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-category
1529 (uri (bioconductor-uri "Category" version))
1532 "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
1533 (properties `((upstream-name . "Category")))
1534 (build-system r-build-system)
1536 `(("r-annotate" ,r-annotate)
1537 ("r-annotationdbi" ,r-annotationdbi)
1538 ("r-biobase" ,r-biobase)
1539 ("r-biocgenerics" ,r-biocgenerics)
1540 ("r-genefilter" ,r-genefilter)
1541 ("r-graph" ,r-graph)
1542 ("r-gseabase" ,r-gseabase)
1543 ("r-matrix" ,r-matrix)
1546 (home-page "https://bioconductor.org/packages/Category")
1547 (synopsis "Category analysis")
1549 "This package provides a collection of tools for performing category
1551 (license license:artistic2.0)))
1553 (define-public r-deseq2
1560 (uri (bioconductor-uri "DESeq2" version))
1563 "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp"))))
1564 (properties `((upstream-name . "DESeq2")))
1565 (build-system r-build-system)
1567 `(("r-biobase" ,r-biobase)
1568 ("r-biocgenerics" ,r-biocgenerics)
1569 ("r-biocparallel" ,r-biocparallel)
1570 ("r-genefilter" ,r-genefilter)
1571 ("r-geneplotter" ,r-geneplotter)
1572 ("r-genomicranges" ,r-genomicranges)
1573 ("r-ggplot2" ,r-ggplot2)
1574 ("r-iranges" ,r-iranges)
1575 ("r-locfit" ,r-locfit)
1577 ("r-rcpparmadillo" ,r-rcpparmadillo)
1578 ("r-s4vectors" ,r-s4vectors)
1579 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1581 `(("r-knitr" ,r-knitr)))
1582 (home-page "https://bioconductor.org/packages/DESeq2")
1583 (synopsis "Differential gene expression analysis")
1585 "This package provides functions to estimate variance-mean dependence in
1586 count data from high-throughput nucleotide sequencing assays and test for
1587 differential expression based on a model using the negative binomial
1589 (license license:lgpl3+)))
1591 (define-public r-dexseq
1598 (uri (bioconductor-uri "DEXSeq" version))
1601 "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
1602 (properties `((upstream-name . "DEXSeq")))
1603 (build-system r-build-system)
1605 `(("r-annotationdbi" ,r-annotationdbi)
1606 ("r-biobase" ,r-biobase)
1607 ("r-biocgenerics" ,r-biocgenerics)
1608 ("r-biocparallel" ,r-biocparallel)
1609 ("r-biomart" ,r-biomart)
1610 ("r-deseq2" ,r-deseq2)
1611 ("r-genefilter" ,r-genefilter)
1612 ("r-geneplotter" ,r-geneplotter)
1613 ("r-genomicranges" ,r-genomicranges)
1614 ("r-hwriter" ,r-hwriter)
1615 ("r-iranges" ,r-iranges)
1616 ("r-rcolorbrewer" ,r-rcolorbrewer)
1617 ("r-rsamtools" ,r-rsamtools)
1618 ("r-s4vectors" ,r-s4vectors)
1619 ("r-statmod" ,r-statmod)
1620 ("r-stringr" ,r-stringr)
1621 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1623 `(("r-knitr" ,r-knitr)))
1624 (home-page "https://bioconductor.org/packages/DEXSeq")
1625 (synopsis "Inference of differential exon usage in RNA-Seq")
1627 "This package is focused on finding differential exon usage using RNA-seq
1628 exon counts between samples with different experimental designs. It provides
1629 functions that allows the user to make the necessary statistical tests based
1630 on a model that uses the negative binomial distribution to estimate the
1631 variance between biological replicates and generalized linear models for
1632 testing. The package also provides functions for the visualization and
1633 exploration of the results.")
1634 (license license:gpl3+)))
1636 (define-public r-genefilter
1638 (name "r-genefilter")
1643 (uri (bioconductor-uri "genefilter" version))
1646 "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
1647 (build-system r-build-system)
1649 `(("gfortran" ,gfortran)
1650 ("r-knitr" ,r-knitr)))
1652 `(("r-annotate" ,r-annotate)
1653 ("r-annotationdbi" ,r-annotationdbi)
1654 ("r-biobase" ,r-biobase)
1655 ("r-biocgenerics" ,r-biocgenerics)
1656 ("r-survival" ,r-survival)))
1657 (home-page "https://bioconductor.org/packages/genefilter")
1658 (synopsis "Filter genes from high-throughput experiments")
1660 "This package provides basic functions for filtering genes from
1661 high-throughput sequencing experiments.")
1662 (license license:artistic2.0)))
1664 (define-public r-gostats
1671 (uri (bioconductor-uri "GOstats" version))
1674 "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
1675 (properties `((upstream-name . "GOstats")))
1676 (build-system r-build-system)
1678 `(("r-annotate" ,r-annotate)
1679 ("r-annotationdbi" ,r-annotationdbi)
1680 ("r-annotationforge" ,r-annotationforge)
1681 ("r-biobase" ,r-biobase)
1682 ("r-category" ,r-category)
1683 ("r-go-db" ,r-go-db)
1684 ("r-graph" ,r-graph)
1685 ("r-rgraphviz" ,r-rgraphviz)
1686 ("r-rbgl" ,r-rbgl)))
1687 (home-page "https://bioconductor.org/packages/GOstats")
1688 (synopsis "Tools for manipulating GO and microarrays")
1690 "This package provides a set of tools for interacting with GO and
1691 microarray data. A variety of basic manipulation tools for graphs, hypothesis
1692 testing and other simple calculations.")
1693 (license license:artistic2.0)))
1695 (define-public r-gseabase
1702 (uri (bioconductor-uri "GSEABase" version))
1705 "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
1706 (properties `((upstream-name . "GSEABase")))
1707 (build-system r-build-system)
1709 `(("r-annotate" ,r-annotate)
1710 ("r-annotationdbi" ,r-annotationdbi)
1711 ("r-biobase" ,r-biobase)
1712 ("r-biocgenerics" ,r-biocgenerics)
1713 ("r-graph" ,r-graph)
1716 `(("r-knitr" ,r-knitr)))
1717 (home-page "https://bioconductor.org/packages/GSEABase")
1718 (synopsis "Gene set enrichment data structures and methods")
1720 "This package provides classes and methods to support @dfn{Gene Set
1721 Enrichment Analysis} (GSEA).")
1722 (license license:artistic2.0)))
1724 (define-public r-hpar
1731 (uri (bioconductor-uri "hpar" version))
1734 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
1735 (build-system r-build-system)
1737 `(("r-knitr" ,r-knitr)))
1738 (home-page "https://bioconductor.org/packages/hpar/")
1739 (synopsis "Human Protein Atlas in R")
1740 (description "This package provides a simple interface to and data from
1741 the Human Protein Atlas project.")
1742 (license license:artistic2.0)))
1744 (define-public r-rbgl
1751 (uri (bioconductor-uri "RBGL" version))
1754 "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
1755 (properties `((upstream-name . "RBGL")))
1756 (build-system r-build-system)
1759 ("r-graph" ,r-graph)))
1760 (home-page "https://www.bioconductor.org/packages/RBGL")
1761 (synopsis "Interface to the Boost graph library")
1763 "This package provides a fairly extensive and comprehensive interface to
1764 the graph algorithms contained in the Boost library.")
1765 (license license:artistic2.0)))
1767 (define-public r-regioner
1774 (uri (bioconductor-uri "regioneR" version))
1777 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
1778 (properties `((upstream-name . "regioneR")))
1779 (build-system r-build-system)
1781 `(("r-biostrings" ,r-biostrings)
1782 ("r-bsgenome" ,r-bsgenome)
1783 ("r-genomeinfodb" ,r-genomeinfodb)
1784 ("r-genomicranges" ,r-genomicranges)
1785 ("r-iranges" ,r-iranges)
1786 ("r-memoise" ,r-memoise)
1787 ("r-rtracklayer" ,r-rtracklayer)
1788 ("r-s4vectors" ,r-s4vectors)))
1790 `(("r-knitr" ,r-knitr)))
1791 (home-page "https://bioconductor.org/packages/regioneR/")
1792 (synopsis "Association analysis of genomic regions")
1793 (description "This package offers a statistical framework based on
1794 customizable permutation tests to assess the association between genomic
1795 region sets and other genomic features.")
1796 (license license:artistic2.0)))
1798 (define-public r-reportingtools
1800 (name "r-reportingtools")
1805 (uri (bioconductor-uri "ReportingTools" version))
1808 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
1810 `((upstream-name . "ReportingTools")))
1811 (build-system r-build-system)
1813 `(("r-annotate" ,r-annotate)
1814 ("r-annotationdbi" ,r-annotationdbi)
1815 ("r-biobase" ,r-biobase)
1816 ("r-biocgenerics" ,r-biocgenerics)
1817 ("r-category" ,r-category)
1818 ("r-deseq2" ,r-deseq2)
1819 ("r-edger" ,r-edger)
1820 ("r-ggbio" ,r-ggbio)
1821 ("r-ggplot2" ,r-ggplot2)
1822 ("r-gostats" ,r-gostats)
1823 ("r-gseabase" ,r-gseabase)
1824 ("r-hwriter" ,r-hwriter)
1825 ("r-iranges" ,r-iranges)
1826 ("r-knitr" ,r-knitr)
1827 ("r-lattice" ,r-lattice)
1828 ("r-limma" ,r-limma)
1829 ("r-pfam-db" ,r-pfam-db)
1830 ("r-r-utils" ,r-r-utils)
1833 `(("r-knitr" ,r-knitr)))
1834 (home-page "https://bioconductor.org/packages/ReportingTools/")
1835 (synopsis "Tools for making reports in various formats")
1837 "The ReportingTools package enables users to easily display reports of
1838 analysis results generated from sources such as microarray and sequencing
1839 data. The package allows users to create HTML pages that may be viewed on a
1840 web browser, or in other formats. Users can generate tables with sortable and
1841 filterable columns, make and display plots, and link table entries to other
1842 data sources such as NCBI or larger plots within the HTML page. Using the
1843 package, users can also produce a table of contents page to link various
1844 reports together for a particular project that can be viewed in a web
1846 (license license:artistic2.0)))
1848 (define-public r-shortread
1850 (name "r-shortread")
1855 (uri (bioconductor-uri "ShortRead" version))
1858 "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
1859 (properties `((upstream-name . "ShortRead")))
1860 (build-system r-build-system)
1864 `(("r-biobase" ,r-biobase)
1865 ("r-biocgenerics" ,r-biocgenerics)
1866 ("r-biocparallel" ,r-biocparallel)
1867 ("r-biostrings" ,r-biostrings)
1868 ("r-genomeinfodb" ,r-genomeinfodb)
1869 ("r-genomicalignments" ,r-genomicalignments)
1870 ("r-genomicranges" ,r-genomicranges)
1871 ("r-rhtslib" ,r-rhtslib)
1872 ("r-hwriter" ,r-hwriter)
1873 ("r-iranges" ,r-iranges)
1874 ("r-lattice" ,r-lattice)
1875 ("r-latticeextra" ,r-latticeextra)
1876 ("r-rsamtools" ,r-rsamtools)
1877 ("r-s4vectors" ,r-s4vectors)
1878 ("r-xvector" ,r-xvector)
1879 ("r-zlibbioc" ,r-zlibbioc)))
1880 (home-page "https://bioconductor.org/packages/ShortRead")
1881 (synopsis "FASTQ input and manipulation tools")
1883 "This package implements sampling, iteration, and input of FASTQ files.
1884 It includes functions for filtering and trimming reads, and for generating a
1885 quality assessment report. Data are represented as
1886 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
1887 purposes. The package also contains legacy support for early single-end,
1888 ungapped alignment formats.")
1889 (license license:artistic2.0)))
1891 (define-public r-systempiper
1893 (name "r-systempiper")
1898 (uri (bioconductor-uri "systemPipeR" version))
1901 "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
1902 (properties `((upstream-name . "systemPipeR")))
1903 (build-system r-build-system)
1905 `(("r-annotate" ,r-annotate)
1906 ("r-assertthat" ,r-assertthat)
1907 ("r-batchtools" ,r-batchtools)
1908 ("r-biostrings" ,r-biostrings)
1909 ("r-deseq2" ,r-deseq2)
1911 ("r-edger" ,r-edger)
1912 ("r-genomicfeatures" ,r-genomicfeatures)
1913 ("r-genomicranges" ,r-genomicranges)
1914 ("r-ggplot2" ,r-ggplot2)
1915 ("r-go-db" ,r-go-db)
1916 ("r-gostats" ,r-gostats)
1917 ("r-iranges" ,r-iranges)
1918 ("r-limma" ,r-limma)
1919 ("r-magrittr" ,r-magrittr)
1920 ("r-pheatmap" ,r-pheatmap)
1921 ("r-rjson" ,r-rjson)
1922 ("r-rsamtools" ,r-rsamtools)
1924 ("r-shortread" ,r-shortread)
1925 ("r-stringr" ,r-stringr)
1926 ("r-summarizedexperiment" ,r-summarizedexperiment)
1928 ("r-variantannotation" ,r-variantannotation)))
1930 `(("r-knitr" ,r-knitr)))
1931 (home-page "https://github.com/tgirke/systemPipeR")
1932 (synopsis "Next generation sequencing workflow and reporting environment")
1934 "This R package provides tools for building and running automated
1935 end-to-end analysis workflows for a wide range of @dfn{next generation
1936 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
1937 Important features include a uniform workflow interface across different NGS
1938 applications, automated report generation, and support for running both R and
1939 command-line software, such as NGS aligners or peak/variant callers, on local
1940 computers or compute clusters. Efficient handling of complex sample sets and
1941 experimental designs is facilitated by a consistently implemented sample
1942 annotation infrastructure.")
1943 (license license:artistic2.0)))
1945 (define-public r-geneplotter
1947 (name "r-geneplotter")
1952 (uri (bioconductor-uri "geneplotter" version))
1955 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
1956 (build-system r-build-system)
1958 `(("r-annotate" ,r-annotate)
1959 ("r-annotationdbi" ,r-annotationdbi)
1960 ("r-biobase" ,r-biobase)
1961 ("r-biocgenerics" ,r-biocgenerics)
1962 ("r-lattice" ,r-lattice)
1963 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1964 (home-page "https://bioconductor.org/packages/geneplotter")
1965 (synopsis "Graphics functions for genomic data")
1967 "This package provides functions for plotting genomic data.")
1968 (license license:artistic2.0)))
1970 (define-public r-oligoclasses
1972 (name "r-oligoclasses")
1977 (uri (bioconductor-uri "oligoClasses" version))
1980 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
1981 (properties `((upstream-name . "oligoClasses")))
1982 (build-system r-build-system)
1984 `(("r-affyio" ,r-affyio)
1985 ("r-biobase" ,r-biobase)
1986 ("r-biocgenerics" ,r-biocgenerics)
1987 ("r-biocmanager" ,r-biocmanager)
1988 ("r-biostrings" ,r-biostrings)
1991 ("r-foreach" ,r-foreach)
1992 ("r-genomicranges" ,r-genomicranges)
1993 ("r-iranges" ,r-iranges)
1994 ("r-rsqlite" ,r-rsqlite)
1995 ("r-s4vectors" ,r-s4vectors)
1996 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1997 (home-page "https://bioconductor.org/packages/oligoClasses/")
1998 (synopsis "Classes for high-throughput arrays")
2000 "This package contains class definitions, validity checks, and
2001 initialization methods for classes used by the @code{oligo} and @code{crlmm}
2003 (license license:gpl2+)))
2005 (define-public r-oligo
2012 (uri (bioconductor-uri "oligo" version))
2015 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
2016 (properties `((upstream-name . "oligo")))
2017 (build-system r-build-system)
2018 (inputs `(("zlib" ,zlib)))
2020 `(("r-affxparser" ,r-affxparser)
2021 ("r-affyio" ,r-affyio)
2022 ("r-biobase" ,r-biobase)
2023 ("r-biocgenerics" ,r-biocgenerics)
2024 ("r-biostrings" ,r-biostrings)
2027 ("r-oligoclasses" ,r-oligoclasses)
2028 ("r-preprocesscore" ,r-preprocesscore)
2029 ("r-rsqlite" ,r-rsqlite)
2030 ("r-zlibbioc" ,r-zlibbioc)))
2032 `(("r-knitr" ,r-knitr)))
2033 (home-page "https://bioconductor.org/packages/oligo/")
2034 (synopsis "Preprocessing tools for oligonucleotide arrays")
2036 "This package provides a package to analyze oligonucleotide
2037 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
2038 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
2039 (license license:lgpl2.0+)))
2041 (define-public r-qvalue
2048 (uri (bioconductor-uri "qvalue" version))
2051 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
2052 (build-system r-build-system)
2054 `(("r-ggplot2" ,r-ggplot2)
2055 ("r-reshape2" ,r-reshape2)))
2057 `(("r-knitr" ,r-knitr)))
2058 (home-page "https://github.com/StoreyLab/qvalue")
2059 (synopsis "Q-value estimation for false discovery rate control")
2061 "This package takes a list of p-values resulting from the simultaneous
2062 testing of many hypotheses and estimates their q-values and local @dfn{false
2063 discovery rate} (FDR) values. The q-value of a test measures the proportion
2064 of false positives incurred when that particular test is called significant.
2065 The local FDR measures the posterior probability the null hypothesis is true
2066 given the test's p-value. Various plots are automatically generated, allowing
2067 one to make sensible significance cut-offs. The software can be applied to
2068 problems in genomics, brain imaging, astrophysics, and data mining.")
2069 ;; Any version of the LGPL.
2070 (license license:lgpl3+)))
2072 (define r-rcppnumerical
2074 (name "r-rcppnumerical")
2078 (uri (cran-uri "RcppNumerical" version))
2081 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
2082 (properties `((upstream-name . "RcppNumerical")))
2083 (build-system r-build-system)
2085 `(("r-rcpp" ,r-rcpp)
2086 ("r-rcppeigen" ,r-rcppeigen)))
2088 `(("r-knitr" ,r-knitr)))
2089 (home-page "https://github.com/yixuan/RcppNumerical")
2090 (synopsis "Rcpp integration for numerical computing libraries")
2091 (description "This package provides a collection of open source libraries
2092 for numerical computing (numerical integration, optimization, etc.) and their
2093 integration with @code{Rcpp}.")
2094 (license license:gpl2+)))
2096 (define-public r-apeglm
2102 (uri (bioconductor-uri "apeglm" version))
2105 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
2106 (properties `((upstream-name . "apeglm")))
2107 (build-system r-build-system)
2109 `(("r-emdbook" ,r-emdbook)
2110 ("r-genomicranges" ,r-genomicranges)
2112 ("r-rcppeigen" ,r-rcppeigen)
2113 ("r-rcppnumerical" ,r-rcppnumerical)
2114 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2115 (native-inputs `(("r-knitr" ,r-knitr)))
2116 (home-page "https://bioconductor.org/packages/apeglm")
2117 (synopsis "Approximate posterior estimation for GLM coefficients")
2118 (description "This package provides Bayesian shrinkage estimators for
2119 effect sizes for a variety of GLM models, using approximation of the
2120 posterior for individual coefficients.")
2121 (license license:gpl2)))
2123 (define-public r-greylistchip
2125 (name "r-greylistchip")
2129 (uri (bioconductor-uri "GreyListChIP" version))
2132 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
2133 (properties `((upstream-name . "GreyListChIP")))
2134 (build-system r-build-system)
2136 `(("r-bsgenome" ,r-bsgenome)
2137 ("r-genomeinfodb" ,r-genomeinfodb)
2138 ("r-genomicalignments" ,r-genomicalignments)
2139 ("r-genomicranges" ,r-genomicranges)
2141 ("r-rsamtools" ,r-rsamtools)
2142 ("r-rtracklayer" ,r-rtracklayer)
2143 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2144 (home-page "https://bioconductor.org/packages/GreyListChIP")
2145 (synopsis "Greylist artefact regions based on ChIP inputs")
2146 (description "This package identifies regions of ChIP experiments with high
2147 signal in the input, that lead to spurious peaks during peak calling.")
2148 (license license:artistic2.0)))
2150 (define-public r-diffbind
2157 (uri (bioconductor-uri "DiffBind" version))
2160 "0kxn59v93hl5pq8d156lnbz0sslpnxyjcfrvq2gzgd91sd587qmn"))))
2161 (properties `((upstream-name . "DiffBind")))
2162 (build-system r-build-system)
2164 `(("r-amap" ,r-amap)
2165 ("r-apeglm" ,r-apeglm)
2167 ("r-biocparallel" ,r-biocparallel)
2168 ("r-deseq2" ,r-deseq2)
2169 ("r-dplyr" ,r-dplyr)
2170 ("r-genomicalignments" ,r-genomicalignments)
2171 ("r-genomicranges" ,r-genomicranges)
2172 ("r-ggplot2" ,r-ggplot2)
2173 ("r-ggrepel" ,r-ggrepel)
2174 ("r-gplots" ,r-gplots)
2175 ("r-greylistchip" ,r-greylistchip)
2176 ("r-iranges" ,r-iranges)
2177 ("r-lattice" ,r-lattice)
2178 ("r-limma" ,r-limma)
2179 ("r-locfit" ,r-locfit)
2180 ("r-rcolorbrewer" , r-rcolorbrewer)
2182 ("r-rhtslib" ,r-rhtslib)
2183 ("r-rsamtools" ,r-rsamtools)
2184 ("r-s4vectors" ,r-s4vectors)
2185 ("r-summarizedexperiment" ,r-summarizedexperiment)
2186 ("r-systempiper" ,r-systempiper)))
2187 (home-page "https://bioconductor.org/packages/DiffBind")
2188 (synopsis "Differential binding analysis of ChIP-Seq peak data")
2190 "This package computes differentially bound sites from multiple
2191 ChIP-seq experiments using affinity (quantitative) data. Also enables
2192 occupancy (overlap) analysis and plotting functions.")
2193 (license license:artistic2.0)))
2195 (define-public r-ripseeker
2197 (name "r-ripseeker")
2202 (uri (bioconductor-uri "RIPSeeker" version))
2205 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
2206 (properties `((upstream-name . "RIPSeeker")))
2207 (build-system r-build-system)
2209 `(("r-s4vectors" ,r-s4vectors)
2210 ("r-iranges" ,r-iranges)
2211 ("r-genomicranges" ,r-genomicranges)
2212 ("r-summarizedexperiment" ,r-summarizedexperiment)
2213 ("r-rsamtools" ,r-rsamtools)
2214 ("r-genomicalignments" ,r-genomicalignments)
2215 ("r-rtracklayer" ,r-rtracklayer)))
2216 (home-page "https://bioconductor.org/packages/RIPSeeker")
2218 "Identifying protein-associated transcripts from RIP-seq experiments")
2220 "This package infers and discriminates RIP peaks from RIP-seq alignments
2221 using two-state HMM with negative binomial emission probability. While
2222 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
2223 a suite of bioinformatics tools integrated within this self-contained software
2224 package comprehensively addressing issues ranging from post-alignments
2225 processing to visualization and annotation.")
2226 (license license:gpl2)))
2228 (define-public r-multtest
2235 (uri (bioconductor-uri "multtest" version))
2238 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
2239 (build-system r-build-system)
2241 `(("r-survival" ,r-survival)
2242 ("r-biocgenerics" ,r-biocgenerics)
2243 ("r-biobase" ,r-biobase)
2244 ("r-mass" ,r-mass)))
2245 (home-page "https://bioconductor.org/packages/multtest")
2246 (synopsis "Resampling-based multiple hypothesis testing")
2248 "This package can do non-parametric bootstrap and permutation
2249 resampling-based multiple testing procedures (including empirical Bayes
2250 methods) for controlling the family-wise error rate (FWER), generalized
2251 family-wise error rate (gFWER), tail probability of the proportion of
2252 false positives (TPPFP), and false discovery rate (FDR). Several choices
2253 of bootstrap-based null distribution are implemented (centered, centered
2254 and scaled, quantile-transformed). Single-step and step-wise methods are
2255 available. Tests based on a variety of T- and F-statistics (including
2256 T-statistics based on regression parameters from linear and survival models
2257 as well as those based on correlation parameters) are included. When probing
2258 hypotheses with T-statistics, users may also select a potentially faster null
2259 distribution which is multivariate normal with mean zero and variance
2260 covariance matrix derived from the vector influence function. Results are
2261 reported in terms of adjusted P-values, confidence regions and test statistic
2262 cutoffs. The procedures are directly applicable to identifying differentially
2263 expressed genes in DNA microarray experiments.")
2264 (license license:lgpl3)))
2266 (define-public r-graph
2272 (uri (bioconductor-uri "graph" version))
2275 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
2276 (build-system r-build-system)
2278 `(("r-biocgenerics" ,r-biocgenerics)))
2279 (home-page "https://bioconductor.org/packages/graph")
2280 (synopsis "Handle graph data structures in R")
2282 "This package implements some simple graph handling capabilities for R.")
2283 (license license:artistic2.0)))
2285 ;; This is a CRAN package, but it depends on a Bioconductor package.
2286 (define-public r-ggm
2293 (uri (cran-uri "ggm" version))
2296 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
2297 (properties `((upstream-name . "ggm")))
2298 (build-system r-build-system)
2300 `(("r-graph" ,r-graph)
2301 ("r-igraph" ,r-igraph)))
2302 (home-page "https://cran.r-project.org/package=ggm")
2303 (synopsis "Functions for graphical Markov models")
2305 "This package provides functions and datasets for maximum likelihood
2306 fitting of some classes of graphical Markov models.")
2307 (license license:gpl2+)))
2309 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
2310 (define-public r-perfmeas
2317 (uri (cran-uri "PerfMeas" version))
2320 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
2321 (properties `((upstream-name . "PerfMeas")))
2322 (build-system r-build-system)
2324 `(("r-graph" ,r-graph)
2325 ("r-limma" ,r-limma)
2326 ("r-rbgl" ,r-rbgl)))
2327 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
2328 (synopsis "Performance measures for ranking and classification tasks")
2330 "This package implements different performance measures for
2331 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
2332 a given recall, F-score for single and multiple classes are available.")
2333 (license license:gpl2+)))
2335 ;; This is a CRAN package, but it depends on a Bioconductor package.
2336 (define-public r-codedepends
2338 (name "r-codedepends")
2343 (uri (cran-uri "CodeDepends" version))
2346 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
2347 (properties `((upstream-name . "CodeDepends")))
2348 (build-system r-build-system)
2350 `(("r-codetools" ,r-codetools)
2351 ("r-graph" ,r-graph)
2353 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2354 (synopsis "Analysis of R code for reproducible research and code comprehension")
2356 "This package provides tools for analyzing R expressions or blocks of
2357 code and determining the dependencies between them. It focuses on R scripts,
2358 but can be used on the bodies of functions. There are many facilities
2359 including the ability to summarize or get a high-level view of code,
2360 determining dependencies between variables, code improvement suggestions.")
2361 ;; Any version of the GPL
2362 (license (list license:gpl2+ license:gpl3+))))
2364 (define-public r-chippeakanno
2366 (name "r-chippeakanno")
2371 (uri (bioconductor-uri "ChIPpeakAnno" version))
2374 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
2375 (properties `((upstream-name . "ChIPpeakAnno")))
2376 (build-system r-build-system)
2378 `(("r-annotationdbi" ,r-annotationdbi)
2379 ("r-biocgenerics" ,r-biocgenerics)
2380 ("r-biomart" ,r-biomart)
2381 ("r-biostrings" ,r-biostrings)
2383 ("r-ensembldb" ,r-ensembldb)
2384 ("r-genomeinfodb" ,r-genomeinfodb)
2385 ("r-genomicalignments" ,r-genomicalignments)
2386 ("r-genomicfeatures" ,r-genomicfeatures)
2387 ("r-genomicranges" ,r-genomicranges)
2388 ("r-ggplot2" ,r-ggplot2)
2389 ("r-graph" ,r-graph)
2390 ("r-iranges" ,r-iranges)
2391 ("r-keggrest" ,r-keggrest)
2392 ("r-matrixstats" ,r-matrixstats)
2393 ("r-multtest" ,r-multtest)
2395 ("r-regioner" ,r-regioner)
2396 ("r-rsamtools" ,r-rsamtools)
2397 ("r-rtracklayer" ,r-rtracklayer)
2398 ("r-s4vectors" ,r-s4vectors)
2399 ("r-summarizedexperiment" ,r-summarizedexperiment)
2400 ("r-venndiagram" ,r-venndiagram)))
2402 `(("r-knitr" ,r-knitr)))
2403 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2404 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2406 "The package includes functions to retrieve the sequences around the peak,
2407 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2408 custom features such as most conserved elements and other transcription factor
2409 binding sites supplied by users. Starting 2.0.5, new functions have been added
2410 for finding the peaks with bi-directional promoters with summary statistics
2411 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2412 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2413 enrichedGO (addGeneIDs).")
2414 (license license:gpl2+)))
2416 (define-public r-matrixgenerics
2418 (name "r-matrixgenerics")
2422 (uri (bioconductor-uri "MatrixGenerics" version))
2425 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
2427 `((upstream-name . "MatrixGenerics")))
2428 (build-system r-build-system)
2430 `(("r-matrixstats" ,r-matrixstats)))
2431 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2432 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2434 "This package provides S4 generic functions modeled after the
2435 @code{matrixStats} API for alternative matrix implementations. Packages with
2436 alternative matrix implementation can depend on this package and implement the
2437 generic functions that are defined here for a useful set of row and column
2438 summary statistics. Other package developers can import this package and
2439 handle a different matrix implementations without worrying about
2440 incompatibilities.")
2441 (license license:artistic2.0)))
2443 (define-public r-marray
2449 (uri (bioconductor-uri "marray" version))
2451 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
2452 (build-system r-build-system)
2454 `(("r-limma" ,r-limma)))
2455 (home-page "https://bioconductor.org/packages/marray")
2456 (synopsis "Exploratory analysis for two-color spotted microarray data")
2457 (description "This package contains class definitions for two-color spotted
2458 microarray data. It also includes functions for data input, diagnostic plots,
2459 normalization and quality checking.")
2460 (license license:lgpl2.0+)))
2462 (define-public r-cghbase
2468 (uri (bioconductor-uri "CGHbase" version))
2470 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
2471 (properties `((upstream-name . "CGHbase")))
2472 (build-system r-build-system)
2474 `(("r-biobase" ,r-biobase)
2475 ("r-marray" ,r-marray)))
2476 (home-page "https://bioconductor.org/packages/CGHbase")
2477 (synopsis "Base functions and classes for arrayCGH data analysis")
2478 (description "This package contains functions and classes that are needed by
2479 the @code{arrayCGH} packages.")
2480 (license license:gpl2+)))
2482 (define-public r-cghcall
2488 (uri (bioconductor-uri "CGHcall" version))
2490 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
2491 (properties `((upstream-name . "CGHcall")))
2492 (build-system r-build-system)
2494 `(("r-biobase" ,r-biobase)
2495 ("r-cghbase" ,r-cghbase)
2496 ("r-impute" ,r-impute)
2497 ("r-dnacopy" ,r-dnacopy)
2498 ("r-snowfall" ,r-snowfall)))
2499 (home-page "https://bioconductor.org/packages/CGHcall")
2500 (synopsis "Base functions and classes for arrayCGH data analysis")
2501 (description "This package contains functions and classes that are needed by
2502 @code{arrayCGH} packages.")
2503 (license license:gpl2+)))
2505 (define-public r-qdnaseq
2511 (uri (bioconductor-uri "QDNAseq" version))
2513 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
2514 (properties `((upstream-name . "QDNAseq")))
2515 (build-system r-build-system)
2517 `(("r-biobase" ,r-biobase)
2518 ("r-cghbase" ,r-cghbase)
2519 ("r-cghcall" ,r-cghcall)
2520 ("r-dnacopy" ,r-dnacopy)
2521 ("r-future" ,r-future)
2522 ("r-future-apply" ,r-future-apply)
2523 ("r-genomicranges" ,r-genomicranges)
2524 ("r-iranges" ,r-iranges)
2525 ("r-matrixstats" ,r-matrixstats)
2526 ("r-r-utils" ,r-r-utils)
2527 ("r-rsamtools" ,r-rsamtools)))
2528 (home-page "https://bioconductor.org/packages/QDNAseq")
2529 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2530 (description "The genome is divided into non-overlapping fixed-sized bins,
2531 number of sequence reads in each counted, adjusted with a simultaneous
2532 two-dimensional loess correction for sequence mappability and GC content, and
2533 filtered to remove spurious regions in the genome. Downstream steps of
2534 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2536 (license license:gpl2+)))
2538 (define-public r-bayseq
2545 (uri (bioconductor-uri "baySeq" version))
2548 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
2549 (properties `((upstream-name . "baySeq")))
2550 (build-system r-build-system)
2552 `(("r-abind" ,r-abind)
2553 ("r-edger" ,r-edger)
2554 ("r-genomicranges" ,r-genomicranges)))
2555 (home-page "https://bioconductor.org/packages/baySeq/")
2556 (synopsis "Bayesian analysis of differential expression patterns in count data")
2558 "This package identifies differential expression in high-throughput count
2559 data, such as that derived from next-generation sequencing machines,
2560 calculating estimated posterior likelihoods of differential expression (or
2561 more complex hypotheses) via empirical Bayesian methods.")
2562 (license license:gpl3)))
2564 (define-public r-chipcomp
2571 (uri (bioconductor-uri "ChIPComp" version))
2574 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
2575 (properties `((upstream-name . "ChIPComp")))
2576 (build-system r-build-system)
2578 `(("r-biocgenerics" ,r-biocgenerics)
2579 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2580 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2581 ("r-genomeinfodb" ,r-genomeinfodb)
2582 ("r-genomicranges" ,r-genomicranges)
2583 ("r-iranges" ,r-iranges)
2584 ("r-limma" ,r-limma)
2585 ("r-rsamtools" ,r-rsamtools)
2586 ("r-rtracklayer" ,r-rtracklayer)
2587 ("r-s4vectors" ,r-s4vectors)))
2588 (home-page "https://bioconductor.org/packages/ChIPComp")
2589 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2591 "ChIPComp implements a statistical method for quantitative comparison of
2592 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2593 sites across multiple conditions considering matching control in ChIP-seq
2595 ;; Any version of the GPL.
2596 (license license:gpl3+)))
2598 (define-public r-riboprofiling
2600 (name "r-riboprofiling")
2605 (uri (bioconductor-uri "RiboProfiling" version))
2608 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
2609 (properties `((upstream-name . "RiboProfiling")))
2610 (build-system r-build-system)
2612 `(("r-biocgenerics" ,r-biocgenerics)
2613 ("r-biostrings" ,r-biostrings)
2614 ("r-data-table" ,r-data-table)
2615 ("r-genomeinfodb" ,r-genomeinfodb)
2616 ("r-genomicalignments" ,r-genomicalignments)
2617 ("r-genomicfeatures" ,r-genomicfeatures)
2618 ("r-genomicranges" ,r-genomicranges)
2619 ("r-ggbio" ,r-ggbio)
2620 ("r-ggplot2" ,r-ggplot2)
2621 ("r-iranges" ,r-iranges)
2623 ("r-reshape2" ,r-reshape2)
2624 ("r-rsamtools" ,r-rsamtools)
2625 ("r-rtracklayer" ,r-rtracklayer)
2626 ("r-s4vectors" ,r-s4vectors)
2627 ("r-sqldf" ,r-sqldf)))
2629 `(("r-knitr" ,r-knitr)))
2630 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2631 (synopsis "Ribosome profiling data analysis")
2632 (description "Starting with a BAM file, this package provides the
2633 necessary functions for quality assessment, read start position recalibration,
2634 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2635 of count data: pairs, log fold-change, codon frequency and coverage
2636 assessment, principal component analysis on codon coverage.")
2637 (license license:gpl3)))
2639 (define-public r-riboseqr
2646 (uri (bioconductor-uri "riboSeqR" version))
2649 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
2650 (properties `((upstream-name . "riboSeqR")))
2651 (build-system r-build-system)
2653 `(("r-abind" ,r-abind)
2654 ("r-bayseq" ,r-bayseq)
2655 ("r-genomeinfodb" ,r-genomeinfodb)
2656 ("r-genomicranges" ,r-genomicranges)
2657 ("r-iranges" ,r-iranges)
2658 ("r-rsamtools" ,r-rsamtools)
2659 ("r-seqlogo" ,r-seqlogo)))
2660 (home-page "https://bioconductor.org/packages/riboSeqR/")
2661 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2663 "This package provides plotting functions, frameshift detection and
2664 parsing of genetic sequencing data from ribosome profiling experiments.")
2665 (license license:gpl3)))
2667 (define-public r-interactionset
2669 (name "r-interactionset")
2674 (uri (bioconductor-uri "InteractionSet" version))
2677 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
2679 `((upstream-name . "InteractionSet")))
2680 (build-system r-build-system)
2682 `(("r-biocgenerics" ,r-biocgenerics)
2683 ("r-genomeinfodb" ,r-genomeinfodb)
2684 ("r-genomicranges" ,r-genomicranges)
2685 ("r-iranges" ,r-iranges)
2686 ("r-matrix" ,r-matrix)
2688 ("r-s4vectors" ,r-s4vectors)
2689 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2691 `(("r-knitr" ,r-knitr)))
2692 (home-page "https://bioconductor.org/packages/InteractionSet")
2693 (synopsis "Base classes for storing genomic interaction data")
2695 "This package provides the @code{GInteractions},
2696 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2697 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2699 (license license:gpl3)))
2701 (define-public r-genomicinteractions
2703 (name "r-genomicinteractions")
2708 (uri (bioconductor-uri "GenomicInteractions" version))
2711 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
2713 `((upstream-name . "GenomicInteractions")))
2714 (build-system r-build-system)
2716 `(("r-biobase" ,r-biobase)
2717 ("r-biocgenerics" ,r-biocgenerics)
2718 ("r-data-table" ,r-data-table)
2719 ("r-dplyr" ,r-dplyr)
2720 ("r-genomeinfodb" ,r-genomeinfodb)
2721 ("r-genomicranges" ,r-genomicranges)
2722 ("r-ggplot2" ,r-ggplot2)
2723 ("r-gridextra" ,r-gridextra)
2725 ("r-igraph" ,r-igraph)
2726 ("r-interactionset" ,r-interactionset)
2727 ("r-iranges" ,r-iranges)
2728 ("r-rsamtools" ,r-rsamtools)
2729 ("r-rtracklayer" ,r-rtracklayer)
2730 ("r-s4vectors" ,r-s4vectors)
2731 ("r-stringr" ,r-stringr)))
2733 `(("r-knitr" ,r-knitr)))
2734 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2735 (synopsis "R package for handling genomic interaction data")
2737 "This R package provides tools for handling genomic interaction data,
2738 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2739 information and producing various plots and statistics.")
2740 (license license:gpl3)))
2742 (define-public r-ctc
2749 (uri (bioconductor-uri "ctc" version))
2752 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
2753 (build-system r-build-system)
2754 (propagated-inputs `(("r-amap" ,r-amap)))
2755 (home-page "https://bioconductor.org/packages/ctc/")
2756 (synopsis "Cluster and tree conversion")
2758 "This package provides tools for exporting and importing classification
2759 trees and clusters to other programs.")
2760 (license license:gpl2)))
2762 (define-public r-goseq
2769 (uri (bioconductor-uri "goseq" version))
2772 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
2773 (build-system r-build-system)
2775 `(("r-annotationdbi" ,r-annotationdbi)
2776 ("r-biasedurn" ,r-biasedurn)
2777 ("r-biocgenerics" ,r-biocgenerics)
2778 ("r-genelendatabase" ,r-genelendatabase)
2779 ("r-go-db" ,r-go-db)
2780 ("r-mgcv" ,r-mgcv)))
2781 (home-page "https://bioconductor.org/packages/goseq/")
2782 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2784 "This package provides tools to detect Gene Ontology and/or other user
2785 defined categories which are over/under represented in RNA-seq data.")
2786 (license license:lgpl2.0+)))
2788 (define-public r-glimma
2795 (uri (bioconductor-uri "Glimma" version))
2798 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
2799 (properties `((upstream-name . "Glimma")))
2800 (build-system r-build-system)
2802 `(("r-deseq2" ,r-deseq2)
2803 ("r-edger" ,r-edger)
2804 ("r-htmlwidgets" ,r-htmlwidgets)
2805 ("r-jsonlite" ,r-jsonlite)
2806 ("r-limma" ,r-limma)
2807 ("r-s4vectors" ,r-s4vectors)
2808 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2810 `(("r-knitr" ,r-knitr)))
2811 (home-page "https://github.com/Shians/Glimma")
2812 (synopsis "Interactive HTML graphics")
2814 "This package generates interactive visualisations for analysis of
2815 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2816 HTML page. The interactions are built on top of the popular static
2817 representations of analysis results in order to provide additional
2819 (license license:lgpl3)))
2821 (define-public r-rots
2828 (uri (bioconductor-uri "ROTS" version))
2831 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
2832 (properties `((upstream-name . "ROTS")))
2833 (build-system r-build-system)
2835 `(("r-biobase" ,r-biobase)
2836 ("r-rcpp" ,r-rcpp)))
2837 (home-page "https://bioconductor.org/packages/ROTS/")
2838 (synopsis "Reproducibility-Optimized Test Statistic")
2840 "This package provides tools for calculating the
2841 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2843 (license license:gpl2+)))
2845 (define-public r-plgem
2852 (uri (bioconductor-uri "plgem" version))
2855 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
2856 (build-system r-build-system)
2858 `(("r-biobase" ,r-biobase)
2859 ("r-mass" ,r-mass)))
2860 (home-page "http://www.genopolis.it")
2861 (synopsis "Detect differential expression in microarray and proteomics datasets")
2863 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2864 model the variance-versus-mean dependence that exists in a variety of
2865 genome-wide datasets, including microarray and proteomics data. The use of
2866 PLGEM has been shown to improve the detection of differentially expressed
2867 genes or proteins in these datasets.")
2868 (license license:gpl2)))
2870 (define-public r-inspect
2877 (uri (bioconductor-uri "INSPEcT" version))
2880 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
2881 (properties `((upstream-name . "INSPEcT")))
2882 (build-system r-build-system)
2884 `(("r-biobase" ,r-biobase)
2885 ("r-biocgenerics" ,r-biocgenerics)
2886 ("r-biocparallel" ,r-biocparallel)
2887 ("r-deseq2" ,r-deseq2)
2888 ("r-desolve" ,r-desolve)
2889 ("r-gdata" ,r-gdata)
2890 ("r-genomeinfodb" ,r-genomeinfodb)
2891 ("r-genomicalignments" ,r-genomicalignments)
2892 ("r-genomicfeatures" ,r-genomicfeatures)
2893 ("r-genomicranges" ,r-genomicranges)
2894 ("r-iranges" ,r-iranges)
2895 ("r-kernsmooth" ,r-kernsmooth)
2896 ("r-plgem" ,r-plgem)
2898 ("r-rootsolve" ,r-rootsolve)
2899 ("r-rsamtools" ,r-rsamtools)
2900 ("r-rtracklayer" ,r-rtracklayer)
2901 ("r-s4vectors" ,r-s4vectors)
2902 ("r-shiny" ,r-shiny)
2903 ("r-summarizedexperiment" ,r-summarizedexperiment)
2904 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2905 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2907 `(("r-knitr" ,r-knitr)))
2908 (home-page "https://bioconductor.org/packages/INSPEcT")
2909 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2911 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2912 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2913 order to evaluate synthesis, processing and degradation rates and assess via
2914 modeling the rates that determines changes in mature mRNA levels.")
2915 (license license:gpl2)))
2917 (define-public r-dnabarcodes
2919 (name "r-dnabarcodes")
2924 (uri (bioconductor-uri "DNABarcodes" version))
2927 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
2928 (properties `((upstream-name . "DNABarcodes")))
2929 (build-system r-build-system)
2932 ("r-matrix" ,r-matrix)
2933 ("r-rcpp" ,r-rcpp)))
2935 `(("r-knitr" ,r-knitr)))
2936 (home-page "https://bioconductor.org/packages/DNABarcodes")
2937 (synopsis "Create and analyze DNA barcodes")
2939 "This package offers tools to create DNA barcode sets capable of
2940 correcting insertion, deletion, and substitution errors. Existing barcodes
2941 can be analyzed regarding their minimal, maximal and average distances between
2942 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2943 demultiplexed, i.e. assigned to their original reference barcode.")
2944 (license license:gpl2)))
2946 (define-public r-ruvseq
2953 (uri (bioconductor-uri "RUVSeq" version))
2956 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
2957 (properties `((upstream-name . "RUVSeq")))
2958 (build-system r-build-system)
2960 `(("r-biobase" ,r-biobase)
2961 ("r-edaseq" ,r-edaseq)
2962 ("r-edger" ,r-edger)
2963 ("r-mass" ,r-mass)))
2965 `(("r-knitr" ,r-knitr)))
2966 (home-page "https://github.com/drisso/RUVSeq")
2967 (synopsis "Remove unwanted variation from RNA-Seq data")
2969 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2970 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2972 (license license:artistic2.0)))
2974 (define-public r-biocneighbors
2976 (name "r-biocneighbors")
2981 (uri (bioconductor-uri "BiocNeighbors" version))
2984 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
2985 (properties `((upstream-name . "BiocNeighbors")))
2986 (build-system r-build-system)
2988 `(("r-biocparallel" ,r-biocparallel)
2989 ("r-matrix" ,r-matrix)
2991 ("r-rcpphnsw" ,r-rcpphnsw)
2992 ("r-s4vectors" ,r-s4vectors)))
2994 `(("r-knitr" ,r-knitr)))
2995 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2996 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2998 "This package implements exact and approximate methods for nearest
2999 neighbor detection, in a framework that allows them to be easily switched
3000 within Bioconductor packages or workflows. The exact algorithm is implemented
3001 using pre-clustering with the k-means algorithm. Functions are also provided
3002 to search for all neighbors within a given distance. Parallelization is
3003 achieved for all methods using the BiocParallel framework.")
3004 (license license:gpl3)))
3006 (define-public r-biocsingular
3008 (name "r-biocsingular")
3013 (uri (bioconductor-uri "BiocSingular" version))
3016 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
3017 (properties `((upstream-name . "BiocSingular")))
3018 (build-system r-build-system)
3020 `(("r-beachmat" ,r-beachmat)
3021 ("r-biocgenerics" ,r-biocgenerics)
3022 ("r-biocparallel" ,r-biocparallel)
3023 ("r-delayedarray" ,r-delayedarray)
3024 ("r-irlba" ,r-irlba)
3025 ("r-matrix" ,r-matrix)
3028 ("r-s4vectors" ,r-s4vectors)))
3030 `(("r-knitr" ,r-knitr)))
3031 (home-page "https://github.com/LTLA/BiocSingular")
3032 (synopsis "Singular value decomposition for Bioconductor packages")
3034 "This package implements exact and approximate methods for singular value
3035 decomposition and principal components analysis, in a framework that allows
3036 them to be easily switched within Bioconductor packages or workflows. Where
3037 possible, parallelization is achieved using the BiocParallel framework.")
3038 (license license:gpl3)))
3040 (define-public r-destiny
3047 (uri (bioconductor-uri "destiny" version))
3050 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
3051 (build-system r-build-system)
3053 `(("r-biobase" ,r-biobase)
3054 ("r-biocgenerics" ,r-biocgenerics)
3055 ("r-ggplot-multistats" ,r-ggplot-multistats)
3056 ("r-ggplot2" ,r-ggplot2)
3057 ("r-ggthemes" ,r-ggthemes)
3058 ("r-irlba" ,r-irlba)
3059 ("r-knn-covertree" ,r-knn-covertree)
3060 ("r-matrix" ,r-matrix)
3061 ("r-pcamethods" ,r-pcamethods)
3062 ("r-proxy" ,r-proxy)
3064 ("r-rcppeigen" ,r-rcppeigen)
3065 ("r-rcpphnsw" ,r-rcpphnsw)
3066 ("r-rspectra" ,r-rspectra)
3067 ("r-scales" ,r-scales)
3068 ("r-scatterplot3d" ,r-scatterplot3d)
3069 ("r-singlecellexperiment" ,r-singlecellexperiment)
3070 ("r-smoother" ,r-smoother)
3071 ("r-summarizedexperiment" ,r-summarizedexperiment)
3072 ("r-tidyr" ,r-tidyr)
3073 ("r-tidyselect" ,r-tidyselect)
3076 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
3077 (home-page "https://bioconductor.org/packages/destiny/")
3078 (synopsis "Create and plot diffusion maps")
3079 (description "This package provides tools to create and plot diffusion
3081 ;; Any version of the GPL
3082 (license license:gpl3+)))
3084 (define-public r-savr
3091 (uri (bioconductor-uri "savR" version))
3094 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
3095 (properties `((upstream-name . "savR")))
3096 (build-system r-build-system)
3098 `(("r-ggplot2" ,r-ggplot2)
3099 ("r-gridextra" ,r-gridextra)
3100 ("r-reshape2" ,r-reshape2)
3101 ("r-scales" ,r-scales)
3103 (home-page "https://github.com/bcalder/savR")
3104 (synopsis "Parse and analyze Illumina SAV files")
3106 "This package provides tools to parse Illumina Sequence Analysis
3107 Viewer (SAV) files, access data, and generate QC plots.")
3108 (license license:agpl3+)))
3110 (define-public r-chipexoqual
3112 (name "r-chipexoqual")
3117 (uri (bioconductor-uri "ChIPexoQual" version))
3120 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
3121 (properties `((upstream-name . "ChIPexoQual")))
3122 (build-system r-build-system)
3124 `(("r-biocparallel" ,r-biocparallel)
3125 ("r-biovizbase" ,r-biovizbase)
3126 ("r-broom" ,r-broom)
3127 ("r-data-table" ,r-data-table)
3128 ("r-dplyr" ,r-dplyr)
3129 ("r-genomeinfodb" ,r-genomeinfodb)
3130 ("r-genomicalignments" ,r-genomicalignments)
3131 ("r-genomicranges" ,r-genomicranges)
3132 ("r-ggplot2" ,r-ggplot2)
3133 ("r-hexbin" ,r-hexbin)
3134 ("r-iranges" ,r-iranges)
3135 ("r-rcolorbrewer" ,r-rcolorbrewer)
3136 ("r-rmarkdown" ,r-rmarkdown)
3137 ("r-rsamtools" ,r-rsamtools)
3138 ("r-s4vectors" ,r-s4vectors)
3139 ("r-scales" ,r-scales)
3140 ("r-viridis" ,r-viridis)))
3142 `(("r-knitr" ,r-knitr)))
3143 (home-page "https://github.com/keleslab/ChIPexoQual")
3144 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
3146 "This package provides a quality control pipeline for ChIP-exo/nexus
3148 (license license:gpl2+)))
3150 (define-public r-copynumber
3152 (name "r-copynumber")
3156 (uri (bioconductor-uri "copynumber" version))
3159 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
3160 (build-system r-build-system)
3162 `(("r-s4vectors" ,r-s4vectors)
3163 ("r-iranges" ,r-iranges)
3164 ("r-genomicranges" ,r-genomicranges)
3165 ("r-biocgenerics" ,r-biocgenerics)))
3166 (home-page "https://bioconductor.org/packages/copynumber")
3167 (synopsis "Segmentation of single- and multi-track copy number data")
3169 "This package segments single- and multi-track copy number data by a
3170 penalized least squares regression method.")
3171 (license license:artistic2.0)))
3173 (define-public r-dnacopy
3180 (uri (bioconductor-uri "DNAcopy" version))
3183 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
3184 (properties `((upstream-name . "DNAcopy")))
3185 (build-system r-build-system)
3186 (native-inputs `(("gfortran" ,gfortran)))
3187 (home-page "https://bioconductor.org/packages/DNAcopy")
3188 (synopsis "DNA copy number data analysis")
3190 "This package implements the @dfn{circular binary segmentation} (CBS)
3191 algorithm to segment DNA copy number data and identify genomic regions with
3192 abnormal copy number.")
3193 (license license:gpl2+)))
3195 ;; This is a CRAN package, but it uncharacteristically depends on a
3196 ;; Bioconductor package.
3197 (define-public r-htscluster
3199 (name "r-htscluster")
3204 (uri (cran-uri "HTSCluster" version))
3207 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
3208 (properties `((upstream-name . "HTSCluster")))
3209 (build-system r-build-system)
3211 `(("r-capushe" ,r-capushe)
3212 ("r-edger" ,r-edger)
3213 ("r-plotrix" ,r-plotrix)))
3214 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
3215 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
3217 "This package provides a Poisson mixture model is implemented to cluster
3218 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
3219 estimation is performed using either the EM or CEM algorithm, and the slope
3220 heuristics are used for model selection (i.e., to choose the number of
3222 (license license:gpl3+)))
3224 (define-public r-deds
3231 (uri (bioconductor-uri "DEDS" version))
3234 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
3235 (properties `((upstream-name . "DEDS")))
3236 (build-system r-build-system)
3237 (home-page "https://bioconductor.org/packages/DEDS/")
3238 (synopsis "Differential expression via distance summary for microarray data")
3240 "This library contains functions that calculate various statistics of
3241 differential expression for microarray data, including t statistics, fold
3242 change, F statistics, SAM, moderated t and F statistics and B statistics. It
3243 also implements a new methodology called DEDS (Differential Expression via
3244 Distance Summary), which selects differentially expressed genes by integrating
3245 and summarizing a set of statistics using a weighted distance approach.")
3246 ;; Any version of the LGPL.
3247 (license license:lgpl3+)))
3249 ;; This is a CRAN package, but since it depends on a Bioconductor package we
3251 (define-public r-nbpseq
3258 (uri (cran-uri "NBPSeq" version))
3261 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
3262 (properties `((upstream-name . "NBPSeq")))
3263 (build-system r-build-system)
3265 `(("r-qvalue" ,r-qvalue)))
3266 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
3267 (synopsis "Negative binomial models for RNA-Seq data")
3269 "This package provides negative binomial models for two-group comparisons
3270 and regression inferences from RNA-sequencing data.")
3271 (license license:gpl2)))
3273 (define-public r-ebseq
3280 (uri (bioconductor-uri "EBSeq" version))
3283 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3284 (properties `((upstream-name . "EBSeq")))
3285 (build-system r-build-system)
3287 `(("r-blockmodeling" ,r-blockmodeling)
3288 ("r-gplots" ,r-gplots)
3289 ("r-testthat" ,r-testthat)))
3290 (home-page "https://bioconductor.org/packages/EBSeq")
3291 (synopsis "Differential expression analysis of RNA-seq data")
3293 "This package provides tools for differential expression analysis at both
3294 gene and isoform level using RNA-seq data")
3295 (license license:artistic2.0)))
3297 (define-public r-karyoploter
3299 (name "r-karyoploter")
3303 (uri (bioconductor-uri "karyoploteR" version))
3306 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
3307 (build-system r-build-system)
3309 `(("r-annotationdbi" ,r-annotationdbi)
3310 ("r-bamsignals" ,r-bamsignals)
3311 ("r-bezier" ,r-bezier)
3312 ("r-biovizbase" ,r-biovizbase)
3313 ("r-digest" ,r-digest)
3314 ("r-genomeinfodb" ,r-genomeinfodb)
3315 ("r-genomicfeatures" ,r-genomicfeatures)
3316 ("r-genomicranges" ,r-genomicranges)
3317 ("r-iranges" ,r-iranges)
3318 ("r-memoise" ,r-memoise)
3319 ("r-regioner" ,r-regioner)
3320 ("r-rsamtools" ,r-rsamtools)
3321 ("r-rtracklayer" ,r-rtracklayer)
3322 ("r-s4vectors" ,r-s4vectors)
3323 ("r-variantannotation" ,r-variantannotation)))
3325 `(("r-knitr" ,r-knitr)))
3326 (home-page "https://bioconductor.org/packages/karyoploteR/")
3327 (synopsis "Plot customizable linear genomes displaying arbitrary data")
3328 (description "This package creates karyotype plots of arbitrary genomes and
3329 offers a complete set of functions to plot arbitrary data on them. It mimics
3330 many R base graphics functions coupling them with a coordinate change function
3331 automatically mapping the chromosome and data coordinates into the plot
3333 (license license:artistic2.0)))
3335 (define-public r-lpsymphony
3337 (name "r-lpsymphony")
3342 (uri (bioconductor-uri "lpsymphony" version))
3345 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
3346 (build-system r-build-system)
3350 `(("pkg-config" ,pkg-config)
3351 ("r-knitr" ,r-knitr)))
3352 (home-page "https://r-forge.r-project.org/projects/rsymphony")
3353 (synopsis "Symphony integer linear programming solver in R")
3355 "This package was derived from Rsymphony. The package provides an R
3356 interface to SYMPHONY, a linear programming solver written in C++. The main
3357 difference between this package and Rsymphony is that it includes the solver
3358 source code, while Rsymphony expects to find header and library files on the
3359 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3360 to install interface to SYMPHONY.")
3361 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3362 ;; lpsimphony is released under the same terms.
3363 (license license:epl1.0)))
3365 (define-public r-ihw
3372 (uri (bioconductor-uri "IHW" version))
3375 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3376 (properties `((upstream-name . "IHW")))
3377 (build-system r-build-system)
3379 `(("r-biocgenerics" ,r-biocgenerics)
3380 ("r-fdrtool" ,r-fdrtool)
3381 ("r-lpsymphony" ,r-lpsymphony)
3382 ("r-slam" ,r-slam)))
3384 `(("r-knitr" ,r-knitr)))
3385 (home-page "https://bioconductor.org/packages/IHW")
3386 (synopsis "Independent hypothesis weighting")
3388 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3389 procedure that increases power compared to the method of Benjamini and
3390 Hochberg by assigning data-driven weights to each hypothesis. The input to
3391 IHW is a two-column table of p-values and covariates. The covariate can be
3392 any continuous-valued or categorical variable that is thought to be
3393 informative on the statistical properties of each hypothesis test, while it is
3394 independent of the p-value under the null hypothesis.")
3395 (license license:artistic2.0)))
3397 (define-public r-icobra
3404 (uri (bioconductor-uri "iCOBRA" version))
3407 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3408 (properties `((upstream-name . "iCOBRA")))
3409 (build-system r-build-system)
3411 `(("r-dplyr" ,r-dplyr)
3413 ("r-ggplot2" ,r-ggplot2)
3414 ("r-limma" ,r-limma)
3415 ("r-reshape2" ,r-reshape2)
3417 ("r-scales" ,r-scales)
3418 ("r-shiny" ,r-shiny)
3419 ("r-shinybs" ,r-shinybs)
3420 ("r-shinydashboard" ,r-shinydashboard)
3421 ("r-upsetr" ,r-upsetr)))
3423 `(("r-knitr" ,r-knitr)))
3424 (home-page "https://bioconductor.org/packages/iCOBRA")
3425 (synopsis "Comparison and visualization of ranking and assignment methods")
3427 "This package provides functions for calculation and visualization of
3428 performance metrics for evaluation of ranking and binary
3429 classification (assignment) methods. It also contains a Shiny application for
3430 interactive exploration of results.")
3431 (license license:gpl2+)))
3433 (define-public r-mast
3440 (uri (bioconductor-uri "MAST" version))
3443 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
3444 (properties `((upstream-name . "MAST")))
3445 (build-system r-build-system)
3447 `(("r-abind" ,r-abind)
3448 ("r-biobase" ,r-biobase)
3449 ("r-biocgenerics" ,r-biocgenerics)
3450 ("r-data-table" ,r-data-table)
3451 ("r-ggplot2" ,r-ggplot2)
3453 ("r-progress" ,r-progress)
3454 ("r-reshape2" ,r-reshape2)
3455 ("r-s4vectors" ,r-s4vectors)
3456 ("r-singlecellexperiment" ,r-singlecellexperiment)
3457 ("r-stringr" ,r-stringr)
3458 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3460 `(("r-knitr" ,r-knitr)))
3461 (home-page "https://github.com/RGLab/MAST/")
3462 (synopsis "Model-based analysis of single cell transcriptomics")
3464 "This package provides methods and models for handling zero-inflated
3465 single cell assay data.")
3466 (license license:gpl2+)))
3468 (define-public r-monocle
3475 (uri (bioconductor-uri "monocle" version))
3478 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
3479 (build-system r-build-system)
3481 `(("r-biobase" ,r-biobase)
3482 ("r-biocgenerics" ,r-biocgenerics)
3483 ("r-biocviews" ,r-biocviews)
3484 ("r-cluster" ,r-cluster)
3485 ("r-combinat" ,r-combinat)
3486 ("r-ddrtree" ,r-ddrtree)
3487 ("r-densityclust" ,r-densityclust)
3488 ("r-dplyr" ,r-dplyr)
3489 ("r-fastica" ,r-fastica)
3490 ("r-ggplot2" ,r-ggplot2)
3491 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3492 ("r-igraph" ,r-igraph)
3493 ("r-irlba" ,r-irlba)
3494 ("r-limma" ,r-limma)
3496 ("r-matrix" ,r-matrix)
3497 ("r-matrixstats" ,r-matrixstats)
3498 ("r-pheatmap" ,r-pheatmap)
3500 ("r-proxy" ,r-proxy)
3501 ("r-qlcmatrix" ,r-qlcmatrix)
3504 ("r-reshape2" ,r-reshape2)
3505 ("r-rtsne" ,r-rtsne)
3507 ("r-stringr" ,r-stringr)
3508 ("r-tibble" ,r-tibble)
3510 ("r-viridis" ,r-viridis)))
3512 `(("r-knitr" ,r-knitr)))
3513 (home-page "https://bioconductor.org/packages/monocle")
3514 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3516 "Monocle performs differential expression and time-series analysis for
3517 single-cell expression experiments. It orders individual cells according to
3518 progress through a biological process, without knowing ahead of time which
3519 genes define progress through that process. Monocle also performs
3520 differential expression analysis, clustering, visualization, and other useful
3521 tasks on single cell expression data. It is designed to work with RNA-Seq and
3522 qPCR data, but could be used with other types as well.")
3523 (license license:artistic2.0)))
3525 (define-public r-monocle3
3533 (url "https://github.com/cole-trapnell-lab/monocle3")
3535 (file-name (git-file-name name version))
3538 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3539 (build-system r-build-system)
3541 `(("r-biobase" ,r-biobase)
3542 ("r-biocgenerics" ,r-biocgenerics)
3543 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3544 ("r-dplyr" ,r-dplyr)
3545 ("r-ggplot2" ,r-ggplot2)
3546 ("r-ggrepel" ,r-ggrepel)
3548 ("r-htmlwidgets" ,r-htmlwidgets)
3549 ("r-igraph" ,r-igraph)
3550 ("r-irlba" ,r-irlba)
3551 ("r-limma" ,r-limma)
3552 ("r-lmtest" ,r-lmtest)
3554 ("r-matrix" ,r-matrix)
3555 ("r-matrix-utils" ,r-matrix-utils)
3556 ("r-pbapply" ,r-pbapply)
3557 ("r-pbmcapply" ,r-pbmcapply)
3558 ("r-pheatmap" ,r-pheatmap)
3559 ("r-plotly" ,r-plotly)
3561 ("r-proxy" ,r-proxy)
3563 ("r-purrr" ,r-purrr)
3566 ("r-rcppparallel" ,r-rcppparallel)
3567 ("r-reshape2" ,r-reshape2)
3568 ("r-reticulate" ,r-reticulate)
3569 ("r-rhpcblasctl" ,r-rhpcblasctl)
3570 ("r-rtsne" ,r-rtsne)
3571 ("r-shiny" ,r-shiny)
3573 ("r-spdep" ,r-spdep)
3574 ("r-speedglm" ,r-speedglm)
3575 ("r-stringr" ,r-stringr)
3576 ("r-singlecellexperiment" ,r-singlecellexperiment)
3577 ("r-tibble" ,r-tibble)
3578 ("r-tidyr" ,r-tidyr)
3580 ("r-viridis" ,r-viridis)))
3581 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3582 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3584 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3585 (license license:expat)))
3587 (define-public r-noiseq
3594 (uri (bioconductor-uri "NOISeq" version))
3597 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
3598 (properties `((upstream-name . "NOISeq")))
3599 (build-system r-build-system)
3601 `(("r-biobase" ,r-biobase)
3602 ("r-matrix" ,r-matrix)))
3603 (home-page "https://bioconductor.org/packages/NOISeq")
3604 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3606 "This package provides tools to support the analysis of RNA-seq
3607 expression data or other similar kind of data. It provides exploratory plots
3608 to evaluate saturation, count distribution, expression per chromosome, type of
3609 detected features, features length, etc. It also supports the analysis of
3610 differential expression between two experimental conditions with no parametric
3612 (license license:artistic2.0)))
3614 (define-public r-scdd
3621 (uri (bioconductor-uri "scDD" version))
3624 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
3625 (properties `((upstream-name . "scDD")))
3626 (build-system r-build-system)
3629 ("r-biocparallel" ,r-biocparallel)
3630 ("r-ebseq" ,r-ebseq)
3631 ("r-fields" ,r-fields)
3632 ("r-ggplot2" ,r-ggplot2)
3633 ("r-mclust" ,r-mclust)
3634 ("r-outliers" ,r-outliers)
3635 ("r-s4vectors" ,r-s4vectors)
3636 ("r-scran" ,r-scran)
3637 ("r-singlecellexperiment" ,r-singlecellexperiment)
3638 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3640 `(("r-knitr" ,r-knitr)))
3641 (home-page "https://github.com/kdkorthauer/scDD")
3642 (synopsis "Mixture modeling of single-cell RNA-seq data")
3644 "This package implements a method to analyze single-cell RNA-seq data
3645 utilizing flexible Dirichlet Process mixture models. Genes with differential
3646 distributions of expression are classified into several interesting patterns
3647 of differences between two conditions. The package also includes functions
3648 for simulating data with these patterns from negative binomial
3650 (license license:gpl2)))
3652 (define-public r-scone
3659 (uri (bioconductor-uri "scone" version))
3662 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
3663 (build-system r-build-system)
3665 `(("r-aroma-light" ,r-aroma-light)
3666 ("r-biocparallel" ,r-biocparallel)
3668 ("r-class" ,r-class)
3669 ("r-cluster" ,r-cluster)
3670 ("r-compositions" ,r-compositions)
3671 ("r-diptest" ,r-diptest)
3672 ("r-edger" ,r-edger)
3674 ("r-gplots" ,r-gplots)
3675 ("r-hexbin" ,r-hexbin)
3676 ("r-limma" ,r-limma)
3677 ("r-matrixstats" ,r-matrixstats)
3678 ("r-mixtools" ,r-mixtools)
3679 ("r-rarpack" ,r-rarpack)
3680 ("r-rcolorbrewer" ,r-rcolorbrewer)
3681 ("r-rhdf5" ,r-rhdf5)
3682 ("r-ruvseq" ,r-ruvseq)
3683 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3685 `(("r-knitr" ,r-knitr)))
3686 (home-page "https://bioconductor.org/packages/scone")
3687 (synopsis "Single cell overview of normalized expression data")
3689 "SCONE is an R package for comparing and ranking the performance of
3690 different normalization schemes for single-cell RNA-seq and other
3691 high-throughput analyses.")
3692 (license license:artistic2.0)))
3694 (define-public r-geoquery
3701 (uri (bioconductor-uri "GEOquery" version))
3704 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
3705 (properties `((upstream-name . "GEOquery")))
3706 (build-system r-build-system)
3708 `(("r-biobase" ,r-biobase)
3709 ("r-dplyr" ,r-dplyr)
3711 ("r-limma" ,r-limma)
3712 ("r-magrittr" ,r-magrittr)
3713 ("r-readr" ,r-readr)
3714 ("r-tidyr" ,r-tidyr)
3715 ("r-xml2" ,r-xml2)))
3717 `(("r-knitr" ,r-knitr)))
3718 (home-page "https://github.com/seandavi/GEOquery/")
3719 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3721 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3722 microarray data. Given the rich and varied nature of this resource, it is
3723 only natural to want to apply BioConductor tools to these data. GEOquery is
3724 the bridge between GEO and BioConductor.")
3725 (license license:gpl2)))
3727 (define-public r-illuminaio
3729 (name "r-illuminaio")
3734 (uri (bioconductor-uri "illuminaio" version))
3737 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
3738 (build-system r-build-system)
3740 `(("r-base64" ,r-base64)))
3741 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3742 (synopsis "Parse Illumina microarray output files")
3744 "This package provides tools for parsing Illumina's microarray output
3745 files, including IDAT.")
3746 (license license:gpl2)))
3748 (define-public r-siggenes
3755 (uri (bioconductor-uri "siggenes" version))
3758 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
3759 (build-system r-build-system)
3761 `(("r-biobase" ,r-biobase)
3762 ("r-multtest" ,r-multtest)
3763 ("r-scrime" ,r-scrime)))
3764 (home-page "https://bioconductor.org/packages/siggenes/")
3766 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3768 "This package provides tools for the identification of differentially
3769 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3770 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3771 Bayes Analyses of Microarrays} (EBAM).")
3772 (license license:lgpl2.0+)))
3774 (define-public r-bumphunter
3776 (name "r-bumphunter")
3781 (uri (bioconductor-uri "bumphunter" version))
3784 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
3785 (build-system r-build-system)
3787 `(("r-annotationdbi" ,r-annotationdbi)
3788 ("r-biocgenerics" ,r-biocgenerics)
3789 ("r-dorng" ,r-dorng)
3790 ("r-foreach" ,r-foreach)
3791 ("r-genomeinfodb" ,r-genomeinfodb)
3792 ("r-genomicfeatures" ,r-genomicfeatures)
3793 ("r-genomicranges" ,r-genomicranges)
3794 ("r-iranges" ,r-iranges)
3795 ("r-iterators" ,r-iterators)
3796 ("r-limma" ,r-limma)
3797 ("r-locfit" ,r-locfit)
3798 ("r-matrixstats" ,r-matrixstats)
3799 ("r-s4vectors" ,r-s4vectors)))
3800 (home-page "https://github.com/ririzarr/bumphunter")
3801 (synopsis "Find bumps in genomic data")
3803 "This package provides tools for finding bumps in genomic data in order
3804 to identify differentially methylated regions in epigenetic epidemiology
3806 (license license:artistic2.0)))
3808 (define-public r-minfi
3815 (uri (bioconductor-uri "minfi" version))
3818 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
3819 (build-system r-build-system)
3821 `(("r-beanplot" ,r-beanplot)
3822 ("r-biobase" ,r-biobase)
3823 ("r-biocgenerics" ,r-biocgenerics)
3824 ("r-biocparallel" ,r-biocparallel)
3825 ("r-biostrings" ,r-biostrings)
3826 ("r-bumphunter" ,r-bumphunter)
3827 ("r-data-table" ,r-data-table)
3828 ("r-delayedarray" ,r-delayedarray)
3829 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3830 ("r-genefilter" ,r-genefilter)
3831 ("r-genomeinfodb" ,r-genomeinfodb)
3832 ("r-genomicranges" ,r-genomicranges)
3833 ("r-geoquery" ,r-geoquery)
3834 ("r-hdf5array" ,r-hdf5array)
3835 ("r-illuminaio" ,r-illuminaio)
3836 ("r-iranges" ,r-iranges)
3837 ("r-lattice" ,r-lattice)
3838 ("r-limma" ,r-limma)
3840 ("r-mclust" ,r-mclust)
3842 ("r-nor1mix" ,r-nor1mix)
3843 ("r-preprocesscore" ,r-preprocesscore)
3844 ("r-quadprog" ,r-quadprog)
3845 ("r-rcolorbrewer" ,r-rcolorbrewer)
3846 ("r-reshape" ,r-reshape)
3847 ("r-s4vectors" ,r-s4vectors)
3848 ("r-siggenes" ,r-siggenes)
3849 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3851 `(("r-knitr" ,r-knitr)))
3852 (home-page "https://github.com/hansenlab/minfi")
3853 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3855 "This package provides tools to analyze and visualize Illumina Infinium
3856 methylation arrays.")
3857 (license license:artistic2.0)))
3859 (define-public r-methylumi
3861 (name "r-methylumi")
3866 (uri (bioconductor-uri "methylumi" version))
3869 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
3870 (build-system r-build-system)
3872 `(("r-annotate" ,r-annotate)
3873 ("r-annotationdbi" ,r-annotationdbi)
3874 ("r-biobase" ,r-biobase)
3875 ("r-biocgenerics" ,r-biocgenerics)
3876 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3877 ("r-genefilter" ,r-genefilter)
3878 ("r-genomeinfodb" ,r-genomeinfodb)
3879 ("r-genomicranges" ,r-genomicranges)
3880 ("r-ggplot2" ,r-ggplot2)
3881 ("r-illuminaio" ,r-illuminaio)
3882 ("r-iranges" ,r-iranges)
3883 ("r-lattice" ,r-lattice)
3884 ("r-matrixstats" ,r-matrixstats)
3885 ("r-minfi" ,r-minfi)
3886 ("r-reshape2" ,r-reshape2)
3887 ("r-s4vectors" ,r-s4vectors)
3888 ("r-scales" ,r-scales)
3889 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3891 `(("r-knitr" ,r-knitr)))
3892 (home-page "https://bioconductor.org/packages/methylumi")
3893 (synopsis "Handle Illumina methylation data")
3895 "This package provides classes for holding and manipulating Illumina
3896 methylation data. Based on eSet, it can contain MIAME information, sample
3897 information, feature information, and multiple matrices of data. An
3898 \"intelligent\" import function, methylumiR can read the Illumina text files
3899 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3900 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3901 background correction, and quality control features for GoldenGate, Infinium,
3902 and Infinium HD arrays are also included.")
3903 (license license:gpl2)))
3905 (define-public r-lumi
3912 (uri (bioconductor-uri "lumi" version))
3915 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
3916 (build-system r-build-system)
3918 `(("r-affy" ,r-affy)
3919 ("r-annotate" ,r-annotate)
3920 ("r-annotationdbi" ,r-annotationdbi)
3921 ("r-biobase" ,r-biobase)
3923 ("r-genomicfeatures" ,r-genomicfeatures)
3924 ("r-genomicranges" ,r-genomicranges)
3925 ("r-kernsmooth" ,r-kernsmooth)
3926 ("r-lattice" ,r-lattice)
3928 ("r-methylumi" ,r-methylumi)
3930 ("r-nleqslv" ,r-nleqslv)
3931 ("r-preprocesscore" ,r-preprocesscore)
3932 ("r-rsqlite" ,r-rsqlite)))
3933 (home-page "https://bioconductor.org/packages/lumi")
3934 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3936 "The lumi package provides an integrated solution for the Illumina
3937 microarray data analysis. It includes functions of Illumina
3938 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3939 variance stabilization, normalization and gene annotation at the probe level.
3940 It also includes the functions of processing Illumina methylation microarrays,
3941 especially Illumina Infinium methylation microarrays.")
3942 (license license:lgpl2.0+)))
3944 (define-public r-linnorm
3951 (uri (bioconductor-uri "Linnorm" version))
3954 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
3955 (properties `((upstream-name . "Linnorm")))
3956 (build-system r-build-system)
3958 `(("r-amap" ,r-amap)
3959 ("r-apcluster" ,r-apcluster)
3960 ("r-ellipse" ,r-ellipse)
3961 ("r-fastcluster" ,r-fastcluster)
3963 ("r-ggdendro" ,r-ggdendro)
3964 ("r-ggplot2" ,r-ggplot2)
3965 ("r-gmodels" ,r-gmodels)
3966 ("r-igraph" ,r-igraph)
3967 ("r-limma" ,r-limma)
3969 ("r-mclust" ,r-mclust)
3971 ("r-rcpparmadillo" ,r-rcpparmadillo)
3972 ("r-rtsne" ,r-rtsne)
3973 ("r-statmod" ,r-statmod)
3974 ("r-vegan" ,r-vegan)
3977 `(("r-knitr" ,r-knitr)))
3978 (home-page "http://www.jjwanglab.org/Linnorm/")
3979 (synopsis "Linear model and normality based transformation method")
3981 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3982 count data or any large scale count data. It transforms such datasets for
3983 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3984 the following pipelines are implemented:
3987 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3988 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3989 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3990 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3991 @item Differential expression analysis or differential peak detection using
3992 limma (@code{Linnorm.limma})
3993 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3994 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3995 @item Stable gene selection for scRNA-seq data; for users without or who do
3996 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3997 @item Data imputation (@code{Linnorm.DataImput}).
4000 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
4001 @code{RnaXSim} function is included for simulating RNA-seq data for the
4002 evaluation of DEG analysis methods.")
4003 (license license:expat)))
4005 (define-public r-ioniser
4012 (uri (bioconductor-uri "IONiseR" version))
4015 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
4016 (properties `((upstream-name . "IONiseR")))
4017 (build-system r-build-system)
4019 `(("r-biocgenerics" ,r-biocgenerics)
4020 ("r-biocparallel" ,r-biocparallel)
4021 ("r-biostrings" ,r-biostrings)
4022 ("r-bit64" ,r-bit64)
4023 ("r-dplyr" ,r-dplyr)
4024 ("r-ggplot2" ,r-ggplot2)
4025 ("r-magrittr" ,r-magrittr)
4026 ("r-rhdf5" ,r-rhdf5)
4027 ("r-shortread" ,r-shortread)
4028 ("r-stringr" ,r-stringr)
4029 ("r-tibble" ,r-tibble)
4030 ("r-tidyr" ,r-tidyr)
4031 ("r-xvector" ,r-xvector)))
4033 `(("r-knitr" ,r-knitr)))
4034 (home-page "https://bioconductor.org/packages/IONiseR/")
4035 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
4037 "IONiseR provides tools for the quality assessment of Oxford Nanopore
4038 MinION data. It extracts summary statistics from a set of fast5 files and can
4039 be used either before or after base calling. In addition to standard
4040 summaries of the read-types produced, it provides a number of plots for
4041 visualising metrics relative to experiment run time or spatially over the
4042 surface of a flowcell.")
4043 (license license:expat)))
4045 ;; This is a CRAN package, but it depends on packages from Bioconductor.
4046 (define-public r-gkmsvm
4053 (uri (cran-uri "gkmSVM" version))
4056 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
4057 (properties `((upstream-name . "gkmSVM")))
4058 (build-system r-build-system)
4060 `(("r-kernlab" ,r-kernlab)
4063 ("r-seqinr" ,r-seqinr)))
4064 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
4065 (synopsis "Gapped-kmer support vector machine")
4067 "This R package provides tools for training gapped-kmer SVM classifiers
4068 for DNA and protein sequences. This package supports several sequence
4069 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
4070 (license license:gpl2+)))
4072 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
4073 (define-public r-mutoss
4080 (uri (cran-uri "mutoss" version))
4083 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
4084 (properties `((upstream-name . "mutoss")))
4085 (build-system r-build-system)
4087 `(("r-multcomp" ,r-multcomp)
4088 ("r-multtest" ,r-multtest)
4089 ("r-mvtnorm" ,r-mvtnorm)
4090 ("r-plotrix" ,r-plotrix)))
4091 (home-page "https://github.com/kornl/mutoss/")
4092 (synopsis "Unified multiple testing procedures")
4094 "This package is designed to ease the application and comparison of
4095 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
4096 are standardized and usable by the accompanying mutossGUI package.")
4097 ;; Any version of the GPL.
4098 (license (list license:gpl2+ license:gpl3+))))
4100 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
4101 ;; from Bioconductor, so we put it here.
4102 (define-public r-metap
4109 (uri (cran-uri "metap" version))
4112 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
4113 (build-system r-build-system)
4115 `(("r-lattice" ,r-lattice)
4116 ("r-mutoss" ,r-mutoss)
4117 ("r-rdpack" ,r-rdpack)
4118 ("r-tfisher" ,r-tfisher)))
4119 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4120 (synopsis "Meta-analysis of significance values")
4122 "The canonical way to perform meta-analysis involves using effect sizes.
4123 When they are not available this package provides a number of methods for
4124 meta-analysis of significance values including the methods of Edgington,
4125 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4126 published results; and a routine for graphical display.")
4127 (license license:gpl2)))
4129 (define-public r-triform
4136 (uri (bioconductor-uri "triform" version))
4139 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
4140 (build-system r-build-system)
4142 `(("r-biocgenerics" ,r-biocgenerics)
4143 ("r-iranges" ,r-iranges)
4144 ("r-yaml" ,r-yaml)))
4145 (home-page "https://bioconductor.org/packages/triform/")
4146 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
4148 "The Triform algorithm uses model-free statistics to identify peak-like
4149 distributions of TF ChIP sequencing reads, taking advantage of an improved
4150 peak definition in combination with known profile characteristics.")
4151 (license license:gpl2)))
4153 (define-public r-varianttools
4155 (name "r-varianttools")
4160 (uri (bioconductor-uri "VariantTools" version))
4163 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
4164 (properties `((upstream-name . "VariantTools")))
4165 (build-system r-build-system)
4167 `(("r-biobase" ,r-biobase)
4168 ("r-biocgenerics" ,r-biocgenerics)
4169 ("r-biocparallel" ,r-biocparallel)
4170 ("r-biostrings" ,r-biostrings)
4171 ("r-bsgenome" ,r-bsgenome)
4172 ("r-genomeinfodb" ,r-genomeinfodb)
4173 ("r-genomicfeatures" ,r-genomicfeatures)
4174 ("r-genomicranges" ,r-genomicranges)
4175 ("r-iranges" ,r-iranges)
4176 ("r-matrix" ,r-matrix)
4177 ("r-rsamtools" ,r-rsamtools)
4178 ("r-rtracklayer" ,r-rtracklayer)
4179 ("r-s4vectors" ,r-s4vectors)
4180 ("r-variantannotation" ,r-variantannotation)))
4181 (home-page "https://bioconductor.org/packages/VariantTools/")
4182 (synopsis "Tools for exploratory analysis of variant calls")
4184 "Explore, diagnose, and compare variant calls using filters. The
4185 VariantTools package supports a workflow for loading data, calling single
4186 sample variants and tumor-specific somatic mutations or other sample-specific
4187 variant types (e.g., RNA editing). Most of the functions operate on
4188 alignments (BAM files) or datasets of called variants. The user is expected
4189 to have already aligned the reads with a separate tool, e.g., GSNAP via
4191 (license license:artistic2.0)))
4193 (define-public r-heatplus
4200 (uri (bioconductor-uri "Heatplus" version))
4203 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
4204 (properties `((upstream-name . "Heatplus")))
4205 (build-system r-build-system)
4207 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
4208 (home-page "https://github.com/alexploner/Heatplus")
4209 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
4211 "This package provides tools to display a rectangular heatmap (intensity
4212 plot) of a data matrix. By default, both samples (columns) and features (row)
4213 of the matrix are sorted according to a hierarchical clustering, and the
4214 corresponding dendrogram is plotted. Optionally, panels with additional
4215 information about samples and features can be added to the plot.")
4216 (license license:gpl2+)))
4218 (define-public r-gosemsim
4225 (uri (bioconductor-uri "GOSemSim" version))
4228 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
4229 (properties `((upstream-name . "GOSemSim")))
4230 (build-system r-build-system)
4232 `(("r-annotationdbi" ,r-annotationdbi)
4233 ("r-go-db" ,r-go-db)
4234 ("r-rcpp" ,r-rcpp)))
4236 `(("r-knitr" ,r-knitr)))
4237 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
4238 (synopsis "GO-terms semantic similarity measures")
4240 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
4241 quantitative ways to compute similarities between genes and gene groups, and
4242 have became important basis for many bioinformatics analysis approaches.
4243 GOSemSim is an R package for semantic similarity computation among GO terms,
4244 sets of GO terms, gene products and gene clusters.")
4245 (license license:artistic2.0)))
4247 (define-public r-anota
4254 (uri (bioconductor-uri "anota" version))
4257 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
4258 (build-system r-build-system)
4260 `(("r-multtest" ,r-multtest)
4261 ("r-qvalue" ,r-qvalue)))
4262 (home-page "https://bioconductor.org/packages/anota/")
4263 (synopsis "Analysis of translational activity")
4265 "Genome wide studies of translational control is emerging as a tool to
4266 study various biological conditions. The output from such analysis is both
4267 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
4268 involved in translation (the actively translating mRNA level) for each mRNA.
4269 The standard analysis of such data strives towards identifying differential
4270 translational between two or more sample classes - i.e. differences in
4271 actively translated mRNA levels that are independent of underlying differences
4272 in cytosolic mRNA levels. This package allows for such analysis using partial
4273 variances and the random variance model. As 10s of thousands of mRNAs are
4274 analyzed in parallel the library performs a number of tests to assure that
4275 the data set is suitable for such analysis.")
4276 (license license:gpl3)))
4278 (define-public r-sigpathway
4280 (name "r-sigpathway")
4285 (uri (bioconductor-uri "sigPathway" version))
4288 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
4289 (properties `((upstream-name . "sigPathway")))
4290 (build-system r-build-system)
4291 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
4292 (synopsis "Pathway analysis")
4294 "This package is used to conduct pathway analysis by calculating the NT_k
4295 and NE_k statistics in a statistical framework for determining whether a
4296 specified group of genes for a pathway has a coordinated association with a
4297 phenotype of interest.")
4298 (license license:gpl2)))
4300 (define-public r-fgsea
4307 (uri (bioconductor-uri "fgsea" version))
4310 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
4311 (build-system r-build-system)
4314 ("r-biocparallel" ,r-biocparallel)
4315 ("r-data-table" ,r-data-table)
4316 ("r-fastmatch" ,r-fastmatch)
4317 ("r-ggplot2" ,r-ggplot2)
4318 ("r-gridextra" ,r-gridextra)
4319 ("r-matrix" ,r-matrix)
4320 ("r-rcpp" ,r-rcpp)))
4322 `(("r-knitr" ,r-knitr)))
4323 (home-page "https://github.com/ctlab/fgsea/")
4324 (synopsis "Fast gene set enrichment analysis")
4326 "The package implements an algorithm for fast gene set enrichment
4327 analysis. Using the fast algorithm makes more permutations and gets
4328 more fine grained p-values, which allows using accurate standard approaches
4329 to multiple hypothesis correction.")
4330 (license license:expat)))
4332 (define-public r-dose
4339 (uri (bioconductor-uri "DOSE" version))
4342 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
4343 (properties `((upstream-name . "DOSE")))
4344 (build-system r-build-system)
4346 `(("r-annotationdbi" ,r-annotationdbi)
4347 ("r-biocparallel" ,r-biocparallel)
4348 ("r-do-db" ,r-do-db)
4349 ("r-fgsea" ,r-fgsea)
4350 ("r-ggplot2" ,r-ggplot2)
4351 ("r-gosemsim" ,r-gosemsim)
4352 ("r-qvalue" ,r-qvalue)
4353 ("r-reshape2" ,r-reshape2)))
4355 `(("r-knitr" ,r-knitr)))
4356 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4357 (synopsis "Disease ontology semantic and enrichment analysis")
4359 "This package implements five methods proposed by Resnik, Schlicker,
4360 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4361 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4362 including hypergeometric model and gene set enrichment analysis are also
4363 implemented for discovering disease associations of high-throughput biological
4365 (license license:artistic2.0)))
4367 (define-public r-enrichplot
4369 (name "r-enrichplot")
4374 (uri (bioconductor-uri "enrichplot" version))
4377 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4378 (build-system r-build-system)
4380 `(("r-cowplot" ,r-cowplot)
4382 ("r-ggplot2" ,r-ggplot2)
4383 ("r-ggraph" ,r-ggraph)
4384 ("r-gosemsim" ,r-gosemsim)
4385 ("r-igraph" ,r-igraph)
4386 ("r-magrittr" ,r-magrittr)
4388 ("r-purrr" ,r-purrr)
4389 ("r-rcolorbrewer" ,r-rcolorbrewer)
4390 ("r-reshape2" ,r-reshape2)
4391 ("r-scatterpie" ,r-scatterpie)
4392 ("r-shadowtext" ,r-shadowtext)))
4394 `(("r-knitr" ,r-knitr)))
4395 (home-page "https://github.com/GuangchuangYu/enrichplot")
4396 (synopsis "Visualization of functional enrichment result")
4398 "The enrichplot package implements several visualization methods for
4399 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4400 All the visualization methods are developed based on ggplot2 graphics.")
4401 (license license:artistic2.0)))
4403 (define-public r-clusterprofiler
4405 (name "r-clusterprofiler")
4410 (uri (bioconductor-uri "clusterProfiler" version))
4413 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4415 `((upstream-name . "clusterProfiler")))
4416 (build-system r-build-system)
4418 `(("r-annotationdbi" ,r-annotationdbi)
4420 ("r-downloader" ,r-downloader)
4421 ("r-dplyr" ,r-dplyr)
4422 ("r-enrichplot" ,r-enrichplot)
4423 ("r-go-db" ,r-go-db)
4424 ("r-gosemsim" ,r-gosemsim)
4425 ("r-magrittr" ,r-magrittr)
4427 ("r-qvalue" ,r-qvalue)
4428 ("r-rlang" ,r-rlang)
4429 ("r-rvcheck" ,r-rvcheck)
4430 ("r-tidyr" ,r-tidyr)))
4432 `(("r-knitr" ,r-knitr)))
4433 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4434 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4436 "This package implements methods to analyze and visualize functional
4437 profiles (GO and KEGG) of gene and gene clusters.")
4438 (license license:artistic2.0)))
4440 (define-public r-mlinterfaces
4442 (name "r-mlinterfaces")
4447 (uri (bioconductor-uri "MLInterfaces" version))
4450 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4451 (properties `((upstream-name . "MLInterfaces")))
4452 (build-system r-build-system)
4454 `(("r-annotate" ,r-annotate)
4455 ("r-biobase" ,r-biobase)
4456 ("r-biocgenerics" ,r-biocgenerics)
4457 ("r-cluster" ,r-cluster)
4460 ("r-gdata" ,r-gdata)
4461 ("r-genefilter" ,r-genefilter)
4462 ("r-ggvis" ,r-ggvis)
4463 ("r-hwriter" ,r-hwriter)
4465 ("r-mlbench" ,r-mlbench)
4467 ("r-rcolorbrewer" ,r-rcolorbrewer)
4469 ("r-rpart" ,r-rpart)
4470 ("r-sfsmisc" ,r-sfsmisc)
4471 ("r-shiny" ,r-shiny)
4472 ("r-threejs" ,r-threejs)))
4473 (home-page "https://bioconductor.org/packages/MLInterfaces/")
4474 (synopsis "Interfaces to R machine learning procedures")
4476 "This package provides uniform interfaces to machine learning code for
4477 data in R and Bioconductor containers.")
4478 ;; Any version of the LGPL.
4479 (license license:lgpl2.1+)))
4481 (define-public r-annaffy
4488 (uri (bioconductor-uri "annaffy" version))
4491 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
4492 (build-system r-build-system)
4495 (modify-phases %standard-phases
4496 (add-after 'unpack 'remove-reference-to-non-free-data
4498 (substitute* "DESCRIPTION"
4502 `(("r-annotationdbi" ,r-annotationdbi)
4503 ("r-biobase" ,r-biobase)
4505 ("r-go-db" ,r-go-db)))
4506 (home-page "https://bioconductor.org/packages/annaffy/")
4507 (synopsis "Annotation tools for Affymetrix biological metadata")
4509 "This package provides functions for handling data from Bioconductor
4510 Affymetrix annotation data packages. It produces compact HTML and text
4511 reports including experimental data and URL links to many online databases.
4512 It allows searching of biological metadata using various criteria.")
4513 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4514 ;; the LGPL 2.1 is included.
4515 (license license:lgpl2.1+)))
4517 (define-public r-a4core
4524 (uri (bioconductor-uri "a4Core" version))
4527 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
4528 (properties `((upstream-name . "a4Core")))
4529 (build-system r-build-system)
4531 `(("r-biobase" ,r-biobase)
4532 ("r-glmnet" ,r-glmnet)))
4534 `(("r-knitr" ,r-knitr)))
4535 (home-page "https://bioconductor.org/packages/a4Core")
4536 (synopsis "Automated Affymetrix array analysis core package")
4538 "This is the core package for the automated analysis of Affymetrix
4540 (license license:gpl3)))
4542 (define-public r-a4classif
4544 (name "r-a4classif")
4549 (uri (bioconductor-uri "a4Classif" version))
4552 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
4553 (properties `((upstream-name . "a4Classif")))
4554 (build-system r-build-system)
4556 `(("r-a4core" ,r-a4core)
4557 ("r-a4preproc" ,r-a4preproc)
4558 ("r-biobase" ,r-biobase)
4559 ("r-glmnet" ,r-glmnet)
4562 ("r-varselrf" ,r-varselrf)))
4564 `(("r-knitr" ,r-knitr)))
4565 (home-page "https://bioconductor.org/packages/a4Classif/")
4566 (synopsis "Automated Affymetrix array analysis classification package")
4568 "This is the classification package for the automated analysis of
4569 Affymetrix arrays.")
4570 (license license:gpl3)))
4572 (define-public r-a4preproc
4574 (name "r-a4preproc")
4579 (uri (bioconductor-uri "a4Preproc" version))
4582 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
4583 (properties `((upstream-name . "a4Preproc")))
4584 (build-system r-build-system)
4586 `(("r-biobase" ,r-biobase)
4587 ("r-biocgenerics" ,r-biocgenerics)))
4589 `(("r-knitr" ,r-knitr)))
4590 (home-page "https://bioconductor.org/packages/a4Preproc/")
4591 (synopsis "Automated Affymetrix array analysis preprocessing package")
4593 "This is a package for the automated analysis of Affymetrix arrays. It
4594 is used for preprocessing the arrays.")
4595 (license license:gpl3)))
4597 (define-public r-a4reporting
4599 (name "r-a4reporting")
4604 (uri (bioconductor-uri "a4Reporting" version))
4607 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
4608 (properties `((upstream-name . "a4Reporting")))
4609 (build-system r-build-system)
4611 `(("r-xtable" ,r-xtable)))
4613 `(("r-knitr" ,r-knitr)))
4614 (home-page "https://bioconductor.org/packages/a4Reporting/")
4615 (synopsis "Automated Affymetrix array analysis reporting package")
4617 "This is a package for the automated analysis of Affymetrix arrays. It
4618 provides reporting features.")
4619 (license license:gpl3)))
4621 (define-public r-a4base
4628 (uri (bioconductor-uri "a4Base" version))
4631 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
4632 (properties `((upstream-name . "a4Base")))
4633 (build-system r-build-system)
4635 `(("r-a4core" ,r-a4core)
4636 ("r-a4preproc" ,r-a4preproc)
4637 ("r-annaffy" ,r-annaffy)
4638 ("r-biobase" ,r-biobase)
4639 ("r-genefilter" ,r-genefilter)
4640 ("r-glmnet" ,r-glmnet)
4641 ("r-gplots" ,r-gplots)
4642 ("r-limma" ,r-limma)
4644 ("r-multtest" ,r-multtest)))
4645 (home-page "https://bioconductor.org/packages/a4Base/")
4646 (synopsis "Automated Affymetrix array analysis base package")
4648 "This package provides basic features for the automated analysis of
4649 Affymetrix arrays.")
4650 (license license:gpl3)))
4659 (uri (bioconductor-uri "a4" version))
4662 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
4663 (build-system r-build-system)
4665 `(("r-a4base" ,r-a4base)
4666 ("r-a4classif" ,r-a4classif)
4667 ("r-a4core" ,r-a4core)
4668 ("r-a4preproc" ,r-a4preproc)
4669 ("r-a4reporting" ,r-a4reporting)))
4670 (home-page "https://bioconductor.org/packages/a4/")
4671 (synopsis "Automated Affymetrix array analysis umbrella package")
4673 "This package provides a software suite for the automated analysis of
4674 Affymetrix arrays.")
4675 (license license:gpl3)))
4677 (define-public r-abseqr
4684 (uri (bioconductor-uri "abseqR" version))
4687 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
4688 (properties `((upstream-name . "abseqR")))
4689 (build-system r-build-system)
4691 `(("pandoc" ,pandoc)))
4693 `(("r-biocparallel" ,r-biocparallel)
4694 ("r-biocstyle" ,r-biocstyle)
4695 ("r-circlize" ,r-circlize)
4696 ("r-flexdashboard" ,r-flexdashboard)
4697 ("r-ggcorrplot" ,r-ggcorrplot)
4698 ("r-ggdendro" ,r-ggdendro)
4699 ("r-ggplot2" ,r-ggplot2)
4700 ("r-gridextra" ,r-gridextra)
4701 ("r-knitr" ,r-knitr)
4702 ("r-plotly" ,r-plotly)
4705 ("r-rcolorbrewer" ,r-rcolorbrewer)
4706 ("r-reshape2" ,r-reshape2)
4707 ("r-rmarkdown" ,r-rmarkdown)
4708 ("r-stringr" ,r-stringr)
4709 ("r-vegan" ,r-vegan)
4710 ("r-venndiagram" ,r-venndiagram)))
4712 `(("r-knitr" ,r-knitr)))
4713 (home-page "https://github.com/malhamdoosh/abseqR")
4714 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4716 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4717 sequencing datasets generated from antibody libraries and abseqR is one of its
4718 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4719 capabilities and allows them to generate interactive HTML reports for the
4720 convenience of viewing and sharing with other researchers. Additionally,
4721 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4722 further downstream analysis on its output.")
4723 (license license:gpl3)))
4725 (define-public r-bacon
4732 (uri (bioconductor-uri "bacon" version))
4735 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
4736 (build-system r-build-system)
4738 `(("r-biocparallel" ,r-biocparallel)
4739 ("r-ellipse" ,r-ellipse)
4740 ("r-ggplot2" ,r-ggplot2)))
4742 `(("r-knitr" ,r-knitr)))
4743 (home-page "https://bioconductor.org/packages/bacon/")
4744 (synopsis "Controlling bias and inflation in association studies")
4746 "Bacon can be used to remove inflation and bias often observed in
4747 epigenome- and transcriptome-wide association studies. To this end bacon
4748 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4749 fitting a three-component normal mixture on z-scores.")
4750 (license license:gpl2+)))
4752 (define-public r-rgadem
4759 (uri (bioconductor-uri "rGADEM" version))
4762 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
4763 (properties `((upstream-name . "rGADEM")))
4764 (build-system r-build-system)
4766 `(("r-biostrings" ,r-biostrings)
4767 ("r-bsgenome" ,r-bsgenome)
4768 ("r-genomicranges" ,r-genomicranges)
4769 ("r-iranges" ,r-iranges)
4770 ("r-seqlogo" ,r-seqlogo)))
4771 (home-page "https://bioconductor.org/packages/rGADEM/")
4772 (synopsis "De novo sequence motif discovery")
4774 "rGADEM is an efficient de novo motif discovery tool for large-scale
4775 genomic sequence data.")
4776 (license license:artistic2.0)))
4778 (define-public r-motiv
4785 (uri (bioconductor-uri "MotIV" version))
4788 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4789 (properties `((upstream-name . "MotIV")))
4790 (build-system r-build-system)
4794 `(("r-biocgenerics" ,r-biocgenerics)
4795 ("r-biostrings" ,r-biostrings)
4796 ("r-genomicranges" ,r-genomicranges)
4797 ("r-iranges" ,r-iranges)
4798 ("r-lattice" ,r-lattice)
4799 ("r-rgadem" ,r-rgadem)
4800 ("r-s4vectors" ,r-s4vectors)))
4801 (home-page "https://bioconductor.org/packages/MotIV/")
4802 (synopsis "Motif identification and validation")
4804 "This package is used for the identification and validation of sequence
4805 motifs. It makes use of STAMP for comparing a set of motifs to a given
4806 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4807 distributions, modules and filter motifs.")
4808 (license license:gpl2)))
4810 (define-public r-motifdb
4816 (uri (bioconductor-uri "MotifDb" version))
4818 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
4819 (properties `((upstream-name . "MotifDb")))
4820 (build-system r-build-system)
4822 `(("r-biocgenerics" ,r-biocgenerics)
4823 ("r-biostrings" ,r-biostrings)
4824 ("r-genomicranges" ,r-genomicranges)
4825 ("r-iranges" ,r-iranges)
4826 ("r-rtracklayer" ,r-rtracklayer)
4827 ("r-s4vectors" ,r-s4vectors)
4828 ("r-splitstackshape" ,r-splitstackshape)))
4830 `(("r-knitr" ,r-knitr)))
4831 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4832 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4833 (description "This package provides more than 2000 annotated position
4834 frequency matrices from nine public sources, for multiple organisms.")
4835 (license license:artistic2.0)))
4837 (define-public r-motifbreakr
4839 (name "r-motifbreakr")
4843 (uri (bioconductor-uri "motifbreakR" version))
4845 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
4846 (properties `((upstream-name . "motifbreakR")))
4847 (build-system r-build-system)
4849 `(("r-biocgenerics" ,r-biocgenerics)
4850 ("r-biocparallel" ,r-biocparallel)
4851 ("r-biostrings" ,r-biostrings)
4852 ("r-bsgenome" ,r-bsgenome)
4853 ("r-genomeinfodb" ,r-genomeinfodb)
4854 ("r-genomicranges" ,r-genomicranges)
4855 ("r-grimport" ,r-grimport)
4857 ("r-iranges" ,r-iranges)
4858 ("r-matrixstats" ,r-matrixstats)
4859 ("r-motifdb" ,r-motifdb)
4860 ("r-motifstack" ,r-motifstack)
4861 ("r-rtracklayer" ,r-rtracklayer)
4862 ("r-s4vectors" ,r-s4vectors)
4863 ("r-stringr" ,r-stringr)
4864 ("r-summarizedexperiment" ,r-summarizedexperiment)
4865 ("r-tfmpvalue" ,r-tfmpvalue)
4866 ("r-variantannotation" ,r-variantannotation)))
4868 `(("r-knitr" ,r-knitr)))
4869 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4870 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4871 (description "This package allows biologists to judge in the first place
4872 whether the sequence surrounding the polymorphism is a good match, and in
4873 the second place how much information is gained or lost in one allele of
4874 the polymorphism relative to another. This package gives a choice of
4875 algorithms for interrogation of genomes with motifs from public sources:
4877 @item a weighted-sum probability matrix;
4878 @item log-probabilities;
4879 @item weighted by relative entropy.
4882 This package can predict effects for novel or previously described variants in
4883 public databases, making it suitable for tasks beyond the scope of its original
4884 design. Lastly, it can be used to interrogate any genome curated within
4886 (license license:gpl2+)))
4888 (define-public r-motifstack
4890 (name "r-motifstack")
4895 (uri (bioconductor-uri "motifStack" version))
4898 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
4899 (properties `((upstream-name . "motifStack")))
4900 (build-system r-build-system)
4902 `(("r-ade4" ,r-ade4)
4903 ("r-biostrings" ,r-biostrings)
4904 ("r-ggplot2" ,r-ggplot2)
4905 ("r-htmlwidgets" ,r-htmlwidgets)
4908 `(("r-knitr" ,r-knitr)))
4909 (home-page "https://bioconductor.org/packages/motifStack/")
4910 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4912 "The motifStack package is designed for graphic representation of
4913 multiple motifs with different similarity scores. It works with both DNA/RNA
4914 sequence motifs and amino acid sequence motifs. In addition, it provides the
4915 flexibility for users to customize the graphic parameters such as the font
4916 type and symbol colors.")
4917 (license license:gpl2+)))
4919 (define-public r-genomicscores
4921 (name "r-genomicscores")
4926 (uri (bioconductor-uri "GenomicScores" version))
4929 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
4930 (properties `((upstream-name . "GenomicScores")))
4931 (build-system r-build-system)
4933 `(("r-annotationhub" ,r-annotationhub)
4934 ("r-biobase" ,r-biobase)
4935 ("r-biocfilecache" ,r-biocfilecache)
4936 ("r-biocgenerics" ,r-biocgenerics)
4937 ("r-biocmanager" ,r-biocmanager)
4938 ("r-biostrings" ,r-biostrings)
4939 ("r-delayedarray" ,r-delayedarray)
4940 ("r-genomeinfodb" ,r-genomeinfodb)
4941 ("r-genomicranges" ,r-genomicranges)
4942 ("r-hdf5array" ,r-hdf5array)
4943 ("r-iranges" ,r-iranges)
4944 ("r-rhdf5" ,r-rhdf5)
4945 ("r-s4vectors" ,r-s4vectors)
4948 `(("r-knitr" ,r-knitr)))
4949 (home-page "https://github.com/rcastelo/GenomicScores/")
4950 (synopsis "Work with genome-wide position-specific scores")
4952 "This package provides infrastructure to store and access genome-wide
4953 position-specific scores within R and Bioconductor.")
4954 (license license:artistic2.0)))
4956 (define-public r-atacseqqc
4958 (name "r-atacseqqc")
4963 (uri (bioconductor-uri "ATACseqQC" version))
4966 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
4967 (properties `((upstream-name . "ATACseqQC")))
4968 (build-system r-build-system)
4970 `(("r-biocgenerics" ,r-biocgenerics)
4971 ("r-biostrings" ,r-biostrings)
4972 ("r-bsgenome" ,r-bsgenome)
4973 ("r-chippeakanno" ,r-chippeakanno)
4974 ("r-edger" ,r-edger)
4975 ("r-genomeinfodb" ,r-genomeinfodb)
4976 ("r-genomicalignments" ,r-genomicalignments)
4977 ("r-genomicranges" ,r-genomicranges)
4978 ("r-genomicscores" ,r-genomicscores)
4979 ("r-iranges" ,r-iranges)
4980 ("r-kernsmooth" ,r-kernsmooth)
4981 ("r-limma" ,r-limma)
4982 ("r-motifstack" ,r-motifstack)
4983 ("r-preseqr" ,r-preseqr)
4984 ("r-randomforest" ,r-randomforest)
4985 ("r-rsamtools" ,r-rsamtools)
4986 ("r-rtracklayer" ,r-rtracklayer)
4987 ("r-s4vectors" ,r-s4vectors)))
4989 `(("r-knitr" ,r-knitr)))
4990 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4991 (synopsis "ATAC-seq quality control")
4993 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4994 sequencing, is a rapid and sensitive method for chromatin accessibility
4995 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4996 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4997 assess whether their ATAC-seq experiment is successful. It includes
4998 diagnostic plots of fragment size distribution, proportion of mitochondria
4999 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
5001 (license license:gpl2+)))
5003 (define-public r-gofuncr
5010 (uri (bioconductor-uri "GOfuncR" version))
5013 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
5014 (properties `((upstream-name . "GOfuncR")))
5015 (build-system r-build-system)
5017 `(("r-annotationdbi" ,r-annotationdbi)
5018 ("r-genomicranges" ,r-genomicranges)
5019 ("r-gtools" ,r-gtools)
5020 ("r-iranges" ,r-iranges)
5021 ("r-mapplots" ,r-mapplots)
5023 ("r-vioplot" ,r-vioplot)))
5025 `(("r-knitr" ,r-knitr)))
5026 (home-page "https://bioconductor.org/packages/GOfuncR/")
5027 (synopsis "Gene ontology enrichment using FUNC")
5029 "GOfuncR performs a gene ontology enrichment analysis based on the
5030 ontology enrichment software FUNC. GO-annotations are obtained from
5031 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
5032 included in the package and updated regularly. GOfuncR provides the standard
5033 candidate vs background enrichment analysis using the hypergeometric test, as
5034 well as three additional tests:
5037 @item the Wilcoxon rank-sum test that is used when genes are ranked,
5038 @item a binomial test that is used when genes are associated with two counts,
5040 @item a Chi-square or Fisher's exact test that is used in cases when genes are
5041 associated with four counts.
5044 To correct for multiple testing and interdependency of the tests, family-wise
5045 error rates are computed based on random permutations of the gene-associated
5046 variables. GOfuncR also provides tools for exploring the ontology graph and
5047 the annotations, and options to take gene-length or spatial clustering of
5048 genes into account. It is also possible to provide custom gene coordinates,
5049 annotations and ontologies.")
5050 (license license:gpl2+)))
5052 (define-public r-abaenrichment
5054 (name "r-abaenrichment")
5059 (uri (bioconductor-uri "ABAEnrichment" version))
5062 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
5063 (properties `((upstream-name . "ABAEnrichment")))
5064 (build-system r-build-system)
5066 `(("r-abadata" ,r-abadata)
5067 ("r-data-table" ,r-data-table)
5068 ("r-gofuncr" ,r-gofuncr)
5069 ("r-gplots" ,r-gplots)
5070 ("r-gtools" ,r-gtools)
5071 ("r-rcpp" ,r-rcpp)))
5073 `(("r-knitr" ,r-knitr)))
5074 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
5075 (synopsis "Gene expression enrichment in human brain regions")
5077 "The package ABAEnrichment is designed to test for enrichment of user
5078 defined candidate genes in the set of expressed genes in different human brain
5079 regions. The core function @code{aba_enrich} integrates the expression of the
5080 candidate gene set (averaged across donors) and the structural information of
5081 the brain using an ontology, both provided by the Allen Brain Atlas project.")
5082 (license license:gpl2+)))
5084 (define-public r-annotationfuncs
5086 (name "r-annotationfuncs")
5091 (uri (bioconductor-uri "AnnotationFuncs" version))
5094 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
5096 `((upstream-name . "AnnotationFuncs")))
5097 (build-system r-build-system)
5099 `(("r-annotationdbi" ,r-annotationdbi)
5101 (home-page "https://www.iysik.com/r/annotationfuncs")
5102 (synopsis "Annotation translation functions")
5104 "This package provides functions for handling translating between
5105 different identifieres using the Biocore Data Team data-packages (e.g.
5106 @code{org.Bt.eg.db}).")
5107 (license license:gpl2)))
5109 (define-public r-annotationtools
5111 (name "r-annotationtools")
5116 (uri (bioconductor-uri "annotationTools" version))
5119 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
5121 `((upstream-name . "annotationTools")))
5122 (build-system r-build-system)
5123 (propagated-inputs `(("r-biobase" ,r-biobase)))
5124 (home-page "https://bioconductor.org/packages/annotationTools/")
5125 (synopsis "Annotate microarrays and perform gene expression analyses")
5127 "This package provides functions to annotate microarrays, find orthologs,
5128 and integrate heterogeneous gene expression profiles using annotation and
5129 other molecular biology information available as flat file database (plain
5131 ;; Any version of the GPL.
5132 (license (list license:gpl2+))))
5134 (define-public r-allelicimbalance
5136 (name "r-allelicimbalance")
5141 (uri (bioconductor-uri "AllelicImbalance" version))
5144 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
5146 `((upstream-name . "AllelicImbalance")))
5147 (build-system r-build-system)
5149 `(("r-annotationdbi" ,r-annotationdbi)
5150 ("r-biocgenerics" ,r-biocgenerics)
5151 ("r-biostrings" ,r-biostrings)
5152 ("r-bsgenome" ,r-bsgenome)
5153 ("r-genomeinfodb" ,r-genomeinfodb)
5154 ("r-genomicalignments" ,r-genomicalignments)
5155 ("r-genomicfeatures" ,r-genomicfeatures)
5156 ("r-genomicranges" ,r-genomicranges)
5157 ("r-gridextra" ,r-gridextra)
5159 ("r-iranges" ,r-iranges)
5160 ("r-lattice" ,r-lattice)
5161 ("r-latticeextra" ,r-latticeextra)
5163 ("r-rsamtools" ,r-rsamtools)
5164 ("r-s4vectors" ,r-s4vectors)
5165 ("r-seqinr" ,r-seqinr)
5166 ("r-summarizedexperiment" ,r-summarizedexperiment)
5167 ("r-variantannotation" ,r-variantannotation)))
5169 `(("r-knitr" ,r-knitr)))
5170 (home-page "https://github.com/pappewaio/AllelicImbalance")
5171 (synopsis "Investigate allele-specific expression")
5173 "This package provides a framework for allele-specific expression
5174 investigation using RNA-seq data.")
5175 (license license:gpl3)))
5177 (define-public r-aucell
5184 (uri (bioconductor-uri "AUCell" version))
5187 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
5188 (properties `((upstream-name . "AUCell")))
5189 (build-system r-build-system)
5191 `(("r-biocgenerics" ,r-biocgenerics)
5192 ("r-data-table" ,r-data-table)
5193 ("r-gseabase" ,r-gseabase)
5194 ("r-mixtools" ,r-mixtools)
5195 ("r-r-utils" ,r-r-utils)
5196 ("r-s4vectors" ,r-s4vectors)
5197 ("r-shiny" ,r-shiny)
5198 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5200 `(("r-knitr" ,r-knitr)))
5201 (home-page "https://bioconductor.org/packages/AUCell/")
5202 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
5204 "AUCell identifies cells with active gene sets (e.g. signatures,
5205 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
5206 Under the Curve} (AUC) to calculate whether a critical subset of the input
5207 gene set is enriched within the expressed genes for each cell. The
5208 distribution of AUC scores across all the cells allows exploring the relative
5209 expression of the signature. Since the scoring method is ranking-based,
5210 AUCell is independent of the gene expression units and the normalization
5211 procedure. In addition, since the cells are evaluated individually, it can
5212 easily be applied to bigger datasets, subsetting the expression matrix if
5214 (license license:gpl3)))
5216 (define-public r-ebimage
5223 (uri (bioconductor-uri "EBImage" version))
5226 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5227 (properties `((upstream-name . "EBImage")))
5228 (build-system r-build-system)
5230 `(("r-abind" ,r-abind)
5231 ("r-biocgenerics" ,r-biocgenerics)
5232 ("r-fftwtools" ,r-fftwtools)
5233 ("r-htmltools" ,r-htmltools)
5234 ("r-htmlwidgets" ,r-htmlwidgets)
5236 ("r-locfit" ,r-locfit)
5238 ("r-rcurl" ,r-rcurl)
5239 ("r-tiff" ,r-tiff)))
5241 `(("r-knitr" ,r-knitr))) ; for vignettes
5242 (home-page "https://github.com/aoles/EBImage")
5243 (synopsis "Image processing and analysis toolbox for R")
5245 "EBImage provides general purpose functionality for image processing and
5246 analysis. In the context of (high-throughput) microscopy-based cellular
5247 assays, EBImage offers tools to segment cells and extract quantitative
5248 cellular descriptors. This allows the automation of such tasks using the R
5249 programming language and facilitates the use of other tools in the R
5250 environment for signal processing, statistical modeling, machine learning and
5251 visualization with image data.")
5252 ;; Any version of the LGPL.
5253 (license license:lgpl2.1+)))
5255 (define-public r-yamss
5262 (uri (bioconductor-uri "yamss" version))
5265 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
5266 (build-system r-build-system)
5268 `(("r-biocgenerics" ,r-biocgenerics)
5269 ("r-data-table" ,r-data-table)
5270 ("r-ebimage" ,r-ebimage)
5271 ("r-iranges" ,r-iranges)
5272 ("r-limma" ,r-limma)
5273 ("r-matrix" ,r-matrix)
5275 ("r-s4vectors" ,r-s4vectors)
5276 ("r-summarizedexperiment"
5277 ,r-summarizedexperiment)))
5279 `(("r-knitr" ,r-knitr)))
5280 (home-page "https://github.com/hansenlab/yamss")
5281 (synopsis "Tools for high-throughput metabolomics")
5283 "This package provides tools to analyze and visualize high-throughput
5284 metabolomics data acquired using chromatography-mass spectrometry. These tools
5285 preprocess data in a way that enables reliable and powerful differential
5287 (license license:artistic2.0)))
5289 (define-public r-gtrellis
5296 (uri (bioconductor-uri "gtrellis" version))
5299 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
5300 (build-system r-build-system)
5302 `(("r-circlize" ,r-circlize)
5303 ("r-genomicranges" ,r-genomicranges)
5304 ("r-getoptlong" ,r-getoptlong)
5305 ("r-iranges" ,r-iranges)))
5307 `(("r-knitr" ,r-knitr)))
5308 (home-page "https://github.com/jokergoo/gtrellis")
5309 (synopsis "Genome level Trellis layout")
5311 "Genome level Trellis graph visualizes genomic data conditioned by
5312 genomic categories (e.g. chromosomes). For each genomic category, multiple
5313 dimensional data which are represented as tracks describe different features
5314 from different aspects. This package provides high flexibility to arrange
5315 genomic categories and to add self-defined graphics in the plot.")
5316 (license license:expat)))
5318 (define-public r-somaticsignatures
5320 (name "r-somaticsignatures")
5325 (uri (bioconductor-uri "SomaticSignatures" version))
5328 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
5330 `((upstream-name . "SomaticSignatures")))
5331 (build-system r-build-system)
5333 `(("r-biobase" ,r-biobase)
5334 ("r-biostrings" ,r-biostrings)
5335 ("r-genomeinfodb" ,r-genomeinfodb)
5336 ("r-genomicranges" ,r-genomicranges)
5337 ("r-ggbio" ,r-ggbio)
5338 ("r-ggplot2" ,r-ggplot2)
5339 ("r-iranges" ,r-iranges)
5341 ("r-pcamethods" ,r-pcamethods)
5342 ("r-proxy" ,r-proxy)
5343 ("r-reshape2" ,r-reshape2)
5344 ("r-s4vectors" ,r-s4vectors)
5345 ("r-variantannotation" ,r-variantannotation)))
5347 `(("r-knitr" ,r-knitr)))
5348 (home-page "https://github.com/juliangehring/SomaticSignatures")
5349 (synopsis "Somatic signatures")
5351 "This package identifies mutational signatures of @dfn{single nucleotide
5352 variants} (SNVs). It provides a infrastructure related to the methodology
5353 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5354 decomposition algorithms.")
5355 (license license:expat)))
5357 (define-public r-yapsa
5364 (uri (bioconductor-uri "YAPSA" version))
5367 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5368 (properties `((upstream-name . "YAPSA")))
5369 (build-system r-build-system)
5371 `(("r-biostrings" ,r-biostrings)
5372 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5373 ("r-circlize" ,r-circlize)
5374 ("r-complexheatmap" ,r-complexheatmap)
5375 ("r-corrplot" ,r-corrplot)
5376 ("r-dendextend" ,r-dendextend)
5377 ("r-doparallel" ,r-doparallel)
5378 ("r-dplyr" ,r-dplyr)
5379 ("r-genomeinfodb" ,r-genomeinfodb)
5380 ("r-genomicranges" ,r-genomicranges)
5381 ("r-getoptlong" ,r-getoptlong)
5382 ("r-ggbeeswarm" ,r-ggbeeswarm)
5383 ("r-ggplot2" ,r-ggplot2)
5384 ("r-gridextra" ,r-gridextra)
5385 ("r-gtrellis" ,r-gtrellis)
5386 ("r-keggrest" ,r-keggrest)
5387 ("r-limsolve" ,r-limsolve)
5388 ("r-magrittr" ,r-magrittr)
5389 ("r-pmcmr" ,r-pmcmr)
5390 ("r-pracma" ,r-pracma)
5391 ("r-reshape2" ,r-reshape2)
5392 ("r-somaticsignatures" ,r-somaticsignatures)
5393 ("r-variantannotation" ,r-variantannotation)))
5395 `(("r-knitr" ,r-knitr)))
5396 (home-page "https://bioconductor.org/packages/YAPSA/")
5397 (synopsis "Yet another package for signature analysis")
5399 "This package provides functions and routines useful in the analysis of
5400 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5401 functions to perform a signature analysis with known signatures and a
5402 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5404 (license license:gpl3)))
5406 (define-public r-gcrma
5413 (uri (bioconductor-uri "gcrma" version))
5416 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5417 (build-system r-build-system)
5419 `(("r-affy" ,r-affy)
5420 ("r-affyio" ,r-affyio)
5421 ("r-biobase" ,r-biobase)
5422 ("r-biocmanager" ,r-biocmanager)
5423 ("r-biostrings" ,r-biostrings)
5424 ("r-xvector" ,r-xvector)))
5425 (home-page "https://bioconductor.org/packages/gcrma/")
5426 (synopsis "Background adjustment using sequence information")
5428 "Gcrma adjusts for background intensities in Affymetrix array data which
5429 include optical noise and @dfn{non-specific binding} (NSB). The main function
5430 @code{gcrma} converts background adjusted probe intensities to expression
5431 measures using the same normalization and summarization methods as a
5432 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5433 to estimate probe affinity to NSB. The sequence information is summarized in
5434 a more complex way than the simple GC content. Instead, the base types (A, T,
5435 G or C) at each position along the probe determine the affinity of each probe.
5436 The parameters of the position-specific base contributions to the probe
5437 affinity is estimated in an NSB experiment in which only NSB but no
5438 gene-specific binding is expected.")
5439 ;; Any version of the LGPL
5440 (license license:lgpl2.1+)))
5442 (define-public r-simpleaffy
5444 (name "r-simpleaffy")
5449 (uri (bioconductor-uri "simpleaffy" version))
5452 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5453 (build-system r-build-system)
5455 `(("r-affy" ,r-affy)
5456 ("r-biobase" ,r-biobase)
5457 ("r-biocgenerics" ,r-biocgenerics)
5458 ("r-gcrma" ,r-gcrma)
5459 ("r-genefilter" ,r-genefilter)))
5460 (home-page "https://bioconductor.org/packages/simpleaffy/")
5461 (synopsis "Very simple high level analysis of Affymetrix data")
5463 "This package provides high level functions for reading Affy @file{.CEL}
5464 files, phenotypic data, and then computing simple things with it, such as
5465 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5466 library. It also has some basic scatter plot functions and mechanisms for
5467 generating high resolution journal figures.")
5468 (license license:gpl2+)))
5470 (define-public r-yaqcaffy
5477 (uri (bioconductor-uri "yaqcaffy" version))
5480 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
5481 (build-system r-build-system)
5483 `(("r-simpleaffy" ,r-simpleaffy)))
5484 (home-page "https://bioconductor.org/packages/yaqcaffy/")
5485 (synopsis "Affymetrix quality control and reproducibility analysis")
5487 "This is a package that can be used for quality control of Affymetrix
5488 GeneChip expression data and reproducibility analysis of human whole genome
5489 chips with the MAQC reference datasets.")
5490 (license license:artistic2.0)))
5492 (define-public r-quantro
5499 (uri (bioconductor-uri "quantro" version))
5502 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
5503 (build-system r-build-system)
5505 `(("r-biobase" ,r-biobase)
5506 ("r-doparallel" ,r-doparallel)
5507 ("r-foreach" ,r-foreach)
5508 ("r-ggplot2" ,r-ggplot2)
5509 ("r-iterators" ,r-iterators)
5510 ("r-minfi" ,r-minfi)
5511 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5513 `(("r-knitr" ,r-knitr)))
5514 (home-page "https://bioconductor.org/packages/quantro/")
5515 (synopsis "Test for when to use quantile normalization")
5517 "This package provides a data-driven test for the assumptions of quantile
5518 normalization using raw data such as objects that inherit eSets (e.g.
5519 ExpressionSet, MethylSet). Group level information about each sample (such as
5520 Tumor / Normal status) must also be provided because the test assesses if
5521 there are global differences in the distributions between the user-defined
5523 (license license:gpl3+)))
5525 (define-public r-yarn
5532 (uri (bioconductor-uri "yarn" version))
5535 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
5536 (build-system r-build-system)
5538 `(("r-biobase" ,r-biobase)
5539 ("r-biomart" ,r-biomart)
5540 ("r-downloader" ,r-downloader)
5541 ("r-edger" ,r-edger)
5542 ("r-gplots" ,r-gplots)
5543 ("r-limma" ,r-limma)
5544 ("r-matrixstats" ,r-matrixstats)
5545 ("r-preprocesscore" ,r-preprocesscore)
5546 ("r-quantro" ,r-quantro)
5547 ("r-rcolorbrewer" ,r-rcolorbrewer)
5548 ("r-readr" ,r-readr)))
5550 `(("r-knitr" ,r-knitr)))
5551 (home-page "https://bioconductor.org/packages/yarn/")
5552 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5554 "Expedite large RNA-Seq analyses using a combination of previously
5555 developed tools. YARN is meant to make it easier for the user in performing
5556 basic mis-annotation quality control, filtering, and condition-aware
5557 normalization. YARN leverages many Bioconductor tools and statistical
5558 techniques to account for the large heterogeneity and sparsity found in very
5559 large RNA-seq experiments.")
5560 (license license:artistic2.0)))
5562 (define-public r-roar
5569 (uri (bioconductor-uri "roar" version))
5572 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
5573 (build-system r-build-system)
5575 `(("r-biocgenerics" ,r-biocgenerics)
5576 ("r-genomeinfodb" ,r-genomeinfodb)
5577 ("r-genomicalignments" ,r-genomicalignments)
5578 ("r-genomicranges" ,r-genomicranges)
5579 ("r-iranges" ,r-iranges)
5580 ("r-rtracklayer" ,r-rtracklayer)
5581 ("r-s4vectors" ,r-s4vectors)
5582 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5583 (home-page "https://github.com/vodkatad/roar/")
5584 (synopsis "Identify differential APA usage from RNA-seq alignments")
5586 "This package provides tools for identifying preferential usage of APA
5587 sites, comparing two biological conditions, starting from known alternative
5588 sites and alignments obtained from standard RNA-seq experiments.")
5589 (license license:gpl3)))
5591 (define-public r-xbseq
5598 (uri (bioconductor-uri "XBSeq" version))
5601 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
5602 (properties `((upstream-name . "XBSeq")))
5603 (build-system r-build-system)
5605 `(("r-biobase" ,r-biobase)
5606 ("r-deseq2" ,r-deseq2)
5607 ("r-dplyr" ,r-dplyr)
5608 ("r-ggplot2" ,r-ggplot2)
5609 ("r-locfit" ,r-locfit)
5610 ("r-magrittr" ,r-magrittr)
5611 ("r-matrixstats" ,r-matrixstats)
5612 ("r-pracma" ,r-pracma)
5613 ("r-roar" ,r-roar)))
5615 `(("r-knitr" ,r-knitr)))
5616 (home-page "https://github.com/Liuy12/XBSeq")
5617 (synopsis "Test for differential expression for RNA-seq data")
5619 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5620 expression} (DE), where a statistical model was established based on the
5621 assumption that observed signals are the convolution of true expression
5622 signals and sequencing noises. The mapped reads in non-exonic regions are
5623 considered as sequencing noises, which follows a Poisson distribution. Given
5624 measurable observed signal and background noise from RNA-seq data, true
5625 expression signals, assuming governed by the negative binomial distribution,
5626 can be delineated and thus the accurate detection of differential expressed
5628 (license license:gpl3+)))
5630 (define-public r-massspecwavelet
5632 (name "r-massspecwavelet")
5637 (uri (bioconductor-uri "MassSpecWavelet" version))
5640 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
5642 `((upstream-name . "MassSpecWavelet")))
5643 (build-system r-build-system)
5645 `(("r-waveslim" ,r-waveslim)))
5646 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5647 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5649 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5650 data mainly through the use of wavelet transforms. It supports peak detection
5651 based on @dfn{Continuous Wavelet Transform} (CWT).")
5652 (license license:lgpl2.0+)))
5654 (define-public r-xcms
5661 (uri (bioconductor-uri "xcms" version))
5664 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
5665 (build-system r-build-system)
5667 `(("r-biobase" ,r-biobase)
5668 ("r-biocgenerics" ,r-biocgenerics)
5669 ("r-biocparallel" ,r-biocparallel)
5670 ("r-iranges" ,r-iranges)
5671 ("r-lattice" ,r-lattice)
5672 ("r-massspecwavelet" ,r-massspecwavelet)
5673 ("r-mscoreutils" ,r-mscoreutils)
5674 ("r-msnbase" ,r-msnbase)
5677 ("r-protgenerics" ,r-protgenerics)
5679 ("r-rcolorbrewer" ,r-rcolorbrewer)
5680 ("r-robustbase" ,r-robustbase)
5681 ("r-s4vectors" ,r-s4vectors)
5682 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5684 `(("r-knitr" ,r-knitr)))
5685 (home-page "https://bioconductor.org/packages/xcms/")
5686 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5688 "This package provides a framework for processing and visualization of
5689 chromatographically separated and single-spectra mass spectral data. It
5690 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5691 data for high-throughput, untargeted analyte profiling.")
5692 (license license:gpl2+)))
5694 (define-public r-wrench
5701 (uri (bioconductor-uri "Wrench" version))
5704 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
5705 (properties `((upstream-name . "Wrench")))
5706 (build-system r-build-system)
5708 `(("r-limma" ,r-limma)
5709 ("r-locfit" ,r-locfit)
5710 ("r-matrixstats" ,r-matrixstats)))
5712 `(("r-knitr" ,r-knitr)))
5713 (home-page "https://github.com/HCBravoLab/Wrench")
5714 (synopsis "Wrench normalization for sparse count data")
5716 "Wrench is a package for normalization sparse genomic count data, like
5717 that arising from 16s metagenomic surveys.")
5718 (license license:artistic2.0)))
5720 (define-public r-wiggleplotr
5722 (name "r-wiggleplotr")
5727 (uri (bioconductor-uri "wiggleplotr" version))
5730 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
5731 (build-system r-build-system)
5733 `(("r-assertthat" ,r-assertthat)
5734 ("r-cowplot" ,r-cowplot)
5735 ("r-dplyr" ,r-dplyr)
5736 ("r-genomeinfodb" ,r-genomeinfodb)
5737 ("r-genomicranges" ,r-genomicranges)
5738 ("r-ggplot2" ,r-ggplot2)
5739 ("r-iranges" ,r-iranges)
5740 ("r-purrr" ,r-purrr)
5741 ("r-rtracklayer" ,r-rtracklayer)
5742 ("r-s4vectors" ,r-s4vectors)))
5744 `(("r-knitr" ,r-knitr)))
5745 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5746 (synopsis "Make read coverage plots from BigWig files")
5748 "This package provides tools to visualize read coverage from sequencing
5749 experiments together with genomic annotations (genes, transcripts, peaks).
5750 Introns of long transcripts can be rescaled to a fixed length for better
5751 visualization of exonic read coverage.")
5752 (license license:asl2.0)))
5754 (define-public r-widgettools
5756 (name "r-widgettools")
5761 (uri (bioconductor-uri "widgetTools" version))
5764 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
5765 (properties `((upstream-name . "widgetTools")))
5766 (build-system r-build-system)
5767 (home-page "https://bioconductor.org/packages/widgetTools/")
5768 (synopsis "Tools for creating interactive tcltk widgets")
5770 "This package contains tools to support the construction of tcltk
5772 ;; Any version of the LGPL.
5773 (license license:lgpl3+)))
5775 (define-public r-webbioc
5782 (uri (bioconductor-uri "webbioc" version))
5785 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
5786 (build-system r-build-system)
5788 `(("netpbm" ,netpbm)
5791 `(("r-affy" ,r-affy)
5792 ("r-annaffy" ,r-annaffy)
5793 ("r-biobase" ,r-biobase)
5794 ("r-biocmanager" ,r-biocmanager)
5795 ("r-gcrma" ,r-gcrma)
5796 ("r-multtest" ,r-multtest)
5797 ("r-qvalue" ,r-qvalue)
5799 (home-page "https://www.bioconductor.org/")
5800 (synopsis "Bioconductor web interface")
5802 "This package provides an integrated web interface for doing microarray
5803 analysis using several of the Bioconductor packages. It is intended to be
5804 deployed as a centralized bioinformatics resource for use by many users.
5805 Currently only Affymetrix oligonucleotide analysis is supported.")
5806 (license license:gpl2+)))
5808 (define-public r-zfpkm
5815 (uri (bioconductor-uri "zFPKM" version))
5818 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
5819 (properties `((upstream-name . "zFPKM")))
5820 (build-system r-build-system)
5822 `(("r-checkmate" ,r-checkmate)
5823 ("r-dplyr" ,r-dplyr)
5824 ("r-ggplot2" ,r-ggplot2)
5825 ("r-summarizedexperiment" ,r-summarizedexperiment)
5826 ("r-tidyr" ,r-tidyr)))
5828 `(("r-knitr" ,r-knitr)))
5829 (home-page "https://github.com/ronammar/zFPKM/")
5830 (synopsis "Functions to facilitate zFPKM transformations")
5832 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5833 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5835 (license license:gpl3)))
5837 (define-public r-rbowtie2
5844 (uri (bioconductor-uri "Rbowtie2" version))
5847 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
5848 (properties `((upstream-name . "Rbowtie2")))
5849 (build-system r-build-system)
5853 `(("r-knitr" ,r-knitr)))
5854 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5855 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5857 "This package provides an R wrapper of the popular @code{bowtie2}
5858 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5859 rapid adapter trimming, identification, and read merging.")
5860 (license license:gpl3+)))
5862 (define-public r-progeny
5869 (uri (bioconductor-uri "progeny" version))
5872 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
5873 (build-system r-build-system)
5875 `(("r-biobase" ,r-biobase)
5876 ("r-dplyr" ,r-dplyr)
5877 ("r-ggplot2" ,r-ggplot2)
5878 ("r-ggrepel" ,r-ggrepel)
5879 ("r-gridextra" ,r-gridextra)
5880 ("r-tidyr" ,r-tidyr)))
5882 `(("r-knitr" ,r-knitr)))
5883 (home-page "https://github.com/saezlab/progeny")
5884 (synopsis "Pathway responsive gene activity inference")
5886 "This package provides a function to infer pathway activity from gene
5887 expression. It contains the linear model inferred in the publication
5888 \"Perturbation-response genes reveal signaling footprints in cancer gene
5890 (license license:asl2.0)))
5892 (define-public r-arrmnormalization
5894 (name "r-arrmnormalization")
5899 (uri (bioconductor-uri "ARRmNormalization" version))
5902 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
5904 `((upstream-name . "ARRmNormalization")))
5905 (build-system r-build-system)
5906 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5907 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5908 (synopsis "Adaptive robust regression normalization for methylation data")
5910 "This is a package to perform the @dfn{Adaptive Robust Regression
5911 method} (ARRm) for the normalization of methylation data from the Illumina
5912 Infinium HumanMethylation 450k assay.")
5913 (license license:artistic2.0)))
5915 (define-public r-biocfilecache
5917 (name "r-biocfilecache")
5922 (uri (bioconductor-uri "BiocFileCache" version))
5925 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
5926 (properties `((upstream-name . "BiocFileCache")))
5927 (build-system r-build-system)
5929 `(("r-curl" ,r-curl)
5931 ("r-dbplyr" ,r-dbplyr)
5932 ("r-dplyr" ,r-dplyr)
5934 ("r-rappdirs" ,r-rappdirs)
5935 ("r-rsqlite" ,r-rsqlite)))
5937 `(("r-knitr" ,r-knitr)))
5938 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5939 (synopsis "Manage files across sessions")
5941 "This package creates a persistent on-disk cache of files that the user
5942 can add, update, and retrieve. It is useful for managing resources (such as
5943 custom Txdb objects) that are costly or difficult to create, web resources,
5944 and data files used across sessions.")
5945 (license license:artistic2.0)))
5947 (define-public r-iclusterplus
5949 (name "r-iclusterplus")
5954 (uri (bioconductor-uri "iClusterPlus" version))
5957 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
5958 (properties `((upstream-name . "iClusterPlus")))
5959 (build-system r-build-system)
5960 (native-inputs `(("gfortran" ,gfortran)))
5961 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5962 (synopsis "Integrative clustering of multi-type genomic data")
5964 "iClusterPlus is developed for integrative clustering analysis of
5965 multi-type genomic data and is an enhanced version of iCluster proposed and
5966 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5967 from the experiments where biological samples (e.g. tumor samples) are
5968 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5969 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5970 on. In the iClusterPlus model, binary observations such as somatic mutation
5971 are modeled as Binomial processes; categorical observations such as copy
5972 number states are realizations of Multinomial random variables; counts are
5973 modeled as Poisson random processes; and continuous measures are modeled by
5974 Gaussian distributions.")
5975 (license license:gpl2+)))
5977 (define-public r-rbowtie
5984 (uri (bioconductor-uri "Rbowtie" version))
5987 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
5988 (properties `((upstream-name . "Rbowtie")))
5989 (build-system r-build-system)
5993 `(("r-knitr" ,r-knitr)))
5994 (home-page "https://bioconductor.org/packages/Rbowtie/")
5995 (synopsis "R bowtie wrapper")
5997 "This package provides an R wrapper around the popular bowtie short read
5998 aligner and around SpliceMap, a de novo splice junction discovery and
6000 (license license:artistic2.0)))
6002 (define-public r-sgseq
6009 (uri (bioconductor-uri "SGSeq" version))
6012 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
6013 (properties `((upstream-name . "SGSeq")))
6014 (build-system r-build-system)
6016 `(("r-annotationdbi" ,r-annotationdbi)
6017 ("r-biocgenerics" ,r-biocgenerics)
6018 ("r-biostrings" ,r-biostrings)
6019 ("r-genomeinfodb" ,r-genomeinfodb)
6020 ("r-genomicalignments" ,r-genomicalignments)
6021 ("r-genomicfeatures" ,r-genomicfeatures)
6022 ("r-genomicranges" ,r-genomicranges)
6023 ("r-igraph" ,r-igraph)
6024 ("r-iranges" ,r-iranges)
6025 ("r-rsamtools" ,r-rsamtools)
6026 ("r-rtracklayer" ,r-rtracklayer)
6027 ("r-runit" ,r-runit)
6028 ("r-s4vectors" ,r-s4vectors)
6029 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6031 `(("r-knitr" ,r-knitr)))
6032 (home-page "https://bioconductor.org/packages/SGSeq/")
6033 (synopsis "Splice event prediction and quantification from RNA-seq data")
6035 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
6036 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
6037 represented as a splice graph, which can be obtained from existing annotation
6038 or predicted from the mapped sequence reads. Splice events are identified
6039 from the graph and are quantified locally using structurally compatible reads
6040 at the start or end of each splice variant. The software includes functions
6041 for splice event prediction, quantification, visualization and
6043 (license license:artistic2.0)))
6045 (define-public r-rhisat2
6052 (uri (bioconductor-uri "Rhisat2" version))
6055 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
6056 (properties `((upstream-name . "Rhisat2")))
6057 (build-system r-build-system)
6060 (modify-phases %standard-phases
6061 (add-after 'unpack 'make-reproducible
6063 (substitute* "src/Makefile"
6064 (("`hostname`") "guix")
6066 ;; Avoid shelling out to "which".
6067 (("^CC =.*") (which "gcc"))
6068 (("^CPP =.*") (which "g++")))
6071 `(("r-genomicfeatures" ,r-genomicfeatures)
6072 ("r-genomicranges" ,r-genomicranges)
6073 ("r-sgseq" ,r-sgseq)))
6075 `(("r-knitr" ,r-knitr)))
6076 (home-page "https://github.com/fmicompbio/Rhisat2")
6077 (synopsis "R Wrapper for HISAT2 sequence aligner")
6079 "This package provides an R interface to the HISAT2 spliced short-read
6080 aligner by Kim et al. (2015). The package contains wrapper functions to
6081 create a genome index and to perform the read alignment to the generated
6083 (license license:gpl3)))
6085 (define-public r-quasr
6092 (uri (bioconductor-uri "QuasR" version))
6095 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
6096 (properties `((upstream-name . "QuasR")))
6097 (build-system r-build-system)
6099 `(("r-annotationdbi" ,r-annotationdbi)
6100 ("r-biobase" ,r-biobase)
6101 ("r-biocgenerics" ,r-biocgenerics)
6102 ("r-biocmanager" ,r-biocmanager)
6103 ("r-biocparallel" ,r-biocparallel)
6104 ("r-biostrings" ,r-biostrings)
6105 ("r-bsgenome" ,r-bsgenome)
6106 ("r-genomeinfodb" ,r-genomeinfodb)
6107 ("r-genomicalignments" ,r-genomicalignments)
6108 ("r-genomicfeatures" ,r-genomicfeatures)
6109 ("r-genomicfiles" ,r-genomicfiles)
6110 ("r-genomicranges" ,r-genomicranges)
6111 ("r-iranges" ,r-iranges)
6112 ("r-rbowtie" ,r-rbowtie)
6113 ("r-rhisat2" ,r-rhisat2)
6114 ("r-rhtslib" ,r-rhtslib)
6115 ("r-rsamtools" ,r-rsamtools)
6116 ("r-rtracklayer" ,r-rtracklayer)
6117 ("r-s4vectors" ,r-s4vectors)
6118 ("r-shortread" ,r-shortread)))
6120 `(("r-knitr" ,r-knitr)))
6121 (home-page "https://bioconductor.org/packages/QuasR/")
6122 (synopsis "Quantify and annotate short reads in R")
6124 "This package provides a framework for the quantification and analysis of
6125 short genomic reads. It covers a complete workflow starting from raw sequence
6126 reads, over creation of alignments and quality control plots, to the
6127 quantification of genomic regions of interest.")
6128 (license license:gpl2)))
6130 (define-public r-rqc
6137 (uri (bioconductor-uri "Rqc" version))
6140 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
6141 (properties `((upstream-name . "Rqc")))
6142 (build-system r-build-system)
6144 `(("r-biocgenerics" ,r-biocgenerics)
6145 ("r-biocparallel" ,r-biocparallel)
6146 ("r-biocstyle" ,r-biocstyle)
6147 ("r-biostrings" ,r-biostrings)
6148 ("r-biovizbase" ,r-biovizbase)
6149 ("r-genomicalignments" ,r-genomicalignments)
6150 ("r-genomicfiles" ,r-genomicfiles)
6151 ("r-ggplot2" ,r-ggplot2)
6152 ("r-iranges" ,r-iranges)
6153 ("r-knitr" ,r-knitr)
6154 ("r-markdown" ,r-markdown)
6157 ("r-reshape2" ,r-reshape2)
6158 ("r-rsamtools" ,r-rsamtools)
6159 ("r-s4vectors" ,r-s4vectors)
6160 ("r-shiny" ,r-shiny)
6161 ("r-shortread" ,r-shortread)))
6163 `(("r-knitr" ,r-knitr)))
6164 (home-page "https://github.com/labbcb/Rqc")
6165 (synopsis "Quality control tool for high-throughput sequencing data")
6167 "Rqc is an optimized tool designed for quality control and assessment of
6168 high-throughput sequencing data. It performs parallel processing of entire
6169 files and produces a report which contains a set of high-resolution
6171 (license license:gpl2+)))
6173 (define-public r-birewire
6180 (uri (bioconductor-uri "BiRewire" version))
6183 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
6184 (properties `((upstream-name . "BiRewire")))
6185 (build-system r-build-system)
6187 `(("r-igraph" ,r-igraph)
6188 ("r-matrix" ,r-matrix)
6190 ("r-tsne" ,r-tsne)))
6191 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
6192 (synopsis "Tools for randomization of bipartite graphs")
6194 "This package provides functions for bipartite network rewiring through N
6195 consecutive switching steps and for the computation of the minimal number of
6196 switching steps to be performed in order to maximise the dissimilarity with
6197 respect to the original network. It includes functions for the analysis of
6198 the introduced randomness across the switching steps and several other
6199 routines to analyse the resulting networks and their natural projections.")
6200 (license license:gpl3)))
6202 (define-public r-birta
6209 (uri (bioconductor-uri "birta" version))
6212 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
6213 (build-system r-build-system)
6215 `(("r-biobase" ,r-biobase)
6216 ("r-limma" ,r-limma)
6217 ("r-mass" ,r-mass)))
6218 (home-page "https://bioconductor.org/packages/birta")
6219 (synopsis "Bayesian inference of regulation of transcriptional activity")
6221 "Expression levels of mRNA molecules are regulated by different
6222 processes, comprising inhibition or activation by transcription factors and
6223 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
6224 Inference of Regulation of Transcriptional Activity) uses the regulatory
6225 networks of transcription factors and miRNAs together with mRNA and miRNA
6226 expression data to predict switches in regulatory activity between two
6227 conditions. A Bayesian network is used to model the regulatory structure and
6228 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
6229 (license license:gpl2+)))
6231 (define-public r-multidataset
6233 (name "r-multidataset")
6238 (uri (bioconductor-uri "MultiDataSet" version))
6241 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
6242 (properties `((upstream-name . "MultiDataSet")))
6243 (build-system r-build-system)
6245 `(("r-biobase" ,r-biobase)
6246 ("r-biocgenerics" ,r-biocgenerics)
6247 ("r-genomicranges" ,r-genomicranges)
6248 ("r-ggplot2" ,r-ggplot2)
6249 ("r-ggrepel" ,r-ggrepel)
6250 ("r-iranges" ,r-iranges)
6251 ("r-limma" ,r-limma)
6252 ("r-qqman" ,r-qqman)
6253 ("r-s4vectors" ,r-s4vectors)
6254 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6256 `(("r-knitr" ,r-knitr)))
6257 (home-page "https://bioconductor.org/packages/MultiDataSet/")
6258 (synopsis "Implementation of MultiDataSet and ResultSet")
6260 "This package provides an implementation of the BRGE's (Bioinformatic
6261 Research Group in Epidemiology from Center for Research in Environmental
6262 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
6263 integrating multi omics data sets and ResultSet is a container for omics
6264 results. This package contains base classes for MEAL and rexposome
6266 (license license:expat)))
6268 (define-public r-ropls
6275 (uri (bioconductor-uri "ropls" version))
6278 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
6279 (build-system r-build-system)
6281 `(("r-biobase" ,r-biobase)
6282 ("r-multidataset" ,r-multidataset)))
6284 `(("r-knitr" ,r-knitr))) ; for vignettes
6285 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
6286 (synopsis "Multivariate analysis and feature selection of omics data")
6288 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
6289 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
6290 regression, classification, and feature selection of omics data where the
6291 number of variables exceeds the number of samples and with multicollinearity
6292 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
6293 separately model the variation correlated (predictive) to the factor of
6294 interest and the uncorrelated (orthogonal) variation. While performing
6295 similarly to PLS, OPLS facilitates interpretation.
6297 This package provides imlementations of PCA, PLS, and OPLS for multivariate
6298 analysis and feature selection of omics data. In addition to scores, loadings
6299 and weights plots, the package provides metrics and graphics to determine the
6300 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
6301 validity of the model by permutation testing, detect outliers, and perform
6302 feature selection (e.g. with Variable Importance in Projection or regression
6304 (license license:cecill)))
6306 (define-public r-biosigner
6308 (name "r-biosigner")
6313 (uri (bioconductor-uri "biosigner" version))
6316 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
6317 (build-system r-build-system)
6319 `(("r-biobase" ,r-biobase)
6320 ("r-e1071" ,r-e1071)
6321 ("r-multidataset" ,r-multidataset)
6322 ("r-randomforest" ,r-randomforest)
6323 ("r-ropls" ,r-ropls)))
6325 `(("r-knitr" ,r-knitr)))
6326 (home-page "https://bioconductor.org/packages/biosigner/")
6327 (synopsis "Signature discovery from omics data")
6329 "Feature selection is critical in omics data analysis to extract
6330 restricted and meaningful molecular signatures from complex and high-dimension
6331 data, and to build robust classifiers. This package implements a method to
6332 assess the relevance of the variables for the prediction performances of the
6333 classifier. The approach can be run in parallel with the PLS-DA, Random
6334 Forest, and SVM binary classifiers. The signatures and the corresponding
6335 'restricted' models are returned, enabling future predictions on new
6337 (license license:cecill)))
6339 (define-public r-annotatr
6346 (uri (bioconductor-uri "annotatr" version))
6349 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
6350 (build-system r-build-system)
6352 `(("r-annotationdbi" ,r-annotationdbi)
6353 ("r-annotationhub" ,r-annotationhub)
6354 ("r-dplyr" ,r-dplyr)
6355 ("r-genomeinfodb" ,r-genomeinfodb)
6356 ("r-genomicfeatures" ,r-genomicfeatures)
6357 ("r-genomicranges" ,r-genomicranges)
6358 ("r-ggplot2" ,r-ggplot2)
6359 ("r-iranges" ,r-iranges)
6360 ("r-readr" ,r-readr)
6361 ("r-regioner" ,r-regioner)
6362 ("r-reshape2" ,r-reshape2)
6363 ("r-rtracklayer" ,r-rtracklayer)
6364 ("r-s4vectors" ,r-s4vectors)))
6366 `(("r-knitr" ,r-knitr)))
6367 (home-page "https://bioconductor.org/packages/annotatr/")
6368 (synopsis "Annotation of genomic regions to genomic annotations")
6370 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6371 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6372 to investigate the intersecting genomic annotations. Such annotations include
6373 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6374 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6375 enhancers. The annotatr package provides an easy way to summarize and
6376 visualize the intersection of genomic sites/regions with genomic
6378 (license license:gpl3)))
6380 (define-public r-rsubread
6387 (uri (bioconductor-uri "Rsubread" version))
6390 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
6391 (properties `((upstream-name . "Rsubread")))
6392 (build-system r-build-system)
6393 (inputs `(("zlib" ,zlib)))
6395 `(("r-matrix" ,r-matrix)))
6396 (home-page "https://bioconductor.org/packages/Rsubread/")
6397 (synopsis "Subread sequence alignment and counting for R")
6399 "This package provides tools for alignment, quantification and analysis
6400 of second and third generation sequencing data. It includes functionality for
6401 read mapping, read counting, SNP calling, structural variant detection and
6402 gene fusion discovery. It can be applied to all major sequencing techologies
6403 and to both short and long sequence reads.")
6404 (license license:gpl3)))
6406 (define-public r-flowutils
6408 (name "r-flowutils")
6413 (uri (bioconductor-uri "flowUtils" version))
6416 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6417 (properties `((upstream-name . "flowUtils")))
6418 (build-system r-build-system)
6420 `(("r-biobase" ,r-biobase)
6421 ("r-corpcor" ,r-corpcor)
6422 ("r-flowcore" ,r-flowcore)
6423 ("r-graph" ,r-graph)
6424 ("r-runit" ,r-runit)
6426 (home-page "https://github.com/jspidlen/flowUtils")
6427 (synopsis "Utilities for flow cytometry")
6429 "This package provides utilities for flow cytometry data.")
6430 (license license:artistic2.0)))
6432 (define-public r-consensusclusterplus
6434 (name "r-consensusclusterplus")
6439 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6442 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6444 `((upstream-name . "ConsensusClusterPlus")))
6445 (build-system r-build-system)
6448 ("r-biobase" ,r-biobase)
6449 ("r-cluster" ,r-cluster)))
6450 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6451 (synopsis "Clustering algorithm")
6453 "This package provides an implementation of an algorithm for determining
6454 cluster count and membership by stability evidence in unsupervised analysis.")
6455 (license license:gpl2)))
6457 (define-public r-cytolib
6464 (uri (bioconductor-uri "cytolib" version))
6467 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
6468 (properties `((upstream-name . "cytolib")))
6469 (build-system r-build-system)
6472 (modify-phases %standard-phases
6473 (add-after 'unpack 'fix-linking
6475 (substitute* "src/Makevars.in"
6476 ;; This is to avoid having a plain directory on the list of
6477 ;; libraries to link.
6478 (("\\(RHDF5_LIBS\\)" match)
6479 (string-append match "/libhdf5.a")))
6482 `(("r-knitr" ,r-knitr)
6483 ("pkg-config" ,pkg-config)))
6487 ("r-rcpparmadillo" ,r-rcpparmadillo)
6488 ("r-rcppparallel" ,r-rcppparallel)
6489 ("r-rhdf5lib" ,r-rhdf5lib)
6490 ("r-rprotobuflib" ,r-rprotobuflib)))
6491 (home-page "https://bioconductor.org/packages/cytolib/")
6492 (synopsis "C++ infrastructure for working with gated cytometry")
6494 "This package provides the core data structure and API to represent and
6495 interact with gated cytometry data.")
6496 (license license:artistic2.0)))
6498 (define-public r-flowcore
6505 (uri (bioconductor-uri "flowCore" version))
6508 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
6509 (properties `((upstream-name . "flowCore")))
6510 (build-system r-build-system)
6513 ("r-biobase" ,r-biobase)
6514 ("r-biocgenerics" ,r-biocgenerics)
6515 ("r-cytolib" ,r-cytolib)
6516 ("r-matrixstats" ,r-matrixstats)
6518 ("r-rcpparmadillo" ,r-rcpparmadillo)
6519 ("r-rprotobuflib" ,r-rprotobuflib)
6520 ("r-s4vectors" ,r-s4vectors)))
6522 `(("r-knitr" ,r-knitr)))
6523 (home-page "https://bioconductor.org/packages/flowCore")
6524 (synopsis "Basic structures for flow cytometry data")
6526 "This package provides S4 data structures and basic functions to deal
6527 with flow cytometry data.")
6528 (license license:artistic2.0)))
6530 (define-public r-flowmeans
6532 (name "r-flowmeans")
6537 (uri (bioconductor-uri "flowMeans" version))
6540 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
6541 (properties `((upstream-name . "flowMeans")))
6542 (build-system r-build-system)
6544 `(("r-biobase" ,r-biobase)
6545 ("r-feature" ,r-feature)
6546 ("r-flowcore" ,r-flowcore)
6547 ("r-rrcov" ,r-rrcov)))
6548 (home-page "https://bioconductor.org/packages/flowMeans")
6549 (synopsis "Non-parametric flow cytometry data gating")
6551 "This package provides tools to identify cell populations in Flow
6552 Cytometry data using non-parametric clustering and segmented-regression-based
6553 change point detection.")
6554 (license license:artistic2.0)))
6556 (define-public r-ncdfflow
6563 (uri (bioconductor-uri "ncdfFlow" version))
6566 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
6567 (properties `((upstream-name . "ncdfFlow")))
6568 (build-system r-build-system)
6571 (modify-phases %standard-phases
6572 (add-after 'unpack 'fix-linking
6574 (substitute* "src/Makevars"
6575 ;; This is to avoid having a plain directory on the list of
6576 ;; libraries to link.
6577 (("\\(RHDF5_LIBS\\)" match)
6578 (string-append match "/libhdf5.a")))
6582 ("r-biobase" ,r-biobase)
6583 ("r-biocgenerics" ,r-biocgenerics)
6584 ("r-flowcore" ,r-flowcore)
6586 ("r-rcpparmadillo" ,r-rcpparmadillo)
6587 ("r-rhdf5lib" ,r-rhdf5lib)
6588 ("r-zlibbioc" ,r-zlibbioc)))
6590 `(("r-knitr" ,r-knitr)))
6591 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6592 (synopsis "HDF5 based storage for flow cytometry data")
6594 "This package provides HDF5 storage based methods and functions for
6595 manipulation of flow cytometry data.")
6596 (license license:artistic2.0)))
6598 (define-public r-ggcyto
6605 (uri (bioconductor-uri "ggcyto" version))
6608 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
6609 (properties `((upstream-name . "ggcyto")))
6610 (build-system r-build-system)
6612 `(("r-data-table" ,r-data-table)
6613 ("r-flowcore" ,r-flowcore)
6614 ("r-flowworkspace" ,r-flowworkspace)
6615 ("r-ggplot2" ,r-ggplot2)
6616 ("r-gridextra" ,r-gridextra)
6617 ("r-hexbin" ,r-hexbin)
6618 ("r-ncdfflow" ,r-ncdfflow)
6620 ("r-rcolorbrewer" ,r-rcolorbrewer)
6621 ("r-rlang" ,r-rlang)
6622 ("r-scales" ,r-scales)))
6624 `(("r-knitr" ,r-knitr)))
6625 (home-page "https://github.com/RGLab/ggcyto/issues")
6626 (synopsis "Visualize Cytometry data with ggplot")
6628 "With the dedicated fortify method implemented for @code{flowSet},
6629 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6630 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6631 and some custom layers also make it easy to add gates and population
6632 statistics to the plot.")
6633 (license license:artistic2.0)))
6635 (define-public r-flowviz
6642 (uri (bioconductor-uri "flowViz" version))
6645 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
6646 (properties `((upstream-name . "flowViz")))
6647 (build-system r-build-system)
6649 `(("r-biobase" ,r-biobase)
6650 ("r-flowcore" ,r-flowcore)
6651 ("r-hexbin" ,r-hexbin)
6652 ("r-idpmisc" ,r-idpmisc)
6653 ("r-kernsmooth" ,r-kernsmooth)
6654 ("r-lattice" ,r-lattice)
6655 ("r-latticeextra" ,r-latticeextra)
6657 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6659 `(("r-knitr" ,r-knitr)))
6660 (home-page "https://bioconductor.org/packages/flowViz/")
6661 (synopsis "Visualization for flow cytometry")
6663 "This package provides visualization tools for flow cytometry data.")
6664 (license license:artistic2.0)))
6666 (define-public r-flowclust
6668 (name "r-flowclust")
6673 (uri (bioconductor-uri "flowClust" version))
6676 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
6677 (properties `((upstream-name . "flowClust")))
6678 (build-system r-build-system)
6681 (list "--configure-args=--enable-bundled-gsl=no")))
6683 `(("r-biobase" ,r-biobase)
6684 ("r-biocgenerics" ,r-biocgenerics)
6686 ("r-corpcor" ,r-corpcor)
6687 ("r-ellipse" ,r-ellipse)
6688 ("r-flowcore" ,r-flowcore)
6689 ("r-flowviz" ,r-flowviz)
6690 ("r-graph" ,r-graph)
6691 ("r-mnormt" ,r-mnormt)))
6695 `(("pkg-config" ,pkg-config)
6696 ("r-knitr" ,r-knitr)))
6697 (home-page "https://bioconductor.org/packages/flowClust")
6698 (synopsis "Clustering for flow cytometry")
6700 "This package provides robust model-based clustering using a t-mixture
6701 model with Box-Cox transformation.")
6702 (license license:artistic2.0)))
6704 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6705 ;; make it use our protobuf package instead.
6706 (define-public r-rprotobuflib
6708 (name "r-rprotobuflib")
6713 (uri (bioconductor-uri "RProtoBufLib" version))
6716 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
6717 (properties `((upstream-name . "RProtoBufLib")))
6718 (build-system r-build-system)
6721 (modify-phases %standard-phases
6722 (add-after 'unpack 'unpack-bundled-sources
6724 (with-directory-excursion "src"
6725 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6728 `(("r-knitr" ,r-knitr)))
6729 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6730 (synopsis "C++ headers and static libraries of Protocol buffers")
6732 "This package provides the headers and static library of Protocol buffers
6733 for other R packages to compile and link against.")
6734 (license license:bsd-3)))
6736 (define-public r-flowworkspace
6738 (name "r-flowworkspace")
6743 (uri (bioconductor-uri "flowWorkspace" version))
6746 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
6747 (properties `((upstream-name . "flowWorkspace")))
6748 (build-system r-build-system)
6751 (modify-phases %standard-phases
6752 (add-after 'unpack 'fix-linking
6754 (substitute* "src/Makevars"
6755 ;; This is to avoid having a plain directory on the list of
6756 ;; libraries to link.
6757 (("\\{h5lib\\}" match)
6758 (string-append match "/libhdf5.a")))
6761 `(("r-aws-s3" ,r-aws-s3)
6762 ("r-aws-signature" ,r-aws-signature)
6764 ("r-biobase" ,r-biobase)
6765 ("r-biocgenerics" ,r-biocgenerics)
6766 ("r-cytolib" ,r-cytolib)
6767 ("r-data-table" ,r-data-table)
6768 ("r-digest" ,r-digest)
6769 ("r-dplyr" ,r-dplyr)
6770 ("r-flowcore" ,r-flowcore)
6771 ("r-ggplot2" ,r-ggplot2)
6772 ("r-graph" ,r-graph)
6773 ("r-lattice" ,r-lattice)
6774 ("r-latticeextra" ,r-latticeextra)
6775 ("r-matrixstats" ,r-matrixstats)
6776 ("r-ncdfflow" ,r-ncdfflow)
6779 ("r-rcpparmadillo" ,r-rcpparmadillo)
6780 ("r-rcppparallel" ,r-rcppparallel)
6781 ("r-rgraphviz" ,r-rgraphviz)
6782 ("r-rhdf5lib" ,r-rhdf5lib)
6783 ("r-rprotobuflib" ,r-rprotobuflib)
6784 ("r-scales" ,r-scales)
6787 `(("r-knitr" ,r-knitr)))
6788 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6789 (synopsis "Infrastructure for working with cytometry data")
6791 "This package is designed to facilitate comparison of automated gating
6792 methods against manual gating done in flowJo. This package allows you to
6793 import basic flowJo workspaces into BioConductor and replicate the gating from
6794 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6795 samples, compensation, and transformation are performed so that the output
6796 matches the flowJo analysis.")
6797 (license license:artistic2.0)))
6799 (define-public r-flowstats
6801 (name "r-flowstats")
6806 (uri (bioconductor-uri "flowStats" version))
6809 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
6810 (properties `((upstream-name . "flowStats")))
6811 (build-system r-build-system)
6813 `(("r-biobase" ,r-biobase)
6814 ("r-biocgenerics" ,r-biocgenerics)
6815 ("r-cluster" ,r-cluster)
6817 ("r-flowcore" ,r-flowcore)
6818 ("r-flowviz" ,r-flowviz)
6819 ("r-flowworkspace" ,r-flowworkspace)
6820 ("r-kernsmooth" ,r-kernsmooth)
6822 ("r-lattice" ,r-lattice)
6824 ("r-ncdfflow" ,r-ncdfflow)
6825 ("r-rcolorbrewer" ,r-rcolorbrewer)
6826 ("r-rrcov" ,r-rrcov)))
6827 (home-page "http://www.github.com/RGLab/flowStats")
6828 (synopsis "Statistical methods for the analysis of flow cytometry data")
6830 "This package provides methods and functionality to analyze flow data
6831 that is beyond the basic infrastructure provided by the @code{flowCore}
6833 (license license:artistic2.0)))
6835 (define-public r-opencyto
6842 (uri (bioconductor-uri "openCyto" version))
6845 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
6846 (properties `((upstream-name . "openCyto")))
6847 (build-system r-build-system)
6849 `(("r-biobase" ,r-biobase)
6850 ("r-biocgenerics" ,r-biocgenerics)
6852 ("r-data-table" ,r-data-table)
6853 ("r-flowclust" ,r-flowclust)
6854 ("r-flowcore" ,r-flowcore)
6855 ("r-flowstats" ,r-flowstats)
6856 ("r-flowviz" ,r-flowviz)
6857 ("r-flowworkspace" ,r-flowworkspace)
6858 ("r-graph" ,r-graph)
6859 ("r-gtools" ,r-gtools)
6861 ("r-lattice" ,r-lattice)
6863 ("r-ncdfflow" ,r-ncdfflow)
6865 ("r-r-utils" ,r-r-utils)
6867 ("r-rcolorbrewer" ,r-rcolorbrewer)
6869 ("r-rrcov" ,r-rrcov)))
6871 `(("r-knitr" ,r-knitr)))
6872 (home-page "https://bioconductor.org/packages/openCyto")
6873 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6875 "This package is designed to facilitate the automated gating methods in a
6876 sequential way to mimic the manual gating strategy.")
6877 (license license:artistic2.0)))
6879 (define-public r-cytoml
6886 (uri (bioconductor-uri "CytoML" version))
6889 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
6890 (properties `((upstream-name . "CytoML")))
6891 (build-system r-build-system)
6894 (modify-phases %standard-phases
6895 (add-after 'unpack 'fix-linking
6897 (substitute* "src/Makevars.in"
6898 ;; This is to avoid having a plain directory on the list of
6899 ;; libraries to link.
6900 (("\\{h5lib\\}" match)
6901 (string-append match "/libhdf5.a")))
6904 `(("libxml2" ,libxml2)))
6906 `(("r-base64enc" ,r-base64enc)
6908 ("r-biobase" ,r-biobase)
6909 ("r-corpcor" ,r-corpcor)
6910 ("r-cytolib" ,r-cytolib)
6911 ("r-data-table" ,r-data-table)
6912 ("r-dplyr" ,r-dplyr)
6913 ("r-flowcore" ,r-flowcore)
6914 ("r-flowworkspace" ,r-flowworkspace)
6915 ("r-ggcyto" ,r-ggcyto)
6916 ("r-graph" ,r-graph)
6917 ("r-jsonlite" ,r-jsonlite)
6918 ("r-lattice" ,r-lattice)
6919 ("r-opencyto" ,r-opencyto)
6923 ("r-rcpparmadillo" ,r-rcpparmadillo)
6924 ("r-rcppparallel" ,r-rcppparallel)
6925 ("r-rgraphviz" ,r-rgraphviz)
6926 ("r-rhdf5lib" ,r-rhdf5lib)
6927 ("r-rprotobuflib" ,r-rprotobuflib)
6928 ("r-runit" ,r-runit)
6929 ("r-tibble" ,r-tibble)
6932 ("r-yaml" ,r-yaml)))
6934 `(("r-knitr" ,r-knitr)))
6935 (home-page "https://github.com/RGLab/CytoML")
6936 (synopsis "GatingML interface for cross platform cytometry data sharing")
6938 "This package provides an interface to implementations of the GatingML2.0
6939 standard to exchange gated cytometry data with other software platforms.")
6940 (license license:artistic2.0)))
6942 (define-public r-flowsom
6949 (uri (bioconductor-uri "FlowSOM" version))
6952 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
6953 (properties `((upstream-name . "FlowSOM")))
6954 (build-system r-build-system)
6956 `(("r-biocgenerics" ,r-biocgenerics)
6957 ("r-consensusclusterplus" ,r-consensusclusterplus)
6958 ("r-cytoml" ,r-cytoml)
6959 ("r-flowcore" ,r-flowcore)
6960 ("r-flowworkspace" ,r-flowworkspace)
6961 ("r-igraph" ,r-igraph)
6962 ("r-rcolorbrewer" ,r-rcolorbrewer)
6965 (home-page "https://bioconductor.org/packages/FlowSOM/")
6966 (synopsis "Visualize and interpret cytometry data")
6968 "FlowSOM offers visualization options for cytometry data, by using
6969 self-organizing map clustering and minimal spanning trees.")
6970 (license license:gpl2+)))
6972 (define-public r-mixomics
6979 (uri (bioconductor-uri "mixOmics" version))
6982 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
6983 (properties `((upstream-name . "mixOmics")))
6984 (build-system r-build-system)
6986 `(("r-corpcor" ,r-corpcor)
6987 ("r-dplyr" ,r-dplyr)
6988 ("r-ellipse" ,r-ellipse)
6989 ("r-ggrepel" ,r-ggrepel)
6990 ("r-ggplot2" ,r-ggplot2)
6991 ("r-gridextra" ,r-gridextra)
6992 ("r-igraph" ,r-igraph)
6993 ("r-lattice" ,r-lattice)
6995 ("r-matrixstats" ,r-matrixstats)
6996 ("r-rarpack" ,r-rarpack)
6997 ("r-rcolorbrewer" ,r-rcolorbrewer)
6998 ("r-reshape2" ,r-reshape2)
6999 ("r-tidyr" ,r-tidyr)))
7001 `(("r-knitr" ,r-knitr)))
7002 (home-page "http://www.mixOmics.org")
7003 (synopsis "Multivariate methods for exploration of biological datasets")
7005 "mixOmics offers a wide range of multivariate methods for the exploration
7006 and integration of biological datasets with a particular focus on variable
7007 selection. The package proposes several sparse multivariate models we have
7008 developed to identify the key variables that are highly correlated, and/or
7009 explain the biological outcome of interest. The data that can be analysed
7010 with mixOmics may come from high throughput sequencing technologies, such as
7011 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
7012 also beyond the realm of omics (e.g. spectral imaging). The methods
7013 implemented in mixOmics can also handle missing values without having to
7014 delete entire rows with missing data.")
7015 (license license:gpl2+)))
7017 (define-public r-depecher
7018 (package ;Source/Weave error
7024 (uri (bioconductor-uri "DepecheR" version))
7027 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
7028 (properties `((upstream-name . "DepecheR")))
7029 (build-system r-build-system)
7031 `(("r-beanplot" ,r-beanplot)
7032 ("r-dosnow" ,r-dosnow)
7033 ("r-dplyr" ,r-dplyr)
7035 ("r-foreach" ,r-foreach)
7036 ("r-ggplot2" ,r-ggplot2)
7037 ("r-gmodels" ,r-gmodels)
7038 ("r-gplots" ,r-gplots)
7040 ("r-matrixstats" ,r-matrixstats)
7041 ("r-mixomics" ,r-mixomics)
7042 ("r-moments" ,r-moments)
7044 ("r-rcppeigen" ,r-rcppeigen)
7045 ("r-reshape2" ,r-reshape2)
7046 ("r-robustbase" ,r-robustbase)
7047 ("r-viridis" ,r-viridis)))
7049 `(("r-knitr" ,r-knitr)))
7050 (home-page "https://bioconductor.org/packages/DepecheR/")
7051 (synopsis "Identify traits of clusters in high-dimensional entities")
7053 "The purpose of this package is to identify traits in a dataset that can
7054 separate groups. This is done on two levels. First, clustering is performed,
7055 using an implementation of sparse K-means. Secondly, the generated clusters
7056 are used to predict outcomes of groups of individuals based on their
7057 distribution of observations in the different clusters. As certain clusters
7058 with separating information will be identified, and these clusters are defined
7059 by a sparse number of variables, this method can reduce the complexity of
7060 data, to only emphasize the data that actually matters.")
7061 (license license:expat)))
7063 (define-public r-rcistarget
7065 (name "r-rcistarget")
7070 (uri (bioconductor-uri "RcisTarget" version))
7073 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
7074 (properties `((upstream-name . "RcisTarget")))
7075 (build-system r-build-system)
7077 `(("r-aucell" ,r-aucell)
7078 ("r-biocgenerics" ,r-biocgenerics)
7079 ("r-data-table" ,r-data-table)
7080 ("r-feather" ,r-feather)
7081 ("r-gseabase" ,r-gseabase)
7082 ("r-r-utils" ,r-r-utils)
7083 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7085 `(("r-knitr" ,r-knitr)))
7086 (home-page "https://aertslab.org/#scenic")
7087 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
7089 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
7090 over-represented on a gene list. In a first step, RcisTarget selects DNA
7091 motifs that are significantly over-represented in the surroundings of the
7092 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
7093 achieved by using a database that contains genome-wide cross-species rankings
7094 for each motif. The motifs that are then annotated to TFs and those that have
7095 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
7096 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
7097 genes in the gene-set that are ranked above the leading edge).")
7098 (license license:gpl3)))
7100 (define-public r-cicero
7107 (uri (bioconductor-uri "cicero" version))
7110 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
7111 (build-system r-build-system)
7113 `(("r-assertthat" ,r-assertthat)
7114 ("r-biobase" ,r-biobase)
7115 ("r-biocgenerics" ,r-biocgenerics)
7116 ("r-data-table" ,r-data-table)
7117 ("r-dplyr" ,r-dplyr)
7119 ("r-genomicranges" ,r-genomicranges)
7120 ("r-ggplot2" ,r-ggplot2)
7121 ("r-glasso" ,r-glasso)
7123 ("r-igraph" ,r-igraph)
7124 ("r-iranges" ,r-iranges)
7125 ("r-matrix" ,r-matrix)
7126 ("r-monocle" ,r-monocle)
7128 ("r-reshape2" ,r-reshape2)
7129 ("r-s4vectors" ,r-s4vectors)
7130 ("r-stringi" ,r-stringi)
7131 ("r-stringr" ,r-stringr)
7132 ("r-tibble" ,r-tibble)
7133 ("r-tidyr" ,r-tidyr)
7134 ("r-vgam" ,r-vgam)))
7136 `(("r-knitr" ,r-knitr)))
7137 (home-page "https://bioconductor.org/packages/cicero/")
7138 (synopsis "Predict cis-co-accessibility from single-cell data")
7140 "Cicero computes putative cis-regulatory maps from single-cell chromatin
7141 accessibility data. It also extends the monocle package for use in chromatin
7142 accessibility data.")
7143 (license license:expat)))
7145 ;; This is the latest commit on the "monocle3" branch.
7146 (define-public r-cicero-monocle3
7147 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
7149 (package (inherit r-cicero)
7150 (name "r-cicero-monocle3")
7151 (version (git-version "1.3.2" revision commit))
7156 (url "https://github.com/cole-trapnell-lab/cicero-release")
7158 (file-name (git-file-name name version))
7161 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
7163 `(("r-monocle3" ,r-monocle3)
7164 ,@(alist-delete "r-monocle"
7165 (package-propagated-inputs r-cicero)))))))
7167 (define-public r-circrnaprofiler
7169 (name "r-circrnaprofiler")
7174 (uri (bioconductor-uri "circRNAprofiler" version))
7177 "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
7179 `((upstream-name . "circRNAprofiler")))
7180 (build-system r-build-system)
7182 `(("r-annotationhub" ,r-annotationhub)
7183 ("r-biostrings" ,r-biostrings)
7184 ("r-bsgenome" ,r-bsgenome)
7185 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7186 ("r-deseq2" ,r-deseq2)
7187 ("r-dplyr" ,r-dplyr)
7188 ("r-edger" ,r-edger)
7189 ("r-genomeinfodb" ,r-genomeinfodb)
7190 ("r-genomicranges" ,r-genomicranges)
7191 ("r-ggplot2" ,r-ggplot2)
7192 ("r-gwascat" ,r-gwascat)
7193 ("r-iranges" ,r-iranges)
7194 ("r-magrittr" ,r-magrittr)
7195 ("r-r-utils" ,r-r-utils)
7196 ("r-readr" ,r-readr)
7197 ("r-reshape2" ,r-reshape2)
7198 ("r-rlang" ,r-rlang)
7199 ("r-rtracklayer" ,r-rtracklayer)
7200 ("r-s4vectors" ,r-s4vectors)
7201 ("r-seqinr" ,r-seqinr)
7202 ("r-stringi" ,r-stringi)
7203 ("r-stringr" ,r-stringr)
7204 ("r-universalmotif" ,r-universalmotif)))
7206 `(("r-knitr" ,r-knitr)))
7208 "https://github.com/Aufiero/circRNAprofiler")
7210 "Computational framework for the downstream analysis of circular RNA's")
7212 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
7213 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
7214 framework allows to combine and analyze circRNAs previously detected by
7215 multiple publicly available annotation-based circRNA detection tools. It
7216 covers different aspects of circRNAs analysis from differential expression
7217 analysis, evolutionary conservation, biogenesis to functional analysis.")
7218 (license license:gpl3)))
7220 (define-public r-cistopic
7221 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
7225 (version (git-version "0.2.1" revision commit))
7230 (url "https://github.com/aertslab/cisTopic")
7232 (file-name (git-file-name name version))
7235 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
7236 (build-system r-build-system)
7238 `(("r-aucell" ,r-aucell)
7239 ("r-data-table" ,r-data-table)
7240 ("r-dplyr" ,r-dplyr)
7241 ("r-dosnow" ,r-dosnow)
7243 ("r-feather" ,r-feather)
7244 ("r-fitdistrplus" ,r-fitdistrplus)
7245 ("r-genomicranges" ,r-genomicranges)
7246 ("r-ggplot2" ,r-ggplot2)
7248 ("r-matrix" ,r-matrix)
7250 ("r-rcistarget" ,r-rcistarget)
7251 ("r-rtracklayer" ,r-rtracklayer)
7252 ("r-s4vectors" ,r-s4vectors)))
7253 (home-page "https://github.com/aertslab/cisTopic")
7254 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
7256 "The sparse nature of single cell epigenomics data can be overruled using
7257 probabilistic modelling methods such as @dfn{Latent Dirichlet
7258 Allocation} (LDA). This package allows the probabilistic modelling of
7259 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
7260 includes functionalities to identify cell states based on the contribution of
7261 cisTopics and explore the nature and regulatory proteins driving them.")
7262 (license license:gpl3))))
7264 (define-public r-genie3
7271 (uri (bioconductor-uri "GENIE3" version))
7274 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
7275 (properties `((upstream-name . "GENIE3")))
7276 (build-system r-build-system)
7277 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
7279 `(("r-knitr" ,r-knitr)))
7280 (home-page "https://bioconductor.org/packages/GENIE3")
7281 (synopsis "Gene network inference with ensemble of trees")
7283 "This package implements the GENIE3 algorithm for inferring gene
7284 regulatory networks from expression data.")
7285 (license license:gpl2+)))
7287 (define-public r-roc
7294 (uri (bioconductor-uri "ROC" version))
7297 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
7298 (properties `((upstream-name . "ROC")))
7299 (build-system r-build-system)
7301 `(("r-knitr" ,r-knitr)))
7302 (home-page "https://www.bioconductor.org/packages/ROC/")
7303 (synopsis "Utilities for ROC curves")
7305 "This package provides utilities for @dfn{Receiver Operating
7306 Characteristic} (ROC) curves, with a focus on micro arrays.")
7307 (license license:artistic2.0)))
7309 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
7311 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
7316 (uri (bioconductor-uri
7317 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
7318 version 'annotation))
7321 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
7324 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
7325 (build-system r-build-system)
7326 (propagated-inputs `(("r-minfi" ,r-minfi)))
7328 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
7329 (synopsis "Annotation for Illumina's 450k methylation arrays")
7331 "This package provides manifests and annotation for Illumina's 450k array
7333 (license license:artistic2.0)))
7335 (define-public r-watermelon
7337 (name "r-watermelon")
7342 (uri (bioconductor-uri "wateRmelon" version))
7345 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
7346 (properties `((upstream-name . "wateRmelon")))
7347 (build-system r-build-system)
7349 `(("r-biobase" ,r-biobase)
7350 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
7351 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
7352 ("r-illuminaio" ,r-illuminaio)
7353 ("r-limma" ,r-limma)
7355 ("r-matrixstats" ,r-matrixstats)
7356 ("r-methylumi" ,r-methylumi)
7358 (home-page "https://bioconductor.org/packages/wateRmelon/")
7359 (synopsis "Illumina 450 methylation array normalization and metrics")
7361 "The standard index of DNA methylation (beta) is computed from methylated
7362 and unmethylated signal intensities. Betas calculated from raw signal
7363 intensities perform well, but using 11 methylomic datasets we demonstrate that
7364 quantile normalization methods produce marked improvement. The commonly used
7365 procedure of normalizing betas is inferior to the separate normalization of M
7366 and U, and it is also advantageous to normalize Type I and Type II assays
7367 separately. This package provides 15 flavours of betas and three performance
7368 metrics, with methods for objects produced by the @code{methylumi} and
7369 @code{minfi} packages.")
7370 (license license:gpl3)))
7372 (define-public r-gdsfmt
7379 (uri (bioconductor-uri "gdsfmt" version))
7382 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
7383 (modules '((guix build utils)))
7384 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
7385 ;; them and link with system libraries instead.
7388 (for-each delete-file-recursively
7392 (substitute* "src/Makevars"
7393 (("all: \\$\\(SHLIB\\)") "all:")
7394 (("\\$\\(SHLIB\\): liblzma.a") "")
7395 (("(ZLIB|LZ4)/.*") "")
7396 (("CoreArray/dVLIntGDS.cpp.*")
7397 "CoreArray/dVLIntGDS.cpp")
7398 (("CoreArray/dVLIntGDS.o.*")
7399 "CoreArray/dVLIntGDS.o")
7400 (("PKG_LIBS = ./liblzma.a")
7401 "PKG_LIBS = -llz4"))
7402 (substitute* "src/CoreArray/dStream.h"
7403 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
7404 (string-append "include <" header ">")))
7406 (properties `((upstream-name . "gdsfmt")))
7407 (build-system r-build-system)
7413 `(("r-knitr" ,r-knitr)))
7414 (home-page "http://corearray.sourceforge.net/")
7416 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7418 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7419 Data Structure} (GDS) data files, which are portable across platforms with
7420 hierarchical structure to store multiple scalable array-oriented data sets
7421 with metadata information. It is suited for large-scale datasets, especially
7422 for data which are much larger than the available random-access memory. The
7423 @code{gdsfmt} package offers efficient operations specifically designed for
7424 integers of less than 8 bits, since a diploid genotype, like
7425 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7426 byte. Data compression and decompression are available with relatively
7427 efficient random access. It is also allowed to read a GDS file in parallel
7428 with multiple R processes supported by the package @code{parallel}.")
7429 (license license:lgpl3)))
7431 (define-public r-bigmelon
7438 (uri (bioconductor-uri "bigmelon" version))
7441 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7442 (properties `((upstream-name . "bigmelon")))
7443 (build-system r-build-system)
7445 `(("r-biobase" ,r-biobase)
7446 ("r-biocgenerics" ,r-biocgenerics)
7447 ("r-gdsfmt" ,r-gdsfmt)
7448 ("r-geoquery" ,r-geoquery)
7449 ("r-methylumi" ,r-methylumi)
7450 ("r-minfi" ,r-minfi)
7451 ("r-watermelon" ,r-watermelon)))
7452 (home-page "https://bioconductor.org/packages/bigmelon/")
7453 (synopsis "Illumina methylation array analysis for large experiments")
7455 "This package provides methods for working with Illumina arrays using the
7456 @code{gdsfmt} package.")
7457 (license license:gpl3)))
7459 (define-public r-seqbias
7466 (uri (bioconductor-uri "seqbias" version))
7469 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
7470 (properties `((upstream-name . "seqbias")))
7471 (build-system r-build-system)
7473 `(("r-biostrings" ,r-biostrings)
7474 ("r-genomicranges" ,r-genomicranges)
7475 ("r-rhtslib" ,r-rhtslib)))
7476 (home-page "https://bioconductor.org/packages/seqbias/")
7477 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
7479 "This package implements a model of per-position sequencing bias in
7480 high-throughput sequencing data using a simple Bayesian network, the structure
7481 and parameters of which are trained on a set of aligned reads and a reference
7483 (license license:lgpl3)))
7485 (define-public r-snplocs-hsapiens-dbsnp144-grch37
7487 (name "r-snplocs-hsapiens-dbsnp144-grch37")
7491 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
7492 version 'annotation))
7495 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
7496 (build-system r-build-system)
7497 ;; As this package provides little more than a very large data file it
7498 ;; doesn't make sense to build substitutes.
7499 (arguments `(#:substitutable? #f))
7501 `(("r-biocgenerics" ,r-biocgenerics)
7502 ("r-s4vectors" ,r-s4vectors)
7503 ("r-iranges" ,r-iranges)
7504 ("r-genomeinfodb" ,r-genomeinfodb)
7505 ("r-genomicranges" ,r-genomicranges)
7506 ("r-bsgenome" ,r-bsgenome)
7507 ("r-biostrings" ,r-biostrings)))
7509 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
7510 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
7511 (description "This package provides SNP locations and alleles for Homo
7512 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
7513 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
7514 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
7515 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
7516 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
7517 the mitochondrion chromosome. Therefore, the SNPs in this package can be
7518 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
7519 correct position but this injection will exclude chrM (i.e. nothing will be
7520 injected in that sequence).")
7521 (license license:artistic2.0)))
7523 (define-public r-reqon
7530 (uri (bioconductor-uri "ReQON" version))
7533 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
7534 (properties `((upstream-name . "ReQON")))
7535 (build-system r-build-system)
7537 `(("r-rjava" ,r-rjava)
7538 ("r-rsamtools" ,r-rsamtools)
7539 ("r-seqbias" ,r-seqbias)))
7540 (home-page "https://bioconductor.org/packages/ReQON/")
7541 (synopsis "Recalibrating quality of nucleotides")
7543 "This package provides an implementation of an algorithm for
7544 recalibrating the base quality scores for aligned sequencing data in BAM
7546 (license license:gpl2)))
7548 (define-public r-wavcluster
7550 (name "r-wavcluster")
7555 (uri (bioconductor-uri "wavClusteR" version))
7558 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
7559 (properties `((upstream-name . "wavClusteR")))
7560 (build-system r-build-system)
7562 `(("r-biocgenerics" ,r-biocgenerics)
7563 ("r-biostrings" ,r-biostrings)
7564 ("r-foreach" ,r-foreach)
7565 ("r-genomicfeatures" ,r-genomicfeatures)
7566 ("r-genomicranges" ,r-genomicranges)
7567 ("r-ggplot2" ,r-ggplot2)
7568 ("r-hmisc" ,r-hmisc)
7569 ("r-iranges" ,r-iranges)
7570 ("r-mclust" ,r-mclust)
7571 ("r-rsamtools" ,r-rsamtools)
7572 ("r-rtracklayer" ,r-rtracklayer)
7573 ("r-s4vectors" ,r-s4vectors)
7574 ("r-seqinr" ,r-seqinr)
7575 ("r-stringr" ,r-stringr)))
7577 `(("r-knitr" ,r-knitr)))
7578 (home-page "https://bioconductor.org/packages/wavClusteR/")
7579 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
7581 "This package provides an integrated pipeline for the analysis of
7582 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7583 sequencing errors, SNPs and additional non-experimental sources by a non-
7584 parametric mixture model. The protein binding sites (clusters) are then
7585 resolved at high resolution and cluster statistics are estimated using a
7586 rigorous Bayesian framework. Post-processing of the results, data export for
7587 UCSC genome browser visualization and motif search analysis are provided. In
7588 addition, the package integrates RNA-Seq data to estimate the False
7589 Discovery Rate of cluster detection. Key functions support parallel multicore
7590 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7591 be applied to the analysis of other NGS data obtained from experimental
7592 procedures that induce nucleotide substitutions (e.g. BisSeq).")
7593 (license license:gpl2)))
7595 (define-public r-timeseriesexperiment
7597 (name "r-timeseriesexperiment")
7602 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7605 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
7607 `((upstream-name . "TimeSeriesExperiment")))
7608 (build-system r-build-system)
7610 `(("r-deseq2" ,r-deseq2)
7611 ("r-dplyr" ,r-dplyr)
7612 ("r-dynamictreecut" ,r-dynamictreecut)
7613 ("r-edger" ,r-edger)
7614 ("r-ggplot2" ,r-ggplot2)
7615 ("r-hmisc" ,r-hmisc)
7616 ("r-limma" ,r-limma)
7617 ("r-magrittr" ,r-magrittr)
7618 ("r-proxy" ,r-proxy)
7619 ("r-s4vectors" ,r-s4vectors)
7620 ("r-summarizedexperiment" ,r-summarizedexperiment)
7621 ("r-tibble" ,r-tibble)
7622 ("r-tidyr" ,r-tidyr)
7623 ("r-vegan" ,r-vegan)
7624 ("r-viridis" ,r-viridis)))
7626 `(("r-knitr" ,r-knitr)))
7627 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7628 (synopsis "Analysis for short time-series data")
7630 "This package is a visualization and analysis toolbox for short time
7631 course data which includes dimensionality reduction, clustering, two-sample
7632 differential expression testing and gene ranking techniques. The package also
7633 provides methods for retrieving enriched pathways.")
7634 (license license:lgpl3+)))
7636 (define-public r-variantfiltering
7638 (name "r-variantfiltering")
7643 (uri (bioconductor-uri "VariantFiltering" version))
7646 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
7648 `((upstream-name . "VariantFiltering")))
7649 (build-system r-build-system)
7651 `(("r-annotationdbi" ,r-annotationdbi)
7652 ("r-biobase" ,r-biobase)
7653 ("r-biocgenerics" ,r-biocgenerics)
7654 ("r-biocparallel" ,r-biocparallel)
7655 ("r-biostrings" ,r-biostrings)
7656 ("r-bsgenome" ,r-bsgenome)
7658 ("r-genomeinfodb" ,r-genomeinfodb)
7659 ("r-genomicfeatures" ,r-genomicfeatures)
7660 ("r-genomicranges" ,r-genomicranges)
7661 ("r-genomicscores" ,r-genomicscores)
7662 ("r-graph" ,r-graph)
7664 ("r-iranges" ,r-iranges)
7666 ("r-rsamtools" ,r-rsamtools)
7667 ("r-s4vectors" ,r-s4vectors)
7668 ("r-shiny" ,r-shiny)
7669 ("r-shinyjs" ,r-shinyjs)
7670 ("r-shinythemes" ,r-shinythemes)
7671 ("r-shinytree" ,r-shinytree)
7672 ("r-summarizedexperiment" ,r-summarizedexperiment)
7673 ("r-variantannotation" ,r-variantannotation)
7674 ("r-xvector" ,r-xvector)))
7675 (home-page "https://github.com/rcastelo/VariantFiltering")
7676 (synopsis "Filtering of coding and non-coding genetic variants")
7678 "Filter genetic variants using different criteria such as inheritance
7679 model, amino acid change consequence, minor allele frequencies across human
7680 populations, splice site strength, conservation, etc.")
7681 (license license:artistic2.0)))
7683 (define-public r-genomegraphs
7685 (name "r-genomegraphs")
7690 (uri (bioconductor-uri "GenomeGraphs" version))
7693 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7694 (properties `((upstream-name . "GenomeGraphs")))
7695 (build-system r-build-system)
7697 `(("r-biomart" ,r-biomart)))
7698 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7699 (synopsis "Plotting genomic information from Ensembl")
7701 "Genomic data analyses requires integrated visualization of known genomic
7702 information and new experimental data. GenomeGraphs uses the biomaRt package
7703 to perform live annotation queries to Ensembl and translates this to e.g.
7704 gene/transcript structures in viewports of the grid graphics package. This
7705 results in genomic information plotted together with your data. Another
7706 strength of GenomeGraphs is to plot different data types such as array CGH,
7707 gene expression, sequencing and other data, together in one plot using the
7708 same genome coordinate system.")
7709 (license license:artistic2.0)))
7711 (define-public r-wavetiling
7713 (name "r-wavetiling")
7718 (uri (bioconductor-uri "waveTiling" version))
7721 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7722 (properties `((upstream-name . "waveTiling")))
7723 (build-system r-build-system)
7725 `(("r-affy" ,r-affy)
7726 ("r-biobase" ,r-biobase)
7727 ("r-biostrings" ,r-biostrings)
7728 ("r-genomegraphs" ,r-genomegraphs)
7729 ("r-genomicranges" ,r-genomicranges)
7730 ("r-iranges" ,r-iranges)
7731 ("r-oligo" ,r-oligo)
7732 ("r-oligoclasses" ,r-oligoclasses)
7733 ("r-preprocesscore" ,r-preprocesscore)
7734 ("r-waveslim" ,r-waveslim)))
7735 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7736 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7738 "This package is designed to conduct transcriptome analysis for tiling
7739 arrays based on fast wavelet-based functional models.")
7740 (license license:gpl2+)))
7742 (define-public r-variancepartition
7744 (name "r-variancepartition")
7749 (uri (bioconductor-uri "variancePartition" version))
7752 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
7754 `((upstream-name . "variancePartition")))
7755 (build-system r-build-system)
7757 `(("r-biobase" ,r-biobase)
7758 ("r-biocparallel" ,r-biocparallel)
7759 ("r-colorramps" ,r-colorramps)
7760 ("r-doparallel" ,r-doparallel)
7761 ("r-foreach" ,r-foreach)
7762 ("r-ggplot2" ,r-ggplot2)
7763 ("r-gplots" ,r-gplots)
7764 ("r-iterators" ,r-iterators)
7765 ("r-limma" ,r-limma)
7767 ("r-lmertest" ,r-lmertest)
7769 ("r-pbkrtest" ,r-pbkrtest)
7770 ("r-progress" ,r-progress)
7771 ("r-reshape2" ,r-reshape2)
7772 ("r-scales" ,r-scales)))
7774 `(("r-knitr" ,r-knitr)))
7775 (home-page "https://bioconductor.org/packages/variancePartition/")
7776 (synopsis "Analyze variation in gene expression experiments")
7778 "This is a package providing tools to quantify and interpret multiple
7779 sources of biological and technical variation in gene expression experiments.
7780 It uses a linear mixed model to quantify variation in gene expression
7781 attributable to individual, tissue, time point, or technical variables. The
7782 package includes dream differential expression analysis for repeated
7784 (license license:gpl2+)))
7786 (define-public r-htqpcr
7793 (uri (bioconductor-uri "HTqPCR" version))
7796 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
7797 (properties `((upstream-name . "HTqPCR")))
7798 (build-system r-build-system)
7800 `(("r-affy" ,r-affy)
7801 ("r-biobase" ,r-biobase)
7802 ("r-gplots" ,r-gplots)
7803 ("r-limma" ,r-limma)
7804 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7805 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7806 "groups/bertone/software/HTqPCR.pdf"))
7807 (synopsis "Automated analysis of high-throughput qPCR data")
7809 "Analysis of Ct values from high throughput quantitative real-time
7810 PCR (qPCR) assays across multiple conditions or replicates. The input data
7811 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7812 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7813 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7814 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7815 loading, quality assessment, normalization, visualization and parametric or
7816 non-parametric testing for statistical significance in Ct values between
7817 features (e.g. genes, microRNAs).")
7818 (license license:artistic2.0)))
7820 (define-public r-unifiedwmwqpcr
7822 (name "r-unifiedwmwqpcr")
7827 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7830 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
7832 `((upstream-name . "unifiedWMWqPCR")))
7833 (build-system r-build-system)
7835 `(("r-biocgenerics" ,r-biocgenerics)
7836 ("r-htqpcr" ,r-htqpcr)))
7837 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7838 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7840 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7841 data. This modified test allows for testing differential expression in qPCR
7843 (license license:gpl2+)))
7845 (define-public r-universalmotif
7847 (name "r-universalmotif")
7852 (uri (bioconductor-uri "universalmotif" version))
7855 "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
7857 `((upstream-name . "universalmotif")))
7858 (build-system r-build-system)
7861 (modify-phases %standard-phases
7862 (add-after 'unpack 'fix-reference-to-strip
7864 (substitute* "src/Makevars"
7865 (("/usr/bin/strip") (which "strip"))))))))
7867 `(("r-biocgenerics" ,r-biocgenerics)
7868 ("r-biostrings" ,r-biostrings)
7869 ("r-ggplot2" ,r-ggplot2)
7870 ("r-ggseqlogo" ,r-ggseqlogo)
7871 ("r-iranges" ,r-iranges)
7874 ("r-rcppthread" ,r-rcppthread)
7875 ("r-rdpack" ,r-rdpack)
7876 ("r-rlang" ,r-rlang)
7877 ("r-s4vectors" ,r-s4vectors)
7878 ("r-yaml" ,r-yaml)))
7880 `(("r-knitr" ,r-knitr)))
7882 "https://bioconductor.org/packages/universalmotif/")
7884 "Specific structures importer, modifier, and exporter for R")
7886 "This package allows importing most common @dfn{specific structure}
7887 (motif) types into R for use by functions provided by other Bioconductor
7888 motif-related packages. Motifs can be exported into most major motif formats
7889 from various classes as defined by other Bioconductor packages. A suite of
7890 motif and sequence manipulation and analysis functions are included, including
7891 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
7892 motifs, and others.")
7893 (license license:gpl3)))
7895 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7897 (define-public r-activedriverwgs
7899 (name "r-activedriverwgs")
7904 (uri (cran-uri "ActiveDriverWGS" version))
7907 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
7909 `((upstream-name . "ActiveDriverWGS")))
7910 (build-system r-build-system)
7912 `(("r-biostrings" ,r-biostrings)
7913 ("r-bsgenome" ,r-bsgenome)
7914 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7915 ("r-genomeinfodb" ,r-genomeinfodb)
7916 ("r-genomicranges" ,r-genomicranges)
7917 ("r-iranges" ,r-iranges)
7918 ("r-s4vectors" ,r-s4vectors)))
7920 `(("r-knitr" ,r-knitr)))
7921 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7922 (synopsis "Driver discovery tool for cancer whole genomes")
7924 "This package provides a method for finding an enrichment of cancer
7925 simple somatic mutations (SNVs and Indels) in functional elements across the
7926 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7927 using whole genome sequencing data.")
7928 (license license:gpl3)))
7930 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7932 (define-public r-activepathways
7934 (name "r-activepathways")
7939 (uri (cran-uri "ActivePathways" version))
7942 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7944 `((upstream-name . "ActivePathways")))
7945 (build-system r-build-system)
7947 `(("r-data-table" ,r-data-table)
7948 ("r-ggplot2" ,r-ggplot2)))
7950 `(("r-knitr" ,r-knitr)))
7951 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7952 (synopsis "Multivariate pathway enrichment analysis")
7954 "This package represents an integrative method of analyzing multi omics
7955 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7956 uses a statistical data fusion approach, rationalizes contributing evidence
7957 and highlights associated genes, improving systems-level understanding of
7958 cellular organization in health and disease.")
7959 (license license:gpl3)))
7961 (define-public r-bgmix
7968 (uri (bioconductor-uri "BGmix" version))
7971 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
7972 (properties `((upstream-name . "BGmix")))
7973 (build-system r-build-system)
7975 `(("r-kernsmooth" ,r-kernsmooth)))
7976 (home-page "https://bioconductor.org/packages/BGmix/")
7977 (synopsis "Bayesian models for differential gene expression")
7979 "This package provides fully Bayesian mixture models for differential
7981 (license license:gpl2)))
7983 (define-public r-bgx
7990 (uri (bioconductor-uri "bgx" version))
7993 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
7994 (properties `((upstream-name . "bgx")))
7995 (build-system r-build-system)
7997 `(("r-affy" ,r-affy)
7998 ("r-biobase" ,r-biobase)
7999 ("r-gcrma" ,r-gcrma)
8000 ("r-rcpp" ,r-rcpp)))
8001 (home-page "https://bioconductor.org/packages/bgx/")
8002 (synopsis "Bayesian gene expression")
8004 "This package provides tools for Bayesian integrated analysis of
8005 Affymetrix GeneChips.")
8006 (license license:gpl2)))
8008 (define-public r-bhc
8015 (uri (bioconductor-uri "BHC" version))
8018 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
8019 (properties `((upstream-name . "BHC")))
8020 (build-system r-build-system)
8021 (home-page "https://bioconductor.org/packages/BHC/")
8022 (synopsis "Bayesian hierarchical clustering")
8024 "The method implemented in this package performs bottom-up hierarchical
8025 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
8026 in the data and Bayesian model selection to decide at each step which clusters
8027 to merge. This avoids several limitations of traditional methods, for example
8028 how many clusters there should be and how to choose a principled distance
8029 metric. This implementation accepts multinomial (i.e. discrete, with 2+
8030 categories) or time-series data. This version also includes a randomised
8031 algorithm which is more efficient for larger data sets.")
8032 (license license:gpl3)))
8034 (define-public r-bicare
8041 (uri (bioconductor-uri "BicARE" version))
8044 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
8045 (properties `((upstream-name . "BicARE")))
8046 (build-system r-build-system)
8048 `(("r-biobase" ,r-biobase)
8049 ("r-gseabase" ,r-gseabase)
8050 ("r-multtest" ,r-multtest)))
8051 (home-page "http://bioinfo.curie.fr")
8052 (synopsis "Biclustering analysis and results exploration")
8054 "This is a package for biclustering analysis and exploration of
8056 (license license:gpl2)))
8058 (define-public r-bifet
8065 (uri (bioconductor-uri "BiFET" version))
8068 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
8069 (properties `((upstream-name . "BiFET")))
8070 (build-system r-build-system)
8072 `(("r-genomicranges" ,r-genomicranges)
8073 ("r-poibin" ,r-poibin)))
8075 `(("r-knitr" ,r-knitr)))
8076 (home-page "https://bioconductor.org/packages/BiFET")
8077 (synopsis "Bias-free footprint enrichment test")
8079 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
8080 over-represented in target regions compared to background regions after
8081 correcting for the bias arising from the imbalance in read counts and GC
8082 contents between the target and background regions. For a given TF k, BiFET
8083 tests the null hypothesis that the target regions have the same probability of
8084 having footprints for the TF k as the background regions while correcting for
8085 the read count and GC content bias.")
8086 (license license:gpl3)))
8088 (define-public r-rsbml
8095 (uri (bioconductor-uri "rsbml" version))
8098 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
8099 (properties `((upstream-name . "rsbml")))
8100 (build-system r-build-system)
8102 `(("libsbml" ,libsbml)
8105 `(("r-biocgenerics" ,r-biocgenerics)
8106 ("r-graph" ,r-graph)))
8108 `(("pkg-config" ,pkg-config)))
8109 (home-page "http://www.sbml.org")
8110 (synopsis "R support for SBML")
8112 "This package provides an R interface to libsbml for SBML parsing,
8113 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
8114 (license license:artistic2.0)))
8116 (define-public r-hypergraph
8118 (name "r-hypergraph")
8123 (uri (bioconductor-uri "hypergraph" version))
8126 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
8127 (properties `((upstream-name . "hypergraph")))
8128 (build-system r-build-system)
8130 `(("r-graph" ,r-graph)))
8131 (home-page "https://bioconductor.org/packages/hypergraph")
8132 (synopsis "Hypergraph data structures")
8134 "This package implements some simple capabilities for representing and
8135 manipulating hypergraphs.")
8136 (license license:artistic2.0)))
8138 (define-public r-hyperdraw
8140 (name "r-hyperdraw")
8145 (uri (bioconductor-uri "hyperdraw" version))
8148 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
8149 (properties `((upstream-name . "hyperdraw")))
8150 (build-system r-build-system)
8151 (inputs `(("graphviz" ,graphviz)))
8153 `(("r-graph" ,r-graph)
8154 ("r-hypergraph" ,r-hypergraph)
8155 ("r-rgraphviz" ,r-rgraphviz)))
8156 (home-page "https://bioconductor.org/packages/hyperdraw")
8157 (synopsis "Visualizing hypergraphs")
8159 "This package provides functions for visualizing hypergraphs.")
8160 (license license:gpl2+)))
8162 (define-public r-biggr
8169 (uri (bioconductor-uri "BiGGR" version))
8172 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
8173 (properties `((upstream-name . "BiGGR")))
8174 (build-system r-build-system)
8176 `(("r-hyperdraw" ,r-hyperdraw)
8177 ("r-hypergraph" ,r-hypergraph)
8179 ("r-limsolve" ,r-limsolve)
8180 ("r-rsbml" ,r-rsbml)
8181 ("r-stringr" ,r-stringr)))
8182 (home-page "https://bioconductor.org/packages/BiGGR/")
8183 (synopsis "Constraint based modeling using metabolic reconstruction databases")
8185 "This package provides an interface to simulate metabolic reconstruction
8186 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
8187 reconstruction databases. The package facilitates @dfn{flux balance
8188 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
8189 networks and estimated fluxes can be visualized with hypergraphs.")
8190 (license license:gpl3+)))
8192 (define-public r-bigmemoryextras
8194 (name "r-bigmemoryextras")
8199 (uri (bioconductor-uri "bigmemoryExtras" version))
8202 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
8204 `((upstream-name . "bigmemoryExtras")))
8205 (build-system r-build-system)
8207 `(("r-bigmemory" ,r-bigmemory)))
8209 `(("r-knitr" ,r-knitr)))
8210 (home-page "https://github.com/phaverty/bigmemoryExtras")
8211 (synopsis "Extension of the bigmemory package")
8213 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
8214 safety and convenience features to the @code{filebacked.big.matrix} class from
8215 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
8216 monitoring and gracefully restoring the connection to on-disk data and it also
8217 protects against accidental data modification with a file-system-based
8218 permissions system. Utilities are provided for using @code{BigMatrix}-derived
8219 classes as @code{assayData} matrices within the @code{Biobase} package's
8220 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
8221 related to attaching to, and indexing into, file-backed matrices with
8222 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
8223 a file-backed matrix with factor properties.")
8224 (license license:artistic2.0)))
8226 (define-public r-bigpint
8233 (uri (bioconductor-uri "bigPint" version))
8236 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
8237 (properties `((upstream-name . "bigPint")))
8238 (build-system r-build-system)
8240 `(("r-delayedarray" ,r-delayedarray)
8241 ("r-dplyr" ,r-dplyr)
8242 ("r-ggally" ,r-ggally)
8243 ("r-ggplot2" ,r-ggplot2)
8244 ("r-gridextra" ,r-gridextra)
8245 ("r-hexbin" ,r-hexbin)
8246 ("r-hmisc" ,r-hmisc)
8247 ("r-htmlwidgets" ,r-htmlwidgets)
8248 ("r-plotly" ,r-plotly)
8250 ("r-rcolorbrewer" ,r-rcolorbrewer)
8251 ("r-reshape" ,r-reshape)
8252 ("r-shiny" ,r-shiny)
8253 ("r-shinycssloaders" ,r-shinycssloaders)
8254 ("r-shinydashboard" ,r-shinydashboard)
8255 ("r-stringr" ,r-stringr)
8256 ("r-summarizedexperiment" ,r-summarizedexperiment)
8257 ("r-tidyr" ,r-tidyr)))
8259 `(("r-knitr" ,r-knitr)))
8260 (home-page "https://github.com/lindsayrutter/bigPint")
8261 (synopsis "Big multivariate data plotted interactively")
8263 "This package provides methods for visualizing large multivariate
8264 datasets using static and interactive scatterplot matrices, parallel
8265 coordinate plots, volcano plots, and litre plots. It includes examples for
8266 visualizing RNA-sequencing datasets and differentially expressed genes.")
8267 (license license:gpl3)))
8269 (define-public r-chemminer
8271 (name "r-chemminer")
8276 (uri (bioconductor-uri "ChemmineR" version))
8279 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
8280 (properties `((upstream-name . "ChemmineR")))
8281 (build-system r-build-system)
8283 `(("r-base64enc" ,r-base64enc)
8285 ("r-biocgenerics" ,r-biocgenerics)
8287 ("r-digest" ,r-digest)
8289 ("r-ggplot2" ,r-ggplot2)
8290 ("r-gridextra" ,r-gridextra)
8293 ("r-rcurl" ,r-rcurl)
8294 ("r-rjson" ,r-rjson)
8295 ("r-rsvg" ,r-rsvg)))
8297 `(("r-knitr" ,r-knitr)))
8298 (home-page "https://github.com/girke-lab/ChemmineR")
8299 (synopsis "Cheminformatics toolkit for R")
8301 "ChemmineR is a cheminformatics package for analyzing drug-like small
8302 molecule data in R. It contains functions for efficient processing of large
8303 numbers of molecules, physicochemical/structural property predictions,
8304 structural similarity searching, classification and clustering of compound
8305 libraries with a wide spectrum of algorithms. In addition, it offers
8306 visualization functions for compound clustering results and chemical
8308 (license license:artistic2.0)))
8310 (define-public r-bioassayr
8312 (name "r-bioassayr")
8317 (uri (bioconductor-uri "bioassayR" version))
8320 "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
8321 (properties `((upstream-name . "bioassayR")))
8322 (build-system r-build-system)
8324 `(("r-biocgenerics" ,r-biocgenerics)
8325 ("r-chemminer" ,r-chemminer)
8327 ("r-matrix" ,r-matrix)
8328 ("r-rjson" ,r-rjson)
8329 ("r-rsqlite" ,r-rsqlite)
8332 `(("r-knitr" ,r-knitr)))
8333 (home-page "https://github.com/girke-lab/bioassayR")
8334 (synopsis "Cross-target analysis of small molecule bioactivity")
8336 "bioassayR is a computational tool that enables simultaneous analysis of
8337 thousands of bioassay experiments performed over a diverse set of compounds
8338 and biological targets. Unique features include support for large-scale
8339 cross-target analyses of both public and custom bioassays, generation of
8340 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
8341 preloaded database that provides access to a substantial portion of publicly
8342 available bioactivity data.")
8343 (license license:artistic2.0)))
8345 (define-public r-biobroom
8352 (uri (bioconductor-uri "biobroom" version))
8355 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
8356 (properties `((upstream-name . "biobroom")))
8357 (build-system r-build-system)
8359 `(("r-biobase" ,r-biobase)
8360 ("r-broom" ,r-broom)
8361 ("r-dplyr" ,r-dplyr)
8362 ("r-tidyr" ,r-tidyr)))
8364 `(("r-knitr" ,r-knitr)))
8365 (home-page "https://github.com/StoreyLab/biobroom")
8366 (synopsis "Turn Bioconductor objects into tidy data frames")
8368 "This package contains methods for converting standard objects
8369 constructed by bioinformatics packages, especially those in Bioconductor, and
8370 converting them to @code{tidy} data. It thus serves as a complement to the
8371 @code{broom} package, and follows the same tidy, augment, glance division of
8372 tidying methods. Tidying data makes it easy to recombine, reshape and
8373 visualize bioinformatics analyses.")
8374 ;; Any version of the LGPL.
8375 (license license:lgpl3+)))
8377 (define-public r-graphite
8384 (uri (bioconductor-uri "graphite" version))
8387 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
8388 (properties `((upstream-name . "graphite")))
8389 (build-system r-build-system)
8391 `(("r-annotationdbi" ,r-annotationdbi)
8392 ("r-checkmate" ,r-checkmate)
8393 ("r-graph" ,r-graph)
8395 ("r-rappdirs" ,r-rappdirs)))
8396 (home-page "https://bioconductor.org/packages/graphite/")
8397 (synopsis "Networks from pathway databases")
8399 "Graphite provides networks derived from eight public pathway databases,
8400 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
8402 (license license:agpl3+)))
8404 (define-public r-reactomepa
8406 (name "r-reactomepa")
8411 (uri (bioconductor-uri "ReactomePA" version))
8414 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
8415 (properties `((upstream-name . "ReactomePA")))
8416 (build-system r-build-system)
8418 `(("r-annotationdbi" ,r-annotationdbi)
8420 ("r-enrichplot" ,r-enrichplot)
8421 ("r-ggplot2" ,r-ggplot2)
8422 ("r-ggraph" ,r-ggraph)
8423 ("r-graphite" ,r-graphite)
8424 ("r-igraph" ,r-igraph)
8425 ("r-reactome-db" ,r-reactome-db)))
8427 `(("r-knitr" ,r-knitr)))
8428 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
8429 (synopsis "Reactome pathway analysis")
8431 "This package provides functions for pathway analysis based on the
8432 REACTOME pathway database. It implements enrichment analysis, gene set
8433 enrichment analysis and several functions for visualization.")
8434 (license license:gpl2)))
8436 (define-public r-ebarrays
8443 (uri (bioconductor-uri "EBarrays" version))
8446 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
8447 (properties `((upstream-name . "EBarrays")))
8448 (build-system r-build-system)
8450 `(("r-biobase" ,r-biobase)
8451 ("r-cluster" ,r-cluster)
8452 ("r-lattice" ,r-lattice)))
8453 (home-page "https://bioconductor.org/packages/EBarrays/")
8454 (synopsis "Gene clustering and differential expression identification")
8456 "EBarrays provides tools for the analysis of replicated/unreplicated
8458 (license license:gpl2+)))
8460 (define-public r-bioccasestudies
8462 (name "r-bioccasestudies")
8467 (uri (bioconductor-uri "BiocCaseStudies" version))
8470 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
8472 `((upstream-name . "BiocCaseStudies")))
8473 (build-system r-build-system)
8474 (propagated-inputs `(("r-biobase" ,r-biobase)))
8475 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
8476 (synopsis "Support for the case studies monograph")
8478 "This package provides software and data to support the case studies
8480 (license license:artistic2.0)))
8482 (define-public r-biocgraph
8484 (name "r-biocgraph")
8489 (uri (bioconductor-uri "biocGraph" version))
8492 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
8493 (properties `((upstream-name . "biocGraph")))
8494 (build-system r-build-system)
8496 `(("r-biocgenerics" ,r-biocgenerics)
8497 ("r-geneplotter" ,r-geneplotter)
8498 ("r-graph" ,r-graph)
8499 ("r-rgraphviz" ,r-rgraphviz)))
8500 (home-page "https://bioconductor.org/packages/biocGraph/")
8501 (synopsis "Graph examples and use cases in Bioinformatics")
8503 "This package provides examples and code that make use of the
8504 different graph related packages produced by Bioconductor.")
8505 (license license:artistic2.0)))
8507 (define-public r-experimenthub
8509 (name "r-experimenthub")
8514 (uri (bioconductor-uri "ExperimentHub" version))
8517 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
8518 (properties `((upstream-name . "ExperimentHub")))
8519 (build-system r-build-system)
8521 `(("r-annotationhub" ,r-annotationhub)
8522 ("r-biocfilecache" ,r-biocfilecache)
8523 ("r-biocgenerics" ,r-biocgenerics)
8524 ("r-biocmanager" ,r-biocmanager)
8526 ("r-rappdirs" ,r-rappdirs)
8527 ("r-s4vectors" ,r-s4vectors)))
8529 `(("r-knitr" ,r-knitr)))
8530 (home-page "https://bioconductor.org/packages/ExperimentHub/")
8531 (synopsis "Client to access ExperimentHub resources")
8533 "This package provides a client for the Bioconductor ExperimentHub web
8534 resource. ExperimentHub provides a central location where curated data from
8535 experiments, publications or training courses can be accessed. Each resource
8536 has associated metadata, tags and date of modification. The client creates
8537 and manages a local cache of files retrieved enabling quick and reproducible
8539 (license license:artistic2.0)))
8541 (define-public r-multiassayexperiment
8543 (name "r-multiassayexperiment")
8548 (uri (bioconductor-uri "MultiAssayExperiment" version))
8551 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
8553 `((upstream-name . "MultiAssayExperiment")))
8554 (build-system r-build-system)
8556 `(("r-biobase" ,r-biobase)
8557 ("r-biocgenerics" ,r-biocgenerics)
8558 ("r-genomicranges" ,r-genomicranges)
8559 ("r-iranges" ,r-iranges)
8560 ("r-s4vectors" ,r-s4vectors)
8561 ("r-summarizedexperiment" ,r-summarizedexperiment)
8562 ("r-tidyr" ,r-tidyr)))
8564 `(("r-knitr" ,r-knitr)))
8565 (home-page "https://waldronlab.io/MultiAssayExperiment/")
8566 (synopsis "Integration of multi-omics experiments in Bioconductor")
8568 "MultiAssayExperiment harmonizes data management of multiple assays
8569 performed on an overlapping set of specimens. It provides a familiar
8570 Bioconductor user experience by extending concepts from
8571 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
8572 classes for individual assays, and allowing subsetting by genomic ranges or
8574 (license license:artistic2.0)))
8576 (define-public r-bioconcotk
8578 (name "r-bioconcotk")
8583 (uri (bioconductor-uri "BiocOncoTK" version))
8586 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
8587 (properties `((upstream-name . "BiocOncoTK")))
8588 (build-system r-build-system)
8590 `(("r-bigrquery" ,r-bigrquery)
8592 ("r-complexheatmap" ,r-complexheatmap)
8593 ("r-curatedtcgadata" ,r-curatedtcgadata)
8595 ("r-dplyr" ,r-dplyr)
8597 ("r-genomicfeatures" ,r-genomicfeatures)
8598 ("r-genomicranges" ,r-genomicranges)
8599 ("r-ggplot2" ,r-ggplot2)
8600 ("r-ggpubr" ,r-ggpubr)
8601 ("r-graph" ,r-graph)
8603 ("r-iranges" ,r-iranges)
8604 ("r-magrittr" ,r-magrittr)
8606 ("r-rgraphviz" ,r-rgraphviz)
8607 ("r-rjson" ,r-rjson)
8608 ("r-s4vectors" ,r-s4vectors)
8609 ("r-scales" ,r-scales)
8610 ("r-shiny" ,r-shiny)
8611 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8613 `(("r-knitr" ,r-knitr)))
8614 (home-page "https://bioconductor.org/packages/BiocOncoTK")
8615 (synopsis "Bioconductor components for general cancer genomics")
8617 "The purpose of this package is to provide a central interface to various
8618 tools for genome-scale analysis of cancer studies.")
8619 (license license:artistic2.0)))
8621 (define-public r-biocor
8628 (uri (bioconductor-uri "BioCor" version))
8631 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
8632 (properties `((upstream-name . "BioCor")))
8633 (build-system r-build-system)
8635 `(("r-biocparallel" ,r-biocparallel)
8636 ("r-gseabase" ,r-gseabase)
8637 ("r-matrix" ,r-matrix)))
8639 `(("r-knitr" ,r-knitr)))
8640 (home-page "https://llrs.github.io/BioCor/")
8641 (synopsis "Functional similarities")
8643 "This package provides tools to calculate functional similarities based
8644 on the pathways described on KEGG and REACTOME or in gene sets. These
8645 similarities can be calculated for pathways or gene sets, genes, or clusters
8646 and combined with other similarities. They can be used to improve networks,
8647 gene selection, testing relationships, and so on.")
8648 (license license:expat)))
8650 (define-public r-biocpkgtools
8652 (name "r-biocpkgtools")
8657 (uri (bioconductor-uri "BiocPkgTools" version))
8660 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
8661 (properties `((upstream-name . "BiocPkgTools")))
8662 (build-system r-build-system)
8664 `(("r-biocfilecache" ,r-biocfilecache)
8665 ("r-biocmanager" ,r-biocmanager)
8666 ("r-biocviews" ,r-biocviews)
8667 ("r-dplyr" ,r-dplyr)
8670 ("r-graph" ,r-graph)
8671 ("r-htmltools" ,r-htmltools)
8672 ("r-htmlwidgets" ,r-htmlwidgets)
8674 ("r-igraph" ,r-igraph)
8675 ("r-jsonlite" ,r-jsonlite)
8676 ("r-magrittr" ,r-magrittr)
8677 ("r-rappdirs" ,r-rappdirs)
8679 ("r-readr" ,r-readr)
8681 ("r-rlang" ,r-rlang)
8682 ("r-rvest" ,r-rvest)
8683 ("r-stringr" ,r-stringr)
8684 ("r-tibble" ,r-tibble)
8685 ("r-tidyr" ,r-tidyr)
8686 ("r-tidyselect" ,r-tidyselect)
8687 ("r-xml2" ,r-xml2)))
8689 `(("r-knitr" ,r-knitr)))
8690 (home-page "https://github.com/seandavi/BiocPkgTools")
8691 (synopsis "Collection of tools for learning about Bioconductor packages")
8693 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8694 and build status. This package is a simple collection of functions to access
8695 that metadata from R. The goal is to expose metadata for data mining and
8696 value-added functionality such as package searching, text mining, and
8697 analytics on packages.")
8698 (license license:expat)))
8700 (define-public r-biocset
8707 (uri (bioconductor-uri "BiocSet" version))
8710 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
8711 (properties `((upstream-name . "BiocSet")))
8712 (build-system r-build-system)
8714 `(("r-annotationdbi" ,r-annotationdbi)
8715 ("r-biocio" ,r-biocio)
8716 ("r-dplyr" ,r-dplyr)
8717 ("r-keggrest" ,r-keggrest)
8718 ("r-ontologyindex" ,r-ontologyindex)
8720 ("r-rlang" ,r-rlang)
8721 ("r-s4vectors" ,r-s4vectors)
8722 ("r-tibble" ,r-tibble)
8723 ("r-tidyr" ,r-tidyr)))
8725 `(("r-knitr" ,r-knitr)))
8727 "https://bioconductor.org/packages/BiocSet")
8729 "Representing Different Biological Sets")
8731 "BiocSet displays different biological sets in a triple tibble format.
8732 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
8733 The user has the ability to activate one of these three tibbles to perform
8734 common functions from the @code{dplyr} package. Mapping functionality and
8735 accessing web references for elements/sets are also available in BiocSet.")
8736 (license license:artistic2.0)))
8738 (define-public r-biocworkflowtools
8740 (name "r-biocworkflowtools")
8745 (uri (bioconductor-uri "BiocWorkflowTools" version))
8748 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
8750 `((upstream-name . "BiocWorkflowTools")))
8751 (build-system r-build-system)
8753 `(("r-biocstyle" ,r-biocstyle)
8754 ("r-bookdown" ,r-bookdown)
8755 ("r-git2r" ,r-git2r)
8757 ("r-knitr" ,r-knitr)
8758 ("r-rmarkdown" ,r-rmarkdown)
8759 ("r-rstudioapi" ,r-rstudioapi)
8760 ("r-stringr" ,r-stringr)
8761 ("r-usethis" ,r-usethis)))
8763 `(("r-knitr" ,r-knitr)))
8764 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8765 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8767 "This package provides functions to ease the transition between
8768 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8769 (license license:expat)))
8771 (define-public r-biodist
8778 (uri (bioconductor-uri "bioDist" version))
8781 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
8782 (properties `((upstream-name . "bioDist")))
8783 (build-system r-build-system)
8785 `(("r-biobase" ,r-biobase)
8786 ("r-kernsmooth" ,r-kernsmooth)))
8787 (home-page "https://bioconductor.org/packages/bioDist/")
8788 (synopsis "Different distance measures")
8790 "This package provides a collection of software tools for calculating
8791 distance measures.")
8792 (license license:artistic2.0)))
8794 (define-public r-pcatools
8801 (uri (bioconductor-uri "PCAtools" version))
8804 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
8805 (properties `((upstream-name . "PCAtools")))
8806 (build-system r-build-system)
8808 `(("r-beachmat" ,r-beachmat)
8810 ("r-biocparallel" ,r-biocparallel)
8811 ("r-biocsingular" ,r-biocsingular)
8812 ("r-cowplot" ,r-cowplot)
8813 ("r-delayedarray" ,r-delayedarray)
8814 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8815 ("r-dqrng" ,r-dqrng)
8816 ("r-ggplot2" ,r-ggplot2)
8817 ("r-ggrepel" ,r-ggrepel)
8818 ("r-lattice" ,r-lattice)
8819 ("r-matrix" ,r-matrix)
8821 ("r-reshape2" ,r-reshape2)))
8822 (native-inputs `(("r-knitr" ,r-knitr)))
8823 (home-page "https://github.com/kevinblighe/PCAtools")
8824 (synopsis "PCAtools: everything Principal Components Analysis")
8826 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8827 structure of the data without the need to build any model to represent it.
8828 This \"summary\" of the data is arrived at through a process of reduction that
8829 can transform the large number of variables into a lesser number that are
8830 uncorrelated (i.e. the 'principal components'), while at the same time being
8831 capable of easy interpretation on the original data. PCAtools provides
8832 functions for data exploration via PCA, and allows the user to generate
8833 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8834 can also identify an optimal number of principal components via different
8835 metrics, such as the elbow method and Horn's parallel analysis, which has
8836 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8837 dimensional mass cytometry data.")
8838 (license license:gpl3)))
8840 (define-public r-rgreat
8847 (uri (bioconductor-uri "rGREAT" version))
8850 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
8851 (properties `((upstream-name . "rGREAT")))
8852 (build-system r-build-system)
8854 `(("r-genomicranges" ,r-genomicranges)
8855 ("r-getoptlong" ,r-getoptlong)
8856 ("r-iranges" ,r-iranges)
8857 ("r-rcurl" ,r-rcurl)
8858 ("r-rjson" ,r-rjson)))
8859 (native-inputs `(("r-knitr" ,r-knitr)))
8860 (home-page "https://github.com/jokergoo/rGREAT")
8861 (synopsis "Client for GREAT analysis")
8863 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8864 Tool) analysis automatic by constructing a HTTP POST request according to
8865 user's input and automatically retrieving results from GREAT web server.")
8866 (license license:expat)))
8868 (define-public r-m3c
8875 (uri (bioconductor-uri "M3C" version))
8878 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
8879 (properties `((upstream-name . "M3C")))
8880 (build-system r-build-system)
8882 `(("r-cluster" ,r-cluster)
8883 ("r-corpcor" ,r-corpcor)
8884 ("r-doparallel" ,r-doparallel)
8885 ("r-dosnow" ,r-dosnow)
8886 ("r-foreach" ,r-foreach)
8887 ("r-ggplot2" ,r-ggplot2)
8888 ("r-matrix" ,r-matrix)
8889 ("r-matrixcalc" ,r-matrixcalc)
8890 ("r-rtsne" ,r-rtsne)
8891 ("r-umap" ,r-umap)))
8892 (native-inputs `(("r-knitr" ,r-knitr)))
8893 (home-page "https://bioconductor.org/packages/M3C")
8894 (synopsis "Monte Carlo reference-based consensus clustering")
8896 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8897 simulation to eliminate overestimation of @code{K} and can reject the null
8898 hypothesis @code{K=1}.")
8899 (license license:agpl3+)))
8901 (define-public r-icens
8908 (uri (bioconductor-uri "Icens" version))
8911 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
8912 (properties `((upstream-name . "Icens")))
8913 (build-system r-build-system)
8915 `(("r-survival" ,r-survival)))
8916 (home-page "https://bioconductor.org/packages/Icens")
8917 (synopsis "NPMLE for censored and truncated data")
8919 "This package provides many functions for computing the
8920 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8922 (license license:artistic2.0)))
8924 ;; This is a CRAN package but it depends on r-icens, which is published on
8926 (define-public r-interval
8933 (uri (cran-uri "interval" version))
8936 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
8937 (properties `((upstream-name . "interval")))
8938 (build-system r-build-system)
8940 `(("r-icens" ,r-icens)
8941 ("r-mlecens" ,r-mlecens)
8943 ("r-survival" ,r-survival)))
8944 (home-page "https://cran.r-project.org/web/packages/interval/")
8945 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8947 "This package provides functions to fit nonparametric survival curves,
8948 plot them, and perform logrank or Wilcoxon type tests.")
8949 (license license:gpl2+)))
8951 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8952 ;; Bioconductor package.
8953 (define-public r-fhtest
8960 (uri (cran-uri "FHtest" version))
8963 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
8964 (properties `((upstream-name . "FHtest")))
8965 (build-system r-build-system)
8967 `(("r-interval" ,r-interval)
8968 ("r-kmsurv" ,r-kmsurv)
8971 ("r-survival" ,r-survival)))
8972 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8973 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8975 "This package provides functions to compare two or more survival curves
8979 @item The Fleming-Harrington test for right-censored data based on
8980 permutations and on counting processes.
8981 @item An extension of the Fleming-Harrington test for interval-censored data
8982 based on a permutation distribution and on a score vector distribution.
8985 (license license:gpl2+)))
8987 (define-public r-fourcseq
8994 (uri (bioconductor-uri "FourCSeq" version))
8996 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
8997 (properties `((upstream-name . "FourCSeq")))
8998 (build-system r-build-system)
9000 `(("r-biobase" ,r-biobase)
9001 ("r-biostrings" ,r-biostrings)
9002 ("r-deseq2" ,r-deseq2)
9004 ("r-genomicalignments" ,r-genomicalignments)
9005 ("r-genomicranges" ,r-genomicranges)
9006 ("r-ggbio" ,r-ggbio)
9007 ("r-ggplot2" ,r-ggplot2)
9008 ("r-gtools" ,r-gtools)
9010 ("r-matrix" ,r-matrix)
9011 ("r-reshape2" ,r-reshape2)
9012 ("r-rsamtools" ,r-rsamtools)
9013 ("r-rtracklayer" ,r-rtracklayer)
9014 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9016 `(("r-knitr" ,r-knitr)))
9018 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
9019 (synopsis "Analysis of multiplexed 4C sequencing data")
9021 "This package is an R package dedicated to the analysis of (multiplexed)
9022 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
9023 interactions between DNA elements and identify differential interactions
9024 between conditions. The statistical analysis in R starts with individual bam
9025 files for each sample as inputs. To obtain these files, the package contains
9026 a Python script to demultiplex libraries and trim off primer sequences. With
9027 a standard alignment software the required bam files can be then be
9029 (license license:gpl3+)))
9031 (define-public r-preprocesscore
9033 (name "r-preprocesscore")
9038 (uri (bioconductor-uri "preprocessCore" version))
9041 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
9043 `((upstream-name . "preprocessCore")))
9044 (build-system r-build-system)
9045 (home-page "https://github.com/bmbolstad/preprocessCore")
9046 (synopsis "Collection of pre-processing functions")
9048 "This package provides a library of core pre-processing and normalization
9050 (license license:lgpl2.0+)))
9052 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
9053 ;; Bioconductor package.
9054 (define-public r-wgcna
9061 (uri (cran-uri "WGCNA" version))
9064 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
9065 (properties `((upstream-name . "WGCNA")))
9066 (build-system r-build-system)
9068 `(("r-annotationdbi" ,r-annotationdbi)
9069 ("r-doparallel" ,r-doparallel)
9070 ("r-dynamictreecut" ,r-dynamictreecut)
9071 ("r-fastcluster" ,r-fastcluster)
9072 ("r-foreach" ,r-foreach)
9073 ("r-go-db" ,r-go-db)
9074 ("r-hmisc" ,r-hmisc)
9075 ("r-impute" ,r-impute)
9077 ("r-survival" ,r-survival)
9078 ("r-matrixstats" ,r-matrixstats)
9079 ("r-preprocesscore" ,r-preprocesscore)))
9081 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
9082 (synopsis "Weighted correlation network analysis")
9084 "This package provides functions necessary to perform Weighted
9085 Correlation Network Analysis on high-dimensional data. It includes functions
9086 for rudimentary data cleaning, construction and summarization of correlation
9087 networks, module identification and functions for relating both variables and
9088 modules to sample traits. It also includes a number of utility functions for
9089 data manipulation and visualization.")
9090 (license license:gpl2+)))
9092 (define-public r-rgraphviz
9094 (name "r-rgraphviz")
9099 (uri (bioconductor-uri "Rgraphviz" version))
9102 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
9103 (properties `((upstream-name . "Rgraphviz")))
9104 (build-system r-build-system)
9107 (modify-phases %standard-phases
9108 (add-after 'unpack 'make-reproducible
9110 ;; The replacement value is taken from src/graphviz/builddate.h
9111 (substitute* "src/graphviz/configure"
9112 (("VERSION_DATE=.*")
9113 "VERSION_DATE=20200427.2341\n"))
9115 ;; FIXME: Rgraphviz bundles the sources of an older variant of
9116 ;; graphviz. It does not build with the latest version of graphviz, so
9117 ;; we do not add graphviz to the inputs.
9118 (inputs `(("zlib" ,zlib)))
9120 `(("r-graph" ,r-graph)))
9122 `(("pkg-config" ,pkg-config)))
9123 (home-page "https://bioconductor.org/packages/Rgraphviz")
9124 (synopsis "Plotting capabilities for R graph objects")
9126 "This package interfaces R with the graphviz library for plotting R graph
9127 objects from the @code{graph} package.")
9128 (license license:epl1.0)))
9130 (define-public r-fithic
9136 (uri (bioconductor-uri "FitHiC" version))
9139 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
9140 (properties `((upstream-name . "FitHiC")))
9141 (build-system r-build-system)
9143 `(("r-data-table" ,r-data-table)
9144 ("r-fdrtool" ,r-fdrtool)
9145 ("r-rcpp" ,r-rcpp)))
9147 `(("r-knitr" ,r-knitr)))
9148 (home-page "https://bioconductor.org/packages/FitHiC")
9149 (synopsis "Confidence estimation for intra-chromosomal contact maps")
9151 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
9152 intra-chromosomal contact maps produced by genome-wide genome architecture
9153 assays such as Hi-C.")
9154 (license license:gpl2+)))
9156 (define-public r-hitc
9162 (uri (bioconductor-uri "HiTC" version))
9165 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
9166 (properties `((upstream-name . "HiTC")))
9167 (build-system r-build-system)
9169 `(("r-biostrings" ,r-biostrings)
9170 ("r-genomeinfodb" ,r-genomeinfodb)
9171 ("r-genomicranges" ,r-genomicranges)
9172 ("r-iranges" ,r-iranges)
9173 ("r-matrix" ,r-matrix)
9174 ("r-rcolorbrewer" ,r-rcolorbrewer)
9175 ("r-rtracklayer" ,r-rtracklayer)))
9176 (home-page "https://bioconductor.org/packages/HiTC")
9177 (synopsis "High throughput chromosome conformation capture analysis")
9179 "The HiTC package was developed to explore high-throughput \"C\" data
9180 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
9181 quality controls, normalization, visualization, and further analysis are also
9183 (license license:artistic2.0)))
9185 (define-public r-hdf5array
9187 (name "r-hdf5array")
9192 (uri (bioconductor-uri "HDF5Array" version))
9195 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
9196 (properties `((upstream-name . "HDF5Array")))
9197 (build-system r-build-system)
9200 (modify-phases %standard-phases
9201 (add-after 'unpack 'fix-linking
9203 (substitute* "src/Makevars"
9204 ;; This is to avoid having a plain directory on the list of
9205 ;; libraries to link.
9206 (("\\(RHDF5LIB_LIBS\\)" match)
9207 (string-append match "/libhdf5.a")))
9212 `(("r-biocgenerics" ,r-biocgenerics)
9213 ("r-delayedarray" ,r-delayedarray)
9214 ("r-iranges" ,r-iranges)
9215 ("r-matrix" ,r-matrix)
9216 ("r-rhdf5" ,r-rhdf5)
9217 ("r-rhdf5lib" ,r-rhdf5lib)
9218 ("r-s4vectors" ,r-s4vectors)))
9219 (home-page "https://bioconductor.org/packages/HDF5Array")
9220 (synopsis "HDF5 back end for DelayedArray objects")
9221 (description "This package provides an array-like container for convenient
9222 access and manipulation of HDF5 datasets. It supports delayed operations and
9224 (license license:artistic2.0)))
9226 (define-public r-rhdf5lib
9233 (uri (bioconductor-uri "Rhdf5lib" version))
9236 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
9237 (modules '((guix build utils)))
9240 ;; Delete bundled binaries
9241 (delete-file-recursively "src/wininclude/")
9242 (delete-file-recursively "src/winlib-4.9.3/")
9243 (delete-file-recursively "src/winlib-8.3.0/")
9244 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
9246 (properties `((upstream-name . "Rhdf5lib")))
9247 (build-system r-build-system)
9250 (modify-phases %standard-phases
9251 (add-after 'unpack 'do-not-use-bundled-hdf5
9252 (lambda* (#:key inputs #:allow-other-keys)
9253 (for-each delete-file '("configure" "configure.ac"))
9254 ;; Do not make other packages link with the proprietary libsz.
9255 (substitute* "R/zzz.R"
9256 ((" \"%s/libsz.a\"") ""))
9257 (with-directory-excursion "src"
9258 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
9259 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
9261 ;; Remove timestamp and host system information to make
9262 ;; the build reproducible.
9263 (substitute* "hdf5/src/libhdf5.settings.in"
9264 (("Configured on: @CONFIG_DATE@")
9265 "Configured on: Guix")
9266 (("Uname information:.*")
9267 "Uname information: Linux\n")
9268 ;; Remove unnecessary store reference.
9270 "C Compiler: GCC\n"))
9271 (rename-file "hdf5/src/libhdf5.settings.in"
9272 "hdf5/src/libhdf5.settings")
9273 (rename-file "Makevars.in" "Makevars")
9274 (substitute* "Makevars"
9275 (("@ZLIB_LIB@") "-lz")
9276 (("@ZLIB_INCLUDE@") "")
9277 (("HDF5_CXX_LIB=.*")
9278 (string-append "HDF5_CXX_LIB="
9279 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
9281 (string-append "HDF5_LIB="
9282 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
9283 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
9284 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
9285 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
9286 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
9288 (string-append "HDF5_HL_LIB="
9289 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
9290 (("HDF5_HL_CXX_LIB=.*")
9291 (string-append "HDF5_HL_CXX_LIB="
9292 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
9293 ;; szip is non-free software
9294 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
9295 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
9300 `(("hdf5" ,hdf5-1.10)))
9302 `(("hdf5-source" ,(package-source hdf5-1.10))
9303 ("r-knitr" ,r-knitr)))
9304 (home-page "https://bioconductor.org/packages/Rhdf5lib")
9305 (synopsis "HDF5 library as an R package")
9306 (description "This package provides C and C++ HDF5 libraries for use in R
9308 (license license:artistic2.0)))
9310 (define-public r-beachmat
9317 (uri (bioconductor-uri "beachmat" version))
9320 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
9321 (build-system r-build-system)
9323 `(("r-biocgenerics" ,r-biocgenerics)
9324 ("r-delayedarray" ,r-delayedarray)
9325 ("r-matrix" ,r-matrix)))
9327 `(("r-knitr" ,r-knitr)))
9328 (home-page "https://bioconductor.org/packages/beachmat")
9329 (synopsis "Compiling Bioconductor to handle each matrix type")
9330 (description "This package provides a consistent C++ class interface for a
9331 variety of commonly used matrix types, including sparse and HDF5-backed
9333 (license license:gpl3)))
9335 ;; This package includes files that have been taken from kentutils. Some
9336 ;; parts of kentutils are not released under a free license, but this package
9337 ;; only uses files that are also found in the free parts of kentutils.
9338 (define-public r-cner
9345 (uri (bioconductor-uri "CNEr" version))
9347 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
9348 (properties `((upstream-name . "CNEr")))
9349 (build-system r-build-system)
9350 (inputs `(("zlib" ,zlib)))
9352 `(("r-annotate" ,r-annotate)
9353 ("r-biocgenerics" ,r-biocgenerics)
9354 ("r-biostrings" ,r-biostrings)
9356 ("r-genomeinfodb" ,r-genomeinfodb)
9357 ("r-genomicalignments" ,r-genomicalignments)
9358 ("r-genomicranges" ,r-genomicranges)
9359 ("r-ggplot2" ,r-ggplot2)
9360 ("r-go-db" ,r-go-db)
9361 ("r-iranges" ,r-iranges)
9362 ("r-keggrest" ,r-keggrest)
9363 ("r-powerlaw" ,r-powerlaw)
9364 ("r-r-utils" ,r-r-utils)
9365 ("r-readr" ,r-readr)
9366 ("r-reshape2" ,r-reshape2)
9367 ("r-rsqlite" ,r-rsqlite)
9368 ("r-rtracklayer" ,r-rtracklayer)
9369 ("r-s4vectors" ,r-s4vectors)
9370 ("r-xvector" ,r-xvector)))
9372 `(("r-knitr" ,r-knitr)))
9373 (home-page "https://github.com/ge11232002/CNEr")
9374 (synopsis "CNE Detection and Visualization")
9376 "This package provides tools for large-scale identification and
9377 advanced visualization of sets of conserved noncoding elements.")
9378 ;; For all files in src/ucsc "license is hereby granted for all use -
9379 ;; public, private or commercial"; this includes those files that don't
9380 ;; have a license header, because they are included in the free parts of
9381 ;; the kentutils package.
9382 (license (list license:gpl2
9383 (license:non-copyleft
9384 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
9386 (define-public r-tfbstools
9388 (name "r-tfbstools")
9393 (uri (bioconductor-uri "TFBSTools" version))
9396 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
9397 (properties `((upstream-name . "TFBSTools")))
9398 (build-system r-build-system)
9400 `(("r-biobase" ,r-biobase)
9401 ("r-biocgenerics" ,r-biocgenerics)
9402 ("r-biocparallel" ,r-biocparallel)
9403 ("r-biostrings" ,r-biostrings)
9404 ("r-bsgenome" ,r-bsgenome)
9405 ("r-catools" ,r-catools)
9408 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
9409 ("r-genomeinfodb" ,r-genomeinfodb)
9410 ("r-genomicranges" ,r-genomicranges)
9411 ("r-gtools" ,r-gtools)
9412 ("r-iranges" ,r-iranges)
9413 ("r-rsqlite" ,r-rsqlite)
9414 ("r-rtracklayer" ,r-rtracklayer)
9415 ("r-s4vectors" ,r-s4vectors)
9416 ("r-seqlogo" ,r-seqlogo)
9417 ("r-tfmpvalue" ,r-tfmpvalue)
9419 ("r-xvector" ,r-xvector)))
9420 (native-inputs `(("r-knitr" ,r-knitr)))
9421 (home-page "https://github.com/ge11232002/TFBSTools")
9422 (synopsis "Transcription factor binding site (TFBS) analysis")
9424 "TFBSTools is a package for the analysis and manipulation of
9425 transcription factor binding sites. It includes matrices conversion
9426 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
9427 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
9428 scan putative TFBS from sequence/alignment, query JASPAR database and
9429 provides a wrapper of de novo motif discovery software.")
9430 (license license:gpl2)))
9432 (define-public r-motifmatchr
9434 (name "r-motifmatchr")
9439 (uri (bioconductor-uri "motifmatchr" version))
9442 "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
9443 (properties `((upstream-name . "motifmatchr")))
9444 (build-system r-build-system)
9446 `(("r-biostrings" ,r-biostrings)
9447 ("r-bsgenome" ,r-bsgenome)
9448 ("r-genomeinfodb" ,r-genomeinfodb)
9449 ("r-genomicranges" ,r-genomicranges)
9450 ("r-iranges" ,r-iranges)
9451 ("r-matrix" ,r-matrix)
9453 ("r-rcpparmadillo" ,r-rcpparmadillo)
9454 ("r-rsamtools" ,r-rsamtools)
9455 ("r-s4vectors" ,r-s4vectors)
9456 ("r-summarizedexperiment" ,r-summarizedexperiment)
9457 ("r-tfbstools" ,r-tfbstools)))
9458 (native-inputs `(("r-knitr" ,r-knitr)))
9459 (home-page "https://bioconductor.org/packages/motifmatchr")
9460 (synopsis "Fast motif matching in R")
9462 "Quickly find motif matches for many motifs and many sequences.
9463 This package wraps C++ code from the MOODS motif calling library.")
9464 (license license:gpl3)))
9466 (define-public r-chromvar
9473 (uri (bioconductor-uri "chromVAR" version))
9475 (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
9476 (properties `((upstream-name . "chromVAR")))
9477 (build-system r-build-system)
9479 `(("r-biocgenerics" ,r-biocgenerics)
9480 ("r-biocparallel" ,r-biocparallel)
9481 ("r-biostrings" ,r-biostrings)
9482 ("r-bsgenome" ,r-bsgenome)
9484 ("r-genomeinfodb" ,r-genomeinfodb)
9485 ("r-genomicranges" ,r-genomicranges)
9486 ("r-ggplot2" ,r-ggplot2)
9487 ("r-iranges" ,r-iranges)
9488 ("r-matrix" ,r-matrix)
9489 ("r-miniui" ,r-miniui)
9490 ("r-nabor" ,r-nabor)
9491 ("r-plotly" ,r-plotly)
9492 ("r-rcolorbrewer" ,r-rcolorbrewer)
9494 ("r-rcpparmadillo" ,r-rcpparmadillo)
9495 ("r-rsamtools" ,r-rsamtools)
9496 ("r-rtsne" ,r-rtsne)
9497 ("r-s4vectors" ,r-s4vectors)
9498 ("r-shiny" ,r-shiny)
9499 ("r-summarizedexperiment" ,r-summarizedexperiment)
9500 ("r-tfbstools" ,r-tfbstools)))
9501 (native-inputs `(("r-knitr" ,r-knitr)))
9502 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
9503 (synopsis "Determine chromatin variation across regions")
9505 "This package @code{r-chromvar} determines variation in chromatin
9506 accessibility across sets of annotations or peaks. @code{r-chromvar} is
9507 designed primarily for single-cell or sparse chromatin accessibility data like
9508 single cell assay for transposase-accessible chromatin using
9509 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
9510 sequence (@code{DNAse-seq}) experiments.")
9511 (license license:expat)))
9513 (define-public r-singlecellexperiment
9515 (name "r-singlecellexperiment")
9520 (uri (bioconductor-uri "SingleCellExperiment" version))
9523 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
9525 `((upstream-name . "SingleCellExperiment")))
9526 (build-system r-build-system)
9528 `(("r-biocgenerics" ,r-biocgenerics)
9529 ("r-s4vectors" ,r-s4vectors)
9530 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9532 `(("r-knitr" ,r-knitr)))
9533 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
9534 (synopsis "S4 classes for single cell data")
9535 (description "This package defines an S4 class for storing data from
9536 single-cell experiments. This includes specialized methods to store and
9537 retrieve spike-in information, dimensionality reduction coordinates and size
9538 factors for each cell, along with the usual metadata for genes and
9540 (license license:gpl3)))
9542 (define-public r-scuttle
9549 (uri (bioconductor-uri "scuttle" version))
9552 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
9553 (properties `((upstream-name . "scuttle")))
9554 (build-system r-build-system)
9556 `(("r-beachmat" ,r-beachmat)
9557 ("r-biocgenerics" ,r-biocgenerics)
9558 ("r-biocparallel" ,r-biocparallel)
9559 ("r-delayedarray" ,r-delayedarray)
9560 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9561 ("r-genomicranges" ,r-genomicranges)
9562 ("r-matrix" ,r-matrix)
9564 ("r-s4vectors" ,r-s4vectors)
9565 ("r-singlecellexperiment" ,r-singlecellexperiment)
9566 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9567 (native-inputs `(("r-knitr" ,r-knitr)))
9568 (home-page "https://bioconductor.org/packages/scuttle")
9569 (synopsis "Single-cell RNA-Seq analysis utilities")
9571 "This package provides basic utility functions for performing single-cell
9572 analyses, focusing on simple normalization, quality control and data
9573 transformations. It also provides some helper functions to assist development
9574 of other packages.")
9575 (license license:gpl3)))
9577 (define-public r-scater
9583 (uri (bioconductor-uri "scater" version))
9586 "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535"))))
9587 (build-system r-build-system)
9589 `(("r-biocgenerics" ,r-biocgenerics)
9590 ("r-biocneighbors" ,r-biocneighbors)
9591 ("r-biocparallel" ,r-biocparallel)
9592 ("r-biocsingular" ,r-biocsingular)
9593 ("r-delayedarray" ,r-delayedarray)
9594 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9595 ("r-ggbeeswarm" ,r-ggbeeswarm)
9596 ("r-ggplot2" ,r-ggplot2)
9597 ("r-gridextra" ,r-gridextra)
9598 ("r-matrix" ,r-matrix)
9599 ("r-rlang" ,r-rlang)
9600 ("r-s4vectors" ,r-s4vectors)
9601 ("r-scuttle" ,r-scuttle)
9602 ("r-singlecellexperiment" ,r-singlecellexperiment)
9603 ("r-summarizedexperiment" ,r-summarizedexperiment)
9604 ("r-viridis" ,r-viridis)))
9606 `(("r-knitr" ,r-knitr)))
9607 (home-page "https://github.com/davismcc/scater")
9608 (synopsis "Single-cell analysis toolkit for gene expression data in R")
9609 (description "This package provides a collection of tools for doing
9610 various analyses of single-cell RNA-seq gene expression data, with a focus on
9612 (license license:gpl2+)))
9614 (define-public r-scran
9621 (uri (bioconductor-uri "scran" version))
9624 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
9625 (build-system r-build-system)
9627 `(("r-beachmat" ,r-beachmat)
9629 ("r-biocgenerics" ,r-biocgenerics)
9630 ("r-biocneighbors" ,r-biocneighbors)
9631 ("r-biocparallel" ,r-biocparallel)
9632 ("r-biocsingular" ,r-biocsingular)
9633 ("r-bluster" ,r-bluster)
9634 ("r-delayedarray" ,r-delayedarray)
9635 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9636 ("r-dqrng" ,r-dqrng)
9637 ("r-edger" ,r-edger)
9638 ("r-igraph" ,r-igraph)
9639 ("r-limma" ,r-limma)
9640 ("r-matrix" ,r-matrix)
9642 ("r-s4vectors" ,r-s4vectors)
9643 ("r-scuttle" ,r-scuttle)
9644 ("r-singlecellexperiment" ,r-singlecellexperiment)
9645 ("r-statmod" ,r-statmod)
9646 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9648 `(("r-knitr" ,r-knitr)))
9649 (home-page "https://bioconductor.org/packages/scran")
9650 (synopsis "Methods for single-cell RNA-Seq data analysis")
9651 (description "This package implements a variety of low-level analyses of
9652 single-cell RNA-seq data. Methods are provided for normalization of
9653 cell-specific biases, assignment of cell cycle phase, and detection of highly
9654 variable and significantly correlated genes.")
9655 (license license:gpl3)))
9657 (define-public r-sparsematrixstats
9659 (name "r-sparsematrixstats")
9664 (uri (bioconductor-uri "sparseMatrixStats" version))
9667 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
9669 `((upstream-name . "sparseMatrixStats")))
9670 (build-system r-build-system)
9672 `(("r-matrix" ,r-matrix)
9673 ("r-matrixgenerics" ,r-matrixgenerics)
9674 ("r-matrixstats" ,r-matrixstats)
9675 ("r-rcpp" ,r-rcpp)))
9676 (native-inputs `(("r-knitr" ,r-knitr)))
9677 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
9678 (synopsis "Summary statistics for rows and columns of sparse matrices")
9680 "This package provides high performance functions for row and column
9681 operations on sparse matrices. Currently, the optimizations are limited to
9682 data in the column sparse format.")
9683 (license license:expat)))
9685 (define-public r-delayedmatrixstats
9687 (name "r-delayedmatrixstats")
9692 (uri (bioconductor-uri "DelayedMatrixStats" version))
9695 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
9697 `((upstream-name . "DelayedMatrixStats")))
9698 (build-system r-build-system)
9700 `(("r-biocparallel" ,r-biocparallel)
9701 ("r-delayedarray" ,r-delayedarray)
9702 ("r-hdf5array" ,r-hdf5array)
9703 ("r-iranges" ,r-iranges)
9704 ("r-matrix" ,r-matrix)
9705 ("r-matrixgenerics" ,r-matrixgenerics)
9706 ("r-matrixstats" ,r-matrixstats)
9707 ("r-s4vectors" ,r-s4vectors)
9708 ("r-sparsematrixstats" ,r-sparsematrixstats)))
9710 `(("r-knitr" ,r-knitr)))
9711 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
9712 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
9714 "This package provides a port of the @code{matrixStats} API for use with
9715 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
9716 contains high-performing functions operating on rows and columns of
9717 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
9718 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
9719 are optimized per data type and for subsetted calculations such that both
9720 memory usage and processing time is minimized.")
9721 (license license:expat)))
9723 (define-public r-mscoreutils
9725 (name "r-mscoreutils")
9730 (uri (bioconductor-uri "MsCoreUtils" version))
9733 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
9734 (properties `((upstream-name . "MsCoreUtils")))
9735 (build-system r-build-system)
9737 `(("r-mass" ,r-mass)
9739 ("r-s4vectors" ,r-s4vectors)))
9741 `(("r-knitr" ,r-knitr)))
9742 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
9743 (synopsis "Core utils for mass spectrometry data")
9745 "This package defines low-level functions for mass spectrometry data and
9746 is independent of any high-level data structures. These functions include
9747 mass spectra processing functions (noise estimation, smoothing, binning),
9748 quantitative aggregation functions (median polish, robust summarisation,
9749 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
9750 well as misc helper functions, that are used across high-level data structure
9751 within the R for Mass Spectrometry packages.")
9752 (license license:artistic2.0)))
9754 (define-public r-biocio
9761 (uri (bioconductor-uri "BiocIO" version))
9764 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
9765 (properties `((upstream-name . "BiocIO")))
9766 (build-system r-build-system)
9768 `(("r-biocgenerics" ,r-biocgenerics)
9769 ("r-genomicranges" ,r-genomicranges)
9770 ("r-rcurl" ,r-rcurl)
9771 ("r-s4vectors" ,r-s4vectors)))
9773 `(("r-knitr" ,r-knitr)))
9774 (home-page "https://bioconductor.org/packages/BiocIO")
9775 (synopsis "Standard input and output for Bioconductor packages")
9777 "This package implements `import()` and `export()` standard generics for
9778 importing and exporting biological data formats. `import()` supports
9779 whole-file as well as chunk-wise iterative import. The `import()` interface
9780 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
9781 row or element-like components of the file resource), `select()` (on
9782 column-like components of the file resource) and `collect()`. The `import()`
9783 interface optionally provides transparent access to remote (e.g. via https)
9784 as well as local access. Developers can register a file extension, e.g.,
9785 `.loom` for dispatch from character-based URIs to specific `import()` /
9786 `export()` methods based on classes representing file types, e.g.,
9788 (license license:artistic2.0)))
9790 (define-public r-msmseda
9797 (uri (bioconductor-uri "msmsEDA" version))
9800 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
9801 (properties `((upstream-name . "msmsEDA")))
9802 (build-system r-build-system)
9804 `(("r-gplots" ,r-gplots)
9806 ("r-msnbase" ,r-msnbase)
9807 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9809 "https://bioconductor.org/packages/msmsEDA")
9810 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
9812 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
9813 experiments, and visualize de influence of the involved factors.")
9814 (license license:gpl2)))
9816 (define-public r-msmstests
9818 (name "r-msmstests")
9823 (uri (bioconductor-uri "msmsTests" version))
9826 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
9827 (properties `((upstream-name . "msmsTests")))
9828 (build-system r-build-system)
9830 `(("r-edger" ,r-edger)
9831 ("r-msmseda" ,r-msmseda)
9832 ("r-msnbase" ,r-msnbase)
9833 ("r-qvalue" ,r-qvalue)))
9835 "https://bioconductor.org/packages/msmsTests")
9836 (synopsis "Differential LC-MS/MS expression tests")
9838 "This packages provides statistical tests for label-free LC-MS/MS data
9839 by spectral counts, to discover differentially expressed proteins between two
9840 biological conditions. Three tests are available: Poisson GLM regression,
9841 quasi-likelihood GLM regression, and the negative binomial of the edgeR
9842 package.The three models admit blocking factors to control for nuissance
9843 variables.To assure a good level of reproducibility a post-test filter is
9844 available, where we may set the minimum effect size considered biologicaly
9845 relevant, and the minimum expression of the most abundant condition.")
9846 (license license:gpl2)))
9848 (define-public r-catalyst
9855 (uri (bioconductor-uri "CATALYST" version))
9858 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
9859 (properties `((upstream-name . "CATALYST")))
9860 (build-system r-build-system)
9862 `(("r-circlize" ,r-circlize)
9863 ("r-complexheatmap" ,r-complexheatmap)
9864 ("r-consensusclusterplus" ,r-consensusclusterplus)
9865 ("r-cowplot" ,r-cowplot)
9866 ("r-data-table" ,r-data-table)
9867 ("r-dplyr" ,r-dplyr)
9869 ("r-flowcore" ,r-flowcore)
9870 ("r-flowsom" ,r-flowsom)
9871 ("r-ggplot2" ,r-ggplot2)
9872 ("r-ggrepel" ,r-ggrepel)
9873 ("r-ggridges" ,r-ggridges)
9874 ("r-gridextra" ,r-gridextra)
9875 ("r-magrittr" ,r-magrittr)
9876 ("r-matrix" ,r-matrix)
9877 ("r-matrixstats" ,r-matrixstats)
9879 ("r-purrr" ,r-purrr)
9880 ("r-rcolorbrewer" ,r-rcolorbrewer)
9881 ("r-reshape2" ,r-reshape2)
9882 ("r-rtsne" ,r-rtsne)
9883 ("r-s4vectors" ,r-s4vectors)
9884 ("r-scales" ,r-scales)
9885 ("r-scater" ,r-scater)
9886 ("r-singlecellexperiment" ,r-singlecellexperiment)
9887 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9889 `(("r-knitr" ,r-knitr)))
9891 "https://github.com/HelenaLC/CATALYST")
9892 (synopsis "Cytometry data analysis tools")
9894 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
9895 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
9896 reporters to label antibodies, thereby substantially decreasing spectral
9897 overlap and allowing for examination of over 50 parameters at the single cell
9898 level. While spectral overlap is significantly less pronounced in CyTOF than
9899 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
9900 and oxide formation can impede data interpretability. We designed
9901 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
9902 preprocessing of cytometry data, including i) normalization using bead
9903 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
9904 (license license:gpl2+)))
9906 (define-public r-erma
9913 (uri (bioconductor-uri "erma" version))
9916 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
9917 (build-system r-build-system)
9919 `(("r-annotationdbi" ,r-annotationdbi)
9920 ("r-biobase" ,r-biobase)
9921 ("r-biocgenerics" ,r-biocgenerics)
9922 ("r-biocparallel" ,r-biocparallel)
9923 ("r-genomeinfodb" ,r-genomeinfodb)
9924 ("r-genomicfiles" ,r-genomicfiles)
9925 ("r-genomicranges" ,r-genomicranges)
9926 ("r-ggplot2" ,r-ggplot2)
9927 ("r-homo-sapiens" ,r-homo-sapiens)
9928 ("r-iranges" ,r-iranges)
9929 ("r-rtracklayer" ,r-rtracklayer)
9930 ("r-s4vectors" ,r-s4vectors)
9931 ("r-shiny" ,r-shiny)
9932 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9934 `(("r-knitr" ,r-knitr)))
9935 (home-page "https://bioconductor.org/packages/erma")
9936 (synopsis "Epigenomic road map adventures")
9938 "The epigenomics road map describes locations of epigenetic marks in DNA
9939 from a variety of cell types. Of interest are locations of histone
9940 modifications, sites of DNA methylation, and regions of accessible chromatin.
9941 This package presents a selection of elements of the road map including
9942 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
9943 by Ernst and Kellis.")
9944 (license license:artistic2.0)))
9946 (define-public r-ggbio
9953 (uri (bioconductor-uri "ggbio" version))
9956 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
9957 (build-system r-build-system)
9960 (modify-phases %standard-phases
9961 ;; See https://github.com/tengfei/ggbio/issues/117
9962 ;; This fix will be included in the next release.
9963 (add-after 'unpack 'fix-typo
9965 (substitute* "R/GGbio-class.R"
9966 (("fechable") "fetchable"))
9969 `(("r-annotationdbi" ,r-annotationdbi)
9970 ("r-annotationfilter" ,r-annotationfilter)
9971 ("r-biobase" ,r-biobase)
9972 ("r-biocgenerics" ,r-biocgenerics)
9973 ("r-biostrings" ,r-biostrings)
9974 ("r-biovizbase" ,r-biovizbase)
9975 ("r-bsgenome" ,r-bsgenome)
9976 ("r-ensembldb" ,r-ensembldb)
9977 ("r-genomeinfodb" ,r-genomeinfodb)
9978 ("r-genomicalignments" ,r-genomicalignments)
9979 ("r-genomicfeatures" ,r-genomicfeatures)
9980 ("r-genomicranges" ,r-genomicranges)
9981 ("r-ggally" ,r-ggally)
9982 ("r-ggplot2" ,r-ggplot2)
9983 ("r-gridextra" ,r-gridextra)
9984 ("r-gtable" ,r-gtable)
9985 ("r-hmisc" ,r-hmisc)
9986 ("r-iranges" ,r-iranges)
9987 ("r-organismdbi" ,r-organismdbi)
9988 ("r-reshape2" ,r-reshape2)
9989 ("r-rlang" ,r-rlang)
9990 ("r-rsamtools" ,r-rsamtools)
9991 ("r-rtracklayer" ,r-rtracklayer)
9992 ("r-s4vectors" ,r-s4vectors)
9993 ("r-scales" ,r-scales)
9994 ("r-summarizedexperiment" ,r-summarizedexperiment)
9995 ("r-variantannotation" ,r-variantannotation)))
9997 `(("r-knitr" ,r-knitr)))
9998 (home-page "http://www.tengfei.name/ggbio/")
9999 (synopsis "Visualization tools for genomic data")
10001 "The ggbio package extends and specializes the grammar of graphics for
10002 biological data. The graphics are designed to answer common scientific
10003 questions, in particular those often asked of high throughput genomics data.
10004 All core Bioconductor data structures are supported, where appropriate. The
10005 package supports detailed views of particular genomic regions, as well as
10006 genome-wide overviews. Supported overviews include ideograms and grand linear
10007 views. High-level plots include sequence fragment length, edge-linked
10008 interval to data view, mismatch pileup, and several splicing summaries.")
10009 (license license:artistic2.0)))
10011 (define-public r-gqtlbase
10013 (name "r-gqtlbase")
10018 (uri (bioconductor-uri "gQTLBase" version))
10021 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
10022 (properties `((upstream-name . "gQTLBase")))
10023 (build-system r-build-system)
10026 (modify-phases %standard-phases
10027 ;; This is an upstream bug.
10028 (add-after 'unpack 'fix-imports
10030 (substitute* "NAMESPACE"
10031 ((".*maxffmode.*") "")
10032 (("importFrom\\(ff,.*") "import(ff)\n"))
10035 `(("r-batchjobs" ,r-batchjobs)
10036 ("r-bbmisc" ,r-bbmisc)
10037 ("r-biocgenerics" ,r-biocgenerics)
10039 ("r-doparallel" ,r-doparallel)
10041 ("r-ffbase" ,r-ffbase)
10042 ("r-foreach" ,r-foreach)
10043 ("r-genomicfiles" ,r-genomicfiles)
10044 ("r-genomicranges" ,r-genomicranges)
10045 ("r-rtracklayer" ,r-rtracklayer)
10046 ("r-s4vectors" ,r-s4vectors)
10047 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10049 `(("r-knitr" ,r-knitr)))
10050 (home-page "https://bioconductor.org/packages/gQTLBase")
10051 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10053 "The purpose of this package is to simplify the storage and interrogation
10054 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10056 (license license:artistic2.0)))
10058 (define-public r-gqtlstats
10060 (name "r-gqtlstats")
10065 (uri (bioconductor-uri "gQTLstats" version))
10068 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
10069 (properties `((upstream-name . "gQTLstats")))
10070 (build-system r-build-system)
10072 `(("r-annotationdbi" ,r-annotationdbi)
10073 ("r-batchjobs" ,r-batchjobs)
10074 ("r-bbmisc" ,r-bbmisc)
10075 ("r-beeswarm" ,r-beeswarm)
10076 ("r-biobase" ,r-biobase)
10077 ("r-biocgenerics" ,r-biocgenerics)
10078 ("r-doparallel" ,r-doparallel)
10079 ("r-dplyr" ,r-dplyr)
10081 ("r-ffbase" ,r-ffbase)
10082 ("r-foreach" ,r-foreach)
10083 ("r-genomeinfodb" ,r-genomeinfodb)
10084 ("r-genomicfeatures" ,r-genomicfeatures)
10085 ("r-genomicfiles" ,r-genomicfiles)
10086 ("r-genomicranges" ,r-genomicranges)
10087 ("r-ggbeeswarm" ,r-ggbeeswarm)
10088 ("r-ggplot2" ,r-ggplot2)
10089 ("r-gqtlbase" ,r-gqtlbase)
10090 ("r-hardyweinberg" ,r-hardyweinberg)
10091 ("r-homo-sapiens" ,r-homo-sapiens)
10092 ("r-iranges" ,r-iranges)
10093 ("r-limma" ,r-limma)
10095 ("r-plotly" ,r-plotly)
10096 ("r-reshape2" ,r-reshape2)
10097 ("r-s4vectors" ,r-s4vectors)
10098 ("r-shiny" ,r-shiny)
10099 ("r-snpstats" ,r-snpstats)
10100 ("r-summarizedexperiment" ,r-summarizedexperiment)
10101 ("r-variantannotation" ,r-variantannotation)))
10103 `(("r-knitr" ,r-knitr)))
10104 (home-page "https://bioconductor.org/packages/gQTLstats")
10105 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10107 "This package provides tools for the computationally efficient analysis
10108 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10109 The software in this package aims to support refinements and functional
10110 interpretation of members of a collection of association statistics on a
10111 family of feature/genome hypotheses.")
10112 (license license:artistic2.0)))
10114 (define-public r-gviz
10121 (uri (bioconductor-uri "Gviz" version))
10124 "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
10125 (properties `((upstream-name . "Gviz")))
10126 (build-system r-build-system)
10128 `(("r-annotationdbi" ,r-annotationdbi)
10129 ("r-biobase" ,r-biobase)
10130 ("r-biocgenerics" ,r-biocgenerics)
10131 ("r-biomart" ,r-biomart)
10132 ("r-biostrings" ,r-biostrings)
10133 ("r-biovizbase" ,r-biovizbase)
10134 ("r-bsgenome" ,r-bsgenome)
10135 ("r-digest" ,r-digest)
10136 ("r-ensembldb" ,r-ensembldb)
10137 ("r-genomeinfodb" ,r-genomeinfodb)
10138 ("r-genomicalignments" ,r-genomicalignments)
10139 ("r-genomicfeatures" ,r-genomicfeatures)
10140 ("r-genomicranges" ,r-genomicranges)
10141 ("r-iranges" ,r-iranges)
10142 ("r-lattice" ,r-lattice)
10143 ("r-latticeextra" ,r-latticeextra)
10144 ("r-matrixstats" ,r-matrixstats)
10145 ("r-rcolorbrewer" ,r-rcolorbrewer)
10146 ("r-rsamtools" ,r-rsamtools)
10147 ("r-rtracklayer" ,r-rtracklayer)
10148 ("r-s4vectors" ,r-s4vectors)
10149 ("r-xvector" ,r-xvector)))
10151 `(("r-knitr" ,r-knitr)))
10152 (home-page "https://bioconductor.org/packages/Gviz")
10153 (synopsis "Plotting data and annotation information along genomic coordinates")
10155 "Genomic data analyses requires integrated visualization of known genomic
10156 information and new experimental data. Gviz uses the biomaRt and the
10157 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10158 and translates this to e.g. gene/transcript structures in viewports of the
10159 grid graphics package. This results in genomic information plotted together
10161 (license license:artistic2.0)))
10163 (define-public r-gwascat
10170 (uri (bioconductor-uri "gwascat" version))
10173 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
10174 (build-system r-build-system)
10176 `(("r-annotationdbi" ,r-annotationdbi)
10177 ("r-biocfilecache" ,r-biocfilecache)
10178 ("r-biostrings" ,r-biostrings)
10179 ("r-genomeinfodb" ,r-genomeinfodb)
10180 ("r-genomicfeatures" ,r-genomicfeatures)
10181 ("r-genomicranges" ,r-genomicranges)
10182 ("r-iranges" ,r-iranges)
10183 ("r-readr" ,r-readr)
10184 ("r-s4vectors" ,r-s4vectors)
10185 ("r-snpstats" ,r-snpstats)
10186 ("r-variantannotation" ,r-variantannotation)))
10188 `(("r-knitr" ,r-knitr)))
10189 (home-page "https://bioconductor.org/packages/gwascat")
10190 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10192 "This package provides tools for representing and modeling data in the
10193 EMBL-EBI GWAS catalog.")
10194 (license license:artistic2.0)))
10196 (define-public r-kegggraph
10198 (name "r-kegggraph")
10203 (uri (bioconductor-uri "KEGGgraph" version))
10205 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
10206 (properties `((upstream-name . "KEGGgraph")))
10207 (build-system r-build-system)
10209 `(("r-graph" ,r-graph)
10210 ("r-rcurl" ,r-rcurl)
10212 (home-page "https://bioconductor.org/packages/KEGGgraph")
10213 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
10215 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
10216 object as well as a collection of tools to analyze, dissect and visualize these
10217 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
10218 maintaining all essential pathway attributes. The package offers
10219 functionalities including parsing, graph operation, visualization and etc.")
10220 (license license:gpl2+)))
10222 (define-public r-ldblock
10229 (uri (bioconductor-uri "ldblock" version))
10232 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
10233 (build-system r-build-system)
10235 `(("r-biocgenerics" ,r-biocgenerics)
10236 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
10237 ("r-ensembldb" ,r-ensembldb)
10238 ("r-genomeinfodb" ,r-genomeinfodb)
10239 ("r-genomicfiles" ,r-genomicfiles)
10241 ("r-matrix" ,r-matrix)
10242 ("r-rsamtools" ,r-rsamtools)
10243 ("r-snpstats" ,r-snpstats)
10244 ("r-variantannotation" ,r-variantannotation)))
10246 `(("r-knitr" ,r-knitr)))
10247 (home-page "https://bioconductor.org/packages/ldblock")
10248 (synopsis "Data structures for linkage disequilibrium measures in populations")
10250 "This package defines data structures for @dfn{linkage
10251 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10252 handling of existing population-level data for the purpose of flexibly
10253 defining LD blocks.")
10254 (license license:artistic2.0)))
10256 ;; This is a CRAN package, but it depends on r-snpstats, which is a
10257 ;; Bioconductor package.
10258 (define-public r-ldheatmap
10260 (name "r-ldheatmap")
10265 (uri (cran-uri "LDheatmap" version))
10268 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
10269 (properties `((upstream-name . "LDheatmap")))
10270 (build-system r-build-system)
10272 `(("r-genetics" ,r-genetics)
10274 ("r-snpstats" ,r-snpstats)))
10275 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
10276 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
10278 "This package provides tools to produce a graphical display, as a heat
10279 map, of measures of pairwise linkage disequilibria between SNPs. Users may
10280 optionally include the physical locations or genetic map distances of each SNP
10282 (license license:gpl3)))
10284 (define-public r-pathview
10286 (name "r-pathview")
10291 (uri (bioconductor-uri "pathview" version))
10293 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
10294 (properties `((upstream-name . "pathview")))
10295 (build-system r-build-system)
10297 `(("r-annotationdbi" ,r-annotationdbi)
10298 ("r-graph" ,r-graph)
10299 ("r-kegggraph" ,r-kegggraph)
10300 ("r-keggrest" ,r-keggrest)
10301 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10303 ("r-rgraphviz" ,r-rgraphviz)
10305 (home-page "https://pathview.uncc.edu/")
10306 (synopsis "Tool set for pathway based data integration and visualization")
10308 "@code{r-pathview} is a tool set for pathway based data integration and
10309 visualization. It maps and renders a wide variety of biological data on
10310 relevant pathway graphs. All users need is to supply their data and specify
10311 the target pathway. This package automatically downloads the pathway graph
10312 data, parses the data file, maps user data to the pathway, and render pathway
10313 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
10314 integrates with pathway and gene set (enrichment) analysis tools for
10315 large-scale and fully automated analysis.")
10316 (license license:gpl3+)))
10318 (define-public r-snpstats
10320 (name "r-snpstats")
10325 (uri (bioconductor-uri "snpStats" version))
10328 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
10329 (properties `((upstream-name . "snpStats")))
10330 (build-system r-build-system)
10331 (inputs `(("zlib" ,zlib)))
10333 `(("r-biocgenerics" ,r-biocgenerics)
10334 ("r-matrix" ,r-matrix)
10335 ("r-survival" ,r-survival)
10336 ("r-zlibbioc" ,r-zlibbioc)))
10337 (home-page "https://bioconductor.org/packages/snpStats")
10338 (synopsis "Methods for SNP association studies")
10340 "This package provides classes and statistical methods for large
10341 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
10342 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10343 (license license:gpl3)))
10345 (define-public r-sushi
10351 (uri (bioconductor-uri "Sushi" version))
10354 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
10355 (properties `((upstream-name . "Sushi")))
10356 (build-system r-build-system)
10358 `(("r-biomart" ,r-biomart)
10360 (home-page "https://bioconductor.org/packages/Sushi")
10361 (synopsis "Tools for visualizing genomics data")
10363 "This package provides flexible, quantitative, and integrative genomic
10364 visualizations for publication-quality multi-panel figures.")
10365 (license license:gpl2+)))