1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
5 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
7 ;;; This file is part of GNU Guix.
9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
10 ;;; under the terms of the GNU General Public License as published by
11 ;;; the Free Software Foundation; either version 3 of the License, or (at
12 ;;; your option) any later version.
14 ;;; GNU Guix is distributed in the hope that it will be useful, but
15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 ;;; GNU General Public License for more details.
19 ;;; You should have received a copy of the GNU General Public License
20 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
22 (define-module (gnu packages bioconductor)
23 #:use-module ((guix licenses) #:prefix license:)
24 #:use-module (guix packages)
25 #:use-module (guix download)
26 #:use-module (guix git-download)
27 #:use-module (guix build-system r)
28 #:use-module (gnu packages)
29 #:use-module (gnu packages base)
30 #:use-module (gnu packages bioinformatics)
31 #:use-module (gnu packages cran)
32 #:use-module (gnu packages compression)
33 #:use-module (gnu packages gcc)
34 #:use-module (gnu packages graph)
35 #:use-module (gnu packages haskell-xyz)
36 #:use-module (gnu packages image)
37 #:use-module (gnu packages maths)
38 #:use-module (gnu packages netpbm)
39 #:use-module (gnu packages perl)
40 #:use-module (gnu packages pkg-config)
41 #:use-module (gnu packages statistics)
42 #:use-module (gnu packages web)
43 #:use-module (srfi srfi-1))
48 (define-public r-bsgenome-celegans-ucsc-ce6
50 (name "r-bsgenome-celegans-ucsc-ce6")
54 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
58 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
60 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
61 (build-system r-build-system)
63 `(("r-bsgenome" ,r-bsgenome)))
65 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
66 (synopsis "Full genome sequences for Worm")
68 "This package provides full genome sequences for Caenorhabditis
69 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
71 (license license:artistic2.0)))
73 (define-public r-bsgenome-celegans-ucsc-ce10
75 (name "r-bsgenome-celegans-ucsc-ce10")
79 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
83 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
85 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
86 (build-system r-build-system)
88 `(("r-bsgenome" ,r-bsgenome)))
90 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
91 (synopsis "Full genome sequences for Worm")
93 "This package provides full genome sequences for Caenorhabditis
94 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
96 (license license:artistic2.0)))
98 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
100 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
104 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
105 version 'annotation))
108 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
110 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
111 (build-system r-build-system)
113 `(("r-bsgenome" ,r-bsgenome)))
115 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
116 (synopsis "Full genome sequences for Fly")
118 "This package provides full genome sequences for Drosophila
119 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
121 (license license:artistic2.0)))
123 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
125 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
129 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
130 version 'annotation))
133 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
135 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
136 (build-system r-build-system)
138 `(("r-bsgenome" ,r-bsgenome)))
140 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
141 (synopsis "Full genome sequences for Fly")
143 "This package provides full genome sequences for Drosophila
144 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
145 Biostrings objects.")
146 (license license:artistic2.0)))
148 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
150 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
154 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
155 version 'annotation))
158 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
160 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
161 (build-system r-build-system)
163 `(("r-bsgenome" ,r-bsgenome)
164 ("r-bsgenome-dmelanogaster-ucsc-dm3"
165 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
166 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
167 (synopsis "Full masked genome sequences for Fly")
169 "This package provides full masked genome sequences for Drosophila
170 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
171 Biostrings objects. The sequences are the same as in
172 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
173 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
174 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
175 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
176 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
177 (license license:artistic2.0)))
179 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
181 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
185 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
186 version 'annotation))
189 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
191 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
192 (build-system r-build-system)
194 `(("r-bsgenome" ,r-bsgenome)))
196 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
197 (synopsis "Full genome sequences for Homo sapiens")
199 "This package provides full genome sequences for Homo sapiens from
200 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
205 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
209 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
210 version 'annotation))
213 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
215 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
216 (build-system r-build-system)
218 `(("r-bsgenome" ,r-bsgenome)
219 ("r-bsgenome-hsapiens-ucsc-hg19"
220 ,r-bsgenome-hsapiens-ucsc-hg19)))
221 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
222 (synopsis "Full masked genome sequences for Homo sapiens")
224 "This package provides full genome sequences for Homo sapiens (Human) as
225 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
226 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
227 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
228 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
229 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
230 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
232 (license license:artistic2.0)))
234 (define-public r-bsgenome-mmusculus-ucsc-mm9
236 (name "r-bsgenome-mmusculus-ucsc-mm9")
240 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
241 version 'annotation))
244 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
246 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
247 (build-system r-build-system)
249 `(("r-bsgenome" ,r-bsgenome)))
251 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
252 (synopsis "Full genome sequences for Mouse")
254 "This package provides full genome sequences for Mus musculus (Mouse) as
255 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
256 (license license:artistic2.0)))
258 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
260 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
264 ;; We cannot use bioconductor-uri here because this tarball is
265 ;; located under "data/annotation/" instead of "bioc/".
266 (uri (string-append "http://www.bioconductor.org/packages/"
267 "release/data/annotation/src/contrib/"
268 "BSgenome.Mmusculus.UCSC.mm9.masked_"
272 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
274 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
275 (build-system r-build-system)
277 `(("r-bsgenome" ,r-bsgenome)
278 ("r-bsgenome-mmusculus-ucsc-mm9"
279 ,r-bsgenome-mmusculus-ucsc-mm9)))
280 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
281 (synopsis "Full masked genome sequences for Mouse")
283 "This package provides full genome sequences for Mus musculus (Mouse) as
284 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
285 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
286 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
287 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
288 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
289 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
291 (license license:artistic2.0)))
293 (define-public r-bsgenome-mmusculus-ucsc-mm10
295 (name "r-bsgenome-mmusculus-ucsc-mm10")
299 ;; We cannot use bioconductor-uri here because this tarball is
300 ;; located under "data/annotation/" instead of "bioc/".
301 (uri (string-append "https://www.bioconductor.org/packages/"
302 "release/data/annotation/src/contrib/"
303 "BSgenome.Mmusculus.UCSC.mm10_"
307 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
309 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
310 (build-system r-build-system)
311 ;; As this package provides little more than a very large data file it
312 ;; doesn't make sense to build substitutes.
313 (arguments `(#:substitutable? #f))
315 `(("r-bsgenome" ,r-bsgenome)))
317 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
318 (synopsis "Full genome sequences for Mouse")
320 "This package provides full genome sequences for Mus
321 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
322 in Biostrings objects.")
323 (license license:artistic2.0)))
325 (define-public r-org-ce-eg-db
327 (name "r-org-ce-eg-db")
331 ;; We cannot use bioconductor-uri here because this tarball is
332 ;; located under "data/annotation/" instead of "bioc/".
333 (uri (string-append "https://www.bioconductor.org/packages/"
334 "release/data/annotation/src/contrib/"
335 "org.Ce.eg.db_" version ".tar.gz"))
338 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
340 `((upstream-name . "org.Ce.eg.db")))
341 (build-system r-build-system)
343 `(("r-annotationdbi" ,r-annotationdbi)))
344 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
345 (synopsis "Genome wide annotation for Worm")
347 "This package provides mappings from Entrez gene identifiers to various
348 annotations for the genome of the model worm Caenorhabditis elegans.")
349 (license license:artistic2.0)))
351 (define-public r-org-dm-eg-db
353 (name "r-org-dm-eg-db")
357 ;; We cannot use bioconductor-uri here because this tarball is
358 ;; located under "data/annotation/" instead of "bioc/".
359 (uri (string-append "https://www.bioconductor.org/packages/"
360 "release/data/annotation/src/contrib/"
361 "org.Dm.eg.db_" version ".tar.gz"))
364 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
366 `((upstream-name . "org.Dm.eg.db")))
367 (build-system r-build-system)
369 `(("r-annotationdbi" ,r-annotationdbi)))
370 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
371 (synopsis "Genome wide annotation for Fly")
373 "This package provides mappings from Entrez gene identifiers to various
374 annotations for the genome of the model fruit fly Drosophila melanogaster.")
375 (license license:artistic2.0)))
377 (define-public r-org-dr-eg-db
379 (name "r-org-dr-eg-db")
383 ;; We cannot use bioconductor-uri here because this tarball is
384 ;; located under "data/annotation/" instead of "bioc/".
385 (uri (string-append "https://www.bioconductor.org/packages/"
386 "release/data/annotation/src/contrib/"
387 "org.Dr.eg.db_" version ".tar.gz"))
390 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
392 `((upstream-name . "org.Dr.eg.db")))
393 (build-system r-build-system)
395 `(("r-annotationdbi" ,r-annotationdbi)))
396 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
397 (synopsis "Annotation for Zebrafish")
399 "This package provides genome wide annotations for Zebrafish, primarily
400 based on mapping using Entrez Gene identifiers.")
401 (license license:artistic2.0)))
403 (define-public r-org-hs-eg-db
405 (name "r-org-hs-eg-db")
409 ;; We cannot use bioconductor-uri here because this tarball is
410 ;; located under "data/annotation/" instead of "bioc/".
411 (uri (string-append "https://www.bioconductor.org/packages/"
412 "release/data/annotation/src/contrib/"
413 "org.Hs.eg.db_" version ".tar.gz"))
416 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
418 `((upstream-name . "org.Hs.eg.db")))
419 (build-system r-build-system)
421 `(("r-annotationdbi" ,r-annotationdbi)))
422 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
423 (synopsis "Genome wide annotation for Human")
425 "This package contains genome-wide annotations for Human, primarily based
426 on mapping using Entrez Gene identifiers.")
427 (license license:artistic2.0)))
429 (define-public r-org-mm-eg-db
431 (name "r-org-mm-eg-db")
435 ;; We cannot use bioconductor-uri here because this tarball is
436 ;; located under "data/annotation/" instead of "bioc/".
437 (uri (string-append "https://www.bioconductor.org/packages/"
438 "release/data/annotation/src/contrib/"
439 "org.Mm.eg.db_" version ".tar.gz"))
442 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
444 `((upstream-name . "org.Mm.eg.db")))
445 (build-system r-build-system)
447 `(("r-annotationdbi" ,r-annotationdbi)))
448 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
449 (synopsis "Genome wide annotation for Mouse")
451 "This package provides mappings from Entrez gene identifiers to various
452 annotations for the genome of the model mouse Mus musculus.")
453 (license license:artistic2.0)))
455 (define-public r-bsgenome-hsapiens-ucsc-hg19
457 (name "r-bsgenome-hsapiens-ucsc-hg19")
461 ;; We cannot use bioconductor-uri here because this tarball is
462 ;; located under "data/annotation/" instead of "bioc/".
463 (uri (string-append "https://www.bioconductor.org/packages/"
464 "release/data/annotation/src/contrib/"
465 "BSgenome.Hsapiens.UCSC.hg19_"
469 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
471 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
472 (build-system r-build-system)
473 ;; As this package provides little more than a very large data file it
474 ;; doesn't make sense to build substitutes.
475 (arguments `(#:substitutable? #f))
477 `(("r-bsgenome" ,r-bsgenome)))
479 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
480 (synopsis "Full genome sequences for Homo sapiens")
482 "This package provides full genome sequences for Homo sapiens as provided
483 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
484 (license license:artistic2.0)))
486 (define-public r-ensdb-hsapiens-v75
488 (name "r-ensdb-hsapiens-v75")
493 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
496 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
498 `((upstream-name . "EnsDb.Hsapiens.v75")))
499 (build-system r-build-system)
501 `(("r-ensembldb" ,r-ensembldb)))
502 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
503 (synopsis "Ensembl based annotation package")
505 "This package exposes an annotation database generated from Ensembl.")
506 (license license:artistic2.0)))
508 (define-public r-genelendatabase
510 (name "r-genelendatabase")
515 ;; We cannot use bioconductor-uri here because this tarball is
516 ;; located under "data/experiment/" instead of "bioc/".
517 (uri (string-append "https://bioconductor.org/packages/"
518 "release/data/experiment/src/contrib"
519 "/geneLenDataBase_" version ".tar.gz"))
522 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
524 `((upstream-name . "geneLenDataBase")))
525 (build-system r-build-system)
527 `(("r-rtracklayer" ,r-rtracklayer)
528 ("r-genomicfeatures" ,r-genomicfeatures)))
529 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
530 (synopsis "Lengths of mRNA transcripts for a number of genomes")
532 "This package provides the lengths of mRNA transcripts for a number of
533 genomes and gene ID formats, largely based on the UCSC table browser.")
534 (license license:lgpl2.0+)))
536 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
538 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
542 ;; We cannot use bioconductor-uri here because this tarball is
543 ;; located under "data/annotation/" instead of "bioc/".
544 (uri (string-append "https://bioconductor.org/packages/"
545 "release/data/annotation/src/contrib"
546 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
550 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
552 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
553 (build-system r-build-system)
554 ;; As this package provides little more than a very large data file it
555 ;; doesn't make sense to build substitutes.
556 (arguments `(#:substitutable? #f))
558 `(("r-genomicfeatures" ,r-genomicfeatures)))
560 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
561 (synopsis "Annotation package for human genome in TxDb format")
563 "This package provides an annotation database of Homo sapiens genome
564 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
565 track. The database is exposed as a @code{TxDb} object.")
566 (license license:artistic2.0)))
568 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
570 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
574 ;; We cannot use bioconductor-uri here because this tarball is
575 ;; located under "data/annotation/" instead of "bioc/".
576 (uri (string-append "https://bioconductor.org/packages/"
577 "release/data/annotation/src/contrib"
578 "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
582 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
584 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
585 (build-system r-build-system)
587 `(("r-genomicfeatures" ,r-genomicfeatures)))
589 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
590 (synopsis "Annotation package for human genome in TxDb format")
592 "This package provides an annotation database of Homo sapiens genome
593 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
594 track. The database is exposed as a @code{TxDb} object.")
595 (license license:artistic2.0)))
597 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
599 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
603 ;; We cannot use bioconductor-uri here because this tarball is
604 ;; located under "data/annotation/" instead of "bioc/".
605 (uri (string-append "https://bioconductor.org/packages/"
606 "release/data/annotation/src/contrib"
607 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
611 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
613 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
614 (build-system r-build-system)
616 `(("r-genomicfeatures" ,r-genomicfeatures)
617 ("r-annotationdbi" ,r-annotationdbi)))
619 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
620 (synopsis "Annotation package for mouse genome in TxDb format")
622 "This package provides an annotation database of Mouse genome data. It
623 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
624 database is exposed as a @code{TxDb} object.")
625 (license license:artistic2.0)))
627 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
629 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
633 ;; We cannot use bioconductor-uri here because this tarball is
634 ;; located under "data/annotation/" instead of "bioc/".
635 (uri (string-append "https://www.bioconductor.org/packages/"
636 "release/data/annotation/src/contrib/"
637 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
641 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
643 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
644 (build-system r-build-system)
645 ;; As this package provides little more than a very large data file it
646 ;; doesn't make sense to build substitutes.
647 (arguments `(#:substitutable? #f))
649 `(("r-bsgenome" ,r-bsgenome)
650 ("r-genomicfeatures" ,r-genomicfeatures)
651 ("r-annotationdbi" ,r-annotationdbi)))
653 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
654 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
656 "This package loads a TxDb object, which is an R interface to
657 prefabricated databases contained in this package. This package provides
658 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
659 based on the knownGene track.")
660 (license license:artistic2.0)))
662 (define-public r-txdb-celegans-ucsc-ce6-ensgene
664 (name "r-txdb-celegans-ucsc-ce6-ensgene")
669 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
670 version 'annotation))
673 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
675 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
676 (build-system r-build-system)
678 `(("r-annotationdbi" ,r-annotationdbi)
679 ("r-genomicfeatures" ,r-genomicfeatures)))
680 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
681 (synopsis "Annotation package for C elegans TxDb objects")
683 "This package exposes a C elegans annotation database generated from UCSC
684 by exposing these as TxDb objects.")
685 (license license:artistic2.0)))
687 (define-public r-fdb-infiniummethylation-hg19
689 (name "r-fdb-infiniummethylation-hg19")
693 ;; We cannot use bioconductor-uri here because this tarball is
694 ;; located under "data/annotation/" instead of "bioc/".
695 (uri (string-append "https://www.bioconductor.org/packages/"
696 "release/data/annotation/src/contrib/"
697 "FDb.InfiniumMethylation.hg19_"
701 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
703 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
704 (build-system r-build-system)
706 `(("r-biostrings" ,r-biostrings)
707 ("r-genomicfeatures" ,r-genomicfeatures)
708 ("r-annotationdbi" ,r-annotationdbi)
709 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
710 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
711 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
712 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
714 "This is an annotation package for Illumina Infinium DNA methylation
715 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
717 (license license:artistic2.0)))
719 (define-public r-illuminahumanmethylationepicmanifest
721 (name "r-illuminahumanmethylationepicmanifest")
725 ;; We cannot use bioconductor-uri here because this tarball is
726 ;; located under "data/annotation/" instead of "bioc/".
727 (uri (string-append "https://www.bioconductor.org/packages/"
728 "release/data/annotation/src/contrib/"
729 "IlluminaHumanMethylationEPICmanifest_"
733 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
735 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
736 (build-system r-build-system)
738 `(("r-minfi" ,r-minfi)))
739 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
740 (synopsis "Manifest for Illumina's EPIC methylation arrays")
742 "This is a manifest package for Illumina's EPIC methylation arrays.")
743 (license license:artistic2.0)))
745 (define-public r-do-db
751 ;; We cannot use bioconductor-uri here because this tarball is
752 ;; located under "data/annotation/" instead of "bioc/".
753 (uri (string-append "https://www.bioconductor.org/packages/"
754 "release/data/annotation/src/contrib/"
755 "DO.db_" version ".tar.gz"))
758 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
760 `((upstream-name . "DO.db")))
761 (build-system r-build-system)
763 `(("r-annotationdbi" ,r-annotationdbi)))
764 (home-page "https://www.bioconductor.org/packages/DO.db/")
765 (synopsis "Annotation maps describing the entire Disease Ontology")
767 "This package provides a set of annotation maps describing the entire
769 (license license:artistic2.0)))
771 (define-public r-pfam-db
778 (uri (bioconductor-uri "PFAM.db" version 'annotation))
781 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
782 (properties `((upstream-name . "PFAM.db")))
783 (build-system r-build-system)
785 `(("r-annotationdbi" ,r-annotationdbi)))
786 (home-page "https://bioconductor.org/packages/PFAM.db")
787 (synopsis "Set of protein ID mappings for PFAM")
789 "This package provides a set of protein ID mappings for PFAM, assembled
790 using data from public repositories.")
791 (license license:artistic2.0)))
793 (define-public r-phastcons100way-ucsc-hg19
795 (name "r-phastcons100way-ucsc-hg19")
800 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
801 version 'annotation))
804 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
806 `((upstream-name . "phastCons100way.UCSC.hg19")))
807 (build-system r-build-system)
809 `(("r-bsgenome" ,r-bsgenome)
810 ("r-genomeinfodb" ,r-genomeinfodb)
811 ("r-genomicranges" ,r-genomicranges)
812 ("r-genomicscores" ,r-genomicscores)
813 ("r-iranges" ,r-iranges)
814 ("r-s4vectors" ,r-s4vectors)))
815 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
816 (synopsis "UCSC phastCons conservation scores for hg19")
818 "This package provides UCSC phastCons conservation scores for the human
819 genome (hg19) calculated from multiple alignments with other 99 vertebrate
821 (license license:artistic2.0)))
826 (define-public r-abadata
832 ;; We cannot use bioconductor-uri here because this tarball is
833 ;; located under "data/experiment/" instead of "bioc/".
834 (uri (string-append "https://www.bioconductor.org/packages/"
835 "release/data/experiment/src/contrib/"
836 "ABAData_" version ".tar.gz"))
839 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
841 `((upstream-name . "ABAData")))
842 (build-system r-build-system)
844 `(("r-annotationdbi" ,r-annotationdbi)))
845 (home-page "https://www.bioconductor.org/packages/ABAData/")
846 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
848 "This package provides the data for the gene expression enrichment
849 analysis conducted in the package ABAEnrichment. The package includes three
850 datasets which are derived from the Allen Brain Atlas:
853 @item Gene expression data from Human Brain (adults) averaged across donors,
854 @item Gene expression data from the Developing Human Brain pooled into five
855 age categories and averaged across donors, and
856 @item a developmental effect score based on the Developing Human Brain
860 All datasets are restricted to protein coding genes.")
861 (license license:gpl2+)))
863 (define-public r-arrmdata
869 ;; We cannot use bioconductor-uri here because this tarball is
870 ;; located under "data/experiment/" instead of "bioc/".
871 (uri (string-append "https://www.bioconductor.org/packages/"
872 "release/data/experiment/src/contrib/"
873 "ARRmData_" version ".tar.gz"))
876 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
878 `((upstream-name . "ARRmData")))
879 (build-system r-build-system)
880 (home-page "https://www.bioconductor.org/packages/ARRmData/")
881 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
883 "This package provides raw beta values from 36 samples across 3 groups
884 from Illumina 450k methylation arrays.")
885 (license license:artistic2.0)))
887 (define-public r-hsmmsinglecell
889 (name "r-hsmmsinglecell")
893 ;; We cannot use bioconductor-uri here because this tarball is
894 ;; located under "data/experiment/" instead of "bioc/".
895 (uri (string-append "https://www.bioconductor.org/packages/"
896 "release/data/experiment/src/contrib/"
897 "HSMMSingleCell_" version ".tar.gz"))
900 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
902 `((upstream-name . "HSMMSingleCell")))
903 (build-system r-build-system)
904 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
905 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
907 "Skeletal myoblasts undergo a well-characterized sequence of
908 morphological and transcriptional changes during differentiation. In this
909 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
910 under high mitogen conditions (GM) and then differentiated by switching to
911 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
912 hundred cells taken over a time-course of serum-induced differentiation.
913 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
914 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
915 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
916 which were then sequenced to a depth of ~4 million reads per library,
917 resulting in a complete gene expression profile for each cell.")
918 (license license:artistic2.0)))
926 ;; We cannot use bioconductor-uri here because this tarball is
927 ;; located under "data/experiment/" instead of "bioc/".
928 (uri (string-append "https://www.bioconductor.org/packages/"
929 "release/data/experiment/src/contrib/"
930 "ALL_" version ".tar.gz"))
933 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
934 (properties `((upstream-name . "ALL")))
935 (build-system r-build-system)
937 `(("r-biobase" ,r-biobase)))
938 (home-page "https://bioconductor.org/packages/ALL")
939 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
941 "The data consist of microarrays from 128 different individuals with
942 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
943 are available. The data have been normalized (using rma) and it is the
944 jointly normalized data that are available here. The data are presented in
945 the form of an @code{exprSet} object.")
946 (license license:artistic2.0)))
948 (define-public r-affydata
955 (uri (bioconductor-uri "affydata" version 'experiment))
958 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
959 (properties `((upstream-name . "affydata")))
960 (build-system r-build-system)
962 `(("r-affy" ,r-affy)))
963 (home-page "https://bioconductor.org/packages/affydata/")
964 (synopsis "Affymetrix data for demonstration purposes")
966 "This package provides example datasets that represent 'real world
967 examples' of Affymetrix data, unlike the artificial examples included in the
968 package @code{affy}.")
969 (license license:gpl2+)))
974 (define-public r-biocgenerics
976 (name "r-biocgenerics")
980 (uri (bioconductor-uri "BiocGenerics" version))
983 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
985 `((upstream-name . "BiocGenerics")))
986 (build-system r-build-system)
987 (home-page "https://bioconductor.org/packages/BiocGenerics")
988 (synopsis "S4 generic functions for Bioconductor")
990 "This package provides S4 generic functions needed by many Bioconductor
992 (license license:artistic2.0)))
994 (define-public r-affycomp
1001 (uri (bioconductor-uri "affycomp" version))
1004 "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
1005 (properties `((upstream-name . "affycomp")))
1006 (build-system r-build-system)
1007 (propagated-inputs `(("r-biobase" ,r-biobase)))
1008 (home-page "https://bioconductor.org/packages/affycomp/")
1009 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1011 "The package contains functions that can be used to compare expression
1012 measures for Affymetrix Oligonucleotide Arrays.")
1013 (license license:gpl2+)))
1015 (define-public r-affycompatible
1017 (name "r-affycompatible")
1022 (uri (bioconductor-uri "AffyCompatible" version))
1025 "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
1027 `((upstream-name . "AffyCompatible")))
1028 (build-system r-build-system)
1030 `(("r-biostrings" ,r-biostrings)
1031 ("r-rcurl" ,r-rcurl)
1033 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1034 (synopsis "Work with Affymetrix GeneChip files")
1036 "This package provides an interface to Affymetrix chip annotation and
1037 sample attribute files. The package allows an easy way for users to download
1038 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1039 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1040 Command Console} (AGCC)-compatible sample annotation files.")
1041 (license license:artistic2.0)))
1043 (define-public r-affycontam
1045 (name "r-affycontam")
1050 (uri (bioconductor-uri "affyContam" version))
1053 "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
1054 (properties `((upstream-name . "affyContam")))
1055 (build-system r-build-system)
1057 `(("r-affy" ,r-affy)
1058 ("r-affydata" ,r-affydata)
1059 ("r-biobase" ,r-biobase)))
1060 (home-page "https://bioconductor.org/packages/affyContam/")
1061 (synopsis "Structured corruption of Affymetrix CEL file data")
1063 "Microarray quality assessment is a major concern of microarray analysts.
1064 This package provides some simple approaches to in silico creation of quality
1065 problems in CEL-level data to help evaluate performance of quality metrics.")
1066 (license license:artistic2.0)))
1068 (define-public r-affycoretools
1070 (name "r-affycoretools")
1075 (uri (bioconductor-uri "affycoretools" version))
1078 "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s"))))
1079 (properties `((upstream-name . "affycoretools")))
1080 (build-system r-build-system)
1082 `(("r-affy" ,r-affy)
1083 ("r-annotationdbi" ,r-annotationdbi)
1084 ("r-biobase" ,r-biobase)
1085 ("r-biocgenerics" ,r-biocgenerics)
1087 ("r-edger" ,r-edger)
1088 ("r-gcrma" ,r-gcrma)
1089 ("r-ggplot2" ,r-ggplot2)
1090 ("r-gostats" ,r-gostats)
1091 ("r-gplots" ,r-gplots)
1092 ("r-hwriter" ,r-hwriter)
1093 ("r-lattice" ,r-lattice)
1094 ("r-limma" ,r-limma)
1095 ("r-oligoclasses" ,r-oligoclasses)
1096 ("r-reportingtools" ,r-reportingtools)
1097 ("r-rsqlite" ,r-rsqlite)
1098 ("r-s4vectors" ,r-s4vectors)
1099 ("r-xtable" ,r-xtable)))
1100 (home-page "https://bioconductor.org/packages/affycoretools/")
1101 (synopsis "Functions for analyses with Affymetrix GeneChips")
1103 "This package provides various wrapper functions that have been written
1104 to streamline the more common analyses that a Biostatistician might see.")
1105 (license license:artistic2.0)))
1107 (define-public r-affxparser
1109 (name "r-affxparser")
1114 (uri (bioconductor-uri "affxparser" version))
1117 "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33"))))
1118 (properties `((upstream-name . "affxparser")))
1119 (build-system r-build-system)
1120 (home-page "https://github.com/HenrikBengtsson/affxparser")
1121 (synopsis "Affymetrix File Parsing SDK")
1123 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1124 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1125 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1126 are supported. Currently, there are methods for reading @dfn{chip definition
1127 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1128 either in full or in part. For example, probe signals from a few probesets
1129 can be extracted very quickly from a set of CEL files into a convenient list
1131 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1133 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1135 (define-public r-annotate
1142 (uri (bioconductor-uri "annotate" version))
1145 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
1146 (build-system r-build-system)
1148 `(("r-annotationdbi" ,r-annotationdbi)
1149 ("r-biobase" ,r-biobase)
1150 ("r-biocgenerics" ,r-biocgenerics)
1152 ("r-rcurl" ,r-rcurl)
1154 ("r-xtable" ,r-xtable)))
1156 "https://bioconductor.org/packages/annotate")
1157 (synopsis "Annotation for microarrays")
1158 (description "This package provides R environments for the annotation of
1160 (license license:artistic2.0)))
1162 (define-public r-hpar
1169 (uri (bioconductor-uri "hpar" version))
1172 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
1173 (build-system r-build-system)
1174 (home-page "https://bioconductor.org/packages/hpar/")
1175 (synopsis "Human Protein Atlas in R")
1176 (description "This package provides a simple interface to and data from
1177 the Human Protein Atlas project.")
1178 (license license:artistic2.0)))
1180 (define-public r-regioner
1187 (uri (bioconductor-uri "regioneR" version))
1190 "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
1191 (properties `((upstream-name . "regioneR")))
1192 (build-system r-build-system)
1194 `(("r-biostrings" ,r-biostrings)
1195 ("r-bsgenome" ,r-bsgenome)
1196 ("r-genomeinfodb" ,r-genomeinfodb)
1197 ("r-genomicranges" ,r-genomicranges)
1198 ("r-iranges" ,r-iranges)
1199 ("r-memoise" ,r-memoise)
1200 ("r-rtracklayer" ,r-rtracklayer)
1201 ("r-s4vectors" ,r-s4vectors)))
1202 (home-page "https://bioconductor.org/packages/regioneR/")
1203 (synopsis "Association analysis of genomic regions")
1204 (description "This package offers a statistical framework based on
1205 customizable permutation tests to assess the association between genomic
1206 region sets and other genomic features.")
1207 (license license:artistic2.0)))
1209 (define-public r-reportingtools
1211 (name "r-reportingtools")
1216 (uri (bioconductor-uri "ReportingTools" version))
1219 "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
1221 `((upstream-name . "ReportingTools")))
1222 (build-system r-build-system)
1224 `(("r-annotate" ,r-annotate)
1225 ("r-annotationdbi" ,r-annotationdbi)
1226 ("r-biobase" ,r-biobase)
1227 ("r-biocgenerics" ,r-biocgenerics)
1228 ("r-category" ,r-category)
1229 ("r-deseq2" ,r-deseq2)
1230 ("r-edger" ,r-edger)
1231 ("r-ggbio" ,r-ggbio)
1232 ("r-ggplot2" ,r-ggplot2)
1233 ("r-gostats" ,r-gostats)
1234 ("r-gseabase" ,r-gseabase)
1235 ("r-hwriter" ,r-hwriter)
1236 ("r-iranges" ,r-iranges)
1237 ("r-knitr" ,r-knitr)
1238 ("r-lattice" ,r-lattice)
1239 ("r-limma" ,r-limma)
1240 ("r-pfam-db" ,r-pfam-db)
1241 ("r-r-utils" ,r-r-utils)
1243 (home-page "https://bioconductor.org/packages/ReportingTools/")
1244 (synopsis "Tools for making reports in various formats")
1246 "The ReportingTools package enables users to easily display reports of
1247 analysis results generated from sources such as microarray and sequencing
1248 data. The package allows users to create HTML pages that may be viewed on a
1249 web browser, or in other formats. Users can generate tables with sortable and
1250 filterable columns, make and display plots, and link table entries to other
1251 data sources such as NCBI or larger plots within the HTML page. Using the
1252 package, users can also produce a table of contents page to link various
1253 reports together for a particular project that can be viewed in a web
1255 (license license:artistic2.0)))
1257 (define-public r-geneplotter
1259 (name "r-geneplotter")
1264 (uri (bioconductor-uri "geneplotter" version))
1267 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1268 (build-system r-build-system)
1270 `(("r-annotate" ,r-annotate)
1271 ("r-annotationdbi" ,r-annotationdbi)
1272 ("r-biobase" ,r-biobase)
1273 ("r-biocgenerics" ,r-biocgenerics)
1274 ("r-lattice" ,r-lattice)
1275 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1276 (home-page "https://bioconductor.org/packages/geneplotter")
1277 (synopsis "Graphics functions for genomic data")
1279 "This package provides functions for plotting genomic data.")
1280 (license license:artistic2.0)))
1282 (define-public r-oligoclasses
1284 (name "r-oligoclasses")
1289 (uri (bioconductor-uri "oligoClasses" version))
1292 "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72"))))
1293 (properties `((upstream-name . "oligoClasses")))
1294 (build-system r-build-system)
1296 `(("r-affyio" ,r-affyio)
1297 ("r-biobase" ,r-biobase)
1298 ("r-biocgenerics" ,r-biocgenerics)
1299 ("r-biocmanager" ,r-biocmanager)
1300 ("r-biostrings" ,r-biostrings)
1303 ("r-foreach" ,r-foreach)
1304 ("r-genomicranges" ,r-genomicranges)
1305 ("r-iranges" ,r-iranges)
1306 ("r-rsqlite" ,r-rsqlite)
1307 ("r-s4vectors" ,r-s4vectors)
1308 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1309 (home-page "https://bioconductor.org/packages/oligoClasses/")
1310 (synopsis "Classes for high-throughput arrays")
1312 "This package contains class definitions, validity checks, and
1313 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1315 (license license:gpl2+)))
1317 (define-public r-oligo
1324 (uri (bioconductor-uri "oligo" version))
1327 "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df"))))
1328 (properties `((upstream-name . "oligo")))
1329 (build-system r-build-system)
1330 (inputs `(("zlib" ,zlib)))
1332 `(("r-affxparser" ,r-affxparser)
1333 ("r-affyio" ,r-affyio)
1334 ("r-biobase" ,r-biobase)
1335 ("r-biocgenerics" ,r-biocgenerics)
1336 ("r-biostrings" ,r-biostrings)
1339 ("r-oligoclasses" ,r-oligoclasses)
1340 ("r-preprocesscore" ,r-preprocesscore)
1341 ("r-rsqlite" ,r-rsqlite)
1342 ("r-zlibbioc" ,r-zlibbioc)))
1343 (home-page "https://bioconductor.org/packages/oligo/")
1344 (synopsis "Preprocessing tools for oligonucleotide arrays")
1346 "This package provides a package to analyze oligonucleotide
1347 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1348 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1349 (license license:lgpl2.0+)))
1351 (define-public r-qvalue
1358 (uri (bioconductor-uri "qvalue" version))
1361 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1362 (build-system r-build-system)
1364 `(("r-ggplot2" ,r-ggplot2)
1365 ("r-reshape2" ,r-reshape2)))
1366 (home-page "http://github.com/jdstorey/qvalue")
1367 (synopsis "Q-value estimation for false discovery rate control")
1369 "This package takes a list of p-values resulting from the simultaneous
1370 testing of many hypotheses and estimates their q-values and local @dfn{false
1371 discovery rate} (FDR) values. The q-value of a test measures the proportion
1372 of false positives incurred when that particular test is called significant.
1373 The local FDR measures the posterior probability the null hypothesis is true
1374 given the test's p-value. Various plots are automatically generated, allowing
1375 one to make sensible significance cut-offs. The software can be applied to
1376 problems in genomics, brain imaging, astrophysics, and data mining.")
1377 ;; Any version of the LGPL.
1378 (license license:lgpl3+)))
1380 (define-public r-diffbind
1387 (uri (bioconductor-uri "DiffBind" version))
1390 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1391 (properties `((upstream-name . "DiffBind")))
1392 (build-system r-build-system)
1396 `(("r-amap" ,r-amap)
1397 ("r-biocparallel" ,r-biocparallel)
1398 ("r-deseq2" ,r-deseq2)
1399 ("r-dplyr" ,r-dplyr)
1400 ("r-edger" ,r-edger)
1401 ("r-genomicalignments" ,r-genomicalignments)
1402 ("r-genomicranges" ,r-genomicranges)
1403 ("r-ggplot2" ,r-ggplot2)
1404 ("r-ggrepel" ,r-ggrepel)
1405 ("r-gplots" ,r-gplots)
1406 ("r-iranges" ,r-iranges)
1407 ("r-lattice" ,r-lattice)
1408 ("r-limma" ,r-limma)
1409 ("r-locfit" ,r-locfit)
1410 ("r-rcolorbrewer" , r-rcolorbrewer)
1412 ("r-rhtslib" ,r-rhtslib)
1413 ("r-rsamtools" ,r-rsamtools)
1414 ("r-s4vectors" ,r-s4vectors)
1415 ("r-summarizedexperiment" ,r-summarizedexperiment)
1416 ("r-systempiper" ,r-systempiper)))
1417 (home-page "http://bioconductor.org/packages/DiffBind")
1418 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1420 "This package computes differentially bound sites from multiple
1421 ChIP-seq experiments using affinity (quantitative) data. Also enables
1422 occupancy (overlap) analysis and plotting functions.")
1423 (license license:artistic2.0)))
1425 (define-public r-ripseeker
1427 (name "r-ripseeker")
1432 (uri (bioconductor-uri "RIPSeeker" version))
1435 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1436 (properties `((upstream-name . "RIPSeeker")))
1437 (build-system r-build-system)
1439 `(("r-s4vectors" ,r-s4vectors)
1440 ("r-iranges" ,r-iranges)
1441 ("r-genomicranges" ,r-genomicranges)
1442 ("r-summarizedexperiment" ,r-summarizedexperiment)
1443 ("r-rsamtools" ,r-rsamtools)
1444 ("r-genomicalignments" ,r-genomicalignments)
1445 ("r-rtracklayer" ,r-rtracklayer)))
1446 (home-page "http://bioconductor.org/packages/RIPSeeker")
1448 "Identifying protein-associated transcripts from RIP-seq experiments")
1450 "This package infers and discriminates RIP peaks from RIP-seq alignments
1451 using two-state HMM with negative binomial emission probability. While
1452 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1453 a suite of bioinformatics tools integrated within this self-contained software
1454 package comprehensively addressing issues ranging from post-alignments
1455 processing to visualization and annotation.")
1456 (license license:gpl2)))
1458 (define-public r-multtest
1465 (uri (bioconductor-uri "multtest" version))
1468 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1469 (build-system r-build-system)
1471 `(("r-survival" ,r-survival)
1472 ("r-biocgenerics" ,r-biocgenerics)
1473 ("r-biobase" ,r-biobase)
1474 ("r-mass" ,r-mass)))
1475 (home-page "http://bioconductor.org/packages/multtest")
1476 (synopsis "Resampling-based multiple hypothesis testing")
1478 "This package can do non-parametric bootstrap and permutation
1479 resampling-based multiple testing procedures (including empirical Bayes
1480 methods) for controlling the family-wise error rate (FWER), generalized
1481 family-wise error rate (gFWER), tail probability of the proportion of
1482 false positives (TPPFP), and false discovery rate (FDR). Several choices
1483 of bootstrap-based null distribution are implemented (centered, centered
1484 and scaled, quantile-transformed). Single-step and step-wise methods are
1485 available. Tests based on a variety of T- and F-statistics (including
1486 T-statistics based on regression parameters from linear and survival models
1487 as well as those based on correlation parameters) are included. When probing
1488 hypotheses with T-statistics, users may also select a potentially faster null
1489 distribution which is multivariate normal with mean zero and variance
1490 covariance matrix derived from the vector influence function. Results are
1491 reported in terms of adjusted P-values, confidence regions and test statistic
1492 cutoffs. The procedures are directly applicable to identifying differentially
1493 expressed genes in DNA microarray experiments.")
1494 (license license:lgpl3)))
1496 (define-public r-graph
1502 (uri (bioconductor-uri "graph" version))
1505 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1506 (build-system r-build-system)
1508 `(("r-biocgenerics" ,r-biocgenerics)))
1509 (home-page "https://bioconductor.org/packages/graph")
1510 (synopsis "Handle graph data structures in R")
1512 "This package implements some simple graph handling capabilities for R.")
1513 (license license:artistic2.0)))
1515 (define-public r-codedepends
1517 (name "r-codedepends")
1522 (uri (cran-uri "CodeDepends" version))
1525 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1526 (properties `((upstream-name . "CodeDepends")))
1527 (build-system r-build-system)
1529 `(("r-codetools" ,r-codetools)
1530 ("r-graph" ,r-graph)
1532 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1533 (synopsis "Analysis of R code for reproducible research and code comprehension")
1535 "This package provides tools for analyzing R expressions or blocks of
1536 code and determining the dependencies between them. It focuses on R scripts,
1537 but can be used on the bodies of functions. There are many facilities
1538 including the ability to summarize or get a high-level view of code,
1539 determining dependencies between variables, code improvement suggestions.")
1540 ;; Any version of the GPL
1541 (license (list license:gpl2+ license:gpl3+))))
1543 (define-public r-chippeakanno
1545 (name "r-chippeakanno")
1550 (uri (bioconductor-uri "ChIPpeakAnno" version))
1553 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1554 (properties `((upstream-name . "ChIPpeakAnno")))
1555 (build-system r-build-system)
1557 `(("r-annotationdbi" ,r-annotationdbi)
1558 ("r-biobase" ,r-biobase)
1559 ("r-biocgenerics" ,r-biocgenerics)
1560 ("r-biocmanager" ,r-biocmanager)
1561 ("r-biomart" ,r-biomart)
1562 ("r-biostrings" ,r-biostrings)
1563 ("r-bsgenome" ,r-bsgenome)
1565 ("r-delayedarray" ,r-delayedarray)
1566 ("r-ensembldb" ,r-ensembldb)
1567 ("r-genomeinfodb" ,r-genomeinfodb)
1568 ("r-genomicalignments" ,r-genomicalignments)
1569 ("r-genomicfeatures" ,r-genomicfeatures)
1570 ("r-genomicranges" ,r-genomicranges)
1571 ("r-go-db" ,r-go-db)
1572 ("r-graph" ,r-graph)
1574 ("r-iranges" ,r-iranges)
1575 ("r-limma" ,r-limma)
1576 ("r-matrixstats" ,r-matrixstats)
1577 ("r-multtest" ,r-multtest)
1579 ("r-regioner" ,r-regioner)
1580 ("r-rsamtools" ,r-rsamtools)
1581 ("r-rtracklayer" ,r-rtracklayer)
1582 ("r-s4vectors" ,r-s4vectors)
1583 ("r-seqinr" ,r-seqinr)
1584 ("r-summarizedexperiment" ,r-summarizedexperiment)
1585 ("r-venndiagram" ,r-venndiagram)))
1586 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1587 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1589 "The package includes functions to retrieve the sequences around the peak,
1590 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1591 custom features such as most conserved elements and other transcription factor
1592 binding sites supplied by users. Starting 2.0.5, new functions have been added
1593 for finding the peaks with bi-directional promoters with summary statistics
1594 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1595 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1596 enrichedGO (addGeneIDs).")
1597 (license license:gpl2+)))
1599 (define-public r-marray
1605 (uri (bioconductor-uri "marray" version))
1607 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1608 (build-system r-build-system)
1610 `(("r-limma" ,r-limma)))
1611 (home-page "http://bioconductor.org/packages/marray")
1612 (synopsis "Exploratory analysis for two-color spotted microarray data")
1613 (description "This package contains class definitions for two-color spotted
1614 microarray data. It also includes functions for data input, diagnostic plots,
1615 normalization and quality checking.")
1616 (license license:lgpl2.0+)))
1618 (define-public r-cghbase
1624 (uri (bioconductor-uri "CGHbase" version))
1626 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1627 (properties `((upstream-name . "CGHbase")))
1628 (build-system r-build-system)
1630 `(("r-biobase" ,r-biobase)
1631 ("r-marray" ,r-marray)))
1632 (home-page "http://bioconductor.org/packages/CGHbase")
1633 (synopsis "Base functions and classes for arrayCGH data analysis")
1634 (description "This package contains functions and classes that are needed by
1635 the @code{arrayCGH} packages.")
1636 (license license:gpl2+)))
1638 (define-public r-cghcall
1644 (uri (bioconductor-uri "CGHcall" version))
1646 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1647 (properties `((upstream-name . "CGHcall")))
1648 (build-system r-build-system)
1650 `(("r-biobase" ,r-biobase)
1651 ("r-cghbase" ,r-cghbase)
1652 ("r-impute" ,r-impute)
1653 ("r-dnacopy" ,r-dnacopy)
1654 ("r-snowfall" ,r-snowfall)))
1655 (home-page "http://bioconductor.org/packages/CGHcall")
1656 (synopsis "Base functions and classes for arrayCGH data analysis")
1657 (description "This package contains functions and classes that are needed by
1658 @code{arrayCGH} packages.")
1659 (license license:gpl2+)))
1661 (define-public r-qdnaseq
1667 (uri (bioconductor-uri "QDNAseq" version))
1669 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1670 (properties `((upstream-name . "QDNAseq")))
1671 (build-system r-build-system)
1673 `(("r-biobase" ,r-biobase)
1674 ("r-biocparallel" ,r-biocparallel)
1675 ("r-cghbase" ,r-cghbase)
1676 ("r-cghcall" ,r-cghcall)
1677 ("r-dnacopy" ,r-dnacopy)
1678 ("r-genomicranges" ,r-genomicranges)
1679 ("r-iranges" ,r-iranges)
1680 ("r-matrixstats" ,r-matrixstats)
1681 ("r-r-utils" ,r-r-utils)
1682 ("r-rsamtools" ,r-rsamtools)))
1683 (home-page "http://bioconductor.org/packages/QDNAseq")
1684 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1685 (description "The genome is divided into non-overlapping fixed-sized bins,
1686 number of sequence reads in each counted, adjusted with a simultaneous
1687 two-dimensional loess correction for sequence mappability and GC content, and
1688 filtered to remove spurious regions in the genome. Downstream steps of
1689 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1691 (license license:gpl2+)))
1693 (define-public r-bayseq
1700 (uri (bioconductor-uri "baySeq" version))
1703 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1704 (properties `((upstream-name . "baySeq")))
1705 (build-system r-build-system)
1707 `(("r-abind" ,r-abind)
1708 ("r-edger" ,r-edger)
1709 ("r-genomicranges" ,r-genomicranges)))
1710 (home-page "https://bioconductor.org/packages/baySeq/")
1711 (synopsis "Bayesian analysis of differential expression patterns in count data")
1713 "This package identifies differential expression in high-throughput count
1714 data, such as that derived from next-generation sequencing machines,
1715 calculating estimated posterior likelihoods of differential expression (or
1716 more complex hypotheses) via empirical Bayesian methods.")
1717 (license license:gpl3)))
1719 (define-public r-chipcomp
1726 (uri (bioconductor-uri "ChIPComp" version))
1729 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1730 (properties `((upstream-name . "ChIPComp")))
1731 (build-system r-build-system)
1733 `(("r-biocgenerics" ,r-biocgenerics)
1734 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1735 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1736 ("r-genomeinfodb" ,r-genomeinfodb)
1737 ("r-genomicranges" ,r-genomicranges)
1738 ("r-iranges" ,r-iranges)
1739 ("r-limma" ,r-limma)
1740 ("r-rsamtools" ,r-rsamtools)
1741 ("r-rtracklayer" ,r-rtracklayer)
1742 ("r-s4vectors" ,r-s4vectors)))
1743 (home-page "https://bioconductor.org/packages/ChIPComp")
1744 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1746 "ChIPComp implements a statistical method for quantitative comparison of
1747 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1748 sites across multiple conditions considering matching control in ChIP-seq
1750 ;; Any version of the GPL.
1751 (license license:gpl3+)))
1753 (define-public r-riboprofiling
1755 (name "r-riboprofiling")
1760 (uri (bioconductor-uri "RiboProfiling" version))
1763 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1764 (properties `((upstream-name . "RiboProfiling")))
1765 (build-system r-build-system)
1767 `(("r-biocgenerics" ,r-biocgenerics)
1768 ("r-biostrings" ,r-biostrings)
1769 ("r-data-table" ,r-data-table)
1770 ("r-genomeinfodb" ,r-genomeinfodb)
1771 ("r-genomicalignments" ,r-genomicalignments)
1772 ("r-genomicfeatures" ,r-genomicfeatures)
1773 ("r-genomicranges" ,r-genomicranges)
1774 ("r-ggbio" ,r-ggbio)
1775 ("r-ggplot2" ,r-ggplot2)
1776 ("r-iranges" ,r-iranges)
1778 ("r-reshape2" ,r-reshape2)
1779 ("r-rsamtools" ,r-rsamtools)
1780 ("r-rtracklayer" ,r-rtracklayer)
1781 ("r-s4vectors" ,r-s4vectors)
1782 ("r-sqldf" ,r-sqldf)))
1783 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1784 (synopsis "Ribosome profiling data analysis")
1785 (description "Starting with a BAM file, this package provides the
1786 necessary functions for quality assessment, read start position recalibration,
1787 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1788 of count data: pairs, log fold-change, codon frequency and coverage
1789 assessment, principal component analysis on codon coverage.")
1790 (license license:gpl3)))
1792 (define-public r-riboseqr
1799 (uri (bioconductor-uri "riboSeqR" version))
1802 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1803 (properties `((upstream-name . "riboSeqR")))
1804 (build-system r-build-system)
1806 `(("r-abind" ,r-abind)
1807 ("r-bayseq" ,r-bayseq)
1808 ("r-genomeinfodb" ,r-genomeinfodb)
1809 ("r-genomicranges" ,r-genomicranges)
1810 ("r-iranges" ,r-iranges)
1811 ("r-rsamtools" ,r-rsamtools)
1812 ("r-seqlogo" ,r-seqlogo)))
1813 (home-page "https://bioconductor.org/packages/riboSeqR/")
1814 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1816 "This package provides plotting functions, frameshift detection and
1817 parsing of genetic sequencing data from ribosome profiling experiments.")
1818 (license license:gpl3)))
1820 (define-public r-interactionset
1822 (name "r-interactionset")
1827 (uri (bioconductor-uri "InteractionSet" version))
1830 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1832 `((upstream-name . "InteractionSet")))
1833 (build-system r-build-system)
1835 `(("r-biocgenerics" ,r-biocgenerics)
1836 ("r-genomeinfodb" ,r-genomeinfodb)
1837 ("r-genomicranges" ,r-genomicranges)
1838 ("r-iranges" ,r-iranges)
1839 ("r-matrix" ,r-matrix)
1841 ("r-s4vectors" ,r-s4vectors)
1842 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1843 (home-page "https://bioconductor.org/packages/InteractionSet")
1844 (synopsis "Base classes for storing genomic interaction data")
1846 "This package provides the @code{GInteractions},
1847 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1848 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1850 (license license:gpl3)))
1852 (define-public r-genomicinteractions
1854 (name "r-genomicinteractions")
1859 (uri (bioconductor-uri "GenomicInteractions" version))
1862 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1864 `((upstream-name . "GenomicInteractions")))
1865 (build-system r-build-system)
1867 `(("r-biobase" ,r-biobase)
1868 ("r-biocgenerics" ,r-biocgenerics)
1869 ("r-data-table" ,r-data-table)
1870 ("r-dplyr" ,r-dplyr)
1871 ("r-genomeinfodb" ,r-genomeinfodb)
1872 ("r-genomicranges" ,r-genomicranges)
1873 ("r-ggplot2" ,r-ggplot2)
1874 ("r-gridextra" ,r-gridextra)
1876 ("r-igraph" ,r-igraph)
1877 ("r-interactionset" ,r-interactionset)
1878 ("r-iranges" ,r-iranges)
1879 ("r-rsamtools" ,r-rsamtools)
1880 ("r-rtracklayer" ,r-rtracklayer)
1881 ("r-s4vectors" ,r-s4vectors)
1882 ("r-stringr" ,r-stringr)))
1883 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1884 (synopsis "R package for handling genomic interaction data")
1886 "This R package provides tools for handling genomic interaction data,
1887 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1888 information and producing various plots and statistics.")
1889 (license license:gpl3)))
1891 (define-public r-ctc
1898 (uri (bioconductor-uri "ctc" version))
1901 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1902 (build-system r-build-system)
1903 (propagated-inputs `(("r-amap" ,r-amap)))
1904 (home-page "https://bioconductor.org/packages/ctc/")
1905 (synopsis "Cluster and tree conversion")
1907 "This package provides tools for exporting and importing classification
1908 trees and clusters to other programs.")
1909 (license license:gpl2)))
1911 (define-public r-goseq
1918 (uri (bioconductor-uri "goseq" version))
1921 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1922 (build-system r-build-system)
1924 `(("r-annotationdbi" ,r-annotationdbi)
1925 ("r-biasedurn" ,r-biasedurn)
1926 ("r-biocgenerics" ,r-biocgenerics)
1927 ("r-genelendatabase" ,r-genelendatabase)
1928 ("r-go-db" ,r-go-db)
1929 ("r-mgcv" ,r-mgcv)))
1930 (home-page "https://bioconductor.org/packages/goseq/")
1931 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1933 "This package provides tools to detect Gene Ontology and/or other user
1934 defined categories which are over/under represented in RNA-seq data.")
1935 (license license:lgpl2.0+)))
1937 (define-public r-glimma
1944 (uri (bioconductor-uri "Glimma" version))
1947 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1948 (properties `((upstream-name . "Glimma")))
1949 (build-system r-build-system)
1951 `(("r-edger" ,r-edger)
1952 ("r-jsonlite" ,r-jsonlite)
1953 ("r-s4vectors" ,r-s4vectors)))
1954 (home-page "https://github.com/Shians/Glimma")
1955 (synopsis "Interactive HTML graphics")
1957 "This package generates interactive visualisations for analysis of
1958 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1959 HTML page. The interactions are built on top of the popular static
1960 representations of analysis results in order to provide additional
1962 (license license:lgpl3)))
1964 (define-public r-rots
1971 (uri (bioconductor-uri "ROTS" version))
1974 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1975 (properties `((upstream-name . "ROTS")))
1976 (build-system r-build-system)
1978 `(("r-biobase" ,r-biobase)
1979 ("r-rcpp" ,r-rcpp)))
1980 (home-page "https://bioconductor.org/packages/ROTS/")
1981 (synopsis "Reproducibility-Optimized Test Statistic")
1983 "This package provides tools for calculating the
1984 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1986 (license license:gpl2+)))
1988 (define-public r-plgem
1995 (uri (bioconductor-uri "plgem" version))
1998 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1999 (build-system r-build-system)
2001 `(("r-biobase" ,r-biobase)
2002 ("r-mass" ,r-mass)))
2003 (home-page "http://www.genopolis.it")
2004 (synopsis "Detect differential expression in microarray and proteomics datasets")
2006 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2007 model the variance-versus-mean dependence that exists in a variety of
2008 genome-wide datasets, including microarray and proteomics data. The use of
2009 PLGEM has been shown to improve the detection of differentially expressed
2010 genes or proteins in these datasets.")
2011 (license license:gpl2)))
2013 (define-public r-inspect
2020 (uri (bioconductor-uri "INSPEcT" version))
2023 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
2024 (properties `((upstream-name . "INSPEcT")))
2025 (build-system r-build-system)
2027 `(("r-biobase" ,r-biobase)
2028 ("r-biocgenerics" ,r-biocgenerics)
2029 ("r-biocparallel" ,r-biocparallel)
2030 ("r-deseq2" ,r-deseq2)
2031 ("r-desolve" ,r-desolve)
2032 ("r-genomicalignments" ,r-genomicalignments)
2033 ("r-genomicfeatures" ,r-genomicfeatures)
2034 ("r-genomicranges" ,r-genomicranges)
2035 ("r-iranges" ,r-iranges)
2036 ("r-plgem" ,r-plgem)
2037 ("r-preprocesscore" ,r-preprocesscore)
2039 ("r-rootsolve" ,r-rootsolve)
2040 ("r-rsamtools" ,r-rsamtools)
2041 ("r-s4vectors" ,r-s4vectors)
2042 ("r-shiny" ,r-shiny)
2043 ("r-summarizedexperiment" ,r-summarizedexperiment)
2044 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2045 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2046 (home-page "https://bioconductor.org/packages/INSPEcT")
2047 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2049 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2050 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2051 order to evaluate synthesis, processing and degradation rates and assess via
2052 modeling the rates that determines changes in mature mRNA levels.")
2053 (license license:gpl2)))
2055 (define-public r-dnabarcodes
2057 (name "r-dnabarcodes")
2062 (uri (bioconductor-uri "DNABarcodes" version))
2065 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
2066 (properties `((upstream-name . "DNABarcodes")))
2067 (build-system r-build-system)
2070 ("r-matrix" ,r-matrix)
2071 ("r-rcpp" ,r-rcpp)))
2072 (home-page "https://bioconductor.org/packages/DNABarcodes")
2073 (synopsis "Create and analyze DNA barcodes")
2075 "This package offers tools to create DNA barcode sets capable of
2076 correcting insertion, deletion, and substitution errors. Existing barcodes
2077 can be analyzed regarding their minimal, maximal and average distances between
2078 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2079 demultiplexed, i.e. assigned to their original reference barcode.")
2080 (license license:gpl2)))
2082 (define-public r-ruvseq
2089 (uri (bioconductor-uri "RUVSeq" version))
2092 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
2093 (properties `((upstream-name . "RUVSeq")))
2094 (build-system r-build-system)
2096 `(("r-biobase" ,r-biobase)
2097 ("r-edaseq" ,r-edaseq)
2098 ("r-edger" ,r-edger)
2099 ("r-mass" ,r-mass)))
2100 (home-page "https://github.com/drisso/RUVSeq")
2101 (synopsis "Remove unwanted variation from RNA-Seq data")
2103 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2104 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2106 (license license:artistic2.0)))
2108 (define-public r-biocneighbors
2110 (name "r-biocneighbors")
2115 (uri (bioconductor-uri "BiocNeighbors" version))
2118 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
2119 (properties `((upstream-name . "BiocNeighbors")))
2120 (build-system r-build-system)
2122 `(("r-biocgenerics" ,r-biocgenerics)
2123 ("r-biocparallel" ,r-biocparallel)
2125 ("r-rcppannoy" ,r-rcppannoy)
2126 ("r-rcpphnsw" ,r-rcpphnsw)
2127 ("r-s4vectors" ,r-s4vectors)))
2128 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2129 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2131 "This package implements exact and approximate methods for nearest
2132 neighbor detection, in a framework that allows them to be easily switched
2133 within Bioconductor packages or workflows. The exact algorithm is implemented
2134 using pre-clustering with the k-means algorithm. Functions are also provided
2135 to search for all neighbors within a given distance. Parallelization is
2136 achieved for all methods using the BiocParallel framework.")
2137 (license license:gpl3)))
2139 (define-public r-biocsingular
2141 (name "r-biocsingular")
2146 (uri (bioconductor-uri "BiocSingular" version))
2149 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
2150 (properties `((upstream-name . "BiocSingular")))
2151 (build-system r-build-system)
2153 `(("r-beachmat" ,r-beachmat)
2154 ("r-biocgenerics" ,r-biocgenerics)
2155 ("r-biocparallel" ,r-biocparallel)
2156 ("r-delayedarray" ,r-delayedarray)
2157 ("r-irlba" ,r-irlba)
2158 ("r-matrix" ,r-matrix)
2161 ("r-s4vectors" ,r-s4vectors)))
2162 (home-page "https://github.com/LTLA/BiocSingular")
2163 (synopsis "Singular value decomposition for Bioconductor packages")
2165 "This package implements exact and approximate methods for singular value
2166 decomposition and principal components analysis, in a framework that allows
2167 them to be easily switched within Bioconductor packages or workflows. Where
2168 possible, parallelization is achieved using the BiocParallel framework.")
2169 (license license:gpl3)))
2171 (define-public r-destiny
2178 (uri (bioconductor-uri "destiny" version))
2181 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
2182 (build-system r-build-system)
2184 `(("r-biobase" ,r-biobase)
2185 ("r-biocgenerics" ,r-biocgenerics)
2186 ("r-ggplot2" ,r-ggplot2)
2187 ("r-ggthemes" ,r-ggthemes)
2188 ("r-igraph" ,r-igraph)
2189 ("r-matrix" ,r-matrix)
2190 ("r-proxy" ,r-proxy)
2192 ("r-rcppeigen" ,r-rcppeigen)
2193 ("r-scales" ,r-scales)
2194 ("r-scatterplot3d" ,r-scatterplot3d)
2195 ("r-smoother" ,r-smoother)
2196 ("r-summarizedexperiment" ,r-summarizedexperiment)
2198 (home-page "https://bioconductor.org/packages/destiny/")
2199 (synopsis "Create and plot diffusion maps")
2200 (description "This package provides tools to create and plot diffusion
2202 ;; Any version of the GPL
2203 (license license:gpl3+)))
2205 (define-public r-savr
2212 (uri (bioconductor-uri "savR" version))
2215 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
2216 (properties `((upstream-name . "savR")))
2217 (build-system r-build-system)
2219 `(("r-ggplot2" ,r-ggplot2)
2220 ("r-gridextra" ,r-gridextra)
2221 ("r-reshape2" ,r-reshape2)
2222 ("r-scales" ,r-scales)
2224 (home-page "https://github.com/bcalder/savR")
2225 (synopsis "Parse and analyze Illumina SAV files")
2227 "This package provides tools to parse Illumina Sequence Analysis
2228 Viewer (SAV) files, access data, and generate QC plots.")
2229 (license license:agpl3+)))
2231 (define-public r-chipexoqual
2233 (name "r-chipexoqual")
2238 (uri (bioconductor-uri "ChIPexoQual" version))
2241 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
2242 (properties `((upstream-name . "ChIPexoQual")))
2243 (build-system r-build-system)
2245 `(("r-biocparallel" ,r-biocparallel)
2246 ("r-biovizbase" ,r-biovizbase)
2247 ("r-broom" ,r-broom)
2248 ("r-data-table" ,r-data-table)
2249 ("r-dplyr" ,r-dplyr)
2250 ("r-genomeinfodb" ,r-genomeinfodb)
2251 ("r-genomicalignments" ,r-genomicalignments)
2252 ("r-genomicranges" ,r-genomicranges)
2253 ("r-ggplot2" ,r-ggplot2)
2254 ("r-hexbin" ,r-hexbin)
2255 ("r-iranges" ,r-iranges)
2256 ("r-rcolorbrewer" ,r-rcolorbrewer)
2257 ("r-rmarkdown" ,r-rmarkdown)
2258 ("r-rsamtools" ,r-rsamtools)
2259 ("r-s4vectors" ,r-s4vectors)
2260 ("r-scales" ,r-scales)
2261 ("r-viridis" ,r-viridis)))
2262 (home-page "https://github.com/keleslab/ChIPexoQual")
2263 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2265 "This package provides a quality control pipeline for ChIP-exo/nexus
2267 (license license:gpl2+)))
2269 (define-public r-copynumber
2271 (name "r-copynumber")
2275 (uri (bioconductor-uri "copynumber" version))
2278 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
2279 (build-system r-build-system)
2281 `(("r-s4vectors" ,r-s4vectors)
2282 ("r-iranges" ,r-iranges)
2283 ("r-genomicranges" ,r-genomicranges)
2284 ("r-biocgenerics" ,r-biocgenerics)))
2285 (home-page "https://bioconductor.org/packages/copynumber")
2286 (synopsis "Segmentation of single- and multi-track copy number data")
2288 "This package segments single- and multi-track copy number data by a
2289 penalized least squares regression method.")
2290 (license license:artistic2.0)))
2292 (define-public r-dnacopy
2299 (uri (bioconductor-uri "DNAcopy" version))
2302 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2303 (properties `((upstream-name . "DNAcopy")))
2304 (build-system r-build-system)
2305 (native-inputs `(("gfortran" ,gfortran)))
2306 (home-page "https://bioconductor.org/packages/DNAcopy")
2307 (synopsis "DNA copy number data analysis")
2309 "This package implements the @dfn{circular binary segmentation} (CBS)
2310 algorithm to segment DNA copy number data and identify genomic regions with
2311 abnormal copy number.")
2312 (license license:gpl2+)))
2314 ;; This is a CRAN package, but it uncharacteristically depends on a
2315 ;; Bioconductor package.
2316 (define-public r-htscluster
2318 (name "r-htscluster")
2323 (uri (cran-uri "HTSCluster" version))
2326 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2327 (properties `((upstream-name . "HTSCluster")))
2328 (build-system r-build-system)
2330 `(("r-capushe" ,r-capushe)
2331 ("r-edger" ,r-edger)
2332 ("r-plotrix" ,r-plotrix)))
2333 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2334 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2336 "This package provides a Poisson mixture model is implemented to cluster
2337 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2338 estimation is performed using either the EM or CEM algorithm, and the slope
2339 heuristics are used for model selection (i.e., to choose the number of
2341 (license license:gpl3+)))
2343 (define-public r-deds
2350 (uri (bioconductor-uri "DEDS" version))
2353 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2354 (properties `((upstream-name . "DEDS")))
2355 (build-system r-build-system)
2356 (home-page "https://bioconductor.org/packages/DEDS/")
2357 (synopsis "Differential expression via distance summary for microarray data")
2359 "This library contains functions that calculate various statistics of
2360 differential expression for microarray data, including t statistics, fold
2361 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2362 also implements a new methodology called DEDS (Differential Expression via
2363 Distance Summary), which selects differentially expressed genes by integrating
2364 and summarizing a set of statistics using a weighted distance approach.")
2365 ;; Any version of the LGPL.
2366 (license license:lgpl3+)))
2368 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2370 (define-public r-nbpseq
2377 (uri (cran-uri "NBPSeq" version))
2380 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2381 (properties `((upstream-name . "NBPSeq")))
2382 (build-system r-build-system)
2384 `(("r-qvalue" ,r-qvalue)))
2385 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2386 (synopsis "Negative binomial models for RNA-Seq data")
2388 "This package provides negative binomial models for two-group comparisons
2389 and regression inferences from RNA-sequencing data.")
2390 (license license:gpl2)))
2392 (define-public r-ebseq
2399 (uri (bioconductor-uri "EBSeq" version))
2402 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2403 (properties `((upstream-name . "EBSeq")))
2404 (build-system r-build-system)
2406 `(("r-blockmodeling" ,r-blockmodeling)
2407 ("r-gplots" ,r-gplots)
2408 ("r-testthat" ,r-testthat)))
2409 (home-page "https://bioconductor.org/packages/EBSeq")
2410 (synopsis "Differential expression analysis of RNA-seq data")
2412 "This package provides tools for differential expression analysis at both
2413 gene and isoform level using RNA-seq data")
2414 (license license:artistic2.0)))
2416 (define-public r-lpsymphony
2418 (name "r-lpsymphony")
2423 (uri (bioconductor-uri "lpsymphony" version))
2426 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2427 (build-system r-build-system)
2429 `(("gfortran" ,gfortran)
2432 `(("pkg-config" ,pkg-config)))
2433 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2434 (synopsis "Symphony integer linear programming solver in R")
2436 "This package was derived from Rsymphony. The package provides an R
2437 interface to SYMPHONY, a linear programming solver written in C++. The main
2438 difference between this package and Rsymphony is that it includes the solver
2439 source code, while Rsymphony expects to find header and library files on the
2440 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2441 to install interface to SYMPHONY.")
2442 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2443 ;; lpsimphony is released under the same terms.
2444 (license license:epl1.0)))
2446 (define-public r-ihw
2453 (uri (bioconductor-uri "IHW" version))
2456 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2457 (properties `((upstream-name . "IHW")))
2458 (build-system r-build-system)
2460 `(("r-biocgenerics" ,r-biocgenerics)
2461 ("r-fdrtool" ,r-fdrtool)
2462 ("r-lpsymphony" ,r-lpsymphony)
2463 ("r-slam" ,r-slam)))
2464 (home-page "https://bioconductor.org/packages/IHW")
2465 (synopsis "Independent hypothesis weighting")
2467 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2468 procedure that increases power compared to the method of Benjamini and
2469 Hochberg by assigning data-driven weights to each hypothesis. The input to
2470 IHW is a two-column table of p-values and covariates. The covariate can be
2471 any continuous-valued or categorical variable that is thought to be
2472 informative on the statistical properties of each hypothesis test, while it is
2473 independent of the p-value under the null hypothesis.")
2474 (license license:artistic2.0)))
2476 (define-public r-icobra
2483 (uri (bioconductor-uri "iCOBRA" version))
2486 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2487 (properties `((upstream-name . "iCOBRA")))
2488 (build-system r-build-system)
2490 `(("r-dplyr" ,r-dplyr)
2492 ("r-ggplot2" ,r-ggplot2)
2493 ("r-limma" ,r-limma)
2494 ("r-reshape2" ,r-reshape2)
2496 ("r-scales" ,r-scales)
2497 ("r-shiny" ,r-shiny)
2498 ("r-shinybs" ,r-shinybs)
2499 ("r-shinydashboard" ,r-shinydashboard)
2500 ("r-upsetr" ,r-upsetr)))
2501 (home-page "https://bioconductor.org/packages/iCOBRA")
2502 (synopsis "Comparison and visualization of ranking and assignment methods")
2504 "This package provides functions for calculation and visualization of
2505 performance metrics for evaluation of ranking and binary
2506 classification (assignment) methods. It also contains a Shiny application for
2507 interactive exploration of results.")
2508 (license license:gpl2+)))
2510 (define-public r-mast
2517 (uri (bioconductor-uri "MAST" version))
2520 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2521 (properties `((upstream-name . "MAST")))
2522 (build-system r-build-system)
2524 `(("r-abind" ,r-abind)
2526 ("r-biobase" ,r-biobase)
2527 ("r-biocgenerics" ,r-biocgenerics)
2528 ("r-data-table" ,r-data-table)
2529 ("r-ggplot2" ,r-ggplot2)
2531 ("r-progress" ,r-progress)
2532 ("r-reshape2" ,r-reshape2)
2533 ("r-s4vectors" ,r-s4vectors)
2534 ("r-singlecellexperiment" ,r-singlecellexperiment)
2535 ("r-stringr" ,r-stringr)
2536 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2537 (home-page "https://github.com/RGLab/MAST/")
2538 (synopsis "Model-based analysis of single cell transcriptomics")
2540 "This package provides methods and models for handling zero-inflated
2541 single cell assay data.")
2542 (license license:gpl2+)))
2544 (define-public r-monocle
2551 (uri (bioconductor-uri "monocle" version))
2554 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2555 (build-system r-build-system)
2557 `(("r-biobase" ,r-biobase)
2558 ("r-biocgenerics" ,r-biocgenerics)
2559 ("r-biocviews" ,r-biocviews)
2560 ("r-cluster" ,r-cluster)
2561 ("r-combinat" ,r-combinat)
2562 ("r-ddrtree" ,r-ddrtree)
2563 ("r-densityclust" ,r-densityclust)
2564 ("r-dplyr" ,r-dplyr)
2565 ("r-fastica" ,r-fastica)
2566 ("r-ggplot2" ,r-ggplot2)
2567 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2568 ("r-igraph" ,r-igraph)
2569 ("r-irlba" ,r-irlba)
2570 ("r-limma" ,r-limma)
2572 ("r-matrix" ,r-matrix)
2573 ("r-matrixstats" ,r-matrixstats)
2574 ("r-pheatmap" ,r-pheatmap)
2576 ("r-proxy" ,r-proxy)
2577 ("r-qlcmatrix" ,r-qlcmatrix)
2580 ("r-reshape2" ,r-reshape2)
2581 ("r-rtsne" ,r-rtsne)
2583 ("r-stringr" ,r-stringr)
2584 ("r-tibble" ,r-tibble)
2586 ("r-viridis" ,r-viridis)))
2587 (home-page "https://bioconductor.org/packages/monocle")
2588 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2590 "Monocle performs differential expression and time-series analysis for
2591 single-cell expression experiments. It orders individual cells according to
2592 progress through a biological process, without knowing ahead of time which
2593 genes define progress through that process. Monocle also performs
2594 differential expression analysis, clustering, visualization, and other useful
2595 tasks on single cell expression data. It is designed to work with RNA-Seq and
2596 qPCR data, but could be used with other types as well.")
2597 (license license:artistic2.0)))
2599 (define-public r-monocle3
2607 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2609 (file-name (git-file-name name version))
2612 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2613 (build-system r-build-system)
2615 `(("r-biobase" ,r-biobase)
2616 ("r-biocgenerics" ,r-biocgenerics)
2617 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2618 ("r-dplyr" ,r-dplyr)
2619 ("r-ggplot2" ,r-ggplot2)
2620 ("r-ggrepel" ,r-ggrepel)
2622 ("r-htmlwidgets" ,r-htmlwidgets)
2623 ("r-igraph" ,r-igraph)
2624 ("r-irlba" ,r-irlba)
2625 ("r-limma" ,r-limma)
2626 ("r-lmtest" ,r-lmtest)
2628 ("r-matrix" ,r-matrix)
2629 ("r-matrix-utils" ,r-matrix-utils)
2630 ("r-pbapply" ,r-pbapply)
2631 ("r-pbmcapply" ,r-pbmcapply)
2632 ("r-pheatmap" ,r-pheatmap)
2633 ("r-plotly" ,r-plotly)
2635 ("r-proxy" ,r-proxy)
2637 ("r-purrr" ,r-purrr)
2640 ("r-rcppparallel" ,r-rcppparallel)
2641 ("r-reshape2" ,r-reshape2)
2642 ("r-reticulate" ,r-reticulate)
2643 ("r-rhpcblasctl" ,r-rhpcblasctl)
2644 ("r-rtsne" ,r-rtsne)
2645 ("r-shiny" ,r-shiny)
2647 ("r-spdep" ,r-spdep)
2648 ("r-speedglm" ,r-speedglm)
2649 ("r-stringr" ,r-stringr)
2650 ("r-singlecellexperiment" ,r-singlecellexperiment)
2651 ("r-tibble" ,r-tibble)
2652 ("r-tidyr" ,r-tidyr)
2654 ("r-viridis" ,r-viridis)))
2655 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2656 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2658 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2659 (license license:expat)))
2661 (define-public r-noiseq
2668 (uri (bioconductor-uri "NOISeq" version))
2671 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2672 (properties `((upstream-name . "NOISeq")))
2673 (build-system r-build-system)
2675 `(("r-biobase" ,r-biobase)
2676 ("r-matrix" ,r-matrix)))
2677 (home-page "https://bioconductor.org/packages/NOISeq")
2678 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2680 "This package provides tools to support the analysis of RNA-seq
2681 expression data or other similar kind of data. It provides exploratory plots
2682 to evaluate saturation, count distribution, expression per chromosome, type of
2683 detected features, features length, etc. It also supports the analysis of
2684 differential expression between two experimental conditions with no parametric
2686 (license license:artistic2.0)))
2688 (define-public r-scdd
2695 (uri (bioconductor-uri "scDD" version))
2698 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2699 (properties `((upstream-name . "scDD")))
2700 (build-system r-build-system)
2703 ("r-biocparallel" ,r-biocparallel)
2704 ("r-ebseq" ,r-ebseq)
2705 ("r-fields" ,r-fields)
2706 ("r-ggplot2" ,r-ggplot2)
2707 ("r-mclust" ,r-mclust)
2708 ("r-outliers" ,r-outliers)
2709 ("r-s4vectors" ,r-s4vectors)
2710 ("r-scran" ,r-scran)
2711 ("r-singlecellexperiment" ,r-singlecellexperiment)
2712 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2713 (home-page "https://github.com/kdkorthauer/scDD")
2714 (synopsis "Mixture modeling of single-cell RNA-seq data")
2716 "This package implements a method to analyze single-cell RNA-seq data
2717 utilizing flexible Dirichlet Process mixture models. Genes with differential
2718 distributions of expression are classified into several interesting patterns
2719 of differences between two conditions. The package also includes functions
2720 for simulating data with these patterns from negative binomial
2722 (license license:gpl2)))
2724 (define-public r-scone
2731 (uri (bioconductor-uri "scone" version))
2734 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2735 (build-system r-build-system)
2737 `(("r-aroma-light" ,r-aroma-light)
2738 ("r-biocparallel" ,r-biocparallel)
2740 ("r-class" ,r-class)
2741 ("r-cluster" ,r-cluster)
2742 ("r-compositions" ,r-compositions)
2743 ("r-diptest" ,r-diptest)
2744 ("r-edger" ,r-edger)
2746 ("r-gplots" ,r-gplots)
2747 ("r-hexbin" ,r-hexbin)
2748 ("r-limma" ,r-limma)
2749 ("r-matrixstats" ,r-matrixstats)
2750 ("r-mixtools" ,r-mixtools)
2751 ("r-rarpack" ,r-rarpack)
2752 ("r-rcolorbrewer" ,r-rcolorbrewer)
2753 ("r-rhdf5" ,r-rhdf5)
2754 ("r-ruvseq" ,r-ruvseq)
2755 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2756 (home-page "https://bioconductor.org/packages/scone")
2757 (synopsis "Single cell overview of normalized expression data")
2759 "SCONE is an R package for comparing and ranking the performance of
2760 different normalization schemes for single-cell RNA-seq and other
2761 high-throughput analyses.")
2762 (license license:artistic2.0)))
2764 (define-public r-geoquery
2771 (uri (bioconductor-uri "GEOquery" version))
2774 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2775 (properties `((upstream-name . "GEOquery")))
2776 (build-system r-build-system)
2778 `(("r-biobase" ,r-biobase)
2779 ("r-dplyr" ,r-dplyr)
2781 ("r-limma" ,r-limma)
2782 ("r-magrittr" ,r-magrittr)
2783 ("r-readr" ,r-readr)
2784 ("r-tidyr" ,r-tidyr)
2785 ("r-xml2" ,r-xml2)))
2786 (home-page "https://github.com/seandavi/GEOquery/")
2787 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2789 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2790 microarray data. Given the rich and varied nature of this resource, it is
2791 only natural to want to apply BioConductor tools to these data. GEOquery is
2792 the bridge between GEO and BioConductor.")
2793 (license license:gpl2)))
2795 (define-public r-illuminaio
2797 (name "r-illuminaio")
2802 (uri (bioconductor-uri "illuminaio" version))
2805 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2806 (build-system r-build-system)
2808 `(("r-base64" ,r-base64)))
2809 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2810 (synopsis "Parse Illumina microarray output files")
2812 "This package provides tools for parsing Illumina's microarray output
2813 files, including IDAT.")
2814 (license license:gpl2)))
2816 (define-public r-siggenes
2823 (uri (bioconductor-uri "siggenes" version))
2826 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2827 (build-system r-build-system)
2829 `(("r-biobase" ,r-biobase)
2830 ("r-multtest" ,r-multtest)
2831 ("r-scrime" ,r-scrime)))
2832 (home-page "https://bioconductor.org/packages/siggenes/")
2834 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2836 "This package provides tools for the identification of differentially
2837 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2838 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2839 Bayes Analyses of Microarrays} (EBAM).")
2840 (license license:lgpl2.0+)))
2842 (define-public r-bumphunter
2844 (name "r-bumphunter")
2849 (uri (bioconductor-uri "bumphunter" version))
2852 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2853 (build-system r-build-system)
2855 `(("r-annotationdbi" ,r-annotationdbi)
2856 ("r-biocgenerics" ,r-biocgenerics)
2857 ("r-dorng" ,r-dorng)
2858 ("r-foreach" ,r-foreach)
2859 ("r-genomeinfodb" ,r-genomeinfodb)
2860 ("r-genomicfeatures" ,r-genomicfeatures)
2861 ("r-genomicranges" ,r-genomicranges)
2862 ("r-iranges" ,r-iranges)
2863 ("r-iterators" ,r-iterators)
2864 ("r-limma" ,r-limma)
2865 ("r-locfit" ,r-locfit)
2866 ("r-matrixstats" ,r-matrixstats)
2867 ("r-s4vectors" ,r-s4vectors)))
2868 (home-page "https://github.com/ririzarr/bumphunter")
2869 (synopsis "Find bumps in genomic data")
2871 "This package provides tools for finding bumps in genomic data in order
2872 to identify differentially methylated regions in epigenetic epidemiology
2874 (license license:artistic2.0)))
2876 (define-public r-minfi
2883 (uri (bioconductor-uri "minfi" version))
2886 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2887 (build-system r-build-system)
2889 `(("r-beanplot" ,r-beanplot)
2890 ("r-biobase" ,r-biobase)
2891 ("r-biocgenerics" ,r-biocgenerics)
2892 ("r-biocparallel" ,r-biocparallel)
2893 ("r-biostrings" ,r-biostrings)
2894 ("r-bumphunter" ,r-bumphunter)
2895 ("r-data-table" ,r-data-table)
2896 ("r-delayedarray" ,r-delayedarray)
2897 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2898 ("r-genefilter" ,r-genefilter)
2899 ("r-genomeinfodb" ,r-genomeinfodb)
2900 ("r-genomicranges" ,r-genomicranges)
2901 ("r-geoquery" ,r-geoquery)
2902 ("r-hdf5array" ,r-hdf5array)
2903 ("r-illuminaio" ,r-illuminaio)
2904 ("r-iranges" ,r-iranges)
2905 ("r-lattice" ,r-lattice)
2906 ("r-limma" ,r-limma)
2908 ("r-mclust" ,r-mclust)
2910 ("r-nor1mix" ,r-nor1mix)
2911 ("r-preprocesscore" ,r-preprocesscore)
2912 ("r-quadprog" ,r-quadprog)
2913 ("r-rcolorbrewer" ,r-rcolorbrewer)
2914 ("r-reshape" ,r-reshape)
2915 ("r-s4vectors" ,r-s4vectors)
2916 ("r-siggenes" ,r-siggenes)
2917 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2918 (home-page "https://github.com/hansenlab/minfi")
2919 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2921 "This package provides tools to analyze and visualize Illumina Infinium
2922 methylation arrays.")
2923 (license license:artistic2.0)))
2925 (define-public r-methylumi
2927 (name "r-methylumi")
2932 (uri (bioconductor-uri "methylumi" version))
2935 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2936 (build-system r-build-system)
2938 `(("r-annotate" ,r-annotate)
2939 ("r-annotationdbi" ,r-annotationdbi)
2940 ("r-biobase" ,r-biobase)
2941 ("r-biocgenerics" ,r-biocgenerics)
2942 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2943 ("r-genefilter" ,r-genefilter)
2944 ("r-genomeinfodb" ,r-genomeinfodb)
2945 ("r-genomicranges" ,r-genomicranges)
2946 ("r-ggplot2" ,r-ggplot2)
2947 ("r-illuminaio" ,r-illuminaio)
2948 ("r-iranges" ,r-iranges)
2949 ("r-lattice" ,r-lattice)
2950 ("r-matrixstats" ,r-matrixstats)
2951 ("r-minfi" ,r-minfi)
2952 ("r-reshape2" ,r-reshape2)
2953 ("r-s4vectors" ,r-s4vectors)
2954 ("r-scales" ,r-scales)
2955 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2956 (home-page "https://bioconductor.org/packages/methylumi")
2957 (synopsis "Handle Illumina methylation data")
2959 "This package provides classes for holding and manipulating Illumina
2960 methylation data. Based on eSet, it can contain MIAME information, sample
2961 information, feature information, and multiple matrices of data. An
2962 \"intelligent\" import function, methylumiR can read the Illumina text files
2963 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2964 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2965 background correction, and quality control features for GoldenGate, Infinium,
2966 and Infinium HD arrays are also included.")
2967 (license license:gpl2)))
2969 (define-public r-lumi
2976 (uri (bioconductor-uri "lumi" version))
2979 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2980 (build-system r-build-system)
2982 `(("r-affy" ,r-affy)
2983 ("r-annotate" ,r-annotate)
2984 ("r-annotationdbi" ,r-annotationdbi)
2985 ("r-biobase" ,r-biobase)
2987 ("r-genomicfeatures" ,r-genomicfeatures)
2988 ("r-genomicranges" ,r-genomicranges)
2989 ("r-kernsmooth" ,r-kernsmooth)
2990 ("r-lattice" ,r-lattice)
2992 ("r-methylumi" ,r-methylumi)
2994 ("r-nleqslv" ,r-nleqslv)
2995 ("r-preprocesscore" ,r-preprocesscore)
2996 ("r-rsqlite" ,r-rsqlite)))
2997 (home-page "https://bioconductor.org/packages/lumi")
2998 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3000 "The lumi package provides an integrated solution for the Illumina
3001 microarray data analysis. It includes functions of Illumina
3002 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3003 variance stabilization, normalization and gene annotation at the probe level.
3004 It also includes the functions of processing Illumina methylation microarrays,
3005 especially Illumina Infinium methylation microarrays.")
3006 (license license:lgpl2.0+)))
3008 (define-public r-linnorm
3015 (uri (bioconductor-uri "Linnorm" version))
3018 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
3019 (properties `((upstream-name . "Linnorm")))
3020 (build-system r-build-system)
3022 `(("r-amap" ,r-amap)
3023 ("r-apcluster" ,r-apcluster)
3024 ("r-ellipse" ,r-ellipse)
3025 ("r-fastcluster" ,r-fastcluster)
3027 ("r-ggdendro" ,r-ggdendro)
3028 ("r-ggplot2" ,r-ggplot2)
3029 ("r-gmodels" ,r-gmodels)
3030 ("r-igraph" ,r-igraph)
3031 ("r-limma" ,r-limma)
3033 ("r-mclust" ,r-mclust)
3035 ("r-rcpparmadillo" ,r-rcpparmadillo)
3036 ("r-rtsne" ,r-rtsne)
3037 ("r-statmod" ,r-statmod)
3038 ("r-vegan" ,r-vegan)
3040 (home-page "http://www.jjwanglab.org/Linnorm/")
3041 (synopsis "Linear model and normality based transformation method")
3043 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3044 count data or any large scale count data. It transforms such datasets for
3045 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3046 the following pipelines are implemented:
3049 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3050 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3051 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3052 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3053 @item Differential expression analysis or differential peak detection using
3054 limma (@code{Linnorm.limma})
3055 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3056 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3057 @item Stable gene selection for scRNA-seq data; for users without or who do
3058 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3059 @item Data imputation (@code{Linnorm.DataImput}).
3062 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3063 @code{RnaXSim} function is included for simulating RNA-seq data for the
3064 evaluation of DEG analysis methods.")
3065 (license license:expat)))
3067 (define-public r-ioniser
3074 (uri (bioconductor-uri "IONiseR" version))
3077 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
3078 (properties `((upstream-name . "IONiseR")))
3079 (build-system r-build-system)
3081 `(("r-biocgenerics" ,r-biocgenerics)
3082 ("r-biocparallel" ,r-biocparallel)
3083 ("r-biostrings" ,r-biostrings)
3084 ("r-bit64" ,r-bit64)
3085 ("r-dplyr" ,r-dplyr)
3086 ("r-ggplot2" ,r-ggplot2)
3087 ("r-magrittr" ,r-magrittr)
3088 ("r-rhdf5" ,r-rhdf5)
3089 ("r-shortread" ,r-shortread)
3090 ("r-stringr" ,r-stringr)
3091 ("r-tibble" ,r-tibble)
3092 ("r-tidyr" ,r-tidyr)
3093 ("r-xvector" ,r-xvector)))
3094 (home-page "https://bioconductor.org/packages/IONiseR/")
3095 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3097 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3098 MinION data. It extracts summary statistics from a set of fast5 files and can
3099 be used either before or after base calling. In addition to standard
3100 summaries of the read-types produced, it provides a number of plots for
3101 visualising metrics relative to experiment run time or spatially over the
3102 surface of a flowcell.")
3103 (license license:expat)))
3105 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3106 (define-public r-gkmsvm
3113 (uri (cran-uri "gkmSVM" version))
3116 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3117 (properties `((upstream-name . "gkmSVM")))
3118 (build-system r-build-system)
3120 `(("r-biocgenerics" ,r-biocgenerics)
3121 ("r-biostrings" ,r-biostrings)
3122 ("r-genomeinfodb" ,r-genomeinfodb)
3123 ("r-genomicranges" ,r-genomicranges)
3124 ("r-iranges" ,r-iranges)
3125 ("r-kernlab" ,r-kernlab)
3128 ("r-rtracklayer" ,r-rtracklayer)
3129 ("r-s4vectors" ,r-s4vectors)
3130 ("r-seqinr" ,r-seqinr)))
3131 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3132 (synopsis "Gapped-kmer support vector machine")
3134 "This R package provides tools for training gapped-kmer SVM classifiers
3135 for DNA and protein sequences. This package supports several sequence
3136 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3137 (license license:gpl2+)))
3139 (define-public r-triform
3146 (uri (bioconductor-uri "triform" version))
3149 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
3150 (build-system r-build-system)
3152 `(("r-biocgenerics" ,r-biocgenerics)
3153 ("r-iranges" ,r-iranges)
3154 ("r-yaml" ,r-yaml)))
3155 (home-page "https://bioconductor.org/packages/triform/")
3156 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3158 "The Triform algorithm uses model-free statistics to identify peak-like
3159 distributions of TF ChIP sequencing reads, taking advantage of an improved
3160 peak definition in combination with known profile characteristics.")
3161 (license license:gpl2)))
3163 (define-public r-varianttools
3165 (name "r-varianttools")
3170 (uri (bioconductor-uri "VariantTools" version))
3173 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
3174 (properties `((upstream-name . "VariantTools")))
3175 (build-system r-build-system)
3177 `(("r-biobase" ,r-biobase)
3178 ("r-biocgenerics" ,r-biocgenerics)
3179 ("r-biocparallel" ,r-biocparallel)
3180 ("r-biostrings" ,r-biostrings)
3181 ("r-bsgenome" ,r-bsgenome)
3182 ("r-genomeinfodb" ,r-genomeinfodb)
3183 ("r-genomicfeatures" ,r-genomicfeatures)
3184 ("r-genomicranges" ,r-genomicranges)
3185 ("r-iranges" ,r-iranges)
3186 ("r-matrix" ,r-matrix)
3187 ("r-rsamtools" ,r-rsamtools)
3188 ("r-rtracklayer" ,r-rtracklayer)
3189 ("r-s4vectors" ,r-s4vectors)
3190 ("r-variantannotation" ,r-variantannotation)))
3191 (home-page "https://bioconductor.org/packages/VariantTools/")
3192 (synopsis "Tools for exploratory analysis of variant calls")
3194 "Explore, diagnose, and compare variant calls using filters. The
3195 VariantTools package supports a workflow for loading data, calling single
3196 sample variants and tumor-specific somatic mutations or other sample-specific
3197 variant types (e.g., RNA editing). Most of the functions operate on
3198 alignments (BAM files) or datasets of called variants. The user is expected
3199 to have already aligned the reads with a separate tool, e.g., GSNAP via
3201 (license license:artistic2.0)))
3203 (define-public r-heatplus
3210 (uri (bioconductor-uri "Heatplus" version))
3213 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
3214 (properties `((upstream-name . "Heatplus")))
3215 (build-system r-build-system)
3217 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3218 (home-page "https://github.com/alexploner/Heatplus")
3219 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3221 "This package provides tools to display a rectangular heatmap (intensity
3222 plot) of a data matrix. By default, both samples (columns) and features (row)
3223 of the matrix are sorted according to a hierarchical clustering, and the
3224 corresponding dendrogram is plotted. Optionally, panels with additional
3225 information about samples and features can be added to the plot.")
3226 (license license:gpl2+)))
3228 (define-public r-gosemsim
3235 (uri (bioconductor-uri "GOSemSim" version))
3238 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
3239 (properties `((upstream-name . "GOSemSim")))
3240 (build-system r-build-system)
3242 `(("r-annotationdbi" ,r-annotationdbi)
3243 ("r-go-db" ,r-go-db)
3244 ("r-rcpp" ,r-rcpp)))
3245 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3246 (synopsis "GO-terms semantic similarity measures")
3248 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3249 quantitative ways to compute similarities between genes and gene groups, and
3250 have became important basis for many bioinformatics analysis approaches.
3251 GOSemSim is an R package for semantic similarity computation among GO terms,
3252 sets of GO terms, gene products and gene clusters.")
3253 (license license:artistic2.0)))
3255 (define-public r-anota
3262 (uri (bioconductor-uri "anota" version))
3265 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
3266 (build-system r-build-system)
3268 `(("r-multtest" ,r-multtest)
3269 ("r-qvalue" ,r-qvalue)))
3270 (home-page "https://bioconductor.org/packages/anota/")
3271 (synopsis "Analysis of translational activity")
3273 "Genome wide studies of translational control is emerging as a tool to
3274 study various biological conditions. The output from such analysis is both
3275 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3276 involved in translation (the actively translating mRNA level) for each mRNA.
3277 The standard analysis of such data strives towards identifying differential
3278 translational between two or more sample classes - i.e. differences in
3279 actively translated mRNA levels that are independent of underlying differences
3280 in cytosolic mRNA levels. This package allows for such analysis using partial
3281 variances and the random variance model. As 10s of thousands of mRNAs are
3282 analyzed in parallel the library performs a number of tests to assure that
3283 the data set is suitable for such analysis.")
3284 (license license:gpl3)))
3286 (define-public r-sigpathway
3288 (name "r-sigpathway")
3293 (uri (bioconductor-uri "sigPathway" version))
3296 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3297 (properties `((upstream-name . "sigPathway")))
3298 (build-system r-build-system)
3299 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3300 (synopsis "Pathway analysis")
3302 "This package is used to conduct pathway analysis by calculating the NT_k
3303 and NE_k statistics in a statistical framework for determining whether a
3304 specified group of genes for a pathway has a coordinated association with a
3305 phenotype of interest.")
3306 (license license:gpl2)))
3308 (define-public r-fgsea
3315 (uri (bioconductor-uri "fgsea" version))
3318 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3319 (build-system r-build-system)
3322 ("r-biocparallel" ,r-biocparallel)
3323 ("r-data-table" ,r-data-table)
3324 ("r-fastmatch" ,r-fastmatch)
3325 ("r-ggplot2" ,r-ggplot2)
3326 ("r-gridextra" ,r-gridextra)
3327 ("r-matrix" ,r-matrix)
3328 ("r-rcpp" ,r-rcpp)))
3329 (home-page "https://github.com/ctlab/fgsea/")
3330 (synopsis "Fast gene set enrichment analysis")
3332 "The package implements an algorithm for fast gene set enrichment
3333 analysis. Using the fast algorithm allows to make more permutations and get
3334 more fine grained p-values, which allows to use accurate stantard approaches
3335 to multiple hypothesis correction.")
3336 (license license:expat)))
3338 (define-public r-dose
3345 (uri (bioconductor-uri "DOSE" version))
3348 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3349 (properties `((upstream-name . "DOSE")))
3350 (build-system r-build-system)
3352 `(("r-annotationdbi" ,r-annotationdbi)
3353 ("r-biocparallel" ,r-biocparallel)
3354 ("r-do-db" ,r-do-db)
3355 ("r-fgsea" ,r-fgsea)
3356 ("r-ggplot2" ,r-ggplot2)
3357 ("r-gosemsim" ,r-gosemsim)
3358 ("r-qvalue" ,r-qvalue)
3359 ("r-reshape2" ,r-reshape2)
3360 ("r-s4vectors" ,r-s4vectors)))
3361 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3362 (synopsis "Disease ontology semantic and enrichment analysis")
3364 "This package implements five methods proposed by Resnik, Schlicker,
3365 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3366 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3367 including hypergeometric model and gene set enrichment analysis are also
3368 implemented for discovering disease associations of high-throughput biological
3370 (license license:artistic2.0)))
3372 (define-public r-enrichplot
3374 (name "r-enrichplot")
3379 (uri (bioconductor-uri "enrichplot" version))
3382 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3383 (build-system r-build-system)
3385 `(("r-annotationdbi" ,r-annotationdbi)
3386 ("r-cowplot" ,r-cowplot)
3388 ("r-europepmc" ,r-europepmc)
3389 ("r-ggplot2" ,r-ggplot2)
3390 ("r-ggplotify" ,r-ggplotify)
3391 ("r-ggraph" ,r-ggraph)
3392 ("r-ggridges" ,r-ggridges)
3393 ("r-gosemsim" ,r-gosemsim)
3394 ("r-gridextra" ,r-gridextra)
3395 ("r-igraph" ,r-igraph)
3396 ("r-purrr" ,r-purrr)
3397 ("r-rcolorbrewer" ,r-rcolorbrewer)
3398 ("r-reshape2" ,r-reshape2)
3399 ("r-upsetr" ,r-upsetr)))
3400 (home-page "https://github.com/GuangchuangYu/enrichplot")
3401 (synopsis "Visualization of functional enrichment result")
3403 "The enrichplot package implements several visualization methods for
3404 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3405 All the visualization methods are developed based on ggplot2 graphics.")
3406 (license license:artistic2.0)))
3408 (define-public r-clusterprofiler
3410 (name "r-clusterprofiler")
3415 (uri (bioconductor-uri "clusterProfiler" version))
3418 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3420 `((upstream-name . "clusterProfiler")))
3421 (build-system r-build-system)
3423 `(("r-annotationdbi" ,r-annotationdbi)
3425 ("r-enrichplot" ,r-enrichplot)
3426 ("r-ggplot2" ,r-ggplot2)
3427 ("r-go-db" ,r-go-db)
3428 ("r-gosemsim" ,r-gosemsim)
3429 ("r-magrittr" ,r-magrittr)
3431 ("r-qvalue" ,r-qvalue)
3432 ("r-rvcheck" ,r-rvcheck)
3433 ("r-tidyr" ,r-tidyr)))
3434 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3435 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3437 "This package implements methods to analyze and visualize functional
3438 profiles (GO and KEGG) of gene and gene clusters.")
3439 (license license:artistic2.0)))
3441 (define-public r-mlinterfaces
3443 (name "r-mlinterfaces")
3448 (uri (bioconductor-uri "MLInterfaces" version))
3451 "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh"))))
3452 (properties `((upstream-name . "MLInterfaces")))
3453 (build-system r-build-system)
3455 `(("r-annotate" ,r-annotate)
3456 ("r-biobase" ,r-biobase)
3457 ("r-biocgenerics" ,r-biocgenerics)
3458 ("r-cluster" ,r-cluster)
3461 ("r-gdata" ,r-gdata)
3462 ("r-genefilter" ,r-genefilter)
3463 ("r-ggvis" ,r-ggvis)
3464 ("r-hwriter" ,r-hwriter)
3466 ("r-mlbench" ,r-mlbench)
3468 ("r-rcolorbrewer" ,r-rcolorbrewer)
3470 ("r-rpart" ,r-rpart)
3471 ("r-sfsmisc" ,r-sfsmisc)
3472 ("r-shiny" ,r-shiny)
3473 ("r-threejs" ,r-threejs)))
3474 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3475 (synopsis "Interfaces to R machine learning procedures")
3477 "This package provides uniform interfaces to machine learning code for
3478 data in R and Bioconductor containers.")
3479 ;; Any version of the LGPL.
3480 (license license:lgpl2.1+)))
3482 (define-public r-annaffy
3489 (uri (bioconductor-uri "annaffy" version))
3492 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3493 (build-system r-build-system)
3496 (modify-phases %standard-phases
3497 (add-after 'unpack 'remove-reference-to-non-free-data
3499 (substitute* "DESCRIPTION"
3503 `(("r-annotationdbi" ,r-annotationdbi)
3504 ("r-biobase" ,r-biobase)
3506 ("r-go-db" ,r-go-db)))
3507 (home-page "https://bioconductor.org/packages/annaffy/")
3508 (synopsis "Annotation tools for Affymetrix biological metadata")
3510 "This package provides functions for handling data from Bioconductor
3511 Affymetrix annotation data packages. It produces compact HTML and text
3512 reports including experimental data and URL links to many online databases.
3513 It allows searching of biological metadata using various criteria.")
3514 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3515 ;; the LGPL 2.1 is included.
3516 (license license:lgpl2.1+)))
3518 (define-public r-a4core
3525 (uri (bioconductor-uri "a4Core" version))
3528 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3529 (properties `((upstream-name . "a4Core")))
3530 (build-system r-build-system)
3532 `(("r-biobase" ,r-biobase)
3533 ("r-glmnet" ,r-glmnet)))
3534 (home-page "https://bioconductor.org/packages/a4Core")
3535 (synopsis "Automated Affymetrix array analysis core package")
3537 "This is the core package for the automated analysis of Affymetrix
3539 (license license:gpl3)))
3541 (define-public r-a4classif
3543 (name "r-a4classif")
3548 (uri (bioconductor-uri "a4Classif" version))
3551 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3552 (properties `((upstream-name . "a4Classif")))
3553 (build-system r-build-system)
3555 `(("r-a4core" ,r-a4core)
3556 ("r-a4preproc" ,r-a4preproc)
3557 ("r-glmnet" ,r-glmnet)
3558 ("r-mlinterfaces" ,r-mlinterfaces)
3561 ("r-varselrf" ,r-varselrf)))
3562 (home-page "https://bioconductor.org/packages/a4Classif/")
3563 (synopsis "Automated Affymetrix array analysis classification package")
3565 "This is the classification package for the automated analysis of
3566 Affymetrix arrays.")
3567 (license license:gpl3)))
3569 (define-public r-a4preproc
3571 (name "r-a4preproc")
3576 (uri (bioconductor-uri "a4Preproc" version))
3579 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3580 (properties `((upstream-name . "a4Preproc")))
3581 (build-system r-build-system)
3583 `(("r-annotationdbi" ,r-annotationdbi)))
3584 (home-page "https://bioconductor.org/packages/a4Preproc/")
3585 (synopsis "Automated Affymetrix array analysis preprocessing package")
3587 "This is a package for the automated analysis of Affymetrix arrays. It
3588 is used for preprocessing the arrays.")
3589 (license license:gpl3)))
3591 (define-public r-a4reporting
3593 (name "r-a4reporting")
3598 (uri (bioconductor-uri "a4Reporting" version))
3601 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3602 (properties `((upstream-name . "a4Reporting")))
3603 (build-system r-build-system)
3605 `(("r-annaffy" ,r-annaffy)
3606 ("r-xtable" ,r-xtable)))
3607 (home-page "https://bioconductor.org/packages/a4Reporting/")
3608 (synopsis "Automated Affymetrix array analysis reporting package")
3610 "This is a package for the automated analysis of Affymetrix arrays. It
3611 provides reporting features.")
3612 (license license:gpl3)))
3614 (define-public r-a4base
3621 (uri (bioconductor-uri "a4Base" version))
3624 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3625 (properties `((upstream-name . "a4Base")))
3626 (build-system r-build-system)
3628 `(("r-a4core" ,r-a4core)
3629 ("r-a4preproc" ,r-a4preproc)
3630 ("r-annaffy" ,r-annaffy)
3631 ("r-annotationdbi" ,r-annotationdbi)
3632 ("r-biobase" ,r-biobase)
3633 ("r-genefilter" ,r-genefilter)
3634 ("r-glmnet" ,r-glmnet)
3635 ("r-gplots" ,r-gplots)
3636 ("r-limma" ,r-limma)
3638 ("r-multtest" ,r-multtest)))
3639 (home-page "https://bioconductor.org/packages/a4Base/")
3640 (synopsis "Automated Affymetrix array analysis base package")
3642 "This package provides basic features for the automated analysis of
3643 Affymetrix arrays.")
3644 (license license:gpl3)))
3653 (uri (bioconductor-uri "a4" version))
3656 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3657 (build-system r-build-system)
3659 `(("r-a4base" ,r-a4base)
3660 ("r-a4classif" ,r-a4classif)
3661 ("r-a4core" ,r-a4core)
3662 ("r-a4preproc" ,r-a4preproc)
3663 ("r-a4reporting" ,r-a4reporting)))
3664 (home-page "https://bioconductor.org/packages/a4/")
3665 (synopsis "Automated Affymetrix array analysis umbrella package")
3667 "This package provides a software suite for the automated analysis of
3668 Affymetrix arrays.")
3669 (license license:gpl3)))
3671 (define-public r-abseqr
3678 (uri (bioconductor-uri "abseqR" version))
3681 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3682 (properties `((upstream-name . "abseqR")))
3683 (build-system r-build-system)
3685 `(("pandoc" ,ghc-pandoc)))
3687 `(("r-biocparallel" ,r-biocparallel)
3688 ("r-biocstyle" ,r-biocstyle)
3689 ("r-circlize" ,r-circlize)
3690 ("r-flexdashboard" ,r-flexdashboard)
3691 ("r-ggcorrplot" ,r-ggcorrplot)
3692 ("r-ggdendro" ,r-ggdendro)
3693 ("r-ggplot2" ,r-ggplot2)
3694 ("r-gridextra" ,r-gridextra)
3695 ("r-knitr" ,r-knitr)
3696 ("r-plotly" ,r-plotly)
3699 ("r-rcolorbrewer" ,r-rcolorbrewer)
3700 ("r-reshape2" ,r-reshape2)
3701 ("r-rmarkdown" ,r-rmarkdown)
3702 ("r-stringr" ,r-stringr)
3703 ("r-vegan" ,r-vegan)
3704 ("r-venndiagram" ,r-venndiagram)))
3705 (home-page "https://github.com/malhamdoosh/abseqR")
3706 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3708 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3709 sequencing datasets generated from antibody libraries and abseqR is one of its
3710 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3711 capabilities and allows them to generate interactive HTML reports for the
3712 convenience of viewing and sharing with other researchers. Additionally,
3713 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3714 further downstream analysis on its output.")
3715 (license license:gpl3)))
3717 (define-public r-bacon
3724 (uri (bioconductor-uri "bacon" version))
3727 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3728 (build-system r-build-system)
3730 `(("r-biocparallel" ,r-biocparallel)
3731 ("r-ellipse" ,r-ellipse)
3732 ("r-ggplot2" ,r-ggplot2)))
3733 (home-page "https://bioconductor.org/packages/bacon/")
3734 (synopsis "Controlling bias and inflation in association studies")
3736 "Bacon can be used to remove inflation and bias often observed in
3737 epigenome- and transcriptome-wide association studies. To this end bacon
3738 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3739 fitting a three-component normal mixture on z-scores.")
3740 (license license:gpl2+)))
3742 (define-public r-rgadem
3749 (uri (bioconductor-uri "rGADEM" version))
3752 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3753 (properties `((upstream-name . "rGADEM")))
3754 (build-system r-build-system)
3756 `(("r-biostrings" ,r-biostrings)
3757 ("r-bsgenome" ,r-bsgenome)
3758 ("r-iranges" ,r-iranges)
3759 ("r-seqlogo" ,r-seqlogo)))
3760 (home-page "https://bioconductor.org/packages/rGADEM/")
3761 (synopsis "De novo sequence motif discovery")
3763 "rGADEM is an efficient de novo motif discovery tool for large-scale
3764 genomic sequence data.")
3765 (license license:artistic2.0)))
3767 (define-public r-motiv
3774 (uri (bioconductor-uri "MotIV" version))
3777 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3778 (properties `((upstream-name . "MotIV")))
3779 (build-system r-build-system)
3783 `(("r-biocgenerics" ,r-biocgenerics)
3784 ("r-biostrings" ,r-biostrings)
3785 ("r-iranges" ,r-iranges)
3786 ("r-lattice" ,r-lattice)
3787 ("r-rgadem" ,r-rgadem)
3788 ("r-s4vectors" ,r-s4vectors)))
3789 (home-page "https://bioconductor.org/packages/MotIV/")
3790 (synopsis "Motif identification and validation")
3792 "This package is used for the identification and validation of sequence
3793 motifs. It makes use of STAMP for comparing a set of motifs to a given
3794 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3795 distributions, modules and filter motifs.")
3796 (license license:gpl2)))
3798 (define-public r-motifstack
3800 (name "r-motifstack")
3805 (uri (bioconductor-uri "motifStack" version))
3808 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3809 (properties `((upstream-name . "motifStack")))
3810 (build-system r-build-system)
3812 `(("r-ade4" ,r-ade4)
3813 ("r-biostrings" ,r-biostrings)
3814 ("r-grimport2" ,r-grimport2)
3815 ("r-htmlwidgets" ,r-htmlwidgets)
3816 ("r-motiv" ,r-motiv)
3817 ("r-scales" ,r-scales)
3819 (home-page "https://bioconductor.org/packages/motifStack/")
3820 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3822 "The motifStack package is designed for graphic representation of
3823 multiple motifs with different similarity scores. It works with both DNA/RNA
3824 sequence motifs and amino acid sequence motifs. In addition, it provides the
3825 flexibility for users to customize the graphic parameters such as the font
3826 type and symbol colors.")
3827 (license license:gpl2+)))
3829 (define-public r-genomicscores
3831 (name "r-genomicscores")
3836 (uri (bioconductor-uri "GenomicScores" version))
3839 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3840 (properties `((upstream-name . "GenomicScores")))
3841 (build-system r-build-system)
3843 `(("r-annotationhub" ,r-annotationhub)
3844 ("r-biobase" ,r-biobase)
3845 ("r-biocgenerics" ,r-biocgenerics)
3846 ("r-biostrings" ,r-biostrings)
3847 ("r-bsgenome" ,r-bsgenome)
3848 ("r-genomeinfodb" ,r-genomeinfodb)
3849 ("r-genomicranges" ,r-genomicranges)
3850 ("r-iranges" ,r-iranges)
3851 ("r-s4vectors" ,r-s4vectors)
3853 (home-page "https://github.com/rcastelo/GenomicScores/")
3854 (synopsis "Work with genome-wide position-specific scores")
3856 "This package provides infrastructure to store and access genome-wide
3857 position-specific scores within R and Bioconductor.")
3858 (license license:artistic2.0)))
3860 (define-public r-atacseqqc
3862 (name "r-atacseqqc")
3867 (uri (bioconductor-uri "ATACseqQC" version))
3870 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3871 (properties `((upstream-name . "ATACseqQC")))
3872 (build-system r-build-system)
3874 `(("r-biocgenerics" ,r-biocgenerics)
3875 ("r-biostrings" ,r-biostrings)
3876 ("r-bsgenome" ,r-bsgenome)
3877 ("r-chippeakanno" ,r-chippeakanno)
3878 ("r-edger" ,r-edger)
3879 ("r-genomeinfodb" ,r-genomeinfodb)
3880 ("r-genomicalignments" ,r-genomicalignments)
3881 ("r-genomicranges" ,r-genomicranges)
3882 ("r-genomicscores" ,r-genomicscores)
3883 ("r-iranges" ,r-iranges)
3884 ("r-kernsmooth" ,r-kernsmooth)
3885 ("r-limma" ,r-limma)
3886 ("r-motifstack" ,r-motifstack)
3887 ("r-preseqr" ,r-preseqr)
3888 ("r-randomforest" ,r-randomforest)
3889 ("r-rsamtools" ,r-rsamtools)
3890 ("r-rtracklayer" ,r-rtracklayer)
3891 ("r-s4vectors" ,r-s4vectors)))
3892 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3893 (synopsis "ATAC-seq quality control")
3895 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3896 sequencing, is a rapid and sensitive method for chromatin accessibility
3897 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3898 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3899 assess whether their ATAC-seq experiment is successful. It includes
3900 diagnostic plots of fragment size distribution, proportion of mitochondria
3901 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3903 (license license:gpl2+)))
3905 (define-public r-gofuncr
3912 (uri (bioconductor-uri "GOfuncR" version))
3915 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3916 (properties `((upstream-name . "GOfuncR")))
3917 (build-system r-build-system)
3919 `(("r-annotationdbi" ,r-annotationdbi)
3920 ("r-genomicranges" ,r-genomicranges)
3921 ("r-gtools" ,r-gtools)
3922 ("r-iranges" ,r-iranges)
3923 ("r-mapplots" ,r-mapplots)
3925 ("r-vioplot" ,r-vioplot)))
3926 (home-page "https://bioconductor.org/packages/GOfuncR/")
3927 (synopsis "Gene ontology enrichment using FUNC")
3929 "GOfuncR performs a gene ontology enrichment analysis based on the
3930 ontology enrichment software FUNC. GO-annotations are obtained from
3931 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3932 included in the package and updated regularly. GOfuncR provides the standard
3933 candidate vs background enrichment analysis using the hypergeometric test, as
3934 well as three additional tests:
3937 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3938 @item a binomial test that is used when genes are associated with two counts,
3940 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3941 associated with four counts.
3944 To correct for multiple testing and interdependency of the tests, family-wise
3945 error rates are computed based on random permutations of the gene-associated
3946 variables. GOfuncR also provides tools for exploring the ontology graph and
3947 the annotations, and options to take gene-length or spatial clustering of
3948 genes into account. It is also possible to provide custom gene coordinates,
3949 annotations and ontologies.")
3950 (license license:gpl2+)))
3952 (define-public r-abaenrichment
3954 (name "r-abaenrichment")
3959 (uri (bioconductor-uri "ABAEnrichment" version))
3962 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
3963 (properties `((upstream-name . "ABAEnrichment")))
3964 (build-system r-build-system)
3966 `(("r-abadata" ,r-abadata)
3967 ("r-data-table" ,r-data-table)
3968 ("r-gofuncr" ,r-gofuncr)
3969 ("r-gplots" ,r-gplots)
3970 ("r-gtools" ,r-gtools)
3971 ("r-rcpp" ,r-rcpp)))
3972 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3973 (synopsis "Gene expression enrichment in human brain regions")
3975 "The package ABAEnrichment is designed to test for enrichment of user
3976 defined candidate genes in the set of expressed genes in different human brain
3977 regions. The core function @code{aba_enrich} integrates the expression of the
3978 candidate gene set (averaged across donors) and the structural information of
3979 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3980 (license license:gpl2+)))
3982 (define-public r-annotationfuncs
3984 (name "r-annotationfuncs")
3989 (uri (bioconductor-uri "AnnotationFuncs" version))
3992 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3994 `((upstream-name . "AnnotationFuncs")))
3995 (build-system r-build-system)
3997 `(("r-annotationdbi" ,r-annotationdbi)
3999 (home-page "https://www.iysik.com/r/annotationfuncs")
4000 (synopsis "Annotation translation functions")
4002 "This package provides functions for handling translating between
4003 different identifieres using the Biocore Data Team data-packages (e.g.
4004 @code{org.Bt.eg.db}).")
4005 (license license:gpl2)))
4007 (define-public r-annotationtools
4009 (name "r-annotationtools")
4014 (uri (bioconductor-uri "annotationTools" version))
4017 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
4019 `((upstream-name . "annotationTools")))
4020 (build-system r-build-system)
4021 (propagated-inputs `(("r-biobase" ,r-biobase)))
4022 (home-page "https://bioconductor.org/packages/annotationTools/")
4023 (synopsis "Annotate microarrays and perform gene expression analyses")
4025 "This package provides functions to annotate microarrays, find orthologs,
4026 and integrate heterogeneous gene expression profiles using annotation and
4027 other molecular biology information available as flat file database (plain
4029 ;; Any version of the GPL.
4030 (license (list license:gpl2+))))
4032 (define-public r-allelicimbalance
4034 (name "r-allelicimbalance")
4039 (uri (bioconductor-uri "AllelicImbalance" version))
4042 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
4044 `((upstream-name . "AllelicImbalance")))
4045 (build-system r-build-system)
4047 `(("r-annotationdbi" ,r-annotationdbi)
4048 ("r-biocgenerics" ,r-biocgenerics)
4049 ("r-biostrings" ,r-biostrings)
4050 ("r-bsgenome" ,r-bsgenome)
4051 ("r-genomeinfodb" ,r-genomeinfodb)
4052 ("r-genomicalignments" ,r-genomicalignments)
4053 ("r-genomicfeatures" ,r-genomicfeatures)
4054 ("r-genomicranges" ,r-genomicranges)
4055 ("r-gridextra" ,r-gridextra)
4057 ("r-iranges" ,r-iranges)
4058 ("r-lattice" ,r-lattice)
4059 ("r-latticeextra" ,r-latticeextra)
4061 ("r-rsamtools" ,r-rsamtools)
4062 ("r-s4vectors" ,r-s4vectors)
4063 ("r-seqinr" ,r-seqinr)
4064 ("r-summarizedexperiment" ,r-summarizedexperiment)
4065 ("r-variantannotation" ,r-variantannotation)))
4066 (home-page "https://github.com/pappewaio/AllelicImbalance")
4067 (synopsis "Investigate allele-specific expression")
4069 "This package provides a framework for allele-specific expression
4070 investigation using RNA-seq data.")
4071 (license license:gpl3)))
4073 (define-public r-aucell
4080 (uri (bioconductor-uri "AUCell" version))
4083 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
4084 (properties `((upstream-name . "AUCell")))
4085 (build-system r-build-system)
4087 `(("r-data-table" ,r-data-table)
4088 ("r-gseabase" ,r-gseabase)
4089 ("r-mixtools" ,r-mixtools)
4090 ("r-r-utils" ,r-r-utils)
4091 ("r-shiny" ,r-shiny)
4092 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4093 (home-page "https://bioconductor.org/packages/AUCell/")
4094 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4096 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4097 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4098 Under the Curve} (AUC) to calculate whether a critical subset of the input
4099 gene set is enriched within the expressed genes for each cell. The
4100 distribution of AUC scores across all the cells allows exploring the relative
4101 expression of the signature. Since the scoring method is ranking-based,
4102 AUCell is independent of the gene expression units and the normalization
4103 procedure. In addition, since the cells are evaluated individually, it can
4104 easily be applied to bigger datasets, subsetting the expression matrix if
4106 (license license:gpl3)))
4108 (define-public r-ebimage
4115 (uri (bioconductor-uri "EBImage" version))
4118 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
4119 (properties `((upstream-name . "EBImage")))
4120 (build-system r-build-system)
4122 `(("r-abind" ,r-abind)
4123 ("r-biocgenerics" ,r-biocgenerics)
4124 ("r-fftwtools" ,r-fftwtools)
4125 ("r-htmltools" ,r-htmltools)
4126 ("r-htmlwidgets" ,r-htmlwidgets)
4128 ("r-locfit" ,r-locfit)
4130 ("r-rcurl" ,r-rcurl)
4131 ("r-tiff" ,r-tiff)))
4133 `(("r-knitr" ,r-knitr))) ; for vignettes
4134 (home-page "https://github.com/aoles/EBImage")
4135 (synopsis "Image processing and analysis toolbox for R")
4137 "EBImage provides general purpose functionality for image processing and
4138 analysis. In the context of (high-throughput) microscopy-based cellular
4139 assays, EBImage offers tools to segment cells and extract quantitative
4140 cellular descriptors. This allows the automation of such tasks using the R
4141 programming language and facilitates the use of other tools in the R
4142 environment for signal processing, statistical modeling, machine learning and
4143 visualization with image data.")
4144 ;; Any version of the LGPL.
4145 (license license:lgpl2.1+)))
4147 (define-public r-yamss
4154 (uri (bioconductor-uri "yamss" version))
4157 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
4158 (build-system r-build-system)
4160 `(("r-biocgenerics" ,r-biocgenerics)
4161 ("r-data-table" ,r-data-table)
4162 ("r-ebimage" ,r-ebimage)
4163 ("r-iranges" ,r-iranges)
4164 ("r-limma" ,r-limma)
4165 ("r-matrix" ,r-matrix)
4167 ("r-s4vectors" ,r-s4vectors)
4168 ("r-summarizedexperiment"
4169 ,r-summarizedexperiment)))
4170 (home-page "https://github.com/hansenlab/yamss")
4171 (synopsis "Tools for high-throughput metabolomics")
4173 "This package provides tools to analyze and visualize high-throughput
4174 metabolomics data acquired using chromatography-mass spectrometry. These tools
4175 preprocess data in a way that enables reliable and powerful differential
4177 (license license:artistic2.0)))
4179 (define-public r-gtrellis
4186 (uri (bioconductor-uri "gtrellis" version))
4189 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
4190 (build-system r-build-system)
4192 `(("r-circlize" ,r-circlize)
4193 ("r-genomicranges" ,r-genomicranges)
4194 ("r-getoptlong" ,r-getoptlong)
4195 ("r-iranges" ,r-iranges)))
4196 (home-page "https://github.com/jokergoo/gtrellis")
4197 (synopsis "Genome level Trellis layout")
4199 "Genome level Trellis graph visualizes genomic data conditioned by
4200 genomic categories (e.g. chromosomes). For each genomic category, multiple
4201 dimensional data which are represented as tracks describe different features
4202 from different aspects. This package provides high flexibility to arrange
4203 genomic categories and to add self-defined graphics in the plot.")
4204 (license license:expat)))
4206 (define-public r-somaticsignatures
4208 (name "r-somaticsignatures")
4213 (uri (bioconductor-uri "SomaticSignatures" version))
4216 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
4218 `((upstream-name . "SomaticSignatures")))
4219 (build-system r-build-system)
4221 `(("r-biobase" ,r-biobase)
4222 ("r-biostrings" ,r-biostrings)
4223 ("r-genomeinfodb" ,r-genomeinfodb)
4224 ("r-genomicranges" ,r-genomicranges)
4225 ("r-ggbio" ,r-ggbio)
4226 ("r-ggplot2" ,r-ggplot2)
4227 ("r-iranges" ,r-iranges)
4229 ("r-pcamethods" ,r-pcamethods)
4230 ("r-proxy" ,r-proxy)
4231 ("r-reshape2" ,r-reshape2)
4232 ("r-s4vectors" ,r-s4vectors)
4233 ("r-variantannotation" ,r-variantannotation)))
4234 (home-page "https://github.com/juliangehring/SomaticSignatures")
4235 (synopsis "Somatic signatures")
4237 "This package identifies mutational signatures of @dfn{single nucleotide
4238 variants} (SNVs). It provides a infrastructure related to the methodology
4239 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4240 decomposition algorithms.")
4241 (license license:expat)))
4243 (define-public r-yapsa
4250 (uri (bioconductor-uri "YAPSA" version))
4253 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
4254 (properties `((upstream-name . "YAPSA")))
4255 (build-system r-build-system)
4257 `(("r-circlize" ,r-circlize)
4258 ("r-complexheatmap" ,r-complexheatmap)
4259 ("r-corrplot" ,r-corrplot)
4260 ("r-dendextend" ,r-dendextend)
4261 ("r-genomeinfodb" ,r-genomeinfodb)
4262 ("r-genomicranges" ,r-genomicranges)
4263 ("r-getoptlong" ,r-getoptlong)
4264 ("r-ggplot2" ,r-ggplot2)
4265 ("r-gridextra" ,r-gridextra)
4266 ("r-gtrellis" ,r-gtrellis)
4267 ("r-keggrest" ,r-keggrest)
4269 ("r-pmcmr" ,r-pmcmr)
4270 ("r-reshape2" ,r-reshape2)
4271 ("r-somaticsignatures" ,r-somaticsignatures)
4272 ("r-variantannotation" ,r-variantannotation)))
4273 (home-page "https://bioconductor.org/packages/YAPSA/")
4274 (synopsis "Yet another package for signature analysis")
4276 "This package provides functions and routines useful in the analysis of
4277 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4278 functions to perform a signature analysis with known signatures and a
4279 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4281 (license license:gpl3)))
4283 (define-public r-gcrma
4290 (uri (bioconductor-uri "gcrma" version))
4293 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4294 (build-system r-build-system)
4296 `(("r-affy" ,r-affy)
4297 ("r-affyio" ,r-affyio)
4298 ("r-biobase" ,r-biobase)
4299 ("r-biocmanager" ,r-biocmanager)
4300 ("r-biostrings" ,r-biostrings)
4301 ("r-xvector" ,r-xvector)))
4302 (home-page "https://bioconductor.org/packages/gcrma/")
4303 (synopsis "Background adjustment using sequence information")
4305 "Gcrma adjusts for background intensities in Affymetrix array data which
4306 include optical noise and @dfn{non-specific binding} (NSB). The main function
4307 @code{gcrma} converts background adjusted probe intensities to expression
4308 measures using the same normalization and summarization methods as a
4309 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4310 to estimate probe affinity to NSB. The sequence information is summarized in
4311 a more complex way than the simple GC content. Instead, the base types (A, T,
4312 G or C) at each position along the probe determine the affinity of each probe.
4313 The parameters of the position-specific base contributions to the probe
4314 affinity is estimated in an NSB experiment in which only NSB but no
4315 gene-specific bidning is expected.")
4316 ;; Any version of the LGPL
4317 (license license:lgpl2.1+)))
4319 (define-public r-simpleaffy
4321 (name "r-simpleaffy")
4326 (uri (bioconductor-uri "simpleaffy" version))
4329 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4330 (build-system r-build-system)
4332 `(("r-affy" ,r-affy)
4333 ("r-biobase" ,r-biobase)
4334 ("r-biocgenerics" ,r-biocgenerics)
4335 ("r-gcrma" ,r-gcrma)
4336 ("r-genefilter" ,r-genefilter)))
4337 (home-page "https://bioconductor.org/packages/simpleaffy/")
4338 (synopsis "Very simple high level analysis of Affymetrix data")
4340 "This package provides high level functions for reading Affy @file{.CEL}
4341 files, phenotypic data, and then computing simple things with it, such as
4342 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4343 library. It also has some basic scatter plot functions and mechanisms for
4344 generating high resolution journal figures.")
4345 (license license:gpl2+)))
4347 (define-public r-yaqcaffy
4354 (uri (bioconductor-uri "yaqcaffy" version))
4357 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4358 (build-system r-build-system)
4360 `(("r-simpleaffy" ,r-simpleaffy)))
4361 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4362 (synopsis "Affymetrix quality control and reproducibility analysis")
4364 "This is a package that can be used for quality control of Affymetrix
4365 GeneChip expression data and reproducibility analysis of human whole genome
4366 chips with the MAQC reference datasets.")
4367 (license license:artistic2.0)))
4369 (define-public r-quantro
4376 (uri (bioconductor-uri "quantro" version))
4379 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4380 (build-system r-build-system)
4382 `(("r-biobase" ,r-biobase)
4383 ("r-doparallel" ,r-doparallel)
4384 ("r-foreach" ,r-foreach)
4385 ("r-ggplot2" ,r-ggplot2)
4386 ("r-iterators" ,r-iterators)
4387 ("r-minfi" ,r-minfi)
4388 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4389 (home-page "https://bioconductor.org/packages/quantro/")
4390 (synopsis "Test for when to use quantile normalization")
4392 "This package provides a data-driven test for the assumptions of quantile
4393 normalization using raw data such as objects that inherit eSets (e.g.
4394 ExpressionSet, MethylSet). Group level information about each sample (such as
4395 Tumor / Normal status) must also be provided because the test assesses if
4396 there are global differences in the distributions between the user-defined
4398 (license license:gpl3+)))
4400 (define-public r-yarn
4407 (uri (bioconductor-uri "yarn" version))
4410 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4411 (build-system r-build-system)
4413 `(("r-biobase" ,r-biobase)
4414 ("r-biomart" ,r-biomart)
4415 ("r-downloader" ,r-downloader)
4416 ("r-edger" ,r-edger)
4417 ("r-gplots" ,r-gplots)
4418 ("r-limma" ,r-limma)
4419 ("r-matrixstats" ,r-matrixstats)
4420 ("r-preprocesscore" ,r-preprocesscore)
4421 ("r-quantro" ,r-quantro)
4422 ("r-rcolorbrewer" ,r-rcolorbrewer)
4423 ("r-readr" ,r-readr)))
4424 (home-page "https://bioconductor.org/packages/yarn/")
4425 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4427 "Expedite large RNA-Seq analyses using a combination of previously
4428 developed tools. YARN is meant to make it easier for the user in performing
4429 basic mis-annotation quality control, filtering, and condition-aware
4430 normalization. YARN leverages many Bioconductor tools and statistical
4431 techniques to account for the large heterogeneity and sparsity found in very
4432 large RNA-seq experiments.")
4433 (license license:artistic2.0)))
4435 (define-public r-roar
4442 (uri (bioconductor-uri "roar" version))
4445 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4446 (build-system r-build-system)
4448 `(("r-biocgenerics" ,r-biocgenerics)
4449 ("r-genomeinfodb" ,r-genomeinfodb)
4450 ("r-genomicalignments" ,r-genomicalignments)
4451 ("r-genomicranges" ,r-genomicranges)
4452 ("r-iranges" ,r-iranges)
4453 ("r-rtracklayer" ,r-rtracklayer)
4454 ("r-s4vectors" ,r-s4vectors)
4455 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4456 (home-page "https://github.com/vodkatad/roar/")
4457 (synopsis "Identify differential APA usage from RNA-seq alignments")
4459 "This package provides tools for identifying preferential usage of APA
4460 sites, comparing two biological conditions, starting from known alternative
4461 sites and alignments obtained from standard RNA-seq experiments.")
4462 (license license:gpl3)))
4464 (define-public r-xbseq
4471 (uri (bioconductor-uri "XBSeq" version))
4474 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4475 (properties `((upstream-name . "XBSeq")))
4476 (build-system r-build-system)
4478 `(("r-biobase" ,r-biobase)
4479 ("r-deseq2" ,r-deseq2)
4480 ("r-dplyr" ,r-dplyr)
4481 ("r-ggplot2" ,r-ggplot2)
4482 ("r-locfit" ,r-locfit)
4483 ("r-magrittr" ,r-magrittr)
4484 ("r-matrixstats" ,r-matrixstats)
4485 ("r-pracma" ,r-pracma)
4486 ("r-roar" ,r-roar)))
4487 (home-page "https://github.com/Liuy12/XBSeq")
4488 (synopsis "Test for differential expression for RNA-seq data")
4490 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4491 expression} (DE), where a statistical model was established based on the
4492 assumption that observed signals are the convolution of true expression
4493 signals and sequencing noises. The mapped reads in non-exonic regions are
4494 considered as sequencing noises, which follows a Poisson distribution. Given
4495 measurable observed signal and background noise from RNA-seq data, true
4496 expression signals, assuming governed by the negative binomial distribution,
4497 can be delineated and thus the accurate detection of differential expressed
4499 (license license:gpl3+)))
4501 (define-public r-massspecwavelet
4503 (name "r-massspecwavelet")
4508 (uri (bioconductor-uri "MassSpecWavelet" version))
4511 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4513 `((upstream-name . "MassSpecWavelet")))
4514 (build-system r-build-system)
4516 `(("r-waveslim" ,r-waveslim)))
4517 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4518 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4520 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4521 data mainly through the use of wavelet transforms. It supports peak detection
4522 based on @dfn{Continuous Wavelet Transform} (CWT).")
4523 (license license:lgpl2.0+)))
4525 (define-public r-xcms
4532 (uri (bioconductor-uri "xcms" version))
4535 "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v"))))
4536 (build-system r-build-system)
4538 `(("r-biobase" ,r-biobase)
4539 ("r-biocgenerics" ,r-biocgenerics)
4540 ("r-biocparallel" ,r-biocparallel)
4541 ("r-lattice" ,r-lattice)
4542 ("r-massspecwavelet" ,r-massspecwavelet)
4543 ("r-msnbase" ,r-msnbase)
4544 ("r-multtest" ,r-multtest)
4547 ("r-protgenerics" ,r-protgenerics)
4549 ("r-rcolorbrewer" ,r-rcolorbrewer)
4550 ("r-robustbase" ,r-robustbase)
4551 ("r-s4vectors" ,r-s4vectors)))
4552 (home-page "https://bioconductor.org/packages/xcms/")
4553 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4555 "This package provides a framework for processing and visualization of
4556 chromatographically separated and single-spectra mass spectral data. It
4557 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4558 data for high-throughput, untargeted analyte profiling.")
4559 (license license:gpl2+)))
4561 (define-public r-wrench
4568 (uri (bioconductor-uri "Wrench" version))
4571 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4572 (properties `((upstream-name . "Wrench")))
4573 (build-system r-build-system)
4575 `(("r-limma" ,r-limma)
4576 ("r-locfit" ,r-locfit)
4577 ("r-matrixstats" ,r-matrixstats)))
4578 (home-page "https://github.com/HCBravoLab/Wrench")
4579 (synopsis "Wrench normalization for sparse count data")
4581 "Wrench is a package for normalization sparse genomic count data, like
4582 that arising from 16s metagenomic surveys.")
4583 (license license:artistic2.0)))
4585 (define-public r-wiggleplotr
4587 (name "r-wiggleplotr")
4592 (uri (bioconductor-uri "wiggleplotr" version))
4595 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4596 (build-system r-build-system)
4598 `(("r-assertthat" ,r-assertthat)
4599 ("r-cowplot" ,r-cowplot)
4600 ("r-dplyr" ,r-dplyr)
4601 ("r-genomeinfodb" ,r-genomeinfodb)
4602 ("r-genomicranges" ,r-genomicranges)
4603 ("r-ggplot2" ,r-ggplot2)
4604 ("r-iranges" ,r-iranges)
4605 ("r-purrr" ,r-purrr)
4606 ("r-rtracklayer" ,r-rtracklayer)
4607 ("r-s4vectors" ,r-s4vectors)))
4608 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4609 (synopsis "Make read coverage plots from BigWig files")
4611 "This package provides tools to visualize read coverage from sequencing
4612 experiments together with genomic annotations (genes, transcripts, peaks).
4613 Introns of long transcripts can be rescaled to a fixed length for better
4614 visualization of exonic read coverage.")
4615 (license license:asl2.0)))
4617 (define-public r-widgettools
4619 (name "r-widgettools")
4624 (uri (bioconductor-uri "widgetTools" version))
4627 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4628 (properties `((upstream-name . "widgetTools")))
4629 (build-system r-build-system)
4630 (home-page "https://bioconductor.org/packages/widgetTools/")
4631 (synopsis "Tools for creating interactive tcltk widgets")
4633 "This package contains tools to support the construction of tcltk
4635 ;; Any version of the LGPL.
4636 (license license:lgpl3+)))
4638 (define-public r-webbioc
4645 (uri (bioconductor-uri "webbioc" version))
4648 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4649 (build-system r-build-system)
4651 `(("netpbm" ,netpbm)
4654 `(("r-affy" ,r-affy)
4655 ("r-annaffy" ,r-annaffy)
4656 ("r-biobase" ,r-biobase)
4657 ("r-biocmanager" ,r-biocmanager)
4658 ("r-gcrma" ,r-gcrma)
4659 ("r-multtest" ,r-multtest)
4660 ("r-qvalue" ,r-qvalue)
4662 (home-page "https://www.bioconductor.org/")
4663 (synopsis "Bioconductor web interface")
4665 "This package provides an integrated web interface for doing microarray
4666 analysis using several of the Bioconductor packages. It is intended to be
4667 deployed as a centralized bioinformatics resource for use by many users.
4668 Currently only Affymetrix oligonucleotide analysis is supported.")
4669 (license license:gpl2+)))
4671 (define-public r-zfpkm
4678 (uri (bioconductor-uri "zFPKM" version))
4681 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4682 (properties `((upstream-name . "zFPKM")))
4683 (build-system r-build-system)
4685 `(("r-checkmate" ,r-checkmate)
4686 ("r-dplyr" ,r-dplyr)
4687 ("r-ggplot2" ,r-ggplot2)
4688 ("r-summarizedexperiment" ,r-summarizedexperiment)
4689 ("r-tidyr" ,r-tidyr)))
4690 (home-page "https://github.com/ronammar/zFPKM/")
4691 (synopsis "Functions to facilitate zFPKM transformations")
4693 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4694 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4696 (license license:gpl3)))
4698 (define-public r-rbowtie2
4705 (uri (bioconductor-uri "Rbowtie2" version))
4708 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4709 (properties `((upstream-name . "Rbowtie2")))
4710 (build-system r-build-system)
4713 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4714 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4716 "This package provides an R wrapper of the popular @code{bowtie2}
4717 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4718 rapid adapter trimming, identification, and read merging.")
4719 (license license:gpl3+)))
4721 (define-public r-progeny
4728 (uri (bioconductor-uri "progeny" version))
4731 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4732 (build-system r-build-system)
4733 (propagated-inputs `(("r-biobase" ,r-biobase)))
4734 (home-page "https://github.com/saezlab/progeny")
4735 (synopsis "Pathway responsive gene activity inference")
4737 "This package provides a function to infer pathway activity from gene
4738 expression. It contains the linear model inferred in the publication
4739 \"Perturbation-response genes reveal signaling footprints in cancer gene
4741 (license license:asl2.0)))
4743 (define-public r-arrmnormalization
4745 (name "r-arrmnormalization")
4750 (uri (bioconductor-uri "ARRmNormalization" version))
4753 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4755 `((upstream-name . "ARRmNormalization")))
4756 (build-system r-build-system)
4757 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4758 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4759 (synopsis "Adaptive robust regression normalization for methylation data")
4761 "This is a package to perform the @dfn{Adaptive Robust Regression
4762 method} (ARRm) for the normalization of methylation data from the Illumina
4763 Infinium HumanMethylation 450k assay.")
4764 (license license:artistic2.0)))
4766 (define-public r-biocfilecache
4768 (name "r-biocfilecache")
4773 (uri (bioconductor-uri "BiocFileCache" version))
4776 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4777 (properties `((upstream-name . "BiocFileCache")))
4778 (build-system r-build-system)
4780 `(("r-curl" ,r-curl)
4782 ("r-dbplyr" ,r-dbplyr)
4783 ("r-dplyr" ,r-dplyr)
4785 ("r-rappdirs" ,r-rappdirs)
4786 ("r-rsqlite" ,r-rsqlite)))
4787 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4788 (synopsis "Manage files across sessions")
4790 "This package creates a persistent on-disk cache of files that the user
4791 can add, update, and retrieve. It is useful for managing resources (such as
4792 custom Txdb objects) that are costly or difficult to create, web resources,
4793 and data files used across sessions.")
4794 (license license:artistic2.0)))
4796 (define-public r-iclusterplus
4798 (name "r-iclusterplus")
4803 (uri (bioconductor-uri "iClusterPlus" version))
4806 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4807 (properties `((upstream-name . "iClusterPlus")))
4808 (build-system r-build-system)
4809 (native-inputs `(("gfortran" ,gfortran)))
4810 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4811 (synopsis "Integrative clustering of multi-type genomic data")
4813 "iClusterPlus is developed for integrative clustering analysis of
4814 multi-type genomic data and is an enhanced version of iCluster proposed and
4815 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4816 from the experiments where biological samples (e.g. tumor samples) are
4817 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4818 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4819 on. In the iClusterPlus model, binary observations such as somatic mutation
4820 are modeled as Binomial processes; categorical observations such as copy
4821 number states are realizations of Multinomial random variables; counts are
4822 modeled as Poisson random processes; and continuous measures are modeled by
4823 Gaussian distributions.")
4824 (license license:gpl2+)))
4826 (define-public r-rbowtie
4833 (uri (bioconductor-uri "Rbowtie" version))
4836 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4837 (properties `((upstream-name . "Rbowtie")))
4838 (build-system r-build-system)
4841 (home-page "https://bioconductor.org/packages/Rbowtie/")
4842 (synopsis "R bowtie wrapper")
4844 "This package provides an R wrapper around the popular bowtie short read
4845 aligner and around SpliceMap, a de novo splice junction discovery and
4847 (license license:artistic2.0)))
4849 (define-public r-sgseq
4856 (uri (bioconductor-uri "SGSeq" version))
4859 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4860 (properties `((upstream-name . "SGSeq")))
4861 (build-system r-build-system)
4863 `(("r-annotationdbi" ,r-annotationdbi)
4864 ("r-biocgenerics" ,r-biocgenerics)
4865 ("r-biostrings" ,r-biostrings)
4866 ("r-genomeinfodb" ,r-genomeinfodb)
4867 ("r-genomicalignments" ,r-genomicalignments)
4868 ("r-genomicfeatures" ,r-genomicfeatures)
4869 ("r-genomicranges" ,r-genomicranges)
4870 ("r-igraph" ,r-igraph)
4871 ("r-iranges" ,r-iranges)
4872 ("r-rsamtools" ,r-rsamtools)
4873 ("r-rtracklayer" ,r-rtracklayer)
4874 ("r-runit" ,r-runit)
4875 ("r-s4vectors" ,r-s4vectors)
4876 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4877 (home-page "https://bioconductor.org/packages/SGSeq/")
4878 (synopsis "Splice event prediction and quantification from RNA-seq data")
4880 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4881 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4882 represented as a splice graph, which can be obtained from existing annotation
4883 or predicted from the mapped sequence reads. Splice events are identified
4884 from the graph and are quantified locally using structurally compatible reads
4885 at the start or end of each splice variant. The software includes functions
4886 for splice event prediction, quantification, visualization and
4888 (license license:artistic2.0)))
4890 (define-public r-rhisat2
4897 (uri (bioconductor-uri "Rhisat2" version))
4900 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4901 (properties `((upstream-name . "Rhisat2")))
4902 (build-system r-build-system)
4904 `(("which" ,which)))
4906 `(("r-genomicfeatures" ,r-genomicfeatures)
4907 ("r-genomicranges" ,r-genomicranges)
4908 ("r-sgseq" ,r-sgseq)))
4909 (home-page "https://github.com/fmicompbio/Rhisat2")
4910 (synopsis "R Wrapper for HISAT2 sequence aligner")
4912 "This package provides an R interface to the HISAT2 spliced short-read
4913 aligner by Kim et al. (2015). The package contains wrapper functions to
4914 create a genome index and to perform the read alignment to the generated
4916 (license license:gpl3)))
4918 (define-public r-quasr
4925 (uri (bioconductor-uri "QuasR" version))
4928 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4929 (properties `((upstream-name . "QuasR")))
4930 (build-system r-build-system)
4934 `(("r-annotationdbi" ,r-annotationdbi)
4935 ("r-biobase" ,r-biobase)
4936 ("r-biocgenerics" ,r-biocgenerics)
4937 ("r-biocmanager" ,r-biocmanager)
4938 ("r-biocparallel" ,r-biocparallel)
4939 ("r-biostrings" ,r-biostrings)
4940 ("r-bsgenome" ,r-bsgenome)
4941 ("r-genomeinfodb" ,r-genomeinfodb)
4942 ("r-genomicalignments" ,r-genomicalignments)
4943 ("r-genomicfeatures" ,r-genomicfeatures)
4944 ("r-genomicfiles" ,r-genomicfiles)
4945 ("r-genomicranges" ,r-genomicranges)
4946 ("r-iranges" ,r-iranges)
4947 ("r-rbowtie" ,r-rbowtie)
4948 ("r-rhisat2" ,r-rhisat2)
4949 ("r-rhtslib" ,r-rhtslib)
4950 ("r-rsamtools" ,r-rsamtools)
4951 ("r-rtracklayer" ,r-rtracklayer)
4952 ("r-s4vectors" ,r-s4vectors)
4953 ("r-shortread" ,r-shortread)))
4954 (home-page "https://bioconductor.org/packages/QuasR/")
4955 (synopsis "Quantify and annotate short reads in R")
4957 "This package provides a framework for the quantification and analysis of
4958 short genomic reads. It covers a complete workflow starting from raw sequence
4959 reads, over creation of alignments and quality control plots, to the
4960 quantification of genomic regions of interest.")
4961 (license license:gpl2)))
4963 (define-public r-rqc
4970 (uri (bioconductor-uri "Rqc" version))
4973 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4974 (properties `((upstream-name . "Rqc")))
4975 (build-system r-build-system)
4977 `(("r-biocgenerics" ,r-biocgenerics)
4978 ("r-biocparallel" ,r-biocparallel)
4979 ("r-biocstyle" ,r-biocstyle)
4980 ("r-biostrings" ,r-biostrings)
4981 ("r-biovizbase" ,r-biovizbase)
4982 ("r-genomicalignments" ,r-genomicalignments)
4983 ("r-genomicfiles" ,r-genomicfiles)
4984 ("r-ggplot2" ,r-ggplot2)
4985 ("r-iranges" ,r-iranges)
4986 ("r-knitr" ,r-knitr)
4987 ("r-markdown" ,r-markdown)
4990 ("r-reshape2" ,r-reshape2)
4991 ("r-rsamtools" ,r-rsamtools)
4992 ("r-s4vectors" ,r-s4vectors)
4993 ("r-shiny" ,r-shiny)
4994 ("r-shortread" ,r-shortread)))
4995 (home-page "https://github.com/labbcb/Rqc")
4996 (synopsis "Quality control tool for high-throughput sequencing data")
4998 "Rqc is an optimized tool designed for quality control and assessment of
4999 high-throughput sequencing data. It performs parallel processing of entire
5000 files and produces a report which contains a set of high-resolution
5002 (license license:gpl2+)))
5004 (define-public r-birewire
5011 (uri (bioconductor-uri "BiRewire" version))
5014 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
5015 (properties `((upstream-name . "BiRewire")))
5016 (build-system r-build-system)
5018 `(("r-igraph" ,r-igraph)
5019 ("r-matrix" ,r-matrix)
5021 ("r-tsne" ,r-tsne)))
5022 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5023 (synopsis "Tools for randomization of bipartite graphs")
5025 "This package provides functions for bipartite network rewiring through N
5026 consecutive switching steps and for the computation of the minimal number of
5027 switching steps to be performed in order to maximise the dissimilarity with
5028 respect to the original network. It includes functions for the analysis of
5029 the introduced randomness across the switching steps and several other
5030 routines to analyse the resulting networks and their natural projections.")
5031 (license license:gpl3)))
5033 (define-public r-birta
5040 (uri (bioconductor-uri "birta" version))
5043 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
5044 (build-system r-build-system)
5046 `(("r-biobase" ,r-biobase)
5047 ("r-limma" ,r-limma)
5048 ("r-mass" ,r-mass)))
5049 (home-page "https://bioconductor.org/packages/birta")
5050 (synopsis "Bayesian inference of regulation of transcriptional activity")
5052 "Expression levels of mRNA molecules are regulated by different
5053 processes, comprising inhibition or activation by transcription factors and
5054 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5055 Inference of Regulation of Transcriptional Activity) uses the regulatory
5056 networks of transcription factors and miRNAs together with mRNA and miRNA
5057 expression data to predict switches in regulatory activity between two
5058 conditions. A Bayesian network is used to model the regulatory structure and
5059 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5060 (license license:gpl2+)))
5062 (define-public r-ropls
5069 (uri (bioconductor-uri "ropls" version))
5072 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
5073 (build-system r-build-system)
5074 (propagated-inputs `(("r-biobase" ,r-biobase)))
5076 `(("r-knitr" ,r-knitr))) ; for vignettes
5077 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5078 (synopsis "Multivariate analysis and feature selection of omics data")
5080 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5081 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5082 regression, classification, and feature selection of omics data where the
5083 number of variables exceeds the number of samples and with multicollinearity
5084 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5085 separately model the variation correlated (predictive) to the factor of
5086 interest and the uncorrelated (orthogonal) variation. While performing
5087 similarly to PLS, OPLS facilitates interpretation.
5089 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5090 analysis and feature selection of omics data. In addition to scores, loadings
5091 and weights plots, the package provides metrics and graphics to determine the
5092 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5093 validity of the model by permutation testing, detect outliers, and perform
5094 feature selection (e.g. with Variable Importance in Projection or regression
5096 (license license:cecill)))
5098 (define-public r-biosigner
5100 (name "r-biosigner")
5105 (uri (bioconductor-uri "biosigner" version))
5108 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
5109 (build-system r-build-system)
5111 `(("r-biobase" ,r-biobase)
5112 ("r-e1071" ,r-e1071)
5113 ("r-randomforest" ,r-randomforest)
5114 ("r-ropls" ,r-ropls)))
5116 `(("r-knitr" ,r-knitr)
5117 ("r-rmarkdown" ,r-rmarkdown)
5118 ("pandoc" ,ghc-pandoc)
5119 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5120 (home-page "https://bioconductor.org/packages/biosigner/")
5121 (synopsis "Signature discovery from omics data")
5123 "Feature selection is critical in omics data analysis to extract
5124 restricted and meaningful molecular signatures from complex and high-dimension
5125 data, and to build robust classifiers. This package implements a method to
5126 assess the relevance of the variables for the prediction performances of the
5127 classifier. The approach can be run in parallel with the PLS-DA, Random
5128 Forest, and SVM binary classifiers. The signatures and the corresponding
5129 'restricted' models are returned, enabling future predictions on new
5131 (license license:cecill)))
5133 (define-public r-annotatr
5140 (uri (bioconductor-uri "annotatr" version))
5143 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
5144 (build-system r-build-system)
5146 `(("r-annotationdbi" ,r-annotationdbi)
5147 ("r-annotationhub" ,r-annotationhub)
5148 ("r-dplyr" ,r-dplyr)
5149 ("r-genomeinfodb" ,r-genomeinfodb)
5150 ("r-genomicfeatures" ,r-genomicfeatures)
5151 ("r-genomicranges" ,r-genomicranges)
5152 ("r-ggplot2" ,r-ggplot2)
5153 ("r-iranges" ,r-iranges)
5154 ("r-readr" ,r-readr)
5155 ("r-regioner" ,r-regioner)
5156 ("r-reshape2" ,r-reshape2)
5157 ("r-rtracklayer" ,r-rtracklayer)
5158 ("r-s4vectors" ,r-s4vectors)))
5159 (home-page "https://bioconductor.org/packages/annotatr/")
5160 (synopsis "Annotation of genomic regions to genomic annotations")
5162 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5163 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5164 to investigate the intersecting genomic annotations. Such annotations include
5165 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5166 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5167 enhancers. The annotatr package provides an easy way to summarize and
5168 visualize the intersection of genomic sites/regions with genomic
5170 (license license:gpl3)))
5172 (define-public r-rsubread
5179 (uri (bioconductor-uri "Rsubread" version))
5182 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
5183 (properties `((upstream-name . "Rsubread")))
5184 (build-system r-build-system)
5185 (inputs `(("zlib" ,zlib)))
5186 (home-page "https://bioconductor.org/packages/Rsubread/")
5187 (synopsis "Subread sequence alignment and counting for R")
5189 "This package provides tools for alignment, quantification and analysis
5190 of second and third generation sequencing data. It includes functionality for
5191 read mapping, read counting, SNP calling, structural variant detection and
5192 gene fusion discovery. It can be applied to all major sequencing techologies
5193 and to both short and long sequence reads.")
5194 (license license:gpl3)))
5196 (define-public r-flowutils
5198 (name "r-flowutils")
5203 (uri (bioconductor-uri "flowUtils" version))
5206 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
5207 (properties `((upstream-name . "flowUtils")))
5208 (build-system r-build-system)
5210 `(("r-biobase" ,r-biobase)
5211 ("r-corpcor" ,r-corpcor)
5212 ("r-flowcore" ,r-flowcore)
5213 ("r-graph" ,r-graph)
5214 ("r-runit" ,r-runit)
5216 (home-page "https://github.com/jspidlen/flowUtils")
5217 (synopsis "Utilities for flow cytometry")
5219 "This package provides utilities for flow cytometry data.")
5220 (license license:artistic2.0)))
5222 (define-public r-consensusclusterplus
5224 (name "r-consensusclusterplus")
5229 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5232 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
5234 `((upstream-name . "ConsensusClusterPlus")))
5235 (build-system r-build-system)
5238 ("r-biobase" ,r-biobase)
5239 ("r-cluster" ,r-cluster)))
5240 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5241 (synopsis "Clustering algorithm")
5243 "This package provides an implementation of an algorithm for determining
5244 cluster count and membership by stability evidence in unsupervised analysis.")
5245 (license license:gpl2)))
5247 (define-public r-flowcore
5254 (uri (bioconductor-uri "flowCore" version))
5257 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
5258 (properties `((upstream-name . "flowCore")))
5259 (build-system r-build-system)
5262 ("r-biobase" ,r-biobase)
5263 ("r-biocgenerics" ,r-biocgenerics)
5264 ("r-corpcor" ,r-corpcor)
5265 ("r-graph" ,r-graph)
5267 ("r-matrixstats" ,r-matrixstats)
5269 ("r-rrcov" ,r-rrcov)))
5270 (home-page "https://bioconductor.org/packages/flowCore")
5271 (synopsis "Basic structures for flow cytometry data")
5273 "This package provides S4 data structures and basic functions to deal
5274 with flow cytometry data.")
5275 (license license:artistic2.0)))
5277 (define-public r-flowmeans
5279 (name "r-flowmeans")
5284 (uri (bioconductor-uri "flowMeans" version))
5287 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
5288 (properties `((upstream-name . "flowMeans")))
5289 (build-system r-build-system)
5291 `(("r-biobase" ,r-biobase)
5292 ("r-feature" ,r-feature)
5293 ("r-flowcore" ,r-flowcore)
5294 ("r-rrcov" ,r-rrcov)))
5295 (home-page "https://bioconductor.org/packages/flowMeans")
5296 (synopsis "Non-parametric flow cytometry data gating")
5298 "This package provides tools to identify cell populations in Flow
5299 Cytometry data using non-parametric clustering and segmented-regression-based
5300 change point detection.")
5301 (license license:artistic2.0)))
5303 (define-public r-flowsom
5310 (uri (bioconductor-uri "FlowSOM" version))
5313 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5314 (properties `((upstream-name . "FlowSOM")))
5315 (build-system r-build-system)
5317 `(("r-biocgenerics" ,r-biocgenerics)
5318 ("r-consensusclusterplus" ,r-consensusclusterplus)
5319 ("r-flowcore" ,r-flowcore)
5320 ("r-flowutils" ,r-flowutils)
5321 ("r-igraph" ,r-igraph)
5324 (home-page "https://bioconductor.org/packages/FlowSOM/")
5325 (synopsis "Visualize and interpret cytometry data")
5327 "FlowSOM offers visualization options for cytometry data, by using
5328 self-organizing map clustering and minimal spanning trees.")
5329 (license license:gpl2+)))
5331 (define-public r-mixomics
5338 (uri (bioconductor-uri "mixOmics" version))
5341 "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
5342 (properties `((upstream-name . "mixOmics")))
5343 (build-system r-build-system)
5345 `(("r-corpcor" ,r-corpcor)
5346 ("r-dplyr" ,r-dplyr)
5347 ("r-ellipse" ,r-ellipse)
5348 ("r-ggplot2" ,r-ggplot2)
5349 ("r-gridextra" ,r-gridextra)
5350 ("r-igraph" ,r-igraph)
5351 ("r-lattice" ,r-lattice)
5353 ("r-matrixstats" ,r-matrixstats)
5354 ("r-rarpack" ,r-rarpack)
5355 ("r-rcolorbrewer" ,r-rcolorbrewer)
5356 ("r-reshape2" ,r-reshape2)
5357 ("r-tidyr" ,r-tidyr)))
5358 (home-page "http://www.mixOmics.org")
5359 (synopsis "Multivariate methods for exploration of biological datasets")
5361 "mixOmics offers a wide range of multivariate methods for the exploration
5362 and integration of biological datasets with a particular focus on variable
5363 selection. The package proposes several sparse multivariate models we have
5364 developed to identify the key variables that are highly correlated, and/or
5365 explain the biological outcome of interest. The data that can be analysed
5366 with mixOmics may come from high throughput sequencing technologies, such as
5367 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5368 also beyond the realm of omics (e.g. spectral imaging). The methods
5369 implemented in mixOmics can also handle missing values without having to
5370 delete entire rows with missing data.")
5371 (license license:gpl2+)))
5373 (define-public r-depecher
5380 (uri (bioconductor-uri "DepecheR" version))
5383 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5384 (properties `((upstream-name . "DepecheR")))
5385 (build-system r-build-system)
5388 (modify-phases %standard-phases
5389 (add-after 'unpack 'fix-syntax-error
5391 (substitute* "src/Makevars"
5395 `(("r-beanplot" ,r-beanplot)
5396 ("r-biocparallel" ,r-biocparallel)
5397 ("r-dosnow" ,r-dosnow)
5398 ("r-dplyr" ,r-dplyr)
5399 ("r-foreach" ,r-foreach)
5400 ("r-ggplot2" ,r-ggplot2)
5401 ("r-gplots" ,r-gplots)
5403 ("r-matrixstats" ,r-matrixstats)
5404 ("r-mixomics" ,r-mixomics)
5405 ("r-moments" ,r-moments)
5407 ("r-rcppeigen" ,r-rcppeigen)
5408 ("r-reshape2" ,r-reshape2)
5409 ("r-viridis" ,r-viridis)))
5410 (home-page "https://bioconductor.org/packages/DepecheR/")
5411 (synopsis "Identify traits of clusters in high-dimensional entities")
5413 "The purpose of this package is to identify traits in a dataset that can
5414 separate groups. This is done on two levels. First, clustering is performed,
5415 using an implementation of sparse K-means. Secondly, the generated clusters
5416 are used to predict outcomes of groups of individuals based on their
5417 distribution of observations in the different clusters. As certain clusters
5418 with separating information will be identified, and these clusters are defined
5419 by a sparse number of variables, this method can reduce the complexity of
5420 data, to only emphasize the data that actually matters.")
5421 (license license:expat)))
5423 (define-public r-rcistarget
5425 (name "r-rcistarget")
5430 (uri (bioconductor-uri "RcisTarget" version))
5433 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5434 (properties `((upstream-name . "RcisTarget")))
5435 (build-system r-build-system)
5437 `(("r-aucell" ,r-aucell)
5438 ("r-biocgenerics" ,r-biocgenerics)
5439 ("r-data-table" ,r-data-table)
5440 ("r-feather" ,r-feather)
5441 ("r-gseabase" ,r-gseabase)
5442 ("r-r-utils" ,r-r-utils)
5443 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5444 (home-page "https://aertslab.org/#scenic")
5445 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5447 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5448 over-represented on a gene list. In a first step, RcisTarget selects DNA
5449 motifs that are significantly over-represented in the surroundings of the
5450 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5451 achieved by using a database that contains genome-wide cross-species rankings
5452 for each motif. The motifs that are then annotated to TFs and those that have
5453 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5454 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5455 genes in the gene-set that are ranked above the leading edge).")
5456 (license license:gpl3)))
5458 (define-public r-cicero
5465 (uri (bioconductor-uri "cicero" version))
5468 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5469 (build-system r-build-system)
5471 `(("r-assertthat" ,r-assertthat)
5472 ("r-biobase" ,r-biobase)
5473 ("r-biocgenerics" ,r-biocgenerics)
5474 ("r-data-table" ,r-data-table)
5475 ("r-dplyr" ,r-dplyr)
5477 ("r-genomicranges" ,r-genomicranges)
5478 ("r-ggplot2" ,r-ggplot2)
5479 ("r-glasso" ,r-glasso)
5481 ("r-igraph" ,r-igraph)
5482 ("r-iranges" ,r-iranges)
5483 ("r-matrix" ,r-matrix)
5484 ("r-monocle" ,r-monocle)
5486 ("r-reshape2" ,r-reshape2)
5487 ("r-s4vectors" ,r-s4vectors)
5488 ("r-stringr" ,r-stringr)
5489 ("r-tibble" ,r-tibble)
5490 ("r-vgam" ,r-vgam)))
5491 (home-page "https://bioconductor.org/packages/cicero/")
5492 (synopsis "Predict cis-co-accessibility from single-cell data")
5494 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5495 accessibility data. It also extends the monocle package for use in chromatin
5496 accessibility data.")
5497 (license license:expat)))
5499 ;; This is the latest commit on the "monocle3" branch.
5500 (define-public r-cicero-monocle3
5501 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5503 (package (inherit r-cicero)
5504 (name "r-cicero-monocle3")
5505 (version (git-version "1.3.2" revision commit))
5510 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5512 (file-name (git-file-name name version))
5515 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5517 `(("r-monocle3" ,r-monocle3)
5518 ,@(alist-delete "r-monocle"
5519 (package-propagated-inputs r-cicero)))))))
5521 (define-public r-cistopic
5522 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5526 (version (git-version "0.2.1" revision commit))
5531 (url "https://github.com/aertslab/cisTopic.git")
5533 (file-name (git-file-name name version))
5536 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5537 (build-system r-build-system)
5539 `(("r-aucell" ,r-aucell)
5540 ("r-data-table" ,r-data-table)
5541 ("r-dplyr" ,r-dplyr)
5542 ("r-dosnow" ,r-dosnow)
5544 ("r-feather" ,r-feather)
5545 ("r-fitdistrplus" ,r-fitdistrplus)
5546 ("r-genomicranges" ,r-genomicranges)
5547 ("r-ggplot2" ,r-ggplot2)
5549 ("r-matrix" ,r-matrix)
5551 ("r-rcistarget" ,r-rcistarget)
5552 ("r-rtracklayer" ,r-rtracklayer)
5553 ("r-s4vectors" ,r-s4vectors)))
5554 (home-page "https://github.com/aertslab/cisTopic")
5555 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5557 "The sparse nature of single cell epigenomics data can be overruled using
5558 probabilistic modelling methods such as @dfn{Latent Dirichlet
5559 Allocation} (LDA). This package allows the probabilistic modelling of
5560 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5561 includes functionalities to identify cell states based on the contribution of
5562 cisTopics and explore the nature and regulatory proteins driving them.")
5563 (license license:gpl3))))
5565 (define-public r-genie3
5572 (uri (bioconductor-uri "GENIE3" version))
5575 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5576 (properties `((upstream-name . "GENIE3")))
5577 (build-system r-build-system)
5578 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5579 (home-page "https://bioconductor.org/packages/GENIE3")
5580 (synopsis "Gene network inference with ensemble of trees")
5582 "This package implements the GENIE3 algorithm for inferring gene
5583 regulatory networks from expression data.")
5584 (license license:gpl2+)))
5586 (define-public r-roc
5593 (uri (bioconductor-uri "ROC" version))
5596 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5597 (properties `((upstream-name . "ROC")))
5598 (build-system r-build-system)
5599 (home-page "https://www.bioconductor.org/packages/ROC/")
5600 (synopsis "Utilities for ROC curves")
5602 "This package provides utilities for @dfn{Receiver Operating
5603 Characteristic} (ROC) curves, with a focus on micro arrays.")
5604 (license license:artistic2.0)))
5606 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5608 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5613 (uri (bioconductor-uri
5614 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5615 version 'annotation))
5618 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5621 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5622 (build-system r-build-system)
5623 (propagated-inputs `(("r-minfi" ,r-minfi)))
5625 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5626 (synopsis "Annotation for Illumina's 450k methylation arrays")
5628 "This package provides manifests and annotation for Illumina's 450k array
5630 (license license:artistic2.0)))
5632 (define-public r-watermelon
5634 (name "r-watermelon")
5639 (uri (bioconductor-uri "wateRmelon" version))
5642 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
5643 (properties `((upstream-name . "wateRmelon")))
5644 (build-system r-build-system)
5646 `(("r-biobase" ,r-biobase)
5647 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
5648 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
5649 ("r-illuminaio" ,r-illuminaio)
5650 ("r-limma" ,r-limma)
5652 ("r-matrixstats" ,r-matrixstats)
5653 ("r-methylumi" ,r-methylumi)
5655 (home-page "https://bioconductor.org/packages/wateRmelon/")
5656 (synopsis "Illumina 450 methylation array normalization and metrics")
5658 "The standard index of DNA methylation (beta) is computed from methylated
5659 and unmethylated signal intensities. Betas calculated from raw signal
5660 intensities perform well, but using 11 methylomic datasets we demonstrate that
5661 quantile normalization methods produce marked improvement. The commonly used
5662 procedure of normalizing betas is inferior to the separate normalization of M
5663 and U, and it is also advantageous to normalize Type I and Type II assays
5664 separately. This package provides 15 flavours of betas and three performance
5665 metrics, with methods for objects produced by the @code{methylumi} and
5666 @code{minfi} packages.")
5667 (license license:gpl3)))
5669 (define-public r-gdsfmt
5676 (uri (bioconductor-uri "gdsfmt" version))
5679 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
5680 (modules '((guix build utils)))
5681 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
5682 ;; them and link with system libraries instead.
5685 (for-each delete-file-recursively
5689 (substitute* "src/Makevars"
5690 (("all: \\$\\(SHLIB\\)") "all:")
5691 (("\\$\\(SHLIB\\): liblzma.a") "")
5692 (("(ZLIB|LZ4)/.*") "")
5693 (("CoreArray/dVLIntGDS.cpp.*")
5694 "CoreArray/dVLIntGDS.cpp")
5695 (("CoreArray/dVLIntGDS.o.*")
5696 "CoreArray/dVLIntGDS.o")
5697 (("PKG_LIBS = ./liblzma.a")
5698 "PKG_LIBS = -llz4"))
5699 (substitute* "src/CoreArray/dStream.h"
5700 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
5701 (string-append "include <" header ">")))
5703 (properties `((upstream-name . "gdsfmt")))
5704 (build-system r-build-system)
5709 (home-page "http://corearray.sourceforge.net/")
5711 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
5713 "This package provides a high-level R interface to CoreArray @dfn{Genomic
5714 Data Structure} (GDS) data files, which are portable across platforms with
5715 hierarchical structure to store multiple scalable array-oriented data sets
5716 with metadata information. It is suited for large-scale datasets, especially
5717 for data which are much larger than the available random-access memory. The
5718 @code{gdsfmt} package offers efficient operations specifically designed for
5719 integers of less than 8 bits, since a diploid genotype, like
5720 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
5721 byte. Data compression and decompression are available with relatively
5722 efficient random access. It is also allowed to read a GDS file in parallel
5723 with multiple R processes supported by the package @code{parallel}.")
5724 (license license:lgpl3)))
5726 (define-public r-bigmelon
5733 (uri (bioconductor-uri "bigmelon" version))
5736 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
5737 (properties `((upstream-name . "bigmelon")))
5738 (build-system r-build-system)
5740 `(("r-biobase" ,r-biobase)
5741 ("r-biocgenerics" ,r-biocgenerics)
5742 ("r-gdsfmt" ,r-gdsfmt)
5743 ("r-geoquery" ,r-geoquery)
5744 ("r-methylumi" ,r-methylumi)
5745 ("r-minfi" ,r-minfi)
5746 ("r-watermelon" ,r-watermelon)))
5747 (home-page "https://bioconductor.org/packages/bigmelon/")
5748 (synopsis "Illumina methylation array analysis for large experiments")
5750 "This package provides methods for working with Illumina arrays using the
5751 @code{gdsfmt} package.")
5752 (license license:gpl3)))
5754 (define-public r-seqbias
5761 (uri (bioconductor-uri "seqbias" version))
5764 "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
5765 (properties `((upstream-name . "seqbias")))
5766 (build-system r-build-system)
5768 `(("r-biostrings" ,r-biostrings)
5769 ("r-genomicranges" ,r-genomicranges)
5770 ("r-rhtslib" ,r-rhtslib)))
5772 `(("zlib" ,zlib))) ; This comes from rhtslib.
5773 (home-page "https://bioconductor.org/packages/seqbias/")
5774 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
5776 "This package implements a model of per-position sequencing bias in
5777 high-throughput sequencing data using a simple Bayesian network, the structure
5778 and parameters of which are trained on a set of aligned reads and a reference
5780 (license license:lgpl3)))
5782 (define-public r-reqon
5789 (uri (bioconductor-uri "ReQON" version))
5792 "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
5793 (properties `((upstream-name . "ReQON")))
5794 (build-system r-build-system)
5796 `(("r-rjava" ,r-rjava)
5797 ("r-rsamtools" ,r-rsamtools)
5798 ("r-seqbias" ,r-seqbias)))
5799 (home-page "https://bioconductor.org/packages/ReQON/")
5800 (synopsis "Recalibrating quality of nucleotides")
5802 "This package provides an implementation of an algorithm for
5803 recalibrating the base quality scores for aligned sequencing data in BAM
5805 (license license:gpl2)))
5807 (define-public r-wavcluster
5809 (name "r-wavcluster")
5814 (uri (bioconductor-uri "wavClusteR" version))
5817 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
5818 (properties `((upstream-name . "wavClusteR")))
5819 (build-system r-build-system)
5821 `(("r-biocgenerics" ,r-biocgenerics)
5822 ("r-biostrings" ,r-biostrings)
5823 ("r-foreach" ,r-foreach)
5824 ("r-genomicfeatures" ,r-genomicfeatures)
5825 ("r-genomicranges" ,r-genomicranges)
5826 ("r-ggplot2" ,r-ggplot2)
5827 ("r-hmisc" ,r-hmisc)
5828 ("r-iranges" ,r-iranges)
5829 ("r-mclust" ,r-mclust)
5830 ("r-rsamtools" ,r-rsamtools)
5831 ("r-rtracklayer" ,r-rtracklayer)
5832 ("r-s4vectors" ,r-s4vectors)
5833 ("r-seqinr" ,r-seqinr)
5834 ("r-stringr" ,r-stringr)
5835 ("r-wmtsa" ,r-wmtsa)))
5836 (home-page "https://bioconductor.org/packages/wavClusteR/")
5837 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
5839 "This package provides an integrated pipeline for the analysis of
5840 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
5841 sequencing errors, SNPs and additional non-experimental sources by a non-
5842 parametric mixture model. The protein binding sites (clusters) are then
5843 resolved at high resolution and cluster statistics are estimated using a
5844 rigorous Bayesian framework. Post-processing of the results, data export for
5845 UCSC genome browser visualization and motif search analysis are provided. In
5846 addition, the package allows to integrate RNA-Seq data to estimate the False
5847 Discovery Rate of cluster detection. Key functions support parallel multicore
5848 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
5849 be applied to the analysis of other NGS data obtained from experimental
5850 procedures that induce nucleotide substitutions (e.g. BisSeq).")
5851 (license license:gpl2)))
5853 (define-public r-timeseriesexperiment
5855 (name "r-timeseriesexperiment")
5860 (uri (bioconductor-uri "TimeSeriesExperiment" version))
5863 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
5865 `((upstream-name . "TimeSeriesExperiment")))
5866 (build-system r-build-system)
5868 `(("r-deseq2" ,r-deseq2)
5869 ("r-dplyr" ,r-dplyr)
5870 ("r-dynamictreecut" ,r-dynamictreecut)
5871 ("r-edger" ,r-edger)
5872 ("r-ggplot2" ,r-ggplot2)
5873 ("r-hmisc" ,r-hmisc)
5874 ("r-limma" ,r-limma)
5875 ("r-magrittr" ,r-magrittr)
5876 ("r-proxy" ,r-proxy)
5877 ("r-s4vectors" ,r-s4vectors)
5878 ("r-summarizedexperiment" ,r-summarizedexperiment)
5879 ("r-tibble" ,r-tibble)
5880 ("r-tidyr" ,r-tidyr)
5881 ("r-vegan" ,r-vegan)
5882 ("r-viridis" ,r-viridis)))
5883 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
5884 (synopsis "Analysis for short time-series data")
5886 "This package is a visualization and analysis toolbox for short time
5887 course data which includes dimensionality reduction, clustering, two-sample
5888 differential expression testing and gene ranking techniques. The package also
5889 provides methods for retrieving enriched pathways.")
5890 (license license:lgpl3+)))
5892 (define-public r-variantfiltering
5894 (name "r-variantfiltering")
5899 (uri (bioconductor-uri "VariantFiltering" version))
5902 "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
5904 `((upstream-name . "VariantFiltering")))
5905 (build-system r-build-system)
5907 `(("r-annotationdbi" ,r-annotationdbi)
5908 ("r-biobase" ,r-biobase)
5909 ("r-biocgenerics" ,r-biocgenerics)
5910 ("r-biocparallel" ,r-biocparallel)
5911 ("r-biostrings" ,r-biostrings)
5912 ("r-bsgenome" ,r-bsgenome)
5914 ("r-genomeinfodb" ,r-genomeinfodb)
5915 ("r-genomicfeatures" ,r-genomicfeatures)
5916 ("r-genomicranges" ,r-genomicranges)
5917 ("r-genomicscores" ,r-genomicscores)
5918 ("r-graph" ,r-graph)
5920 ("r-iranges" ,r-iranges)
5922 ("r-rsamtools" ,r-rsamtools)
5923 ("r-s4vectors" ,r-s4vectors)
5924 ("r-shiny" ,r-shiny)
5925 ("r-shinyjs" ,r-shinyjs)
5926 ("r-shinythemes" ,r-shinythemes)
5927 ("r-shinytree" ,r-shinytree)
5928 ("r-summarizedexperiment" ,r-summarizedexperiment)
5929 ("r-variantannotation" ,r-variantannotation)
5930 ("r-xvector" ,r-xvector)))
5931 (home-page "https://github.com/rcastelo/VariantFiltering")
5932 (synopsis "Filtering of coding and non-coding genetic variants")
5934 "Filter genetic variants using different criteria such as inheritance
5935 model, amino acid change consequence, minor allele frequencies across human
5936 populations, splice site strength, conservation, etc.")
5937 (license license:artistic2.0)))
5939 (define-public r-genomegraphs
5941 (name "r-genomegraphs")
5946 (uri (bioconductor-uri "GenomeGraphs" version))
5949 "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd"))))
5950 (properties `((upstream-name . "GenomeGraphs")))
5951 (build-system r-build-system)
5953 `(("r-biomart" ,r-biomart)))
5954 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
5955 (synopsis "Plotting genomic information from Ensembl")
5957 "Genomic data analyses requires integrated visualization of known genomic
5958 information and new experimental data. GenomeGraphs uses the biomaRt package
5959 to perform live annotation queries to Ensembl and translates this to e.g.
5960 gene/transcript structures in viewports of the grid graphics package. This
5961 results in genomic information plotted together with your data. Another
5962 strength of GenomeGraphs is to plot different data types such as array CGH,
5963 gene expression, sequencing and other data, together in one plot using the
5964 same genome coordinate system.")
5965 (license license:artistic2.0)))
5967 (define-public r-wavetiling
5969 (name "r-wavetiling")
5974 (uri (bioconductor-uri "waveTiling" version))
5977 "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir"))))
5978 (properties `((upstream-name . "waveTiling")))
5979 (build-system r-build-system)
5981 `(("r-affy" ,r-affy)
5982 ("r-biobase" ,r-biobase)
5983 ("r-biostrings" ,r-biostrings)
5984 ("r-genomegraphs" ,r-genomegraphs)
5985 ("r-genomicranges" ,r-genomicranges)
5986 ("r-iranges" ,r-iranges)
5987 ("r-oligo" ,r-oligo)
5988 ("r-oligoclasses" ,r-oligoclasses)
5989 ("r-preprocesscore" ,r-preprocesscore)
5990 ("r-waveslim" ,r-waveslim)))
5991 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
5992 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
5994 "This package is designed to conduct transcriptome analysis for tiling
5995 arrays based on fast wavelet-based functional models.")
5996 (license license:gpl2+)))
5998 (define-public r-variancepartition
6000 (name "r-variancepartition")
6005 (uri (bioconductor-uri "variancePartition" version))
6008 "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
6010 `((upstream-name . "variancePartition")))
6011 (build-system r-build-system)
6013 `(("r-biobase" ,r-biobase)
6014 ("r-biocparallel" ,r-biocparallel)
6015 ("r-colorramps" ,r-colorramps)
6016 ("r-doparallel" ,r-doparallel)
6017 ("r-foreach" ,r-foreach)
6018 ("r-ggplot2" ,r-ggplot2)
6019 ("r-gplots" ,r-gplots)
6020 ("r-iterators" ,r-iterators)
6021 ("r-limma" ,r-limma)
6023 ("r-lmertest" ,r-lmertest)
6025 ("r-pbkrtest" ,r-pbkrtest)
6026 ("r-progress" ,r-progress)
6027 ("r-reshape2" ,r-reshape2)
6028 ("r-scales" ,r-scales)))
6029 (home-page "https://bioconductor.org/packages/variancePartition/")
6030 (synopsis "Analyze variation in gene expression experiments")
6032 "This is a package providing tools to quantify and interpret multiple
6033 sources of biological and technical variation in gene expression experiments.
6034 It uses a linear mixed model to quantify variation in gene expression
6035 attributable to individual, tissue, time point, or technical variables. The
6036 package includes dream differential expression analysis for repeated
6038 (license license:gpl2+)))
6040 (define-public r-htqpcr
6047 (uri (bioconductor-uri "HTqPCR" version))
6050 "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
6051 (properties `((upstream-name . "HTqPCR")))
6052 (build-system r-build-system)
6054 `(("r-affy" ,r-affy)
6055 ("r-biobase" ,r-biobase)
6056 ("r-gplots" ,r-gplots)
6057 ("r-limma" ,r-limma)
6058 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6059 (home-page "http://www.ebi.ac.uk/bertone/software")
6060 (synopsis "Automated analysis of high-throughput qPCR data")
6062 "Analysis of Ct values from high throughput quantitative real-time
6063 PCR (qPCR) assays across multiple conditions or replicates. The input data
6064 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6065 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6066 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6067 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6068 loading, quality assessment, normalization, visualization and parametric or
6069 non-parametric testing for statistical significance in Ct values between
6070 features (e.g. genes, microRNAs).")
6071 (license license:artistic2.0)))
6073 (define-public r-unifiedwmwqpcr
6075 (name "r-unifiedwmwqpcr")
6080 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6083 "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
6085 `((upstream-name . "unifiedWMWqPCR")))
6086 (build-system r-build-system)
6088 `(("r-biocgenerics" ,r-biocgenerics)
6089 ("r-htqpcr" ,r-htqpcr)))
6090 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6091 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6093 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6094 data. This modified test allows for testing differential expression in qPCR
6096 (license license:gpl2+)))