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-gseabase
1640 (uri (bioconductor-uri "GSEABase" version))
1643 "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
1644 (properties `((upstream-name . "GSEABase")))
1645 (build-system r-build-system)
1647 `(("r-annotate" ,r-annotate)
1648 ("r-annotationdbi" ,r-annotationdbi)
1649 ("r-biobase" ,r-biobase)
1650 ("r-biocgenerics" ,r-biocgenerics)
1651 ("r-graph" ,r-graph)
1654 `(("r-knitr" ,r-knitr)))
1655 (home-page "https://bioconductor.org/packages/GSEABase")
1656 (synopsis "Gene set enrichment data structures and methods")
1658 "This package provides classes and methods to support @dfn{Gene Set
1659 Enrichment Analysis} (GSEA).")
1660 (license license:artistic2.0)))
1662 (define-public r-hpar
1669 (uri (bioconductor-uri "hpar" version))
1672 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
1673 (build-system r-build-system)
1675 `(("r-knitr" ,r-knitr)))
1676 (home-page "https://bioconductor.org/packages/hpar/")
1677 (synopsis "Human Protein Atlas in R")
1678 (description "This package provides a simple interface to and data from
1679 the Human Protein Atlas project.")
1680 (license license:artistic2.0)))
1682 (define-public r-rbgl
1689 (uri (bioconductor-uri "RBGL" version))
1692 "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
1693 (properties `((upstream-name . "RBGL")))
1694 (build-system r-build-system)
1697 ("r-graph" ,r-graph)))
1698 (home-page "https://www.bioconductor.org/packages/RBGL")
1699 (synopsis "Interface to the Boost graph library")
1701 "This package provides a fairly extensive and comprehensive interface to
1702 the graph algorithms contained in the Boost library.")
1703 (license license:artistic2.0)))
1705 (define-public r-regioner
1712 (uri (bioconductor-uri "regioneR" version))
1715 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
1716 (properties `((upstream-name . "regioneR")))
1717 (build-system r-build-system)
1719 `(("r-biostrings" ,r-biostrings)
1720 ("r-bsgenome" ,r-bsgenome)
1721 ("r-genomeinfodb" ,r-genomeinfodb)
1722 ("r-genomicranges" ,r-genomicranges)
1723 ("r-iranges" ,r-iranges)
1724 ("r-memoise" ,r-memoise)
1725 ("r-rtracklayer" ,r-rtracklayer)
1726 ("r-s4vectors" ,r-s4vectors)))
1728 `(("r-knitr" ,r-knitr)))
1729 (home-page "https://bioconductor.org/packages/regioneR/")
1730 (synopsis "Association analysis of genomic regions")
1731 (description "This package offers a statistical framework based on
1732 customizable permutation tests to assess the association between genomic
1733 region sets and other genomic features.")
1734 (license license:artistic2.0)))
1736 (define-public r-reportingtools
1738 (name "r-reportingtools")
1743 (uri (bioconductor-uri "ReportingTools" version))
1746 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
1748 `((upstream-name . "ReportingTools")))
1749 (build-system r-build-system)
1751 `(("r-annotate" ,r-annotate)
1752 ("r-annotationdbi" ,r-annotationdbi)
1753 ("r-biobase" ,r-biobase)
1754 ("r-biocgenerics" ,r-biocgenerics)
1755 ("r-category" ,r-category)
1756 ("r-deseq2" ,r-deseq2)
1757 ("r-edger" ,r-edger)
1758 ("r-ggbio" ,r-ggbio)
1759 ("r-ggplot2" ,r-ggplot2)
1760 ("r-gostats" ,r-gostats)
1761 ("r-gseabase" ,r-gseabase)
1762 ("r-hwriter" ,r-hwriter)
1763 ("r-iranges" ,r-iranges)
1764 ("r-knitr" ,r-knitr)
1765 ("r-lattice" ,r-lattice)
1766 ("r-limma" ,r-limma)
1767 ("r-pfam-db" ,r-pfam-db)
1768 ("r-r-utils" ,r-r-utils)
1771 `(("r-knitr" ,r-knitr)))
1772 (home-page "https://bioconductor.org/packages/ReportingTools/")
1773 (synopsis "Tools for making reports in various formats")
1775 "The ReportingTools package enables users to easily display reports of
1776 analysis results generated from sources such as microarray and sequencing
1777 data. The package allows users to create HTML pages that may be viewed on a
1778 web browser, or in other formats. Users can generate tables with sortable and
1779 filterable columns, make and display plots, and link table entries to other
1780 data sources such as NCBI or larger plots within the HTML page. Using the
1781 package, users can also produce a table of contents page to link various
1782 reports together for a particular project that can be viewed in a web
1784 (license license:artistic2.0)))
1786 (define-public r-geneplotter
1788 (name "r-geneplotter")
1793 (uri (bioconductor-uri "geneplotter" version))
1796 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
1797 (build-system r-build-system)
1799 `(("r-annotate" ,r-annotate)
1800 ("r-annotationdbi" ,r-annotationdbi)
1801 ("r-biobase" ,r-biobase)
1802 ("r-biocgenerics" ,r-biocgenerics)
1803 ("r-lattice" ,r-lattice)
1804 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1805 (home-page "https://bioconductor.org/packages/geneplotter")
1806 (synopsis "Graphics functions for genomic data")
1808 "This package provides functions for plotting genomic data.")
1809 (license license:artistic2.0)))
1811 (define-public r-oligoclasses
1813 (name "r-oligoclasses")
1818 (uri (bioconductor-uri "oligoClasses" version))
1821 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
1822 (properties `((upstream-name . "oligoClasses")))
1823 (build-system r-build-system)
1825 `(("r-affyio" ,r-affyio)
1826 ("r-biobase" ,r-biobase)
1827 ("r-biocgenerics" ,r-biocgenerics)
1828 ("r-biocmanager" ,r-biocmanager)
1829 ("r-biostrings" ,r-biostrings)
1832 ("r-foreach" ,r-foreach)
1833 ("r-genomicranges" ,r-genomicranges)
1834 ("r-iranges" ,r-iranges)
1835 ("r-rsqlite" ,r-rsqlite)
1836 ("r-s4vectors" ,r-s4vectors)
1837 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1838 (home-page "https://bioconductor.org/packages/oligoClasses/")
1839 (synopsis "Classes for high-throughput arrays")
1841 "This package contains class definitions, validity checks, and
1842 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1844 (license license:gpl2+)))
1846 (define-public r-oligo
1853 (uri (bioconductor-uri "oligo" version))
1856 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
1857 (properties `((upstream-name . "oligo")))
1858 (build-system r-build-system)
1859 (inputs `(("zlib" ,zlib)))
1861 `(("r-affxparser" ,r-affxparser)
1862 ("r-affyio" ,r-affyio)
1863 ("r-biobase" ,r-biobase)
1864 ("r-biocgenerics" ,r-biocgenerics)
1865 ("r-biostrings" ,r-biostrings)
1868 ("r-oligoclasses" ,r-oligoclasses)
1869 ("r-preprocesscore" ,r-preprocesscore)
1870 ("r-rsqlite" ,r-rsqlite)
1871 ("r-zlibbioc" ,r-zlibbioc)))
1873 `(("r-knitr" ,r-knitr)))
1874 (home-page "https://bioconductor.org/packages/oligo/")
1875 (synopsis "Preprocessing tools for oligonucleotide arrays")
1877 "This package provides a package to analyze oligonucleotide
1878 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1879 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1880 (license license:lgpl2.0+)))
1882 (define-public r-qvalue
1889 (uri (bioconductor-uri "qvalue" version))
1892 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
1893 (build-system r-build-system)
1895 `(("r-ggplot2" ,r-ggplot2)
1896 ("r-reshape2" ,r-reshape2)))
1898 `(("r-knitr" ,r-knitr)))
1899 (home-page "https://github.com/StoreyLab/qvalue")
1900 (synopsis "Q-value estimation for false discovery rate control")
1902 "This package takes a list of p-values resulting from the simultaneous
1903 testing of many hypotheses and estimates their q-values and local @dfn{false
1904 discovery rate} (FDR) values. The q-value of a test measures the proportion
1905 of false positives incurred when that particular test is called significant.
1906 The local FDR measures the posterior probability the null hypothesis is true
1907 given the test's p-value. Various plots are automatically generated, allowing
1908 one to make sensible significance cut-offs. The software can be applied to
1909 problems in genomics, brain imaging, astrophysics, and data mining.")
1910 ;; Any version of the LGPL.
1911 (license license:lgpl3+)))
1913 (define r-rcppnumerical
1915 (name "r-rcppnumerical")
1919 (uri (cran-uri "RcppNumerical" version))
1922 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
1923 (properties `((upstream-name . "RcppNumerical")))
1924 (build-system r-build-system)
1926 `(("r-rcpp" ,r-rcpp)
1927 ("r-rcppeigen" ,r-rcppeigen)))
1929 `(("r-knitr" ,r-knitr)))
1930 (home-page "https://github.com/yixuan/RcppNumerical")
1931 (synopsis "Rcpp integration for numerical computing libraries")
1932 (description "This package provides a collection of open source libraries
1933 for numerical computing (numerical integration, optimization, etc.) and their
1934 integration with @code{Rcpp}.")
1935 (license license:gpl2+)))
1937 (define-public r-apeglm
1943 (uri (bioconductor-uri "apeglm" version))
1946 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
1947 (properties `((upstream-name . "apeglm")))
1948 (build-system r-build-system)
1950 `(("r-emdbook" ,r-emdbook)
1951 ("r-genomicranges" ,r-genomicranges)
1953 ("r-rcppeigen" ,r-rcppeigen)
1954 ("r-rcppnumerical" ,r-rcppnumerical)
1955 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1956 (native-inputs `(("r-knitr" ,r-knitr)))
1957 (home-page "https://bioconductor.org/packages/apeglm")
1958 (synopsis "Approximate posterior estimation for GLM coefficients")
1959 (description "This package provides Bayesian shrinkage estimators for
1960 effect sizes for a variety of GLM models, using approximation of the
1961 posterior for individual coefficients.")
1962 (license license:gpl2)))
1964 (define-public r-greylistchip
1966 (name "r-greylistchip")
1970 (uri (bioconductor-uri "GreyListChIP" version))
1973 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
1974 (properties `((upstream-name . "GreyListChIP")))
1975 (build-system r-build-system)
1977 `(("r-bsgenome" ,r-bsgenome)
1978 ("r-genomeinfodb" ,r-genomeinfodb)
1979 ("r-genomicalignments" ,r-genomicalignments)
1980 ("r-genomicranges" ,r-genomicranges)
1982 ("r-rsamtools" ,r-rsamtools)
1983 ("r-rtracklayer" ,r-rtracklayer)
1984 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1985 (home-page "https://bioconductor.org/packages/GreyListChIP")
1986 (synopsis "Greylist artefact regions based on ChIP inputs")
1987 (description "This package identifies regions of ChIP experiments with high
1988 signal in the input, that lead to spurious peaks during peak calling.")
1989 (license license:artistic2.0)))
1991 (define-public r-diffbind
1998 (uri (bioconductor-uri "DiffBind" version))
2001 "0kxn59v93hl5pq8d156lnbz0sslpnxyjcfrvq2gzgd91sd587qmn"))))
2002 (properties `((upstream-name . "DiffBind")))
2003 (build-system r-build-system)
2005 `(("r-amap" ,r-amap)
2006 ("r-apeglm" ,r-apeglm)
2008 ("r-biocparallel" ,r-biocparallel)
2009 ("r-deseq2" ,r-deseq2)
2010 ("r-dplyr" ,r-dplyr)
2011 ("r-genomicalignments" ,r-genomicalignments)
2012 ("r-genomicranges" ,r-genomicranges)
2013 ("r-ggplot2" ,r-ggplot2)
2014 ("r-ggrepel" ,r-ggrepel)
2015 ("r-gplots" ,r-gplots)
2016 ("r-greylistchip" ,r-greylistchip)
2017 ("r-iranges" ,r-iranges)
2018 ("r-lattice" ,r-lattice)
2019 ("r-limma" ,r-limma)
2020 ("r-locfit" ,r-locfit)
2021 ("r-rcolorbrewer" , r-rcolorbrewer)
2023 ("r-rhtslib" ,r-rhtslib)
2024 ("r-rsamtools" ,r-rsamtools)
2025 ("r-s4vectors" ,r-s4vectors)
2026 ("r-summarizedexperiment" ,r-summarizedexperiment)
2027 ("r-systempiper" ,r-systempiper)))
2028 (home-page "https://bioconductor.org/packages/DiffBind")
2029 (synopsis "Differential binding analysis of ChIP-Seq peak data")
2031 "This package computes differentially bound sites from multiple
2032 ChIP-seq experiments using affinity (quantitative) data. Also enables
2033 occupancy (overlap) analysis and plotting functions.")
2034 (license license:artistic2.0)))
2036 (define-public r-ripseeker
2038 (name "r-ripseeker")
2043 (uri (bioconductor-uri "RIPSeeker" version))
2046 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
2047 (properties `((upstream-name . "RIPSeeker")))
2048 (build-system r-build-system)
2050 `(("r-s4vectors" ,r-s4vectors)
2051 ("r-iranges" ,r-iranges)
2052 ("r-genomicranges" ,r-genomicranges)
2053 ("r-summarizedexperiment" ,r-summarizedexperiment)
2054 ("r-rsamtools" ,r-rsamtools)
2055 ("r-genomicalignments" ,r-genomicalignments)
2056 ("r-rtracklayer" ,r-rtracklayer)))
2057 (home-page "https://bioconductor.org/packages/RIPSeeker")
2059 "Identifying protein-associated transcripts from RIP-seq experiments")
2061 "This package infers and discriminates RIP peaks from RIP-seq alignments
2062 using two-state HMM with negative binomial emission probability. While
2063 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
2064 a suite of bioinformatics tools integrated within this self-contained software
2065 package comprehensively addressing issues ranging from post-alignments
2066 processing to visualization and annotation.")
2067 (license license:gpl2)))
2069 (define-public r-multtest
2076 (uri (bioconductor-uri "multtest" version))
2079 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
2080 (build-system r-build-system)
2082 `(("r-survival" ,r-survival)
2083 ("r-biocgenerics" ,r-biocgenerics)
2084 ("r-biobase" ,r-biobase)
2085 ("r-mass" ,r-mass)))
2086 (home-page "https://bioconductor.org/packages/multtest")
2087 (synopsis "Resampling-based multiple hypothesis testing")
2089 "This package can do non-parametric bootstrap and permutation
2090 resampling-based multiple testing procedures (including empirical Bayes
2091 methods) for controlling the family-wise error rate (FWER), generalized
2092 family-wise error rate (gFWER), tail probability of the proportion of
2093 false positives (TPPFP), and false discovery rate (FDR). Several choices
2094 of bootstrap-based null distribution are implemented (centered, centered
2095 and scaled, quantile-transformed). Single-step and step-wise methods are
2096 available. Tests based on a variety of T- and F-statistics (including
2097 T-statistics based on regression parameters from linear and survival models
2098 as well as those based on correlation parameters) are included. When probing
2099 hypotheses with T-statistics, users may also select a potentially faster null
2100 distribution which is multivariate normal with mean zero and variance
2101 covariance matrix derived from the vector influence function. Results are
2102 reported in terms of adjusted P-values, confidence regions and test statistic
2103 cutoffs. The procedures are directly applicable to identifying differentially
2104 expressed genes in DNA microarray experiments.")
2105 (license license:lgpl3)))
2107 (define-public r-graph
2113 (uri (bioconductor-uri "graph" version))
2116 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
2117 (build-system r-build-system)
2119 `(("r-biocgenerics" ,r-biocgenerics)))
2120 (home-page "https://bioconductor.org/packages/graph")
2121 (synopsis "Handle graph data structures in R")
2123 "This package implements some simple graph handling capabilities for R.")
2124 (license license:artistic2.0)))
2126 ;; This is a CRAN package, but it depends on a Bioconductor package.
2127 (define-public r-ggm
2134 (uri (cran-uri "ggm" version))
2137 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
2138 (properties `((upstream-name . "ggm")))
2139 (build-system r-build-system)
2141 `(("r-graph" ,r-graph)
2142 ("r-igraph" ,r-igraph)))
2143 (home-page "https://cran.r-project.org/package=ggm")
2144 (synopsis "Functions for graphical Markov models")
2146 "This package provides functions and datasets for maximum likelihood
2147 fitting of some classes of graphical Markov models.")
2148 (license license:gpl2+)))
2150 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
2151 (define-public r-perfmeas
2158 (uri (cran-uri "PerfMeas" version))
2161 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
2162 (properties `((upstream-name . "PerfMeas")))
2163 (build-system r-build-system)
2165 `(("r-graph" ,r-graph)
2166 ("r-limma" ,r-limma)
2167 ("r-rbgl" ,r-rbgl)))
2168 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
2169 (synopsis "Performance measures for ranking and classification tasks")
2171 "This package implements different performance measures for
2172 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
2173 a given recall, F-score for single and multiple classes are available.")
2174 (license license:gpl2+)))
2176 ;; This is a CRAN package, but it depends on a Bioconductor package.
2177 (define-public r-codedepends
2179 (name "r-codedepends")
2184 (uri (cran-uri "CodeDepends" version))
2187 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
2188 (properties `((upstream-name . "CodeDepends")))
2189 (build-system r-build-system)
2191 `(("r-codetools" ,r-codetools)
2192 ("r-graph" ,r-graph)
2194 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2195 (synopsis "Analysis of R code for reproducible research and code comprehension")
2197 "This package provides tools for analyzing R expressions or blocks of
2198 code and determining the dependencies between them. It focuses on R scripts,
2199 but can be used on the bodies of functions. There are many facilities
2200 including the ability to summarize or get a high-level view of code,
2201 determining dependencies between variables, code improvement suggestions.")
2202 ;; Any version of the GPL
2203 (license (list license:gpl2+ license:gpl3+))))
2205 (define-public r-chippeakanno
2207 (name "r-chippeakanno")
2212 (uri (bioconductor-uri "ChIPpeakAnno" version))
2215 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
2216 (properties `((upstream-name . "ChIPpeakAnno")))
2217 (build-system r-build-system)
2219 `(("r-annotationdbi" ,r-annotationdbi)
2220 ("r-biocgenerics" ,r-biocgenerics)
2221 ("r-biomart" ,r-biomart)
2222 ("r-biostrings" ,r-biostrings)
2224 ("r-ensembldb" ,r-ensembldb)
2225 ("r-genomeinfodb" ,r-genomeinfodb)
2226 ("r-genomicalignments" ,r-genomicalignments)
2227 ("r-genomicfeatures" ,r-genomicfeatures)
2228 ("r-genomicranges" ,r-genomicranges)
2229 ("r-ggplot2" ,r-ggplot2)
2230 ("r-graph" ,r-graph)
2231 ("r-iranges" ,r-iranges)
2232 ("r-keggrest" ,r-keggrest)
2233 ("r-matrixstats" ,r-matrixstats)
2234 ("r-multtest" ,r-multtest)
2236 ("r-regioner" ,r-regioner)
2237 ("r-rsamtools" ,r-rsamtools)
2238 ("r-rtracklayer" ,r-rtracklayer)
2239 ("r-s4vectors" ,r-s4vectors)
2240 ("r-summarizedexperiment" ,r-summarizedexperiment)
2241 ("r-venndiagram" ,r-venndiagram)))
2243 `(("r-knitr" ,r-knitr)))
2244 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2245 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2247 "The package includes functions to retrieve the sequences around the peak,
2248 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2249 custom features such as most conserved elements and other transcription factor
2250 binding sites supplied by users. Starting 2.0.5, new functions have been added
2251 for finding the peaks with bi-directional promoters with summary statistics
2252 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2253 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2254 enrichedGO (addGeneIDs).")
2255 (license license:gpl2+)))
2257 (define-public r-matrixgenerics
2259 (name "r-matrixgenerics")
2263 (uri (bioconductor-uri "MatrixGenerics" version))
2266 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
2268 `((upstream-name . "MatrixGenerics")))
2269 (build-system r-build-system)
2271 `(("r-matrixstats" ,r-matrixstats)))
2272 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2273 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2275 "This package provides S4 generic functions modeled after the
2276 @code{matrixStats} API for alternative matrix implementations. Packages with
2277 alternative matrix implementation can depend on this package and implement the
2278 generic functions that are defined here for a useful set of row and column
2279 summary statistics. Other package developers can import this package and
2280 handle a different matrix implementations without worrying about
2281 incompatibilities.")
2282 (license license:artistic2.0)))
2284 (define-public r-marray
2290 (uri (bioconductor-uri "marray" version))
2292 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
2293 (build-system r-build-system)
2295 `(("r-limma" ,r-limma)))
2296 (home-page "https://bioconductor.org/packages/marray")
2297 (synopsis "Exploratory analysis for two-color spotted microarray data")
2298 (description "This package contains class definitions for two-color spotted
2299 microarray data. It also includes functions for data input, diagnostic plots,
2300 normalization and quality checking.")
2301 (license license:lgpl2.0+)))
2303 (define-public r-cghbase
2309 (uri (bioconductor-uri "CGHbase" version))
2311 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
2312 (properties `((upstream-name . "CGHbase")))
2313 (build-system r-build-system)
2315 `(("r-biobase" ,r-biobase)
2316 ("r-marray" ,r-marray)))
2317 (home-page "https://bioconductor.org/packages/CGHbase")
2318 (synopsis "Base functions and classes for arrayCGH data analysis")
2319 (description "This package contains functions and classes that are needed by
2320 the @code{arrayCGH} packages.")
2321 (license license:gpl2+)))
2323 (define-public r-cghcall
2329 (uri (bioconductor-uri "CGHcall" version))
2331 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
2332 (properties `((upstream-name . "CGHcall")))
2333 (build-system r-build-system)
2335 `(("r-biobase" ,r-biobase)
2336 ("r-cghbase" ,r-cghbase)
2337 ("r-impute" ,r-impute)
2338 ("r-dnacopy" ,r-dnacopy)
2339 ("r-snowfall" ,r-snowfall)))
2340 (home-page "https://bioconductor.org/packages/CGHcall")
2341 (synopsis "Base functions and classes for arrayCGH data analysis")
2342 (description "This package contains functions and classes that are needed by
2343 @code{arrayCGH} packages.")
2344 (license license:gpl2+)))
2346 (define-public r-qdnaseq
2352 (uri (bioconductor-uri "QDNAseq" version))
2354 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
2355 (properties `((upstream-name . "QDNAseq")))
2356 (build-system r-build-system)
2358 `(("r-biobase" ,r-biobase)
2359 ("r-cghbase" ,r-cghbase)
2360 ("r-cghcall" ,r-cghcall)
2361 ("r-dnacopy" ,r-dnacopy)
2362 ("r-future" ,r-future)
2363 ("r-future-apply" ,r-future-apply)
2364 ("r-genomicranges" ,r-genomicranges)
2365 ("r-iranges" ,r-iranges)
2366 ("r-matrixstats" ,r-matrixstats)
2367 ("r-r-utils" ,r-r-utils)
2368 ("r-rsamtools" ,r-rsamtools)))
2369 (home-page "https://bioconductor.org/packages/QDNAseq")
2370 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2371 (description "The genome is divided into non-overlapping fixed-sized bins,
2372 number of sequence reads in each counted, adjusted with a simultaneous
2373 two-dimensional loess correction for sequence mappability and GC content, and
2374 filtered to remove spurious regions in the genome. Downstream steps of
2375 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2377 (license license:gpl2+)))
2379 (define-public r-bayseq
2386 (uri (bioconductor-uri "baySeq" version))
2389 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
2390 (properties `((upstream-name . "baySeq")))
2391 (build-system r-build-system)
2393 `(("r-abind" ,r-abind)
2394 ("r-edger" ,r-edger)
2395 ("r-genomicranges" ,r-genomicranges)))
2396 (home-page "https://bioconductor.org/packages/baySeq/")
2397 (synopsis "Bayesian analysis of differential expression patterns in count data")
2399 "This package identifies differential expression in high-throughput count
2400 data, such as that derived from next-generation sequencing machines,
2401 calculating estimated posterior likelihoods of differential expression (or
2402 more complex hypotheses) via empirical Bayesian methods.")
2403 (license license:gpl3)))
2405 (define-public r-chipcomp
2412 (uri (bioconductor-uri "ChIPComp" version))
2415 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
2416 (properties `((upstream-name . "ChIPComp")))
2417 (build-system r-build-system)
2419 `(("r-biocgenerics" ,r-biocgenerics)
2420 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2421 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2422 ("r-genomeinfodb" ,r-genomeinfodb)
2423 ("r-genomicranges" ,r-genomicranges)
2424 ("r-iranges" ,r-iranges)
2425 ("r-limma" ,r-limma)
2426 ("r-rsamtools" ,r-rsamtools)
2427 ("r-rtracklayer" ,r-rtracklayer)
2428 ("r-s4vectors" ,r-s4vectors)))
2429 (home-page "https://bioconductor.org/packages/ChIPComp")
2430 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2432 "ChIPComp implements a statistical method for quantitative comparison of
2433 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2434 sites across multiple conditions considering matching control in ChIP-seq
2436 ;; Any version of the GPL.
2437 (license license:gpl3+)))
2439 (define-public r-riboprofiling
2441 (name "r-riboprofiling")
2446 (uri (bioconductor-uri "RiboProfiling" version))
2449 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
2450 (properties `((upstream-name . "RiboProfiling")))
2451 (build-system r-build-system)
2453 `(("r-biocgenerics" ,r-biocgenerics)
2454 ("r-biostrings" ,r-biostrings)
2455 ("r-data-table" ,r-data-table)
2456 ("r-genomeinfodb" ,r-genomeinfodb)
2457 ("r-genomicalignments" ,r-genomicalignments)
2458 ("r-genomicfeatures" ,r-genomicfeatures)
2459 ("r-genomicranges" ,r-genomicranges)
2460 ("r-ggbio" ,r-ggbio)
2461 ("r-ggplot2" ,r-ggplot2)
2462 ("r-iranges" ,r-iranges)
2464 ("r-reshape2" ,r-reshape2)
2465 ("r-rsamtools" ,r-rsamtools)
2466 ("r-rtracklayer" ,r-rtracklayer)
2467 ("r-s4vectors" ,r-s4vectors)
2468 ("r-sqldf" ,r-sqldf)))
2470 `(("r-knitr" ,r-knitr)))
2471 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2472 (synopsis "Ribosome profiling data analysis")
2473 (description "Starting with a BAM file, this package provides the
2474 necessary functions for quality assessment, read start position recalibration,
2475 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2476 of count data: pairs, log fold-change, codon frequency and coverage
2477 assessment, principal component analysis on codon coverage.")
2478 (license license:gpl3)))
2480 (define-public r-riboseqr
2487 (uri (bioconductor-uri "riboSeqR" version))
2490 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
2491 (properties `((upstream-name . "riboSeqR")))
2492 (build-system r-build-system)
2494 `(("r-abind" ,r-abind)
2495 ("r-bayseq" ,r-bayseq)
2496 ("r-genomeinfodb" ,r-genomeinfodb)
2497 ("r-genomicranges" ,r-genomicranges)
2498 ("r-iranges" ,r-iranges)
2499 ("r-rsamtools" ,r-rsamtools)
2500 ("r-seqlogo" ,r-seqlogo)))
2501 (home-page "https://bioconductor.org/packages/riboSeqR/")
2502 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2504 "This package provides plotting functions, frameshift detection and
2505 parsing of genetic sequencing data from ribosome profiling experiments.")
2506 (license license:gpl3)))
2508 (define-public r-interactionset
2510 (name "r-interactionset")
2515 (uri (bioconductor-uri "InteractionSet" version))
2518 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
2520 `((upstream-name . "InteractionSet")))
2521 (build-system r-build-system)
2523 `(("r-biocgenerics" ,r-biocgenerics)
2524 ("r-genomeinfodb" ,r-genomeinfodb)
2525 ("r-genomicranges" ,r-genomicranges)
2526 ("r-iranges" ,r-iranges)
2527 ("r-matrix" ,r-matrix)
2529 ("r-s4vectors" ,r-s4vectors)
2530 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2532 `(("r-knitr" ,r-knitr)))
2533 (home-page "https://bioconductor.org/packages/InteractionSet")
2534 (synopsis "Base classes for storing genomic interaction data")
2536 "This package provides the @code{GInteractions},
2537 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2538 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2540 (license license:gpl3)))
2542 (define-public r-genomicinteractions
2544 (name "r-genomicinteractions")
2549 (uri (bioconductor-uri "GenomicInteractions" version))
2552 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
2554 `((upstream-name . "GenomicInteractions")))
2555 (build-system r-build-system)
2557 `(("r-biobase" ,r-biobase)
2558 ("r-biocgenerics" ,r-biocgenerics)
2559 ("r-data-table" ,r-data-table)
2560 ("r-dplyr" ,r-dplyr)
2561 ("r-genomeinfodb" ,r-genomeinfodb)
2562 ("r-genomicranges" ,r-genomicranges)
2563 ("r-ggplot2" ,r-ggplot2)
2564 ("r-gridextra" ,r-gridextra)
2566 ("r-igraph" ,r-igraph)
2567 ("r-interactionset" ,r-interactionset)
2568 ("r-iranges" ,r-iranges)
2569 ("r-rsamtools" ,r-rsamtools)
2570 ("r-rtracklayer" ,r-rtracklayer)
2571 ("r-s4vectors" ,r-s4vectors)
2572 ("r-stringr" ,r-stringr)))
2574 `(("r-knitr" ,r-knitr)))
2575 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2576 (synopsis "R package for handling genomic interaction data")
2578 "This R package provides tools for handling genomic interaction data,
2579 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2580 information and producing various plots and statistics.")
2581 (license license:gpl3)))
2583 (define-public r-ctc
2590 (uri (bioconductor-uri "ctc" version))
2593 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
2594 (build-system r-build-system)
2595 (propagated-inputs `(("r-amap" ,r-amap)))
2596 (home-page "https://bioconductor.org/packages/ctc/")
2597 (synopsis "Cluster and tree conversion")
2599 "This package provides tools for exporting and importing classification
2600 trees and clusters to other programs.")
2601 (license license:gpl2)))
2603 (define-public r-goseq
2610 (uri (bioconductor-uri "goseq" version))
2613 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
2614 (build-system r-build-system)
2616 `(("r-annotationdbi" ,r-annotationdbi)
2617 ("r-biasedurn" ,r-biasedurn)
2618 ("r-biocgenerics" ,r-biocgenerics)
2619 ("r-genelendatabase" ,r-genelendatabase)
2620 ("r-go-db" ,r-go-db)
2621 ("r-mgcv" ,r-mgcv)))
2622 (home-page "https://bioconductor.org/packages/goseq/")
2623 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2625 "This package provides tools to detect Gene Ontology and/or other user
2626 defined categories which are over/under represented in RNA-seq data.")
2627 (license license:lgpl2.0+)))
2629 (define-public r-glimma
2636 (uri (bioconductor-uri "Glimma" version))
2639 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
2640 (properties `((upstream-name . "Glimma")))
2641 (build-system r-build-system)
2643 `(("r-deseq2" ,r-deseq2)
2644 ("r-edger" ,r-edger)
2645 ("r-htmlwidgets" ,r-htmlwidgets)
2646 ("r-jsonlite" ,r-jsonlite)
2647 ("r-limma" ,r-limma)
2648 ("r-s4vectors" ,r-s4vectors)
2649 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2651 `(("r-knitr" ,r-knitr)))
2652 (home-page "https://github.com/Shians/Glimma")
2653 (synopsis "Interactive HTML graphics")
2655 "This package generates interactive visualisations for analysis of
2656 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2657 HTML page. The interactions are built on top of the popular static
2658 representations of analysis results in order to provide additional
2660 (license license:lgpl3)))
2662 (define-public r-rots
2669 (uri (bioconductor-uri "ROTS" version))
2672 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
2673 (properties `((upstream-name . "ROTS")))
2674 (build-system r-build-system)
2676 `(("r-biobase" ,r-biobase)
2677 ("r-rcpp" ,r-rcpp)))
2678 (home-page "https://bioconductor.org/packages/ROTS/")
2679 (synopsis "Reproducibility-Optimized Test Statistic")
2681 "This package provides tools for calculating the
2682 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2684 (license license:gpl2+)))
2686 (define-public r-plgem
2693 (uri (bioconductor-uri "plgem" version))
2696 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
2697 (build-system r-build-system)
2699 `(("r-biobase" ,r-biobase)
2700 ("r-mass" ,r-mass)))
2701 (home-page "http://www.genopolis.it")
2702 (synopsis "Detect differential expression in microarray and proteomics datasets")
2704 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2705 model the variance-versus-mean dependence that exists in a variety of
2706 genome-wide datasets, including microarray and proteomics data. The use of
2707 PLGEM has been shown to improve the detection of differentially expressed
2708 genes or proteins in these datasets.")
2709 (license license:gpl2)))
2711 (define-public r-inspect
2718 (uri (bioconductor-uri "INSPEcT" version))
2721 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
2722 (properties `((upstream-name . "INSPEcT")))
2723 (build-system r-build-system)
2725 `(("r-biobase" ,r-biobase)
2726 ("r-biocgenerics" ,r-biocgenerics)
2727 ("r-biocparallel" ,r-biocparallel)
2728 ("r-deseq2" ,r-deseq2)
2729 ("r-desolve" ,r-desolve)
2730 ("r-gdata" ,r-gdata)
2731 ("r-genomeinfodb" ,r-genomeinfodb)
2732 ("r-genomicalignments" ,r-genomicalignments)
2733 ("r-genomicfeatures" ,r-genomicfeatures)
2734 ("r-genomicranges" ,r-genomicranges)
2735 ("r-iranges" ,r-iranges)
2736 ("r-kernsmooth" ,r-kernsmooth)
2737 ("r-plgem" ,r-plgem)
2739 ("r-rootsolve" ,r-rootsolve)
2740 ("r-rsamtools" ,r-rsamtools)
2741 ("r-rtracklayer" ,r-rtracklayer)
2742 ("r-s4vectors" ,r-s4vectors)
2743 ("r-shiny" ,r-shiny)
2744 ("r-summarizedexperiment" ,r-summarizedexperiment)
2745 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2746 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2748 `(("r-knitr" ,r-knitr)))
2749 (home-page "https://bioconductor.org/packages/INSPEcT")
2750 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2752 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2753 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2754 order to evaluate synthesis, processing and degradation rates and assess via
2755 modeling the rates that determines changes in mature mRNA levels.")
2756 (license license:gpl2)))
2758 (define-public r-dnabarcodes
2760 (name "r-dnabarcodes")
2765 (uri (bioconductor-uri "DNABarcodes" version))
2768 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
2769 (properties `((upstream-name . "DNABarcodes")))
2770 (build-system r-build-system)
2773 ("r-matrix" ,r-matrix)
2774 ("r-rcpp" ,r-rcpp)))
2776 `(("r-knitr" ,r-knitr)))
2777 (home-page "https://bioconductor.org/packages/DNABarcodes")
2778 (synopsis "Create and analyze DNA barcodes")
2780 "This package offers tools to create DNA barcode sets capable of
2781 correcting insertion, deletion, and substitution errors. Existing barcodes
2782 can be analyzed regarding their minimal, maximal and average distances between
2783 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2784 demultiplexed, i.e. assigned to their original reference barcode.")
2785 (license license:gpl2)))
2787 (define-public r-ruvseq
2794 (uri (bioconductor-uri "RUVSeq" version))
2797 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
2798 (properties `((upstream-name . "RUVSeq")))
2799 (build-system r-build-system)
2801 `(("r-biobase" ,r-biobase)
2802 ("r-edaseq" ,r-edaseq)
2803 ("r-edger" ,r-edger)
2804 ("r-mass" ,r-mass)))
2806 `(("r-knitr" ,r-knitr)))
2807 (home-page "https://github.com/drisso/RUVSeq")
2808 (synopsis "Remove unwanted variation from RNA-Seq data")
2810 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2811 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2813 (license license:artistic2.0)))
2815 (define-public r-biocneighbors
2817 (name "r-biocneighbors")
2822 (uri (bioconductor-uri "BiocNeighbors" version))
2825 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
2826 (properties `((upstream-name . "BiocNeighbors")))
2827 (build-system r-build-system)
2829 `(("r-biocparallel" ,r-biocparallel)
2830 ("r-matrix" ,r-matrix)
2832 ("r-rcpphnsw" ,r-rcpphnsw)
2833 ("r-s4vectors" ,r-s4vectors)))
2835 `(("r-knitr" ,r-knitr)))
2836 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2837 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2839 "This package implements exact and approximate methods for nearest
2840 neighbor detection, in a framework that allows them to be easily switched
2841 within Bioconductor packages or workflows. The exact algorithm is implemented
2842 using pre-clustering with the k-means algorithm. Functions are also provided
2843 to search for all neighbors within a given distance. Parallelization is
2844 achieved for all methods using the BiocParallel framework.")
2845 (license license:gpl3)))
2847 (define-public r-biocsingular
2849 (name "r-biocsingular")
2854 (uri (bioconductor-uri "BiocSingular" version))
2857 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
2858 (properties `((upstream-name . "BiocSingular")))
2859 (build-system r-build-system)
2861 `(("r-beachmat" ,r-beachmat)
2862 ("r-biocgenerics" ,r-biocgenerics)
2863 ("r-biocparallel" ,r-biocparallel)
2864 ("r-delayedarray" ,r-delayedarray)
2865 ("r-irlba" ,r-irlba)
2866 ("r-matrix" ,r-matrix)
2869 ("r-s4vectors" ,r-s4vectors)))
2871 `(("r-knitr" ,r-knitr)))
2872 (home-page "https://github.com/LTLA/BiocSingular")
2873 (synopsis "Singular value decomposition for Bioconductor packages")
2875 "This package implements exact and approximate methods for singular value
2876 decomposition and principal components analysis, in a framework that allows
2877 them to be easily switched within Bioconductor packages or workflows. Where
2878 possible, parallelization is achieved using the BiocParallel framework.")
2879 (license license:gpl3)))
2881 (define-public r-destiny
2888 (uri (bioconductor-uri "destiny" version))
2891 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
2892 (build-system r-build-system)
2894 `(("r-biobase" ,r-biobase)
2895 ("r-biocgenerics" ,r-biocgenerics)
2896 ("r-ggplot-multistats" ,r-ggplot-multistats)
2897 ("r-ggplot2" ,r-ggplot2)
2898 ("r-ggthemes" ,r-ggthemes)
2899 ("r-irlba" ,r-irlba)
2900 ("r-knn-covertree" ,r-knn-covertree)
2901 ("r-matrix" ,r-matrix)
2902 ("r-pcamethods" ,r-pcamethods)
2903 ("r-proxy" ,r-proxy)
2905 ("r-rcppeigen" ,r-rcppeigen)
2906 ("r-rcpphnsw" ,r-rcpphnsw)
2907 ("r-rspectra" ,r-rspectra)
2908 ("r-scales" ,r-scales)
2909 ("r-scatterplot3d" ,r-scatterplot3d)
2910 ("r-singlecellexperiment" ,r-singlecellexperiment)
2911 ("r-smoother" ,r-smoother)
2912 ("r-summarizedexperiment" ,r-summarizedexperiment)
2913 ("r-tidyr" ,r-tidyr)
2914 ("r-tidyselect" ,r-tidyselect)
2917 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2918 (home-page "https://bioconductor.org/packages/destiny/")
2919 (synopsis "Create and plot diffusion maps")
2920 (description "This package provides tools to create and plot diffusion
2922 ;; Any version of the GPL
2923 (license license:gpl3+)))
2925 (define-public r-savr
2932 (uri (bioconductor-uri "savR" version))
2935 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
2936 (properties `((upstream-name . "savR")))
2937 (build-system r-build-system)
2939 `(("r-ggplot2" ,r-ggplot2)
2940 ("r-gridextra" ,r-gridextra)
2941 ("r-reshape2" ,r-reshape2)
2942 ("r-scales" ,r-scales)
2944 (home-page "https://github.com/bcalder/savR")
2945 (synopsis "Parse and analyze Illumina SAV files")
2947 "This package provides tools to parse Illumina Sequence Analysis
2948 Viewer (SAV) files, access data, and generate QC plots.")
2949 (license license:agpl3+)))
2951 (define-public r-chipexoqual
2953 (name "r-chipexoqual")
2958 (uri (bioconductor-uri "ChIPexoQual" version))
2961 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
2962 (properties `((upstream-name . "ChIPexoQual")))
2963 (build-system r-build-system)
2965 `(("r-biocparallel" ,r-biocparallel)
2966 ("r-biovizbase" ,r-biovizbase)
2967 ("r-broom" ,r-broom)
2968 ("r-data-table" ,r-data-table)
2969 ("r-dplyr" ,r-dplyr)
2970 ("r-genomeinfodb" ,r-genomeinfodb)
2971 ("r-genomicalignments" ,r-genomicalignments)
2972 ("r-genomicranges" ,r-genomicranges)
2973 ("r-ggplot2" ,r-ggplot2)
2974 ("r-hexbin" ,r-hexbin)
2975 ("r-iranges" ,r-iranges)
2976 ("r-rcolorbrewer" ,r-rcolorbrewer)
2977 ("r-rmarkdown" ,r-rmarkdown)
2978 ("r-rsamtools" ,r-rsamtools)
2979 ("r-s4vectors" ,r-s4vectors)
2980 ("r-scales" ,r-scales)
2981 ("r-viridis" ,r-viridis)))
2983 `(("r-knitr" ,r-knitr)))
2984 (home-page "https://github.com/keleslab/ChIPexoQual")
2985 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2987 "This package provides a quality control pipeline for ChIP-exo/nexus
2989 (license license:gpl2+)))
2991 (define-public r-copynumber
2993 (name "r-copynumber")
2997 (uri (bioconductor-uri "copynumber" version))
3000 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
3001 (build-system r-build-system)
3003 `(("r-s4vectors" ,r-s4vectors)
3004 ("r-iranges" ,r-iranges)
3005 ("r-genomicranges" ,r-genomicranges)
3006 ("r-biocgenerics" ,r-biocgenerics)))
3007 (home-page "https://bioconductor.org/packages/copynumber")
3008 (synopsis "Segmentation of single- and multi-track copy number data")
3010 "This package segments single- and multi-track copy number data by a
3011 penalized least squares regression method.")
3012 (license license:artistic2.0)))
3014 (define-public r-dnacopy
3021 (uri (bioconductor-uri "DNAcopy" version))
3024 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
3025 (properties `((upstream-name . "DNAcopy")))
3026 (build-system r-build-system)
3027 (native-inputs `(("gfortran" ,gfortran)))
3028 (home-page "https://bioconductor.org/packages/DNAcopy")
3029 (synopsis "DNA copy number data analysis")
3031 "This package implements the @dfn{circular binary segmentation} (CBS)
3032 algorithm to segment DNA copy number data and identify genomic regions with
3033 abnormal copy number.")
3034 (license license:gpl2+)))
3036 ;; This is a CRAN package, but it uncharacteristically depends on a
3037 ;; Bioconductor package.
3038 (define-public r-htscluster
3040 (name "r-htscluster")
3045 (uri (cran-uri "HTSCluster" version))
3048 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
3049 (properties `((upstream-name . "HTSCluster")))
3050 (build-system r-build-system)
3052 `(("r-capushe" ,r-capushe)
3053 ("r-edger" ,r-edger)
3054 ("r-plotrix" ,r-plotrix)))
3055 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
3056 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
3058 "This package provides a Poisson mixture model is implemented to cluster
3059 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
3060 estimation is performed using either the EM or CEM algorithm, and the slope
3061 heuristics are used for model selection (i.e., to choose the number of
3063 (license license:gpl3+)))
3065 (define-public r-deds
3072 (uri (bioconductor-uri "DEDS" version))
3075 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
3076 (properties `((upstream-name . "DEDS")))
3077 (build-system r-build-system)
3078 (home-page "https://bioconductor.org/packages/DEDS/")
3079 (synopsis "Differential expression via distance summary for microarray data")
3081 "This library contains functions that calculate various statistics of
3082 differential expression for microarray data, including t statistics, fold
3083 change, F statistics, SAM, moderated t and F statistics and B statistics. It
3084 also implements a new methodology called DEDS (Differential Expression via
3085 Distance Summary), which selects differentially expressed genes by integrating
3086 and summarizing a set of statistics using a weighted distance approach.")
3087 ;; Any version of the LGPL.
3088 (license license:lgpl3+)))
3090 ;; This is a CRAN package, but since it depends on a Bioconductor package we
3092 (define-public r-nbpseq
3099 (uri (cran-uri "NBPSeq" version))
3102 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
3103 (properties `((upstream-name . "NBPSeq")))
3104 (build-system r-build-system)
3106 `(("r-qvalue" ,r-qvalue)))
3107 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
3108 (synopsis "Negative binomial models for RNA-Seq data")
3110 "This package provides negative binomial models for two-group comparisons
3111 and regression inferences from RNA-sequencing data.")
3112 (license license:gpl2)))
3114 (define-public r-ebseq
3121 (uri (bioconductor-uri "EBSeq" version))
3124 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3125 (properties `((upstream-name . "EBSeq")))
3126 (build-system r-build-system)
3128 `(("r-blockmodeling" ,r-blockmodeling)
3129 ("r-gplots" ,r-gplots)
3130 ("r-testthat" ,r-testthat)))
3131 (home-page "https://bioconductor.org/packages/EBSeq")
3132 (synopsis "Differential expression analysis of RNA-seq data")
3134 "This package provides tools for differential expression analysis at both
3135 gene and isoform level using RNA-seq data")
3136 (license license:artistic2.0)))
3138 (define-public r-karyoploter
3140 (name "r-karyoploter")
3144 (uri (bioconductor-uri "karyoploteR" version))
3147 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
3148 (build-system r-build-system)
3150 `(("r-annotationdbi" ,r-annotationdbi)
3151 ("r-bamsignals" ,r-bamsignals)
3152 ("r-bezier" ,r-bezier)
3153 ("r-biovizbase" ,r-biovizbase)
3154 ("r-digest" ,r-digest)
3155 ("r-genomeinfodb" ,r-genomeinfodb)
3156 ("r-genomicfeatures" ,r-genomicfeatures)
3157 ("r-genomicranges" ,r-genomicranges)
3158 ("r-iranges" ,r-iranges)
3159 ("r-memoise" ,r-memoise)
3160 ("r-regioner" ,r-regioner)
3161 ("r-rsamtools" ,r-rsamtools)
3162 ("r-rtracklayer" ,r-rtracklayer)
3163 ("r-s4vectors" ,r-s4vectors)
3164 ("r-variantannotation" ,r-variantannotation)))
3166 `(("r-knitr" ,r-knitr)))
3167 (home-page "https://bioconductor.org/packages/karyoploteR/")
3168 (synopsis "Plot customizable linear genomes displaying arbitrary data")
3169 (description "This package creates karyotype plots of arbitrary genomes and
3170 offers a complete set of functions to plot arbitrary data on them. It mimics
3171 many R base graphics functions coupling them with a coordinate change function
3172 automatically mapping the chromosome and data coordinates into the plot
3174 (license license:artistic2.0)))
3176 (define-public r-lpsymphony
3178 (name "r-lpsymphony")
3183 (uri (bioconductor-uri "lpsymphony" version))
3186 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
3187 (build-system r-build-system)
3191 `(("pkg-config" ,pkg-config)
3192 ("r-knitr" ,r-knitr)))
3193 (home-page "https://r-forge.r-project.org/projects/rsymphony")
3194 (synopsis "Symphony integer linear programming solver in R")
3196 "This package was derived from Rsymphony. The package provides an R
3197 interface to SYMPHONY, a linear programming solver written in C++. The main
3198 difference between this package and Rsymphony is that it includes the solver
3199 source code, while Rsymphony expects to find header and library files on the
3200 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3201 to install interface to SYMPHONY.")
3202 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3203 ;; lpsimphony is released under the same terms.
3204 (license license:epl1.0)))
3206 (define-public r-ihw
3213 (uri (bioconductor-uri "IHW" version))
3216 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3217 (properties `((upstream-name . "IHW")))
3218 (build-system r-build-system)
3220 `(("r-biocgenerics" ,r-biocgenerics)
3221 ("r-fdrtool" ,r-fdrtool)
3222 ("r-lpsymphony" ,r-lpsymphony)
3223 ("r-slam" ,r-slam)))
3225 `(("r-knitr" ,r-knitr)))
3226 (home-page "https://bioconductor.org/packages/IHW")
3227 (synopsis "Independent hypothesis weighting")
3229 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3230 procedure that increases power compared to the method of Benjamini and
3231 Hochberg by assigning data-driven weights to each hypothesis. The input to
3232 IHW is a two-column table of p-values and covariates. The covariate can be
3233 any continuous-valued or categorical variable that is thought to be
3234 informative on the statistical properties of each hypothesis test, while it is
3235 independent of the p-value under the null hypothesis.")
3236 (license license:artistic2.0)))
3238 (define-public r-icobra
3245 (uri (bioconductor-uri "iCOBRA" version))
3248 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3249 (properties `((upstream-name . "iCOBRA")))
3250 (build-system r-build-system)
3252 `(("r-dplyr" ,r-dplyr)
3254 ("r-ggplot2" ,r-ggplot2)
3255 ("r-limma" ,r-limma)
3256 ("r-reshape2" ,r-reshape2)
3258 ("r-scales" ,r-scales)
3259 ("r-shiny" ,r-shiny)
3260 ("r-shinybs" ,r-shinybs)
3261 ("r-shinydashboard" ,r-shinydashboard)
3262 ("r-upsetr" ,r-upsetr)))
3264 `(("r-knitr" ,r-knitr)))
3265 (home-page "https://bioconductor.org/packages/iCOBRA")
3266 (synopsis "Comparison and visualization of ranking and assignment methods")
3268 "This package provides functions for calculation and visualization of
3269 performance metrics for evaluation of ranking and binary
3270 classification (assignment) methods. It also contains a Shiny application for
3271 interactive exploration of results.")
3272 (license license:gpl2+)))
3274 (define-public r-mast
3281 (uri (bioconductor-uri "MAST" version))
3284 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
3285 (properties `((upstream-name . "MAST")))
3286 (build-system r-build-system)
3288 `(("r-abind" ,r-abind)
3289 ("r-biobase" ,r-biobase)
3290 ("r-biocgenerics" ,r-biocgenerics)
3291 ("r-data-table" ,r-data-table)
3292 ("r-ggplot2" ,r-ggplot2)
3294 ("r-progress" ,r-progress)
3295 ("r-reshape2" ,r-reshape2)
3296 ("r-s4vectors" ,r-s4vectors)
3297 ("r-singlecellexperiment" ,r-singlecellexperiment)
3298 ("r-stringr" ,r-stringr)
3299 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3301 `(("r-knitr" ,r-knitr)))
3302 (home-page "https://github.com/RGLab/MAST/")
3303 (synopsis "Model-based analysis of single cell transcriptomics")
3305 "This package provides methods and models for handling zero-inflated
3306 single cell assay data.")
3307 (license license:gpl2+)))
3309 (define-public r-monocle
3316 (uri (bioconductor-uri "monocle" version))
3319 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
3320 (build-system r-build-system)
3322 `(("r-biobase" ,r-biobase)
3323 ("r-biocgenerics" ,r-biocgenerics)
3324 ("r-biocviews" ,r-biocviews)
3325 ("r-cluster" ,r-cluster)
3326 ("r-combinat" ,r-combinat)
3327 ("r-ddrtree" ,r-ddrtree)
3328 ("r-densityclust" ,r-densityclust)
3329 ("r-dplyr" ,r-dplyr)
3330 ("r-fastica" ,r-fastica)
3331 ("r-ggplot2" ,r-ggplot2)
3332 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3333 ("r-igraph" ,r-igraph)
3334 ("r-irlba" ,r-irlba)
3335 ("r-limma" ,r-limma)
3337 ("r-matrix" ,r-matrix)
3338 ("r-matrixstats" ,r-matrixstats)
3339 ("r-pheatmap" ,r-pheatmap)
3341 ("r-proxy" ,r-proxy)
3342 ("r-qlcmatrix" ,r-qlcmatrix)
3345 ("r-reshape2" ,r-reshape2)
3346 ("r-rtsne" ,r-rtsne)
3348 ("r-stringr" ,r-stringr)
3349 ("r-tibble" ,r-tibble)
3351 ("r-viridis" ,r-viridis)))
3353 `(("r-knitr" ,r-knitr)))
3354 (home-page "https://bioconductor.org/packages/monocle")
3355 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3357 "Monocle performs differential expression and time-series analysis for
3358 single-cell expression experiments. It orders individual cells according to
3359 progress through a biological process, without knowing ahead of time which
3360 genes define progress through that process. Monocle also performs
3361 differential expression analysis, clustering, visualization, and other useful
3362 tasks on single cell expression data. It is designed to work with RNA-Seq and
3363 qPCR data, but could be used with other types as well.")
3364 (license license:artistic2.0)))
3366 (define-public r-monocle3
3374 (url "https://github.com/cole-trapnell-lab/monocle3")
3376 (file-name (git-file-name name version))
3379 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3380 (build-system r-build-system)
3382 `(("r-biobase" ,r-biobase)
3383 ("r-biocgenerics" ,r-biocgenerics)
3384 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3385 ("r-dplyr" ,r-dplyr)
3386 ("r-ggplot2" ,r-ggplot2)
3387 ("r-ggrepel" ,r-ggrepel)
3389 ("r-htmlwidgets" ,r-htmlwidgets)
3390 ("r-igraph" ,r-igraph)
3391 ("r-irlba" ,r-irlba)
3392 ("r-limma" ,r-limma)
3393 ("r-lmtest" ,r-lmtest)
3395 ("r-matrix" ,r-matrix)
3396 ("r-matrix-utils" ,r-matrix-utils)
3397 ("r-pbapply" ,r-pbapply)
3398 ("r-pbmcapply" ,r-pbmcapply)
3399 ("r-pheatmap" ,r-pheatmap)
3400 ("r-plotly" ,r-plotly)
3402 ("r-proxy" ,r-proxy)
3404 ("r-purrr" ,r-purrr)
3407 ("r-rcppparallel" ,r-rcppparallel)
3408 ("r-reshape2" ,r-reshape2)
3409 ("r-reticulate" ,r-reticulate)
3410 ("r-rhpcblasctl" ,r-rhpcblasctl)
3411 ("r-rtsne" ,r-rtsne)
3412 ("r-shiny" ,r-shiny)
3414 ("r-spdep" ,r-spdep)
3415 ("r-speedglm" ,r-speedglm)
3416 ("r-stringr" ,r-stringr)
3417 ("r-singlecellexperiment" ,r-singlecellexperiment)
3418 ("r-tibble" ,r-tibble)
3419 ("r-tidyr" ,r-tidyr)
3421 ("r-viridis" ,r-viridis)))
3422 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3423 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3425 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3426 (license license:expat)))
3428 (define-public r-noiseq
3435 (uri (bioconductor-uri "NOISeq" version))
3438 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
3439 (properties `((upstream-name . "NOISeq")))
3440 (build-system r-build-system)
3442 `(("r-biobase" ,r-biobase)
3443 ("r-matrix" ,r-matrix)))
3444 (home-page "https://bioconductor.org/packages/NOISeq")
3445 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3447 "This package provides tools to support the analysis of RNA-seq
3448 expression data or other similar kind of data. It provides exploratory plots
3449 to evaluate saturation, count distribution, expression per chromosome, type of
3450 detected features, features length, etc. It also supports the analysis of
3451 differential expression between two experimental conditions with no parametric
3453 (license license:artistic2.0)))
3455 (define-public r-scdd
3462 (uri (bioconductor-uri "scDD" version))
3465 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
3466 (properties `((upstream-name . "scDD")))
3467 (build-system r-build-system)
3470 ("r-biocparallel" ,r-biocparallel)
3471 ("r-ebseq" ,r-ebseq)
3472 ("r-fields" ,r-fields)
3473 ("r-ggplot2" ,r-ggplot2)
3474 ("r-mclust" ,r-mclust)
3475 ("r-outliers" ,r-outliers)
3476 ("r-s4vectors" ,r-s4vectors)
3477 ("r-scran" ,r-scran)
3478 ("r-singlecellexperiment" ,r-singlecellexperiment)
3479 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3481 `(("r-knitr" ,r-knitr)))
3482 (home-page "https://github.com/kdkorthauer/scDD")
3483 (synopsis "Mixture modeling of single-cell RNA-seq data")
3485 "This package implements a method to analyze single-cell RNA-seq data
3486 utilizing flexible Dirichlet Process mixture models. Genes with differential
3487 distributions of expression are classified into several interesting patterns
3488 of differences between two conditions. The package also includes functions
3489 for simulating data with these patterns from negative binomial
3491 (license license:gpl2)))
3493 (define-public r-scone
3500 (uri (bioconductor-uri "scone" version))
3503 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
3504 (build-system r-build-system)
3506 `(("r-aroma-light" ,r-aroma-light)
3507 ("r-biocparallel" ,r-biocparallel)
3509 ("r-class" ,r-class)
3510 ("r-cluster" ,r-cluster)
3511 ("r-compositions" ,r-compositions)
3512 ("r-diptest" ,r-diptest)
3513 ("r-edger" ,r-edger)
3515 ("r-gplots" ,r-gplots)
3516 ("r-hexbin" ,r-hexbin)
3517 ("r-limma" ,r-limma)
3518 ("r-matrixstats" ,r-matrixstats)
3519 ("r-mixtools" ,r-mixtools)
3520 ("r-rarpack" ,r-rarpack)
3521 ("r-rcolorbrewer" ,r-rcolorbrewer)
3522 ("r-rhdf5" ,r-rhdf5)
3523 ("r-ruvseq" ,r-ruvseq)
3524 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3526 `(("r-knitr" ,r-knitr)))
3527 (home-page "https://bioconductor.org/packages/scone")
3528 (synopsis "Single cell overview of normalized expression data")
3530 "SCONE is an R package for comparing and ranking the performance of
3531 different normalization schemes for single-cell RNA-seq and other
3532 high-throughput analyses.")
3533 (license license:artistic2.0)))
3535 (define-public r-geoquery
3542 (uri (bioconductor-uri "GEOquery" version))
3545 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
3546 (properties `((upstream-name . "GEOquery")))
3547 (build-system r-build-system)
3549 `(("r-biobase" ,r-biobase)
3550 ("r-dplyr" ,r-dplyr)
3552 ("r-limma" ,r-limma)
3553 ("r-magrittr" ,r-magrittr)
3554 ("r-readr" ,r-readr)
3555 ("r-tidyr" ,r-tidyr)
3556 ("r-xml2" ,r-xml2)))
3558 `(("r-knitr" ,r-knitr)))
3559 (home-page "https://github.com/seandavi/GEOquery/")
3560 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3562 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3563 microarray data. Given the rich and varied nature of this resource, it is
3564 only natural to want to apply BioConductor tools to these data. GEOquery is
3565 the bridge between GEO and BioConductor.")
3566 (license license:gpl2)))
3568 (define-public r-illuminaio
3570 (name "r-illuminaio")
3575 (uri (bioconductor-uri "illuminaio" version))
3578 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
3579 (build-system r-build-system)
3581 `(("r-base64" ,r-base64)))
3582 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3583 (synopsis "Parse Illumina microarray output files")
3585 "This package provides tools for parsing Illumina's microarray output
3586 files, including IDAT.")
3587 (license license:gpl2)))
3589 (define-public r-siggenes
3596 (uri (bioconductor-uri "siggenes" version))
3599 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
3600 (build-system r-build-system)
3602 `(("r-biobase" ,r-biobase)
3603 ("r-multtest" ,r-multtest)
3604 ("r-scrime" ,r-scrime)))
3605 (home-page "https://bioconductor.org/packages/siggenes/")
3607 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3609 "This package provides tools for the identification of differentially
3610 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3611 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3612 Bayes Analyses of Microarrays} (EBAM).")
3613 (license license:lgpl2.0+)))
3615 (define-public r-bumphunter
3617 (name "r-bumphunter")
3622 (uri (bioconductor-uri "bumphunter" version))
3625 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
3626 (build-system r-build-system)
3628 `(("r-annotationdbi" ,r-annotationdbi)
3629 ("r-biocgenerics" ,r-biocgenerics)
3630 ("r-dorng" ,r-dorng)
3631 ("r-foreach" ,r-foreach)
3632 ("r-genomeinfodb" ,r-genomeinfodb)
3633 ("r-genomicfeatures" ,r-genomicfeatures)
3634 ("r-genomicranges" ,r-genomicranges)
3635 ("r-iranges" ,r-iranges)
3636 ("r-iterators" ,r-iterators)
3637 ("r-limma" ,r-limma)
3638 ("r-locfit" ,r-locfit)
3639 ("r-matrixstats" ,r-matrixstats)
3640 ("r-s4vectors" ,r-s4vectors)))
3641 (home-page "https://github.com/ririzarr/bumphunter")
3642 (synopsis "Find bumps in genomic data")
3644 "This package provides tools for finding bumps in genomic data in order
3645 to identify differentially methylated regions in epigenetic epidemiology
3647 (license license:artistic2.0)))
3649 (define-public r-minfi
3656 (uri (bioconductor-uri "minfi" version))
3659 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
3660 (build-system r-build-system)
3662 `(("r-beanplot" ,r-beanplot)
3663 ("r-biobase" ,r-biobase)
3664 ("r-biocgenerics" ,r-biocgenerics)
3665 ("r-biocparallel" ,r-biocparallel)
3666 ("r-biostrings" ,r-biostrings)
3667 ("r-bumphunter" ,r-bumphunter)
3668 ("r-data-table" ,r-data-table)
3669 ("r-delayedarray" ,r-delayedarray)
3670 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3671 ("r-genefilter" ,r-genefilter)
3672 ("r-genomeinfodb" ,r-genomeinfodb)
3673 ("r-genomicranges" ,r-genomicranges)
3674 ("r-geoquery" ,r-geoquery)
3675 ("r-hdf5array" ,r-hdf5array)
3676 ("r-illuminaio" ,r-illuminaio)
3677 ("r-iranges" ,r-iranges)
3678 ("r-lattice" ,r-lattice)
3679 ("r-limma" ,r-limma)
3681 ("r-mclust" ,r-mclust)
3683 ("r-nor1mix" ,r-nor1mix)
3684 ("r-preprocesscore" ,r-preprocesscore)
3685 ("r-quadprog" ,r-quadprog)
3686 ("r-rcolorbrewer" ,r-rcolorbrewer)
3687 ("r-reshape" ,r-reshape)
3688 ("r-s4vectors" ,r-s4vectors)
3689 ("r-siggenes" ,r-siggenes)
3690 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3692 `(("r-knitr" ,r-knitr)))
3693 (home-page "https://github.com/hansenlab/minfi")
3694 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3696 "This package provides tools to analyze and visualize Illumina Infinium
3697 methylation arrays.")
3698 (license license:artistic2.0)))
3700 (define-public r-methylumi
3702 (name "r-methylumi")
3707 (uri (bioconductor-uri "methylumi" version))
3710 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
3711 (build-system r-build-system)
3713 `(("r-annotate" ,r-annotate)
3714 ("r-annotationdbi" ,r-annotationdbi)
3715 ("r-biobase" ,r-biobase)
3716 ("r-biocgenerics" ,r-biocgenerics)
3717 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3718 ("r-genefilter" ,r-genefilter)
3719 ("r-genomeinfodb" ,r-genomeinfodb)
3720 ("r-genomicranges" ,r-genomicranges)
3721 ("r-ggplot2" ,r-ggplot2)
3722 ("r-illuminaio" ,r-illuminaio)
3723 ("r-iranges" ,r-iranges)
3724 ("r-lattice" ,r-lattice)
3725 ("r-matrixstats" ,r-matrixstats)
3726 ("r-minfi" ,r-minfi)
3727 ("r-reshape2" ,r-reshape2)
3728 ("r-s4vectors" ,r-s4vectors)
3729 ("r-scales" ,r-scales)
3730 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3732 `(("r-knitr" ,r-knitr)))
3733 (home-page "https://bioconductor.org/packages/methylumi")
3734 (synopsis "Handle Illumina methylation data")
3736 "This package provides classes for holding and manipulating Illumina
3737 methylation data. Based on eSet, it can contain MIAME information, sample
3738 information, feature information, and multiple matrices of data. An
3739 \"intelligent\" import function, methylumiR can read the Illumina text files
3740 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3741 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3742 background correction, and quality control features for GoldenGate, Infinium,
3743 and Infinium HD arrays are also included.")
3744 (license license:gpl2)))
3746 (define-public r-lumi
3753 (uri (bioconductor-uri "lumi" version))
3756 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
3757 (build-system r-build-system)
3759 `(("r-affy" ,r-affy)
3760 ("r-annotate" ,r-annotate)
3761 ("r-annotationdbi" ,r-annotationdbi)
3762 ("r-biobase" ,r-biobase)
3764 ("r-genomicfeatures" ,r-genomicfeatures)
3765 ("r-genomicranges" ,r-genomicranges)
3766 ("r-kernsmooth" ,r-kernsmooth)
3767 ("r-lattice" ,r-lattice)
3769 ("r-methylumi" ,r-methylumi)
3771 ("r-nleqslv" ,r-nleqslv)
3772 ("r-preprocesscore" ,r-preprocesscore)
3773 ("r-rsqlite" ,r-rsqlite)))
3774 (home-page "https://bioconductor.org/packages/lumi")
3775 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3777 "The lumi package provides an integrated solution for the Illumina
3778 microarray data analysis. It includes functions of Illumina
3779 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3780 variance stabilization, normalization and gene annotation at the probe level.
3781 It also includes the functions of processing Illumina methylation microarrays,
3782 especially Illumina Infinium methylation microarrays.")
3783 (license license:lgpl2.0+)))
3785 (define-public r-linnorm
3792 (uri (bioconductor-uri "Linnorm" version))
3795 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
3796 (properties `((upstream-name . "Linnorm")))
3797 (build-system r-build-system)
3799 `(("r-amap" ,r-amap)
3800 ("r-apcluster" ,r-apcluster)
3801 ("r-ellipse" ,r-ellipse)
3802 ("r-fastcluster" ,r-fastcluster)
3804 ("r-ggdendro" ,r-ggdendro)
3805 ("r-ggplot2" ,r-ggplot2)
3806 ("r-gmodels" ,r-gmodels)
3807 ("r-igraph" ,r-igraph)
3808 ("r-limma" ,r-limma)
3810 ("r-mclust" ,r-mclust)
3812 ("r-rcpparmadillo" ,r-rcpparmadillo)
3813 ("r-rtsne" ,r-rtsne)
3814 ("r-statmod" ,r-statmod)
3815 ("r-vegan" ,r-vegan)
3818 `(("r-knitr" ,r-knitr)))
3819 (home-page "http://www.jjwanglab.org/Linnorm/")
3820 (synopsis "Linear model and normality based transformation method")
3822 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3823 count data or any large scale count data. It transforms such datasets for
3824 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3825 the following pipelines are implemented:
3828 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3829 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3830 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3831 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3832 @item Differential expression analysis or differential peak detection using
3833 limma (@code{Linnorm.limma})
3834 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3835 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3836 @item Stable gene selection for scRNA-seq data; for users without or who do
3837 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3838 @item Data imputation (@code{Linnorm.DataImput}).
3841 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3842 @code{RnaXSim} function is included for simulating RNA-seq data for the
3843 evaluation of DEG analysis methods.")
3844 (license license:expat)))
3846 (define-public r-ioniser
3853 (uri (bioconductor-uri "IONiseR" version))
3856 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
3857 (properties `((upstream-name . "IONiseR")))
3858 (build-system r-build-system)
3860 `(("r-biocgenerics" ,r-biocgenerics)
3861 ("r-biocparallel" ,r-biocparallel)
3862 ("r-biostrings" ,r-biostrings)
3863 ("r-bit64" ,r-bit64)
3864 ("r-dplyr" ,r-dplyr)
3865 ("r-ggplot2" ,r-ggplot2)
3866 ("r-magrittr" ,r-magrittr)
3867 ("r-rhdf5" ,r-rhdf5)
3868 ("r-shortread" ,r-shortread)
3869 ("r-stringr" ,r-stringr)
3870 ("r-tibble" ,r-tibble)
3871 ("r-tidyr" ,r-tidyr)
3872 ("r-xvector" ,r-xvector)))
3874 `(("r-knitr" ,r-knitr)))
3875 (home-page "https://bioconductor.org/packages/IONiseR/")
3876 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3878 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3879 MinION data. It extracts summary statistics from a set of fast5 files and can
3880 be used either before or after base calling. In addition to standard
3881 summaries of the read-types produced, it provides a number of plots for
3882 visualising metrics relative to experiment run time or spatially over the
3883 surface of a flowcell.")
3884 (license license:expat)))
3886 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3887 (define-public r-gkmsvm
3894 (uri (cran-uri "gkmSVM" version))
3897 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3898 (properties `((upstream-name . "gkmSVM")))
3899 (build-system r-build-system)
3901 `(("r-kernlab" ,r-kernlab)
3904 ("r-seqinr" ,r-seqinr)))
3905 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3906 (synopsis "Gapped-kmer support vector machine")
3908 "This R package provides tools for training gapped-kmer SVM classifiers
3909 for DNA and protein sequences. This package supports several sequence
3910 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3911 (license license:gpl2+)))
3913 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3914 (define-public r-mutoss
3921 (uri (cran-uri "mutoss" version))
3924 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3925 (properties `((upstream-name . "mutoss")))
3926 (build-system r-build-system)
3928 `(("r-multcomp" ,r-multcomp)
3929 ("r-multtest" ,r-multtest)
3930 ("r-mvtnorm" ,r-mvtnorm)
3931 ("r-plotrix" ,r-plotrix)))
3932 (home-page "https://github.com/kornl/mutoss/")
3933 (synopsis "Unified multiple testing procedures")
3935 "This package is designed to ease the application and comparison of
3936 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3937 are standardized and usable by the accompanying mutossGUI package.")
3938 ;; Any version of the GPL.
3939 (license (list license:gpl2+ license:gpl3+))))
3941 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3942 ;; from Bioconductor, so we put it here.
3943 (define-public r-metap
3950 (uri (cran-uri "metap" version))
3953 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3954 (build-system r-build-system)
3956 `(("r-lattice" ,r-lattice)
3957 ("r-mutoss" ,r-mutoss)
3958 ("r-rdpack" ,r-rdpack)
3959 ("r-tfisher" ,r-tfisher)))
3960 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3961 (synopsis "Meta-analysis of significance values")
3963 "The canonical way to perform meta-analysis involves using effect sizes.
3964 When they are not available this package provides a number of methods for
3965 meta-analysis of significance values including the methods of Edgington,
3966 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3967 published results; and a routine for graphical display.")
3968 (license license:gpl2)))
3970 (define-public r-triform
3977 (uri (bioconductor-uri "triform" version))
3980 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3981 (build-system r-build-system)
3983 `(("r-biocgenerics" ,r-biocgenerics)
3984 ("r-iranges" ,r-iranges)
3985 ("r-yaml" ,r-yaml)))
3986 (home-page "https://bioconductor.org/packages/triform/")
3987 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3989 "The Triform algorithm uses model-free statistics to identify peak-like
3990 distributions of TF ChIP sequencing reads, taking advantage of an improved
3991 peak definition in combination with known profile characteristics.")
3992 (license license:gpl2)))
3994 (define-public r-varianttools
3996 (name "r-varianttools")
4001 (uri (bioconductor-uri "VariantTools" version))
4004 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
4005 (properties `((upstream-name . "VariantTools")))
4006 (build-system r-build-system)
4008 `(("r-biobase" ,r-biobase)
4009 ("r-biocgenerics" ,r-biocgenerics)
4010 ("r-biocparallel" ,r-biocparallel)
4011 ("r-biostrings" ,r-biostrings)
4012 ("r-bsgenome" ,r-bsgenome)
4013 ("r-genomeinfodb" ,r-genomeinfodb)
4014 ("r-genomicfeatures" ,r-genomicfeatures)
4015 ("r-genomicranges" ,r-genomicranges)
4016 ("r-iranges" ,r-iranges)
4017 ("r-matrix" ,r-matrix)
4018 ("r-rsamtools" ,r-rsamtools)
4019 ("r-rtracklayer" ,r-rtracklayer)
4020 ("r-s4vectors" ,r-s4vectors)
4021 ("r-variantannotation" ,r-variantannotation)))
4022 (home-page "https://bioconductor.org/packages/VariantTools/")
4023 (synopsis "Tools for exploratory analysis of variant calls")
4025 "Explore, diagnose, and compare variant calls using filters. The
4026 VariantTools package supports a workflow for loading data, calling single
4027 sample variants and tumor-specific somatic mutations or other sample-specific
4028 variant types (e.g., RNA editing). Most of the functions operate on
4029 alignments (BAM files) or datasets of called variants. The user is expected
4030 to have already aligned the reads with a separate tool, e.g., GSNAP via
4032 (license license:artistic2.0)))
4034 (define-public r-heatplus
4041 (uri (bioconductor-uri "Heatplus" version))
4044 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
4045 (properties `((upstream-name . "Heatplus")))
4046 (build-system r-build-system)
4048 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
4049 (home-page "https://github.com/alexploner/Heatplus")
4050 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
4052 "This package provides tools to display a rectangular heatmap (intensity
4053 plot) of a data matrix. By default, both samples (columns) and features (row)
4054 of the matrix are sorted according to a hierarchical clustering, and the
4055 corresponding dendrogram is plotted. Optionally, panels with additional
4056 information about samples and features can be added to the plot.")
4057 (license license:gpl2+)))
4059 (define-public r-gosemsim
4066 (uri (bioconductor-uri "GOSemSim" version))
4069 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
4070 (properties `((upstream-name . "GOSemSim")))
4071 (build-system r-build-system)
4073 `(("r-annotationdbi" ,r-annotationdbi)
4074 ("r-go-db" ,r-go-db)
4075 ("r-rcpp" ,r-rcpp)))
4077 `(("r-knitr" ,r-knitr)))
4078 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
4079 (synopsis "GO-terms semantic similarity measures")
4081 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
4082 quantitative ways to compute similarities between genes and gene groups, and
4083 have became important basis for many bioinformatics analysis approaches.
4084 GOSemSim is an R package for semantic similarity computation among GO terms,
4085 sets of GO terms, gene products and gene clusters.")
4086 (license license:artistic2.0)))
4088 (define-public r-anota
4095 (uri (bioconductor-uri "anota" version))
4098 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
4099 (build-system r-build-system)
4101 `(("r-multtest" ,r-multtest)
4102 ("r-qvalue" ,r-qvalue)))
4103 (home-page "https://bioconductor.org/packages/anota/")
4104 (synopsis "Analysis of translational activity")
4106 "Genome wide studies of translational control is emerging as a tool to
4107 study various biological conditions. The output from such analysis is both
4108 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
4109 involved in translation (the actively translating mRNA level) for each mRNA.
4110 The standard analysis of such data strives towards identifying differential
4111 translational between two or more sample classes - i.e. differences in
4112 actively translated mRNA levels that are independent of underlying differences
4113 in cytosolic mRNA levels. This package allows for such analysis using partial
4114 variances and the random variance model. As 10s of thousands of mRNAs are
4115 analyzed in parallel the library performs a number of tests to assure that
4116 the data set is suitable for such analysis.")
4117 (license license:gpl3)))
4119 (define-public r-sigpathway
4121 (name "r-sigpathway")
4126 (uri (bioconductor-uri "sigPathway" version))
4129 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
4130 (properties `((upstream-name . "sigPathway")))
4131 (build-system r-build-system)
4132 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
4133 (synopsis "Pathway analysis")
4135 "This package is used to conduct pathway analysis by calculating the NT_k
4136 and NE_k statistics in a statistical framework for determining whether a
4137 specified group of genes for a pathway has a coordinated association with a
4138 phenotype of interest.")
4139 (license license:gpl2)))
4141 (define-public r-fgsea
4148 (uri (bioconductor-uri "fgsea" version))
4151 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
4152 (build-system r-build-system)
4155 ("r-biocparallel" ,r-biocparallel)
4156 ("r-data-table" ,r-data-table)
4157 ("r-fastmatch" ,r-fastmatch)
4158 ("r-ggplot2" ,r-ggplot2)
4159 ("r-gridextra" ,r-gridextra)
4160 ("r-matrix" ,r-matrix)
4161 ("r-rcpp" ,r-rcpp)))
4163 `(("r-knitr" ,r-knitr)))
4164 (home-page "https://github.com/ctlab/fgsea/")
4165 (synopsis "Fast gene set enrichment analysis")
4167 "The package implements an algorithm for fast gene set enrichment
4168 analysis. Using the fast algorithm makes more permutations and gets
4169 more fine grained p-values, which allows using accurate standard approaches
4170 to multiple hypothesis correction.")
4171 (license license:expat)))
4173 (define-public r-dose
4180 (uri (bioconductor-uri "DOSE" version))
4183 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
4184 (properties `((upstream-name . "DOSE")))
4185 (build-system r-build-system)
4187 `(("r-annotationdbi" ,r-annotationdbi)
4188 ("r-biocparallel" ,r-biocparallel)
4189 ("r-do-db" ,r-do-db)
4190 ("r-fgsea" ,r-fgsea)
4191 ("r-ggplot2" ,r-ggplot2)
4192 ("r-gosemsim" ,r-gosemsim)
4193 ("r-qvalue" ,r-qvalue)
4194 ("r-reshape2" ,r-reshape2)))
4196 `(("r-knitr" ,r-knitr)))
4197 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4198 (synopsis "Disease ontology semantic and enrichment analysis")
4200 "This package implements five methods proposed by Resnik, Schlicker,
4201 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4202 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4203 including hypergeometric model and gene set enrichment analysis are also
4204 implemented for discovering disease associations of high-throughput biological
4206 (license license:artistic2.0)))
4208 (define-public r-enrichplot
4210 (name "r-enrichplot")
4215 (uri (bioconductor-uri "enrichplot" version))
4218 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4219 (build-system r-build-system)
4221 `(("r-cowplot" ,r-cowplot)
4223 ("r-ggplot2" ,r-ggplot2)
4224 ("r-ggraph" ,r-ggraph)
4225 ("r-gosemsim" ,r-gosemsim)
4226 ("r-igraph" ,r-igraph)
4227 ("r-magrittr" ,r-magrittr)
4229 ("r-purrr" ,r-purrr)
4230 ("r-rcolorbrewer" ,r-rcolorbrewer)
4231 ("r-reshape2" ,r-reshape2)
4232 ("r-scatterpie" ,r-scatterpie)
4233 ("r-shadowtext" ,r-shadowtext)))
4235 `(("r-knitr" ,r-knitr)))
4236 (home-page "https://github.com/GuangchuangYu/enrichplot")
4237 (synopsis "Visualization of functional enrichment result")
4239 "The enrichplot package implements several visualization methods for
4240 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4241 All the visualization methods are developed based on ggplot2 graphics.")
4242 (license license:artistic2.0)))
4244 (define-public r-clusterprofiler
4246 (name "r-clusterprofiler")
4251 (uri (bioconductor-uri "clusterProfiler" version))
4254 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4256 `((upstream-name . "clusterProfiler")))
4257 (build-system r-build-system)
4259 `(("r-annotationdbi" ,r-annotationdbi)
4261 ("r-downloader" ,r-downloader)
4262 ("r-dplyr" ,r-dplyr)
4263 ("r-enrichplot" ,r-enrichplot)
4264 ("r-go-db" ,r-go-db)
4265 ("r-gosemsim" ,r-gosemsim)
4266 ("r-magrittr" ,r-magrittr)
4268 ("r-qvalue" ,r-qvalue)
4269 ("r-rlang" ,r-rlang)
4270 ("r-rvcheck" ,r-rvcheck)
4271 ("r-tidyr" ,r-tidyr)))
4273 `(("r-knitr" ,r-knitr)))
4274 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4275 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4277 "This package implements methods to analyze and visualize functional
4278 profiles (GO and KEGG) of gene and gene clusters.")
4279 (license license:artistic2.0)))
4281 (define-public r-mlinterfaces
4283 (name "r-mlinterfaces")
4288 (uri (bioconductor-uri "MLInterfaces" version))
4291 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4292 (properties `((upstream-name . "MLInterfaces")))
4293 (build-system r-build-system)
4295 `(("r-annotate" ,r-annotate)
4296 ("r-biobase" ,r-biobase)
4297 ("r-biocgenerics" ,r-biocgenerics)
4298 ("r-cluster" ,r-cluster)
4301 ("r-gdata" ,r-gdata)
4302 ("r-genefilter" ,r-genefilter)
4303 ("r-ggvis" ,r-ggvis)
4304 ("r-hwriter" ,r-hwriter)
4306 ("r-mlbench" ,r-mlbench)
4308 ("r-rcolorbrewer" ,r-rcolorbrewer)
4310 ("r-rpart" ,r-rpart)
4311 ("r-sfsmisc" ,r-sfsmisc)
4312 ("r-shiny" ,r-shiny)
4313 ("r-threejs" ,r-threejs)))
4314 (home-page "https://bioconductor.org/packages/MLInterfaces/")
4315 (synopsis "Interfaces to R machine learning procedures")
4317 "This package provides uniform interfaces to machine learning code for
4318 data in R and Bioconductor containers.")
4319 ;; Any version of the LGPL.
4320 (license license:lgpl2.1+)))
4322 (define-public r-annaffy
4329 (uri (bioconductor-uri "annaffy" version))
4332 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
4333 (build-system r-build-system)
4336 (modify-phases %standard-phases
4337 (add-after 'unpack 'remove-reference-to-non-free-data
4339 (substitute* "DESCRIPTION"
4343 `(("r-annotationdbi" ,r-annotationdbi)
4344 ("r-biobase" ,r-biobase)
4346 ("r-go-db" ,r-go-db)))
4347 (home-page "https://bioconductor.org/packages/annaffy/")
4348 (synopsis "Annotation tools for Affymetrix biological metadata")
4350 "This package provides functions for handling data from Bioconductor
4351 Affymetrix annotation data packages. It produces compact HTML and text
4352 reports including experimental data and URL links to many online databases.
4353 It allows searching of biological metadata using various criteria.")
4354 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4355 ;; the LGPL 2.1 is included.
4356 (license license:lgpl2.1+)))
4358 (define-public r-a4core
4365 (uri (bioconductor-uri "a4Core" version))
4368 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
4369 (properties `((upstream-name . "a4Core")))
4370 (build-system r-build-system)
4372 `(("r-biobase" ,r-biobase)
4373 ("r-glmnet" ,r-glmnet)))
4375 `(("r-knitr" ,r-knitr)))
4376 (home-page "https://bioconductor.org/packages/a4Core")
4377 (synopsis "Automated Affymetrix array analysis core package")
4379 "This is the core package for the automated analysis of Affymetrix
4381 (license license:gpl3)))
4383 (define-public r-a4classif
4385 (name "r-a4classif")
4390 (uri (bioconductor-uri "a4Classif" version))
4393 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
4394 (properties `((upstream-name . "a4Classif")))
4395 (build-system r-build-system)
4397 `(("r-a4core" ,r-a4core)
4398 ("r-a4preproc" ,r-a4preproc)
4399 ("r-biobase" ,r-biobase)
4400 ("r-glmnet" ,r-glmnet)
4403 ("r-varselrf" ,r-varselrf)))
4405 `(("r-knitr" ,r-knitr)))
4406 (home-page "https://bioconductor.org/packages/a4Classif/")
4407 (synopsis "Automated Affymetrix array analysis classification package")
4409 "This is the classification package for the automated analysis of
4410 Affymetrix arrays.")
4411 (license license:gpl3)))
4413 (define-public r-a4preproc
4415 (name "r-a4preproc")
4420 (uri (bioconductor-uri "a4Preproc" version))
4423 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
4424 (properties `((upstream-name . "a4Preproc")))
4425 (build-system r-build-system)
4427 `(("r-biobase" ,r-biobase)
4428 ("r-biocgenerics" ,r-biocgenerics)))
4430 `(("r-knitr" ,r-knitr)))
4431 (home-page "https://bioconductor.org/packages/a4Preproc/")
4432 (synopsis "Automated Affymetrix array analysis preprocessing package")
4434 "This is a package for the automated analysis of Affymetrix arrays. It
4435 is used for preprocessing the arrays.")
4436 (license license:gpl3)))
4438 (define-public r-a4reporting
4440 (name "r-a4reporting")
4445 (uri (bioconductor-uri "a4Reporting" version))
4448 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
4449 (properties `((upstream-name . "a4Reporting")))
4450 (build-system r-build-system)
4452 `(("r-xtable" ,r-xtable)))
4454 `(("r-knitr" ,r-knitr)))
4455 (home-page "https://bioconductor.org/packages/a4Reporting/")
4456 (synopsis "Automated Affymetrix array analysis reporting package")
4458 "This is a package for the automated analysis of Affymetrix arrays. It
4459 provides reporting features.")
4460 (license license:gpl3)))
4462 (define-public r-a4base
4469 (uri (bioconductor-uri "a4Base" version))
4472 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
4473 (properties `((upstream-name . "a4Base")))
4474 (build-system r-build-system)
4476 `(("r-a4core" ,r-a4core)
4477 ("r-a4preproc" ,r-a4preproc)
4478 ("r-annaffy" ,r-annaffy)
4479 ("r-biobase" ,r-biobase)
4480 ("r-genefilter" ,r-genefilter)
4481 ("r-glmnet" ,r-glmnet)
4482 ("r-gplots" ,r-gplots)
4483 ("r-limma" ,r-limma)
4485 ("r-multtest" ,r-multtest)))
4486 (home-page "https://bioconductor.org/packages/a4Base/")
4487 (synopsis "Automated Affymetrix array analysis base package")
4489 "This package provides basic features for the automated analysis of
4490 Affymetrix arrays.")
4491 (license license:gpl3)))
4500 (uri (bioconductor-uri "a4" version))
4503 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
4504 (build-system r-build-system)
4506 `(("r-a4base" ,r-a4base)
4507 ("r-a4classif" ,r-a4classif)
4508 ("r-a4core" ,r-a4core)
4509 ("r-a4preproc" ,r-a4preproc)
4510 ("r-a4reporting" ,r-a4reporting)))
4511 (home-page "https://bioconductor.org/packages/a4/")
4512 (synopsis "Automated Affymetrix array analysis umbrella package")
4514 "This package provides a software suite for the automated analysis of
4515 Affymetrix arrays.")
4516 (license license:gpl3)))
4518 (define-public r-abseqr
4525 (uri (bioconductor-uri "abseqR" version))
4528 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
4529 (properties `((upstream-name . "abseqR")))
4530 (build-system r-build-system)
4532 `(("pandoc" ,pandoc)))
4534 `(("r-biocparallel" ,r-biocparallel)
4535 ("r-biocstyle" ,r-biocstyle)
4536 ("r-circlize" ,r-circlize)
4537 ("r-flexdashboard" ,r-flexdashboard)
4538 ("r-ggcorrplot" ,r-ggcorrplot)
4539 ("r-ggdendro" ,r-ggdendro)
4540 ("r-ggplot2" ,r-ggplot2)
4541 ("r-gridextra" ,r-gridextra)
4542 ("r-knitr" ,r-knitr)
4543 ("r-plotly" ,r-plotly)
4546 ("r-rcolorbrewer" ,r-rcolorbrewer)
4547 ("r-reshape2" ,r-reshape2)
4548 ("r-rmarkdown" ,r-rmarkdown)
4549 ("r-stringr" ,r-stringr)
4550 ("r-vegan" ,r-vegan)
4551 ("r-venndiagram" ,r-venndiagram)))
4553 `(("r-knitr" ,r-knitr)))
4554 (home-page "https://github.com/malhamdoosh/abseqR")
4555 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4557 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4558 sequencing datasets generated from antibody libraries and abseqR is one of its
4559 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4560 capabilities and allows them to generate interactive HTML reports for the
4561 convenience of viewing and sharing with other researchers. Additionally,
4562 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4563 further downstream analysis on its output.")
4564 (license license:gpl3)))
4566 (define-public r-bacon
4573 (uri (bioconductor-uri "bacon" version))
4576 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
4577 (build-system r-build-system)
4579 `(("r-biocparallel" ,r-biocparallel)
4580 ("r-ellipse" ,r-ellipse)
4581 ("r-ggplot2" ,r-ggplot2)))
4583 `(("r-knitr" ,r-knitr)))
4584 (home-page "https://bioconductor.org/packages/bacon/")
4585 (synopsis "Controlling bias and inflation in association studies")
4587 "Bacon can be used to remove inflation and bias often observed in
4588 epigenome- and transcriptome-wide association studies. To this end bacon
4589 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4590 fitting a three-component normal mixture on z-scores.")
4591 (license license:gpl2+)))
4593 (define-public r-rgadem
4600 (uri (bioconductor-uri "rGADEM" version))
4603 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
4604 (properties `((upstream-name . "rGADEM")))
4605 (build-system r-build-system)
4607 `(("r-biostrings" ,r-biostrings)
4608 ("r-bsgenome" ,r-bsgenome)
4609 ("r-genomicranges" ,r-genomicranges)
4610 ("r-iranges" ,r-iranges)
4611 ("r-seqlogo" ,r-seqlogo)))
4612 (home-page "https://bioconductor.org/packages/rGADEM/")
4613 (synopsis "De novo sequence motif discovery")
4615 "rGADEM is an efficient de novo motif discovery tool for large-scale
4616 genomic sequence data.")
4617 (license license:artistic2.0)))
4619 (define-public r-motiv
4626 (uri (bioconductor-uri "MotIV" version))
4629 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4630 (properties `((upstream-name . "MotIV")))
4631 (build-system r-build-system)
4635 `(("r-biocgenerics" ,r-biocgenerics)
4636 ("r-biostrings" ,r-biostrings)
4637 ("r-genomicranges" ,r-genomicranges)
4638 ("r-iranges" ,r-iranges)
4639 ("r-lattice" ,r-lattice)
4640 ("r-rgadem" ,r-rgadem)
4641 ("r-s4vectors" ,r-s4vectors)))
4642 (home-page "https://bioconductor.org/packages/MotIV/")
4643 (synopsis "Motif identification and validation")
4645 "This package is used for the identification and validation of sequence
4646 motifs. It makes use of STAMP for comparing a set of motifs to a given
4647 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4648 distributions, modules and filter motifs.")
4649 (license license:gpl2)))
4651 (define-public r-motifdb
4657 (uri (bioconductor-uri "MotifDb" version))
4659 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
4660 (properties `((upstream-name . "MotifDb")))
4661 (build-system r-build-system)
4663 `(("r-biocgenerics" ,r-biocgenerics)
4664 ("r-biostrings" ,r-biostrings)
4665 ("r-genomicranges" ,r-genomicranges)
4666 ("r-iranges" ,r-iranges)
4667 ("r-rtracklayer" ,r-rtracklayer)
4668 ("r-s4vectors" ,r-s4vectors)
4669 ("r-splitstackshape" ,r-splitstackshape)))
4671 `(("r-knitr" ,r-knitr)))
4672 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4673 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4674 (description "This package provides more than 2000 annotated position
4675 frequency matrices from nine public sources, for multiple organisms.")
4676 (license license:artistic2.0)))
4678 (define-public r-motifbreakr
4680 (name "r-motifbreakr")
4684 (uri (bioconductor-uri "motifbreakR" version))
4686 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
4687 (properties `((upstream-name . "motifbreakR")))
4688 (build-system r-build-system)
4690 `(("r-biocgenerics" ,r-biocgenerics)
4691 ("r-biocparallel" ,r-biocparallel)
4692 ("r-biostrings" ,r-biostrings)
4693 ("r-bsgenome" ,r-bsgenome)
4694 ("r-genomeinfodb" ,r-genomeinfodb)
4695 ("r-genomicranges" ,r-genomicranges)
4696 ("r-grimport" ,r-grimport)
4698 ("r-iranges" ,r-iranges)
4699 ("r-matrixstats" ,r-matrixstats)
4700 ("r-motifdb" ,r-motifdb)
4701 ("r-motifstack" ,r-motifstack)
4702 ("r-rtracklayer" ,r-rtracklayer)
4703 ("r-s4vectors" ,r-s4vectors)
4704 ("r-stringr" ,r-stringr)
4705 ("r-summarizedexperiment" ,r-summarizedexperiment)
4706 ("r-tfmpvalue" ,r-tfmpvalue)
4707 ("r-variantannotation" ,r-variantannotation)))
4709 `(("r-knitr" ,r-knitr)))
4710 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4711 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4712 (description "This package allows biologists to judge in the first place
4713 whether the sequence surrounding the polymorphism is a good match, and in
4714 the second place how much information is gained or lost in one allele of
4715 the polymorphism relative to another. This package gives a choice of
4716 algorithms for interrogation of genomes with motifs from public sources:
4718 @item a weighted-sum probability matrix;
4719 @item log-probabilities;
4720 @item weighted by relative entropy.
4723 This package can predict effects for novel or previously described variants in
4724 public databases, making it suitable for tasks beyond the scope of its original
4725 design. Lastly, it can be used to interrogate any genome curated within
4727 (license license:gpl2+)))
4729 (define-public r-motifstack
4731 (name "r-motifstack")
4736 (uri (bioconductor-uri "motifStack" version))
4739 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
4740 (properties `((upstream-name . "motifStack")))
4741 (build-system r-build-system)
4743 `(("r-ade4" ,r-ade4)
4744 ("r-biostrings" ,r-biostrings)
4745 ("r-ggplot2" ,r-ggplot2)
4746 ("r-htmlwidgets" ,r-htmlwidgets)
4749 `(("r-knitr" ,r-knitr)))
4750 (home-page "https://bioconductor.org/packages/motifStack/")
4751 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4753 "The motifStack package is designed for graphic representation of
4754 multiple motifs with different similarity scores. It works with both DNA/RNA
4755 sequence motifs and amino acid sequence motifs. In addition, it provides the
4756 flexibility for users to customize the graphic parameters such as the font
4757 type and symbol colors.")
4758 (license license:gpl2+)))
4760 (define-public r-genomicscores
4762 (name "r-genomicscores")
4767 (uri (bioconductor-uri "GenomicScores" version))
4770 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
4771 (properties `((upstream-name . "GenomicScores")))
4772 (build-system r-build-system)
4774 `(("r-annotationhub" ,r-annotationhub)
4775 ("r-biobase" ,r-biobase)
4776 ("r-biocfilecache" ,r-biocfilecache)
4777 ("r-biocgenerics" ,r-biocgenerics)
4778 ("r-biocmanager" ,r-biocmanager)
4779 ("r-biostrings" ,r-biostrings)
4780 ("r-delayedarray" ,r-delayedarray)
4781 ("r-genomeinfodb" ,r-genomeinfodb)
4782 ("r-genomicranges" ,r-genomicranges)
4783 ("r-hdf5array" ,r-hdf5array)
4784 ("r-iranges" ,r-iranges)
4785 ("r-rhdf5" ,r-rhdf5)
4786 ("r-s4vectors" ,r-s4vectors)
4789 `(("r-knitr" ,r-knitr)))
4790 (home-page "https://github.com/rcastelo/GenomicScores/")
4791 (synopsis "Work with genome-wide position-specific scores")
4793 "This package provides infrastructure to store and access genome-wide
4794 position-specific scores within R and Bioconductor.")
4795 (license license:artistic2.0)))
4797 (define-public r-atacseqqc
4799 (name "r-atacseqqc")
4804 (uri (bioconductor-uri "ATACseqQC" version))
4807 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
4808 (properties `((upstream-name . "ATACseqQC")))
4809 (build-system r-build-system)
4811 `(("r-biocgenerics" ,r-biocgenerics)
4812 ("r-biostrings" ,r-biostrings)
4813 ("r-bsgenome" ,r-bsgenome)
4814 ("r-chippeakanno" ,r-chippeakanno)
4815 ("r-edger" ,r-edger)
4816 ("r-genomeinfodb" ,r-genomeinfodb)
4817 ("r-genomicalignments" ,r-genomicalignments)
4818 ("r-genomicranges" ,r-genomicranges)
4819 ("r-genomicscores" ,r-genomicscores)
4820 ("r-iranges" ,r-iranges)
4821 ("r-kernsmooth" ,r-kernsmooth)
4822 ("r-limma" ,r-limma)
4823 ("r-motifstack" ,r-motifstack)
4824 ("r-preseqr" ,r-preseqr)
4825 ("r-randomforest" ,r-randomforest)
4826 ("r-rsamtools" ,r-rsamtools)
4827 ("r-rtracklayer" ,r-rtracklayer)
4828 ("r-s4vectors" ,r-s4vectors)))
4830 `(("r-knitr" ,r-knitr)))
4831 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4832 (synopsis "ATAC-seq quality control")
4834 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4835 sequencing, is a rapid and sensitive method for chromatin accessibility
4836 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4837 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4838 assess whether their ATAC-seq experiment is successful. It includes
4839 diagnostic plots of fragment size distribution, proportion of mitochondria
4840 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4842 (license license:gpl2+)))
4844 (define-public r-gofuncr
4851 (uri (bioconductor-uri "GOfuncR" version))
4854 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
4855 (properties `((upstream-name . "GOfuncR")))
4856 (build-system r-build-system)
4858 `(("r-annotationdbi" ,r-annotationdbi)
4859 ("r-genomicranges" ,r-genomicranges)
4860 ("r-gtools" ,r-gtools)
4861 ("r-iranges" ,r-iranges)
4862 ("r-mapplots" ,r-mapplots)
4864 ("r-vioplot" ,r-vioplot)))
4866 `(("r-knitr" ,r-knitr)))
4867 (home-page "https://bioconductor.org/packages/GOfuncR/")
4868 (synopsis "Gene ontology enrichment using FUNC")
4870 "GOfuncR performs a gene ontology enrichment analysis based on the
4871 ontology enrichment software FUNC. GO-annotations are obtained from
4872 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4873 included in the package and updated regularly. GOfuncR provides the standard
4874 candidate vs background enrichment analysis using the hypergeometric test, as
4875 well as three additional tests:
4878 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4879 @item a binomial test that is used when genes are associated with two counts,
4881 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4882 associated with four counts.
4885 To correct for multiple testing and interdependency of the tests, family-wise
4886 error rates are computed based on random permutations of the gene-associated
4887 variables. GOfuncR also provides tools for exploring the ontology graph and
4888 the annotations, and options to take gene-length or spatial clustering of
4889 genes into account. It is also possible to provide custom gene coordinates,
4890 annotations and ontologies.")
4891 (license license:gpl2+)))
4893 (define-public r-abaenrichment
4895 (name "r-abaenrichment")
4900 (uri (bioconductor-uri "ABAEnrichment" version))
4903 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
4904 (properties `((upstream-name . "ABAEnrichment")))
4905 (build-system r-build-system)
4907 `(("r-abadata" ,r-abadata)
4908 ("r-data-table" ,r-data-table)
4909 ("r-gofuncr" ,r-gofuncr)
4910 ("r-gplots" ,r-gplots)
4911 ("r-gtools" ,r-gtools)
4912 ("r-rcpp" ,r-rcpp)))
4914 `(("r-knitr" ,r-knitr)))
4915 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4916 (synopsis "Gene expression enrichment in human brain regions")
4918 "The package ABAEnrichment is designed to test for enrichment of user
4919 defined candidate genes in the set of expressed genes in different human brain
4920 regions. The core function @code{aba_enrich} integrates the expression of the
4921 candidate gene set (averaged across donors) and the structural information of
4922 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4923 (license license:gpl2+)))
4925 (define-public r-annotationfuncs
4927 (name "r-annotationfuncs")
4932 (uri (bioconductor-uri "AnnotationFuncs" version))
4935 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
4937 `((upstream-name . "AnnotationFuncs")))
4938 (build-system r-build-system)
4940 `(("r-annotationdbi" ,r-annotationdbi)
4942 (home-page "https://www.iysik.com/r/annotationfuncs")
4943 (synopsis "Annotation translation functions")
4945 "This package provides functions for handling translating between
4946 different identifieres using the Biocore Data Team data-packages (e.g.
4947 @code{org.Bt.eg.db}).")
4948 (license license:gpl2)))
4950 (define-public r-annotationtools
4952 (name "r-annotationtools")
4957 (uri (bioconductor-uri "annotationTools" version))
4960 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
4962 `((upstream-name . "annotationTools")))
4963 (build-system r-build-system)
4964 (propagated-inputs `(("r-biobase" ,r-biobase)))
4965 (home-page "https://bioconductor.org/packages/annotationTools/")
4966 (synopsis "Annotate microarrays and perform gene expression analyses")
4968 "This package provides functions to annotate microarrays, find orthologs,
4969 and integrate heterogeneous gene expression profiles using annotation and
4970 other molecular biology information available as flat file database (plain
4972 ;; Any version of the GPL.
4973 (license (list license:gpl2+))))
4975 (define-public r-allelicimbalance
4977 (name "r-allelicimbalance")
4982 (uri (bioconductor-uri "AllelicImbalance" version))
4985 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
4987 `((upstream-name . "AllelicImbalance")))
4988 (build-system r-build-system)
4990 `(("r-annotationdbi" ,r-annotationdbi)
4991 ("r-biocgenerics" ,r-biocgenerics)
4992 ("r-biostrings" ,r-biostrings)
4993 ("r-bsgenome" ,r-bsgenome)
4994 ("r-genomeinfodb" ,r-genomeinfodb)
4995 ("r-genomicalignments" ,r-genomicalignments)
4996 ("r-genomicfeatures" ,r-genomicfeatures)
4997 ("r-genomicranges" ,r-genomicranges)
4998 ("r-gridextra" ,r-gridextra)
5000 ("r-iranges" ,r-iranges)
5001 ("r-lattice" ,r-lattice)
5002 ("r-latticeextra" ,r-latticeextra)
5004 ("r-rsamtools" ,r-rsamtools)
5005 ("r-s4vectors" ,r-s4vectors)
5006 ("r-seqinr" ,r-seqinr)
5007 ("r-summarizedexperiment" ,r-summarizedexperiment)
5008 ("r-variantannotation" ,r-variantannotation)))
5010 `(("r-knitr" ,r-knitr)))
5011 (home-page "https://github.com/pappewaio/AllelicImbalance")
5012 (synopsis "Investigate allele-specific expression")
5014 "This package provides a framework for allele-specific expression
5015 investigation using RNA-seq data.")
5016 (license license:gpl3)))
5018 (define-public r-aucell
5025 (uri (bioconductor-uri "AUCell" version))
5028 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
5029 (properties `((upstream-name . "AUCell")))
5030 (build-system r-build-system)
5032 `(("r-biocgenerics" ,r-biocgenerics)
5033 ("r-data-table" ,r-data-table)
5034 ("r-gseabase" ,r-gseabase)
5035 ("r-mixtools" ,r-mixtools)
5036 ("r-r-utils" ,r-r-utils)
5037 ("r-s4vectors" ,r-s4vectors)
5038 ("r-shiny" ,r-shiny)
5039 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5041 `(("r-knitr" ,r-knitr)))
5042 (home-page "https://bioconductor.org/packages/AUCell/")
5043 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
5045 "AUCell identifies cells with active gene sets (e.g. signatures,
5046 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
5047 Under the Curve} (AUC) to calculate whether a critical subset of the input
5048 gene set is enriched within the expressed genes for each cell. The
5049 distribution of AUC scores across all the cells allows exploring the relative
5050 expression of the signature. Since the scoring method is ranking-based,
5051 AUCell is independent of the gene expression units and the normalization
5052 procedure. In addition, since the cells are evaluated individually, it can
5053 easily be applied to bigger datasets, subsetting the expression matrix if
5055 (license license:gpl3)))
5057 (define-public r-ebimage
5064 (uri (bioconductor-uri "EBImage" version))
5067 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5068 (properties `((upstream-name . "EBImage")))
5069 (build-system r-build-system)
5071 `(("r-abind" ,r-abind)
5072 ("r-biocgenerics" ,r-biocgenerics)
5073 ("r-fftwtools" ,r-fftwtools)
5074 ("r-htmltools" ,r-htmltools)
5075 ("r-htmlwidgets" ,r-htmlwidgets)
5077 ("r-locfit" ,r-locfit)
5079 ("r-rcurl" ,r-rcurl)
5080 ("r-tiff" ,r-tiff)))
5082 `(("r-knitr" ,r-knitr))) ; for vignettes
5083 (home-page "https://github.com/aoles/EBImage")
5084 (synopsis "Image processing and analysis toolbox for R")
5086 "EBImage provides general purpose functionality for image processing and
5087 analysis. In the context of (high-throughput) microscopy-based cellular
5088 assays, EBImage offers tools to segment cells and extract quantitative
5089 cellular descriptors. This allows the automation of such tasks using the R
5090 programming language and facilitates the use of other tools in the R
5091 environment for signal processing, statistical modeling, machine learning and
5092 visualization with image data.")
5093 ;; Any version of the LGPL.
5094 (license license:lgpl2.1+)))
5096 (define-public r-yamss
5103 (uri (bioconductor-uri "yamss" version))
5106 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
5107 (build-system r-build-system)
5109 `(("r-biocgenerics" ,r-biocgenerics)
5110 ("r-data-table" ,r-data-table)
5111 ("r-ebimage" ,r-ebimage)
5112 ("r-iranges" ,r-iranges)
5113 ("r-limma" ,r-limma)
5114 ("r-matrix" ,r-matrix)
5116 ("r-s4vectors" ,r-s4vectors)
5117 ("r-summarizedexperiment"
5118 ,r-summarizedexperiment)))
5120 `(("r-knitr" ,r-knitr)))
5121 (home-page "https://github.com/hansenlab/yamss")
5122 (synopsis "Tools for high-throughput metabolomics")
5124 "This package provides tools to analyze and visualize high-throughput
5125 metabolomics data acquired using chromatography-mass spectrometry. These tools
5126 preprocess data in a way that enables reliable and powerful differential
5128 (license license:artistic2.0)))
5130 (define-public r-gtrellis
5137 (uri (bioconductor-uri "gtrellis" version))
5140 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
5141 (build-system r-build-system)
5143 `(("r-circlize" ,r-circlize)
5144 ("r-genomicranges" ,r-genomicranges)
5145 ("r-getoptlong" ,r-getoptlong)
5146 ("r-iranges" ,r-iranges)))
5148 `(("r-knitr" ,r-knitr)))
5149 (home-page "https://github.com/jokergoo/gtrellis")
5150 (synopsis "Genome level Trellis layout")
5152 "Genome level Trellis graph visualizes genomic data conditioned by
5153 genomic categories (e.g. chromosomes). For each genomic category, multiple
5154 dimensional data which are represented as tracks describe different features
5155 from different aspects. This package provides high flexibility to arrange
5156 genomic categories and to add self-defined graphics in the plot.")
5157 (license license:expat)))
5159 (define-public r-somaticsignatures
5161 (name "r-somaticsignatures")
5166 (uri (bioconductor-uri "SomaticSignatures" version))
5169 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
5171 `((upstream-name . "SomaticSignatures")))
5172 (build-system r-build-system)
5174 `(("r-biobase" ,r-biobase)
5175 ("r-biostrings" ,r-biostrings)
5176 ("r-genomeinfodb" ,r-genomeinfodb)
5177 ("r-genomicranges" ,r-genomicranges)
5178 ("r-ggbio" ,r-ggbio)
5179 ("r-ggplot2" ,r-ggplot2)
5180 ("r-iranges" ,r-iranges)
5182 ("r-pcamethods" ,r-pcamethods)
5183 ("r-proxy" ,r-proxy)
5184 ("r-reshape2" ,r-reshape2)
5185 ("r-s4vectors" ,r-s4vectors)
5186 ("r-variantannotation" ,r-variantannotation)))
5188 `(("r-knitr" ,r-knitr)))
5189 (home-page "https://github.com/juliangehring/SomaticSignatures")
5190 (synopsis "Somatic signatures")
5192 "This package identifies mutational signatures of @dfn{single nucleotide
5193 variants} (SNVs). It provides a infrastructure related to the methodology
5194 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5195 decomposition algorithms.")
5196 (license license:expat)))
5198 (define-public r-yapsa
5205 (uri (bioconductor-uri "YAPSA" version))
5208 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5209 (properties `((upstream-name . "YAPSA")))
5210 (build-system r-build-system)
5212 `(("r-biostrings" ,r-biostrings)
5213 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5214 ("r-circlize" ,r-circlize)
5215 ("r-complexheatmap" ,r-complexheatmap)
5216 ("r-corrplot" ,r-corrplot)
5217 ("r-dendextend" ,r-dendextend)
5218 ("r-doparallel" ,r-doparallel)
5219 ("r-dplyr" ,r-dplyr)
5220 ("r-genomeinfodb" ,r-genomeinfodb)
5221 ("r-genomicranges" ,r-genomicranges)
5222 ("r-getoptlong" ,r-getoptlong)
5223 ("r-ggbeeswarm" ,r-ggbeeswarm)
5224 ("r-ggplot2" ,r-ggplot2)
5225 ("r-gridextra" ,r-gridextra)
5226 ("r-gtrellis" ,r-gtrellis)
5227 ("r-keggrest" ,r-keggrest)
5228 ("r-limsolve" ,r-limsolve)
5229 ("r-magrittr" ,r-magrittr)
5230 ("r-pmcmr" ,r-pmcmr)
5231 ("r-pracma" ,r-pracma)
5232 ("r-reshape2" ,r-reshape2)
5233 ("r-somaticsignatures" ,r-somaticsignatures)
5234 ("r-variantannotation" ,r-variantannotation)))
5236 `(("r-knitr" ,r-knitr)))
5237 (home-page "https://bioconductor.org/packages/YAPSA/")
5238 (synopsis "Yet another package for signature analysis")
5240 "This package provides functions and routines useful in the analysis of
5241 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5242 functions to perform a signature analysis with known signatures and a
5243 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5245 (license license:gpl3)))
5247 (define-public r-gcrma
5254 (uri (bioconductor-uri "gcrma" version))
5257 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5258 (build-system r-build-system)
5260 `(("r-affy" ,r-affy)
5261 ("r-affyio" ,r-affyio)
5262 ("r-biobase" ,r-biobase)
5263 ("r-biocmanager" ,r-biocmanager)
5264 ("r-biostrings" ,r-biostrings)
5265 ("r-xvector" ,r-xvector)))
5266 (home-page "https://bioconductor.org/packages/gcrma/")
5267 (synopsis "Background adjustment using sequence information")
5269 "Gcrma adjusts for background intensities in Affymetrix array data which
5270 include optical noise and @dfn{non-specific binding} (NSB). The main function
5271 @code{gcrma} converts background adjusted probe intensities to expression
5272 measures using the same normalization and summarization methods as a
5273 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5274 to estimate probe affinity to NSB. The sequence information is summarized in
5275 a more complex way than the simple GC content. Instead, the base types (A, T,
5276 G or C) at each position along the probe determine the affinity of each probe.
5277 The parameters of the position-specific base contributions to the probe
5278 affinity is estimated in an NSB experiment in which only NSB but no
5279 gene-specific binding is expected.")
5280 ;; Any version of the LGPL
5281 (license license:lgpl2.1+)))
5283 (define-public r-simpleaffy
5285 (name "r-simpleaffy")
5290 (uri (bioconductor-uri "simpleaffy" version))
5293 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5294 (build-system r-build-system)
5296 `(("r-affy" ,r-affy)
5297 ("r-biobase" ,r-biobase)
5298 ("r-biocgenerics" ,r-biocgenerics)
5299 ("r-gcrma" ,r-gcrma)
5300 ("r-genefilter" ,r-genefilter)))
5301 (home-page "https://bioconductor.org/packages/simpleaffy/")
5302 (synopsis "Very simple high level analysis of Affymetrix data")
5304 "This package provides high level functions for reading Affy @file{.CEL}
5305 files, phenotypic data, and then computing simple things with it, such as
5306 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5307 library. It also has some basic scatter plot functions and mechanisms for
5308 generating high resolution journal figures.")
5309 (license license:gpl2+)))
5311 (define-public r-yaqcaffy
5318 (uri (bioconductor-uri "yaqcaffy" version))
5321 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
5322 (build-system r-build-system)
5324 `(("r-simpleaffy" ,r-simpleaffy)))
5325 (home-page "https://bioconductor.org/packages/yaqcaffy/")
5326 (synopsis "Affymetrix quality control and reproducibility analysis")
5328 "This is a package that can be used for quality control of Affymetrix
5329 GeneChip expression data and reproducibility analysis of human whole genome
5330 chips with the MAQC reference datasets.")
5331 (license license:artistic2.0)))
5333 (define-public r-quantro
5340 (uri (bioconductor-uri "quantro" version))
5343 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
5344 (build-system r-build-system)
5346 `(("r-biobase" ,r-biobase)
5347 ("r-doparallel" ,r-doparallel)
5348 ("r-foreach" ,r-foreach)
5349 ("r-ggplot2" ,r-ggplot2)
5350 ("r-iterators" ,r-iterators)
5351 ("r-minfi" ,r-minfi)
5352 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5354 `(("r-knitr" ,r-knitr)))
5355 (home-page "https://bioconductor.org/packages/quantro/")
5356 (synopsis "Test for when to use quantile normalization")
5358 "This package provides a data-driven test for the assumptions of quantile
5359 normalization using raw data such as objects that inherit eSets (e.g.
5360 ExpressionSet, MethylSet). Group level information about each sample (such as
5361 Tumor / Normal status) must also be provided because the test assesses if
5362 there are global differences in the distributions between the user-defined
5364 (license license:gpl3+)))
5366 (define-public r-yarn
5373 (uri (bioconductor-uri "yarn" version))
5376 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
5377 (build-system r-build-system)
5379 `(("r-biobase" ,r-biobase)
5380 ("r-biomart" ,r-biomart)
5381 ("r-downloader" ,r-downloader)
5382 ("r-edger" ,r-edger)
5383 ("r-gplots" ,r-gplots)
5384 ("r-limma" ,r-limma)
5385 ("r-matrixstats" ,r-matrixstats)
5386 ("r-preprocesscore" ,r-preprocesscore)
5387 ("r-quantro" ,r-quantro)
5388 ("r-rcolorbrewer" ,r-rcolorbrewer)
5389 ("r-readr" ,r-readr)))
5391 `(("r-knitr" ,r-knitr)))
5392 (home-page "https://bioconductor.org/packages/yarn/")
5393 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5395 "Expedite large RNA-Seq analyses using a combination of previously
5396 developed tools. YARN is meant to make it easier for the user in performing
5397 basic mis-annotation quality control, filtering, and condition-aware
5398 normalization. YARN leverages many Bioconductor tools and statistical
5399 techniques to account for the large heterogeneity and sparsity found in very
5400 large RNA-seq experiments.")
5401 (license license:artistic2.0)))
5403 (define-public r-roar
5410 (uri (bioconductor-uri "roar" version))
5413 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
5414 (build-system r-build-system)
5416 `(("r-biocgenerics" ,r-biocgenerics)
5417 ("r-genomeinfodb" ,r-genomeinfodb)
5418 ("r-genomicalignments" ,r-genomicalignments)
5419 ("r-genomicranges" ,r-genomicranges)
5420 ("r-iranges" ,r-iranges)
5421 ("r-rtracklayer" ,r-rtracklayer)
5422 ("r-s4vectors" ,r-s4vectors)
5423 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5424 (home-page "https://github.com/vodkatad/roar/")
5425 (synopsis "Identify differential APA usage from RNA-seq alignments")
5427 "This package provides tools for identifying preferential usage of APA
5428 sites, comparing two biological conditions, starting from known alternative
5429 sites and alignments obtained from standard RNA-seq experiments.")
5430 (license license:gpl3)))
5432 (define-public r-xbseq
5439 (uri (bioconductor-uri "XBSeq" version))
5442 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
5443 (properties `((upstream-name . "XBSeq")))
5444 (build-system r-build-system)
5446 `(("r-biobase" ,r-biobase)
5447 ("r-deseq2" ,r-deseq2)
5448 ("r-dplyr" ,r-dplyr)
5449 ("r-ggplot2" ,r-ggplot2)
5450 ("r-locfit" ,r-locfit)
5451 ("r-magrittr" ,r-magrittr)
5452 ("r-matrixstats" ,r-matrixstats)
5453 ("r-pracma" ,r-pracma)
5454 ("r-roar" ,r-roar)))
5456 `(("r-knitr" ,r-knitr)))
5457 (home-page "https://github.com/Liuy12/XBSeq")
5458 (synopsis "Test for differential expression for RNA-seq data")
5460 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5461 expression} (DE), where a statistical model was established based on the
5462 assumption that observed signals are the convolution of true expression
5463 signals and sequencing noises. The mapped reads in non-exonic regions are
5464 considered as sequencing noises, which follows a Poisson distribution. Given
5465 measurable observed signal and background noise from RNA-seq data, true
5466 expression signals, assuming governed by the negative binomial distribution,
5467 can be delineated and thus the accurate detection of differential expressed
5469 (license license:gpl3+)))
5471 (define-public r-massspecwavelet
5473 (name "r-massspecwavelet")
5478 (uri (bioconductor-uri "MassSpecWavelet" version))
5481 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
5483 `((upstream-name . "MassSpecWavelet")))
5484 (build-system r-build-system)
5486 `(("r-waveslim" ,r-waveslim)))
5487 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5488 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5490 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5491 data mainly through the use of wavelet transforms. It supports peak detection
5492 based on @dfn{Continuous Wavelet Transform} (CWT).")
5493 (license license:lgpl2.0+)))
5495 (define-public r-xcms
5502 (uri (bioconductor-uri "xcms" version))
5505 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
5506 (build-system r-build-system)
5508 `(("r-biobase" ,r-biobase)
5509 ("r-biocgenerics" ,r-biocgenerics)
5510 ("r-biocparallel" ,r-biocparallel)
5511 ("r-iranges" ,r-iranges)
5512 ("r-lattice" ,r-lattice)
5513 ("r-massspecwavelet" ,r-massspecwavelet)
5514 ("r-mscoreutils" ,r-mscoreutils)
5515 ("r-msnbase" ,r-msnbase)
5518 ("r-protgenerics" ,r-protgenerics)
5520 ("r-rcolorbrewer" ,r-rcolorbrewer)
5521 ("r-robustbase" ,r-robustbase)
5522 ("r-s4vectors" ,r-s4vectors)
5523 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5525 `(("r-knitr" ,r-knitr)))
5526 (home-page "https://bioconductor.org/packages/xcms/")
5527 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5529 "This package provides a framework for processing and visualization of
5530 chromatographically separated and single-spectra mass spectral data. It
5531 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5532 data for high-throughput, untargeted analyte profiling.")
5533 (license license:gpl2+)))
5535 (define-public r-wrench
5542 (uri (bioconductor-uri "Wrench" version))
5545 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
5546 (properties `((upstream-name . "Wrench")))
5547 (build-system r-build-system)
5549 `(("r-limma" ,r-limma)
5550 ("r-locfit" ,r-locfit)
5551 ("r-matrixstats" ,r-matrixstats)))
5553 `(("r-knitr" ,r-knitr)))
5554 (home-page "https://github.com/HCBravoLab/Wrench")
5555 (synopsis "Wrench normalization for sparse count data")
5557 "Wrench is a package for normalization sparse genomic count data, like
5558 that arising from 16s metagenomic surveys.")
5559 (license license:artistic2.0)))
5561 (define-public r-wiggleplotr
5563 (name "r-wiggleplotr")
5568 (uri (bioconductor-uri "wiggleplotr" version))
5571 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
5572 (build-system r-build-system)
5574 `(("r-assertthat" ,r-assertthat)
5575 ("r-cowplot" ,r-cowplot)
5576 ("r-dplyr" ,r-dplyr)
5577 ("r-genomeinfodb" ,r-genomeinfodb)
5578 ("r-genomicranges" ,r-genomicranges)
5579 ("r-ggplot2" ,r-ggplot2)
5580 ("r-iranges" ,r-iranges)
5581 ("r-purrr" ,r-purrr)
5582 ("r-rtracklayer" ,r-rtracklayer)
5583 ("r-s4vectors" ,r-s4vectors)))
5585 `(("r-knitr" ,r-knitr)))
5586 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5587 (synopsis "Make read coverage plots from BigWig files")
5589 "This package provides tools to visualize read coverage from sequencing
5590 experiments together with genomic annotations (genes, transcripts, peaks).
5591 Introns of long transcripts can be rescaled to a fixed length for better
5592 visualization of exonic read coverage.")
5593 (license license:asl2.0)))
5595 (define-public r-widgettools
5597 (name "r-widgettools")
5602 (uri (bioconductor-uri "widgetTools" version))
5605 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
5606 (properties `((upstream-name . "widgetTools")))
5607 (build-system r-build-system)
5608 (home-page "https://bioconductor.org/packages/widgetTools/")
5609 (synopsis "Tools for creating interactive tcltk widgets")
5611 "This package contains tools to support the construction of tcltk
5613 ;; Any version of the LGPL.
5614 (license license:lgpl3+)))
5616 (define-public r-webbioc
5623 (uri (bioconductor-uri "webbioc" version))
5626 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
5627 (build-system r-build-system)
5629 `(("netpbm" ,netpbm)
5632 `(("r-affy" ,r-affy)
5633 ("r-annaffy" ,r-annaffy)
5634 ("r-biobase" ,r-biobase)
5635 ("r-biocmanager" ,r-biocmanager)
5636 ("r-gcrma" ,r-gcrma)
5637 ("r-multtest" ,r-multtest)
5638 ("r-qvalue" ,r-qvalue)
5640 (home-page "https://www.bioconductor.org/")
5641 (synopsis "Bioconductor web interface")
5643 "This package provides an integrated web interface for doing microarray
5644 analysis using several of the Bioconductor packages. It is intended to be
5645 deployed as a centralized bioinformatics resource for use by many users.
5646 Currently only Affymetrix oligonucleotide analysis is supported.")
5647 (license license:gpl2+)))
5649 (define-public r-zfpkm
5656 (uri (bioconductor-uri "zFPKM" version))
5659 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
5660 (properties `((upstream-name . "zFPKM")))
5661 (build-system r-build-system)
5663 `(("r-checkmate" ,r-checkmate)
5664 ("r-dplyr" ,r-dplyr)
5665 ("r-ggplot2" ,r-ggplot2)
5666 ("r-summarizedexperiment" ,r-summarizedexperiment)
5667 ("r-tidyr" ,r-tidyr)))
5669 `(("r-knitr" ,r-knitr)))
5670 (home-page "https://github.com/ronammar/zFPKM/")
5671 (synopsis "Functions to facilitate zFPKM transformations")
5673 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5674 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5676 (license license:gpl3)))
5678 (define-public r-rbowtie2
5685 (uri (bioconductor-uri "Rbowtie2" version))
5688 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
5689 (properties `((upstream-name . "Rbowtie2")))
5690 (build-system r-build-system)
5694 `(("r-knitr" ,r-knitr)))
5695 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5696 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5698 "This package provides an R wrapper of the popular @code{bowtie2}
5699 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5700 rapid adapter trimming, identification, and read merging.")
5701 (license license:gpl3+)))
5703 (define-public r-progeny
5710 (uri (bioconductor-uri "progeny" version))
5713 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
5714 (build-system r-build-system)
5716 `(("r-biobase" ,r-biobase)
5717 ("r-dplyr" ,r-dplyr)
5718 ("r-ggplot2" ,r-ggplot2)
5719 ("r-ggrepel" ,r-ggrepel)
5720 ("r-gridextra" ,r-gridextra)
5721 ("r-tidyr" ,r-tidyr)))
5723 `(("r-knitr" ,r-knitr)))
5724 (home-page "https://github.com/saezlab/progeny")
5725 (synopsis "Pathway responsive gene activity inference")
5727 "This package provides a function to infer pathway activity from gene
5728 expression. It contains the linear model inferred in the publication
5729 \"Perturbation-response genes reveal signaling footprints in cancer gene
5731 (license license:asl2.0)))
5733 (define-public r-arrmnormalization
5735 (name "r-arrmnormalization")
5740 (uri (bioconductor-uri "ARRmNormalization" version))
5743 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
5745 `((upstream-name . "ARRmNormalization")))
5746 (build-system r-build-system)
5747 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5748 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5749 (synopsis "Adaptive robust regression normalization for methylation data")
5751 "This is a package to perform the @dfn{Adaptive Robust Regression
5752 method} (ARRm) for the normalization of methylation data from the Illumina
5753 Infinium HumanMethylation 450k assay.")
5754 (license license:artistic2.0)))
5756 (define-public r-biocfilecache
5758 (name "r-biocfilecache")
5763 (uri (bioconductor-uri "BiocFileCache" version))
5766 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
5767 (properties `((upstream-name . "BiocFileCache")))
5768 (build-system r-build-system)
5770 `(("r-curl" ,r-curl)
5772 ("r-dbplyr" ,r-dbplyr)
5773 ("r-dplyr" ,r-dplyr)
5775 ("r-rappdirs" ,r-rappdirs)
5776 ("r-rsqlite" ,r-rsqlite)))
5778 `(("r-knitr" ,r-knitr)))
5779 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5780 (synopsis "Manage files across sessions")
5782 "This package creates a persistent on-disk cache of files that the user
5783 can add, update, and retrieve. It is useful for managing resources (such as
5784 custom Txdb objects) that are costly or difficult to create, web resources,
5785 and data files used across sessions.")
5786 (license license:artistic2.0)))
5788 (define-public r-iclusterplus
5790 (name "r-iclusterplus")
5795 (uri (bioconductor-uri "iClusterPlus" version))
5798 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
5799 (properties `((upstream-name . "iClusterPlus")))
5800 (build-system r-build-system)
5801 (native-inputs `(("gfortran" ,gfortran)))
5802 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5803 (synopsis "Integrative clustering of multi-type genomic data")
5805 "iClusterPlus is developed for integrative clustering analysis of
5806 multi-type genomic data and is an enhanced version of iCluster proposed and
5807 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5808 from the experiments where biological samples (e.g. tumor samples) are
5809 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5810 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5811 on. In the iClusterPlus model, binary observations such as somatic mutation
5812 are modeled as Binomial processes; categorical observations such as copy
5813 number states are realizations of Multinomial random variables; counts are
5814 modeled as Poisson random processes; and continuous measures are modeled by
5815 Gaussian distributions.")
5816 (license license:gpl2+)))
5818 (define-public r-rbowtie
5825 (uri (bioconductor-uri "Rbowtie" version))
5828 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
5829 (properties `((upstream-name . "Rbowtie")))
5830 (build-system r-build-system)
5834 `(("r-knitr" ,r-knitr)))
5835 (home-page "https://bioconductor.org/packages/Rbowtie/")
5836 (synopsis "R bowtie wrapper")
5838 "This package provides an R wrapper around the popular bowtie short read
5839 aligner and around SpliceMap, a de novo splice junction discovery and
5841 (license license:artistic2.0)))
5843 (define-public r-sgseq
5850 (uri (bioconductor-uri "SGSeq" version))
5853 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
5854 (properties `((upstream-name . "SGSeq")))
5855 (build-system r-build-system)
5857 `(("r-annotationdbi" ,r-annotationdbi)
5858 ("r-biocgenerics" ,r-biocgenerics)
5859 ("r-biostrings" ,r-biostrings)
5860 ("r-genomeinfodb" ,r-genomeinfodb)
5861 ("r-genomicalignments" ,r-genomicalignments)
5862 ("r-genomicfeatures" ,r-genomicfeatures)
5863 ("r-genomicranges" ,r-genomicranges)
5864 ("r-igraph" ,r-igraph)
5865 ("r-iranges" ,r-iranges)
5866 ("r-rsamtools" ,r-rsamtools)
5867 ("r-rtracklayer" ,r-rtracklayer)
5868 ("r-runit" ,r-runit)
5869 ("r-s4vectors" ,r-s4vectors)
5870 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5872 `(("r-knitr" ,r-knitr)))
5873 (home-page "https://bioconductor.org/packages/SGSeq/")
5874 (synopsis "Splice event prediction and quantification from RNA-seq data")
5876 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5877 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5878 represented as a splice graph, which can be obtained from existing annotation
5879 or predicted from the mapped sequence reads. Splice events are identified
5880 from the graph and are quantified locally using structurally compatible reads
5881 at the start or end of each splice variant. The software includes functions
5882 for splice event prediction, quantification, visualization and
5884 (license license:artistic2.0)))
5886 (define-public r-rhisat2
5893 (uri (bioconductor-uri "Rhisat2" version))
5896 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
5897 (properties `((upstream-name . "Rhisat2")))
5898 (build-system r-build-system)
5901 (modify-phases %standard-phases
5902 (add-after 'unpack 'make-reproducible
5904 (substitute* "src/Makefile"
5905 (("`hostname`") "guix")
5907 ;; Avoid shelling out to "which".
5908 (("^CC =.*") (which "gcc"))
5909 (("^CPP =.*") (which "g++")))
5912 `(("r-genomicfeatures" ,r-genomicfeatures)
5913 ("r-genomicranges" ,r-genomicranges)
5914 ("r-sgseq" ,r-sgseq)))
5916 `(("r-knitr" ,r-knitr)))
5917 (home-page "https://github.com/fmicompbio/Rhisat2")
5918 (synopsis "R Wrapper for HISAT2 sequence aligner")
5920 "This package provides an R interface to the HISAT2 spliced short-read
5921 aligner by Kim et al. (2015). The package contains wrapper functions to
5922 create a genome index and to perform the read alignment to the generated
5924 (license license:gpl3)))
5926 (define-public r-quasr
5933 (uri (bioconductor-uri "QuasR" version))
5936 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
5937 (properties `((upstream-name . "QuasR")))
5938 (build-system r-build-system)
5940 `(("r-annotationdbi" ,r-annotationdbi)
5941 ("r-biobase" ,r-biobase)
5942 ("r-biocgenerics" ,r-biocgenerics)
5943 ("r-biocmanager" ,r-biocmanager)
5944 ("r-biocparallel" ,r-biocparallel)
5945 ("r-biostrings" ,r-biostrings)
5946 ("r-bsgenome" ,r-bsgenome)
5947 ("r-genomeinfodb" ,r-genomeinfodb)
5948 ("r-genomicalignments" ,r-genomicalignments)
5949 ("r-genomicfeatures" ,r-genomicfeatures)
5950 ("r-genomicfiles" ,r-genomicfiles)
5951 ("r-genomicranges" ,r-genomicranges)
5952 ("r-iranges" ,r-iranges)
5953 ("r-rbowtie" ,r-rbowtie)
5954 ("r-rhisat2" ,r-rhisat2)
5955 ("r-rhtslib" ,r-rhtslib)
5956 ("r-rsamtools" ,r-rsamtools)
5957 ("r-rtracklayer" ,r-rtracklayer)
5958 ("r-s4vectors" ,r-s4vectors)
5959 ("r-shortread" ,r-shortread)))
5961 `(("r-knitr" ,r-knitr)))
5962 (home-page "https://bioconductor.org/packages/QuasR/")
5963 (synopsis "Quantify and annotate short reads in R")
5965 "This package provides a framework for the quantification and analysis of
5966 short genomic reads. It covers a complete workflow starting from raw sequence
5967 reads, over creation of alignments and quality control plots, to the
5968 quantification of genomic regions of interest.")
5969 (license license:gpl2)))
5971 (define-public r-rqc
5978 (uri (bioconductor-uri "Rqc" version))
5981 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
5982 (properties `((upstream-name . "Rqc")))
5983 (build-system r-build-system)
5985 `(("r-biocgenerics" ,r-biocgenerics)
5986 ("r-biocparallel" ,r-biocparallel)
5987 ("r-biocstyle" ,r-biocstyle)
5988 ("r-biostrings" ,r-biostrings)
5989 ("r-biovizbase" ,r-biovizbase)
5990 ("r-genomicalignments" ,r-genomicalignments)
5991 ("r-genomicfiles" ,r-genomicfiles)
5992 ("r-ggplot2" ,r-ggplot2)
5993 ("r-iranges" ,r-iranges)
5994 ("r-knitr" ,r-knitr)
5995 ("r-markdown" ,r-markdown)
5998 ("r-reshape2" ,r-reshape2)
5999 ("r-rsamtools" ,r-rsamtools)
6000 ("r-s4vectors" ,r-s4vectors)
6001 ("r-shiny" ,r-shiny)
6002 ("r-shortread" ,r-shortread)))
6004 `(("r-knitr" ,r-knitr)))
6005 (home-page "https://github.com/labbcb/Rqc")
6006 (synopsis "Quality control tool for high-throughput sequencing data")
6008 "Rqc is an optimized tool designed for quality control and assessment of
6009 high-throughput sequencing data. It performs parallel processing of entire
6010 files and produces a report which contains a set of high-resolution
6012 (license license:gpl2+)))
6014 (define-public r-birewire
6021 (uri (bioconductor-uri "BiRewire" version))
6024 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
6025 (properties `((upstream-name . "BiRewire")))
6026 (build-system r-build-system)
6028 `(("r-igraph" ,r-igraph)
6029 ("r-matrix" ,r-matrix)
6031 ("r-tsne" ,r-tsne)))
6032 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
6033 (synopsis "Tools for randomization of bipartite graphs")
6035 "This package provides functions for bipartite network rewiring through N
6036 consecutive switching steps and for the computation of the minimal number of
6037 switching steps to be performed in order to maximise the dissimilarity with
6038 respect to the original network. It includes functions for the analysis of
6039 the introduced randomness across the switching steps and several other
6040 routines to analyse the resulting networks and their natural projections.")
6041 (license license:gpl3)))
6043 (define-public r-birta
6050 (uri (bioconductor-uri "birta" version))
6053 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
6054 (build-system r-build-system)
6056 `(("r-biobase" ,r-biobase)
6057 ("r-limma" ,r-limma)
6058 ("r-mass" ,r-mass)))
6059 (home-page "https://bioconductor.org/packages/birta")
6060 (synopsis "Bayesian inference of regulation of transcriptional activity")
6062 "Expression levels of mRNA molecules are regulated by different
6063 processes, comprising inhibition or activation by transcription factors and
6064 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
6065 Inference of Regulation of Transcriptional Activity) uses the regulatory
6066 networks of transcription factors and miRNAs together with mRNA and miRNA
6067 expression data to predict switches in regulatory activity between two
6068 conditions. A Bayesian network is used to model the regulatory structure and
6069 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
6070 (license license:gpl2+)))
6072 (define-public r-multidataset
6074 (name "r-multidataset")
6079 (uri (bioconductor-uri "MultiDataSet" version))
6082 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
6083 (properties `((upstream-name . "MultiDataSet")))
6084 (build-system r-build-system)
6086 `(("r-biobase" ,r-biobase)
6087 ("r-biocgenerics" ,r-biocgenerics)
6088 ("r-genomicranges" ,r-genomicranges)
6089 ("r-ggplot2" ,r-ggplot2)
6090 ("r-ggrepel" ,r-ggrepel)
6091 ("r-iranges" ,r-iranges)
6092 ("r-limma" ,r-limma)
6093 ("r-qqman" ,r-qqman)
6094 ("r-s4vectors" ,r-s4vectors)
6095 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6097 `(("r-knitr" ,r-knitr)))
6098 (home-page "https://bioconductor.org/packages/MultiDataSet/")
6099 (synopsis "Implementation of MultiDataSet and ResultSet")
6101 "This package provides an implementation of the BRGE's (Bioinformatic
6102 Research Group in Epidemiology from Center for Research in Environmental
6103 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
6104 integrating multi omics data sets and ResultSet is a container for omics
6105 results. This package contains base classes for MEAL and rexposome
6107 (license license:expat)))
6109 (define-public r-ropls
6116 (uri (bioconductor-uri "ropls" version))
6119 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
6120 (build-system r-build-system)
6122 `(("r-biobase" ,r-biobase)
6123 ("r-multidataset" ,r-multidataset)))
6125 `(("r-knitr" ,r-knitr))) ; for vignettes
6126 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
6127 (synopsis "Multivariate analysis and feature selection of omics data")
6129 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
6130 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
6131 regression, classification, and feature selection of omics data where the
6132 number of variables exceeds the number of samples and with multicollinearity
6133 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
6134 separately model the variation correlated (predictive) to the factor of
6135 interest and the uncorrelated (orthogonal) variation. While performing
6136 similarly to PLS, OPLS facilitates interpretation.
6138 This package provides imlementations of PCA, PLS, and OPLS for multivariate
6139 analysis and feature selection of omics data. In addition to scores, loadings
6140 and weights plots, the package provides metrics and graphics to determine the
6141 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
6142 validity of the model by permutation testing, detect outliers, and perform
6143 feature selection (e.g. with Variable Importance in Projection or regression
6145 (license license:cecill)))
6147 (define-public r-biosigner
6149 (name "r-biosigner")
6154 (uri (bioconductor-uri "biosigner" version))
6157 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
6158 (build-system r-build-system)
6160 `(("r-biobase" ,r-biobase)
6161 ("r-e1071" ,r-e1071)
6162 ("r-multidataset" ,r-multidataset)
6163 ("r-randomforest" ,r-randomforest)
6164 ("r-ropls" ,r-ropls)))
6166 `(("r-knitr" ,r-knitr)))
6167 (home-page "https://bioconductor.org/packages/biosigner/")
6168 (synopsis "Signature discovery from omics data")
6170 "Feature selection is critical in omics data analysis to extract
6171 restricted and meaningful molecular signatures from complex and high-dimension
6172 data, and to build robust classifiers. This package implements a method to
6173 assess the relevance of the variables for the prediction performances of the
6174 classifier. The approach can be run in parallel with the PLS-DA, Random
6175 Forest, and SVM binary classifiers. The signatures and the corresponding
6176 'restricted' models are returned, enabling future predictions on new
6178 (license license:cecill)))
6180 (define-public r-annotatr
6187 (uri (bioconductor-uri "annotatr" version))
6190 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
6191 (build-system r-build-system)
6193 `(("r-annotationdbi" ,r-annotationdbi)
6194 ("r-annotationhub" ,r-annotationhub)
6195 ("r-dplyr" ,r-dplyr)
6196 ("r-genomeinfodb" ,r-genomeinfodb)
6197 ("r-genomicfeatures" ,r-genomicfeatures)
6198 ("r-genomicranges" ,r-genomicranges)
6199 ("r-ggplot2" ,r-ggplot2)
6200 ("r-iranges" ,r-iranges)
6201 ("r-readr" ,r-readr)
6202 ("r-regioner" ,r-regioner)
6203 ("r-reshape2" ,r-reshape2)
6204 ("r-rtracklayer" ,r-rtracklayer)
6205 ("r-s4vectors" ,r-s4vectors)))
6207 `(("r-knitr" ,r-knitr)))
6208 (home-page "https://bioconductor.org/packages/annotatr/")
6209 (synopsis "Annotation of genomic regions to genomic annotations")
6211 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6212 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6213 to investigate the intersecting genomic annotations. Such annotations include
6214 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6215 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6216 enhancers. The annotatr package provides an easy way to summarize and
6217 visualize the intersection of genomic sites/regions with genomic
6219 (license license:gpl3)))
6221 (define-public r-rsubread
6228 (uri (bioconductor-uri "Rsubread" version))
6231 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
6232 (properties `((upstream-name . "Rsubread")))
6233 (build-system r-build-system)
6234 (inputs `(("zlib" ,zlib)))
6236 `(("r-matrix" ,r-matrix)))
6237 (home-page "https://bioconductor.org/packages/Rsubread/")
6238 (synopsis "Subread sequence alignment and counting for R")
6240 "This package provides tools for alignment, quantification and analysis
6241 of second and third generation sequencing data. It includes functionality for
6242 read mapping, read counting, SNP calling, structural variant detection and
6243 gene fusion discovery. It can be applied to all major sequencing techologies
6244 and to both short and long sequence reads.")
6245 (license license:gpl3)))
6247 (define-public r-flowutils
6249 (name "r-flowutils")
6254 (uri (bioconductor-uri "flowUtils" version))
6257 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6258 (properties `((upstream-name . "flowUtils")))
6259 (build-system r-build-system)
6261 `(("r-biobase" ,r-biobase)
6262 ("r-corpcor" ,r-corpcor)
6263 ("r-flowcore" ,r-flowcore)
6264 ("r-graph" ,r-graph)
6265 ("r-runit" ,r-runit)
6267 (home-page "https://github.com/jspidlen/flowUtils")
6268 (synopsis "Utilities for flow cytometry")
6270 "This package provides utilities for flow cytometry data.")
6271 (license license:artistic2.0)))
6273 (define-public r-consensusclusterplus
6275 (name "r-consensusclusterplus")
6280 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6283 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6285 `((upstream-name . "ConsensusClusterPlus")))
6286 (build-system r-build-system)
6289 ("r-biobase" ,r-biobase)
6290 ("r-cluster" ,r-cluster)))
6291 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6292 (synopsis "Clustering algorithm")
6294 "This package provides an implementation of an algorithm for determining
6295 cluster count and membership by stability evidence in unsupervised analysis.")
6296 (license license:gpl2)))
6298 (define-public r-cytolib
6305 (uri (bioconductor-uri "cytolib" version))
6308 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
6309 (properties `((upstream-name . "cytolib")))
6310 (build-system r-build-system)
6313 (modify-phases %standard-phases
6314 (add-after 'unpack 'fix-linking
6316 (substitute* "src/Makevars.in"
6317 ;; This is to avoid having a plain directory on the list of
6318 ;; libraries to link.
6319 (("\\(RHDF5_LIBS\\)" match)
6320 (string-append match "/libhdf5.a")))
6323 `(("r-knitr" ,r-knitr)
6324 ("pkg-config" ,pkg-config)))
6328 ("r-rcpparmadillo" ,r-rcpparmadillo)
6329 ("r-rcppparallel" ,r-rcppparallel)
6330 ("r-rhdf5lib" ,r-rhdf5lib)
6331 ("r-rprotobuflib" ,r-rprotobuflib)))
6332 (home-page "https://bioconductor.org/packages/cytolib/")
6333 (synopsis "C++ infrastructure for working with gated cytometry")
6335 "This package provides the core data structure and API to represent and
6336 interact with gated cytometry data.")
6337 (license license:artistic2.0)))
6339 (define-public r-flowcore
6346 (uri (bioconductor-uri "flowCore" version))
6349 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
6350 (properties `((upstream-name . "flowCore")))
6351 (build-system r-build-system)
6354 ("r-biobase" ,r-biobase)
6355 ("r-biocgenerics" ,r-biocgenerics)
6356 ("r-cytolib" ,r-cytolib)
6357 ("r-matrixstats" ,r-matrixstats)
6359 ("r-rcpparmadillo" ,r-rcpparmadillo)
6360 ("r-rprotobuflib" ,r-rprotobuflib)
6361 ("r-s4vectors" ,r-s4vectors)))
6363 `(("r-knitr" ,r-knitr)))
6364 (home-page "https://bioconductor.org/packages/flowCore")
6365 (synopsis "Basic structures for flow cytometry data")
6367 "This package provides S4 data structures and basic functions to deal
6368 with flow cytometry data.")
6369 (license license:artistic2.0)))
6371 (define-public r-flowmeans
6373 (name "r-flowmeans")
6378 (uri (bioconductor-uri "flowMeans" version))
6381 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
6382 (properties `((upstream-name . "flowMeans")))
6383 (build-system r-build-system)
6385 `(("r-biobase" ,r-biobase)
6386 ("r-feature" ,r-feature)
6387 ("r-flowcore" ,r-flowcore)
6388 ("r-rrcov" ,r-rrcov)))
6389 (home-page "https://bioconductor.org/packages/flowMeans")
6390 (synopsis "Non-parametric flow cytometry data gating")
6392 "This package provides tools to identify cell populations in Flow
6393 Cytometry data using non-parametric clustering and segmented-regression-based
6394 change point detection.")
6395 (license license:artistic2.0)))
6397 (define-public r-ncdfflow
6404 (uri (bioconductor-uri "ncdfFlow" version))
6407 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
6408 (properties `((upstream-name . "ncdfFlow")))
6409 (build-system r-build-system)
6412 (modify-phases %standard-phases
6413 (add-after 'unpack 'fix-linking
6415 (substitute* "src/Makevars"
6416 ;; This is to avoid having a plain directory on the list of
6417 ;; libraries to link.
6418 (("\\(RHDF5_LIBS\\)" match)
6419 (string-append match "/libhdf5.a")))
6423 ("r-biobase" ,r-biobase)
6424 ("r-biocgenerics" ,r-biocgenerics)
6425 ("r-flowcore" ,r-flowcore)
6427 ("r-rcpparmadillo" ,r-rcpparmadillo)
6428 ("r-rhdf5lib" ,r-rhdf5lib)
6429 ("r-zlibbioc" ,r-zlibbioc)))
6431 `(("r-knitr" ,r-knitr)))
6432 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6433 (synopsis "HDF5 based storage for flow cytometry data")
6435 "This package provides HDF5 storage based methods and functions for
6436 manipulation of flow cytometry data.")
6437 (license license:artistic2.0)))
6439 (define-public r-ggcyto
6446 (uri (bioconductor-uri "ggcyto" version))
6449 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
6450 (properties `((upstream-name . "ggcyto")))
6451 (build-system r-build-system)
6453 `(("r-data-table" ,r-data-table)
6454 ("r-flowcore" ,r-flowcore)
6455 ("r-flowworkspace" ,r-flowworkspace)
6456 ("r-ggplot2" ,r-ggplot2)
6457 ("r-gridextra" ,r-gridextra)
6458 ("r-hexbin" ,r-hexbin)
6459 ("r-ncdfflow" ,r-ncdfflow)
6461 ("r-rcolorbrewer" ,r-rcolorbrewer)
6462 ("r-rlang" ,r-rlang)
6463 ("r-scales" ,r-scales)))
6465 `(("r-knitr" ,r-knitr)))
6466 (home-page "https://github.com/RGLab/ggcyto/issues")
6467 (synopsis "Visualize Cytometry data with ggplot")
6469 "With the dedicated fortify method implemented for @code{flowSet},
6470 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6471 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6472 and some custom layers also make it easy to add gates and population
6473 statistics to the plot.")
6474 (license license:artistic2.0)))
6476 (define-public r-flowviz
6483 (uri (bioconductor-uri "flowViz" version))
6486 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
6487 (properties `((upstream-name . "flowViz")))
6488 (build-system r-build-system)
6490 `(("r-biobase" ,r-biobase)
6491 ("r-flowcore" ,r-flowcore)
6492 ("r-hexbin" ,r-hexbin)
6493 ("r-idpmisc" ,r-idpmisc)
6494 ("r-kernsmooth" ,r-kernsmooth)
6495 ("r-lattice" ,r-lattice)
6496 ("r-latticeextra" ,r-latticeextra)
6498 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6500 `(("r-knitr" ,r-knitr)))
6501 (home-page "https://bioconductor.org/packages/flowViz/")
6502 (synopsis "Visualization for flow cytometry")
6504 "This package provides visualization tools for flow cytometry data.")
6505 (license license:artistic2.0)))
6507 (define-public r-flowclust
6509 (name "r-flowclust")
6514 (uri (bioconductor-uri "flowClust" version))
6517 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
6518 (properties `((upstream-name . "flowClust")))
6519 (build-system r-build-system)
6522 (list "--configure-args=--enable-bundled-gsl=no")))
6524 `(("r-biobase" ,r-biobase)
6525 ("r-biocgenerics" ,r-biocgenerics)
6527 ("r-corpcor" ,r-corpcor)
6528 ("r-ellipse" ,r-ellipse)
6529 ("r-flowcore" ,r-flowcore)
6530 ("r-flowviz" ,r-flowviz)
6531 ("r-graph" ,r-graph)
6532 ("r-mnormt" ,r-mnormt)))
6536 `(("pkg-config" ,pkg-config)
6537 ("r-knitr" ,r-knitr)))
6538 (home-page "https://bioconductor.org/packages/flowClust")
6539 (synopsis "Clustering for flow cytometry")
6541 "This package provides robust model-based clustering using a t-mixture
6542 model with Box-Cox transformation.")
6543 (license license:artistic2.0)))
6545 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6546 ;; make it use our protobuf package instead.
6547 (define-public r-rprotobuflib
6549 (name "r-rprotobuflib")
6554 (uri (bioconductor-uri "RProtoBufLib" version))
6557 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
6558 (properties `((upstream-name . "RProtoBufLib")))
6559 (build-system r-build-system)
6562 (modify-phases %standard-phases
6563 (add-after 'unpack 'unpack-bundled-sources
6565 (with-directory-excursion "src"
6566 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6569 `(("r-knitr" ,r-knitr)))
6570 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6571 (synopsis "C++ headers and static libraries of Protocol buffers")
6573 "This package provides the headers and static library of Protocol buffers
6574 for other R packages to compile and link against.")
6575 (license license:bsd-3)))
6577 (define-public r-flowworkspace
6579 (name "r-flowworkspace")
6584 (uri (bioconductor-uri "flowWorkspace" version))
6587 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
6588 (properties `((upstream-name . "flowWorkspace")))
6589 (build-system r-build-system)
6592 (modify-phases %standard-phases
6593 (add-after 'unpack 'fix-linking
6595 (substitute* "src/Makevars"
6596 ;; This is to avoid having a plain directory on the list of
6597 ;; libraries to link.
6598 (("\\{h5lib\\}" match)
6599 (string-append match "/libhdf5.a")))
6602 `(("r-aws-s3" ,r-aws-s3)
6603 ("r-aws-signature" ,r-aws-signature)
6605 ("r-biobase" ,r-biobase)
6606 ("r-biocgenerics" ,r-biocgenerics)
6607 ("r-cytolib" ,r-cytolib)
6608 ("r-data-table" ,r-data-table)
6609 ("r-digest" ,r-digest)
6610 ("r-dplyr" ,r-dplyr)
6611 ("r-flowcore" ,r-flowcore)
6612 ("r-ggplot2" ,r-ggplot2)
6613 ("r-graph" ,r-graph)
6614 ("r-lattice" ,r-lattice)
6615 ("r-latticeextra" ,r-latticeextra)
6616 ("r-matrixstats" ,r-matrixstats)
6617 ("r-ncdfflow" ,r-ncdfflow)
6620 ("r-rcpparmadillo" ,r-rcpparmadillo)
6621 ("r-rcppparallel" ,r-rcppparallel)
6622 ("r-rgraphviz" ,r-rgraphviz)
6623 ("r-rhdf5lib" ,r-rhdf5lib)
6624 ("r-rprotobuflib" ,r-rprotobuflib)
6625 ("r-scales" ,r-scales)
6628 `(("r-knitr" ,r-knitr)))
6629 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6630 (synopsis "Infrastructure for working with cytometry data")
6632 "This package is designed to facilitate comparison of automated gating
6633 methods against manual gating done in flowJo. This package allows you to
6634 import basic flowJo workspaces into BioConductor and replicate the gating from
6635 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6636 samples, compensation, and transformation are performed so that the output
6637 matches the flowJo analysis.")
6638 (license license:artistic2.0)))
6640 (define-public r-flowstats
6642 (name "r-flowstats")
6647 (uri (bioconductor-uri "flowStats" version))
6650 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
6651 (properties `((upstream-name . "flowStats")))
6652 (build-system r-build-system)
6654 `(("r-biobase" ,r-biobase)
6655 ("r-biocgenerics" ,r-biocgenerics)
6656 ("r-cluster" ,r-cluster)
6658 ("r-flowcore" ,r-flowcore)
6659 ("r-flowviz" ,r-flowviz)
6660 ("r-flowworkspace" ,r-flowworkspace)
6661 ("r-kernsmooth" ,r-kernsmooth)
6663 ("r-lattice" ,r-lattice)
6665 ("r-ncdfflow" ,r-ncdfflow)
6666 ("r-rcolorbrewer" ,r-rcolorbrewer)
6667 ("r-rrcov" ,r-rrcov)))
6668 (home-page "http://www.github.com/RGLab/flowStats")
6669 (synopsis "Statistical methods for the analysis of flow cytometry data")
6671 "This package provides methods and functionality to analyze flow data
6672 that is beyond the basic infrastructure provided by the @code{flowCore}
6674 (license license:artistic2.0)))
6676 (define-public r-opencyto
6683 (uri (bioconductor-uri "openCyto" version))
6686 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
6687 (properties `((upstream-name . "openCyto")))
6688 (build-system r-build-system)
6690 `(("r-biobase" ,r-biobase)
6691 ("r-biocgenerics" ,r-biocgenerics)
6693 ("r-data-table" ,r-data-table)
6694 ("r-flowclust" ,r-flowclust)
6695 ("r-flowcore" ,r-flowcore)
6696 ("r-flowstats" ,r-flowstats)
6697 ("r-flowviz" ,r-flowviz)
6698 ("r-flowworkspace" ,r-flowworkspace)
6699 ("r-graph" ,r-graph)
6700 ("r-gtools" ,r-gtools)
6702 ("r-lattice" ,r-lattice)
6704 ("r-ncdfflow" ,r-ncdfflow)
6706 ("r-r-utils" ,r-r-utils)
6708 ("r-rcolorbrewer" ,r-rcolorbrewer)
6710 ("r-rrcov" ,r-rrcov)))
6712 `(("r-knitr" ,r-knitr)))
6713 (home-page "https://bioconductor.org/packages/openCyto")
6714 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6716 "This package is designed to facilitate the automated gating methods in a
6717 sequential way to mimic the manual gating strategy.")
6718 (license license:artistic2.0)))
6720 (define-public r-cytoml
6727 (uri (bioconductor-uri "CytoML" version))
6730 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
6731 (properties `((upstream-name . "CytoML")))
6732 (build-system r-build-system)
6735 (modify-phases %standard-phases
6736 (add-after 'unpack 'fix-linking
6738 (substitute* "src/Makevars.in"
6739 ;; This is to avoid having a plain directory on the list of
6740 ;; libraries to link.
6741 (("\\{h5lib\\}" match)
6742 (string-append match "/libhdf5.a")))
6745 `(("libxml2" ,libxml2)))
6747 `(("r-base64enc" ,r-base64enc)
6749 ("r-biobase" ,r-biobase)
6750 ("r-corpcor" ,r-corpcor)
6751 ("r-cytolib" ,r-cytolib)
6752 ("r-data-table" ,r-data-table)
6753 ("r-dplyr" ,r-dplyr)
6754 ("r-flowcore" ,r-flowcore)
6755 ("r-flowworkspace" ,r-flowworkspace)
6756 ("r-ggcyto" ,r-ggcyto)
6757 ("r-graph" ,r-graph)
6758 ("r-jsonlite" ,r-jsonlite)
6759 ("r-lattice" ,r-lattice)
6760 ("r-opencyto" ,r-opencyto)
6764 ("r-rcpparmadillo" ,r-rcpparmadillo)
6765 ("r-rcppparallel" ,r-rcppparallel)
6766 ("r-rgraphviz" ,r-rgraphviz)
6767 ("r-rhdf5lib" ,r-rhdf5lib)
6768 ("r-rprotobuflib" ,r-rprotobuflib)
6769 ("r-runit" ,r-runit)
6770 ("r-tibble" ,r-tibble)
6773 ("r-yaml" ,r-yaml)))
6775 `(("r-knitr" ,r-knitr)))
6776 (home-page "https://github.com/RGLab/CytoML")
6777 (synopsis "GatingML interface for cross platform cytometry data sharing")
6779 "This package provides an interface to implementations of the GatingML2.0
6780 standard to exchange gated cytometry data with other software platforms.")
6781 (license license:artistic2.0)))
6783 (define-public r-flowsom
6790 (uri (bioconductor-uri "FlowSOM" version))
6793 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
6794 (properties `((upstream-name . "FlowSOM")))
6795 (build-system r-build-system)
6797 `(("r-biocgenerics" ,r-biocgenerics)
6798 ("r-consensusclusterplus" ,r-consensusclusterplus)
6799 ("r-cytoml" ,r-cytoml)
6800 ("r-flowcore" ,r-flowcore)
6801 ("r-flowworkspace" ,r-flowworkspace)
6802 ("r-igraph" ,r-igraph)
6803 ("r-rcolorbrewer" ,r-rcolorbrewer)
6806 (home-page "https://bioconductor.org/packages/FlowSOM/")
6807 (synopsis "Visualize and interpret cytometry data")
6809 "FlowSOM offers visualization options for cytometry data, by using
6810 self-organizing map clustering and minimal spanning trees.")
6811 (license license:gpl2+)))
6813 (define-public r-mixomics
6820 (uri (bioconductor-uri "mixOmics" version))
6823 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
6824 (properties `((upstream-name . "mixOmics")))
6825 (build-system r-build-system)
6827 `(("r-corpcor" ,r-corpcor)
6828 ("r-dplyr" ,r-dplyr)
6829 ("r-ellipse" ,r-ellipse)
6830 ("r-ggrepel" ,r-ggrepel)
6831 ("r-ggplot2" ,r-ggplot2)
6832 ("r-gridextra" ,r-gridextra)
6833 ("r-igraph" ,r-igraph)
6834 ("r-lattice" ,r-lattice)
6836 ("r-matrixstats" ,r-matrixstats)
6837 ("r-rarpack" ,r-rarpack)
6838 ("r-rcolorbrewer" ,r-rcolorbrewer)
6839 ("r-reshape2" ,r-reshape2)
6840 ("r-tidyr" ,r-tidyr)))
6842 `(("r-knitr" ,r-knitr)))
6843 (home-page "http://www.mixOmics.org")
6844 (synopsis "Multivariate methods for exploration of biological datasets")
6846 "mixOmics offers a wide range of multivariate methods for the exploration
6847 and integration of biological datasets with a particular focus on variable
6848 selection. The package proposes several sparse multivariate models we have
6849 developed to identify the key variables that are highly correlated, and/or
6850 explain the biological outcome of interest. The data that can be analysed
6851 with mixOmics may come from high throughput sequencing technologies, such as
6852 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6853 also beyond the realm of omics (e.g. spectral imaging). The methods
6854 implemented in mixOmics can also handle missing values without having to
6855 delete entire rows with missing data.")
6856 (license license:gpl2+)))
6858 (define-public r-depecher
6859 (package ;Source/Weave error
6865 (uri (bioconductor-uri "DepecheR" version))
6868 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
6869 (properties `((upstream-name . "DepecheR")))
6870 (build-system r-build-system)
6872 `(("r-beanplot" ,r-beanplot)
6873 ("r-dosnow" ,r-dosnow)
6874 ("r-dplyr" ,r-dplyr)
6876 ("r-foreach" ,r-foreach)
6877 ("r-ggplot2" ,r-ggplot2)
6878 ("r-gmodels" ,r-gmodels)
6879 ("r-gplots" ,r-gplots)
6881 ("r-matrixstats" ,r-matrixstats)
6882 ("r-mixomics" ,r-mixomics)
6883 ("r-moments" ,r-moments)
6885 ("r-rcppeigen" ,r-rcppeigen)
6886 ("r-reshape2" ,r-reshape2)
6887 ("r-robustbase" ,r-robustbase)
6888 ("r-viridis" ,r-viridis)))
6890 `(("r-knitr" ,r-knitr)))
6891 (home-page "https://bioconductor.org/packages/DepecheR/")
6892 (synopsis "Identify traits of clusters in high-dimensional entities")
6894 "The purpose of this package is to identify traits in a dataset that can
6895 separate groups. This is done on two levels. First, clustering is performed,
6896 using an implementation of sparse K-means. Secondly, the generated clusters
6897 are used to predict outcomes of groups of individuals based on their
6898 distribution of observations in the different clusters. As certain clusters
6899 with separating information will be identified, and these clusters are defined
6900 by a sparse number of variables, this method can reduce the complexity of
6901 data, to only emphasize the data that actually matters.")
6902 (license license:expat)))
6904 (define-public r-rcistarget
6906 (name "r-rcistarget")
6911 (uri (bioconductor-uri "RcisTarget" version))
6914 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
6915 (properties `((upstream-name . "RcisTarget")))
6916 (build-system r-build-system)
6918 `(("r-aucell" ,r-aucell)
6919 ("r-biocgenerics" ,r-biocgenerics)
6920 ("r-data-table" ,r-data-table)
6921 ("r-feather" ,r-feather)
6922 ("r-gseabase" ,r-gseabase)
6923 ("r-r-utils" ,r-r-utils)
6924 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6926 `(("r-knitr" ,r-knitr)))
6927 (home-page "https://aertslab.org/#scenic")
6928 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6930 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6931 over-represented on a gene list. In a first step, RcisTarget selects DNA
6932 motifs that are significantly over-represented in the surroundings of the
6933 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6934 achieved by using a database that contains genome-wide cross-species rankings
6935 for each motif. The motifs that are then annotated to TFs and those that have
6936 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6937 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6938 genes in the gene-set that are ranked above the leading edge).")
6939 (license license:gpl3)))
6941 (define-public r-cicero
6948 (uri (bioconductor-uri "cicero" version))
6951 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
6952 (build-system r-build-system)
6954 `(("r-assertthat" ,r-assertthat)
6955 ("r-biobase" ,r-biobase)
6956 ("r-biocgenerics" ,r-biocgenerics)
6957 ("r-data-table" ,r-data-table)
6958 ("r-dplyr" ,r-dplyr)
6960 ("r-genomicranges" ,r-genomicranges)
6961 ("r-ggplot2" ,r-ggplot2)
6962 ("r-glasso" ,r-glasso)
6964 ("r-igraph" ,r-igraph)
6965 ("r-iranges" ,r-iranges)
6966 ("r-matrix" ,r-matrix)
6967 ("r-monocle" ,r-monocle)
6969 ("r-reshape2" ,r-reshape2)
6970 ("r-s4vectors" ,r-s4vectors)
6971 ("r-stringi" ,r-stringi)
6972 ("r-stringr" ,r-stringr)
6973 ("r-tibble" ,r-tibble)
6974 ("r-tidyr" ,r-tidyr)
6975 ("r-vgam" ,r-vgam)))
6977 `(("r-knitr" ,r-knitr)))
6978 (home-page "https://bioconductor.org/packages/cicero/")
6979 (synopsis "Predict cis-co-accessibility from single-cell data")
6981 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6982 accessibility data. It also extends the monocle package for use in chromatin
6983 accessibility data.")
6984 (license license:expat)))
6986 ;; This is the latest commit on the "monocle3" branch.
6987 (define-public r-cicero-monocle3
6988 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6990 (package (inherit r-cicero)
6991 (name "r-cicero-monocle3")
6992 (version (git-version "1.3.2" revision commit))
6997 (url "https://github.com/cole-trapnell-lab/cicero-release")
6999 (file-name (git-file-name name version))
7002 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
7004 `(("r-monocle3" ,r-monocle3)
7005 ,@(alist-delete "r-monocle"
7006 (package-propagated-inputs r-cicero)))))))
7008 (define-public r-circrnaprofiler
7010 (name "r-circrnaprofiler")
7015 (uri (bioconductor-uri "circRNAprofiler" version))
7018 "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
7020 `((upstream-name . "circRNAprofiler")))
7021 (build-system r-build-system)
7023 `(("r-annotationhub" ,r-annotationhub)
7024 ("r-biostrings" ,r-biostrings)
7025 ("r-bsgenome" ,r-bsgenome)
7026 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7027 ("r-deseq2" ,r-deseq2)
7028 ("r-dplyr" ,r-dplyr)
7029 ("r-edger" ,r-edger)
7030 ("r-genomeinfodb" ,r-genomeinfodb)
7031 ("r-genomicranges" ,r-genomicranges)
7032 ("r-ggplot2" ,r-ggplot2)
7033 ("r-gwascat" ,r-gwascat)
7034 ("r-iranges" ,r-iranges)
7035 ("r-magrittr" ,r-magrittr)
7036 ("r-r-utils" ,r-r-utils)
7037 ("r-readr" ,r-readr)
7038 ("r-reshape2" ,r-reshape2)
7039 ("r-rlang" ,r-rlang)
7040 ("r-rtracklayer" ,r-rtracklayer)
7041 ("r-s4vectors" ,r-s4vectors)
7042 ("r-seqinr" ,r-seqinr)
7043 ("r-stringi" ,r-stringi)
7044 ("r-stringr" ,r-stringr)
7045 ("r-universalmotif" ,r-universalmotif)))
7047 `(("r-knitr" ,r-knitr)))
7049 "https://github.com/Aufiero/circRNAprofiler")
7051 "Computational framework for the downstream analysis of circular RNA's")
7053 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
7054 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
7055 framework allows to combine and analyze circRNAs previously detected by
7056 multiple publicly available annotation-based circRNA detection tools. It
7057 covers different aspects of circRNAs analysis from differential expression
7058 analysis, evolutionary conservation, biogenesis to functional analysis.")
7059 (license license:gpl3)))
7061 (define-public r-cistopic
7062 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
7066 (version (git-version "0.2.1" revision commit))
7071 (url "https://github.com/aertslab/cisTopic")
7073 (file-name (git-file-name name version))
7076 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
7077 (build-system r-build-system)
7079 `(("r-aucell" ,r-aucell)
7080 ("r-data-table" ,r-data-table)
7081 ("r-dplyr" ,r-dplyr)
7082 ("r-dosnow" ,r-dosnow)
7084 ("r-feather" ,r-feather)
7085 ("r-fitdistrplus" ,r-fitdistrplus)
7086 ("r-genomicranges" ,r-genomicranges)
7087 ("r-ggplot2" ,r-ggplot2)
7089 ("r-matrix" ,r-matrix)
7091 ("r-rcistarget" ,r-rcistarget)
7092 ("r-rtracklayer" ,r-rtracklayer)
7093 ("r-s4vectors" ,r-s4vectors)))
7094 (home-page "https://github.com/aertslab/cisTopic")
7095 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
7097 "The sparse nature of single cell epigenomics data can be overruled using
7098 probabilistic modelling methods such as @dfn{Latent Dirichlet
7099 Allocation} (LDA). This package allows the probabilistic modelling of
7100 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
7101 includes functionalities to identify cell states based on the contribution of
7102 cisTopics and explore the nature and regulatory proteins driving them.")
7103 (license license:gpl3))))
7105 (define-public r-genie3
7112 (uri (bioconductor-uri "GENIE3" version))
7115 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
7116 (properties `((upstream-name . "GENIE3")))
7117 (build-system r-build-system)
7118 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
7120 `(("r-knitr" ,r-knitr)))
7121 (home-page "https://bioconductor.org/packages/GENIE3")
7122 (synopsis "Gene network inference with ensemble of trees")
7124 "This package implements the GENIE3 algorithm for inferring gene
7125 regulatory networks from expression data.")
7126 (license license:gpl2+)))
7128 (define-public r-roc
7135 (uri (bioconductor-uri "ROC" version))
7138 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
7139 (properties `((upstream-name . "ROC")))
7140 (build-system r-build-system)
7142 `(("r-knitr" ,r-knitr)))
7143 (home-page "https://www.bioconductor.org/packages/ROC/")
7144 (synopsis "Utilities for ROC curves")
7146 "This package provides utilities for @dfn{Receiver Operating
7147 Characteristic} (ROC) curves, with a focus on micro arrays.")
7148 (license license:artistic2.0)))
7150 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
7152 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
7157 (uri (bioconductor-uri
7158 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
7159 version 'annotation))
7162 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
7165 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
7166 (build-system r-build-system)
7167 (propagated-inputs `(("r-minfi" ,r-minfi)))
7169 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
7170 (synopsis "Annotation for Illumina's 450k methylation arrays")
7172 "This package provides manifests and annotation for Illumina's 450k array
7174 (license license:artistic2.0)))
7176 (define-public r-watermelon
7178 (name "r-watermelon")
7183 (uri (bioconductor-uri "wateRmelon" version))
7186 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
7187 (properties `((upstream-name . "wateRmelon")))
7188 (build-system r-build-system)
7190 `(("r-biobase" ,r-biobase)
7191 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
7192 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
7193 ("r-illuminaio" ,r-illuminaio)
7194 ("r-limma" ,r-limma)
7196 ("r-matrixstats" ,r-matrixstats)
7197 ("r-methylumi" ,r-methylumi)
7199 (home-page "https://bioconductor.org/packages/wateRmelon/")
7200 (synopsis "Illumina 450 methylation array normalization and metrics")
7202 "The standard index of DNA methylation (beta) is computed from methylated
7203 and unmethylated signal intensities. Betas calculated from raw signal
7204 intensities perform well, but using 11 methylomic datasets we demonstrate that
7205 quantile normalization methods produce marked improvement. The commonly used
7206 procedure of normalizing betas is inferior to the separate normalization of M
7207 and U, and it is also advantageous to normalize Type I and Type II assays
7208 separately. This package provides 15 flavours of betas and three performance
7209 metrics, with methods for objects produced by the @code{methylumi} and
7210 @code{minfi} packages.")
7211 (license license:gpl3)))
7213 (define-public r-gdsfmt
7220 (uri (bioconductor-uri "gdsfmt" version))
7223 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
7224 (modules '((guix build utils)))
7225 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
7226 ;; them and link with system libraries instead.
7229 (for-each delete-file-recursively
7233 (substitute* "src/Makevars"
7234 (("all: \\$\\(SHLIB\\)") "all:")
7235 (("\\$\\(SHLIB\\): liblzma.a") "")
7236 (("(ZLIB|LZ4)/.*") "")
7237 (("CoreArray/dVLIntGDS.cpp.*")
7238 "CoreArray/dVLIntGDS.cpp")
7239 (("CoreArray/dVLIntGDS.o.*")
7240 "CoreArray/dVLIntGDS.o")
7241 (("PKG_LIBS = ./liblzma.a")
7242 "PKG_LIBS = -llz4"))
7243 (substitute* "src/CoreArray/dStream.h"
7244 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
7245 (string-append "include <" header ">")))
7247 (properties `((upstream-name . "gdsfmt")))
7248 (build-system r-build-system)
7254 `(("r-knitr" ,r-knitr)))
7255 (home-page "http://corearray.sourceforge.net/")
7257 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7259 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7260 Data Structure} (GDS) data files, which are portable across platforms with
7261 hierarchical structure to store multiple scalable array-oriented data sets
7262 with metadata information. It is suited for large-scale datasets, especially
7263 for data which are much larger than the available random-access memory. The
7264 @code{gdsfmt} package offers efficient operations specifically designed for
7265 integers of less than 8 bits, since a diploid genotype, like
7266 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7267 byte. Data compression and decompression are available with relatively
7268 efficient random access. It is also allowed to read a GDS file in parallel
7269 with multiple R processes supported by the package @code{parallel}.")
7270 (license license:lgpl3)))
7272 (define-public r-bigmelon
7279 (uri (bioconductor-uri "bigmelon" version))
7282 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7283 (properties `((upstream-name . "bigmelon")))
7284 (build-system r-build-system)
7286 `(("r-biobase" ,r-biobase)
7287 ("r-biocgenerics" ,r-biocgenerics)
7288 ("r-gdsfmt" ,r-gdsfmt)
7289 ("r-geoquery" ,r-geoquery)
7290 ("r-methylumi" ,r-methylumi)
7291 ("r-minfi" ,r-minfi)
7292 ("r-watermelon" ,r-watermelon)))
7293 (home-page "https://bioconductor.org/packages/bigmelon/")
7294 (synopsis "Illumina methylation array analysis for large experiments")
7296 "This package provides methods for working with Illumina arrays using the
7297 @code{gdsfmt} package.")
7298 (license license:gpl3)))
7300 (define-public r-seqbias
7307 (uri (bioconductor-uri "seqbias" version))
7310 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
7311 (properties `((upstream-name . "seqbias")))
7312 (build-system r-build-system)
7314 `(("r-biostrings" ,r-biostrings)
7315 ("r-genomicranges" ,r-genomicranges)
7316 ("r-rhtslib" ,r-rhtslib)))
7317 (home-page "https://bioconductor.org/packages/seqbias/")
7318 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
7320 "This package implements a model of per-position sequencing bias in
7321 high-throughput sequencing data using a simple Bayesian network, the structure
7322 and parameters of which are trained on a set of aligned reads and a reference
7324 (license license:lgpl3)))
7326 (define-public r-snplocs-hsapiens-dbsnp144-grch37
7328 (name "r-snplocs-hsapiens-dbsnp144-grch37")
7332 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
7333 version 'annotation))
7336 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
7337 (build-system r-build-system)
7338 ;; As this package provides little more than a very large data file it
7339 ;; doesn't make sense to build substitutes.
7340 (arguments `(#:substitutable? #f))
7342 `(("r-biocgenerics" ,r-biocgenerics)
7343 ("r-s4vectors" ,r-s4vectors)
7344 ("r-iranges" ,r-iranges)
7345 ("r-genomeinfodb" ,r-genomeinfodb)
7346 ("r-genomicranges" ,r-genomicranges)
7347 ("r-bsgenome" ,r-bsgenome)
7348 ("r-biostrings" ,r-biostrings)))
7350 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
7351 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
7352 (description "This package provides SNP locations and alleles for Homo
7353 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
7354 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
7355 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
7356 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
7357 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
7358 the mitochondrion chromosome. Therefore, the SNPs in this package can be
7359 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
7360 correct position but this injection will exclude chrM (i.e. nothing will be
7361 injected in that sequence).")
7362 (license license:artistic2.0)))
7364 (define-public r-reqon
7371 (uri (bioconductor-uri "ReQON" version))
7374 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
7375 (properties `((upstream-name . "ReQON")))
7376 (build-system r-build-system)
7378 `(("r-rjava" ,r-rjava)
7379 ("r-rsamtools" ,r-rsamtools)
7380 ("r-seqbias" ,r-seqbias)))
7381 (home-page "https://bioconductor.org/packages/ReQON/")
7382 (synopsis "Recalibrating quality of nucleotides")
7384 "This package provides an implementation of an algorithm for
7385 recalibrating the base quality scores for aligned sequencing data in BAM
7387 (license license:gpl2)))
7389 (define-public r-wavcluster
7391 (name "r-wavcluster")
7396 (uri (bioconductor-uri "wavClusteR" version))
7399 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
7400 (properties `((upstream-name . "wavClusteR")))
7401 (build-system r-build-system)
7403 `(("r-biocgenerics" ,r-biocgenerics)
7404 ("r-biostrings" ,r-biostrings)
7405 ("r-foreach" ,r-foreach)
7406 ("r-genomicfeatures" ,r-genomicfeatures)
7407 ("r-genomicranges" ,r-genomicranges)
7408 ("r-ggplot2" ,r-ggplot2)
7409 ("r-hmisc" ,r-hmisc)
7410 ("r-iranges" ,r-iranges)
7411 ("r-mclust" ,r-mclust)
7412 ("r-rsamtools" ,r-rsamtools)
7413 ("r-rtracklayer" ,r-rtracklayer)
7414 ("r-s4vectors" ,r-s4vectors)
7415 ("r-seqinr" ,r-seqinr)
7416 ("r-stringr" ,r-stringr)))
7418 `(("r-knitr" ,r-knitr)))
7419 (home-page "https://bioconductor.org/packages/wavClusteR/")
7420 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
7422 "This package provides an integrated pipeline for the analysis of
7423 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7424 sequencing errors, SNPs and additional non-experimental sources by a non-
7425 parametric mixture model. The protein binding sites (clusters) are then
7426 resolved at high resolution and cluster statistics are estimated using a
7427 rigorous Bayesian framework. Post-processing of the results, data export for
7428 UCSC genome browser visualization and motif search analysis are provided. In
7429 addition, the package integrates RNA-Seq data to estimate the False
7430 Discovery Rate of cluster detection. Key functions support parallel multicore
7431 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7432 be applied to the analysis of other NGS data obtained from experimental
7433 procedures that induce nucleotide substitutions (e.g. BisSeq).")
7434 (license license:gpl2)))
7436 (define-public r-timeseriesexperiment
7438 (name "r-timeseriesexperiment")
7443 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7446 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
7448 `((upstream-name . "TimeSeriesExperiment")))
7449 (build-system r-build-system)
7451 `(("r-deseq2" ,r-deseq2)
7452 ("r-dplyr" ,r-dplyr)
7453 ("r-dynamictreecut" ,r-dynamictreecut)
7454 ("r-edger" ,r-edger)
7455 ("r-ggplot2" ,r-ggplot2)
7456 ("r-hmisc" ,r-hmisc)
7457 ("r-limma" ,r-limma)
7458 ("r-magrittr" ,r-magrittr)
7459 ("r-proxy" ,r-proxy)
7460 ("r-s4vectors" ,r-s4vectors)
7461 ("r-summarizedexperiment" ,r-summarizedexperiment)
7462 ("r-tibble" ,r-tibble)
7463 ("r-tidyr" ,r-tidyr)
7464 ("r-vegan" ,r-vegan)
7465 ("r-viridis" ,r-viridis)))
7467 `(("r-knitr" ,r-knitr)))
7468 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7469 (synopsis "Analysis for short time-series data")
7471 "This package is a visualization and analysis toolbox for short time
7472 course data which includes dimensionality reduction, clustering, two-sample
7473 differential expression testing and gene ranking techniques. The package also
7474 provides methods for retrieving enriched pathways.")
7475 (license license:lgpl3+)))
7477 (define-public r-variantfiltering
7479 (name "r-variantfiltering")
7484 (uri (bioconductor-uri "VariantFiltering" version))
7487 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
7489 `((upstream-name . "VariantFiltering")))
7490 (build-system r-build-system)
7492 `(("r-annotationdbi" ,r-annotationdbi)
7493 ("r-biobase" ,r-biobase)
7494 ("r-biocgenerics" ,r-biocgenerics)
7495 ("r-biocparallel" ,r-biocparallel)
7496 ("r-biostrings" ,r-biostrings)
7497 ("r-bsgenome" ,r-bsgenome)
7499 ("r-genomeinfodb" ,r-genomeinfodb)
7500 ("r-genomicfeatures" ,r-genomicfeatures)
7501 ("r-genomicranges" ,r-genomicranges)
7502 ("r-genomicscores" ,r-genomicscores)
7503 ("r-graph" ,r-graph)
7505 ("r-iranges" ,r-iranges)
7507 ("r-rsamtools" ,r-rsamtools)
7508 ("r-s4vectors" ,r-s4vectors)
7509 ("r-shiny" ,r-shiny)
7510 ("r-shinyjs" ,r-shinyjs)
7511 ("r-shinythemes" ,r-shinythemes)
7512 ("r-shinytree" ,r-shinytree)
7513 ("r-summarizedexperiment" ,r-summarizedexperiment)
7514 ("r-variantannotation" ,r-variantannotation)
7515 ("r-xvector" ,r-xvector)))
7516 (home-page "https://github.com/rcastelo/VariantFiltering")
7517 (synopsis "Filtering of coding and non-coding genetic variants")
7519 "Filter genetic variants using different criteria such as inheritance
7520 model, amino acid change consequence, minor allele frequencies across human
7521 populations, splice site strength, conservation, etc.")
7522 (license license:artistic2.0)))
7524 (define-public r-genomegraphs
7526 (name "r-genomegraphs")
7531 (uri (bioconductor-uri "GenomeGraphs" version))
7534 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7535 (properties `((upstream-name . "GenomeGraphs")))
7536 (build-system r-build-system)
7538 `(("r-biomart" ,r-biomart)))
7539 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7540 (synopsis "Plotting genomic information from Ensembl")
7542 "Genomic data analyses requires integrated visualization of known genomic
7543 information and new experimental data. GenomeGraphs uses the biomaRt package
7544 to perform live annotation queries to Ensembl and translates this to e.g.
7545 gene/transcript structures in viewports of the grid graphics package. This
7546 results in genomic information plotted together with your data. Another
7547 strength of GenomeGraphs is to plot different data types such as array CGH,
7548 gene expression, sequencing and other data, together in one plot using the
7549 same genome coordinate system.")
7550 (license license:artistic2.0)))
7552 (define-public r-wavetiling
7554 (name "r-wavetiling")
7559 (uri (bioconductor-uri "waveTiling" version))
7562 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7563 (properties `((upstream-name . "waveTiling")))
7564 (build-system r-build-system)
7566 `(("r-affy" ,r-affy)
7567 ("r-biobase" ,r-biobase)
7568 ("r-biostrings" ,r-biostrings)
7569 ("r-genomegraphs" ,r-genomegraphs)
7570 ("r-genomicranges" ,r-genomicranges)
7571 ("r-iranges" ,r-iranges)
7572 ("r-oligo" ,r-oligo)
7573 ("r-oligoclasses" ,r-oligoclasses)
7574 ("r-preprocesscore" ,r-preprocesscore)
7575 ("r-waveslim" ,r-waveslim)))
7576 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7577 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7579 "This package is designed to conduct transcriptome analysis for tiling
7580 arrays based on fast wavelet-based functional models.")
7581 (license license:gpl2+)))
7583 (define-public r-variancepartition
7585 (name "r-variancepartition")
7590 (uri (bioconductor-uri "variancePartition" version))
7593 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
7595 `((upstream-name . "variancePartition")))
7596 (build-system r-build-system)
7598 `(("r-biobase" ,r-biobase)
7599 ("r-biocparallel" ,r-biocparallel)
7600 ("r-colorramps" ,r-colorramps)
7601 ("r-doparallel" ,r-doparallel)
7602 ("r-foreach" ,r-foreach)
7603 ("r-ggplot2" ,r-ggplot2)
7604 ("r-gplots" ,r-gplots)
7605 ("r-iterators" ,r-iterators)
7606 ("r-limma" ,r-limma)
7608 ("r-lmertest" ,r-lmertest)
7610 ("r-pbkrtest" ,r-pbkrtest)
7611 ("r-progress" ,r-progress)
7612 ("r-reshape2" ,r-reshape2)
7613 ("r-scales" ,r-scales)))
7615 `(("r-knitr" ,r-knitr)))
7616 (home-page "https://bioconductor.org/packages/variancePartition/")
7617 (synopsis "Analyze variation in gene expression experiments")
7619 "This is a package providing tools to quantify and interpret multiple
7620 sources of biological and technical variation in gene expression experiments.
7621 It uses a linear mixed model to quantify variation in gene expression
7622 attributable to individual, tissue, time point, or technical variables. The
7623 package includes dream differential expression analysis for repeated
7625 (license license:gpl2+)))
7627 (define-public r-htqpcr
7634 (uri (bioconductor-uri "HTqPCR" version))
7637 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
7638 (properties `((upstream-name . "HTqPCR")))
7639 (build-system r-build-system)
7641 `(("r-affy" ,r-affy)
7642 ("r-biobase" ,r-biobase)
7643 ("r-gplots" ,r-gplots)
7644 ("r-limma" ,r-limma)
7645 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7646 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7647 "groups/bertone/software/HTqPCR.pdf"))
7648 (synopsis "Automated analysis of high-throughput qPCR data")
7650 "Analysis of Ct values from high throughput quantitative real-time
7651 PCR (qPCR) assays across multiple conditions or replicates. The input data
7652 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7653 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7654 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7655 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7656 loading, quality assessment, normalization, visualization and parametric or
7657 non-parametric testing for statistical significance in Ct values between
7658 features (e.g. genes, microRNAs).")
7659 (license license:artistic2.0)))
7661 (define-public r-unifiedwmwqpcr
7663 (name "r-unifiedwmwqpcr")
7668 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7671 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
7673 `((upstream-name . "unifiedWMWqPCR")))
7674 (build-system r-build-system)
7676 `(("r-biocgenerics" ,r-biocgenerics)
7677 ("r-htqpcr" ,r-htqpcr)))
7678 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7679 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7681 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7682 data. This modified test allows for testing differential expression in qPCR
7684 (license license:gpl2+)))
7686 (define-public r-universalmotif
7688 (name "r-universalmotif")
7693 (uri (bioconductor-uri "universalmotif" version))
7696 "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
7698 `((upstream-name . "universalmotif")))
7699 (build-system r-build-system)
7702 (modify-phases %standard-phases
7703 (add-after 'unpack 'fix-reference-to-strip
7705 (substitute* "src/Makevars"
7706 (("/usr/bin/strip") (which "strip"))))))))
7708 `(("r-biocgenerics" ,r-biocgenerics)
7709 ("r-biostrings" ,r-biostrings)
7710 ("r-ggplot2" ,r-ggplot2)
7711 ("r-ggseqlogo" ,r-ggseqlogo)
7712 ("r-iranges" ,r-iranges)
7715 ("r-rcppthread" ,r-rcppthread)
7716 ("r-rdpack" ,r-rdpack)
7717 ("r-rlang" ,r-rlang)
7718 ("r-s4vectors" ,r-s4vectors)
7719 ("r-yaml" ,r-yaml)))
7721 `(("r-knitr" ,r-knitr)))
7723 "https://bioconductor.org/packages/universalmotif/")
7725 "Specific structures importer, modifier, and exporter for R")
7727 "This package allows importing most common @dfn{specific structure}
7728 (motif) types into R for use by functions provided by other Bioconductor
7729 motif-related packages. Motifs can be exported into most major motif formats
7730 from various classes as defined by other Bioconductor packages. A suite of
7731 motif and sequence manipulation and analysis functions are included, including
7732 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
7733 motifs, and others.")
7734 (license license:gpl3)))
7736 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7738 (define-public r-activedriverwgs
7740 (name "r-activedriverwgs")
7745 (uri (cran-uri "ActiveDriverWGS" version))
7748 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
7750 `((upstream-name . "ActiveDriverWGS")))
7751 (build-system r-build-system)
7753 `(("r-biostrings" ,r-biostrings)
7754 ("r-bsgenome" ,r-bsgenome)
7755 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7756 ("r-genomeinfodb" ,r-genomeinfodb)
7757 ("r-genomicranges" ,r-genomicranges)
7758 ("r-iranges" ,r-iranges)
7759 ("r-s4vectors" ,r-s4vectors)))
7761 `(("r-knitr" ,r-knitr)))
7762 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7763 (synopsis "Driver discovery tool for cancer whole genomes")
7765 "This package provides a method for finding an enrichment of cancer
7766 simple somatic mutations (SNVs and Indels) in functional elements across the
7767 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7768 using whole genome sequencing data.")
7769 (license license:gpl3)))
7771 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7773 (define-public r-activepathways
7775 (name "r-activepathways")
7780 (uri (cran-uri "ActivePathways" version))
7783 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7785 `((upstream-name . "ActivePathways")))
7786 (build-system r-build-system)
7788 `(("r-data-table" ,r-data-table)
7789 ("r-ggplot2" ,r-ggplot2)))
7791 `(("r-knitr" ,r-knitr)))
7792 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7793 (synopsis "Multivariate pathway enrichment analysis")
7795 "This package represents an integrative method of analyzing multi omics
7796 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7797 uses a statistical data fusion approach, rationalizes contributing evidence
7798 and highlights associated genes, improving systems-level understanding of
7799 cellular organization in health and disease.")
7800 (license license:gpl3)))
7802 (define-public r-bgmix
7809 (uri (bioconductor-uri "BGmix" version))
7812 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
7813 (properties `((upstream-name . "BGmix")))
7814 (build-system r-build-system)
7816 `(("r-kernsmooth" ,r-kernsmooth)))
7817 (home-page "https://bioconductor.org/packages/BGmix/")
7818 (synopsis "Bayesian models for differential gene expression")
7820 "This package provides fully Bayesian mixture models for differential
7822 (license license:gpl2)))
7824 (define-public r-bgx
7831 (uri (bioconductor-uri "bgx" version))
7834 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
7835 (properties `((upstream-name . "bgx")))
7836 (build-system r-build-system)
7838 `(("r-affy" ,r-affy)
7839 ("r-biobase" ,r-biobase)
7840 ("r-gcrma" ,r-gcrma)
7841 ("r-rcpp" ,r-rcpp)))
7842 (home-page "https://bioconductor.org/packages/bgx/")
7843 (synopsis "Bayesian gene expression")
7845 "This package provides tools for Bayesian integrated analysis of
7846 Affymetrix GeneChips.")
7847 (license license:gpl2)))
7849 (define-public r-bhc
7856 (uri (bioconductor-uri "BHC" version))
7859 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
7860 (properties `((upstream-name . "BHC")))
7861 (build-system r-build-system)
7862 (home-page "https://bioconductor.org/packages/BHC/")
7863 (synopsis "Bayesian hierarchical clustering")
7865 "The method implemented in this package performs bottom-up hierarchical
7866 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7867 in the data and Bayesian model selection to decide at each step which clusters
7868 to merge. This avoids several limitations of traditional methods, for example
7869 how many clusters there should be and how to choose a principled distance
7870 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7871 categories) or time-series data. This version also includes a randomised
7872 algorithm which is more efficient for larger data sets.")
7873 (license license:gpl3)))
7875 (define-public r-bicare
7882 (uri (bioconductor-uri "BicARE" version))
7885 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
7886 (properties `((upstream-name . "BicARE")))
7887 (build-system r-build-system)
7889 `(("r-biobase" ,r-biobase)
7890 ("r-gseabase" ,r-gseabase)
7891 ("r-multtest" ,r-multtest)))
7892 (home-page "http://bioinfo.curie.fr")
7893 (synopsis "Biclustering analysis and results exploration")
7895 "This is a package for biclustering analysis and exploration of
7897 (license license:gpl2)))
7899 (define-public r-bifet
7906 (uri (bioconductor-uri "BiFET" version))
7909 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
7910 (properties `((upstream-name . "BiFET")))
7911 (build-system r-build-system)
7913 `(("r-genomicranges" ,r-genomicranges)
7914 ("r-poibin" ,r-poibin)))
7916 `(("r-knitr" ,r-knitr)))
7917 (home-page "https://bioconductor.org/packages/BiFET")
7918 (synopsis "Bias-free footprint enrichment test")
7920 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7921 over-represented in target regions compared to background regions after
7922 correcting for the bias arising from the imbalance in read counts and GC
7923 contents between the target and background regions. For a given TF k, BiFET
7924 tests the null hypothesis that the target regions have the same probability of
7925 having footprints for the TF k as the background regions while correcting for
7926 the read count and GC content bias.")
7927 (license license:gpl3)))
7929 (define-public r-rsbml
7936 (uri (bioconductor-uri "rsbml" version))
7939 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
7940 (properties `((upstream-name . "rsbml")))
7941 (build-system r-build-system)
7943 `(("libsbml" ,libsbml)
7946 `(("r-biocgenerics" ,r-biocgenerics)
7947 ("r-graph" ,r-graph)))
7949 `(("pkg-config" ,pkg-config)))
7950 (home-page "http://www.sbml.org")
7951 (synopsis "R support for SBML")
7953 "This package provides an R interface to libsbml for SBML parsing,
7954 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7955 (license license:artistic2.0)))
7957 (define-public r-hypergraph
7959 (name "r-hypergraph")
7964 (uri (bioconductor-uri "hypergraph" version))
7967 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
7968 (properties `((upstream-name . "hypergraph")))
7969 (build-system r-build-system)
7971 `(("r-graph" ,r-graph)))
7972 (home-page "https://bioconductor.org/packages/hypergraph")
7973 (synopsis "Hypergraph data structures")
7975 "This package implements some simple capabilities for representing and
7976 manipulating hypergraphs.")
7977 (license license:artistic2.0)))
7979 (define-public r-hyperdraw
7981 (name "r-hyperdraw")
7986 (uri (bioconductor-uri "hyperdraw" version))
7989 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
7990 (properties `((upstream-name . "hyperdraw")))
7991 (build-system r-build-system)
7992 (inputs `(("graphviz" ,graphviz)))
7994 `(("r-graph" ,r-graph)
7995 ("r-hypergraph" ,r-hypergraph)
7996 ("r-rgraphviz" ,r-rgraphviz)))
7997 (home-page "https://bioconductor.org/packages/hyperdraw")
7998 (synopsis "Visualizing hypergraphs")
8000 "This package provides functions for visualizing hypergraphs.")
8001 (license license:gpl2+)))
8003 (define-public r-biggr
8010 (uri (bioconductor-uri "BiGGR" version))
8013 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
8014 (properties `((upstream-name . "BiGGR")))
8015 (build-system r-build-system)
8017 `(("r-hyperdraw" ,r-hyperdraw)
8018 ("r-hypergraph" ,r-hypergraph)
8020 ("r-limsolve" ,r-limsolve)
8021 ("r-rsbml" ,r-rsbml)
8022 ("r-stringr" ,r-stringr)))
8023 (home-page "https://bioconductor.org/packages/BiGGR/")
8024 (synopsis "Constraint based modeling using metabolic reconstruction databases")
8026 "This package provides an interface to simulate metabolic reconstruction
8027 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
8028 reconstruction databases. The package facilitates @dfn{flux balance
8029 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
8030 networks and estimated fluxes can be visualized with hypergraphs.")
8031 (license license:gpl3+)))
8033 (define-public r-bigmemoryextras
8035 (name "r-bigmemoryextras")
8040 (uri (bioconductor-uri "bigmemoryExtras" version))
8043 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
8045 `((upstream-name . "bigmemoryExtras")))
8046 (build-system r-build-system)
8048 `(("r-bigmemory" ,r-bigmemory)))
8050 `(("r-knitr" ,r-knitr)))
8051 (home-page "https://github.com/phaverty/bigmemoryExtras")
8052 (synopsis "Extension of the bigmemory package")
8054 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
8055 safety and convenience features to the @code{filebacked.big.matrix} class from
8056 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
8057 monitoring and gracefully restoring the connection to on-disk data and it also
8058 protects against accidental data modification with a file-system-based
8059 permissions system. Utilities are provided for using @code{BigMatrix}-derived
8060 classes as @code{assayData} matrices within the @code{Biobase} package's
8061 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
8062 related to attaching to, and indexing into, file-backed matrices with
8063 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
8064 a file-backed matrix with factor properties.")
8065 (license license:artistic2.0)))
8067 (define-public r-bigpint
8074 (uri (bioconductor-uri "bigPint" version))
8077 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
8078 (properties `((upstream-name . "bigPint")))
8079 (build-system r-build-system)
8081 `(("r-delayedarray" ,r-delayedarray)
8082 ("r-dplyr" ,r-dplyr)
8083 ("r-ggally" ,r-ggally)
8084 ("r-ggplot2" ,r-ggplot2)
8085 ("r-gridextra" ,r-gridextra)
8086 ("r-hexbin" ,r-hexbin)
8087 ("r-hmisc" ,r-hmisc)
8088 ("r-htmlwidgets" ,r-htmlwidgets)
8089 ("r-plotly" ,r-plotly)
8091 ("r-rcolorbrewer" ,r-rcolorbrewer)
8092 ("r-reshape" ,r-reshape)
8093 ("r-shiny" ,r-shiny)
8094 ("r-shinycssloaders" ,r-shinycssloaders)
8095 ("r-shinydashboard" ,r-shinydashboard)
8096 ("r-stringr" ,r-stringr)
8097 ("r-summarizedexperiment" ,r-summarizedexperiment)
8098 ("r-tidyr" ,r-tidyr)))
8100 `(("r-knitr" ,r-knitr)))
8101 (home-page "https://github.com/lindsayrutter/bigPint")
8102 (synopsis "Big multivariate data plotted interactively")
8104 "This package provides methods for visualizing large multivariate
8105 datasets using static and interactive scatterplot matrices, parallel
8106 coordinate plots, volcano plots, and litre plots. It includes examples for
8107 visualizing RNA-sequencing datasets and differentially expressed genes.")
8108 (license license:gpl3)))
8110 (define-public r-chemminer
8112 (name "r-chemminer")
8117 (uri (bioconductor-uri "ChemmineR" version))
8120 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
8121 (properties `((upstream-name . "ChemmineR")))
8122 (build-system r-build-system)
8124 `(("r-base64enc" ,r-base64enc)
8126 ("r-biocgenerics" ,r-biocgenerics)
8128 ("r-digest" ,r-digest)
8130 ("r-ggplot2" ,r-ggplot2)
8131 ("r-gridextra" ,r-gridextra)
8134 ("r-rcurl" ,r-rcurl)
8135 ("r-rjson" ,r-rjson)
8136 ("r-rsvg" ,r-rsvg)))
8138 `(("r-knitr" ,r-knitr)))
8139 (home-page "https://github.com/girke-lab/ChemmineR")
8140 (synopsis "Cheminformatics toolkit for R")
8142 "ChemmineR is a cheminformatics package for analyzing drug-like small
8143 molecule data in R. It contains functions for efficient processing of large
8144 numbers of molecules, physicochemical/structural property predictions,
8145 structural similarity searching, classification and clustering of compound
8146 libraries with a wide spectrum of algorithms. In addition, it offers
8147 visualization functions for compound clustering results and chemical
8149 (license license:artistic2.0)))
8151 (define-public r-bioassayr
8153 (name "r-bioassayr")
8158 (uri (bioconductor-uri "bioassayR" version))
8161 "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
8162 (properties `((upstream-name . "bioassayR")))
8163 (build-system r-build-system)
8165 `(("r-biocgenerics" ,r-biocgenerics)
8166 ("r-chemminer" ,r-chemminer)
8168 ("r-matrix" ,r-matrix)
8169 ("r-rjson" ,r-rjson)
8170 ("r-rsqlite" ,r-rsqlite)
8173 `(("r-knitr" ,r-knitr)))
8174 (home-page "https://github.com/girke-lab/bioassayR")
8175 (synopsis "Cross-target analysis of small molecule bioactivity")
8177 "bioassayR is a computational tool that enables simultaneous analysis of
8178 thousands of bioassay experiments performed over a diverse set of compounds
8179 and biological targets. Unique features include support for large-scale
8180 cross-target analyses of both public and custom bioassays, generation of
8181 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
8182 preloaded database that provides access to a substantial portion of publicly
8183 available bioactivity data.")
8184 (license license:artistic2.0)))
8186 (define-public r-biobroom
8193 (uri (bioconductor-uri "biobroom" version))
8196 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
8197 (properties `((upstream-name . "biobroom")))
8198 (build-system r-build-system)
8200 `(("r-biobase" ,r-biobase)
8201 ("r-broom" ,r-broom)
8202 ("r-dplyr" ,r-dplyr)
8203 ("r-tidyr" ,r-tidyr)))
8205 `(("r-knitr" ,r-knitr)))
8206 (home-page "https://github.com/StoreyLab/biobroom")
8207 (synopsis "Turn Bioconductor objects into tidy data frames")
8209 "This package contains methods for converting standard objects
8210 constructed by bioinformatics packages, especially those in Bioconductor, and
8211 converting them to @code{tidy} data. It thus serves as a complement to the
8212 @code{broom} package, and follows the same tidy, augment, glance division of
8213 tidying methods. Tidying data makes it easy to recombine, reshape and
8214 visualize bioinformatics analyses.")
8215 ;; Any version of the LGPL.
8216 (license license:lgpl3+)))
8218 (define-public r-graphite
8225 (uri (bioconductor-uri "graphite" version))
8228 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
8229 (properties `((upstream-name . "graphite")))
8230 (build-system r-build-system)
8232 `(("r-annotationdbi" ,r-annotationdbi)
8233 ("r-checkmate" ,r-checkmate)
8234 ("r-graph" ,r-graph)
8236 ("r-rappdirs" ,r-rappdirs)))
8237 (home-page "https://bioconductor.org/packages/graphite/")
8238 (synopsis "Networks from pathway databases")
8240 "Graphite provides networks derived from eight public pathway databases,
8241 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
8243 (license license:agpl3+)))
8245 (define-public r-reactomepa
8247 (name "r-reactomepa")
8252 (uri (bioconductor-uri "ReactomePA" version))
8255 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
8256 (properties `((upstream-name . "ReactomePA")))
8257 (build-system r-build-system)
8259 `(("r-annotationdbi" ,r-annotationdbi)
8261 ("r-enrichplot" ,r-enrichplot)
8262 ("r-ggplot2" ,r-ggplot2)
8263 ("r-ggraph" ,r-ggraph)
8264 ("r-graphite" ,r-graphite)
8265 ("r-igraph" ,r-igraph)
8266 ("r-reactome-db" ,r-reactome-db)))
8268 `(("r-knitr" ,r-knitr)))
8269 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
8270 (synopsis "Reactome pathway analysis")
8272 "This package provides functions for pathway analysis based on the
8273 REACTOME pathway database. It implements enrichment analysis, gene set
8274 enrichment analysis and several functions for visualization.")
8275 (license license:gpl2)))
8277 (define-public r-ebarrays
8284 (uri (bioconductor-uri "EBarrays" version))
8287 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
8288 (properties `((upstream-name . "EBarrays")))
8289 (build-system r-build-system)
8291 `(("r-biobase" ,r-biobase)
8292 ("r-cluster" ,r-cluster)
8293 ("r-lattice" ,r-lattice)))
8294 (home-page "https://bioconductor.org/packages/EBarrays/")
8295 (synopsis "Gene clustering and differential expression identification")
8297 "EBarrays provides tools for the analysis of replicated/unreplicated
8299 (license license:gpl2+)))
8301 (define-public r-bioccasestudies
8303 (name "r-bioccasestudies")
8308 (uri (bioconductor-uri "BiocCaseStudies" version))
8311 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
8313 `((upstream-name . "BiocCaseStudies")))
8314 (build-system r-build-system)
8315 (propagated-inputs `(("r-biobase" ,r-biobase)))
8316 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
8317 (synopsis "Support for the case studies monograph")
8319 "This package provides software and data to support the case studies
8321 (license license:artistic2.0)))
8323 (define-public r-biocgraph
8325 (name "r-biocgraph")
8330 (uri (bioconductor-uri "biocGraph" version))
8333 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
8334 (properties `((upstream-name . "biocGraph")))
8335 (build-system r-build-system)
8337 `(("r-biocgenerics" ,r-biocgenerics)
8338 ("r-geneplotter" ,r-geneplotter)
8339 ("r-graph" ,r-graph)
8340 ("r-rgraphviz" ,r-rgraphviz)))
8341 (home-page "https://bioconductor.org/packages/biocGraph/")
8342 (synopsis "Graph examples and use cases in Bioinformatics")
8344 "This package provides examples and code that make use of the
8345 different graph related packages produced by Bioconductor.")
8346 (license license:artistic2.0)))
8348 (define-public r-experimenthub
8350 (name "r-experimenthub")
8355 (uri (bioconductor-uri "ExperimentHub" version))
8358 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
8359 (properties `((upstream-name . "ExperimentHub")))
8360 (build-system r-build-system)
8362 `(("r-annotationhub" ,r-annotationhub)
8363 ("r-biocfilecache" ,r-biocfilecache)
8364 ("r-biocgenerics" ,r-biocgenerics)
8365 ("r-biocmanager" ,r-biocmanager)
8367 ("r-rappdirs" ,r-rappdirs)
8368 ("r-s4vectors" ,r-s4vectors)))
8370 `(("r-knitr" ,r-knitr)))
8371 (home-page "https://bioconductor.org/packages/ExperimentHub/")
8372 (synopsis "Client to access ExperimentHub resources")
8374 "This package provides a client for the Bioconductor ExperimentHub web
8375 resource. ExperimentHub provides a central location where curated data from
8376 experiments, publications or training courses can be accessed. Each resource
8377 has associated metadata, tags and date of modification. The client creates
8378 and manages a local cache of files retrieved enabling quick and reproducible
8380 (license license:artistic2.0)))
8382 (define-public r-multiassayexperiment
8384 (name "r-multiassayexperiment")
8389 (uri (bioconductor-uri "MultiAssayExperiment" version))
8392 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
8394 `((upstream-name . "MultiAssayExperiment")))
8395 (build-system r-build-system)
8397 `(("r-biobase" ,r-biobase)
8398 ("r-biocgenerics" ,r-biocgenerics)
8399 ("r-genomicranges" ,r-genomicranges)
8400 ("r-iranges" ,r-iranges)
8401 ("r-s4vectors" ,r-s4vectors)
8402 ("r-summarizedexperiment" ,r-summarizedexperiment)
8403 ("r-tidyr" ,r-tidyr)))
8405 `(("r-knitr" ,r-knitr)))
8406 (home-page "https://waldronlab.io/MultiAssayExperiment/")
8407 (synopsis "Integration of multi-omics experiments in Bioconductor")
8409 "MultiAssayExperiment harmonizes data management of multiple assays
8410 performed on an overlapping set of specimens. It provides a familiar
8411 Bioconductor user experience by extending concepts from
8412 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
8413 classes for individual assays, and allowing subsetting by genomic ranges or
8415 (license license:artistic2.0)))
8417 (define-public r-bioconcotk
8419 (name "r-bioconcotk")
8424 (uri (bioconductor-uri "BiocOncoTK" version))
8427 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
8428 (properties `((upstream-name . "BiocOncoTK")))
8429 (build-system r-build-system)
8431 `(("r-bigrquery" ,r-bigrquery)
8433 ("r-complexheatmap" ,r-complexheatmap)
8434 ("r-curatedtcgadata" ,r-curatedtcgadata)
8436 ("r-dplyr" ,r-dplyr)
8438 ("r-genomicfeatures" ,r-genomicfeatures)
8439 ("r-genomicranges" ,r-genomicranges)
8440 ("r-ggplot2" ,r-ggplot2)
8441 ("r-ggpubr" ,r-ggpubr)
8442 ("r-graph" ,r-graph)
8444 ("r-iranges" ,r-iranges)
8445 ("r-magrittr" ,r-magrittr)
8447 ("r-rgraphviz" ,r-rgraphviz)
8448 ("r-rjson" ,r-rjson)
8449 ("r-s4vectors" ,r-s4vectors)
8450 ("r-scales" ,r-scales)
8451 ("r-shiny" ,r-shiny)
8452 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8454 `(("r-knitr" ,r-knitr)))
8455 (home-page "https://bioconductor.org/packages/BiocOncoTK")
8456 (synopsis "Bioconductor components for general cancer genomics")
8458 "The purpose of this package is to provide a central interface to various
8459 tools for genome-scale analysis of cancer studies.")
8460 (license license:artistic2.0)))
8462 (define-public r-biocor
8469 (uri (bioconductor-uri "BioCor" version))
8472 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
8473 (properties `((upstream-name . "BioCor")))
8474 (build-system r-build-system)
8476 `(("r-biocparallel" ,r-biocparallel)
8477 ("r-gseabase" ,r-gseabase)
8478 ("r-matrix" ,r-matrix)))
8480 `(("r-knitr" ,r-knitr)))
8481 (home-page "https://llrs.github.io/BioCor/")
8482 (synopsis "Functional similarities")
8484 "This package provides tools to calculate functional similarities based
8485 on the pathways described on KEGG and REACTOME or in gene sets. These
8486 similarities can be calculated for pathways or gene sets, genes, or clusters
8487 and combined with other similarities. They can be used to improve networks,
8488 gene selection, testing relationships, and so on.")
8489 (license license:expat)))
8491 (define-public r-biocpkgtools
8493 (name "r-biocpkgtools")
8498 (uri (bioconductor-uri "BiocPkgTools" version))
8501 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
8502 (properties `((upstream-name . "BiocPkgTools")))
8503 (build-system r-build-system)
8505 `(("r-biocfilecache" ,r-biocfilecache)
8506 ("r-biocmanager" ,r-biocmanager)
8507 ("r-biocviews" ,r-biocviews)
8508 ("r-dplyr" ,r-dplyr)
8511 ("r-graph" ,r-graph)
8512 ("r-htmltools" ,r-htmltools)
8513 ("r-htmlwidgets" ,r-htmlwidgets)
8515 ("r-igraph" ,r-igraph)
8516 ("r-jsonlite" ,r-jsonlite)
8517 ("r-magrittr" ,r-magrittr)
8518 ("r-rappdirs" ,r-rappdirs)
8520 ("r-readr" ,r-readr)
8522 ("r-rlang" ,r-rlang)
8523 ("r-rvest" ,r-rvest)
8524 ("r-stringr" ,r-stringr)
8525 ("r-tibble" ,r-tibble)
8526 ("r-tidyr" ,r-tidyr)
8527 ("r-tidyselect" ,r-tidyselect)
8528 ("r-xml2" ,r-xml2)))
8530 `(("r-knitr" ,r-knitr)))
8531 (home-page "https://github.com/seandavi/BiocPkgTools")
8532 (synopsis "Collection of tools for learning about Bioconductor packages")
8534 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8535 and build status. This package is a simple collection of functions to access
8536 that metadata from R. The goal is to expose metadata for data mining and
8537 value-added functionality such as package searching, text mining, and
8538 analytics on packages.")
8539 (license license:expat)))
8541 (define-public r-biocset
8548 (uri (bioconductor-uri "BiocSet" version))
8551 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
8552 (properties `((upstream-name . "BiocSet")))
8553 (build-system r-build-system)
8555 `(("r-annotationdbi" ,r-annotationdbi)
8556 ("r-biocio" ,r-biocio)
8557 ("r-dplyr" ,r-dplyr)
8558 ("r-keggrest" ,r-keggrest)
8559 ("r-ontologyindex" ,r-ontologyindex)
8561 ("r-rlang" ,r-rlang)
8562 ("r-s4vectors" ,r-s4vectors)
8563 ("r-tibble" ,r-tibble)
8564 ("r-tidyr" ,r-tidyr)))
8566 `(("r-knitr" ,r-knitr)))
8568 "https://bioconductor.org/packages/BiocSet")
8570 "Representing Different Biological Sets")
8572 "BiocSet displays different biological sets in a triple tibble format.
8573 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
8574 The user has the ability to activate one of these three tibbles to perform
8575 common functions from the @code{dplyr} package. Mapping functionality and
8576 accessing web references for elements/sets are also available in BiocSet.")
8577 (license license:artistic2.0)))
8579 (define-public r-biocworkflowtools
8581 (name "r-biocworkflowtools")
8586 (uri (bioconductor-uri "BiocWorkflowTools" version))
8589 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
8591 `((upstream-name . "BiocWorkflowTools")))
8592 (build-system r-build-system)
8594 `(("r-biocstyle" ,r-biocstyle)
8595 ("r-bookdown" ,r-bookdown)
8596 ("r-git2r" ,r-git2r)
8598 ("r-knitr" ,r-knitr)
8599 ("r-rmarkdown" ,r-rmarkdown)
8600 ("r-rstudioapi" ,r-rstudioapi)
8601 ("r-stringr" ,r-stringr)
8602 ("r-usethis" ,r-usethis)))
8604 `(("r-knitr" ,r-knitr)))
8605 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8606 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8608 "This package provides functions to ease the transition between
8609 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8610 (license license:expat)))
8612 (define-public r-biodist
8619 (uri (bioconductor-uri "bioDist" version))
8622 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
8623 (properties `((upstream-name . "bioDist")))
8624 (build-system r-build-system)
8626 `(("r-biobase" ,r-biobase)
8627 ("r-kernsmooth" ,r-kernsmooth)))
8628 (home-page "https://bioconductor.org/packages/bioDist/")
8629 (synopsis "Different distance measures")
8631 "This package provides a collection of software tools for calculating
8632 distance measures.")
8633 (license license:artistic2.0)))
8635 (define-public r-pcatools
8642 (uri (bioconductor-uri "PCAtools" version))
8645 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
8646 (properties `((upstream-name . "PCAtools")))
8647 (build-system r-build-system)
8649 `(("r-beachmat" ,r-beachmat)
8651 ("r-biocparallel" ,r-biocparallel)
8652 ("r-biocsingular" ,r-biocsingular)
8653 ("r-cowplot" ,r-cowplot)
8654 ("r-delayedarray" ,r-delayedarray)
8655 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8656 ("r-dqrng" ,r-dqrng)
8657 ("r-ggplot2" ,r-ggplot2)
8658 ("r-ggrepel" ,r-ggrepel)
8659 ("r-lattice" ,r-lattice)
8660 ("r-matrix" ,r-matrix)
8662 ("r-reshape2" ,r-reshape2)))
8663 (native-inputs `(("r-knitr" ,r-knitr)))
8664 (home-page "https://github.com/kevinblighe/PCAtools")
8665 (synopsis "PCAtools: everything Principal Components Analysis")
8667 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8668 structure of the data without the need to build any model to represent it.
8669 This \"summary\" of the data is arrived at through a process of reduction that
8670 can transform the large number of variables into a lesser number that are
8671 uncorrelated (i.e. the 'principal components'), while at the same time being
8672 capable of easy interpretation on the original data. PCAtools provides
8673 functions for data exploration via PCA, and allows the user to generate
8674 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8675 can also identify an optimal number of principal components via different
8676 metrics, such as the elbow method and Horn's parallel analysis, which has
8677 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8678 dimensional mass cytometry data.")
8679 (license license:gpl3)))
8681 (define-public r-rgreat
8688 (uri (bioconductor-uri "rGREAT" version))
8691 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
8692 (properties `((upstream-name . "rGREAT")))
8693 (build-system r-build-system)
8695 `(("r-genomicranges" ,r-genomicranges)
8696 ("r-getoptlong" ,r-getoptlong)
8697 ("r-iranges" ,r-iranges)
8698 ("r-rcurl" ,r-rcurl)
8699 ("r-rjson" ,r-rjson)))
8700 (native-inputs `(("r-knitr" ,r-knitr)))
8701 (home-page "https://github.com/jokergoo/rGREAT")
8702 (synopsis "Client for GREAT analysis")
8704 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8705 Tool) analysis automatic by constructing a HTTP POST request according to
8706 user's input and automatically retrieving results from GREAT web server.")
8707 (license license:expat)))
8709 (define-public r-m3c
8716 (uri (bioconductor-uri "M3C" version))
8719 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
8720 (properties `((upstream-name . "M3C")))
8721 (build-system r-build-system)
8723 `(("r-cluster" ,r-cluster)
8724 ("r-corpcor" ,r-corpcor)
8725 ("r-doparallel" ,r-doparallel)
8726 ("r-dosnow" ,r-dosnow)
8727 ("r-foreach" ,r-foreach)
8728 ("r-ggplot2" ,r-ggplot2)
8729 ("r-matrix" ,r-matrix)
8730 ("r-matrixcalc" ,r-matrixcalc)
8731 ("r-rtsne" ,r-rtsne)
8732 ("r-umap" ,r-umap)))
8733 (native-inputs `(("r-knitr" ,r-knitr)))
8734 (home-page "https://bioconductor.org/packages/M3C")
8735 (synopsis "Monte Carlo reference-based consensus clustering")
8737 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8738 simulation to eliminate overestimation of @code{K} and can reject the null
8739 hypothesis @code{K=1}.")
8740 (license license:agpl3+)))
8742 (define-public r-icens
8749 (uri (bioconductor-uri "Icens" version))
8752 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
8753 (properties `((upstream-name . "Icens")))
8754 (build-system r-build-system)
8756 `(("r-survival" ,r-survival)))
8757 (home-page "https://bioconductor.org/packages/Icens")
8758 (synopsis "NPMLE for censored and truncated data")
8760 "This package provides many functions for computing the
8761 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8763 (license license:artistic2.0)))
8765 ;; This is a CRAN package but it depends on r-icens, which is published on
8767 (define-public r-interval
8774 (uri (cran-uri "interval" version))
8777 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
8778 (properties `((upstream-name . "interval")))
8779 (build-system r-build-system)
8781 `(("r-icens" ,r-icens)
8782 ("r-mlecens" ,r-mlecens)
8784 ("r-survival" ,r-survival)))
8785 (home-page "https://cran.r-project.org/web/packages/interval/")
8786 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8788 "This package provides functions to fit nonparametric survival curves,
8789 plot them, and perform logrank or Wilcoxon type tests.")
8790 (license license:gpl2+)))
8792 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8793 ;; Bioconductor package.
8794 (define-public r-fhtest
8801 (uri (cran-uri "FHtest" version))
8804 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
8805 (properties `((upstream-name . "FHtest")))
8806 (build-system r-build-system)
8808 `(("r-interval" ,r-interval)
8809 ("r-kmsurv" ,r-kmsurv)
8812 ("r-survival" ,r-survival)))
8813 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8814 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8816 "This package provides functions to compare two or more survival curves
8820 @item The Fleming-Harrington test for right-censored data based on
8821 permutations and on counting processes.
8822 @item An extension of the Fleming-Harrington test for interval-censored data
8823 based on a permutation distribution and on a score vector distribution.
8826 (license license:gpl2+)))
8828 (define-public r-fourcseq
8835 (uri (bioconductor-uri "FourCSeq" version))
8837 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
8838 (properties `((upstream-name . "FourCSeq")))
8839 (build-system r-build-system)
8841 `(("r-biobase" ,r-biobase)
8842 ("r-biostrings" ,r-biostrings)
8843 ("r-deseq2" ,r-deseq2)
8845 ("r-genomicalignments" ,r-genomicalignments)
8846 ("r-genomicranges" ,r-genomicranges)
8847 ("r-ggbio" ,r-ggbio)
8848 ("r-ggplot2" ,r-ggplot2)
8849 ("r-gtools" ,r-gtools)
8851 ("r-matrix" ,r-matrix)
8852 ("r-reshape2" ,r-reshape2)
8853 ("r-rsamtools" ,r-rsamtools)
8854 ("r-rtracklayer" ,r-rtracklayer)
8855 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8857 `(("r-knitr" ,r-knitr)))
8859 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8860 (synopsis "Analysis of multiplexed 4C sequencing data")
8862 "This package is an R package dedicated to the analysis of (multiplexed)
8863 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8864 interactions between DNA elements and identify differential interactions
8865 between conditions. The statistical analysis in R starts with individual bam
8866 files for each sample as inputs. To obtain these files, the package contains
8867 a Python script to demultiplex libraries and trim off primer sequences. With
8868 a standard alignment software the required bam files can be then be
8870 (license license:gpl3+)))
8872 (define-public r-preprocesscore
8874 (name "r-preprocesscore")
8879 (uri (bioconductor-uri "preprocessCore" version))
8882 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
8884 `((upstream-name . "preprocessCore")))
8885 (build-system r-build-system)
8886 (home-page "https://github.com/bmbolstad/preprocessCore")
8887 (synopsis "Collection of pre-processing functions")
8889 "This package provides a library of core pre-processing and normalization
8891 (license license:lgpl2.0+)))
8893 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
8894 ;; Bioconductor package.
8895 (define-public r-wgcna
8902 (uri (cran-uri "WGCNA" version))
8905 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
8906 (properties `((upstream-name . "WGCNA")))
8907 (build-system r-build-system)
8909 `(("r-annotationdbi" ,r-annotationdbi)
8910 ("r-doparallel" ,r-doparallel)
8911 ("r-dynamictreecut" ,r-dynamictreecut)
8912 ("r-fastcluster" ,r-fastcluster)
8913 ("r-foreach" ,r-foreach)
8914 ("r-go-db" ,r-go-db)
8915 ("r-hmisc" ,r-hmisc)
8916 ("r-impute" ,r-impute)
8918 ("r-survival" ,r-survival)
8919 ("r-matrixstats" ,r-matrixstats)
8920 ("r-preprocesscore" ,r-preprocesscore)))
8922 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8923 (synopsis "Weighted correlation network analysis")
8925 "This package provides functions necessary to perform Weighted
8926 Correlation Network Analysis on high-dimensional data. It includes functions
8927 for rudimentary data cleaning, construction and summarization of correlation
8928 networks, module identification and functions for relating both variables and
8929 modules to sample traits. It also includes a number of utility functions for
8930 data manipulation and visualization.")
8931 (license license:gpl2+)))
8933 (define-public r-rgraphviz
8935 (name "r-rgraphviz")
8940 (uri (bioconductor-uri "Rgraphviz" version))
8943 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
8944 (properties `((upstream-name . "Rgraphviz")))
8945 (build-system r-build-system)
8948 (modify-phases %standard-phases
8949 (add-after 'unpack 'make-reproducible
8951 ;; The replacement value is taken from src/graphviz/builddate.h
8952 (substitute* "src/graphviz/configure"
8953 (("VERSION_DATE=.*")
8954 "VERSION_DATE=20200427.2341\n"))
8956 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8957 ;; graphviz. It does not build with the latest version of graphviz, so
8958 ;; we do not add graphviz to the inputs.
8959 (inputs `(("zlib" ,zlib)))
8961 `(("r-graph" ,r-graph)))
8963 `(("pkg-config" ,pkg-config)))
8964 (home-page "https://bioconductor.org/packages/Rgraphviz")
8965 (synopsis "Plotting capabilities for R graph objects")
8967 "This package interfaces R with the graphviz library for plotting R graph
8968 objects from the @code{graph} package.")
8969 (license license:epl1.0)))
8971 (define-public r-fithic
8977 (uri (bioconductor-uri "FitHiC" version))
8980 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
8981 (properties `((upstream-name . "FitHiC")))
8982 (build-system r-build-system)
8984 `(("r-data-table" ,r-data-table)
8985 ("r-fdrtool" ,r-fdrtool)
8986 ("r-rcpp" ,r-rcpp)))
8988 `(("r-knitr" ,r-knitr)))
8989 (home-page "https://bioconductor.org/packages/FitHiC")
8990 (synopsis "Confidence estimation for intra-chromosomal contact maps")
8992 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
8993 intra-chromosomal contact maps produced by genome-wide genome architecture
8994 assays such as Hi-C.")
8995 (license license:gpl2+)))
8997 (define-public r-hitc
9003 (uri (bioconductor-uri "HiTC" version))
9006 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
9007 (properties `((upstream-name . "HiTC")))
9008 (build-system r-build-system)
9010 `(("r-biostrings" ,r-biostrings)
9011 ("r-genomeinfodb" ,r-genomeinfodb)
9012 ("r-genomicranges" ,r-genomicranges)
9013 ("r-iranges" ,r-iranges)
9014 ("r-matrix" ,r-matrix)
9015 ("r-rcolorbrewer" ,r-rcolorbrewer)
9016 ("r-rtracklayer" ,r-rtracklayer)))
9017 (home-page "https://bioconductor.org/packages/HiTC")
9018 (synopsis "High throughput chromosome conformation capture analysis")
9020 "The HiTC package was developed to explore high-throughput \"C\" data
9021 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
9022 quality controls, normalization, visualization, and further analysis are also
9024 (license license:artistic2.0)))
9026 (define-public r-hdf5array
9028 (name "r-hdf5array")
9033 (uri (bioconductor-uri "HDF5Array" version))
9036 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
9037 (properties `((upstream-name . "HDF5Array")))
9038 (build-system r-build-system)
9041 (modify-phases %standard-phases
9042 (add-after 'unpack 'fix-linking
9044 (substitute* "src/Makevars"
9045 ;; This is to avoid having a plain directory on the list of
9046 ;; libraries to link.
9047 (("\\(RHDF5LIB_LIBS\\)" match)
9048 (string-append match "/libhdf5.a")))
9053 `(("r-biocgenerics" ,r-biocgenerics)
9054 ("r-delayedarray" ,r-delayedarray)
9055 ("r-iranges" ,r-iranges)
9056 ("r-matrix" ,r-matrix)
9057 ("r-rhdf5" ,r-rhdf5)
9058 ("r-rhdf5lib" ,r-rhdf5lib)
9059 ("r-s4vectors" ,r-s4vectors)))
9060 (home-page "https://bioconductor.org/packages/HDF5Array")
9061 (synopsis "HDF5 back end for DelayedArray objects")
9062 (description "This package provides an array-like container for convenient
9063 access and manipulation of HDF5 datasets. It supports delayed operations and
9065 (license license:artistic2.0)))
9067 (define-public r-rhdf5lib
9074 (uri (bioconductor-uri "Rhdf5lib" version))
9077 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
9078 (modules '((guix build utils)))
9081 ;; Delete bundled binaries
9082 (delete-file-recursively "src/wininclude/")
9083 (delete-file-recursively "src/winlib-4.9.3/")
9084 (delete-file-recursively "src/winlib-8.3.0/")
9085 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
9087 (properties `((upstream-name . "Rhdf5lib")))
9088 (build-system r-build-system)
9091 (modify-phases %standard-phases
9092 (add-after 'unpack 'do-not-use-bundled-hdf5
9093 (lambda* (#:key inputs #:allow-other-keys)
9094 (for-each delete-file '("configure" "configure.ac"))
9095 ;; Do not make other packages link with the proprietary libsz.
9096 (substitute* "R/zzz.R"
9097 ((" \"%s/libsz.a\"") ""))
9098 (with-directory-excursion "src"
9099 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
9100 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
9102 ;; Remove timestamp and host system information to make
9103 ;; the build reproducible.
9104 (substitute* "hdf5/src/libhdf5.settings.in"
9105 (("Configured on: @CONFIG_DATE@")
9106 "Configured on: Guix")
9107 (("Uname information:.*")
9108 "Uname information: Linux\n")
9109 ;; Remove unnecessary store reference.
9111 "C Compiler: GCC\n"))
9112 (rename-file "hdf5/src/libhdf5.settings.in"
9113 "hdf5/src/libhdf5.settings")
9114 (rename-file "Makevars.in" "Makevars")
9115 (substitute* "Makevars"
9116 (("@ZLIB_LIB@") "-lz")
9117 (("@ZLIB_INCLUDE@") "")
9118 (("HDF5_CXX_LIB=.*")
9119 (string-append "HDF5_CXX_LIB="
9120 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
9122 (string-append "HDF5_LIB="
9123 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
9124 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
9125 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
9126 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
9127 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
9129 (string-append "HDF5_HL_LIB="
9130 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
9131 (("HDF5_HL_CXX_LIB=.*")
9132 (string-append "HDF5_HL_CXX_LIB="
9133 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
9134 ;; szip is non-free software
9135 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
9136 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
9141 `(("hdf5" ,hdf5-1.10)))
9143 `(("hdf5-source" ,(package-source hdf5-1.10))
9144 ("r-knitr" ,r-knitr)))
9145 (home-page "https://bioconductor.org/packages/Rhdf5lib")
9146 (synopsis "HDF5 library as an R package")
9147 (description "This package provides C and C++ HDF5 libraries for use in R
9149 (license license:artistic2.0)))
9151 (define-public r-beachmat
9158 (uri (bioconductor-uri "beachmat" version))
9161 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
9162 (build-system r-build-system)
9164 `(("r-biocgenerics" ,r-biocgenerics)
9165 ("r-delayedarray" ,r-delayedarray)
9166 ("r-matrix" ,r-matrix)))
9168 `(("r-knitr" ,r-knitr)))
9169 (home-page "https://bioconductor.org/packages/beachmat")
9170 (synopsis "Compiling Bioconductor to handle each matrix type")
9171 (description "This package provides a consistent C++ class interface for a
9172 variety of commonly used matrix types, including sparse and HDF5-backed
9174 (license license:gpl3)))
9176 ;; This package includes files that have been taken from kentutils. Some
9177 ;; parts of kentutils are not released under a free license, but this package
9178 ;; only uses files that are also found in the free parts of kentutils.
9179 (define-public r-cner
9186 (uri (bioconductor-uri "CNEr" version))
9188 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
9189 (properties `((upstream-name . "CNEr")))
9190 (build-system r-build-system)
9191 (inputs `(("zlib" ,zlib)))
9193 `(("r-annotate" ,r-annotate)
9194 ("r-biocgenerics" ,r-biocgenerics)
9195 ("r-biostrings" ,r-biostrings)
9197 ("r-genomeinfodb" ,r-genomeinfodb)
9198 ("r-genomicalignments" ,r-genomicalignments)
9199 ("r-genomicranges" ,r-genomicranges)
9200 ("r-ggplot2" ,r-ggplot2)
9201 ("r-go-db" ,r-go-db)
9202 ("r-iranges" ,r-iranges)
9203 ("r-keggrest" ,r-keggrest)
9204 ("r-powerlaw" ,r-powerlaw)
9205 ("r-r-utils" ,r-r-utils)
9206 ("r-readr" ,r-readr)
9207 ("r-reshape2" ,r-reshape2)
9208 ("r-rsqlite" ,r-rsqlite)
9209 ("r-rtracklayer" ,r-rtracklayer)
9210 ("r-s4vectors" ,r-s4vectors)
9211 ("r-xvector" ,r-xvector)))
9213 `(("r-knitr" ,r-knitr)))
9214 (home-page "https://github.com/ge11232002/CNEr")
9215 (synopsis "CNE Detection and Visualization")
9217 "This package provides tools for large-scale identification and
9218 advanced visualization of sets of conserved noncoding elements.")
9219 ;; For all files in src/ucsc "license is hereby granted for all use -
9220 ;; public, private or commercial"; this includes those files that don't
9221 ;; have a license header, because they are included in the free parts of
9222 ;; the kentutils package.
9223 (license (list license:gpl2
9224 (license:non-copyleft
9225 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
9227 (define-public r-tfbstools
9229 (name "r-tfbstools")
9234 (uri (bioconductor-uri "TFBSTools" version))
9237 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
9238 (properties `((upstream-name . "TFBSTools")))
9239 (build-system r-build-system)
9241 `(("r-biobase" ,r-biobase)
9242 ("r-biocgenerics" ,r-biocgenerics)
9243 ("r-biocparallel" ,r-biocparallel)
9244 ("r-biostrings" ,r-biostrings)
9245 ("r-bsgenome" ,r-bsgenome)
9246 ("r-catools" ,r-catools)
9249 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
9250 ("r-genomeinfodb" ,r-genomeinfodb)
9251 ("r-genomicranges" ,r-genomicranges)
9252 ("r-gtools" ,r-gtools)
9253 ("r-iranges" ,r-iranges)
9254 ("r-rsqlite" ,r-rsqlite)
9255 ("r-rtracklayer" ,r-rtracklayer)
9256 ("r-s4vectors" ,r-s4vectors)
9257 ("r-seqlogo" ,r-seqlogo)
9258 ("r-tfmpvalue" ,r-tfmpvalue)
9260 ("r-xvector" ,r-xvector)))
9261 (native-inputs `(("r-knitr" ,r-knitr)))
9262 (home-page "https://github.com/ge11232002/TFBSTools")
9263 (synopsis "Transcription factor binding site (TFBS) analysis")
9265 "TFBSTools is a package for the analysis and manipulation of
9266 transcription factor binding sites. It includes matrices conversion
9267 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
9268 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
9269 scan putative TFBS from sequence/alignment, query JASPAR database and
9270 provides a wrapper of de novo motif discovery software.")
9271 (license license:gpl2)))
9273 (define-public r-motifmatchr
9275 (name "r-motifmatchr")
9280 (uri (bioconductor-uri "motifmatchr" version))
9283 "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
9284 (properties `((upstream-name . "motifmatchr")))
9285 (build-system r-build-system)
9287 `(("r-biostrings" ,r-biostrings)
9288 ("r-bsgenome" ,r-bsgenome)
9289 ("r-genomeinfodb" ,r-genomeinfodb)
9290 ("r-genomicranges" ,r-genomicranges)
9291 ("r-iranges" ,r-iranges)
9292 ("r-matrix" ,r-matrix)
9294 ("r-rcpparmadillo" ,r-rcpparmadillo)
9295 ("r-rsamtools" ,r-rsamtools)
9296 ("r-s4vectors" ,r-s4vectors)
9297 ("r-summarizedexperiment" ,r-summarizedexperiment)
9298 ("r-tfbstools" ,r-tfbstools)))
9299 (native-inputs `(("r-knitr" ,r-knitr)))
9300 (home-page "https://bioconductor.org/packages/motifmatchr")
9301 (synopsis "Fast motif matching in R")
9303 "Quickly find motif matches for many motifs and many sequences.
9304 This package wraps C++ code from the MOODS motif calling library.")
9305 (license license:gpl3)))
9307 (define-public r-chromvar
9314 (uri (bioconductor-uri "chromVAR" version))
9316 (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
9317 (properties `((upstream-name . "chromVAR")))
9318 (build-system r-build-system)
9320 `(("r-biocgenerics" ,r-biocgenerics)
9321 ("r-biocparallel" ,r-biocparallel)
9322 ("r-biostrings" ,r-biostrings)
9323 ("r-bsgenome" ,r-bsgenome)
9325 ("r-genomeinfodb" ,r-genomeinfodb)
9326 ("r-genomicranges" ,r-genomicranges)
9327 ("r-ggplot2" ,r-ggplot2)
9328 ("r-iranges" ,r-iranges)
9329 ("r-matrix" ,r-matrix)
9330 ("r-miniui" ,r-miniui)
9331 ("r-nabor" ,r-nabor)
9332 ("r-plotly" ,r-plotly)
9333 ("r-rcolorbrewer" ,r-rcolorbrewer)
9335 ("r-rcpparmadillo" ,r-rcpparmadillo)
9336 ("r-rsamtools" ,r-rsamtools)
9337 ("r-rtsne" ,r-rtsne)
9338 ("r-s4vectors" ,r-s4vectors)
9339 ("r-shiny" ,r-shiny)
9340 ("r-summarizedexperiment" ,r-summarizedexperiment)
9341 ("r-tfbstools" ,r-tfbstools)))
9342 (native-inputs `(("r-knitr" ,r-knitr)))
9343 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
9344 (synopsis "Determine chromatin variation across regions")
9346 "This package @code{r-chromvar} determines variation in chromatin
9347 accessibility across sets of annotations or peaks. @code{r-chromvar} is
9348 designed primarily for single-cell or sparse chromatin accessibility data like
9349 single cell assay for transposase-accessible chromatin using
9350 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
9351 sequence (@code{DNAse-seq}) experiments.")
9352 (license license:expat)))
9354 (define-public r-singlecellexperiment
9356 (name "r-singlecellexperiment")
9361 (uri (bioconductor-uri "SingleCellExperiment" version))
9364 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
9366 `((upstream-name . "SingleCellExperiment")))
9367 (build-system r-build-system)
9369 `(("r-biocgenerics" ,r-biocgenerics)
9370 ("r-s4vectors" ,r-s4vectors)
9371 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9373 `(("r-knitr" ,r-knitr)))
9374 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
9375 (synopsis "S4 classes for single cell data")
9376 (description "This package defines an S4 class for storing data from
9377 single-cell experiments. This includes specialized methods to store and
9378 retrieve spike-in information, dimensionality reduction coordinates and size
9379 factors for each cell, along with the usual metadata for genes and
9381 (license license:gpl3)))
9383 (define-public r-scuttle
9390 (uri (bioconductor-uri "scuttle" version))
9393 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
9394 (properties `((upstream-name . "scuttle")))
9395 (build-system r-build-system)
9397 `(("r-beachmat" ,r-beachmat)
9398 ("r-biocgenerics" ,r-biocgenerics)
9399 ("r-biocparallel" ,r-biocparallel)
9400 ("r-delayedarray" ,r-delayedarray)
9401 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9402 ("r-genomicranges" ,r-genomicranges)
9403 ("r-matrix" ,r-matrix)
9405 ("r-s4vectors" ,r-s4vectors)
9406 ("r-singlecellexperiment" ,r-singlecellexperiment)
9407 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9408 (native-inputs `(("r-knitr" ,r-knitr)))
9409 (home-page "https://bioconductor.org/packages/scuttle")
9410 (synopsis "Single-cell RNA-Seq analysis utilities")
9412 "This package provides basic utility functions for performing single-cell
9413 analyses, focusing on simple normalization, quality control and data
9414 transformations. It also provides some helper functions to assist development
9415 of other packages.")
9416 (license license:gpl3)))
9418 (define-public r-scater
9424 (uri (bioconductor-uri "scater" version))
9427 "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535"))))
9428 (build-system r-build-system)
9430 `(("r-biocgenerics" ,r-biocgenerics)
9431 ("r-biocneighbors" ,r-biocneighbors)
9432 ("r-biocparallel" ,r-biocparallel)
9433 ("r-biocsingular" ,r-biocsingular)
9434 ("r-delayedarray" ,r-delayedarray)
9435 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9436 ("r-ggbeeswarm" ,r-ggbeeswarm)
9437 ("r-ggplot2" ,r-ggplot2)
9438 ("r-gridextra" ,r-gridextra)
9439 ("r-matrix" ,r-matrix)
9440 ("r-rlang" ,r-rlang)
9441 ("r-s4vectors" ,r-s4vectors)
9442 ("r-scuttle" ,r-scuttle)
9443 ("r-singlecellexperiment" ,r-singlecellexperiment)
9444 ("r-summarizedexperiment" ,r-summarizedexperiment)
9445 ("r-viridis" ,r-viridis)))
9447 `(("r-knitr" ,r-knitr)))
9448 (home-page "https://github.com/davismcc/scater")
9449 (synopsis "Single-cell analysis toolkit for gene expression data in R")
9450 (description "This package provides a collection of tools for doing
9451 various analyses of single-cell RNA-seq gene expression data, with a focus on
9453 (license license:gpl2+)))
9455 (define-public r-scran
9462 (uri (bioconductor-uri "scran" version))
9465 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
9466 (build-system r-build-system)
9468 `(("r-beachmat" ,r-beachmat)
9470 ("r-biocgenerics" ,r-biocgenerics)
9471 ("r-biocneighbors" ,r-biocneighbors)
9472 ("r-biocparallel" ,r-biocparallel)
9473 ("r-biocsingular" ,r-biocsingular)
9474 ("r-bluster" ,r-bluster)
9475 ("r-delayedarray" ,r-delayedarray)
9476 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9477 ("r-dqrng" ,r-dqrng)
9478 ("r-edger" ,r-edger)
9479 ("r-igraph" ,r-igraph)
9480 ("r-limma" ,r-limma)
9481 ("r-matrix" ,r-matrix)
9483 ("r-s4vectors" ,r-s4vectors)
9484 ("r-scuttle" ,r-scuttle)
9485 ("r-singlecellexperiment" ,r-singlecellexperiment)
9486 ("r-statmod" ,r-statmod)
9487 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9489 `(("r-knitr" ,r-knitr)))
9490 (home-page "https://bioconductor.org/packages/scran")
9491 (synopsis "Methods for single-cell RNA-Seq data analysis")
9492 (description "This package implements a variety of low-level analyses of
9493 single-cell RNA-seq data. Methods are provided for normalization of
9494 cell-specific biases, assignment of cell cycle phase, and detection of highly
9495 variable and significantly correlated genes.")
9496 (license license:gpl3)))
9498 (define-public r-sparsematrixstats
9500 (name "r-sparsematrixstats")
9505 (uri (bioconductor-uri "sparseMatrixStats" version))
9508 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
9510 `((upstream-name . "sparseMatrixStats")))
9511 (build-system r-build-system)
9513 `(("r-matrix" ,r-matrix)
9514 ("r-matrixgenerics" ,r-matrixgenerics)
9515 ("r-matrixstats" ,r-matrixstats)
9516 ("r-rcpp" ,r-rcpp)))
9517 (native-inputs `(("r-knitr" ,r-knitr)))
9518 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
9519 (synopsis "Summary statistics for rows and columns of sparse matrices")
9521 "This package provides high performance functions for row and column
9522 operations on sparse matrices. Currently, the optimizations are limited to
9523 data in the column sparse format.")
9524 (license license:expat)))
9526 (define-public r-delayedmatrixstats
9528 (name "r-delayedmatrixstats")
9533 (uri (bioconductor-uri "DelayedMatrixStats" version))
9536 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
9538 `((upstream-name . "DelayedMatrixStats")))
9539 (build-system r-build-system)
9541 `(("r-biocparallel" ,r-biocparallel)
9542 ("r-delayedarray" ,r-delayedarray)
9543 ("r-hdf5array" ,r-hdf5array)
9544 ("r-iranges" ,r-iranges)
9545 ("r-matrix" ,r-matrix)
9546 ("r-matrixgenerics" ,r-matrixgenerics)
9547 ("r-matrixstats" ,r-matrixstats)
9548 ("r-s4vectors" ,r-s4vectors)
9549 ("r-sparsematrixstats" ,r-sparsematrixstats)))
9551 `(("r-knitr" ,r-knitr)))
9552 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
9553 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
9555 "This package provides a port of the @code{matrixStats} API for use with
9556 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
9557 contains high-performing functions operating on rows and columns of
9558 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
9559 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
9560 are optimized per data type and for subsetted calculations such that both
9561 memory usage and processing time is minimized.")
9562 (license license:expat)))
9564 (define-public r-mscoreutils
9566 (name "r-mscoreutils")
9571 (uri (bioconductor-uri "MsCoreUtils" version))
9574 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
9575 (properties `((upstream-name . "MsCoreUtils")))
9576 (build-system r-build-system)
9578 `(("r-mass" ,r-mass)
9580 ("r-s4vectors" ,r-s4vectors)))
9582 `(("r-knitr" ,r-knitr)))
9583 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
9584 (synopsis "Core utils for mass spectrometry data")
9586 "This package defines low-level functions for mass spectrometry data and
9587 is independent of any high-level data structures. These functions include
9588 mass spectra processing functions (noise estimation, smoothing, binning),
9589 quantitative aggregation functions (median polish, robust summarisation,
9590 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
9591 well as misc helper functions, that are used across high-level data structure
9592 within the R for Mass Spectrometry packages.")
9593 (license license:artistic2.0)))
9595 (define-public r-biocio
9602 (uri (bioconductor-uri "BiocIO" version))
9605 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
9606 (properties `((upstream-name . "BiocIO")))
9607 (build-system r-build-system)
9609 `(("r-biocgenerics" ,r-biocgenerics)
9610 ("r-genomicranges" ,r-genomicranges)
9611 ("r-rcurl" ,r-rcurl)
9612 ("r-s4vectors" ,r-s4vectors)))
9614 `(("r-knitr" ,r-knitr)))
9615 (home-page "https://bioconductor.org/packages/BiocIO")
9616 (synopsis "Standard input and output for Bioconductor packages")
9618 "This package implements `import()` and `export()` standard generics for
9619 importing and exporting biological data formats. `import()` supports
9620 whole-file as well as chunk-wise iterative import. The `import()` interface
9621 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
9622 row or element-like components of the file resource), `select()` (on
9623 column-like components of the file resource) and `collect()`. The `import()`
9624 interface optionally provides transparent access to remote (e.g. via https)
9625 as well as local access. Developers can register a file extension, e.g.,
9626 `.loom` for dispatch from character-based URIs to specific `import()` /
9627 `export()` methods based on classes representing file types, e.g.,
9629 (license license:artistic2.0)))
9631 (define-public r-msmseda
9638 (uri (bioconductor-uri "msmsEDA" version))
9641 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
9642 (properties `((upstream-name . "msmsEDA")))
9643 (build-system r-build-system)
9645 `(("r-gplots" ,r-gplots)
9647 ("r-msnbase" ,r-msnbase)
9648 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9650 "https://bioconductor.org/packages/msmsEDA")
9651 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
9653 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
9654 experiments, and visualize de influence of the involved factors.")
9655 (license license:gpl2)))
9657 (define-public r-msmstests
9659 (name "r-msmstests")
9664 (uri (bioconductor-uri "msmsTests" version))
9667 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
9668 (properties `((upstream-name . "msmsTests")))
9669 (build-system r-build-system)
9671 `(("r-edger" ,r-edger)
9672 ("r-msmseda" ,r-msmseda)
9673 ("r-msnbase" ,r-msnbase)
9674 ("r-qvalue" ,r-qvalue)))
9676 "https://bioconductor.org/packages/msmsTests")
9677 (synopsis "Differential LC-MS/MS expression tests")
9679 "This packages provides statistical tests for label-free LC-MS/MS data
9680 by spectral counts, to discover differentially expressed proteins between two
9681 biological conditions. Three tests are available: Poisson GLM regression,
9682 quasi-likelihood GLM regression, and the negative binomial of the edgeR
9683 package.The three models admit blocking factors to control for nuissance
9684 variables.To assure a good level of reproducibility a post-test filter is
9685 available, where we may set the minimum effect size considered biologicaly
9686 relevant, and the minimum expression of the most abundant condition.")
9687 (license license:gpl2)))
9689 (define-public r-catalyst
9696 (uri (bioconductor-uri "CATALYST" version))
9699 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
9700 (properties `((upstream-name . "CATALYST")))
9701 (build-system r-build-system)
9703 `(("r-circlize" ,r-circlize)
9704 ("r-complexheatmap" ,r-complexheatmap)
9705 ("r-consensusclusterplus" ,r-consensusclusterplus)
9706 ("r-cowplot" ,r-cowplot)
9707 ("r-data-table" ,r-data-table)
9708 ("r-dplyr" ,r-dplyr)
9710 ("r-flowcore" ,r-flowcore)
9711 ("r-flowsom" ,r-flowsom)
9712 ("r-ggplot2" ,r-ggplot2)
9713 ("r-ggrepel" ,r-ggrepel)
9714 ("r-ggridges" ,r-ggridges)
9715 ("r-gridextra" ,r-gridextra)
9716 ("r-magrittr" ,r-magrittr)
9717 ("r-matrix" ,r-matrix)
9718 ("r-matrixstats" ,r-matrixstats)
9720 ("r-purrr" ,r-purrr)
9721 ("r-rcolorbrewer" ,r-rcolorbrewer)
9722 ("r-reshape2" ,r-reshape2)
9723 ("r-rtsne" ,r-rtsne)
9724 ("r-s4vectors" ,r-s4vectors)
9725 ("r-scales" ,r-scales)
9726 ("r-scater" ,r-scater)
9727 ("r-singlecellexperiment" ,r-singlecellexperiment)
9728 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9730 `(("r-knitr" ,r-knitr)))
9732 "https://github.com/HelenaLC/CATALYST")
9733 (synopsis "Cytometry data analysis tools")
9735 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
9736 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
9737 reporters to label antibodies, thereby substantially decreasing spectral
9738 overlap and allowing for examination of over 50 parameters at the single cell
9739 level. While spectral overlap is significantly less pronounced in CyTOF than
9740 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
9741 and oxide formation can impede data interpretability. We designed
9742 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
9743 preprocessing of cytometry data, including i) normalization using bead
9744 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
9745 (license license:gpl2+)))
9747 (define-public r-erma
9754 (uri (bioconductor-uri "erma" version))
9757 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
9758 (build-system r-build-system)
9760 `(("r-annotationdbi" ,r-annotationdbi)
9761 ("r-biobase" ,r-biobase)
9762 ("r-biocgenerics" ,r-biocgenerics)
9763 ("r-biocparallel" ,r-biocparallel)
9764 ("r-genomeinfodb" ,r-genomeinfodb)
9765 ("r-genomicfiles" ,r-genomicfiles)
9766 ("r-genomicranges" ,r-genomicranges)
9767 ("r-ggplot2" ,r-ggplot2)
9768 ("r-homo-sapiens" ,r-homo-sapiens)
9769 ("r-iranges" ,r-iranges)
9770 ("r-rtracklayer" ,r-rtracklayer)
9771 ("r-s4vectors" ,r-s4vectors)
9772 ("r-shiny" ,r-shiny)
9773 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9775 `(("r-knitr" ,r-knitr)))
9776 (home-page "https://bioconductor.org/packages/erma")
9777 (synopsis "Epigenomic road map adventures")
9779 "The epigenomics road map describes locations of epigenetic marks in DNA
9780 from a variety of cell types. Of interest are locations of histone
9781 modifications, sites of DNA methylation, and regions of accessible chromatin.
9782 This package presents a selection of elements of the road map including
9783 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
9784 by Ernst and Kellis.")
9785 (license license:artistic2.0)))
9787 (define-public r-ggbio
9794 (uri (bioconductor-uri "ggbio" version))
9797 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
9798 (build-system r-build-system)
9801 (modify-phases %standard-phases
9802 ;; See https://github.com/tengfei/ggbio/issues/117
9803 ;; This fix will be included in the next release.
9804 (add-after 'unpack 'fix-typo
9806 (substitute* "R/GGbio-class.R"
9807 (("fechable") "fetchable"))
9810 `(("r-annotationdbi" ,r-annotationdbi)
9811 ("r-annotationfilter" ,r-annotationfilter)
9812 ("r-biobase" ,r-biobase)
9813 ("r-biocgenerics" ,r-biocgenerics)
9814 ("r-biostrings" ,r-biostrings)
9815 ("r-biovizbase" ,r-biovizbase)
9816 ("r-bsgenome" ,r-bsgenome)
9817 ("r-ensembldb" ,r-ensembldb)
9818 ("r-genomeinfodb" ,r-genomeinfodb)
9819 ("r-genomicalignments" ,r-genomicalignments)
9820 ("r-genomicfeatures" ,r-genomicfeatures)
9821 ("r-genomicranges" ,r-genomicranges)
9822 ("r-ggally" ,r-ggally)
9823 ("r-ggplot2" ,r-ggplot2)
9824 ("r-gridextra" ,r-gridextra)
9825 ("r-gtable" ,r-gtable)
9826 ("r-hmisc" ,r-hmisc)
9827 ("r-iranges" ,r-iranges)
9828 ("r-organismdbi" ,r-organismdbi)
9829 ("r-reshape2" ,r-reshape2)
9830 ("r-rlang" ,r-rlang)
9831 ("r-rsamtools" ,r-rsamtools)
9832 ("r-rtracklayer" ,r-rtracklayer)
9833 ("r-s4vectors" ,r-s4vectors)
9834 ("r-scales" ,r-scales)
9835 ("r-summarizedexperiment" ,r-summarizedexperiment)
9836 ("r-variantannotation" ,r-variantannotation)))
9838 `(("r-knitr" ,r-knitr)))
9839 (home-page "http://www.tengfei.name/ggbio/")
9840 (synopsis "Visualization tools for genomic data")
9842 "The ggbio package extends and specializes the grammar of graphics for
9843 biological data. The graphics are designed to answer common scientific
9844 questions, in particular those often asked of high throughput genomics data.
9845 All core Bioconductor data structures are supported, where appropriate. The
9846 package supports detailed views of particular genomic regions, as well as
9847 genome-wide overviews. Supported overviews include ideograms and grand linear
9848 views. High-level plots include sequence fragment length, edge-linked
9849 interval to data view, mismatch pileup, and several splicing summaries.")
9850 (license license:artistic2.0)))
9852 (define-public r-gqtlbase
9859 (uri (bioconductor-uri "gQTLBase" version))
9862 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
9863 (properties `((upstream-name . "gQTLBase")))
9864 (build-system r-build-system)
9867 (modify-phases %standard-phases
9868 ;; This is an upstream bug.
9869 (add-after 'unpack 'fix-imports
9871 (substitute* "NAMESPACE"
9872 ((".*maxffmode.*") "")
9873 (("importFrom\\(ff,.*") "import(ff)\n"))
9876 `(("r-batchjobs" ,r-batchjobs)
9877 ("r-bbmisc" ,r-bbmisc)
9878 ("r-biocgenerics" ,r-biocgenerics)
9880 ("r-doparallel" ,r-doparallel)
9882 ("r-ffbase" ,r-ffbase)
9883 ("r-foreach" ,r-foreach)
9884 ("r-genomicfiles" ,r-genomicfiles)
9885 ("r-genomicranges" ,r-genomicranges)
9886 ("r-rtracklayer" ,r-rtracklayer)
9887 ("r-s4vectors" ,r-s4vectors)
9888 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9890 `(("r-knitr" ,r-knitr)))
9891 (home-page "https://bioconductor.org/packages/gQTLBase")
9892 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
9894 "The purpose of this package is to simplify the storage and interrogation
9895 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
9897 (license license:artistic2.0)))
9899 (define-public r-gqtlstats
9901 (name "r-gqtlstats")
9906 (uri (bioconductor-uri "gQTLstats" version))
9909 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
9910 (properties `((upstream-name . "gQTLstats")))
9911 (build-system r-build-system)
9913 `(("r-annotationdbi" ,r-annotationdbi)
9914 ("r-batchjobs" ,r-batchjobs)
9915 ("r-bbmisc" ,r-bbmisc)
9916 ("r-beeswarm" ,r-beeswarm)
9917 ("r-biobase" ,r-biobase)
9918 ("r-biocgenerics" ,r-biocgenerics)
9919 ("r-doparallel" ,r-doparallel)
9920 ("r-dplyr" ,r-dplyr)
9922 ("r-ffbase" ,r-ffbase)
9923 ("r-foreach" ,r-foreach)
9924 ("r-genomeinfodb" ,r-genomeinfodb)
9925 ("r-genomicfeatures" ,r-genomicfeatures)
9926 ("r-genomicfiles" ,r-genomicfiles)
9927 ("r-genomicranges" ,r-genomicranges)
9928 ("r-ggbeeswarm" ,r-ggbeeswarm)
9929 ("r-ggplot2" ,r-ggplot2)
9930 ("r-gqtlbase" ,r-gqtlbase)
9931 ("r-hardyweinberg" ,r-hardyweinberg)
9932 ("r-homo-sapiens" ,r-homo-sapiens)
9933 ("r-iranges" ,r-iranges)
9934 ("r-limma" ,r-limma)
9936 ("r-plotly" ,r-plotly)
9937 ("r-reshape2" ,r-reshape2)
9938 ("r-s4vectors" ,r-s4vectors)
9939 ("r-shiny" ,r-shiny)
9940 ("r-snpstats" ,r-snpstats)
9941 ("r-summarizedexperiment" ,r-summarizedexperiment)
9942 ("r-variantannotation" ,r-variantannotation)))
9944 `(("r-knitr" ,r-knitr)))
9945 (home-page "https://bioconductor.org/packages/gQTLstats")
9946 (synopsis "Computationally efficient analysis for eQTL and allied studies")
9948 "This package provides tools for the computationally efficient analysis
9949 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
9950 The software in this package aims to support refinements and functional
9951 interpretation of members of a collection of association statistics on a
9952 family of feature/genome hypotheses.")
9953 (license license:artistic2.0)))
9955 (define-public r-gviz
9962 (uri (bioconductor-uri "Gviz" version))
9965 "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
9966 (properties `((upstream-name . "Gviz")))
9967 (build-system r-build-system)
9969 `(("r-annotationdbi" ,r-annotationdbi)
9970 ("r-biobase" ,r-biobase)
9971 ("r-biocgenerics" ,r-biocgenerics)
9972 ("r-biomart" ,r-biomart)
9973 ("r-biostrings" ,r-biostrings)
9974 ("r-biovizbase" ,r-biovizbase)
9975 ("r-bsgenome" ,r-bsgenome)
9976 ("r-digest" ,r-digest)
9977 ("r-ensembldb" ,r-ensembldb)
9978 ("r-genomeinfodb" ,r-genomeinfodb)
9979 ("r-genomicalignments" ,r-genomicalignments)
9980 ("r-genomicfeatures" ,r-genomicfeatures)
9981 ("r-genomicranges" ,r-genomicranges)
9982 ("r-iranges" ,r-iranges)
9983 ("r-lattice" ,r-lattice)
9984 ("r-latticeextra" ,r-latticeextra)
9985 ("r-matrixstats" ,r-matrixstats)
9986 ("r-rcolorbrewer" ,r-rcolorbrewer)
9987 ("r-rsamtools" ,r-rsamtools)
9988 ("r-rtracklayer" ,r-rtracklayer)
9989 ("r-s4vectors" ,r-s4vectors)
9990 ("r-xvector" ,r-xvector)))
9992 `(("r-knitr" ,r-knitr)))
9993 (home-page "https://bioconductor.org/packages/Gviz")
9994 (synopsis "Plotting data and annotation information along genomic coordinates")
9996 "Genomic data analyses requires integrated visualization of known genomic
9997 information and new experimental data. Gviz uses the biomaRt and the
9998 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
9999 and translates this to e.g. gene/transcript structures in viewports of the
10000 grid graphics package. This results in genomic information plotted together
10002 (license license:artistic2.0)))
10004 (define-public r-gwascat
10011 (uri (bioconductor-uri "gwascat" version))
10014 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
10015 (build-system r-build-system)
10017 `(("r-annotationdbi" ,r-annotationdbi)
10018 ("r-biocfilecache" ,r-biocfilecache)
10019 ("r-biostrings" ,r-biostrings)
10020 ("r-genomeinfodb" ,r-genomeinfodb)
10021 ("r-genomicfeatures" ,r-genomicfeatures)
10022 ("r-genomicranges" ,r-genomicranges)
10023 ("r-iranges" ,r-iranges)
10024 ("r-readr" ,r-readr)
10025 ("r-s4vectors" ,r-s4vectors)
10026 ("r-snpstats" ,r-snpstats)
10027 ("r-variantannotation" ,r-variantannotation)))
10029 `(("r-knitr" ,r-knitr)))
10030 (home-page "https://bioconductor.org/packages/gwascat")
10031 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10033 "This package provides tools for representing and modeling data in the
10034 EMBL-EBI GWAS catalog.")
10035 (license license:artistic2.0)))
10037 (define-public r-kegggraph
10039 (name "r-kegggraph")
10044 (uri (bioconductor-uri "KEGGgraph" version))
10046 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
10047 (properties `((upstream-name . "KEGGgraph")))
10048 (build-system r-build-system)
10050 `(("r-graph" ,r-graph)
10051 ("r-rcurl" ,r-rcurl)
10053 (home-page "https://bioconductor.org/packages/KEGGgraph")
10054 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
10056 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
10057 object as well as a collection of tools to analyze, dissect and visualize these
10058 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
10059 maintaining all essential pathway attributes. The package offers
10060 functionalities including parsing, graph operation, visualization and etc.")
10061 (license license:gpl2+)))
10063 (define-public r-ldblock
10070 (uri (bioconductor-uri "ldblock" version))
10073 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
10074 (build-system r-build-system)
10076 `(("r-biocgenerics" ,r-biocgenerics)
10077 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
10078 ("r-ensembldb" ,r-ensembldb)
10079 ("r-genomeinfodb" ,r-genomeinfodb)
10080 ("r-genomicfiles" ,r-genomicfiles)
10082 ("r-matrix" ,r-matrix)
10083 ("r-rsamtools" ,r-rsamtools)
10084 ("r-snpstats" ,r-snpstats)
10085 ("r-variantannotation" ,r-variantannotation)))
10087 `(("r-knitr" ,r-knitr)))
10088 (home-page "https://bioconductor.org/packages/ldblock")
10089 (synopsis "Data structures for linkage disequilibrium measures in populations")
10091 "This package defines data structures for @dfn{linkage
10092 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10093 handling of existing population-level data for the purpose of flexibly
10094 defining LD blocks.")
10095 (license license:artistic2.0)))
10097 ;; This is a CRAN package, but it depends on r-snpstats, which is a
10098 ;; Bioconductor package.
10099 (define-public r-ldheatmap
10101 (name "r-ldheatmap")
10106 (uri (cran-uri "LDheatmap" version))
10109 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
10110 (properties `((upstream-name . "LDheatmap")))
10111 (build-system r-build-system)
10113 `(("r-genetics" ,r-genetics)
10115 ("r-snpstats" ,r-snpstats)))
10116 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
10117 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
10119 "This package provides tools to produce a graphical display, as a heat
10120 map, of measures of pairwise linkage disequilibria between SNPs. Users may
10121 optionally include the physical locations or genetic map distances of each SNP
10123 (license license:gpl3)))
10125 (define-public r-pathview
10127 (name "r-pathview")
10132 (uri (bioconductor-uri "pathview" version))
10134 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
10135 (properties `((upstream-name . "pathview")))
10136 (build-system r-build-system)
10138 `(("r-annotationdbi" ,r-annotationdbi)
10139 ("r-graph" ,r-graph)
10140 ("r-kegggraph" ,r-kegggraph)
10141 ("r-keggrest" ,r-keggrest)
10142 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10144 ("r-rgraphviz" ,r-rgraphviz)
10146 (home-page "https://pathview.uncc.edu/")
10147 (synopsis "Tool set for pathway based data integration and visualization")
10149 "@code{r-pathview} is a tool set for pathway based data integration and
10150 visualization. It maps and renders a wide variety of biological data on
10151 relevant pathway graphs. All users need is to supply their data and specify
10152 the target pathway. This package automatically downloads the pathway graph
10153 data, parses the data file, maps user data to the pathway, and render pathway
10154 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
10155 integrates with pathway and gene set (enrichment) analysis tools for
10156 large-scale and fully automated analysis.")
10157 (license license:gpl3+)))
10159 (define-public r-snpstats
10161 (name "r-snpstats")
10166 (uri (bioconductor-uri "snpStats" version))
10169 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
10170 (properties `((upstream-name . "snpStats")))
10171 (build-system r-build-system)
10172 (inputs `(("zlib" ,zlib)))
10174 `(("r-biocgenerics" ,r-biocgenerics)
10175 ("r-matrix" ,r-matrix)
10176 ("r-survival" ,r-survival)
10177 ("r-zlibbioc" ,r-zlibbioc)))
10178 (home-page "https://bioconductor.org/packages/snpStats")
10179 (synopsis "Methods for SNP association studies")
10181 "This package provides classes and statistical methods for large
10182 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
10183 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10184 (license license:gpl3)))
10186 (define-public r-sushi
10192 (uri (bioconductor-uri "Sushi" version))
10195 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
10196 (properties `((upstream-name . "Sushi")))
10197 (build-system r-build-system)
10199 `(("r-biomart" ,r-biomart)
10201 (home-page "https://bioconductor.org/packages/Sushi")
10202 (synopsis "Tools for visualizing genomics data")
10204 "This package provides flexible, quantitative, and integrative genomic
10205 visualizations for publication-quality multi-panel figures.")
10206 (license license:gpl2+)))