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 ;; We cannot use bioconductor-uri here because this tarball is
80 ;; located under "data/annotation/" instead of "bioc/".
81 (uri (string-append "https://www.bioconductor.org/packages/"
82 "release/data/annotation/src/contrib/"
83 "BSgenome.Celegans.UCSC.ce10_"
87 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
89 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
90 (build-system r-build-system)
91 ;; As this package provides little more than a very large data file it
92 ;; doesn't make sense to build substitutes.
93 (arguments `(#:substitutable? #f))
95 `(("r-bsgenome" ,r-bsgenome)))
97 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
98 (synopsis "Full genome sequences for Worm")
100 "This package provides full genome sequences for Caenorhabditis
101 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
103 (license license:artistic2.0)))
105 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
107 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
111 ;; We cannot use bioconductor-uri here because this tarball is
112 ;; located under "data/annotation/" instead of "bioc/".
113 (uri (string-append "https://www.bioconductor.org/packages/"
114 "release/data/annotation/src/contrib/"
115 "BSgenome.Dmelanogaster.UCSC.dm6_"
119 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
121 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
122 (build-system r-build-system)
123 ;; As this package provides little more than a very large data file it
124 ;; doesn't make sense to build substitutes.
125 (arguments `(#:substitutable? #f))
127 `(("r-bsgenome" ,r-bsgenome)))
129 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
130 (synopsis "Full genome sequences for Fly")
132 "This package provides full genome sequences for Drosophila
133 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
135 (license license:artistic2.0)))
137 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
139 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
143 ;; We cannot use bioconductor-uri here because this tarball is
144 ;; located under "data/annotation/" instead of "bioc/".
145 (uri (string-append "https://www.bioconductor.org/packages/"
146 "release/data/annotation/src/contrib/"
147 "BSgenome.Dmelanogaster.UCSC.dm3_"
151 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
153 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
154 (build-system r-build-system)
155 ;; As this package provides little more than a very large data file it
156 ;; doesn't make sense to build substitutes.
157 (arguments `(#:substitutable? #f))
159 `(("r-bsgenome" ,r-bsgenome)))
161 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
162 (synopsis "Full genome sequences for Fly")
164 "This package provides full genome sequences for Drosophila
165 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
166 Biostrings objects.")
167 (license license:artistic2.0)))
169 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
171 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
175 ;; We cannot use bioconductor-uri here because this tarball is
176 ;; located under "data/annotation/" instead of "bioc/".
177 (uri (string-append "http://www.bioconductor.org/packages/"
178 "release/data/annotation/src/contrib/"
179 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
183 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
185 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
186 (build-system r-build-system)
188 `(("r-bsgenome" ,r-bsgenome)
189 ("r-bsgenome-dmelanogaster-ucsc-dm3"
190 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
191 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
192 (synopsis "Full masked genome sequences for Fly")
194 "This package provides full masked genome sequences for Drosophila
195 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
196 Biostrings objects. The sequences are the same as in
197 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
198 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
199 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
200 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
201 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
202 (license license:artistic2.0)))
204 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
206 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
210 ;; We cannot use bioconductor-uri here because this tarball is
211 ;; located under "data/annotation/" instead of "bioc/".
212 (uri (string-append "https://www.bioconductor.org/packages/"
213 "release/data/annotation/src/contrib/"
214 "BSgenome.Hsapiens.1000genomes.hs37d5_"
218 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
220 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
221 (build-system r-build-system)
222 ;; As this package provides little more than a very large data file it
223 ;; doesn't make sense to build substitutes.
224 (arguments `(#:substitutable? #f))
226 `(("r-bsgenome" ,r-bsgenome)))
228 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
229 (synopsis "Full genome sequences for Homo sapiens")
231 "This package provides full genome sequences for Homo sapiens from
232 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
233 (license license:artistic2.0)))
235 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
237 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
241 ;; We cannot use bioconductor-uri here because this tarball is
242 ;; located under "data/annotation/" instead of "bioc/".
243 (uri (string-append "http://www.bioconductor.org/packages/"
244 "release/data/annotation/src/contrib/"
245 "BSgenome.Hsapiens.UCSC.hg19.masked_"
249 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
251 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
252 (build-system r-build-system)
254 `(("r-bsgenome" ,r-bsgenome)
255 ("r-bsgenome-hsapiens-ucsc-hg19"
256 ,r-bsgenome-hsapiens-ucsc-hg19)))
257 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
258 (synopsis "Full masked genome sequences for Homo sapiens")
260 "This package provides full genome sequences for Homo sapiens (Human) as
261 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
262 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
263 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
264 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
265 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
266 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
268 (license license:artistic2.0)))
270 (define-public r-bsgenome-mmusculus-ucsc-mm9
272 (name "r-bsgenome-mmusculus-ucsc-mm9")
276 ;; We cannot use bioconductor-uri here because this tarball is
277 ;; located under "data/annotation/" instead of "bioc/".
278 (uri (string-append "https://www.bioconductor.org/packages/"
279 "release/data/annotation/src/contrib/"
280 "BSgenome.Mmusculus.UCSC.mm9_"
284 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
286 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
287 (build-system r-build-system)
288 ;; As this package provides little more than a very large data file it
289 ;; doesn't make sense to build substitutes.
290 (arguments `(#:substitutable? #f))
292 `(("r-bsgenome" ,r-bsgenome)))
294 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
295 (synopsis "Full genome sequences for Mouse")
297 "This package provides full genome sequences for Mus musculus (Mouse) as
298 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
299 (license license:artistic2.0)))
301 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
303 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
307 ;; We cannot use bioconductor-uri here because this tarball is
308 ;; located under "data/annotation/" instead of "bioc/".
309 (uri (string-append "http://www.bioconductor.org/packages/"
310 "release/data/annotation/src/contrib/"
311 "BSgenome.Mmusculus.UCSC.mm9.masked_"
315 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
317 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
318 (build-system r-build-system)
320 `(("r-bsgenome" ,r-bsgenome)
321 ("r-bsgenome-mmusculus-ucsc-mm9"
322 ,r-bsgenome-mmusculus-ucsc-mm9)))
323 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
324 (synopsis "Full masked genome sequences for Mouse")
326 "This package provides full genome sequences for Mus musculus (Mouse) as
327 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
328 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
329 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
330 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
331 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
332 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
334 (license license:artistic2.0)))
336 (define-public r-bsgenome-mmusculus-ucsc-mm10
338 (name "r-bsgenome-mmusculus-ucsc-mm10")
342 ;; We cannot use bioconductor-uri here because this tarball is
343 ;; located under "data/annotation/" instead of "bioc/".
344 (uri (string-append "https://www.bioconductor.org/packages/"
345 "release/data/annotation/src/contrib/"
346 "BSgenome.Mmusculus.UCSC.mm10_"
350 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
352 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
353 (build-system r-build-system)
354 ;; As this package provides little more than a very large data file it
355 ;; doesn't make sense to build substitutes.
356 (arguments `(#:substitutable? #f))
358 `(("r-bsgenome" ,r-bsgenome)))
360 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
361 (synopsis "Full genome sequences for Mouse")
363 "This package provides full genome sequences for Mus
364 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
365 in Biostrings objects.")
366 (license license:artistic2.0)))
368 (define-public r-org-ce-eg-db
370 (name "r-org-ce-eg-db")
374 ;; We cannot use bioconductor-uri here because this tarball is
375 ;; located under "data/annotation/" instead of "bioc/".
376 (uri (string-append "https://www.bioconductor.org/packages/"
377 "release/data/annotation/src/contrib/"
378 "org.Ce.eg.db_" version ".tar.gz"))
381 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
383 `((upstream-name . "org.Ce.eg.db")))
384 (build-system r-build-system)
386 `(("r-annotationdbi" ,r-annotationdbi)))
387 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
388 (synopsis "Genome wide annotation for Worm")
390 "This package provides mappings from Entrez gene identifiers to various
391 annotations for the genome of the model worm Caenorhabditis elegans.")
392 (license license:artistic2.0)))
394 (define-public r-org-dm-eg-db
396 (name "r-org-dm-eg-db")
400 ;; We cannot use bioconductor-uri here because this tarball is
401 ;; located under "data/annotation/" instead of "bioc/".
402 (uri (string-append "https://www.bioconductor.org/packages/"
403 "release/data/annotation/src/contrib/"
404 "org.Dm.eg.db_" version ".tar.gz"))
407 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
409 `((upstream-name . "org.Dm.eg.db")))
410 (build-system r-build-system)
412 `(("r-annotationdbi" ,r-annotationdbi)))
413 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
414 (synopsis "Genome wide annotation for Fly")
416 "This package provides mappings from Entrez gene identifiers to various
417 annotations for the genome of the model fruit fly Drosophila melanogaster.")
418 (license license:artistic2.0)))
420 (define-public r-org-dr-eg-db
422 (name "r-org-dr-eg-db")
426 ;; We cannot use bioconductor-uri here because this tarball is
427 ;; located under "data/annotation/" instead of "bioc/".
428 (uri (string-append "https://www.bioconductor.org/packages/"
429 "release/data/annotation/src/contrib/"
430 "org.Dr.eg.db_" version ".tar.gz"))
433 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
435 `((upstream-name . "org.Dr.eg.db")))
436 (build-system r-build-system)
438 `(("r-annotationdbi" ,r-annotationdbi)))
439 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
440 (synopsis "Annotation for Zebrafish")
442 "This package provides genome wide annotations for Zebrafish, primarily
443 based on mapping using Entrez Gene identifiers.")
444 (license license:artistic2.0)))
446 (define-public r-org-hs-eg-db
448 (name "r-org-hs-eg-db")
452 ;; We cannot use bioconductor-uri here because this tarball is
453 ;; located under "data/annotation/" instead of "bioc/".
454 (uri (string-append "https://www.bioconductor.org/packages/"
455 "release/data/annotation/src/contrib/"
456 "org.Hs.eg.db_" version ".tar.gz"))
459 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
461 `((upstream-name . "org.Hs.eg.db")))
462 (build-system r-build-system)
464 `(("r-annotationdbi" ,r-annotationdbi)))
465 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
466 (synopsis "Genome wide annotation for Human")
468 "This package contains genome-wide annotations for Human, primarily based
469 on mapping using Entrez Gene identifiers.")
470 (license license:artistic2.0)))
472 (define-public r-org-mm-eg-db
474 (name "r-org-mm-eg-db")
478 ;; We cannot use bioconductor-uri here because this tarball is
479 ;; located under "data/annotation/" instead of "bioc/".
480 (uri (string-append "https://www.bioconductor.org/packages/"
481 "release/data/annotation/src/contrib/"
482 "org.Mm.eg.db_" version ".tar.gz"))
485 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
487 `((upstream-name . "org.Mm.eg.db")))
488 (build-system r-build-system)
490 `(("r-annotationdbi" ,r-annotationdbi)))
491 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
492 (synopsis "Genome wide annotation for Mouse")
494 "This package provides mappings from Entrez gene identifiers to various
495 annotations for the genome of the model mouse Mus musculus.")
496 (license license:artistic2.0)))
498 (define-public r-bsgenome-hsapiens-ucsc-hg19
500 (name "r-bsgenome-hsapiens-ucsc-hg19")
504 ;; We cannot use bioconductor-uri here because this tarball is
505 ;; located under "data/annotation/" instead of "bioc/".
506 (uri (string-append "https://www.bioconductor.org/packages/"
507 "release/data/annotation/src/contrib/"
508 "BSgenome.Hsapiens.UCSC.hg19_"
512 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
514 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
515 (build-system r-build-system)
516 ;; As this package provides little more than a very large data file it
517 ;; doesn't make sense to build substitutes.
518 (arguments `(#:substitutable? #f))
520 `(("r-bsgenome" ,r-bsgenome)))
522 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
523 (synopsis "Full genome sequences for Homo sapiens")
525 "This package provides full genome sequences for Homo sapiens as provided
526 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
527 (license license:artistic2.0)))
529 (define-public r-ensdb-hsapiens-v75
531 (name "r-ensdb-hsapiens-v75")
536 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
539 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
541 `((upstream-name . "EnsDb.Hsapiens.v75")))
542 (build-system r-build-system)
544 `(("r-ensembldb" ,r-ensembldb)))
545 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
546 (synopsis "Ensembl based annotation package")
548 "This package exposes an annotation database generated from Ensembl.")
549 (license license:artistic2.0)))
551 (define-public r-genelendatabase
553 (name "r-genelendatabase")
558 ;; We cannot use bioconductor-uri here because this tarball is
559 ;; located under "data/experiment/" instead of "bioc/".
560 (uri (string-append "https://bioconductor.org/packages/"
561 "release/data/experiment/src/contrib"
562 "/geneLenDataBase_" version ".tar.gz"))
565 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
567 `((upstream-name . "geneLenDataBase")))
568 (build-system r-build-system)
570 `(("r-rtracklayer" ,r-rtracklayer)
571 ("r-genomicfeatures" ,r-genomicfeatures)))
572 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
573 (synopsis "Lengths of mRNA transcripts for a number of genomes")
575 "This package provides the lengths of mRNA transcripts for a number of
576 genomes and gene ID formats, largely based on the UCSC table browser.")
577 (license license:lgpl2.0+)))
579 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
581 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
585 ;; We cannot use bioconductor-uri here because this tarball is
586 ;; located under "data/annotation/" instead of "bioc/".
587 (uri (string-append "https://bioconductor.org/packages/"
588 "release/data/annotation/src/contrib"
589 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
593 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
595 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
596 (build-system r-build-system)
597 ;; As this package provides little more than a very large data file it
598 ;; doesn't make sense to build substitutes.
599 (arguments `(#:substitutable? #f))
601 `(("r-genomicfeatures" ,r-genomicfeatures)))
603 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
604 (synopsis "Annotation package for human genome in TxDb format")
606 "This package provides an annotation database of Homo sapiens genome
607 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
608 track. The database is exposed as a @code{TxDb} object.")
609 (license license:artistic2.0)))
611 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
613 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
617 ;; We cannot use bioconductor-uri here because this tarball is
618 ;; located under "data/annotation/" instead of "bioc/".
619 (uri (string-append "https://bioconductor.org/packages/"
620 "release/data/annotation/src/contrib"
621 "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
625 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
627 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
628 (build-system r-build-system)
630 `(("r-genomicfeatures" ,r-genomicfeatures)))
632 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
633 (synopsis "Annotation package for human genome in TxDb format")
635 "This package provides an annotation database of Homo sapiens genome
636 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
637 track. The database is exposed as a @code{TxDb} object.")
638 (license license:artistic2.0)))
640 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
642 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
646 ;; We cannot use bioconductor-uri here because this tarball is
647 ;; located under "data/annotation/" instead of "bioc/".
648 (uri (string-append "https://bioconductor.org/packages/"
649 "release/data/annotation/src/contrib"
650 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
654 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
656 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
657 (build-system r-build-system)
659 `(("r-genomicfeatures" ,r-genomicfeatures)
660 ("r-annotationdbi" ,r-annotationdbi)))
662 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
663 (synopsis "Annotation package for mouse genome in TxDb format")
665 "This package provides an annotation database of Mouse genome data. It
666 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
667 database is exposed as a @code{TxDb} object.")
668 (license license:artistic2.0)))
670 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
672 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
676 ;; We cannot use bioconductor-uri here because this tarball is
677 ;; located under "data/annotation/" instead of "bioc/".
678 (uri (string-append "https://www.bioconductor.org/packages/"
679 "release/data/annotation/src/contrib/"
680 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
684 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
686 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
687 (build-system r-build-system)
688 ;; As this package provides little more than a very large data file it
689 ;; doesn't make sense to build substitutes.
690 (arguments `(#:substitutable? #f))
692 `(("r-bsgenome" ,r-bsgenome)
693 ("r-genomicfeatures" ,r-genomicfeatures)
694 ("r-annotationdbi" ,r-annotationdbi)))
696 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
697 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
699 "This package loads a TxDb object, which is an R interface to
700 prefabricated databases contained in this package. This package provides
701 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
702 based on the knownGene track.")
703 (license license:artistic2.0)))
705 (define-public r-txdb-celegans-ucsc-ce6-ensgene
707 (name "r-txdb-celegans-ucsc-ce6-ensgene")
712 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
713 version 'annotation))
716 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
718 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
719 (build-system r-build-system)
721 `(("r-annotationdbi" ,r-annotationdbi)
722 ("r-genomicfeatures" ,r-genomicfeatures)))
723 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
724 (synopsis "Annotation package for C elegans TxDb objects")
726 "This package exposes a C elegans annotation database generated from UCSC
727 by exposing these as TxDb objects.")
728 (license license:artistic2.0)))
730 (define-public r-fdb-infiniummethylation-hg19
732 (name "r-fdb-infiniummethylation-hg19")
736 ;; We cannot use bioconductor-uri here because this tarball is
737 ;; located under "data/annotation/" instead of "bioc/".
738 (uri (string-append "https://www.bioconductor.org/packages/"
739 "release/data/annotation/src/contrib/"
740 "FDb.InfiniumMethylation.hg19_"
744 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
746 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
747 (build-system r-build-system)
749 `(("r-biostrings" ,r-biostrings)
750 ("r-genomicfeatures" ,r-genomicfeatures)
751 ("r-annotationdbi" ,r-annotationdbi)
752 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
753 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
754 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
755 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
757 "This is an annotation package for Illumina Infinium DNA methylation
758 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
760 (license license:artistic2.0)))
762 (define-public r-illuminahumanmethylationepicmanifest
764 (name "r-illuminahumanmethylationepicmanifest")
768 ;; We cannot use bioconductor-uri here because this tarball is
769 ;; located under "data/annotation/" instead of "bioc/".
770 (uri (string-append "https://www.bioconductor.org/packages/"
771 "release/data/annotation/src/contrib/"
772 "IlluminaHumanMethylationEPICmanifest_"
776 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
778 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
779 (build-system r-build-system)
781 `(("r-minfi" ,r-minfi)))
782 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
783 (synopsis "Manifest for Illumina's EPIC methylation arrays")
785 "This is a manifest package for Illumina's EPIC methylation arrays.")
786 (license license:artistic2.0)))
788 (define-public r-do-db
794 ;; We cannot use bioconductor-uri here because this tarball is
795 ;; located under "data/annotation/" instead of "bioc/".
796 (uri (string-append "https://www.bioconductor.org/packages/"
797 "release/data/annotation/src/contrib/"
798 "DO.db_" version ".tar.gz"))
801 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
803 `((upstream-name . "DO.db")))
804 (build-system r-build-system)
806 `(("r-annotationdbi" ,r-annotationdbi)))
807 (home-page "https://www.bioconductor.org/packages/DO.db/")
808 (synopsis "Annotation maps describing the entire Disease Ontology")
810 "This package provides a set of annotation maps describing the entire
812 (license license:artistic2.0)))
814 (define-public r-pfam-db
821 (uri (bioconductor-uri "PFAM.db" version 'annotation))
824 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
825 (properties `((upstream-name . "PFAM.db")))
826 (build-system r-build-system)
828 `(("r-annotationdbi" ,r-annotationdbi)))
829 (home-page "https://bioconductor.org/packages/PFAM.db")
830 (synopsis "Set of protein ID mappings for PFAM")
832 "This package provides a set of protein ID mappings for PFAM, assembled
833 using data from public repositories.")
834 (license license:artistic2.0)))
836 (define-public r-phastcons100way-ucsc-hg19
838 (name "r-phastcons100way-ucsc-hg19")
843 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
844 version 'annotation))
847 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
849 `((upstream-name . "phastCons100way.UCSC.hg19")))
850 (build-system r-build-system)
852 `(("r-bsgenome" ,r-bsgenome)
853 ("r-genomeinfodb" ,r-genomeinfodb)
854 ("r-genomicranges" ,r-genomicranges)
855 ("r-genomicscores" ,r-genomicscores)
856 ("r-iranges" ,r-iranges)
857 ("r-s4vectors" ,r-s4vectors)))
858 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
859 (synopsis "UCSC phastCons conservation scores for hg19")
861 "This package provides UCSC phastCons conservation scores for the human
862 genome (hg19) calculated from multiple alignments with other 99 vertebrate
864 (license license:artistic2.0)))
869 (define-public r-abadata
875 ;; We cannot use bioconductor-uri here because this tarball is
876 ;; located under "data/experiment/" instead of "bioc/".
877 (uri (string-append "https://www.bioconductor.org/packages/"
878 "release/data/experiment/src/contrib/"
879 "ABAData_" version ".tar.gz"))
882 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
884 `((upstream-name . "ABAData")))
885 (build-system r-build-system)
887 `(("r-annotationdbi" ,r-annotationdbi)))
888 (home-page "https://www.bioconductor.org/packages/ABAData/")
889 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
891 "This package provides the data for the gene expression enrichment
892 analysis conducted in the package ABAEnrichment. The package includes three
893 datasets which are derived from the Allen Brain Atlas:
896 @item Gene expression data from Human Brain (adults) averaged across donors,
897 @item Gene expression data from the Developing Human Brain pooled into five
898 age categories and averaged across donors, and
899 @item a developmental effect score based on the Developing Human Brain
903 All datasets are restricted to protein coding genes.")
904 (license license:gpl2+)))
906 (define-public r-arrmdata
912 ;; We cannot use bioconductor-uri here because this tarball is
913 ;; located under "data/experiment/" instead of "bioc/".
914 (uri (string-append "https://www.bioconductor.org/packages/"
915 "release/data/experiment/src/contrib/"
916 "ARRmData_" version ".tar.gz"))
919 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
921 `((upstream-name . "ARRmData")))
922 (build-system r-build-system)
923 (home-page "https://www.bioconductor.org/packages/ARRmData/")
924 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
926 "This package provides raw beta values from 36 samples across 3 groups
927 from Illumina 450k methylation arrays.")
928 (license license:artistic2.0)))
930 (define-public r-hsmmsinglecell
932 (name "r-hsmmsinglecell")
936 ;; We cannot use bioconductor-uri here because this tarball is
937 ;; located under "data/experiment/" instead of "bioc/".
938 (uri (string-append "https://www.bioconductor.org/packages/"
939 "release/data/experiment/src/contrib/"
940 "HSMMSingleCell_" version ".tar.gz"))
943 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
945 `((upstream-name . "HSMMSingleCell")))
946 (build-system r-build-system)
947 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
948 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
950 "Skeletal myoblasts undergo a well-characterized sequence of
951 morphological and transcriptional changes during differentiation. In this
952 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
953 under high mitogen conditions (GM) and then differentiated by switching to
954 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
955 hundred cells taken over a time-course of serum-induced differentiation.
956 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
957 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
958 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
959 which were then sequenced to a depth of ~4 million reads per library,
960 resulting in a complete gene expression profile for each cell.")
961 (license license:artistic2.0)))
969 ;; We cannot use bioconductor-uri here because this tarball is
970 ;; located under "data/experiment/" instead of "bioc/".
971 (uri (string-append "https://www.bioconductor.org/packages/"
972 "release/data/experiment/src/contrib/"
973 "ALL_" version ".tar.gz"))
976 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
977 (properties `((upstream-name . "ALL")))
978 (build-system r-build-system)
980 `(("r-biobase" ,r-biobase)))
981 (home-page "https://bioconductor.org/packages/ALL")
982 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
984 "The data consist of microarrays from 128 different individuals with
985 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
986 are available. The data have been normalized (using rma) and it is the
987 jointly normalized data that are available here. The data are presented in
988 the form of an @code{exprSet} object.")
989 (license license:artistic2.0)))
991 (define-public r-affydata
998 (uri (bioconductor-uri "affydata" version 'experiment))
1001 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1002 (properties `((upstream-name . "affydata")))
1003 (build-system r-build-system)
1005 `(("r-affy" ,r-affy)))
1006 (home-page "https://bioconductor.org/packages/affydata/")
1007 (synopsis "Affymetrix data for demonstration purposes")
1009 "This package provides example datasets that represent 'real world
1010 examples' of Affymetrix data, unlike the artificial examples included in the
1011 package @code{affy}.")
1012 (license license:gpl2+)))
1017 (define-public r-biocgenerics
1019 (name "r-biocgenerics")
1023 (uri (bioconductor-uri "BiocGenerics" version))
1026 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
1028 `((upstream-name . "BiocGenerics")))
1029 (build-system r-build-system)
1030 (home-page "https://bioconductor.org/packages/BiocGenerics")
1031 (synopsis "S4 generic functions for Bioconductor")
1033 "This package provides S4 generic functions needed by many Bioconductor
1035 (license license:artistic2.0)))
1037 (define-public r-affycomp
1044 (uri (bioconductor-uri "affycomp" version))
1047 "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
1048 (properties `((upstream-name . "affycomp")))
1049 (build-system r-build-system)
1050 (propagated-inputs `(("r-biobase" ,r-biobase)))
1051 (home-page "https://bioconductor.org/packages/affycomp/")
1052 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1054 "The package contains functions that can be used to compare expression
1055 measures for Affymetrix Oligonucleotide Arrays.")
1056 (license license:gpl2+)))
1058 (define-public r-affycompatible
1060 (name "r-affycompatible")
1065 (uri (bioconductor-uri "AffyCompatible" version))
1068 "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
1070 `((upstream-name . "AffyCompatible")))
1071 (build-system r-build-system)
1073 `(("r-biostrings" ,r-biostrings)
1074 ("r-rcurl" ,r-rcurl)
1076 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1077 (synopsis "Work with Affymetrix GeneChip files")
1079 "This package provides an interface to Affymetrix chip annotation and
1080 sample attribute files. The package allows an easy way for users to download
1081 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1082 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1083 Command Console} (AGCC)-compatible sample annotation files.")
1084 (license license:artistic2.0)))
1086 (define-public r-affycontam
1088 (name "r-affycontam")
1093 (uri (bioconductor-uri "affyContam" version))
1096 "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
1097 (properties `((upstream-name . "affyContam")))
1098 (build-system r-build-system)
1100 `(("r-affy" ,r-affy)
1101 ("r-affydata" ,r-affydata)
1102 ("r-biobase" ,r-biobase)))
1103 (home-page "https://bioconductor.org/packages/affyContam/")
1104 (synopsis "Structured corruption of Affymetrix CEL file data")
1106 "Microarray quality assessment is a major concern of microarray analysts.
1107 This package provides some simple approaches to in silico creation of quality
1108 problems in CEL-level data to help evaluate performance of quality metrics.")
1109 (license license:artistic2.0)))
1111 (define-public r-affycoretools
1113 (name "r-affycoretools")
1118 (uri (bioconductor-uri "affycoretools" version))
1121 "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s"))))
1122 (properties `((upstream-name . "affycoretools")))
1123 (build-system r-build-system)
1125 `(("r-affy" ,r-affy)
1126 ("r-annotationdbi" ,r-annotationdbi)
1127 ("r-biobase" ,r-biobase)
1128 ("r-biocgenerics" ,r-biocgenerics)
1130 ("r-edger" ,r-edger)
1131 ("r-gcrma" ,r-gcrma)
1132 ("r-ggplot2" ,r-ggplot2)
1133 ("r-gostats" ,r-gostats)
1134 ("r-gplots" ,r-gplots)
1135 ("r-hwriter" ,r-hwriter)
1136 ("r-lattice" ,r-lattice)
1137 ("r-limma" ,r-limma)
1138 ("r-oligoclasses" ,r-oligoclasses)
1139 ("r-reportingtools" ,r-reportingtools)
1140 ("r-rsqlite" ,r-rsqlite)
1141 ("r-s4vectors" ,r-s4vectors)
1142 ("r-xtable" ,r-xtable)))
1143 (home-page "https://bioconductor.org/packages/affycoretools/")
1144 (synopsis "Functions for analyses with Affymetrix GeneChips")
1146 "This package provides various wrapper functions that have been written
1147 to streamline the more common analyses that a Biostatistician might see.")
1148 (license license:artistic2.0)))
1150 (define-public r-affxparser
1152 (name "r-affxparser")
1157 (uri (bioconductor-uri "affxparser" version))
1160 "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33"))))
1161 (properties `((upstream-name . "affxparser")))
1162 (build-system r-build-system)
1163 (home-page "https://github.com/HenrikBengtsson/affxparser")
1164 (synopsis "Affymetrix File Parsing SDK")
1166 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1167 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1168 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1169 are supported. Currently, there are methods for reading @dfn{chip definition
1170 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1171 either in full or in part. For example, probe signals from a few probesets
1172 can be extracted very quickly from a set of CEL files into a convenient list
1174 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1176 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1178 (define-public r-annotate
1185 (uri (bioconductor-uri "annotate" version))
1188 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
1189 (build-system r-build-system)
1191 `(("r-annotationdbi" ,r-annotationdbi)
1192 ("r-biobase" ,r-biobase)
1193 ("r-biocgenerics" ,r-biocgenerics)
1195 ("r-rcurl" ,r-rcurl)
1197 ("r-xtable" ,r-xtable)))
1199 "https://bioconductor.org/packages/annotate")
1200 (synopsis "Annotation for microarrays")
1201 (description "This package provides R environments for the annotation of
1203 (license license:artistic2.0)))
1205 (define-public r-hpar
1212 (uri (bioconductor-uri "hpar" version))
1215 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
1216 (build-system r-build-system)
1217 (home-page "https://bioconductor.org/packages/hpar/")
1218 (synopsis "Human Protein Atlas in R")
1219 (description "This package provides a simple interface to and data from
1220 the Human Protein Atlas project.")
1221 (license license:artistic2.0)))
1223 (define-public r-regioner
1230 (uri (bioconductor-uri "regioneR" version))
1233 "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
1234 (properties `((upstream-name . "regioneR")))
1235 (build-system r-build-system)
1237 `(("r-biostrings" ,r-biostrings)
1238 ("r-bsgenome" ,r-bsgenome)
1239 ("r-genomeinfodb" ,r-genomeinfodb)
1240 ("r-genomicranges" ,r-genomicranges)
1241 ("r-iranges" ,r-iranges)
1242 ("r-memoise" ,r-memoise)
1243 ("r-rtracklayer" ,r-rtracklayer)
1244 ("r-s4vectors" ,r-s4vectors)))
1245 (home-page "https://bioconductor.org/packages/regioneR/")
1246 (synopsis "Association analysis of genomic regions")
1247 (description "This package offers a statistical framework based on
1248 customizable permutation tests to assess the association between genomic
1249 region sets and other genomic features.")
1250 (license license:artistic2.0)))
1252 (define-public r-reportingtools
1254 (name "r-reportingtools")
1259 (uri (bioconductor-uri "ReportingTools" version))
1262 "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
1264 `((upstream-name . "ReportingTools")))
1265 (build-system r-build-system)
1267 `(("r-annotate" ,r-annotate)
1268 ("r-annotationdbi" ,r-annotationdbi)
1269 ("r-biobase" ,r-biobase)
1270 ("r-biocgenerics" ,r-biocgenerics)
1271 ("r-category" ,r-category)
1272 ("r-deseq2" ,r-deseq2)
1273 ("r-edger" ,r-edger)
1274 ("r-ggbio" ,r-ggbio)
1275 ("r-ggplot2" ,r-ggplot2)
1276 ("r-gostats" ,r-gostats)
1277 ("r-gseabase" ,r-gseabase)
1278 ("r-hwriter" ,r-hwriter)
1279 ("r-iranges" ,r-iranges)
1280 ("r-knitr" ,r-knitr)
1281 ("r-lattice" ,r-lattice)
1282 ("r-limma" ,r-limma)
1283 ("r-pfam-db" ,r-pfam-db)
1284 ("r-r-utils" ,r-r-utils)
1286 (home-page "https://bioconductor.org/packages/ReportingTools/")
1287 (synopsis "Tools for making reports in various formats")
1289 "The ReportingTools package enables users to easily display reports of
1290 analysis results generated from sources such as microarray and sequencing
1291 data. The package allows users to create HTML pages that may be viewed on a
1292 web browser, or in other formats. Users can generate tables with sortable and
1293 filterable columns, make and display plots, and link table entries to other
1294 data sources such as NCBI or larger plots within the HTML page. Using the
1295 package, users can also produce a table of contents page to link various
1296 reports together for a particular project that can be viewed in a web
1298 (license license:artistic2.0)))
1300 (define-public r-geneplotter
1302 (name "r-geneplotter")
1307 (uri (bioconductor-uri "geneplotter" version))
1310 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1311 (build-system r-build-system)
1313 `(("r-annotate" ,r-annotate)
1314 ("r-annotationdbi" ,r-annotationdbi)
1315 ("r-biobase" ,r-biobase)
1316 ("r-biocgenerics" ,r-biocgenerics)
1317 ("r-lattice" ,r-lattice)
1318 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1319 (home-page "https://bioconductor.org/packages/geneplotter")
1320 (synopsis "Graphics functions for genomic data")
1322 "This package provides functions for plotting genomic data.")
1323 (license license:artistic2.0)))
1325 (define-public r-oligoclasses
1327 (name "r-oligoclasses")
1332 (uri (bioconductor-uri "oligoClasses" version))
1335 "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72"))))
1336 (properties `((upstream-name . "oligoClasses")))
1337 (build-system r-build-system)
1339 `(("r-affyio" ,r-affyio)
1340 ("r-biobase" ,r-biobase)
1341 ("r-biocgenerics" ,r-biocgenerics)
1342 ("r-biocmanager" ,r-biocmanager)
1343 ("r-biostrings" ,r-biostrings)
1346 ("r-foreach" ,r-foreach)
1347 ("r-genomicranges" ,r-genomicranges)
1348 ("r-iranges" ,r-iranges)
1349 ("r-rsqlite" ,r-rsqlite)
1350 ("r-s4vectors" ,r-s4vectors)
1351 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1352 (home-page "https://bioconductor.org/packages/oligoClasses/")
1353 (synopsis "Classes for high-throughput arrays")
1355 "This package contains class definitions, validity checks, and
1356 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1358 (license license:gpl2+)))
1360 (define-public r-oligo
1367 (uri (bioconductor-uri "oligo" version))
1370 "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df"))))
1371 (properties `((upstream-name . "oligo")))
1372 (build-system r-build-system)
1373 (inputs `(("zlib" ,zlib)))
1375 `(("r-affxparser" ,r-affxparser)
1376 ("r-affyio" ,r-affyio)
1377 ("r-biobase" ,r-biobase)
1378 ("r-biocgenerics" ,r-biocgenerics)
1379 ("r-biostrings" ,r-biostrings)
1382 ("r-oligoclasses" ,r-oligoclasses)
1383 ("r-preprocesscore" ,r-preprocesscore)
1384 ("r-rsqlite" ,r-rsqlite)
1385 ("r-zlibbioc" ,r-zlibbioc)))
1386 (home-page "https://bioconductor.org/packages/oligo/")
1387 (synopsis "Preprocessing tools for oligonucleotide arrays")
1389 "This package provides a package to analyze oligonucleotide
1390 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1391 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1392 (license license:lgpl2.0+)))
1394 (define-public r-qvalue
1401 (uri (bioconductor-uri "qvalue" version))
1404 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1405 (build-system r-build-system)
1407 `(("r-ggplot2" ,r-ggplot2)
1408 ("r-reshape2" ,r-reshape2)))
1409 (home-page "http://github.com/jdstorey/qvalue")
1410 (synopsis "Q-value estimation for false discovery rate control")
1412 "This package takes a list of p-values resulting from the simultaneous
1413 testing of many hypotheses and estimates their q-values and local @dfn{false
1414 discovery rate} (FDR) values. The q-value of a test measures the proportion
1415 of false positives incurred when that particular test is called significant.
1416 The local FDR measures the posterior probability the null hypothesis is true
1417 given the test's p-value. Various plots are automatically generated, allowing
1418 one to make sensible significance cut-offs. The software can be applied to
1419 problems in genomics, brain imaging, astrophysics, and data mining.")
1420 ;; Any version of the LGPL.
1421 (license license:lgpl3+)))
1423 (define-public r-diffbind
1430 (uri (bioconductor-uri "DiffBind" version))
1433 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1434 (properties `((upstream-name . "DiffBind")))
1435 (build-system r-build-system)
1439 `(("r-amap" ,r-amap)
1440 ("r-biocparallel" ,r-biocparallel)
1441 ("r-deseq2" ,r-deseq2)
1442 ("r-dplyr" ,r-dplyr)
1443 ("r-edger" ,r-edger)
1444 ("r-genomicalignments" ,r-genomicalignments)
1445 ("r-genomicranges" ,r-genomicranges)
1446 ("r-ggplot2" ,r-ggplot2)
1447 ("r-ggrepel" ,r-ggrepel)
1448 ("r-gplots" ,r-gplots)
1449 ("r-iranges" ,r-iranges)
1450 ("r-lattice" ,r-lattice)
1451 ("r-limma" ,r-limma)
1452 ("r-locfit" ,r-locfit)
1453 ("r-rcolorbrewer" , r-rcolorbrewer)
1455 ("r-rhtslib" ,r-rhtslib)
1456 ("r-rsamtools" ,r-rsamtools)
1457 ("r-s4vectors" ,r-s4vectors)
1458 ("r-summarizedexperiment" ,r-summarizedexperiment)
1459 ("r-systempiper" ,r-systempiper)))
1460 (home-page "http://bioconductor.org/packages/DiffBind")
1461 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1463 "This package computes differentially bound sites from multiple
1464 ChIP-seq experiments using affinity (quantitative) data. Also enables
1465 occupancy (overlap) analysis and plotting functions.")
1466 (license license:artistic2.0)))
1468 (define-public r-ripseeker
1470 (name "r-ripseeker")
1475 (uri (bioconductor-uri "RIPSeeker" version))
1478 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1479 (properties `((upstream-name . "RIPSeeker")))
1480 (build-system r-build-system)
1482 `(("r-s4vectors" ,r-s4vectors)
1483 ("r-iranges" ,r-iranges)
1484 ("r-genomicranges" ,r-genomicranges)
1485 ("r-summarizedexperiment" ,r-summarizedexperiment)
1486 ("r-rsamtools" ,r-rsamtools)
1487 ("r-genomicalignments" ,r-genomicalignments)
1488 ("r-rtracklayer" ,r-rtracklayer)))
1489 (home-page "http://bioconductor.org/packages/RIPSeeker")
1491 "Identifying protein-associated transcripts from RIP-seq experiments")
1493 "This package infers and discriminates RIP peaks from RIP-seq alignments
1494 using two-state HMM with negative binomial emission probability. While
1495 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1496 a suite of bioinformatics tools integrated within this self-contained software
1497 package comprehensively addressing issues ranging from post-alignments
1498 processing to visualization and annotation.")
1499 (license license:gpl2)))
1501 (define-public r-multtest
1508 (uri (bioconductor-uri "multtest" version))
1511 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1512 (build-system r-build-system)
1514 `(("r-survival" ,r-survival)
1515 ("r-biocgenerics" ,r-biocgenerics)
1516 ("r-biobase" ,r-biobase)
1517 ("r-mass" ,r-mass)))
1518 (home-page "http://bioconductor.org/packages/multtest")
1519 (synopsis "Resampling-based multiple hypothesis testing")
1521 "This package can do non-parametric bootstrap and permutation
1522 resampling-based multiple testing procedures (including empirical Bayes
1523 methods) for controlling the family-wise error rate (FWER), generalized
1524 family-wise error rate (gFWER), tail probability of the proportion of
1525 false positives (TPPFP), and false discovery rate (FDR). Several choices
1526 of bootstrap-based null distribution are implemented (centered, centered
1527 and scaled, quantile-transformed). Single-step and step-wise methods are
1528 available. Tests based on a variety of T- and F-statistics (including
1529 T-statistics based on regression parameters from linear and survival models
1530 as well as those based on correlation parameters) are included. When probing
1531 hypotheses with T-statistics, users may also select a potentially faster null
1532 distribution which is multivariate normal with mean zero and variance
1533 covariance matrix derived from the vector influence function. Results are
1534 reported in terms of adjusted P-values, confidence regions and test statistic
1535 cutoffs. The procedures are directly applicable to identifying differentially
1536 expressed genes in DNA microarray experiments.")
1537 (license license:lgpl3)))
1539 (define-public r-graph
1545 (uri (bioconductor-uri "graph" version))
1548 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1549 (build-system r-build-system)
1551 `(("r-biocgenerics" ,r-biocgenerics)))
1552 (home-page "https://bioconductor.org/packages/graph")
1553 (synopsis "Handle graph data structures in R")
1555 "This package implements some simple graph handling capabilities for R.")
1556 (license license:artistic2.0)))
1558 (define-public r-codedepends
1560 (name "r-codedepends")
1565 (uri (cran-uri "CodeDepends" version))
1568 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1569 (properties `((upstream-name . "CodeDepends")))
1570 (build-system r-build-system)
1572 `(("r-codetools" ,r-codetools)
1573 ("r-graph" ,r-graph)
1575 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1576 (synopsis "Analysis of R code for reproducible research and code comprehension")
1578 "This package provides tools for analyzing R expressions or blocks of
1579 code and determining the dependencies between them. It focuses on R scripts,
1580 but can be used on the bodies of functions. There are many facilities
1581 including the ability to summarize or get a high-level view of code,
1582 determining dependencies between variables, code improvement suggestions.")
1583 ;; Any version of the GPL
1584 (license (list license:gpl2+ license:gpl3+))))
1586 (define-public r-chippeakanno
1588 (name "r-chippeakanno")
1593 (uri (bioconductor-uri "ChIPpeakAnno" version))
1596 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1597 (properties `((upstream-name . "ChIPpeakAnno")))
1598 (build-system r-build-system)
1600 `(("r-annotationdbi" ,r-annotationdbi)
1601 ("r-biobase" ,r-biobase)
1602 ("r-biocgenerics" ,r-biocgenerics)
1603 ("r-biocmanager" ,r-biocmanager)
1604 ("r-biomart" ,r-biomart)
1605 ("r-biostrings" ,r-biostrings)
1606 ("r-bsgenome" ,r-bsgenome)
1608 ("r-delayedarray" ,r-delayedarray)
1609 ("r-ensembldb" ,r-ensembldb)
1610 ("r-genomeinfodb" ,r-genomeinfodb)
1611 ("r-genomicalignments" ,r-genomicalignments)
1612 ("r-genomicfeatures" ,r-genomicfeatures)
1613 ("r-genomicranges" ,r-genomicranges)
1614 ("r-go-db" ,r-go-db)
1615 ("r-graph" ,r-graph)
1617 ("r-iranges" ,r-iranges)
1618 ("r-limma" ,r-limma)
1619 ("r-matrixstats" ,r-matrixstats)
1620 ("r-multtest" ,r-multtest)
1622 ("r-regioner" ,r-regioner)
1623 ("r-rsamtools" ,r-rsamtools)
1624 ("r-rtracklayer" ,r-rtracklayer)
1625 ("r-s4vectors" ,r-s4vectors)
1626 ("r-seqinr" ,r-seqinr)
1627 ("r-summarizedexperiment" ,r-summarizedexperiment)
1628 ("r-venndiagram" ,r-venndiagram)))
1629 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1630 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1632 "The package includes functions to retrieve the sequences around the peak,
1633 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1634 custom features such as most conserved elements and other transcription factor
1635 binding sites supplied by users. Starting 2.0.5, new functions have been added
1636 for finding the peaks with bi-directional promoters with summary statistics
1637 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1638 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1639 enrichedGO (addGeneIDs).")
1640 (license license:gpl2+)))
1642 (define-public r-marray
1648 (uri (bioconductor-uri "marray" version))
1650 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1651 (build-system r-build-system)
1653 `(("r-limma" ,r-limma)))
1654 (home-page "http://bioconductor.org/packages/marray")
1655 (synopsis "Exploratory analysis for two-color spotted microarray data")
1656 (description "This package contains class definitions for two-color spotted
1657 microarray data. It also includes functions for data input, diagnostic plots,
1658 normalization and quality checking.")
1659 (license license:lgpl2.0+)))
1661 (define-public r-cghbase
1667 (uri (bioconductor-uri "CGHbase" version))
1669 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1670 (properties `((upstream-name . "CGHbase")))
1671 (build-system r-build-system)
1673 `(("r-biobase" ,r-biobase)
1674 ("r-marray" ,r-marray)))
1675 (home-page "http://bioconductor.org/packages/CGHbase")
1676 (synopsis "Base functions and classes for arrayCGH data analysis")
1677 (description "This package contains functions and classes that are needed by
1678 the @code{arrayCGH} packages.")
1679 (license license:gpl2+)))
1681 (define-public r-cghcall
1687 (uri (bioconductor-uri "CGHcall" version))
1689 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1690 (properties `((upstream-name . "CGHcall")))
1691 (build-system r-build-system)
1693 `(("r-biobase" ,r-biobase)
1694 ("r-cghbase" ,r-cghbase)
1695 ("r-impute" ,r-impute)
1696 ("r-dnacopy" ,r-dnacopy)
1697 ("r-snowfall" ,r-snowfall)))
1698 (home-page "http://bioconductor.org/packages/CGHcall")
1699 (synopsis "Base functions and classes for arrayCGH data analysis")
1700 (description "This package contains functions and classes that are needed by
1701 @code{arrayCGH} packages.")
1702 (license license:gpl2+)))
1704 (define-public r-qdnaseq
1710 (uri (bioconductor-uri "QDNAseq" version))
1712 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1713 (properties `((upstream-name . "QDNAseq")))
1714 (build-system r-build-system)
1716 `(("r-biobase" ,r-biobase)
1717 ("r-biocparallel" ,r-biocparallel)
1718 ("r-cghbase" ,r-cghbase)
1719 ("r-cghcall" ,r-cghcall)
1720 ("r-dnacopy" ,r-dnacopy)
1721 ("r-genomicranges" ,r-genomicranges)
1722 ("r-iranges" ,r-iranges)
1723 ("r-matrixstats" ,r-matrixstats)
1724 ("r-r-utils" ,r-r-utils)
1725 ("r-rsamtools" ,r-rsamtools)))
1726 (home-page "http://bioconductor.org/packages/QDNAseq")
1727 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1728 (description "The genome is divided into non-overlapping fixed-sized bins,
1729 number of sequence reads in each counted, adjusted with a simultaneous
1730 two-dimensional loess correction for sequence mappability and GC content, and
1731 filtered to remove spurious regions in the genome. Downstream steps of
1732 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1734 (license license:gpl2+)))
1736 (define-public r-bayseq
1743 (uri (bioconductor-uri "baySeq" version))
1746 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1747 (properties `((upstream-name . "baySeq")))
1748 (build-system r-build-system)
1750 `(("r-abind" ,r-abind)
1751 ("r-edger" ,r-edger)
1752 ("r-genomicranges" ,r-genomicranges)))
1753 (home-page "https://bioconductor.org/packages/baySeq/")
1754 (synopsis "Bayesian analysis of differential expression patterns in count data")
1756 "This package identifies differential expression in high-throughput count
1757 data, such as that derived from next-generation sequencing machines,
1758 calculating estimated posterior likelihoods of differential expression (or
1759 more complex hypotheses) via empirical Bayesian methods.")
1760 (license license:gpl3)))
1762 (define-public r-chipcomp
1769 (uri (bioconductor-uri "ChIPComp" version))
1772 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1773 (properties `((upstream-name . "ChIPComp")))
1774 (build-system r-build-system)
1776 `(("r-biocgenerics" ,r-biocgenerics)
1777 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1778 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1779 ("r-genomeinfodb" ,r-genomeinfodb)
1780 ("r-genomicranges" ,r-genomicranges)
1781 ("r-iranges" ,r-iranges)
1782 ("r-limma" ,r-limma)
1783 ("r-rsamtools" ,r-rsamtools)
1784 ("r-rtracklayer" ,r-rtracklayer)
1785 ("r-s4vectors" ,r-s4vectors)))
1786 (home-page "https://bioconductor.org/packages/ChIPComp")
1787 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1789 "ChIPComp implements a statistical method for quantitative comparison of
1790 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1791 sites across multiple conditions considering matching control in ChIP-seq
1793 ;; Any version of the GPL.
1794 (license license:gpl3+)))
1796 (define-public r-riboprofiling
1798 (name "r-riboprofiling")
1803 (uri (bioconductor-uri "RiboProfiling" version))
1806 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1807 (properties `((upstream-name . "RiboProfiling")))
1808 (build-system r-build-system)
1810 `(("r-biocgenerics" ,r-biocgenerics)
1811 ("r-biostrings" ,r-biostrings)
1812 ("r-data-table" ,r-data-table)
1813 ("r-genomeinfodb" ,r-genomeinfodb)
1814 ("r-genomicalignments" ,r-genomicalignments)
1815 ("r-genomicfeatures" ,r-genomicfeatures)
1816 ("r-genomicranges" ,r-genomicranges)
1817 ("r-ggbio" ,r-ggbio)
1818 ("r-ggplot2" ,r-ggplot2)
1819 ("r-iranges" ,r-iranges)
1821 ("r-reshape2" ,r-reshape2)
1822 ("r-rsamtools" ,r-rsamtools)
1823 ("r-rtracklayer" ,r-rtracklayer)
1824 ("r-s4vectors" ,r-s4vectors)
1825 ("r-sqldf" ,r-sqldf)))
1826 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1827 (synopsis "Ribosome profiling data analysis")
1828 (description "Starting with a BAM file, this package provides the
1829 necessary functions for quality assessment, read start position recalibration,
1830 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1831 of count data: pairs, log fold-change, codon frequency and coverage
1832 assessment, principal component analysis on codon coverage.")
1833 (license license:gpl3)))
1835 (define-public r-riboseqr
1842 (uri (bioconductor-uri "riboSeqR" version))
1845 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1846 (properties `((upstream-name . "riboSeqR")))
1847 (build-system r-build-system)
1849 `(("r-abind" ,r-abind)
1850 ("r-bayseq" ,r-bayseq)
1851 ("r-genomeinfodb" ,r-genomeinfodb)
1852 ("r-genomicranges" ,r-genomicranges)
1853 ("r-iranges" ,r-iranges)
1854 ("r-rsamtools" ,r-rsamtools)
1855 ("r-seqlogo" ,r-seqlogo)))
1856 (home-page "https://bioconductor.org/packages/riboSeqR/")
1857 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1859 "This package provides plotting functions, frameshift detection and
1860 parsing of genetic sequencing data from ribosome profiling experiments.")
1861 (license license:gpl3)))
1863 (define-public r-interactionset
1865 (name "r-interactionset")
1870 (uri (bioconductor-uri "InteractionSet" version))
1873 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1875 `((upstream-name . "InteractionSet")))
1876 (build-system r-build-system)
1878 `(("r-biocgenerics" ,r-biocgenerics)
1879 ("r-genomeinfodb" ,r-genomeinfodb)
1880 ("r-genomicranges" ,r-genomicranges)
1881 ("r-iranges" ,r-iranges)
1882 ("r-matrix" ,r-matrix)
1884 ("r-s4vectors" ,r-s4vectors)
1885 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1886 (home-page "https://bioconductor.org/packages/InteractionSet")
1887 (synopsis "Base classes for storing genomic interaction data")
1889 "This package provides the @code{GInteractions},
1890 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1891 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1893 (license license:gpl3)))
1895 (define-public r-genomicinteractions
1897 (name "r-genomicinteractions")
1902 (uri (bioconductor-uri "GenomicInteractions" version))
1905 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1907 `((upstream-name . "GenomicInteractions")))
1908 (build-system r-build-system)
1910 `(("r-biobase" ,r-biobase)
1911 ("r-biocgenerics" ,r-biocgenerics)
1912 ("r-data-table" ,r-data-table)
1913 ("r-dplyr" ,r-dplyr)
1914 ("r-genomeinfodb" ,r-genomeinfodb)
1915 ("r-genomicranges" ,r-genomicranges)
1916 ("r-ggplot2" ,r-ggplot2)
1917 ("r-gridextra" ,r-gridextra)
1919 ("r-igraph" ,r-igraph)
1920 ("r-interactionset" ,r-interactionset)
1921 ("r-iranges" ,r-iranges)
1922 ("r-rsamtools" ,r-rsamtools)
1923 ("r-rtracklayer" ,r-rtracklayer)
1924 ("r-s4vectors" ,r-s4vectors)
1925 ("r-stringr" ,r-stringr)))
1926 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1927 (synopsis "R package for handling genomic interaction data")
1929 "This R package provides tools for handling genomic interaction data,
1930 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1931 information and producing various plots and statistics.")
1932 (license license:gpl3)))
1934 (define-public r-ctc
1941 (uri (bioconductor-uri "ctc" version))
1944 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1945 (build-system r-build-system)
1946 (propagated-inputs `(("r-amap" ,r-amap)))
1947 (home-page "https://bioconductor.org/packages/ctc/")
1948 (synopsis "Cluster and tree conversion")
1950 "This package provides tools for exporting and importing classification
1951 trees and clusters to other programs.")
1952 (license license:gpl2)))
1954 (define-public r-goseq
1961 (uri (bioconductor-uri "goseq" version))
1964 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1965 (build-system r-build-system)
1967 `(("r-annotationdbi" ,r-annotationdbi)
1968 ("r-biasedurn" ,r-biasedurn)
1969 ("r-biocgenerics" ,r-biocgenerics)
1970 ("r-genelendatabase" ,r-genelendatabase)
1971 ("r-go-db" ,r-go-db)
1972 ("r-mgcv" ,r-mgcv)))
1973 (home-page "https://bioconductor.org/packages/goseq/")
1974 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1976 "This package provides tools to detect Gene Ontology and/or other user
1977 defined categories which are over/under represented in RNA-seq data.")
1978 (license license:lgpl2.0+)))
1980 (define-public r-glimma
1987 (uri (bioconductor-uri "Glimma" version))
1990 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1991 (properties `((upstream-name . "Glimma")))
1992 (build-system r-build-system)
1994 `(("r-edger" ,r-edger)
1995 ("r-jsonlite" ,r-jsonlite)
1996 ("r-s4vectors" ,r-s4vectors)))
1997 (home-page "https://github.com/Shians/Glimma")
1998 (synopsis "Interactive HTML graphics")
2000 "This package generates interactive visualisations for analysis of
2001 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2002 HTML page. The interactions are built on top of the popular static
2003 representations of analysis results in order to provide additional
2005 (license license:lgpl3)))
2007 (define-public r-rots
2014 (uri (bioconductor-uri "ROTS" version))
2017 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
2018 (properties `((upstream-name . "ROTS")))
2019 (build-system r-build-system)
2021 `(("r-biobase" ,r-biobase)
2022 ("r-rcpp" ,r-rcpp)))
2023 (home-page "https://bioconductor.org/packages/ROTS/")
2024 (synopsis "Reproducibility-Optimized Test Statistic")
2026 "This package provides tools for calculating the
2027 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2029 (license license:gpl2+)))
2031 (define-public r-plgem
2038 (uri (bioconductor-uri "plgem" version))
2041 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
2042 (build-system r-build-system)
2044 `(("r-biobase" ,r-biobase)
2045 ("r-mass" ,r-mass)))
2046 (home-page "http://www.genopolis.it")
2047 (synopsis "Detect differential expression in microarray and proteomics datasets")
2049 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2050 model the variance-versus-mean dependence that exists in a variety of
2051 genome-wide datasets, including microarray and proteomics data. The use of
2052 PLGEM has been shown to improve the detection of differentially expressed
2053 genes or proteins in these datasets.")
2054 (license license:gpl2)))
2056 (define-public r-inspect
2063 (uri (bioconductor-uri "INSPEcT" version))
2066 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
2067 (properties `((upstream-name . "INSPEcT")))
2068 (build-system r-build-system)
2070 `(("r-biobase" ,r-biobase)
2071 ("r-biocgenerics" ,r-biocgenerics)
2072 ("r-biocparallel" ,r-biocparallel)
2073 ("r-deseq2" ,r-deseq2)
2074 ("r-desolve" ,r-desolve)
2075 ("r-genomicalignments" ,r-genomicalignments)
2076 ("r-genomicfeatures" ,r-genomicfeatures)
2077 ("r-genomicranges" ,r-genomicranges)
2078 ("r-iranges" ,r-iranges)
2079 ("r-plgem" ,r-plgem)
2080 ("r-preprocesscore" ,r-preprocesscore)
2082 ("r-rootsolve" ,r-rootsolve)
2083 ("r-rsamtools" ,r-rsamtools)
2084 ("r-s4vectors" ,r-s4vectors)
2085 ("r-shiny" ,r-shiny)
2086 ("r-summarizedexperiment" ,r-summarizedexperiment)
2087 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2088 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2089 (home-page "https://bioconductor.org/packages/INSPEcT")
2090 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2092 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2093 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2094 order to evaluate synthesis, processing and degradation rates and assess via
2095 modeling the rates that determines changes in mature mRNA levels.")
2096 (license license:gpl2)))
2098 (define-public r-dnabarcodes
2100 (name "r-dnabarcodes")
2105 (uri (bioconductor-uri "DNABarcodes" version))
2108 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
2109 (properties `((upstream-name . "DNABarcodes")))
2110 (build-system r-build-system)
2113 ("r-matrix" ,r-matrix)
2114 ("r-rcpp" ,r-rcpp)))
2115 (home-page "https://bioconductor.org/packages/DNABarcodes")
2116 (synopsis "Create and analyze DNA barcodes")
2118 "This package offers tools to create DNA barcode sets capable of
2119 correcting insertion, deletion, and substitution errors. Existing barcodes
2120 can be analyzed regarding their minimal, maximal and average distances between
2121 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2122 demultiplexed, i.e. assigned to their original reference barcode.")
2123 (license license:gpl2)))
2125 (define-public r-ruvseq
2132 (uri (bioconductor-uri "RUVSeq" version))
2135 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
2136 (properties `((upstream-name . "RUVSeq")))
2137 (build-system r-build-system)
2139 `(("r-biobase" ,r-biobase)
2140 ("r-edaseq" ,r-edaseq)
2141 ("r-edger" ,r-edger)
2142 ("r-mass" ,r-mass)))
2143 (home-page "https://github.com/drisso/RUVSeq")
2144 (synopsis "Remove unwanted variation from RNA-Seq data")
2146 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2147 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2149 (license license:artistic2.0)))
2151 (define-public r-biocneighbors
2153 (name "r-biocneighbors")
2158 (uri (bioconductor-uri "BiocNeighbors" version))
2161 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
2162 (properties `((upstream-name . "BiocNeighbors")))
2163 (build-system r-build-system)
2165 `(("r-biocgenerics" ,r-biocgenerics)
2166 ("r-biocparallel" ,r-biocparallel)
2168 ("r-rcppannoy" ,r-rcppannoy)
2169 ("r-rcpphnsw" ,r-rcpphnsw)
2170 ("r-s4vectors" ,r-s4vectors)))
2171 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2172 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2174 "This package implements exact and approximate methods for nearest
2175 neighbor detection, in a framework that allows them to be easily switched
2176 within Bioconductor packages or workflows. The exact algorithm is implemented
2177 using pre-clustering with the k-means algorithm. Functions are also provided
2178 to search for all neighbors within a given distance. Parallelization is
2179 achieved for all methods using the BiocParallel framework.")
2180 (license license:gpl3)))
2182 (define-public r-biocsingular
2184 (name "r-biocsingular")
2189 (uri (bioconductor-uri "BiocSingular" version))
2192 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
2193 (properties `((upstream-name . "BiocSingular")))
2194 (build-system r-build-system)
2196 `(("r-beachmat" ,r-beachmat)
2197 ("r-biocgenerics" ,r-biocgenerics)
2198 ("r-biocparallel" ,r-biocparallel)
2199 ("r-delayedarray" ,r-delayedarray)
2200 ("r-irlba" ,r-irlba)
2201 ("r-matrix" ,r-matrix)
2204 ("r-s4vectors" ,r-s4vectors)))
2205 (home-page "https://github.com/LTLA/BiocSingular")
2206 (synopsis "Singular value decomposition for Bioconductor packages")
2208 "This package implements exact and approximate methods for singular value
2209 decomposition and principal components analysis, in a framework that allows
2210 them to be easily switched within Bioconductor packages or workflows. Where
2211 possible, parallelization is achieved using the BiocParallel framework.")
2212 (license license:gpl3)))
2214 (define-public r-destiny
2221 (uri (bioconductor-uri "destiny" version))
2224 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
2225 (build-system r-build-system)
2227 `(("r-biobase" ,r-biobase)
2228 ("r-biocgenerics" ,r-biocgenerics)
2229 ("r-ggplot2" ,r-ggplot2)
2230 ("r-ggthemes" ,r-ggthemes)
2231 ("r-igraph" ,r-igraph)
2232 ("r-matrix" ,r-matrix)
2233 ("r-proxy" ,r-proxy)
2235 ("r-rcppeigen" ,r-rcppeigen)
2236 ("r-scales" ,r-scales)
2237 ("r-scatterplot3d" ,r-scatterplot3d)
2238 ("r-smoother" ,r-smoother)
2239 ("r-summarizedexperiment" ,r-summarizedexperiment)
2241 (home-page "https://bioconductor.org/packages/destiny/")
2242 (synopsis "Create and plot diffusion maps")
2243 (description "This package provides tools to create and plot diffusion
2245 ;; Any version of the GPL
2246 (license license:gpl3+)))
2248 (define-public r-savr
2255 (uri (bioconductor-uri "savR" version))
2258 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
2259 (properties `((upstream-name . "savR")))
2260 (build-system r-build-system)
2262 `(("r-ggplot2" ,r-ggplot2)
2263 ("r-gridextra" ,r-gridextra)
2264 ("r-reshape2" ,r-reshape2)
2265 ("r-scales" ,r-scales)
2267 (home-page "https://github.com/bcalder/savR")
2268 (synopsis "Parse and analyze Illumina SAV files")
2270 "This package provides tools to parse Illumina Sequence Analysis
2271 Viewer (SAV) files, access data, and generate QC plots.")
2272 (license license:agpl3+)))
2274 (define-public r-chipexoqual
2276 (name "r-chipexoqual")
2281 (uri (bioconductor-uri "ChIPexoQual" version))
2284 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
2285 (properties `((upstream-name . "ChIPexoQual")))
2286 (build-system r-build-system)
2288 `(("r-biocparallel" ,r-biocparallel)
2289 ("r-biovizbase" ,r-biovizbase)
2290 ("r-broom" ,r-broom)
2291 ("r-data-table" ,r-data-table)
2292 ("r-dplyr" ,r-dplyr)
2293 ("r-genomeinfodb" ,r-genomeinfodb)
2294 ("r-genomicalignments" ,r-genomicalignments)
2295 ("r-genomicranges" ,r-genomicranges)
2296 ("r-ggplot2" ,r-ggplot2)
2297 ("r-hexbin" ,r-hexbin)
2298 ("r-iranges" ,r-iranges)
2299 ("r-rcolorbrewer" ,r-rcolorbrewer)
2300 ("r-rmarkdown" ,r-rmarkdown)
2301 ("r-rsamtools" ,r-rsamtools)
2302 ("r-s4vectors" ,r-s4vectors)
2303 ("r-scales" ,r-scales)
2304 ("r-viridis" ,r-viridis)))
2305 (home-page "https://github.com/keleslab/ChIPexoQual")
2306 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2308 "This package provides a quality control pipeline for ChIP-exo/nexus
2310 (license license:gpl2+)))
2312 (define-public r-copynumber
2314 (name "r-copynumber")
2318 (uri (bioconductor-uri "copynumber" version))
2321 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
2322 (build-system r-build-system)
2324 `(("r-s4vectors" ,r-s4vectors)
2325 ("r-iranges" ,r-iranges)
2326 ("r-genomicranges" ,r-genomicranges)
2327 ("r-biocgenerics" ,r-biocgenerics)))
2328 (home-page "https://bioconductor.org/packages/copynumber")
2329 (synopsis "Segmentation of single- and multi-track copy number data")
2331 "This package segments single- and multi-track copy number data by a
2332 penalized least squares regression method.")
2333 (license license:artistic2.0)))
2335 (define-public r-dnacopy
2342 (uri (bioconductor-uri "DNAcopy" version))
2345 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2346 (properties `((upstream-name . "DNAcopy")))
2347 (build-system r-build-system)
2348 (native-inputs `(("gfortran" ,gfortran)))
2349 (home-page "https://bioconductor.org/packages/DNAcopy")
2350 (synopsis "DNA copy number data analysis")
2352 "This package implements the @dfn{circular binary segmentation} (CBS)
2353 algorithm to segment DNA copy number data and identify genomic regions with
2354 abnormal copy number.")
2355 (license license:gpl2+)))
2357 ;; This is a CRAN package, but it uncharacteristically depends on a
2358 ;; Bioconductor package.
2359 (define-public r-htscluster
2361 (name "r-htscluster")
2366 (uri (cran-uri "HTSCluster" version))
2369 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2370 (properties `((upstream-name . "HTSCluster")))
2371 (build-system r-build-system)
2373 `(("r-capushe" ,r-capushe)
2374 ("r-edger" ,r-edger)
2375 ("r-plotrix" ,r-plotrix)))
2376 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2377 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2379 "This package provides a Poisson mixture model is implemented to cluster
2380 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2381 estimation is performed using either the EM or CEM algorithm, and the slope
2382 heuristics are used for model selection (i.e., to choose the number of
2384 (license license:gpl3+)))
2386 (define-public r-deds
2393 (uri (bioconductor-uri "DEDS" version))
2396 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2397 (properties `((upstream-name . "DEDS")))
2398 (build-system r-build-system)
2399 (home-page "https://bioconductor.org/packages/DEDS/")
2400 (synopsis "Differential expression via distance summary for microarray data")
2402 "This library contains functions that calculate various statistics of
2403 differential expression for microarray data, including t statistics, fold
2404 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2405 also implements a new methodology called DEDS (Differential Expression via
2406 Distance Summary), which selects differentially expressed genes by integrating
2407 and summarizing a set of statistics using a weighted distance approach.")
2408 ;; Any version of the LGPL.
2409 (license license:lgpl3+)))
2411 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2413 (define-public r-nbpseq
2420 (uri (cran-uri "NBPSeq" version))
2423 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2424 (properties `((upstream-name . "NBPSeq")))
2425 (build-system r-build-system)
2427 `(("r-qvalue" ,r-qvalue)))
2428 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2429 (synopsis "Negative binomial models for RNA-Seq data")
2431 "This package provides negative binomial models for two-group comparisons
2432 and regression inferences from RNA-sequencing data.")
2433 (license license:gpl2)))
2435 (define-public r-ebseq
2442 (uri (bioconductor-uri "EBSeq" version))
2445 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2446 (properties `((upstream-name . "EBSeq")))
2447 (build-system r-build-system)
2449 `(("r-blockmodeling" ,r-blockmodeling)
2450 ("r-gplots" ,r-gplots)
2451 ("r-testthat" ,r-testthat)))
2452 (home-page "https://bioconductor.org/packages/EBSeq")
2453 (synopsis "Differential expression analysis of RNA-seq data")
2455 "This package provides tools for differential expression analysis at both
2456 gene and isoform level using RNA-seq data")
2457 (license license:artistic2.0)))
2459 (define-public r-lpsymphony
2461 (name "r-lpsymphony")
2466 (uri (bioconductor-uri "lpsymphony" version))
2469 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2470 (build-system r-build-system)
2472 `(("gfortran" ,gfortran)
2475 `(("pkg-config" ,pkg-config)))
2476 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2477 (synopsis "Symphony integer linear programming solver in R")
2479 "This package was derived from Rsymphony. The package provides an R
2480 interface to SYMPHONY, a linear programming solver written in C++. The main
2481 difference between this package and Rsymphony is that it includes the solver
2482 source code, while Rsymphony expects to find header and library files on the
2483 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2484 to install interface to SYMPHONY.")
2485 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2486 ;; lpsimphony is released under the same terms.
2487 (license license:epl1.0)))
2489 (define-public r-ihw
2496 (uri (bioconductor-uri "IHW" version))
2499 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2500 (properties `((upstream-name . "IHW")))
2501 (build-system r-build-system)
2503 `(("r-biocgenerics" ,r-biocgenerics)
2504 ("r-fdrtool" ,r-fdrtool)
2505 ("r-lpsymphony" ,r-lpsymphony)
2506 ("r-slam" ,r-slam)))
2507 (home-page "https://bioconductor.org/packages/IHW")
2508 (synopsis "Independent hypothesis weighting")
2510 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2511 procedure that increases power compared to the method of Benjamini and
2512 Hochberg by assigning data-driven weights to each hypothesis. The input to
2513 IHW is a two-column table of p-values and covariates. The covariate can be
2514 any continuous-valued or categorical variable that is thought to be
2515 informative on the statistical properties of each hypothesis test, while it is
2516 independent of the p-value under the null hypothesis.")
2517 (license license:artistic2.0)))
2519 (define-public r-icobra
2526 (uri (bioconductor-uri "iCOBRA" version))
2529 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2530 (properties `((upstream-name . "iCOBRA")))
2531 (build-system r-build-system)
2533 `(("r-dplyr" ,r-dplyr)
2535 ("r-ggplot2" ,r-ggplot2)
2536 ("r-limma" ,r-limma)
2537 ("r-reshape2" ,r-reshape2)
2539 ("r-scales" ,r-scales)
2540 ("r-shiny" ,r-shiny)
2541 ("r-shinybs" ,r-shinybs)
2542 ("r-shinydashboard" ,r-shinydashboard)
2543 ("r-upsetr" ,r-upsetr)))
2544 (home-page "https://bioconductor.org/packages/iCOBRA")
2545 (synopsis "Comparison and visualization of ranking and assignment methods")
2547 "This package provides functions for calculation and visualization of
2548 performance metrics for evaluation of ranking and binary
2549 classification (assignment) methods. It also contains a Shiny application for
2550 interactive exploration of results.")
2551 (license license:gpl2+)))
2553 (define-public r-mast
2560 (uri (bioconductor-uri "MAST" version))
2563 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2564 (properties `((upstream-name . "MAST")))
2565 (build-system r-build-system)
2567 `(("r-abind" ,r-abind)
2569 ("r-biobase" ,r-biobase)
2570 ("r-biocgenerics" ,r-biocgenerics)
2571 ("r-data-table" ,r-data-table)
2572 ("r-ggplot2" ,r-ggplot2)
2574 ("r-progress" ,r-progress)
2575 ("r-reshape2" ,r-reshape2)
2576 ("r-s4vectors" ,r-s4vectors)
2577 ("r-singlecellexperiment" ,r-singlecellexperiment)
2578 ("r-stringr" ,r-stringr)
2579 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2580 (home-page "https://github.com/RGLab/MAST/")
2581 (synopsis "Model-based analysis of single cell transcriptomics")
2583 "This package provides methods and models for handling zero-inflated
2584 single cell assay data.")
2585 (license license:gpl2+)))
2587 (define-public r-monocle
2594 (uri (bioconductor-uri "monocle" version))
2597 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2598 (build-system r-build-system)
2600 `(("r-biobase" ,r-biobase)
2601 ("r-biocgenerics" ,r-biocgenerics)
2602 ("r-biocviews" ,r-biocviews)
2603 ("r-cluster" ,r-cluster)
2604 ("r-combinat" ,r-combinat)
2605 ("r-ddrtree" ,r-ddrtree)
2606 ("r-densityclust" ,r-densityclust)
2607 ("r-dplyr" ,r-dplyr)
2608 ("r-fastica" ,r-fastica)
2609 ("r-ggplot2" ,r-ggplot2)
2610 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2611 ("r-igraph" ,r-igraph)
2612 ("r-irlba" ,r-irlba)
2613 ("r-limma" ,r-limma)
2615 ("r-matrix" ,r-matrix)
2616 ("r-matrixstats" ,r-matrixstats)
2617 ("r-pheatmap" ,r-pheatmap)
2619 ("r-proxy" ,r-proxy)
2620 ("r-qlcmatrix" ,r-qlcmatrix)
2623 ("r-reshape2" ,r-reshape2)
2624 ("r-rtsne" ,r-rtsne)
2626 ("r-stringr" ,r-stringr)
2627 ("r-tibble" ,r-tibble)
2629 ("r-viridis" ,r-viridis)))
2630 (home-page "https://bioconductor.org/packages/monocle")
2631 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2633 "Monocle performs differential expression and time-series analysis for
2634 single-cell expression experiments. It orders individual cells according to
2635 progress through a biological process, without knowing ahead of time which
2636 genes define progress through that process. Monocle also performs
2637 differential expression analysis, clustering, visualization, and other useful
2638 tasks on single cell expression data. It is designed to work with RNA-Seq and
2639 qPCR data, but could be used with other types as well.")
2640 (license license:artistic2.0)))
2642 (define-public r-monocle3
2650 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2652 (file-name (git-file-name name version))
2655 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2656 (build-system r-build-system)
2658 `(("r-biobase" ,r-biobase)
2659 ("r-biocgenerics" ,r-biocgenerics)
2660 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2661 ("r-dplyr" ,r-dplyr)
2662 ("r-ggplot2" ,r-ggplot2)
2663 ("r-ggrepel" ,r-ggrepel)
2665 ("r-htmlwidgets" ,r-htmlwidgets)
2666 ("r-igraph" ,r-igraph)
2667 ("r-irlba" ,r-irlba)
2668 ("r-limma" ,r-limma)
2669 ("r-lmtest" ,r-lmtest)
2671 ("r-matrix" ,r-matrix)
2672 ("r-matrix-utils" ,r-matrix-utils)
2673 ("r-pbapply" ,r-pbapply)
2674 ("r-pbmcapply" ,r-pbmcapply)
2675 ("r-pheatmap" ,r-pheatmap)
2676 ("r-plotly" ,r-plotly)
2678 ("r-proxy" ,r-proxy)
2680 ("r-purrr" ,r-purrr)
2683 ("r-rcppparallel" ,r-rcppparallel)
2684 ("r-reshape2" ,r-reshape2)
2685 ("r-reticulate" ,r-reticulate)
2686 ("r-rhpcblasctl" ,r-rhpcblasctl)
2687 ("r-rtsne" ,r-rtsne)
2688 ("r-shiny" ,r-shiny)
2690 ("r-spdep" ,r-spdep)
2691 ("r-speedglm" ,r-speedglm)
2692 ("r-stringr" ,r-stringr)
2693 ("r-singlecellexperiment" ,r-singlecellexperiment)
2694 ("r-tibble" ,r-tibble)
2695 ("r-tidyr" ,r-tidyr)
2697 ("r-viridis" ,r-viridis)))
2698 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2699 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2701 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2702 (license license:expat)))
2704 (define-public r-noiseq
2711 (uri (bioconductor-uri "NOISeq" version))
2714 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2715 (properties `((upstream-name . "NOISeq")))
2716 (build-system r-build-system)
2718 `(("r-biobase" ,r-biobase)
2719 ("r-matrix" ,r-matrix)))
2720 (home-page "https://bioconductor.org/packages/NOISeq")
2721 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2723 "This package provides tools to support the analysis of RNA-seq
2724 expression data or other similar kind of data. It provides exploratory plots
2725 to evaluate saturation, count distribution, expression per chromosome, type of
2726 detected features, features length, etc. It also supports the analysis of
2727 differential expression between two experimental conditions with no parametric
2729 (license license:artistic2.0)))
2731 (define-public r-scdd
2738 (uri (bioconductor-uri "scDD" version))
2741 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2742 (properties `((upstream-name . "scDD")))
2743 (build-system r-build-system)
2746 ("r-biocparallel" ,r-biocparallel)
2747 ("r-ebseq" ,r-ebseq)
2748 ("r-fields" ,r-fields)
2749 ("r-ggplot2" ,r-ggplot2)
2750 ("r-mclust" ,r-mclust)
2751 ("r-outliers" ,r-outliers)
2752 ("r-s4vectors" ,r-s4vectors)
2753 ("r-scran" ,r-scran)
2754 ("r-singlecellexperiment" ,r-singlecellexperiment)
2755 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2756 (home-page "https://github.com/kdkorthauer/scDD")
2757 (synopsis "Mixture modeling of single-cell RNA-seq data")
2759 "This package implements a method to analyze single-cell RNA-seq data
2760 utilizing flexible Dirichlet Process mixture models. Genes with differential
2761 distributions of expression are classified into several interesting patterns
2762 of differences between two conditions. The package also includes functions
2763 for simulating data with these patterns from negative binomial
2765 (license license:gpl2)))
2767 (define-public r-scone
2774 (uri (bioconductor-uri "scone" version))
2777 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2778 (build-system r-build-system)
2780 `(("r-aroma-light" ,r-aroma-light)
2781 ("r-biocparallel" ,r-biocparallel)
2783 ("r-class" ,r-class)
2784 ("r-cluster" ,r-cluster)
2785 ("r-compositions" ,r-compositions)
2786 ("r-diptest" ,r-diptest)
2787 ("r-edger" ,r-edger)
2789 ("r-gplots" ,r-gplots)
2790 ("r-hexbin" ,r-hexbin)
2791 ("r-limma" ,r-limma)
2792 ("r-matrixstats" ,r-matrixstats)
2793 ("r-mixtools" ,r-mixtools)
2794 ("r-rarpack" ,r-rarpack)
2795 ("r-rcolorbrewer" ,r-rcolorbrewer)
2796 ("r-rhdf5" ,r-rhdf5)
2797 ("r-ruvseq" ,r-ruvseq)
2798 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2799 (home-page "https://bioconductor.org/packages/scone")
2800 (synopsis "Single cell overview of normalized expression data")
2802 "SCONE is an R package for comparing and ranking the performance of
2803 different normalization schemes for single-cell RNA-seq and other
2804 high-throughput analyses.")
2805 (license license:artistic2.0)))
2807 (define-public r-geoquery
2814 (uri (bioconductor-uri "GEOquery" version))
2817 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2818 (properties `((upstream-name . "GEOquery")))
2819 (build-system r-build-system)
2821 `(("r-biobase" ,r-biobase)
2822 ("r-dplyr" ,r-dplyr)
2824 ("r-limma" ,r-limma)
2825 ("r-magrittr" ,r-magrittr)
2826 ("r-readr" ,r-readr)
2827 ("r-tidyr" ,r-tidyr)
2828 ("r-xml2" ,r-xml2)))
2829 (home-page "https://github.com/seandavi/GEOquery/")
2830 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2832 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2833 microarray data. Given the rich and varied nature of this resource, it is
2834 only natural to want to apply BioConductor tools to these data. GEOquery is
2835 the bridge between GEO and BioConductor.")
2836 (license license:gpl2)))
2838 (define-public r-illuminaio
2840 (name "r-illuminaio")
2845 (uri (bioconductor-uri "illuminaio" version))
2848 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2849 (build-system r-build-system)
2851 `(("r-base64" ,r-base64)))
2852 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2853 (synopsis "Parse Illumina microarray output files")
2855 "This package provides tools for parsing Illumina's microarray output
2856 files, including IDAT.")
2857 (license license:gpl2)))
2859 (define-public r-siggenes
2866 (uri (bioconductor-uri "siggenes" version))
2869 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2870 (build-system r-build-system)
2872 `(("r-biobase" ,r-biobase)
2873 ("r-multtest" ,r-multtest)
2874 ("r-scrime" ,r-scrime)))
2875 (home-page "https://bioconductor.org/packages/siggenes/")
2877 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2879 "This package provides tools for the identification of differentially
2880 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2881 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2882 Bayes Analyses of Microarrays} (EBAM).")
2883 (license license:lgpl2.0+)))
2885 (define-public r-bumphunter
2887 (name "r-bumphunter")
2892 (uri (bioconductor-uri "bumphunter" version))
2895 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2896 (build-system r-build-system)
2898 `(("r-annotationdbi" ,r-annotationdbi)
2899 ("r-biocgenerics" ,r-biocgenerics)
2900 ("r-dorng" ,r-dorng)
2901 ("r-foreach" ,r-foreach)
2902 ("r-genomeinfodb" ,r-genomeinfodb)
2903 ("r-genomicfeatures" ,r-genomicfeatures)
2904 ("r-genomicranges" ,r-genomicranges)
2905 ("r-iranges" ,r-iranges)
2906 ("r-iterators" ,r-iterators)
2907 ("r-limma" ,r-limma)
2908 ("r-locfit" ,r-locfit)
2909 ("r-matrixstats" ,r-matrixstats)
2910 ("r-s4vectors" ,r-s4vectors)))
2911 (home-page "https://github.com/ririzarr/bumphunter")
2912 (synopsis "Find bumps in genomic data")
2914 "This package provides tools for finding bumps in genomic data in order
2915 to identify differentially methylated regions in epigenetic epidemiology
2917 (license license:artistic2.0)))
2919 (define-public r-minfi
2926 (uri (bioconductor-uri "minfi" version))
2929 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2930 (build-system r-build-system)
2932 `(("r-beanplot" ,r-beanplot)
2933 ("r-biobase" ,r-biobase)
2934 ("r-biocgenerics" ,r-biocgenerics)
2935 ("r-biocparallel" ,r-biocparallel)
2936 ("r-biostrings" ,r-biostrings)
2937 ("r-bumphunter" ,r-bumphunter)
2938 ("r-data-table" ,r-data-table)
2939 ("r-delayedarray" ,r-delayedarray)
2940 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2941 ("r-genefilter" ,r-genefilter)
2942 ("r-genomeinfodb" ,r-genomeinfodb)
2943 ("r-genomicranges" ,r-genomicranges)
2944 ("r-geoquery" ,r-geoquery)
2945 ("r-hdf5array" ,r-hdf5array)
2946 ("r-illuminaio" ,r-illuminaio)
2947 ("r-iranges" ,r-iranges)
2948 ("r-lattice" ,r-lattice)
2949 ("r-limma" ,r-limma)
2951 ("r-mclust" ,r-mclust)
2953 ("r-nor1mix" ,r-nor1mix)
2954 ("r-preprocesscore" ,r-preprocesscore)
2955 ("r-quadprog" ,r-quadprog)
2956 ("r-rcolorbrewer" ,r-rcolorbrewer)
2957 ("r-reshape" ,r-reshape)
2958 ("r-s4vectors" ,r-s4vectors)
2959 ("r-siggenes" ,r-siggenes)
2960 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2961 (home-page "https://github.com/hansenlab/minfi")
2962 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2964 "This package provides tools to analyze and visualize Illumina Infinium
2965 methylation arrays.")
2966 (license license:artistic2.0)))
2968 (define-public r-methylumi
2970 (name "r-methylumi")
2975 (uri (bioconductor-uri "methylumi" version))
2978 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2979 (build-system r-build-system)
2981 `(("r-annotate" ,r-annotate)
2982 ("r-annotationdbi" ,r-annotationdbi)
2983 ("r-biobase" ,r-biobase)
2984 ("r-biocgenerics" ,r-biocgenerics)
2985 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2986 ("r-genefilter" ,r-genefilter)
2987 ("r-genomeinfodb" ,r-genomeinfodb)
2988 ("r-genomicranges" ,r-genomicranges)
2989 ("r-ggplot2" ,r-ggplot2)
2990 ("r-illuminaio" ,r-illuminaio)
2991 ("r-iranges" ,r-iranges)
2992 ("r-lattice" ,r-lattice)
2993 ("r-matrixstats" ,r-matrixstats)
2994 ("r-minfi" ,r-minfi)
2995 ("r-reshape2" ,r-reshape2)
2996 ("r-s4vectors" ,r-s4vectors)
2997 ("r-scales" ,r-scales)
2998 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2999 (home-page "https://bioconductor.org/packages/methylumi")
3000 (synopsis "Handle Illumina methylation data")
3002 "This package provides classes for holding and manipulating Illumina
3003 methylation data. Based on eSet, it can contain MIAME information, sample
3004 information, feature information, and multiple matrices of data. An
3005 \"intelligent\" import function, methylumiR can read the Illumina text files
3006 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3007 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3008 background correction, and quality control features for GoldenGate, Infinium,
3009 and Infinium HD arrays are also included.")
3010 (license license:gpl2)))
3012 (define-public r-lumi
3019 (uri (bioconductor-uri "lumi" version))
3022 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
3023 (build-system r-build-system)
3025 `(("r-affy" ,r-affy)
3026 ("r-annotate" ,r-annotate)
3027 ("r-annotationdbi" ,r-annotationdbi)
3028 ("r-biobase" ,r-biobase)
3030 ("r-genomicfeatures" ,r-genomicfeatures)
3031 ("r-genomicranges" ,r-genomicranges)
3032 ("r-kernsmooth" ,r-kernsmooth)
3033 ("r-lattice" ,r-lattice)
3035 ("r-methylumi" ,r-methylumi)
3037 ("r-nleqslv" ,r-nleqslv)
3038 ("r-preprocesscore" ,r-preprocesscore)
3039 ("r-rsqlite" ,r-rsqlite)))
3040 (home-page "https://bioconductor.org/packages/lumi")
3041 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3043 "The lumi package provides an integrated solution for the Illumina
3044 microarray data analysis. It includes functions of Illumina
3045 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3046 variance stabilization, normalization and gene annotation at the probe level.
3047 It also includes the functions of processing Illumina methylation microarrays,
3048 especially Illumina Infinium methylation microarrays.")
3049 (license license:lgpl2.0+)))
3051 (define-public r-linnorm
3058 (uri (bioconductor-uri "Linnorm" version))
3061 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
3062 (properties `((upstream-name . "Linnorm")))
3063 (build-system r-build-system)
3065 `(("r-amap" ,r-amap)
3066 ("r-apcluster" ,r-apcluster)
3067 ("r-ellipse" ,r-ellipse)
3068 ("r-fastcluster" ,r-fastcluster)
3070 ("r-ggdendro" ,r-ggdendro)
3071 ("r-ggplot2" ,r-ggplot2)
3072 ("r-gmodels" ,r-gmodels)
3073 ("r-igraph" ,r-igraph)
3074 ("r-limma" ,r-limma)
3076 ("r-mclust" ,r-mclust)
3078 ("r-rcpparmadillo" ,r-rcpparmadillo)
3079 ("r-rtsne" ,r-rtsne)
3080 ("r-statmod" ,r-statmod)
3081 ("r-vegan" ,r-vegan)
3083 (home-page "http://www.jjwanglab.org/Linnorm/")
3084 (synopsis "Linear model and normality based transformation method")
3086 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3087 count data or any large scale count data. It transforms such datasets for
3088 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3089 the following pipelines are implemented:
3092 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3093 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3094 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3095 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3096 @item Differential expression analysis or differential peak detection using
3097 limma (@code{Linnorm.limma})
3098 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3099 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3100 @item Stable gene selection for scRNA-seq data; for users without or who do
3101 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3102 @item Data imputation (@code{Linnorm.DataImput}).
3105 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3106 @code{RnaXSim} function is included for simulating RNA-seq data for the
3107 evaluation of DEG analysis methods.")
3108 (license license:expat)))
3110 (define-public r-ioniser
3117 (uri (bioconductor-uri "IONiseR" version))
3120 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
3121 (properties `((upstream-name . "IONiseR")))
3122 (build-system r-build-system)
3124 `(("r-biocgenerics" ,r-biocgenerics)
3125 ("r-biocparallel" ,r-biocparallel)
3126 ("r-biostrings" ,r-biostrings)
3127 ("r-bit64" ,r-bit64)
3128 ("r-dplyr" ,r-dplyr)
3129 ("r-ggplot2" ,r-ggplot2)
3130 ("r-magrittr" ,r-magrittr)
3131 ("r-rhdf5" ,r-rhdf5)
3132 ("r-shortread" ,r-shortread)
3133 ("r-stringr" ,r-stringr)
3134 ("r-tibble" ,r-tibble)
3135 ("r-tidyr" ,r-tidyr)
3136 ("r-xvector" ,r-xvector)))
3137 (home-page "https://bioconductor.org/packages/IONiseR/")
3138 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3140 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3141 MinION data. It extracts summary statistics from a set of fast5 files and can
3142 be used either before or after base calling. In addition to standard
3143 summaries of the read-types produced, it provides a number of plots for
3144 visualising metrics relative to experiment run time or spatially over the
3145 surface of a flowcell.")
3146 (license license:expat)))
3148 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3149 (define-public r-gkmsvm
3156 (uri (cran-uri "gkmSVM" version))
3159 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3160 (properties `((upstream-name . "gkmSVM")))
3161 (build-system r-build-system)
3163 `(("r-biocgenerics" ,r-biocgenerics)
3164 ("r-biostrings" ,r-biostrings)
3165 ("r-genomeinfodb" ,r-genomeinfodb)
3166 ("r-genomicranges" ,r-genomicranges)
3167 ("r-iranges" ,r-iranges)
3168 ("r-kernlab" ,r-kernlab)
3171 ("r-rtracklayer" ,r-rtracklayer)
3172 ("r-s4vectors" ,r-s4vectors)
3173 ("r-seqinr" ,r-seqinr)))
3174 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3175 (synopsis "Gapped-kmer support vector machine")
3177 "This R package provides tools for training gapped-kmer SVM classifiers
3178 for DNA and protein sequences. This package supports several sequence
3179 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3180 (license license:gpl2+)))
3182 (define-public r-triform
3189 (uri (bioconductor-uri "triform" version))
3192 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
3193 (build-system r-build-system)
3195 `(("r-biocgenerics" ,r-biocgenerics)
3196 ("r-iranges" ,r-iranges)
3197 ("r-yaml" ,r-yaml)))
3198 (home-page "https://bioconductor.org/packages/triform/")
3199 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3201 "The Triform algorithm uses model-free statistics to identify peak-like
3202 distributions of TF ChIP sequencing reads, taking advantage of an improved
3203 peak definition in combination with known profile characteristics.")
3204 (license license:gpl2)))
3206 (define-public r-varianttools
3208 (name "r-varianttools")
3213 (uri (bioconductor-uri "VariantTools" version))
3216 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
3217 (properties `((upstream-name . "VariantTools")))
3218 (build-system r-build-system)
3220 `(("r-biobase" ,r-biobase)
3221 ("r-biocgenerics" ,r-biocgenerics)
3222 ("r-biocparallel" ,r-biocparallel)
3223 ("r-biostrings" ,r-biostrings)
3224 ("r-bsgenome" ,r-bsgenome)
3225 ("r-genomeinfodb" ,r-genomeinfodb)
3226 ("r-genomicfeatures" ,r-genomicfeatures)
3227 ("r-genomicranges" ,r-genomicranges)
3228 ("r-iranges" ,r-iranges)
3229 ("r-matrix" ,r-matrix)
3230 ("r-rsamtools" ,r-rsamtools)
3231 ("r-rtracklayer" ,r-rtracklayer)
3232 ("r-s4vectors" ,r-s4vectors)
3233 ("r-variantannotation" ,r-variantannotation)))
3234 (home-page "https://bioconductor.org/packages/VariantTools/")
3235 (synopsis "Tools for exploratory analysis of variant calls")
3237 "Explore, diagnose, and compare variant calls using filters. The
3238 VariantTools package supports a workflow for loading data, calling single
3239 sample variants and tumor-specific somatic mutations or other sample-specific
3240 variant types (e.g., RNA editing). Most of the functions operate on
3241 alignments (BAM files) or datasets of called variants. The user is expected
3242 to have already aligned the reads with a separate tool, e.g., GSNAP via
3244 (license license:artistic2.0)))
3246 (define-public r-heatplus
3253 (uri (bioconductor-uri "Heatplus" version))
3256 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
3257 (properties `((upstream-name . "Heatplus")))
3258 (build-system r-build-system)
3260 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3261 (home-page "https://github.com/alexploner/Heatplus")
3262 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3264 "This package provides tools to display a rectangular heatmap (intensity
3265 plot) of a data matrix. By default, both samples (columns) and features (row)
3266 of the matrix are sorted according to a hierarchical clustering, and the
3267 corresponding dendrogram is plotted. Optionally, panels with additional
3268 information about samples and features can be added to the plot.")
3269 (license license:gpl2+)))
3271 (define-public r-gosemsim
3278 (uri (bioconductor-uri "GOSemSim" version))
3281 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
3282 (properties `((upstream-name . "GOSemSim")))
3283 (build-system r-build-system)
3285 `(("r-annotationdbi" ,r-annotationdbi)
3286 ("r-go-db" ,r-go-db)
3287 ("r-rcpp" ,r-rcpp)))
3288 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3289 (synopsis "GO-terms semantic similarity measures")
3291 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3292 quantitative ways to compute similarities between genes and gene groups, and
3293 have became important basis for many bioinformatics analysis approaches.
3294 GOSemSim is an R package for semantic similarity computation among GO terms,
3295 sets of GO terms, gene products and gene clusters.")
3296 (license license:artistic2.0)))
3298 (define-public r-anota
3305 (uri (bioconductor-uri "anota" version))
3308 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
3309 (build-system r-build-system)
3311 `(("r-multtest" ,r-multtest)
3312 ("r-qvalue" ,r-qvalue)))
3313 (home-page "https://bioconductor.org/packages/anota/")
3314 (synopsis "Analysis of translational activity")
3316 "Genome wide studies of translational control is emerging as a tool to
3317 study various biological conditions. The output from such analysis is both
3318 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3319 involved in translation (the actively translating mRNA level) for each mRNA.
3320 The standard analysis of such data strives towards identifying differential
3321 translational between two or more sample classes - i.e. differences in
3322 actively translated mRNA levels that are independent of underlying differences
3323 in cytosolic mRNA levels. This package allows for such analysis using partial
3324 variances and the random variance model. As 10s of thousands of mRNAs are
3325 analyzed in parallel the library performs a number of tests to assure that
3326 the data set is suitable for such analysis.")
3327 (license license:gpl3)))
3329 (define-public r-sigpathway
3331 (name "r-sigpathway")
3336 (uri (bioconductor-uri "sigPathway" version))
3339 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3340 (properties `((upstream-name . "sigPathway")))
3341 (build-system r-build-system)
3342 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3343 (synopsis "Pathway analysis")
3345 "This package is used to conduct pathway analysis by calculating the NT_k
3346 and NE_k statistics in a statistical framework for determining whether a
3347 specified group of genes for a pathway has a coordinated association with a
3348 phenotype of interest.")
3349 (license license:gpl2)))
3351 (define-public r-fgsea
3358 (uri (bioconductor-uri "fgsea" version))
3361 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3362 (build-system r-build-system)
3365 ("r-biocparallel" ,r-biocparallel)
3366 ("r-data-table" ,r-data-table)
3367 ("r-fastmatch" ,r-fastmatch)
3368 ("r-ggplot2" ,r-ggplot2)
3369 ("r-gridextra" ,r-gridextra)
3370 ("r-matrix" ,r-matrix)
3371 ("r-rcpp" ,r-rcpp)))
3372 (home-page "https://github.com/ctlab/fgsea/")
3373 (synopsis "Fast gene set enrichment analysis")
3375 "The package implements an algorithm for fast gene set enrichment
3376 analysis. Using the fast algorithm allows to make more permutations and get
3377 more fine grained p-values, which allows to use accurate stantard approaches
3378 to multiple hypothesis correction.")
3379 (license license:expat)))
3381 (define-public r-dose
3388 (uri (bioconductor-uri "DOSE" version))
3391 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3392 (properties `((upstream-name . "DOSE")))
3393 (build-system r-build-system)
3395 `(("r-annotationdbi" ,r-annotationdbi)
3396 ("r-biocparallel" ,r-biocparallel)
3397 ("r-do-db" ,r-do-db)
3398 ("r-fgsea" ,r-fgsea)
3399 ("r-ggplot2" ,r-ggplot2)
3400 ("r-gosemsim" ,r-gosemsim)
3401 ("r-qvalue" ,r-qvalue)
3402 ("r-reshape2" ,r-reshape2)
3403 ("r-s4vectors" ,r-s4vectors)))
3404 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3405 (synopsis "Disease ontology semantic and enrichment analysis")
3407 "This package implements five methods proposed by Resnik, Schlicker,
3408 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3409 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3410 including hypergeometric model and gene set enrichment analysis are also
3411 implemented for discovering disease associations of high-throughput biological
3413 (license license:artistic2.0)))
3415 (define-public r-enrichplot
3417 (name "r-enrichplot")
3422 (uri (bioconductor-uri "enrichplot" version))
3425 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3426 (build-system r-build-system)
3428 `(("r-annotationdbi" ,r-annotationdbi)
3429 ("r-cowplot" ,r-cowplot)
3431 ("r-europepmc" ,r-europepmc)
3432 ("r-ggplot2" ,r-ggplot2)
3433 ("r-ggplotify" ,r-ggplotify)
3434 ("r-ggraph" ,r-ggraph)
3435 ("r-ggridges" ,r-ggridges)
3436 ("r-gosemsim" ,r-gosemsim)
3437 ("r-gridextra" ,r-gridextra)
3438 ("r-igraph" ,r-igraph)
3439 ("r-purrr" ,r-purrr)
3440 ("r-rcolorbrewer" ,r-rcolorbrewer)
3441 ("r-reshape2" ,r-reshape2)
3442 ("r-upsetr" ,r-upsetr)))
3443 (home-page "https://github.com/GuangchuangYu/enrichplot")
3444 (synopsis "Visualization of functional enrichment result")
3446 "The enrichplot package implements several visualization methods for
3447 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3448 All the visualization methods are developed based on ggplot2 graphics.")
3449 (license license:artistic2.0)))
3451 (define-public r-clusterprofiler
3453 (name "r-clusterprofiler")
3458 (uri (bioconductor-uri "clusterProfiler" version))
3461 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3463 `((upstream-name . "clusterProfiler")))
3464 (build-system r-build-system)
3466 `(("r-annotationdbi" ,r-annotationdbi)
3468 ("r-enrichplot" ,r-enrichplot)
3469 ("r-ggplot2" ,r-ggplot2)
3470 ("r-go-db" ,r-go-db)
3471 ("r-gosemsim" ,r-gosemsim)
3472 ("r-magrittr" ,r-magrittr)
3474 ("r-qvalue" ,r-qvalue)
3475 ("r-rvcheck" ,r-rvcheck)
3476 ("r-tidyr" ,r-tidyr)))
3477 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3478 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3480 "This package implements methods to analyze and visualize functional
3481 profiles (GO and KEGG) of gene and gene clusters.")
3482 (license license:artistic2.0)))
3484 (define-public r-mlinterfaces
3486 (name "r-mlinterfaces")
3491 (uri (bioconductor-uri "MLInterfaces" version))
3494 "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh"))))
3495 (properties `((upstream-name . "MLInterfaces")))
3496 (build-system r-build-system)
3498 `(("r-annotate" ,r-annotate)
3499 ("r-biobase" ,r-biobase)
3500 ("r-biocgenerics" ,r-biocgenerics)
3501 ("r-cluster" ,r-cluster)
3504 ("r-gdata" ,r-gdata)
3505 ("r-genefilter" ,r-genefilter)
3506 ("r-ggvis" ,r-ggvis)
3507 ("r-hwriter" ,r-hwriter)
3509 ("r-mlbench" ,r-mlbench)
3511 ("r-rcolorbrewer" ,r-rcolorbrewer)
3513 ("r-rpart" ,r-rpart)
3514 ("r-sfsmisc" ,r-sfsmisc)
3515 ("r-shiny" ,r-shiny)
3516 ("r-threejs" ,r-threejs)))
3517 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3518 (synopsis "Interfaces to R machine learning procedures")
3520 "This package provides uniform interfaces to machine learning code for
3521 data in R and Bioconductor containers.")
3522 ;; Any version of the LGPL.
3523 (license license:lgpl2.1+)))
3525 (define-public r-annaffy
3532 (uri (bioconductor-uri "annaffy" version))
3535 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3536 (build-system r-build-system)
3539 (modify-phases %standard-phases
3540 (add-after 'unpack 'remove-reference-to-non-free-data
3542 (substitute* "DESCRIPTION"
3546 `(("r-annotationdbi" ,r-annotationdbi)
3547 ("r-biobase" ,r-biobase)
3549 ("r-go-db" ,r-go-db)))
3550 (home-page "https://bioconductor.org/packages/annaffy/")
3551 (synopsis "Annotation tools for Affymetrix biological metadata")
3553 "This package provides functions for handling data from Bioconductor
3554 Affymetrix annotation data packages. It produces compact HTML and text
3555 reports including experimental data and URL links to many online databases.
3556 It allows searching of biological metadata using various criteria.")
3557 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3558 ;; the LGPL 2.1 is included.
3559 (license license:lgpl2.1+)))
3561 (define-public r-a4core
3568 (uri (bioconductor-uri "a4Core" version))
3571 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3572 (properties `((upstream-name . "a4Core")))
3573 (build-system r-build-system)
3575 `(("r-biobase" ,r-biobase)
3576 ("r-glmnet" ,r-glmnet)))
3577 (home-page "https://bioconductor.org/packages/a4Core")
3578 (synopsis "Automated Affymetrix array analysis core package")
3580 "This is the core package for the automated analysis of Affymetrix
3582 (license license:gpl3)))
3584 (define-public r-a4classif
3586 (name "r-a4classif")
3591 (uri (bioconductor-uri "a4Classif" version))
3594 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3595 (properties `((upstream-name . "a4Classif")))
3596 (build-system r-build-system)
3598 `(("r-a4core" ,r-a4core)
3599 ("r-a4preproc" ,r-a4preproc)
3600 ("r-glmnet" ,r-glmnet)
3601 ("r-mlinterfaces" ,r-mlinterfaces)
3604 ("r-varselrf" ,r-varselrf)))
3605 (home-page "https://bioconductor.org/packages/a4Classif/")
3606 (synopsis "Automated Affymetrix array analysis classification package")
3608 "This is the classification package for the automated analysis of
3609 Affymetrix arrays.")
3610 (license license:gpl3)))
3612 (define-public r-a4preproc
3614 (name "r-a4preproc")
3619 (uri (bioconductor-uri "a4Preproc" version))
3622 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3623 (properties `((upstream-name . "a4Preproc")))
3624 (build-system r-build-system)
3626 `(("r-annotationdbi" ,r-annotationdbi)))
3627 (home-page "https://bioconductor.org/packages/a4Preproc/")
3628 (synopsis "Automated Affymetrix array analysis preprocessing package")
3630 "This is a package for the automated analysis of Affymetrix arrays. It
3631 is used for preprocessing the arrays.")
3632 (license license:gpl3)))
3634 (define-public r-a4reporting
3636 (name "r-a4reporting")
3641 (uri (bioconductor-uri "a4Reporting" version))
3644 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3645 (properties `((upstream-name . "a4Reporting")))
3646 (build-system r-build-system)
3648 `(("r-annaffy" ,r-annaffy)
3649 ("r-xtable" ,r-xtable)))
3650 (home-page "https://bioconductor.org/packages/a4Reporting/")
3651 (synopsis "Automated Affymetrix array analysis reporting package")
3653 "This is a package for the automated analysis of Affymetrix arrays. It
3654 provides reporting features.")
3655 (license license:gpl3)))
3657 (define-public r-a4base
3664 (uri (bioconductor-uri "a4Base" version))
3667 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3668 (properties `((upstream-name . "a4Base")))
3669 (build-system r-build-system)
3671 `(("r-a4core" ,r-a4core)
3672 ("r-a4preproc" ,r-a4preproc)
3673 ("r-annaffy" ,r-annaffy)
3674 ("r-annotationdbi" ,r-annotationdbi)
3675 ("r-biobase" ,r-biobase)
3676 ("r-genefilter" ,r-genefilter)
3677 ("r-glmnet" ,r-glmnet)
3678 ("r-gplots" ,r-gplots)
3679 ("r-limma" ,r-limma)
3681 ("r-multtest" ,r-multtest)))
3682 (home-page "https://bioconductor.org/packages/a4Base/")
3683 (synopsis "Automated Affymetrix array analysis base package")
3685 "This package provides basic features for the automated analysis of
3686 Affymetrix arrays.")
3687 (license license:gpl3)))
3696 (uri (bioconductor-uri "a4" version))
3699 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3700 (build-system r-build-system)
3702 `(("r-a4base" ,r-a4base)
3703 ("r-a4classif" ,r-a4classif)
3704 ("r-a4core" ,r-a4core)
3705 ("r-a4preproc" ,r-a4preproc)
3706 ("r-a4reporting" ,r-a4reporting)))
3707 (home-page "https://bioconductor.org/packages/a4/")
3708 (synopsis "Automated Affymetrix array analysis umbrella package")
3710 "This package provides a software suite for the automated analysis of
3711 Affymetrix arrays.")
3712 (license license:gpl3)))
3714 (define-public r-abseqr
3721 (uri (bioconductor-uri "abseqR" version))
3724 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3725 (properties `((upstream-name . "abseqR")))
3726 (build-system r-build-system)
3728 `(("pandoc" ,ghc-pandoc)))
3730 `(("r-biocparallel" ,r-biocparallel)
3731 ("r-biocstyle" ,r-biocstyle)
3732 ("r-circlize" ,r-circlize)
3733 ("r-flexdashboard" ,r-flexdashboard)
3734 ("r-ggcorrplot" ,r-ggcorrplot)
3735 ("r-ggdendro" ,r-ggdendro)
3736 ("r-ggplot2" ,r-ggplot2)
3737 ("r-gridextra" ,r-gridextra)
3738 ("r-knitr" ,r-knitr)
3739 ("r-plotly" ,r-plotly)
3742 ("r-rcolorbrewer" ,r-rcolorbrewer)
3743 ("r-reshape2" ,r-reshape2)
3744 ("r-rmarkdown" ,r-rmarkdown)
3745 ("r-stringr" ,r-stringr)
3746 ("r-vegan" ,r-vegan)
3747 ("r-venndiagram" ,r-venndiagram)))
3748 (home-page "https://github.com/malhamdoosh/abseqR")
3749 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3751 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3752 sequencing datasets generated from antibody libraries and abseqR is one of its
3753 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3754 capabilities and allows them to generate interactive HTML reports for the
3755 convenience of viewing and sharing with other researchers. Additionally,
3756 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3757 further downstream analysis on its output.")
3758 (license license:gpl3)))
3760 (define-public r-bacon
3767 (uri (bioconductor-uri "bacon" version))
3770 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3771 (build-system r-build-system)
3773 `(("r-biocparallel" ,r-biocparallel)
3774 ("r-ellipse" ,r-ellipse)
3775 ("r-ggplot2" ,r-ggplot2)))
3776 (home-page "https://bioconductor.org/packages/bacon/")
3777 (synopsis "Controlling bias and inflation in association studies")
3779 "Bacon can be used to remove inflation and bias often observed in
3780 epigenome- and transcriptome-wide association studies. To this end bacon
3781 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3782 fitting a three-component normal mixture on z-scores.")
3783 (license license:gpl2+)))
3785 (define-public r-rgadem
3792 (uri (bioconductor-uri "rGADEM" version))
3795 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3796 (properties `((upstream-name . "rGADEM")))
3797 (build-system r-build-system)
3799 `(("r-biostrings" ,r-biostrings)
3800 ("r-bsgenome" ,r-bsgenome)
3801 ("r-iranges" ,r-iranges)
3802 ("r-seqlogo" ,r-seqlogo)))
3803 (home-page "https://bioconductor.org/packages/rGADEM/")
3804 (synopsis "De novo sequence motif discovery")
3806 "rGADEM is an efficient de novo motif discovery tool for large-scale
3807 genomic sequence data.")
3808 (license license:artistic2.0)))
3810 (define-public r-motiv
3817 (uri (bioconductor-uri "MotIV" version))
3820 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3821 (properties `((upstream-name . "MotIV")))
3822 (build-system r-build-system)
3826 `(("r-biocgenerics" ,r-biocgenerics)
3827 ("r-biostrings" ,r-biostrings)
3828 ("r-iranges" ,r-iranges)
3829 ("r-lattice" ,r-lattice)
3830 ("r-rgadem" ,r-rgadem)
3831 ("r-s4vectors" ,r-s4vectors)))
3832 (home-page "https://bioconductor.org/packages/MotIV/")
3833 (synopsis "Motif identification and validation")
3835 "This package is used for the identification and validation of sequence
3836 motifs. It makes use of STAMP for comparing a set of motifs to a given
3837 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3838 distributions, modules and filter motifs.")
3839 (license license:gpl2)))
3841 (define-public r-motifstack
3843 (name "r-motifstack")
3848 (uri (bioconductor-uri "motifStack" version))
3851 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3852 (properties `((upstream-name . "motifStack")))
3853 (build-system r-build-system)
3855 `(("r-ade4" ,r-ade4)
3856 ("r-biostrings" ,r-biostrings)
3857 ("r-grimport2" ,r-grimport2)
3858 ("r-htmlwidgets" ,r-htmlwidgets)
3859 ("r-motiv" ,r-motiv)
3860 ("r-scales" ,r-scales)
3862 (home-page "https://bioconductor.org/packages/motifStack/")
3863 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3865 "The motifStack package is designed for graphic representation of
3866 multiple motifs with different similarity scores. It works with both DNA/RNA
3867 sequence motifs and amino acid sequence motifs. In addition, it provides the
3868 flexibility for users to customize the graphic parameters such as the font
3869 type and symbol colors.")
3870 (license license:gpl2+)))
3872 (define-public r-genomicscores
3874 (name "r-genomicscores")
3879 (uri (bioconductor-uri "GenomicScores" version))
3882 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3883 (properties `((upstream-name . "GenomicScores")))
3884 (build-system r-build-system)
3886 `(("r-annotationhub" ,r-annotationhub)
3887 ("r-biobase" ,r-biobase)
3888 ("r-biocgenerics" ,r-biocgenerics)
3889 ("r-biostrings" ,r-biostrings)
3890 ("r-bsgenome" ,r-bsgenome)
3891 ("r-genomeinfodb" ,r-genomeinfodb)
3892 ("r-genomicranges" ,r-genomicranges)
3893 ("r-iranges" ,r-iranges)
3894 ("r-s4vectors" ,r-s4vectors)
3896 (home-page "https://github.com/rcastelo/GenomicScores/")
3897 (synopsis "Work with genome-wide position-specific scores")
3899 "This package provides infrastructure to store and access genome-wide
3900 position-specific scores within R and Bioconductor.")
3901 (license license:artistic2.0)))
3903 (define-public r-atacseqqc
3905 (name "r-atacseqqc")
3910 (uri (bioconductor-uri "ATACseqQC" version))
3913 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3914 (properties `((upstream-name . "ATACseqQC")))
3915 (build-system r-build-system)
3917 `(("r-biocgenerics" ,r-biocgenerics)
3918 ("r-biostrings" ,r-biostrings)
3919 ("r-bsgenome" ,r-bsgenome)
3920 ("r-chippeakanno" ,r-chippeakanno)
3921 ("r-edger" ,r-edger)
3922 ("r-genomeinfodb" ,r-genomeinfodb)
3923 ("r-genomicalignments" ,r-genomicalignments)
3924 ("r-genomicranges" ,r-genomicranges)
3925 ("r-genomicscores" ,r-genomicscores)
3926 ("r-iranges" ,r-iranges)
3927 ("r-kernsmooth" ,r-kernsmooth)
3928 ("r-limma" ,r-limma)
3929 ("r-motifstack" ,r-motifstack)
3930 ("r-preseqr" ,r-preseqr)
3931 ("r-randomforest" ,r-randomforest)
3932 ("r-rsamtools" ,r-rsamtools)
3933 ("r-rtracklayer" ,r-rtracklayer)
3934 ("r-s4vectors" ,r-s4vectors)))
3935 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3936 (synopsis "ATAC-seq quality control")
3938 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3939 sequencing, is a rapid and sensitive method for chromatin accessibility
3940 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3941 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3942 assess whether their ATAC-seq experiment is successful. It includes
3943 diagnostic plots of fragment size distribution, proportion of mitochondria
3944 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3946 (license license:gpl2+)))
3948 (define-public r-gofuncr
3955 (uri (bioconductor-uri "GOfuncR" version))
3958 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3959 (properties `((upstream-name . "GOfuncR")))
3960 (build-system r-build-system)
3962 `(("r-annotationdbi" ,r-annotationdbi)
3963 ("r-genomicranges" ,r-genomicranges)
3964 ("r-gtools" ,r-gtools)
3965 ("r-iranges" ,r-iranges)
3966 ("r-mapplots" ,r-mapplots)
3968 ("r-vioplot" ,r-vioplot)))
3969 (home-page "https://bioconductor.org/packages/GOfuncR/")
3970 (synopsis "Gene ontology enrichment using FUNC")
3972 "GOfuncR performs a gene ontology enrichment analysis based on the
3973 ontology enrichment software FUNC. GO-annotations are obtained from
3974 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3975 included in the package and updated regularly. GOfuncR provides the standard
3976 candidate vs background enrichment analysis using the hypergeometric test, as
3977 well as three additional tests:
3980 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3981 @item a binomial test that is used when genes are associated with two counts,
3983 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3984 associated with four counts.
3987 To correct for multiple testing and interdependency of the tests, family-wise
3988 error rates are computed based on random permutations of the gene-associated
3989 variables. GOfuncR also provides tools for exploring the ontology graph and
3990 the annotations, and options to take gene-length or spatial clustering of
3991 genes into account. It is also possible to provide custom gene coordinates,
3992 annotations and ontologies.")
3993 (license license:gpl2+)))
3995 (define-public r-abaenrichment
3997 (name "r-abaenrichment")
4002 (uri (bioconductor-uri "ABAEnrichment" version))
4005 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
4006 (properties `((upstream-name . "ABAEnrichment")))
4007 (build-system r-build-system)
4009 `(("r-abadata" ,r-abadata)
4010 ("r-data-table" ,r-data-table)
4011 ("r-gofuncr" ,r-gofuncr)
4012 ("r-gplots" ,r-gplots)
4013 ("r-gtools" ,r-gtools)
4014 ("r-rcpp" ,r-rcpp)))
4015 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4016 (synopsis "Gene expression enrichment in human brain regions")
4018 "The package ABAEnrichment is designed to test for enrichment of user
4019 defined candidate genes in the set of expressed genes in different human brain
4020 regions. The core function @code{aba_enrich} integrates the expression of the
4021 candidate gene set (averaged across donors) and the structural information of
4022 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4023 (license license:gpl2+)))
4025 (define-public r-annotationfuncs
4027 (name "r-annotationfuncs")
4032 (uri (bioconductor-uri "AnnotationFuncs" version))
4035 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
4037 `((upstream-name . "AnnotationFuncs")))
4038 (build-system r-build-system)
4040 `(("r-annotationdbi" ,r-annotationdbi)
4042 (home-page "https://www.iysik.com/r/annotationfuncs")
4043 (synopsis "Annotation translation functions")
4045 "This package provides functions for handling translating between
4046 different identifieres using the Biocore Data Team data-packages (e.g.
4047 @code{org.Bt.eg.db}).")
4048 (license license:gpl2)))
4050 (define-public r-annotationtools
4052 (name "r-annotationtools")
4057 (uri (bioconductor-uri "annotationTools" version))
4060 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
4062 `((upstream-name . "annotationTools")))
4063 (build-system r-build-system)
4064 (propagated-inputs `(("r-biobase" ,r-biobase)))
4065 (home-page "https://bioconductor.org/packages/annotationTools/")
4066 (synopsis "Annotate microarrays and perform gene expression analyses")
4068 "This package provides functions to annotate microarrays, find orthologs,
4069 and integrate heterogeneous gene expression profiles using annotation and
4070 other molecular biology information available as flat file database (plain
4072 ;; Any version of the GPL.
4073 (license (list license:gpl2+))))
4075 (define-public r-allelicimbalance
4077 (name "r-allelicimbalance")
4082 (uri (bioconductor-uri "AllelicImbalance" version))
4085 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
4087 `((upstream-name . "AllelicImbalance")))
4088 (build-system r-build-system)
4090 `(("r-annotationdbi" ,r-annotationdbi)
4091 ("r-biocgenerics" ,r-biocgenerics)
4092 ("r-biostrings" ,r-biostrings)
4093 ("r-bsgenome" ,r-bsgenome)
4094 ("r-genomeinfodb" ,r-genomeinfodb)
4095 ("r-genomicalignments" ,r-genomicalignments)
4096 ("r-genomicfeatures" ,r-genomicfeatures)
4097 ("r-genomicranges" ,r-genomicranges)
4098 ("r-gridextra" ,r-gridextra)
4100 ("r-iranges" ,r-iranges)
4101 ("r-lattice" ,r-lattice)
4102 ("r-latticeextra" ,r-latticeextra)
4104 ("r-rsamtools" ,r-rsamtools)
4105 ("r-s4vectors" ,r-s4vectors)
4106 ("r-seqinr" ,r-seqinr)
4107 ("r-summarizedexperiment" ,r-summarizedexperiment)
4108 ("r-variantannotation" ,r-variantannotation)))
4109 (home-page "https://github.com/pappewaio/AllelicImbalance")
4110 (synopsis "Investigate allele-specific expression")
4112 "This package provides a framework for allele-specific expression
4113 investigation using RNA-seq data.")
4114 (license license:gpl3)))
4116 (define-public r-aucell
4123 (uri (bioconductor-uri "AUCell" version))
4126 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
4127 (properties `((upstream-name . "AUCell")))
4128 (build-system r-build-system)
4130 `(("r-data-table" ,r-data-table)
4131 ("r-gseabase" ,r-gseabase)
4132 ("r-mixtools" ,r-mixtools)
4133 ("r-r-utils" ,r-r-utils)
4134 ("r-shiny" ,r-shiny)
4135 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4136 (home-page "https://bioconductor.org/packages/AUCell/")
4137 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4139 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4140 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4141 Under the Curve} (AUC) to calculate whether a critical subset of the input
4142 gene set is enriched within the expressed genes for each cell. The
4143 distribution of AUC scores across all the cells allows exploring the relative
4144 expression of the signature. Since the scoring method is ranking-based,
4145 AUCell is independent of the gene expression units and the normalization
4146 procedure. In addition, since the cells are evaluated individually, it can
4147 easily be applied to bigger datasets, subsetting the expression matrix if
4149 (license license:gpl3)))
4151 (define-public r-ebimage
4158 (uri (bioconductor-uri "EBImage" version))
4161 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
4162 (properties `((upstream-name . "EBImage")))
4163 (build-system r-build-system)
4165 `(("r-abind" ,r-abind)
4166 ("r-biocgenerics" ,r-biocgenerics)
4167 ("r-fftwtools" ,r-fftwtools)
4168 ("r-htmltools" ,r-htmltools)
4169 ("r-htmlwidgets" ,r-htmlwidgets)
4171 ("r-locfit" ,r-locfit)
4173 ("r-rcurl" ,r-rcurl)
4174 ("r-tiff" ,r-tiff)))
4176 `(("r-knitr" ,r-knitr))) ; for vignettes
4177 (home-page "https://github.com/aoles/EBImage")
4178 (synopsis "Image processing and analysis toolbox for R")
4180 "EBImage provides general purpose functionality for image processing and
4181 analysis. In the context of (high-throughput) microscopy-based cellular
4182 assays, EBImage offers tools to segment cells and extract quantitative
4183 cellular descriptors. This allows the automation of such tasks using the R
4184 programming language and facilitates the use of other tools in the R
4185 environment for signal processing, statistical modeling, machine learning and
4186 visualization with image data.")
4187 ;; Any version of the LGPL.
4188 (license license:lgpl2.1+)))
4190 (define-public r-yamss
4197 (uri (bioconductor-uri "yamss" version))
4200 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
4201 (build-system r-build-system)
4203 `(("r-biocgenerics" ,r-biocgenerics)
4204 ("r-data-table" ,r-data-table)
4205 ("r-ebimage" ,r-ebimage)
4206 ("r-iranges" ,r-iranges)
4207 ("r-limma" ,r-limma)
4208 ("r-matrix" ,r-matrix)
4210 ("r-s4vectors" ,r-s4vectors)
4211 ("r-summarizedexperiment"
4212 ,r-summarizedexperiment)))
4213 (home-page "https://github.com/hansenlab/yamss")
4214 (synopsis "Tools for high-throughput metabolomics")
4216 "This package provides tools to analyze and visualize high-throughput
4217 metabolomics data acquired using chromatography-mass spectrometry. These tools
4218 preprocess data in a way that enables reliable and powerful differential
4220 (license license:artistic2.0)))
4222 (define-public r-gtrellis
4229 (uri (bioconductor-uri "gtrellis" version))
4232 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
4233 (build-system r-build-system)
4235 `(("r-circlize" ,r-circlize)
4236 ("r-genomicranges" ,r-genomicranges)
4237 ("r-getoptlong" ,r-getoptlong)
4238 ("r-iranges" ,r-iranges)))
4239 (home-page "https://github.com/jokergoo/gtrellis")
4240 (synopsis "Genome level Trellis layout")
4242 "Genome level Trellis graph visualizes genomic data conditioned by
4243 genomic categories (e.g. chromosomes). For each genomic category, multiple
4244 dimensional data which are represented as tracks describe different features
4245 from different aspects. This package provides high flexibility to arrange
4246 genomic categories and to add self-defined graphics in the plot.")
4247 (license license:expat)))
4249 (define-public r-somaticsignatures
4251 (name "r-somaticsignatures")
4256 (uri (bioconductor-uri "SomaticSignatures" version))
4259 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
4261 `((upstream-name . "SomaticSignatures")))
4262 (build-system r-build-system)
4264 `(("r-biobase" ,r-biobase)
4265 ("r-biostrings" ,r-biostrings)
4266 ("r-genomeinfodb" ,r-genomeinfodb)
4267 ("r-genomicranges" ,r-genomicranges)
4268 ("r-ggbio" ,r-ggbio)
4269 ("r-ggplot2" ,r-ggplot2)
4270 ("r-iranges" ,r-iranges)
4272 ("r-pcamethods" ,r-pcamethods)
4273 ("r-proxy" ,r-proxy)
4274 ("r-reshape2" ,r-reshape2)
4275 ("r-s4vectors" ,r-s4vectors)
4276 ("r-variantannotation" ,r-variantannotation)))
4277 (home-page "https://github.com/juliangehring/SomaticSignatures")
4278 (synopsis "Somatic signatures")
4280 "This package identifies mutational signatures of @dfn{single nucleotide
4281 variants} (SNVs). It provides a infrastructure related to the methodology
4282 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4283 decomposition algorithms.")
4284 (license license:expat)))
4286 (define-public r-yapsa
4293 (uri (bioconductor-uri "YAPSA" version))
4296 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
4297 (properties `((upstream-name . "YAPSA")))
4298 (build-system r-build-system)
4300 `(("r-circlize" ,r-circlize)
4301 ("r-complexheatmap" ,r-complexheatmap)
4302 ("r-corrplot" ,r-corrplot)
4303 ("r-dendextend" ,r-dendextend)
4304 ("r-genomeinfodb" ,r-genomeinfodb)
4305 ("r-genomicranges" ,r-genomicranges)
4306 ("r-getoptlong" ,r-getoptlong)
4307 ("r-ggplot2" ,r-ggplot2)
4308 ("r-gridextra" ,r-gridextra)
4309 ("r-gtrellis" ,r-gtrellis)
4310 ("r-keggrest" ,r-keggrest)
4312 ("r-pmcmr" ,r-pmcmr)
4313 ("r-reshape2" ,r-reshape2)
4314 ("r-somaticsignatures" ,r-somaticsignatures)
4315 ("r-variantannotation" ,r-variantannotation)))
4316 (home-page "https://bioconductor.org/packages/YAPSA/")
4317 (synopsis "Yet another package for signature analysis")
4319 "This package provides functions and routines useful in the analysis of
4320 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4321 functions to perform a signature analysis with known signatures and a
4322 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4324 (license license:gpl3)))
4326 (define-public r-gcrma
4333 (uri (bioconductor-uri "gcrma" version))
4336 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4337 (build-system r-build-system)
4339 `(("r-affy" ,r-affy)
4340 ("r-affyio" ,r-affyio)
4341 ("r-biobase" ,r-biobase)
4342 ("r-biocmanager" ,r-biocmanager)
4343 ("r-biostrings" ,r-biostrings)
4344 ("r-xvector" ,r-xvector)))
4345 (home-page "https://bioconductor.org/packages/gcrma/")
4346 (synopsis "Background adjustment using sequence information")
4348 "Gcrma adjusts for background intensities in Affymetrix array data which
4349 include optical noise and @dfn{non-specific binding} (NSB). The main function
4350 @code{gcrma} converts background adjusted probe intensities to expression
4351 measures using the same normalization and summarization methods as a
4352 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4353 to estimate probe affinity to NSB. The sequence information is summarized in
4354 a more complex way than the simple GC content. Instead, the base types (A, T,
4355 G or C) at each position along the probe determine the affinity of each probe.
4356 The parameters of the position-specific base contributions to the probe
4357 affinity is estimated in an NSB experiment in which only NSB but no
4358 gene-specific bidning is expected.")
4359 ;; Any version of the LGPL
4360 (license license:lgpl2.1+)))
4362 (define-public r-simpleaffy
4364 (name "r-simpleaffy")
4369 (uri (bioconductor-uri "simpleaffy" version))
4372 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4373 (build-system r-build-system)
4375 `(("r-affy" ,r-affy)
4376 ("r-biobase" ,r-biobase)
4377 ("r-biocgenerics" ,r-biocgenerics)
4378 ("r-gcrma" ,r-gcrma)
4379 ("r-genefilter" ,r-genefilter)))
4380 (home-page "https://bioconductor.org/packages/simpleaffy/")
4381 (synopsis "Very simple high level analysis of Affymetrix data")
4383 "This package provides high level functions for reading Affy @file{.CEL}
4384 files, phenotypic data, and then computing simple things with it, such as
4385 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4386 library. It also has some basic scatter plot functions and mechanisms for
4387 generating high resolution journal figures.")
4388 (license license:gpl2+)))
4390 (define-public r-yaqcaffy
4397 (uri (bioconductor-uri "yaqcaffy" version))
4400 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4401 (build-system r-build-system)
4403 `(("r-simpleaffy" ,r-simpleaffy)))
4404 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4405 (synopsis "Affymetrix quality control and reproducibility analysis")
4407 "This is a package that can be used for quality control of Affymetrix
4408 GeneChip expression data and reproducibility analysis of human whole genome
4409 chips with the MAQC reference datasets.")
4410 (license license:artistic2.0)))
4412 (define-public r-quantro
4419 (uri (bioconductor-uri "quantro" version))
4422 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4423 (build-system r-build-system)
4425 `(("r-biobase" ,r-biobase)
4426 ("r-doparallel" ,r-doparallel)
4427 ("r-foreach" ,r-foreach)
4428 ("r-ggplot2" ,r-ggplot2)
4429 ("r-iterators" ,r-iterators)
4430 ("r-minfi" ,r-minfi)
4431 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4432 (home-page "https://bioconductor.org/packages/quantro/")
4433 (synopsis "Test for when to use quantile normalization")
4435 "This package provides a data-driven test for the assumptions of quantile
4436 normalization using raw data such as objects that inherit eSets (e.g.
4437 ExpressionSet, MethylSet). Group level information about each sample (such as
4438 Tumor / Normal status) must also be provided because the test assesses if
4439 there are global differences in the distributions between the user-defined
4441 (license license:gpl3+)))
4443 (define-public r-yarn
4450 (uri (bioconductor-uri "yarn" version))
4453 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4454 (build-system r-build-system)
4456 `(("r-biobase" ,r-biobase)
4457 ("r-biomart" ,r-biomart)
4458 ("r-downloader" ,r-downloader)
4459 ("r-edger" ,r-edger)
4460 ("r-gplots" ,r-gplots)
4461 ("r-limma" ,r-limma)
4462 ("r-matrixstats" ,r-matrixstats)
4463 ("r-preprocesscore" ,r-preprocesscore)
4464 ("r-quantro" ,r-quantro)
4465 ("r-rcolorbrewer" ,r-rcolorbrewer)
4466 ("r-readr" ,r-readr)))
4467 (home-page "https://bioconductor.org/packages/yarn/")
4468 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4470 "Expedite large RNA-Seq analyses using a combination of previously
4471 developed tools. YARN is meant to make it easier for the user in performing
4472 basic mis-annotation quality control, filtering, and condition-aware
4473 normalization. YARN leverages many Bioconductor tools and statistical
4474 techniques to account for the large heterogeneity and sparsity found in very
4475 large RNA-seq experiments.")
4476 (license license:artistic2.0)))
4478 (define-public r-roar
4485 (uri (bioconductor-uri "roar" version))
4488 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4489 (build-system r-build-system)
4491 `(("r-biocgenerics" ,r-biocgenerics)
4492 ("r-genomeinfodb" ,r-genomeinfodb)
4493 ("r-genomicalignments" ,r-genomicalignments)
4494 ("r-genomicranges" ,r-genomicranges)
4495 ("r-iranges" ,r-iranges)
4496 ("r-rtracklayer" ,r-rtracklayer)
4497 ("r-s4vectors" ,r-s4vectors)
4498 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4499 (home-page "https://github.com/vodkatad/roar/")
4500 (synopsis "Identify differential APA usage from RNA-seq alignments")
4502 "This package provides tools for identifying preferential usage of APA
4503 sites, comparing two biological conditions, starting from known alternative
4504 sites and alignments obtained from standard RNA-seq experiments.")
4505 (license license:gpl3)))
4507 (define-public r-xbseq
4514 (uri (bioconductor-uri "XBSeq" version))
4517 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4518 (properties `((upstream-name . "XBSeq")))
4519 (build-system r-build-system)
4521 `(("r-biobase" ,r-biobase)
4522 ("r-deseq2" ,r-deseq2)
4523 ("r-dplyr" ,r-dplyr)
4524 ("r-ggplot2" ,r-ggplot2)
4525 ("r-locfit" ,r-locfit)
4526 ("r-magrittr" ,r-magrittr)
4527 ("r-matrixstats" ,r-matrixstats)
4528 ("r-pracma" ,r-pracma)
4529 ("r-roar" ,r-roar)))
4530 (home-page "https://github.com/Liuy12/XBSeq")
4531 (synopsis "Test for differential expression for RNA-seq data")
4533 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4534 expression} (DE), where a statistical model was established based on the
4535 assumption that observed signals are the convolution of true expression
4536 signals and sequencing noises. The mapped reads in non-exonic regions are
4537 considered as sequencing noises, which follows a Poisson distribution. Given
4538 measurable observed signal and background noise from RNA-seq data, true
4539 expression signals, assuming governed by the negative binomial distribution,
4540 can be delineated and thus the accurate detection of differential expressed
4542 (license license:gpl3+)))
4544 (define-public r-massspecwavelet
4546 (name "r-massspecwavelet")
4551 (uri (bioconductor-uri "MassSpecWavelet" version))
4554 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4556 `((upstream-name . "MassSpecWavelet")))
4557 (build-system r-build-system)
4559 `(("r-waveslim" ,r-waveslim)))
4560 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4561 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4563 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4564 data mainly through the use of wavelet transforms. It supports peak detection
4565 based on @dfn{Continuous Wavelet Transform} (CWT).")
4566 (license license:lgpl2.0+)))
4568 (define-public r-xcms
4575 (uri (bioconductor-uri "xcms" version))
4578 "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v"))))
4579 (build-system r-build-system)
4581 `(("r-biobase" ,r-biobase)
4582 ("r-biocgenerics" ,r-biocgenerics)
4583 ("r-biocparallel" ,r-biocparallel)
4584 ("r-lattice" ,r-lattice)
4585 ("r-massspecwavelet" ,r-massspecwavelet)
4586 ("r-msnbase" ,r-msnbase)
4587 ("r-multtest" ,r-multtest)
4590 ("r-protgenerics" ,r-protgenerics)
4592 ("r-rcolorbrewer" ,r-rcolorbrewer)
4593 ("r-robustbase" ,r-robustbase)
4594 ("r-s4vectors" ,r-s4vectors)))
4595 (home-page "https://bioconductor.org/packages/xcms/")
4596 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4598 "This package provides a framework for processing and visualization of
4599 chromatographically separated and single-spectra mass spectral data. It
4600 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4601 data for high-throughput, untargeted analyte profiling.")
4602 (license license:gpl2+)))
4604 (define-public r-wrench
4611 (uri (bioconductor-uri "Wrench" version))
4614 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4615 (properties `((upstream-name . "Wrench")))
4616 (build-system r-build-system)
4618 `(("r-limma" ,r-limma)
4619 ("r-locfit" ,r-locfit)
4620 ("r-matrixstats" ,r-matrixstats)))
4621 (home-page "https://github.com/HCBravoLab/Wrench")
4622 (synopsis "Wrench normalization for sparse count data")
4624 "Wrench is a package for normalization sparse genomic count data, like
4625 that arising from 16s metagenomic surveys.")
4626 (license license:artistic2.0)))
4628 (define-public r-wiggleplotr
4630 (name "r-wiggleplotr")
4635 (uri (bioconductor-uri "wiggleplotr" version))
4638 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4639 (build-system r-build-system)
4641 `(("r-assertthat" ,r-assertthat)
4642 ("r-cowplot" ,r-cowplot)
4643 ("r-dplyr" ,r-dplyr)
4644 ("r-genomeinfodb" ,r-genomeinfodb)
4645 ("r-genomicranges" ,r-genomicranges)
4646 ("r-ggplot2" ,r-ggplot2)
4647 ("r-iranges" ,r-iranges)
4648 ("r-purrr" ,r-purrr)
4649 ("r-rtracklayer" ,r-rtracklayer)
4650 ("r-s4vectors" ,r-s4vectors)))
4651 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4652 (synopsis "Make read coverage plots from BigWig files")
4654 "This package provides tools to visualize read coverage from sequencing
4655 experiments together with genomic annotations (genes, transcripts, peaks).
4656 Introns of long transcripts can be rescaled to a fixed length for better
4657 visualization of exonic read coverage.")
4658 (license license:asl2.0)))
4660 (define-public r-widgettools
4662 (name "r-widgettools")
4667 (uri (bioconductor-uri "widgetTools" version))
4670 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4671 (properties `((upstream-name . "widgetTools")))
4672 (build-system r-build-system)
4673 (home-page "https://bioconductor.org/packages/widgetTools/")
4674 (synopsis "Tools for creating interactive tcltk widgets")
4676 "This package contains tools to support the construction of tcltk
4678 ;; Any version of the LGPL.
4679 (license license:lgpl3+)))
4681 (define-public r-webbioc
4688 (uri (bioconductor-uri "webbioc" version))
4691 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4692 (build-system r-build-system)
4694 `(("netpbm" ,netpbm)
4697 `(("r-affy" ,r-affy)
4698 ("r-annaffy" ,r-annaffy)
4699 ("r-biobase" ,r-biobase)
4700 ("r-biocmanager" ,r-biocmanager)
4701 ("r-gcrma" ,r-gcrma)
4702 ("r-multtest" ,r-multtest)
4703 ("r-qvalue" ,r-qvalue)
4705 (home-page "https://www.bioconductor.org/")
4706 (synopsis "Bioconductor web interface")
4708 "This package provides an integrated web interface for doing microarray
4709 analysis using several of the Bioconductor packages. It is intended to be
4710 deployed as a centralized bioinformatics resource for use by many users.
4711 Currently only Affymetrix oligonucleotide analysis is supported.")
4712 (license license:gpl2+)))
4714 (define-public r-zfpkm
4721 (uri (bioconductor-uri "zFPKM" version))
4724 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4725 (properties `((upstream-name . "zFPKM")))
4726 (build-system r-build-system)
4728 `(("r-checkmate" ,r-checkmate)
4729 ("r-dplyr" ,r-dplyr)
4730 ("r-ggplot2" ,r-ggplot2)
4731 ("r-summarizedexperiment" ,r-summarizedexperiment)
4732 ("r-tidyr" ,r-tidyr)))
4733 (home-page "https://github.com/ronammar/zFPKM/")
4734 (synopsis "Functions to facilitate zFPKM transformations")
4736 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4737 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4739 (license license:gpl3)))
4741 (define-public r-rbowtie2
4748 (uri (bioconductor-uri "Rbowtie2" version))
4751 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4752 (properties `((upstream-name . "Rbowtie2")))
4753 (build-system r-build-system)
4756 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4757 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4759 "This package provides an R wrapper of the popular @code{bowtie2}
4760 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4761 rapid adapter trimming, identification, and read merging.")
4762 (license license:gpl3+)))
4764 (define-public r-progeny
4771 (uri (bioconductor-uri "progeny" version))
4774 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4775 (build-system r-build-system)
4776 (propagated-inputs `(("r-biobase" ,r-biobase)))
4777 (home-page "https://github.com/saezlab/progeny")
4778 (synopsis "Pathway responsive gene activity inference")
4780 "This package provides a function to infer pathway activity from gene
4781 expression. It contains the linear model inferred in the publication
4782 \"Perturbation-response genes reveal signaling footprints in cancer gene
4784 (license license:asl2.0)))
4786 (define-public r-arrmnormalization
4788 (name "r-arrmnormalization")
4793 (uri (bioconductor-uri "ARRmNormalization" version))
4796 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4798 `((upstream-name . "ARRmNormalization")))
4799 (build-system r-build-system)
4800 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4801 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4802 (synopsis "Adaptive robust regression normalization for methylation data")
4804 "This is a package to perform the @dfn{Adaptive Robust Regression
4805 method} (ARRm) for the normalization of methylation data from the Illumina
4806 Infinium HumanMethylation 450k assay.")
4807 (license license:artistic2.0)))
4809 (define-public r-biocfilecache
4811 (name "r-biocfilecache")
4816 (uri (bioconductor-uri "BiocFileCache" version))
4819 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4820 (properties `((upstream-name . "BiocFileCache")))
4821 (build-system r-build-system)
4823 `(("r-curl" ,r-curl)
4825 ("r-dbplyr" ,r-dbplyr)
4826 ("r-dplyr" ,r-dplyr)
4828 ("r-rappdirs" ,r-rappdirs)
4829 ("r-rsqlite" ,r-rsqlite)))
4830 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4831 (synopsis "Manage files across sessions")
4833 "This package creates a persistent on-disk cache of files that the user
4834 can add, update, and retrieve. It is useful for managing resources (such as
4835 custom Txdb objects) that are costly or difficult to create, web resources,
4836 and data files used across sessions.")
4837 (license license:artistic2.0)))
4839 (define-public r-iclusterplus
4841 (name "r-iclusterplus")
4846 (uri (bioconductor-uri "iClusterPlus" version))
4849 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4850 (properties `((upstream-name . "iClusterPlus")))
4851 (build-system r-build-system)
4852 (native-inputs `(("gfortran" ,gfortran)))
4853 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4854 (synopsis "Integrative clustering of multi-type genomic data")
4856 "iClusterPlus is developed for integrative clustering analysis of
4857 multi-type genomic data and is an enhanced version of iCluster proposed and
4858 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4859 from the experiments where biological samples (e.g. tumor samples) are
4860 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4861 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4862 on. In the iClusterPlus model, binary observations such as somatic mutation
4863 are modeled as Binomial processes; categorical observations such as copy
4864 number states are realizations of Multinomial random variables; counts are
4865 modeled as Poisson random processes; and continuous measures are modeled by
4866 Gaussian distributions.")
4867 (license license:gpl2+)))
4869 (define-public r-rbowtie
4876 (uri (bioconductor-uri "Rbowtie" version))
4879 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4880 (properties `((upstream-name . "Rbowtie")))
4881 (build-system r-build-system)
4884 (home-page "https://bioconductor.org/packages/Rbowtie/")
4885 (synopsis "R bowtie wrapper")
4887 "This package provides an R wrapper around the popular bowtie short read
4888 aligner and around SpliceMap, a de novo splice junction discovery and
4890 (license license:artistic2.0)))
4892 (define-public r-sgseq
4899 (uri (bioconductor-uri "SGSeq" version))
4902 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4903 (properties `((upstream-name . "SGSeq")))
4904 (build-system r-build-system)
4906 `(("r-annotationdbi" ,r-annotationdbi)
4907 ("r-biocgenerics" ,r-biocgenerics)
4908 ("r-biostrings" ,r-biostrings)
4909 ("r-genomeinfodb" ,r-genomeinfodb)
4910 ("r-genomicalignments" ,r-genomicalignments)
4911 ("r-genomicfeatures" ,r-genomicfeatures)
4912 ("r-genomicranges" ,r-genomicranges)
4913 ("r-igraph" ,r-igraph)
4914 ("r-iranges" ,r-iranges)
4915 ("r-rsamtools" ,r-rsamtools)
4916 ("r-rtracklayer" ,r-rtracklayer)
4917 ("r-runit" ,r-runit)
4918 ("r-s4vectors" ,r-s4vectors)
4919 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4920 (home-page "https://bioconductor.org/packages/SGSeq/")
4921 (synopsis "Splice event prediction and quantification from RNA-seq data")
4923 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4924 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4925 represented as a splice graph, which can be obtained from existing annotation
4926 or predicted from the mapped sequence reads. Splice events are identified
4927 from the graph and are quantified locally using structurally compatible reads
4928 at the start or end of each splice variant. The software includes functions
4929 for splice event prediction, quantification, visualization and
4931 (license license:artistic2.0)))
4933 (define-public r-rhisat2
4940 (uri (bioconductor-uri "Rhisat2" version))
4943 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4944 (properties `((upstream-name . "Rhisat2")))
4945 (build-system r-build-system)
4947 `(("which" ,which)))
4949 `(("r-genomicfeatures" ,r-genomicfeatures)
4950 ("r-genomicranges" ,r-genomicranges)
4951 ("r-sgseq" ,r-sgseq)))
4952 (home-page "https://github.com/fmicompbio/Rhisat2")
4953 (synopsis "R Wrapper for HISAT2 sequence aligner")
4955 "This package provides an R interface to the HISAT2 spliced short-read
4956 aligner by Kim et al. (2015). The package contains wrapper functions to
4957 create a genome index and to perform the read alignment to the generated
4959 (license license:gpl3)))
4961 (define-public r-quasr
4968 (uri (bioconductor-uri "QuasR" version))
4971 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4972 (properties `((upstream-name . "QuasR")))
4973 (build-system r-build-system)
4977 `(("r-annotationdbi" ,r-annotationdbi)
4978 ("r-biobase" ,r-biobase)
4979 ("r-biocgenerics" ,r-biocgenerics)
4980 ("r-biocmanager" ,r-biocmanager)
4981 ("r-biocparallel" ,r-biocparallel)
4982 ("r-biostrings" ,r-biostrings)
4983 ("r-bsgenome" ,r-bsgenome)
4984 ("r-genomeinfodb" ,r-genomeinfodb)
4985 ("r-genomicalignments" ,r-genomicalignments)
4986 ("r-genomicfeatures" ,r-genomicfeatures)
4987 ("r-genomicfiles" ,r-genomicfiles)
4988 ("r-genomicranges" ,r-genomicranges)
4989 ("r-iranges" ,r-iranges)
4990 ("r-rbowtie" ,r-rbowtie)
4991 ("r-rhisat2" ,r-rhisat2)
4992 ("r-rhtslib" ,r-rhtslib)
4993 ("r-rsamtools" ,r-rsamtools)
4994 ("r-rtracklayer" ,r-rtracklayer)
4995 ("r-s4vectors" ,r-s4vectors)
4996 ("r-shortread" ,r-shortread)))
4997 (home-page "https://bioconductor.org/packages/QuasR/")
4998 (synopsis "Quantify and annotate short reads in R")
5000 "This package provides a framework for the quantification and analysis of
5001 short genomic reads. It covers a complete workflow starting from raw sequence
5002 reads, over creation of alignments and quality control plots, to the
5003 quantification of genomic regions of interest.")
5004 (license license:gpl2)))
5006 (define-public r-rqc
5013 (uri (bioconductor-uri "Rqc" version))
5016 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
5017 (properties `((upstream-name . "Rqc")))
5018 (build-system r-build-system)
5020 `(("r-biocgenerics" ,r-biocgenerics)
5021 ("r-biocparallel" ,r-biocparallel)
5022 ("r-biocstyle" ,r-biocstyle)
5023 ("r-biostrings" ,r-biostrings)
5024 ("r-biovizbase" ,r-biovizbase)
5025 ("r-genomicalignments" ,r-genomicalignments)
5026 ("r-genomicfiles" ,r-genomicfiles)
5027 ("r-ggplot2" ,r-ggplot2)
5028 ("r-iranges" ,r-iranges)
5029 ("r-knitr" ,r-knitr)
5030 ("r-markdown" ,r-markdown)
5033 ("r-reshape2" ,r-reshape2)
5034 ("r-rsamtools" ,r-rsamtools)
5035 ("r-s4vectors" ,r-s4vectors)
5036 ("r-shiny" ,r-shiny)
5037 ("r-shortread" ,r-shortread)))
5038 (home-page "https://github.com/labbcb/Rqc")
5039 (synopsis "Quality control tool for high-throughput sequencing data")
5041 "Rqc is an optimized tool designed for quality control and assessment of
5042 high-throughput sequencing data. It performs parallel processing of entire
5043 files and produces a report which contains a set of high-resolution
5045 (license license:gpl2+)))
5047 (define-public r-birewire
5054 (uri (bioconductor-uri "BiRewire" version))
5057 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
5058 (properties `((upstream-name . "BiRewire")))
5059 (build-system r-build-system)
5061 `(("r-igraph" ,r-igraph)
5062 ("r-matrix" ,r-matrix)
5064 ("r-tsne" ,r-tsne)))
5065 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5066 (synopsis "Tools for randomization of bipartite graphs")
5068 "This package provides functions for bipartite network rewiring through N
5069 consecutive switching steps and for the computation of the minimal number of
5070 switching steps to be performed in order to maximise the dissimilarity with
5071 respect to the original network. It includes functions for the analysis of
5072 the introduced randomness across the switching steps and several other
5073 routines to analyse the resulting networks and their natural projections.")
5074 (license license:gpl3)))
5076 (define-public r-birta
5083 (uri (bioconductor-uri "birta" version))
5086 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
5087 (build-system r-build-system)
5089 `(("r-biobase" ,r-biobase)
5090 ("r-limma" ,r-limma)
5091 ("r-mass" ,r-mass)))
5092 (home-page "https://bioconductor.org/packages/birta")
5093 (synopsis "Bayesian inference of regulation of transcriptional activity")
5095 "Expression levels of mRNA molecules are regulated by different
5096 processes, comprising inhibition or activation by transcription factors and
5097 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5098 Inference of Regulation of Transcriptional Activity) uses the regulatory
5099 networks of transcription factors and miRNAs together with mRNA and miRNA
5100 expression data to predict switches in regulatory activity between two
5101 conditions. A Bayesian network is used to model the regulatory structure and
5102 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5103 (license license:gpl2+)))
5105 (define-public r-ropls
5112 (uri (bioconductor-uri "ropls" version))
5115 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
5116 (build-system r-build-system)
5117 (propagated-inputs `(("r-biobase" ,r-biobase)))
5119 `(("r-knitr" ,r-knitr))) ; for vignettes
5120 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5121 (synopsis "Multivariate analysis and feature selection of omics data")
5123 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5124 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5125 regression, classification, and feature selection of omics data where the
5126 number of variables exceeds the number of samples and with multicollinearity
5127 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5128 separately model the variation correlated (predictive) to the factor of
5129 interest and the uncorrelated (orthogonal) variation. While performing
5130 similarly to PLS, OPLS facilitates interpretation.
5132 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5133 analysis and feature selection of omics data. In addition to scores, loadings
5134 and weights plots, the package provides metrics and graphics to determine the
5135 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5136 validity of the model by permutation testing, detect outliers, and perform
5137 feature selection (e.g. with Variable Importance in Projection or regression
5139 (license license:cecill)))
5141 (define-public r-biosigner
5143 (name "r-biosigner")
5148 (uri (bioconductor-uri "biosigner" version))
5151 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
5152 (build-system r-build-system)
5154 `(("r-biobase" ,r-biobase)
5155 ("r-e1071" ,r-e1071)
5156 ("r-randomforest" ,r-randomforest)
5157 ("r-ropls" ,r-ropls)))
5159 `(("r-knitr" ,r-knitr)
5160 ("r-rmarkdown" ,r-rmarkdown)
5161 ("pandoc" ,ghc-pandoc)
5162 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5163 (home-page "https://bioconductor.org/packages/biosigner/")
5164 (synopsis "Signature discovery from omics data")
5166 "Feature selection is critical in omics data analysis to extract
5167 restricted and meaningful molecular signatures from complex and high-dimension
5168 data, and to build robust classifiers. This package implements a method to
5169 assess the relevance of the variables for the prediction performances of the
5170 classifier. The approach can be run in parallel with the PLS-DA, Random
5171 Forest, and SVM binary classifiers. The signatures and the corresponding
5172 'restricted' models are returned, enabling future predictions on new
5174 (license license:cecill)))
5176 (define-public r-annotatr
5183 (uri (bioconductor-uri "annotatr" version))
5186 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
5187 (build-system r-build-system)
5189 `(("r-annotationdbi" ,r-annotationdbi)
5190 ("r-annotationhub" ,r-annotationhub)
5191 ("r-dplyr" ,r-dplyr)
5192 ("r-genomeinfodb" ,r-genomeinfodb)
5193 ("r-genomicfeatures" ,r-genomicfeatures)
5194 ("r-genomicranges" ,r-genomicranges)
5195 ("r-ggplot2" ,r-ggplot2)
5196 ("r-iranges" ,r-iranges)
5197 ("r-readr" ,r-readr)
5198 ("r-regioner" ,r-regioner)
5199 ("r-reshape2" ,r-reshape2)
5200 ("r-rtracklayer" ,r-rtracklayer)
5201 ("r-s4vectors" ,r-s4vectors)))
5202 (home-page "https://bioconductor.org/packages/annotatr/")
5203 (synopsis "Annotation of genomic regions to genomic annotations")
5205 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5206 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5207 to investigate the intersecting genomic annotations. Such annotations include
5208 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5209 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5210 enhancers. The annotatr package provides an easy way to summarize and
5211 visualize the intersection of genomic sites/regions with genomic
5213 (license license:gpl3)))
5215 (define-public r-rsubread
5222 (uri (bioconductor-uri "Rsubread" version))
5225 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
5226 (properties `((upstream-name . "Rsubread")))
5227 (build-system r-build-system)
5228 (inputs `(("zlib" ,zlib)))
5229 (home-page "https://bioconductor.org/packages/Rsubread/")
5230 (synopsis "Subread sequence alignment and counting for R")
5232 "This package provides tools for alignment, quantification and analysis
5233 of second and third generation sequencing data. It includes functionality for
5234 read mapping, read counting, SNP calling, structural variant detection and
5235 gene fusion discovery. It can be applied to all major sequencing techologies
5236 and to both short and long sequence reads.")
5237 (license license:gpl3)))
5239 (define-public r-flowutils
5241 (name "r-flowutils")
5246 (uri (bioconductor-uri "flowUtils" version))
5249 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
5250 (properties `((upstream-name . "flowUtils")))
5251 (build-system r-build-system)
5253 `(("r-biobase" ,r-biobase)
5254 ("r-corpcor" ,r-corpcor)
5255 ("r-flowcore" ,r-flowcore)
5256 ("r-graph" ,r-graph)
5257 ("r-runit" ,r-runit)
5259 (home-page "https://github.com/jspidlen/flowUtils")
5260 (synopsis "Utilities for flow cytometry")
5262 "This package provides utilities for flow cytometry data.")
5263 (license license:artistic2.0)))
5265 (define-public r-consensusclusterplus
5267 (name "r-consensusclusterplus")
5272 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5275 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
5277 `((upstream-name . "ConsensusClusterPlus")))
5278 (build-system r-build-system)
5281 ("r-biobase" ,r-biobase)
5282 ("r-cluster" ,r-cluster)))
5283 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5284 (synopsis "Clustering algorithm")
5286 "This package provides an implementation of an algorithm for determining
5287 cluster count and membership by stability evidence in unsupervised analysis.")
5288 (license license:gpl2)))
5290 (define-public r-flowcore
5297 (uri (bioconductor-uri "flowCore" version))
5300 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
5301 (properties `((upstream-name . "flowCore")))
5302 (build-system r-build-system)
5305 ("r-biobase" ,r-biobase)
5306 ("r-biocgenerics" ,r-biocgenerics)
5307 ("r-corpcor" ,r-corpcor)
5308 ("r-graph" ,r-graph)
5310 ("r-matrixstats" ,r-matrixstats)
5312 ("r-rrcov" ,r-rrcov)))
5313 (home-page "https://bioconductor.org/packages/flowCore")
5314 (synopsis "Basic structures for flow cytometry data")
5316 "This package provides S4 data structures and basic functions to deal
5317 with flow cytometry data.")
5318 (license license:artistic2.0)))
5320 (define-public r-flowmeans
5322 (name "r-flowmeans")
5327 (uri (bioconductor-uri "flowMeans" version))
5330 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
5331 (properties `((upstream-name . "flowMeans")))
5332 (build-system r-build-system)
5334 `(("r-biobase" ,r-biobase)
5335 ("r-feature" ,r-feature)
5336 ("r-flowcore" ,r-flowcore)
5337 ("r-rrcov" ,r-rrcov)))
5338 (home-page "https://bioconductor.org/packages/flowMeans")
5339 (synopsis "Non-parametric flow cytometry data gating")
5341 "This package provides tools to identify cell populations in Flow
5342 Cytometry data using non-parametric clustering and segmented-regression-based
5343 change point detection.")
5344 (license license:artistic2.0)))
5346 (define-public r-flowsom
5353 (uri (bioconductor-uri "FlowSOM" version))
5356 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5357 (properties `((upstream-name . "FlowSOM")))
5358 (build-system r-build-system)
5360 `(("r-biocgenerics" ,r-biocgenerics)
5361 ("r-consensusclusterplus" ,r-consensusclusterplus)
5362 ("r-flowcore" ,r-flowcore)
5363 ("r-flowutils" ,r-flowutils)
5364 ("r-igraph" ,r-igraph)
5367 (home-page "https://bioconductor.org/packages/FlowSOM/")
5368 (synopsis "Visualize and interpret cytometry data")
5370 "FlowSOM offers visualization options for cytometry data, by using
5371 self-organizing map clustering and minimal spanning trees.")
5372 (license license:gpl2+)))
5374 (define-public r-mixomics
5381 (uri (bioconductor-uri "mixOmics" version))
5384 "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
5385 (properties `((upstream-name . "mixOmics")))
5386 (build-system r-build-system)
5388 `(("r-corpcor" ,r-corpcor)
5389 ("r-dplyr" ,r-dplyr)
5390 ("r-ellipse" ,r-ellipse)
5391 ("r-ggplot2" ,r-ggplot2)
5392 ("r-gridextra" ,r-gridextra)
5393 ("r-igraph" ,r-igraph)
5394 ("r-lattice" ,r-lattice)
5396 ("r-matrixstats" ,r-matrixstats)
5397 ("r-rarpack" ,r-rarpack)
5398 ("r-rcolorbrewer" ,r-rcolorbrewer)
5399 ("r-reshape2" ,r-reshape2)
5400 ("r-tidyr" ,r-tidyr)))
5401 (home-page "http://www.mixOmics.org")
5402 (synopsis "Multivariate methods for exploration of biological datasets")
5404 "mixOmics offers a wide range of multivariate methods for the exploration
5405 and integration of biological datasets with a particular focus on variable
5406 selection. The package proposes several sparse multivariate models we have
5407 developed to identify the key variables that are highly correlated, and/or
5408 explain the biological outcome of interest. The data that can be analysed
5409 with mixOmics may come from high throughput sequencing technologies, such as
5410 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5411 also beyond the realm of omics (e.g. spectral imaging). The methods
5412 implemented in mixOmics can also handle missing values without having to
5413 delete entire rows with missing data.")
5414 (license license:gpl2+)))
5416 (define-public r-depecher
5423 (uri (bioconductor-uri "DepecheR" version))
5426 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5427 (properties `((upstream-name . "DepecheR")))
5428 (build-system r-build-system)
5431 (modify-phases %standard-phases
5432 (add-after 'unpack 'fix-syntax-error
5434 (substitute* "src/Makevars"
5438 `(("r-beanplot" ,r-beanplot)
5439 ("r-biocparallel" ,r-biocparallel)
5440 ("r-dosnow" ,r-dosnow)
5441 ("r-dplyr" ,r-dplyr)
5442 ("r-foreach" ,r-foreach)
5443 ("r-ggplot2" ,r-ggplot2)
5444 ("r-gplots" ,r-gplots)
5446 ("r-matrixstats" ,r-matrixstats)
5447 ("r-mixomics" ,r-mixomics)
5448 ("r-moments" ,r-moments)
5450 ("r-rcppeigen" ,r-rcppeigen)
5451 ("r-reshape2" ,r-reshape2)
5452 ("r-viridis" ,r-viridis)))
5453 (home-page "https://bioconductor.org/packages/DepecheR/")
5454 (synopsis "Identify traits of clusters in high-dimensional entities")
5456 "The purpose of this package is to identify traits in a dataset that can
5457 separate groups. This is done on two levels. First, clustering is performed,
5458 using an implementation of sparse K-means. Secondly, the generated clusters
5459 are used to predict outcomes of groups of individuals based on their
5460 distribution of observations in the different clusters. As certain clusters
5461 with separating information will be identified, and these clusters are defined
5462 by a sparse number of variables, this method can reduce the complexity of
5463 data, to only emphasize the data that actually matters.")
5464 (license license:expat)))
5466 (define-public r-rcistarget
5468 (name "r-rcistarget")
5473 (uri (bioconductor-uri "RcisTarget" version))
5476 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5477 (properties `((upstream-name . "RcisTarget")))
5478 (build-system r-build-system)
5480 `(("r-aucell" ,r-aucell)
5481 ("r-biocgenerics" ,r-biocgenerics)
5482 ("r-data-table" ,r-data-table)
5483 ("r-feather" ,r-feather)
5484 ("r-gseabase" ,r-gseabase)
5485 ("r-r-utils" ,r-r-utils)
5486 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5487 (home-page "https://aertslab.org/#scenic")
5488 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5490 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5491 over-represented on a gene list. In a first step, RcisTarget selects DNA
5492 motifs that are significantly over-represented in the surroundings of the
5493 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5494 achieved by using a database that contains genome-wide cross-species rankings
5495 for each motif. The motifs that are then annotated to TFs and those that have
5496 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5497 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5498 genes in the gene-set that are ranked above the leading edge).")
5499 (license license:gpl3)))
5501 (define-public r-cicero
5508 (uri (bioconductor-uri "cicero" version))
5511 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5512 (build-system r-build-system)
5514 `(("r-assertthat" ,r-assertthat)
5515 ("r-biobase" ,r-biobase)
5516 ("r-biocgenerics" ,r-biocgenerics)
5517 ("r-data-table" ,r-data-table)
5518 ("r-dplyr" ,r-dplyr)
5520 ("r-genomicranges" ,r-genomicranges)
5521 ("r-ggplot2" ,r-ggplot2)
5522 ("r-glasso" ,r-glasso)
5524 ("r-igraph" ,r-igraph)
5525 ("r-iranges" ,r-iranges)
5526 ("r-matrix" ,r-matrix)
5527 ("r-monocle" ,r-monocle)
5529 ("r-reshape2" ,r-reshape2)
5530 ("r-s4vectors" ,r-s4vectors)
5531 ("r-stringr" ,r-stringr)
5532 ("r-tibble" ,r-tibble)
5533 ("r-vgam" ,r-vgam)))
5534 (home-page "https://bioconductor.org/packages/cicero/")
5535 (synopsis "Predict cis-co-accessibility from single-cell data")
5537 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5538 accessibility data. It also extends the monocle package for use in chromatin
5539 accessibility data.")
5540 (license license:expat)))
5542 ;; This is the latest commit on the "monocle3" branch.
5543 (define-public r-cicero-monocle3
5544 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5546 (package (inherit r-cicero)
5547 (name "r-cicero-monocle3")
5548 (version (git-version "1.3.2" revision commit))
5553 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5555 (file-name (git-file-name name version))
5558 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5560 `(("r-monocle3" ,r-monocle3)
5561 ,@(alist-delete "r-monocle"
5562 (package-propagated-inputs r-cicero)))))))
5564 (define-public r-cistopic
5565 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5569 (version (git-version "0.2.1" revision commit))
5574 (url "https://github.com/aertslab/cisTopic.git")
5576 (file-name (git-file-name name version))
5579 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5580 (build-system r-build-system)
5582 `(("r-aucell" ,r-aucell)
5583 ("r-data-table" ,r-data-table)
5584 ("r-dplyr" ,r-dplyr)
5585 ("r-dosnow" ,r-dosnow)
5587 ("r-feather" ,r-feather)
5588 ("r-fitdistrplus" ,r-fitdistrplus)
5589 ("r-genomicranges" ,r-genomicranges)
5590 ("r-ggplot2" ,r-ggplot2)
5592 ("r-matrix" ,r-matrix)
5594 ("r-rcistarget" ,r-rcistarget)
5595 ("r-rtracklayer" ,r-rtracklayer)
5596 ("r-s4vectors" ,r-s4vectors)))
5597 (home-page "https://github.com/aertslab/cisTopic")
5598 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5600 "The sparse nature of single cell epigenomics data can be overruled using
5601 probabilistic modelling methods such as @dfn{Latent Dirichlet
5602 Allocation} (LDA). This package allows the probabilistic modelling of
5603 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5604 includes functionalities to identify cell states based on the contribution of
5605 cisTopics and explore the nature and regulatory proteins driving them.")
5606 (license license:gpl3))))
5608 (define-public r-genie3
5615 (uri (bioconductor-uri "GENIE3" version))
5618 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5619 (properties `((upstream-name . "GENIE3")))
5620 (build-system r-build-system)
5621 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5622 (home-page "https://bioconductor.org/packages/GENIE3")
5623 (synopsis "Gene network inference with ensemble of trees")
5625 "This package implements the GENIE3 algorithm for inferring gene
5626 regulatory networks from expression data.")
5627 (license license:gpl2+)))
5629 (define-public r-roc
5636 (uri (bioconductor-uri "ROC" version))
5639 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5640 (properties `((upstream-name . "ROC")))
5641 (build-system r-build-system)
5642 (home-page "https://www.bioconductor.org/packages/ROC/")
5643 (synopsis "Utilities for ROC curves")
5645 "This package provides utilities for @dfn{Receiver Operating
5646 Characteristic} (ROC) curves, with a focus on micro arrays.")
5647 (license license:artistic2.0)))
5649 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5651 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5656 (uri (bioconductor-uri
5657 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5658 version 'annotation))
5661 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5664 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5665 (build-system r-build-system)
5666 (propagated-inputs `(("r-minfi" ,r-minfi)))
5668 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5669 (synopsis "Annotation for Illumina's 450k methylation arrays")
5671 "This package provides manifests and annotation for Illumina's 450k array
5673 (license license:artistic2.0)))
5675 (define-public r-watermelon
5677 (name "r-watermelon")
5682 (uri (bioconductor-uri "wateRmelon" version))
5685 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
5686 (properties `((upstream-name . "wateRmelon")))
5687 (build-system r-build-system)
5689 `(("r-biobase" ,r-biobase)
5690 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
5691 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
5692 ("r-illuminaio" ,r-illuminaio)
5693 ("r-limma" ,r-limma)
5695 ("r-matrixstats" ,r-matrixstats)
5696 ("r-methylumi" ,r-methylumi)
5698 (home-page "https://bioconductor.org/packages/wateRmelon/")
5699 (synopsis "Illumina 450 methylation array normalization and metrics")
5701 "The standard index of DNA methylation (beta) is computed from methylated
5702 and unmethylated signal intensities. Betas calculated from raw signal
5703 intensities perform well, but using 11 methylomic datasets we demonstrate that
5704 quantile normalization methods produce marked improvement. The commonly used
5705 procedure of normalizing betas is inferior to the separate normalization of M
5706 and U, and it is also advantageous to normalize Type I and Type II assays
5707 separately. This package provides 15 flavours of betas and three performance
5708 metrics, with methods for objects produced by the @code{methylumi} and
5709 @code{minfi} packages.")
5710 (license license:gpl3)))
5712 (define-public r-gdsfmt
5719 (uri (bioconductor-uri "gdsfmt" version))
5722 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
5723 (modules '((guix build utils)))
5724 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
5725 ;; them and link with system libraries instead.
5728 (for-each delete-file-recursively
5732 (substitute* "src/Makevars"
5733 (("all: \\$\\(SHLIB\\)") "all:")
5734 (("\\$\\(SHLIB\\): liblzma.a") "")
5735 (("(ZLIB|LZ4)/.*") "")
5736 (("CoreArray/dVLIntGDS.cpp.*")
5737 "CoreArray/dVLIntGDS.cpp")
5738 (("CoreArray/dVLIntGDS.o.*")
5739 "CoreArray/dVLIntGDS.o")
5740 (("PKG_LIBS = ./liblzma.a")
5741 "PKG_LIBS = -llz4"))
5742 (substitute* "src/CoreArray/dStream.h"
5743 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
5744 (string-append "include <" header ">")))
5746 (properties `((upstream-name . "gdsfmt")))
5747 (build-system r-build-system)
5752 (home-page "http://corearray.sourceforge.net/")
5754 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
5756 "This package provides a high-level R interface to CoreArray @dfn{Genomic
5757 Data Structure} (GDS) data files, which are portable across platforms with
5758 hierarchical structure to store multiple scalable array-oriented data sets
5759 with metadata information. It is suited for large-scale datasets, especially
5760 for data which are much larger than the available random-access memory. The
5761 @code{gdsfmt} package offers efficient operations specifically designed for
5762 integers of less than 8 bits, since a diploid genotype, like
5763 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
5764 byte. Data compression and decompression are available with relatively
5765 efficient random access. It is also allowed to read a GDS file in parallel
5766 with multiple R processes supported by the package @code{parallel}.")
5767 (license license:lgpl3)))
5769 (define-public r-bigmelon
5776 (uri (bioconductor-uri "bigmelon" version))
5779 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
5780 (properties `((upstream-name . "bigmelon")))
5781 (build-system r-build-system)
5783 `(("r-biobase" ,r-biobase)
5784 ("r-biocgenerics" ,r-biocgenerics)
5785 ("r-gdsfmt" ,r-gdsfmt)
5786 ("r-geoquery" ,r-geoquery)
5787 ("r-methylumi" ,r-methylumi)
5788 ("r-minfi" ,r-minfi)
5789 ("r-watermelon" ,r-watermelon)))
5790 (home-page "https://bioconductor.org/packages/bigmelon/")
5791 (synopsis "Illumina methylation array analysis for large experiments")
5793 "This package provides methods for working with Illumina arrays using the
5794 @code{gdsfmt} package.")
5795 (license license:gpl3)))
5797 (define-public r-seqbias
5804 (uri (bioconductor-uri "seqbias" version))
5807 "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
5808 (properties `((upstream-name . "seqbias")))
5809 (build-system r-build-system)
5811 `(("r-biostrings" ,r-biostrings)
5812 ("r-genomicranges" ,r-genomicranges)
5813 ("r-rhtslib" ,r-rhtslib)))
5815 `(("zlib" ,zlib))) ; This comes from rhtslib.
5816 (home-page "https://bioconductor.org/packages/seqbias/")
5817 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
5819 "This package implements a model of per-position sequencing bias in
5820 high-throughput sequencing data using a simple Bayesian network, the structure
5821 and parameters of which are trained on a set of aligned reads and a reference
5823 (license license:lgpl3)))
5825 (define-public r-reqon
5832 (uri (bioconductor-uri "ReQON" version))
5835 "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
5836 (properties `((upstream-name . "ReQON")))
5837 (build-system r-build-system)
5839 `(("r-rjava" ,r-rjava)
5840 ("r-rsamtools" ,r-rsamtools)
5841 ("r-seqbias" ,r-seqbias)))
5842 (home-page "https://bioconductor.org/packages/ReQON/")
5843 (synopsis "Recalibrating quality of nucleotides")
5845 "This package provides an implementation of an algorithm for
5846 recalibrating the base quality scores for aligned sequencing data in BAM
5848 (license license:gpl2)))
5850 (define-public r-wavcluster
5852 (name "r-wavcluster")
5857 (uri (bioconductor-uri "wavClusteR" version))
5860 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
5861 (properties `((upstream-name . "wavClusteR")))
5862 (build-system r-build-system)
5864 `(("r-biocgenerics" ,r-biocgenerics)
5865 ("r-biostrings" ,r-biostrings)
5866 ("r-foreach" ,r-foreach)
5867 ("r-genomicfeatures" ,r-genomicfeatures)
5868 ("r-genomicranges" ,r-genomicranges)
5869 ("r-ggplot2" ,r-ggplot2)
5870 ("r-hmisc" ,r-hmisc)
5871 ("r-iranges" ,r-iranges)
5872 ("r-mclust" ,r-mclust)
5873 ("r-rsamtools" ,r-rsamtools)
5874 ("r-rtracklayer" ,r-rtracklayer)
5875 ("r-s4vectors" ,r-s4vectors)
5876 ("r-seqinr" ,r-seqinr)
5877 ("r-stringr" ,r-stringr)
5878 ("r-wmtsa" ,r-wmtsa)))
5879 (home-page "https://bioconductor.org/packages/wavClusteR/")
5880 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
5882 "This package provides an integrated pipeline for the analysis of
5883 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
5884 sequencing errors, SNPs and additional non-experimental sources by a non-
5885 parametric mixture model. The protein binding sites (clusters) are then
5886 resolved at high resolution and cluster statistics are estimated using a
5887 rigorous Bayesian framework. Post-processing of the results, data export for
5888 UCSC genome browser visualization and motif search analysis are provided. In
5889 addition, the package allows to integrate RNA-Seq data to estimate the False
5890 Discovery Rate of cluster detection. Key functions support parallel multicore
5891 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
5892 be applied to the analysis of other NGS data obtained from experimental
5893 procedures that induce nucleotide substitutions (e.g. BisSeq).")
5894 (license license:gpl2)))
5896 (define-public r-timeseriesexperiment
5898 (name "r-timeseriesexperiment")
5903 (uri (bioconductor-uri "TimeSeriesExperiment" version))
5906 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
5908 `((upstream-name . "TimeSeriesExperiment")))
5909 (build-system r-build-system)
5911 `(("r-deseq2" ,r-deseq2)
5912 ("r-dplyr" ,r-dplyr)
5913 ("r-dynamictreecut" ,r-dynamictreecut)
5914 ("r-edger" ,r-edger)
5915 ("r-ggplot2" ,r-ggplot2)
5916 ("r-hmisc" ,r-hmisc)
5917 ("r-limma" ,r-limma)
5918 ("r-magrittr" ,r-magrittr)
5919 ("r-proxy" ,r-proxy)
5920 ("r-s4vectors" ,r-s4vectors)
5921 ("r-summarizedexperiment" ,r-summarizedexperiment)
5922 ("r-tibble" ,r-tibble)
5923 ("r-tidyr" ,r-tidyr)
5924 ("r-vegan" ,r-vegan)
5925 ("r-viridis" ,r-viridis)))
5926 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
5927 (synopsis "Analysis for short time-series data")
5929 "This package is a visualization and analysis toolbox for short time
5930 course data which includes dimensionality reduction, clustering, two-sample
5931 differential expression testing and gene ranking techniques. The package also
5932 provides methods for retrieving enriched pathways.")
5933 (license license:lgpl3+)))
5935 (define-public r-variantfiltering
5937 (name "r-variantfiltering")
5942 (uri (bioconductor-uri "VariantFiltering" version))
5945 "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
5947 `((upstream-name . "VariantFiltering")))
5948 (build-system r-build-system)
5950 `(("r-annotationdbi" ,r-annotationdbi)
5951 ("r-biobase" ,r-biobase)
5952 ("r-biocgenerics" ,r-biocgenerics)
5953 ("r-biocparallel" ,r-biocparallel)
5954 ("r-biostrings" ,r-biostrings)
5955 ("r-bsgenome" ,r-bsgenome)
5957 ("r-genomeinfodb" ,r-genomeinfodb)
5958 ("r-genomicfeatures" ,r-genomicfeatures)
5959 ("r-genomicranges" ,r-genomicranges)
5960 ("r-genomicscores" ,r-genomicscores)
5961 ("r-graph" ,r-graph)
5963 ("r-iranges" ,r-iranges)
5965 ("r-rsamtools" ,r-rsamtools)
5966 ("r-s4vectors" ,r-s4vectors)
5967 ("r-shiny" ,r-shiny)
5968 ("r-shinyjs" ,r-shinyjs)
5969 ("r-shinythemes" ,r-shinythemes)
5970 ("r-shinytree" ,r-shinytree)
5971 ("r-summarizedexperiment" ,r-summarizedexperiment)
5972 ("r-variantannotation" ,r-variantannotation)
5973 ("r-xvector" ,r-xvector)))
5974 (home-page "https://github.com/rcastelo/VariantFiltering")
5975 (synopsis "Filtering of coding and non-coding genetic variants")
5977 "Filter genetic variants using different criteria such as inheritance
5978 model, amino acid change consequence, minor allele frequencies across human
5979 populations, splice site strength, conservation, etc.")
5980 (license license:artistic2.0)))
5982 (define-public r-genomegraphs
5984 (name "r-genomegraphs")
5989 (uri (bioconductor-uri "GenomeGraphs" version))
5992 "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd"))))
5993 (properties `((upstream-name . "GenomeGraphs")))
5994 (build-system r-build-system)
5996 `(("r-biomart" ,r-biomart)))
5997 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
5998 (synopsis "Plotting genomic information from Ensembl")
6000 "Genomic data analyses requires integrated visualization of known genomic
6001 information and new experimental data. GenomeGraphs uses the biomaRt package
6002 to perform live annotation queries to Ensembl and translates this to e.g.
6003 gene/transcript structures in viewports of the grid graphics package. This
6004 results in genomic information plotted together with your data. Another
6005 strength of GenomeGraphs is to plot different data types such as array CGH,
6006 gene expression, sequencing and other data, together in one plot using the
6007 same genome coordinate system.")
6008 (license license:artistic2.0)))
6010 (define-public r-wavetiling
6012 (name "r-wavetiling")
6017 (uri (bioconductor-uri "waveTiling" version))
6020 "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir"))))
6021 (properties `((upstream-name . "waveTiling")))
6022 (build-system r-build-system)
6024 `(("r-affy" ,r-affy)
6025 ("r-biobase" ,r-biobase)
6026 ("r-biostrings" ,r-biostrings)
6027 ("r-genomegraphs" ,r-genomegraphs)
6028 ("r-genomicranges" ,r-genomicranges)
6029 ("r-iranges" ,r-iranges)
6030 ("r-oligo" ,r-oligo)
6031 ("r-oligoclasses" ,r-oligoclasses)
6032 ("r-preprocesscore" ,r-preprocesscore)
6033 ("r-waveslim" ,r-waveslim)))
6034 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6035 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6037 "This package is designed to conduct transcriptome analysis for tiling
6038 arrays based on fast wavelet-based functional models.")
6039 (license license:gpl2+)))
6041 (define-public r-variancepartition
6043 (name "r-variancepartition")
6048 (uri (bioconductor-uri "variancePartition" version))
6051 "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
6053 `((upstream-name . "variancePartition")))
6054 (build-system r-build-system)
6056 `(("r-biobase" ,r-biobase)
6057 ("r-biocparallel" ,r-biocparallel)
6058 ("r-colorramps" ,r-colorramps)
6059 ("r-doparallel" ,r-doparallel)
6060 ("r-foreach" ,r-foreach)
6061 ("r-ggplot2" ,r-ggplot2)
6062 ("r-gplots" ,r-gplots)
6063 ("r-iterators" ,r-iterators)
6064 ("r-limma" ,r-limma)
6066 ("r-lmertest" ,r-lmertest)
6068 ("r-pbkrtest" ,r-pbkrtest)
6069 ("r-progress" ,r-progress)
6070 ("r-reshape2" ,r-reshape2)
6071 ("r-scales" ,r-scales)))
6072 (home-page "https://bioconductor.org/packages/variancePartition/")
6073 (synopsis "Analyze variation in gene expression experiments")
6075 "This is a package providing tools to quantify and interpret multiple
6076 sources of biological and technical variation in gene expression experiments.
6077 It uses a linear mixed model to quantify variation in gene expression
6078 attributable to individual, tissue, time point, or technical variables. The
6079 package includes dream differential expression analysis for repeated
6081 (license license:gpl2+)))
6083 (define-public r-htqpcr
6090 (uri (bioconductor-uri "HTqPCR" version))
6093 "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
6094 (properties `((upstream-name . "HTqPCR")))
6095 (build-system r-build-system)
6097 `(("r-affy" ,r-affy)
6098 ("r-biobase" ,r-biobase)
6099 ("r-gplots" ,r-gplots)
6100 ("r-limma" ,r-limma)
6101 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6102 (home-page "http://www.ebi.ac.uk/bertone/software")
6103 (synopsis "Automated analysis of high-throughput qPCR data")
6105 "Analysis of Ct values from high throughput quantitative real-time
6106 PCR (qPCR) assays across multiple conditions or replicates. The input data
6107 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6108 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6109 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6110 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6111 loading, quality assessment, normalization, visualization and parametric or
6112 non-parametric testing for statistical significance in Ct values between
6113 features (e.g. genes, microRNAs).")
6114 (license license:artistic2.0)))
6116 (define-public r-unifiedwmwqpcr
6118 (name "r-unifiedwmwqpcr")
6123 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6126 "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
6128 `((upstream-name . "unifiedWMWqPCR")))
6129 (build-system r-build-system)
6131 `(("r-biocgenerics" ,r-biocgenerics)
6132 ("r-htqpcr" ,r-htqpcr)))
6133 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6134 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6136 "This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6137 data. This modified test allows for testing differential expression in qPCR
6139 (license license:gpl2+)))