiment))
996 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
997 (properties `((upstream-name . "ALL")))
998 (build-system r-build-system)
1000 `(("r-biobase" ,r-biobase)))
1001 (home-page "https://bioconductor.org/packages/ALL")
1002 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1004 "The data consist of microarrays from 128 different individuals with
1005 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1006 are available. The data have been normalized (using rma) and it is the
1007 jointly normalized data that are available here. The data are presented in
1008 the form of an @code{exprSet} object.")
1009 (license license:artistic2.0)))
1011 (define-public r-affydata
1018 (uri (bioconductor-uri "affydata" version 'experiment))
1021 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1022 (properties `((upstream-name . "affydata")))
1023 (build-system r-build-system)
1025 `(("r-affy" ,r-affy)))
1026 (home-page "https://bioconductor.org/packages/affydata/")
1027 (synopsis "Affymetrix data for demonstration purposes")
1029 "This package provides example datasets that represent 'real world
1030 examples' of Affymetrix data, unlike the artificial examples included in the
1031 package @code{affy}.")
1032 (license license:gpl2+)))
1034 (define-public r-gagedata
1041 (uri (bioconductor-uri "gageData" version 'experiment))
1043 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
1044 (properties `((upstream-name . "gageData")))
1045 (build-system r-build-system)
1046 (home-page "https://bioconductor.org/packages/gageData")
1047 (synopsis "Auxillary data for gage package")
1049 "This is a supportive data package for the software package @code{gage}.
1050 However, the data supplied here are also useful for gene set or pathway
1051 analysis or microarray data analysis in general. In this package, we provide
1052 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1053 BMP6 (originally published as an demo dataset for GAGE, also registered as
1054 GSE13604 in GEO). This package also includes commonly used gene set data based
1055 on KEGG pathways and GO terms for major research species, including human,
1056 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1057 yeast are also included.")
1058 (license license:gpl2+)))
1060 (define-public r-curatedtcgadata
1062 (name "r-curatedtcgadata")
1067 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1070 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1072 `((upstream-name . "curatedTCGAData")))
1073 (build-system r-build-system)
1075 `(("r-annotationhub" ,r-annotationhub)
1076 ("r-experimenthub" ,r-experimenthub)
1077 ("r-hdf5array" ,r-hdf5array)
1078 ("r-multiassayexperiment" ,r-multiassayexperiment)
1079 ("r-s4vectors" ,r-s4vectors)
1080 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1081 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1082 (synopsis "Curated data from The Cancer Genome Atlas")
1084 "This package provides publicly available data from The Cancer Genome
1085 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1086 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1087 number, mutation, microRNA, protein, and others) with clinical / pathological
1088 data. It also links assay barcodes with patient identifiers, enabling
1089 harmonized subsetting of rows (features) and columns (patients / samples)
1090 across the entire multi-'omics experiment.")
1091 (license license:artistic2.0)))
1096 (define-public r-biocversion
1098 (name "r-biocversion")
1103 (uri (bioconductor-uri "BiocVersion" version))
1106 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
1107 (properties `((upstream-name . "BiocVersion")))
1108 (build-system r-build-system)
1109 (home-page "https://bioconductor.org/packages/BiocVersion/")
1110 (synopsis "Set the appropriate version of Bioconductor packages")
1112 "This package provides repository information for the appropriate version
1114 (license license:artistic2.0)))
1116 (define-public r-biocgenerics
1118 (name "r-biocgenerics")
1122 (uri (bioconductor-uri "BiocGenerics" version))
1125 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
1127 `((upstream-name . "BiocGenerics")))
1128 (build-system r-build-system)
1129 (home-page "https://bioconductor.org/packages/BiocGenerics")
1130 (synopsis "S4 generic functions for Bioconductor")
1132 "This package provides S4 generic functions needed by many Bioconductor
1134 (license license:artistic2.0)))
1136 (define-public r-coverageview
1138 (name "r-coverageview")
1142 (uri (bioconductor-uri "CoverageView" version))
1145 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
1146 (build-system r-build-system)
1148 `(("r-s4vectors" ,r-s4vectors)
1149 ("r-iranges" ,r-iranges)
1150 ("r-genomicranges" ,r-genomicranges)
1151 ("r-genomicalignments" ,r-genomicalignments)
1152 ("r-rtracklayer" ,r-rtracklayer)
1153 ("r-rsamtools" ,r-rsamtools)))
1154 (home-page "https://bioconductor.org/packages/CoverageView/")
1155 (synopsis "Coverage visualization package for R")
1156 (description "This package provides a framework for the visualization of
1157 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1158 be also used for genome-wide nucleosome positioning experiments or other
1159 experiment types where it is important to have a framework in order to inspect
1160 how the coverage distributed across the genome.")
1161 (license license:artistic2.0)))
1163 (define-public r-cummerbund
1165 (name "r-cummerbund")
1169 (uri (bioconductor-uri "cummeRbund" version))
1172 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
1173 (build-system r-build-system)
1175 `(("r-biobase" ,r-biobase)
1176 ("r-biocgenerics" ,r-biocgenerics)
1177 ("r-fastcluster" ,r-fastcluster)
1178 ("r-ggplot2" ,r-ggplot2)
1181 ("r-reshape2" ,r-reshape2)
1182 ("r-rsqlite" ,r-rsqlite)
1183 ("r-rtracklayer" ,r-rtracklayer)
1184 ("r-s4vectors" ,r-s4vectors)))
1185 (home-page "https://bioconductor.org/packages/cummeRbund/")
1186 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1187 (description "This package allows for persistent storage, access,
1188 exploration, and manipulation of Cufflinks high-throughput sequencing
1189 data. In addition, provides numerous plotting functions for commonly
1190 used visualizations.")
1191 (license license:artistic2.0)))
1193 (define-public r-bluster
1199 (uri (bioconductor-uri "bluster" version))
1202 "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
1203 (properties `((upstream-name . "bluster")))
1204 (build-system r-build-system)
1206 `(("r-biocneighbors" ,r-biocneighbors)
1207 ("r-biocparallel" ,r-biocparallel)
1208 ("r-igraph" ,r-igraph)
1209 ("r-matrix" ,r-matrix)
1211 ("r-s4vectors" ,r-s4vectors)))
1213 `(("r-knitr" ,r-knitr)))
1214 (home-page "https://bioconductor.org/packages/bluster")
1215 (synopsis "Clustering algorithms for Bioconductor")
1216 (description"This package wraps common clustering algorithms in an easily
1217 extended S4 framework. Backends are implemented for hierarchical, k-means
1218 and graph-based clustering. Several utilities are also provided to compare
1219 and evaluate clustering results.")
1220 (license license:gpl3)))
1222 (define-public r-ideoviz
1228 (uri (bioconductor-uri "IdeoViz" version))
1231 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
1232 (build-system r-build-system)
1234 `(("r-biobase" ,r-biobase)
1235 ("r-iranges" ,r-iranges)
1236 ("r-genomicranges" ,r-genomicranges)
1237 ("r-rcolorbrewer" ,r-rcolorbrewer)
1238 ("r-rtracklayer" ,r-rtracklayer)
1239 ("r-genomeinfodb" ,r-genomeinfodb)))
1240 (home-page "https://bioconductor.org/packages/IdeoViz/")
1241 (synopsis "Plots data along a chromosomal ideogram")
1242 (description "This package provides functions to plot data associated with
1243 arbitrary genomic intervals along chromosomal ideogram.")
1244 (license license:gpl2)))
1246 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
1247 ;; from Bioconductor.
1248 (define-public r-deconstructsigs
1250 (name "r-deconstructsigs")
1254 (uri (cran-uri "deconstructSigs" version))
1257 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
1259 `((upstream-name . "deconstructSigs")))
1260 (build-system r-build-system)
1262 `(("r-bsgenome" ,r-bsgenome)
1263 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1264 ("r-genomeinfodb" ,r-genomeinfodb)
1265 ("r-reshape2" ,r-reshape2)))
1266 (home-page "https://github.com/raerose01/deconstructSigs")
1267 (synopsis "Identifies signatures present in a tumor sample")
1268 (description "This package takes sample information in the form of the
1269 fraction of mutations in each of 96 trinucleotide contexts and identifies
1270 the weighted combination of published signatures that, when summed, most
1271 closely reconstructs the mutational profile.")
1272 (license license:gpl2+)))
1274 ;; This is a CRAN package, but it depends on Bioconductor packages.
1275 (define-public r-nmf
1282 (uri (cran-uri "NMF" version))
1285 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
1286 (properties `((upstream-name . "NMF")))
1287 (build-system r-build-system)
1289 `(("r-cluster" ,r-cluster)
1290 ("r-biobase" ,r-biobase)
1291 ("r-biocmanager" ,r-biocmanager)
1292 ("r-bigmemory" ,r-bigmemory) ; suggested
1293 ("r-synchronicity" ,r-synchronicity) ; suggested
1294 ("r-colorspace" ,r-colorspace)
1295 ("r-digest" ,r-digest)
1296 ("r-doparallel" ,r-doparallel)
1297 ("r-foreach" ,r-foreach)
1298 ("r-ggplot2" ,r-ggplot2)
1299 ("r-gridbase" ,r-gridbase)
1300 ("r-pkgmaker" ,r-pkgmaker)
1301 ("r-rcolorbrewer" ,r-rcolorbrewer)
1302 ("r-registry" ,r-registry)
1303 ("r-reshape2" ,r-reshape2)
1304 ("r-rngtools" ,r-rngtools)
1305 ("r-stringr" ,r-stringr)))
1307 `(("r-knitr" ,r-knitr)))
1308 (home-page "http://renozao.github.io/NMF")
1309 (synopsis "Algorithms and framework for nonnegative matrix factorization")
1311 "This package provides a framework to perform Non-negative Matrix
1312 Factorization (NMF). The package implements a set of already published
1313 algorithms and seeding methods, and provides a framework to test, develop and
1314 plug new or custom algorithms. Most of the built-in algorithms have been
1315 optimized in C++, and the main interface function provides an easy way of
1316 performing parallel computations on multicore machines.")
1317 (license license:gpl2+)))
1319 (define-public r-affycomp
1326 (uri (bioconductor-uri "affycomp" version))
1329 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
1330 (properties `((upstream-name . "affycomp")))
1331 (build-system r-build-system)
1332 (propagated-inputs `(("r-biobase" ,r-biobase)))
1333 (home-page "https://bioconductor.org/packages/affycomp/")
1334 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1336 "The package contains functions that can be used to compare expression
1337 measures for Affymetrix Oligonucleotide Arrays.")
1338 (license license:gpl2+)))
1340 (define-public r-affycompatible
1342 (name "r-affycompatible")
1347 (uri (bioconductor-uri "AffyCompatible" version))
1350 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
1352 `((upstream-name . "AffyCompatible")))
1353 (build-system r-build-system)
1355 `(("r-biostrings" ,r-biostrings)
1356 ("r-rcurl" ,r-rcurl)
1358 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1359 (synopsis "Work with Affymetrix GeneChip files")
1361 "This package provides an interface to Affymetrix chip annotation and
1362 sample attribute files. The package allows an easy way for users to download
1363 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1364 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1365 Command Console} (AGCC)-compatible sample annotation files.")
1366 (license license:artistic2.0)))
1368 (define-public r-affycontam
1370 (name "r-affycontam")
1375 (uri (bioconductor-uri "affyContam" version))
1378 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
1379 (properties `((upstream-name . "affyContam")))
1380 (build-system r-build-system)
1382 `(("r-affy" ,r-affy)
1383 ("r-affydata" ,r-affydata)
1384 ("r-biobase" ,r-biobase)))
1385 (home-page "https://bioconductor.org/packages/affyContam/")
1386 (synopsis "Structured corruption of Affymetrix CEL file data")
1388 "Microarray quality assessment is a major concern of microarray analysts.
1389 This package provides some simple approaches to in silico creation of quality
1390 problems in CEL-level data to help evaluate performance of quality metrics.")
1391 (license license:artistic2.0)))
1393 (define-public r-affycoretools
1395 (name "r-affycoretools")
1400 (uri (bioconductor-uri "affycoretools" version))
1403 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
1404 (properties `((upstream-name . "affycoretools")))
1405 (build-system r-build-system)
1407 `(("r-affy" ,r-affy)
1408 ("r-annotationdbi" ,r-annotationdbi)
1409 ("r-biobase" ,r-biobase)
1410 ("r-biocgenerics" ,r-biocgenerics)
1412 ("r-edger" ,r-edger)
1413 ("r-gcrma" ,r-gcrma)
1414 ("r-glimma" ,r-glimma)
1415 ("r-ggplot2" ,r-ggplot2)
1416 ("r-gostats" ,r-gostats)
1417 ("r-gplots" ,r-gplots)
1418 ("r-hwriter" ,r-hwriter)
1419 ("r-lattice" ,r-lattice)
1420 ("r-limma" ,r-limma)
1421 ("r-oligoclasses" ,r-oligoclasses)
1422 ("r-reportingtools" ,r-reportingtools)
1423 ("r-rsqlite" ,r-rsqlite)
1424 ("r-s4vectors" ,r-s4vectors)
1425 ("r-xtable" ,r-xtable)))
1427 `(("r-knitr" ,r-knitr)))
1428 (home-page "https://bioconductor.org/packages/affycoretools/")
1429 (synopsis "Functions for analyses with Affymetrix GeneChips")
1431 "This package provides various wrapper functions that have been written
1432 to streamline the more common analyses that a Biostatistician might see.")
1433 (license license:artistic2.0)))
1435 (define-public r-affxparser
1437 (name "r-affxparser")
1442 (uri (bioconductor-uri "affxparser" version))
1445 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
1446 (properties `((upstream-name . "affxparser")))
1447 (build-system r-build-system)
1448 (home-page "https://github.com/HenrikBengtsson/affxparser")
1449 (synopsis "Affymetrix File Parsing SDK")
1451 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1452 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1453 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1454 are supported. Currently, there are methods for reading @dfn{chip definition
1455 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1456 either in full or in part. For example, probe signals from a few probesets
1457 can be extracted very quickly from a set of CEL files into a convenient list
1459 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1461 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1463 (define-public r-annotate
1470 (uri (bioconductor-uri "annotate" version))
1473 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
1474 (build-system r-build-system)
1476 `(("r-annotationdbi" ,r-annotationdbi)
1477 ("r-biobase" ,r-biobase)
1478 ("r-biocgenerics" ,r-biocgenerics)
1482 ("r-xtable" ,r-xtable)))
1484 "https://bioconductor.org/packages/annotate")
1485 (synopsis "Annotation for microarrays")
1486 (description "This package provides R environments for the annotation of
1488 (license license:artistic2.0)))
1490 (define-public r-annotationforge
1492 (name "r-annotationforge")
1497 (uri (bioconductor-uri "AnnotationForge" version))
1500 "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
1502 `((upstream-name . "AnnotationForge")))
1503 (build-system r-build-system)
1505 `(("r-annotationdbi" ,r-annotationdbi)
1506 ("r-biobase" ,r-biobase)
1507 ("r-biocgenerics" ,r-biocgenerics)
1509 ("r-rcurl" ,r-rcurl)
1510 ("r-rsqlite" ,r-rsqlite)
1511 ("r-s4vectors" ,r-s4vectors)
1514 `(("r-knitr" ,r-knitr)))
1515 (home-page "https://bioconductor.org/packages/AnnotationForge")
1516 (synopsis "Code for building annotation database packages")
1518 "This package provides code for generating Annotation packages and their
1519 databases. Packages produced are intended to be used with AnnotationDbi.")
1520 (license license:artistic2.0)))
1522 (define-public r-deseq2
1529 (uri (bioconductor-uri "DESeq2" version))
1532 "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
1533 (properties `((upstream-name . "DESeq2")))
1534 (build-system r-build-system)
1536 `(("r-biobase" ,r-biobase)
1537 ("r-biocgenerics" ,r-biocgenerics)
1538 ("r-biocparallel" ,r-biocparallel)
1539 ("r-genefilter" ,r-genefilter)
1540 ("r-geneplotter" ,r-geneplotter)
1541 ("r-genomicranges" ,r-genomicranges)
1542 ("r-ggplot2" ,r-ggplot2)
1543 ("r-iranges" ,r-iranges)
1544 ("r-locfit" ,r-locfit)
1546 ("r-rcpparmadillo" ,r-rcpparmadillo)
1547 ("r-s4vectors" ,r-s4vectors)
1548 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1550 `(("r-knitr" ,r-knitr)))
1551 (home-page "https://bioconductor.org/packages/DESeq2")
1552 (synopsis "Differential gene expression analysis")
1554 "This package provides functions to estimate variance-mean dependence in
1555 count data from high-throughput nucleotide sequencing assays and test for
1556 differential expression based on a model using the negative binomial
1558 (license license:lgpl3+)))
1560 (define-public r-dexseq
1567 (uri (bioconductor-uri "DEXSeq" version))
1570 "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
1571 (properties `((upstream-name . "DEXSeq")))
1572 (build-system r-build-system)
1574 `(("r-annotationdbi" ,r-annotationdbi)
1575 ("r-biobase" ,r-biobase)
1576 ("r-biocgenerics" ,r-biocgenerics)
1577 ("r-biocparallel" ,r-biocparallel)
1578 ("r-biomart" ,r-biomart)
1579 ("r-deseq2" ,r-deseq2)
1580 ("r-genefilter" ,r-genefilter)
1581 ("r-geneplotter" ,r-geneplotter)
1582 ("r-genomicranges" ,r-genomicranges)
1583 ("r-hwriter" ,r-hwriter)
1584 ("r-iranges" ,r-iranges)
1585 ("r-rcolorbrewer" ,r-rcolorbrewer)
1586 ("r-rsamtools" ,r-rsamtools)
1587 ("r-s4vectors" ,r-s4vectors)
1588 ("r-statmod" ,r-statmod)
1589 ("r-stringr" ,r-stringr)
1590 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1592 `(("r-knitr" ,r-knitr)))
1593 (home-page "https://bioconductor.org/packages/DEXSeq")
1594 (synopsis "Inference of differential exon usage in RNA-Seq")
1596 "This package is focused on finding differential exon usage using RNA-seq
1597 exon counts between samples with different experimental designs. It provides
1598 functions that allows the user to make the necessary statistical tests based
1599 on a model that uses the negative binomial distribution to estimate the
1600 variance between biological replicates and generalized linear models for
1601 testing. The package also provides functions for the visualization and
1602 exploration of the results.")
1603 (license license:gpl3+)))
1605 (define-public r-genefilter
1607 (name "r-genefilter")
1612 (uri (bioconductor-uri "genefilter" version))
1615 "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
1616 (build-system r-build-system)
1618 `(("gfortran" ,gfortran)
1619 ("r-knitr" ,r-knitr)))
1621 `(("r-annotate" ,r-annotate)
1622 ("r-annotationdbi" ,r-annotationdbi)
1623 ("r-biobase" ,r-biobase)
1624 ("r-biocgenerics" ,r-biocgenerics)
1625 ("r-survival" ,r-survival)))
1626 (home-page "https://bioconductor.org/packages/genefilter")
1627 (synopsis "Filter genes from high-throughput experiments")
1629 "This package provides basic functions for filtering genes from
1630 high-throughput sequencing experiments.")
1631 (license license:artistic2.0)))
1633 (define-public r-hpar
1640 (uri (bioconductor-uri "hpar" version))
1643 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
1644 (build-system r-build-system)
1646 `(("r-knitr" ,r-knitr)))
1647 (home-page "https://bioconductor.org/packages/hpar/")
1648 (synopsis "Human Protein Atlas in R")
1649 (description "This package provides a simple interface to and data from
1650 the Human Protein Atlas project.")
1651 (license license:artistic2.0)))
1653 (define-public r-regioner
1660 (uri (bioconductor-uri "regioneR" version))
1663 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
1664 (properties `((upstream-name . "regioneR")))
1665 (build-system r-build-system)
1667 `(("r-biostrings" ,r-biostrings)
1668 ("r-bsgenome" ,r-bsgenome)
1669 ("r-genomeinfodb" ,r-genomeinfodb)
1670 ("r-genomicranges" ,r-genomicranges)
1671 ("r-iranges" ,r-iranges)
1672 ("r-memoise" ,r-memoise)
1673 ("r-rtracklayer" ,r-rtracklayer)
1674 ("r-s4vectors" ,r-s4vectors)))
1676 `(("r-knitr" ,r-knitr)))
1677 (home-page "https://bioconductor.org/packages/regioneR/")
1678 (synopsis "Association analysis of genomic regions")
1679 (description "This package offers a statistical framework based on
1680 customizable permutation tests to assess the association between genomic
1681 region sets and other genomic features.")
1682 (license license:artistic2.0)))
1684 (define-public r-reportingtools
1686 (name "r-reportingtools")
1691 (uri (bioconductor-uri "ReportingTools" version))
1694 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
1696 `((upstream-name . "ReportingTools")))
1697 (build-system r-build-system)
1699 `(("r-annotate" ,r-annotate)
1700 ("r-annotationdbi" ,r-annotationdbi)
1701 ("r-biobase" ,r-biobase)
1702 ("r-biocgenerics" ,r-biocgenerics)
1703 ("r-category" ,r-category)
1704 ("r-deseq2" ,r-deseq2)
1705 ("r-edger" ,r-edger)
1706 ("r-ggbio" ,r-ggbio)
1707 ("r-ggplot2" ,r-ggplot2)
1708 ("r-gostats" ,r-gostats)
1709 ("r-gseabase" ,r-gseabase)
1710 ("r-hwriter" ,r-hwriter)
1711 ("r-iranges" ,r-iranges)
1712 ("r-knitr" ,r-knitr)
1713 ("r-lattice" ,r-lattice)
1714 ("r-limma" ,r-limma)
1715 ("r-pfam-db" ,r-pfam-db)
1716 ("r-r-utils" ,r-r-utils)
1719 `(("r-knitr" ,r-knitr)))
1720 (home-page "https://bioconductor.org/packages/ReportingTools/")
1721 (synopsis "Tools for making reports in various formats")
1723 "The ReportingTools package enables users to easily display reports of
1724 analysis results generated from sources such as microarray and sequencing
1725 data. The package allows users to create HTML pages that may be viewed on a
1726 web browser, or in other formats. Users can generate tables with sortable and
1727 filterable columns, make and display plots, and link table entries to other
1728 data sources such as NCBI or larger plots within the HTML page. Using the
1729 package, users can also produce a table of contents page to link various
1730 reports together for a particular project that can be viewed in a web
1732 (license license:artistic2.0)))
1734 (define-public r-geneplotter
1736 (name "r-geneplotter")
1741 (uri (bioconductor-uri "geneplotter" version))
1744 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
1745 (build-system r-build-system)
1747 `(("r-annotate" ,r-annotate)
1748 ("r-annotationdbi" ,r-annotationdbi)
1749 ("r-biobase" ,r-biobase)
1750 ("r-biocgenerics" ,r-biocgenerics)
1751 ("r-lattice" ,r-lattice)
1752 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1753 (home-page "https://bioconductor.org/packages/geneplotter")
1754 (synopsis "Graphics functions for genomic data")
1756 "This package provides functions for plotting genomic data.")
1757 (license license:artistic2.0)))
1759 (define-public r-oligoclasses
1761 (name "r-oligoclasses")
1766 (uri (bioconductor-uri "oligoClasses" version))
1769 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
1770 (properties `((upstream-name . "oligoClasses")))
1771 (build-system r-build-system)
1773 `(("r-affyio" ,r-affyio)
1774 ("r-biobase" ,r-biobase)
1775 ("r-biocgenerics" ,r-biocgenerics)
1776 ("r-biocmanager" ,r-biocmanager)
1777 ("r-biostrings" ,r-biostrings)
1780 ("r-foreach" ,r-foreach)
1781 ("r-genomicranges" ,r-genomicranges)
1782 ("r-iranges" ,r-iranges)
1783 ("r-rsqlite" ,r-rsqlite)
1784 ("r-s4vectors" ,r-s4vectors)
1785 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1786 (home-page "https://bioconductor.org/packages/oligoClasses/")
1787 (synopsis "Classes for high-throughput arrays")
1789 "This package contains class definitions, validity checks, and
1790 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1792 (license license:gpl2+)))
1794 (define-public r-oligo
1801 (uri (bioconductor-uri "oligo" version))
1804 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
1805 (properties `((upstream-name . "oligo")))
1806 (build-system r-build-system)
1807 (inputs `(("zlib" ,zlib)))
1809 `(("r-affxparser" ,r-affxparser)
1810 ("r-affyio" ,r-affyio)
1811 ("r-biobase" ,r-biobase)
1812 ("r-biocgenerics" ,r-biocgenerics)
1813 ("r-biostrings" ,r-biostrings)
1816 ("r-oligoclasses" ,r-oligoclasses)
1817 ("r-preprocesscore" ,r-preprocesscore)
1818 ("r-rsqlite" ,r-rsqlite)
1819 ("r-zlibbioc" ,r-zlibbioc)))
1821 `(("r-knitr" ,r-knitr)))
1822 (home-page "https://bioconductor.org/packages/oligo/")
1823 (synopsis "Preprocessing tools for oligonucleotide arrays")
1825 "This package provides a package to analyze oligonucleotide
1826 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1827 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1828 (license license:lgpl2.0+)))
1830 (define-public r-qvalue
1837 (uri (bioconductor-uri "qvalue" version))
1840 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
1841 (build-system r-build-system)
1843 `(("r-ggplot2" ,r-ggplot2)
1844 ("r-reshape2" ,r-reshape2)))
1846 `(("r-knitr" ,r-knitr)))
1847 (home-page "https://github.com/StoreyLab/qvalue")
1848 (synopsis "Q-value estimation for false discovery rate control")
1850 "This package takes a list of p-values resulting from the simultaneous
1851 testing of many hypotheses and estimates their q-values and local @dfn{false
1852 discovery rate} (FDR) values. The q-value of a test measures the proportion
1853 of false positives incurred when that particular test is called significant.
1854 The local FDR measures the posterior probability the null hypothesis is true
1855 given the test's p-value. Various plots are automatically generated, allowing
1856 one to make sensible significance cut-offs. The software can be applied to
1857 problems in genomics, brain imaging, astrophysics, and data mining.")
1858 ;; Any version of the LGPL.
1859 (license license:lgpl3+)))
1861 (define r-rcppnumerical
1863 (name "r-rcppnumerical")
1867 (uri (cran-uri "RcppNumerical" version))
1870 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
1871 (properties `((upstream-name . "RcppNumerical")))
1872 (build-system r-build-system)
1874 `(("r-rcpp" ,r-rcpp)
1875 ("r-rcppeigen" ,r-rcppeigen)))
1877 `(("r-knitr" ,r-knitr)))
1878 (home-page "https://github.com/yixuan/RcppNumerical")
1879 (synopsis "Rcpp integration for numerical computing libraries")
1880 (description "This package provides a collection of open source libraries
1881 for numerical computing (numerical integration, optimization, etc.) and their
1882 integration with @code{Rcpp}.")
1883 (license license:gpl2+)))
1885 (define-public r-apeglm
1891 (uri (bioconductor-uri "apeglm" version))
1894 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
1895 (properties `((upstream-name . "apeglm")))
1896 (build-system r-build-system)
1898 `(("r-emdbook" ,r-emdbook)
1899 ("r-genomicranges" ,r-genomicranges)
1901 ("r-rcppeigen" ,r-rcppeigen)
1902 ("r-rcppnumerical" ,r-rcppnumerical)
1903 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1904 (native-inputs `(("r-knitr" ,r-knitr)))
1905 (home-page "https://bioconductor.org/packages/apeglm")
1906 (synopsis "Approximate posterior estimation for GLM coefficients")
1907 (description "This package provides Bayesian shrinkage estimators for
1908 effect sizes for a variety of GLM models, using approximation of the
1909 posterior for individual coefficients.")
1910 (license license:gpl2)))
1912 (define-public r-greylistchip
1914 (name "r-greylistchip")
1918 (uri (bioconductor-uri "GreyListChIP" version))
1921 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
1922 (properties `((upstream-name . "GreyListChIP")))
1923 (build-system r-build-system)
1925 `(("r-bsgenome" ,r-bsgenome)
1926 ("r-genomeinfodb" ,r-genomeinfodb)
1927 ("r-genomicalignments" ,r-genomicalignments)
1928 ("r-genomicranges" ,r-genomicranges)
1930 ("r-rsamtools" ,r-rsamtools)
1931 ("r-rtracklayer" ,r-rtracklayer)
1932 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1933 (home-page "https://bioconductor.org/packages/GreyListChIP")
1934 (synopsis "Greylist artefact regions based on ChIP inputs")
1935 (description "This package identifies regions of ChIP experiments with high
1936 signal in the input, that lead to spurious peaks during peak calling.")
1937 (license license:artistic2.0)))
1939 (define-public r-diffbind
1946 (uri (bioconductor-uri "DiffBind" version))
1949 "0kxn59v93hl5pq8d156lnbz0sslpnxyjcfrvq2gzgd91sd587qmn"))))
1950 (properties `((upstream-name . "DiffBind")))
1951 (build-system r-build-system)
1953 `(("r-amap" ,r-amap)
1954 ("r-apeglm" ,r-apeglm)
1956 ("r-biocparallel" ,r-biocparallel)
1957 ("r-deseq2" ,r-deseq2)
1958 ("r-dplyr" ,r-dplyr)
1959 ("r-genomicalignments" ,r-genomicalignments)
1960 ("r-genomicranges" ,r-genomicranges)
1961 ("r-ggplot2" ,r-ggplot2)
1962 ("r-ggrepel" ,r-ggrepel)
1963 ("r-gplots" ,r-gplots)
1964 ("r-greylistchip" ,r-greylistchip)
1965 ("r-iranges" ,r-iranges)
1966 ("r-lattice" ,r-lattice)
1967 ("r-limma" ,r-limma)
1968 ("r-locfit" ,r-locfit)
1969 ("r-rcolorbrewer" , r-rcolorbrewer)
1971 ("r-rhtslib" ,r-rhtslib)
1972 ("r-rsamtools" ,r-rsamtools)
1973 ("r-s4vectors" ,r-s4vectors)
1974 ("r-summarizedexperiment" ,r-summarizedexperiment)
1975 ("r-systempiper" ,r-systempiper)))
1976 (home-page "https://bioconductor.org/packages/DiffBind")
1977 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1979 "This package computes differentially bound sites from multiple
1980 ChIP-seq experiments using affinity (quantitative) data. Also enables
1981 occupancy (overlap) analysis and plotting functions.")
1982 (license license:artistic2.0)))
1984 (define-public r-ripseeker
1986 (name "r-ripseeker")
1991 (uri (bioconductor-uri "RIPSeeker" version))
1994 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1995 (properties `((upstream-name . "RIPSeeker")))
1996 (build-system r-build-system)
1998 `(("r-s4vectors" ,r-s4vectors)
1999 ("r-iranges" ,r-iranges)
2000 ("r-genomicranges" ,r-genomicranges)
2001 ("r-summarizedexperiment" ,r-summarizedexperiment)
2002 ("r-rsamtools" ,r-rsamtools)
2003 ("r-genomicalignments" ,r-genomicalignments)
2004 ("r-rtracklayer" ,r-rtracklayer)))
2005 (home-page "https://bioconductor.org/packages/RIPSeeker")
2007 "Identifying protein-associated transcripts from RIP-seq experiments")
2009 "This package infers and discriminates RIP peaks from RIP-seq alignments
2010 using two-state HMM with negative binomial emission probability. While
2011 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
2012 a suite of bioinformatics tools integrated within this self-contained software
2013 package comprehensively addressing issues ranging from post-alignments
2014 processing to visualization and annotation.")
2015 (license license:gpl2)))
2017 (define-public r-multtest
2024 (uri (bioconductor-uri "multtest" version))
2027 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
2028 (build-system r-build-system)
2030 `(("r-survival" ,r-survival)
2031 ("r-biocgenerics" ,r-biocgenerics)
2032 ("r-biobase" ,r-biobase)
2033 ("r-mass" ,r-mass)))
2034 (home-page "https://bioconductor.org/packages/multtest")
2035 (synopsis "Resampling-based multiple hypothesis testing")
2037 "This package can do non-parametric bootstrap and permutation
2038 resampling-based multiple testing procedures (including empirical Bayes
2039 methods) for controlling the family-wise error rate (FWER), generalized
2040 family-wise error rate (gFWER), tail probability of the proportion of
2041 false positives (TPPFP), and false discovery rate (FDR). Several choices
2042 of bootstrap-based null distribution are implemented (centered, centered
2043 and scaled, quantile-transformed). Single-step and step-wise methods are
2044 available. Tests based on a variety of T- and F-statistics (including
2045 T-statistics based on regression parameters from linear and survival models
2046 as well as those based on correlation parameters) are included. When probing
2047 hypotheses with T-statistics, users may also select a potentially faster null
2048 distribution which is multivariate normal with mean zero and variance
2049 covariance matrix derived from the vector influence function. Results are
2050 reported in terms of adjusted P-values, confidence regions and test statistic
2051 cutoffs. The procedures are directly applicable to identifying differentially
2052 expressed genes in DNA microarray experiments.")
2053 (license license:lgpl3)))
2055 (define-public r-graph
2061 (uri (bioconductor-uri "graph" version))
2064 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
2065 (build-system r-build-system)
2067 `(("r-biocgenerics" ,r-biocgenerics)))
2068 (home-page "https://bioconductor.org/packages/graph")
2069 (synopsis "Handle graph data structures in R")
2071 "This package implements some simple graph handling capabilities for R.")
2072 (license license:artistic2.0)))
2074 ;; This is a CRAN package, but it depends on a Bioconductor package.
2075 (define-public r-ggm
2082 (uri (cran-uri "ggm" version))
2085 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
2086 (properties `((upstream-name . "ggm")))
2087 (build-system r-build-system)
2089 `(("r-graph" ,r-graph)
2090 ("r-igraph" ,r-igraph)))
2091 (home-page "https://cran.r-project.org/package=ggm")
2092 (synopsis "Functions for graphical Markov models")
2094 "This package provides functions and datasets for maximum likelihood
2095 fitting of some classes of graphical Markov models.")
2096 (license license:gpl2+)))
2098 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
2099 (define-public r-perfmeas
2106 (uri (cran-uri "PerfMeas" version))
2109 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
2110 (properties `((upstream-name . "PerfMeas")))
2111 (build-system r-build-system)
2113 `(("r-graph" ,r-graph)
2114 ("r-limma" ,r-limma)
2115 ("r-rbgl" ,r-rbgl)))
2116 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
2117 (synopsis "Performance measures for ranking and classification tasks")
2119 "This package implements different performance measures for
2120 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
2121 a given recall, F-score for single and multiple classes are available.")
2122 (license license:gpl2+)))
2124 ;; This is a CRAN package, but it depends on a Bioconductor package.
2125 (define-public r-codedepends
2127 (name "r-codedepends")
2132 (uri (cran-uri "CodeDepends" version))
2135 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
2136 (properties `((upstream-name . "CodeDepends")))
2137 (build-system r-build-system)
2139 `(("r-codetools" ,r-codetools)
2140 ("r-graph" ,r-graph)
2142 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2143 (synopsis "Analysis of R code for reproducible research and code comprehension")
2145 "This package provides tools for analyzing R expressions or blocks of
2146 code and determining the dependencies between them. It focuses on R scripts,
2147 but can be used on the bodies of functions. There are many facilities
2148 including the ability to summarize or get a high-level view of code,
2149 determining dependencies between variables, code improvement suggestions.")
2150 ;; Any version of the GPL
2151 (license (list license:gpl2+ license:gpl3+))))
2153 (define-public r-chippeakanno
2155 (name "r-chippeakanno")
2160 (uri (bioconductor-uri "ChIPpeakAnno" version))
2163 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
2164 (properties `((upstream-name . "ChIPpeakAnno")))
2165 (build-system r-build-system)
2167 `(("r-annotationdbi" ,r-annotationdbi)
2168 ("r-biocgenerics" ,r-biocgenerics)
2169 ("r-biomart" ,r-biomart)
2170 ("r-biostrings" ,r-biostrings)
2172 ("r-ensembldb" ,r-ensembldb)
2173 ("r-genomeinfodb" ,r-genomeinfodb)
2174 ("r-genomicalignments" ,r-genomicalignments)
2175 ("r-genomicfeatures" ,r-genomicfeatures)
2176 ("r-genomicranges" ,r-genomicranges)
2177 ("r-ggplot2" ,r-ggplot2)
2178 ("r-graph" ,r-graph)
2179 ("r-iranges" ,r-iranges)
2180 ("r-keggrest" ,r-keggrest)
2181 ("r-matrixstats" ,r-matrixstats)
2182 ("r-multtest" ,r-multtest)
2184 ("r-regioner" ,r-regioner)
2185 ("r-rsamtools" ,r-rsamtools)
2186 ("r-rtracklayer" ,r-rtracklayer)
2187 ("r-s4vectors" ,r-s4vectors)
2188 ("r-summarizedexperiment" ,r-summarizedexperiment)
2189 ("r-venndiagram" ,r-venndiagram)))
2191 `(("r-knitr" ,r-knitr)))
2192 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2193 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2195 "The package includes functions to retrieve the sequences around the peak,
2196 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2197 custom features such as most conserved elements and other transcription factor
2198 binding sites supplied by users. Starting 2.0.5, new functions have been added
2199 for finding the peaks with bi-directional promoters with summary statistics
2200 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2201 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2202 enrichedGO (addGeneIDs).")
2203 (license license:gpl2+)))
2205 (define-public r-matrixgenerics
2207 (name "r-matrixgenerics")
2211 (uri (bioconductor-uri "MatrixGenerics" version))
2214 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
2216 `((upstream-name . "MatrixGenerics")))
2217 (build-system r-build-system)
2219 `(("r-matrixstats" ,r-matrixstats)))
2220 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2221 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2223 "This package provides S4 generic functions modeled after the
2224 @code{matrixStats} API for alternative matrix implementations. Packages with
2225 alternative matrix implementation can depend on this package and implement the
2226 generic functions that are defined here for a useful set of row and column
2227 summary statistics. Other package developers can import this package and
2228 handle a different matrix implementations without worrying about
2229 incompatibilities.")
2230 (license license:artistic2.0)))
2232 (define-public r-marray
2238 (uri (bioconductor-uri "marray" version))
2240 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
2241 (build-system r-build-system)
2243 `(("r-limma" ,r-limma)))
2244 (home-page "https://bioconductor.org/packages/marray")
2245 (synopsis "Exploratory analysis for two-color spotted microarray data")
2246 (description "This package contains class definitions for two-color spotted
2247 microarray data. It also includes functions for data input, diagnostic plots,
2248 normalization and quality checking.")
2249 (license license:lgpl2.0+)))
2251 (define-public r-cghbase
2257 (uri (bioconductor-uri "CGHbase" version))
2259 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
2260 (properties `((upstream-name . "CGHbase")))
2261 (build-system r-build-system)
2263 `(("r-biobase" ,r-biobase)
2264 ("r-marray" ,r-marray)))
2265 (home-page "https://bioconductor.org/packages/CGHbase")
2266 (synopsis "Base functions and classes for arrayCGH data analysis")
2267 (description "This package contains functions and classes that are needed by
2268 the @code{arrayCGH} packages.")
2269 (license license:gpl2+)))
2271 (define-public r-cghcall
2277 (uri (bioconductor-uri "CGHcall" version))
2279 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
2280 (properties `((upstream-name . "CGHcall")))
2281 (build-system r-build-system)
2283 `(("r-biobase" ,r-biobase)
2284 ("r-cghbase" ,r-cghbase)
2285 ("r-impute" ,r-impute)
2286 ("r-dnacopy" ,r-dnacopy)
2287 ("r-snowfall" ,r-snowfall)))
2288 (home-page "https://bioconductor.org/packages/CGHcall")
2289 (synopsis "Base functions and classes for arrayCGH data analysis")
2290 (description "This package contains functions and classes that are needed by
2291 @code{arrayCGH} packages.")
2292 (license license:gpl2+)))
2294 (define-public r-qdnaseq
2300 (uri (bioconductor-uri "QDNAseq" version))
2302 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
2303 (properties `((upstream-name . "QDNAseq")))
2304 (build-system r-build-system)
2306 `(("r-biobase" ,r-biobase)
2307 ("r-cghbase" ,r-cghbase)
2308 ("r-cghcall" ,r-cghcall)
2309 ("r-dnacopy" ,r-dnacopy)
2310 ("r-future" ,r-future)
2311 ("r-future-apply" ,r-future-apply)
2312 ("r-genomicranges" ,r-genomicranges)
2313 ("r-iranges" ,r-iranges)
2314 ("r-matrixstats" ,r-matrixstats)
2315 ("r-r-utils" ,r-r-utils)
2316 ("r-rsamtools" ,r-rsamtools)))
2317 (home-page "https://bioconductor.org/packages/QDNAseq")
2318 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2319 (description "The genome is divided into non-overlapping fixed-sized bins,
2320 number of sequence reads in each counted, adjusted with a simultaneous
2321 two-dimensional loess correction for sequence mappability and GC content, and
2322 filtered to remove spurious regions in the genome. Downstream steps of
2323 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2325 (license license:gpl2+)))
2327 (define-public r-bayseq
2334 (uri (bioconductor-uri "baySeq" version))
2337 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
2338 (properties `((upstream-name . "baySeq")))
2339 (build-system r-build-system)
2341 `(("r-abind" ,r-abind)
2342 ("r-edger" ,r-edger)
2343 ("r-genomicranges" ,r-genomicranges)))
2344 (home-page "https://bioconductor.org/packages/baySeq/")
2345 (synopsis "Bayesian analysis of differential expression patterns in count data")
2347 "This package identifies differential expression in high-throughput count
2348 data, such as that derived from next-generation sequencing machines,
2349 calculating estimated posterior likelihoods of differential expression (or
2350 more complex hypotheses) via empirical Bayesian methods.")
2351 (license license:gpl3)))
2353 (define-public r-chipcomp
2360 (uri (bioconductor-uri "ChIPComp" version))
2363 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
2364 (properties `((upstream-name . "ChIPComp")))
2365 (build-system r-build-system)
2367 `(("r-biocgenerics" ,r-biocgenerics)
2368 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2369 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2370 ("r-genomeinfodb" ,r-genomeinfodb)
2371 ("r-genomicranges" ,r-genomicranges)
2372 ("r-iranges" ,r-iranges)
2373 ("r-limma" ,r-limma)
2374 ("r-rsamtools" ,r-rsamtools)
2375 ("r-rtracklayer" ,r-rtracklayer)
2376 ("r-s4vectors" ,r-s4vectors)))
2377 (home-page "https://bioconductor.org/packages/ChIPComp")
2378 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2380 "ChIPComp implements a statistical method for quantitative comparison of
2381 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2382 sites across multiple conditions considering matching control in ChIP-seq
2384 ;; Any version of the GPL.
2385 (license license:gpl3+)))
2387 (define-public r-riboprofiling
2389 (name "r-riboprofiling")
2394 (uri (bioconductor-uri "RiboProfiling" version))
2397 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
2398 (properties `((upstream-name . "RiboProfiling")))
2399 (build-system r-build-system)
2401 `(("r-biocgenerics" ,r-biocgenerics)
2402 ("r-biostrings" ,r-biostrings)
2403 ("r-data-table" ,r-data-table)
2404 ("r-genomeinfodb" ,r-genomeinfodb)
2405 ("r-genomicalignments" ,r-genomicalignments)
2406 ("r-genomicfeatures" ,r-genomicfeatures)
2407 ("r-genomicranges" ,r-genomicranges)
2408 ("r-ggbio" ,r-ggbio)
2409 ("r-ggplot2" ,r-ggplot2)
2410 ("r-iranges" ,r-iranges)
2412 ("r-reshape2" ,r-reshape2)
2413 ("r-rsamtools" ,r-rsamtools)
2414 ("r-rtracklayer" ,r-rtracklayer)
2415 ("r-s4vectors" ,r-s4vectors)
2416 ("r-sqldf" ,r-sqldf)))
2418 `(("r-knitr" ,r-knitr)))
2419 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2420 (synopsis "Ribosome profiling data analysis")
2421 (description "Starting with a BAM file, this package provides the
2422 necessary functions for quality assessment, read start position recalibration,
2423 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2424 of count data: pairs, log fold-change, codon frequency and coverage
2425 assessment, principal component analysis on codon coverage.")
2426 (license license:gpl3)))
2428 (define-public r-riboseqr
2435 (uri (bioconductor-uri "riboSeqR" version))
2438 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
2439 (properties `((upstream-name . "riboSeqR")))
2440 (build-system r-build-system)
2442 `(("r-abind" ,r-abind)
2443 ("r-bayseq" ,r-bayseq)
2444 ("r-genomeinfodb" ,r-genomeinfodb)
2445 ("r-genomicranges" ,r-genomicranges)
2446 ("r-iranges" ,r-iranges)
2447 ("r-rsamtools" ,r-rsamtools)
2448 ("r-seqlogo" ,r-seqlogo)))
2449 (home-page "https://bioconductor.org/packages/riboSeqR/")
2450 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2452 "This package provides plotting functions, frameshift detection and
2453 parsing of genetic sequencing data from ribosome profiling experiments.")
2454 (license license:gpl3)))
2456 (define-public r-interactionset
2458 (name "r-interactionset")
2463 (uri (bioconductor-uri "InteractionSet" version))
2466 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
2468 `((upstream-name . "InteractionSet")))
2469 (build-system r-build-system)
2471 `(("r-biocgenerics" ,r-biocgenerics)
2472 ("r-genomeinfodb" ,r-genomeinfodb)
2473 ("r-genomicranges" ,r-genomicranges)
2474 ("r-iranges" ,r-iranges)
2475 ("r-matrix" ,r-matrix)
2477 ("r-s4vectors" ,r-s4vectors)
2478 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2480 `(("r-knitr" ,r-knitr)))
2481 (home-page "https://bioconductor.org/packages/InteractionSet")
2482 (synopsis "Base classes for storing genomic interaction data")
2484 "This package provides the @code{GInteractions},
2485 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2486 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2488 (license license:gpl3)))
2490 (define-public r-genomicinteractions
2492 (name "r-genomicinteractions")
2497 (uri (bioconductor-uri "GenomicInteractions" version))
2500 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
2502 `((upstream-name . "GenomicInteractions")))
2503 (build-system r-build-system)
2505 `(("r-biobase" ,r-biobase)
2506 ("r-biocgenerics" ,r-biocgenerics)
2507 ("r-data-table" ,r-data-table)
2508 ("r-dplyr" ,r-dplyr)
2509 ("r-genomeinfodb" ,r-genomeinfodb)
2510 ("r-genomicranges" ,r-genomicranges)
2511 ("r-ggplot2" ,r-ggplot2)
2512 ("r-gridextra" ,r-gridextra)
2514 ("r-igraph" ,r-igraph)
2515 ("r-interactionset" ,r-interactionset)
2516 ("r-iranges" ,r-iranges)
2517 ("r-rsamtools" ,r-rsamtools)
2518 ("r-rtracklayer" ,r-rtracklayer)
2519 ("r-s4vectors" ,r-s4vectors)
2520 ("r-stringr" ,r-stringr)))
2522 `(("r-knitr" ,r-knitr)))
2523 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2524 (synopsis "R package for handling genomic interaction data")
2526 "This R package provides tools for handling genomic interaction data,
2527 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2528 information and producing various plots and statistics.")
2529 (license license:gpl3)))
2531 (define-public r-ctc
2538 (uri (bioconductor-uri "ctc" version))
2541 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
2542 (build-system r-build-system)
2543 (propagated-inputs `(("r-amap" ,r-amap)))
2544 (home-page "https://bioconductor.org/packages/ctc/")
2545 (synopsis "Cluster and tree conversion")
2547 "This package provides tools for exporting and importing classification
2548 trees and clusters to other programs.")
2549 (license license:gpl2)))
2551 (define-public r-goseq
2558 (uri (bioconductor-uri "goseq" version))
2561 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
2562 (build-system r-build-system)
2564 `(("r-annotationdbi" ,r-annotationdbi)
2565 ("r-biasedurn" ,r-biasedurn)
2566 ("r-biocgenerics" ,r-biocgenerics)
2567 ("r-genelendatabase" ,r-genelendatabase)
2568 ("r-go-db" ,r-go-db)
2569 ("r-mgcv" ,r-mgcv)))
2570 (home-page "https://bioconductor.org/packages/goseq/")
2571 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2573 "This package provides tools to detect Gene Ontology and/or other user
2574 defined categories which are over/under represented in RNA-seq data.")
2575 (license license:lgpl2.0+)))
2577 (define-public r-glimma
2584 (uri (bioconductor-uri "Glimma" version))
2587 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
2588 (properties `((upstream-name . "Glimma")))
2589 (build-system r-build-system)
2591 `(("r-deseq2" ,r-deseq2)
2592 ("r-edger" ,r-edger)
2593 ("r-htmlwidgets" ,r-htmlwidgets)
2594 ("r-jsonlite" ,r-jsonlite)
2595 ("r-limma" ,r-limma)
2596 ("r-s4vectors" ,r-s4vectors)
2597 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2599 `(("r-knitr" ,r-knitr)))
2600 (home-page "https://github.com/Shians/Glimma")
2601 (synopsis "Interactive HTML graphics")
2603 "This package generates interactive visualisations for analysis of
2604 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2605 HTML page. The interactions are built on top of the popular static
2606 representations of analysis results in order to provide additional
2608 (license license:lgpl3)))
2610 (define-public r-rots
2617 (uri (bioconductor-uri "ROTS" version))
2620 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
2621 (properties `((upstream-name . "ROTS")))
2622 (build-system r-build-system)
2624 `(("r-biobase" ,r-biobase)
2625 ("r-rcpp" ,r-rcpp)))
2626 (home-page "https://bioconductor.org/packages/ROTS/")
2627 (synopsis "Reproducibility-Optimized Test Statistic")
2629 "This package provides tools for calculating the
2630 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2632 (license license:gpl2+)))
2634 (define-public r-plgem
2641 (uri (bioconductor-uri "plgem" version))
2644 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
2645 (build-system r-build-system)
2647 `(("r-biobase" ,r-biobase)
2648 ("r-mass" ,r-mass)))
2649 (home-page "http://www.genopolis.it")
2650 (synopsis "Detect differential expression in microarray and proteomics datasets")
2652 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2653 model the variance-versus-mean dependence that exists in a variety of
2654 genome-wide datasets, including microarray and proteomics data. The use of
2655 PLGEM has been shown to improve the detection of differentially expressed
2656 genes or proteins in these datasets.")
2657 (license license:gpl2)))
2659 (define-public r-inspect
2666 (uri (bioconductor-uri "INSPEcT" version))
2669 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
2670 (properties `((upstream-name . "INSPEcT")))
2671 (build-system r-build-system)
2673 `(("r-biobase" ,r-biobase)
2674 ("r-biocgenerics" ,r-biocgenerics)
2675 ("r-biocparallel" ,r-biocparallel)
2676 ("r-deseq2" ,r-deseq2)
2677 ("r-desolve" ,r-desolve)
2678 ("r-gdata" ,r-gdata)
2679 ("r-genomeinfodb" ,r-genomeinfodb)
2680 ("r-genomicalignments" ,r-genomicalignments)
2681 ("r-genomicfeatures" ,r-genomicfeatures)
2682 ("r-genomicranges" ,r-genomicranges)
2683 ("r-iranges" ,r-iranges)
2684 ("r-kernsmooth" ,r-kernsmooth)
2685 ("r-plgem" ,r-plgem)
2687 ("r-rootsolve" ,r-rootsolve)
2688 ("r-rsamtools" ,r-rsamtools)
2689 ("r-rtracklayer" ,r-rtracklayer)
2690 ("r-s4vectors" ,r-s4vectors)
2691 ("r-shiny" ,r-shiny)
2692 ("r-summarizedexperiment" ,r-summarizedexperiment)
2693 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2694 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2696 `(("r-knitr" ,r-knitr)))
2697 (home-page "https://bioconductor.org/packages/INSPEcT")
2698 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2700 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2701 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2702 order to evaluate synthesis, processing and degradation rates and assess via
2703 modeling the rates that determines changes in mature mRNA levels.")
2704 (license license:gpl2)))
2706 (define-public r-dnabarcodes
2708 (name "r-dnabarcodes")
2713 (uri (bioconductor-uri "DNABarcodes" version))
2716 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
2717 (properties `((upstream-name . "DNABarcodes")))
2718 (build-system r-build-system)
2721 ("r-matrix" ,r-matrix)
2722 ("r-rcpp" ,r-rcpp)))
2724 `(("r-knitr" ,r-knitr)))
2725 (home-page "https://bioconductor.org/packages/DNABarcodes")
2726 (synopsis "Create and analyze DNA barcodes")
2728 "This package offers tools to create DNA barcode sets capable of
2729 correcting insertion, deletion, and substitution errors. Existing barcodes
2730 can be analyzed regarding their minimal, maximal and average distances between
2731 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2732 demultiplexed, i.e. assigned to their original reference barcode.")
2733 (license license:gpl2)))
2735 (define-public r-ruvseq
2742 (uri (bioconductor-uri "RUVSeq" version))
2745 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
2746 (properties `((upstream-name . "RUVSeq")))
2747 (build-system r-build-system)
2749 `(("r-biobase" ,r-biobase)
2750 ("r-edaseq" ,r-edaseq)
2751 ("r-edger" ,r-edger)
2752 ("r-mass" ,r-mass)))
2754 `(("r-knitr" ,r-knitr)))
2755 (home-page "https://github.com/drisso/RUVSeq")
2756 (synopsis "Remove unwanted variation from RNA-Seq data")
2758 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2759 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2761 (license license:artistic2.0)))
2763 (define-public r-biocneighbors
2765 (name "r-biocneighbors")
2770 (uri (bioconductor-uri "BiocNeighbors" version))
2773 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
2774 (properties `((upstream-name . "BiocNeighbors")))
2775 (build-system r-build-system)
2777 `(("r-biocparallel" ,r-biocparallel)
2778 ("r-matrix" ,r-matrix)
2780 ("r-rcpphnsw" ,r-rcpphnsw)
2781 ("r-s4vectors" ,r-s4vectors)))
2783 `(("r-knitr" ,r-knitr)))
2784 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2785 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2787 "This package implements exact and approximate methods for nearest
2788 neighbor detection, in a framework that allows them to be easily switched
2789 within Bioconductor packages or workflows. The exact algorithm is implemented
2790 using pre-clustering with the k-means algorithm. Functions are also provided
2791 to search for all neighbors within a given distance. Parallelization is
2792 achieved for all methods using the BiocParallel framework.")
2793 (license license:gpl3)))
2795 (define-public r-biocsingular
2797 (name "r-biocsingular")
2802 (uri (bioconductor-uri "BiocSingular" version))
2805 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
2806 (properties `((upstream-name . "BiocSingular")))
2807 (build-system r-build-system)
2809 `(("r-beachmat" ,r-beachmat)
2810 ("r-biocgenerics" ,r-biocgenerics)
2811 ("r-biocparallel" ,r-biocparallel)
2812 ("r-delayedarray" ,r-delayedarray)
2813 ("r-irlba" ,r-irlba)
2814 ("r-matrix" ,r-matrix)
2817 ("r-s4vectors" ,r-s4vectors)))
2819 `(("r-knitr" ,r-knitr)))
2820 (home-page "https://github.com/LTLA/BiocSingular")
2821 (synopsis "Singular value decomposition for Bioconductor packages")
2823 "This package implements exact and approximate methods for singular value
2824 decomposition and principal components analysis, in a framework that allows
2825 them to be easily switched within Bioconductor packages or workflows. Where
2826 possible, parallelization is achieved using the BiocParallel framework.")
2827 (license license:gpl3)))
2829 (define-public r-destiny
2836 (uri (bioconductor-uri "destiny" version))
2839 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
2840 (build-system r-build-system)
2842 `(("r-biobase" ,r-biobase)
2843 ("r-biocgenerics" ,r-biocgenerics)
2844 ("r-ggplot-multistats" ,r-ggplot-multistats)
2845 ("r-ggplot2" ,r-ggplot2)
2846 ("r-ggthemes" ,r-ggthemes)
2847 ("r-irlba" ,r-irlba)
2848 ("r-knn-covertree" ,r-knn-covertree)
2849 ("r-matrix" ,r-matrix)
2850 ("r-pcamethods" ,r-pcamethods)
2851 ("r-proxy" ,r-proxy)
2853 ("r-rcppeigen" ,r-rcppeigen)
2854 ("r-rcpphnsw" ,r-rcpphnsw)
2855 ("r-rspectra" ,r-rspectra)
2856 ("r-scales" ,r-scales)
2857 ("r-scatterplot3d" ,r-scatterplot3d)
2858 ("r-singlecellexperiment" ,r-singlecellexperiment)
2859 ("r-smoother" ,r-smoother)
2860 ("r-summarizedexperiment" ,r-summarizedexperiment)
2861 ("r-tidyr" ,r-tidyr)
2862 ("r-tidyselect" ,r-tidyselect)
2865 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2866 (home-page "https://bioconductor.org/packages/destiny/")
2867 (synopsis "Create and plot diffusion maps")
2868 (description "This package provides tools to create and plot diffusion
2870 ;; Any version of the GPL
2871 (license license:gpl3+)))
2873 (define-public r-savr
2880 (uri (bioconductor-uri "savR" version))
2883 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
2884 (properties `((upstream-name . "savR")))
2885 (build-system r-build-system)
2887 `(("r-ggplot2" ,r-ggplot2)
2888 ("r-gridextra" ,r-gridextra)
2889 ("r-reshape2" ,r-reshape2)
2890 ("r-scales" ,r-scales)
2892 (home-page "https://github.com/bcalder/savR")
2893 (synopsis "Parse and analyze Illumina SAV files")
2895 "This package provides tools to parse Illumina Sequence Analysis
2896 Viewer (SAV) files, access data, and generate QC plots.")
2897 (license license:agpl3+)))
2899 (define-public r-chipexoqual
2901 (name "r-chipexoqual")
2906 (uri (bioconductor-uri "ChIPexoQual" version))
2909 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
2910 (properties `((upstream-name . "ChIPexoQual")))
2911 (build-system r-build-system)
2913 `(("r-biocparallel" ,r-biocparallel)
2914 ("r-biovizbase" ,r-biovizbase)
2915 ("r-broom" ,r-broom)
2916 ("r-data-table" ,r-data-table)
2917 ("r-dplyr" ,r-dplyr)
2918 ("r-genomeinfodb" ,r-genomeinfodb)
2919 ("r-genomicalignments" ,r-genomicalignments)
2920 ("r-genomicranges" ,r-genomicranges)
2921 ("r-ggplot2" ,r-ggplot2)
2922 ("r-hexbin" ,r-hexbin)
2923 ("r-iranges" ,r-iranges)
2924 ("r-rcolorbrewer" ,r-rcolorbrewer)
2925 ("r-rmarkdown" ,r-rmarkdown)
2926 ("r-rsamtools" ,r-rsamtools)
2927 ("r-s4vectors" ,r-s4vectors)
2928 ("r-scales" ,r-scales)
2929 ("r-viridis" ,r-viridis)))
2931 `(("r-knitr" ,r-knitr)))
2932 (home-page "https://github.com/keleslab/ChIPexoQual")
2933 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2935 "This package provides a quality control pipeline for ChIP-exo/nexus
2937 (license license:gpl2+)))
2939 (define-public r-copynumber
2941 (name "r-copynumber")
2945 (uri (bioconductor-uri "copynumber" version))
2948 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
2949 (build-system r-build-system)
2951 `(("r-s4vectors" ,r-s4vectors)
2952 ("r-iranges" ,r-iranges)
2953 ("r-genomicranges" ,r-genomicranges)
2954 ("r-biocgenerics" ,r-biocgenerics)))
2955 (home-page "https://bioconductor.org/packages/copynumber")
2956 (synopsis "Segmentation of single- and multi-track copy number data")
2958 "This package segments single- and multi-track copy number data by a
2959 penalized least squares regression method.")
2960 (license license:artistic2.0)))
2962 (define-public r-dnacopy
2969 (uri (bioconductor-uri "DNAcopy" version))
2972 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
2973 (properties `((upstream-name . "DNAcopy")))
2974 (build-system r-build-system)
2975 (native-inputs `(("gfortran" ,gfortran)))
2976 (home-page "https://bioconductor.org/packages/DNAcopy")
2977 (synopsis "DNA copy number data analysis")
2979 "This package implements the @dfn{circular binary segmentation} (CBS)
2980 algorithm to segment DNA copy number data and identify genomic regions with
2981 abnormal copy number.")
2982 (license license:gpl2+)))
2984 ;; This is a CRAN package, but it uncharacteristically depends on a
2985 ;; Bioconductor package.
2986 (define-public r-htscluster
2988 (name "r-htscluster")
2993 (uri (cran-uri "HTSCluster" version))
2996 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2997 (properties `((upstream-name . "HTSCluster")))
2998 (build-system r-build-system)
3000 `(("r-capushe" ,r-capushe)
3001 ("r-edger" ,r-edger)
3002 ("r-plotrix" ,r-plotrix)))
3003 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
3004 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
3006 "This package provides a Poisson mixture model is implemented to cluster
3007 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
3008 estimation is performed using either the EM or CEM algorithm, and the slope
3009 heuristics are used for model selection (i.e., to choose the number of
3011 (license license:gpl3+)))
3013 (define-public r-deds
3020 (uri (bioconductor-uri "DEDS" version))
3023 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
3024 (properties `((upstream-name . "DEDS")))
3025 (build-system r-build-system)
3026 (home-page "https://bioconductor.org/packages/DEDS/")
3027 (synopsis "Differential expression via distance summary for microarray data")
3029 "This library contains functions that calculate various statistics of
3030 differential expression for microarray data, including t statistics, fold
3031 change, F statistics, SAM, moderated t and F statistics and B statistics. It
3032 also implements a new methodology called DEDS (Differential Expression via
3033 Distance Summary), which selects differentially expressed genes by integrating
3034 and summarizing a set of statistics using a weighted distance approach.")
3035 ;; Any version of the LGPL.
3036 (license license:lgpl3+)))
3038 ;; This is a CRAN package, but since it depends on a Bioconductor package we
3040 (define-public r-nbpseq
3047 (uri (cran-uri "NBPSeq" version))
3050 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
3051 (properties `((upstream-name . "NBPSeq")))
3052 (build-system r-build-system)
3054 `(("r-qvalue" ,r-qvalue)))
3055 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
3056 (synopsis "Negative binomial models for RNA-Seq data")
3058 "This package provides negative binomial models for two-group comparisons
3059 and regression inferences from RNA-sequencing data.")
3060 (license license:gpl2)))
3062 (define-public r-ebseq
3069 (uri (bioconductor-uri "EBSeq" version))
3072 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3073 (properties `((upstream-name . "EBSeq")))
3074 (build-system r-build-system)
3076 `(("r-blockmodeling" ,r-blockmodeling)
3077 ("r-gplots" ,r-gplots)
3078 ("r-testthat" ,r-testthat)))
3079 (home-page "https://bioconductor.org/packages/EBSeq")
3080 (synopsis "Differential expression analysis of RNA-seq data")
3082 "This package provides tools for differential expression analysis at both
3083 gene and isoform level using RNA-seq data")
3084 (license license:artistic2.0)))
3086 (define-public r-karyoploter
3088 (name "r-karyoploter")
3092 (uri (bioconductor-uri "karyoploteR" version))
3095 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
3096 (build-system r-build-system)
3098 `(("r-annotationdbi" ,r-annotationdbi)
3099 ("r-bamsignals" ,r-bamsignals)
3100 ("r-bezier" ,r-bezier)
3101 ("r-biovizbase" ,r-biovizbase)
3102 ("r-digest" ,r-digest)
3103 ("r-genomeinfodb" ,r-genomeinfodb)
3104 ("r-genomicfeatures" ,r-genomicfeatures)
3105 ("r-genomicranges" ,r-genomicranges)
3106 ("r-iranges" ,r-iranges)
3107 ("r-memoise" ,r-memoise)
3108 ("r-regioner" ,r-regioner)
3109 ("r-rsamtools" ,r-rsamtools)
3110 ("r-rtracklayer" ,r-rtracklayer)
3111 ("r-s4vectors" ,r-s4vectors)
3112 ("r-variantannotation" ,r-variantannotation)))
3114 `(("r-knitr" ,r-knitr)))
3115 (home-page "https://bioconductor.org/packages/karyoploteR/")
3116 (synopsis "Plot customizable linear genomes displaying arbitrary data")
3117 (description "This package creates karyotype plots of arbitrary genomes and
3118 offers a complete set of functions to plot arbitrary data on them. It mimics
3119 many R base graphics functions coupling them with a coordinate change function
3120 automatically mapping the chromosome and data coordinates into the plot
3122 (license license:artistic2.0)))
3124 (define-public r-lpsymphony
3126 (name "r-lpsymphony")
3131 (uri (bioconductor-uri "lpsymphony" version))
3134 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
3135 (build-system r-build-system)
3139 `(("pkg-config" ,pkg-config)
3140 ("r-knitr" ,r-knitr)))
3141 (home-page "https://r-forge.r-project.org/projects/rsymphony")
3142 (synopsis "Symphony integer linear programming solver in R")
3144 "This package was derived from Rsymphony. The package provides an R
3145 interface to SYMPHONY, a linear programming solver written in C++. The main
3146 difference between this package and Rsymphony is that it includes the solver
3147 source code, while Rsymphony expects to find header and library files on the
3148 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3149 to install interface to SYMPHONY.")
3150 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3151 ;; lpsimphony is released under the same terms.
3152 (license license:epl1.0)))
3154 (define-public r-ihw
3161 (uri (bioconductor-uri "IHW" version))
3164 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3165 (properties `((upstream-name . "IHW")))
3166 (build-system r-build-system)
3168 `(("r-biocgenerics" ,r-biocgenerics)
3169 ("r-fdrtool" ,r-fdrtool)
3170 ("r-lpsymphony" ,r-lpsymphony)
3171 ("r-slam" ,r-slam)))
3173 `(("r-knitr" ,r-knitr)))
3174 (home-page "https://bioconductor.org/packages/IHW")
3175 (synopsis "Independent hypothesis weighting")
3177 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3178 procedure that increases power compared to the method of Benjamini and
3179 Hochberg by assigning data-driven weights to each hypothesis. The input to
3180 IHW is a two-column table of p-values and covariates. The covariate can be
3181 any continuous-valued or categorical variable that is thought to be
3182 informative on the statistical properties of each hypothesis test, while it is
3183 independent of the p-value under the null hypothesis.")
3184 (license license:artistic2.0)))
3186 (define-public r-icobra
3193 (uri (bioconductor-uri "iCOBRA" version))
3196 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3197 (properties `((upstream-name . "iCOBRA")))
3198 (build-system r-build-system)
3200 `(("r-dplyr" ,r-dplyr)
3202 ("r-ggplot2" ,r-ggplot2)
3203 ("r-limma" ,r-limma)
3204 ("r-reshape2" ,r-reshape2)
3206 ("r-scales" ,r-scales)
3207 ("r-shiny" ,r-shiny)
3208 ("r-shinybs" ,r-shinybs)
3209 ("r-shinydashboard" ,r-shinydashboard)
3210 ("r-upsetr" ,r-upsetr)))
3212 `(("r-knitr" ,r-knitr)))
3213 (home-page "https://bioconductor.org/packages/iCOBRA")
3214 (synopsis "Comparison and visualization of ranking and assignment methods")
3216 "This package provides functions for calculation and visualization of
3217 performance metrics for evaluation of ranking and binary
3218 classification (assignment) methods. It also contains a Shiny application for
3219 interactive exploration of results.")
3220 (license license:gpl2+)))
3222 (define-public r-mast
3229 (uri (bioconductor-uri "MAST" version))
3232 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
3233 (properties `((upstream-name . "MAST")))
3234 (build-system r-build-system)
3236 `(("r-abind" ,r-abind)
3237 ("r-biobase" ,r-biobase)
3238 ("r-biocgenerics" ,r-biocgenerics)
3239 ("r-data-table" ,r-data-table)
3240 ("r-ggplot2" ,r-ggplot2)
3242 ("r-progress" ,r-progress)
3243 ("r-reshape2" ,r-reshape2)
3244 ("r-s4vectors" ,r-s4vectors)
3245 ("r-singlecellexperiment" ,r-singlecellexperiment)
3246 ("r-stringr" ,r-stringr)
3247 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3249 `(("r-knitr" ,r-knitr)))
3250 (home-page "https://github.com/RGLab/MAST/")
3251 (synopsis "Model-based analysis of single cell transcriptomics")
3253 "This package provides methods and models for handling zero-inflated
3254 single cell assay data.")
3255 (license license:gpl2+)))
3257 (define-public r-monocle
3264 (uri (bioconductor-uri "monocle" version))
3267 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
3268 (build-system r-build-system)
3270 `(("r-biobase" ,r-biobase)
3271 ("r-biocgenerics" ,r-biocgenerics)
3272 ("r-biocviews" ,r-biocviews)
3273 ("r-cluster" ,r-cluster)
3274 ("r-combinat" ,r-combinat)
3275 ("r-ddrtree" ,r-ddrtree)
3276 ("r-densityclust" ,r-densityclust)
3277 ("r-dplyr" ,r-dplyr)
3278 ("r-fastica" ,r-fastica)
3279 ("r-ggplot2" ,r-ggplot2)
3280 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3281 ("r-igraph" ,r-igraph)
3282 ("r-irlba" ,r-irlba)
3283 ("r-limma" ,r-limma)
3285 ("r-matrix" ,r-matrix)
3286 ("r-matrixstats" ,r-matrixstats)
3287 ("r-pheatmap" ,r-pheatmap)
3289 ("r-proxy" ,r-proxy)
3290 ("r-qlcmatrix" ,r-qlcmatrix)
3293 ("r-reshape2" ,r-reshape2)
3294 ("r-rtsne" ,r-rtsne)
3296 ("r-stringr" ,r-stringr)
3297 ("r-tibble" ,r-tibble)
3299 ("r-viridis" ,r-viridis)))
3301 `(("r-knitr" ,r-knitr)))
3302 (home-page "https://bioconductor.org/packages/monocle")
3303 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3305 "Monocle performs differential expression and time-series analysis for
3306 single-cell expression experiments. It orders individual cells according to
3307 progress through a biological process, without knowing ahead of time which
3308 genes define progress through that process. Monocle also performs
3309 differential expression analysis, clustering, visualization, and other useful
3310 tasks on single cell expression data. It is designed to work with RNA-Seq and
3311 qPCR data, but could be used with other types as well.")
3312 (license license:artistic2.0)))
3314 (define-public r-monocle3
3322 (url "https://github.com/cole-trapnell-lab/monocle3")
3324 (file-name (git-file-name name version))
3327 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3328 (build-system r-build-system)
3330 `(("r-biobase" ,r-biobase)
3331 ("r-biocgenerics" ,r-biocgenerics)
3332 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3333 ("r-dplyr" ,r-dplyr)
3334 ("r-ggplot2" ,r-ggplot2)
3335 ("r-ggrepel" ,r-ggrepel)
3337 ("r-htmlwidgets" ,r-htmlwidgets)
3338 ("r-igraph" ,r-igraph)
3339 ("r-irlba" ,r-irlba)
3340 ("r-limma" ,r-limma)
3341 ("r-lmtest" ,r-lmtest)
3343 ("r-matrix" ,r-matrix)
3344 ("r-matrix-utils" ,r-matrix-utils)
3345 ("r-pbapply" ,r-pbapply)
3346 ("r-pbmcapply" ,r-pbmcapply)
3347 ("r-pheatmap" ,r-pheatmap)
3348 ("r-plotly" ,r-plotly)
3350 ("r-proxy" ,r-proxy)
3352 ("r-purrr" ,r-purrr)
3355 ("r-rcppparallel" ,r-rcppparallel)
3356 ("r-reshape2" ,r-reshape2)
3357 ("r-reticulate" ,r-reticulate)
3358 ("r-rhpcblasctl" ,r-rhpcblasctl)
3359 ("r-rtsne" ,r-rtsne)
3360 ("r-shiny" ,r-shiny)
3362 ("r-spdep" ,r-spdep)
3363 ("r-speedglm" ,r-speedglm)
3364 ("r-stringr" ,r-stringr)
3365 ("r-singlecellexperiment" ,r-singlecellexperiment)
3366 ("r-tibble" ,r-tibble)
3367 ("r-tidyr" ,r-tidyr)
3369 ("r-viridis" ,r-viridis)))
3370 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3371 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3373 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3374 (license license:expat)))
3376 (define-public r-noiseq
3383 (uri (bioconductor-uri "NOISeq" version))
3386 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
3387 (properties `((upstream-name . "NOISeq")))
3388 (build-system r-build-system)
3390 `(("r-biobase" ,r-biobase)
3391 ("r-matrix" ,r-matrix)))
3392 (home-page "https://bioconductor.org/packages/NOISeq")
3393 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3395 "This package provides tools to support the analysis of RNA-seq
3396 expression data or other similar kind of data. It provides exploratory plots
3397 to evaluate saturation, count distribution, expression per chromosome, type of
3398 detected features, features length, etc. It also supports the analysis of
3399 differential expression between two experimental conditions with no parametric
3401 (license license:artistic2.0)))
3403 (define-public r-scdd
3410 (uri (bioconductor-uri "scDD" version))
3413 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
3414 (properties `((upstream-name . "scDD")))
3415 (build-system r-build-system)
3418 ("r-biocparallel" ,r-biocparallel)
3419 ("r-ebseq" ,r-ebseq)
3420 ("r-fields" ,r-fields)
3421 ("r-ggplot2" ,r-ggplot2)
3422 ("r-mclust" ,r-mclust)
3423 ("r-outliers" ,r-outliers)
3424 ("r-s4vectors" ,r-s4vectors)
3425 ("r-scran" ,r-scran)
3426 ("r-singlecellexperiment" ,r-singlecellexperiment)
3427 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3429 `(("r-knitr" ,r-knitr)))
3430 (home-page "https://github.com/kdkorthauer/scDD")
3431 (synopsis "Mixture modeling of single-cell RNA-seq data")
3433 "This package implements a method to analyze single-cell RNA-seq data
3434 utilizing flexible Dirichlet Process mixture models. Genes with differential
3435 distributions of expression are classified into several interesting patterns
3436 of differences between two conditions. The package also includes functions
3437 for simulating data with these patterns from negative binomial
3439 (license license:gpl2)))
3441 (define-public r-scone
3448 (uri (bioconductor-uri "scone" version))
3451 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
3452 (build-system r-build-system)
3454 `(("r-aroma-light" ,r-aroma-light)
3455 ("r-biocparallel" ,r-biocparallel)
3457 ("r-class" ,r-class)
3458 ("r-cluster" ,r-cluster)
3459 ("r-compositions" ,r-compositions)
3460 ("r-diptest" ,r-diptest)
3461 ("r-edger" ,r-edger)
3463 ("r-gplots" ,r-gplots)
3464 ("r-hexbin" ,r-hexbin)
3465 ("r-limma" ,r-limma)
3466 ("r-matrixstats" ,r-matrixstats)
3467 ("r-mixtools" ,r-mixtools)
3468 ("r-rarpack" ,r-rarpack)
3469 ("r-rcolorbrewer" ,r-rcolorbrewer)
3470 ("r-rhdf5" ,r-rhdf5)
3471 ("r-ruvseq" ,r-ruvseq)
3472 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3474 `(("r-knitr" ,r-knitr)))
3475 (home-page "https://bioconductor.org/packages/scone")
3476 (synopsis "Single cell overview of normalized expression data")
3478 "SCONE is an R package for comparing and ranking the performance of
3479 different normalization schemes for single-cell RNA-seq and other
3480 high-throughput analyses.")
3481 (license license:artistic2.0)))
3483 (define-public r-geoquery
3490 (uri (bioconductor-uri "GEOquery" version))
3493 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
3494 (properties `((upstream-name . "GEOquery")))
3495 (build-system r-build-system)
3497 `(("r-biobase" ,r-biobase)
3498 ("r-dplyr" ,r-dplyr)
3500 ("r-limma" ,r-limma)
3501 ("r-magrittr" ,r-magrittr)
3502 ("r-readr" ,r-readr)
3503 ("r-tidyr" ,r-tidyr)
3504 ("r-xml2" ,r-xml2)))
3506 `(("r-knitr" ,r-knitr)))
3507 (home-page "https://github.com/seandavi/GEOquery/")
3508 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3510 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3511 microarray data. Given the rich and varied nature of this resource, it is
3512 only natural to want to apply BioConductor tools to these data. GEOquery is
3513 the bridge between GEO and BioConductor.")
3514 (license license:gpl2)))
3516 (define-public r-illuminaio
3518 (name "r-illuminaio")
3523 (uri (bioconductor-uri "illuminaio" version))
3526 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
3527 (build-system r-build-system)
3529 `(("r-base64" ,r-base64)))
3530 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3531 (synopsis "Parse Illumina microarray output files")
3533 "This package provides tools for parsing Illumina's microarray output
3534 files, including IDAT.")
3535 (license license:gpl2)))
3537 (define-public r-siggenes
3544 (uri (bioconductor-uri "siggenes" version))
3547 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
3548 (build-system r-build-system)
3550 `(("r-biobase" ,r-biobase)
3551 ("r-multtest" ,r-multtest)
3552 ("r-scrime" ,r-scrime)))
3553 (home-page "https://bioconductor.org/packages/siggenes/")
3555 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3557 "This package provides tools for the identification of differentially
3558 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3559 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3560 Bayes Analyses of Microarrays} (EBAM).")
3561 (license license:lgpl2.0+)))
3563 (define-public r-bumphunter
3565 (name "r-bumphunter")
3570 (uri (bioconductor-uri "bumphunter" version))
3573 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
3574 (build-system r-build-system)
3576 `(("r-annotationdbi" ,r-annotationdbi)
3577 ("r-biocgenerics" ,r-biocgenerics)
3578 ("r-dorng" ,r-dorng)
3579 ("r-foreach" ,r-foreach)
3580 ("r-genomeinfodb" ,r-genomeinfodb)
3581 ("r-genomicfeatures" ,r-genomicfeatures)
3582 ("r-genomicranges" ,r-genomicranges)
3583 ("r-iranges" ,r-iranges)
3584 ("r-iterators" ,r-iterators)
3585 ("r-limma" ,r-limma)
3586 ("r-locfit" ,r-locfit)
3587 ("r-matrixstats" ,r-matrixstats)
3588 ("r-s4vectors" ,r-s4vectors)))
3589 (home-page "https://github.com/ririzarr/bumphunter")
3590 (synopsis "Find bumps in genomic data")
3592 "This package provides tools for finding bumps in genomic data in order
3593 to identify differentially methylated regions in epigenetic epidemiology
3595 (license license:artistic2.0)))
3597 (define-public r-minfi
3604 (uri (bioconductor-uri "minfi" version))
3607 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
3608 (build-system r-build-system)
3610 `(("r-beanplot" ,r-beanplot)
3611 ("r-biobase" ,r-biobase)
3612 ("r-biocgenerics" ,r-biocgenerics)
3613 ("r-biocparallel" ,r-biocparallel)
3614 ("r-biostrings" ,r-biostrings)
3615 ("r-bumphunter" ,r-bumphunter)
3616 ("r-data-table" ,r-data-table)
3617 ("r-delayedarray" ,r-delayedarray)
3618 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3619 ("r-genefilter" ,r-genefilter)
3620 ("r-genomeinfodb" ,r-genomeinfodb)
3621 ("r-genomicranges" ,r-genomicranges)
3622 ("r-geoquery" ,r-geoquery)
3623 ("r-hdf5array" ,r-hdf5array)
3624 ("r-illuminaio" ,r-illuminaio)
3625 ("r-iranges" ,r-iranges)
3626 ("r-lattice" ,r-lattice)
3627 ("r-limma" ,r-limma)
3629 ("r-mclust" ,r-mclust)
3631 ("r-nor1mix" ,r-nor1mix)
3632 ("r-preprocesscore" ,r-preprocesscore)
3633 ("r-quadprog" ,r-quadprog)
3634 ("r-rcolorbrewer" ,r-rcolorbrewer)
3635 ("r-reshape" ,r-reshape)
3636 ("r-s4vectors" ,r-s4vectors)
3637 ("r-siggenes" ,r-siggenes)
3638 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3640 `(("r-knitr" ,r-knitr)))
3641 (home-page "https://github.com/hansenlab/minfi")
3642 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3644 "This package provides tools to analyze and visualize Illumina Infinium
3645 methylation arrays.")
3646 (license license:artistic2.0)))
3648 (define-public r-methylumi
3650 (name "r-methylumi")
3655 (uri (bioconductor-uri "methylumi" version))
3658 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
3659 (build-system r-build-system)
3661 `(("r-annotate" ,r-annotate)
3662 ("r-annotationdbi" ,r-annotationdbi)
3663 ("r-biobase" ,r-biobase)
3664 ("r-biocgenerics" ,r-biocgenerics)
3665 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3666 ("r-genefilter" ,r-genefilter)
3667 ("r-genomeinfodb" ,r-genomeinfodb)
3668 ("r-genomicranges" ,r-genomicranges)
3669 ("r-ggplot2" ,r-ggplot2)
3670 ("r-illuminaio" ,r-illuminaio)
3671 ("r-iranges" ,r-iranges)
3672 ("r-lattice" ,r-lattice)
3673 ("r-matrixstats" ,r-matrixstats)
3674 ("r-minfi" ,r-minfi)
3675 ("r-reshape2" ,r-reshape2)
3676 ("r-s4vectors" ,r-s4vectors)
3677 ("r-scales" ,r-scales)
3678 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3680 `(("r-knitr" ,r-knitr)))
3681 (home-page "https://bioconductor.org/packages/methylumi")
3682 (synopsis "Handle Illumina methylation data")
3684 "This package provides classes for holding and manipulating Illumina
3685 methylation data. Based on eSet, it can contain MIAME information, sample
3686 information, feature information, and multiple matrices of data. An
3687 \"intelligent\" import function, methylumiR can read the Illumina text files
3688 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3689 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3690 background correction, and quality control features for GoldenGate, Infinium,
3691 and Infinium HD arrays are also included.")
3692 (license license:gpl2)))
3694 (define-public r-lumi
3701 (uri (bioconductor-uri "lumi" version))
3704 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
3705 (build-system r-build-system)
3707 `(("r-affy" ,r-affy)
3708 ("r-annotate" ,r-annotate)
3709 ("r-annotationdbi" ,r-annotationdbi)
3710 ("r-biobase" ,r-biobase)
3712 ("r-genomicfeatures" ,r-genomicfeatures)
3713 ("r-genomicranges" ,r-genomicranges)
3714 ("r-kernsmooth" ,r-kernsmooth)
3715 ("r-lattice" ,r-lattice)
3717 ("r-methylumi" ,r-methylumi)
3719 ("r-nleqslv" ,r-nleqslv)
3720 ("r-preprocesscore" ,r-preprocesscore)
3721 ("r-rsqlite" ,r-rsqlite)))
3722 (home-page "https://bioconductor.org/packages/lumi")
3723 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3725 "The lumi package provides an integrated solution for the Illumina
3726 microarray data analysis. It includes functions of Illumina
3727 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3728 variance stabilization, normalization and gene annotation at the probe level.
3729 It also includes the functions of processing Illumina methylation microarrays,
3730 especially Illumina Infinium methylation microarrays.")
3731 (license license:lgpl2.0+)))
3733 (define-public r-linnorm
3740 (uri (bioconductor-uri "Linnorm" version))
3743 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
3744 (properties `((upstream-name . "Linnorm")))
3745 (build-system r-build-system)
3747 `(("r-amap" ,r-amap)
3748 ("r-apcluster" ,r-apcluster)
3749 ("r-ellipse" ,r-ellipse)
3750 ("r-fastcluster" ,r-fastcluster)
3752 ("r-ggdendro" ,r-ggdendro)
3753 ("r-ggplot2" ,r-ggplot2)
3754 ("r-gmodels" ,r-gmodels)
3755 ("r-igraph" ,r-igraph)
3756 ("r-limma" ,r-limma)
3758 ("r-mclust" ,r-mclust)
3760 ("r-rcpparmadillo" ,r-rcpparmadillo)
3761 ("r-rtsne" ,r-rtsne)
3762 ("r-statmod" ,r-statmod)
3763 ("r-vegan" ,r-vegan)
3766 `(("r-knitr" ,r-knitr)))
3767 (home-page "http://www.jjwanglab.org/Linnorm/")
3768 (synopsis "Linear model and normality based transformation method")
3770 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3771 count data or any large scale count data. It transforms such datasets for
3772 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3773 the following pipelines are implemented:
3776 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3777 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3778 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3779 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3780 @item Differential expression analysis or differential peak detection using
3781 limma (@code{Linnorm.limma})
3782 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3783 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3784 @item Stable gene selection for scRNA-seq data; for users without or who do
3785 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3786 @item Data imputation (@code{Linnorm.DataImput}).
3789 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3790 @code{RnaXSim} function is included for simulating RNA-seq data for the
3791 evaluation of DEG analysis methods.")
3792 (license license:expat)))
3794 (define-public r-ioniser
3801 (uri (bioconductor-uri "IONiseR" version))
3804 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
3805 (properties `((upstream-name . "IONiseR")))
3806 (build-system r-build-system)
3808 `(("r-biocgenerics" ,r-biocgenerics)
3809 ("r-biocparallel" ,r-biocparallel)
3810 ("r-biostrings" ,r-biostrings)
3811 ("r-bit64" ,r-bit64)
3812 ("r-dplyr" ,r-dplyr)
3813 ("r-ggplot2" ,r-ggplot2)
3814 ("r-magrittr" ,r-magrittr)
3815 ("r-rhdf5" ,r-rhdf5)
3816 ("r-shortread" ,r-shortread)
3817 ("r-stringr" ,r-stringr)
3818 ("r-tibble" ,r-tibble)
3819 ("r-tidyr" ,r-tidyr)
3820 ("r-xvector" ,r-xvector)))
3822 `(("r-knitr" ,r-knitr)))
3823 (home-page "https://bioconductor.org/packages/IONiseR/")
3824 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3826 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3827 MinION data. It extracts summary statistics from a set of fast5 files and can
3828 be used either before or after base calling. In addition to standard
3829 summaries of the read-types produced, it provides a number of plots for
3830 visualising metrics relative to experiment run time or spatially over the
3831 surface of a flowcell.")
3832 (license license:expat)))
3834 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3835 (define-public r-gkmsvm
3842 (uri (cran-uri "gkmSVM" version))
3845 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3846 (properties `((upstream-name . "gkmSVM")))
3847 (build-system r-build-system)
3849 `(("r-kernlab" ,r-kernlab)
3852 ("r-seqinr" ,r-seqinr)))
3853 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3854 (synopsis "Gapped-kmer support vector machine")
3856 "This R package provides tools for training gapped-kmer SVM classifiers
3857 for DNA and protein sequences. This package supports several sequence
3858 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3859 (license license:gpl2+)))
3861 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3862 (define-public r-mutoss
3869 (uri (cran-uri "mutoss" version))
3872 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3873 (properties `((upstream-name . "mutoss")))
3874 (build-system r-build-system)
3876 `(("r-multcomp" ,r-multcomp)
3877 ("r-multtest" ,r-multtest)
3878 ("r-mvtnorm" ,r-mvtnorm)
3879 ("r-plotrix" ,r-plotrix)))
3880 (home-page "https://github.com/kornl/mutoss/")
3881 (synopsis "Unified multiple testing procedures")
3883 "This package is designed to ease the application and comparison of
3884 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3885 are standardized and usable by the accompanying mutossGUI package.")
3886 ;; Any version of the GPL.
3887 (license (list license:gpl2+ license:gpl3+))))
3889 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3890 ;; from Bioconductor, so we put it here.
3891 (define-public r-metap
3898 (uri (cran-uri "metap" version))
3901 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3902 (build-system r-build-system)
3904 `(("r-lattice" ,r-lattice)
3905 ("r-mutoss" ,r-mutoss)
3906 ("r-rdpack" ,r-rdpack)
3907 ("r-tfisher" ,r-tfisher)))
3908 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3909 (synopsis "Meta-analysis of significance values")
3911 "The canonical way to perform meta-analysis involves using effect sizes.
3912 When they are not available this package provides a number of methods for
3913 meta-analysis of significance values including the methods of Edgington,
3914 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3915 published results; and a routine for graphical display.")
3916 (license license:gpl2)))
3918 (define-public r-triform
3925 (uri (bioconductor-uri "triform" version))
3928 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3929 (build-system r-build-system)
3931 `(("r-biocgenerics" ,r-biocgenerics)
3932 ("r-iranges" ,r-iranges)
3933 ("r-yaml" ,r-yaml)))
3934 (home-page "https://bioconductor.org/packages/triform/")
3935 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3937 "The Triform algorithm uses model-free statistics to identify peak-like
3938 distributions of TF ChIP sequencing reads, taking advantage of an improved
3939 peak definition in combination with known profile characteristics.")
3940 (license license:gpl2)))
3942 (define-public r-varianttools
3944 (name "r-varianttools")
3949 (uri (bioconductor-uri "VariantTools" version))
3952 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
3953 (properties `((upstream-name . "VariantTools")))
3954 (build-system r-build-system)
3956 `(("r-biobase" ,r-biobase)
3957 ("r-biocgenerics" ,r-biocgenerics)
3958 ("r-biocparallel" ,r-biocparallel)
3959 ("r-biostrings" ,r-biostrings)
3960 ("r-bsgenome" ,r-bsgenome)
3961 ("r-genomeinfodb" ,r-genomeinfodb)
3962 ("r-genomicfeatures" ,r-genomicfeatures)
3963 ("r-genomicranges" ,r-genomicranges)
3964 ("r-iranges" ,r-iranges)
3965 ("r-matrix" ,r-matrix)
3966 ("r-rsamtools" ,r-rsamtools)
3967 ("r-rtracklayer" ,r-rtracklayer)
3968 ("r-s4vectors" ,r-s4vectors)
3969 ("r-variantannotation" ,r-variantannotation)))
3970 (home-page "https://bioconductor.org/packages/VariantTools/")
3971 (synopsis "Tools for exploratory analysis of variant calls")
3973 "Explore, diagnose, and compare variant calls using filters. The
3974 VariantTools package supports a workflow for loading data, calling single
3975 sample variants and tumor-specific somatic mutations or other sample-specific
3976 variant types (e.g., RNA editing). Most of the functions operate on
3977 alignments (BAM files) or datasets of called variants. The user is expected
3978 to have already aligned the reads with a separate tool, e.g., GSNAP via
3980 (license license:artistic2.0)))
3982 (define-public r-heatplus
3989 (uri (bioconductor-uri "Heatplus" version))
3992 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
3993 (properties `((upstream-name . "Heatplus")))
3994 (build-system r-build-system)
3996 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3997 (home-page "https://github.com/alexploner/Heatplus")
3998 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
4000 "This package provides tools to display a rectangular heatmap (intensity
4001 plot) of a data matrix. By default, both samples (columns) and features (row)
4002 of the matrix are sorted according to a hierarchical clustering, and the
4003 corresponding dendrogram is plotted. Optionally, panels with additional
4004 information about samples and features can be added to the plot.")
4005 (license license:gpl2+)))
4007 (define-public r-gosemsim
4014 (uri (bioconductor-uri "GOSemSim" version))
4017 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
4018 (properties `((upstream-name . "GOSemSim")))
4019 (build-system r-build-system)
4021 `(("r-annotationdbi" ,r-annotationdbi)
4022 ("r-go-db" ,r-go-db)
4023 ("r-rcpp" ,r-rcpp)))
4025 `(("r-knitr" ,r-knitr)))
4026 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
4027 (synopsis "GO-terms semantic similarity measures")
4029 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
4030 quantitative ways to compute similarities between genes and gene groups, and
4031 have became important basis for many bioinformatics analysis approaches.
4032 GOSemSim is an R package for semantic similarity computation among GO terms,
4033 sets of GO terms, gene products and gene clusters.")
4034 (license license:artistic2.0)))
4036 (define-public r-anota
4043 (uri (bioconductor-uri "anota" version))
4046 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
4047 (build-system r-build-system)
4049 `(("r-multtest" ,r-multtest)
4050 ("r-qvalue" ,r-qvalue)))
4051 (home-page "https://bioconductor.org/packages/anota/")
4052 (synopsis "Analysis of translational activity")
4054 "Genome wide studies of translational control is emerging as a tool to
4055 study various biological conditions. The output from such analysis is both
4056 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
4057 involved in translation (the actively translating mRNA level) for each mRNA.
4058 The standard analysis of such data strives towards identifying differential
4059 translational between two or more sample classes - i.e. differences in
4060 actively translated mRNA levels that are independent of underlying differences
4061 in cytosolic mRNA levels. This package allows for such analysis using partial
4062 variances and the random variance model. As 10s of thousands of mRNAs are
4063 analyzed in parallel the library performs a number of tests to assure that
4064 the data set is suitable for such analysis.")
4065 (license license:gpl3)))
4067 (define-public r-sigpathway
4069 (name "r-sigpathway")
4074 (uri (bioconductor-uri "sigPathway" version))
4077 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
4078 (properties `((upstream-name . "sigPathway")))
4079 (build-system r-build-system)
4080 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
4081 (synopsis "Pathway analysis")
4083 "This package is used to conduct pathway analysis by calculating the NT_k
4084 and NE_k statistics in a statistical framework for determining whether a
4085 specified group of genes for a pathway has a coordinated association with a
4086 phenotype of interest.")
4087 (license license:gpl2)))
4089 (define-public r-fgsea
4096 (uri (bioconductor-uri "fgsea" version))
4099 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
4100 (build-system r-build-system)
4103 ("r-biocparallel" ,r-biocparallel)
4104 ("r-data-table" ,r-data-table)
4105 ("r-fastmatch" ,r-fastmatch)
4106 ("r-ggplot2" ,r-ggplot2)
4107 ("r-gridextra" ,r-gridextra)
4108 ("r-matrix" ,r-matrix)
4109 ("r-rcpp" ,r-rcpp)))
4111 `(("r-knitr" ,r-knitr)))
4112 (home-page "https://github.com/ctlab/fgsea/")
4113 (synopsis "Fast gene set enrichment analysis")
4115 "The package implements an algorithm for fast gene set enrichment
4116 analysis. Using the fast algorithm makes more permutations and gets
4117 more fine grained p-values, which allows using accurate standard approaches
4118 to multiple hypothesis correction.")
4119 (license license:expat)))
4121 (define-public r-dose
4128 (uri (bioconductor-uri "DOSE" version))
4131 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
4132 (properties `((upstream-name . "DOSE")))
4133 (build-system r-build-system)
4135 `(("r-annotationdbi" ,r-annotationdbi)
4136 ("r-biocparallel" ,r-biocparallel)
4137 ("r-do-db" ,r-do-db)
4138 ("r-fgsea" ,r-fgsea)
4139 ("r-ggplot2" ,r-ggplot2)
4140 ("r-gosemsim" ,r-gosemsim)
4141 ("r-qvalue" ,r-qvalue)
4142 ("r-reshape2" ,r-reshape2)))
4144 `(("r-knitr" ,r-knitr)))
4145 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4146 (synopsis "Disease ontology semantic and enrichment analysis")
4148 "This package implements five methods proposed by Resnik, Schlicker,
4149 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4150 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4151 including hypergeometric model and gene set enrichment analysis are also
4152 implemented for discovering disease associations of high-throughput biological
4154 (license license:artistic2.0)))
4156 (define-public r-enrichplot
4158 (name "r-enrichplot")
4163 (uri (bioconductor-uri "enrichplot" version))
4166 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4167 (build-system r-build-system)
4169 `(("r-cowplot" ,r-cowplot)
4171 ("r-ggplot2" ,r-ggplot2)
4172 ("r-ggraph" ,r-ggraph)
4173 ("r-gosemsim" ,r-gosemsim)
4174 ("r-igraph" ,r-igraph)
4175 ("r-magrittr" ,r-magrittr)
4177 ("r-purrr" ,r-purrr)
4178 ("r-rcolorbrewer" ,r-rcolorbrewer)
4179 ("r-reshape2" ,r-reshape2)
4180 ("r-scatterpie" ,r-scatterpie)
4181 ("r-shadowtext" ,r-shadowtext)))
4183 `(("r-knitr" ,r-knitr)))
4184 (home-page "https://github.com/GuangchuangYu/enrichplot")
4185 (synopsis "Visualization of functional enrichment result")
4187 "The enrichplot package implements several visualization methods for
4188 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4189 All the visualization methods are developed based on ggplot2 graphics.")
4190 (license license:artistic2.0)))
4192 (define-public r-clusterprofiler
4194 (name "r-clusterprofiler")
4199 (uri (bioconductor-uri "clusterProfiler" version))
4202 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4204 `((upstream-name . "clusterProfiler")))
4205 (build-system r-build-system)
4207 `(("r-annotationdbi" ,r-annotationdbi)
4209 ("r-downloader" ,r-downloader)
4210 ("r-dplyr" ,r-dplyr)
4211 ("r-enrichplot" ,r-enrichplot)
4212 ("r-go-db" ,r-go-db)
4213 ("r-gosemsim" ,r-gosemsim)
4214 ("r-magrittr" ,r-magrittr)
4216 ("r-qvalue" ,r-qvalue)
4217 ("r-rlang" ,r-rlang)
4218 ("r-rvcheck" ,r-rvcheck)
4219 ("r-tidyr" ,r-tidyr)))
4221 `(("r-knitr" ,r-knitr)))
4222 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4223 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4225 "This package implements methods to analyze and visualize functional
4226 profiles (GO and KEGG) of gene and gene clusters.")
4227 (license license:artistic2.0)))
4229 (define-public r-mlinterfaces
4231 (name "r-mlinterfaces")
4236 (uri (bioconductor-uri "MLInterfaces" version))
4239 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4240 (properties `((upstream-name . "MLInterfaces")))
4241 (build-system r-build-system)
4243 `(("r-annotate" ,r-annotate)
4244 ("r-biobase" ,r-biobase)
4245 ("r-biocgenerics" ,r-biocgenerics)
4246 ("r-cluster" ,r-cluster)
4249 ("r-gdata" ,r-gdata)
4250 ("r-genefilter" ,r-genefilter)
4251 ("r-ggvis" ,r-ggvis)
4252 ("r-hwriter" ,r-hwriter)
4254 ("r-mlbench" ,r-mlbench)
4256 ("r-rcolorbrewer" ,r-rcolorbrewer)
4258 ("r-rpart" ,r-rpart)
4259 ("r-sfsmisc" ,r-sfsmisc)
4260 ("r-shiny" ,r-shiny)
4261 ("r-threejs" ,r-threejs)))
4262 (home-page "https://bioconductor.org/packages/MLInterfaces/")
4263 (synopsis "Interfaces to R machine learning procedures")
4265 "This package provides uniform interfaces to machine learning code for
4266 data in R and Bioconductor containers.")
4267 ;; Any version of the LGPL.
4268 (license license:lgpl2.1+)))
4270 (define-public r-annaffy
4277 (uri (bioconductor-uri "annaffy" version))
4280 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
4281 (build-system r-build-system)
4284 (modify-phases %standard-phases
4285 (add-after 'unpack 'remove-reference-to-non-free-data
4287 (substitute* "DESCRIPTION"
4291 `(("r-annotationdbi" ,r-annotationdbi)
4292 ("r-biobase" ,r-biobase)
4294 ("r-go-db" ,r-go-db)))
4295 (home-page "https://bioconductor.org/packages/annaffy/")
4296 (synopsis "Annotation tools for Affymetrix biological metadata")
4298 "This package provides functions for handling data from Bioconductor
4299 Affymetrix annotation data packages. It produces compact HTML and text
4300 reports including experimental data and URL links to many online databases.
4301 It allows searching of biological metadata using various criteria.")
4302 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4303 ;; the LGPL 2.1 is included.
4304 (license license:lgpl2.1+)))
4306 (define-public r-a4core
4313 (uri (bioconductor-uri "a4Core" version))
4316 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
4317 (properties `((upstream-name . "a4Core")))
4318 (build-system r-build-system)
4320 `(("r-biobase" ,r-biobase)
4321 ("r-glmnet" ,r-glmnet)))
4323 `(("r-knitr" ,r-knitr)))
4324 (home-page "https://bioconductor.org/packages/a4Core")
4325 (synopsis "Automated Affymetrix array analysis core package")
4327 "This is the core package for the automated analysis of Affymetrix
4329 (license license:gpl3)))
4331 (define-public r-a4classif
4333 (name "r-a4classif")
4338 (uri (bioconductor-uri "a4Classif" version))
4341 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
4342 (properties `((upstream-name . "a4Classif")))
4343 (build-system r-build-system)
4345 `(("r-a4core" ,r-a4core)
4346 ("r-a4preproc" ,r-a4preproc)
4347 ("r-biobase" ,r-biobase)
4348 ("r-glmnet" ,r-glmnet)
4351 ("r-varselrf" ,r-varselrf)))
4353 `(("r-knitr" ,r-knitr)))
4354 (home-page "https://bioconductor.org/packages/a4Classif/")
4355 (synopsis "Automated Affymetrix array analysis classification package")
4357 "This is the classification package for the automated analysis of
4358 Affymetrix arrays.")
4359 (license license:gpl3)))
4361 (define-public r-a4preproc
4363 (name "r-a4preproc")
4368 (uri (bioconductor-uri "a4Preproc" version))
4371 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
4372 (properties `((upstream-name . "a4Preproc")))
4373 (build-system r-build-system)
4375 `(("r-biobase" ,r-biobase)
4376 ("r-biocgenerics" ,r-biocgenerics)))
4378 `(("r-knitr" ,r-knitr)))
4379 (home-page "https://bioconductor.org/packages/a4Preproc/")
4380 (synopsis "Automated Affymetrix array analysis preprocessing package")
4382 "This is a package for the automated analysis of Affymetrix arrays. It
4383 is used for preprocessing the arrays.")
4384 (license license:gpl3)))
4386 (define-public r-a4reporting
4388 (name "r-a4reporting")
4393 (uri (bioconductor-uri "a4Reporting" version))
4396 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
4397 (properties `((upstream-name . "a4Reporting")))
4398 (build-system r-build-system)
4400 `(("r-xtable" ,r-xtable)))
4402 `(("r-knitr" ,r-knitr)))
4403 (home-page "https://bioconductor.org/packages/a4Reporting/")
4404 (synopsis "Automated Affymetrix array analysis reporting package")
4406 "This is a package for the automated analysis of Affymetrix arrays. It
4407 provides reporting features.")
4408 (license license:gpl3)))
4410 (define-public r-a4base
4417 (uri (bioconductor-uri "a4Base" version))
4420 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
4421 (properties `((upstream-name . "a4Base")))
4422 (build-system r-build-system)
4424 `(("r-a4core" ,r-a4core)
4425 ("r-a4preproc" ,r-a4preproc)
4426 ("r-annaffy" ,r-annaffy)
4427 ("r-biobase" ,r-biobase)
4428 ("r-genefilter" ,r-genefilter)
4429 ("r-glmnet" ,r-glmnet)
4430 ("r-gplots" ,r-gplots)
4431 ("r-limma" ,r-limma)
4433 ("r-multtest" ,r-multtest)))
4434 (home-page "https://bioconductor.org/packages/a4Base/")
4435 (synopsis "Automated Affymetrix array analysis base package")
4437 "This package provides basic features for the automated analysis of
4438 Affymetrix arrays.")
4439 (license license:gpl3)))
4448 (uri (bioconductor-uri "a4" version))
4451 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
4452 (build-system r-build-system)
4454 `(("r-a4base" ,r-a4base)
4455 ("r-a4classif" ,r-a4classif)
4456 ("r-a4core" ,r-a4core)
4457 ("r-a4preproc" ,r-a4preproc)
4458 ("r-a4reporting" ,r-a4reporting)))
4459 (home-page "https://bioconductor.org/packages/a4/")
4460 (synopsis "Automated Affymetrix array analysis umbrella package")
4462 "This package provides a software suite for the automated analysis of
4463 Affymetrix arrays.")
4464 (license license:gpl3)))
4466 (define-public r-abseqr
4473 (uri (bioconductor-uri "abseqR" version))
4476 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
4477 (properties `((upstream-name . "abseqR")))
4478 (build-system r-build-system)
4480 `(("pandoc" ,pandoc)))
4482 `(("r-biocparallel" ,r-biocparallel)
4483 ("r-biocstyle" ,r-biocstyle)
4484 ("r-circlize" ,r-circlize)
4485 ("r-flexdashboard" ,r-flexdashboard)
4486 ("r-ggcorrplot" ,r-ggcorrplot)
4487 ("r-ggdendro" ,r-ggdendro)
4488 ("r-ggplot2" ,r-ggplot2)
4489 ("r-gridextra" ,r-gridextra)
4490 ("r-knitr" ,r-knitr)
4491 ("r-plotly" ,r-plotly)
4494 ("r-rcolorbrewer" ,r-rcolorbrewer)
4495 ("r-reshape2" ,r-reshape2)
4496 ("r-rmarkdown" ,r-rmarkdown)
4497 ("r-stringr" ,r-stringr)
4498 ("r-vegan" ,r-vegan)
4499 ("r-venndiagram" ,r-venndiagram)))
4501 `(("r-knitr" ,r-knitr)))
4502 (home-page "https://github.com/malhamdoosh/abseqR")
4503 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4505 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4506 sequencing datasets generated from antibody libraries and abseqR is one of its
4507 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4508 capabilities and allows them to generate interactive HTML reports for the
4509 convenience of viewing and sharing with other researchers. Additionally,
4510 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4511 further downstream analysis on its output.")
4512 (license license:gpl3)))
4514 (define-public r-bacon
4521 (uri (bioconductor-uri "bacon" version))
4524 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
4525 (build-system r-build-system)
4527 `(("r-biocparallel" ,r-biocparallel)
4528 ("r-ellipse" ,r-ellipse)
4529 ("r-ggplot2" ,r-ggplot2)))
4531 `(("r-knitr" ,r-knitr)))
4532 (home-page "https://bioconductor.org/packages/bacon/")
4533 (synopsis "Controlling bias and inflation in association studies")
4535 "Bacon can be used to remove inflation and bias often observed in
4536 epigenome- and transcriptome-wide association studies. To this end bacon
4537 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4538 fitting a three-component normal mixture on z-scores.")
4539 (license license:gpl2+)))
4541 (define-public r-rgadem
4548 (uri (bioconductor-uri "rGADEM" version))
4551 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
4552 (properties `((upstream-name . "rGADEM")))
4553 (build-system r-build-system)
4555 `(("r-biostrings" ,r-biostrings)
4556 ("r-bsgenome" ,r-bsgenome)
4557 ("r-genomicranges" ,r-genomicranges)
4558 ("r-iranges" ,r-iranges)
4559 ("r-seqlogo" ,r-seqlogo)))
4560 (home-page "https://bioconductor.org/packages/rGADEM/")
4561 (synopsis "De novo sequence motif discovery")
4563 "rGADEM is an efficient de novo motif discovery tool for large-scale
4564 genomic sequence data.")
4565 (license license:artistic2.0)))
4567 (define-public r-motiv
4574 (uri (bioconductor-uri "MotIV" version))
4577 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4578 (properties `((upstream-name . "MotIV")))
4579 (build-system r-build-system)
4583 `(("r-biocgenerics" ,r-biocgenerics)
4584 ("r-biostrings" ,r-biostrings)
4585 ("r-genomicranges" ,r-genomicranges)
4586 ("r-iranges" ,r-iranges)
4587 ("r-lattice" ,r-lattice)
4588 ("r-rgadem" ,r-rgadem)
4589 ("r-s4vectors" ,r-s4vectors)))
4590 (home-page "https://bioconductor.org/packages/MotIV/")
4591 (synopsis "Motif identification and validation")
4593 "This package is used for the identification and validation of sequence
4594 motifs. It makes use of STAMP for comparing a set of motifs to a given
4595 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4596 distributions, modules and filter motifs.")
4597 (license license:gpl2)))
4599 (define-public r-motifdb
4605 (uri (bioconductor-uri "MotifDb" version))
4607 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
4608 (properties `((upstream-name . "MotifDb")))
4609 (build-system r-build-system)
4611 `(("r-biocgenerics" ,r-biocgenerics)
4612 ("r-biostrings" ,r-biostrings)
4613 ("r-genomicranges" ,r-genomicranges)
4614 ("r-iranges" ,r-iranges)
4615 ("r-rtracklayer" ,r-rtracklayer)
4616 ("r-s4vectors" ,r-s4vectors)
4617 ("r-splitstackshape" ,r-splitstackshape)))
4619 `(("r-knitr" ,r-knitr)))
4620 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4621 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4622 (description "This package provides more than 2000 annotated position
4623 frequency matrices from nine public sources, for multiple organisms.")
4624 (license license:artistic2.0)))
4626 (define-public r-motifbreakr
4628 (name "r-motifbreakr")
4632 (uri (bioconductor-uri "motifbreakR" version))
4634 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
4635 (properties `((upstream-name . "motifbreakR")))
4636 (build-system r-build-system)
4638 `(("r-biocgenerics" ,r-biocgenerics)
4639 ("r-biocparallel" ,r-biocparallel)
4640 ("r-biostrings" ,r-biostrings)
4641 ("r-bsgenome" ,r-bsgenome)
4642 ("r-genomeinfodb" ,r-genomeinfodb)
4643 ("r-genomicranges" ,r-genomicranges)
4644 ("r-grimport" ,r-grimport)
4646 ("r-iranges" ,r-iranges)
4647 ("r-matrixstats" ,r-matrixstats)
4648 ("r-motifdb" ,r-motifdb)
4649 ("r-motifstack" ,r-motifstack)
4650 ("r-rtracklayer" ,r-rtracklayer)
4651 ("r-s4vectors" ,r-s4vectors)
4652 ("r-stringr" ,r-stringr)
4653 ("r-summarizedexperiment" ,r-summarizedexperiment)
4654 ("r-tfmpvalue" ,r-tfmpvalue)
4655 ("r-variantannotation" ,r-variantannotation)))
4657 `(("r-knitr" ,r-knitr)))
4658 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4659 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4660 (description "This package allows biologists to judge in the first place
4661 whether the sequence surrounding the polymorphism is a good match, and in
4662 the second place how much information is gained or lost in one allele of
4663 the polymorphism relative to another. This package gives a choice of
4664 algorithms for interrogation of genomes with motifs from public sources:
4666 @item a weighted-sum probability matrix;
4667 @item log-probabilities;
4668 @item weighted by relative entropy.
4671 This package can predict effects for novel or previously described variants in
4672 public databases, making it suitable for tasks beyond the scope of its original
4673 design. Lastly, it can be used to interrogate any genome curated within
4675 (license license:gpl2+)))
4677 (define-public r-motifstack
4679 (name "r-motifstack")
4684 (uri (bioconductor-uri "motifStack" version))
4687 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
4688 (properties `((upstream-name . "motifStack")))
4689 (build-system r-build-system)
4691 `(("r-ade4" ,r-ade4)
4692 ("r-biostrings" ,r-biostrings)
4693 ("r-ggplot2" ,r-ggplot2)
4694 ("r-htmlwidgets" ,r-htmlwidgets)
4697 `(("r-knitr" ,r-knitr)))
4698 (home-page "https://bioconductor.org/packages/motifStack/")
4699 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4701 "The motifStack package is designed for graphic representation of
4702 multiple motifs with different similarity scores. It works with both DNA/RNA
4703 sequence motifs and amino acid sequence motifs. In addition, it provides the
4704 flexibility for users to customize the graphic parameters such as the font
4705 type and symbol colors.")
4706 (license license:gpl2+)))
4708 (define-public r-genomicscores
4710 (name "r-genomicscores")
4715 (uri (bioconductor-uri "GenomicScores" version))
4718 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
4719 (properties `((upstream-name . "GenomicScores")))
4720 (build-system r-build-system)
4722 `(("r-annotationhub" ,r-annotationhub)
4723 ("r-biobase" ,r-biobase)
4724 ("r-biocfilecache" ,r-biocfilecache)
4725 ("r-biocgenerics" ,r-biocgenerics)
4726 ("r-biocmanager" ,r-biocmanager)
4727 ("r-biostrings" ,r-biostrings)
4728 ("r-delayedarray" ,r-delayedarray)
4729 ("r-genomeinfodb" ,r-genomeinfodb)
4730 ("r-genomicranges" ,r-genomicranges)
4731 ("r-hdf5array" ,r-hdf5array)
4732 ("r-iranges" ,r-iranges)
4733 ("r-rhdf5" ,r-rhdf5)
4734 ("r-s4vectors" ,r-s4vectors)
4737 `(("r-knitr" ,r-knitr)))
4738 (home-page "https://github.com/rcastelo/GenomicScores/")
4739 (synopsis "Work with genome-wide position-specific scores")
4741 "This package provides infrastructure to store and access genome-wide
4742 position-specific scores within R and Bioconductor.")
4743 (license license:artistic2.0)))
4745 (define-public r-atacseqqc
4747 (name "r-atacseqqc")
4752 (uri (bioconductor-uri "ATACseqQC" version))
4755 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
4756 (properties `((upstream-name . "ATACseqQC")))
4757 (build-system r-build-system)
4759 `(("r-biocgenerics" ,r-biocgenerics)
4760 ("r-biostrings" ,r-biostrings)
4761 ("r-bsgenome" ,r-bsgenome)
4762 ("r-chippeakanno" ,r-chippeakanno)
4763 ("r-edger" ,r-edger)
4764 ("r-genomeinfodb" ,r-genomeinfodb)
4765 ("r-genomicalignments" ,r-genomicalignments)
4766 ("r-genomicranges" ,r-genomicranges)
4767 ("r-genomicscores" ,r-genomicscores)
4768 ("r-iranges" ,r-iranges)
4769 ("r-kernsmooth" ,r-kernsmooth)
4770 ("r-limma" ,r-limma)
4771 ("r-motifstack" ,r-motifstack)
4772 ("r-preseqr" ,r-preseqr)
4773 ("r-randomforest" ,r-randomforest)
4774 ("r-rsamtools" ,r-rsamtools)
4775 ("r-rtracklayer" ,r-rtracklayer)
4776 ("r-s4vectors" ,r-s4vectors)))
4778 `(("r-knitr" ,r-knitr)))
4779 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4780 (synopsis "ATAC-seq quality control")
4782 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4783 sequencing, is a rapid and sensitive method for chromatin accessibility
4784 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4785 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4786 assess whether their ATAC-seq experiment is successful. It includes
4787 diagnostic plots of fragment size distribution, proportion of mitochondria
4788 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4790 (license license:gpl2+)))
4792 (define-public r-gofuncr
4799 (uri (bioconductor-uri "GOfuncR" version))
4802 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
4803 (properties `((upstream-name . "GOfuncR")))
4804 (build-system r-build-system)
4806 `(("r-annotationdbi" ,r-annotationdbi)
4807 ("r-genomicranges" ,r-genomicranges)
4808 ("r-gtools" ,r-gtools)
4809 ("r-iranges" ,r-iranges)
4810 ("r-mapplots" ,r-mapplots)
4812 ("r-vioplot" ,r-vioplot)))
4814 `(("r-knitr" ,r-knitr)))
4815 (home-page "https://bioconductor.org/packages/GOfuncR/")
4816 (synopsis "Gene ontology enrichment using FUNC")
4818 "GOfuncR performs a gene ontology enrichment analysis based on the
4819 ontology enrichment software FUNC. GO-annotations are obtained from
4820 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4821 included in the package and updated regularly. GOfuncR provides the standard
4822 candidate vs background enrichment analysis using the hypergeometric test, as
4823 well as three additional tests:
4826 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4827 @item a binomial test that is used when genes are associated with two counts,
4829 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4830 associated with four counts.
4833 To correct for multiple testing and interdependency of the tests, family-wise
4834 error rates are computed based on random permutations of the gene-associated
4835 variables. GOfuncR also provides tools for exploring the ontology graph and
4836 the annotations, and options to take gene-length or spatial clustering of
4837 genes into account. It is also possible to provide custom gene coordinates,
4838 annotations and ontologies.")
4839 (license license:gpl2+)))
4841 (define-public r-abaenrichment
4843 (name "r-abaenrichment")
4848 (uri (bioconductor-uri "ABAEnrichment" version))
4851 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
4852 (properties `((upstream-name . "ABAEnrichment")))
4853 (build-system r-build-system)
4855 `(("r-abadata" ,r-abadata)
4856 ("r-data-table" ,r-data-table)
4857 ("r-gofuncr" ,r-gofuncr)
4858 ("r-gplots" ,r-gplots)
4859 ("r-gtools" ,r-gtools)
4860 ("r-rcpp" ,r-rcpp)))
4862 `(("r-knitr" ,r-knitr)))
4863 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4864 (synopsis "Gene expression enrichment in human brain regions")
4866 "The package ABAEnrichment is designed to test for enrichment of user
4867 defined candidate genes in the set of expressed genes in different human brain
4868 regions. The core function @code{aba_enrich} integrates the expression of the
4869 candidate gene set (averaged across donors) and the structural information of
4870 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4871 (license license:gpl2+)))
4873 (define-public r-annotationfuncs
4875 (name "r-annotationfuncs")
4880 (uri (bioconductor-uri "AnnotationFuncs" version))
4883 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
4885 `((upstream-name . "AnnotationFuncs")))
4886 (build-system r-build-system)
4888 `(("r-annotationdbi" ,r-annotationdbi)
4890 (home-page "https://www.iysik.com/r/annotationfuncs")
4891 (synopsis "Annotation translation functions")
4893 "This package provides functions for handling translating between
4894 different identifieres using the Biocore Data Team data-packages (e.g.
4895 @code{org.Bt.eg.db}).")
4896 (license license:gpl2)))
4898 (define-public r-annotationtools
4900 (name "r-annotationtools")
4905 (uri (bioconductor-uri "annotationTools" version))
4908 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
4910 `((upstream-name . "annotationTools")))
4911 (build-system r-build-system)
4912 (propagated-inputs `(("r-biobase" ,r-biobase)))
4913 (home-page "https://bioconductor.org/packages/annotationTools/")
4914 (synopsis "Annotate microarrays and perform gene expression analyses")
4916 "This package provides functions to annotate microarrays, find orthologs,
4917 and integrate heterogeneous gene expression profiles using annotation and
4918 other molecular biology information available as flat file database (plain
4920 ;; Any version of the GPL.
4921 (license (list license:gpl2+))))
4923 (define-public r-allelicimbalance
4925 (name "r-allelicimbalance")
4930 (uri (bioconductor-uri "AllelicImbalance" version))
4933 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
4935 `((upstream-name . "AllelicImbalance")))
4936 (build-system r-build-system)
4938 `(("r-annotationdbi" ,r-annotationdbi)
4939 ("r-biocgenerics" ,r-biocgenerics)
4940 ("r-biostrings" ,r-biostrings)
4941 ("r-bsgenome" ,r-bsgenome)
4942 ("r-genomeinfodb" ,r-genomeinfodb)
4943 ("r-genomicalignments" ,r-genomicalignments)
4944 ("r-genomicfeatures" ,r-genomicfeatures)
4945 ("r-genomicranges" ,r-genomicranges)
4946 ("r-gridextra" ,r-gridextra)
4948 ("r-iranges" ,r-iranges)
4949 ("r-lattice" ,r-lattice)
4950 ("r-latticeextra" ,r-latticeextra)
4952 ("r-rsamtools" ,r-rsamtools)
4953 ("r-s4vectors" ,r-s4vectors)
4954 ("r-seqinr" ,r-seqinr)
4955 ("r-summarizedexperiment" ,r-summarizedexperiment)
4956 ("r-variantannotation" ,r-variantannotation)))
4958 `(("r-knitr" ,r-knitr)))
4959 (home-page "https://github.com/pappewaio/AllelicImbalance")
4960 (synopsis "Investigate allele-specific expression")
4962 "This package provides a framework for allele-specific expression
4963 investigation using RNA-seq data.")
4964 (license license:gpl3)))
4966 (define-public r-aucell
4973 (uri (bioconductor-uri "AUCell" version))
4976 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
4977 (properties `((upstream-name . "AUCell")))
4978 (build-system r-build-system)
4980 `(("r-biocgenerics" ,r-biocgenerics)
4981 ("r-data-table" ,r-data-table)
4982 ("r-gseabase" ,r-gseabase)
4983 ("r-mixtools" ,r-mixtools)
4984 ("r-r-utils" ,r-r-utils)
4985 ("r-s4vectors" ,r-s4vectors)
4986 ("r-shiny" ,r-shiny)
4987 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4989 `(("r-knitr" ,r-knitr)))
4990 (home-page "https://bioconductor.org/packages/AUCell/")
4991 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4993 "AUCell identifies cells with active gene sets (e.g. signatures,
4994 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4995 Under the Curve} (AUC) to calculate whether a critical subset of the input
4996 gene set is enriched within the expressed genes for each cell. The
4997 distribution of AUC scores across all the cells allows exploring the relative
4998 expression of the signature. Since the scoring method is ranking-based,
4999 AUCell is independent of the gene expression units and the normalization
5000 procedure. In addition, since the cells are evaluated individually, it can
5001 easily be applied to bigger datasets, subsetting the expression matrix if
5003 (license license:gpl3)))
5005 (define-public r-ebimage
5012 (uri (bioconductor-uri "EBImage" version))
5015 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5016 (properties `((upstream-name . "EBImage")))
5017 (build-system r-build-system)
5019 `(("r-abind" ,r-abind)
5020 ("r-biocgenerics" ,r-biocgenerics)
5021 ("r-fftwtools" ,r-fftwtools)
5022 ("r-htmltools" ,r-htmltools)
5023 ("r-htmlwidgets" ,r-htmlwidgets)
5025 ("r-locfit" ,r-locfit)
5027 ("r-rcurl" ,r-rcurl)
5028 ("r-tiff" ,r-tiff)))
5030 `(("r-knitr" ,r-knitr))) ; for vignettes
5031 (home-page "https://github.com/aoles/EBImage")
5032 (synopsis "Image processing and analysis toolbox for R")
5034 "EBImage provides general purpose functionality for image processing and
5035 analysis. In the context of (high-throughput) microscopy-based cellular
5036 assays, EBImage offers tools to segment cells and extract quantitative
5037 cellular descriptors. This allows the automation of such tasks using the R
5038 programming language and facilitates the use of other tools in the R
5039 environment for signal processing, statistical modeling, machine learning and
5040 visualization with image data.")
5041 ;; Any version of the LGPL.
5042 (license license:lgpl2.1+)))
5044 (define-public r-yamss
5051 (uri (bioconductor-uri "yamss" version))
5054 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
5055 (build-system r-build-system)
5057 `(("r-biocgenerics" ,r-biocgenerics)
5058 ("r-data-table" ,r-data-table)
5059 ("r-ebimage" ,r-ebimage)
5060 ("r-iranges" ,r-iranges)
5061 ("r-limma" ,r-limma)
5062 ("r-matrix" ,r-matrix)
5064 ("r-s4vectors" ,r-s4vectors)
5065 ("r-summarizedexperiment"
5066 ,r-summarizedexperiment)))
5068 `(("r-knitr" ,r-knitr)))
5069 (home-page "https://github.com/hansenlab/yamss")
5070 (synopsis "Tools for high-throughput metabolomics")
5072 "This package provides tools to analyze and visualize high-throughput
5073 metabolomics data acquired using chromatography-mass spectrometry. These tools
5074 preprocess data in a way that enables reliable and powerful differential
5076 (license license:artistic2.0)))
5078 (define-public r-gtrellis
5085 (uri (bioconductor-uri "gtrellis" version))
5088 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
5089 (build-system r-build-system)
5091 `(("r-circlize" ,r-circlize)
5092 ("r-genomicranges" ,r-genomicranges)
5093 ("r-getoptlong" ,r-getoptlong)
5094 ("r-iranges" ,r-iranges)))
5096 `(("r-knitr" ,r-knitr)))
5097 (home-page "https://github.com/jokergoo/gtrellis")
5098 (synopsis "Genome level Trellis layout")
5100 "Genome level Trellis graph visualizes genomic data conditioned by
5101 genomic categories (e.g. chromosomes). For each genomic category, multiple
5102 dimensional data which are represented as tracks describe different features
5103 from different aspects. This package provides high flexibility to arrange
5104 genomic categories and to add self-defined graphics in the plot.")
5105 (license license:expat)))
5107 (define-public r-somaticsignatures
5109 (name "r-somaticsignatures")
5114 (uri (bioconductor-uri "SomaticSignatures" version))
5117 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
5119 `((upstream-name . "SomaticSignatures")))
5120 (build-system r-build-system)
5122 `(("r-biobase" ,r-biobase)
5123 ("r-biostrings" ,r-biostrings)
5124 ("r-genomeinfodb" ,r-genomeinfodb)
5125 ("r-genomicranges" ,r-genomicranges)
5126 ("r-ggbio" ,r-ggbio)
5127 ("r-ggplot2" ,r-ggplot2)
5128 ("r-iranges" ,r-iranges)
5130 ("r-pcamethods" ,r-pcamethods)
5131 ("r-proxy" ,r-proxy)
5132 ("r-reshape2" ,r-reshape2)
5133 ("r-s4vectors" ,r-s4vectors)
5134 ("r-variantannotation" ,r-variantannotation)))
5136 `(("r-knitr" ,r-knitr)))
5137 (home-page "https://github.com/juliangehring/SomaticSignatures")
5138 (synopsis "Somatic signatures")
5140 "This package identifies mutational signatures of @dfn{single nucleotide
5141 variants} (SNVs). It provides a infrastructure related to the methodology
5142 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5143 decomposition algorithms.")
5144 (license license:expat)))
5146 (define-public r-yapsa
5153 (uri (bioconductor-uri "YAPSA" version))
5156 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5157 (properties `((upstream-name . "YAPSA")))
5158 (build-system r-build-system)
5160 `(("r-biostrings" ,r-biostrings)
5161 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5162 ("r-circlize" ,r-circlize)
5163 ("r-complexheatmap" ,r-complexheatmap)
5164 ("r-corrplot" ,r-corrplot)
5165 ("r-dendextend" ,r-dendextend)
5166 ("r-doparallel" ,r-doparallel)
5167 ("r-dplyr" ,r-dplyr)
5168 ("r-genomeinfodb" ,r-genomeinfodb)
5169 ("r-genomicranges" ,r-genomicranges)
5170 ("r-getoptlong" ,r-getoptlong)
5171 ("r-ggbeeswarm" ,r-ggbeeswarm)
5172 ("r-ggplot2" ,r-ggplot2)
5173 ("r-gridextra" ,r-gridextra)
5174 ("r-gtrellis" ,r-gtrellis)
5175 ("r-keggrest" ,r-keggrest)
5176 ("r-limsolve" ,r-limsolve)
5177 ("r-magrittr" ,r-magrittr)
5178 ("r-pmcmr" ,r-pmcmr)
5179 ("r-pracma" ,r-pracma)
5180 ("r-reshape2" ,r-reshape2)
5181 ("r-somaticsignatures" ,r-somaticsignatures)
5182 ("r-variantannotation" ,r-variantannotation)))
5184 `(("r-knitr" ,r-knitr)))
5185 (home-page "https://bioconductor.org/packages/YAPSA/")
5186 (synopsis "Yet another package for signature analysis")
5188 "This package provides functions and routines useful in the analysis of
5189 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5190 functions to perform a signature analysis with known signatures and a
5191 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5193 (license license:gpl3)))
5195 (define-public r-gcrma
5202 (uri (bioconductor-uri "gcrma" version))
5205 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5206 (build-system r-build-system)
5208 `(("r-affy" ,r-affy)
5209 ("r-affyio" ,r-affyio)
5210 ("r-biobase" ,r-biobase)
5211 ("r-biocmanager" ,r-biocmanager)
5212 ("r-biostrings" ,r-biostrings)
5213 ("r-xvector" ,r-xvector)))
5214 (home-page "https://bioconductor.org/packages/gcrma/")
5215 (synopsis "Background adjustment using sequence information")
5217 "Gcrma adjusts for background intensities in Affymetrix array data which
5218 include optical noise and @dfn{non-specific binding} (NSB). The main function
5219 @code{gcrma} converts background adjusted probe intensities to expression
5220 measures using the same normalization and summarization methods as a
5221 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5222 to estimate probe affinity to NSB. The sequence information is summarized in
5223 a more complex way than the simple GC content. Instead, the base types (A, T,
5224 G or C) at each position along the probe determine the affinity of each probe.
5225 The parameters of the position-specific base contributions to the probe
5226 affinity is estimated in an NSB experiment in which only NSB but no
5227 gene-specific binding is expected.")
5228 ;; Any version of the LGPL
5229 (license license:lgpl2.1+)))
5231 (define-public r-simpleaffy
5233 (name "r-simpleaffy")
5238 (uri (bioconductor-uri "simpleaffy" version))
5241 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5242 (build-system r-build-system)
5244 `(("r-affy" ,r-affy)
5245 ("r-biobase" ,r-biobase)
5246 ("r-biocgenerics" ,r-biocgenerics)
5247 ("r-gcrma" ,r-gcrma)
5248 ("r-genefilter" ,r-genefilter)))
5249 (home-page "https://bioconductor.org/packages/simpleaffy/")
5250 (synopsis "Very simple high level analysis of Affymetrix data")
5252 "This package provides high level functions for reading Affy @file{.CEL}
5253 files, phenotypic data, and then computing simple things with it, such as
5254 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5255 library. It also has some basic scatter plot functions and mechanisms for
5256 generating high resolution journal figures.")
5257 (license license:gpl2+)))
5259 (define-public r-yaqcaffy
5266 (uri (bioconductor-uri "yaqcaffy" version))
5269 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
5270 (build-system r-build-system)
5272 `(("r-simpleaffy" ,r-simpleaffy)))
5273 (home-page "https://bioconductor.org/packages/yaqcaffy/")
5274 (synopsis "Affymetrix quality control and reproducibility analysis")
5276 "This is a package that can be used for quality control of Affymetrix
5277 GeneChip expression data and reproducibility analysis of human whole genome
5278 chips with the MAQC reference datasets.")
5279 (license license:artistic2.0)))
5281 (define-public r-quantro
5288 (uri (bioconductor-uri "quantro" version))
5291 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
5292 (build-system r-build-system)
5294 `(("r-biobase" ,r-biobase)
5295 ("r-doparallel" ,r-doparallel)
5296 ("r-foreach" ,r-foreach)
5297 ("r-ggplot2" ,r-ggplot2)
5298 ("r-iterators" ,r-iterators)
5299 ("r-minfi" ,r-minfi)
5300 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5302 `(("r-knitr" ,r-knitr)))
5303 (home-page "https://bioconductor.org/packages/quantro/")
5304 (synopsis "Test for when to use quantile normalization")
5306 "This package provides a data-driven test for the assumptions of quantile
5307 normalization using raw data such as objects that inherit eSets (e.g.
5308 ExpressionSet, MethylSet). Group level information about each sample (such as
5309 Tumor / Normal status) must also be provided because the test assesses if
5310 there are global differences in the distributions between the user-defined
5312 (license license:gpl3+)))
5314 (define-public r-yarn
5321 (uri (bioconductor-uri "yarn" version))
5324 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
5325 (build-system r-build-system)
5327 `(("r-biobase" ,r-biobase)
5328 ("r-biomart" ,r-biomart)
5329 ("r-downloader" ,r-downloader)
5330 ("r-edger" ,r-edger)
5331 ("r-gplots" ,r-gplots)
5332 ("r-limma" ,r-limma)
5333 ("r-matrixstats" ,r-matrixstats)
5334 ("r-preprocesscore" ,r-preprocesscore)
5335 ("r-quantro" ,r-quantro)
5336 ("r-rcolorbrewer" ,r-rcolorbrewer)
5337 ("r-readr" ,r-readr)))
5339 `(("r-knitr" ,r-knitr)))
5340 (home-page "https://bioconductor.org/packages/yarn/")
5341 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5343 "Expedite large RNA-Seq analyses using a combination of previously
5344 developed tools. YARN is meant to make it easier for the user in performing
5345 basic mis-annotation quality control, filtering, and condition-aware
5346 normalization. YARN leverages many Bioconductor tools and statistical
5347 techniques to account for the large heterogeneity and sparsity found in very
5348 large RNA-seq experiments.")
5349 (license license:artistic2.0)))
5351 (define-public r-roar
5358 (uri (bioconductor-uri "roar" version))
5361 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
5362 (build-system r-build-system)
5364 `(("r-biocgenerics" ,r-biocgenerics)
5365 ("r-genomeinfodb" ,r-genomeinfodb)
5366 ("r-genomicalignments" ,r-genomicalignments)
5367 ("r-genomicranges" ,r-genomicranges)
5368 ("r-iranges" ,r-iranges)
5369 ("r-rtracklayer" ,r-rtracklayer)
5370 ("r-s4vectors" ,r-s4vectors)
5371 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5372 (home-page "https://github.com/vodkatad/roar/")
5373 (synopsis "Identify differential APA usage from RNA-seq alignments")
5375 "This package provides tools for identifying preferential usage of APA
5376 sites, comparing two biological conditions, starting from known alternative
5377 sites and alignments obtained from standard RNA-seq experiments.")
5378 (license license:gpl3)))
5380 (define-public r-xbseq
5387 (uri (bioconductor-uri "XBSeq" version))
5390 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
5391 (properties `((upstream-name . "XBSeq")))
5392 (build-system r-build-system)
5394 `(("r-biobase" ,r-biobase)
5395 ("r-deseq2" ,r-deseq2)
5396 ("r-dplyr" ,r-dplyr)
5397 ("r-ggplot2" ,r-ggplot2)
5398 ("r-locfit" ,r-locfit)
5399 ("r-magrittr" ,r-magrittr)
5400 ("r-matrixstats" ,r-matrixstats)
5401 ("r-pracma" ,r-pracma)
5402 ("r-roar" ,r-roar)))
5404 `(("r-knitr" ,r-knitr)))
5405 (home-page "https://github.com/Liuy12/XBSeq")
5406 (synopsis "Test for differential expression for RNA-seq data")
5408 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5409 expression} (DE), where a statistical model was established based on the
5410 assumption that observed signals are the convolution of true expression
5411 signals and sequencing noises. The mapped reads in non-exonic regions are
5412 considered as sequencing noises, which follows a Poisson distribution. Given
5413 measurable observed signal and background noise from RNA-seq data, true
5414 expression signals, assuming governed by the negative binomial distribution,
5415 can be delineated and thus the accurate detection of differential expressed
5417 (license license:gpl3+)))
5419 (define-public r-massspecwavelet
5421 (name "r-massspecwavelet")
5426 (uri (bioconductor-uri "MassSpecWavelet" version))
5429 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
5431 `((upstream-name . "MassSpecWavelet")))
5432 (build-system r-build-system)
5434 `(("r-waveslim" ,r-waveslim)))
5435 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5436 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5438 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5439 data mainly through the use of wavelet transforms. It supports peak detection
5440 based on @dfn{Continuous Wavelet Transform} (CWT).")
5441 (license license:lgpl2.0+)))
5443 (define-public r-xcms
5450 (uri (bioconductor-uri "xcms" version))
5453 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
5454 (build-system r-build-system)
5456 `(("r-biobase" ,r-biobase)
5457 ("r-biocgenerics" ,r-biocgenerics)
5458 ("r-biocparallel" ,r-biocparallel)
5459 ("r-iranges" ,r-iranges)
5460 ("r-lattice" ,r-lattice)
5461 ("r-massspecwavelet" ,r-massspecwavelet)
5462 ("r-mscoreutils" ,r-mscoreutils)
5463 ("r-msnbase" ,r-msnbase)
5466 ("r-protgenerics" ,r-protgenerics)
5468 ("r-rcolorbrewer" ,r-rcolorbrewer)
5469 ("r-robustbase" ,r-robustbase)
5470 ("r-s4vectors" ,r-s4vectors)
5471 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5473 `(("r-knitr" ,r-knitr)))
5474 (home-page "https://bioconductor.org/packages/xcms/")
5475 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5477 "This package provides a framework for processing and visualization of
5478 chromatographically separated and single-spectra mass spectral data. It
5479 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5480 data for high-throughput, untargeted analyte profiling.")
5481 (license license:gpl2+)))
5483 (define-public r-wrench
5490 (uri (bioconductor-uri "Wrench" version))
5493 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
5494 (properties `((upstream-name . "Wrench")))
5495 (build-system r-build-system)
5497 `(("r-limma" ,r-limma)
5498 ("r-locfit" ,r-locfit)
5499 ("r-matrixstats" ,r-matrixstats)))
5501 `(("r-knitr" ,r-knitr)))
5502 (home-page "https://github.com/HCBravoLab/Wrench")
5503 (synopsis "Wrench normalization for sparse count data")
5505 "Wrench is a package for normalization sparse genomic count data, like
5506 that arising from 16s metagenomic surveys.")
5507 (license license:artistic2.0)))
5509 (define-public r-wiggleplotr
5511 (name "r-wiggleplotr")
5516 (uri (bioconductor-uri "wiggleplotr" version))
5519 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
5520 (build-system r-build-system)
5522 `(("r-assertthat" ,r-assertthat)
5523 ("r-cowplot" ,r-cowplot)
5524 ("r-dplyr" ,r-dplyr)
5525 ("r-genomeinfodb" ,r-genomeinfodb)
5526 ("r-genomicranges" ,r-genomicranges)
5527 ("r-ggplot2" ,r-ggplot2)
5528 ("r-iranges" ,r-iranges)
5529 ("r-purrr" ,r-purrr)
5530 ("r-rtracklayer" ,r-rtracklayer)
5531 ("r-s4vectors" ,r-s4vectors)))
5533 `(("r-knitr" ,r-knitr)))
5534 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5535 (synopsis "Make read coverage plots from BigWig files")
5537 "This package provides tools to visualize read coverage from sequencing
5538 experiments together with genomic annotations (genes, transcripts, peaks).
5539 Introns of long transcripts can be rescaled to a fixed length for better
5540 visualization of exonic read coverage.")
5541 (license license:asl2.0)))
5543 (define-public r-widgettools
5545 (name "r-widgettools")
5550 (uri (bioconductor-uri "widgetTools" version))
5553 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
5554 (properties `((upstream-name . "widgetTools")))
5555 (build-system r-build-system)
5556 (home-page "https://bioconductor.org/packages/widgetTools/")
5557 (synopsis "Tools for creating interactive tcltk widgets")
5559 "This package contains tools to support the construction of tcltk
5561 ;; Any version of the LGPL.
5562 (license license:lgpl3+)))
5564 (define-public r-webbioc
5571 (uri (bioconductor-uri "webbioc" version))
5574 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
5575 (build-system r-build-system)
5577 `(("netpbm" ,netpbm)
5580 `(("r-affy" ,r-affy)
5581 ("r-annaffy" ,r-annaffy)
5582 ("r-biobase" ,r-biobase)
5583 ("r-biocmanager" ,r-biocmanager)
5584 ("r-gcrma" ,r-gcrma)
5585 ("r-multtest" ,r-multtest)
5586 ("r-qvalue" ,r-qvalue)
5588 (home-page "https://www.bioconductor.org/")
5589 (synopsis "Bioconductor web interface")
5591 "This package provides an integrated web interface for doing microarray
5592 analysis using several of the Bioconductor packages. It is intended to be
5593 deployed as a centralized bioinformatics resource for use by many users.
5594 Currently only Affymetrix oligonucleotide analysis is supported.")
5595 (license license:gpl2+)))
5597 (define-public r-zfpkm
5604 (uri (bioconductor-uri "zFPKM" version))
5607 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
5608 (properties `((upstream-name . "zFPKM")))
5609 (build-system r-build-system)
5611 `(("r-checkmate" ,r-checkmate)
5612 ("r-dplyr" ,r-dplyr)
5613 ("r-ggplot2" ,r-ggplot2)
5614 ("r-summarizedexperiment" ,r-summarizedexperiment)
5615 ("r-tidyr" ,r-tidyr)))
5617 `(("r-knitr" ,r-knitr)))
5618 (home-page "https://github.com/ronammar/zFPKM/")
5619 (synopsis "Functions to facilitate zFPKM transformations")
5621 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5622 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5624 (license license:gpl3)))
5626 (define-public r-rbowtie2
5633 (uri (bioconductor-uri "Rbowtie2" version))
5636 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
5637 (properties `((upstream-name . "Rbowtie2")))
5638 (build-system r-build-system)
5642 `(("r-knitr" ,r-knitr)))
5643 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5644 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5646 "This package provides an R wrapper of the popular @code{bowtie2}
5647 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5648 rapid adapter trimming, identification, and read merging.")
5649 (license license:gpl3+)))
5651 (define-public r-progeny
5658 (uri (bioconductor-uri "progeny" version))
5661 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
5662 (build-system r-build-system)
5664 `(("r-biobase" ,r-biobase)
5665 ("r-dplyr" ,r-dplyr)
5666 ("r-ggplot2" ,r-ggplot2)
5667 ("r-ggrepel" ,r-ggrepel)
5668 ("r-gridextra" ,r-gridextra)
5669 ("r-tidyr" ,r-tidyr)))
5671 `(("r-knitr" ,r-knitr)))
5672 (home-page "https://github.com/saezlab/progeny")
5673 (synopsis "Pathway responsive gene activity inference")
5675 "This package provides a function to infer pathway activity from gene
5676 expression. It contains the linear model inferred in the publication
5677 \"Perturbation-response genes reveal signaling footprints in cancer gene
5679 (license license:asl2.0)))
5681 (define-public r-arrmnormalization
5683 (name "r-arrmnormalization")
5688 (uri (bioconductor-uri "ARRmNormalization" version))
5691 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
5693 `((upstream-name . "ARRmNormalization")))
5694 (build-system r-build-system)
5695 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5696 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5697 (synopsis "Adaptive robust regression normalization for methylation data")
5699 "This is a package to perform the @dfn{Adaptive Robust Regression
5700 method} (ARRm) for the normalization of methylation data from the Illumina
5701 Infinium HumanMethylation 450k assay.")
5702 (license license:artistic2.0)))
5704 (define-public r-biocfilecache
5706 (name "r-biocfilecache")
5711 (uri (bioconductor-uri "BiocFileCache" version))
5714 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
5715 (properties `((upstream-name . "BiocFileCache")))
5716 (build-system r-build-system)
5718 `(("r-curl" ,r-curl)
5720 ("r-dbplyr" ,r-dbplyr)
5721 ("r-dplyr" ,r-dplyr)
5723 ("r-rappdirs" ,r-rappdirs)
5724 ("r-rsqlite" ,r-rsqlite)))
5726 `(("r-knitr" ,r-knitr)))
5727 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5728 (synopsis "Manage files across sessions")
5730 "This package creates a persistent on-disk cache of files that the user
5731 can add, update, and retrieve. It is useful for managing resources (such as
5732 custom Txdb objects) that are costly or difficult to create, web resources,
5733 and data files used across sessions.")
5734 (license license:artistic2.0)))
5736 (define-public r-iclusterplus
5738 (name "r-iclusterplus")
5743 (uri (bioconductor-uri "iClusterPlus" version))
5746 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
5747 (properties `((upstream-name . "iClusterPlus")))
5748 (build-system r-build-system)
5749 (native-inputs `(("gfortran" ,gfortran)))
5750 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5751 (synopsis "Integrative clustering of multi-type genomic data")
5753 "iClusterPlus is developed for integrative clustering analysis of
5754 multi-type genomic data and is an enhanced version of iCluster proposed and
5755 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5756 from the experiments where biological samples (e.g. tumor samples) are
5757 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5758 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5759 on. In the iClusterPlus model, binary observations such as somatic mutation
5760 are modeled as Binomial processes; categorical observations such as copy
5761 number states are realizations of Multinomial random variables; counts are
5762 modeled as Poisson random processes; and continuous measures are modeled by
5763 Gaussian distributions.")
5764 (license license:gpl2+)))
5766 (define-public r-rbowtie
5773 (uri (bioconductor-uri "Rbowtie" version))
5776 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
5777 (properties `((upstream-name . "Rbowtie")))
5778 (build-system r-build-system)
5782 `(("r-knitr" ,r-knitr)))
5783 (home-page "https://bioconductor.org/packages/Rbowtie/")
5784 (synopsis "R bowtie wrapper")
5786 "This package provides an R wrapper around the popular bowtie short read
5787 aligner and around SpliceMap, a de novo splice junction discovery and
5789 (license license:artistic2.0)))
5791 (define-public r-sgseq
5798 (uri (bioconductor-uri "SGSeq" version))
5801 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
5802 (properties `((upstream-name . "SGSeq")))
5803 (build-system r-build-system)
5805 `(("r-annotationdbi" ,r-annotationdbi)
5806 ("r-biocgenerics" ,r-biocgenerics)
5807 ("r-biostrings" ,r-biostrings)
5808 ("r-genomeinfodb" ,r-genomeinfodb)
5809 ("r-genomicalignments" ,r-genomicalignments)
5810 ("r-genomicfeatures" ,r-genomicfeatures)
5811 ("r-genomicranges" ,r-genomicranges)
5812 ("r-igraph" ,r-igraph)
5813 ("r-iranges" ,r-iranges)
5814 ("r-rsamtools" ,r-rsamtools)
5815 ("r-rtracklayer" ,r-rtracklayer)
5816 ("r-runit" ,r-runit)
5817 ("r-s4vectors" ,r-s4vectors)
5818 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5820 `(("r-knitr" ,r-knitr)))
5821 (home-page "https://bioconductor.org/packages/SGSeq/")
5822 (synopsis "Splice event prediction and quantification from RNA-seq data")
5824 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5825 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5826 represented as a splice graph, which can be obtained from existing annotation
5827 or predicted from the mapped sequence reads. Splice events are identified
5828 from the graph and are quantified locally using structurally compatible reads
5829 at the start or end of each splice variant. The software includes functions
5830 for splice event prediction, quantification, visualization and
5832 (license license:artistic2.0)))
5834 (define-public r-rhisat2
5841 (uri (bioconductor-uri "Rhisat2" version))
5844 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
5845 (properties `((upstream-name . "Rhisat2")))
5846 (build-system r-build-system)
5849 (modify-phases %standard-phases
5850 (add-after 'unpack 'make-reproducible
5852 (substitute* "src/Makefile"
5853 (("`hostname`") "guix")
5855 ;; Avoid shelling out to "which".
5856 (("^CC =.*") (which "gcc"))
5857 (("^CPP =.*") (which "g++")))
5860 `(("r-genomicfeatures" ,r-genomicfeatures)
5861 ("r-genomicranges" ,r-genomicranges)
5862 ("r-sgseq" ,r-sgseq)))
5864 `(("r-knitr" ,r-knitr)))
5865 (home-page "https://github.com/fmicompbio/Rhisat2")
5866 (synopsis "R Wrapper for HISAT2 sequence aligner")
5868 "This package provides an R interface to the HISAT2 spliced short-read
5869 aligner by Kim et al. (2015). The package contains wrapper functions to
5870 create a genome index and to perform the read alignment to the generated
5872 (license license:gpl3)))
5874 (define-public r-quasr
5881 (uri (bioconductor-uri "QuasR" version))
5884 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
5885 (properties `((upstream-name . "QuasR")))
5886 (build-system r-build-system)
5888 `(("r-annotationdbi" ,r-annotationdbi)
5889 ("r-biobase" ,r-biobase)
5890 ("r-biocgenerics" ,r-biocgenerics)
5891 ("r-biocmanager" ,r-biocmanager)
5892 ("r-biocparallel" ,r-biocparallel)
5893 ("r-biostrings" ,r-biostrings)
5894 ("r-bsgenome" ,r-bsgenome)
5895 ("r-genomeinfodb" ,r-genomeinfodb)
5896 ("r-genomicalignments" ,r-genomicalignments)
5897 ("r-genomicfeatures" ,r-genomicfeatures)
5898 ("r-genomicfiles" ,r-genomicfiles)
5899 ("r-genomicranges" ,r-genomicranges)
5900 ("r-iranges" ,r-iranges)
5901 ("r-rbowtie" ,r-rbowtie)
5902 ("r-rhisat2" ,r-rhisat2)
5903 ("r-rhtslib" ,r-rhtslib)
5904 ("r-rsamtools" ,r-rsamtools)
5905 ("r-rtracklayer" ,r-rtracklayer)
5906 ("r-s4vectors" ,r-s4vectors)
5907 ("r-shortread" ,r-shortread)))
5909 `(("r-knitr" ,r-knitr)))
5910 (home-page "https://bioconductor.org/packages/QuasR/")
5911 (synopsis "Quantify and annotate short reads in R")
5913 "This package provides a framework for the quantification and analysis of
5914 short genomic reads. It covers a complete workflow starting from raw sequence
5915 reads, over creation of alignments and quality control plots, to the
5916 quantification of genomic regions of interest.")
5917 (license license:gpl2)))
5919 (define-public r-rqc
5926 (uri (bioconductor-uri "Rqc" version))
5929 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
5930 (properties `((upstream-name . "Rqc")))
5931 (build-system r-build-system)
5933 `(("r-biocgenerics" ,r-biocgenerics)
5934 ("r-biocparallel" ,r-biocparallel)
5935 ("r-biocstyle" ,r-biocstyle)
5936 ("r-biostrings" ,r-biostrings)
5937 ("r-biovizbase" ,r-biovizbase)
5938 ("r-genomicalignments" ,r-genomicalignments)
5939 ("r-genomicfiles" ,r-genomicfiles)
5940 ("r-ggplot2" ,r-ggplot2)
5941 ("r-iranges" ,r-iranges)
5942 ("r-knitr" ,r-knitr)
5943 ("r-markdown" ,r-markdown)
5946 ("r-reshape2" ,r-reshape2)
5947 ("r-rsamtools" ,r-rsamtools)
5948 ("r-s4vectors" ,r-s4vectors)
5949 ("r-shiny" ,r-shiny)
5950 ("r-shortread" ,r-shortread)))
5952 `(("r-knitr" ,r-knitr)))
5953 (home-page "https://github.com/labbcb/Rqc")
5954 (synopsis "Quality control tool for high-throughput sequencing data")
5956 "Rqc is an optimized tool designed for quality control and assessment of
5957 high-throughput sequencing data. It performs parallel processing of entire
5958 files and produces a report which contains a set of high-resolution
5960 (license license:gpl2+)))
5962 (define-public r-birewire
5969 (uri (bioconductor-uri "BiRewire" version))
5972 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
5973 (properties `((upstream-name . "BiRewire")))
5974 (build-system r-build-system)
5976 `(("r-igraph" ,r-igraph)
5977 ("r-matrix" ,r-matrix)
5979 ("r-tsne" ,r-tsne)))
5980 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5981 (synopsis "Tools for randomization of bipartite graphs")
5983 "This package provides functions for bipartite network rewiring through N
5984 consecutive switching steps and for the computation of the minimal number of
5985 switching steps to be performed in order to maximise the dissimilarity with
5986 respect to the original network. It includes functions for the analysis of
5987 the introduced randomness across the switching steps and several other
5988 routines to analyse the resulting networks and their natural projections.")
5989 (license license:gpl3)))
5991 (define-public r-birta
5998 (uri (bioconductor-uri "birta" version))
6001 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
6002 (build-system r-build-system)
6004 `(("r-biobase" ,r-biobase)
6005 ("r-limma" ,r-limma)
6006 ("r-mass" ,r-mass)))
6007 (home-page "https://bioconductor.org/packages/birta")
6008 (synopsis "Bayesian inference of regulation of transcriptional activity")
6010 "Expression levels of mRNA molecules are regulated by different
6011 processes, comprising inhibition or activation by transcription factors and
6012 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
6013 Inference of Regulation of Transcriptional Activity) uses the regulatory
6014 networks of transcription factors and miRNAs together with mRNA and miRNA
6015 expression data to predict switches in regulatory activity between two
6016 conditions. A Bayesian network is used to model the regulatory structure and
6017 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
6018 (license license:gpl2+)))
6020 (define-public r-multidataset
6022 (name "r-multidataset")
6027 (uri (bioconductor-uri "MultiDataSet" version))
6030 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
6031 (properties `((upstream-name . "MultiDataSet")))
6032 (build-system r-build-system)
6034 `(("r-biobase" ,r-biobase)
6035 ("r-biocgenerics" ,r-biocgenerics)
6036 ("r-genomicranges" ,r-genomicranges)
6037 ("r-ggplot2" ,r-ggplot2)
6038 ("r-ggrepel" ,r-ggrepel)
6039 ("r-iranges" ,r-iranges)
6040 ("r-limma" ,r-limma)
6041 ("r-qqman" ,r-qqman)
6042 ("r-s4vectors" ,r-s4vectors)
6043 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6045 `(("r-knitr" ,r-knitr)))
6046 (home-page "https://bioconductor.org/packages/MultiDataSet/")
6047 (synopsis "Implementation of MultiDataSet and ResultSet")
6049 "This package provides an implementation of the BRGE's (Bioinformatic
6050 Research Group in Epidemiology from Center for Research in Environmental
6051 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
6052 integrating multi omics data sets and ResultSet is a container for omics
6053 results. This package contains base classes for MEAL and rexposome
6055 (license license:expat)))
6057 (define-public r-ropls
6064 (uri (bioconductor-uri "ropls" version))
6067 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
6068 (build-system r-build-system)
6070 `(("r-biobase" ,r-biobase)
6071 ("r-multidataset" ,r-multidataset)))
6073 `(("r-knitr" ,r-knitr))) ; for vignettes
6074 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
6075 (synopsis "Multivariate analysis and feature selection of omics data")
6077 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
6078 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
6079 regression, classification, and feature selection of omics data where the
6080 number of variables exceeds the number of samples and with multicollinearity
6081 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
6082 separately model the variation correlated (predictive) to the factor of
6083 interest and the uncorrelated (orthogonal) variation. While performing
6084 similarly to PLS, OPLS facilitates interpretation.
6086 This package provides imlementations of PCA, PLS, and OPLS for multivariate
6087 analysis and feature selection of omics data. In addition to scores, loadings
6088 and weights plots, the package provides metrics and graphics to determine the
6089 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
6090 validity of the model by permutation testing, detect outliers, and perform
6091 feature selection (e.g. with Variable Importance in Projection or regression
6093 (license license:cecill)))
6095 (define-public r-biosigner
6097 (name "r-biosigner")
6102 (uri (bioconductor-uri "biosigner" version))
6105 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
6106 (build-system r-build-system)
6108 `(("r-biobase" ,r-biobase)
6109 ("r-e1071" ,r-e1071)
6110 ("r-multidataset" ,r-multidataset)
6111 ("r-randomforest" ,r-randomforest)
6112 ("r-ropls" ,r-ropls)))
6114 `(("r-knitr" ,r-knitr)))
6115 (home-page "https://bioconductor.org/packages/biosigner/")
6116 (synopsis "Signature discovery from omics data")
6118 "Feature selection is critical in omics data analysis to extract
6119 restricted and meaningful molecular signatures from complex and high-dimension
6120 data, and to build robust classifiers. This package implements a method to
6121 assess the relevance of the variables for the prediction performances of the
6122 classifier. The approach can be run in parallel with the PLS-DA, Random
6123 Forest, and SVM binary classifiers. The signatures and the corresponding
6124 'restricted' models are returned, enabling future predictions on new
6126 (license license:cecill)))
6128 (define-public r-annotatr
6135 (uri (bioconductor-uri "annotatr" version))
6138 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
6139 (build-system r-build-system)
6141 `(("r-annotationdbi" ,r-annotationdbi)
6142 ("r-annotationhub" ,r-annotationhub)
6143 ("r-dplyr" ,r-dplyr)
6144 ("r-genomeinfodb" ,r-genomeinfodb)
6145 ("r-genomicfeatures" ,r-genomicfeatures)
6146 ("r-genomicranges" ,r-genomicranges)
6147 ("r-ggplot2" ,r-ggplot2)
6148 ("r-iranges" ,r-iranges)
6149 ("r-readr" ,r-readr)
6150 ("r-regioner" ,r-regioner)
6151 ("r-reshape2" ,r-reshape2)
6152 ("r-rtracklayer" ,r-rtracklayer)
6153 ("r-s4vectors" ,r-s4vectors)))
6155 `(("r-knitr" ,r-knitr)))
6156 (home-page "https://bioconductor.org/packages/annotatr/")
6157 (synopsis "Annotation of genomic regions to genomic annotations")
6159 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6160 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6161 to investigate the intersecting genomic annotations. Such annotations include
6162 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6163 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6164 enhancers. The annotatr package provides an easy way to summarize and
6165 visualize the intersection of genomic sites/regions with genomic
6167 (license license:gpl3)))
6169 (define-public r-rsubread
6176 (uri (bioconductor-uri "Rsubread" version))
6179 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
6180 (properties `((upstream-name . "Rsubread")))
6181 (build-system r-build-system)
6182 (inputs `(("zlib" ,zlib)))
6184 `(("r-matrix" ,r-matrix)))
6185 (home-page "https://bioconductor.org/packages/Rsubread/")
6186 (synopsis "Subread sequence alignment and counting for R")
6188 "This package provides tools for alignment, quantification and analysis
6189 of second and third generation sequencing data. It includes functionality for
6190 read mapping, read counting, SNP calling, structural variant detection and
6191 gene fusion discovery. It can be applied to all major sequencing techologies
6192 and to both short and long sequence reads.")
6193 (license license:gpl3)))
6195 (define-public r-flowutils
6197 (name "r-flowutils")
6202 (uri (bioconductor-uri "flowUtils" version))
6205 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6206 (properties `((upstream-name . "flowUtils")))
6207 (build-system r-build-system)
6209 `(("r-biobase" ,r-biobase)
6210 ("r-corpcor" ,r-corpcor)
6211 ("r-flowcore" ,r-flowcore)
6212 ("r-graph" ,r-graph)
6213 ("r-runit" ,r-runit)
6215 (home-page "https://github.com/jspidlen/flowUtils")
6216 (synopsis "Utilities for flow cytometry")
6218 "This package provides utilities for flow cytometry data.")
6219 (license license:artistic2.0)))
6221 (define-public r-consensusclusterplus
6223 (name "r-consensusclusterplus")
6228 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6231 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6233 `((upstream-name . "ConsensusClusterPlus")))
6234 (build-system r-build-system)
6237 ("r-biobase" ,r-biobase)
6238 ("r-cluster" ,r-cluster)))
6239 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6240 (synopsis "Clustering algorithm")
6242 "This package provides an implementation of an algorithm for determining
6243 cluster count and membership by stability evidence in unsupervised analysis.")
6244 (license license:gpl2)))
6246 (define-public r-cytolib
6253 (uri (bioconductor-uri "cytolib" version))
6256 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
6257 (properties `((upstream-name . "cytolib")))
6258 (build-system r-build-system)
6261 (modify-phases %standard-phases
6262 (add-after 'unpack 'fix-linking
6264 (substitute* "src/Makevars.in"
6265 ;; This is to avoid having a plain directory on the list of
6266 ;; libraries to link.
6267 (("\\(RHDF5_LIBS\\)" match)
6268 (string-append match "/libhdf5.a")))
6271 `(("r-knitr" ,r-knitr)
6272 ("pkg-config" ,pkg-config)))
6276 ("r-rcpparmadillo" ,r-rcpparmadillo)
6277 ("r-rcppparallel" ,r-rcppparallel)
6278 ("r-rhdf5lib" ,r-rhdf5lib)
6279 ("r-rprotobuflib" ,r-rprotobuflib)))
6280 (home-page "https://bioconductor.org/packages/cytolib/")
6281 (synopsis "C++ infrastructure for working with gated cytometry")
6283 "This package provides the core data structure and API to represent and
6284 interact with gated cytometry data.")
6285 (license license:artistic2.0)))
6287 (define-public r-flowcore
6294 (uri (bioconductor-uri "flowCore" version))
6297 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
6298 (properties `((upstream-name . "flowCore")))
6299 (build-system r-build-system)
6302 ("r-biobase" ,r-biobase)
6303 ("r-biocgenerics" ,r-biocgenerics)
6304 ("r-cytolib" ,r-cytolib)
6305 ("r-matrixstats" ,r-matrixstats)
6307 ("r-rcpparmadillo" ,r-rcpparmadillo)
6308 ("r-rprotobuflib" ,r-rprotobuflib)
6309 ("r-s4vectors" ,r-s4vectors)))
6311 `(("r-knitr" ,r-knitr)))
6312 (home-page "https://bioconductor.org/packages/flowCore")
6313 (synopsis "Basic structures for flow cytometry data")
6315 "This package provides S4 data structures and basic functions to deal
6316 with flow cytometry data.")
6317 (license license:artistic2.0)))
6319 (define-public r-flowmeans
6321 (name "r-flowmeans")
6326 (uri (bioconductor-uri "flowMeans" version))
6329 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
6330 (properties `((upstream-name . "flowMeans")))
6331 (build-system r-build-system)
6333 `(("r-biobase" ,r-biobase)
6334 ("r-feature" ,r-feature)
6335 ("r-flowcore" ,r-flowcore)
6336 ("r-rrcov" ,r-rrcov)))
6337 (home-page "https://bioconductor.org/packages/flowMeans")
6338 (synopsis "Non-parametric flow cytometry data gating")
6340 "This package provides tools to identify cell populations in Flow
6341 Cytometry data using non-parametric clustering and segmented-regression-based
6342 change point detection.")
6343 (license license:artistic2.0)))
6345 (define-public r-ncdfflow
6352 (uri (bioconductor-uri "ncdfFlow" version))
6355 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
6356 (properties `((upstream-name . "ncdfFlow")))
6357 (build-system r-build-system)
6360 (modify-phases %standard-phases
6361 (add-after 'unpack 'fix-linking
6363 (substitute* "src/Makevars"
6364 ;; This is to avoid having a plain directory on the list of
6365 ;; libraries to link.
6366 (("\\(RHDF5_LIBS\\)" match)
6367 (string-append match "/libhdf5.a")))
6371 ("r-biobase" ,r-biobase)
6372 ("r-biocgenerics" ,r-biocgenerics)
6373 ("r-flowcore" ,r-flowcore)
6375 ("r-rcpparmadillo" ,r-rcpparmadillo)
6376 ("r-rhdf5lib" ,r-rhdf5lib)
6377 ("r-zlibbioc" ,r-zlibbioc)))
6379 `(("r-knitr" ,r-knitr)))
6380 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6381 (synopsis "HDF5 based storage for flow cytometry data")
6383 "This package provides HDF5 storage based methods and functions for
6384 manipulation of flow cytometry data.")
6385 (license license:artistic2.0)))
6387 (define-public r-ggcyto
6394 (uri (bioconductor-uri "ggcyto" version))
6397 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
6398 (properties `((upstream-name . "ggcyto")))
6399 (build-system r-build-system)
6401 `(("r-data-table" ,r-data-table)
6402 ("r-flowcore" ,r-flowcore)
6403 ("r-flowworkspace" ,r-flowworkspace)
6404 ("r-ggplot2" ,r-ggplot2)
6405 ("r-gridextra" ,r-gridextra)
6406 ("r-hexbin" ,r-hexbin)
6407 ("r-ncdfflow" ,r-ncdfflow)
6409 ("r-rcolorbrewer" ,r-rcolorbrewer)
6410 ("r-rlang" ,r-rlang)
6411 ("r-scales" ,r-scales)))
6413 `(("r-knitr" ,r-knitr)))
6414 (home-page "https://github.com/RGLab/ggcyto/issues")
6415 (synopsis "Visualize Cytometry data with ggplot")
6417 "With the dedicated fortify method implemented for @code{flowSet},
6418 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6419 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6420 and some custom layers also make it easy to add gates and population
6421 statistics to the plot.")
6422 (license license:artistic2.0)))
6424 (define-public r-flowviz
6431 (uri (bioconductor-uri "flowViz" version))
6434 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
6435 (properties `((upstream-name . "flowViz")))
6436 (build-system r-build-system)
6438 `(("r-biobase" ,r-biobase)
6439 ("r-flowcore" ,r-flowcore)
6440 ("r-hexbin" ,r-hexbin)
6441 ("r-idpmisc" ,r-idpmisc)
6442 ("r-kernsmooth" ,r-kernsmooth)
6443 ("r-lattice" ,r-lattice)
6444 ("r-latticeextra" ,r-latticeextra)
6446 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6448 `(("r-knitr" ,r-knitr)))
6449 (home-page "https://bioconductor.org/packages/flowViz/")
6450 (synopsis "Visualization for flow cytometry")
6452 "This package provides visualization tools for flow cytometry data.")
6453 (license license:artistic2.0)))
6455 (define-public r-flowclust
6457 (name "r-flowclust")
6462 (uri (bioconductor-uri "flowClust" version))
6465 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
6466 (properties `((upstream-name . "flowClust")))
6467 (build-system r-build-system)
6470 (list "--configure-args=--enable-bundled-gsl=no")))
6472 `(("r-biobase" ,r-biobase)
6473 ("r-biocgenerics" ,r-biocgenerics)
6475 ("r-corpcor" ,r-corpcor)
6476 ("r-ellipse" ,r-ellipse)
6477 ("r-flowcore" ,r-flowcore)
6478 ("r-flowviz" ,r-flowviz)
6479 ("r-graph" ,r-graph)
6480 ("r-mnormt" ,r-mnormt)))
6484 `(("pkg-config" ,pkg-config)
6485 ("r-knitr" ,r-knitr)))
6486 (home-page "https://bioconductor.org/packages/flowClust")
6487 (synopsis "Clustering for flow cytometry")
6489 "This package provides robust model-based clustering using a t-mixture
6490 model with Box-Cox transformation.")
6491 (license license:artistic2.0)))
6493 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6494 ;; make it use our protobuf package instead.
6495 (define-public r-rprotobuflib
6497 (name "r-rprotobuflib")
6502 (uri (bioconductor-uri "RProtoBufLib" version))
6505 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
6506 (properties `((upstream-name . "RProtoBufLib")))
6507 (build-system r-build-system)
6510 (modify-phases %standard-phases
6511 (add-after 'unpack 'unpack-bundled-sources
6513 (with-directory-excursion "src"
6514 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6517 `(("r-knitr" ,r-knitr)))
6518 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6519 (synopsis "C++ headers and static libraries of Protocol buffers")
6521 "This package provides the headers and static library of Protocol buffers
6522 for other R packages to compile and link against.")
6523 (license license:bsd-3)))
6525 (define-public r-flowworkspace
6527 (name "r-flowworkspace")
6532 (uri (bioconductor-uri "flowWorkspace" version))
6535 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
6536 (properties `((upstream-name . "flowWorkspace")))
6537 (build-system r-build-system)
6540 (modify-phases %standard-phases
6541 (add-after 'unpack 'fix-linking
6543 (substitute* "src/Makevars"
6544 ;; This is to avoid having a plain directory on the list of
6545 ;; libraries to link.
6546 (("\\{h5lib\\}" match)
6547 (string-append match "/libhdf5.a")))
6550 `(("r-aws-s3" ,r-aws-s3)
6551 ("r-aws-signature" ,r-aws-signature)
6553 ("r-biobase" ,r-biobase)
6554 ("r-biocgenerics" ,r-biocgenerics)
6555 ("r-cytolib" ,r-cytolib)
6556 ("r-data-table" ,r-data-table)
6557 ("r-digest" ,r-digest)
6558 ("r-dplyr" ,r-dplyr)
6559 ("r-flowcore" ,r-flowcore)
6560 ("r-ggplot2" ,r-ggplot2)
6561 ("r-graph" ,r-graph)
6562 ("r-lattice" ,r-lattice)
6563 ("r-latticeextra" ,r-latticeextra)
6564 ("r-matrixstats" ,r-matrixstats)
6565 ("r-ncdfflow" ,r-ncdfflow)
6568 ("r-rcpparmadillo" ,r-rcpparmadillo)
6569 ("r-rcppparallel" ,r-rcppparallel)
6570 ("r-rgraphviz" ,r-rgraphviz)
6571 ("r-rhdf5lib" ,r-rhdf5lib)
6572 ("r-rprotobuflib" ,r-rprotobuflib)
6573 ("r-scales" ,r-scales)
6576 `(("r-knitr" ,r-knitr)))
6577 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6578 (synopsis "Infrastructure for working with cytometry data")
6580 "This package is designed to facilitate comparison of automated gating
6581 methods against manual gating done in flowJo. This package allows you to
6582 import basic flowJo workspaces into BioConductor and replicate the gating from
6583 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6584 samples, compensation, and transformation are performed so that the output
6585 matches the flowJo analysis.")
6586 (license license:artistic2.0)))
6588 (define-public r-flowstats
6590 (name "r-flowstats")
6595 (uri (bioconductor-uri "flowStats" version))
6598 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
6599 (properties `((upstream-name . "flowStats")))
6600 (build-system r-build-system)
6602 `(("r-biobase" ,r-biobase)
6603 ("r-biocgenerics" ,r-biocgenerics)
6604 ("r-cluster" ,r-cluster)
6606 ("r-flowcore" ,r-flowcore)
6607 ("r-flowviz" ,r-flowviz)
6608 ("r-flowworkspace" ,r-flowworkspace)
6609 ("r-kernsmooth" ,r-kernsmooth)
6611 ("r-lattice" ,r-lattice)
6613 ("r-ncdfflow" ,r-ncdfflow)
6614 ("r-rcolorbrewer" ,r-rcolorbrewer)
6615 ("r-rrcov" ,r-rrcov)))
6616 (home-page "http://www.github.com/RGLab/flowStats")
6617 (synopsis "Statistical methods for the analysis of flow cytometry data")
6619 "This package provides methods and functionality to analyze flow data
6620 that is beyond the basic infrastructure provided by the @code{flowCore}
6622 (license license:artistic2.0)))
6624 (define-public r-opencyto
6631 (uri (bioconductor-uri "openCyto" version))
6634 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
6635 (properties `((upstream-name . "openCyto")))
6636 (build-system r-build-system)
6638 `(("r-biobase" ,r-biobase)
6639 ("r-biocgenerics" ,r-biocgenerics)
6641 ("r-data-table" ,r-data-table)
6642 ("r-flowclust" ,r-flowclust)
6643 ("r-flowcore" ,r-flowcore)
6644 ("r-flowstats" ,r-flowstats)
6645 ("r-flowviz" ,r-flowviz)
6646 ("r-flowworkspace" ,r-flowworkspace)
6647 ("r-graph" ,r-graph)
6648 ("r-gtools" ,r-gtools)
6650 ("r-lattice" ,r-lattice)
6652 ("r-ncdfflow" ,r-ncdfflow)
6654 ("r-r-utils" ,r-r-utils)
6656 ("r-rcolorbrewer" ,r-rcolorbrewer)
6658 ("r-rrcov" ,r-rrcov)))
6660 `(("r-knitr" ,r-knitr)))
6661 (home-page "https://bioconductor.org/packages/openCyto")
6662 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6664 "This package is designed to facilitate the automated gating methods in a
6665 sequential way to mimic the manual gating strategy.")
6666 (license license:artistic2.0)))
6668 (define-public r-cytoml
6675 (uri (bioconductor-uri "CytoML" version))
6678 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
6679 (properties `((upstream-name . "CytoML")))
6680 (build-system r-build-system)
6683 (modify-phases %standard-phases
6684 (add-after 'unpack 'fix-linking
6686 (substitute* "src/Makevars.in"
6687 ;; This is to avoid having a plain directory on the list of
6688 ;; libraries to link.
6689 (("\\{h5lib\\}" match)
6690 (string-append match "/libhdf5.a")))
6693 `(("libxml2" ,libxml2)))
6695 `(("r-base64enc" ,r-base64enc)
6697 ("r-biobase" ,r-biobase)
6698 ("r-corpcor" ,r-corpcor)
6699 ("r-cytolib" ,r-cytolib)
6700 ("r-data-table" ,r-data-table)
6701 ("r-dplyr" ,r-dplyr)
6702 ("r-flowcore" ,r-flowcore)
6703 ("r-flowworkspace" ,r-flowworkspace)
6704 ("r-ggcyto" ,r-ggcyto)
6705 ("r-graph" ,r-graph)
6706 ("r-jsonlite" ,r-jsonlite)
6707 ("r-lattice" ,r-lattice)
6708 ("r-opencyto" ,r-opencyto)
6712 ("r-rcpparmadillo" ,r-rcpparmadillo)
6713 ("r-rcppparallel" ,r-rcppparallel)
6714 ("r-rgraphviz" ,r-rgraphviz)
6715 ("r-rhdf5lib" ,r-rhdf5lib)
6716 ("r-rprotobuflib" ,r-rprotobuflib)
6717 ("r-runit" ,r-runit)
6718 ("r-tibble" ,r-tibble)
6721 ("r-yaml" ,r-yaml)))
6723 `(("r-knitr" ,r-knitr)))
6724 (home-page "https://github.com/RGLab/CytoML")
6725 (synopsis "GatingML interface for cross platform cytometry data sharing")
6727 "This package provides an interface to implementations of the GatingML2.0
6728 standard to exchange gated cytometry data with other software platforms.")
6729 (license license:artistic2.0)))
6731 (define-public r-flowsom
6738 (uri (bioconductor-uri "FlowSOM" version))
6741 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
6742 (properties `((upstream-name . "FlowSOM")))
6743 (build-system r-build-system)
6745 `(("r-biocgenerics" ,r-biocgenerics)
6746 ("r-consensusclusterplus" ,r-consensusclusterplus)
6747 ("r-cytoml" ,r-cytoml)
6748 ("r-flowcore" ,r-flowcore)
6749 ("r-flowworkspace" ,r-flowworkspace)
6750 ("r-igraph" ,r-igraph)
6751 ("r-rcolorbrewer" ,r-rcolorbrewer)
6754 (home-page "https://bioconductor.org/packages/FlowSOM/")
6755 (synopsis "Visualize and interpret cytometry data")
6757 "FlowSOM offers visualization options for cytometry data, by using
6758 self-organizing map clustering and minimal spanning trees.")
6759 (license license:gpl2+)))
6761 (define-public r-mixomics
6768 (uri (bioconductor-uri "mixOmics" version))
6771 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
6772 (properties `((upstream-name . "mixOmics")))
6773 (build-system r-build-system)
6775 `(("r-corpcor" ,r-corpcor)
6776 ("r-dplyr" ,r-dplyr)
6777 ("r-ellipse" ,r-ellipse)
6778 ("r-ggrepel" ,r-ggrepel)
6779 ("r-ggplot2" ,r-ggplot2)
6780 ("r-gridextra" ,r-gridextra)
6781 ("r-igraph" ,r-igraph)
6782 ("r-lattice" ,r-lattice)
6784 ("r-matrixstats" ,r-matrixstats)
6785 ("r-rarpack" ,r-rarpack)
6786 ("r-rcolorbrewer" ,r-rcolorbrewer)
6787 ("r-reshape2" ,r-reshape2)
6788 ("r-tidyr" ,r-tidyr)))
6790 `(("r-knitr" ,r-knitr)))
6791 (home-page "http://www.mixOmics.org")
6792 (synopsis "Multivariate methods for exploration of biological datasets")
6794 "mixOmics offers a wide range of multivariate methods for the exploration
6795 and integration of biological datasets with a particular focus on variable
6796 selection. The package proposes several sparse multivariate models we have
6797 developed to identify the key variables that are highly correlated, and/or
6798 explain the biological outcome of interest. The data that can be analysed
6799 with mixOmics may come from high throughput sequencing technologies, such as
6800 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6801 also beyond the realm of omics (e.g. spectral imaging). The methods
6802 implemented in mixOmics can also handle missing values without having to
6803 delete entire rows with missing data.")
6804 (license license:gpl2+)))
6806 (define-public r-depecher
6807 (package ;Source/Weave error
6813 (uri (bioconductor-uri "DepecheR" version))
6816 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
6817 (properties `((upstream-name . "DepecheR")))
6818 (build-system r-build-system)
6820 `(("r-beanplot" ,r-beanplot)
6821 ("r-dosnow" ,r-dosnow)
6822 ("r-dplyr" ,r-dplyr)
6824 ("r-foreach" ,r-foreach)
6825 ("r-ggplot2" ,r-ggplot2)
6826 ("r-gmodels" ,r-gmodels)
6827 ("r-gplots" ,r-gplots)
6829 ("r-matrixstats" ,r-matrixstats)
6830 ("r-mixomics" ,r-mixomics)
6831 ("r-moments" ,r-moments)
6833 ("r-rcppeigen" ,r-rcppeigen)
6834 ("r-reshape2" ,r-reshape2)
6835 ("r-robustbase" ,r-robustbase)
6836 ("r-viridis" ,r-viridis)))
6838 `(("r-knitr" ,r-knitr)))
6839 (home-page "https://bioconductor.org/packages/DepecheR/")
6840 (synopsis "Identify traits of clusters in high-dimensional entities")
6842 "The purpose of this package is to identify traits in a dataset that can
6843 separate groups. This is done on two levels. First, clustering is performed,
6844 using an implementation of sparse K-means. Secondly, the generated clusters
6845 are used to predict outcomes of groups of individuals based on their
6846 distribution of observations in the different clusters. As certain clusters
6847 with separating information will be identified, and these clusters are defined
6848 by a sparse number of variables, this method can reduce the complexity of
6849 data, to only emphasize the data that actually matters.")
6850 (license license:expat)))
6852 (define-public r-rcistarget
6854 (name "r-rcistarget")
6859 (uri (bioconductor-uri "RcisTarget" version))
6862 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
6863 (properties `((upstream-name . "RcisTarget")))
6864 (build-system r-build-system)
6866 `(("r-aucell" ,r-aucell)
6867 ("r-biocgenerics" ,r-biocgenerics)
6868 ("r-data-table" ,r-data-table)
6869 ("r-feather" ,r-feather)
6870 ("r-gseabase" ,r-gseabase)
6871 ("r-r-utils" ,r-r-utils)
6872 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6874 `(("r-knitr" ,r-knitr)))
6875 (home-page "https://aertslab.org/#scenic")
6876 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6878 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6879 over-represented on a gene list. In a first step, RcisTarget selects DNA
6880 motifs that are significantly over-represented in the surroundings of the
6881 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6882 achieved by using a database that contains genome-wide cross-species rankings
6883 for each motif. The motifs that are then annotated to TFs and those that have
6884 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6885 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6886 genes in the gene-set that are ranked above the leading edge).")
6887 (license license:gpl3)))
6889 (define-public r-cicero
6896 (uri (bioconductor-uri "cicero" version))
6899 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
6900 (build-system r-build-system)
6902 `(("r-assertthat" ,r-assertthat)
6903 ("r-biobase" ,r-biobase)
6904 ("r-biocgenerics" ,r-biocgenerics)
6905 ("r-data-table" ,r-data-table)
6906 ("r-dplyr" ,r-dplyr)
6908 ("r-genomicranges" ,r-genomicranges)
6909 ("r-ggplot2" ,r-ggplot2)
6910 ("r-glasso" ,r-glasso)
6912 ("r-igraph" ,r-igraph)
6913 ("r-iranges" ,r-iranges)
6914 ("r-matrix" ,r-matrix)
6915 ("r-monocle" ,r-monocle)
6917 ("r-reshape2" ,r-reshape2)
6918 ("r-s4vectors" ,r-s4vectors)
6919 ("r-stringi" ,r-stringi)
6920 ("r-stringr" ,r-stringr)
6921 ("r-tibble" ,r-tibble)
6922 ("r-tidyr" ,r-tidyr)
6923 ("r-vgam" ,r-vgam)))
6925 `(("r-knitr" ,r-knitr)))
6926 (home-page "https://bioconductor.org/packages/cicero/")
6927 (synopsis "Predict cis-co-accessibility from single-cell data")
6929 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6930 accessibility data. It also extends the monocle package for use in chromatin
6931 accessibility data.")
6932 (license license:expat)))
6934 ;; This is the latest commit on the "monocle3" branch.
6935 (define-public r-cicero-monocle3
6936 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6938 (package (inherit r-cicero)
6939 (name "r-cicero-monocle3")
6940 (version (git-version "1.3.2" revision commit))
6945 (url "https://github.com/cole-trapnell-lab/cicero-release")
6947 (file-name (git-file-name name version))
6950 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6952 `(("r-monocle3" ,r-monocle3)
6953 ,@(alist-delete "r-monocle"
6954 (package-propagated-inputs r-cicero)))))))
6956 (define-public r-circrnaprofiler
6958 (name "r-circrnaprofiler")
6963 (uri (bioconductor-uri "circRNAprofiler" version))
6966 "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
6968 `((upstream-name . "circRNAprofiler")))
6969 (build-system r-build-system)
6971 `(("r-annotationhub" ,r-annotationhub)
6972 ("r-biostrings" ,r-biostrings)
6973 ("r-bsgenome" ,r-bsgenome)
6974 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
6975 ("r-deseq2" ,r-deseq2)
6976 ("r-dplyr" ,r-dplyr)
6977 ("r-edger" ,r-edger)
6978 ("r-genomeinfodb" ,r-genomeinfodb)
6979 ("r-genomicranges" ,r-genomicranges)
6980 ("r-ggplot2" ,r-ggplot2)
6981 ("r-gwascat" ,r-gwascat)
6982 ("r-iranges" ,r-iranges)
6983 ("r-magrittr" ,r-magrittr)
6984 ("r-r-utils" ,r-r-utils)
6985 ("r-readr" ,r-readr)
6986 ("r-reshape2" ,r-reshape2)
6987 ("r-rlang" ,r-rlang)
6988 ("r-rtracklayer" ,r-rtracklayer)
6989 ("r-s4vectors" ,r-s4vectors)
6990 ("r-seqinr" ,r-seqinr)
6991 ("r-stringi" ,r-stringi)
6992 ("r-stringr" ,r-stringr)
6993 ("r-universalmotif" ,r-universalmotif)))
6995 `(("r-knitr" ,r-knitr)))
6997 "https://github.com/Aufiero/circRNAprofiler")
6999 "Computational framework for the downstream analysis of circular RNA's")
7001 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
7002 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
7003 framework allows to combine and analyze circRNAs previously detected by
7004 multiple publicly available annotation-based circRNA detection tools. It
7005 covers different aspects of circRNAs analysis from differential expression
7006 analysis, evolutionary conservation, biogenesis to functional analysis.")
7007 (license license:gpl3)))
7009 (define-public r-cistopic
7010 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
7014 (version (git-version "0.2.1" revision commit))
7019 (url "https://github.com/aertslab/cisTopic")
7021 (file-name (git-file-name name version))
7024 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
7025 (build-system r-build-system)
7027 `(("r-aucell" ,r-aucell)
7028 ("r-data-table" ,r-data-table)
7029 ("r-dplyr" ,r-dplyr)
7030 ("r-dosnow" ,r-dosnow)
7032 ("r-feather" ,r-feather)
7033 ("r-fitdistrplus" ,r-fitdistrplus)
7034 ("r-genomicranges" ,r-genomicranges)
7035 ("r-ggplot2" ,r-ggplot2)
7037 ("r-matrix" ,r-matrix)
7039 ("r-rcistarget" ,r-rcistarget)
7040 ("r-rtracklayer" ,r-rtracklayer)
7041 ("r-s4vectors" ,r-s4vectors)))
7042 (home-page "https://github.com/aertslab/cisTopic")
7043 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
7045 "The sparse nature of single cell epigenomics data can be overruled using
7046 probabilistic modelling methods such as @dfn{Latent Dirichlet
7047 Allocation} (LDA). This package allows the probabilistic modelling of
7048 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
7049 includes functionalities to identify cell states based on the contribution of
7050 cisTopics and explore the nature and regulatory proteins driving them.")
7051 (license license:gpl3))))
7053 (define-public r-genie3
7060 (uri (bioconductor-uri "GENIE3" version))
7063 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
7064 (properties `((upstream-name . "GENIE3")))
7065 (build-system r-build-system)
7066 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
7068 `(("r-knitr" ,r-knitr)))
7069 (home-page "https://bioconductor.org/packages/GENIE3")
7070 (synopsis "Gene network inference with ensemble of trees")
7072 "This package implements the GENIE3 algorithm for inferring gene
7073 regulatory networks from expression data.")
7074 (license license:gpl2+)))
7076 (define-public r-roc
7083 (uri (bioconductor-uri "ROC" version))
7086 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
7087 (properties `((upstream-name . "ROC")))
7088 (build-system r-build-system)
7090 `(("r-knitr" ,r-knitr)))
7091 (home-page "https://www.bioconductor.org/packages/ROC/")
7092 (synopsis "Utilities for ROC curves")
7094 "This package provides utilities for @dfn{Receiver Operating
7095 Characteristic} (ROC) curves, with a focus on micro arrays.")
7096 (license license:artistic2.0)))
7098 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
7100 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
7105 (uri (bioconductor-uri
7106 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
7107 version 'annotation))
7110 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
7113 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
7114 (build-system r-build-system)
7115 (propagated-inputs `(("r-minfi" ,r-minfi)))
7117 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
7118 (synopsis "Annotation for Illumina's 450k methylation arrays")
7120 "This package provides manifests and annotation for Illumina's 450k array
7122 (license license:artistic2.0)))
7124 (define-public r-watermelon
7126 (name "r-watermelon")
7131 (uri (bioconductor-uri "wateRmelon" version))
7134 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
7135 (properties `((upstream-name . "wateRmelon")))
7136 (build-system r-build-system)
7138 `(("r-biobase" ,r-biobase)
7139 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
7140 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
7141 ("r-illuminaio" ,r-illuminaio)
7142 ("r-limma" ,r-limma)
7144 ("r-matrixstats" ,r-matrixstats)
7145 ("r-methylumi" ,r-methylumi)
7147 (home-page "https://bioconductor.org/packages/wateRmelon/")
7148 (synopsis "Illumina 450 methylation array normalization and metrics")
7150 "The standard index of DNA methylation (beta) is computed from methylated
7151 and unmethylated signal intensities. Betas calculated from raw signal
7152 intensities perform well, but using 11 methylomic datasets we demonstrate that
7153 quantile normalization methods produce marked improvement. The commonly used
7154 procedure of normalizing betas is inferior to the separate normalization of M
7155 and U, and it is also advantageous to normalize Type I and Type II assays
7156 separately. This package provides 15 flavours of betas and three performance
7157 metrics, with methods for objects produced by the @code{methylumi} and
7158 @code{minfi} packages.")
7159 (license license:gpl3)))
7161 (define-public r-gdsfmt
7168 (uri (bioconductor-uri "gdsfmt" version))
7171 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
7172 (modules '((guix build utils)))
7173 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
7174 ;; them and link with system libraries instead.
7177 (for-each delete-file-recursively
7181 (substitute* "src/Makevars"
7182 (("all: \\$\\(SHLIB\\)") "all:")
7183 (("\\$\\(SHLIB\\): liblzma.a") "")
7184 (("(ZLIB|LZ4)/.*") "")
7185 (("CoreArray/dVLIntGDS.cpp.*")
7186 "CoreArray/dVLIntGDS.cpp")
7187 (("CoreArray/dVLIntGDS.o.*")
7188 "CoreArray/dVLIntGDS.o")
7189 (("PKG_LIBS = ./liblzma.a")
7190 "PKG_LIBS = -llz4"))
7191 (substitute* "src/CoreArray/dStream.h"
7192 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
7193 (string-append "include <" header ">")))
7195 (properties `((upstream-name . "gdsfmt")))
7196 (build-system r-build-system)
7202 `(("r-knitr" ,r-knitr)))
7203 (home-page "http://corearray.sourceforge.net/")
7205 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7207 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7208 Data Structure} (GDS) data files, which are portable across platforms with
7209 hierarchical structure to store multiple scalable array-oriented data sets
7210 with metadata information. It is suited for large-scale datasets, especially
7211 for data which are much larger than the available random-access memory. The
7212 @code{gdsfmt} package offers efficient operations specifically designed for
7213 integers of less than 8 bits, since a diploid genotype, like
7214 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7215 byte. Data compression and decompression are available with relatively
7216 efficient random access. It is also allowed to read a GDS file in parallel
7217 with multiple R processes supported by the package @code{parallel}.")
7218 (license license:lgpl3)))
7220 (define-public r-bigmelon
7227 (uri (bioconductor-uri "bigmelon" version))
7230 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7231 (properties `((upstream-name . "bigmelon")))
7232 (build-system r-build-system)
7234 `(("r-biobase" ,r-biobase)
7235 ("r-biocgenerics" ,r-biocgenerics)
7236 ("r-gdsfmt" ,r-gdsfmt)
7237 ("r-geoquery" ,r-geoquery)
7238 ("r-methylumi" ,r-methylumi)
7239 ("r-minfi" ,r-minfi)
7240 ("r-watermelon" ,r-watermelon)))
7241 (home-page "https://bioconductor.org/packages/bigmelon/")
7242 (synopsis "Illumina methylation array analysis for large experiments")
7244 "This package provides methods for working with Illumina arrays using the
7245 @code{gdsfmt} package.")
7246 (license license:gpl3)))
7248 (define-public r-seqbias
7255 (uri (bioconductor-uri "seqbias" version))
7258 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
7259 (properties `((upstream-name . "seqbias")))
7260 (build-system r-build-system)
7262 `(("r-biostrings" ,r-biostrings)
7263 ("r-genomicranges" ,r-genomicranges)
7264 ("r-rhtslib" ,r-rhtslib)))
7265 (home-page "https://bioconductor.org/packages/seqbias/")
7266 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
7268 "This package implements a model of per-position sequencing bias in
7269 high-throughput sequencing data using a simple Bayesian network, the structure
7270 and parameters of which are trained on a set of aligned reads and a reference
7272 (license license:lgpl3)))
7274 (define-public r-snplocs-hsapiens-dbsnp144-grch37
7276 (name "r-snplocs-hsapiens-dbsnp144-grch37")
7280 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
7281 version 'annotation))
7284 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
7285 (build-system r-build-system)
7286 ;; As this package provides little more than a very large data file it
7287 ;; doesn't make sense to build substitutes.
7288 (arguments `(#:substitutable? #f))
7290 `(("r-biocgenerics" ,r-biocgenerics)
7291 ("r-s4vectors" ,r-s4vectors)
7292 ("r-iranges" ,r-iranges)
7293 ("r-genomeinfodb" ,r-genomeinfodb)
7294 ("r-genomicranges" ,r-genomicranges)
7295 ("r-bsgenome" ,r-bsgenome)
7296 ("r-biostrings" ,r-biostrings)))
7298 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
7299 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
7300 (description "This package provides SNP locations and alleles for Homo
7301 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
7302 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
7303 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
7304 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
7305 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
7306 the mitochondrion chromosome. Therefore, the SNPs in this package can be
7307 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
7308 correct position but this injection will exclude chrM (i.e. nothing will be
7309 injected in that sequence).")
7310 (license license:artistic2.0)))
7312 (define-public r-reqon
7319 (uri (bioconductor-uri "ReQON" version))
7322 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
7323 (properties `((upstream-name . "ReQON")))
7324 (build-system r-build-system)
7326 `(("r-rjava" ,r-rjava)
7327 ("r-rsamtools" ,r-rsamtools)
7328 ("r-seqbias" ,r-seqbias)))
7329 (home-page "https://bioconductor.org/packages/ReQON/")
7330 (synopsis "Recalibrating quality of nucleotides")
7332 "This package provides an implementation of an algorithm for
7333 recalibrating the base quality scores for aligned sequencing data in BAM
7335 (license license:gpl2)))
7337 (define-public r-wavcluster
7339 (name "r-wavcluster")
7344 (uri (bioconductor-uri "wavClusteR" version))
7347 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
7348 (properties `((upstream-name . "wavClusteR")))
7349 (build-system r-build-system)
7351 `(("r-biocgenerics" ,r-biocgenerics)
7352 ("r-biostrings" ,r-biostrings)
7353 ("r-foreach" ,r-foreach)
7354 ("r-genomicfeatures" ,r-genomicfeatures)
7355 ("r-genomicranges" ,r-genomicranges)
7356 ("r-ggplot2" ,r-ggplot2)
7357 ("r-hmisc" ,r-hmisc)
7358 ("r-iranges" ,r-iranges)
7359 ("r-mclust" ,r-mclust)
7360 ("r-rsamtools" ,r-rsamtools)
7361 ("r-rtracklayer" ,r-rtracklayer)
7362 ("r-s4vectors" ,r-s4vectors)
7363 ("r-seqinr" ,r-seqinr)
7364 ("r-stringr" ,r-stringr)))
7366 `(("r-knitr" ,r-knitr)))
7367 (home-page "https://bioconductor.org/packages/wavClusteR/")
7368 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
7370 "This package provides an integrated pipeline for the analysis of
7371 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7372 sequencing errors, SNPs and additional non-experimental sources by a non-
7373 parametric mixture model. The protein binding sites (clusters) are then
7374 resolved at high resolution and cluster statistics are estimated using a
7375 rigorous Bayesian framework. Post-processing of the results, data export for
7376 UCSC genome browser visualization and motif search analysis are provided. In
7377 addition, the package integrates RNA-Seq data to estimate the False
7378 Discovery Rate of cluster detection. Key functions support parallel multicore
7379 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7380 be applied to the analysis of other NGS data obtained from experimental
7381 procedures that induce nucleotide substitutions (e.g. BisSeq).")
7382 (license license:gpl2)))
7384 (define-public r-timeseriesexperiment
7386 (name "r-timeseriesexperiment")
7391 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7394 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
7396 `((upstream-name . "TimeSeriesExperiment")))
7397 (build-system r-build-system)
7399 `(("r-deseq2" ,r-deseq2)
7400 ("r-dplyr" ,r-dplyr)
7401 ("r-dynamictreecut" ,r-dynamictreecut)
7402 ("r-edger" ,r-edger)
7403 ("r-ggplot2" ,r-ggplot2)
7404 ("r-hmisc" ,r-hmisc)
7405 ("r-limma" ,r-limma)
7406 ("r-magrittr" ,r-magrittr)
7407 ("r-proxy" ,r-proxy)
7408 ("r-s4vectors" ,r-s4vectors)
7409 ("r-summarizedexperiment" ,r-summarizedexperiment)
7410 ("r-tibble" ,r-tibble)
7411 ("r-tidyr" ,r-tidyr)
7412 ("r-vegan" ,r-vegan)
7413 ("r-viridis" ,r-viridis)))
7415 `(("r-knitr" ,r-knitr)))
7416 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7417 (synopsis "Analysis for short time-series data")
7419 "This package is a visualization and analysis toolbox for short time
7420 course data which includes dimensionality reduction, clustering, two-sample
7421 differential expression testing and gene ranking techniques. The package also
7422 provides methods for retrieving enriched pathways.")
7423 (license license:lgpl3+)))
7425 (define-public r-variantfiltering
7427 (name "r-variantfiltering")
7432 (uri (bioconductor-uri "VariantFiltering" version))
7435 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
7437 `((upstream-name . "VariantFiltering")))
7438 (build-system r-build-system)
7440 `(("r-annotationdbi" ,r-annotationdbi)
7441 ("r-biobase" ,r-biobase)
7442 ("r-biocgenerics" ,r-biocgenerics)
7443 ("r-biocparallel" ,r-biocparallel)
7444 ("r-biostrings" ,r-biostrings)
7445 ("r-bsgenome" ,r-bsgenome)
7447 ("r-genomeinfodb" ,r-genomeinfodb)
7448 ("r-genomicfeatures" ,r-genomicfeatures)
7449 ("r-genomicranges" ,r-genomicranges)
7450 ("r-genomicscores" ,r-genomicscores)
7451 ("r-graph" ,r-graph)
7453 ("r-iranges" ,r-iranges)
7455 ("r-rsamtools" ,r-rsamtools)
7456 ("r-s4vectors" ,r-s4vectors)
7457 ("r-shiny" ,r-shiny)
7458 ("r-shinyjs" ,r-shinyjs)
7459 ("r-shinythemes" ,r-shinythemes)
7460 ("r-shinytree" ,r-shinytree)
7461 ("r-summarizedexperiment" ,r-summarizedexperiment)
7462 ("r-variantannotation" ,r-variantannotation)
7463 ("r-xvector" ,r-xvector)))
7464 (home-page "https://github.com/rcastelo/VariantFiltering")
7465 (synopsis "Filtering of coding and non-coding genetic variants")
7467 "Filter genetic variants using different criteria such as inheritance
7468 model, amino acid change consequence, minor allele frequencies across human
7469 populations, splice site strength, conservation, etc.")
7470 (license license:artistic2.0)))
7472 (define-public r-genomegraphs
7474 (name "r-genomegraphs")
7479 (uri (bioconductor-uri "GenomeGraphs" version))
7482 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7483 (properties `((upstream-name . "GenomeGraphs")))
7484 (build-system r-build-system)
7486 `(("r-biomart" ,r-biomart)))
7487 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7488 (synopsis "Plotting genomic information from Ensembl")
7490 "Genomic data analyses requires integrated visualization of known genomic
7491 information and new experimental data. GenomeGraphs uses the biomaRt package
7492 to perform live annotation queries to Ensembl and translates this to e.g.
7493 gene/transcript structures in viewports of the grid graphics package. This
7494 results in genomic information plotted together with your data. Another
7495 strength of GenomeGraphs is to plot different data types such as array CGH,
7496 gene expression, sequencing and other data, together in one plot using the
7497 same genome coordinate system.")
7498 (license license:artistic2.0)))
7500 (define-public r-wavetiling
7502 (name "r-wavetiling")
7507 (uri (bioconductor-uri "waveTiling" version))
7510 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7511 (properties `((upstream-name . "waveTiling")))
7512 (build-system r-build-system)
7514 `(("r-affy" ,r-affy)
7515 ("r-biobase" ,r-biobase)
7516 ("r-biostrings" ,r-biostrings)
7517 ("r-genomegraphs" ,r-genomegraphs)
7518 ("r-genomicranges" ,r-genomicranges)
7519 ("r-iranges" ,r-iranges)
7520 ("r-oligo" ,r-oligo)
7521 ("r-oligoclasses" ,r-oligoclasses)
7522 ("r-preprocesscore" ,r-preprocesscore)
7523 ("r-waveslim" ,r-waveslim)))
7524 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7525 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7527 "This package is designed to conduct transcriptome analysis for tiling
7528 arrays based on fast wavelet-based functional models.")
7529 (license license:gpl2+)))
7531 (define-public r-variancepartition
7533 (name "r-variancepartition")
7538 (uri (bioconductor-uri "variancePartition" version))
7541 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
7543 `((upstream-name . "variancePartition")))
7544 (build-system r-build-system)
7546 `(("r-biobase" ,r-biobase)
7547 ("r-biocparallel" ,r-biocparallel)
7548 ("r-colorramps" ,r-colorramps)
7549 ("r-doparallel" ,r-doparallel)
7550 ("r-foreach" ,r-foreach)
7551 ("r-ggplot2" ,r-ggplot2)
7552 ("r-gplots" ,r-gplots)
7553 ("r-iterators" ,r-iterators)
7554 ("r-limma" ,r-limma)
7556 ("r-lmertest" ,r-lmertest)
7558 ("r-pbkrtest" ,r-pbkrtest)
7559 ("r-progress" ,r-progress)
7560 ("r-reshape2" ,r-reshape2)
7561 ("r-scales" ,r-scales)))
7563 `(("r-knitr" ,r-knitr)))
7564 (home-page "https://bioconductor.org/packages/variancePartition/")
7565 (synopsis "Analyze variation in gene expression experiments")
7567 "This is a package providing tools to quantify and interpret multiple
7568 sources of biological and technical variation in gene expression experiments.
7569 It uses a linear mixed model to quantify variation in gene expression
7570 attributable to individual, tissue, time point, or technical variables. The
7571 package includes dream differential expression analysis for repeated
7573 (license license:gpl2+)))
7575 (define-public r-htqpcr
7582 (uri (bioconductor-uri "HTqPCR" version))
7585 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
7586 (properties `((upstream-name . "HTqPCR")))
7587 (build-system r-build-system)
7589 `(("r-affy" ,r-affy)
7590 ("r-biobase" ,r-biobase)
7591 ("r-gplots" ,r-gplots)
7592 ("r-limma" ,r-limma)
7593 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7594 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7595 "groups/bertone/software/HTqPCR.pdf"))
7596 (synopsis "Automated analysis of high-throughput qPCR data")
7598 "Analysis of Ct values from high throughput quantitative real-time
7599 PCR (qPCR) assays across multiple conditions or replicates. The input data
7600 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7601 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7602 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7603 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7604 loading, quality assessment, normalization, visualization and parametric or
7605 non-parametric testing for statistical significance in Ct values between
7606 features (e.g. genes, microRNAs).")
7607 (license license:artistic2.0)))
7609 (define-public r-unifiedwmwqpcr
7611 (name "r-unifiedwmwqpcr")
7616 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7619 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
7621 `((upstream-name . "unifiedWMWqPCR")))
7622 (build-system r-build-system)
7624 `(("r-biocgenerics" ,r-biocgenerics)
7625 ("r-htqpcr" ,r-htqpcr)))
7626 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7627 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7629 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7630 data. This modified test allows for testing differential expression in qPCR
7632 (license license:gpl2+)))
7634 (define-public r-universalmotif
7636 (name "r-universalmotif")
7641 (uri (bioconductor-uri "universalmotif" version))
7644 "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
7646 `((upstream-name . "universalmotif")))
7647 (build-system r-build-system)
7650 (modify-phases %standard-phases
7651 (add-after 'unpack 'fix-reference-to-strip
7653 (substitute* "src/Makevars"
7654 (("/usr/bin/strip") (which "strip"))))))))
7656 `(("r-biocgenerics" ,r-biocgenerics)
7657 ("r-biostrings" ,r-biostrings)
7658 ("r-ggplot2" ,r-ggplot2)
7659 ("r-ggseqlogo" ,r-ggseqlogo)
7660 ("r-iranges" ,r-iranges)
7663 ("r-rcppthread" ,r-rcppthread)
7664 ("r-rdpack" ,r-rdpack)
7665 ("r-rlang" ,r-rlang)
7666 ("r-s4vectors" ,r-s4vectors)
7667 ("r-yaml" ,r-yaml)))
7669 `(("r-knitr" ,r-knitr)))
7671 "https://bioconductor.org/packages/universalmotif/")
7673 "Specific structures importer, modifier, and exporter for R")
7675 "This package allows importing most common @dfn{specific structure}
7676 (motif) types into R for use by functions provided by other Bioconductor
7677 motif-related packages. Motifs can be exported into most major motif formats
7678 from various classes as defined by other Bioconductor packages. A suite of
7679 motif and sequence manipulation and analysis functions are included, including
7680 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
7681 motifs, and others.")
7682 (license license:gpl3)))
7684 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7686 (define-public r-activedriverwgs
7688 (name "r-activedriverwgs")
7693 (uri (cran-uri "ActiveDriverWGS" version))
7696 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
7698 `((upstream-name . "ActiveDriverWGS")))
7699 (build-system r-build-system)
7701 `(("r-biostrings" ,r-biostrings)
7702 ("r-bsgenome" ,r-bsgenome)
7703 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7704 ("r-genomeinfodb" ,r-genomeinfodb)
7705 ("r-genomicranges" ,r-genomicranges)
7706 ("r-iranges" ,r-iranges)
7707 ("r-s4vectors" ,r-s4vectors)))
7709 `(("r-knitr" ,r-knitr)))
7710 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7711 (synopsis "Driver discovery tool for cancer whole genomes")
7713 "This package provides a method for finding an enrichment of cancer
7714 simple somatic mutations (SNVs and Indels) in functional elements across the
7715 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7716 using whole genome sequencing data.")
7717 (license license:gpl3)))
7719 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7721 (define-public r-activepathways
7723 (name "r-activepathways")
7728 (uri (cran-uri "ActivePathways" version))
7731 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7733 `((upstream-name . "ActivePathways")))
7734 (build-system r-build-system)
7736 `(("r-data-table" ,r-data-table)
7737 ("r-ggplot2" ,r-ggplot2)))
7739 `(("r-knitr" ,r-knitr)))
7740 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7741 (synopsis "Multivariate pathway enrichment analysis")
7743 "This package represents an integrative method of analyzing multi omics
7744 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7745 uses a statistical data fusion approach, rationalizes contributing evidence
7746 and highlights associated genes, improving systems-level understanding of
7747 cellular organization in health and disease.")
7748 (license license:gpl3)))
7750 (define-public r-bgmix
7757 (uri (bioconductor-uri "BGmix" version))
7760 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
7761 (properties `((upstream-name . "BGmix")))
7762 (build-system r-build-system)
7764 `(("r-kernsmooth" ,r-kernsmooth)))
7765 (home-page "https://bioconductor.org/packages/BGmix/")
7766 (synopsis "Bayesian models for differential gene expression")
7768 "This package provides fully Bayesian mixture models for differential
7770 (license license:gpl2)))
7772 (define-public r-bgx
7779 (uri (bioconductor-uri "bgx" version))
7782 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
7783 (properties `((upstream-name . "bgx")))
7784 (build-system r-build-system)
7786 `(("r-affy" ,r-affy)
7787 ("r-biobase" ,r-biobase)
7788 ("r-gcrma" ,r-gcrma)
7789 ("r-rcpp" ,r-rcpp)))
7790 (home-page "https://bioconductor.org/packages/bgx/")
7791 (synopsis "Bayesian gene expression")
7793 "This package provides tools for Bayesian integrated analysis of
7794 Affymetrix GeneChips.")
7795 (license license:gpl2)))
7797 (define-public r-bhc
7804 (uri (bioconductor-uri "BHC" version))
7807 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
7808 (properties `((upstream-name . "BHC")))
7809 (build-system r-build-system)
7810 (home-page "https://bioconductor.org/packages/BHC/")
7811 (synopsis "Bayesian hierarchical clustering")
7813 "The method implemented in this package performs bottom-up hierarchical
7814 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7815 in the data and Bayesian model selection to decide at each step which clusters
7816 to merge. This avoids several limitations of traditional methods, for example
7817 how many clusters there should be and how to choose a principled distance
7818 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7819 categories) or time-series data. This version also includes a randomised
7820 algorithm which is more efficient for larger data sets.")
7821 (license license:gpl3)))
7823 (define-public r-bicare
7830 (uri (bioconductor-uri "BicARE" version))
7833 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
7834 (properties `((upstream-name . "BicARE")))
7835 (build-system r-build-system)
7837 `(("r-biobase" ,r-biobase)
7838 ("r-gseabase" ,r-gseabase)
7839 ("r-multtest" ,r-multtest)))
7840 (home-page "http://bioinfo.curie.fr")
7841 (synopsis "Biclustering analysis and results exploration")
7843 "This is a package for biclustering analysis and exploration of
7845 (license license:gpl2)))
7847 (define-public r-bifet
7854 (uri (bioconductor-uri "BiFET" version))
7857 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
7858 (properties `((upstream-name . "BiFET")))
7859 (build-system r-build-system)
7861 `(("r-genomicranges" ,r-genomicranges)
7862 ("r-poibin" ,r-poibin)))
7864 `(("r-knitr" ,r-knitr)))
7865 (home-page "https://bioconductor.org/packages/BiFET")
7866 (synopsis "Bias-free footprint enrichment test")
7868 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7869 over-represented in target regions compared to background regions after
7870 correcting for the bias arising from the imbalance in read counts and GC
7871 contents between the target and background regions. For a given TF k, BiFET
7872 tests the null hypothesis that the target regions have the same probability of
7873 having footprints for the TF k as the background regions while correcting for
7874 the read count and GC content bias.")
7875 (license license:gpl3)))
7877 (define-public r-rsbml
7884 (uri (bioconductor-uri "rsbml" version))
7887 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
7888 (properties `((upstream-name . "rsbml")))
7889 (build-system r-build-system)
7891 `(("libsbml" ,libsbml)
7894 `(("r-biocgenerics" ,r-biocgenerics)
7895 ("r-graph" ,r-graph)))
7897 `(("pkg-config" ,pkg-config)))
7898 (home-page "http://www.sbml.org")
7899 (synopsis "R support for SBML")
7901 "This package provides an R interface to libsbml for SBML parsing,
7902 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7903 (license license:artistic2.0)))
7905 (define-public r-hypergraph
7907 (name "r-hypergraph")
7912 (uri (bioconductor-uri "hypergraph" version))
7915 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
7916 (properties `((upstream-name . "hypergraph")))
7917 (build-system r-build-system)
7919 `(("r-graph" ,r-graph)))
7920 (home-page "https://bioconductor.org/packages/hypergraph")
7921 (synopsis "Hypergraph data structures")
7923 "This package implements some simple capabilities for representing and
7924 manipulating hypergraphs.")
7925 (license license:artistic2.0)))
7927 (define-public r-hyperdraw
7929 (name "r-hyperdraw")
7934 (uri (bioconductor-uri "hyperdraw" version))
7937 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
7938 (properties `((upstream-name . "hyperdraw")))
7939 (build-system r-build-system)
7940 (inputs `(("graphviz" ,graphviz)))
7942 `(("r-graph" ,r-graph)
7943 ("r-hypergraph" ,r-hypergraph)
7944 ("r-rgraphviz" ,r-rgraphviz)))
7945 (home-page "https://bioconductor.org/packages/hyperdraw")
7946 (synopsis "Visualizing hypergraphs")
7948 "This package provides functions for visualizing hypergraphs.")
7949 (license license:gpl2+)))
7951 (define-public r-biggr
7958 (uri (bioconductor-uri "BiGGR" version))
7961 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
7962 (properties `((upstream-name . "BiGGR")))
7963 (build-system r-build-system)
7965 `(("r-hyperdraw" ,r-hyperdraw)
7966 ("r-hypergraph" ,r-hypergraph)
7968 ("r-limsolve" ,r-limsolve)
7969 ("r-rsbml" ,r-rsbml)
7970 ("r-stringr" ,r-stringr)))
7971 (home-page "https://bioconductor.org/packages/BiGGR/")
7972 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7974 "This package provides an interface to simulate metabolic reconstruction
7975 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7976 reconstruction databases. The package facilitates @dfn{flux balance
7977 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7978 networks and estimated fluxes can be visualized with hypergraphs.")
7979 (license license:gpl3+)))
7981 (define-public r-bigmemoryextras
7983 (name "r-bigmemoryextras")
7988 (uri (bioconductor-uri "bigmemoryExtras" version))
7991 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
7993 `((upstream-name . "bigmemoryExtras")))
7994 (build-system r-build-system)
7996 `(("r-bigmemory" ,r-bigmemory)))
7998 `(("r-knitr" ,r-knitr)))
7999 (home-page "https://github.com/phaverty/bigmemoryExtras")
8000 (synopsis "Extension of the bigmemory package")
8002 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
8003 safety and convenience features to the @code{filebacked.big.matrix} class from
8004 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
8005 monitoring and gracefully restoring the connection to on-disk data and it also
8006 protects against accidental data modification with a file-system-based
8007 permissions system. Utilities are provided for using @code{BigMatrix}-derived
8008 classes as @code{assayData} matrices within the @code{Biobase} package's
8009 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
8010 related to attaching to, and indexing into, file-backed matrices with
8011 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
8012 a file-backed matrix with factor properties.")
8013 (license license:artistic2.0)))
8015 (define-public r-bigpint
8022 (uri (bioconductor-uri "bigPint" version))
8025 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
8026 (properties `((upstream-name . "bigPint")))
8027 (build-system r-build-system)
8029 `(("r-delayedarray" ,r-delayedarray)
8030 ("r-dplyr" ,r-dplyr)
8031 ("r-ggally" ,r-ggally)
8032 ("r-ggplot2" ,r-ggplot2)
8033 ("r-gridextra" ,r-gridextra)
8034 ("r-hexbin" ,r-hexbin)
8035 ("r-hmisc" ,r-hmisc)
8036 ("r-htmlwidgets" ,r-htmlwidgets)
8037 ("r-plotly" ,r-plotly)
8039 ("r-rcolorbrewer" ,r-rcolorbrewer)
8040 ("r-reshape" ,r-reshape)
8041 ("r-shiny" ,r-shiny)
8042 ("r-shinycssloaders" ,r-shinycssloaders)
8043 ("r-shinydashboard" ,r-shinydashboard)
8044 ("r-stringr" ,r-stringr)
8045 ("r-summarizedexperiment" ,r-summarizedexperiment)
8046 ("r-tidyr" ,r-tidyr)))
8048 `(("r-knitr" ,r-knitr)))
8049 (home-page "https://github.com/lindsayrutter/bigPint")
8050 (synopsis "Big multivariate data plotted interactively")
8052 "This package provides methods for visualizing large multivariate
8053 datasets using static and interactive scatterplot matrices, parallel
8054 coordinate plots, volcano plots, and litre plots. It includes examples for
8055 visualizing RNA-sequencing datasets and differentially expressed genes.")
8056 (license license:gpl3)))
8058 (define-public r-chemminer
8060 (name "r-chemminer")
8065 (uri (bioconductor-uri "ChemmineR" version))
8068 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
8069 (properties `((upstream-name . "ChemmineR")))
8070 (build-system r-build-system)
8072 `(("r-base64enc" ,r-base64enc)
8074 ("r-biocgenerics" ,r-biocgenerics)
8076 ("r-digest" ,r-digest)
8078 ("r-ggplot2" ,r-ggplot2)
8079 ("r-gridextra" ,r-gridextra)
8082 ("r-rcurl" ,r-rcurl)
8083 ("r-rjson" ,r-rjson)
8084 ("r-rsvg" ,r-rsvg)))
8086 `(("r-knitr" ,r-knitr)))
8087 (home-page "https://github.com/girke-lab/ChemmineR")
8088 (synopsis "Cheminformatics toolkit for R")
8090 "ChemmineR is a cheminformatics package for analyzing drug-like small
8091 molecule data in R. It contains functions for efficient processing of large
8092 numbers of molecules, physicochemical/structural property predictions,
8093 structural similarity searching, classification and clustering of compound
8094 libraries with a wide spectrum of algorithms. In addition, it offers
8095 visualization functions for compound clustering results and chemical
8097 (license license:artistic2.0)))
8099 (define-public r-bioassayr
8101 (name "r-bioassayr")
8106 (uri (bioconductor-uri "bioassayR" version))
8109 "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
8110 (properties `((upstream-name . "bioassayR")))
8111 (build-system r-build-system)
8113 `(("r-biocgenerics" ,r-biocgenerics)
8114 ("r-chemminer" ,r-chemminer)
8116 ("r-matrix" ,r-matrix)
8117 ("r-rjson" ,r-rjson)
8118 ("r-rsqlite" ,r-rsqlite)
8121 `(("r-knitr" ,r-knitr)))
8122 (home-page "https://github.com/girke-lab/bioassayR")
8123 (synopsis "Cross-target analysis of small molecule bioactivity")
8125 "bioassayR is a computational tool that enables simultaneous analysis of
8126 thousands of bioassay experiments performed over a diverse set of compounds
8127 and biological targets. Unique features include support for large-scale
8128 cross-target analyses of both public and custom bioassays, generation of
8129 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
8130 preloaded database that provides access to a substantial portion of publicly
8131 available bioactivity data.")
8132 (license license:artistic2.0)))
8134 (define-public r-biobroom
8141 (uri (bioconductor-uri "biobroom" version))
8144 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
8145 (properties `((upstream-name . "biobroom")))
8146 (build-system r-build-system)
8148 `(("r-biobase" ,r-biobase)
8149 ("r-broom" ,r-broom)
8150 ("r-dplyr" ,r-dplyr)
8151 ("r-tidyr" ,r-tidyr)))
8153 `(("r-knitr" ,r-knitr)))
8154 (home-page "https://github.com/StoreyLab/biobroom")
8155 (synopsis "Turn Bioconductor objects into tidy data frames")
8157 "This package contains methods for converting standard objects
8158 constructed by bioinformatics packages, especially those in Bioconductor, and
8159 converting them to @code{tidy} data. It thus serves as a complement to the
8160 @code{broom} package, and follows the same tidy, augment, glance division of
8161 tidying methods. Tidying data makes it easy to recombine, reshape and
8162 visualize bioinformatics analyses.")
8163 ;; Any version of the LGPL.
8164 (license license:lgpl3+)))
8166 (define-public r-graphite
8173 (uri (bioconductor-uri "graphite" version))
8176 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
8177 (properties `((upstream-name . "graphite")))
8178 (build-system r-build-system)
8180 `(("r-annotationdbi" ,r-annotationdbi)
8181 ("r-checkmate" ,r-checkmate)
8182 ("r-graph" ,r-graph)
8184 ("r-rappdirs" ,r-rappdirs)))
8185 (home-page "https://bioconductor.org/packages/graphite/")
8186 (synopsis "Networks from pathway databases")
8188 "Graphite provides networks derived from eight public pathway databases,
8189 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
8191 (license license:agpl3+)))
8193 (define-public r-reactomepa
8195 (name "r-reactomepa")
8200 (uri (bioconductor-uri "ReactomePA" version))
8203 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
8204 (properties `((upstream-name . "ReactomePA")))
8205 (build-system r-build-system)
8207 `(("r-annotationdbi" ,r-annotationdbi)
8209 ("r-enrichplot" ,r-enrichplot)
8210 ("r-ggplot2" ,r-ggplot2)
8211 ("r-ggraph" ,r-ggraph)
8212 ("r-graphite" ,r-graphite)
8213 ("r-igraph" ,r-igraph)
8214 ("r-reactome-db" ,r-reactome-db)))
8216 `(("r-knitr" ,r-knitr)))
8217 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
8218 (synopsis "Reactome pathway analysis")
8220 "This package provides functions for pathway analysis based on the
8221 REACTOME pathway database. It implements enrichment analysis, gene set
8222 enrichment analysis and several functions for visualization.")
8223 (license license:gpl2)))
8225 (define-public r-ebarrays
8232 (uri (bioconductor-uri "EBarrays" version))
8235 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
8236 (properties `((upstream-name . "EBarrays")))
8237 (build-system r-build-system)
8239 `(("r-biobase" ,r-biobase)
8240 ("r-cluster" ,r-cluster)
8241 ("r-lattice" ,r-lattice)))
8242 (home-page "https://bioconductor.org/packages/EBarrays/")
8243 (synopsis "Gene clustering and differential expression identification")
8245 "EBarrays provides tools for the analysis of replicated/unreplicated
8247 (license license:gpl2+)))
8249 (define-public r-bioccasestudies
8251 (name "r-bioccasestudies")
8256 (uri (bioconductor-uri "BiocCaseStudies" version))
8259 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
8261 `((upstream-name . "BiocCaseStudies")))
8262 (build-system r-build-system)
8263 (propagated-inputs `(("r-biobase" ,r-biobase)))
8264 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
8265 (synopsis "Support for the case studies monograph")
8267 "This package provides software and data to support the case studies
8269 (license license:artistic2.0)))
8271 (define-public r-biocgraph
8273 (name "r-biocgraph")
8278 (uri (bioconductor-uri "biocGraph" version))
8281 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
8282 (properties `((upstream-name . "biocGraph")))
8283 (build-system r-build-system)
8285 `(("r-biocgenerics" ,r-biocgenerics)
8286 ("r-geneplotter" ,r-geneplotter)
8287 ("r-graph" ,r-graph)
8288 ("r-rgraphviz" ,r-rgraphviz)))
8289 (home-page "https://bioconductor.org/packages/biocGraph/")
8290 (synopsis "Graph examples and use cases in Bioinformatics")
8292 "This package provides examples and code that make use of the
8293 different graph related packages produced by Bioconductor.")
8294 (license license:artistic2.0)))
8296 (define-public r-experimenthub
8298 (name "r-experimenthub")
8303 (uri (bioconductor-uri "ExperimentHub" version))
8306 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
8307 (properties `((upstream-name . "ExperimentHub")))
8308 (build-system r-build-system)
8310 `(("r-annotationhub" ,r-annotationhub)
8311 ("r-biocfilecache" ,r-biocfilecache)
8312 ("r-biocgenerics" ,r-biocgenerics)
8313 ("r-biocmanager" ,r-biocmanager)
8315 ("r-rappdirs" ,r-rappdirs)
8316 ("r-s4vectors" ,r-s4vectors)))
8318 `(("r-knitr" ,r-knitr)))
8319 (home-page "https://bioconductor.org/packages/ExperimentHub/")
8320 (synopsis "Client to access ExperimentHub resources")
8322 "This package provides a client for the Bioconductor ExperimentHub web
8323 resource. ExperimentHub provides a central location where curated data from
8324 experiments, publications or training courses can be accessed. Each resource
8325 has associated metadata, tags and date of modification. The client creates
8326 and manages a local cache of files retrieved enabling quick and reproducible
8328 (license license:artistic2.0)))
8330 (define-public r-multiassayexperiment
8332 (name "r-multiassayexperiment")
8337 (uri (bioconductor-uri "MultiAssayExperiment" version))
8340 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
8342 `((upstream-name . "MultiAssayExperiment")))
8343 (build-system r-build-system)
8345 `(("r-biobase" ,r-biobase)
8346 ("r-biocgenerics" ,r-biocgenerics)
8347 ("r-genomicranges" ,r-genomicranges)
8348 ("r-iranges" ,r-iranges)
8349 ("r-s4vectors" ,r-s4vectors)
8350 ("r-summarizedexperiment" ,r-summarizedexperiment)
8351 ("r-tidyr" ,r-tidyr)))
8353 `(("r-knitr" ,r-knitr)))
8354 (home-page "https://waldronlab.io/MultiAssayExperiment/")
8355 (synopsis "Integration of multi-omics experiments in Bioconductor")
8357 "MultiAssayExperiment harmonizes data management of multiple assays
8358 performed on an overlapping set of specimens. It provides a familiar
8359 Bioconductor user experience by extending concepts from
8360 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
8361 classes for individual assays, and allowing subsetting by genomic ranges or
8363 (license license:artistic2.0)))
8365 (define-public r-bioconcotk
8367 (name "r-bioconcotk")
8372 (uri (bioconductor-uri "BiocOncoTK" version))
8375 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
8376 (properties `((upstream-name . "BiocOncoTK")))
8377 (build-system r-build-system)
8379 `(("r-bigrquery" ,r-bigrquery)
8381 ("r-complexheatmap" ,r-complexheatmap)
8382 ("r-curatedtcgadata" ,r-curatedtcgadata)
8384 ("r-dplyr" ,r-dplyr)
8386 ("r-genomicfeatures" ,r-genomicfeatures)
8387 ("r-genomicranges" ,r-genomicranges)
8388 ("r-ggplot2" ,r-ggplot2)
8389 ("r-ggpubr" ,r-ggpubr)
8390 ("r-graph" ,r-graph)
8392 ("r-iranges" ,r-iranges)
8393 ("r-magrittr" ,r-magrittr)
8395 ("r-rgraphviz" ,r-rgraphviz)
8396 ("r-rjson" ,r-rjson)
8397 ("r-s4vectors" ,r-s4vectors)
8398 ("r-scales" ,r-scales)
8399 ("r-shiny" ,r-shiny)
8400 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8402 `(("r-knitr" ,r-knitr)))
8403 (home-page "https://bioconductor.org/packages/BiocOncoTK")
8404 (synopsis "Bioconductor components for general cancer genomics")
8406 "The purpose of this package is to provide a central interface to various
8407 tools for genome-scale analysis of cancer studies.")
8408 (license license:artistic2.0)))
8410 (define-public r-biocor
8417 (uri (bioconductor-uri "BioCor" version))
8420 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
8421 (properties `((upstream-name . "BioCor")))
8422 (build-system r-build-system)
8424 `(("r-biocparallel" ,r-biocparallel)
8425 ("r-gseabase" ,r-gseabase)
8426 ("r-matrix" ,r-matrix)))
8428 `(("r-knitr" ,r-knitr)))
8429 (home-page "https://llrs.github.io/BioCor/")
8430 (synopsis "Functional similarities")
8432 "This package provides tools to calculate functional similarities based
8433 on the pathways described on KEGG and REACTOME or in gene sets. These
8434 similarities can be calculated for pathways or gene sets, genes, or clusters
8435 and combined with other similarities. They can be used to improve networks,
8436 gene selection, testing relationships, and so on.")
8437 (license license:expat)))
8439 (define-public r-biocpkgtools
8441 (name "r-biocpkgtools")
8446 (uri (bioconductor-uri "BiocPkgTools" version))
8449 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
8450 (properties `((upstream-name . "BiocPkgTools")))
8451 (build-system r-build-system)
8453 `(("r-biocfilecache" ,r-biocfilecache)
8454 ("r-biocmanager" ,r-biocmanager)
8455 ("r-biocviews" ,r-biocviews)
8456 ("r-dplyr" ,r-dplyr)
8459 ("r-graph" ,r-graph)
8460 ("r-htmltools" ,r-htmltools)
8461 ("r-htmlwidgets" ,r-htmlwidgets)
8463 ("r-igraph" ,r-igraph)
8464 ("r-jsonlite" ,r-jsonlite)
8465 ("r-magrittr" ,r-magrittr)
8466 ("r-rappdirs" ,r-rappdirs)
8468 ("r-readr" ,r-readr)
8470 ("r-rlang" ,r-rlang)
8471 ("r-rvest" ,r-rvest)
8472 ("r-stringr" ,r-stringr)
8473 ("r-tibble" ,r-tibble)
8474 ("r-tidyr" ,r-tidyr)
8475 ("r-tidyselect" ,r-tidyselect)
8476 ("r-xml2" ,r-xml2)))
8478 `(("r-knitr" ,r-knitr)))
8479 (home-page "https://github.com/seandavi/BiocPkgTools")
8480 (synopsis "Collection of tools for learning about Bioconductor packages")
8482 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8483 and build status. This package is a simple collection of functions to access
8484 that metadata from R. The goal is to expose metadata for data mining and
8485 value-added functionality such as package searching, text mining, and
8486 analytics on packages.")
8487 (license license:expat)))
8489 (define-public r-biocset
8496 (uri (bioconductor-uri "BiocSet" version))
8499 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
8500 (properties `((upstream-name . "BiocSet")))
8501 (build-system r-build-system)
8503 `(("r-annotationdbi" ,r-annotationdbi)
8504 ("r-biocio" ,r-biocio)
8505 ("r-dplyr" ,r-dplyr)
8506 ("r-keggrest" ,r-keggrest)
8507 ("r-ontologyindex" ,r-ontologyindex)
8509 ("r-rlang" ,r-rlang)
8510 ("r-s4vectors" ,r-s4vectors)
8511 ("r-tibble" ,r-tibble)
8512 ("r-tidyr" ,r-tidyr)))
8514 `(("r-knitr" ,r-knitr)))
8516 "https://bioconductor.org/packages/BiocSet")
8518 "Representing Different Biological Sets")
8520 "BiocSet displays different biological sets in a triple tibble format.
8521 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
8522 The user has the ability to activate one of these three tibbles to perform
8523 common functions from the @code{dplyr} package. Mapping functionality and
8524 accessing web references for elements/sets are also available in BiocSet.")
8525 (license license:artistic2.0)))
8527 (define-public r-biocworkflowtools
8529 (name "r-biocworkflowtools")
8534 (uri (bioconductor-uri "BiocWorkflowTools" version))
8537 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
8539 `((upstream-name . "BiocWorkflowTools")))
8540 (build-system r-build-system)
8542 `(("r-biocstyle" ,r-biocstyle)
8543 ("r-bookdown" ,r-bookdown)
8544 ("r-git2r" ,r-git2r)
8546 ("r-knitr" ,r-knitr)
8547 ("r-rmarkdown" ,r-rmarkdown)
8548 ("r-rstudioapi" ,r-rstudioapi)
8549 ("r-stringr" ,r-stringr)
8550 ("r-usethis" ,r-usethis)))
8552 `(("r-knitr" ,r-knitr)))
8553 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8554 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8556 "This package provides functions to ease the transition between
8557 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8558 (license license:expat)))
8560 (define-public r-biodist
8567 (uri (bioconductor-uri "bioDist" version))
8570 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
8571 (properties `((upstream-name . "bioDist")))
8572 (build-system r-build-system)
8574 `(("r-biobase" ,r-biobase)
8575 ("r-kernsmooth" ,r-kernsmooth)))
8576 (home-page "https://bioconductor.org/packages/bioDist/")
8577 (synopsis "Different distance measures")
8579 "This package provides a collection of software tools for calculating
8580 distance measures.")
8581 (license license:artistic2.0)))
8583 (define-public r-pcatools
8590 (uri (bioconductor-uri "PCAtools" version))
8593 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
8594 (properties `((upstream-name . "PCAtools")))
8595 (build-system r-build-system)
8597 `(("r-beachmat" ,r-beachmat)
8599 ("r-biocparallel" ,r-biocparallel)
8600 ("r-biocsingular" ,r-biocsingular)
8601 ("r-cowplot" ,r-cowplot)
8602 ("r-delayedarray" ,r-delayedarray)
8603 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8604 ("r-dqrng" ,r-dqrng)
8605 ("r-ggplot2" ,r-ggplot2)
8606 ("r-ggrepel" ,r-ggrepel)
8607 ("r-lattice" ,r-lattice)
8608 ("r-matrix" ,r-matrix)
8610 ("r-reshape2" ,r-reshape2)))
8611 (native-inputs `(("r-knitr" ,r-knitr)))
8612 (home-page "https://github.com/kevinblighe/PCAtools")
8613 (synopsis "PCAtools: everything Principal Components Analysis")
8615 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8616 structure of the data without the need to build any model to represent it.
8617 This \"summary\" of the data is arrived at through a process of reduction that
8618 can transform the large number of variables into a lesser number that are
8619 uncorrelated (i.e. the 'principal components'), while at the same time being
8620 capable of easy interpretation on the original data. PCAtools provides
8621 functions for data exploration via PCA, and allows the user to generate
8622 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8623 can also identify an optimal number of principal components via different
8624 metrics, such as the elbow method and Horn's parallel analysis, which has
8625 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8626 dimensional mass cytometry data.")
8627 (license license:gpl3)))
8629 (define-public r-rgreat
8636 (uri (bioconductor-uri "rGREAT" version))
8639 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
8640 (properties `((upstream-name . "rGREAT")))
8641 (build-system r-build-system)
8643 `(("r-genomicranges" ,r-genomicranges)
8644 ("r-getoptlong" ,r-getoptlong)
8645 ("r-iranges" ,r-iranges)
8646 ("r-rcurl" ,r-rcurl)
8647 ("r-rjson" ,r-rjson)))
8648 (native-inputs `(("r-knitr" ,r-knitr)))
8649 (home-page "https://github.com/jokergoo/rGREAT")
8650 (synopsis "Client for GREAT analysis")
8652 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8653 Tool) analysis automatic by constructing a HTTP POST request according to
8654 user's input and automatically retrieving results from GREAT web server.")
8655 (license license:expat)))
8657 (define-public r-m3c
8664 (uri (bioconductor-uri "M3C" version))
8667 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
8668 (properties `((upstream-name . "M3C")))
8669 (build-system r-build-system)
8671 `(("r-cluster" ,r-cluster)
8672 ("r-corpcor" ,r-corpcor)
8673 ("r-doparallel" ,r-doparallel)
8674 ("r-dosnow" ,r-dosnow)
8675 ("r-foreach" ,r-foreach)
8676 ("r-ggplot2" ,r-ggplot2)
8677 ("r-matrix" ,r-matrix)
8678 ("r-matrixcalc" ,r-matrixcalc)
8679 ("r-rtsne" ,r-rtsne)
8680 ("r-umap" ,r-umap)))
8681 (native-inputs `(("r-knitr" ,r-knitr)))
8682 (home-page "https://bioconductor.org/packages/M3C")
8683 (synopsis "Monte Carlo reference-based consensus clustering")
8685 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8686 simulation to eliminate overestimation of @code{K} and can reject the null
8687 hypothesis @code{K=1}.")
8688 (license license:agpl3+)))
8690 (define-public r-icens
8697 (uri (bioconductor-uri "Icens" version))
8700 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
8701 (properties `((upstream-name . "Icens")))
8702 (build-system r-build-system)
8704 `(("r-survival" ,r-survival)))
8705 (home-page "https://bioconductor.org/packages/Icens")
8706 (synopsis "NPMLE for censored and truncated data")
8708 "This package provides many functions for computing the
8709 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8711 (license license:artistic2.0)))
8713 ;; This is a CRAN package but it depends on r-icens, which is published on
8715 (define-public r-interval
8722 (uri (cran-uri "interval" version))
8725 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
8726 (properties `((upstream-name . "interval")))
8727 (build-system r-build-system)
8729 `(("r-icens" ,r-icens)
8730 ("r-mlecens" ,r-mlecens)
8732 ("r-survival" ,r-survival)))
8733 (home-page "https://cran.r-project.org/web/packages/interval/")
8734 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8736 "This package provides functions to fit nonparametric survival curves,
8737 plot them, and perform logrank or Wilcoxon type tests.")
8738 (license license:gpl2+)))
8740 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8741 ;; Bioconductor package.
8742 (define-public r-fhtest
8749 (uri (cran-uri "FHtest" version))
8752 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
8753 (properties `((upstream-name . "FHtest")))
8754 (build-system r-build-system)
8756 `(("r-interval" ,r-interval)
8757 ("r-kmsurv" ,r-kmsurv)
8760 ("r-survival" ,r-survival)))
8761 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8762 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8764 "This package provides functions to compare two or more survival curves
8768 @item The Fleming-Harrington test for right-censored data based on
8769 permutations and on counting processes.
8770 @item An extension of the Fleming-Harrington test for interval-censored data
8771 based on a permutation distribution and on a score vector distribution.
8774 (license license:gpl2+)))
8776 (define-public r-fourcseq
8783 (uri (bioconductor-uri "FourCSeq" version))
8785 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
8786 (properties `((upstream-name . "FourCSeq")))
8787 (build-system r-build-system)
8789 `(("r-biobase" ,r-biobase)
8790 ("r-biostrings" ,r-biostrings)
8791 ("r-deseq2" ,r-deseq2)
8793 ("r-genomicalignments" ,r-genomicalignments)
8794 ("r-genomicranges" ,r-genomicranges)
8795 ("r-ggbio" ,r-ggbio)
8796 ("r-ggplot2" ,r-ggplot2)
8797 ("r-gtools" ,r-gtools)
8799 ("r-matrix" ,r-matrix)
8800 ("r-reshape2" ,r-reshape2)
8801 ("r-rsamtools" ,r-rsamtools)
8802 ("r-rtracklayer" ,r-rtracklayer)
8803 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8805 `(("r-knitr" ,r-knitr)))
8807 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8808 (synopsis "Analysis of multiplexed 4C sequencing data")
8810 "This package is an R package dedicated to the analysis of (multiplexed)
8811 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8812 interactions between DNA elements and identify differential interactions
8813 between conditions. The statistical analysis in R starts with individual bam
8814 files for each sample as inputs. To obtain these files, the package contains
8815 a Python script to demultiplex libraries and trim off primer sequences. With
8816 a standard alignment software the required bam files can be then be
8818 (license license:gpl3+)))
8820 (define-public r-preprocesscore
8822 (name "r-preprocesscore")
8827 (uri (bioconductor-uri "preprocessCore" version))
8830 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
8832 `((upstream-name . "preprocessCore")))
8833 (build-system r-build-system)
8834 (home-page "https://github.com/bmbolstad/preprocessCore")
8835 (synopsis "Collection of pre-processing functions")
8837 "This package provides a library of core pre-processing and normalization
8839 (license license:lgpl2.0+)))
8841 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
8842 ;; Bioconductor package.
8843 (define-public r-wgcna
8850 (uri (cran-uri "WGCNA" version))
8853 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
8854 (properties `((upstream-name . "WGCNA")))
8855 (build-system r-build-system)
8857 `(("r-annotationdbi" ,r-annotationdbi)
8858 ("r-doparallel" ,r-doparallel)
8859 ("r-dynamictreecut" ,r-dynamictreecut)
8860 ("r-fastcluster" ,r-fastcluster)
8861 ("r-foreach" ,r-foreach)
8862 ("r-go-db" ,r-go-db)
8863 ("r-hmisc" ,r-hmisc)
8864 ("r-impute" ,r-impute)
8866 ("r-survival" ,r-survival)
8867 ("r-matrixstats" ,r-matrixstats)
8868 ("r-preprocesscore" ,r-preprocesscore)))
8870 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8871 (synopsis "Weighted correlation network analysis")
8873 "This package provides functions necessary to perform Weighted
8874 Correlation Network Analysis on high-dimensional data. It includes functions
8875 for rudimentary data cleaning, construction and summarization of correlation
8876 networks, module identification and functions for relating both variables and
8877 modules to sample traits. It also includes a number of utility functions for
8878 data manipulation and visualization.")
8879 (license license:gpl2+)))
8881 (define-public r-rgraphviz
8883 (name "r-rgraphviz")
8888 (uri (bioconductor-uri "Rgraphviz" version))
8891 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
8892 (properties `((upstream-name . "Rgraphviz")))
8893 (build-system r-build-system)
8896 (modify-phases %standard-phases
8897 (add-after 'unpack 'make-reproducible
8899 ;; The replacement value is taken from src/graphviz/builddate.h
8900 (substitute* "src/graphviz/configure"
8901 (("VERSION_DATE=.*")
8902 "VERSION_DATE=20200427.2341\n"))
8904 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8905 ;; graphviz. It does not build with the latest version of graphviz, so
8906 ;; we do not add graphviz to the inputs.
8907 (inputs `(("zlib" ,zlib)))
8909 `(("r-graph" ,r-graph)))
8911 `(("pkg-config" ,pkg-config)))
8912 (home-page "https://bioconductor.org/packages/Rgraphviz")
8913 (synopsis "Plotting capabilities for R graph objects")
8915 "This package interfaces R with the graphviz library for plotting R graph
8916 objects from the @code{graph} package.")
8917 (license license:epl1.0)))
8919 (define-public r-fithic
8925 (uri (bioconductor-uri "FitHiC" version))
8928 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
8929 (properties `((upstream-name . "FitHiC")))
8930 (build-system r-build-system)
8932 `(("r-data-table" ,r-data-table)
8933 ("r-fdrtool" ,r-fdrtool)
8934 ("r-rcpp" ,r-rcpp)))
8936 `(("r-knitr" ,r-knitr)))
8937 (home-page "https://bioconductor.org/packages/FitHiC")
8938 (synopsis "Confidence estimation for intra-chromosomal contact maps")
8940 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
8941 intra-chromosomal contact maps produced by genome-wide genome architecture
8942 assays such as Hi-C.")
8943 (license license:gpl2+)))
8945 (define-public r-hitc
8951 (uri (bioconductor-uri "HiTC" version))
8954 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
8955 (properties `((upstream-name . "HiTC")))
8956 (build-system r-build-system)
8958 `(("r-biostrings" ,r-biostrings)
8959 ("r-genomeinfodb" ,r-genomeinfodb)
8960 ("r-genomicranges" ,r-genomicranges)
8961 ("r-iranges" ,r-iranges)
8962 ("r-matrix" ,r-matrix)
8963 ("r-rcolorbrewer" ,r-rcolorbrewer)
8964 ("r-rtracklayer" ,r-rtracklayer)))
8965 (home-page "https://bioconductor.org/packages/HiTC")
8966 (synopsis "High throughput chromosome conformation capture analysis")
8968 "The HiTC package was developed to explore high-throughput \"C\" data
8969 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
8970 quality controls, normalization, visualization, and further analysis are also
8972 (license license:artistic2.0)))
8974 (define-public r-hdf5array
8976 (name "r-hdf5array")
8981 (uri (bioconductor-uri "HDF5Array" version))
8984 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
8985 (properties `((upstream-name . "HDF5Array")))
8986 (build-system r-build-system)
8989 (modify-phases %standard-phases
8990 (add-after 'unpack 'fix-linking
8992 (substitute* "src/Makevars"
8993 ;; This is to avoid having a plain directory on the list of
8994 ;; libraries to link.
8995 (("\\(RHDF5LIB_LIBS\\)" match)
8996 (string-append match "/libhdf5.a")))
9001 `(("r-biocgenerics" ,r-biocgenerics)
9002 ("r-delayedarray" ,r-delayedarray)
9003 ("r-iranges" ,r-iranges)
9004 ("r-matrix" ,r-matrix)
9005 ("r-rhdf5" ,r-rhdf5)
9006 ("r-rhdf5lib" ,r-rhdf5lib)
9007 ("r-s4vectors" ,r-s4vectors)))
9008 (home-page "https://bioconductor.org/packages/HDF5Array")
9009 (synopsis "HDF5 back end for DelayedArray objects")
9010 (description "This package provides an array-like container for convenient
9011 access and manipulation of HDF5 datasets. It supports delayed operations and
9013 (license license:artistic2.0)))
9015 (define-public r-rhdf5lib
9022 (uri (bioconductor-uri "Rhdf5lib" version))
9025 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
9026 (modules '((guix build utils)))
9029 ;; Delete bundled binaries
9030 (delete-file-recursively "src/wininclude/")
9031 (delete-file-recursively "src/winlib-4.9.3/")
9032 (delete-file-recursively "src/winlib-8.3.0/")
9033 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
9035 (properties `((upstream-name . "Rhdf5lib")))
9036 (build-system r-build-system)
9039 (modify-phases %standard-phases
9040 (add-after 'unpack 'do-not-use-bundled-hdf5
9041 (lambda* (#:key inputs #:allow-other-keys)
9042 (for-each delete-file '("configure" "configure.ac"))
9043 ;; Do not make other packages link with the proprietary libsz.
9044 (substitute* "R/zzz.R"
9045 ((" \"%s/libsz.a\"") ""))
9046 (with-directory-excursion "src"
9047 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
9048 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
9050 ;; Remove timestamp and host system information to make
9051 ;; the build reproducible.
9052 (substitute* "hdf5/src/libhdf5.settings.in"
9053 (("Configured on: @CONFIG_DATE@")
9054 "Configured on: Guix")
9055 (("Uname information:.*")
9056 "Uname information: Linux\n")
9057 ;; Remove unnecessary store reference.
9059 "C Compiler: GCC\n"))
9060 (rename-file "hdf5/src/libhdf5.settings.in"
9061 "hdf5/src/libhdf5.settings")
9062 (rename-file "Makevars.in" "Makevars")
9063 (substitute* "Makevars"
9064 (("@ZLIB_LIB@") "-lz")
9065 (("@ZLIB_INCLUDE@") "")
9066 (("HDF5_CXX_LIB=.*")
9067 (string-append "HDF5_CXX_LIB="
9068 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
9070 (string-append "HDF5_LIB="
9071 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
9072 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
9073 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
9074 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
9075 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
9077 (string-append "HDF5_HL_LIB="
9078 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
9079 (("HDF5_HL_CXX_LIB=.*")
9080 (string-append "HDF5_HL_CXX_LIB="
9081 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
9082 ;; szip is non-free software
9083 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
9084 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
9089 `(("hdf5" ,hdf5-1.10)))
9091 `(("hdf5-source" ,(package-source hdf5-1.10))
9092 ("r-knitr" ,r-knitr)))
9093 (home-page "https://bioconductor.org/packages/Rhdf5lib")
9094 (synopsis "HDF5 library as an R package")
9095 (description "This package provides C and C++ HDF5 libraries for use in R
9097 (license license:artistic2.0)))
9099 (define-public r-beachmat
9106 (uri (bioconductor-uri "beachmat" version))
9109 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
9110 (build-system r-build-system)
9112 `(("r-biocgenerics" ,r-biocgenerics)
9113 ("r-delayedarray" ,r-delayedarray)
9114 ("r-matrix" ,r-matrix)))
9116 `(("r-knitr" ,r-knitr)))
9117 (home-page "https://bioconductor.org/packages/beachmat")
9118 (synopsis "Compiling Bioconductor to handle each matrix type")
9119 (description "This package provides a consistent C++ class interface for a
9120 variety of commonly used matrix types, including sparse and HDF5-backed
9122 (license license:gpl3)))
9124 ;; This package includes files that have been taken from kentutils. Some
9125 ;; parts of kentutils are not released under a free license, but this package
9126 ;; only uses files that are also found in the free parts of kentutils.
9127 (define-public r-cner
9134 (uri (bioconductor-uri "CNEr" version))
9136 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
9137 (properties `((upstream-name . "CNEr")))
9138 (build-system r-build-system)
9139 (inputs `(("zlib" ,zlib)))
9141 `(("r-annotate" ,r-annotate)
9142 ("r-biocgenerics" ,r-biocgenerics)
9143 ("r-biostrings" ,r-biostrings)
9145 ("r-genomeinfodb" ,r-genomeinfodb)
9146 ("r-genomicalignments" ,r-genomicalignments)
9147 ("r-genomicranges" ,r-genomicranges)
9148 ("r-ggplot2" ,r-ggplot2)
9149 ("r-go-db" ,r-go-db)
9150 ("r-iranges" ,r-iranges)
9151 ("r-keggrest" ,r-keggrest)
9152 ("r-powerlaw" ,r-powerlaw)
9153 ("r-r-utils" ,r-r-utils)
9154 ("r-readr" ,r-readr)
9155 ("r-reshape2" ,r-reshape2)
9156 ("r-rsqlite" ,r-rsqlite)
9157 ("r-rtracklayer" ,r-rtracklayer)
9158 ("r-s4vectors" ,r-s4vectors)
9159 ("r-xvector" ,r-xvector)))
9161 `(("r-knitr" ,r-knitr)))
9162 (home-page "https://github.com/ge11232002/CNEr")
9163 (synopsis "CNE Detection and Visualization")
9165 "This package provides tools for large-scale identification and
9166 advanced visualization of sets of conserved noncoding elements.")
9167 ;; For all files in src/ucsc "license is hereby granted for all use -
9168 ;; public, private or commercial"; this includes those files that don't
9169 ;; have a license header, because they are included in the free parts of
9170 ;; the kentutils package.
9171 (license (list license:gpl2
9172 (license:non-copyleft
9173 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
9175 (define-public r-tfbstools
9177 (name "r-tfbstools")
9182 (uri (bioconductor-uri "TFBSTools" version))
9185 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
9186 (properties `((upstream-name . "TFBSTools")))
9187 (build-system r-build-system)
9189 `(("r-biobase" ,r-biobase)
9190 ("r-biocgenerics" ,r-biocgenerics)
9191 ("r-biocparallel" ,r-biocparallel)
9192 ("r-biostrings" ,r-biostrings)
9193 ("r-bsgenome" ,r-bsgenome)
9194 ("r-catools" ,r-catools)
9197 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
9198 ("r-genomeinfodb" ,r-genomeinfodb)
9199 ("r-genomicranges" ,r-genomicranges)
9200 ("r-gtools" ,r-gtools)
9201 ("r-iranges" ,r-iranges)
9202 ("r-rsqlite" ,r-rsqlite)
9203 ("r-rtracklayer" ,r-rtracklayer)
9204 ("r-s4vectors" ,r-s4vectors)
9205 ("r-seqlogo" ,r-seqlogo)
9206 ("r-tfmpvalue" ,r-tfmpvalue)
9208 ("r-xvector" ,r-xvector)))
9209 (native-inputs `(("r-knitr" ,r-knitr)))
9210 (home-page "https://github.com/ge11232002/TFBSTools")
9211 (synopsis "Transcription factor binding site (TFBS) analysis")
9213 "TFBSTools is a package for the analysis and manipulation of
9214 transcription factor binding sites. It includes matrices conversion
9215 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
9216 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
9217 scan putative TFBS from sequence/alignment, query JASPAR database and
9218 provides a wrapper of de novo motif discovery software.")
9219 (license license:gpl2)))
9221 (define-public r-motifmatchr
9223 (name "r-motifmatchr")
9228 (uri (bioconductor-uri "motifmatchr" version))
9231 "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
9232 (properties `((upstream-name . "motifmatchr")))
9233 (build-system r-build-system)
9235 `(("r-biostrings" ,r-biostrings)
9236 ("r-bsgenome" ,r-bsgenome)
9237 ("r-genomeinfodb" ,r-genomeinfodb)
9238 ("r-genomicranges" ,r-genomicranges)
9239 ("r-iranges" ,r-iranges)
9240 ("r-matrix" ,r-matrix)
9242 ("r-rcpparmadillo" ,r-rcpparmadillo)
9243 ("r-rsamtools" ,r-rsamtools)
9244 ("r-s4vectors" ,r-s4vectors)
9245 ("r-summarizedexperiment" ,r-summarizedexperiment)
9246 ("r-tfbstools" ,r-tfbstools)))
9247 (native-inputs `(("r-knitr" ,r-knitr)))
9248 (home-page "https://bioconductor.org/packages/motifmatchr")
9249 (synopsis "Fast motif matching in R")
9251 "Quickly find motif matches for many motifs and many sequences.
9252 This package wraps C++ code from the MOODS motif calling library.")
9253 (license license:gpl3)))
9255 (define-public r-chromvar
9262 (uri (bioconductor-uri "chromVAR" version))
9264 (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
9265 (properties `((upstream-name . "chromVAR")))
9266 (build-system r-build-system)
9268 `(("r-biocgenerics" ,r-biocgenerics)
9269 ("r-biocparallel" ,r-biocparallel)
9270 ("r-biostrings" ,r-biostrings)
9271 ("r-bsgenome" ,r-bsgenome)
9273 ("r-genomeinfodb" ,r-genomeinfodb)
9274 ("r-genomicranges" ,r-genomicranges)
9275 ("r-ggplot2" ,r-ggplot2)
9276 ("r-iranges" ,r-iranges)
9277 ("r-matrix" ,r-matrix)
9278 ("r-miniui" ,r-miniui)
9279 ("r-nabor" ,r-nabor)
9280 ("r-plotly" ,r-plotly)
9281 ("r-rcolorbrewer" ,r-rcolorbrewer)
9283 ("r-rcpparmadillo" ,r-rcpparmadillo)
9284 ("r-rsamtools" ,r-rsamtools)
9285 ("r-rtsne" ,r-rtsne)
9286 ("r-s4vectors" ,r-s4vectors)
9287 ("r-shiny" ,r-shiny)
9288 ("r-summarizedexperiment" ,r-summarizedexperiment)
9289 ("r-tfbstools" ,r-tfbstools)))
9290 (native-inputs `(("r-knitr" ,r-knitr)))
9291 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
9292 (synopsis "Determine chromatin variation across regions")
9294 "This package @code{r-chromvar} determines variation in chromatin
9295 accessibility across sets of annotations or peaks. @code{r-chromvar} is
9296 designed primarily for single-cell or sparse chromatin accessibility data like
9297 single cell assay for transposase-accessible chromatin using
9298 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
9299 sequence (@code{DNAse-seq}) experiments.")
9300 (license license:expat)))
9302 (define-public r-singlecellexperiment
9304 (name "r-singlecellexperiment")
9309 (uri (bioconductor-uri "SingleCellExperiment" version))
9312 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
9314 `((upstream-name . "SingleCellExperiment")))
9315 (build-system r-build-system)
9317 `(("r-biocgenerics" ,r-biocgenerics)
9318 ("r-s4vectors" ,r-s4vectors)
9319 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9321 `(("r-knitr" ,r-knitr)))
9322 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
9323 (synopsis "S4 classes for single cell data")
9324 (description "This package defines an S4 class for storing data from
9325 single-cell experiments. This includes specialized methods to store and
9326 retrieve spike-in information, dimensionality reduction coordinates and size
9327 factors for each cell, along with the usual metadata for genes and
9329 (license license:gpl3)))
9331 (define-public r-scuttle
9338 (uri (bioconductor-uri "scuttle" version))
9341 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
9342 (properties `((upstream-name . "scuttle")))
9343 (build-system r-build-system)
9345 `(("r-beachmat" ,r-beachmat)
9346 ("r-biocgenerics" ,r-biocgenerics)
9347 ("r-biocparallel" ,r-biocparallel)
9348 ("r-delayedarray" ,r-delayedarray)
9349 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9350 ("r-genomicranges" ,r-genomicranges)
9351 ("r-matrix" ,r-matrix)
9353 ("r-s4vectors" ,r-s4vectors)
9354 ("r-singlecellexperiment" ,r-singlecellexperiment)
9355 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9356 (native-inputs `(("r-knitr" ,r-knitr)))
9357 (home-page "https://bioconductor.org/packages/scuttle")
9358 (synopsis "Single-cell RNA-Seq analysis utilities")
9360 "This package provides basic utility functions for performing single-cell
9361 analyses, focusing on simple normalization, quality control and data
9362 transformations. It also provides some helper functions to assist development
9363 of other packages.")
9364 (license license:gpl3)))
9366 (define-public r-scater
9372 (uri (bioconductor-uri "scater" version))
9375 "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535"))))
9376 (build-system r-build-system)
9378 `(("r-biocgenerics" ,r-biocgenerics)
9379 ("r-biocneighbors" ,r-biocneighbors)
9380 ("r-biocparallel" ,r-biocparallel)
9381 ("r-biocsingular" ,r-biocsingular)
9382 ("r-delayedarray" ,r-delayedarray)
9383 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9384 ("r-ggbeeswarm" ,r-ggbeeswarm)
9385 ("r-ggplot2" ,r-ggplot2)
9386 ("r-gridextra" ,r-gridextra)
9387 ("r-matrix" ,r-matrix)
9388 ("r-rlang" ,r-rlang)
9389 ("r-s4vectors" ,r-s4vectors)
9390 ("r-scuttle" ,r-scuttle)
9391 ("r-singlecellexperiment" ,r-singlecellexperiment)
9392 ("r-summarizedexperiment" ,r-summarizedexperiment)
9393 ("r-viridis" ,r-viridis)))
9395 `(("r-knitr" ,r-knitr)))
9396 (home-page "https://github.com/davismcc/scater")
9397 (synopsis "Single-cell analysis toolkit for gene expression data in R")
9398 (description "This package provides a collection of tools for doing
9399 various analyses of single-cell RNA-seq gene expression data, with a focus on
9401 (license license:gpl2+)))
9403 (define-public r-scran
9410 (uri (bioconductor-uri "scran" version))
9413 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
9414 (build-system r-build-system)
9416 `(("r-beachmat" ,r-beachmat)
9418 ("r-biocgenerics" ,r-biocgenerics)
9419 ("r-biocneighbors" ,r-biocneighbors)
9420 ("r-biocparallel" ,r-biocparallel)
9421 ("r-biocsingular" ,r-biocsingular)
9422 ("r-bluster" ,r-bluster)
9423 ("r-delayedarray" ,r-delayedarray)
9424 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9425 ("r-dqrng" ,r-dqrng)
9426 ("r-edger" ,r-edger)
9427 ("r-igraph" ,r-igraph)
9428 ("r-limma" ,r-limma)
9429 ("r-matrix" ,r-matrix)
9431 ("r-s4vectors" ,r-s4vectors)
9432 ("r-scuttle" ,r-scuttle)
9433 ("r-singlecellexperiment" ,r-singlecellexperiment)
9434 ("r-statmod" ,r-statmod)
9435 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9437 `(("r-knitr" ,r-knitr)))
9438 (home-page "https://bioconductor.org/packages/scran")
9439 (synopsis "Methods for single-cell RNA-Seq data analysis")
9440 (description "This package implements a variety of low-level analyses of
9441 single-cell RNA-seq data. Methods are provided for normalization of
9442 cell-specific biases, assignment of cell cycle phase, and detection of highly
9443 variable and significantly correlated genes.")
9444 (license license:gpl3)))
9446 (define-public r-sparsematrixstats
9448 (name "r-sparsematrixstats")
9453 (uri (bioconductor-uri "sparseMatrixStats" version))
9456 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
9458 `((upstream-name . "sparseMatrixStats")))
9459 (build-system r-build-system)
9461 `(("r-matrix" ,r-matrix)
9462 ("r-matrixgenerics" ,r-matrixgenerics)
9463 ("r-matrixstats" ,r-matrixstats)
9464 ("r-rcpp" ,r-rcpp)))
9465 (native-inputs `(("r-knitr" ,r-knitr)))
9466 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
9467 (synopsis "Summary statistics for rows and columns of sparse matrices")
9469 "This package provides high performance functions for row and column
9470 operations on sparse matrices. Currently, the optimizations are limited to
9471 data in the column sparse format.")
9472 (license license:expat)))
9474 (define-public r-delayedmatrixstats
9476 (name "r-delayedmatrixstats")
9481 (uri (bioconductor-uri "DelayedMatrixStats" version))
9484 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
9486 `((upstream-name . "DelayedMatrixStats")))
9487 (build-system r-build-system)
9489 `(("r-biocparallel" ,r-biocparallel)
9490 ("r-delayedarray" ,r-delayedarray)
9491 ("r-hdf5array" ,r-hdf5array)
9492 ("r-iranges" ,r-iranges)
9493 ("r-matrix" ,r-matrix)
9494 ("r-matrixgenerics" ,r-matrixgenerics)
9495 ("r-matrixstats" ,r-matrixstats)
9496 ("r-s4vectors" ,r-s4vectors)
9497 ("r-sparsematrixstats" ,r-sparsematrixstats)))
9499 `(("r-knitr" ,r-knitr)))
9500 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
9501 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
9503 "This package provides a port of the @code{matrixStats} API for use with
9504 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
9505 contains high-performing functions operating on rows and columns of
9506 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
9507 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
9508 are optimized per data type and for subsetted calculations such that both
9509 memory usage and processing time is minimized.")
9510 (license license:expat)))
9512 (define-public r-mscoreutils
9514 (name "r-mscoreutils")
9519 (uri (bioconductor-uri "MsCoreUtils" version))
9522 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
9523 (properties `((upstream-name . "MsCoreUtils")))
9524 (build-system r-build-system)
9526 `(("r-mass" ,r-mass)
9528 ("r-s4vectors" ,r-s4vectors)))
9530 `(("r-knitr" ,r-knitr)))
9531 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
9532 (synopsis "Core utils for mass spectrometry data")
9534 "This package defines low-level functions for mass spectrometry data and
9535 is independent of any high-level data structures. These functions include
9536 mass spectra processing functions (noise estimation, smoothing, binning),
9537 quantitative aggregation functions (median polish, robust summarisation,
9538 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
9539 well as misc helper functions, that are used across high-level data structure
9540 within the R for Mass Spectrometry packages.")
9541 (license license:artistic2.0)))
9543 (define-public r-biocio
9550 (uri (bioconductor-uri "BiocIO" version))
9553 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
9554 (properties `((upstream-name . "BiocIO")))
9555 (build-system r-build-system)
9557 `(("r-biocgenerics" ,r-biocgenerics)
9558 ("r-genomicranges" ,r-genomicranges)
9559 ("r-rcurl" ,r-rcurl)
9560 ("r-s4vectors" ,r-s4vectors)))
9562 `(("r-knitr" ,r-knitr)))
9563 (home-page "https://bioconductor.org/packages/BiocIO")
9564 (synopsis "Standard input and output for Bioconductor packages")
9566 "This package implements `import()` and `export()` standard generics for
9567 importing and exporting biological data formats. `import()` supports
9568 whole-file as well as chunk-wise iterative import. The `import()` interface
9569 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
9570 row or element-like components of the file resource), `select()` (on
9571 column-like components of the file resource) and `collect()`. The `import()`
9572 interface optionally provides transparent access to remote (e.g. via https)
9573 as well as local access. Developers can register a file extension, e.g.,
9574 `.loom` for dispatch from character-based URIs to specific `import()` /
9575 `export()` methods based on classes representing file types, e.g.,
9577 (license license:artistic2.0)))
9579 (define-public r-msmseda
9586 (uri (bioconductor-uri "msmsEDA" version))
9589 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
9590 (properties `((upstream-name . "msmsEDA")))
9591 (build-system r-build-system)
9593 `(("r-gplots" ,r-gplots)
9595 ("r-msnbase" ,r-msnbase)
9596 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9598 "https://bioconductor.org/packages/msmsEDA")
9599 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
9601 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
9602 experiments, and visualize de influence of the involved factors.")
9603 (license license:gpl2)))
9605 (define-public r-msmstests
9607 (name "r-msmstests")
9612 (uri (bioconductor-uri "msmsTests" version))
9615 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
9616 (properties `((upstream-name . "msmsTests")))
9617 (build-system r-build-system)
9619 `(("r-edger" ,r-edger)
9620 ("r-msmseda" ,r-msmseda)
9621 ("r-msnbase" ,r-msnbase)
9622 ("r-qvalue" ,r-qvalue)))
9624 "https://bioconductor.org/packages/msmsTests")
9625 (synopsis "Differential LC-MS/MS expression tests")
9627 "This packages provides statistical tests for label-free LC-MS/MS data
9628 by spectral counts, to discover differentially expressed proteins between two
9629 biological conditions. Three tests are available: Poisson GLM regression,
9630 quasi-likelihood GLM regression, and the negative binomial of the edgeR
9631 package.The three models admit blocking factors to control for nuissance
9632 variables.To assure a good level of reproducibility a post-test filter is
9633 available, where we may set the minimum effect size considered biologicaly
9634 relevant, and the minimum expression of the most abundant condition.")
9635 (license license:gpl2)))
9637 (define-public r-catalyst
9644 (uri (bioconductor-uri "CATALYST" version))
9647 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
9648 (properties `((upstream-name . "CATALYST")))
9649 (build-system r-build-system)
9651 `(("r-circlize" ,r-circlize)
9652 ("r-complexheatmap" ,r-complexheatmap)
9653 ("r-consensusclusterplus" ,r-consensusclusterplus)
9654 ("r-cowplot" ,r-cowplot)
9655 ("r-data-table" ,r-data-table)
9656 ("r-dplyr" ,r-dplyr)
9658 ("r-flowcore" ,r-flowcore)
9659 ("r-flowsom" ,r-flowsom)
9660 ("r-ggplot2" ,r-ggplot2)
9661 ("r-ggrepel" ,r-ggrepel)
9662 ("r-ggridges" ,r-ggridges)
9663 ("r-gridextra" ,r-gridextra)
9664 ("r-magrittr" ,r-magrittr)
9665 ("r-matrix" ,r-matrix)
9666 ("r-matrixstats" ,r-matrixstats)
9668 ("r-purrr" ,r-purrr)
9669 ("r-rcolorbrewer" ,r-rcolorbrewer)
9670 ("r-reshape2" ,r-reshape2)
9671 ("r-rtsne" ,r-rtsne)
9672 ("r-s4vectors" ,r-s4vectors)
9673 ("r-scales" ,r-scales)
9674 ("r-scater" ,r-scater)
9675 ("r-singlecellexperiment" ,r-singlecellexperiment)
9676 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9678 `(("r-knitr" ,r-knitr)))
9680 "https://github.com/HelenaLC/CATALYST")
9681 (synopsis "Cytometry data analysis tools")
9683 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
9684 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
9685 reporters to label antibodies, thereby substantially decreasing spectral
9686 overlap and allowing for examination of over 50 parameters at the single cell
9687 level. While spectral overlap is significantly less pronounced in CyTOF than
9688 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
9689 and oxide formation can impede data interpretability. We designed
9690 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
9691 preprocessing of cytometry data, including i) normalization using bead
9692 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
9693 (license license:gpl2+)))
9695 (define-public r-erma
9702 (uri (bioconductor-uri "erma" version))
9705 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
9706 (build-system r-build-system)
9708 `(("r-annotationdbi" ,r-annotationdbi)
9709 ("r-biobase" ,r-biobase)
9710 ("r-biocgenerics" ,r-biocgenerics)
9711 ("r-biocparallel" ,r-biocparallel)
9712 ("r-genomeinfodb" ,r-genomeinfodb)
9713 ("r-genomicfiles" ,r-genomicfiles)
9714 ("r-genomicranges" ,r-genomicranges)
9715 ("r-ggplot2" ,r-ggplot2)
9716 ("r-homo-sapiens" ,r-homo-sapiens)
9717 ("r-iranges" ,r-iranges)
9718 ("r-rtracklayer" ,r-rtracklayer)
9719 ("r-s4vectors" ,r-s4vectors)
9720 ("r-shiny" ,r-shiny)
9721 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9723 `(("r-knitr" ,r-knitr)))
9724 (home-page "https://bioconductor.org/packages/erma")
9725 (synopsis "Epigenomic road map adventures")
9727 "The epigenomics road map describes locations of epigenetic marks in DNA
9728 from a variety of cell types. Of interest are locations of histone
9729 modifications, sites of DNA methylation, and regions of accessible chromatin.
9730 This package presents a selection of elements of the road map including
9731 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
9732 by Ernst and Kellis.")
9733 (license license:artistic2.0)))
9735 (define-public r-ggbio
9742 (uri (bioconductor-uri "ggbio" version))
9745 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
9746 (build-system r-build-system)
9749 (modify-phases %standard-phases
9750 ;; See https://github.com/tengfei/ggbio/issues/117
9751 ;; This fix will be included in the next release.
9752 (add-after 'unpack 'fix-typo
9754 (substitute* "R/GGbio-class.R"
9755 (("fechable") "fetchable"))
9758 `(("r-annotationdbi" ,r-annotationdbi)
9759 ("r-annotationfilter" ,r-annotationfilter)
9760 ("r-biobase" ,r-biobase)
9761 ("r-biocgenerics" ,r-biocgenerics)
9762 ("r-biostrings" ,r-biostrings)
9763 ("r-biovizbase" ,r-biovizbase)
9764 ("r-bsgenome" ,r-bsgenome)
9765 ("r-ensembldb" ,r-ensembldb)
9766 ("r-genomeinfodb" ,r-genomeinfodb)
9767 ("r-genomicalignments" ,r-genomicalignments)
9768 ("r-genomicfeatures" ,r-genomicfeatures)
9769 ("r-genomicranges" ,r-genomicranges)
9770 ("r-ggally" ,r-ggally)
9771 ("r-ggplot2" ,r-ggplot2)
9772 ("r-gridextra" ,r-gridextra)
9773 ("r-gtable" ,r-gtable)
9774 ("r-hmisc" ,r-hmisc)
9775 ("r-iranges" ,r-iranges)
9776 ("r-organismdbi" ,r-organismdbi)
9777 ("r-reshape2" ,r-reshape2)
9778 ("r-rlang" ,r-rlang)
9779 ("r-rsamtools" ,r-rsamtools)
9780 ("r-rtracklayer" ,r-rtracklayer)
9781 ("r-s4vectors" ,r-s4vectors)
9782 ("r-scales" ,r-scales)
9783 ("r-summarizedexperiment" ,r-summarizedexperiment)
9784 ("r-variantannotation" ,r-variantannotation)))
9786 `(("r-knitr" ,r-knitr)))
9787 (home-page "http://www.tengfei.name/ggbio/")
9788 (synopsis "Visualization tools for genomic data")
9790 "The ggbio package extends and specializes the grammar of graphics for
9791 biological data. The graphics are designed to answer common scientific
9792 questions, in particular those often asked of high throughput genomics data.
9793 All core Bioconductor data structures are supported, where appropriate. The
9794 package supports detailed views of particular genomic regions, as well as
9795 genome-wide overviews. Supported overviews include ideograms and grand linear
9796 views. High-level plots include sequence fragment length, edge-linked
9797 interval to data view, mismatch pileup, and several splicing summaries.")
9798 (license license:artistic2.0)))
9800 (define-public r-gqtlbase
9807 (uri (bioconductor-uri "gQTLBase" version))
9810 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
9811 (properties `((upstream-name . "gQTLBase")))
9812 (build-system r-build-system)
9815 (modify-phases %standard-phases
9816 ;; This is an upstream bug.
9817 (add-after 'unpack 'fix-imports
9819 (substitute* "NAMESPACE"
9820 ((".*maxffmode.*") "")
9821 (("importFrom\\(ff,.*") "import(ff)\n"))
9824 `(("r-batchjobs" ,r-batchjobs)
9825 ("r-bbmisc" ,r-bbmisc)
9826 ("r-biocgenerics" ,r-biocgenerics)
9828 ("r-doparallel" ,r-doparallel)
9830 ("r-ffbase" ,r-ffbase)
9831 ("r-foreach" ,r-foreach)
9832 ("r-genomicfiles" ,r-genomicfiles)
9833 ("r-genomicranges" ,r-genomicranges)
9834 ("r-rtracklayer" ,r-rtracklayer)
9835 ("r-s4vectors" ,r-s4vectors)
9836 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9838 `(("r-knitr" ,r-knitr)))
9839 (home-page "https://bioconductor.org/packages/gQTLBase")
9840 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
9842 "The purpose of this package is to simplify the storage and interrogation
9843 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
9845 (license license:artistic2.0)))
9847 (define-public r-gqtlstats
9849 (name "r-gqtlstats")
9854 (uri (bioconductor-uri "gQTLstats" version))
9857 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
9858 (properties `((upstream-name . "gQTLstats")))
9859 (build-system r-build-system)
9861 `(("r-annotationdbi" ,r-annotationdbi)
9862 ("r-batchjobs" ,r-batchjobs)
9863 ("r-bbmisc" ,r-bbmisc)
9864 ("r-beeswarm" ,r-beeswarm)
9865 ("r-biobase" ,r-biobase)
9866 ("r-biocgenerics" ,r-biocgenerics)
9867 ("r-doparallel" ,r-doparallel)
9868 ("r-dplyr" ,r-dplyr)
9870 ("r-ffbase" ,r-ffbase)
9871 ("r-foreach" ,r-foreach)
9872 ("r-genomeinfodb" ,r-genomeinfodb)
9873 ("r-genomicfeatures" ,r-genomicfeatures)
9874 ("r-genomicfiles" ,r-genomicfiles)
9875 ("r-genomicranges" ,r-genomicranges)
9876 ("r-ggbeeswarm" ,r-ggbeeswarm)
9877 ("r-ggplot2" ,r-ggplot2)
9878 ("r-gqtlbase" ,r-gqtlbase)
9879 ("r-hardyweinberg" ,r-hardyweinberg)
9880 ("r-homo-sapiens" ,r-homo-sapiens)
9881 ("r-iranges" ,r-iranges)
9882 ("r-limma" ,r-limma)
9884 ("r-plotly" ,r-plotly)
9885 ("r-reshape2" ,r-reshape2)
9886 ("r-s4vectors" ,r-s4vectors)
9887 ("r-shiny" ,r-shiny)
9888 ("r-snpstats" ,r-snpstats)
9889 ("r-summarizedexperiment" ,r-summarizedexperiment)
9890 ("r-variantannotation" ,r-variantannotation)))
9892 `(("r-knitr" ,r-knitr)))
9893 (home-page "https://bioconductor.org/packages/gQTLstats")
9894 (synopsis "Computationally efficient analysis for eQTL and allied studies")
9896 "This package provides tools for the computationally efficient analysis
9897 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
9898 The software in this package aims to support refinements and functional
9899 interpretation of members of a collection of association statistics on a
9900 family of feature/genome hypotheses.")
9901 (license license:artistic2.0)))
9903 (define-public r-gviz
9910 (uri (bioconductor-uri "Gviz" version))
9913 "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
9914 (properties `((upstream-name . "Gviz")))
9915 (build-system r-build-system)
9917 `(("r-annotationdbi" ,r-annotationdbi)
9918 ("r-biobase" ,r-biobase)
9919 ("r-biocgenerics" ,r-biocgenerics)
9920 ("r-biomart" ,r-biomart)
9921 ("r-biostrings" ,r-biostrings)
9922 ("r-biovizbase" ,r-biovizbase)
9923 ("r-bsgenome" ,r-bsgenome)
9924 ("r-digest" ,r-digest)
9925 ("r-ensembldb" ,r-ensembldb)
9926 ("r-genomeinfodb" ,r-genomeinfodb)
9927 ("r-genomicalignments" ,r-genomicalignments)
9928 ("r-genomicfeatures" ,r-genomicfeatures)
9929 ("r-genomicranges" ,r-genomicranges)
9930 ("r-iranges" ,r-iranges)
9931 ("r-lattice" ,r-lattice)
9932 ("r-latticeextra" ,r-latticeextra)
9933 ("r-matrixstats" ,r-matrixstats)
9934 ("r-rcolorbrewer" ,r-rcolorbrewer)
9935 ("r-rsamtools" ,r-rsamtools)
9936 ("r-rtracklayer" ,r-rtracklayer)
9937 ("r-s4vectors" ,r-s4vectors)
9938 ("r-xvector" ,r-xvector)))
9940 `(("r-knitr" ,r-knitr)))
9941 (home-page "https://bioconductor.org/packages/Gviz")
9942 (synopsis "Plotting data and annotation information along genomic coordinates")
9944 "Genomic data analyses requires integrated visualization of known genomic
9945 information and new experimental data. Gviz uses the biomaRt and the
9946 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
9947 and translates this to e.g. gene/transcript structures in viewports of the
9948 grid graphics package. This results in genomic information plotted together
9950 (license license:artistic2.0)))
9952 (define-public r-gwascat
9959 (uri (bioconductor-uri "gwascat" version))
9962 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
9963 (build-system r-build-system)
9965 `(("r-annotationdbi" ,r-annotationdbi)
9966 ("r-biocfilecache" ,r-biocfilecache)
9967 ("r-biostrings" ,r-biostrings)
9968 ("r-genomeinfodb" ,r-genomeinfodb)
9969 ("r-genomicfeatures" ,r-genomicfeatures)
9970 ("r-genomicranges" ,r-genomicranges)
9971 ("r-iranges" ,r-iranges)
9972 ("r-readr" ,r-readr)
9973 ("r-s4vectors" ,r-s4vectors)
9974 ("r-snpstats" ,r-snpstats)
9975 ("r-variantannotation" ,r-variantannotation)))
9977 `(("r-knitr" ,r-knitr)))
9978 (home-page "https://bioconductor.org/packages/gwascat")
9979 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
9981 "This package provides tools for representing and modeling data in the
9982 EMBL-EBI GWAS catalog.")
9983 (license license:artistic2.0)))
9985 (define-public r-kegggraph
9987 (name "r-kegggraph")
9992 (uri (bioconductor-uri "KEGGgraph" version))
9994 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
9995 (properties `((upstream-name . "KEGGgraph")))
9996 (build-system r-build-system)
9998 `(("r-graph" ,r-graph)
9999 ("r-rcurl" ,r-rcurl)
10001 (home-page "https://bioconductor.org/packages/KEGGgraph")
10002 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
10004 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
10005 object as well as a collection of tools to analyze, dissect and visualize these
10006 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
10007 maintaining all essential pathway attributes. The package offers
10008 functionalities including parsing, graph operation, visualization and etc.")
10009 (license license:gpl2+)))
10011 (define-public r-ldblock
10018 (uri (bioconductor-uri "ldblock" version))
10021 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
10022 (build-system r-build-system)
10024 `(("r-biocgenerics" ,r-biocgenerics)
10025 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
10026 ("r-ensembldb" ,r-ensembldb)
10027 ("r-genomeinfodb" ,r-genomeinfodb)
10028 ("r-genomicfiles" ,r-genomicfiles)
10030 ("r-matrix" ,r-matrix)
10031 ("r-rsamtools" ,r-rsamtools)
10032 ("r-snpstats" ,r-snpstats)
10033 ("r-variantannotation" ,r-variantannotation)))
10035 `(("r-knitr" ,r-knitr)))
10036 (home-page "https://bioconductor.org/packages/ldblock")
10037 (synopsis "Data structures for linkage disequilibrium measures in populations")
10039 "This package defines data structures for @dfn{linkage
10040 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10041 handling of existing population-level data for the purpose of flexibly
10042 defining LD blocks.")
10043 (license license:artistic2.0)))
10045 ;; This is a CRAN package, but it depends on r-snpstats, which is a
10046 ;; Bioconductor package.
10047 (define-public r-ldheatmap
10049 (name "r-ldheatmap")
10054 (uri (cran-uri "LDheatmap" version))
10057 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
10058 (properties `((upstream-name . "LDheatmap")))
10059 (build-system r-build-system)
10061 `(("r-genetics" ,r-genetics)
10063 ("r-snpstats" ,r-snpstats)))
10064 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
10065 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
10067 "This package provides tools to produce a graphical display, as a heat
10068 map, of measures of pairwise linkage disequilibria between SNPs. Users may
10069 optionally include the physical locations or genetic map distances of each SNP
10071 (license license:gpl3)))
10073 (define-public r-pathview
10075 (name "r-pathview")
10080 (uri (bioconductor-uri "pathview" version))
10082 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
10083 (properties `((upstream-name . "pathview")))
10084 (build-system r-build-system)
10086 `(("r-annotationdbi" ,r-annotationdbi)
10087 ("r-graph" ,r-graph)
10088 ("r-kegggraph" ,r-kegggraph)
10089 ("r-keggrest" ,r-keggrest)
10090 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10092 ("r-rgraphviz" ,r-rgraphviz)
10094 (home-page "https://pathview.uncc.edu/")
10095 (synopsis "Tool set for pathway based data integration and visualization")
10097 "@code{r-pathview} is a tool set for pathway based data integration and
10098 visualization. It maps and renders a wide variety of biological data on
10099 relevant pathway graphs. All users need is to supply their data and specify
10100 the target pathway. This package automatically downloads the pathway graph
10101 data, parses the data file, maps user data to the pathway, and render pathway
10102 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
10103 integrates with pathway and gene set (enrichment) analysis tools for
10104 large-scale and fully automated analysis.")
10105 (license license:gpl3+)))
10107 (define-public r-snpstats
10109 (name "r-snpstats")
10114 (uri (bioconductor-uri "snpStats" version))
10117 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
10118 (properties `((upstream-name . "snpStats")))
10119 (build-system r-build-system)
10120 (inputs `(("zlib" ,zlib)))
10122 `(("r-biocgenerics" ,r-biocgenerics)
10123 ("r-matrix" ,r-matrix)
10124 ("r-survival" ,r-survival)
10125 ("r-zlibbioc" ,r-zlibbioc)))
10126 (home-page "https://bioconductor.org/packages/snpStats")
10127 (synopsis "Methods for SNP association studies")
10129 "This package provides classes and statistical methods for large
10130 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
10131 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10132 (license license:gpl3)))
10134 (define-public r-sushi
10140 (uri (bioconductor-uri "Sushi" version))
10143 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
10144 (properties `((upstream-name . "Sushi")))
10145 (build-system r-build-system)
10147 `(("r-biomart" ,r-biomart)
10149 (home-page "https://bioconductor.org/packages/Sushi")
10150 (synopsis "Tools for visualizing genomics data")
10152 "This package provides flexible, quantitative, and integrative genomic
10153 visualizations for publication-quality multi-panel figures.")
10154 (license license:gpl2+)))