1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
5 ;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune@gmail.com>
6 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
7 ;;; Copyright © 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
8 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
10 ;;; This file is part of GNU Guix.
12 ;;; GNU Guix is free software; you can redistribute it and/or modify it
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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-hpar
1497 (uri (bioconductor-uri "hpar" version))
1500 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
1501 (build-system r-build-system)
1503 `(("r-knitr" ,r-knitr)))
1504 (home-page "https://bioconductor.org/packages/hpar/")
1505 (synopsis "Human Protein Atlas in R")
1506 (description "This package provides a simple interface to and data from
1507 the Human Protein Atlas project.")
1508 (license license:artistic2.0)))
1510 (define-public r-regioner
1517 (uri (bioconductor-uri "regioneR" version))
1520 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
1521 (properties `((upstream-name . "regioneR")))
1522 (build-system r-build-system)
1524 `(("r-biostrings" ,r-biostrings)
1525 ("r-bsgenome" ,r-bsgenome)
1526 ("r-genomeinfodb" ,r-genomeinfodb)
1527 ("r-genomicranges" ,r-genomicranges)
1528 ("r-iranges" ,r-iranges)
1529 ("r-memoise" ,r-memoise)
1530 ("r-rtracklayer" ,r-rtracklayer)
1531 ("r-s4vectors" ,r-s4vectors)))
1533 `(("r-knitr" ,r-knitr)))
1534 (home-page "https://bioconductor.org/packages/regioneR/")
1535 (synopsis "Association analysis of genomic regions")
1536 (description "This package offers a statistical framework based on
1537 customizable permutation tests to assess the association between genomic
1538 region sets and other genomic features.")
1539 (license license:artistic2.0)))
1541 (define-public r-reportingtools
1543 (name "r-reportingtools")
1548 (uri (bioconductor-uri "ReportingTools" version))
1551 "0gkshdhx44yjffqf1xmvik7j5hlhszp1n9ckanaws9ky3iia8j31"))))
1553 `((upstream-name . "ReportingTools")))
1554 (build-system r-build-system)
1556 `(("r-annotate" ,r-annotate)
1557 ("r-annotationdbi" ,r-annotationdbi)
1558 ("r-biobase" ,r-biobase)
1559 ("r-biocgenerics" ,r-biocgenerics)
1560 ("r-category" ,r-category)
1561 ("r-deseq2" ,r-deseq2)
1562 ("r-edger" ,r-edger)
1563 ("r-ggbio" ,r-ggbio)
1564 ("r-ggplot2" ,r-ggplot2)
1565 ("r-gostats" ,r-gostats)
1566 ("r-gseabase" ,r-gseabase)
1567 ("r-hwriter" ,r-hwriter)
1568 ("r-iranges" ,r-iranges)
1569 ("r-knitr" ,r-knitr)
1570 ("r-lattice" ,r-lattice)
1571 ("r-limma" ,r-limma)
1572 ("r-pfam-db" ,r-pfam-db)
1573 ("r-r-utils" ,r-r-utils)
1576 `(("r-knitr" ,r-knitr)))
1577 (home-page "https://bioconductor.org/packages/ReportingTools/")
1578 (synopsis "Tools for making reports in various formats")
1580 "The ReportingTools package enables users to easily display reports of
1581 analysis results generated from sources such as microarray and sequencing
1582 data. The package allows users to create HTML pages that may be viewed on a
1583 web browser, or in other formats. Users can generate tables with sortable and
1584 filterable columns, make and display plots, and link table entries to other
1585 data sources such as NCBI or larger plots within the HTML page. Using the
1586 package, users can also produce a table of contents page to link various
1587 reports together for a particular project that can be viewed in a web
1589 (license license:artistic2.0)))
1591 (define-public r-geneplotter
1593 (name "r-geneplotter")
1598 (uri (bioconductor-uri "geneplotter" version))
1601 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
1602 (build-system r-build-system)
1604 `(("r-annotate" ,r-annotate)
1605 ("r-annotationdbi" ,r-annotationdbi)
1606 ("r-biobase" ,r-biobase)
1607 ("r-biocgenerics" ,r-biocgenerics)
1608 ("r-lattice" ,r-lattice)
1609 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1610 (home-page "https://bioconductor.org/packages/geneplotter")
1611 (synopsis "Graphics functions for genomic data")
1613 "This package provides functions for plotting genomic data.")
1614 (license license:artistic2.0)))
1616 (define-public r-oligoclasses
1618 (name "r-oligoclasses")
1623 (uri (bioconductor-uri "oligoClasses" version))
1626 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
1627 (properties `((upstream-name . "oligoClasses")))
1628 (build-system r-build-system)
1630 `(("r-affyio" ,r-affyio)
1631 ("r-biobase" ,r-biobase)
1632 ("r-biocgenerics" ,r-biocgenerics)
1633 ("r-biocmanager" ,r-biocmanager)
1634 ("r-biostrings" ,r-biostrings)
1637 ("r-foreach" ,r-foreach)
1638 ("r-genomicranges" ,r-genomicranges)
1639 ("r-iranges" ,r-iranges)
1640 ("r-rsqlite" ,r-rsqlite)
1641 ("r-s4vectors" ,r-s4vectors)
1642 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1643 (home-page "https://bioconductor.org/packages/oligoClasses/")
1644 (synopsis "Classes for high-throughput arrays")
1646 "This package contains class definitions, validity checks, and
1647 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1649 (license license:gpl2+)))
1651 (define-public r-oligo
1658 (uri (bioconductor-uri "oligo" version))
1661 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
1662 (properties `((upstream-name . "oligo")))
1663 (build-system r-build-system)
1664 (inputs `(("zlib" ,zlib)))
1666 `(("r-affxparser" ,r-affxparser)
1667 ("r-affyio" ,r-affyio)
1668 ("r-biobase" ,r-biobase)
1669 ("r-biocgenerics" ,r-biocgenerics)
1670 ("r-biostrings" ,r-biostrings)
1673 ("r-oligoclasses" ,r-oligoclasses)
1674 ("r-preprocesscore" ,r-preprocesscore)
1675 ("r-rsqlite" ,r-rsqlite)
1676 ("r-zlibbioc" ,r-zlibbioc)))
1678 `(("r-knitr" ,r-knitr)))
1679 (home-page "https://bioconductor.org/packages/oligo/")
1680 (synopsis "Preprocessing tools for oligonucleotide arrays")
1682 "This package provides a package to analyze oligonucleotide
1683 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1684 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1685 (license license:lgpl2.0+)))
1687 (define-public r-qvalue
1694 (uri (bioconductor-uri "qvalue" version))
1697 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
1698 (build-system r-build-system)
1700 `(("r-ggplot2" ,r-ggplot2)
1701 ("r-reshape2" ,r-reshape2)))
1703 `(("r-knitr" ,r-knitr)))
1704 (home-page "https://github.com/StoreyLab/qvalue")
1705 (synopsis "Q-value estimation for false discovery rate control")
1707 "This package takes a list of p-values resulting from the simultaneous
1708 testing of many hypotheses and estimates their q-values and local @dfn{false
1709 discovery rate} (FDR) values. The q-value of a test measures the proportion
1710 of false positives incurred when that particular test is called significant.
1711 The local FDR measures the posterior probability the null hypothesis is true
1712 given the test's p-value. Various plots are automatically generated, allowing
1713 one to make sensible significance cut-offs. The software can be applied to
1714 problems in genomics, brain imaging, astrophysics, and data mining.")
1715 ;; Any version of the LGPL.
1716 (license license:lgpl3+)))
1718 (define r-rcppnumerical
1720 (name "r-rcppnumerical")
1724 (uri (cran-uri "RcppNumerical" version))
1727 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
1728 (properties `((upstream-name . "RcppNumerical")))
1729 (build-system r-build-system)
1731 `(("r-rcpp" ,r-rcpp)
1732 ("r-rcppeigen" ,r-rcppeigen)))
1734 `(("r-knitr" ,r-knitr)))
1735 (home-page "https://github.com/yixuan/RcppNumerical")
1736 (synopsis "Rcpp integration for numerical computing libraries")
1737 (description "This package provides a collection of open source libraries
1738 for numerical computing (numerical integration, optimization, etc.) and their
1739 integration with @code{Rcpp}.")
1740 (license license:gpl2+)))
1742 (define-public r-apeglm
1748 (uri (bioconductor-uri "apeglm" version))
1751 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
1752 (properties `((upstream-name . "apeglm")))
1753 (build-system r-build-system)
1755 `(("r-emdbook" ,r-emdbook)
1756 ("r-genomicranges" ,r-genomicranges)
1758 ("r-rcppeigen" ,r-rcppeigen)
1759 ("r-rcppnumerical" ,r-rcppnumerical)
1760 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1761 (native-inputs `(("r-knitr" ,r-knitr)))
1762 (home-page "https://bioconductor.org/packages/apeglm")
1763 (synopsis "Approximate posterior estimation for GLM coefficients")
1764 (description "This package provides Bayesian shrinkage estimators for
1765 effect sizes for a variety of GLM models, using approximation of the
1766 posterior for individual coefficients.")
1767 (license license:gpl2)))
1769 (define-public r-greylistchip
1771 (name "r-greylistchip")
1775 (uri (bioconductor-uri "GreyListChIP" version))
1778 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
1779 (properties `((upstream-name . "GreyListChIP")))
1780 (build-system r-build-system)
1782 `(("r-bsgenome" ,r-bsgenome)
1783 ("r-genomeinfodb" ,r-genomeinfodb)
1784 ("r-genomicalignments" ,r-genomicalignments)
1785 ("r-genomicranges" ,r-genomicranges)
1787 ("r-rsamtools" ,r-rsamtools)
1788 ("r-rtracklayer" ,r-rtracklayer)
1789 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1790 (home-page "https://bioconductor.org/packages/GreyListChIP")
1791 (synopsis "Greylist artefact regions based on ChIP inputs")
1792 (description "This package identifies regions of ChIP experiments with high
1793 signal in the input, that lead to spurious peaks during peak calling.")
1794 (license license:artistic2.0)))
1796 (define-public r-diffbind
1803 (uri (bioconductor-uri "DiffBind" version))
1806 "0kxn59v93hl5pq8d156lnbz0sslpnxyjcfrvq2gzgd91sd587qmn"))))
1807 (properties `((upstream-name . "DiffBind")))
1808 (build-system r-build-system)
1810 `(("r-amap" ,r-amap)
1811 ("r-apeglm" ,r-apeglm)
1813 ("r-biocparallel" ,r-biocparallel)
1814 ("r-deseq2" ,r-deseq2)
1815 ("r-dplyr" ,r-dplyr)
1816 ("r-genomicalignments" ,r-genomicalignments)
1817 ("r-genomicranges" ,r-genomicranges)
1818 ("r-ggplot2" ,r-ggplot2)
1819 ("r-ggrepel" ,r-ggrepel)
1820 ("r-gplots" ,r-gplots)
1821 ("r-greylistchip" ,r-greylistchip)
1822 ("r-iranges" ,r-iranges)
1823 ("r-lattice" ,r-lattice)
1824 ("r-limma" ,r-limma)
1825 ("r-locfit" ,r-locfit)
1826 ("r-rcolorbrewer" , r-rcolorbrewer)
1828 ("r-rhtslib" ,r-rhtslib)
1829 ("r-rsamtools" ,r-rsamtools)
1830 ("r-s4vectors" ,r-s4vectors)
1831 ("r-summarizedexperiment" ,r-summarizedexperiment)
1832 ("r-systempiper" ,r-systempiper)))
1833 (home-page "https://bioconductor.org/packages/DiffBind")
1834 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1836 "This package computes differentially bound sites from multiple
1837 ChIP-seq experiments using affinity (quantitative) data. Also enables
1838 occupancy (overlap) analysis and plotting functions.")
1839 (license license:artistic2.0)))
1841 (define-public r-ripseeker
1843 (name "r-ripseeker")
1848 (uri (bioconductor-uri "RIPSeeker" version))
1851 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1852 (properties `((upstream-name . "RIPSeeker")))
1853 (build-system r-build-system)
1855 `(("r-s4vectors" ,r-s4vectors)
1856 ("r-iranges" ,r-iranges)
1857 ("r-genomicranges" ,r-genomicranges)
1858 ("r-summarizedexperiment" ,r-summarizedexperiment)
1859 ("r-rsamtools" ,r-rsamtools)
1860 ("r-genomicalignments" ,r-genomicalignments)
1861 ("r-rtracklayer" ,r-rtracklayer)))
1862 (home-page "https://bioconductor.org/packages/RIPSeeker")
1864 "Identifying protein-associated transcripts from RIP-seq experiments")
1866 "This package infers and discriminates RIP peaks from RIP-seq alignments
1867 using two-state HMM with negative binomial emission probability. While
1868 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1869 a suite of bioinformatics tools integrated within this self-contained software
1870 package comprehensively addressing issues ranging from post-alignments
1871 processing to visualization and annotation.")
1872 (license license:gpl2)))
1874 (define-public r-multtest
1881 (uri (bioconductor-uri "multtest" version))
1884 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
1885 (build-system r-build-system)
1887 `(("r-survival" ,r-survival)
1888 ("r-biocgenerics" ,r-biocgenerics)
1889 ("r-biobase" ,r-biobase)
1890 ("r-mass" ,r-mass)))
1891 (home-page "https://bioconductor.org/packages/multtest")
1892 (synopsis "Resampling-based multiple hypothesis testing")
1894 "This package can do non-parametric bootstrap and permutation
1895 resampling-based multiple testing procedures (including empirical Bayes
1896 methods) for controlling the family-wise error rate (FWER), generalized
1897 family-wise error rate (gFWER), tail probability of the proportion of
1898 false positives (TPPFP), and false discovery rate (FDR). Several choices
1899 of bootstrap-based null distribution are implemented (centered, centered
1900 and scaled, quantile-transformed). Single-step and step-wise methods are
1901 available. Tests based on a variety of T- and F-statistics (including
1902 T-statistics based on regression parameters from linear and survival models
1903 as well as those based on correlation parameters) are included. When probing
1904 hypotheses with T-statistics, users may also select a potentially faster null
1905 distribution which is multivariate normal with mean zero and variance
1906 covariance matrix derived from the vector influence function. Results are
1907 reported in terms of adjusted P-values, confidence regions and test statistic
1908 cutoffs. The procedures are directly applicable to identifying differentially
1909 expressed genes in DNA microarray experiments.")
1910 (license license:lgpl3)))
1912 (define-public r-graph
1918 (uri (bioconductor-uri "graph" version))
1921 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
1922 (build-system r-build-system)
1924 `(("r-biocgenerics" ,r-biocgenerics)))
1925 (home-page "https://bioconductor.org/packages/graph")
1926 (synopsis "Handle graph data structures in R")
1928 "This package implements some simple graph handling capabilities for R.")
1929 (license license:artistic2.0)))
1931 ;; This is a CRAN package, but it depends on a Bioconductor package.
1932 (define-public r-ggm
1939 (uri (cran-uri "ggm" version))
1942 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1943 (properties `((upstream-name . "ggm")))
1944 (build-system r-build-system)
1946 `(("r-graph" ,r-graph)
1947 ("r-igraph" ,r-igraph)))
1948 (home-page "https://cran.r-project.org/package=ggm")
1949 (synopsis "Functions for graphical Markov models")
1951 "This package provides functions and datasets for maximum likelihood
1952 fitting of some classes of graphical Markov models.")
1953 (license license:gpl2+)))
1955 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
1956 (define-public r-perfmeas
1963 (uri (cran-uri "PerfMeas" version))
1966 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
1967 (properties `((upstream-name . "PerfMeas")))
1968 (build-system r-build-system)
1970 `(("r-graph" ,r-graph)
1971 ("r-limma" ,r-limma)
1972 ("r-rbgl" ,r-rbgl)))
1973 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
1974 (synopsis "Performance measures for ranking and classification tasks")
1976 "This package implements different performance measures for
1977 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
1978 a given recall, F-score for single and multiple classes are available.")
1979 (license license:gpl2+)))
1981 ;; This is a CRAN package, but it depends on a Bioconductor package.
1982 (define-public r-codedepends
1984 (name "r-codedepends")
1989 (uri (cran-uri "CodeDepends" version))
1992 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1993 (properties `((upstream-name . "CodeDepends")))
1994 (build-system r-build-system)
1996 `(("r-codetools" ,r-codetools)
1997 ("r-graph" ,r-graph)
1999 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2000 (synopsis "Analysis of R code for reproducible research and code comprehension")
2002 "This package provides tools for analyzing R expressions or blocks of
2003 code and determining the dependencies between them. It focuses on R scripts,
2004 but can be used on the bodies of functions. There are many facilities
2005 including the ability to summarize or get a high-level view of code,
2006 determining dependencies between variables, code improvement suggestions.")
2007 ;; Any version of the GPL
2008 (license (list license:gpl2+ license:gpl3+))))
2010 (define-public r-chippeakanno
2012 (name "r-chippeakanno")
2017 (uri (bioconductor-uri "ChIPpeakAnno" version))
2020 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
2021 (properties `((upstream-name . "ChIPpeakAnno")))
2022 (build-system r-build-system)
2024 `(("r-annotationdbi" ,r-annotationdbi)
2025 ("r-biocgenerics" ,r-biocgenerics)
2026 ("r-biomart" ,r-biomart)
2027 ("r-biostrings" ,r-biostrings)
2029 ("r-ensembldb" ,r-ensembldb)
2030 ("r-genomeinfodb" ,r-genomeinfodb)
2031 ("r-genomicalignments" ,r-genomicalignments)
2032 ("r-genomicfeatures" ,r-genomicfeatures)
2033 ("r-genomicranges" ,r-genomicranges)
2034 ("r-ggplot2" ,r-ggplot2)
2035 ("r-graph" ,r-graph)
2036 ("r-iranges" ,r-iranges)
2037 ("r-keggrest" ,r-keggrest)
2038 ("r-matrixstats" ,r-matrixstats)
2039 ("r-multtest" ,r-multtest)
2041 ("r-regioner" ,r-regioner)
2042 ("r-rsamtools" ,r-rsamtools)
2043 ("r-rtracklayer" ,r-rtracklayer)
2044 ("r-s4vectors" ,r-s4vectors)
2045 ("r-summarizedexperiment" ,r-summarizedexperiment)
2046 ("r-venndiagram" ,r-venndiagram)))
2048 `(("r-knitr" ,r-knitr)))
2049 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2050 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2052 "The package includes functions to retrieve the sequences around the peak,
2053 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2054 custom features such as most conserved elements and other transcription factor
2055 binding sites supplied by users. Starting 2.0.5, new functions have been added
2056 for finding the peaks with bi-directional promoters with summary statistics
2057 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2058 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2059 enrichedGO (addGeneIDs).")
2060 (license license:gpl2+)))
2062 (define-public r-matrixgenerics
2064 (name "r-matrixgenerics")
2068 (uri (bioconductor-uri "MatrixGenerics" version))
2071 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
2073 `((upstream-name . "MatrixGenerics")))
2074 (build-system r-build-system)
2076 `(("r-matrixstats" ,r-matrixstats)))
2077 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2078 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2080 "This package provides S4 generic functions modeled after the
2081 @code{matrixStats} API for alternative matrix implementations. Packages with
2082 alternative matrix implementation can depend on this package and implement the
2083 generic functions that are defined here for a useful set of row and column
2084 summary statistics. Other package developers can import this package and
2085 handle a different matrix implementations without worrying about
2086 incompatibilities.")
2087 (license license:artistic2.0)))
2089 (define-public r-marray
2095 (uri (bioconductor-uri "marray" version))
2097 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
2098 (build-system r-build-system)
2100 `(("r-limma" ,r-limma)))
2101 (home-page "https://bioconductor.org/packages/marray")
2102 (synopsis "Exploratory analysis for two-color spotted microarray data")
2103 (description "This package contains class definitions for two-color spotted
2104 microarray data. It also includes functions for data input, diagnostic plots,
2105 normalization and quality checking.")
2106 (license license:lgpl2.0+)))
2108 (define-public r-cghbase
2114 (uri (bioconductor-uri "CGHbase" version))
2116 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
2117 (properties `((upstream-name . "CGHbase")))
2118 (build-system r-build-system)
2120 `(("r-biobase" ,r-biobase)
2121 ("r-marray" ,r-marray)))
2122 (home-page "https://bioconductor.org/packages/CGHbase")
2123 (synopsis "Base functions and classes for arrayCGH data analysis")
2124 (description "This package contains functions and classes that are needed by
2125 the @code{arrayCGH} packages.")
2126 (license license:gpl2+)))
2128 (define-public r-cghcall
2134 (uri (bioconductor-uri "CGHcall" version))
2136 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
2137 (properties `((upstream-name . "CGHcall")))
2138 (build-system r-build-system)
2140 `(("r-biobase" ,r-biobase)
2141 ("r-cghbase" ,r-cghbase)
2142 ("r-impute" ,r-impute)
2143 ("r-dnacopy" ,r-dnacopy)
2144 ("r-snowfall" ,r-snowfall)))
2145 (home-page "https://bioconductor.org/packages/CGHcall")
2146 (synopsis "Base functions and classes for arrayCGH data analysis")
2147 (description "This package contains functions and classes that are needed by
2148 @code{arrayCGH} packages.")
2149 (license license:gpl2+)))
2151 (define-public r-qdnaseq
2157 (uri (bioconductor-uri "QDNAseq" version))
2159 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
2160 (properties `((upstream-name . "QDNAseq")))
2161 (build-system r-build-system)
2163 `(("r-biobase" ,r-biobase)
2164 ("r-cghbase" ,r-cghbase)
2165 ("r-cghcall" ,r-cghcall)
2166 ("r-dnacopy" ,r-dnacopy)
2167 ("r-future" ,r-future)
2168 ("r-future-apply" ,r-future-apply)
2169 ("r-genomicranges" ,r-genomicranges)
2170 ("r-iranges" ,r-iranges)
2171 ("r-matrixstats" ,r-matrixstats)
2172 ("r-r-utils" ,r-r-utils)
2173 ("r-rsamtools" ,r-rsamtools)))
2174 (home-page "https://bioconductor.org/packages/QDNAseq")
2175 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2176 (description "The genome is divided into non-overlapping fixed-sized bins,
2177 number of sequence reads in each counted, adjusted with a simultaneous
2178 two-dimensional loess correction for sequence mappability and GC content, and
2179 filtered to remove spurious regions in the genome. Downstream steps of
2180 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2182 (license license:gpl2+)))
2184 (define-public r-bayseq
2191 (uri (bioconductor-uri "baySeq" version))
2194 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
2195 (properties `((upstream-name . "baySeq")))
2196 (build-system r-build-system)
2198 `(("r-abind" ,r-abind)
2199 ("r-edger" ,r-edger)
2200 ("r-genomicranges" ,r-genomicranges)))
2201 (home-page "https://bioconductor.org/packages/baySeq/")
2202 (synopsis "Bayesian analysis of differential expression patterns in count data")
2204 "This package identifies differential expression in high-throughput count
2205 data, such as that derived from next-generation sequencing machines,
2206 calculating estimated posterior likelihoods of differential expression (or
2207 more complex hypotheses) via empirical Bayesian methods.")
2208 (license license:gpl3)))
2210 (define-public r-chipcomp
2217 (uri (bioconductor-uri "ChIPComp" version))
2220 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
2221 (properties `((upstream-name . "ChIPComp")))
2222 (build-system r-build-system)
2224 `(("r-biocgenerics" ,r-biocgenerics)
2225 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2226 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2227 ("r-genomeinfodb" ,r-genomeinfodb)
2228 ("r-genomicranges" ,r-genomicranges)
2229 ("r-iranges" ,r-iranges)
2230 ("r-limma" ,r-limma)
2231 ("r-rsamtools" ,r-rsamtools)
2232 ("r-rtracklayer" ,r-rtracklayer)
2233 ("r-s4vectors" ,r-s4vectors)))
2234 (home-page "https://bioconductor.org/packages/ChIPComp")
2235 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2237 "ChIPComp implements a statistical method for quantitative comparison of
2238 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2239 sites across multiple conditions considering matching control in ChIP-seq
2241 ;; Any version of the GPL.
2242 (license license:gpl3+)))
2244 (define-public r-riboprofiling
2246 (name "r-riboprofiling")
2251 (uri (bioconductor-uri "RiboProfiling" version))
2254 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
2255 (properties `((upstream-name . "RiboProfiling")))
2256 (build-system r-build-system)
2258 `(("r-biocgenerics" ,r-biocgenerics)
2259 ("r-biostrings" ,r-biostrings)
2260 ("r-data-table" ,r-data-table)
2261 ("r-genomeinfodb" ,r-genomeinfodb)
2262 ("r-genomicalignments" ,r-genomicalignments)
2263 ("r-genomicfeatures" ,r-genomicfeatures)
2264 ("r-genomicranges" ,r-genomicranges)
2265 ("r-ggbio" ,r-ggbio)
2266 ("r-ggplot2" ,r-ggplot2)
2267 ("r-iranges" ,r-iranges)
2269 ("r-reshape2" ,r-reshape2)
2270 ("r-rsamtools" ,r-rsamtools)
2271 ("r-rtracklayer" ,r-rtracklayer)
2272 ("r-s4vectors" ,r-s4vectors)
2273 ("r-sqldf" ,r-sqldf)))
2275 `(("r-knitr" ,r-knitr)))
2276 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2277 (synopsis "Ribosome profiling data analysis")
2278 (description "Starting with a BAM file, this package provides the
2279 necessary functions for quality assessment, read start position recalibration,
2280 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2281 of count data: pairs, log fold-change, codon frequency and coverage
2282 assessment, principal component analysis on codon coverage.")
2283 (license license:gpl3)))
2285 (define-public r-riboseqr
2292 (uri (bioconductor-uri "riboSeqR" version))
2295 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
2296 (properties `((upstream-name . "riboSeqR")))
2297 (build-system r-build-system)
2299 `(("r-abind" ,r-abind)
2300 ("r-bayseq" ,r-bayseq)
2301 ("r-genomeinfodb" ,r-genomeinfodb)
2302 ("r-genomicranges" ,r-genomicranges)
2303 ("r-iranges" ,r-iranges)
2304 ("r-rsamtools" ,r-rsamtools)
2305 ("r-seqlogo" ,r-seqlogo)))
2306 (home-page "https://bioconductor.org/packages/riboSeqR/")
2307 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2309 "This package provides plotting functions, frameshift detection and
2310 parsing of genetic sequencing data from ribosome profiling experiments.")
2311 (license license:gpl3)))
2313 (define-public r-interactionset
2315 (name "r-interactionset")
2320 (uri (bioconductor-uri "InteractionSet" version))
2323 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
2325 `((upstream-name . "InteractionSet")))
2326 (build-system r-build-system)
2328 `(("r-biocgenerics" ,r-biocgenerics)
2329 ("r-genomeinfodb" ,r-genomeinfodb)
2330 ("r-genomicranges" ,r-genomicranges)
2331 ("r-iranges" ,r-iranges)
2332 ("r-matrix" ,r-matrix)
2334 ("r-s4vectors" ,r-s4vectors)
2335 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2337 `(("r-knitr" ,r-knitr)))
2338 (home-page "https://bioconductor.org/packages/InteractionSet")
2339 (synopsis "Base classes for storing genomic interaction data")
2341 "This package provides the @code{GInteractions},
2342 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2343 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2345 (license license:gpl3)))
2347 (define-public r-genomicinteractions
2349 (name "r-genomicinteractions")
2354 (uri (bioconductor-uri "GenomicInteractions" version))
2357 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
2359 `((upstream-name . "GenomicInteractions")))
2360 (build-system r-build-system)
2362 `(("r-biobase" ,r-biobase)
2363 ("r-biocgenerics" ,r-biocgenerics)
2364 ("r-data-table" ,r-data-table)
2365 ("r-dplyr" ,r-dplyr)
2366 ("r-genomeinfodb" ,r-genomeinfodb)
2367 ("r-genomicranges" ,r-genomicranges)
2368 ("r-ggplot2" ,r-ggplot2)
2369 ("r-gridextra" ,r-gridextra)
2371 ("r-igraph" ,r-igraph)
2372 ("r-interactionset" ,r-interactionset)
2373 ("r-iranges" ,r-iranges)
2374 ("r-rsamtools" ,r-rsamtools)
2375 ("r-rtracklayer" ,r-rtracklayer)
2376 ("r-s4vectors" ,r-s4vectors)
2377 ("r-stringr" ,r-stringr)))
2379 `(("r-knitr" ,r-knitr)))
2380 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2381 (synopsis "R package for handling genomic interaction data")
2383 "This R package provides tools for handling genomic interaction data,
2384 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2385 information and producing various plots and statistics.")
2386 (license license:gpl3)))
2388 (define-public r-ctc
2395 (uri (bioconductor-uri "ctc" version))
2398 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
2399 (build-system r-build-system)
2400 (propagated-inputs `(("r-amap" ,r-amap)))
2401 (home-page "https://bioconductor.org/packages/ctc/")
2402 (synopsis "Cluster and tree conversion")
2404 "This package provides tools for exporting and importing classification
2405 trees and clusters to other programs.")
2406 (license license:gpl2)))
2408 (define-public r-goseq
2415 (uri (bioconductor-uri "goseq" version))
2418 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
2419 (build-system r-build-system)
2421 `(("r-annotationdbi" ,r-annotationdbi)
2422 ("r-biasedurn" ,r-biasedurn)
2423 ("r-biocgenerics" ,r-biocgenerics)
2424 ("r-genelendatabase" ,r-genelendatabase)
2425 ("r-go-db" ,r-go-db)
2426 ("r-mgcv" ,r-mgcv)))
2427 (home-page "https://bioconductor.org/packages/goseq/")
2428 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2430 "This package provides tools to detect Gene Ontology and/or other user
2431 defined categories which are over/under represented in RNA-seq data.")
2432 (license license:lgpl2.0+)))
2434 (define-public r-glimma
2441 (uri (bioconductor-uri "Glimma" version))
2444 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
2445 (properties `((upstream-name . "Glimma")))
2446 (build-system r-build-system)
2448 `(("r-deseq2" ,r-deseq2)
2449 ("r-edger" ,r-edger)
2450 ("r-htmlwidgets" ,r-htmlwidgets)
2451 ("r-jsonlite" ,r-jsonlite)
2452 ("r-limma" ,r-limma)
2453 ("r-s4vectors" ,r-s4vectors)
2454 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2456 `(("r-knitr" ,r-knitr)))
2457 (home-page "https://github.com/Shians/Glimma")
2458 (synopsis "Interactive HTML graphics")
2460 "This package generates interactive visualisations for analysis of
2461 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2462 HTML page. The interactions are built on top of the popular static
2463 representations of analysis results in order to provide additional
2465 (license license:lgpl3)))
2467 (define-public r-rots
2474 (uri (bioconductor-uri "ROTS" version))
2477 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
2478 (properties `((upstream-name . "ROTS")))
2479 (build-system r-build-system)
2481 `(("r-biobase" ,r-biobase)
2482 ("r-rcpp" ,r-rcpp)))
2483 (home-page "https://bioconductor.org/packages/ROTS/")
2484 (synopsis "Reproducibility-Optimized Test Statistic")
2486 "This package provides tools for calculating the
2487 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2489 (license license:gpl2+)))
2491 (define-public r-plgem
2498 (uri (bioconductor-uri "plgem" version))
2501 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
2502 (build-system r-build-system)
2504 `(("r-biobase" ,r-biobase)
2505 ("r-mass" ,r-mass)))
2506 (home-page "http://www.genopolis.it")
2507 (synopsis "Detect differential expression in microarray and proteomics datasets")
2509 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2510 model the variance-versus-mean dependence that exists in a variety of
2511 genome-wide datasets, including microarray and proteomics data. The use of
2512 PLGEM has been shown to improve the detection of differentially expressed
2513 genes or proteins in these datasets.")
2514 (license license:gpl2)))
2516 (define-public r-inspect
2523 (uri (bioconductor-uri "INSPEcT" version))
2526 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
2527 (properties `((upstream-name . "INSPEcT")))
2528 (build-system r-build-system)
2530 `(("r-biobase" ,r-biobase)
2531 ("r-biocgenerics" ,r-biocgenerics)
2532 ("r-biocparallel" ,r-biocparallel)
2533 ("r-deseq2" ,r-deseq2)
2534 ("r-desolve" ,r-desolve)
2535 ("r-gdata" ,r-gdata)
2536 ("r-genomeinfodb" ,r-genomeinfodb)
2537 ("r-genomicalignments" ,r-genomicalignments)
2538 ("r-genomicfeatures" ,r-genomicfeatures)
2539 ("r-genomicranges" ,r-genomicranges)
2540 ("r-iranges" ,r-iranges)
2541 ("r-kernsmooth" ,r-kernsmooth)
2542 ("r-plgem" ,r-plgem)
2544 ("r-rootsolve" ,r-rootsolve)
2545 ("r-rsamtools" ,r-rsamtools)
2546 ("r-rtracklayer" ,r-rtracklayer)
2547 ("r-s4vectors" ,r-s4vectors)
2548 ("r-shiny" ,r-shiny)
2549 ("r-summarizedexperiment" ,r-summarizedexperiment)
2550 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2551 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2553 `(("r-knitr" ,r-knitr)))
2554 (home-page "https://bioconductor.org/packages/INSPEcT")
2555 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2557 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2558 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2559 order to evaluate synthesis, processing and degradation rates and assess via
2560 modeling the rates that determines changes in mature mRNA levels.")
2561 (license license:gpl2)))
2563 (define-public r-dnabarcodes
2565 (name "r-dnabarcodes")
2570 (uri (bioconductor-uri "DNABarcodes" version))
2573 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
2574 (properties `((upstream-name . "DNABarcodes")))
2575 (build-system r-build-system)
2578 ("r-matrix" ,r-matrix)
2579 ("r-rcpp" ,r-rcpp)))
2581 `(("r-knitr" ,r-knitr)))
2582 (home-page "https://bioconductor.org/packages/DNABarcodes")
2583 (synopsis "Create and analyze DNA barcodes")
2585 "This package offers tools to create DNA barcode sets capable of
2586 correcting insertion, deletion, and substitution errors. Existing barcodes
2587 can be analyzed regarding their minimal, maximal and average distances between
2588 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2589 demultiplexed, i.e. assigned to their original reference barcode.")
2590 (license license:gpl2)))
2592 (define-public r-ruvseq
2599 (uri (bioconductor-uri "RUVSeq" version))
2602 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
2603 (properties `((upstream-name . "RUVSeq")))
2604 (build-system r-build-system)
2606 `(("r-biobase" ,r-biobase)
2607 ("r-edaseq" ,r-edaseq)
2608 ("r-edger" ,r-edger)
2609 ("r-mass" ,r-mass)))
2611 `(("r-knitr" ,r-knitr)))
2612 (home-page "https://github.com/drisso/RUVSeq")
2613 (synopsis "Remove unwanted variation from RNA-Seq data")
2615 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2616 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2618 (license license:artistic2.0)))
2620 (define-public r-biocneighbors
2622 (name "r-biocneighbors")
2627 (uri (bioconductor-uri "BiocNeighbors" version))
2630 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
2631 (properties `((upstream-name . "BiocNeighbors")))
2632 (build-system r-build-system)
2634 `(("r-biocparallel" ,r-biocparallel)
2635 ("r-matrix" ,r-matrix)
2637 ("r-rcpphnsw" ,r-rcpphnsw)
2638 ("r-s4vectors" ,r-s4vectors)))
2640 `(("r-knitr" ,r-knitr)))
2641 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2642 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2644 "This package implements exact and approximate methods for nearest
2645 neighbor detection, in a framework that allows them to be easily switched
2646 within Bioconductor packages or workflows. The exact algorithm is implemented
2647 using pre-clustering with the k-means algorithm. Functions are also provided
2648 to search for all neighbors within a given distance. Parallelization is
2649 achieved for all methods using the BiocParallel framework.")
2650 (license license:gpl3)))
2652 (define-public r-biocsingular
2654 (name "r-biocsingular")
2659 (uri (bioconductor-uri "BiocSingular" version))
2662 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
2663 (properties `((upstream-name . "BiocSingular")))
2664 (build-system r-build-system)
2666 `(("r-beachmat" ,r-beachmat)
2667 ("r-biocgenerics" ,r-biocgenerics)
2668 ("r-biocparallel" ,r-biocparallel)
2669 ("r-delayedarray" ,r-delayedarray)
2670 ("r-irlba" ,r-irlba)
2671 ("r-matrix" ,r-matrix)
2674 ("r-s4vectors" ,r-s4vectors)))
2676 `(("r-knitr" ,r-knitr)))
2677 (home-page "https://github.com/LTLA/BiocSingular")
2678 (synopsis "Singular value decomposition for Bioconductor packages")
2680 "This package implements exact and approximate methods for singular value
2681 decomposition and principal components analysis, in a framework that allows
2682 them to be easily switched within Bioconductor packages or workflows. Where
2683 possible, parallelization is achieved using the BiocParallel framework.")
2684 (license license:gpl3)))
2686 (define-public r-destiny
2693 (uri (bioconductor-uri "destiny" version))
2696 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
2697 (build-system r-build-system)
2699 `(("r-biobase" ,r-biobase)
2700 ("r-biocgenerics" ,r-biocgenerics)
2701 ("r-ggplot-multistats" ,r-ggplot-multistats)
2702 ("r-ggplot2" ,r-ggplot2)
2703 ("r-ggthemes" ,r-ggthemes)
2704 ("r-irlba" ,r-irlba)
2705 ("r-knn-covertree" ,r-knn-covertree)
2706 ("r-matrix" ,r-matrix)
2707 ("r-pcamethods" ,r-pcamethods)
2708 ("r-proxy" ,r-proxy)
2710 ("r-rcppeigen" ,r-rcppeigen)
2711 ("r-rcpphnsw" ,r-rcpphnsw)
2712 ("r-rspectra" ,r-rspectra)
2713 ("r-scales" ,r-scales)
2714 ("r-scatterplot3d" ,r-scatterplot3d)
2715 ("r-singlecellexperiment" ,r-singlecellexperiment)
2716 ("r-smoother" ,r-smoother)
2717 ("r-summarizedexperiment" ,r-summarizedexperiment)
2718 ("r-tidyr" ,r-tidyr)
2719 ("r-tidyselect" ,r-tidyselect)
2722 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2723 (home-page "https://bioconductor.org/packages/destiny/")
2724 (synopsis "Create and plot diffusion maps")
2725 (description "This package provides tools to create and plot diffusion
2727 ;; Any version of the GPL
2728 (license license:gpl3+)))
2730 (define-public r-savr
2737 (uri (bioconductor-uri "savR" version))
2740 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
2741 (properties `((upstream-name . "savR")))
2742 (build-system r-build-system)
2744 `(("r-ggplot2" ,r-ggplot2)
2745 ("r-gridextra" ,r-gridextra)
2746 ("r-reshape2" ,r-reshape2)
2747 ("r-scales" ,r-scales)
2749 (home-page "https://github.com/bcalder/savR")
2750 (synopsis "Parse and analyze Illumina SAV files")
2752 "This package provides tools to parse Illumina Sequence Analysis
2753 Viewer (SAV) files, access data, and generate QC plots.")
2754 (license license:agpl3+)))
2756 (define-public r-chipexoqual
2758 (name "r-chipexoqual")
2763 (uri (bioconductor-uri "ChIPexoQual" version))
2766 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
2767 (properties `((upstream-name . "ChIPexoQual")))
2768 (build-system r-build-system)
2770 `(("r-biocparallel" ,r-biocparallel)
2771 ("r-biovizbase" ,r-biovizbase)
2772 ("r-broom" ,r-broom)
2773 ("r-data-table" ,r-data-table)
2774 ("r-dplyr" ,r-dplyr)
2775 ("r-genomeinfodb" ,r-genomeinfodb)
2776 ("r-genomicalignments" ,r-genomicalignments)
2777 ("r-genomicranges" ,r-genomicranges)
2778 ("r-ggplot2" ,r-ggplot2)
2779 ("r-hexbin" ,r-hexbin)
2780 ("r-iranges" ,r-iranges)
2781 ("r-rcolorbrewer" ,r-rcolorbrewer)
2782 ("r-rmarkdown" ,r-rmarkdown)
2783 ("r-rsamtools" ,r-rsamtools)
2784 ("r-s4vectors" ,r-s4vectors)
2785 ("r-scales" ,r-scales)
2786 ("r-viridis" ,r-viridis)))
2788 `(("r-knitr" ,r-knitr)))
2789 (home-page "https://github.com/keleslab/ChIPexoQual")
2790 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2792 "This package provides a quality control pipeline for ChIP-exo/nexus
2794 (license license:gpl2+)))
2796 (define-public r-copynumber
2798 (name "r-copynumber")
2802 (uri (bioconductor-uri "copynumber" version))
2805 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
2806 (build-system r-build-system)
2808 `(("r-s4vectors" ,r-s4vectors)
2809 ("r-iranges" ,r-iranges)
2810 ("r-genomicranges" ,r-genomicranges)
2811 ("r-biocgenerics" ,r-biocgenerics)))
2812 (home-page "https://bioconductor.org/packages/copynumber")
2813 (synopsis "Segmentation of single- and multi-track copy number data")
2815 "This package segments single- and multi-track copy number data by a
2816 penalized least squares regression method.")
2817 (license license:artistic2.0)))
2819 (define-public r-dnacopy
2826 (uri (bioconductor-uri "DNAcopy" version))
2829 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
2830 (properties `((upstream-name . "DNAcopy")))
2831 (build-system r-build-system)
2832 (native-inputs `(("gfortran" ,gfortran)))
2833 (home-page "https://bioconductor.org/packages/DNAcopy")
2834 (synopsis "DNA copy number data analysis")
2836 "This package implements the @dfn{circular binary segmentation} (CBS)
2837 algorithm to segment DNA copy number data and identify genomic regions with
2838 abnormal copy number.")
2839 (license license:gpl2+)))
2841 ;; This is a CRAN package, but it uncharacteristically depends on a
2842 ;; Bioconductor package.
2843 (define-public r-htscluster
2845 (name "r-htscluster")
2850 (uri (cran-uri "HTSCluster" version))
2853 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2854 (properties `((upstream-name . "HTSCluster")))
2855 (build-system r-build-system)
2857 `(("r-capushe" ,r-capushe)
2858 ("r-edger" ,r-edger)
2859 ("r-plotrix" ,r-plotrix)))
2860 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2861 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2863 "This package provides a Poisson mixture model is implemented to cluster
2864 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2865 estimation is performed using either the EM or CEM algorithm, and the slope
2866 heuristics are used for model selection (i.e., to choose the number of
2868 (license license:gpl3+)))
2870 (define-public r-deds
2877 (uri (bioconductor-uri "DEDS" version))
2880 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2881 (properties `((upstream-name . "DEDS")))
2882 (build-system r-build-system)
2883 (home-page "https://bioconductor.org/packages/DEDS/")
2884 (synopsis "Differential expression via distance summary for microarray data")
2886 "This library contains functions that calculate various statistics of
2887 differential expression for microarray data, including t statistics, fold
2888 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2889 also implements a new methodology called DEDS (Differential Expression via
2890 Distance Summary), which selects differentially expressed genes by integrating
2891 and summarizing a set of statistics using a weighted distance approach.")
2892 ;; Any version of the LGPL.
2893 (license license:lgpl3+)))
2895 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2897 (define-public r-nbpseq
2904 (uri (cran-uri "NBPSeq" version))
2907 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2908 (properties `((upstream-name . "NBPSeq")))
2909 (build-system r-build-system)
2911 `(("r-qvalue" ,r-qvalue)))
2912 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2913 (synopsis "Negative binomial models for RNA-Seq data")
2915 "This package provides negative binomial models for two-group comparisons
2916 and regression inferences from RNA-sequencing data.")
2917 (license license:gpl2)))
2919 (define-public r-ebseq
2926 (uri (bioconductor-uri "EBSeq" version))
2929 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
2930 (properties `((upstream-name . "EBSeq")))
2931 (build-system r-build-system)
2933 `(("r-blockmodeling" ,r-blockmodeling)
2934 ("r-gplots" ,r-gplots)
2935 ("r-testthat" ,r-testthat)))
2936 (home-page "https://bioconductor.org/packages/EBSeq")
2937 (synopsis "Differential expression analysis of RNA-seq data")
2939 "This package provides tools for differential expression analysis at both
2940 gene and isoform level using RNA-seq data")
2941 (license license:artistic2.0)))
2943 (define-public r-karyoploter
2945 (name "r-karyoploter")
2949 (uri (bioconductor-uri "karyoploteR" version))
2952 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
2953 (build-system r-build-system)
2955 `(("r-annotationdbi" ,r-annotationdbi)
2956 ("r-bamsignals" ,r-bamsignals)
2957 ("r-bezier" ,r-bezier)
2958 ("r-biovizbase" ,r-biovizbase)
2959 ("r-digest" ,r-digest)
2960 ("r-genomeinfodb" ,r-genomeinfodb)
2961 ("r-genomicfeatures" ,r-genomicfeatures)
2962 ("r-genomicranges" ,r-genomicranges)
2963 ("r-iranges" ,r-iranges)
2964 ("r-memoise" ,r-memoise)
2965 ("r-regioner" ,r-regioner)
2966 ("r-rsamtools" ,r-rsamtools)
2967 ("r-rtracklayer" ,r-rtracklayer)
2968 ("r-s4vectors" ,r-s4vectors)
2969 ("r-variantannotation" ,r-variantannotation)))
2971 `(("r-knitr" ,r-knitr)))
2972 (home-page "https://bioconductor.org/packages/karyoploteR/")
2973 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2974 (description "This package creates karyotype plots of arbitrary genomes and
2975 offers a complete set of functions to plot arbitrary data on them. It mimics
2976 many R base graphics functions coupling them with a coordinate change function
2977 automatically mapping the chromosome and data coordinates into the plot
2979 (license license:artistic2.0)))
2981 (define-public r-lpsymphony
2983 (name "r-lpsymphony")
2988 (uri (bioconductor-uri "lpsymphony" version))
2991 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
2992 (build-system r-build-system)
2996 `(("pkg-config" ,pkg-config)
2997 ("r-knitr" ,r-knitr)))
2998 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2999 (synopsis "Symphony integer linear programming solver in R")
3001 "This package was derived from Rsymphony. The package provides an R
3002 interface to SYMPHONY, a linear programming solver written in C++. The main
3003 difference between this package and Rsymphony is that it includes the solver
3004 source code, while Rsymphony expects to find header and library files on the
3005 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3006 to install interface to SYMPHONY.")
3007 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3008 ;; lpsimphony is released under the same terms.
3009 (license license:epl1.0)))
3011 (define-public r-ihw
3018 (uri (bioconductor-uri "IHW" version))
3021 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3022 (properties `((upstream-name . "IHW")))
3023 (build-system r-build-system)
3025 `(("r-biocgenerics" ,r-biocgenerics)
3026 ("r-fdrtool" ,r-fdrtool)
3027 ("r-lpsymphony" ,r-lpsymphony)
3028 ("r-slam" ,r-slam)))
3030 `(("r-knitr" ,r-knitr)))
3031 (home-page "https://bioconductor.org/packages/IHW")
3032 (synopsis "Independent hypothesis weighting")
3034 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3035 procedure that increases power compared to the method of Benjamini and
3036 Hochberg by assigning data-driven weights to each hypothesis. The input to
3037 IHW is a two-column table of p-values and covariates. The covariate can be
3038 any continuous-valued or categorical variable that is thought to be
3039 informative on the statistical properties of each hypothesis test, while it is
3040 independent of the p-value under the null hypothesis.")
3041 (license license:artistic2.0)))
3043 (define-public r-icobra
3050 (uri (bioconductor-uri "iCOBRA" version))
3053 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3054 (properties `((upstream-name . "iCOBRA")))
3055 (build-system r-build-system)
3057 `(("r-dplyr" ,r-dplyr)
3059 ("r-ggplot2" ,r-ggplot2)
3060 ("r-limma" ,r-limma)
3061 ("r-reshape2" ,r-reshape2)
3063 ("r-scales" ,r-scales)
3064 ("r-shiny" ,r-shiny)
3065 ("r-shinybs" ,r-shinybs)
3066 ("r-shinydashboard" ,r-shinydashboard)
3067 ("r-upsetr" ,r-upsetr)))
3069 `(("r-knitr" ,r-knitr)))
3070 (home-page "https://bioconductor.org/packages/iCOBRA")
3071 (synopsis "Comparison and visualization of ranking and assignment methods")
3073 "This package provides functions for calculation and visualization of
3074 performance metrics for evaluation of ranking and binary
3075 classification (assignment) methods. It also contains a Shiny application for
3076 interactive exploration of results.")
3077 (license license:gpl2+)))
3079 (define-public r-mast
3086 (uri (bioconductor-uri "MAST" version))
3089 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
3090 (properties `((upstream-name . "MAST")))
3091 (build-system r-build-system)
3093 `(("r-abind" ,r-abind)
3094 ("r-biobase" ,r-biobase)
3095 ("r-biocgenerics" ,r-biocgenerics)
3096 ("r-data-table" ,r-data-table)
3097 ("r-ggplot2" ,r-ggplot2)
3099 ("r-progress" ,r-progress)
3100 ("r-reshape2" ,r-reshape2)
3101 ("r-s4vectors" ,r-s4vectors)
3102 ("r-singlecellexperiment" ,r-singlecellexperiment)
3103 ("r-stringr" ,r-stringr)
3104 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3106 `(("r-knitr" ,r-knitr)))
3107 (home-page "https://github.com/RGLab/MAST/")
3108 (synopsis "Model-based analysis of single cell transcriptomics")
3110 "This package provides methods and models for handling zero-inflated
3111 single cell assay data.")
3112 (license license:gpl2+)))
3114 (define-public r-monocle
3121 (uri (bioconductor-uri "monocle" version))
3124 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
3125 (build-system r-build-system)
3127 `(("r-biobase" ,r-biobase)
3128 ("r-biocgenerics" ,r-biocgenerics)
3129 ("r-biocviews" ,r-biocviews)
3130 ("r-cluster" ,r-cluster)
3131 ("r-combinat" ,r-combinat)
3132 ("r-ddrtree" ,r-ddrtree)
3133 ("r-densityclust" ,r-densityclust)
3134 ("r-dplyr" ,r-dplyr)
3135 ("r-fastica" ,r-fastica)
3136 ("r-ggplot2" ,r-ggplot2)
3137 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3138 ("r-igraph" ,r-igraph)
3139 ("r-irlba" ,r-irlba)
3140 ("r-limma" ,r-limma)
3142 ("r-matrix" ,r-matrix)
3143 ("r-matrixstats" ,r-matrixstats)
3144 ("r-pheatmap" ,r-pheatmap)
3146 ("r-proxy" ,r-proxy)
3147 ("r-qlcmatrix" ,r-qlcmatrix)
3150 ("r-reshape2" ,r-reshape2)
3151 ("r-rtsne" ,r-rtsne)
3153 ("r-stringr" ,r-stringr)
3154 ("r-tibble" ,r-tibble)
3156 ("r-viridis" ,r-viridis)))
3158 `(("r-knitr" ,r-knitr)))
3159 (home-page "https://bioconductor.org/packages/monocle")
3160 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3162 "Monocle performs differential expression and time-series analysis for
3163 single-cell expression experiments. It orders individual cells according to
3164 progress through a biological process, without knowing ahead of time which
3165 genes define progress through that process. Monocle also performs
3166 differential expression analysis, clustering, visualization, and other useful
3167 tasks on single cell expression data. It is designed to work with RNA-Seq and
3168 qPCR data, but could be used with other types as well.")
3169 (license license:artistic2.0)))
3171 (define-public r-monocle3
3179 (url "https://github.com/cole-trapnell-lab/monocle3")
3181 (file-name (git-file-name name version))
3184 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3185 (build-system r-build-system)
3187 `(("r-biobase" ,r-biobase)
3188 ("r-biocgenerics" ,r-biocgenerics)
3189 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3190 ("r-dplyr" ,r-dplyr)
3191 ("r-ggplot2" ,r-ggplot2)
3192 ("r-ggrepel" ,r-ggrepel)
3194 ("r-htmlwidgets" ,r-htmlwidgets)
3195 ("r-igraph" ,r-igraph)
3196 ("r-irlba" ,r-irlba)
3197 ("r-limma" ,r-limma)
3198 ("r-lmtest" ,r-lmtest)
3200 ("r-matrix" ,r-matrix)
3201 ("r-matrix-utils" ,r-matrix-utils)
3202 ("r-pbapply" ,r-pbapply)
3203 ("r-pbmcapply" ,r-pbmcapply)
3204 ("r-pheatmap" ,r-pheatmap)
3205 ("r-plotly" ,r-plotly)
3207 ("r-proxy" ,r-proxy)
3209 ("r-purrr" ,r-purrr)
3212 ("r-rcppparallel" ,r-rcppparallel)
3213 ("r-reshape2" ,r-reshape2)
3214 ("r-reticulate" ,r-reticulate)
3215 ("r-rhpcblasctl" ,r-rhpcblasctl)
3216 ("r-rtsne" ,r-rtsne)
3217 ("r-shiny" ,r-shiny)
3219 ("r-spdep" ,r-spdep)
3220 ("r-speedglm" ,r-speedglm)
3221 ("r-stringr" ,r-stringr)
3222 ("r-singlecellexperiment" ,r-singlecellexperiment)
3223 ("r-tibble" ,r-tibble)
3224 ("r-tidyr" ,r-tidyr)
3226 ("r-viridis" ,r-viridis)))
3227 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3228 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3230 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3231 (license license:expat)))
3233 (define-public r-noiseq
3240 (uri (bioconductor-uri "NOISeq" version))
3243 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
3244 (properties `((upstream-name . "NOISeq")))
3245 (build-system r-build-system)
3247 `(("r-biobase" ,r-biobase)
3248 ("r-matrix" ,r-matrix)))
3249 (home-page "https://bioconductor.org/packages/NOISeq")
3250 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3252 "This package provides tools to support the analysis of RNA-seq
3253 expression data or other similar kind of data. It provides exploratory plots
3254 to evaluate saturation, count distribution, expression per chromosome, type of
3255 detected features, features length, etc. It also supports the analysis of
3256 differential expression between two experimental conditions with no parametric
3258 (license license:artistic2.0)))
3260 (define-public r-scdd
3267 (uri (bioconductor-uri "scDD" version))
3270 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
3271 (properties `((upstream-name . "scDD")))
3272 (build-system r-build-system)
3275 ("r-biocparallel" ,r-biocparallel)
3276 ("r-ebseq" ,r-ebseq)
3277 ("r-fields" ,r-fields)
3278 ("r-ggplot2" ,r-ggplot2)
3279 ("r-mclust" ,r-mclust)
3280 ("r-outliers" ,r-outliers)
3281 ("r-s4vectors" ,r-s4vectors)
3282 ("r-scran" ,r-scran)
3283 ("r-singlecellexperiment" ,r-singlecellexperiment)
3284 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3286 `(("r-knitr" ,r-knitr)))
3287 (home-page "https://github.com/kdkorthauer/scDD")
3288 (synopsis "Mixture modeling of single-cell RNA-seq data")
3290 "This package implements a method to analyze single-cell RNA-seq data
3291 utilizing flexible Dirichlet Process mixture models. Genes with differential
3292 distributions of expression are classified into several interesting patterns
3293 of differences between two conditions. The package also includes functions
3294 for simulating data with these patterns from negative binomial
3296 (license license:gpl2)))
3298 (define-public r-scone
3305 (uri (bioconductor-uri "scone" version))
3308 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
3309 (build-system r-build-system)
3311 `(("r-aroma-light" ,r-aroma-light)
3312 ("r-biocparallel" ,r-biocparallel)
3314 ("r-class" ,r-class)
3315 ("r-cluster" ,r-cluster)
3316 ("r-compositions" ,r-compositions)
3317 ("r-diptest" ,r-diptest)
3318 ("r-edger" ,r-edger)
3320 ("r-gplots" ,r-gplots)
3321 ("r-hexbin" ,r-hexbin)
3322 ("r-limma" ,r-limma)
3323 ("r-matrixstats" ,r-matrixstats)
3324 ("r-mixtools" ,r-mixtools)
3325 ("r-rarpack" ,r-rarpack)
3326 ("r-rcolorbrewer" ,r-rcolorbrewer)
3327 ("r-rhdf5" ,r-rhdf5)
3328 ("r-ruvseq" ,r-ruvseq)
3329 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3331 `(("r-knitr" ,r-knitr)))
3332 (home-page "https://bioconductor.org/packages/scone")
3333 (synopsis "Single cell overview of normalized expression data")
3335 "SCONE is an R package for comparing and ranking the performance of
3336 different normalization schemes for single-cell RNA-seq and other
3337 high-throughput analyses.")
3338 (license license:artistic2.0)))
3340 (define-public r-geoquery
3347 (uri (bioconductor-uri "GEOquery" version))
3350 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
3351 (properties `((upstream-name . "GEOquery")))
3352 (build-system r-build-system)
3354 `(("r-biobase" ,r-biobase)
3355 ("r-dplyr" ,r-dplyr)
3357 ("r-limma" ,r-limma)
3358 ("r-magrittr" ,r-magrittr)
3359 ("r-readr" ,r-readr)
3360 ("r-tidyr" ,r-tidyr)
3361 ("r-xml2" ,r-xml2)))
3363 `(("r-knitr" ,r-knitr)))
3364 (home-page "https://github.com/seandavi/GEOquery/")
3365 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3367 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3368 microarray data. Given the rich and varied nature of this resource, it is
3369 only natural to want to apply BioConductor tools to these data. GEOquery is
3370 the bridge between GEO and BioConductor.")
3371 (license license:gpl2)))
3373 (define-public r-illuminaio
3375 (name "r-illuminaio")
3380 (uri (bioconductor-uri "illuminaio" version))
3383 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
3384 (build-system r-build-system)
3386 `(("r-base64" ,r-base64)))
3387 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3388 (synopsis "Parse Illumina microarray output files")
3390 "This package provides tools for parsing Illumina's microarray output
3391 files, including IDAT.")
3392 (license license:gpl2)))
3394 (define-public r-siggenes
3401 (uri (bioconductor-uri "siggenes" version))
3404 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
3405 (build-system r-build-system)
3407 `(("r-biobase" ,r-biobase)
3408 ("r-multtest" ,r-multtest)
3409 ("r-scrime" ,r-scrime)))
3410 (home-page "https://bioconductor.org/packages/siggenes/")
3412 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3414 "This package provides tools for the identification of differentially
3415 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3416 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3417 Bayes Analyses of Microarrays} (EBAM).")
3418 (license license:lgpl2.0+)))
3420 (define-public r-bumphunter
3422 (name "r-bumphunter")
3427 (uri (bioconductor-uri "bumphunter" version))
3430 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
3431 (build-system r-build-system)
3433 `(("r-annotationdbi" ,r-annotationdbi)
3434 ("r-biocgenerics" ,r-biocgenerics)
3435 ("r-dorng" ,r-dorng)
3436 ("r-foreach" ,r-foreach)
3437 ("r-genomeinfodb" ,r-genomeinfodb)
3438 ("r-genomicfeatures" ,r-genomicfeatures)
3439 ("r-genomicranges" ,r-genomicranges)
3440 ("r-iranges" ,r-iranges)
3441 ("r-iterators" ,r-iterators)
3442 ("r-limma" ,r-limma)
3443 ("r-locfit" ,r-locfit)
3444 ("r-matrixstats" ,r-matrixstats)
3445 ("r-s4vectors" ,r-s4vectors)))
3446 (home-page "https://github.com/ririzarr/bumphunter")
3447 (synopsis "Find bumps in genomic data")
3449 "This package provides tools for finding bumps in genomic data in order
3450 to identify differentially methylated regions in epigenetic epidemiology
3452 (license license:artistic2.0)))
3454 (define-public r-minfi
3461 (uri (bioconductor-uri "minfi" version))
3464 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
3465 (build-system r-build-system)
3467 `(("r-beanplot" ,r-beanplot)
3468 ("r-biobase" ,r-biobase)
3469 ("r-biocgenerics" ,r-biocgenerics)
3470 ("r-biocparallel" ,r-biocparallel)
3471 ("r-biostrings" ,r-biostrings)
3472 ("r-bumphunter" ,r-bumphunter)
3473 ("r-data-table" ,r-data-table)
3474 ("r-delayedarray" ,r-delayedarray)
3475 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3476 ("r-genefilter" ,r-genefilter)
3477 ("r-genomeinfodb" ,r-genomeinfodb)
3478 ("r-genomicranges" ,r-genomicranges)
3479 ("r-geoquery" ,r-geoquery)
3480 ("r-hdf5array" ,r-hdf5array)
3481 ("r-illuminaio" ,r-illuminaio)
3482 ("r-iranges" ,r-iranges)
3483 ("r-lattice" ,r-lattice)
3484 ("r-limma" ,r-limma)
3486 ("r-mclust" ,r-mclust)
3488 ("r-nor1mix" ,r-nor1mix)
3489 ("r-preprocesscore" ,r-preprocesscore)
3490 ("r-quadprog" ,r-quadprog)
3491 ("r-rcolorbrewer" ,r-rcolorbrewer)
3492 ("r-reshape" ,r-reshape)
3493 ("r-s4vectors" ,r-s4vectors)
3494 ("r-siggenes" ,r-siggenes)
3495 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3497 `(("r-knitr" ,r-knitr)))
3498 (home-page "https://github.com/hansenlab/minfi")
3499 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3501 "This package provides tools to analyze and visualize Illumina Infinium
3502 methylation arrays.")
3503 (license license:artistic2.0)))
3505 (define-public r-methylumi
3507 (name "r-methylumi")
3512 (uri (bioconductor-uri "methylumi" version))
3515 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
3516 (build-system r-build-system)
3518 `(("r-annotate" ,r-annotate)
3519 ("r-annotationdbi" ,r-annotationdbi)
3520 ("r-biobase" ,r-biobase)
3521 ("r-biocgenerics" ,r-biocgenerics)
3522 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3523 ("r-genefilter" ,r-genefilter)
3524 ("r-genomeinfodb" ,r-genomeinfodb)
3525 ("r-genomicranges" ,r-genomicranges)
3526 ("r-ggplot2" ,r-ggplot2)
3527 ("r-illuminaio" ,r-illuminaio)
3528 ("r-iranges" ,r-iranges)
3529 ("r-lattice" ,r-lattice)
3530 ("r-matrixstats" ,r-matrixstats)
3531 ("r-minfi" ,r-minfi)
3532 ("r-reshape2" ,r-reshape2)
3533 ("r-s4vectors" ,r-s4vectors)
3534 ("r-scales" ,r-scales)
3535 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3537 `(("r-knitr" ,r-knitr)))
3538 (home-page "https://bioconductor.org/packages/methylumi")
3539 (synopsis "Handle Illumina methylation data")
3541 "This package provides classes for holding and manipulating Illumina
3542 methylation data. Based on eSet, it can contain MIAME information, sample
3543 information, feature information, and multiple matrices of data. An
3544 \"intelligent\" import function, methylumiR can read the Illumina text files
3545 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3546 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3547 background correction, and quality control features for GoldenGate, Infinium,
3548 and Infinium HD arrays are also included.")
3549 (license license:gpl2)))
3551 (define-public r-lumi
3558 (uri (bioconductor-uri "lumi" version))
3561 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
3562 (build-system r-build-system)
3564 `(("r-affy" ,r-affy)
3565 ("r-annotate" ,r-annotate)
3566 ("r-annotationdbi" ,r-annotationdbi)
3567 ("r-biobase" ,r-biobase)
3569 ("r-genomicfeatures" ,r-genomicfeatures)
3570 ("r-genomicranges" ,r-genomicranges)
3571 ("r-kernsmooth" ,r-kernsmooth)
3572 ("r-lattice" ,r-lattice)
3574 ("r-methylumi" ,r-methylumi)
3576 ("r-nleqslv" ,r-nleqslv)
3577 ("r-preprocesscore" ,r-preprocesscore)
3578 ("r-rsqlite" ,r-rsqlite)))
3579 (home-page "https://bioconductor.org/packages/lumi")
3580 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3582 "The lumi package provides an integrated solution for the Illumina
3583 microarray data analysis. It includes functions of Illumina
3584 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3585 variance stabilization, normalization and gene annotation at the probe level.
3586 It also includes the functions of processing Illumina methylation microarrays,
3587 especially Illumina Infinium methylation microarrays.")
3588 (license license:lgpl2.0+)))
3590 (define-public r-linnorm
3597 (uri (bioconductor-uri "Linnorm" version))
3600 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
3601 (properties `((upstream-name . "Linnorm")))
3602 (build-system r-build-system)
3604 `(("r-amap" ,r-amap)
3605 ("r-apcluster" ,r-apcluster)
3606 ("r-ellipse" ,r-ellipse)
3607 ("r-fastcluster" ,r-fastcluster)
3609 ("r-ggdendro" ,r-ggdendro)
3610 ("r-ggplot2" ,r-ggplot2)
3611 ("r-gmodels" ,r-gmodels)
3612 ("r-igraph" ,r-igraph)
3613 ("r-limma" ,r-limma)
3615 ("r-mclust" ,r-mclust)
3617 ("r-rcpparmadillo" ,r-rcpparmadillo)
3618 ("r-rtsne" ,r-rtsne)
3619 ("r-statmod" ,r-statmod)
3620 ("r-vegan" ,r-vegan)
3623 `(("r-knitr" ,r-knitr)))
3624 (home-page "http://www.jjwanglab.org/Linnorm/")
3625 (synopsis "Linear model and normality based transformation method")
3627 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3628 count data or any large scale count data. It transforms such datasets for
3629 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3630 the following pipelines are implemented:
3633 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3634 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3635 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3636 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3637 @item Differential expression analysis or differential peak detection using
3638 limma (@code{Linnorm.limma})
3639 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3640 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3641 @item Stable gene selection for scRNA-seq data; for users without or who do
3642 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3643 @item Data imputation (@code{Linnorm.DataImput}).
3646 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3647 @code{RnaXSim} function is included for simulating RNA-seq data for the
3648 evaluation of DEG analysis methods.")
3649 (license license:expat)))
3651 (define-public r-ioniser
3658 (uri (bioconductor-uri "IONiseR" version))
3661 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
3662 (properties `((upstream-name . "IONiseR")))
3663 (build-system r-build-system)
3665 `(("r-biocgenerics" ,r-biocgenerics)
3666 ("r-biocparallel" ,r-biocparallel)
3667 ("r-biostrings" ,r-biostrings)
3668 ("r-bit64" ,r-bit64)
3669 ("r-dplyr" ,r-dplyr)
3670 ("r-ggplot2" ,r-ggplot2)
3671 ("r-magrittr" ,r-magrittr)
3672 ("r-rhdf5" ,r-rhdf5)
3673 ("r-shortread" ,r-shortread)
3674 ("r-stringr" ,r-stringr)
3675 ("r-tibble" ,r-tibble)
3676 ("r-tidyr" ,r-tidyr)
3677 ("r-xvector" ,r-xvector)))
3679 `(("r-knitr" ,r-knitr)))
3680 (home-page "https://bioconductor.org/packages/IONiseR/")
3681 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3683 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3684 MinION data. It extracts summary statistics from a set of fast5 files and can
3685 be used either before or after base calling. In addition to standard
3686 summaries of the read-types produced, it provides a number of plots for
3687 visualising metrics relative to experiment run time or spatially over the
3688 surface of a flowcell.")
3689 (license license:expat)))
3691 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3692 (define-public r-gkmsvm
3699 (uri (cran-uri "gkmSVM" version))
3702 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3703 (properties `((upstream-name . "gkmSVM")))
3704 (build-system r-build-system)
3706 `(("r-kernlab" ,r-kernlab)
3709 ("r-seqinr" ,r-seqinr)))
3710 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3711 (synopsis "Gapped-kmer support vector machine")
3713 "This R package provides tools for training gapped-kmer SVM classifiers
3714 for DNA and protein sequences. This package supports several sequence
3715 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3716 (license license:gpl2+)))
3718 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3719 (define-public r-mutoss
3726 (uri (cran-uri "mutoss" version))
3729 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3730 (properties `((upstream-name . "mutoss")))
3731 (build-system r-build-system)
3733 `(("r-multcomp" ,r-multcomp)
3734 ("r-multtest" ,r-multtest)
3735 ("r-mvtnorm" ,r-mvtnorm)
3736 ("r-plotrix" ,r-plotrix)))
3737 (home-page "https://github.com/kornl/mutoss/")
3738 (synopsis "Unified multiple testing procedures")
3740 "This package is designed to ease the application and comparison of
3741 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3742 are standardized and usable by the accompanying mutossGUI package.")
3743 ;; Any version of the GPL.
3744 (license (list license:gpl2+ license:gpl3+))))
3746 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3747 ;; from Bioconductor, so we put it here.
3748 (define-public r-metap
3755 (uri (cran-uri "metap" version))
3758 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3759 (build-system r-build-system)
3761 `(("r-lattice" ,r-lattice)
3762 ("r-mutoss" ,r-mutoss)
3763 ("r-rdpack" ,r-rdpack)
3764 ("r-tfisher" ,r-tfisher)))
3765 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3766 (synopsis "Meta-analysis of significance values")
3768 "The canonical way to perform meta-analysis involves using effect sizes.
3769 When they are not available this package provides a number of methods for
3770 meta-analysis of significance values including the methods of Edgington,
3771 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3772 published results; and a routine for graphical display.")
3773 (license license:gpl2)))
3775 (define-public r-triform
3782 (uri (bioconductor-uri "triform" version))
3785 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3786 (build-system r-build-system)
3788 `(("r-biocgenerics" ,r-biocgenerics)
3789 ("r-iranges" ,r-iranges)
3790 ("r-yaml" ,r-yaml)))
3791 (home-page "https://bioconductor.org/packages/triform/")
3792 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3794 "The Triform algorithm uses model-free statistics to identify peak-like
3795 distributions of TF ChIP sequencing reads, taking advantage of an improved
3796 peak definition in combination with known profile characteristics.")
3797 (license license:gpl2)))
3799 (define-public r-varianttools
3801 (name "r-varianttools")
3806 (uri (bioconductor-uri "VariantTools" version))
3809 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
3810 (properties `((upstream-name . "VariantTools")))
3811 (build-system r-build-system)
3813 `(("r-biobase" ,r-biobase)
3814 ("r-biocgenerics" ,r-biocgenerics)
3815 ("r-biocparallel" ,r-biocparallel)
3816 ("r-biostrings" ,r-biostrings)
3817 ("r-bsgenome" ,r-bsgenome)
3818 ("r-genomeinfodb" ,r-genomeinfodb)
3819 ("r-genomicfeatures" ,r-genomicfeatures)
3820 ("r-genomicranges" ,r-genomicranges)
3821 ("r-iranges" ,r-iranges)
3822 ("r-matrix" ,r-matrix)
3823 ("r-rsamtools" ,r-rsamtools)
3824 ("r-rtracklayer" ,r-rtracklayer)
3825 ("r-s4vectors" ,r-s4vectors)
3826 ("r-variantannotation" ,r-variantannotation)))
3827 (home-page "https://bioconductor.org/packages/VariantTools/")
3828 (synopsis "Tools for exploratory analysis of variant calls")
3830 "Explore, diagnose, and compare variant calls using filters. The
3831 VariantTools package supports a workflow for loading data, calling single
3832 sample variants and tumor-specific somatic mutations or other sample-specific
3833 variant types (e.g., RNA editing). Most of the functions operate on
3834 alignments (BAM files) or datasets of called variants. The user is expected
3835 to have already aligned the reads with a separate tool, e.g., GSNAP via
3837 (license license:artistic2.0)))
3839 (define-public r-heatplus
3846 (uri (bioconductor-uri "Heatplus" version))
3849 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
3850 (properties `((upstream-name . "Heatplus")))
3851 (build-system r-build-system)
3853 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3854 (home-page "https://github.com/alexploner/Heatplus")
3855 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3857 "This package provides tools to display a rectangular heatmap (intensity
3858 plot) of a data matrix. By default, both samples (columns) and features (row)
3859 of the matrix are sorted according to a hierarchical clustering, and the
3860 corresponding dendrogram is plotted. Optionally, panels with additional
3861 information about samples and features can be added to the plot.")
3862 (license license:gpl2+)))
3864 (define-public r-gosemsim
3871 (uri (bioconductor-uri "GOSemSim" version))
3874 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
3875 (properties `((upstream-name . "GOSemSim")))
3876 (build-system r-build-system)
3878 `(("r-annotationdbi" ,r-annotationdbi)
3879 ("r-go-db" ,r-go-db)
3880 ("r-rcpp" ,r-rcpp)))
3882 `(("r-knitr" ,r-knitr)))
3883 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3884 (synopsis "GO-terms semantic similarity measures")
3886 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3887 quantitative ways to compute similarities between genes and gene groups, and
3888 have became important basis for many bioinformatics analysis approaches.
3889 GOSemSim is an R package for semantic similarity computation among GO terms,
3890 sets of GO terms, gene products and gene clusters.")
3891 (license license:artistic2.0)))
3893 (define-public r-anota
3900 (uri (bioconductor-uri "anota" version))
3903 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
3904 (build-system r-build-system)
3906 `(("r-multtest" ,r-multtest)
3907 ("r-qvalue" ,r-qvalue)))
3908 (home-page "https://bioconductor.org/packages/anota/")
3909 (synopsis "Analysis of translational activity")
3911 "Genome wide studies of translational control is emerging as a tool to
3912 study various biological conditions. The output from such analysis is both
3913 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
3914 involved in translation (the actively translating mRNA level) for each mRNA.
3915 The standard analysis of such data strives towards identifying differential
3916 translational between two or more sample classes - i.e. differences in
3917 actively translated mRNA levels that are independent of underlying differences
3918 in cytosolic mRNA levels. This package allows for such analysis using partial
3919 variances and the random variance model. As 10s of thousands of mRNAs are
3920 analyzed in parallel the library performs a number of tests to assure that
3921 the data set is suitable for such analysis.")
3922 (license license:gpl3)))
3924 (define-public r-sigpathway
3926 (name "r-sigpathway")
3931 (uri (bioconductor-uri "sigPathway" version))
3934 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
3935 (properties `((upstream-name . "sigPathway")))
3936 (build-system r-build-system)
3937 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3938 (synopsis "Pathway analysis")
3940 "This package is used to conduct pathway analysis by calculating the NT_k
3941 and NE_k statistics in a statistical framework for determining whether a
3942 specified group of genes for a pathway has a coordinated association with a
3943 phenotype of interest.")
3944 (license license:gpl2)))
3946 (define-public r-fgsea
3953 (uri (bioconductor-uri "fgsea" version))
3956 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
3957 (build-system r-build-system)
3960 ("r-biocparallel" ,r-biocparallel)
3961 ("r-data-table" ,r-data-table)
3962 ("r-fastmatch" ,r-fastmatch)
3963 ("r-ggplot2" ,r-ggplot2)
3964 ("r-gridextra" ,r-gridextra)
3965 ("r-matrix" ,r-matrix)
3966 ("r-rcpp" ,r-rcpp)))
3968 `(("r-knitr" ,r-knitr)))
3969 (home-page "https://github.com/ctlab/fgsea/")
3970 (synopsis "Fast gene set enrichment analysis")
3972 "The package implements an algorithm for fast gene set enrichment
3973 analysis. Using the fast algorithm makes more permutations and gets
3974 more fine grained p-values, which allows using accurate standard approaches
3975 to multiple hypothesis correction.")
3976 (license license:expat)))
3978 (define-public r-dose
3985 (uri (bioconductor-uri "DOSE" version))
3988 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
3989 (properties `((upstream-name . "DOSE")))
3990 (build-system r-build-system)
3992 `(("r-annotationdbi" ,r-annotationdbi)
3993 ("r-biocparallel" ,r-biocparallel)
3994 ("r-do-db" ,r-do-db)
3995 ("r-fgsea" ,r-fgsea)
3996 ("r-ggplot2" ,r-ggplot2)
3997 ("r-gosemsim" ,r-gosemsim)
3998 ("r-qvalue" ,r-qvalue)
3999 ("r-reshape2" ,r-reshape2)))
4001 `(("r-knitr" ,r-knitr)))
4002 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4003 (synopsis "Disease ontology semantic and enrichment analysis")
4005 "This package implements five methods proposed by Resnik, Schlicker,
4006 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4007 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4008 including hypergeometric model and gene set enrichment analysis are also
4009 implemented for discovering disease associations of high-throughput biological
4011 (license license:artistic2.0)))
4013 (define-public r-enrichplot
4015 (name "r-enrichplot")
4020 (uri (bioconductor-uri "enrichplot" version))
4023 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4024 (build-system r-build-system)
4026 `(("r-cowplot" ,r-cowplot)
4028 ("r-ggplot2" ,r-ggplot2)
4029 ("r-ggraph" ,r-ggraph)
4030 ("r-gosemsim" ,r-gosemsim)
4031 ("r-igraph" ,r-igraph)
4032 ("r-magrittr" ,r-magrittr)
4034 ("r-purrr" ,r-purrr)
4035 ("r-rcolorbrewer" ,r-rcolorbrewer)
4036 ("r-reshape2" ,r-reshape2)
4037 ("r-scatterpie" ,r-scatterpie)
4038 ("r-shadowtext" ,r-shadowtext)))
4040 `(("r-knitr" ,r-knitr)))
4041 (home-page "https://github.com/GuangchuangYu/enrichplot")
4042 (synopsis "Visualization of functional enrichment result")
4044 "The enrichplot package implements several visualization methods for
4045 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4046 All the visualization methods are developed based on ggplot2 graphics.")
4047 (license license:artistic2.0)))
4049 (define-public r-clusterprofiler
4051 (name "r-clusterprofiler")
4056 (uri (bioconductor-uri "clusterProfiler" version))
4059 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4061 `((upstream-name . "clusterProfiler")))
4062 (build-system r-build-system)
4064 `(("r-annotationdbi" ,r-annotationdbi)
4066 ("r-downloader" ,r-downloader)
4067 ("r-dplyr" ,r-dplyr)
4068 ("r-enrichplot" ,r-enrichplot)
4069 ("r-go-db" ,r-go-db)
4070 ("r-gosemsim" ,r-gosemsim)
4071 ("r-magrittr" ,r-magrittr)
4073 ("r-qvalue" ,r-qvalue)
4074 ("r-rlang" ,r-rlang)
4075 ("r-rvcheck" ,r-rvcheck)
4076 ("r-tidyr" ,r-tidyr)))
4078 `(("r-knitr" ,r-knitr)))
4079 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4080 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4082 "This package implements methods to analyze and visualize functional
4083 profiles (GO and KEGG) of gene and gene clusters.")
4084 (license license:artistic2.0)))
4086 (define-public r-mlinterfaces
4088 (name "r-mlinterfaces")
4093 (uri (bioconductor-uri "MLInterfaces" version))
4096 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4097 (properties `((upstream-name . "MLInterfaces")))
4098 (build-system r-build-system)
4100 `(("r-annotate" ,r-annotate)
4101 ("r-biobase" ,r-biobase)
4102 ("r-biocgenerics" ,r-biocgenerics)
4103 ("r-cluster" ,r-cluster)
4106 ("r-gdata" ,r-gdata)
4107 ("r-genefilter" ,r-genefilter)
4108 ("r-ggvis" ,r-ggvis)
4109 ("r-hwriter" ,r-hwriter)
4111 ("r-mlbench" ,r-mlbench)
4113 ("r-rcolorbrewer" ,r-rcolorbrewer)
4115 ("r-rpart" ,r-rpart)
4116 ("r-sfsmisc" ,r-sfsmisc)
4117 ("r-shiny" ,r-shiny)
4118 ("r-threejs" ,r-threejs)))
4119 (home-page "https://bioconductor.org/packages/MLInterfaces/")
4120 (synopsis "Interfaces to R machine learning procedures")
4122 "This package provides uniform interfaces to machine learning code for
4123 data in R and Bioconductor containers.")
4124 ;; Any version of the LGPL.
4125 (license license:lgpl2.1+)))
4127 (define-public r-annaffy
4134 (uri (bioconductor-uri "annaffy" version))
4137 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
4138 (build-system r-build-system)
4141 (modify-phases %standard-phases
4142 (add-after 'unpack 'remove-reference-to-non-free-data
4144 (substitute* "DESCRIPTION"
4148 `(("r-annotationdbi" ,r-annotationdbi)
4149 ("r-biobase" ,r-biobase)
4151 ("r-go-db" ,r-go-db)))
4152 (home-page "https://bioconductor.org/packages/annaffy/")
4153 (synopsis "Annotation tools for Affymetrix biological metadata")
4155 "This package provides functions for handling data from Bioconductor
4156 Affymetrix annotation data packages. It produces compact HTML and text
4157 reports including experimental data and URL links to many online databases.
4158 It allows searching of biological metadata using various criteria.")
4159 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4160 ;; the LGPL 2.1 is included.
4161 (license license:lgpl2.1+)))
4163 (define-public r-a4core
4170 (uri (bioconductor-uri "a4Core" version))
4173 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
4174 (properties `((upstream-name . "a4Core")))
4175 (build-system r-build-system)
4177 `(("r-biobase" ,r-biobase)
4178 ("r-glmnet" ,r-glmnet)))
4180 `(("r-knitr" ,r-knitr)))
4181 (home-page "https://bioconductor.org/packages/a4Core")
4182 (synopsis "Automated Affymetrix array analysis core package")
4184 "This is the core package for the automated analysis of Affymetrix
4186 (license license:gpl3)))
4188 (define-public r-a4classif
4190 (name "r-a4classif")
4195 (uri (bioconductor-uri "a4Classif" version))
4198 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
4199 (properties `((upstream-name . "a4Classif")))
4200 (build-system r-build-system)
4202 `(("r-a4core" ,r-a4core)
4203 ("r-a4preproc" ,r-a4preproc)
4204 ("r-biobase" ,r-biobase)
4205 ("r-glmnet" ,r-glmnet)
4208 ("r-varselrf" ,r-varselrf)))
4210 `(("r-knitr" ,r-knitr)))
4211 (home-page "https://bioconductor.org/packages/a4Classif/")
4212 (synopsis "Automated Affymetrix array analysis classification package")
4214 "This is the classification package for the automated analysis of
4215 Affymetrix arrays.")
4216 (license license:gpl3)))
4218 (define-public r-a4preproc
4220 (name "r-a4preproc")
4225 (uri (bioconductor-uri "a4Preproc" version))
4228 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
4229 (properties `((upstream-name . "a4Preproc")))
4230 (build-system r-build-system)
4232 `(("r-biobase" ,r-biobase)
4233 ("r-biocgenerics" ,r-biocgenerics)))
4235 `(("r-knitr" ,r-knitr)))
4236 (home-page "https://bioconductor.org/packages/a4Preproc/")
4237 (synopsis "Automated Affymetrix array analysis preprocessing package")
4239 "This is a package for the automated analysis of Affymetrix arrays. It
4240 is used for preprocessing the arrays.")
4241 (license license:gpl3)))
4243 (define-public r-a4reporting
4245 (name "r-a4reporting")
4250 (uri (bioconductor-uri "a4Reporting" version))
4253 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
4254 (properties `((upstream-name . "a4Reporting")))
4255 (build-system r-build-system)
4257 `(("r-xtable" ,r-xtable)))
4259 `(("r-knitr" ,r-knitr)))
4260 (home-page "https://bioconductor.org/packages/a4Reporting/")
4261 (synopsis "Automated Affymetrix array analysis reporting package")
4263 "This is a package for the automated analysis of Affymetrix arrays. It
4264 provides reporting features.")
4265 (license license:gpl3)))
4267 (define-public r-a4base
4274 (uri (bioconductor-uri "a4Base" version))
4277 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
4278 (properties `((upstream-name . "a4Base")))
4279 (build-system r-build-system)
4281 `(("r-a4core" ,r-a4core)
4282 ("r-a4preproc" ,r-a4preproc)
4283 ("r-annaffy" ,r-annaffy)
4284 ("r-biobase" ,r-biobase)
4285 ("r-genefilter" ,r-genefilter)
4286 ("r-glmnet" ,r-glmnet)
4287 ("r-gplots" ,r-gplots)
4288 ("r-limma" ,r-limma)
4290 ("r-multtest" ,r-multtest)))
4291 (home-page "https://bioconductor.org/packages/a4Base/")
4292 (synopsis "Automated Affymetrix array analysis base package")
4294 "This package provides basic features for the automated analysis of
4295 Affymetrix arrays.")
4296 (license license:gpl3)))
4305 (uri (bioconductor-uri "a4" version))
4308 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
4309 (build-system r-build-system)
4311 `(("r-a4base" ,r-a4base)
4312 ("r-a4classif" ,r-a4classif)
4313 ("r-a4core" ,r-a4core)
4314 ("r-a4preproc" ,r-a4preproc)
4315 ("r-a4reporting" ,r-a4reporting)))
4316 (home-page "https://bioconductor.org/packages/a4/")
4317 (synopsis "Automated Affymetrix array analysis umbrella package")
4319 "This package provides a software suite for the automated analysis of
4320 Affymetrix arrays.")
4321 (license license:gpl3)))
4323 (define-public r-abseqr
4330 (uri (bioconductor-uri "abseqR" version))
4333 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
4334 (properties `((upstream-name . "abseqR")))
4335 (build-system r-build-system)
4337 `(("pandoc" ,pandoc)))
4339 `(("r-biocparallel" ,r-biocparallel)
4340 ("r-biocstyle" ,r-biocstyle)
4341 ("r-circlize" ,r-circlize)
4342 ("r-flexdashboard" ,r-flexdashboard)
4343 ("r-ggcorrplot" ,r-ggcorrplot)
4344 ("r-ggdendro" ,r-ggdendro)
4345 ("r-ggplot2" ,r-ggplot2)
4346 ("r-gridextra" ,r-gridextra)
4347 ("r-knitr" ,r-knitr)
4348 ("r-plotly" ,r-plotly)
4351 ("r-rcolorbrewer" ,r-rcolorbrewer)
4352 ("r-reshape2" ,r-reshape2)
4353 ("r-rmarkdown" ,r-rmarkdown)
4354 ("r-stringr" ,r-stringr)
4355 ("r-vegan" ,r-vegan)
4356 ("r-venndiagram" ,r-venndiagram)))
4358 `(("r-knitr" ,r-knitr)))
4359 (home-page "https://github.com/malhamdoosh/abseqR")
4360 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4362 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4363 sequencing datasets generated from antibody libraries and abseqR is one of its
4364 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4365 capabilities and allows them to generate interactive HTML reports for the
4366 convenience of viewing and sharing with other researchers. Additionally,
4367 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4368 further downstream analysis on its output.")
4369 (license license:gpl3)))
4371 (define-public r-bacon
4378 (uri (bioconductor-uri "bacon" version))
4381 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
4382 (build-system r-build-system)
4384 `(("r-biocparallel" ,r-biocparallel)
4385 ("r-ellipse" ,r-ellipse)
4386 ("r-ggplot2" ,r-ggplot2)))
4388 `(("r-knitr" ,r-knitr)))
4389 (home-page "https://bioconductor.org/packages/bacon/")
4390 (synopsis "Controlling bias and inflation in association studies")
4392 "Bacon can be used to remove inflation and bias often observed in
4393 epigenome- and transcriptome-wide association studies. To this end bacon
4394 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4395 fitting a three-component normal mixture on z-scores.")
4396 (license license:gpl2+)))
4398 (define-public r-rgadem
4405 (uri (bioconductor-uri "rGADEM" version))
4408 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
4409 (properties `((upstream-name . "rGADEM")))
4410 (build-system r-build-system)
4412 `(("r-biostrings" ,r-biostrings)
4413 ("r-bsgenome" ,r-bsgenome)
4414 ("r-genomicranges" ,r-genomicranges)
4415 ("r-iranges" ,r-iranges)
4416 ("r-seqlogo" ,r-seqlogo)))
4417 (home-page "https://bioconductor.org/packages/rGADEM/")
4418 (synopsis "De novo sequence motif discovery")
4420 "rGADEM is an efficient de novo motif discovery tool for large-scale
4421 genomic sequence data.")
4422 (license license:artistic2.0)))
4424 (define-public r-motiv
4431 (uri (bioconductor-uri "MotIV" version))
4434 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4435 (properties `((upstream-name . "MotIV")))
4436 (build-system r-build-system)
4440 `(("r-biocgenerics" ,r-biocgenerics)
4441 ("r-biostrings" ,r-biostrings)
4442 ("r-genomicranges" ,r-genomicranges)
4443 ("r-iranges" ,r-iranges)
4444 ("r-lattice" ,r-lattice)
4445 ("r-rgadem" ,r-rgadem)
4446 ("r-s4vectors" ,r-s4vectors)))
4447 (home-page "https://bioconductor.org/packages/MotIV/")
4448 (synopsis "Motif identification and validation")
4450 "This package is used for the identification and validation of sequence
4451 motifs. It makes use of STAMP for comparing a set of motifs to a given
4452 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4453 distributions, modules and filter motifs.")
4454 (license license:gpl2)))
4456 (define-public r-motifdb
4462 (uri (bioconductor-uri "MotifDb" version))
4464 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
4465 (properties `((upstream-name . "MotifDb")))
4466 (build-system r-build-system)
4468 `(("r-biocgenerics" ,r-biocgenerics)
4469 ("r-biostrings" ,r-biostrings)
4470 ("r-genomicranges" ,r-genomicranges)
4471 ("r-iranges" ,r-iranges)
4472 ("r-rtracklayer" ,r-rtracklayer)
4473 ("r-s4vectors" ,r-s4vectors)
4474 ("r-splitstackshape" ,r-splitstackshape)))
4476 `(("r-knitr" ,r-knitr)))
4477 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4478 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4479 (description "This package provides more than 2000 annotated position
4480 frequency matrices from nine public sources, for multiple organisms.")
4481 (license license:artistic2.0)))
4483 (define-public r-motifbreakr
4485 (name "r-motifbreakr")
4489 (uri (bioconductor-uri "motifbreakR" version))
4491 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
4492 (properties `((upstream-name . "motifbreakR")))
4493 (build-system r-build-system)
4495 `(("r-biocgenerics" ,r-biocgenerics)
4496 ("r-biocparallel" ,r-biocparallel)
4497 ("r-biostrings" ,r-biostrings)
4498 ("r-bsgenome" ,r-bsgenome)
4499 ("r-genomeinfodb" ,r-genomeinfodb)
4500 ("r-genomicranges" ,r-genomicranges)
4501 ("r-grimport" ,r-grimport)
4503 ("r-iranges" ,r-iranges)
4504 ("r-matrixstats" ,r-matrixstats)
4505 ("r-motifdb" ,r-motifdb)
4506 ("r-motifstack" ,r-motifstack)
4507 ("r-rtracklayer" ,r-rtracklayer)
4508 ("r-s4vectors" ,r-s4vectors)
4509 ("r-stringr" ,r-stringr)
4510 ("r-summarizedexperiment" ,r-summarizedexperiment)
4511 ("r-tfmpvalue" ,r-tfmpvalue)
4512 ("r-variantannotation" ,r-variantannotation)))
4514 `(("r-knitr" ,r-knitr)))
4515 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4516 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4517 (description "This package allows biologists to judge in the first place
4518 whether the sequence surrounding the polymorphism is a good match, and in
4519 the second place how much information is gained or lost in one allele of
4520 the polymorphism relative to another. This package gives a choice of
4521 algorithms for interrogation of genomes with motifs from public sources:
4523 @item a weighted-sum probability matrix;
4524 @item log-probabilities;
4525 @item weighted by relative entropy.
4528 This package can predict effects for novel or previously described variants in
4529 public databases, making it suitable for tasks beyond the scope of its original
4530 design. Lastly, it can be used to interrogate any genome curated within
4532 (license license:gpl2+)))
4534 (define-public r-motifstack
4536 (name "r-motifstack")
4541 (uri (bioconductor-uri "motifStack" version))
4544 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
4545 (properties `((upstream-name . "motifStack")))
4546 (build-system r-build-system)
4548 `(("r-ade4" ,r-ade4)
4549 ("r-biostrings" ,r-biostrings)
4550 ("r-ggplot2" ,r-ggplot2)
4551 ("r-htmlwidgets" ,r-htmlwidgets)
4554 `(("r-knitr" ,r-knitr)))
4555 (home-page "https://bioconductor.org/packages/motifStack/")
4556 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4558 "The motifStack package is designed for graphic representation of
4559 multiple motifs with different similarity scores. It works with both DNA/RNA
4560 sequence motifs and amino acid sequence motifs. In addition, it provides the
4561 flexibility for users to customize the graphic parameters such as the font
4562 type and symbol colors.")
4563 (license license:gpl2+)))
4565 (define-public r-genomicscores
4567 (name "r-genomicscores")
4572 (uri (bioconductor-uri "GenomicScores" version))
4575 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
4576 (properties `((upstream-name . "GenomicScores")))
4577 (build-system r-build-system)
4579 `(("r-annotationhub" ,r-annotationhub)
4580 ("r-biobase" ,r-biobase)
4581 ("r-biocfilecache" ,r-biocfilecache)
4582 ("r-biocgenerics" ,r-biocgenerics)
4583 ("r-biocmanager" ,r-biocmanager)
4584 ("r-biostrings" ,r-biostrings)
4585 ("r-delayedarray" ,r-delayedarray)
4586 ("r-genomeinfodb" ,r-genomeinfodb)
4587 ("r-genomicranges" ,r-genomicranges)
4588 ("r-hdf5array" ,r-hdf5array)
4589 ("r-iranges" ,r-iranges)
4590 ("r-rhdf5" ,r-rhdf5)
4591 ("r-s4vectors" ,r-s4vectors)
4594 `(("r-knitr" ,r-knitr)))
4595 (home-page "https://github.com/rcastelo/GenomicScores/")
4596 (synopsis "Work with genome-wide position-specific scores")
4598 "This package provides infrastructure to store and access genome-wide
4599 position-specific scores within R and Bioconductor.")
4600 (license license:artistic2.0)))
4602 (define-public r-atacseqqc
4604 (name "r-atacseqqc")
4609 (uri (bioconductor-uri "ATACseqQC" version))
4612 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
4613 (properties `((upstream-name . "ATACseqQC")))
4614 (build-system r-build-system)
4616 `(("r-biocgenerics" ,r-biocgenerics)
4617 ("r-biostrings" ,r-biostrings)
4618 ("r-bsgenome" ,r-bsgenome)
4619 ("r-chippeakanno" ,r-chippeakanno)
4620 ("r-edger" ,r-edger)
4621 ("r-genomeinfodb" ,r-genomeinfodb)
4622 ("r-genomicalignments" ,r-genomicalignments)
4623 ("r-genomicranges" ,r-genomicranges)
4624 ("r-genomicscores" ,r-genomicscores)
4625 ("r-iranges" ,r-iranges)
4626 ("r-kernsmooth" ,r-kernsmooth)
4627 ("r-limma" ,r-limma)
4628 ("r-motifstack" ,r-motifstack)
4629 ("r-preseqr" ,r-preseqr)
4630 ("r-randomforest" ,r-randomforest)
4631 ("r-rsamtools" ,r-rsamtools)
4632 ("r-rtracklayer" ,r-rtracklayer)
4633 ("r-s4vectors" ,r-s4vectors)))
4635 `(("r-knitr" ,r-knitr)))
4636 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4637 (synopsis "ATAC-seq quality control")
4639 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4640 sequencing, is a rapid and sensitive method for chromatin accessibility
4641 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4642 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4643 assess whether their ATAC-seq experiment is successful. It includes
4644 diagnostic plots of fragment size distribution, proportion of mitochondria
4645 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4647 (license license:gpl2+)))
4649 (define-public r-gofuncr
4656 (uri (bioconductor-uri "GOfuncR" version))
4659 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
4660 (properties `((upstream-name . "GOfuncR")))
4661 (build-system r-build-system)
4663 `(("r-annotationdbi" ,r-annotationdbi)
4664 ("r-genomicranges" ,r-genomicranges)
4665 ("r-gtools" ,r-gtools)
4666 ("r-iranges" ,r-iranges)
4667 ("r-mapplots" ,r-mapplots)
4669 ("r-vioplot" ,r-vioplot)))
4671 `(("r-knitr" ,r-knitr)))
4672 (home-page "https://bioconductor.org/packages/GOfuncR/")
4673 (synopsis "Gene ontology enrichment using FUNC")
4675 "GOfuncR performs a gene ontology enrichment analysis based on the
4676 ontology enrichment software FUNC. GO-annotations are obtained from
4677 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4678 included in the package and updated regularly. GOfuncR provides the standard
4679 candidate vs background enrichment analysis using the hypergeometric test, as
4680 well as three additional tests:
4683 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4684 @item a binomial test that is used when genes are associated with two counts,
4686 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4687 associated with four counts.
4690 To correct for multiple testing and interdependency of the tests, family-wise
4691 error rates are computed based on random permutations of the gene-associated
4692 variables. GOfuncR also provides tools for exploring the ontology graph and
4693 the annotations, and options to take gene-length or spatial clustering of
4694 genes into account. It is also possible to provide custom gene coordinates,
4695 annotations and ontologies.")
4696 (license license:gpl2+)))
4698 (define-public r-abaenrichment
4700 (name "r-abaenrichment")
4705 (uri (bioconductor-uri "ABAEnrichment" version))
4708 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
4709 (properties `((upstream-name . "ABAEnrichment")))
4710 (build-system r-build-system)
4712 `(("r-abadata" ,r-abadata)
4713 ("r-data-table" ,r-data-table)
4714 ("r-gofuncr" ,r-gofuncr)
4715 ("r-gplots" ,r-gplots)
4716 ("r-gtools" ,r-gtools)
4717 ("r-rcpp" ,r-rcpp)))
4719 `(("r-knitr" ,r-knitr)))
4720 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4721 (synopsis "Gene expression enrichment in human brain regions")
4723 "The package ABAEnrichment is designed to test for enrichment of user
4724 defined candidate genes in the set of expressed genes in different human brain
4725 regions. The core function @code{aba_enrich} integrates the expression of the
4726 candidate gene set (averaged across donors) and the structural information of
4727 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4728 (license license:gpl2+)))
4730 (define-public r-annotationfuncs
4732 (name "r-annotationfuncs")
4737 (uri (bioconductor-uri "AnnotationFuncs" version))
4740 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
4742 `((upstream-name . "AnnotationFuncs")))
4743 (build-system r-build-system)
4745 `(("r-annotationdbi" ,r-annotationdbi)
4747 (home-page "https://www.iysik.com/r/annotationfuncs")
4748 (synopsis "Annotation translation functions")
4750 "This package provides functions for handling translating between
4751 different identifieres using the Biocore Data Team data-packages (e.g.
4752 @code{org.Bt.eg.db}).")
4753 (license license:gpl2)))
4755 (define-public r-annotationtools
4757 (name "r-annotationtools")
4762 (uri (bioconductor-uri "annotationTools" version))
4765 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
4767 `((upstream-name . "annotationTools")))
4768 (build-system r-build-system)
4769 (propagated-inputs `(("r-biobase" ,r-biobase)))
4770 (home-page "https://bioconductor.org/packages/annotationTools/")
4771 (synopsis "Annotate microarrays and perform gene expression analyses")
4773 "This package provides functions to annotate microarrays, find orthologs,
4774 and integrate heterogeneous gene expression profiles using annotation and
4775 other molecular biology information available as flat file database (plain
4777 ;; Any version of the GPL.
4778 (license (list license:gpl2+))))
4780 (define-public r-allelicimbalance
4782 (name "r-allelicimbalance")
4787 (uri (bioconductor-uri "AllelicImbalance" version))
4790 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
4792 `((upstream-name . "AllelicImbalance")))
4793 (build-system r-build-system)
4795 `(("r-annotationdbi" ,r-annotationdbi)
4796 ("r-biocgenerics" ,r-biocgenerics)
4797 ("r-biostrings" ,r-biostrings)
4798 ("r-bsgenome" ,r-bsgenome)
4799 ("r-genomeinfodb" ,r-genomeinfodb)
4800 ("r-genomicalignments" ,r-genomicalignments)
4801 ("r-genomicfeatures" ,r-genomicfeatures)
4802 ("r-genomicranges" ,r-genomicranges)
4803 ("r-gridextra" ,r-gridextra)
4805 ("r-iranges" ,r-iranges)
4806 ("r-lattice" ,r-lattice)
4807 ("r-latticeextra" ,r-latticeextra)
4809 ("r-rsamtools" ,r-rsamtools)
4810 ("r-s4vectors" ,r-s4vectors)
4811 ("r-seqinr" ,r-seqinr)
4812 ("r-summarizedexperiment" ,r-summarizedexperiment)
4813 ("r-variantannotation" ,r-variantannotation)))
4815 `(("r-knitr" ,r-knitr)))
4816 (home-page "https://github.com/pappewaio/AllelicImbalance")
4817 (synopsis "Investigate allele-specific expression")
4819 "This package provides a framework for allele-specific expression
4820 investigation using RNA-seq data.")
4821 (license license:gpl3)))
4823 (define-public r-aucell
4830 (uri (bioconductor-uri "AUCell" version))
4833 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
4834 (properties `((upstream-name . "AUCell")))
4835 (build-system r-build-system)
4837 `(("r-biocgenerics" ,r-biocgenerics)
4838 ("r-data-table" ,r-data-table)
4839 ("r-gseabase" ,r-gseabase)
4840 ("r-mixtools" ,r-mixtools)
4841 ("r-r-utils" ,r-r-utils)
4842 ("r-s4vectors" ,r-s4vectors)
4843 ("r-shiny" ,r-shiny)
4844 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4846 `(("r-knitr" ,r-knitr)))
4847 (home-page "https://bioconductor.org/packages/AUCell/")
4848 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4850 "AUCell identifies cells with active gene sets (e.g. signatures,
4851 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4852 Under the Curve} (AUC) to calculate whether a critical subset of the input
4853 gene set is enriched within the expressed genes for each cell. The
4854 distribution of AUC scores across all the cells allows exploring the relative
4855 expression of the signature. Since the scoring method is ranking-based,
4856 AUCell is independent of the gene expression units and the normalization
4857 procedure. In addition, since the cells are evaluated individually, it can
4858 easily be applied to bigger datasets, subsetting the expression matrix if
4860 (license license:gpl3)))
4862 (define-public r-ebimage
4869 (uri (bioconductor-uri "EBImage" version))
4872 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
4873 (properties `((upstream-name . "EBImage")))
4874 (build-system r-build-system)
4876 `(("r-abind" ,r-abind)
4877 ("r-biocgenerics" ,r-biocgenerics)
4878 ("r-fftwtools" ,r-fftwtools)
4879 ("r-htmltools" ,r-htmltools)
4880 ("r-htmlwidgets" ,r-htmlwidgets)
4882 ("r-locfit" ,r-locfit)
4884 ("r-rcurl" ,r-rcurl)
4885 ("r-tiff" ,r-tiff)))
4887 `(("r-knitr" ,r-knitr))) ; for vignettes
4888 (home-page "https://github.com/aoles/EBImage")
4889 (synopsis "Image processing and analysis toolbox for R")
4891 "EBImage provides general purpose functionality for image processing and
4892 analysis. In the context of (high-throughput) microscopy-based cellular
4893 assays, EBImage offers tools to segment cells and extract quantitative
4894 cellular descriptors. This allows the automation of such tasks using the R
4895 programming language and facilitates the use of other tools in the R
4896 environment for signal processing, statistical modeling, machine learning and
4897 visualization with image data.")
4898 ;; Any version of the LGPL.
4899 (license license:lgpl2.1+)))
4901 (define-public r-yamss
4908 (uri (bioconductor-uri "yamss" version))
4911 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
4912 (build-system r-build-system)
4914 `(("r-biocgenerics" ,r-biocgenerics)
4915 ("r-data-table" ,r-data-table)
4916 ("r-ebimage" ,r-ebimage)
4917 ("r-iranges" ,r-iranges)
4918 ("r-limma" ,r-limma)
4919 ("r-matrix" ,r-matrix)
4921 ("r-s4vectors" ,r-s4vectors)
4922 ("r-summarizedexperiment"
4923 ,r-summarizedexperiment)))
4925 `(("r-knitr" ,r-knitr)))
4926 (home-page "https://github.com/hansenlab/yamss")
4927 (synopsis "Tools for high-throughput metabolomics")
4929 "This package provides tools to analyze and visualize high-throughput
4930 metabolomics data acquired using chromatography-mass spectrometry. These tools
4931 preprocess data in a way that enables reliable and powerful differential
4933 (license license:artistic2.0)))
4935 (define-public r-gtrellis
4942 (uri (bioconductor-uri "gtrellis" version))
4945 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
4946 (build-system r-build-system)
4948 `(("r-circlize" ,r-circlize)
4949 ("r-genomicranges" ,r-genomicranges)
4950 ("r-getoptlong" ,r-getoptlong)
4951 ("r-iranges" ,r-iranges)))
4953 `(("r-knitr" ,r-knitr)))
4954 (home-page "https://github.com/jokergoo/gtrellis")
4955 (synopsis "Genome level Trellis layout")
4957 "Genome level Trellis graph visualizes genomic data conditioned by
4958 genomic categories (e.g. chromosomes). For each genomic category, multiple
4959 dimensional data which are represented as tracks describe different features
4960 from different aspects. This package provides high flexibility to arrange
4961 genomic categories and to add self-defined graphics in the plot.")
4962 (license license:expat)))
4964 (define-public r-somaticsignatures
4966 (name "r-somaticsignatures")
4971 (uri (bioconductor-uri "SomaticSignatures" version))
4974 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
4976 `((upstream-name . "SomaticSignatures")))
4977 (build-system r-build-system)
4979 `(("r-biobase" ,r-biobase)
4980 ("r-biostrings" ,r-biostrings)
4981 ("r-genomeinfodb" ,r-genomeinfodb)
4982 ("r-genomicranges" ,r-genomicranges)
4983 ("r-ggbio" ,r-ggbio)
4984 ("r-ggplot2" ,r-ggplot2)
4985 ("r-iranges" ,r-iranges)
4987 ("r-pcamethods" ,r-pcamethods)
4988 ("r-proxy" ,r-proxy)
4989 ("r-reshape2" ,r-reshape2)
4990 ("r-s4vectors" ,r-s4vectors)
4991 ("r-variantannotation" ,r-variantannotation)))
4993 `(("r-knitr" ,r-knitr)))
4994 (home-page "https://github.com/juliangehring/SomaticSignatures")
4995 (synopsis "Somatic signatures")
4997 "This package identifies mutational signatures of @dfn{single nucleotide
4998 variants} (SNVs). It provides a infrastructure related to the methodology
4999 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5000 decomposition algorithms.")
5001 (license license:expat)))
5003 (define-public r-yapsa
5010 (uri (bioconductor-uri "YAPSA" version))
5013 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5014 (properties `((upstream-name . "YAPSA")))
5015 (build-system r-build-system)
5017 `(("r-biostrings" ,r-biostrings)
5018 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5019 ("r-circlize" ,r-circlize)
5020 ("r-complexheatmap" ,r-complexheatmap)
5021 ("r-corrplot" ,r-corrplot)
5022 ("r-dendextend" ,r-dendextend)
5023 ("r-doparallel" ,r-doparallel)
5024 ("r-dplyr" ,r-dplyr)
5025 ("r-genomeinfodb" ,r-genomeinfodb)
5026 ("r-genomicranges" ,r-genomicranges)
5027 ("r-getoptlong" ,r-getoptlong)
5028 ("r-ggbeeswarm" ,r-ggbeeswarm)
5029 ("r-ggplot2" ,r-ggplot2)
5030 ("r-gridextra" ,r-gridextra)
5031 ("r-gtrellis" ,r-gtrellis)
5032 ("r-keggrest" ,r-keggrest)
5033 ("r-limsolve" ,r-limsolve)
5034 ("r-magrittr" ,r-magrittr)
5035 ("r-pmcmr" ,r-pmcmr)
5036 ("r-pracma" ,r-pracma)
5037 ("r-reshape2" ,r-reshape2)
5038 ("r-somaticsignatures" ,r-somaticsignatures)
5039 ("r-variantannotation" ,r-variantannotation)))
5041 `(("r-knitr" ,r-knitr)))
5042 (home-page "https://bioconductor.org/packages/YAPSA/")
5043 (synopsis "Yet another package for signature analysis")
5045 "This package provides functions and routines useful in the analysis of
5046 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5047 functions to perform a signature analysis with known signatures and a
5048 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5050 (license license:gpl3)))
5052 (define-public r-gcrma
5059 (uri (bioconductor-uri "gcrma" version))
5062 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5063 (build-system r-build-system)
5065 `(("r-affy" ,r-affy)
5066 ("r-affyio" ,r-affyio)
5067 ("r-biobase" ,r-biobase)
5068 ("r-biocmanager" ,r-biocmanager)
5069 ("r-biostrings" ,r-biostrings)
5070 ("r-xvector" ,r-xvector)))
5071 (home-page "https://bioconductor.org/packages/gcrma/")
5072 (synopsis "Background adjustment using sequence information")
5074 "Gcrma adjusts for background intensities in Affymetrix array data which
5075 include optical noise and @dfn{non-specific binding} (NSB). The main function
5076 @code{gcrma} converts background adjusted probe intensities to expression
5077 measures using the same normalization and summarization methods as a
5078 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5079 to estimate probe affinity to NSB. The sequence information is summarized in
5080 a more complex way than the simple GC content. Instead, the base types (A, T,
5081 G or C) at each position along the probe determine the affinity of each probe.
5082 The parameters of the position-specific base contributions to the probe
5083 affinity is estimated in an NSB experiment in which only NSB but no
5084 gene-specific binding is expected.")
5085 ;; Any version of the LGPL
5086 (license license:lgpl2.1+)))
5088 (define-public r-simpleaffy
5090 (name "r-simpleaffy")
5095 (uri (bioconductor-uri "simpleaffy" version))
5098 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5099 (build-system r-build-system)
5101 `(("r-affy" ,r-affy)
5102 ("r-biobase" ,r-biobase)
5103 ("r-biocgenerics" ,r-biocgenerics)
5104 ("r-gcrma" ,r-gcrma)
5105 ("r-genefilter" ,r-genefilter)))
5106 (home-page "https://bioconductor.org/packages/simpleaffy/")
5107 (synopsis "Very simple high level analysis of Affymetrix data")
5109 "This package provides high level functions for reading Affy @file{.CEL}
5110 files, phenotypic data, and then computing simple things with it, such as
5111 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5112 library. It also has some basic scatter plot functions and mechanisms for
5113 generating high resolution journal figures.")
5114 (license license:gpl2+)))
5116 (define-public r-yaqcaffy
5123 (uri (bioconductor-uri "yaqcaffy" version))
5126 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
5127 (build-system r-build-system)
5129 `(("r-simpleaffy" ,r-simpleaffy)))
5130 (home-page "https://bioconductor.org/packages/yaqcaffy/")
5131 (synopsis "Affymetrix quality control and reproducibility analysis")
5133 "This is a package that can be used for quality control of Affymetrix
5134 GeneChip expression data and reproducibility analysis of human whole genome
5135 chips with the MAQC reference datasets.")
5136 (license license:artistic2.0)))
5138 (define-public r-quantro
5145 (uri (bioconductor-uri "quantro" version))
5148 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
5149 (build-system r-build-system)
5151 `(("r-biobase" ,r-biobase)
5152 ("r-doparallel" ,r-doparallel)
5153 ("r-foreach" ,r-foreach)
5154 ("r-ggplot2" ,r-ggplot2)
5155 ("r-iterators" ,r-iterators)
5156 ("r-minfi" ,r-minfi)
5157 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5159 `(("r-knitr" ,r-knitr)))
5160 (home-page "https://bioconductor.org/packages/quantro/")
5161 (synopsis "Test for when to use quantile normalization")
5163 "This package provides a data-driven test for the assumptions of quantile
5164 normalization using raw data such as objects that inherit eSets (e.g.
5165 ExpressionSet, MethylSet). Group level information about each sample (such as
5166 Tumor / Normal status) must also be provided because the test assesses if
5167 there are global differences in the distributions between the user-defined
5169 (license license:gpl3+)))
5171 (define-public r-yarn
5178 (uri (bioconductor-uri "yarn" version))
5181 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
5182 (build-system r-build-system)
5184 `(("r-biobase" ,r-biobase)
5185 ("r-biomart" ,r-biomart)
5186 ("r-downloader" ,r-downloader)
5187 ("r-edger" ,r-edger)
5188 ("r-gplots" ,r-gplots)
5189 ("r-limma" ,r-limma)
5190 ("r-matrixstats" ,r-matrixstats)
5191 ("r-preprocesscore" ,r-preprocesscore)
5192 ("r-quantro" ,r-quantro)
5193 ("r-rcolorbrewer" ,r-rcolorbrewer)
5194 ("r-readr" ,r-readr)))
5196 `(("r-knitr" ,r-knitr)))
5197 (home-page "https://bioconductor.org/packages/yarn/")
5198 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5200 "Expedite large RNA-Seq analyses using a combination of previously
5201 developed tools. YARN is meant to make it easier for the user in performing
5202 basic mis-annotation quality control, filtering, and condition-aware
5203 normalization. YARN leverages many Bioconductor tools and statistical
5204 techniques to account for the large heterogeneity and sparsity found in very
5205 large RNA-seq experiments.")
5206 (license license:artistic2.0)))
5208 (define-public r-roar
5215 (uri (bioconductor-uri "roar" version))
5218 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
5219 (build-system r-build-system)
5221 `(("r-biocgenerics" ,r-biocgenerics)
5222 ("r-genomeinfodb" ,r-genomeinfodb)
5223 ("r-genomicalignments" ,r-genomicalignments)
5224 ("r-genomicranges" ,r-genomicranges)
5225 ("r-iranges" ,r-iranges)
5226 ("r-rtracklayer" ,r-rtracklayer)
5227 ("r-s4vectors" ,r-s4vectors)
5228 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5229 (home-page "https://github.com/vodkatad/roar/")
5230 (synopsis "Identify differential APA usage from RNA-seq alignments")
5232 "This package provides tools for identifying preferential usage of APA
5233 sites, comparing two biological conditions, starting from known alternative
5234 sites and alignments obtained from standard RNA-seq experiments.")
5235 (license license:gpl3)))
5237 (define-public r-xbseq
5244 (uri (bioconductor-uri "XBSeq" version))
5247 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
5248 (properties `((upstream-name . "XBSeq")))
5249 (build-system r-build-system)
5251 `(("r-biobase" ,r-biobase)
5252 ("r-deseq2" ,r-deseq2)
5253 ("r-dplyr" ,r-dplyr)
5254 ("r-ggplot2" ,r-ggplot2)
5255 ("r-locfit" ,r-locfit)
5256 ("r-magrittr" ,r-magrittr)
5257 ("r-matrixstats" ,r-matrixstats)
5258 ("r-pracma" ,r-pracma)
5259 ("r-roar" ,r-roar)))
5261 `(("r-knitr" ,r-knitr)))
5262 (home-page "https://github.com/Liuy12/XBSeq")
5263 (synopsis "Test for differential expression for RNA-seq data")
5265 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5266 expression} (DE), where a statistical model was established based on the
5267 assumption that observed signals are the convolution of true expression
5268 signals and sequencing noises. The mapped reads in non-exonic regions are
5269 considered as sequencing noises, which follows a Poisson distribution. Given
5270 measurable observed signal and background noise from RNA-seq data, true
5271 expression signals, assuming governed by the negative binomial distribution,
5272 can be delineated and thus the accurate detection of differential expressed
5274 (license license:gpl3+)))
5276 (define-public r-massspecwavelet
5278 (name "r-massspecwavelet")
5283 (uri (bioconductor-uri "MassSpecWavelet" version))
5286 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
5288 `((upstream-name . "MassSpecWavelet")))
5289 (build-system r-build-system)
5291 `(("r-waveslim" ,r-waveslim)))
5292 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5293 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5295 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5296 data mainly through the use of wavelet transforms. It supports peak detection
5297 based on @dfn{Continuous Wavelet Transform} (CWT).")
5298 (license license:lgpl2.0+)))
5300 (define-public r-xcms
5307 (uri (bioconductor-uri "xcms" version))
5310 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
5311 (build-system r-build-system)
5313 `(("r-biobase" ,r-biobase)
5314 ("r-biocgenerics" ,r-biocgenerics)
5315 ("r-biocparallel" ,r-biocparallel)
5316 ("r-iranges" ,r-iranges)
5317 ("r-lattice" ,r-lattice)
5318 ("r-massspecwavelet" ,r-massspecwavelet)
5319 ("r-mscoreutils" ,r-mscoreutils)
5320 ("r-msnbase" ,r-msnbase)
5323 ("r-protgenerics" ,r-protgenerics)
5325 ("r-rcolorbrewer" ,r-rcolorbrewer)
5326 ("r-robustbase" ,r-robustbase)
5327 ("r-s4vectors" ,r-s4vectors)
5328 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5330 `(("r-knitr" ,r-knitr)))
5331 (home-page "https://bioconductor.org/packages/xcms/")
5332 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5334 "This package provides a framework for processing and visualization of
5335 chromatographically separated and single-spectra mass spectral data. It
5336 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5337 data for high-throughput, untargeted analyte profiling.")
5338 (license license:gpl2+)))
5340 (define-public r-wrench
5347 (uri (bioconductor-uri "Wrench" version))
5350 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
5351 (properties `((upstream-name . "Wrench")))
5352 (build-system r-build-system)
5354 `(("r-limma" ,r-limma)
5355 ("r-locfit" ,r-locfit)
5356 ("r-matrixstats" ,r-matrixstats)))
5358 `(("r-knitr" ,r-knitr)))
5359 (home-page "https://github.com/HCBravoLab/Wrench")
5360 (synopsis "Wrench normalization for sparse count data")
5362 "Wrench is a package for normalization sparse genomic count data, like
5363 that arising from 16s metagenomic surveys.")
5364 (license license:artistic2.0)))
5366 (define-public r-wiggleplotr
5368 (name "r-wiggleplotr")
5373 (uri (bioconductor-uri "wiggleplotr" version))
5376 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
5377 (build-system r-build-system)
5379 `(("r-assertthat" ,r-assertthat)
5380 ("r-cowplot" ,r-cowplot)
5381 ("r-dplyr" ,r-dplyr)
5382 ("r-genomeinfodb" ,r-genomeinfodb)
5383 ("r-genomicranges" ,r-genomicranges)
5384 ("r-ggplot2" ,r-ggplot2)
5385 ("r-iranges" ,r-iranges)
5386 ("r-purrr" ,r-purrr)
5387 ("r-rtracklayer" ,r-rtracklayer)
5388 ("r-s4vectors" ,r-s4vectors)))
5390 `(("r-knitr" ,r-knitr)))
5391 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5392 (synopsis "Make read coverage plots from BigWig files")
5394 "This package provides tools to visualize read coverage from sequencing
5395 experiments together with genomic annotations (genes, transcripts, peaks).
5396 Introns of long transcripts can be rescaled to a fixed length for better
5397 visualization of exonic read coverage.")
5398 (license license:asl2.0)))
5400 (define-public r-widgettools
5402 (name "r-widgettools")
5407 (uri (bioconductor-uri "widgetTools" version))
5410 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
5411 (properties `((upstream-name . "widgetTools")))
5412 (build-system r-build-system)
5413 (home-page "https://bioconductor.org/packages/widgetTools/")
5414 (synopsis "Tools for creating interactive tcltk widgets")
5416 "This package contains tools to support the construction of tcltk
5418 ;; Any version of the LGPL.
5419 (license license:lgpl3+)))
5421 (define-public r-webbioc
5428 (uri (bioconductor-uri "webbioc" version))
5431 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
5432 (build-system r-build-system)
5434 `(("netpbm" ,netpbm)
5437 `(("r-affy" ,r-affy)
5438 ("r-annaffy" ,r-annaffy)
5439 ("r-biobase" ,r-biobase)
5440 ("r-biocmanager" ,r-biocmanager)
5441 ("r-gcrma" ,r-gcrma)
5442 ("r-multtest" ,r-multtest)
5443 ("r-qvalue" ,r-qvalue)
5445 (home-page "https://www.bioconductor.org/")
5446 (synopsis "Bioconductor web interface")
5448 "This package provides an integrated web interface for doing microarray
5449 analysis using several of the Bioconductor packages. It is intended to be
5450 deployed as a centralized bioinformatics resource for use by many users.
5451 Currently only Affymetrix oligonucleotide analysis is supported.")
5452 (license license:gpl2+)))
5454 (define-public r-zfpkm
5461 (uri (bioconductor-uri "zFPKM" version))
5464 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
5465 (properties `((upstream-name . "zFPKM")))
5466 (build-system r-build-system)
5468 `(("r-checkmate" ,r-checkmate)
5469 ("r-dplyr" ,r-dplyr)
5470 ("r-ggplot2" ,r-ggplot2)
5471 ("r-summarizedexperiment" ,r-summarizedexperiment)
5472 ("r-tidyr" ,r-tidyr)))
5474 `(("r-knitr" ,r-knitr)))
5475 (home-page "https://github.com/ronammar/zFPKM/")
5476 (synopsis "Functions to facilitate zFPKM transformations")
5478 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5479 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5481 (license license:gpl3)))
5483 (define-public r-rbowtie2
5490 (uri (bioconductor-uri "Rbowtie2" version))
5493 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
5494 (properties `((upstream-name . "Rbowtie2")))
5495 (build-system r-build-system)
5499 `(("r-knitr" ,r-knitr)))
5500 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5501 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5503 "This package provides an R wrapper of the popular @code{bowtie2}
5504 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5505 rapid adapter trimming, identification, and read merging.")
5506 (license license:gpl3+)))
5508 (define-public r-progeny
5515 (uri (bioconductor-uri "progeny" version))
5518 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
5519 (build-system r-build-system)
5521 `(("r-biobase" ,r-biobase)
5522 ("r-dplyr" ,r-dplyr)
5523 ("r-ggplot2" ,r-ggplot2)
5524 ("r-ggrepel" ,r-ggrepel)
5525 ("r-gridextra" ,r-gridextra)
5526 ("r-tidyr" ,r-tidyr)))
5528 `(("r-knitr" ,r-knitr)))
5529 (home-page "https://github.com/saezlab/progeny")
5530 (synopsis "Pathway responsive gene activity inference")
5532 "This package provides a function to infer pathway activity from gene
5533 expression. It contains the linear model inferred in the publication
5534 \"Perturbation-response genes reveal signaling footprints in cancer gene
5536 (license license:asl2.0)))
5538 (define-public r-arrmnormalization
5540 (name "r-arrmnormalization")
5545 (uri (bioconductor-uri "ARRmNormalization" version))
5548 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
5550 `((upstream-name . "ARRmNormalization")))
5551 (build-system r-build-system)
5552 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5553 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5554 (synopsis "Adaptive robust regression normalization for methylation data")
5556 "This is a package to perform the @dfn{Adaptive Robust Regression
5557 method} (ARRm) for the normalization of methylation data from the Illumina
5558 Infinium HumanMethylation 450k assay.")
5559 (license license:artistic2.0)))
5561 (define-public r-biocfilecache
5563 (name "r-biocfilecache")
5568 (uri (bioconductor-uri "BiocFileCache" version))
5571 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
5572 (properties `((upstream-name . "BiocFileCache")))
5573 (build-system r-build-system)
5575 `(("r-curl" ,r-curl)
5577 ("r-dbplyr" ,r-dbplyr)
5578 ("r-dplyr" ,r-dplyr)
5580 ("r-rappdirs" ,r-rappdirs)
5581 ("r-rsqlite" ,r-rsqlite)))
5583 `(("r-knitr" ,r-knitr)))
5584 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5585 (synopsis "Manage files across sessions")
5587 "This package creates a persistent on-disk cache of files that the user
5588 can add, update, and retrieve. It is useful for managing resources (such as
5589 custom Txdb objects) that are costly or difficult to create, web resources,
5590 and data files used across sessions.")
5591 (license license:artistic2.0)))
5593 (define-public r-iclusterplus
5595 (name "r-iclusterplus")
5600 (uri (bioconductor-uri "iClusterPlus" version))
5603 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
5604 (properties `((upstream-name . "iClusterPlus")))
5605 (build-system r-build-system)
5606 (native-inputs `(("gfortran" ,gfortran)))
5607 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5608 (synopsis "Integrative clustering of multi-type genomic data")
5610 "iClusterPlus is developed for integrative clustering analysis of
5611 multi-type genomic data and is an enhanced version of iCluster proposed and
5612 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5613 from the experiments where biological samples (e.g. tumor samples) are
5614 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5615 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5616 on. In the iClusterPlus model, binary observations such as somatic mutation
5617 are modeled as Binomial processes; categorical observations such as copy
5618 number states are realizations of Multinomial random variables; counts are
5619 modeled as Poisson random processes; and continuous measures are modeled by
5620 Gaussian distributions.")
5621 (license license:gpl2+)))
5623 (define-public r-rbowtie
5630 (uri (bioconductor-uri "Rbowtie" version))
5633 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
5634 (properties `((upstream-name . "Rbowtie")))
5635 (build-system r-build-system)
5639 `(("r-knitr" ,r-knitr)))
5640 (home-page "https://bioconductor.org/packages/Rbowtie/")
5641 (synopsis "R bowtie wrapper")
5643 "This package provides an R wrapper around the popular bowtie short read
5644 aligner and around SpliceMap, a de novo splice junction discovery and
5646 (license license:artistic2.0)))
5648 (define-public r-sgseq
5655 (uri (bioconductor-uri "SGSeq" version))
5658 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
5659 (properties `((upstream-name . "SGSeq")))
5660 (build-system r-build-system)
5662 `(("r-annotationdbi" ,r-annotationdbi)
5663 ("r-biocgenerics" ,r-biocgenerics)
5664 ("r-biostrings" ,r-biostrings)
5665 ("r-genomeinfodb" ,r-genomeinfodb)
5666 ("r-genomicalignments" ,r-genomicalignments)
5667 ("r-genomicfeatures" ,r-genomicfeatures)
5668 ("r-genomicranges" ,r-genomicranges)
5669 ("r-igraph" ,r-igraph)
5670 ("r-iranges" ,r-iranges)
5671 ("r-rsamtools" ,r-rsamtools)
5672 ("r-rtracklayer" ,r-rtracklayer)
5673 ("r-runit" ,r-runit)
5674 ("r-s4vectors" ,r-s4vectors)
5675 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5677 `(("r-knitr" ,r-knitr)))
5678 (home-page "https://bioconductor.org/packages/SGSeq/")
5679 (synopsis "Splice event prediction and quantification from RNA-seq data")
5681 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5682 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5683 represented as a splice graph, which can be obtained from existing annotation
5684 or predicted from the mapped sequence reads. Splice events are identified
5685 from the graph and are quantified locally using structurally compatible reads
5686 at the start or end of each splice variant. The software includes functions
5687 for splice event prediction, quantification, visualization and
5689 (license license:artistic2.0)))
5691 (define-public r-rhisat2
5698 (uri (bioconductor-uri "Rhisat2" version))
5701 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
5702 (properties `((upstream-name . "Rhisat2")))
5703 (build-system r-build-system)
5706 (modify-phases %standard-phases
5707 (add-after 'unpack 'make-reproducible
5709 (substitute* "src/Makefile"
5710 (("`hostname`") "guix")
5712 ;; Avoid shelling out to "which".
5713 (("^CC =.*") (which "gcc"))
5714 (("^CPP =.*") (which "g++")))
5717 `(("r-genomicfeatures" ,r-genomicfeatures)
5718 ("r-genomicranges" ,r-genomicranges)
5719 ("r-sgseq" ,r-sgseq)))
5721 `(("r-knitr" ,r-knitr)))
5722 (home-page "https://github.com/fmicompbio/Rhisat2")
5723 (synopsis "R Wrapper for HISAT2 sequence aligner")
5725 "This package provides an R interface to the HISAT2 spliced short-read
5726 aligner by Kim et al. (2015). The package contains wrapper functions to
5727 create a genome index and to perform the read alignment to the generated
5729 (license license:gpl3)))
5731 (define-public r-quasr
5738 (uri (bioconductor-uri "QuasR" version))
5741 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
5742 (properties `((upstream-name . "QuasR")))
5743 (build-system r-build-system)
5745 `(("r-annotationdbi" ,r-annotationdbi)
5746 ("r-biobase" ,r-biobase)
5747 ("r-biocgenerics" ,r-biocgenerics)
5748 ("r-biocmanager" ,r-biocmanager)
5749 ("r-biocparallel" ,r-biocparallel)
5750 ("r-biostrings" ,r-biostrings)
5751 ("r-bsgenome" ,r-bsgenome)
5752 ("r-genomeinfodb" ,r-genomeinfodb)
5753 ("r-genomicalignments" ,r-genomicalignments)
5754 ("r-genomicfeatures" ,r-genomicfeatures)
5755 ("r-genomicfiles" ,r-genomicfiles)
5756 ("r-genomicranges" ,r-genomicranges)
5757 ("r-iranges" ,r-iranges)
5758 ("r-rbowtie" ,r-rbowtie)
5759 ("r-rhisat2" ,r-rhisat2)
5760 ("r-rhtslib" ,r-rhtslib)
5761 ("r-rsamtools" ,r-rsamtools)
5762 ("r-rtracklayer" ,r-rtracklayer)
5763 ("r-s4vectors" ,r-s4vectors)
5764 ("r-shortread" ,r-shortread)))
5766 `(("r-knitr" ,r-knitr)))
5767 (home-page "https://bioconductor.org/packages/QuasR/")
5768 (synopsis "Quantify and annotate short reads in R")
5770 "This package provides a framework for the quantification and analysis of
5771 short genomic reads. It covers a complete workflow starting from raw sequence
5772 reads, over creation of alignments and quality control plots, to the
5773 quantification of genomic regions of interest.")
5774 (license license:gpl2)))
5776 (define-public r-rqc
5783 (uri (bioconductor-uri "Rqc" version))
5786 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
5787 (properties `((upstream-name . "Rqc")))
5788 (build-system r-build-system)
5790 `(("r-biocgenerics" ,r-biocgenerics)
5791 ("r-biocparallel" ,r-biocparallel)
5792 ("r-biocstyle" ,r-biocstyle)
5793 ("r-biostrings" ,r-biostrings)
5794 ("r-biovizbase" ,r-biovizbase)
5795 ("r-genomicalignments" ,r-genomicalignments)
5796 ("r-genomicfiles" ,r-genomicfiles)
5797 ("r-ggplot2" ,r-ggplot2)
5798 ("r-iranges" ,r-iranges)
5799 ("r-knitr" ,r-knitr)
5800 ("r-markdown" ,r-markdown)
5803 ("r-reshape2" ,r-reshape2)
5804 ("r-rsamtools" ,r-rsamtools)
5805 ("r-s4vectors" ,r-s4vectors)
5806 ("r-shiny" ,r-shiny)
5807 ("r-shortread" ,r-shortread)))
5809 `(("r-knitr" ,r-knitr)))
5810 (home-page "https://github.com/labbcb/Rqc")
5811 (synopsis "Quality control tool for high-throughput sequencing data")
5813 "Rqc is an optimized tool designed for quality control and assessment of
5814 high-throughput sequencing data. It performs parallel processing of entire
5815 files and produces a report which contains a set of high-resolution
5817 (license license:gpl2+)))
5819 (define-public r-birewire
5826 (uri (bioconductor-uri "BiRewire" version))
5829 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
5830 (properties `((upstream-name . "BiRewire")))
5831 (build-system r-build-system)
5833 `(("r-igraph" ,r-igraph)
5834 ("r-matrix" ,r-matrix)
5836 ("r-tsne" ,r-tsne)))
5837 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5838 (synopsis "Tools for randomization of bipartite graphs")
5840 "This package provides functions for bipartite network rewiring through N
5841 consecutive switching steps and for the computation of the minimal number of
5842 switching steps to be performed in order to maximise the dissimilarity with
5843 respect to the original network. It includes functions for the analysis of
5844 the introduced randomness across the switching steps and several other
5845 routines to analyse the resulting networks and their natural projections.")
5846 (license license:gpl3)))
5848 (define-public r-birta
5855 (uri (bioconductor-uri "birta" version))
5858 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5859 (build-system r-build-system)
5861 `(("r-biobase" ,r-biobase)
5862 ("r-limma" ,r-limma)
5863 ("r-mass" ,r-mass)))
5864 (home-page "https://bioconductor.org/packages/birta")
5865 (synopsis "Bayesian inference of regulation of transcriptional activity")
5867 "Expression levels of mRNA molecules are regulated by different
5868 processes, comprising inhibition or activation by transcription factors and
5869 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5870 Inference of Regulation of Transcriptional Activity) uses the regulatory
5871 networks of transcription factors and miRNAs together with mRNA and miRNA
5872 expression data to predict switches in regulatory activity between two
5873 conditions. A Bayesian network is used to model the regulatory structure and
5874 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5875 (license license:gpl2+)))
5877 (define-public r-multidataset
5879 (name "r-multidataset")
5884 (uri (bioconductor-uri "MultiDataSet" version))
5887 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
5888 (properties `((upstream-name . "MultiDataSet")))
5889 (build-system r-build-system)
5891 `(("r-biobase" ,r-biobase)
5892 ("r-biocgenerics" ,r-biocgenerics)
5893 ("r-genomicranges" ,r-genomicranges)
5894 ("r-ggplot2" ,r-ggplot2)
5895 ("r-ggrepel" ,r-ggrepel)
5896 ("r-iranges" ,r-iranges)
5897 ("r-limma" ,r-limma)
5898 ("r-qqman" ,r-qqman)
5899 ("r-s4vectors" ,r-s4vectors)
5900 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5902 `(("r-knitr" ,r-knitr)))
5903 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5904 (synopsis "Implementation of MultiDataSet and ResultSet")
5906 "This package provides an implementation of the BRGE's (Bioinformatic
5907 Research Group in Epidemiology from Center for Research in Environmental
5908 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5909 integrating multi omics data sets and ResultSet is a container for omics
5910 results. This package contains base classes for MEAL and rexposome
5912 (license license:expat)))
5914 (define-public r-ropls
5921 (uri (bioconductor-uri "ropls" version))
5924 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
5925 (build-system r-build-system)
5927 `(("r-biobase" ,r-biobase)
5928 ("r-multidataset" ,r-multidataset)))
5930 `(("r-knitr" ,r-knitr))) ; for vignettes
5931 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5932 (synopsis "Multivariate analysis and feature selection of omics data")
5934 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5935 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5936 regression, classification, and feature selection of omics data where the
5937 number of variables exceeds the number of samples and with multicollinearity
5938 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5939 separately model the variation correlated (predictive) to the factor of
5940 interest and the uncorrelated (orthogonal) variation. While performing
5941 similarly to PLS, OPLS facilitates interpretation.
5943 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5944 analysis and feature selection of omics data. In addition to scores, loadings
5945 and weights plots, the package provides metrics and graphics to determine the
5946 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5947 validity of the model by permutation testing, detect outliers, and perform
5948 feature selection (e.g. with Variable Importance in Projection or regression
5950 (license license:cecill)))
5952 (define-public r-biosigner
5954 (name "r-biosigner")
5959 (uri (bioconductor-uri "biosigner" version))
5962 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
5963 (build-system r-build-system)
5965 `(("r-biobase" ,r-biobase)
5966 ("r-e1071" ,r-e1071)
5967 ("r-multidataset" ,r-multidataset)
5968 ("r-randomforest" ,r-randomforest)
5969 ("r-ropls" ,r-ropls)))
5971 `(("r-knitr" ,r-knitr)))
5972 (home-page "https://bioconductor.org/packages/biosigner/")
5973 (synopsis "Signature discovery from omics data")
5975 "Feature selection is critical in omics data analysis to extract
5976 restricted and meaningful molecular signatures from complex and high-dimension
5977 data, and to build robust classifiers. This package implements a method to
5978 assess the relevance of the variables for the prediction performances of the
5979 classifier. The approach can be run in parallel with the PLS-DA, Random
5980 Forest, and SVM binary classifiers. The signatures and the corresponding
5981 'restricted' models are returned, enabling future predictions on new
5983 (license license:cecill)))
5985 (define-public r-annotatr
5992 (uri (bioconductor-uri "annotatr" version))
5995 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
5996 (build-system r-build-system)
5998 `(("r-annotationdbi" ,r-annotationdbi)
5999 ("r-annotationhub" ,r-annotationhub)
6000 ("r-dplyr" ,r-dplyr)
6001 ("r-genomeinfodb" ,r-genomeinfodb)
6002 ("r-genomicfeatures" ,r-genomicfeatures)
6003 ("r-genomicranges" ,r-genomicranges)
6004 ("r-ggplot2" ,r-ggplot2)
6005 ("r-iranges" ,r-iranges)
6006 ("r-readr" ,r-readr)
6007 ("r-regioner" ,r-regioner)
6008 ("r-reshape2" ,r-reshape2)
6009 ("r-rtracklayer" ,r-rtracklayer)
6010 ("r-s4vectors" ,r-s4vectors)))
6012 `(("r-knitr" ,r-knitr)))
6013 (home-page "https://bioconductor.org/packages/annotatr/")
6014 (synopsis "Annotation of genomic regions to genomic annotations")
6016 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6017 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6018 to investigate the intersecting genomic annotations. Such annotations include
6019 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6020 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6021 enhancers. The annotatr package provides an easy way to summarize and
6022 visualize the intersection of genomic sites/regions with genomic
6024 (license license:gpl3)))
6026 (define-public r-rsubread
6033 (uri (bioconductor-uri "Rsubread" version))
6036 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
6037 (properties `((upstream-name . "Rsubread")))
6038 (build-system r-build-system)
6039 (inputs `(("zlib" ,zlib)))
6041 `(("r-matrix" ,r-matrix)))
6042 (home-page "https://bioconductor.org/packages/Rsubread/")
6043 (synopsis "Subread sequence alignment and counting for R")
6045 "This package provides tools for alignment, quantification and analysis
6046 of second and third generation sequencing data. It includes functionality for
6047 read mapping, read counting, SNP calling, structural variant detection and
6048 gene fusion discovery. It can be applied to all major sequencing techologies
6049 and to both short and long sequence reads.")
6050 (license license:gpl3)))
6052 (define-public r-flowutils
6054 (name "r-flowutils")
6059 (uri (bioconductor-uri "flowUtils" version))
6062 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6063 (properties `((upstream-name . "flowUtils")))
6064 (build-system r-build-system)
6066 `(("r-biobase" ,r-biobase)
6067 ("r-corpcor" ,r-corpcor)
6068 ("r-flowcore" ,r-flowcore)
6069 ("r-graph" ,r-graph)
6070 ("r-runit" ,r-runit)
6072 (home-page "https://github.com/jspidlen/flowUtils")
6073 (synopsis "Utilities for flow cytometry")
6075 "This package provides utilities for flow cytometry data.")
6076 (license license:artistic2.0)))
6078 (define-public r-consensusclusterplus
6080 (name "r-consensusclusterplus")
6085 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6088 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6090 `((upstream-name . "ConsensusClusterPlus")))
6091 (build-system r-build-system)
6094 ("r-biobase" ,r-biobase)
6095 ("r-cluster" ,r-cluster)))
6096 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6097 (synopsis "Clustering algorithm")
6099 "This package provides an implementation of an algorithm for determining
6100 cluster count and membership by stability evidence in unsupervised analysis.")
6101 (license license:gpl2)))
6103 (define-public r-cytolib
6110 (uri (bioconductor-uri "cytolib" version))
6113 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
6114 (properties `((upstream-name . "cytolib")))
6115 (build-system r-build-system)
6118 (modify-phases %standard-phases
6119 (add-after 'unpack 'fix-linking
6121 (substitute* "src/Makevars.in"
6122 ;; This is to avoid having a plain directory on the list of
6123 ;; libraries to link.
6124 (("\\(RHDF5_LIBS\\)" match)
6125 (string-append match "/libhdf5.a")))
6128 `(("r-knitr" ,r-knitr)
6129 ("pkg-config" ,pkg-config)))
6133 ("r-rcpparmadillo" ,r-rcpparmadillo)
6134 ("r-rcppparallel" ,r-rcppparallel)
6135 ("r-rhdf5lib" ,r-rhdf5lib)
6136 ("r-rprotobuflib" ,r-rprotobuflib)))
6137 (home-page "https://bioconductor.org/packages/cytolib/")
6138 (synopsis "C++ infrastructure for working with gated cytometry")
6140 "This package provides the core data structure and API to represent and
6141 interact with gated cytometry data.")
6142 (license license:artistic2.0)))
6144 (define-public r-flowcore
6151 (uri (bioconductor-uri "flowCore" version))
6154 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
6155 (properties `((upstream-name . "flowCore")))
6156 (build-system r-build-system)
6159 ("r-biobase" ,r-biobase)
6160 ("r-biocgenerics" ,r-biocgenerics)
6161 ("r-cytolib" ,r-cytolib)
6162 ("r-matrixstats" ,r-matrixstats)
6164 ("r-rcpparmadillo" ,r-rcpparmadillo)
6165 ("r-rprotobuflib" ,r-rprotobuflib)
6166 ("r-s4vectors" ,r-s4vectors)))
6168 `(("r-knitr" ,r-knitr)))
6169 (home-page "https://bioconductor.org/packages/flowCore")
6170 (synopsis "Basic structures for flow cytometry data")
6172 "This package provides S4 data structures and basic functions to deal
6173 with flow cytometry data.")
6174 (license license:artistic2.0)))
6176 (define-public r-flowmeans
6178 (name "r-flowmeans")
6183 (uri (bioconductor-uri "flowMeans" version))
6186 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
6187 (properties `((upstream-name . "flowMeans")))
6188 (build-system r-build-system)
6190 `(("r-biobase" ,r-biobase)
6191 ("r-feature" ,r-feature)
6192 ("r-flowcore" ,r-flowcore)
6193 ("r-rrcov" ,r-rrcov)))
6194 (home-page "https://bioconductor.org/packages/flowMeans")
6195 (synopsis "Non-parametric flow cytometry data gating")
6197 "This package provides tools to identify cell populations in Flow
6198 Cytometry data using non-parametric clustering and segmented-regression-based
6199 change point detection.")
6200 (license license:artistic2.0)))
6202 (define-public r-ncdfflow
6209 (uri (bioconductor-uri "ncdfFlow" version))
6212 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
6213 (properties `((upstream-name . "ncdfFlow")))
6214 (build-system r-build-system)
6217 (modify-phases %standard-phases
6218 (add-after 'unpack 'fix-linking
6220 (substitute* "src/Makevars"
6221 ;; This is to avoid having a plain directory on the list of
6222 ;; libraries to link.
6223 (("\\(RHDF5_LIBS\\)" match)
6224 (string-append match "/libhdf5.a")))
6228 ("r-biobase" ,r-biobase)
6229 ("r-biocgenerics" ,r-biocgenerics)
6230 ("r-flowcore" ,r-flowcore)
6232 ("r-rcpparmadillo" ,r-rcpparmadillo)
6233 ("r-rhdf5lib" ,r-rhdf5lib)
6234 ("r-zlibbioc" ,r-zlibbioc)))
6236 `(("r-knitr" ,r-knitr)))
6237 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6238 (synopsis "HDF5 based storage for flow cytometry data")
6240 "This package provides HDF5 storage based methods and functions for
6241 manipulation of flow cytometry data.")
6242 (license license:artistic2.0)))
6244 (define-public r-ggcyto
6251 (uri (bioconductor-uri "ggcyto" version))
6254 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
6255 (properties `((upstream-name . "ggcyto")))
6256 (build-system r-build-system)
6258 `(("r-data-table" ,r-data-table)
6259 ("r-flowcore" ,r-flowcore)
6260 ("r-flowworkspace" ,r-flowworkspace)
6261 ("r-ggplot2" ,r-ggplot2)
6262 ("r-gridextra" ,r-gridextra)
6263 ("r-hexbin" ,r-hexbin)
6264 ("r-ncdfflow" ,r-ncdfflow)
6266 ("r-rcolorbrewer" ,r-rcolorbrewer)
6267 ("r-rlang" ,r-rlang)
6268 ("r-scales" ,r-scales)))
6270 `(("r-knitr" ,r-knitr)))
6271 (home-page "https://github.com/RGLab/ggcyto/issues")
6272 (synopsis "Visualize Cytometry data with ggplot")
6274 "With the dedicated fortify method implemented for @code{flowSet},
6275 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6276 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6277 and some custom layers also make it easy to add gates and population
6278 statistics to the plot.")
6279 (license license:artistic2.0)))
6281 (define-public r-flowviz
6288 (uri (bioconductor-uri "flowViz" version))
6291 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
6292 (properties `((upstream-name . "flowViz")))
6293 (build-system r-build-system)
6295 `(("r-biobase" ,r-biobase)
6296 ("r-flowcore" ,r-flowcore)
6297 ("r-hexbin" ,r-hexbin)
6298 ("r-idpmisc" ,r-idpmisc)
6299 ("r-kernsmooth" ,r-kernsmooth)
6300 ("r-lattice" ,r-lattice)
6301 ("r-latticeextra" ,r-latticeextra)
6303 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6305 `(("r-knitr" ,r-knitr)))
6306 (home-page "https://bioconductor.org/packages/flowViz/")
6307 (synopsis "Visualization for flow cytometry")
6309 "This package provides visualization tools for flow cytometry data.")
6310 (license license:artistic2.0)))
6312 (define-public r-flowclust
6314 (name "r-flowclust")
6319 (uri (bioconductor-uri "flowClust" version))
6322 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
6323 (properties `((upstream-name . "flowClust")))
6324 (build-system r-build-system)
6327 (list "--configure-args=--enable-bundled-gsl=no")))
6329 `(("r-biobase" ,r-biobase)
6330 ("r-biocgenerics" ,r-biocgenerics)
6332 ("r-corpcor" ,r-corpcor)
6333 ("r-ellipse" ,r-ellipse)
6334 ("r-flowcore" ,r-flowcore)
6335 ("r-flowviz" ,r-flowviz)
6336 ("r-graph" ,r-graph)
6337 ("r-mnormt" ,r-mnormt)))
6341 `(("pkg-config" ,pkg-config)
6342 ("r-knitr" ,r-knitr)))
6343 (home-page "https://bioconductor.org/packages/flowClust")
6344 (synopsis "Clustering for flow cytometry")
6346 "This package provides robust model-based clustering using a t-mixture
6347 model with Box-Cox transformation.")
6348 (license license:artistic2.0)))
6350 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6351 ;; make it use our protobuf package instead.
6352 (define-public r-rprotobuflib
6354 (name "r-rprotobuflib")
6359 (uri (bioconductor-uri "RProtoBufLib" version))
6362 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
6363 (properties `((upstream-name . "RProtoBufLib")))
6364 (build-system r-build-system)
6367 (modify-phases %standard-phases
6368 (add-after 'unpack 'unpack-bundled-sources
6370 (with-directory-excursion "src"
6371 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6374 `(("r-knitr" ,r-knitr)))
6375 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6376 (synopsis "C++ headers and static libraries of Protocol buffers")
6378 "This package provides the headers and static library of Protocol buffers
6379 for other R packages to compile and link against.")
6380 (license license:bsd-3)))
6382 (define-public r-flowworkspace
6384 (name "r-flowworkspace")
6389 (uri (bioconductor-uri "flowWorkspace" version))
6392 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
6393 (properties `((upstream-name . "flowWorkspace")))
6394 (build-system r-build-system)
6397 (modify-phases %standard-phases
6398 (add-after 'unpack 'fix-linking
6400 (substitute* "src/Makevars"
6401 ;; This is to avoid having a plain directory on the list of
6402 ;; libraries to link.
6403 (("\\{h5lib\\}" match)
6404 (string-append match "/libhdf5.a")))
6407 `(("r-aws-s3" ,r-aws-s3)
6408 ("r-aws-signature" ,r-aws-signature)
6410 ("r-biobase" ,r-biobase)
6411 ("r-biocgenerics" ,r-biocgenerics)
6412 ("r-cytolib" ,r-cytolib)
6413 ("r-data-table" ,r-data-table)
6414 ("r-digest" ,r-digest)
6415 ("r-dplyr" ,r-dplyr)
6416 ("r-flowcore" ,r-flowcore)
6417 ("r-ggplot2" ,r-ggplot2)
6418 ("r-graph" ,r-graph)
6419 ("r-lattice" ,r-lattice)
6420 ("r-latticeextra" ,r-latticeextra)
6421 ("r-matrixstats" ,r-matrixstats)
6422 ("r-ncdfflow" ,r-ncdfflow)
6425 ("r-rcpparmadillo" ,r-rcpparmadillo)
6426 ("r-rcppparallel" ,r-rcppparallel)
6427 ("r-rgraphviz" ,r-rgraphviz)
6428 ("r-rhdf5lib" ,r-rhdf5lib)
6429 ("r-rprotobuflib" ,r-rprotobuflib)
6430 ("r-scales" ,r-scales)
6433 `(("r-knitr" ,r-knitr)))
6434 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6435 (synopsis "Infrastructure for working with cytometry data")
6437 "This package is designed to facilitate comparison of automated gating
6438 methods against manual gating done in flowJo. This package allows you to
6439 import basic flowJo workspaces into BioConductor and replicate the gating from
6440 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6441 samples, compensation, and transformation are performed so that the output
6442 matches the flowJo analysis.")
6443 (license license:artistic2.0)))
6445 (define-public r-flowstats
6447 (name "r-flowstats")
6452 (uri (bioconductor-uri "flowStats" version))
6455 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
6456 (properties `((upstream-name . "flowStats")))
6457 (build-system r-build-system)
6459 `(("r-biobase" ,r-biobase)
6460 ("r-biocgenerics" ,r-biocgenerics)
6461 ("r-cluster" ,r-cluster)
6463 ("r-flowcore" ,r-flowcore)
6464 ("r-flowviz" ,r-flowviz)
6465 ("r-flowworkspace" ,r-flowworkspace)
6466 ("r-kernsmooth" ,r-kernsmooth)
6468 ("r-lattice" ,r-lattice)
6470 ("r-ncdfflow" ,r-ncdfflow)
6471 ("r-rcolorbrewer" ,r-rcolorbrewer)
6472 ("r-rrcov" ,r-rrcov)))
6473 (home-page "http://www.github.com/RGLab/flowStats")
6474 (synopsis "Statistical methods for the analysis of flow cytometry data")
6476 "This package provides methods and functionality to analyze flow data
6477 that is beyond the basic infrastructure provided by the @code{flowCore}
6479 (license license:artistic2.0)))
6481 (define-public r-opencyto
6488 (uri (bioconductor-uri "openCyto" version))
6491 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
6492 (properties `((upstream-name . "openCyto")))
6493 (build-system r-build-system)
6495 `(("r-biobase" ,r-biobase)
6496 ("r-biocgenerics" ,r-biocgenerics)
6498 ("r-data-table" ,r-data-table)
6499 ("r-flowclust" ,r-flowclust)
6500 ("r-flowcore" ,r-flowcore)
6501 ("r-flowstats" ,r-flowstats)
6502 ("r-flowviz" ,r-flowviz)
6503 ("r-flowworkspace" ,r-flowworkspace)
6504 ("r-graph" ,r-graph)
6505 ("r-gtools" ,r-gtools)
6507 ("r-lattice" ,r-lattice)
6509 ("r-ncdfflow" ,r-ncdfflow)
6511 ("r-r-utils" ,r-r-utils)
6513 ("r-rcolorbrewer" ,r-rcolorbrewer)
6515 ("r-rrcov" ,r-rrcov)))
6517 `(("r-knitr" ,r-knitr)))
6518 (home-page "https://bioconductor.org/packages/openCyto")
6519 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6521 "This package is designed to facilitate the automated gating methods in a
6522 sequential way to mimic the manual gating strategy.")
6523 (license license:artistic2.0)))
6525 (define-public r-cytoml
6532 (uri (bioconductor-uri "CytoML" version))
6535 "1d8x49aqc95x1vx456hya5r7mal80pj9l6wmr5x5pb5r8qyzz6yq"))))
6536 (properties `((upstream-name . "CytoML")))
6537 (build-system r-build-system)
6540 (modify-phases %standard-phases
6541 (add-after 'unpack 'fix-linking
6543 (substitute* "src/Makevars.in"
6544 ;; This is to avoid having a plain directory on the list of
6545 ;; libraries to link.
6546 (("\\{h5lib\\}" match)
6547 (string-append match "/libhdf5.a")))
6550 `(("libxml2" ,libxml2)))
6552 `(("r-base64enc" ,r-base64enc)
6554 ("r-biobase" ,r-biobase)
6555 ("r-corpcor" ,r-corpcor)
6556 ("r-cytolib" ,r-cytolib)
6557 ("r-data-table" ,r-data-table)
6558 ("r-dplyr" ,r-dplyr)
6559 ("r-flowcore" ,r-flowcore)
6560 ("r-flowworkspace" ,r-flowworkspace)
6561 ("r-ggcyto" ,r-ggcyto)
6562 ("r-graph" ,r-graph)
6563 ("r-jsonlite" ,r-jsonlite)
6564 ("r-lattice" ,r-lattice)
6565 ("r-opencyto" ,r-opencyto)
6569 ("r-rcpparmadillo" ,r-rcpparmadillo)
6570 ("r-rcppparallel" ,r-rcppparallel)
6571 ("r-rgraphviz" ,r-rgraphviz)
6572 ("r-rhdf5lib" ,r-rhdf5lib)
6573 ("r-rprotobuflib" ,r-rprotobuflib)
6574 ("r-runit" ,r-runit)
6575 ("r-tibble" ,r-tibble)
6578 ("r-yaml" ,r-yaml)))
6580 `(("r-knitr" ,r-knitr)))
6581 (home-page "https://github.com/RGLab/CytoML")
6582 (synopsis "GatingML interface for cross platform cytometry data sharing")
6584 "This package provides an interface to implementations of the GatingML2.0
6585 standard to exchange gated cytometry data with other software platforms.")
6586 (license license:artistic2.0)))
6588 (define-public r-flowsom
6595 (uri (bioconductor-uri "FlowSOM" version))
6598 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
6599 (properties `((upstream-name . "FlowSOM")))
6600 (build-system r-build-system)
6602 `(("r-biocgenerics" ,r-biocgenerics)
6603 ("r-consensusclusterplus" ,r-consensusclusterplus)
6604 ("r-cytoml" ,r-cytoml)
6605 ("r-flowcore" ,r-flowcore)
6606 ("r-flowworkspace" ,r-flowworkspace)
6607 ("r-igraph" ,r-igraph)
6608 ("r-rcolorbrewer" ,r-rcolorbrewer)
6611 (home-page "https://bioconductor.org/packages/FlowSOM/")
6612 (synopsis "Visualize and interpret cytometry data")
6614 "FlowSOM offers visualization options for cytometry data, by using
6615 self-organizing map clustering and minimal spanning trees.")
6616 (license license:gpl2+)))
6618 (define-public r-mixomics
6625 (uri (bioconductor-uri "mixOmics" version))
6628 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
6629 (properties `((upstream-name . "mixOmics")))
6630 (build-system r-build-system)
6632 `(("r-corpcor" ,r-corpcor)
6633 ("r-dplyr" ,r-dplyr)
6634 ("r-ellipse" ,r-ellipse)
6635 ("r-ggrepel" ,r-ggrepel)
6636 ("r-ggplot2" ,r-ggplot2)
6637 ("r-gridextra" ,r-gridextra)
6638 ("r-igraph" ,r-igraph)
6639 ("r-lattice" ,r-lattice)
6641 ("r-matrixstats" ,r-matrixstats)
6642 ("r-rarpack" ,r-rarpack)
6643 ("r-rcolorbrewer" ,r-rcolorbrewer)
6644 ("r-reshape2" ,r-reshape2)
6645 ("r-tidyr" ,r-tidyr)))
6647 `(("r-knitr" ,r-knitr)))
6648 (home-page "http://www.mixOmics.org")
6649 (synopsis "Multivariate methods for exploration of biological datasets")
6651 "mixOmics offers a wide range of multivariate methods for the exploration
6652 and integration of biological datasets with a particular focus on variable
6653 selection. The package proposes several sparse multivariate models we have
6654 developed to identify the key variables that are highly correlated, and/or
6655 explain the biological outcome of interest. The data that can be analysed
6656 with mixOmics may come from high throughput sequencing technologies, such as
6657 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6658 also beyond the realm of omics (e.g. spectral imaging). The methods
6659 implemented in mixOmics can also handle missing values without having to
6660 delete entire rows with missing data.")
6661 (license license:gpl2+)))
6663 (define-public r-depecher
6664 (package ;Source/Weave error
6670 (uri (bioconductor-uri "DepecheR" version))
6673 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
6674 (properties `((upstream-name . "DepecheR")))
6675 (build-system r-build-system)
6677 `(("r-beanplot" ,r-beanplot)
6678 ("r-dosnow" ,r-dosnow)
6679 ("r-dplyr" ,r-dplyr)
6681 ("r-foreach" ,r-foreach)
6682 ("r-ggplot2" ,r-ggplot2)
6683 ("r-gmodels" ,r-gmodels)
6684 ("r-gplots" ,r-gplots)
6686 ("r-matrixstats" ,r-matrixstats)
6687 ("r-mixomics" ,r-mixomics)
6688 ("r-moments" ,r-moments)
6690 ("r-rcppeigen" ,r-rcppeigen)
6691 ("r-reshape2" ,r-reshape2)
6692 ("r-robustbase" ,r-robustbase)
6693 ("r-viridis" ,r-viridis)))
6695 `(("r-knitr" ,r-knitr)))
6696 (home-page "https://bioconductor.org/packages/DepecheR/")
6697 (synopsis "Identify traits of clusters in high-dimensional entities")
6699 "The purpose of this package is to identify traits in a dataset that can
6700 separate groups. This is done on two levels. First, clustering is performed,
6701 using an implementation of sparse K-means. Secondly, the generated clusters
6702 are used to predict outcomes of groups of individuals based on their
6703 distribution of observations in the different clusters. As certain clusters
6704 with separating information will be identified, and these clusters are defined
6705 by a sparse number of variables, this method can reduce the complexity of
6706 data, to only emphasize the data that actually matters.")
6707 (license license:expat)))
6709 (define-public r-rcistarget
6711 (name "r-rcistarget")
6716 (uri (bioconductor-uri "RcisTarget" version))
6719 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
6720 (properties `((upstream-name . "RcisTarget")))
6721 (build-system r-build-system)
6723 `(("r-aucell" ,r-aucell)
6724 ("r-biocgenerics" ,r-biocgenerics)
6725 ("r-data-table" ,r-data-table)
6726 ("r-feather" ,r-feather)
6727 ("r-gseabase" ,r-gseabase)
6728 ("r-r-utils" ,r-r-utils)
6729 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6731 `(("r-knitr" ,r-knitr)))
6732 (home-page "https://aertslab.org/#scenic")
6733 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6735 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6736 over-represented on a gene list. In a first step, RcisTarget selects DNA
6737 motifs that are significantly over-represented in the surroundings of the
6738 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6739 achieved by using a database that contains genome-wide cross-species rankings
6740 for each motif. The motifs that are then annotated to TFs and those that have
6741 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6742 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6743 genes in the gene-set that are ranked above the leading edge).")
6744 (license license:gpl3)))
6746 (define-public r-cicero
6753 (uri (bioconductor-uri "cicero" version))
6756 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
6757 (build-system r-build-system)
6759 `(("r-assertthat" ,r-assertthat)
6760 ("r-biobase" ,r-biobase)
6761 ("r-biocgenerics" ,r-biocgenerics)
6762 ("r-data-table" ,r-data-table)
6763 ("r-dplyr" ,r-dplyr)
6765 ("r-genomicranges" ,r-genomicranges)
6766 ("r-ggplot2" ,r-ggplot2)
6767 ("r-glasso" ,r-glasso)
6769 ("r-igraph" ,r-igraph)
6770 ("r-iranges" ,r-iranges)
6771 ("r-matrix" ,r-matrix)
6772 ("r-monocle" ,r-monocle)
6774 ("r-reshape2" ,r-reshape2)
6775 ("r-s4vectors" ,r-s4vectors)
6776 ("r-stringi" ,r-stringi)
6777 ("r-stringr" ,r-stringr)
6778 ("r-tibble" ,r-tibble)
6779 ("r-tidyr" ,r-tidyr)
6780 ("r-vgam" ,r-vgam)))
6782 `(("r-knitr" ,r-knitr)))
6783 (home-page "https://bioconductor.org/packages/cicero/")
6784 (synopsis "Predict cis-co-accessibility from single-cell data")
6786 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6787 accessibility data. It also extends the monocle package for use in chromatin
6788 accessibility data.")
6789 (license license:expat)))
6791 ;; This is the latest commit on the "monocle3" branch.
6792 (define-public r-cicero-monocle3
6793 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6795 (package (inherit r-cicero)
6796 (name "r-cicero-monocle3")
6797 (version (git-version "1.3.2" revision commit))
6802 (url "https://github.com/cole-trapnell-lab/cicero-release")
6804 (file-name (git-file-name name version))
6807 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6809 `(("r-monocle3" ,r-monocle3)
6810 ,@(alist-delete "r-monocle"
6811 (package-propagated-inputs r-cicero)))))))
6813 (define-public r-cistopic
6814 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6818 (version (git-version "0.2.1" revision commit))
6823 (url "https://github.com/aertslab/cisTopic")
6825 (file-name (git-file-name name version))
6828 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6829 (build-system r-build-system)
6831 `(("r-aucell" ,r-aucell)
6832 ("r-data-table" ,r-data-table)
6833 ("r-dplyr" ,r-dplyr)
6834 ("r-dosnow" ,r-dosnow)
6836 ("r-feather" ,r-feather)
6837 ("r-fitdistrplus" ,r-fitdistrplus)
6838 ("r-genomicranges" ,r-genomicranges)
6839 ("r-ggplot2" ,r-ggplot2)
6841 ("r-matrix" ,r-matrix)
6843 ("r-rcistarget" ,r-rcistarget)
6844 ("r-rtracklayer" ,r-rtracklayer)
6845 ("r-s4vectors" ,r-s4vectors)))
6846 (home-page "https://github.com/aertslab/cisTopic")
6847 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6849 "The sparse nature of single cell epigenomics data can be overruled using
6850 probabilistic modelling methods such as @dfn{Latent Dirichlet
6851 Allocation} (LDA). This package allows the probabilistic modelling of
6852 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6853 includes functionalities to identify cell states based on the contribution of
6854 cisTopics and explore the nature and regulatory proteins driving them.")
6855 (license license:gpl3))))
6857 (define-public r-genie3
6864 (uri (bioconductor-uri "GENIE3" version))
6867 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
6868 (properties `((upstream-name . "GENIE3")))
6869 (build-system r-build-system)
6870 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6872 `(("r-knitr" ,r-knitr)))
6873 (home-page "https://bioconductor.org/packages/GENIE3")
6874 (synopsis "Gene network inference with ensemble of trees")
6876 "This package implements the GENIE3 algorithm for inferring gene
6877 regulatory networks from expression data.")
6878 (license license:gpl2+)))
6880 (define-public r-roc
6887 (uri (bioconductor-uri "ROC" version))
6890 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
6891 (properties `((upstream-name . "ROC")))
6892 (build-system r-build-system)
6894 `(("r-knitr" ,r-knitr)))
6895 (home-page "https://www.bioconductor.org/packages/ROC/")
6896 (synopsis "Utilities for ROC curves")
6898 "This package provides utilities for @dfn{Receiver Operating
6899 Characteristic} (ROC) curves, with a focus on micro arrays.")
6900 (license license:artistic2.0)))
6902 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6904 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6909 (uri (bioconductor-uri
6910 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6911 version 'annotation))
6914 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6917 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6918 (build-system r-build-system)
6919 (propagated-inputs `(("r-minfi" ,r-minfi)))
6921 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6922 (synopsis "Annotation for Illumina's 450k methylation arrays")
6924 "This package provides manifests and annotation for Illumina's 450k array
6926 (license license:artistic2.0)))
6928 (define-public r-watermelon
6930 (name "r-watermelon")
6935 (uri (bioconductor-uri "wateRmelon" version))
6938 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
6939 (properties `((upstream-name . "wateRmelon")))
6940 (build-system r-build-system)
6942 `(("r-biobase" ,r-biobase)
6943 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6944 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6945 ("r-illuminaio" ,r-illuminaio)
6946 ("r-limma" ,r-limma)
6948 ("r-matrixstats" ,r-matrixstats)
6949 ("r-methylumi" ,r-methylumi)
6951 (home-page "https://bioconductor.org/packages/wateRmelon/")
6952 (synopsis "Illumina 450 methylation array normalization and metrics")
6954 "The standard index of DNA methylation (beta) is computed from methylated
6955 and unmethylated signal intensities. Betas calculated from raw signal
6956 intensities perform well, but using 11 methylomic datasets we demonstrate that
6957 quantile normalization methods produce marked improvement. The commonly used
6958 procedure of normalizing betas is inferior to the separate normalization of M
6959 and U, and it is also advantageous to normalize Type I and Type II assays
6960 separately. This package provides 15 flavours of betas and three performance
6961 metrics, with methods for objects produced by the @code{methylumi} and
6962 @code{minfi} packages.")
6963 (license license:gpl3)))
6965 (define-public r-gdsfmt
6972 (uri (bioconductor-uri "gdsfmt" version))
6975 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
6976 (modules '((guix build utils)))
6977 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6978 ;; them and link with system libraries instead.
6981 (for-each delete-file-recursively
6985 (substitute* "src/Makevars"
6986 (("all: \\$\\(SHLIB\\)") "all:")
6987 (("\\$\\(SHLIB\\): liblzma.a") "")
6988 (("(ZLIB|LZ4)/.*") "")
6989 (("CoreArray/dVLIntGDS.cpp.*")
6990 "CoreArray/dVLIntGDS.cpp")
6991 (("CoreArray/dVLIntGDS.o.*")
6992 "CoreArray/dVLIntGDS.o")
6993 (("PKG_LIBS = ./liblzma.a")
6994 "PKG_LIBS = -llz4"))
6995 (substitute* "src/CoreArray/dStream.h"
6996 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6997 (string-append "include <" header ">")))
6999 (properties `((upstream-name . "gdsfmt")))
7000 (build-system r-build-system)
7006 `(("r-knitr" ,r-knitr)))
7007 (home-page "http://corearray.sourceforge.net/")
7009 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7011 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7012 Data Structure} (GDS) data files, which are portable across platforms with
7013 hierarchical structure to store multiple scalable array-oriented data sets
7014 with metadata information. It is suited for large-scale datasets, especially
7015 for data which are much larger than the available random-access memory. The
7016 @code{gdsfmt} package offers efficient operations specifically designed for
7017 integers of less than 8 bits, since a diploid genotype, like
7018 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7019 byte. Data compression and decompression are available with relatively
7020 efficient random access. It is also allowed to read a GDS file in parallel
7021 with multiple R processes supported by the package @code{parallel}.")
7022 (license license:lgpl3)))
7024 (define-public r-bigmelon
7031 (uri (bioconductor-uri "bigmelon" version))
7034 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7035 (properties `((upstream-name . "bigmelon")))
7036 (build-system r-build-system)
7038 `(("r-biobase" ,r-biobase)
7039 ("r-biocgenerics" ,r-biocgenerics)
7040 ("r-gdsfmt" ,r-gdsfmt)
7041 ("r-geoquery" ,r-geoquery)
7042 ("r-methylumi" ,r-methylumi)
7043 ("r-minfi" ,r-minfi)
7044 ("r-watermelon" ,r-watermelon)))
7045 (home-page "https://bioconductor.org/packages/bigmelon/")
7046 (synopsis "Illumina methylation array analysis for large experiments")
7048 "This package provides methods for working with Illumina arrays using the
7049 @code{gdsfmt} package.")
7050 (license license:gpl3)))
7052 (define-public r-seqbias
7059 (uri (bioconductor-uri "seqbias" version))
7062 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
7063 (properties `((upstream-name . "seqbias")))
7064 (build-system r-build-system)
7066 `(("r-biostrings" ,r-biostrings)
7067 ("r-genomicranges" ,r-genomicranges)
7068 ("r-rhtslib" ,r-rhtslib)))
7069 (home-page "https://bioconductor.org/packages/seqbias/")
7070 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
7072 "This package implements a model of per-position sequencing bias in
7073 high-throughput sequencing data using a simple Bayesian network, the structure
7074 and parameters of which are trained on a set of aligned reads and a reference
7076 (license license:lgpl3)))
7078 (define-public r-snplocs-hsapiens-dbsnp144-grch37
7080 (name "r-snplocs-hsapiens-dbsnp144-grch37")
7084 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
7085 version 'annotation))
7088 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
7089 (build-system r-build-system)
7090 ;; As this package provides little more than a very large data file it
7091 ;; doesn't make sense to build substitutes.
7092 (arguments `(#:substitutable? #f))
7094 `(("r-biocgenerics" ,r-biocgenerics)
7095 ("r-s4vectors" ,r-s4vectors)
7096 ("r-iranges" ,r-iranges)
7097 ("r-genomeinfodb" ,r-genomeinfodb)
7098 ("r-genomicranges" ,r-genomicranges)
7099 ("r-bsgenome" ,r-bsgenome)
7100 ("r-biostrings" ,r-biostrings)))
7102 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
7103 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
7104 (description "This package provides SNP locations and alleles for Homo
7105 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
7106 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
7107 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
7108 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
7109 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
7110 the mitochondrion chromosome. Therefore, the SNPs in this package can be
7111 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
7112 correct position but this injection will exclude chrM (i.e. nothing will be
7113 injected in that sequence).")
7114 (license license:artistic2.0)))
7116 (define-public r-reqon
7123 (uri (bioconductor-uri "ReQON" version))
7126 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
7127 (properties `((upstream-name . "ReQON")))
7128 (build-system r-build-system)
7130 `(("r-rjava" ,r-rjava)
7131 ("r-rsamtools" ,r-rsamtools)
7132 ("r-seqbias" ,r-seqbias)))
7133 (home-page "https://bioconductor.org/packages/ReQON/")
7134 (synopsis "Recalibrating quality of nucleotides")
7136 "This package provides an implementation of an algorithm for
7137 recalibrating the base quality scores for aligned sequencing data in BAM
7139 (license license:gpl2)))
7141 (define-public r-wavcluster
7143 (name "r-wavcluster")
7148 (uri (bioconductor-uri "wavClusteR" version))
7151 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
7152 (properties `((upstream-name . "wavClusteR")))
7153 (build-system r-build-system)
7155 `(("r-biocgenerics" ,r-biocgenerics)
7156 ("r-biostrings" ,r-biostrings)
7157 ("r-foreach" ,r-foreach)
7158 ("r-genomicfeatures" ,r-genomicfeatures)
7159 ("r-genomicranges" ,r-genomicranges)
7160 ("r-ggplot2" ,r-ggplot2)
7161 ("r-hmisc" ,r-hmisc)
7162 ("r-iranges" ,r-iranges)
7163 ("r-mclust" ,r-mclust)
7164 ("r-rsamtools" ,r-rsamtools)
7165 ("r-rtracklayer" ,r-rtracklayer)
7166 ("r-s4vectors" ,r-s4vectors)
7167 ("r-seqinr" ,r-seqinr)
7168 ("r-stringr" ,r-stringr)))
7170 `(("r-knitr" ,r-knitr)))
7171 (home-page "https://bioconductor.org/packages/wavClusteR/")
7172 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
7174 "This package provides an integrated pipeline for the analysis of
7175 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7176 sequencing errors, SNPs and additional non-experimental sources by a non-
7177 parametric mixture model. The protein binding sites (clusters) are then
7178 resolved at high resolution and cluster statistics are estimated using a
7179 rigorous Bayesian framework. Post-processing of the results, data export for
7180 UCSC genome browser visualization and motif search analysis are provided. In
7181 addition, the package integrates RNA-Seq data to estimate the False
7182 Discovery Rate of cluster detection. Key functions support parallel multicore
7183 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7184 be applied to the analysis of other NGS data obtained from experimental
7185 procedures that induce nucleotide substitutions (e.g. BisSeq).")
7186 (license license:gpl2)))
7188 (define-public r-timeseriesexperiment
7190 (name "r-timeseriesexperiment")
7195 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7198 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
7200 `((upstream-name . "TimeSeriesExperiment")))
7201 (build-system r-build-system)
7203 `(("r-deseq2" ,r-deseq2)
7204 ("r-dplyr" ,r-dplyr)
7205 ("r-dynamictreecut" ,r-dynamictreecut)
7206 ("r-edger" ,r-edger)
7207 ("r-ggplot2" ,r-ggplot2)
7208 ("r-hmisc" ,r-hmisc)
7209 ("r-limma" ,r-limma)
7210 ("r-magrittr" ,r-magrittr)
7211 ("r-proxy" ,r-proxy)
7212 ("r-s4vectors" ,r-s4vectors)
7213 ("r-summarizedexperiment" ,r-summarizedexperiment)
7214 ("r-tibble" ,r-tibble)
7215 ("r-tidyr" ,r-tidyr)
7216 ("r-vegan" ,r-vegan)
7217 ("r-viridis" ,r-viridis)))
7219 `(("r-knitr" ,r-knitr)))
7220 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7221 (synopsis "Analysis for short time-series data")
7223 "This package is a visualization and analysis toolbox for short time
7224 course data which includes dimensionality reduction, clustering, two-sample
7225 differential expression testing and gene ranking techniques. The package also
7226 provides methods for retrieving enriched pathways.")
7227 (license license:lgpl3+)))
7229 (define-public r-variantfiltering
7231 (name "r-variantfiltering")
7236 (uri (bioconductor-uri "VariantFiltering" version))
7239 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
7241 `((upstream-name . "VariantFiltering")))
7242 (build-system r-build-system)
7244 `(("r-annotationdbi" ,r-annotationdbi)
7245 ("r-biobase" ,r-biobase)
7246 ("r-biocgenerics" ,r-biocgenerics)
7247 ("r-biocparallel" ,r-biocparallel)
7248 ("r-biostrings" ,r-biostrings)
7249 ("r-bsgenome" ,r-bsgenome)
7251 ("r-genomeinfodb" ,r-genomeinfodb)
7252 ("r-genomicfeatures" ,r-genomicfeatures)
7253 ("r-genomicranges" ,r-genomicranges)
7254 ("r-genomicscores" ,r-genomicscores)
7255 ("r-graph" ,r-graph)
7257 ("r-iranges" ,r-iranges)
7259 ("r-rsamtools" ,r-rsamtools)
7260 ("r-s4vectors" ,r-s4vectors)
7261 ("r-shiny" ,r-shiny)
7262 ("r-shinyjs" ,r-shinyjs)
7263 ("r-shinythemes" ,r-shinythemes)
7264 ("r-shinytree" ,r-shinytree)
7265 ("r-summarizedexperiment" ,r-summarizedexperiment)
7266 ("r-variantannotation" ,r-variantannotation)
7267 ("r-xvector" ,r-xvector)))
7268 (home-page "https://github.com/rcastelo/VariantFiltering")
7269 (synopsis "Filtering of coding and non-coding genetic variants")
7271 "Filter genetic variants using different criteria such as inheritance
7272 model, amino acid change consequence, minor allele frequencies across human
7273 populations, splice site strength, conservation, etc.")
7274 (license license:artistic2.0)))
7276 (define-public r-genomegraphs
7278 (name "r-genomegraphs")
7283 (uri (bioconductor-uri "GenomeGraphs" version))
7286 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7287 (properties `((upstream-name . "GenomeGraphs")))
7288 (build-system r-build-system)
7290 `(("r-biomart" ,r-biomart)))
7291 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7292 (synopsis "Plotting genomic information from Ensembl")
7294 "Genomic data analyses requires integrated visualization of known genomic
7295 information and new experimental data. GenomeGraphs uses the biomaRt package
7296 to perform live annotation queries to Ensembl and translates this to e.g.
7297 gene/transcript structures in viewports of the grid graphics package. This
7298 results in genomic information plotted together with your data. Another
7299 strength of GenomeGraphs is to plot different data types such as array CGH,
7300 gene expression, sequencing and other data, together in one plot using the
7301 same genome coordinate system.")
7302 (license license:artistic2.0)))
7304 (define-public r-wavetiling
7306 (name "r-wavetiling")
7311 (uri (bioconductor-uri "waveTiling" version))
7314 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7315 (properties `((upstream-name . "waveTiling")))
7316 (build-system r-build-system)
7318 `(("r-affy" ,r-affy)
7319 ("r-biobase" ,r-biobase)
7320 ("r-biostrings" ,r-biostrings)
7321 ("r-genomegraphs" ,r-genomegraphs)
7322 ("r-genomicranges" ,r-genomicranges)
7323 ("r-iranges" ,r-iranges)
7324 ("r-oligo" ,r-oligo)
7325 ("r-oligoclasses" ,r-oligoclasses)
7326 ("r-preprocesscore" ,r-preprocesscore)
7327 ("r-waveslim" ,r-waveslim)))
7328 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7329 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7331 "This package is designed to conduct transcriptome analysis for tiling
7332 arrays based on fast wavelet-based functional models.")
7333 (license license:gpl2+)))
7335 (define-public r-variancepartition
7337 (name "r-variancepartition")
7342 (uri (bioconductor-uri "variancePartition" version))
7345 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
7347 `((upstream-name . "variancePartition")))
7348 (build-system r-build-system)
7350 `(("r-biobase" ,r-biobase)
7351 ("r-biocparallel" ,r-biocparallel)
7352 ("r-colorramps" ,r-colorramps)
7353 ("r-doparallel" ,r-doparallel)
7354 ("r-foreach" ,r-foreach)
7355 ("r-ggplot2" ,r-ggplot2)
7356 ("r-gplots" ,r-gplots)
7357 ("r-iterators" ,r-iterators)
7358 ("r-limma" ,r-limma)
7360 ("r-lmertest" ,r-lmertest)
7362 ("r-pbkrtest" ,r-pbkrtest)
7363 ("r-progress" ,r-progress)
7364 ("r-reshape2" ,r-reshape2)
7365 ("r-scales" ,r-scales)))
7367 `(("r-knitr" ,r-knitr)))
7368 (home-page "https://bioconductor.org/packages/variancePartition/")
7369 (synopsis "Analyze variation in gene expression experiments")
7371 "This is a package providing tools to quantify and interpret multiple
7372 sources of biological and technical variation in gene expression experiments.
7373 It uses a linear mixed model to quantify variation in gene expression
7374 attributable to individual, tissue, time point, or technical variables. The
7375 package includes dream differential expression analysis for repeated
7377 (license license:gpl2+)))
7379 (define-public r-htqpcr
7386 (uri (bioconductor-uri "HTqPCR" version))
7389 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
7390 (properties `((upstream-name . "HTqPCR")))
7391 (build-system r-build-system)
7393 `(("r-affy" ,r-affy)
7394 ("r-biobase" ,r-biobase)
7395 ("r-gplots" ,r-gplots)
7396 ("r-limma" ,r-limma)
7397 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7398 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7399 "groups/bertone/software/HTqPCR.pdf"))
7400 (synopsis "Automated analysis of high-throughput qPCR data")
7402 "Analysis of Ct values from high throughput quantitative real-time
7403 PCR (qPCR) assays across multiple conditions or replicates. The input data
7404 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7405 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7406 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7407 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7408 loading, quality assessment, normalization, visualization and parametric or
7409 non-parametric testing for statistical significance in Ct values between
7410 features (e.g. genes, microRNAs).")
7411 (license license:artistic2.0)))
7413 (define-public r-unifiedwmwqpcr
7415 (name "r-unifiedwmwqpcr")
7420 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7423 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
7425 `((upstream-name . "unifiedWMWqPCR")))
7426 (build-system r-build-system)
7428 `(("r-biocgenerics" ,r-biocgenerics)
7429 ("r-htqpcr" ,r-htqpcr)))
7430 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7431 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7433 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7434 data. This modified test allows for testing differential expression in qPCR
7436 (license license:gpl2+)))
7438 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7440 (define-public r-activedriverwgs
7442 (name "r-activedriverwgs")
7447 (uri (cran-uri "ActiveDriverWGS" version))
7450 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
7452 `((upstream-name . "ActiveDriverWGS")))
7453 (build-system r-build-system)
7455 `(("r-biostrings" ,r-biostrings)
7456 ("r-bsgenome" ,r-bsgenome)
7457 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7458 ("r-genomeinfodb" ,r-genomeinfodb)
7459 ("r-genomicranges" ,r-genomicranges)
7460 ("r-iranges" ,r-iranges)
7461 ("r-s4vectors" ,r-s4vectors)))
7463 `(("r-knitr" ,r-knitr)))
7464 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7465 (synopsis "Driver discovery tool for cancer whole genomes")
7467 "This package provides a method for finding an enrichment of cancer
7468 simple somatic mutations (SNVs and Indels) in functional elements across the
7469 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7470 using whole genome sequencing data.")
7471 (license license:gpl3)))
7473 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7475 (define-public r-activepathways
7477 (name "r-activepathways")
7482 (uri (cran-uri "ActivePathways" version))
7485 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7487 `((upstream-name . "ActivePathways")))
7488 (build-system r-build-system)
7490 `(("r-data-table" ,r-data-table)
7491 ("r-ggplot2" ,r-ggplot2)))
7493 `(("r-knitr" ,r-knitr)))
7494 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7495 (synopsis "Multivariate pathway enrichment analysis")
7497 "This package represents an integrative method of analyzing multi omics
7498 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7499 uses a statistical data fusion approach, rationalizes contributing evidence
7500 and highlights associated genes, improving systems-level understanding of
7501 cellular organization in health and disease.")
7502 (license license:gpl3)))
7504 (define-public r-bgmix
7511 (uri (bioconductor-uri "BGmix" version))
7514 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
7515 (properties `((upstream-name . "BGmix")))
7516 (build-system r-build-system)
7518 `(("r-kernsmooth" ,r-kernsmooth)))
7519 (home-page "https://bioconductor.org/packages/BGmix/")
7520 (synopsis "Bayesian models for differential gene expression")
7522 "This package provides fully Bayesian mixture models for differential
7524 (license license:gpl2)))
7526 (define-public r-bgx
7533 (uri (bioconductor-uri "bgx" version))
7536 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
7537 (properties `((upstream-name . "bgx")))
7538 (build-system r-build-system)
7540 `(("r-affy" ,r-affy)
7541 ("r-biobase" ,r-biobase)
7542 ("r-gcrma" ,r-gcrma)
7543 ("r-rcpp" ,r-rcpp)))
7544 (home-page "https://bioconductor.org/packages/bgx/")
7545 (synopsis "Bayesian gene expression")
7547 "This package provides tools for Bayesian integrated analysis of
7548 Affymetrix GeneChips.")
7549 (license license:gpl2)))
7551 (define-public r-bhc
7558 (uri (bioconductor-uri "BHC" version))
7561 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
7562 (properties `((upstream-name . "BHC")))
7563 (build-system r-build-system)
7564 (home-page "https://bioconductor.org/packages/BHC/")
7565 (synopsis "Bayesian hierarchical clustering")
7567 "The method implemented in this package performs bottom-up hierarchical
7568 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7569 in the data and Bayesian model selection to decide at each step which clusters
7570 to merge. This avoids several limitations of traditional methods, for example
7571 how many clusters there should be and how to choose a principled distance
7572 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7573 categories) or time-series data. This version also includes a randomised
7574 algorithm which is more efficient for larger data sets.")
7575 (license license:gpl3)))
7577 (define-public r-bicare
7584 (uri (bioconductor-uri "BicARE" version))
7587 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
7588 (properties `((upstream-name . "BicARE")))
7589 (build-system r-build-system)
7591 `(("r-biobase" ,r-biobase)
7592 ("r-gseabase" ,r-gseabase)
7593 ("r-multtest" ,r-multtest)))
7594 (home-page "http://bioinfo.curie.fr")
7595 (synopsis "Biclustering analysis and results exploration")
7597 "This is a package for biclustering analysis and exploration of
7599 (license license:gpl2)))
7601 (define-public r-bifet
7608 (uri (bioconductor-uri "BiFET" version))
7611 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
7612 (properties `((upstream-name . "BiFET")))
7613 (build-system r-build-system)
7615 `(("r-genomicranges" ,r-genomicranges)
7616 ("r-poibin" ,r-poibin)))
7618 `(("r-knitr" ,r-knitr)))
7619 (home-page "https://bioconductor.org/packages/BiFET")
7620 (synopsis "Bias-free footprint enrichment test")
7622 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7623 over-represented in target regions compared to background regions after
7624 correcting for the bias arising from the imbalance in read counts and GC
7625 contents between the target and background regions. For a given TF k, BiFET
7626 tests the null hypothesis that the target regions have the same probability of
7627 having footprints for the TF k as the background regions while correcting for
7628 the read count and GC content bias.")
7629 (license license:gpl3)))
7631 (define-public r-rsbml
7638 (uri (bioconductor-uri "rsbml" version))
7641 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
7642 (properties `((upstream-name . "rsbml")))
7643 (build-system r-build-system)
7645 `(("libsbml" ,libsbml)
7648 `(("r-biocgenerics" ,r-biocgenerics)
7649 ("r-graph" ,r-graph)))
7651 `(("pkg-config" ,pkg-config)))
7652 (home-page "http://www.sbml.org")
7653 (synopsis "R support for SBML")
7655 "This package provides an R interface to libsbml for SBML parsing,
7656 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7657 (license license:artistic2.0)))
7659 (define-public r-hypergraph
7661 (name "r-hypergraph")
7666 (uri (bioconductor-uri "hypergraph" version))
7669 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
7670 (properties `((upstream-name . "hypergraph")))
7671 (build-system r-build-system)
7673 `(("r-graph" ,r-graph)))
7674 (home-page "https://bioconductor.org/packages/hypergraph")
7675 (synopsis "Hypergraph data structures")
7677 "This package implements some simple capabilities for representing and
7678 manipulating hypergraphs.")
7679 (license license:artistic2.0)))
7681 (define-public r-hyperdraw
7683 (name "r-hyperdraw")
7688 (uri (bioconductor-uri "hyperdraw" version))
7691 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
7692 (properties `((upstream-name . "hyperdraw")))
7693 (build-system r-build-system)
7694 (inputs `(("graphviz" ,graphviz)))
7696 `(("r-graph" ,r-graph)
7697 ("r-hypergraph" ,r-hypergraph)
7698 ("r-rgraphviz" ,r-rgraphviz)))
7699 (home-page "https://bioconductor.org/packages/hyperdraw")
7700 (synopsis "Visualizing hypergraphs")
7702 "This package provides functions for visualizing hypergraphs.")
7703 (license license:gpl2+)))
7705 (define-public r-biggr
7712 (uri (bioconductor-uri "BiGGR" version))
7715 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
7716 (properties `((upstream-name . "BiGGR")))
7717 (build-system r-build-system)
7719 `(("r-hyperdraw" ,r-hyperdraw)
7720 ("r-hypergraph" ,r-hypergraph)
7722 ("r-limsolve" ,r-limsolve)
7723 ("r-rsbml" ,r-rsbml)
7724 ("r-stringr" ,r-stringr)))
7725 (home-page "https://bioconductor.org/packages/BiGGR/")
7726 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7728 "This package provides an interface to simulate metabolic reconstruction
7729 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7730 reconstruction databases. The package facilitates @dfn{flux balance
7731 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7732 networks and estimated fluxes can be visualized with hypergraphs.")
7733 (license license:gpl3+)))
7735 (define-public r-bigmemoryextras
7737 (name "r-bigmemoryextras")
7742 (uri (bioconductor-uri "bigmemoryExtras" version))
7745 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
7747 `((upstream-name . "bigmemoryExtras")))
7748 (build-system r-build-system)
7750 `(("r-bigmemory" ,r-bigmemory)))
7752 `(("r-knitr" ,r-knitr)))
7753 (home-page "https://github.com/phaverty/bigmemoryExtras")
7754 (synopsis "Extension of the bigmemory package")
7756 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7757 safety and convenience features to the @code{filebacked.big.matrix} class from
7758 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7759 monitoring and gracefully restoring the connection to on-disk data and it also
7760 protects against accidental data modification with a file-system-based
7761 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7762 classes as @code{assayData} matrices within the @code{Biobase} package's
7763 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7764 related to attaching to, and indexing into, file-backed matrices with
7765 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7766 a file-backed matrix with factor properties.")
7767 (license license:artistic2.0)))
7769 (define-public r-bigpint
7776 (uri (bioconductor-uri "bigPint" version))
7779 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
7780 (properties `((upstream-name . "bigPint")))
7781 (build-system r-build-system)
7783 `(("r-delayedarray" ,r-delayedarray)
7784 ("r-dplyr" ,r-dplyr)
7785 ("r-ggally" ,r-ggally)
7786 ("r-ggplot2" ,r-ggplot2)
7787 ("r-gridextra" ,r-gridextra)
7788 ("r-hexbin" ,r-hexbin)
7789 ("r-hmisc" ,r-hmisc)
7790 ("r-htmlwidgets" ,r-htmlwidgets)
7791 ("r-plotly" ,r-plotly)
7793 ("r-rcolorbrewer" ,r-rcolorbrewer)
7794 ("r-reshape" ,r-reshape)
7795 ("r-shiny" ,r-shiny)
7796 ("r-shinycssloaders" ,r-shinycssloaders)
7797 ("r-shinydashboard" ,r-shinydashboard)
7798 ("r-stringr" ,r-stringr)
7799 ("r-summarizedexperiment" ,r-summarizedexperiment)
7800 ("r-tidyr" ,r-tidyr)))
7802 `(("r-knitr" ,r-knitr)))
7803 (home-page "https://github.com/lindsayrutter/bigPint")
7804 (synopsis "Big multivariate data plotted interactively")
7806 "This package provides methods for visualizing large multivariate
7807 datasets using static and interactive scatterplot matrices, parallel
7808 coordinate plots, volcano plots, and litre plots. It includes examples for
7809 visualizing RNA-sequencing datasets and differentially expressed genes.")
7810 (license license:gpl3)))
7812 (define-public r-chemminer
7814 (name "r-chemminer")
7819 (uri (bioconductor-uri "ChemmineR" version))
7822 "1853w19042c53whdnrfg1v8f07wpswf2si8q4613yrcamzg2zjkx"))))
7823 (properties `((upstream-name . "ChemmineR")))
7824 (build-system r-build-system)
7826 `(("r-base64enc" ,r-base64enc)
7828 ("r-biocgenerics" ,r-biocgenerics)
7830 ("r-digest" ,r-digest)
7832 ("r-ggplot2" ,r-ggplot2)
7833 ("r-gridextra" ,r-gridextra)
7836 ("r-rcurl" ,r-rcurl)
7837 ("r-rjson" ,r-rjson)
7838 ("r-rsvg" ,r-rsvg)))
7840 `(("r-knitr" ,r-knitr)))
7841 (home-page "https://github.com/girke-lab/ChemmineR")
7842 (synopsis "Cheminformatics toolkit for R")
7844 "ChemmineR is a cheminformatics package for analyzing drug-like small
7845 molecule data in R. It contains functions for efficient processing of large
7846 numbers of molecules, physicochemical/structural property predictions,
7847 structural similarity searching, classification and clustering of compound
7848 libraries with a wide spectrum of algorithms. In addition, it offers
7849 visualization functions for compound clustering results and chemical
7851 (license license:artistic2.0)))
7853 (define-public r-bioassayr
7855 (name "r-bioassayr")
7860 (uri (bioconductor-uri "bioassayR" version))
7863 "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f"))))
7864 (properties `((upstream-name . "bioassayR")))
7865 (build-system r-build-system)
7867 `(("r-biocgenerics" ,r-biocgenerics)
7868 ("r-chemminer" ,r-chemminer)
7870 ("r-matrix" ,r-matrix)
7871 ("r-rjson" ,r-rjson)
7872 ("r-rsqlite" ,r-rsqlite)
7875 `(("r-knitr" ,r-knitr)))
7876 (home-page "https://github.com/TylerBackman/bioassayR")
7877 (synopsis "Cross-target analysis of small molecule bioactivity")
7879 "bioassayR is a computational tool that enables simultaneous analysis of
7880 thousands of bioassay experiments performed over a diverse set of compounds
7881 and biological targets. Unique features include support for large-scale
7882 cross-target analyses of both public and custom bioassays, generation of
7883 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7884 preloaded database that provides access to a substantial portion of publicly
7885 available bioactivity data.")
7886 (license license:artistic2.0)))
7888 (define-public r-biobroom
7895 (uri (bioconductor-uri "biobroom" version))
7898 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
7899 (properties `((upstream-name . "biobroom")))
7900 (build-system r-build-system)
7902 `(("r-biobase" ,r-biobase)
7903 ("r-broom" ,r-broom)
7904 ("r-dplyr" ,r-dplyr)
7905 ("r-tidyr" ,r-tidyr)))
7907 `(("r-knitr" ,r-knitr)))
7908 (home-page "https://github.com/StoreyLab/biobroom")
7909 (synopsis "Turn Bioconductor objects into tidy data frames")
7911 "This package contains methods for converting standard objects
7912 constructed by bioinformatics packages, especially those in Bioconductor, and
7913 converting them to @code{tidy} data. It thus serves as a complement to the
7914 @code{broom} package, and follows the same tidy, augment, glance division of
7915 tidying methods. Tidying data makes it easy to recombine, reshape and
7916 visualize bioinformatics analyses.")
7917 ;; Any version of the LGPL.
7918 (license license:lgpl3+)))
7920 (define-public r-graphite
7927 (uri (bioconductor-uri "graphite" version))
7930 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
7931 (properties `((upstream-name . "graphite")))
7932 (build-system r-build-system)
7934 `(("r-annotationdbi" ,r-annotationdbi)
7935 ("r-checkmate" ,r-checkmate)
7936 ("r-graph" ,r-graph)
7938 ("r-rappdirs" ,r-rappdirs)))
7939 (home-page "https://bioconductor.org/packages/graphite/")
7940 (synopsis "Networks from pathway databases")
7942 "Graphite provides networks derived from eight public pathway databases,
7943 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7945 (license license:agpl3+)))
7947 (define-public r-reactomepa
7949 (name "r-reactomepa")
7954 (uri (bioconductor-uri "ReactomePA" version))
7957 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
7958 (properties `((upstream-name . "ReactomePA")))
7959 (build-system r-build-system)
7961 `(("r-annotationdbi" ,r-annotationdbi)
7963 ("r-enrichplot" ,r-enrichplot)
7964 ("r-ggplot2" ,r-ggplot2)
7965 ("r-ggraph" ,r-ggraph)
7966 ("r-graphite" ,r-graphite)
7967 ("r-igraph" ,r-igraph)
7968 ("r-reactome-db" ,r-reactome-db)))
7970 `(("r-knitr" ,r-knitr)))
7971 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7972 (synopsis "Reactome pathway analysis")
7974 "This package provides functions for pathway analysis based on the
7975 REACTOME pathway database. It implements enrichment analysis, gene set
7976 enrichment analysis and several functions for visualization.")
7977 (license license:gpl2)))
7979 (define-public r-ebarrays
7986 (uri (bioconductor-uri "EBarrays" version))
7989 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
7990 (properties `((upstream-name . "EBarrays")))
7991 (build-system r-build-system)
7993 `(("r-biobase" ,r-biobase)
7994 ("r-cluster" ,r-cluster)
7995 ("r-lattice" ,r-lattice)))
7996 (home-page "https://bioconductor.org/packages/EBarrays/")
7997 (synopsis "Gene clustering and differential expression identification")
7999 "EBarrays provides tools for the analysis of replicated/unreplicated
8001 (license license:gpl2+)))
8003 (define-public r-bioccasestudies
8005 (name "r-bioccasestudies")
8010 (uri (bioconductor-uri "BiocCaseStudies" version))
8013 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
8015 `((upstream-name . "BiocCaseStudies")))
8016 (build-system r-build-system)
8017 (propagated-inputs `(("r-biobase" ,r-biobase)))
8018 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
8019 (synopsis "Support for the case studies monograph")
8021 "This package provides software and data to support the case studies
8023 (license license:artistic2.0)))
8025 (define-public r-biocgraph
8027 (name "r-biocgraph")
8032 (uri (bioconductor-uri "biocGraph" version))
8035 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
8036 (properties `((upstream-name . "biocGraph")))
8037 (build-system r-build-system)
8039 `(("r-biocgenerics" ,r-biocgenerics)
8040 ("r-geneplotter" ,r-geneplotter)
8041 ("r-graph" ,r-graph)
8042 ("r-rgraphviz" ,r-rgraphviz)))
8043 (home-page "https://bioconductor.org/packages/biocGraph/")
8044 (synopsis "Graph examples and use cases in Bioinformatics")
8046 "This package provides examples and code that make use of the
8047 different graph related packages produced by Bioconductor.")
8048 (license license:artistic2.0)))
8050 (define-public r-experimenthub
8052 (name "r-experimenthub")
8057 (uri (bioconductor-uri "ExperimentHub" version))
8060 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
8061 (properties `((upstream-name . "ExperimentHub")))
8062 (build-system r-build-system)
8064 `(("r-annotationhub" ,r-annotationhub)
8065 ("r-biocfilecache" ,r-biocfilecache)
8066 ("r-biocgenerics" ,r-biocgenerics)
8067 ("r-biocmanager" ,r-biocmanager)
8069 ("r-rappdirs" ,r-rappdirs)
8070 ("r-s4vectors" ,r-s4vectors)))
8072 `(("r-knitr" ,r-knitr)))
8073 (home-page "https://bioconductor.org/packages/ExperimentHub/")
8074 (synopsis "Client to access ExperimentHub resources")
8076 "This package provides a client for the Bioconductor ExperimentHub web
8077 resource. ExperimentHub provides a central location where curated data from
8078 experiments, publications or training courses can be accessed. Each resource
8079 has associated metadata, tags and date of modification. The client creates
8080 and manages a local cache of files retrieved enabling quick and reproducible
8082 (license license:artistic2.0)))
8084 (define-public r-multiassayexperiment
8086 (name "r-multiassayexperiment")
8091 (uri (bioconductor-uri "MultiAssayExperiment" version))
8094 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
8096 `((upstream-name . "MultiAssayExperiment")))
8097 (build-system r-build-system)
8099 `(("r-biobase" ,r-biobase)
8100 ("r-biocgenerics" ,r-biocgenerics)
8101 ("r-genomicranges" ,r-genomicranges)
8102 ("r-iranges" ,r-iranges)
8103 ("r-s4vectors" ,r-s4vectors)
8104 ("r-summarizedexperiment" ,r-summarizedexperiment)
8105 ("r-tidyr" ,r-tidyr)))
8107 `(("r-knitr" ,r-knitr)))
8108 (home-page "https://waldronlab.io/MultiAssayExperiment/")
8109 (synopsis "Integration of multi-omics experiments in Bioconductor")
8111 "MultiAssayExperiment harmonizes data management of multiple assays
8112 performed on an overlapping set of specimens. It provides a familiar
8113 Bioconductor user experience by extending concepts from
8114 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
8115 classes for individual assays, and allowing subsetting by genomic ranges or
8117 (license license:artistic2.0)))
8119 (define-public r-bioconcotk
8121 (name "r-bioconcotk")
8126 (uri (bioconductor-uri "BiocOncoTK" version))
8129 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
8130 (properties `((upstream-name . "BiocOncoTK")))
8131 (build-system r-build-system)
8133 `(("r-bigrquery" ,r-bigrquery)
8135 ("r-complexheatmap" ,r-complexheatmap)
8136 ("r-curatedtcgadata" ,r-curatedtcgadata)
8138 ("r-dplyr" ,r-dplyr)
8140 ("r-genomicfeatures" ,r-genomicfeatures)
8141 ("r-genomicranges" ,r-genomicranges)
8142 ("r-ggplot2" ,r-ggplot2)
8143 ("r-ggpubr" ,r-ggpubr)
8144 ("r-graph" ,r-graph)
8146 ("r-iranges" ,r-iranges)
8147 ("r-magrittr" ,r-magrittr)
8149 ("r-rgraphviz" ,r-rgraphviz)
8150 ("r-rjson" ,r-rjson)
8151 ("r-s4vectors" ,r-s4vectors)
8152 ("r-scales" ,r-scales)
8153 ("r-shiny" ,r-shiny)
8154 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8156 `(("r-knitr" ,r-knitr)))
8157 (home-page "https://bioconductor.org/packages/BiocOncoTK")
8158 (synopsis "Bioconductor components for general cancer genomics")
8160 "The purpose of this package is to provide a central interface to various
8161 tools for genome-scale analysis of cancer studies.")
8162 (license license:artistic2.0)))
8164 (define-public r-biocor
8171 (uri (bioconductor-uri "BioCor" version))
8174 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
8175 (properties `((upstream-name . "BioCor")))
8176 (build-system r-build-system)
8178 `(("r-biocparallel" ,r-biocparallel)
8179 ("r-gseabase" ,r-gseabase)
8180 ("r-matrix" ,r-matrix)))
8182 `(("r-knitr" ,r-knitr)))
8183 (home-page "https://llrs.github.io/BioCor/")
8184 (synopsis "Functional similarities")
8186 "This package provides tools to calculate functional similarities based
8187 on the pathways described on KEGG and REACTOME or in gene sets. These
8188 similarities can be calculated for pathways or gene sets, genes, or clusters
8189 and combined with other similarities. They can be used to improve networks,
8190 gene selection, testing relationships, and so on.")
8191 (license license:expat)))
8193 (define-public r-biocpkgtools
8195 (name "r-biocpkgtools")
8200 (uri (bioconductor-uri "BiocPkgTools" version))
8203 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
8204 (properties `((upstream-name . "BiocPkgTools")))
8205 (build-system r-build-system)
8207 `(("r-biocfilecache" ,r-biocfilecache)
8208 ("r-biocmanager" ,r-biocmanager)
8209 ("r-biocviews" ,r-biocviews)
8210 ("r-dplyr" ,r-dplyr)
8213 ("r-graph" ,r-graph)
8214 ("r-htmltools" ,r-htmltools)
8215 ("r-htmlwidgets" ,r-htmlwidgets)
8217 ("r-igraph" ,r-igraph)
8218 ("r-jsonlite" ,r-jsonlite)
8219 ("r-magrittr" ,r-magrittr)
8220 ("r-rappdirs" ,r-rappdirs)
8222 ("r-readr" ,r-readr)
8224 ("r-rlang" ,r-rlang)
8225 ("r-rvest" ,r-rvest)
8226 ("r-stringr" ,r-stringr)
8227 ("r-tibble" ,r-tibble)
8228 ("r-tidyr" ,r-tidyr)
8229 ("r-tidyselect" ,r-tidyselect)
8230 ("r-xml2" ,r-xml2)))
8232 `(("r-knitr" ,r-knitr)))
8233 (home-page "https://github.com/seandavi/BiocPkgTools")
8234 (synopsis "Collection of tools for learning about Bioconductor packages")
8236 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8237 and build status. This package is a simple collection of functions to access
8238 that metadata from R. The goal is to expose metadata for data mining and
8239 value-added functionality such as package searching, text mining, and
8240 analytics on packages.")
8241 (license license:expat)))
8243 (define-public r-biocset
8250 (uri (bioconductor-uri "BiocSet" version))
8253 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
8254 (properties `((upstream-name . "BiocSet")))
8255 (build-system r-build-system)
8257 `(("r-annotationdbi" ,r-annotationdbi)
8258 ("r-biocio" ,r-biocio)
8259 ("r-dplyr" ,r-dplyr)
8260 ("r-keggrest" ,r-keggrest)
8261 ("r-ontologyindex" ,r-ontologyindex)
8263 ("r-rlang" ,r-rlang)
8264 ("r-s4vectors" ,r-s4vectors)
8265 ("r-tibble" ,r-tibble)
8266 ("r-tidyr" ,r-tidyr)))
8268 `(("r-knitr" ,r-knitr)))
8270 "https://bioconductor.org/packages/BiocSet")
8272 "Representing Different Biological Sets")
8274 "BiocSet displays different biological sets in a triple tibble format.
8275 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
8276 The user has the ability to activate one of these three tibbles to perform
8277 common functions from the @code{dplyr} package. Mapping functionality and
8278 accessing web references for elements/sets are also available in BiocSet.")
8279 (license license:artistic2.0)))
8281 (define-public r-biocworkflowtools
8283 (name "r-biocworkflowtools")
8288 (uri (bioconductor-uri "BiocWorkflowTools" version))
8291 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
8293 `((upstream-name . "BiocWorkflowTools")))
8294 (build-system r-build-system)
8296 `(("r-biocstyle" ,r-biocstyle)
8297 ("r-bookdown" ,r-bookdown)
8298 ("r-git2r" ,r-git2r)
8300 ("r-knitr" ,r-knitr)
8301 ("r-rmarkdown" ,r-rmarkdown)
8302 ("r-rstudioapi" ,r-rstudioapi)
8303 ("r-stringr" ,r-stringr)
8304 ("r-usethis" ,r-usethis)))
8306 `(("r-knitr" ,r-knitr)))
8307 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8308 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8310 "This package provides functions to ease the transition between
8311 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8312 (license license:expat)))
8314 (define-public r-biodist
8321 (uri (bioconductor-uri "bioDist" version))
8324 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
8325 (properties `((upstream-name . "bioDist")))
8326 (build-system r-build-system)
8328 `(("r-biobase" ,r-biobase)
8329 ("r-kernsmooth" ,r-kernsmooth)))
8330 (home-page "https://bioconductor.org/packages/bioDist/")
8331 (synopsis "Different distance measures")
8333 "This package provides a collection of software tools for calculating
8334 distance measures.")
8335 (license license:artistic2.0)))
8337 (define-public r-pcatools
8344 (uri (bioconductor-uri "PCAtools" version))
8347 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
8348 (properties `((upstream-name . "PCAtools")))
8349 (build-system r-build-system)
8351 `(("r-beachmat" ,r-beachmat)
8353 ("r-biocparallel" ,r-biocparallel)
8354 ("r-biocsingular" ,r-biocsingular)
8355 ("r-cowplot" ,r-cowplot)
8356 ("r-delayedarray" ,r-delayedarray)
8357 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8358 ("r-dqrng" ,r-dqrng)
8359 ("r-ggplot2" ,r-ggplot2)
8360 ("r-ggrepel" ,r-ggrepel)
8361 ("r-lattice" ,r-lattice)
8362 ("r-matrix" ,r-matrix)
8364 ("r-reshape2" ,r-reshape2)))
8365 (native-inputs `(("r-knitr" ,r-knitr)))
8366 (home-page "https://github.com/kevinblighe/PCAtools")
8367 (synopsis "PCAtools: everything Principal Components Analysis")
8369 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8370 structure of the data without the need to build any model to represent it.
8371 This \"summary\" of the data is arrived at through a process of reduction that
8372 can transform the large number of variables into a lesser number that are
8373 uncorrelated (i.e. the 'principal components'), while at the same time being
8374 capable of easy interpretation on the original data. PCAtools provides
8375 functions for data exploration via PCA, and allows the user to generate
8376 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8377 can also identify an optimal number of principal components via different
8378 metrics, such as the elbow method and Horn's parallel analysis, which has
8379 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8380 dimensional mass cytometry data.")
8381 (license license:gpl3)))
8383 (define-public r-rgreat
8390 (uri (bioconductor-uri "rGREAT" version))
8393 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
8394 (properties `((upstream-name . "rGREAT")))
8395 (build-system r-build-system)
8397 `(("r-genomicranges" ,r-genomicranges)
8398 ("r-getoptlong" ,r-getoptlong)
8399 ("r-iranges" ,r-iranges)
8400 ("r-rcurl" ,r-rcurl)
8401 ("r-rjson" ,r-rjson)))
8402 (native-inputs `(("r-knitr" ,r-knitr)))
8403 (home-page "https://github.com/jokergoo/rGREAT")
8404 (synopsis "Client for GREAT analysis")
8406 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8407 Tool) analysis automatic by constructing a HTTP POST request according to
8408 user's input and automatically retrieving results from GREAT web server.")
8409 (license license:expat)))
8411 (define-public r-m3c
8418 (uri (bioconductor-uri "M3C" version))
8421 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
8422 (properties `((upstream-name . "M3C")))
8423 (build-system r-build-system)
8425 `(("r-cluster" ,r-cluster)
8426 ("r-corpcor" ,r-corpcor)
8427 ("r-doparallel" ,r-doparallel)
8428 ("r-dosnow" ,r-dosnow)
8429 ("r-foreach" ,r-foreach)
8430 ("r-ggplot2" ,r-ggplot2)
8431 ("r-matrix" ,r-matrix)
8432 ("r-matrixcalc" ,r-matrixcalc)
8433 ("r-rtsne" ,r-rtsne)
8434 ("r-umap" ,r-umap)))
8435 (native-inputs `(("r-knitr" ,r-knitr)))
8436 (home-page "https://bioconductor.org/packages/M3C")
8437 (synopsis "Monte Carlo reference-based consensus clustering")
8439 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8440 simulation to eliminate overestimation of @code{K} and can reject the null
8441 hypothesis @code{K=1}.")
8442 (license license:agpl3+)))
8444 (define-public r-icens
8451 (uri (bioconductor-uri "Icens" version))
8454 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
8455 (properties `((upstream-name . "Icens")))
8456 (build-system r-build-system)
8458 `(("r-survival" ,r-survival)))
8459 (home-page "https://bioconductor.org/packages/Icens")
8460 (synopsis "NPMLE for censored and truncated data")
8462 "This package provides many functions for computing the
8463 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8465 (license license:artistic2.0)))
8467 ;; This is a CRAN package but it depends on r-icens, which is published on
8469 (define-public r-interval
8476 (uri (cran-uri "interval" version))
8479 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
8480 (properties `((upstream-name . "interval")))
8481 (build-system r-build-system)
8483 `(("r-icens" ,r-icens)
8484 ("r-mlecens" ,r-mlecens)
8486 ("r-survival" ,r-survival)))
8487 (home-page "https://cran.r-project.org/web/packages/interval/")
8488 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8490 "This package provides functions to fit nonparametric survival curves,
8491 plot them, and perform logrank or Wilcoxon type tests.")
8492 (license license:gpl2+)))
8494 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8495 ;; Bioconductor package.
8496 (define-public r-fhtest
8503 (uri (cran-uri "FHtest" version))
8506 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
8507 (properties `((upstream-name . "FHtest")))
8508 (build-system r-build-system)
8510 `(("r-interval" ,r-interval)
8511 ("r-kmsurv" ,r-kmsurv)
8514 ("r-survival" ,r-survival)))
8515 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8516 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8518 "This package provides functions to compare two or more survival curves
8522 @item The Fleming-Harrington test for right-censored data based on
8523 permutations and on counting processes.
8524 @item An extension of the Fleming-Harrington test for interval-censored data
8525 based on a permutation distribution and on a score vector distribution.
8528 (license license:gpl2+)))
8530 (define-public r-fourcseq
8537 (uri (bioconductor-uri "FourCSeq" version))
8539 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
8540 (properties `((upstream-name . "FourCSeq")))
8541 (build-system r-build-system)
8543 `(("r-biobase" ,r-biobase)
8544 ("r-biostrings" ,r-biostrings)
8545 ("r-deseq2" ,r-deseq2)
8547 ("r-genomicalignments" ,r-genomicalignments)
8548 ("r-genomicranges" ,r-genomicranges)
8549 ("r-ggbio" ,r-ggbio)
8550 ("r-ggplot2" ,r-ggplot2)
8551 ("r-gtools" ,r-gtools)
8553 ("r-matrix" ,r-matrix)
8554 ("r-reshape2" ,r-reshape2)
8555 ("r-rsamtools" ,r-rsamtools)
8556 ("r-rtracklayer" ,r-rtracklayer)
8557 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8559 `(("r-knitr" ,r-knitr)))
8561 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
8562 (synopsis "Analysis of multiplexed 4C sequencing data")
8564 "This package is an R package dedicated to the analysis of (multiplexed)
8565 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
8566 interactions between DNA elements and identify differential interactions
8567 between conditions. The statistical analysis in R starts with individual bam
8568 files for each sample as inputs. To obtain these files, the package contains
8569 a Python script to demultiplex libraries and trim off primer sequences. With
8570 a standard alignment software the required bam files can be then be
8572 (license license:gpl3+)))
8574 (define-public r-preprocesscore
8576 (name "r-preprocesscore")
8581 (uri (bioconductor-uri "preprocessCore" version))
8584 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
8586 `((upstream-name . "preprocessCore")))
8587 (build-system r-build-system)
8588 (home-page "https://github.com/bmbolstad/preprocessCore")
8589 (synopsis "Collection of pre-processing functions")
8591 "This package provides a library of core pre-processing and normalization
8593 (license license:lgpl2.0+)))
8595 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
8596 ;; Bioconductor package.
8597 (define-public r-wgcna
8604 (uri (cran-uri "WGCNA" version))
8607 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
8608 (properties `((upstream-name . "WGCNA")))
8609 (build-system r-build-system)
8611 `(("r-annotationdbi" ,r-annotationdbi)
8612 ("r-doparallel" ,r-doparallel)
8613 ("r-dynamictreecut" ,r-dynamictreecut)
8614 ("r-fastcluster" ,r-fastcluster)
8615 ("r-foreach" ,r-foreach)
8616 ("r-go-db" ,r-go-db)
8617 ("r-hmisc" ,r-hmisc)
8618 ("r-impute" ,r-impute)
8620 ("r-survival" ,r-survival)
8621 ("r-matrixstats" ,r-matrixstats)
8622 ("r-preprocesscore" ,r-preprocesscore)))
8624 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
8625 (synopsis "Weighted correlation network analysis")
8627 "This package provides functions necessary to perform Weighted
8628 Correlation Network Analysis on high-dimensional data. It includes functions
8629 for rudimentary data cleaning, construction and summarization of correlation
8630 networks, module identification and functions for relating both variables and
8631 modules to sample traits. It also includes a number of utility functions for
8632 data manipulation and visualization.")
8633 (license license:gpl2+)))
8635 (define-public r-rgraphviz
8637 (name "r-rgraphviz")
8642 (uri (bioconductor-uri "Rgraphviz" version))
8645 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
8646 (properties `((upstream-name . "Rgraphviz")))
8647 (build-system r-build-system)
8650 (modify-phases %standard-phases
8651 (add-after 'unpack 'make-reproducible
8653 ;; The replacement value is taken from src/graphviz/builddate.h
8654 (substitute* "src/graphviz/configure"
8655 (("VERSION_DATE=.*")
8656 "VERSION_DATE=20200427.2341\n"))
8658 ;; FIXME: Rgraphviz bundles the sources of an older variant of
8659 ;; graphviz. It does not build with the latest version of graphviz, so
8660 ;; we do not add graphviz to the inputs.
8661 (inputs `(("zlib" ,zlib)))
8663 `(("r-graph" ,r-graph)))
8665 `(("pkg-config" ,pkg-config)))
8666 (home-page "https://bioconductor.org/packages/Rgraphviz")
8667 (synopsis "Plotting capabilities for R graph objects")
8669 "This package interfaces R with the graphviz library for plotting R graph
8670 objects from the @code{graph} package.")
8671 (license license:epl1.0)))
8673 (define-public r-fithic
8679 (uri (bioconductor-uri "FitHiC" version))
8682 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
8683 (properties `((upstream-name . "FitHiC")))
8684 (build-system r-build-system)
8686 `(("r-data-table" ,r-data-table)
8687 ("r-fdrtool" ,r-fdrtool)
8688 ("r-rcpp" ,r-rcpp)))
8690 `(("r-knitr" ,r-knitr)))
8691 (home-page "https://bioconductor.org/packages/FitHiC")
8692 (synopsis "Confidence estimation for intra-chromosomal contact maps")
8694 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
8695 intra-chromosomal contact maps produced by genome-wide genome architecture
8696 assays such as Hi-C.")
8697 (license license:gpl2+)))
8699 (define-public r-hitc
8705 (uri (bioconductor-uri "HiTC" version))
8708 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
8709 (properties `((upstream-name . "HiTC")))
8710 (build-system r-build-system)
8712 `(("r-biostrings" ,r-biostrings)
8713 ("r-genomeinfodb" ,r-genomeinfodb)
8714 ("r-genomicranges" ,r-genomicranges)
8715 ("r-iranges" ,r-iranges)
8716 ("r-matrix" ,r-matrix)
8717 ("r-rcolorbrewer" ,r-rcolorbrewer)
8718 ("r-rtracklayer" ,r-rtracklayer)))
8719 (home-page "https://bioconductor.org/packages/HiTC")
8720 (synopsis "High throughput chromosome conformation capture analysis")
8722 "The HiTC package was developed to explore high-throughput \"C\" data
8723 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
8724 quality controls, normalization, visualization, and further analysis are also
8726 (license license:artistic2.0)))
8728 (define-public r-hdf5array
8730 (name "r-hdf5array")
8735 (uri (bioconductor-uri "HDF5Array" version))
8738 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
8739 (properties `((upstream-name . "HDF5Array")))
8740 (build-system r-build-system)
8743 (modify-phases %standard-phases
8744 (add-after 'unpack 'fix-linking
8746 (substitute* "src/Makevars"
8747 ;; This is to avoid having a plain directory on the list of
8748 ;; libraries to link.
8749 (("\\(RHDF5LIB_LIBS\\)" match)
8750 (string-append match "/libhdf5.a")))
8755 `(("r-biocgenerics" ,r-biocgenerics)
8756 ("r-delayedarray" ,r-delayedarray)
8757 ("r-iranges" ,r-iranges)
8758 ("r-matrix" ,r-matrix)
8759 ("r-rhdf5" ,r-rhdf5)
8760 ("r-rhdf5lib" ,r-rhdf5lib)
8761 ("r-s4vectors" ,r-s4vectors)))
8762 (home-page "https://bioconductor.org/packages/HDF5Array")
8763 (synopsis "HDF5 back end for DelayedArray objects")
8764 (description "This package provides an array-like container for convenient
8765 access and manipulation of HDF5 datasets. It supports delayed operations and
8767 (license license:artistic2.0)))
8769 (define-public r-rhdf5lib
8776 (uri (bioconductor-uri "Rhdf5lib" version))
8779 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
8780 (modules '((guix build utils)))
8783 ;; Delete bundled binaries
8784 (delete-file-recursively "src/wininclude/")
8785 (delete-file-recursively "src/winlib-4.9.3/")
8786 (delete-file-recursively "src/winlib-8.3.0/")
8787 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
8789 (properties `((upstream-name . "Rhdf5lib")))
8790 (build-system r-build-system)
8793 (modify-phases %standard-phases
8794 (add-after 'unpack 'do-not-use-bundled-hdf5
8795 (lambda* (#:key inputs #:allow-other-keys)
8796 (for-each delete-file '("configure" "configure.ac"))
8797 ;; Do not make other packages link with the proprietary libsz.
8798 (substitute* "R/zzz.R"
8799 ((" \"%s/libsz.a\"") ""))
8800 (with-directory-excursion "src"
8801 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
8802 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
8804 ;; Remove timestamp and host system information to make
8805 ;; the build reproducible.
8806 (substitute* "hdf5/src/libhdf5.settings.in"
8807 (("Configured on: @CONFIG_DATE@")
8808 "Configured on: Guix")
8809 (("Uname information:.*")
8810 "Uname information: Linux\n")
8811 ;; Remove unnecessary store reference.
8813 "C Compiler: GCC\n"))
8814 (rename-file "hdf5/src/libhdf5.settings.in"
8815 "hdf5/src/libhdf5.settings")
8816 (rename-file "Makevars.in" "Makevars")
8817 (substitute* "Makevars"
8818 (("@ZLIB_LIB@") "-lz")
8819 (("@ZLIB_INCLUDE@") "")
8820 (("HDF5_CXX_LIB=.*")
8821 (string-append "HDF5_CXX_LIB="
8822 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
8824 (string-append "HDF5_LIB="
8825 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
8826 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
8827 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
8828 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
8829 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
8831 (string-append "HDF5_HL_LIB="
8832 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
8833 (("HDF5_HL_CXX_LIB=.*")
8834 (string-append "HDF5_HL_CXX_LIB="
8835 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
8836 ;; szip is non-free software
8837 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
8838 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
8843 `(("hdf5" ,hdf5-1.10)))
8845 `(("hdf5-source" ,(package-source hdf5-1.10))
8846 ("r-knitr" ,r-knitr)))
8847 (home-page "https://bioconductor.org/packages/Rhdf5lib")
8848 (synopsis "HDF5 library as an R package")
8849 (description "This package provides C and C++ HDF5 libraries for use in R
8851 (license license:artistic2.0)))
8853 (define-public r-beachmat
8860 (uri (bioconductor-uri "beachmat" version))
8863 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
8864 (build-system r-build-system)
8866 `(("r-biocgenerics" ,r-biocgenerics)
8867 ("r-delayedarray" ,r-delayedarray)
8868 ("r-matrix" ,r-matrix)))
8870 `(("r-knitr" ,r-knitr)))
8871 (home-page "https://bioconductor.org/packages/beachmat")
8872 (synopsis "Compiling Bioconductor to handle each matrix type")
8873 (description "This package provides a consistent C++ class interface for a
8874 variety of commonly used matrix types, including sparse and HDF5-backed
8876 (license license:gpl3)))
8878 ;; This package includes files that have been taken from kentutils. Some
8879 ;; parts of kentutils are not released under a free license, but this package
8880 ;; only uses files that are also found in the free parts of kentutils.
8881 (define-public r-cner
8888 (uri (bioconductor-uri "CNEr" version))
8890 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
8891 (properties `((upstream-name . "CNEr")))
8892 (build-system r-build-system)
8893 (inputs `(("zlib" ,zlib)))
8895 `(("r-annotate" ,r-annotate)
8896 ("r-biocgenerics" ,r-biocgenerics)
8897 ("r-biostrings" ,r-biostrings)
8899 ("r-genomeinfodb" ,r-genomeinfodb)
8900 ("r-genomicalignments" ,r-genomicalignments)
8901 ("r-genomicranges" ,r-genomicranges)
8902 ("r-ggplot2" ,r-ggplot2)
8903 ("r-go-db" ,r-go-db)
8904 ("r-iranges" ,r-iranges)
8905 ("r-keggrest" ,r-keggrest)
8906 ("r-powerlaw" ,r-powerlaw)
8907 ("r-r-utils" ,r-r-utils)
8908 ("r-readr" ,r-readr)
8909 ("r-reshape2" ,r-reshape2)
8910 ("r-rsqlite" ,r-rsqlite)
8911 ("r-rtracklayer" ,r-rtracklayer)
8912 ("r-s4vectors" ,r-s4vectors)
8913 ("r-xvector" ,r-xvector)))
8915 `(("r-knitr" ,r-knitr)))
8916 (home-page "https://github.com/ge11232002/CNEr")
8917 (synopsis "CNE Detection and Visualization")
8919 "This package provides tools for large-scale identification and
8920 advanced visualization of sets of conserved noncoding elements.")
8921 ;; For all files in src/ucsc "license is hereby granted for all use -
8922 ;; public, private or commercial"; this includes those files that don't
8923 ;; have a license header, because they are included in the free parts of
8924 ;; the kentutils package.
8925 (license (list license:gpl2
8926 (license:non-copyleft
8927 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
8929 (define-public r-tfbstools
8931 (name "r-tfbstools")
8936 (uri (bioconductor-uri "TFBSTools" version))
8939 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
8940 (properties `((upstream-name . "TFBSTools")))
8941 (build-system r-build-system)
8943 `(("r-biobase" ,r-biobase)
8944 ("r-biocgenerics" ,r-biocgenerics)
8945 ("r-biocparallel" ,r-biocparallel)
8946 ("r-biostrings" ,r-biostrings)
8947 ("r-bsgenome" ,r-bsgenome)
8948 ("r-catools" ,r-catools)
8951 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
8952 ("r-genomeinfodb" ,r-genomeinfodb)
8953 ("r-genomicranges" ,r-genomicranges)
8954 ("r-gtools" ,r-gtools)
8955 ("r-iranges" ,r-iranges)
8956 ("r-rsqlite" ,r-rsqlite)
8957 ("r-rtracklayer" ,r-rtracklayer)
8958 ("r-s4vectors" ,r-s4vectors)
8959 ("r-seqlogo" ,r-seqlogo)
8960 ("r-tfmpvalue" ,r-tfmpvalue)
8962 ("r-xvector" ,r-xvector)))
8963 (native-inputs `(("r-knitr" ,r-knitr)))
8964 (home-page "https://github.com/ge11232002/TFBSTools")
8965 (synopsis "Transcription factor binding site (TFBS) analysis")
8967 "TFBSTools is a package for the analysis and manipulation of
8968 transcription factor binding sites. It includes matrices conversion
8969 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
8970 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
8971 scan putative TFBS from sequence/alignment, query JASPAR database and
8972 provides a wrapper of de novo motif discovery software.")
8973 (license license:gpl2)))
8975 (define-public r-singlecellexperiment
8977 (name "r-singlecellexperiment")
8982 (uri (bioconductor-uri "SingleCellExperiment" version))
8985 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
8987 `((upstream-name . "SingleCellExperiment")))
8988 (build-system r-build-system)
8990 `(("r-biocgenerics" ,r-biocgenerics)
8991 ("r-s4vectors" ,r-s4vectors)
8992 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8994 `(("r-knitr" ,r-knitr)))
8995 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
8996 (synopsis "S4 classes for single cell data")
8997 (description "This package defines an S4 class for storing data from
8998 single-cell experiments. This includes specialized methods to store and
8999 retrieve spike-in information, dimensionality reduction coordinates and size
9000 factors for each cell, along with the usual metadata for genes and
9002 (license license:gpl3)))
9004 (define-public r-scuttle
9011 (uri (bioconductor-uri "scuttle" version))
9014 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
9015 (properties `((upstream-name . "scuttle")))
9016 (build-system r-build-system)
9018 `(("r-beachmat" ,r-beachmat)
9019 ("r-biocgenerics" ,r-biocgenerics)
9020 ("r-biocparallel" ,r-biocparallel)
9021 ("r-delayedarray" ,r-delayedarray)
9022 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9023 ("r-genomicranges" ,r-genomicranges)
9024 ("r-matrix" ,r-matrix)
9026 ("r-s4vectors" ,r-s4vectors)
9027 ("r-singlecellexperiment" ,r-singlecellexperiment)
9028 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9029 (native-inputs `(("r-knitr" ,r-knitr)))
9030 (home-page "https://bioconductor.org/packages/scuttle")
9031 (synopsis "Single-cell RNA-Seq analysis utilities")
9033 "This package provides basic utility functions for performing single-cell
9034 analyses, focusing on simple normalization, quality control and data
9035 transformations. It also provides some helper functions to assist development
9036 of other packages.")
9037 (license license:gpl3)))
9039 (define-public r-scater
9045 (uri (bioconductor-uri "scater" version))
9048 "14f7yw277nykxmcm7wlhlsf3nizpwzz24hax1icx73lavfxmc535"))))
9049 (build-system r-build-system)
9051 `(("r-biocgenerics" ,r-biocgenerics)
9052 ("r-biocneighbors" ,r-biocneighbors)
9053 ("r-biocparallel" ,r-biocparallel)
9054 ("r-biocsingular" ,r-biocsingular)
9055 ("r-delayedarray" ,r-delayedarray)
9056 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9057 ("r-ggbeeswarm" ,r-ggbeeswarm)
9058 ("r-ggplot2" ,r-ggplot2)
9059 ("r-gridextra" ,r-gridextra)
9060 ("r-matrix" ,r-matrix)
9061 ("r-rlang" ,r-rlang)
9062 ("r-s4vectors" ,r-s4vectors)
9063 ("r-scuttle" ,r-scuttle)
9064 ("r-singlecellexperiment" ,r-singlecellexperiment)
9065 ("r-summarizedexperiment" ,r-summarizedexperiment)
9066 ("r-viridis" ,r-viridis)))
9068 `(("r-knitr" ,r-knitr)))
9069 (home-page "https://github.com/davismcc/scater")
9070 (synopsis "Single-cell analysis toolkit for gene expression data in R")
9071 (description "This package provides a collection of tools for doing
9072 various analyses of single-cell RNA-seq gene expression data, with a focus on
9074 (license license:gpl2+)))
9076 (define-public r-scran
9083 (uri (bioconductor-uri "scran" version))
9086 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
9087 (build-system r-build-system)
9089 `(("r-beachmat" ,r-beachmat)
9091 ("r-biocgenerics" ,r-biocgenerics)
9092 ("r-biocneighbors" ,r-biocneighbors)
9093 ("r-biocparallel" ,r-biocparallel)
9094 ("r-biocsingular" ,r-biocsingular)
9095 ("r-bluster" ,r-bluster)
9096 ("r-delayedarray" ,r-delayedarray)
9097 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9098 ("r-dqrng" ,r-dqrng)
9099 ("r-edger" ,r-edger)
9100 ("r-igraph" ,r-igraph)
9101 ("r-limma" ,r-limma)
9102 ("r-matrix" ,r-matrix)
9104 ("r-s4vectors" ,r-s4vectors)
9105 ("r-scuttle" ,r-scuttle)
9106 ("r-singlecellexperiment" ,r-singlecellexperiment)
9107 ("r-statmod" ,r-statmod)
9108 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9110 `(("r-knitr" ,r-knitr)))
9111 (home-page "https://bioconductor.org/packages/scran")
9112 (synopsis "Methods for single-cell RNA-Seq data analysis")
9113 (description "This package implements a variety of low-level analyses of
9114 single-cell RNA-seq data. Methods are provided for normalization of
9115 cell-specific biases, assignment of cell cycle phase, and detection of highly
9116 variable and significantly correlated genes.")
9117 (license license:gpl3)))
9119 (define-public r-sparsematrixstats
9121 (name "r-sparsematrixstats")
9126 (uri (bioconductor-uri "sparseMatrixStats" version))
9129 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
9131 `((upstream-name . "sparseMatrixStats")))
9132 (build-system r-build-system)
9134 `(("r-matrix" ,r-matrix)
9135 ("r-matrixgenerics" ,r-matrixgenerics)
9136 ("r-matrixstats" ,r-matrixstats)
9137 ("r-rcpp" ,r-rcpp)))
9138 (native-inputs `(("r-knitr" ,r-knitr)))
9139 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
9140 (synopsis "Summary statistics for rows and columns of sparse matrices")
9142 "This package provides high performance functions for row and column
9143 operations on sparse matrices. Currently, the optimizations are limited to
9144 data in the column sparse format.")
9145 (license license:expat)))
9147 (define-public r-delayedmatrixstats
9149 (name "r-delayedmatrixstats")
9154 (uri (bioconductor-uri "DelayedMatrixStats" version))
9157 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
9159 `((upstream-name . "DelayedMatrixStats")))
9160 (build-system r-build-system)
9162 `(("r-biocparallel" ,r-biocparallel)
9163 ("r-delayedarray" ,r-delayedarray)
9164 ("r-hdf5array" ,r-hdf5array)
9165 ("r-iranges" ,r-iranges)
9166 ("r-matrix" ,r-matrix)
9167 ("r-matrixgenerics" ,r-matrixgenerics)
9168 ("r-matrixstats" ,r-matrixstats)
9169 ("r-s4vectors" ,r-s4vectors)
9170 ("r-sparsematrixstats" ,r-sparsematrixstats)))
9172 `(("r-knitr" ,r-knitr)))
9173 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
9174 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
9176 "This package provides a port of the @code{matrixStats} API for use with
9177 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
9178 contains high-performing functions operating on rows and columns of
9179 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
9180 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
9181 are optimized per data type and for subsetted calculations such that both
9182 memory usage and processing time is minimized.")
9183 (license license:expat)))
9185 (define-public r-mscoreutils
9187 (name "r-mscoreutils")
9192 (uri (bioconductor-uri "MsCoreUtils" version))
9195 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
9196 (properties `((upstream-name . "MsCoreUtils")))
9197 (build-system r-build-system)
9199 `(("r-mass" ,r-mass)
9201 ("r-s4vectors" ,r-s4vectors)))
9203 `(("r-knitr" ,r-knitr)))
9204 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
9205 (synopsis "Core utils for mass spectrometry data")
9207 "This package defines low-level functions for mass spectrometry data and
9208 is independent of any high-level data structures. These functions include
9209 mass spectra processing functions (noise estimation, smoothing, binning),
9210 quantitative aggregation functions (median polish, robust summarisation,
9211 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
9212 well as misc helper functions, that are used across high-level data structure
9213 within the R for Mass Spectrometry packages.")
9214 (license license:artistic2.0)))
9216 (define-public r-biocio
9223 (uri (bioconductor-uri "BiocIO" version))
9226 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
9227 (properties `((upstream-name . "BiocIO")))
9228 (build-system r-build-system)
9230 `(("r-biocgenerics" ,r-biocgenerics)
9231 ("r-genomicranges" ,r-genomicranges)
9232 ("r-rcurl" ,r-rcurl)
9233 ("r-s4vectors" ,r-s4vectors)))
9235 `(("r-knitr" ,r-knitr)))
9236 (home-page "https://bioconductor.org/packages/BiocIO")
9237 (synopsis "Standard input and output for Bioconductor packages")
9239 "This package implements `import()` and `export()` standard generics for
9240 importing and exporting biological data formats. `import()` supports
9241 whole-file as well as chunk-wise iterative import. The `import()` interface
9242 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
9243 row or element-like components of the file resource), `select()` (on
9244 column-like components of the file resource) and `collect()`. The `import()`
9245 interface optionally provides transparent access to remote (e.g. via https)
9246 as well as local access. Developers can register a file extension, e.g.,
9247 `.loom` for dispatch from character-based URIs to specific `import()` /
9248 `export()` methods based on classes representing file types, e.g.,
9250 (license license:artistic2.0)))
9252 (define-public r-msmseda
9259 (uri (bioconductor-uri "msmsEDA" version))
9262 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
9263 (properties `((upstream-name . "msmsEDA")))
9264 (build-system r-build-system)
9266 `(("r-gplots" ,r-gplots)
9268 ("r-msnbase" ,r-msnbase)
9269 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9271 "https://bioconductor.org/packages/msmsEDA")
9272 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
9274 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
9275 experiments, and visualize de influence of the involved factors.")
9276 (license license:gpl2)))
9278 (define-public r-msmstests
9280 (name "r-msmstests")
9285 (uri (bioconductor-uri "msmsTests" version))
9288 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
9289 (properties `((upstream-name . "msmsTests")))
9290 (build-system r-build-system)
9292 `(("r-edger" ,r-edger)
9293 ("r-msmseda" ,r-msmseda)
9294 ("r-msnbase" ,r-msnbase)
9295 ("r-qvalue" ,r-qvalue)))
9297 "https://bioconductor.org/packages/msmsTests")
9298 (synopsis "Differential LC-MS/MS expression tests")
9300 "This packages provides statistical tests for label-free LC-MS/MS data
9301 by spectral counts, to discover differentially expressed proteins between two
9302 biological conditions. Three tests are available: Poisson GLM regression,
9303 quasi-likelihood GLM regression, and the negative binomial of the edgeR
9304 package.The three models admit blocking factors to control for nuissance
9305 variables.To assure a good level of reproducibility a post-test filter is
9306 available, where we may set the minimum effect size considered biologicaly
9307 relevant, and the minimum expression of the most abundant condition.")
9308 (license license:gpl2)))
9310 (define-public r-catalyst
9317 (uri (bioconductor-uri "CATALYST" version))
9320 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
9321 (properties `((upstream-name . "CATALYST")))
9322 (build-system r-build-system)
9324 `(("r-circlize" ,r-circlize)
9325 ("r-complexheatmap" ,r-complexheatmap)
9326 ("r-consensusclusterplus" ,r-consensusclusterplus)
9327 ("r-cowplot" ,r-cowplot)
9328 ("r-data-table" ,r-data-table)
9329 ("r-dplyr" ,r-dplyr)
9331 ("r-flowcore" ,r-flowcore)
9332 ("r-flowsom" ,r-flowsom)
9333 ("r-ggplot2" ,r-ggplot2)
9334 ("r-ggrepel" ,r-ggrepel)
9335 ("r-ggridges" ,r-ggridges)
9336 ("r-gridextra" ,r-gridextra)
9337 ("r-magrittr" ,r-magrittr)
9338 ("r-matrix" ,r-matrix)
9339 ("r-matrixstats" ,r-matrixstats)
9341 ("r-purrr" ,r-purrr)
9342 ("r-rcolorbrewer" ,r-rcolorbrewer)
9343 ("r-reshape2" ,r-reshape2)
9344 ("r-rtsne" ,r-rtsne)
9345 ("r-s4vectors" ,r-s4vectors)
9346 ("r-scales" ,r-scales)
9347 ("r-scater" ,r-scater)
9348 ("r-singlecellexperiment" ,r-singlecellexperiment)
9349 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9351 `(("r-knitr" ,r-knitr)))
9353 "https://github.com/HelenaLC/CATALYST")
9354 (synopsis "Cytometry data analysis tools")
9356 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
9357 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
9358 reporters to label antibodies, thereby substantially decreasing spectral
9359 overlap and allowing for examination of over 50 parameters at the single cell
9360 level. While spectral overlap is significantly less pronounced in CyTOF than
9361 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
9362 and oxide formation can impede data interpretability. We designed
9363 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
9364 preprocessing of cytometry data, including i) normalization using bead
9365 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
9366 (license license:gpl2+)))
9368 (define-public r-erma
9375 (uri (bioconductor-uri "erma" version))
9378 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
9379 (build-system r-build-system)
9381 `(("r-annotationdbi" ,r-annotationdbi)
9382 ("r-biobase" ,r-biobase)
9383 ("r-biocgenerics" ,r-biocgenerics)
9384 ("r-biocparallel" ,r-biocparallel)
9385 ("r-genomeinfodb" ,r-genomeinfodb)
9386 ("r-genomicfiles" ,r-genomicfiles)
9387 ("r-genomicranges" ,r-genomicranges)
9388 ("r-ggplot2" ,r-ggplot2)
9389 ("r-homo-sapiens" ,r-homo-sapiens)
9390 ("r-iranges" ,r-iranges)
9391 ("r-rtracklayer" ,r-rtracklayer)
9392 ("r-s4vectors" ,r-s4vectors)
9393 ("r-shiny" ,r-shiny)
9394 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9396 `(("r-knitr" ,r-knitr)))
9397 (home-page "https://bioconductor.org/packages/erma")
9398 (synopsis "Epigenomic road map adventures")
9400 "The epigenomics road map describes locations of epigenetic marks in DNA
9401 from a variety of cell types. Of interest are locations of histone
9402 modifications, sites of DNA methylation, and regions of accessible chromatin.
9403 This package presents a selection of elements of the road map including
9404 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
9405 by Ernst and Kellis.")
9406 (license license:artistic2.0)))
9408 (define-public r-ggbio
9415 (uri (bioconductor-uri "ggbio" version))
9418 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
9419 (build-system r-build-system)
9422 (modify-phases %standard-phases
9423 ;; See https://github.com/tengfei/ggbio/issues/117
9424 ;; This fix will be included in the next release.
9425 (add-after 'unpack 'fix-typo
9427 (substitute* "R/GGbio-class.R"
9428 (("fechable") "fetchable"))
9431 `(("r-annotationdbi" ,r-annotationdbi)
9432 ("r-annotationfilter" ,r-annotationfilter)
9433 ("r-biobase" ,r-biobase)
9434 ("r-biocgenerics" ,r-biocgenerics)
9435 ("r-biostrings" ,r-biostrings)
9436 ("r-biovizbase" ,r-biovizbase)
9437 ("r-bsgenome" ,r-bsgenome)
9438 ("r-ensembldb" ,r-ensembldb)
9439 ("r-genomeinfodb" ,r-genomeinfodb)
9440 ("r-genomicalignments" ,r-genomicalignments)
9441 ("r-genomicfeatures" ,r-genomicfeatures)
9442 ("r-genomicranges" ,r-genomicranges)
9443 ("r-ggally" ,r-ggally)
9444 ("r-ggplot2" ,r-ggplot2)
9445 ("r-gridextra" ,r-gridextra)
9446 ("r-gtable" ,r-gtable)
9447 ("r-hmisc" ,r-hmisc)
9448 ("r-iranges" ,r-iranges)
9449 ("r-organismdbi" ,r-organismdbi)
9450 ("r-reshape2" ,r-reshape2)
9451 ("r-rlang" ,r-rlang)
9452 ("r-rsamtools" ,r-rsamtools)
9453 ("r-rtracklayer" ,r-rtracklayer)
9454 ("r-s4vectors" ,r-s4vectors)
9455 ("r-scales" ,r-scales)
9456 ("r-summarizedexperiment" ,r-summarizedexperiment)
9457 ("r-variantannotation" ,r-variantannotation)))
9459 `(("r-knitr" ,r-knitr)))
9460 (home-page "http://www.tengfei.name/ggbio/")
9461 (synopsis "Visualization tools for genomic data")
9463 "The ggbio package extends and specializes the grammar of graphics for
9464 biological data. The graphics are designed to answer common scientific
9465 questions, in particular those often asked of high throughput genomics data.
9466 All core Bioconductor data structures are supported, where appropriate. The
9467 package supports detailed views of particular genomic regions, as well as
9468 genome-wide overviews. Supported overviews include ideograms and grand linear
9469 views. High-level plots include sequence fragment length, edge-linked
9470 interval to data view, mismatch pileup, and several splicing summaries.")
9471 (license license:artistic2.0)))
9473 (define-public r-gqtlbase
9480 (uri (bioconductor-uri "gQTLBase" version))
9483 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
9484 (properties `((upstream-name . "gQTLBase")))
9485 (build-system r-build-system)
9488 (modify-phases %standard-phases
9489 ;; This is an upstream bug.
9490 (add-after 'unpack 'fix-imports
9492 (substitute* "NAMESPACE"
9493 ((".*maxffmode.*") "")
9494 (("importFrom\\(ff,.*") "import(ff)\n"))
9497 `(("r-batchjobs" ,r-batchjobs)
9498 ("r-bbmisc" ,r-bbmisc)
9499 ("r-biocgenerics" ,r-biocgenerics)
9501 ("r-doparallel" ,r-doparallel)
9503 ("r-ffbase" ,r-ffbase)
9504 ("r-foreach" ,r-foreach)
9505 ("r-genomicfiles" ,r-genomicfiles)
9506 ("r-genomicranges" ,r-genomicranges)
9507 ("r-rtracklayer" ,r-rtracklayer)
9508 ("r-s4vectors" ,r-s4vectors)
9509 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9511 `(("r-knitr" ,r-knitr)))
9512 (home-page "https://bioconductor.org/packages/gQTLBase")
9513 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
9515 "The purpose of this package is to simplify the storage and interrogation
9516 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
9518 (license license:artistic2.0)))
9520 (define-public r-gqtlstats
9522 (name "r-gqtlstats")
9527 (uri (bioconductor-uri "gQTLstats" version))
9530 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
9531 (properties `((upstream-name . "gQTLstats")))
9532 (build-system r-build-system)
9534 `(("r-annotationdbi" ,r-annotationdbi)
9535 ("r-batchjobs" ,r-batchjobs)
9536 ("r-bbmisc" ,r-bbmisc)
9537 ("r-beeswarm" ,r-beeswarm)
9538 ("r-biobase" ,r-biobase)
9539 ("r-biocgenerics" ,r-biocgenerics)
9540 ("r-doparallel" ,r-doparallel)
9541 ("r-dplyr" ,r-dplyr)
9543 ("r-ffbase" ,r-ffbase)
9544 ("r-foreach" ,r-foreach)
9545 ("r-genomeinfodb" ,r-genomeinfodb)
9546 ("r-genomicfeatures" ,r-genomicfeatures)
9547 ("r-genomicfiles" ,r-genomicfiles)
9548 ("r-genomicranges" ,r-genomicranges)
9549 ("r-ggbeeswarm" ,r-ggbeeswarm)
9550 ("r-ggplot2" ,r-ggplot2)
9551 ("r-gqtlbase" ,r-gqtlbase)
9552 ("r-hardyweinberg" ,r-hardyweinberg)
9553 ("r-homo-sapiens" ,r-homo-sapiens)
9554 ("r-iranges" ,r-iranges)
9555 ("r-limma" ,r-limma)
9557 ("r-plotly" ,r-plotly)
9558 ("r-reshape2" ,r-reshape2)
9559 ("r-s4vectors" ,r-s4vectors)
9560 ("r-shiny" ,r-shiny)
9561 ("r-snpstats" ,r-snpstats)
9562 ("r-summarizedexperiment" ,r-summarizedexperiment)
9563 ("r-variantannotation" ,r-variantannotation)))
9565 `(("r-knitr" ,r-knitr)))
9566 (home-page "https://bioconductor.org/packages/gQTLstats")
9567 (synopsis "Computationally efficient analysis for eQTL and allied studies")
9569 "This package provides tools for the computationally efficient analysis
9570 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
9571 The software in this package aims to support refinements and functional
9572 interpretation of members of a collection of association statistics on a
9573 family of feature/genome hypotheses.")
9574 (license license:artistic2.0)))
9576 (define-public r-gviz
9583 (uri (bioconductor-uri "Gviz" version))
9586 "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
9587 (properties `((upstream-name . "Gviz")))
9588 (build-system r-build-system)
9590 `(("r-annotationdbi" ,r-annotationdbi)
9591 ("r-biobase" ,r-biobase)
9592 ("r-biocgenerics" ,r-biocgenerics)
9593 ("r-biomart" ,r-biomart)
9594 ("r-biostrings" ,r-biostrings)
9595 ("r-biovizbase" ,r-biovizbase)
9596 ("r-bsgenome" ,r-bsgenome)
9597 ("r-digest" ,r-digest)
9598 ("r-ensembldb" ,r-ensembldb)
9599 ("r-genomeinfodb" ,r-genomeinfodb)
9600 ("r-genomicalignments" ,r-genomicalignments)
9601 ("r-genomicfeatures" ,r-genomicfeatures)
9602 ("r-genomicranges" ,r-genomicranges)
9603 ("r-iranges" ,r-iranges)
9604 ("r-lattice" ,r-lattice)
9605 ("r-latticeextra" ,r-latticeextra)
9606 ("r-matrixstats" ,r-matrixstats)
9607 ("r-rcolorbrewer" ,r-rcolorbrewer)
9608 ("r-rsamtools" ,r-rsamtools)
9609 ("r-rtracklayer" ,r-rtracklayer)
9610 ("r-s4vectors" ,r-s4vectors)
9611 ("r-xvector" ,r-xvector)))
9613 `(("r-knitr" ,r-knitr)))
9614 (home-page "https://bioconductor.org/packages/Gviz")
9615 (synopsis "Plotting data and annotation information along genomic coordinates")
9617 "Genomic data analyses requires integrated visualization of known genomic
9618 information and new experimental data. Gviz uses the biomaRt and the
9619 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
9620 and translates this to e.g. gene/transcript structures in viewports of the
9621 grid graphics package. This results in genomic information plotted together
9623 (license license:artistic2.0)))
9625 (define-public r-gwascat
9632 (uri (bioconductor-uri "gwascat" version))
9635 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
9636 (build-system r-build-system)
9638 `(("r-annotationdbi" ,r-annotationdbi)
9639 ("r-biocfilecache" ,r-biocfilecache)
9640 ("r-biostrings" ,r-biostrings)
9641 ("r-genomeinfodb" ,r-genomeinfodb)
9642 ("r-genomicfeatures" ,r-genomicfeatures)
9643 ("r-genomicranges" ,r-genomicranges)
9644 ("r-iranges" ,r-iranges)
9645 ("r-readr" ,r-readr)
9646 ("r-s4vectors" ,r-s4vectors)
9647 ("r-snpstats" ,r-snpstats)
9648 ("r-variantannotation" ,r-variantannotation)))
9650 `(("r-knitr" ,r-knitr)))
9651 (home-page "https://bioconductor.org/packages/gwascat")
9652 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
9654 "This package provides tools for representing and modeling data in the
9655 EMBL-EBI GWAS catalog.")
9656 (license license:artistic2.0)))
9658 (define-public r-kegggraph
9660 (name "r-kegggraph")
9665 (uri (bioconductor-uri "KEGGgraph" version))
9667 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
9668 (properties `((upstream-name . "KEGGgraph")))
9669 (build-system r-build-system)
9671 `(("r-graph" ,r-graph)
9672 ("r-rcurl" ,r-rcurl)
9674 (home-page "https://bioconductor.org/packages/KEGGgraph")
9675 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
9677 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
9678 object as well as a collection of tools to analyze, dissect and visualize these
9679 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
9680 maintaining all essential pathway attributes. The package offers
9681 functionalities including parsing, graph operation, visualization and etc.")
9682 (license license:gpl2+)))
9684 (define-public r-ldblock
9691 (uri (bioconductor-uri "ldblock" version))
9694 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
9695 (build-system r-build-system)
9697 `(("r-biocgenerics" ,r-biocgenerics)
9698 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
9699 ("r-ensembldb" ,r-ensembldb)
9700 ("r-genomeinfodb" ,r-genomeinfodb)
9701 ("r-genomicfiles" ,r-genomicfiles)
9703 ("r-matrix" ,r-matrix)
9704 ("r-rsamtools" ,r-rsamtools)
9705 ("r-snpstats" ,r-snpstats)
9706 ("r-variantannotation" ,r-variantannotation)))
9708 `(("r-knitr" ,r-knitr)))
9709 (home-page "https://bioconductor.org/packages/ldblock")
9710 (synopsis "Data structures for linkage disequilibrium measures in populations")
9712 "This package defines data structures for @dfn{linkage
9713 disequilibrium} (LD) measures in populations. Its purpose is to simplify
9714 handling of existing population-level data for the purpose of flexibly
9715 defining LD blocks.")
9716 (license license:artistic2.0)))
9718 ;; This is a CRAN package, but it depends on r-snpstats, which is a
9719 ;; Bioconductor package.
9720 (define-public r-ldheatmap
9722 (name "r-ldheatmap")
9727 (uri (cran-uri "LDheatmap" version))
9730 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
9731 (properties `((upstream-name . "LDheatmap")))
9732 (build-system r-build-system)
9734 `(("r-genetics" ,r-genetics)
9736 ("r-snpstats" ,r-snpstats)))
9737 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
9738 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
9740 "This package provides tools to produce a graphical display, as a heat
9741 map, of measures of pairwise linkage disequilibria between SNPs. Users may
9742 optionally include the physical locations or genetic map distances of each SNP
9744 (license license:gpl3)))
9746 (define-public r-pathview
9753 (uri (bioconductor-uri "pathview" version))
9755 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
9756 (properties `((upstream-name . "pathview")))
9757 (build-system r-build-system)
9759 `(("r-annotationdbi" ,r-annotationdbi)
9760 ("r-graph" ,r-graph)
9761 ("r-kegggraph" ,r-kegggraph)
9762 ("r-keggrest" ,r-keggrest)
9763 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
9765 ("r-rgraphviz" ,r-rgraphviz)
9767 (home-page "https://pathview.uncc.edu/")
9768 (synopsis "Tool set for pathway based data integration and visualization")
9770 "@code{r-pathview} is a tool set for pathway based data integration and
9771 visualization. It maps and renders a wide variety of biological data on
9772 relevant pathway graphs. All users need is to supply their data and specify
9773 the target pathway. This package automatically downloads the pathway graph
9774 data, parses the data file, maps user data to the pathway, and render pathway
9775 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
9776 integrates with pathway and gene set (enrichment) analysis tools for
9777 large-scale and fully automated analysis.")
9778 (license license:gpl3+)))
9780 (define-public r-snpstats
9787 (uri (bioconductor-uri "snpStats" version))
9790 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
9791 (properties `((upstream-name . "snpStats")))
9792 (build-system r-build-system)
9793 (inputs `(("zlib" ,zlib)))
9795 `(("r-biocgenerics" ,r-biocgenerics)
9796 ("r-matrix" ,r-matrix)
9797 ("r-survival" ,r-survival)
9798 ("r-zlibbioc" ,r-zlibbioc)))
9799 (home-page "https://bioconductor.org/packages/snpStats")
9800 (synopsis "Methods for SNP association studies")
9802 "This package provides classes and statistical methods for large
9803 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
9804 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
9805 (license license:gpl3)))
9807 (define-public r-sushi
9813 (uri (bioconductor-uri "Sushi" version))
9816 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
9817 (properties `((upstream-name . "Sushi")))
9818 (build-system r-build-system)
9820 `(("r-biomart" ,r-biomart)
9822 (home-page "https://bioconductor.org/packages/Sushi")
9823 (synopsis "Tools for visualizing genomics data")
9825 "This package provides flexible, quantitative, and integrative genomic
9826 visualizations for publication-quality multi-panel figures.")
9827 (license license:gpl2+)))