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>
6 ;;; This file is part of GNU Guix.
8 ;;; GNU Guix is free software; you can redistribute it and/or modify it
9 ;;; under the terms of the GNU General Public License as published by
10 ;;; the Free Software Foundation; either version 3 of the License, or (at
11 ;;; your option) any later version.
13 ;;; GNU Guix is distributed in the hope that it will be useful, but
14 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
15 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 ;;; GNU General Public License for more details.
18 ;;; You should have received a copy of the GNU General Public License
19 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
21 (define-module (gnu packages bioconductor)
22 #:use-module ((guix licenses) #:prefix license:)
23 #:use-module (guix packages)
24 #:use-module (guix download)
25 #:use-module (guix build-system r)
26 #:use-module (gnu packages)
27 #:use-module (gnu packages base)
28 #:use-module (gnu packages bioinformatics)
29 #:use-module (gnu packages cran)
30 #:use-module (gnu packages compression)
31 #:use-module (gnu packages gcc)
32 #:use-module (gnu packages graph)
33 #:use-module (gnu packages haskell)
34 #:use-module (gnu packages image)
35 #:use-module (gnu packages maths)
36 #:use-module (gnu packages netpbm)
37 #:use-module (gnu packages perl)
38 #:use-module (gnu packages pkg-config)
39 #:use-module (gnu packages statistics)
40 #:use-module (gnu packages web))
45 (define-public r-bsgenome-celegans-ucsc-ce6
47 (name "r-bsgenome-celegans-ucsc-ce6")
51 ;; We cannot use bioconductor-uri here because this tarball is
52 ;; located under "data/annotation/" instead of "bioc/".
53 (uri (string-append "https://www.bioconductor.org/packages/"
54 "release/data/annotation/src/contrib/"
55 "BSgenome.Celegans.UCSC.ce6_"
59 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
61 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
62 (build-system r-build-system)
63 ;; As this package provides little more than a very large data file it
64 ;; doesn't make sense to build substitutes.
65 (arguments `(#:substitutable? #f))
67 `(("r-bsgenome" ,r-bsgenome)))
69 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
70 (synopsis "Full genome sequences for Worm")
72 "This package provides full genome sequences for Caenorhabditis
73 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
75 (license license:artistic2.0)))
77 (define-public r-bsgenome-celegans-ucsc-ce10
79 (name "r-bsgenome-celegans-ucsc-ce10")
83 ;; We cannot use bioconductor-uri here because this tarball is
84 ;; located under "data/annotation/" instead of "bioc/".
85 (uri (string-append "https://www.bioconductor.org/packages/"
86 "release/data/annotation/src/contrib/"
87 "BSgenome.Celegans.UCSC.ce10_"
91 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
93 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
94 (build-system r-build-system)
95 ;; As this package provides little more than a very large data file it
96 ;; doesn't make sense to build substitutes.
97 (arguments `(#:substitutable? #f))
99 `(("r-bsgenome" ,r-bsgenome)))
101 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
102 (synopsis "Full genome sequences for Worm")
104 "This package provides full genome sequences for Caenorhabditis
105 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
107 (license license:artistic2.0)))
109 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
111 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
115 ;; We cannot use bioconductor-uri here because this tarball is
116 ;; located under "data/annotation/" instead of "bioc/".
117 (uri (string-append "https://www.bioconductor.org/packages/"
118 "release/data/annotation/src/contrib/"
119 "BSgenome.Dmelanogaster.UCSC.dm6_"
123 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
125 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
126 (build-system r-build-system)
127 ;; As this package provides little more than a very large data file it
128 ;; doesn't make sense to build substitutes.
129 (arguments `(#:substitutable? #f))
131 `(("r-bsgenome" ,r-bsgenome)))
133 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
134 (synopsis "Full genome sequences for Fly")
136 "This package provides full genome sequences for Drosophila
137 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
139 (license license:artistic2.0)))
141 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
143 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
147 ;; We cannot use bioconductor-uri here because this tarball is
148 ;; located under "data/annotation/" instead of "bioc/".
149 (uri (string-append "https://www.bioconductor.org/packages/"
150 "release/data/annotation/src/contrib/"
151 "BSgenome.Dmelanogaster.UCSC.dm3_"
155 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
157 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
158 (build-system r-build-system)
159 ;; As this package provides little more than a very large data file it
160 ;; doesn't make sense to build substitutes.
161 (arguments `(#:substitutable? #f))
163 `(("r-bsgenome" ,r-bsgenome)))
165 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
166 (synopsis "Full genome sequences for Fly")
168 "This package provides full genome sequences for Drosophila
169 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
170 Biostrings objects.")
171 (license license:artistic2.0)))
173 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
175 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
179 ;; We cannot use bioconductor-uri here because this tarball is
180 ;; located under "data/annotation/" instead of "bioc/".
181 (uri (string-append "http://www.bioconductor.org/packages/"
182 "release/data/annotation/src/contrib/"
183 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
187 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
189 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
190 (build-system r-build-system)
192 `(("r-bsgenome" ,r-bsgenome)
193 ("r-bsgenome-dmelanogaster-ucsc-dm3"
194 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
195 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
196 (synopsis "Full masked genome sequences for Fly")
198 "This package provides full masked genome sequences for Drosophila
199 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
200 Biostrings objects. The sequences are the same as in
201 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
202 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
203 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
204 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
205 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
206 (license license:artistic2.0)))
208 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
210 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
214 ;; We cannot use bioconductor-uri here because this tarball is
215 ;; located under "data/annotation/" instead of "bioc/".
216 (uri (string-append "https://www.bioconductor.org/packages/"
217 "release/data/annotation/src/contrib/"
218 "BSgenome.Hsapiens.1000genomes.hs37d5_"
222 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
224 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
225 (build-system r-build-system)
226 ;; As this package provides little more than a very large data file it
227 ;; doesn't make sense to build substitutes.
228 (arguments `(#:substitutable? #f))
230 `(("r-bsgenome" ,r-bsgenome)))
232 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
233 (synopsis "Full genome sequences for Homo sapiens")
235 "This package provides full genome sequences for Homo sapiens from
236 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
237 (license license:artistic2.0)))
239 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
241 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
245 ;; We cannot use bioconductor-uri here because this tarball is
246 ;; located under "data/annotation/" instead of "bioc/".
247 (uri (string-append "http://www.bioconductor.org/packages/"
248 "release/data/annotation/src/contrib/"
249 "BSgenome.Hsapiens.UCSC.hg19.masked_"
253 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
255 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
256 (build-system r-build-system)
258 `(("r-bsgenome" ,r-bsgenome)
259 ("r-bsgenome-hsapiens-ucsc-hg19"
260 ,r-bsgenome-hsapiens-ucsc-hg19)))
261 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
262 (synopsis "Full masked genome sequences for Homo sapiens")
264 "This package provides full genome sequences for Homo sapiens (Human) as
265 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
266 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
267 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
268 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
269 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
270 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
272 (license license:artistic2.0)))
274 (define-public r-bsgenome-mmusculus-ucsc-mm9
276 (name "r-bsgenome-mmusculus-ucsc-mm9")
280 ;; We cannot use bioconductor-uri here because this tarball is
281 ;; located under "data/annotation/" instead of "bioc/".
282 (uri (string-append "https://www.bioconductor.org/packages/"
283 "release/data/annotation/src/contrib/"
284 "BSgenome.Mmusculus.UCSC.mm9_"
288 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
290 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
291 (build-system r-build-system)
292 ;; As this package provides little more than a very large data file it
293 ;; doesn't make sense to build substitutes.
294 (arguments `(#:substitutable? #f))
296 `(("r-bsgenome" ,r-bsgenome)))
298 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
299 (synopsis "Full genome sequences for Mouse")
301 "This package provides full genome sequences for Mus musculus (Mouse) as
302 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
303 (license license:artistic2.0)))
305 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
307 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
311 ;; We cannot use bioconductor-uri here because this tarball is
312 ;; located under "data/annotation/" instead of "bioc/".
313 (uri (string-append "http://www.bioconductor.org/packages/"
314 "release/data/annotation/src/contrib/"
315 "BSgenome.Mmusculus.UCSC.mm9.masked_"
319 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
321 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
322 (build-system r-build-system)
324 `(("r-bsgenome" ,r-bsgenome)
325 ("r-bsgenome-mmusculus-ucsc-mm9"
326 ,r-bsgenome-mmusculus-ucsc-mm9)))
327 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
328 (synopsis "Full masked genome sequences for Mouse")
330 "This package provides full genome sequences for Mus musculus (Mouse) as
331 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
332 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
333 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
334 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
335 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
336 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
338 (license license:artistic2.0)))
340 (define-public r-bsgenome-mmusculus-ucsc-mm10
342 (name "r-bsgenome-mmusculus-ucsc-mm10")
346 ;; We cannot use bioconductor-uri here because this tarball is
347 ;; located under "data/annotation/" instead of "bioc/".
348 (uri (string-append "https://www.bioconductor.org/packages/"
349 "release/data/annotation/src/contrib/"
350 "BSgenome.Mmusculus.UCSC.mm10_"
354 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
356 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
357 (build-system r-build-system)
358 ;; As this package provides little more than a very large data file it
359 ;; doesn't make sense to build substitutes.
360 (arguments `(#:substitutable? #f))
362 `(("r-bsgenome" ,r-bsgenome)))
364 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
365 (synopsis "Full genome sequences for Mouse")
367 "This package provides full genome sequences for Mus
368 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
369 in Biostrings objects.")
370 (license license:artistic2.0)))
372 (define-public r-org-ce-eg-db
374 (name "r-org-ce-eg-db")
378 ;; We cannot use bioconductor-uri here because this tarball is
379 ;; located under "data/annotation/" instead of "bioc/".
380 (uri (string-append "https://www.bioconductor.org/packages/"
381 "release/data/annotation/src/contrib/"
382 "org.Ce.eg.db_" version ".tar.gz"))
385 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
387 `((upstream-name . "org.Ce.eg.db")))
388 (build-system r-build-system)
390 `(("r-annotationdbi" ,r-annotationdbi)))
391 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
392 (synopsis "Genome wide annotation for Worm")
394 "This package provides mappings from Entrez gene identifiers to various
395 annotations for the genome of the model worm Caenorhabditis elegans.")
396 (license license:artistic2.0)))
398 (define-public r-org-dm-eg-db
400 (name "r-org-dm-eg-db")
404 ;; We cannot use bioconductor-uri here because this tarball is
405 ;; located under "data/annotation/" instead of "bioc/".
406 (uri (string-append "https://www.bioconductor.org/packages/"
407 "release/data/annotation/src/contrib/"
408 "org.Dm.eg.db_" version ".tar.gz"))
411 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
413 `((upstream-name . "org.Dm.eg.db")))
414 (build-system r-build-system)
416 `(("r-annotationdbi" ,r-annotationdbi)))
417 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
418 (synopsis "Genome wide annotation for Fly")
420 "This package provides mappings from Entrez gene identifiers to various
421 annotations for the genome of the model fruit fly Drosophila melanogaster.")
422 (license license:artistic2.0)))
424 (define-public r-org-dr-eg-db
426 (name "r-org-dr-eg-db")
430 ;; We cannot use bioconductor-uri here because this tarball is
431 ;; located under "data/annotation/" instead of "bioc/".
432 (uri (string-append "https://www.bioconductor.org/packages/"
433 "release/data/annotation/src/contrib/"
434 "org.Dr.eg.db_" version ".tar.gz"))
437 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
439 `((upstream-name . "org.Dr.eg.db")))
440 (build-system r-build-system)
442 `(("r-annotationdbi" ,r-annotationdbi)))
443 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
444 (synopsis "Annotation for Zebrafish")
446 "This package provides genome wide annotations for Zebrafish, primarily
447 based on mapping using Entrez Gene identifiers.")
448 (license license:artistic2.0)))
450 (define-public r-org-hs-eg-db
452 (name "r-org-hs-eg-db")
456 ;; We cannot use bioconductor-uri here because this tarball is
457 ;; located under "data/annotation/" instead of "bioc/".
458 (uri (string-append "https://www.bioconductor.org/packages/"
459 "release/data/annotation/src/contrib/"
460 "org.Hs.eg.db_" version ".tar.gz"))
463 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
465 `((upstream-name . "org.Hs.eg.db")))
466 (build-system r-build-system)
468 `(("r-annotationdbi" ,r-annotationdbi)))
469 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
470 (synopsis "Genome wide annotation for Human")
472 "This package contains genome-wide annotations for Human, primarily based
473 on mapping using Entrez Gene identifiers.")
474 (license license:artistic2.0)))
476 (define-public r-org-mm-eg-db
478 (name "r-org-mm-eg-db")
482 ;; We cannot use bioconductor-uri here because this tarball is
483 ;; located under "data/annotation/" instead of "bioc/".
484 (uri (string-append "https://www.bioconductor.org/packages/"
485 "release/data/annotation/src/contrib/"
486 "org.Mm.eg.db_" version ".tar.gz"))
489 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
491 `((upstream-name . "org.Mm.eg.db")))
492 (build-system r-build-system)
494 `(("r-annotationdbi" ,r-annotationdbi)))
495 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
496 (synopsis "Genome wide annotation for Mouse")
498 "This package provides mappings from Entrez gene identifiers to various
499 annotations for the genome of the model mouse Mus musculus.")
500 (license license:artistic2.0)))
502 (define-public r-bsgenome-hsapiens-ucsc-hg19
504 (name "r-bsgenome-hsapiens-ucsc-hg19")
508 ;; We cannot use bioconductor-uri here because this tarball is
509 ;; located under "data/annotation/" instead of "bioc/".
510 (uri (string-append "https://www.bioconductor.org/packages/"
511 "release/data/annotation/src/contrib/"
512 "BSgenome.Hsapiens.UCSC.hg19_"
516 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
518 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
519 (build-system r-build-system)
520 ;; As this package provides little more than a very large data file it
521 ;; doesn't make sense to build substitutes.
522 (arguments `(#:substitutable? #f))
524 `(("r-bsgenome" ,r-bsgenome)))
526 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
527 (synopsis "Full genome sequences for Homo sapiens")
529 "This package provides full genome sequences for Homo sapiens as provided
530 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
531 (license license:artistic2.0)))
533 (define-public r-genelendatabase
535 (name "r-genelendatabase")
540 ;; We cannot use bioconductor-uri here because this tarball is
541 ;; located under "data/experiment/" instead of "bioc/".
542 (uri (string-append "https://bioconductor.org/packages/"
543 "release/data/experiment/src/contrib"
544 "/geneLenDataBase_" version ".tar.gz"))
547 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
549 `((upstream-name . "geneLenDataBase")))
550 (build-system r-build-system)
552 `(("r-rtracklayer" ,r-rtracklayer)
553 ("r-genomicfeatures" ,r-genomicfeatures)))
554 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
555 (synopsis "Lengths of mRNA transcripts for a number of genomes")
557 "This package provides the lengths of mRNA transcripts for a number of
558 genomes and gene ID formats, largely based on the UCSC table browser.")
559 (license license:lgpl2.0+)))
561 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
563 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
567 ;; We cannot use bioconductor-uri here because this tarball is
568 ;; located under "data/annotation/" instead of "bioc/".
569 (uri (string-append "https://bioconductor.org/packages/"
570 "release/data/annotation/src/contrib"
571 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
575 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
577 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
578 (build-system r-build-system)
579 ;; As this package provides little more than a very large data file it
580 ;; doesn't make sense to build substitutes.
581 (arguments `(#:substitutable? #f))
583 `(("r-genomicfeatures" ,r-genomicfeatures)))
585 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
586 (synopsis "Annotation package for human genome in TxDb format")
588 "This package provides an annotation database of Homo sapiens genome
589 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
590 track. The database is exposed as a @code{TxDb} object.")
591 (license license:artistic2.0)))
593 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
595 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
599 ;; We cannot use bioconductor-uri here because this tarball is
600 ;; located under "data/annotation/" instead of "bioc/".
601 (uri (string-append "https://bioconductor.org/packages/"
602 "release/data/annotation/src/contrib"
603 "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
607 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
609 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
610 (build-system r-build-system)
612 `(("r-genomicfeatures" ,r-genomicfeatures)))
614 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
615 (synopsis "Annotation package for human genome in TxDb format")
617 "This package provides an annotation database of Homo sapiens genome
618 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
619 track. The database is exposed as a @code{TxDb} object.")
620 (license license:artistic2.0)))
622 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
624 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
628 ;; We cannot use bioconductor-uri here because this tarball is
629 ;; located under "data/annotation/" instead of "bioc/".
630 (uri (string-append "https://bioconductor.org/packages/"
631 "release/data/annotation/src/contrib"
632 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
636 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
638 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
639 (build-system r-build-system)
641 `(("r-genomicfeatures" ,r-genomicfeatures)
642 ("r-annotationdbi" ,r-annotationdbi)))
644 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
645 (synopsis "Annotation package for mouse genome in TxDb format")
647 "This package provides an annotation database of Mouse genome data. It
648 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
649 database is exposed as a @code{TxDb} object.")
650 (license license:artistic2.0)))
652 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
654 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
658 ;; We cannot use bioconductor-uri here because this tarball is
659 ;; located under "data/annotation/" instead of "bioc/".
660 (uri (string-append "https://www.bioconductor.org/packages/"
661 "release/data/annotation/src/contrib/"
662 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
666 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
668 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
669 (build-system r-build-system)
670 ;; As this package provides little more than a very large data file it
671 ;; doesn't make sense to build substitutes.
672 (arguments `(#:substitutable? #f))
674 `(("r-bsgenome" ,r-bsgenome)
675 ("r-genomicfeatures" ,r-genomicfeatures)
676 ("r-annotationdbi" ,r-annotationdbi)))
678 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
679 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
681 "This package loads a TxDb object, which is an R interface to
682 prefabricated databases contained in this package. This package provides
683 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
684 based on the knownGene track.")
685 (license license:artistic2.0)))
687 (define-public r-fdb-infiniummethylation-hg19
689 (name "r-fdb-infiniummethylation-hg19")
693 ;; We cannot use bioconductor-uri here because this tarball is
694 ;; located under "data/annotation/" instead of "bioc/".
695 (uri (string-append "https://www.bioconductor.org/packages/"
696 "release/data/annotation/src/contrib/"
697 "FDb.InfiniumMethylation.hg19_"
701 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
703 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
704 (build-system r-build-system)
706 `(("r-biostrings" ,r-biostrings)
707 ("r-genomicfeatures" ,r-genomicfeatures)
708 ("r-annotationdbi" ,r-annotationdbi)
709 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
710 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
711 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
712 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
714 "This is an annotation package for Illumina Infinium DNA methylation
715 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
717 (license license:artistic2.0)))
719 (define-public r-illuminahumanmethylationepicmanifest
721 (name "r-illuminahumanmethylationepicmanifest")
725 ;; We cannot use bioconductor-uri here because this tarball is
726 ;; located under "data/annotation/" instead of "bioc/".
727 (uri (string-append "https://www.bioconductor.org/packages/"
728 "release/data/annotation/src/contrib/"
729 "IlluminaHumanMethylationEPICmanifest_"
733 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
735 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
736 (build-system r-build-system)
738 `(("r-minfi" ,r-minfi)))
739 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
740 (synopsis "Manifest for Illumina's EPIC methylation arrays")
742 "This is a manifest package for Illumina's EPIC methylation arrays.")
743 (license license:artistic2.0)))
745 (define-public r-do-db
751 ;; We cannot use bioconductor-uri here because this tarball is
752 ;; located under "data/annotation/" instead of "bioc/".
753 (uri (string-append "https://www.bioconductor.org/packages/"
754 "release/data/annotation/src/contrib/"
755 "DO.db_" version ".tar.gz"))
758 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
760 `((upstream-name . "DO.db")))
761 (build-system r-build-system)
763 `(("r-annotationdbi" ,r-annotationdbi)))
764 (home-page "https://www.bioconductor.org/packages/DO.db/")
765 (synopsis "Annotation maps describing the entire Disease Ontology")
767 "This package provides a set of annotation maps describing the entire
769 (license license:artistic2.0)))
774 (define-public r-abadata
780 ;; We cannot use bioconductor-uri here because this tarball is
781 ;; located under "data/experiment/" instead of "bioc/".
782 (uri (string-append "https://www.bioconductor.org/packages/"
783 "release/data/experiment/src/contrib/"
784 "ABAData_" version ".tar.gz"))
787 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
789 `((upstream-name . "ABAData")))
790 (build-system r-build-system)
792 `(("r-annotationdbi" ,r-annotationdbi)))
793 (home-page "https://www.bioconductor.org/packages/ABAData/")
794 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
796 "This package provides the data for the gene expression enrichment
797 analysis conducted in the package ABAEnrichment. The package includes three
798 datasets which are derived from the Allen Brain Atlas:
801 @item Gene expression data from Human Brain (adults) averaged across donors,
802 @item Gene expression data from the Developing Human Brain pooled into five
803 age categories and averaged across donors, and
804 @item a developmental effect score based on the Developing Human Brain
808 All datasets are restricted to protein coding genes.")
809 (license license:gpl2+)))
811 (define-public r-arrmdata
817 ;; We cannot use bioconductor-uri here because this tarball is
818 ;; located under "data/experiment/" instead of "bioc/".
819 (uri (string-append "https://www.bioconductor.org/packages/"
820 "release/data/experiment/src/contrib/"
821 "ARRmData_" version ".tar.gz"))
824 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
826 `((upstream-name . "ARRmData")))
827 (build-system r-build-system)
828 (home-page "https://www.bioconductor.org/packages/ARRmData/")
829 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
831 "This package provides raw beta values from 36 samples across 3 groups
832 from Illumina 450k methylation arrays.")
833 (license license:artistic2.0)))
835 (define-public r-hsmmsinglecell
837 (name "r-hsmmsinglecell")
841 ;; We cannot use bioconductor-uri here because this tarball is
842 ;; located under "data/experiment/" instead of "bioc/".
843 (uri (string-append "https://www.bioconductor.org/packages/"
844 "release/data/experiment/src/contrib/"
845 "HSMMSingleCell_" version ".tar.gz"))
848 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
850 `((upstream-name . "HSMMSingleCell")))
851 (build-system r-build-system)
852 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
853 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
855 "Skeletal myoblasts undergo a well-characterized sequence of
856 morphological and transcriptional changes during differentiation. In this
857 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
858 under high mitogen conditions (GM) and then differentiated by switching to
859 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
860 hundred cells taken over a time-course of serum-induced differentiation.
861 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
862 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
863 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
864 which were then sequenced to a depth of ~4 million reads per library,
865 resulting in a complete gene expression profile for each cell.")
866 (license license:artistic2.0)))
874 ;; We cannot use bioconductor-uri here because this tarball is
875 ;; located under "data/experiment/" instead of "bioc/".
876 (uri (string-append "https://www.bioconductor.org/packages/"
877 "release/data/experiment/src/contrib/"
878 "ALL_" version ".tar.gz"))
881 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
882 (properties `((upstream-name . "ALL")))
883 (build-system r-build-system)
885 `(("r-biobase" ,r-biobase)))
886 (home-page "https://bioconductor.org/packages/ALL")
887 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
889 "The data consist of microarrays from 128 different individuals with
890 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
891 are available. The data have been normalized (using rma) and it is the
892 jointly normalized data that are available here. The data are presented in
893 the form of an @code{exprSet} object.")
894 (license license:artistic2.0)))
899 (define-public r-biocgenerics
901 (name "r-biocgenerics")
905 (uri (bioconductor-uri "BiocGenerics" version))
908 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
910 `((upstream-name . "BiocGenerics")))
911 (build-system r-build-system)
912 (home-page "https://bioconductor.org/packages/BiocGenerics")
913 (synopsis "S4 generic functions for Bioconductor")
915 "This package provides S4 generic functions needed by many Bioconductor
917 (license license:artistic2.0)))
919 (define-public r-annotate
926 (uri (bioconductor-uri "annotate" version))
929 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
930 (build-system r-build-system)
932 `(("r-annotationdbi" ,r-annotationdbi)
933 ("r-biobase" ,r-biobase)
934 ("r-biocgenerics" ,r-biocgenerics)
938 ("r-xtable" ,r-xtable)))
940 "https://bioconductor.org/packages/annotate")
941 (synopsis "Annotation for microarrays")
942 (description "This package provides R environments for the annotation of
944 (license license:artistic2.0)))
946 (define-public r-hpar
953 (uri (bioconductor-uri "hpar" version))
956 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
957 (build-system r-build-system)
958 (home-page "https://bioconductor.org/packages/hpar/")
959 (synopsis "Human Protein Atlas in R")
960 (description "This package provides a simple interface to and data from
961 the Human Protein Atlas project.")
962 (license license:artistic2.0)))
964 (define-public r-regioner
971 (uri (bioconductor-uri "regioneR" version))
974 "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
975 (properties `((upstream-name . "regioneR")))
976 (build-system r-build-system)
978 `(("r-biostrings" ,r-biostrings)
979 ("r-bsgenome" ,r-bsgenome)
980 ("r-genomeinfodb" ,r-genomeinfodb)
981 ("r-genomicranges" ,r-genomicranges)
982 ("r-iranges" ,r-iranges)
983 ("r-memoise" ,r-memoise)
984 ("r-rtracklayer" ,r-rtracklayer)
985 ("r-s4vectors" ,r-s4vectors)))
986 (home-page "https://bioconductor.org/packages/regioneR/")
987 (synopsis "Association analysis of genomic regions")
988 (description "This package offers a statistical framework based on
989 customizable permutation tests to assess the association between genomic
990 region sets and other genomic features.")
991 (license license:artistic2.0)))
993 (define-public r-geneplotter
995 (name "r-geneplotter")
1000 (uri (bioconductor-uri "geneplotter" version))
1003 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1004 (build-system r-build-system)
1006 `(("r-annotate" ,r-annotate)
1007 ("r-annotationdbi" ,r-annotationdbi)
1008 ("r-biobase" ,r-biobase)
1009 ("r-biocgenerics" ,r-biocgenerics)
1010 ("r-lattice" ,r-lattice)
1011 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1012 (home-page "https://bioconductor.org/packages/geneplotter")
1013 (synopsis "Graphics functions for genomic data")
1015 "This package provides functions for plotting genomic data.")
1016 (license license:artistic2.0)))
1018 (define-public r-qvalue
1025 (uri (bioconductor-uri "qvalue" version))
1028 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1029 (build-system r-build-system)
1031 `(("r-ggplot2" ,r-ggplot2)
1032 ("r-reshape2" ,r-reshape2)))
1033 (home-page "http://github.com/jdstorey/qvalue")
1034 (synopsis "Q-value estimation for false discovery rate control")
1036 "This package takes a list of p-values resulting from the simultaneous
1037 testing of many hypotheses and estimates their q-values and local @dfn{false
1038 discovery rate} (FDR) values. The q-value of a test measures the proportion
1039 of false positives incurred when that particular test is called significant.
1040 The local FDR measures the posterior probability the null hypothesis is true
1041 given the test's p-value. Various plots are automatically generated, allowing
1042 one to make sensible significance cut-offs. The software can be applied to
1043 problems in genomics, brain imaging, astrophysics, and data mining.")
1044 ;; Any version of the LGPL.
1045 (license license:lgpl3+)))
1047 (define-public r-diffbind
1054 (uri (bioconductor-uri "DiffBind" version))
1057 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1058 (properties `((upstream-name . "DiffBind")))
1059 (build-system r-build-system)
1063 `(("r-amap" ,r-amap)
1064 ("r-biocparallel" ,r-biocparallel)
1065 ("r-deseq2" ,r-deseq2)
1066 ("r-dplyr" ,r-dplyr)
1067 ("r-edger" ,r-edger)
1068 ("r-genomicalignments" ,r-genomicalignments)
1069 ("r-genomicranges" ,r-genomicranges)
1070 ("r-ggplot2" ,r-ggplot2)
1071 ("r-ggrepel" ,r-ggrepel)
1072 ("r-gplots" ,r-gplots)
1073 ("r-iranges" ,r-iranges)
1074 ("r-lattice" ,r-lattice)
1075 ("r-limma" ,r-limma)
1076 ("r-locfit" ,r-locfit)
1077 ("r-rcolorbrewer" , r-rcolorbrewer)
1079 ("r-rhtslib" ,r-rhtslib)
1080 ("r-rsamtools" ,r-rsamtools)
1081 ("r-s4vectors" ,r-s4vectors)
1082 ("r-summarizedexperiment" ,r-summarizedexperiment)
1083 ("r-systempiper" ,r-systempiper)))
1084 (home-page "http://bioconductor.org/packages/DiffBind")
1085 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1087 "This package computes differentially bound sites from multiple
1088 ChIP-seq experiments using affinity (quantitative) data. Also enables
1089 occupancy (overlap) analysis and plotting functions.")
1090 (license license:artistic2.0)))
1092 (define-public r-ripseeker
1094 (name "r-ripseeker")
1099 (uri (bioconductor-uri "RIPSeeker" version))
1102 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1103 (properties `((upstream-name . "RIPSeeker")))
1104 (build-system r-build-system)
1106 `(("r-s4vectors" ,r-s4vectors)
1107 ("r-iranges" ,r-iranges)
1108 ("r-genomicranges" ,r-genomicranges)
1109 ("r-summarizedexperiment" ,r-summarizedexperiment)
1110 ("r-rsamtools" ,r-rsamtools)
1111 ("r-genomicalignments" ,r-genomicalignments)
1112 ("r-rtracklayer" ,r-rtracklayer)))
1113 (home-page "http://bioconductor.org/packages/RIPSeeker")
1115 "Identifying protein-associated transcripts from RIP-seq experiments")
1117 "This package infers and discriminates RIP peaks from RIP-seq alignments
1118 using two-state HMM with negative binomial emission probability. While
1119 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1120 a suite of bioinformatics tools integrated within this self-contained software
1121 package comprehensively addressing issues ranging from post-alignments
1122 processing to visualization and annotation.")
1123 (license license:gpl2)))
1125 (define-public r-multtest
1132 (uri (bioconductor-uri "multtest" version))
1135 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1136 (build-system r-build-system)
1138 `(("r-survival" ,r-survival)
1139 ("r-biocgenerics" ,r-biocgenerics)
1140 ("r-biobase" ,r-biobase)
1141 ("r-mass" ,r-mass)))
1142 (home-page "http://bioconductor.org/packages/multtest")
1143 (synopsis "Resampling-based multiple hypothesis testing")
1145 "This package can do non-parametric bootstrap and permutation
1146 resampling-based multiple testing procedures (including empirical Bayes
1147 methods) for controlling the family-wise error rate (FWER), generalized
1148 family-wise error rate (gFWER), tail probability of the proportion of
1149 false positives (TPPFP), and false discovery rate (FDR). Several choices
1150 of bootstrap-based null distribution are implemented (centered, centered
1151 and scaled, quantile-transformed). Single-step and step-wise methods are
1152 available. Tests based on a variety of T- and F-statistics (including
1153 T-statistics based on regression parameters from linear and survival models
1154 as well as those based on correlation parameters) are included. When probing
1155 hypotheses with T-statistics, users may also select a potentially faster null
1156 distribution which is multivariate normal with mean zero and variance
1157 covariance matrix derived from the vector influence function. Results are
1158 reported in terms of adjusted P-values, confidence regions and test statistic
1159 cutoffs. The procedures are directly applicable to identifying differentially
1160 expressed genes in DNA microarray experiments.")
1161 (license license:lgpl3)))
1163 (define-public r-graph
1169 (uri (bioconductor-uri "graph" version))
1172 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1173 (build-system r-build-system)
1175 `(("r-biocgenerics" ,r-biocgenerics)))
1176 (home-page "https://bioconductor.org/packages/graph")
1177 (synopsis "Handle graph data structures in R")
1179 "This package implements some simple graph handling capabilities for R.")
1180 (license license:artistic2.0)))
1182 (define-public r-codedepends
1184 (name "r-codedepends")
1189 (uri (cran-uri "CodeDepends" version))
1192 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1193 (properties `((upstream-name . "CodeDepends")))
1194 (build-system r-build-system)
1196 `(("r-codetools" ,r-codetools)
1197 ("r-graph" ,r-graph)
1199 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1200 (synopsis "Analysis of R code for reproducible research and code comprehension")
1202 "This package provides tools for analyzing R expressions or blocks of
1203 code and determining the dependencies between them. It focuses on R scripts,
1204 but can be used on the bodies of functions. There are many facilities
1205 including the ability to summarize or get a high-level view of code,
1206 determining dependencies between variables, code improvement suggestions.")
1207 ;; Any version of the GPL
1208 (license (list license:gpl2+ license:gpl3+))))
1210 (define-public r-chippeakanno
1212 (name "r-chippeakanno")
1217 (uri (bioconductor-uri "ChIPpeakAnno" version))
1220 "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
1221 (properties `((upstream-name . "ChIPpeakAnno")))
1222 (build-system r-build-system)
1224 `(("r-annotationdbi" ,r-annotationdbi)
1225 ("r-biobase" ,r-biobase)
1226 ("r-biocgenerics" ,r-biocgenerics)
1227 ("r-biocmanager" ,r-biocmanager)
1228 ("r-biomart" ,r-biomart)
1229 ("r-biostrings" ,r-biostrings)
1230 ("r-bsgenome" ,r-bsgenome)
1232 ("r-delayedarray" ,r-delayedarray)
1233 ("r-ensembldb" ,r-ensembldb)
1234 ("r-genomeinfodb" ,r-genomeinfodb)
1235 ("r-genomicalignments" ,r-genomicalignments)
1236 ("r-genomicfeatures" ,r-genomicfeatures)
1237 ("r-genomicranges" ,r-genomicranges)
1238 ("r-go-db" ,r-go-db)
1239 ("r-graph" ,r-graph)
1241 ("r-iranges" ,r-iranges)
1242 ("r-limma" ,r-limma)
1243 ("r-matrixstats" ,r-matrixstats)
1244 ("r-multtest" ,r-multtest)
1246 ("r-regioner" ,r-regioner)
1247 ("r-rsamtools" ,r-rsamtools)
1248 ("r-rtracklayer" ,r-rtracklayer)
1249 ("r-s4vectors" ,r-s4vectors)
1250 ("r-seqinr" ,r-seqinr)
1251 ("r-summarizedexperiment" ,r-summarizedexperiment)
1252 ("r-venndiagram" ,r-venndiagram)))
1253 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1254 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1256 "The package includes functions to retrieve the sequences around the peak,
1257 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1258 custom features such as most conserved elements and other transcription factor
1259 binding sites supplied by users. Starting 2.0.5, new functions have been added
1260 for finding the peaks with bi-directional promoters with summary statistics
1261 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1262 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1263 enrichedGO (addGeneIDs).")
1264 (license license:gpl2+)))
1266 (define-public r-marray
1272 (uri (bioconductor-uri "marray" version))
1274 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1275 (build-system r-build-system)
1277 `(("r-limma" ,r-limma)))
1278 (home-page "http://bioconductor.org/packages/marray")
1279 (synopsis "Exploratory analysis for two-color spotted microarray data")
1280 (description "This package contains class definitions for two-color spotted
1281 microarray data. It also includes functions for data input, diagnostic plots,
1282 normalization and quality checking.")
1283 (license license:lgpl2.0+)))
1285 (define-public r-cghbase
1291 (uri (bioconductor-uri "CGHbase" version))
1293 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1294 (properties `((upstream-name . "CGHbase")))
1295 (build-system r-build-system)
1297 `(("r-biobase" ,r-biobase)
1298 ("r-marray" ,r-marray)))
1299 (home-page "http://bioconductor.org/packages/CGHbase")
1300 (synopsis "Base functions and classes for arrayCGH data analysis")
1301 (description "This package contains functions and classes that are needed by
1302 the @code{arrayCGH} packages.")
1303 (license license:gpl2+)))
1305 (define-public r-cghcall
1311 (uri (bioconductor-uri "CGHcall" version))
1313 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1314 (properties `((upstream-name . "CGHcall")))
1315 (build-system r-build-system)
1317 `(("r-biobase" ,r-biobase)
1318 ("r-cghbase" ,r-cghbase)
1319 ("r-impute" ,r-impute)
1320 ("r-dnacopy" ,r-dnacopy)
1321 ("r-snowfall" ,r-snowfall)))
1322 (home-page "http://bioconductor.org/packages/CGHcall")
1323 (synopsis "Base functions and classes for arrayCGH data analysis")
1324 (description "This package contains functions and classes that are needed by
1325 @code{arrayCGH} packages.")
1326 (license license:gpl2+)))
1328 (define-public r-qdnaseq
1334 (uri (bioconductor-uri "QDNAseq" version))
1336 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1337 (properties `((upstream-name . "QDNAseq")))
1338 (build-system r-build-system)
1340 `(("r-biobase" ,r-biobase)
1341 ("r-biocparallel" ,r-biocparallel)
1342 ("r-cghbase" ,r-cghbase)
1343 ("r-cghcall" ,r-cghcall)
1344 ("r-dnacopy" ,r-dnacopy)
1345 ("r-genomicranges" ,r-genomicranges)
1346 ("r-iranges" ,r-iranges)
1347 ("r-matrixstats" ,r-matrixstats)
1348 ("r-r-utils" ,r-r-utils)
1349 ("r-rsamtools" ,r-rsamtools)))
1350 (home-page "http://bioconductor.org/packages/QDNAseq")
1351 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1352 (description "The genome is divided into non-overlapping fixed-sized bins,
1353 number of sequence reads in each counted, adjusted with a simultaneous
1354 two-dimensional loess correction for sequence mappability and GC content, and
1355 filtered to remove spurious regions in the genome. Downstream steps of
1356 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1358 (license license:gpl2+)))
1360 (define-public r-bayseq
1367 (uri (bioconductor-uri "baySeq" version))
1370 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1371 (properties `((upstream-name . "baySeq")))
1372 (build-system r-build-system)
1374 `(("r-abind" ,r-abind)
1375 ("r-edger" ,r-edger)
1376 ("r-genomicranges" ,r-genomicranges)))
1377 (home-page "https://bioconductor.org/packages/baySeq/")
1378 (synopsis "Bayesian analysis of differential expression patterns in count data")
1380 "This package identifies differential expression in high-throughput count
1381 data, such as that derived from next-generation sequencing machines,
1382 calculating estimated posterior likelihoods of differential expression (or
1383 more complex hypotheses) via empirical Bayesian methods.")
1384 (license license:gpl3)))
1386 (define-public r-chipcomp
1393 (uri (bioconductor-uri "ChIPComp" version))
1396 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1397 (properties `((upstream-name . "ChIPComp")))
1398 (build-system r-build-system)
1400 `(("r-biocgenerics" ,r-biocgenerics)
1401 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1402 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1403 ("r-genomeinfodb" ,r-genomeinfodb)
1404 ("r-genomicranges" ,r-genomicranges)
1405 ("r-iranges" ,r-iranges)
1406 ("r-limma" ,r-limma)
1407 ("r-rsamtools" ,r-rsamtools)
1408 ("r-rtracklayer" ,r-rtracklayer)
1409 ("r-s4vectors" ,r-s4vectors)))
1410 (home-page "https://bioconductor.org/packages/ChIPComp")
1411 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1413 "ChIPComp implements a statistical method for quantitative comparison of
1414 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1415 sites across multiple conditions considering matching control in ChIP-seq
1417 ;; Any version of the GPL.
1418 (license license:gpl3+)))
1420 (define-public r-riboprofiling
1422 (name "r-riboprofiling")
1427 (uri (bioconductor-uri "RiboProfiling" version))
1430 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1431 (properties `((upstream-name . "RiboProfiling")))
1432 (build-system r-build-system)
1434 `(("r-biocgenerics" ,r-biocgenerics)
1435 ("r-biostrings" ,r-biostrings)
1436 ("r-data-table" ,r-data-table)
1437 ("r-genomeinfodb" ,r-genomeinfodb)
1438 ("r-genomicalignments" ,r-genomicalignments)
1439 ("r-genomicfeatures" ,r-genomicfeatures)
1440 ("r-genomicranges" ,r-genomicranges)
1441 ("r-ggbio" ,r-ggbio)
1442 ("r-ggplot2" ,r-ggplot2)
1443 ("r-iranges" ,r-iranges)
1445 ("r-reshape2" ,r-reshape2)
1446 ("r-rsamtools" ,r-rsamtools)
1447 ("r-rtracklayer" ,r-rtracklayer)
1448 ("r-s4vectors" ,r-s4vectors)
1449 ("r-sqldf" ,r-sqldf)))
1450 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1451 (synopsis "Ribosome profiling data analysis")
1452 (description "Starting with a BAM file, this package provides the
1453 necessary functions for quality assessment, read start position recalibration,
1454 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1455 of count data: pairs, log fold-change, codon frequency and coverage
1456 assessment, principal component analysis on codon coverage.")
1457 (license license:gpl3)))
1459 (define-public r-riboseqr
1466 (uri (bioconductor-uri "riboSeqR" version))
1469 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1470 (properties `((upstream-name . "riboSeqR")))
1471 (build-system r-build-system)
1473 `(("r-abind" ,r-abind)
1474 ("r-bayseq" ,r-bayseq)
1475 ("r-genomeinfodb" ,r-genomeinfodb)
1476 ("r-genomicranges" ,r-genomicranges)
1477 ("r-iranges" ,r-iranges)
1478 ("r-rsamtools" ,r-rsamtools)
1479 ("r-seqlogo" ,r-seqlogo)))
1480 (home-page "https://bioconductor.org/packages/riboSeqR/")
1481 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1483 "This package provides plotting functions, frameshift detection and
1484 parsing of genetic sequencing data from ribosome profiling experiments.")
1485 (license license:gpl3)))
1487 (define-public r-interactionset
1489 (name "r-interactionset")
1494 (uri (bioconductor-uri "InteractionSet" version))
1497 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1499 `((upstream-name . "InteractionSet")))
1500 (build-system r-build-system)
1502 `(("r-biocgenerics" ,r-biocgenerics)
1503 ("r-genomeinfodb" ,r-genomeinfodb)
1504 ("r-genomicranges" ,r-genomicranges)
1505 ("r-iranges" ,r-iranges)
1506 ("r-matrix" ,r-matrix)
1508 ("r-s4vectors" ,r-s4vectors)
1509 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1510 (home-page "https://bioconductor.org/packages/InteractionSet")
1511 (synopsis "Base classes for storing genomic interaction data")
1513 "This package provides the @code{GInteractions},
1514 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1515 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1517 (license license:gpl3)))
1519 (define-public r-genomicinteractions
1521 (name "r-genomicinteractions")
1526 (uri (bioconductor-uri "GenomicInteractions" version))
1529 "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
1531 `((upstream-name . "GenomicInteractions")))
1532 (build-system r-build-system)
1534 `(("r-biobase" ,r-biobase)
1535 ("r-biocgenerics" ,r-biocgenerics)
1536 ("r-data-table" ,r-data-table)
1537 ("r-dplyr" ,r-dplyr)
1538 ("r-genomeinfodb" ,r-genomeinfodb)
1539 ("r-genomicranges" ,r-genomicranges)
1540 ("r-ggplot2" ,r-ggplot2)
1541 ("r-gridextra" ,r-gridextra)
1543 ("r-igraph" ,r-igraph)
1544 ("r-interactionset" ,r-interactionset)
1545 ("r-iranges" ,r-iranges)
1546 ("r-rsamtools" ,r-rsamtools)
1547 ("r-rtracklayer" ,r-rtracklayer)
1548 ("r-s4vectors" ,r-s4vectors)
1549 ("r-stringr" ,r-stringr)))
1550 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1551 (synopsis "R package for handling genomic interaction data")
1553 "This R package provides tools for handling genomic interaction data,
1554 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1555 information and producing various plots and statistics.")
1556 (license license:gpl3)))
1558 (define-public r-ctc
1565 (uri (bioconductor-uri "ctc" version))
1568 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1569 (build-system r-build-system)
1570 (propagated-inputs `(("r-amap" ,r-amap)))
1571 (home-page "https://bioconductor.org/packages/ctc/")
1572 (synopsis "Cluster and tree conversion")
1574 "This package provides tools for exporting and importing classification
1575 trees and clusters to other programs.")
1576 (license license:gpl2)))
1578 (define-public r-goseq
1585 (uri (bioconductor-uri "goseq" version))
1588 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1589 (build-system r-build-system)
1591 `(("r-annotationdbi" ,r-annotationdbi)
1592 ("r-biasedurn" ,r-biasedurn)
1593 ("r-biocgenerics" ,r-biocgenerics)
1594 ("r-genelendatabase" ,r-genelendatabase)
1595 ("r-go-db" ,r-go-db)
1596 ("r-mgcv" ,r-mgcv)))
1597 (home-page "https://bioconductor.org/packages/goseq/")
1598 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1600 "This package provides tools to detect Gene Ontology and/or other user
1601 defined categories which are over/under represented in RNA-seq data.")
1602 (license license:lgpl2.0+)))
1604 (define-public r-glimma
1611 (uri (bioconductor-uri "Glimma" version))
1614 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1615 (properties `((upstream-name . "Glimma")))
1616 (build-system r-build-system)
1618 `(("r-edger" ,r-edger)
1619 ("r-jsonlite" ,r-jsonlite)
1620 ("r-s4vectors" ,r-s4vectors)))
1621 (home-page "https://github.com/Shians/Glimma")
1622 (synopsis "Interactive HTML graphics")
1624 "This package generates interactive visualisations for analysis of
1625 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1626 HTML page. The interactions are built on top of the popular static
1627 representations of analysis results in order to provide additional
1629 (license license:lgpl3)))
1631 (define-public r-rots
1638 (uri (bioconductor-uri "ROTS" version))
1641 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1642 (properties `((upstream-name . "ROTS")))
1643 (build-system r-build-system)
1645 `(("r-biobase" ,r-biobase)
1646 ("r-rcpp" ,r-rcpp)))
1647 (home-page "https://bioconductor.org/packages/ROTS/")
1648 (synopsis "Reproducibility-Optimized Test Statistic")
1650 "This package provides tools for calculating the
1651 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1653 (license license:gpl2+)))
1655 (define-public r-plgem
1662 (uri (bioconductor-uri "plgem" version))
1665 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1666 (build-system r-build-system)
1668 `(("r-biobase" ,r-biobase)
1669 ("r-mass" ,r-mass)))
1670 (home-page "http://www.genopolis.it")
1671 (synopsis "Detect differential expression in microarray and proteomics datasets")
1673 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1674 model the variance-versus-mean dependence that exists in a variety of
1675 genome-wide datasets, including microarray and proteomics data. The use of
1676 PLGEM has been shown to improve the detection of differentially expressed
1677 genes or proteins in these datasets.")
1678 (license license:gpl2)))
1680 (define-public r-inspect
1687 (uri (bioconductor-uri "INSPEcT" version))
1690 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1691 (properties `((upstream-name . "INSPEcT")))
1692 (build-system r-build-system)
1694 `(("r-biobase" ,r-biobase)
1695 ("r-biocgenerics" ,r-biocgenerics)
1696 ("r-biocparallel" ,r-biocparallel)
1697 ("r-deseq2" ,r-deseq2)
1698 ("r-desolve" ,r-desolve)
1699 ("r-genomicalignments" ,r-genomicalignments)
1700 ("r-genomicfeatures" ,r-genomicfeatures)
1701 ("r-genomicranges" ,r-genomicranges)
1702 ("r-iranges" ,r-iranges)
1703 ("r-plgem" ,r-plgem)
1704 ("r-preprocesscore" ,r-preprocesscore)
1706 ("r-rootsolve" ,r-rootsolve)
1707 ("r-rsamtools" ,r-rsamtools)
1708 ("r-s4vectors" ,r-s4vectors)
1709 ("r-shiny" ,r-shiny)
1710 ("r-summarizedexperiment" ,r-summarizedexperiment)
1711 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1712 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1713 (home-page "https://bioconductor.org/packages/INSPEcT")
1714 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1716 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1717 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1718 order to evaluate synthesis, processing and degradation rates and assess via
1719 modeling the rates that determines changes in mature mRNA levels.")
1720 (license license:gpl2)))
1722 (define-public r-dnabarcodes
1724 (name "r-dnabarcodes")
1729 (uri (bioconductor-uri "DNABarcodes" version))
1732 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1733 (properties `((upstream-name . "DNABarcodes")))
1734 (build-system r-build-system)
1737 ("r-matrix" ,r-matrix)
1738 ("r-rcpp" ,r-rcpp)))
1739 (home-page "https://bioconductor.org/packages/DNABarcodes")
1740 (synopsis "Create and analyze DNA barcodes")
1742 "This package offers tools to create DNA barcode sets capable of
1743 correcting insertion, deletion, and substitution errors. Existing barcodes
1744 can be analyzed regarding their minimal, maximal and average distances between
1745 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1746 demultiplexed, i.e. assigned to their original reference barcode.")
1747 (license license:gpl2)))
1749 (define-public r-ruvseq
1756 (uri (bioconductor-uri "RUVSeq" version))
1759 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
1760 (properties `((upstream-name . "RUVSeq")))
1761 (build-system r-build-system)
1763 `(("r-biobase" ,r-biobase)
1764 ("r-edaseq" ,r-edaseq)
1765 ("r-edger" ,r-edger)
1766 ("r-mass" ,r-mass)))
1767 (home-page "https://github.com/drisso/RUVSeq")
1768 (synopsis "Remove unwanted variation from RNA-Seq data")
1770 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1771 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1773 (license license:artistic2.0)))
1775 (define-public r-biocneighbors
1777 (name "r-biocneighbors")
1782 (uri (bioconductor-uri "BiocNeighbors" version))
1785 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
1786 (properties `((upstream-name . "BiocNeighbors")))
1787 (build-system r-build-system)
1789 `(("r-biocgenerics" ,r-biocgenerics)
1790 ("r-biocparallel" ,r-biocparallel)
1792 ("r-rcppannoy" ,r-rcppannoy)
1793 ("r-rcpphnsw" ,r-rcpphnsw)
1794 ("r-s4vectors" ,r-s4vectors)))
1795 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1796 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1798 "This package implements exact and approximate methods for nearest
1799 neighbor detection, in a framework that allows them to be easily switched
1800 within Bioconductor packages or workflows. The exact algorithm is implemented
1801 using pre-clustering with the k-means algorithm. Functions are also provided
1802 to search for all neighbors within a given distance. Parallelization is
1803 achieved for all methods using the BiocParallel framework.")
1804 (license license:gpl3)))
1806 (define-public r-biocsingular
1808 (name "r-biocsingular")
1813 (uri (bioconductor-uri "BiocSingular" version))
1816 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
1817 (properties `((upstream-name . "BiocSingular")))
1818 (build-system r-build-system)
1820 `(("r-beachmat" ,r-beachmat)
1821 ("r-biocgenerics" ,r-biocgenerics)
1822 ("r-biocparallel" ,r-biocparallel)
1823 ("r-delayedarray" ,r-delayedarray)
1824 ("r-irlba" ,r-irlba)
1825 ("r-matrix" ,r-matrix)
1828 ("r-s4vectors" ,r-s4vectors)))
1829 (home-page "https://github.com/LTLA/BiocSingular")
1830 (synopsis "Singular value decomposition for Bioconductor packages")
1832 "This package implements exact and approximate methods for singular value
1833 decomposition and principal components analysis, in a framework that allows
1834 them to be easily switched within Bioconductor packages or workflows. Where
1835 possible, parallelization is achieved using the BiocParallel framework.")
1836 (license license:gpl3)))
1838 (define-public r-destiny
1845 (uri (bioconductor-uri "destiny" version))
1848 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
1849 (build-system r-build-system)
1851 `(("r-biobase" ,r-biobase)
1852 ("r-biocgenerics" ,r-biocgenerics)
1853 ("r-ggplot2" ,r-ggplot2)
1854 ("r-ggthemes" ,r-ggthemes)
1855 ("r-igraph" ,r-igraph)
1856 ("r-matrix" ,r-matrix)
1857 ("r-proxy" ,r-proxy)
1859 ("r-rcppeigen" ,r-rcppeigen)
1860 ("r-scales" ,r-scales)
1861 ("r-scatterplot3d" ,r-scatterplot3d)
1862 ("r-smoother" ,r-smoother)
1863 ("r-summarizedexperiment" ,r-summarizedexperiment)
1865 (home-page "https://bioconductor.org/packages/destiny/")
1866 (synopsis "Create and plot diffusion maps")
1867 (description "This package provides tools to create and plot diffusion
1869 ;; Any version of the GPL
1870 (license license:gpl3+)))
1872 (define-public r-savr
1879 (uri (bioconductor-uri "savR" version))
1882 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
1883 (properties `((upstream-name . "savR")))
1884 (build-system r-build-system)
1886 `(("r-ggplot2" ,r-ggplot2)
1887 ("r-gridextra" ,r-gridextra)
1888 ("r-reshape2" ,r-reshape2)
1889 ("r-scales" ,r-scales)
1891 (home-page "https://github.com/bcalder/savR")
1892 (synopsis "Parse and analyze Illumina SAV files")
1894 "This package provides tools to parse Illumina Sequence Analysis
1895 Viewer (SAV) files, access data, and generate QC plots.")
1896 (license license:agpl3+)))
1898 (define-public r-chipexoqual
1900 (name "r-chipexoqual")
1905 (uri (bioconductor-uri "ChIPexoQual" version))
1908 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
1909 (properties `((upstream-name . "ChIPexoQual")))
1910 (build-system r-build-system)
1912 `(("r-biocparallel" ,r-biocparallel)
1913 ("r-biovizbase" ,r-biovizbase)
1914 ("r-broom" ,r-broom)
1915 ("r-data-table" ,r-data-table)
1916 ("r-dplyr" ,r-dplyr)
1917 ("r-genomeinfodb" ,r-genomeinfodb)
1918 ("r-genomicalignments" ,r-genomicalignments)
1919 ("r-genomicranges" ,r-genomicranges)
1920 ("r-ggplot2" ,r-ggplot2)
1921 ("r-hexbin" ,r-hexbin)
1922 ("r-iranges" ,r-iranges)
1923 ("r-rcolorbrewer" ,r-rcolorbrewer)
1924 ("r-rmarkdown" ,r-rmarkdown)
1925 ("r-rsamtools" ,r-rsamtools)
1926 ("r-s4vectors" ,r-s4vectors)
1927 ("r-scales" ,r-scales)
1928 ("r-viridis" ,r-viridis)))
1929 (home-page "https://github.com/keleslab/ChIPexoQual")
1930 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1932 "This package provides a quality control pipeline for ChIP-exo/nexus
1934 (license license:gpl2+)))
1936 (define-public r-copynumber
1938 (name "r-copynumber")
1942 (uri (bioconductor-uri "copynumber" version))
1945 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
1946 (build-system r-build-system)
1948 `(("r-s4vectors" ,r-s4vectors)
1949 ("r-iranges" ,r-iranges)
1950 ("r-genomicranges" ,r-genomicranges)
1951 ("r-biocgenerics" ,r-biocgenerics)))
1952 (home-page "https://bioconductor.org/packages/copynumber")
1953 (synopsis "Segmentation of single- and multi-track copy number data")
1955 "This package segments single- and multi-track copy number data by a
1956 penalized least squares regression method.")
1957 (license license:artistic2.0)))
1959 (define-public r-dnacopy
1966 (uri (bioconductor-uri "DNAcopy" version))
1969 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
1970 (properties `((upstream-name . "DNAcopy")))
1971 (build-system r-build-system)
1972 (native-inputs `(("gfortran" ,gfortran)))
1973 (home-page "https://bioconductor.org/packages/DNAcopy")
1974 (synopsis "DNA copy number data analysis")
1976 "This package implements the @dfn{circular binary segmentation} (CBS)
1977 algorithm to segment DNA copy number data and identify genomic regions with
1978 abnormal copy number.")
1979 (license license:gpl2+)))
1981 ;; This is a CRAN package, but it uncharacteristically depends on a
1982 ;; Bioconductor package.
1983 (define-public r-htscluster
1985 (name "r-htscluster")
1990 (uri (cran-uri "HTSCluster" version))
1993 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1994 (properties `((upstream-name . "HTSCluster")))
1995 (build-system r-build-system)
1997 `(("r-capushe" ,r-capushe)
1998 ("r-edger" ,r-edger)
1999 ("r-plotrix" ,r-plotrix)))
2000 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2001 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2003 "This package provides a Poisson mixture model is implemented to cluster
2004 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2005 estimation is performed using either the EM or CEM algorithm, and the slope
2006 heuristics are used for model selection (i.e., to choose the number of
2008 (license license:gpl3+)))
2010 (define-public r-deds
2017 (uri (bioconductor-uri "DEDS" version))
2020 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2021 (properties `((upstream-name . "DEDS")))
2022 (build-system r-build-system)
2023 (home-page "https://bioconductor.org/packages/DEDS/")
2024 (synopsis "Differential expression via distance summary for microarray data")
2026 "This library contains functions that calculate various statistics of
2027 differential expression for microarray data, including t statistics, fold
2028 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2029 also implements a new methodology called DEDS (Differential Expression via
2030 Distance Summary), which selects differentially expressed genes by integrating
2031 and summarizing a set of statistics using a weighted distance approach.")
2032 ;; Any version of the LGPL.
2033 (license license:lgpl3+)))
2035 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2037 (define-public r-nbpseq
2044 (uri (cran-uri "NBPSeq" version))
2047 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2048 (properties `((upstream-name . "NBPSeq")))
2049 (build-system r-build-system)
2051 `(("r-qvalue" ,r-qvalue)))
2052 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2053 (synopsis "Negative binomial models for RNA-Seq data")
2055 "This package provides negative binomial models for two-group comparisons
2056 and regression inferences from RNA-sequencing data.")
2057 (license license:gpl2)))
2059 (define-public r-ebseq
2066 (uri (bioconductor-uri "EBSeq" version))
2069 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2070 (properties `((upstream-name . "EBSeq")))
2071 (build-system r-build-system)
2073 `(("r-blockmodeling" ,r-blockmodeling)
2074 ("r-gplots" ,r-gplots)
2075 ("r-testthat" ,r-testthat)))
2076 (home-page "https://bioconductor.org/packages/EBSeq")
2077 (synopsis "Differential expression analysis of RNA-seq data")
2079 "This package provides tools for differential expression analysis at both
2080 gene and isoform level using RNA-seq data")
2081 (license license:artistic2.0)))
2083 (define-public r-lpsymphony
2085 (name "r-lpsymphony")
2090 (uri (bioconductor-uri "lpsymphony" version))
2093 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2094 (build-system r-build-system)
2096 `(("gfortran" ,gfortran)
2099 `(("pkg-config" ,pkg-config)))
2100 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2101 (synopsis "Symphony integer linear programming solver in R")
2103 "This package was derived from Rsymphony. The package provides an R
2104 interface to SYMPHONY, a linear programming solver written in C++. The main
2105 difference between this package and Rsymphony is that it includes the solver
2106 source code, while Rsymphony expects to find header and library files on the
2107 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2108 to install interface to SYMPHONY.")
2109 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2110 ;; lpsimphony is released under the same terms.
2111 (license license:epl1.0)))
2113 (define-public r-ihw
2120 (uri (bioconductor-uri "IHW" version))
2123 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2124 (properties `((upstream-name . "IHW")))
2125 (build-system r-build-system)
2127 `(("r-biocgenerics" ,r-biocgenerics)
2128 ("r-fdrtool" ,r-fdrtool)
2129 ("r-lpsymphony" ,r-lpsymphony)
2130 ("r-slam" ,r-slam)))
2131 (home-page "https://bioconductor.org/packages/IHW")
2132 (synopsis "Independent hypothesis weighting")
2134 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2135 procedure that increases power compared to the method of Benjamini and
2136 Hochberg by assigning data-driven weights to each hypothesis. The input to
2137 IHW is a two-column table of p-values and covariates. The covariate can be
2138 any continuous-valued or categorical variable that is thought to be
2139 informative on the statistical properties of each hypothesis test, while it is
2140 independent of the p-value under the null hypothesis.")
2141 (license license:artistic2.0)))
2143 (define-public r-icobra
2150 (uri (bioconductor-uri "iCOBRA" version))
2153 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2154 (properties `((upstream-name . "iCOBRA")))
2155 (build-system r-build-system)
2157 `(("r-dplyr" ,r-dplyr)
2159 ("r-ggplot2" ,r-ggplot2)
2160 ("r-limma" ,r-limma)
2161 ("r-reshape2" ,r-reshape2)
2163 ("r-scales" ,r-scales)
2164 ("r-shiny" ,r-shiny)
2165 ("r-shinybs" ,r-shinybs)
2166 ("r-shinydashboard" ,r-shinydashboard)
2167 ("r-upsetr" ,r-upsetr)))
2168 (home-page "https://bioconductor.org/packages/iCOBRA")
2169 (synopsis "Comparison and visualization of ranking and assignment methods")
2171 "This package provides functions for calculation and visualization of
2172 performance metrics for evaluation of ranking and binary
2173 classification (assignment) methods. It also contains a Shiny application for
2174 interactive exploration of results.")
2175 (license license:gpl2+)))
2177 (define-public r-mast
2184 (uri (bioconductor-uri "MAST" version))
2187 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2188 (properties `((upstream-name . "MAST")))
2189 (build-system r-build-system)
2191 `(("r-abind" ,r-abind)
2193 ("r-biobase" ,r-biobase)
2194 ("r-biocgenerics" ,r-biocgenerics)
2195 ("r-data-table" ,r-data-table)
2196 ("r-ggplot2" ,r-ggplot2)
2198 ("r-progress" ,r-progress)
2199 ("r-reshape2" ,r-reshape2)
2200 ("r-s4vectors" ,r-s4vectors)
2201 ("r-singlecellexperiment" ,r-singlecellexperiment)
2202 ("r-stringr" ,r-stringr)
2203 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2204 (home-page "https://github.com/RGLab/MAST/")
2205 (synopsis "Model-based analysis of single cell transcriptomics")
2207 "This package provides methods and models for handling zero-inflated
2208 single cell assay data.")
2209 (license license:gpl2+)))
2211 (define-public r-monocle
2218 (uri (bioconductor-uri "monocle" version))
2221 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2222 (build-system r-build-system)
2224 `(("r-biobase" ,r-biobase)
2225 ("r-biocgenerics" ,r-biocgenerics)
2226 ("r-biocviews" ,r-biocviews)
2227 ("r-cluster" ,r-cluster)
2228 ("r-combinat" ,r-combinat)
2229 ("r-ddrtree" ,r-ddrtree)
2230 ("r-densityclust" ,r-densityclust)
2231 ("r-dplyr" ,r-dplyr)
2232 ("r-fastica" ,r-fastica)
2233 ("r-ggplot2" ,r-ggplot2)
2234 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2235 ("r-igraph" ,r-igraph)
2236 ("r-irlba" ,r-irlba)
2237 ("r-limma" ,r-limma)
2239 ("r-matrix" ,r-matrix)
2240 ("r-matrixstats" ,r-matrixstats)
2241 ("r-pheatmap" ,r-pheatmap)
2243 ("r-proxy" ,r-proxy)
2244 ("r-qlcmatrix" ,r-qlcmatrix)
2247 ("r-reshape2" ,r-reshape2)
2248 ("r-rtsne" ,r-rtsne)
2250 ("r-stringr" ,r-stringr)
2251 ("r-tibble" ,r-tibble)
2253 ("r-viridis" ,r-viridis)))
2254 (home-page "https://bioconductor.org/packages/monocle")
2255 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2257 "Monocle performs differential expression and time-series analysis for
2258 single-cell expression experiments. It orders individual cells according to
2259 progress through a biological process, without knowing ahead of time which
2260 genes define progress through that process. Monocle also performs
2261 differential expression analysis, clustering, visualization, and other useful
2262 tasks on single cell expression data. It is designed to work with RNA-Seq and
2263 qPCR data, but could be used with other types as well.")
2264 (license license:artistic2.0)))
2266 (define-public r-noiseq
2273 (uri (bioconductor-uri "NOISeq" version))
2276 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2277 (properties `((upstream-name . "NOISeq")))
2278 (build-system r-build-system)
2280 `(("r-biobase" ,r-biobase)
2281 ("r-matrix" ,r-matrix)))
2282 (home-page "https://bioconductor.org/packages/NOISeq")
2283 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2285 "This package provides tools to support the analysis of RNA-seq
2286 expression data or other similar kind of data. It provides exploratory plots
2287 to evaluate saturation, count distribution, expression per chromosome, type of
2288 detected features, features length, etc. It also supports the analysis of
2289 differential expression between two experimental conditions with no parametric
2291 (license license:artistic2.0)))
2293 (define-public r-scdd
2300 (uri (bioconductor-uri "scDD" version))
2303 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2304 (properties `((upstream-name . "scDD")))
2305 (build-system r-build-system)
2308 ("r-biocparallel" ,r-biocparallel)
2309 ("r-ebseq" ,r-ebseq)
2310 ("r-fields" ,r-fields)
2311 ("r-ggplot2" ,r-ggplot2)
2312 ("r-mclust" ,r-mclust)
2313 ("r-outliers" ,r-outliers)
2314 ("r-s4vectors" ,r-s4vectors)
2315 ("r-scran" ,r-scran)
2316 ("r-singlecellexperiment" ,r-singlecellexperiment)
2317 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2318 (home-page "https://github.com/kdkorthauer/scDD")
2319 (synopsis "Mixture modeling of single-cell RNA-seq data")
2321 "This package implements a method to analyze single-cell RNA-seq data
2322 utilizing flexible Dirichlet Process mixture models. Genes with differential
2323 distributions of expression are classified into several interesting patterns
2324 of differences between two conditions. The package also includes functions
2325 for simulating data with these patterns from negative binomial
2327 (license license:gpl2)))
2329 (define-public r-scone
2336 (uri (bioconductor-uri "scone" version))
2339 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2340 (build-system r-build-system)
2342 `(("r-aroma-light" ,r-aroma-light)
2343 ("r-biocparallel" ,r-biocparallel)
2345 ("r-class" ,r-class)
2346 ("r-cluster" ,r-cluster)
2347 ("r-compositions" ,r-compositions)
2348 ("r-diptest" ,r-diptest)
2349 ("r-edger" ,r-edger)
2351 ("r-gplots" ,r-gplots)
2352 ("r-hexbin" ,r-hexbin)
2353 ("r-limma" ,r-limma)
2354 ("r-matrixstats" ,r-matrixstats)
2355 ("r-mixtools" ,r-mixtools)
2356 ("r-rarpack" ,r-rarpack)
2357 ("r-rcolorbrewer" ,r-rcolorbrewer)
2358 ("r-rhdf5" ,r-rhdf5)
2359 ("r-ruvseq" ,r-ruvseq)
2360 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2361 (home-page "https://bioconductor.org/packages/scone")
2362 (synopsis "Single cell overview of normalized expression data")
2364 "SCONE is an R package for comparing and ranking the performance of
2365 different normalization schemes for single-cell RNA-seq and other
2366 high-throughput analyses.")
2367 (license license:artistic2.0)))
2369 (define-public r-geoquery
2376 (uri (bioconductor-uri "GEOquery" version))
2379 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2380 (properties `((upstream-name . "GEOquery")))
2381 (build-system r-build-system)
2383 `(("r-biobase" ,r-biobase)
2384 ("r-dplyr" ,r-dplyr)
2386 ("r-limma" ,r-limma)
2387 ("r-magrittr" ,r-magrittr)
2388 ("r-readr" ,r-readr)
2389 ("r-tidyr" ,r-tidyr)
2390 ("r-xml2" ,r-xml2)))
2391 (home-page "https://github.com/seandavi/GEOquery/")
2392 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2394 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2395 microarray data. Given the rich and varied nature of this resource, it is
2396 only natural to want to apply BioConductor tools to these data. GEOquery is
2397 the bridge between GEO and BioConductor.")
2398 (license license:gpl2)))
2400 (define-public r-illuminaio
2402 (name "r-illuminaio")
2407 (uri (bioconductor-uri "illuminaio" version))
2410 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2411 (build-system r-build-system)
2413 `(("r-base64" ,r-base64)))
2414 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2415 (synopsis "Parse Illumina microarray output files")
2417 "This package provides tools for parsing Illumina's microarray output
2418 files, including IDAT.")
2419 (license license:gpl2)))
2421 (define-public r-siggenes
2428 (uri (bioconductor-uri "siggenes" version))
2431 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2432 (build-system r-build-system)
2434 `(("r-biobase" ,r-biobase)
2435 ("r-multtest" ,r-multtest)
2436 ("r-scrime" ,r-scrime)))
2437 (home-page "https://bioconductor.org/packages/siggenes/")
2439 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2441 "This package provides tools for the identification of differentially
2442 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2443 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2444 Bayes Analyses of Microarrays} (EBAM).")
2445 (license license:lgpl2.0+)))
2447 (define-public r-bumphunter
2449 (name "r-bumphunter")
2454 (uri (bioconductor-uri "bumphunter" version))
2457 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2458 (build-system r-build-system)
2460 `(("r-annotationdbi" ,r-annotationdbi)
2461 ("r-biocgenerics" ,r-biocgenerics)
2462 ("r-dorng" ,r-dorng)
2463 ("r-foreach" ,r-foreach)
2464 ("r-genomeinfodb" ,r-genomeinfodb)
2465 ("r-genomicfeatures" ,r-genomicfeatures)
2466 ("r-genomicranges" ,r-genomicranges)
2467 ("r-iranges" ,r-iranges)
2468 ("r-iterators" ,r-iterators)
2469 ("r-limma" ,r-limma)
2470 ("r-locfit" ,r-locfit)
2471 ("r-matrixstats" ,r-matrixstats)
2472 ("r-s4vectors" ,r-s4vectors)))
2473 (home-page "https://github.com/ririzarr/bumphunter")
2474 (synopsis "Find bumps in genomic data")
2476 "This package provides tools for finding bumps in genomic data in order
2477 to identify differentially methylated regions in epigenetic epidemiology
2479 (license license:artistic2.0)))
2481 (define-public r-minfi
2488 (uri (bioconductor-uri "minfi" version))
2491 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2492 (build-system r-build-system)
2494 `(("r-beanplot" ,r-beanplot)
2495 ("r-biobase" ,r-biobase)
2496 ("r-biocgenerics" ,r-biocgenerics)
2497 ("r-biocparallel" ,r-biocparallel)
2498 ("r-biostrings" ,r-biostrings)
2499 ("r-bumphunter" ,r-bumphunter)
2500 ("r-data-table" ,r-data-table)
2501 ("r-delayedarray" ,r-delayedarray)
2502 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2503 ("r-genefilter" ,r-genefilter)
2504 ("r-genomeinfodb" ,r-genomeinfodb)
2505 ("r-genomicranges" ,r-genomicranges)
2506 ("r-geoquery" ,r-geoquery)
2507 ("r-hdf5array" ,r-hdf5array)
2508 ("r-illuminaio" ,r-illuminaio)
2509 ("r-iranges" ,r-iranges)
2510 ("r-lattice" ,r-lattice)
2511 ("r-limma" ,r-limma)
2513 ("r-mclust" ,r-mclust)
2515 ("r-nor1mix" ,r-nor1mix)
2516 ("r-preprocesscore" ,r-preprocesscore)
2517 ("r-quadprog" ,r-quadprog)
2518 ("r-rcolorbrewer" ,r-rcolorbrewer)
2519 ("r-reshape" ,r-reshape)
2520 ("r-s4vectors" ,r-s4vectors)
2521 ("r-siggenes" ,r-siggenes)
2522 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2523 (home-page "https://github.com/hansenlab/minfi")
2524 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2526 "This package provides tools to analyze and visualize Illumina Infinium
2527 methylation arrays.")
2528 (license license:artistic2.0)))
2530 (define-public r-methylumi
2532 (name "r-methylumi")
2537 (uri (bioconductor-uri "methylumi" version))
2540 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2541 (build-system r-build-system)
2543 `(("r-annotate" ,r-annotate)
2544 ("r-annotationdbi" ,r-annotationdbi)
2545 ("r-biobase" ,r-biobase)
2546 ("r-biocgenerics" ,r-biocgenerics)
2547 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2548 ("r-genefilter" ,r-genefilter)
2549 ("r-genomeinfodb" ,r-genomeinfodb)
2550 ("r-genomicranges" ,r-genomicranges)
2551 ("r-ggplot2" ,r-ggplot2)
2552 ("r-illuminaio" ,r-illuminaio)
2553 ("r-iranges" ,r-iranges)
2554 ("r-lattice" ,r-lattice)
2555 ("r-matrixstats" ,r-matrixstats)
2556 ("r-minfi" ,r-minfi)
2557 ("r-reshape2" ,r-reshape2)
2558 ("r-s4vectors" ,r-s4vectors)
2559 ("r-scales" ,r-scales)
2560 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2561 (home-page "https://bioconductor.org/packages/methylumi")
2562 (synopsis "Handle Illumina methylation data")
2564 "This package provides classes for holding and manipulating Illumina
2565 methylation data. Based on eSet, it can contain MIAME information, sample
2566 information, feature information, and multiple matrices of data. An
2567 \"intelligent\" import function, methylumiR can read the Illumina text files
2568 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2569 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2570 background correction, and quality control features for GoldenGate, Infinium,
2571 and Infinium HD arrays are also included.")
2572 (license license:gpl2)))
2574 (define-public r-lumi
2581 (uri (bioconductor-uri "lumi" version))
2584 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2585 (build-system r-build-system)
2587 `(("r-affy" ,r-affy)
2588 ("r-annotate" ,r-annotate)
2589 ("r-annotationdbi" ,r-annotationdbi)
2590 ("r-biobase" ,r-biobase)
2592 ("r-genomicfeatures" ,r-genomicfeatures)
2593 ("r-genomicranges" ,r-genomicranges)
2594 ("r-kernsmooth" ,r-kernsmooth)
2595 ("r-lattice" ,r-lattice)
2597 ("r-methylumi" ,r-methylumi)
2599 ("r-nleqslv" ,r-nleqslv)
2600 ("r-preprocesscore" ,r-preprocesscore)
2601 ("r-rsqlite" ,r-rsqlite)))
2602 (home-page "https://bioconductor.org/packages/lumi")
2603 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2605 "The lumi package provides an integrated solution for the Illumina
2606 microarray data analysis. It includes functions of Illumina
2607 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2608 variance stabilization, normalization and gene annotation at the probe level.
2609 It also includes the functions of processing Illumina methylation microarrays,
2610 especially Illumina Infinium methylation microarrays.")
2611 (license license:lgpl2.0+)))
2613 (define-public r-linnorm
2620 (uri (bioconductor-uri "Linnorm" version))
2623 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2624 (properties `((upstream-name . "Linnorm")))
2625 (build-system r-build-system)
2627 `(("r-amap" ,r-amap)
2628 ("r-apcluster" ,r-apcluster)
2629 ("r-ellipse" ,r-ellipse)
2630 ("r-fastcluster" ,r-fastcluster)
2632 ("r-ggdendro" ,r-ggdendro)
2633 ("r-ggplot2" ,r-ggplot2)
2634 ("r-gmodels" ,r-gmodels)
2635 ("r-igraph" ,r-igraph)
2636 ("r-limma" ,r-limma)
2638 ("r-mclust" ,r-mclust)
2640 ("r-rcpparmadillo" ,r-rcpparmadillo)
2641 ("r-rtsne" ,r-rtsne)
2642 ("r-statmod" ,r-statmod)
2643 ("r-vegan" ,r-vegan)
2645 (home-page "http://www.jjwanglab.org/Linnorm/")
2646 (synopsis "Linear model and normality based transformation method")
2648 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2649 count data or any large scale count data. It transforms such datasets for
2650 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2651 the following pipelines are implemented:
2654 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2655 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2656 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2657 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2658 @item Differential expression analysis or differential peak detection using
2659 limma (@code{Linnorm.limma})
2660 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2661 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2662 @item Stable gene selection for scRNA-seq data; for users without or who do
2663 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2664 @item Data imputation (@code{Linnorm.DataImput}).
2667 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2668 @code{RnaXSim} function is included for simulating RNA-seq data for the
2669 evaluation of DEG analysis methods.")
2670 (license license:expat)))
2672 (define-public r-ioniser
2679 (uri (bioconductor-uri "IONiseR" version))
2682 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2683 (properties `((upstream-name . "IONiseR")))
2684 (build-system r-build-system)
2686 `(("r-biocgenerics" ,r-biocgenerics)
2687 ("r-biocparallel" ,r-biocparallel)
2688 ("r-biostrings" ,r-biostrings)
2689 ("r-bit64" ,r-bit64)
2690 ("r-dplyr" ,r-dplyr)
2691 ("r-ggplot2" ,r-ggplot2)
2692 ("r-magrittr" ,r-magrittr)
2693 ("r-rhdf5" ,r-rhdf5)
2694 ("r-shortread" ,r-shortread)
2695 ("r-stringr" ,r-stringr)
2696 ("r-tibble" ,r-tibble)
2697 ("r-tidyr" ,r-tidyr)
2698 ("r-xvector" ,r-xvector)))
2699 (home-page "https://bioconductor.org/packages/IONiseR/")
2700 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2702 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2703 MinION data. It extracts summary statistics from a set of fast5 files and can
2704 be used either before or after base calling. In addition to standard
2705 summaries of the read-types produced, it provides a number of plots for
2706 visualising metrics relative to experiment run time or spatially over the
2707 surface of a flowcell.")
2708 (license license:expat)))
2710 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2711 (define-public r-gkmsvm
2718 (uri (cran-uri "gkmSVM" version))
2721 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2722 (properties `((upstream-name . "gkmSVM")))
2723 (build-system r-build-system)
2725 `(("r-biocgenerics" ,r-biocgenerics)
2726 ("r-biostrings" ,r-biostrings)
2727 ("r-genomeinfodb" ,r-genomeinfodb)
2728 ("r-genomicranges" ,r-genomicranges)
2729 ("r-iranges" ,r-iranges)
2730 ("r-kernlab" ,r-kernlab)
2733 ("r-rtracklayer" ,r-rtracklayer)
2734 ("r-s4vectors" ,r-s4vectors)
2735 ("r-seqinr" ,r-seqinr)))
2736 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2737 (synopsis "Gapped-kmer support vector machine")
2739 "This R package provides tools for training gapped-kmer SVM classifiers
2740 for DNA and protein sequences. This package supports several sequence
2741 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2742 (license license:gpl2+)))
2744 (define-public r-triform
2751 (uri (bioconductor-uri "triform" version))
2754 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
2755 (build-system r-build-system)
2757 `(("r-biocgenerics" ,r-biocgenerics)
2758 ("r-iranges" ,r-iranges)
2759 ("r-yaml" ,r-yaml)))
2760 (home-page "https://bioconductor.org/packages/triform/")
2761 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2763 "The Triform algorithm uses model-free statistics to identify peak-like
2764 distributions of TF ChIP sequencing reads, taking advantage of an improved
2765 peak definition in combination with known profile characteristics.")
2766 (license license:gpl2)))
2768 (define-public r-varianttools
2770 (name "r-varianttools")
2775 (uri (bioconductor-uri "VariantTools" version))
2778 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
2779 (properties `((upstream-name . "VariantTools")))
2780 (build-system r-build-system)
2782 `(("r-biobase" ,r-biobase)
2783 ("r-biocgenerics" ,r-biocgenerics)
2784 ("r-biocparallel" ,r-biocparallel)
2785 ("r-biostrings" ,r-biostrings)
2786 ("r-bsgenome" ,r-bsgenome)
2787 ("r-genomeinfodb" ,r-genomeinfodb)
2788 ("r-genomicfeatures" ,r-genomicfeatures)
2789 ("r-genomicranges" ,r-genomicranges)
2790 ("r-iranges" ,r-iranges)
2791 ("r-matrix" ,r-matrix)
2792 ("r-rsamtools" ,r-rsamtools)
2793 ("r-rtracklayer" ,r-rtracklayer)
2794 ("r-s4vectors" ,r-s4vectors)
2795 ("r-variantannotation" ,r-variantannotation)))
2796 (home-page "https://bioconductor.org/packages/VariantTools/")
2797 (synopsis "Tools for exploratory analysis of variant calls")
2799 "Explore, diagnose, and compare variant calls using filters. The
2800 VariantTools package supports a workflow for loading data, calling single
2801 sample variants and tumor-specific somatic mutations or other sample-specific
2802 variant types (e.g., RNA editing). Most of the functions operate on
2803 alignments (BAM files) or datasets of called variants. The user is expected
2804 to have already aligned the reads with a separate tool, e.g., GSNAP via
2806 (license license:artistic2.0)))
2808 (define-public r-heatplus
2815 (uri (bioconductor-uri "Heatplus" version))
2818 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
2819 (properties `((upstream-name . "Heatplus")))
2820 (build-system r-build-system)
2822 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2823 (home-page "https://github.com/alexploner/Heatplus")
2824 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2826 "This package provides tools to display a rectangular heatmap (intensity
2827 plot) of a data matrix. By default, both samples (columns) and features (row)
2828 of the matrix are sorted according to a hierarchical clustering, and the
2829 corresponding dendrogram is plotted. Optionally, panels with additional
2830 information about samples and features can be added to the plot.")
2831 (license license:gpl2+)))
2833 (define-public r-gosemsim
2840 (uri (bioconductor-uri "GOSemSim" version))
2843 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
2844 (properties `((upstream-name . "GOSemSim")))
2845 (build-system r-build-system)
2847 `(("r-annotationdbi" ,r-annotationdbi)
2848 ("r-go-db" ,r-go-db)
2849 ("r-rcpp" ,r-rcpp)))
2850 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2851 (synopsis "GO-terms semantic similarity measures")
2853 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2854 quantitative ways to compute similarities between genes and gene groups, and
2855 have became important basis for many bioinformatics analysis approaches.
2856 GOSemSim is an R package for semantic similarity computation among GO terms,
2857 sets of GO terms, gene products and gene clusters.")
2858 (license license:artistic2.0)))
2860 (define-public r-anota
2867 (uri (bioconductor-uri "anota" version))
2870 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
2871 (build-system r-build-system)
2873 `(("r-multtest" ,r-multtest)
2874 ("r-qvalue" ,r-qvalue)))
2875 (home-page "https://bioconductor.org/packages/anota/")
2876 (synopsis "Analysis of translational activity")
2878 "Genome wide studies of translational control is emerging as a tool to
2879 study various biological conditions. The output from such analysis is both
2880 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2881 involved in translation (the actively translating mRNA level) for each mRNA.
2882 The standard analysis of such data strives towards identifying differential
2883 translational between two or more sample classes - i.e. differences in
2884 actively translated mRNA levels that are independent of underlying differences
2885 in cytosolic mRNA levels. This package allows for such analysis using partial
2886 variances and the random variance model. As 10s of thousands of mRNAs are
2887 analyzed in parallel the library performs a number of tests to assure that
2888 the data set is suitable for such analysis.")
2889 (license license:gpl3)))
2891 (define-public r-sigpathway
2893 (name "r-sigpathway")
2898 (uri (bioconductor-uri "sigPathway" version))
2901 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
2902 (properties `((upstream-name . "sigPathway")))
2903 (build-system r-build-system)
2904 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2905 (synopsis "Pathway analysis")
2907 "This package is used to conduct pathway analysis by calculating the NT_k
2908 and NE_k statistics in a statistical framework for determining whether a
2909 specified group of genes for a pathway has a coordinated association with a
2910 phenotype of interest.")
2911 (license license:gpl2)))
2913 (define-public r-fgsea
2920 (uri (bioconductor-uri "fgsea" version))
2923 "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
2924 (build-system r-build-system)
2927 ("r-biocparallel" ,r-biocparallel)
2928 ("r-data-table" ,r-data-table)
2929 ("r-fastmatch" ,r-fastmatch)
2930 ("r-ggplot2" ,r-ggplot2)
2931 ("r-gridextra" ,r-gridextra)
2932 ("r-matrix" ,r-matrix)
2933 ("r-rcpp" ,r-rcpp)))
2934 (home-page "https://github.com/ctlab/fgsea/")
2935 (synopsis "Fast gene set enrichment analysis")
2937 "The package implements an algorithm for fast gene set enrichment
2938 analysis. Using the fast algorithm allows to make more permutations and get
2939 more fine grained p-values, which allows to use accurate stantard approaches
2940 to multiple hypothesis correction.")
2941 (license license:expat)))
2943 (define-public r-dose
2950 (uri (bioconductor-uri "DOSE" version))
2953 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
2954 (properties `((upstream-name . "DOSE")))
2955 (build-system r-build-system)
2957 `(("r-annotationdbi" ,r-annotationdbi)
2958 ("r-biocparallel" ,r-biocparallel)
2959 ("r-do-db" ,r-do-db)
2960 ("r-fgsea" ,r-fgsea)
2961 ("r-ggplot2" ,r-ggplot2)
2962 ("r-gosemsim" ,r-gosemsim)
2963 ("r-qvalue" ,r-qvalue)
2964 ("r-reshape2" ,r-reshape2)
2965 ("r-s4vectors" ,r-s4vectors)))
2966 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2967 (synopsis "Disease ontology semantic and enrichment analysis")
2969 "This package implements five methods proposed by Resnik, Schlicker,
2970 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2971 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2972 including hypergeometric model and gene set enrichment analysis are also
2973 implemented for discovering disease associations of high-throughput biological
2975 (license license:artistic2.0)))
2977 (define-public r-enrichplot
2979 (name "r-enrichplot")
2984 (uri (bioconductor-uri "enrichplot" version))
2987 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
2988 (build-system r-build-system)
2990 `(("r-annotationdbi" ,r-annotationdbi)
2991 ("r-cowplot" ,r-cowplot)
2993 ("r-europepmc" ,r-europepmc)
2994 ("r-ggplot2" ,r-ggplot2)
2995 ("r-ggplotify" ,r-ggplotify)
2996 ("r-ggraph" ,r-ggraph)
2997 ("r-ggridges" ,r-ggridges)
2998 ("r-gosemsim" ,r-gosemsim)
2999 ("r-gridextra" ,r-gridextra)
3000 ("r-igraph" ,r-igraph)
3001 ("r-purrr" ,r-purrr)
3002 ("r-rcolorbrewer" ,r-rcolorbrewer)
3003 ("r-reshape2" ,r-reshape2)
3004 ("r-upsetr" ,r-upsetr)))
3005 (home-page "https://github.com/GuangchuangYu/enrichplot")
3006 (synopsis "Visualization of functional enrichment result")
3008 "The enrichplot package implements several visualization methods for
3009 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3010 All the visualization methods are developed based on ggplot2 graphics.")
3011 (license license:artistic2.0)))
3013 (define-public r-clusterprofiler
3015 (name "r-clusterprofiler")
3020 (uri (bioconductor-uri "clusterProfiler" version))
3023 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3025 `((upstream-name . "clusterProfiler")))
3026 (build-system r-build-system)
3028 `(("r-annotationdbi" ,r-annotationdbi)
3030 ("r-enrichplot" ,r-enrichplot)
3031 ("r-ggplot2" ,r-ggplot2)
3032 ("r-go-db" ,r-go-db)
3033 ("r-gosemsim" ,r-gosemsim)
3034 ("r-magrittr" ,r-magrittr)
3036 ("r-qvalue" ,r-qvalue)
3037 ("r-rvcheck" ,r-rvcheck)
3038 ("r-tidyr" ,r-tidyr)))
3039 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3040 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3042 "This package implements methods to analyze and visualize functional
3043 profiles (GO and KEGG) of gene and gene clusters.")
3044 (license license:artistic2.0)))
3046 (define-public r-mlinterfaces
3048 (name "r-mlinterfaces")
3053 (uri (bioconductor-uri "MLInterfaces" version))
3056 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
3057 (properties `((upstream-name . "MLInterfaces")))
3058 (build-system r-build-system)
3060 `(("r-annotate" ,r-annotate)
3061 ("r-biobase" ,r-biobase)
3062 ("r-biocgenerics" ,r-biocgenerics)
3063 ("r-cluster" ,r-cluster)
3066 ("r-gdata" ,r-gdata)
3067 ("r-genefilter" ,r-genefilter)
3068 ("r-ggvis" ,r-ggvis)
3069 ("r-hwriter" ,r-hwriter)
3071 ("r-mlbench" ,r-mlbench)
3073 ("r-rcolorbrewer" ,r-rcolorbrewer)
3075 ("r-rpart" ,r-rpart)
3076 ("r-sfsmisc" ,r-sfsmisc)
3077 ("r-shiny" ,r-shiny)
3078 ("r-threejs" ,r-threejs)))
3079 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3080 (synopsis "Interfaces to R machine learning procedures")
3082 "This package provides uniform interfaces to machine learning code for
3083 data in R and Bioconductor containers.")
3084 ;; Any version of the LGPL.
3085 (license license:lgpl2.1+)))
3087 (define-public r-annaffy
3094 (uri (bioconductor-uri "annaffy" version))
3097 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3098 (build-system r-build-system)
3101 (modify-phases %standard-phases
3102 (add-after 'unpack 'remove-reference-to-non-free-data
3104 (substitute* "DESCRIPTION"
3108 `(("r-annotationdbi" ,r-annotationdbi)
3109 ("r-biobase" ,r-biobase)
3111 ("r-go-db" ,r-go-db)))
3112 (home-page "https://bioconductor.org/packages/annaffy/")
3113 (synopsis "Annotation tools for Affymetrix biological metadata")
3115 "This package provides functions for handling data from Bioconductor
3116 Affymetrix annotation data packages. It produces compact HTML and text
3117 reports including experimental data and URL links to many online databases.
3118 It allows searching of biological metadata using various criteria.")
3119 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3120 ;; the LGPL 2.1 is included.
3121 (license license:lgpl2.1+)))
3123 (define-public r-a4core
3130 (uri (bioconductor-uri "a4Core" version))
3133 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3134 (properties `((upstream-name . "a4Core")))
3135 (build-system r-build-system)
3137 `(("r-biobase" ,r-biobase)
3138 ("r-glmnet" ,r-glmnet)))
3139 (home-page "https://bioconductor.org/packages/a4Core")
3140 (synopsis "Automated Affymetrix array analysis core package")
3142 "This is the core package for the automated analysis of Affymetrix
3144 (license license:gpl3)))
3146 (define-public r-a4classif
3148 (name "r-a4classif")
3153 (uri (bioconductor-uri "a4Classif" version))
3156 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3157 (properties `((upstream-name . "a4Classif")))
3158 (build-system r-build-system)
3160 `(("r-a4core" ,r-a4core)
3161 ("r-a4preproc" ,r-a4preproc)
3162 ("r-glmnet" ,r-glmnet)
3163 ("r-mlinterfaces" ,r-mlinterfaces)
3166 ("r-varselrf" ,r-varselrf)))
3167 (home-page "https://bioconductor.org/packages/a4Classif/")
3168 (synopsis "Automated Affymetrix array analysis classification package")
3170 "This is the classification package for the automated analysis of
3171 Affymetrix arrays.")
3172 (license license:gpl3)))
3174 (define-public r-a4preproc
3176 (name "r-a4preproc")
3181 (uri (bioconductor-uri "a4Preproc" version))
3184 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3185 (properties `((upstream-name . "a4Preproc")))
3186 (build-system r-build-system)
3188 `(("r-annotationdbi" ,r-annotationdbi)))
3189 (home-page "https://bioconductor.org/packages/a4Preproc/")
3190 (synopsis "Automated Affymetrix array analysis preprocessing package")
3192 "This is a package for the automated analysis of Affymetrix arrays. It
3193 is used for preprocessing the arrays.")
3194 (license license:gpl3)))
3196 (define-public r-a4reporting
3198 (name "r-a4reporting")
3203 (uri (bioconductor-uri "a4Reporting" version))
3206 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3207 (properties `((upstream-name . "a4Reporting")))
3208 (build-system r-build-system)
3210 `(("r-annaffy" ,r-annaffy)
3211 ("r-xtable" ,r-xtable)))
3212 (home-page "https://bioconductor.org/packages/a4Reporting/")
3213 (synopsis "Automated Affymetrix array analysis reporting package")
3215 "This is a package for the automated analysis of Affymetrix arrays. It
3216 provides reporting features.")
3217 (license license:gpl3)))
3219 (define-public r-a4base
3226 (uri (bioconductor-uri "a4Base" version))
3229 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3230 (properties `((upstream-name . "a4Base")))
3231 (build-system r-build-system)
3233 `(("r-a4core" ,r-a4core)
3234 ("r-a4preproc" ,r-a4preproc)
3235 ("r-annaffy" ,r-annaffy)
3236 ("r-annotationdbi" ,r-annotationdbi)
3237 ("r-biobase" ,r-biobase)
3238 ("r-genefilter" ,r-genefilter)
3239 ("r-glmnet" ,r-glmnet)
3240 ("r-gplots" ,r-gplots)
3241 ("r-limma" ,r-limma)
3243 ("r-multtest" ,r-multtest)))
3244 (home-page "https://bioconductor.org/packages/a4Base/")
3245 (synopsis "Automated Affymetrix array analysis base package")
3247 "This package provides basic features for the automated analysis of
3248 Affymetrix arrays.")
3249 (license license:gpl3)))
3258 (uri (bioconductor-uri "a4" version))
3261 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3262 (build-system r-build-system)
3264 `(("r-a4base" ,r-a4base)
3265 ("r-a4classif" ,r-a4classif)
3266 ("r-a4core" ,r-a4core)
3267 ("r-a4preproc" ,r-a4preproc)
3268 ("r-a4reporting" ,r-a4reporting)))
3269 (home-page "https://bioconductor.org/packages/a4/")
3270 (synopsis "Automated Affymetrix array analysis umbrella package")
3272 "This package provides a software suite for the automated analysis of
3273 Affymetrix arrays.")
3274 (license license:gpl3)))
3276 (define-public r-abseqr
3283 (uri (bioconductor-uri "abseqR" version))
3286 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3287 (properties `((upstream-name . "abseqR")))
3288 (build-system r-build-system)
3290 `(("pandoc" ,ghc-pandoc)))
3292 `(("r-biocparallel" ,r-biocparallel)
3293 ("r-biocstyle" ,r-biocstyle)
3294 ("r-circlize" ,r-circlize)
3295 ("r-flexdashboard" ,r-flexdashboard)
3296 ("r-ggcorrplot" ,r-ggcorrplot)
3297 ("r-ggdendro" ,r-ggdendro)
3298 ("r-ggplot2" ,r-ggplot2)
3299 ("r-gridextra" ,r-gridextra)
3300 ("r-knitr" ,r-knitr)
3301 ("r-plotly" ,r-plotly)
3304 ("r-rcolorbrewer" ,r-rcolorbrewer)
3305 ("r-reshape2" ,r-reshape2)
3306 ("r-rmarkdown" ,r-rmarkdown)
3307 ("r-stringr" ,r-stringr)
3308 ("r-vegan" ,r-vegan)
3309 ("r-venndiagram" ,r-venndiagram)))
3310 (home-page "https://github.com/malhamdoosh/abseqR")
3311 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3313 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3314 sequencing datasets generated from antibody libraries and abseqR is one of its
3315 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3316 capabilities and allows them to generate interactive HTML reports for the
3317 convenience of viewing and sharing with other researchers. Additionally,
3318 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3319 further downstream analysis on its output.")
3320 (license license:gpl3)))
3322 (define-public r-bacon
3329 (uri (bioconductor-uri "bacon" version))
3332 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3333 (build-system r-build-system)
3335 `(("r-biocparallel" ,r-biocparallel)
3336 ("r-ellipse" ,r-ellipse)
3337 ("r-ggplot2" ,r-ggplot2)))
3338 (home-page "https://bioconductor.org/packages/bacon/")
3339 (synopsis "Controlling bias and inflation in association studies")
3341 "Bacon can be used to remove inflation and bias often observed in
3342 epigenome- and transcriptome-wide association studies. To this end bacon
3343 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3344 fitting a three-component normal mixture on z-scores.")
3345 (license license:gpl2+)))
3347 (define-public r-rgadem
3354 (uri (bioconductor-uri "rGADEM" version))
3357 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3358 (properties `((upstream-name . "rGADEM")))
3359 (build-system r-build-system)
3361 `(("r-biostrings" ,r-biostrings)
3362 ("r-bsgenome" ,r-bsgenome)
3363 ("r-iranges" ,r-iranges)
3364 ("r-seqlogo" ,r-seqlogo)))
3365 (home-page "https://bioconductor.org/packages/rGADEM/")
3366 (synopsis "De novo sequence motif discovery")
3368 "rGADEM is an efficient de novo motif discovery tool for large-scale
3369 genomic sequence data.")
3370 (license license:artistic2.0)))
3372 (define-public r-motiv
3379 (uri (bioconductor-uri "MotIV" version))
3382 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3383 (properties `((upstream-name . "MotIV")))
3384 (build-system r-build-system)
3388 `(("r-biocgenerics" ,r-biocgenerics)
3389 ("r-biostrings" ,r-biostrings)
3390 ("r-iranges" ,r-iranges)
3391 ("r-lattice" ,r-lattice)
3392 ("r-rgadem" ,r-rgadem)
3393 ("r-s4vectors" ,r-s4vectors)))
3394 (home-page "https://bioconductor.org/packages/MotIV/")
3395 (synopsis "Motif identification and validation")
3397 "This package is used for the identification and validation of sequence
3398 motifs. It makes use of STAMP for comparing a set of motifs to a given
3399 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3400 distributions, modules and filter motifs.")
3401 (license license:gpl2)))
3403 (define-public r-motifstack
3405 (name "r-motifstack")
3410 (uri (bioconductor-uri "motifStack" version))
3413 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3414 (properties `((upstream-name . "motifStack")))
3415 (build-system r-build-system)
3417 `(("r-ade4" ,r-ade4)
3418 ("r-biostrings" ,r-biostrings)
3419 ("r-grimport2" ,r-grimport2)
3420 ("r-htmlwidgets" ,r-htmlwidgets)
3421 ("r-motiv" ,r-motiv)
3422 ("r-scales" ,r-scales)
3424 (home-page "https://bioconductor.org/packages/motifStack/")
3425 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3427 "The motifStack package is designed for graphic representation of
3428 multiple motifs with different similarity scores. It works with both DNA/RNA
3429 sequence motifs and amino acid sequence motifs. In addition, it provides the
3430 flexibility for users to customize the graphic parameters such as the font
3431 type and symbol colors.")
3432 (license license:gpl2+)))
3434 (define-public r-genomicscores
3436 (name "r-genomicscores")
3441 (uri (bioconductor-uri "GenomicScores" version))
3444 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3445 (properties `((upstream-name . "GenomicScores")))
3446 (build-system r-build-system)
3448 `(("r-annotationhub" ,r-annotationhub)
3449 ("r-biobase" ,r-biobase)
3450 ("r-biocgenerics" ,r-biocgenerics)
3451 ("r-biostrings" ,r-biostrings)
3452 ("r-bsgenome" ,r-bsgenome)
3453 ("r-genomeinfodb" ,r-genomeinfodb)
3454 ("r-genomicranges" ,r-genomicranges)
3455 ("r-iranges" ,r-iranges)
3456 ("r-s4vectors" ,r-s4vectors)
3458 (home-page "https://github.com/rcastelo/GenomicScores/")
3459 (synopsis "Work with genome-wide position-specific scores")
3461 "This package provides infrastructure to store and access genome-wide
3462 position-specific scores within R and Bioconductor.")
3463 (license license:artistic2.0)))
3465 (define-public r-atacseqqc
3467 (name "r-atacseqqc")
3472 (uri (bioconductor-uri "ATACseqQC" version))
3475 "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
3476 (properties `((upstream-name . "ATACseqQC")))
3477 (build-system r-build-system)
3479 `(("r-biocgenerics" ,r-biocgenerics)
3480 ("r-biostrings" ,r-biostrings)
3481 ("r-bsgenome" ,r-bsgenome)
3482 ("r-chippeakanno" ,r-chippeakanno)
3483 ("r-edger" ,r-edger)
3484 ("r-genomeinfodb" ,r-genomeinfodb)
3485 ("r-genomicalignments" ,r-genomicalignments)
3486 ("r-genomicranges" ,r-genomicranges)
3487 ("r-genomicscores" ,r-genomicscores)
3488 ("r-iranges" ,r-iranges)
3489 ("r-kernsmooth" ,r-kernsmooth)
3490 ("r-limma" ,r-limma)
3491 ("r-motifstack" ,r-motifstack)
3492 ("r-preseqr" ,r-preseqr)
3493 ("r-randomforest" ,r-randomforest)
3494 ("r-rsamtools" ,r-rsamtools)
3495 ("r-rtracklayer" ,r-rtracklayer)
3496 ("r-s4vectors" ,r-s4vectors)))
3497 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3498 (synopsis "ATAC-seq quality control")
3500 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3501 sequencing, is a rapid and sensitive method for chromatin accessibility
3502 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3503 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3504 assess whether their ATAC-seq experiment is successful. It includes
3505 diagnostic plots of fragment size distribution, proportion of mitochondria
3506 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3508 (license license:gpl2+)))
3510 (define-public r-gofuncr
3517 (uri (bioconductor-uri "GOfuncR" version))
3520 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3521 (properties `((upstream-name . "GOfuncR")))
3522 (build-system r-build-system)
3524 `(("r-annotationdbi" ,r-annotationdbi)
3525 ("r-genomicranges" ,r-genomicranges)
3526 ("r-gtools" ,r-gtools)
3527 ("r-iranges" ,r-iranges)
3528 ("r-mapplots" ,r-mapplots)
3530 ("r-vioplot" ,r-vioplot)))
3531 (home-page "https://bioconductor.org/packages/GOfuncR/")
3532 (synopsis "Gene ontology enrichment using FUNC")
3534 "GOfuncR performs a gene ontology enrichment analysis based on the
3535 ontology enrichment software FUNC. GO-annotations are obtained from
3536 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3537 included in the package and updated regularly. GOfuncR provides the standard
3538 candidate vs background enrichment analysis using the hypergeometric test, as
3539 well as three additional tests:
3542 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3543 @item a binomial test that is used when genes are associated with two counts,
3545 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3546 associated with four counts.
3549 To correct for multiple testing and interdependency of the tests, family-wise
3550 error rates are computed based on random permutations of the gene-associated
3551 variables. GOfuncR also provides tools for exploring the ontology graph and
3552 the annotations, and options to take gene-length or spatial clustering of
3553 genes into account. It is also possible to provide custom gene coordinates,
3554 annotations and ontologies.")
3555 (license license:gpl2+)))
3557 (define-public r-abaenrichment
3559 (name "r-abaenrichment")
3564 (uri (bioconductor-uri "ABAEnrichment" version))
3567 "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
3568 (properties `((upstream-name . "ABAEnrichment")))
3569 (build-system r-build-system)
3571 `(("r-abadata" ,r-abadata)
3572 ("r-data-table" ,r-data-table)
3573 ("r-gofuncr" ,r-gofuncr)
3574 ("r-gplots" ,r-gplots)
3575 ("r-gtools" ,r-gtools)
3576 ("r-rcpp" ,r-rcpp)))
3577 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3578 (synopsis "Gene expression enrichment in human brain regions")
3580 "The package ABAEnrichment is designed to test for enrichment of user
3581 defined candidate genes in the set of expressed genes in different human brain
3582 regions. The core function @code{aba_enrich} integrates the expression of the
3583 candidate gene set (averaged across donors) and the structural information of
3584 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3585 (license license:gpl2+)))
3587 (define-public r-annotationfuncs
3589 (name "r-annotationfuncs")
3594 (uri (bioconductor-uri "AnnotationFuncs" version))
3597 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3599 `((upstream-name . "AnnotationFuncs")))
3600 (build-system r-build-system)
3602 `(("r-annotationdbi" ,r-annotationdbi)
3604 (home-page "https://www.iysik.com/r/annotationfuncs")
3605 (synopsis "Annotation translation functions")
3607 "This package provides functions for handling translating between
3608 different identifieres using the Biocore Data Team data-packages (e.g.
3609 @code{org.Bt.eg.db}).")
3610 (license license:gpl2)))
3612 (define-public r-annotationtools
3614 (name "r-annotationtools")
3619 (uri (bioconductor-uri "annotationTools" version))
3622 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3624 `((upstream-name . "annotationTools")))
3625 (build-system r-build-system)
3626 (propagated-inputs `(("r-biobase" ,r-biobase)))
3627 (home-page "https://bioconductor.org/packages/annotationTools/")
3628 (synopsis "Annotate microarrays and perform gene expression analyses")
3630 "This package provides functions to annotate microarrays, find orthologs,
3631 and integrate heterogeneous gene expression profiles using annotation and
3632 other molecular biology information available as flat file database (plain
3634 ;; Any version of the GPL.
3635 (license (list license:gpl2+))))
3637 (define-public r-allelicimbalance
3639 (name "r-allelicimbalance")
3644 (uri (bioconductor-uri "AllelicImbalance" version))
3647 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3649 `((upstream-name . "AllelicImbalance")))
3650 (build-system r-build-system)
3652 `(("r-annotationdbi" ,r-annotationdbi)
3653 ("r-biocgenerics" ,r-biocgenerics)
3654 ("r-biostrings" ,r-biostrings)
3655 ("r-bsgenome" ,r-bsgenome)
3656 ("r-genomeinfodb" ,r-genomeinfodb)
3657 ("r-genomicalignments" ,r-genomicalignments)
3658 ("r-genomicfeatures" ,r-genomicfeatures)
3659 ("r-genomicranges" ,r-genomicranges)
3660 ("r-gridextra" ,r-gridextra)
3662 ("r-iranges" ,r-iranges)
3663 ("r-lattice" ,r-lattice)
3664 ("r-latticeextra" ,r-latticeextra)
3666 ("r-rsamtools" ,r-rsamtools)
3667 ("r-s4vectors" ,r-s4vectors)
3668 ("r-seqinr" ,r-seqinr)
3669 ("r-summarizedexperiment" ,r-summarizedexperiment)
3670 ("r-variantannotation" ,r-variantannotation)))
3671 (home-page "https://github.com/pappewaio/AllelicImbalance")
3672 (synopsis "Investigate allele-specific expression")
3674 "This package provides a framework for allele-specific expression
3675 investigation using RNA-seq data.")
3676 (license license:gpl3)))
3678 (define-public r-aucell
3685 (uri (bioconductor-uri "AUCell" version))
3688 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
3689 (properties `((upstream-name . "AUCell")))
3690 (build-system r-build-system)
3692 `(("r-data-table" ,r-data-table)
3693 ("r-gseabase" ,r-gseabase)
3694 ("r-mixtools" ,r-mixtools)
3695 ("r-r-utils" ,r-r-utils)
3696 ("r-shiny" ,r-shiny)
3697 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3698 (home-page "https://bioconductor.org/packages/AUCell/")
3699 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3701 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3702 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3703 Under the Curve} (AUC) to calculate whether a critical subset of the input
3704 gene set is enriched within the expressed genes for each cell. The
3705 distribution of AUC scores across all the cells allows exploring the relative
3706 expression of the signature. Since the scoring method is ranking-based,
3707 AUCell is independent of the gene expression units and the normalization
3708 procedure. In addition, since the cells are evaluated individually, it can
3709 easily be applied to bigger datasets, subsetting the expression matrix if
3711 (license license:gpl3)))
3713 (define-public r-ebimage
3720 (uri (bioconductor-uri "EBImage" version))
3723 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
3724 (properties `((upstream-name . "EBImage")))
3725 (build-system r-build-system)
3727 `(("r-abind" ,r-abind)
3728 ("r-biocgenerics" ,r-biocgenerics)
3729 ("r-fftwtools" ,r-fftwtools)
3730 ("r-htmltools" ,r-htmltools)
3731 ("r-htmlwidgets" ,r-htmlwidgets)
3733 ("r-locfit" ,r-locfit)
3735 ("r-rcurl" ,r-rcurl)
3736 ("r-tiff" ,r-tiff)))
3738 `(("r-knitr" ,r-knitr))) ; for vignettes
3739 (home-page "https://github.com/aoles/EBImage")
3740 (synopsis "Image processing and analysis toolbox for R")
3742 "EBImage provides general purpose functionality for image processing and
3743 analysis. In the context of (high-throughput) microscopy-based cellular
3744 assays, EBImage offers tools to segment cells and extract quantitative
3745 cellular descriptors. This allows the automation of such tasks using the R
3746 programming language and facilitates the use of other tools in the R
3747 environment for signal processing, statistical modeling, machine learning and
3748 visualization with image data.")
3749 ;; Any version of the LGPL.
3750 (license license:lgpl2.1+)))
3752 (define-public r-yamss
3759 (uri (bioconductor-uri "yamss" version))
3762 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
3763 (build-system r-build-system)
3765 `(("r-biocgenerics" ,r-biocgenerics)
3766 ("r-data-table" ,r-data-table)
3767 ("r-ebimage" ,r-ebimage)
3768 ("r-iranges" ,r-iranges)
3769 ("r-limma" ,r-limma)
3770 ("r-matrix" ,r-matrix)
3772 ("r-s4vectors" ,r-s4vectors)
3773 ("r-summarizedexperiment"
3774 ,r-summarizedexperiment)))
3775 (home-page "https://github.com/hansenlab/yamss")
3776 (synopsis "Tools for high-throughput metabolomics")
3778 "This package provides tools to analyze and visualize high-throughput
3779 metabolomics data acquired using chromatography-mass spectrometry. These tools
3780 preprocess data in a way that enables reliable and powerful differential
3782 (license license:artistic2.0)))
3784 (define-public r-gtrellis
3791 (uri (bioconductor-uri "gtrellis" version))
3794 "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
3795 (build-system r-build-system)
3797 `(("r-circlize" ,r-circlize)
3798 ("r-genomicranges" ,r-genomicranges)
3799 ("r-getoptlong" ,r-getoptlong)
3800 ("r-iranges" ,r-iranges)))
3801 (home-page "https://github.com/jokergoo/gtrellis")
3802 (synopsis "Genome level Trellis layout")
3804 "Genome level Trellis graph visualizes genomic data conditioned by
3805 genomic categories (e.g. chromosomes). For each genomic category, multiple
3806 dimensional data which are represented as tracks describe different features
3807 from different aspects. This package provides high flexibility to arrange
3808 genomic categories and to add self-defined graphics in the plot.")
3809 (license license:expat)))
3811 (define-public r-somaticsignatures
3813 (name "r-somaticsignatures")
3818 (uri (bioconductor-uri "SomaticSignatures" version))
3821 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
3823 `((upstream-name . "SomaticSignatures")))
3824 (build-system r-build-system)
3826 `(("r-biobase" ,r-biobase)
3827 ("r-biostrings" ,r-biostrings)
3828 ("r-genomeinfodb" ,r-genomeinfodb)
3829 ("r-genomicranges" ,r-genomicranges)
3830 ("r-ggbio" ,r-ggbio)
3831 ("r-ggplot2" ,r-ggplot2)
3832 ("r-iranges" ,r-iranges)
3834 ("r-pcamethods" ,r-pcamethods)
3835 ("r-proxy" ,r-proxy)
3836 ("r-reshape2" ,r-reshape2)
3837 ("r-s4vectors" ,r-s4vectors)
3838 ("r-variantannotation" ,r-variantannotation)))
3839 (home-page "https://github.com/juliangehring/SomaticSignatures")
3840 (synopsis "Somatic signatures")
3842 "This package identifies mutational signatures of @dfn{single nucleotide
3843 variants} (SNVs). It provides a infrastructure related to the methodology
3844 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3845 decomposition algorithms.")
3846 (license license:expat)))
3848 (define-public r-yapsa
3855 (uri (bioconductor-uri "YAPSA" version))
3858 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
3859 (properties `((upstream-name . "YAPSA")))
3860 (build-system r-build-system)
3862 `(("r-circlize" ,r-circlize)
3863 ("r-complexheatmap" ,r-complexheatmap)
3864 ("r-corrplot" ,r-corrplot)
3865 ("r-dendextend" ,r-dendextend)
3866 ("r-genomeinfodb" ,r-genomeinfodb)
3867 ("r-genomicranges" ,r-genomicranges)
3868 ("r-getoptlong" ,r-getoptlong)
3869 ("r-ggplot2" ,r-ggplot2)
3870 ("r-gridextra" ,r-gridextra)
3871 ("r-gtrellis" ,r-gtrellis)
3872 ("r-keggrest" ,r-keggrest)
3874 ("r-pmcmr" ,r-pmcmr)
3875 ("r-reshape2" ,r-reshape2)
3876 ("r-somaticsignatures" ,r-somaticsignatures)
3877 ("r-variantannotation" ,r-variantannotation)))
3878 (home-page "https://bioconductor.org/packages/YAPSA/")
3879 (synopsis "Yet another package for signature analysis")
3881 "This package provides functions and routines useful in the analysis of
3882 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3883 functions to perform a signature analysis with known signatures and a
3884 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3886 (license license:gpl3)))
3888 (define-public r-gcrma
3895 (uri (bioconductor-uri "gcrma" version))
3898 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
3899 (build-system r-build-system)
3901 `(("r-affy" ,r-affy)
3902 ("r-affyio" ,r-affyio)
3903 ("r-biobase" ,r-biobase)
3904 ("r-biocmanager" ,r-biocmanager)
3905 ("r-biostrings" ,r-biostrings)
3906 ("r-xvector" ,r-xvector)))
3907 (home-page "https://bioconductor.org/packages/gcrma/")
3908 (synopsis "Background adjustment using sequence information")
3910 "Gcrma adjusts for background intensities in Affymetrix array data which
3911 include optical noise and @dfn{non-specific binding} (NSB). The main function
3912 @code{gcrma} converts background adjusted probe intensities to expression
3913 measures using the same normalization and summarization methods as a
3914 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
3915 to estimate probe affinity to NSB. The sequence information is summarized in
3916 a more complex way than the simple GC content. Instead, the base types (A, T,
3917 G or C) at each position along the probe determine the affinity of each probe.
3918 The parameters of the position-specific base contributions to the probe
3919 affinity is estimated in an NSB experiment in which only NSB but no
3920 gene-specific bidning is expected.")
3921 ;; Any version of the LGPL
3922 (license license:lgpl2.1+)))
3924 (define-public r-simpleaffy
3926 (name "r-simpleaffy")
3931 (uri (bioconductor-uri "simpleaffy" version))
3934 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
3935 (build-system r-build-system)
3937 `(("r-affy" ,r-affy)
3938 ("r-biobase" ,r-biobase)
3939 ("r-biocgenerics" ,r-biocgenerics)
3940 ("r-gcrma" ,r-gcrma)
3941 ("r-genefilter" ,r-genefilter)))
3942 (home-page "https://bioconductor.org/packages/simpleaffy/")
3943 (synopsis "Very simple high level analysis of Affymetrix data")
3945 "This package provides high level functions for reading Affy @file{.CEL}
3946 files, phenotypic data, and then computing simple things with it, such as
3947 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
3948 library. It also has some basic scatter plot functions and mechanisms for
3949 generating high resolution journal figures.")
3950 (license license:gpl2+)))
3952 (define-public r-yaqcaffy
3959 (uri (bioconductor-uri "yaqcaffy" version))
3962 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
3963 (build-system r-build-system)
3965 `(("r-simpleaffy" ,r-simpleaffy)))
3966 (home-page "https://bioconductor.org/packages/yaqcaffy/")
3967 (synopsis "Affymetrix quality control and reproducibility analysis")
3969 "This is a package that can be used for quality control of Affymetrix
3970 GeneChip expression data and reproducibility analysis of human whole genome
3971 chips with the MAQC reference datasets.")
3972 (license license:artistic2.0)))
3974 (define-public r-quantro
3981 (uri (bioconductor-uri "quantro" version))
3984 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
3985 (build-system r-build-system)
3987 `(("r-biobase" ,r-biobase)
3988 ("r-doparallel" ,r-doparallel)
3989 ("r-foreach" ,r-foreach)
3990 ("r-ggplot2" ,r-ggplot2)
3991 ("r-iterators" ,r-iterators)
3992 ("r-minfi" ,r-minfi)
3993 ("r-rcolorbrewer" ,r-rcolorbrewer)))
3994 (home-page "https://bioconductor.org/packages/quantro/")
3995 (synopsis "Test for when to use quantile normalization")
3997 "This package provides a data-driven test for the assumptions of quantile
3998 normalization using raw data such as objects that inherit eSets (e.g.
3999 ExpressionSet, MethylSet). Group level information about each sample (such as
4000 Tumor / Normal status) must also be provided because the test assesses if
4001 there are global differences in the distributions between the user-defined
4003 (license license:gpl3+)))
4005 (define-public r-yarn
4012 (uri (bioconductor-uri "yarn" version))
4015 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4016 (build-system r-build-system)
4018 `(("r-biobase" ,r-biobase)
4019 ("r-biomart" ,r-biomart)
4020 ("r-downloader" ,r-downloader)
4021 ("r-edger" ,r-edger)
4022 ("r-gplots" ,r-gplots)
4023 ("r-limma" ,r-limma)
4024 ("r-matrixstats" ,r-matrixstats)
4025 ("r-preprocesscore" ,r-preprocesscore)
4026 ("r-quantro" ,r-quantro)
4027 ("r-rcolorbrewer" ,r-rcolorbrewer)
4028 ("r-readr" ,r-readr)))
4029 (home-page "https://bioconductor.org/packages/yarn/")
4030 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4032 "Expedite large RNA-Seq analyses using a combination of previously
4033 developed tools. YARN is meant to make it easier for the user in performing
4034 basic mis-annotation quality control, filtering, and condition-aware
4035 normalization. YARN leverages many Bioconductor tools and statistical
4036 techniques to account for the large heterogeneity and sparsity found in very
4037 large RNA-seq experiments.")
4038 (license license:artistic2.0)))
4040 (define-public r-roar
4047 (uri (bioconductor-uri "roar" version))
4050 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4051 (build-system r-build-system)
4053 `(("r-biocgenerics" ,r-biocgenerics)
4054 ("r-genomeinfodb" ,r-genomeinfodb)
4055 ("r-genomicalignments" ,r-genomicalignments)
4056 ("r-genomicranges" ,r-genomicranges)
4057 ("r-iranges" ,r-iranges)
4058 ("r-rtracklayer" ,r-rtracklayer)
4059 ("r-s4vectors" ,r-s4vectors)
4060 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4061 (home-page "https://github.com/vodkatad/roar/")
4062 (synopsis "Identify differential APA usage from RNA-seq alignments")
4064 "This package provides tools for identifying preferential usage of APA
4065 sites, comparing two biological conditions, starting from known alternative
4066 sites and alignments obtained from standard RNA-seq experiments.")
4067 (license license:gpl3)))
4069 (define-public r-xbseq
4076 (uri (bioconductor-uri "XBSeq" version))
4079 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4080 (properties `((upstream-name . "XBSeq")))
4081 (build-system r-build-system)
4083 `(("r-biobase" ,r-biobase)
4084 ("r-deseq2" ,r-deseq2)
4085 ("r-dplyr" ,r-dplyr)
4086 ("r-ggplot2" ,r-ggplot2)
4087 ("r-locfit" ,r-locfit)
4088 ("r-magrittr" ,r-magrittr)
4089 ("r-matrixstats" ,r-matrixstats)
4090 ("r-pracma" ,r-pracma)
4091 ("r-roar" ,r-roar)))
4092 (home-page "https://github.com/Liuy12/XBSeq")
4093 (synopsis "Test for differential expression for RNA-seq data")
4095 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4096 expression} (DE), where a statistical model was established based on the
4097 assumption that observed signals are the convolution of true expression
4098 signals and sequencing noises. The mapped reads in non-exonic regions are
4099 considered as sequencing noises, which follows a Poisson distribution. Given
4100 measurable observed signal and background noise from RNA-seq data, true
4101 expression signals, assuming governed by the negative binomial distribution,
4102 can be delineated and thus the accurate detection of differential expressed
4104 (license license:gpl3+)))
4106 (define-public r-massspecwavelet
4108 (name "r-massspecwavelet")
4113 (uri (bioconductor-uri "MassSpecWavelet" version))
4116 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4118 `((upstream-name . "MassSpecWavelet")))
4119 (build-system r-build-system)
4121 `(("r-waveslim" ,r-waveslim)))
4122 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4123 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4125 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4126 data mainly through the use of wavelet transforms. It supports peak detection
4127 based on @dfn{Continuous Wavelet Transform} (CWT).")
4128 (license license:lgpl2.0+)))
4130 (define-public r-xcms
4137 (uri (bioconductor-uri "xcms" version))
4140 "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
4141 (build-system r-build-system)
4143 `(("r-biobase" ,r-biobase)
4144 ("r-biocgenerics" ,r-biocgenerics)
4145 ("r-biocparallel" ,r-biocparallel)
4146 ("r-lattice" ,r-lattice)
4147 ("r-massspecwavelet" ,r-massspecwavelet)
4148 ("r-msnbase" ,r-msnbase)
4149 ("r-multtest" ,r-multtest)
4152 ("r-protgenerics" ,r-protgenerics)
4154 ("r-rcolorbrewer" ,r-rcolorbrewer)
4155 ("r-robustbase" ,r-robustbase)
4156 ("r-s4vectors" ,r-s4vectors)))
4157 (home-page "https://bioconductor.org/packages/xcms/")
4158 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4160 "This package provides a framework for processing and visualization of
4161 chromatographically separated and single-spectra mass spectral data. It
4162 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4163 data for high-throughput, untargeted analyte profiling.")
4164 (license license:gpl2+)))
4166 (define-public r-wrench
4173 (uri (bioconductor-uri "Wrench" version))
4176 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4177 (properties `((upstream-name . "Wrench")))
4178 (build-system r-build-system)
4180 `(("r-limma" ,r-limma)
4181 ("r-locfit" ,r-locfit)
4182 ("r-matrixstats" ,r-matrixstats)))
4183 (home-page "https://github.com/HCBravoLab/Wrench")
4184 (synopsis "Wrench normalization for sparse count data")
4186 "Wrench is a package for normalization sparse genomic count data, like
4187 that arising from 16s metagenomic surveys.")
4188 (license license:artistic2.0)))
4190 (define-public r-wiggleplotr
4192 (name "r-wiggleplotr")
4197 (uri (bioconductor-uri "wiggleplotr" version))
4200 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4201 (build-system r-build-system)
4203 `(("r-assertthat" ,r-assertthat)
4204 ("r-cowplot" ,r-cowplot)
4205 ("r-dplyr" ,r-dplyr)
4206 ("r-genomeinfodb" ,r-genomeinfodb)
4207 ("r-genomicranges" ,r-genomicranges)
4208 ("r-ggplot2" ,r-ggplot2)
4209 ("r-iranges" ,r-iranges)
4210 ("r-purrr" ,r-purrr)
4211 ("r-rtracklayer" ,r-rtracklayer)
4212 ("r-s4vectors" ,r-s4vectors)))
4213 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4214 (synopsis "Make read coverage plots from BigWig files")
4216 "This package provides tools to visualize read coverage from sequencing
4217 experiments together with genomic annotations (genes, transcripts, peaks).
4218 Introns of long transcripts can be rescaled to a fixed length for better
4219 visualization of exonic read coverage.")
4220 (license license:asl2.0)))
4222 (define-public r-widgettools
4224 (name "r-widgettools")
4229 (uri (bioconductor-uri "widgetTools" version))
4232 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4233 (properties `((upstream-name . "widgetTools")))
4234 (build-system r-build-system)
4235 (home-page "https://bioconductor.org/packages/widgetTools/")
4236 (synopsis "Tools for creating interactive tcltk widgets")
4238 "This package contains tools to support the construction of tcltk
4240 ;; Any version of the LGPL.
4241 (license license:lgpl3+)))
4243 (define-public r-webbioc
4250 (uri (bioconductor-uri "webbioc" version))
4253 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4254 (build-system r-build-system)
4256 `(("netpbm" ,netpbm)
4259 `(("r-affy" ,r-affy)
4260 ("r-annaffy" ,r-annaffy)
4261 ("r-biobase" ,r-biobase)
4262 ("r-biocmanager" ,r-biocmanager)
4263 ("r-gcrma" ,r-gcrma)
4264 ("r-multtest" ,r-multtest)
4265 ("r-qvalue" ,r-qvalue)
4267 (home-page "https://www.bioconductor.org/")
4268 (synopsis "Bioconductor web interface")
4270 "This package provides an integrated web interface for doing microarray
4271 analysis using several of the Bioconductor packages. It is intended to be
4272 deployed as a centralized bioinformatics resource for use by many users.
4273 Currently only Affymetrix oligonucleotide analysis is supported.")
4274 (license license:gpl2+)))
4276 (define-public r-zfpkm
4283 (uri (bioconductor-uri "zFPKM" version))
4286 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4287 (properties `((upstream-name . "zFPKM")))
4288 (build-system r-build-system)
4290 `(("r-checkmate" ,r-checkmate)
4291 ("r-dplyr" ,r-dplyr)
4292 ("r-ggplot2" ,r-ggplot2)
4293 ("r-summarizedexperiment" ,r-summarizedexperiment)
4294 ("r-tidyr" ,r-tidyr)))
4295 (home-page "https://github.com/ronammar/zFPKM/")
4296 (synopsis "Functions to facilitate zFPKM transformations")
4298 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4299 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4301 (license license:gpl3)))
4303 (define-public r-rbowtie2
4310 (uri (bioconductor-uri "Rbowtie2" version))
4313 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4314 (properties `((upstream-name . "Rbowtie2")))
4315 (build-system r-build-system)
4318 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4319 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4321 "This package provides an R wrapper of the popular @code{bowtie2}
4322 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4323 rapid adapter trimming, identification, and read merging.")
4324 (license license:gpl3+)))
4326 (define-public r-progeny
4333 (uri (bioconductor-uri "progeny" version))
4336 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4337 (build-system r-build-system)
4338 (propagated-inputs `(("r-biobase" ,r-biobase)))
4339 (home-page "https://github.com/saezlab/progeny")
4340 (synopsis "Pathway responsive gene activity inference")
4342 "This package provides a function to infer pathway activity from gene
4343 expression. It contains the linear model inferred in the publication
4344 \"Perturbation-response genes reveal signaling footprints in cancer gene
4346 (license license:asl2.0)))
4348 (define-public r-arrmnormalization
4350 (name "r-arrmnormalization")
4355 (uri (bioconductor-uri "ARRmNormalization" version))
4358 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4360 `((upstream-name . "ARRmNormalization")))
4361 (build-system r-build-system)
4362 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4363 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4364 (synopsis "Adaptive robust regression normalization for methylation data")
4366 "This is a package to perform the @dfn{Adaptive Robust Regression
4367 method} (ARRm) for the normalization of methylation data from the Illumina
4368 Infinium HumanMethylation 450k assay.")
4369 (license license:artistic2.0)))
4371 (define-public r-biocfilecache
4373 (name "r-biocfilecache")
4378 (uri (bioconductor-uri "BiocFileCache" version))
4381 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4382 (properties `((upstream-name . "BiocFileCache")))
4383 (build-system r-build-system)
4385 `(("r-curl" ,r-curl)
4387 ("r-dbplyr" ,r-dbplyr)
4388 ("r-dplyr" ,r-dplyr)
4390 ("r-rappdirs" ,r-rappdirs)
4391 ("r-rsqlite" ,r-rsqlite)))
4392 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4393 (synopsis "Manage files across sessions")
4395 "This package creates a persistent on-disk cache of files that the user
4396 can add, update, and retrieve. It is useful for managing resources (such as
4397 custom Txdb objects) that are costly or difficult to create, web resources,
4398 and data files used across sessions.")
4399 (license license:artistic2.0)))
4401 (define-public r-iclusterplus
4403 (name "r-iclusterplus")
4408 (uri (bioconductor-uri "iClusterPlus" version))
4411 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4412 (properties `((upstream-name . "iClusterPlus")))
4413 (build-system r-build-system)
4414 (native-inputs `(("gfortran" ,gfortran)))
4415 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4416 (synopsis "Integrative clustering of multi-type genomic data")
4418 "iClusterPlus is developed for integrative clustering analysis of
4419 multi-type genomic data and is an enhanced version of iCluster proposed and
4420 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4421 from the experiments where biological samples (e.g. tumor samples) are
4422 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4423 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4424 on. In the iClusterPlus model, binary observations such as somatic mutation
4425 are modeled as Binomial processes; categorical observations such as copy
4426 number states are realizations of Multinomial random variables; counts are
4427 modeled as Poisson random processes; and continuous measures are modeled by
4428 Gaussian distributions.")
4429 (license license:gpl2+)))
4431 (define-public r-rbowtie
4438 (uri (bioconductor-uri "Rbowtie" version))
4441 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4442 (properties `((upstream-name . "Rbowtie")))
4443 (build-system r-build-system)
4446 (home-page "https://bioconductor.org/packages/Rbowtie/")
4447 (synopsis "R bowtie wrapper")
4449 "This package provides an R wrapper around the popular bowtie short read
4450 aligner and around SpliceMap, a de novo splice junction discovery and
4452 (license license:artistic2.0)))
4454 (define-public r-sgseq
4461 (uri (bioconductor-uri "SGSeq" version))
4464 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4465 (properties `((upstream-name . "SGSeq")))
4466 (build-system r-build-system)
4468 `(("r-annotationdbi" ,r-annotationdbi)
4469 ("r-biocgenerics" ,r-biocgenerics)
4470 ("r-biostrings" ,r-biostrings)
4471 ("r-genomeinfodb" ,r-genomeinfodb)
4472 ("r-genomicalignments" ,r-genomicalignments)
4473 ("r-genomicfeatures" ,r-genomicfeatures)
4474 ("r-genomicranges" ,r-genomicranges)
4475 ("r-igraph" ,r-igraph)
4476 ("r-iranges" ,r-iranges)
4477 ("r-rsamtools" ,r-rsamtools)
4478 ("r-rtracklayer" ,r-rtracklayer)
4479 ("r-runit" ,r-runit)
4480 ("r-s4vectors" ,r-s4vectors)
4481 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4482 (home-page "https://bioconductor.org/packages/SGSeq/")
4483 (synopsis "Splice event prediction and quantification from RNA-seq data")
4485 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4486 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4487 represented as a splice graph, which can be obtained from existing annotation
4488 or predicted from the mapped sequence reads. Splice events are identified
4489 from the graph and are quantified locally using structurally compatible reads
4490 at the start or end of each splice variant. The software includes functions
4491 for splice event prediction, quantification, visualization and
4493 (license license:artistic2.0)))
4495 (define-public r-rhisat2
4502 (uri (bioconductor-uri "Rhisat2" version))
4505 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4506 (properties `((upstream-name . "Rhisat2")))
4507 (build-system r-build-system)
4509 `(("which" ,which)))
4511 `(("r-genomicfeatures" ,r-genomicfeatures)
4512 ("r-genomicranges" ,r-genomicranges)
4513 ("r-sgseq" ,r-sgseq)))
4514 (home-page "https://github.com/fmicompbio/Rhisat2")
4515 (synopsis "R Wrapper for HISAT2 sequence aligner")
4517 "This package provides an R interface to the HISAT2 spliced short-read
4518 aligner by Kim et al. (2015). The package contains wrapper functions to
4519 create a genome index and to perform the read alignment to the generated
4521 (license license:gpl3)))
4523 (define-public r-quasr
4530 (uri (bioconductor-uri "QuasR" version))
4533 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4534 (properties `((upstream-name . "QuasR")))
4535 (build-system r-build-system)
4539 `(("r-annotationdbi" ,r-annotationdbi)
4540 ("r-biobase" ,r-biobase)
4541 ("r-biocgenerics" ,r-biocgenerics)
4542 ("r-biocmanager" ,r-biocmanager)
4543 ("r-biocparallel" ,r-biocparallel)
4544 ("r-biostrings" ,r-biostrings)
4545 ("r-bsgenome" ,r-bsgenome)
4546 ("r-genomeinfodb" ,r-genomeinfodb)
4547 ("r-genomicalignments" ,r-genomicalignments)
4548 ("r-genomicfeatures" ,r-genomicfeatures)
4549 ("r-genomicfiles" ,r-genomicfiles)
4550 ("r-genomicranges" ,r-genomicranges)
4551 ("r-iranges" ,r-iranges)
4552 ("r-rbowtie" ,r-rbowtie)
4553 ("r-rhisat2" ,r-rhisat2)
4554 ("r-rhtslib" ,r-rhtslib)
4555 ("r-rsamtools" ,r-rsamtools)
4556 ("r-rtracklayer" ,r-rtracklayer)
4557 ("r-s4vectors" ,r-s4vectors)
4558 ("r-shortread" ,r-shortread)))
4559 (home-page "https://bioconductor.org/packages/QuasR/")
4560 (synopsis "Quantify and annotate short reads in R")
4562 "This package provides a framework for the quantification and analysis of
4563 short genomic reads. It covers a complete workflow starting from raw sequence
4564 reads, over creation of alignments and quality control plots, to the
4565 quantification of genomic regions of interest.")
4566 (license license:gpl2)))
4568 (define-public r-rqc
4575 (uri (bioconductor-uri "Rqc" version))
4578 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4579 (properties `((upstream-name . "Rqc")))
4580 (build-system r-build-system)
4582 `(("r-biocgenerics" ,r-biocgenerics)
4583 ("r-biocparallel" ,r-biocparallel)
4584 ("r-biocstyle" ,r-biocstyle)
4585 ("r-biostrings" ,r-biostrings)
4586 ("r-biovizbase" ,r-biovizbase)
4587 ("r-genomicalignments" ,r-genomicalignments)
4588 ("r-genomicfiles" ,r-genomicfiles)
4589 ("r-ggplot2" ,r-ggplot2)
4590 ("r-iranges" ,r-iranges)
4591 ("r-knitr" ,r-knitr)
4592 ("r-markdown" ,r-markdown)
4595 ("r-reshape2" ,r-reshape2)
4596 ("r-rsamtools" ,r-rsamtools)
4597 ("r-s4vectors" ,r-s4vectors)
4598 ("r-shiny" ,r-shiny)
4599 ("r-shortread" ,r-shortread)))
4600 (home-page "https://github.com/labbcb/Rqc")
4601 (synopsis "Quality control tool for high-throughput sequencing data")
4603 "Rqc is an optimized tool designed for quality control and assessment of
4604 high-throughput sequencing data. It performs parallel processing of entire
4605 files and produces a report which contains a set of high-resolution
4607 (license license:gpl2+)))
4609 (define-public r-birewire
4616 (uri (bioconductor-uri "BiRewire" version))
4619 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
4620 (properties `((upstream-name . "BiRewire")))
4621 (build-system r-build-system)
4623 `(("r-igraph" ,r-igraph)
4624 ("r-matrix" ,r-matrix)
4626 ("r-tsne" ,r-tsne)))
4627 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
4628 (synopsis "Tools for randomization of bipartite graphs")
4630 "This package provides functions for bipartite network rewiring through N
4631 consecutive switching steps and for the computation of the minimal number of
4632 switching steps to be performed in order to maximise the dissimilarity with
4633 respect to the original network. It includes functions for the analysis of
4634 the introduced randomness across the switching steps and several other
4635 routines to analyse the resulting networks and their natural projections.")
4636 (license license:gpl3)))
4638 (define-public r-birta
4645 (uri (bioconductor-uri "birta" version))
4648 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
4649 (build-system r-build-system)
4651 `(("r-biobase" ,r-biobase)
4652 ("r-limma" ,r-limma)
4653 ("r-mass" ,r-mass)))
4654 (home-page "https://bioconductor.org/packages/birta")
4655 (synopsis "Bayesian inference of regulation of transcriptional activity")
4657 "Expression levels of mRNA molecules are regulated by different
4658 processes, comprising inhibition or activation by transcription factors and
4659 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
4660 Inference of Regulation of Transcriptional Activity) uses the regulatory
4661 networks of transcription factors and miRNAs together with mRNA and miRNA
4662 expression data to predict switches in regulatory activity between two
4663 conditions. A Bayesian network is used to model the regulatory structure and
4664 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
4665 (license license:gpl2+)))
4667 (define-public r-ropls
4674 (uri (bioconductor-uri "ropls" version))
4677 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
4678 (build-system r-build-system)
4679 (propagated-inputs `(("r-biobase" ,r-biobase)))
4681 `(("r-knitr" ,r-knitr))) ; for vignettes
4682 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
4683 (synopsis "Multivariate analysis and feature selection of omics data")
4685 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
4686 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
4687 regression, classification, and feature selection of omics data where the
4688 number of variables exceeds the number of samples and with multicollinearity
4689 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
4690 separately model the variation correlated (predictive) to the factor of
4691 interest and the uncorrelated (orthogonal) variation. While performing
4692 similarly to PLS, OPLS facilitates interpretation.
4694 This package provides imlementations of PCA, PLS, and OPLS for multivariate
4695 analysis and feature selection of omics data. In addition to scores, loadings
4696 and weights plots, the package provides metrics and graphics to determine the
4697 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
4698 validity of the model by permutation testing, detect outliers, and perform
4699 feature selection (e.g. with Variable Importance in Projection or regression
4701 (license license:cecill)))
4703 (define-public r-biosigner
4705 (name "r-biosigner")
4710 (uri (bioconductor-uri "biosigner" version))
4713 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
4714 (build-system r-build-system)
4716 `(("r-biobase" ,r-biobase)
4717 ("r-e1071" ,r-e1071)
4718 ("r-randomforest" ,r-randomforest)
4719 ("r-ropls" ,r-ropls)))
4721 `(("r-knitr" ,r-knitr)
4722 ("r-rmarkdown" ,r-rmarkdown)
4723 ("pandoc" ,ghc-pandoc)
4724 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
4725 (home-page "https://bioconductor.org/packages/biosigner/")
4726 (synopsis "Signature discovery from omics data")
4728 "Feature selection is critical in omics data analysis to extract
4729 restricted and meaningful molecular signatures from complex and high-dimension
4730 data, and to build robust classifiers. This package implements a method to
4731 assess the relevance of the variables for the prediction performances of the
4732 classifier. The approach can be run in parallel with the PLS-DA, Random
4733 Forest, and SVM binary classifiers. The signatures and the corresponding
4734 'restricted' models are returned, enabling future predictions on new
4736 (license license:cecill)))
4738 (define-public r-annotatr
4745 (uri (bioconductor-uri "annotatr" version))
4748 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
4749 (build-system r-build-system)
4751 `(("r-annotationdbi" ,r-annotationdbi)
4752 ("r-annotationhub" ,r-annotationhub)
4753 ("r-dplyr" ,r-dplyr)
4754 ("r-genomeinfodb" ,r-genomeinfodb)
4755 ("r-genomicfeatures" ,r-genomicfeatures)
4756 ("r-genomicranges" ,r-genomicranges)
4757 ("r-ggplot2" ,r-ggplot2)
4758 ("r-iranges" ,r-iranges)
4759 ("r-readr" ,r-readr)
4760 ("r-regioner" ,r-regioner)
4761 ("r-reshape2" ,r-reshape2)
4762 ("r-rtracklayer" ,r-rtracklayer)
4763 ("r-s4vectors" ,r-s4vectors)))
4764 (home-page "https://bioconductor.org/packages/annotatr/")
4765 (synopsis "Annotation of genomic regions to genomic annotations")
4767 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
4768 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
4769 to investigate the intersecting genomic annotations. Such annotations include
4770 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
4771 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
4772 enhancers. The annotatr package provides an easy way to summarize and
4773 visualize the intersection of genomic sites/regions with genomic
4775 (license license:gpl3)))
4777 (define-public r-rsubread
4784 (uri (bioconductor-uri "Rsubread" version))
4787 "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
4788 (properties `((upstream-name . "Rsubread")))
4789 (build-system r-build-system)
4790 (inputs `(("zlib" ,zlib)))
4791 (home-page "https://bioconductor.org/packages/Rsubread/")
4792 (synopsis "Subread sequence alignment and counting for R")
4794 "This package provides tools for alignment, quantification and analysis
4795 of second and third generation sequencing data. It includes functionality for
4796 read mapping, read counting, SNP calling, structural variant detection and
4797 gene fusion discovery. It can be applied to all major sequencing techologies
4798 and to both short and long sequence reads.")
4799 (license license:gpl3)))
4801 (define-public r-flowutils
4803 (name "r-flowutils")
4808 (uri (bioconductor-uri "flowUtils" version))
4811 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
4812 (properties `((upstream-name . "flowUtils")))
4813 (build-system r-build-system)
4815 `(("r-biobase" ,r-biobase)
4816 ("r-corpcor" ,r-corpcor)
4817 ("r-flowcore" ,r-flowcore)
4818 ("r-graph" ,r-graph)
4819 ("r-runit" ,r-runit)
4821 (home-page "https://github.com/jspidlen/flowUtils")
4822 (synopsis "Utilities for flow cytometry")
4824 "This package provides utilities for flow cytometry data.")
4825 (license license:artistic2.0)))
4827 (define-public r-consensusclusterplus
4829 (name "r-consensusclusterplus")
4834 (uri (bioconductor-uri "ConsensusClusterPlus" version))
4837 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
4839 `((upstream-name . "ConsensusClusterPlus")))
4840 (build-system r-build-system)
4843 ("r-biobase" ,r-biobase)
4844 ("r-cluster" ,r-cluster)))
4845 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
4846 (synopsis "Clustering algorithm")
4848 "This package provides an implementation of an algorithm for determining
4849 cluster count and membership by stability evidence in unsupervised analysis.")
4850 (license license:gpl2)))
4852 (define-public r-flowcore
4859 (uri (bioconductor-uri "flowCore" version))
4862 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
4863 (properties `((upstream-name . "flowCore")))
4864 (build-system r-build-system)
4867 ("r-biobase" ,r-biobase)
4868 ("r-biocgenerics" ,r-biocgenerics)
4869 ("r-corpcor" ,r-corpcor)
4870 ("r-graph" ,r-graph)
4872 ("r-matrixstats" ,r-matrixstats)
4874 ("r-rrcov" ,r-rrcov)))
4875 (home-page "https://bioconductor.org/packages/flowCore")
4876 (synopsis "Basic structures for flow cytometry data")
4878 "This package provides S4 data structures and basic functions to deal
4879 with flow cytometry data.")
4880 (license license:artistic2.0)))
4882 (define-public r-flowmeans
4884 (name "r-flowmeans")
4889 (uri (bioconductor-uri "flowMeans" version))
4892 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
4893 (properties `((upstream-name . "flowMeans")))
4894 (build-system r-build-system)
4896 `(("r-biobase" ,r-biobase)
4897 ("r-feature" ,r-feature)
4898 ("r-flowcore" ,r-flowcore)
4899 ("r-rrcov" ,r-rrcov)))
4900 (home-page "https://bioconductor.org/packages/flowMeans")
4901 (synopsis "Non-parametric flow cytometry data gating")
4903 "This package provides tools to identify cell populations in Flow
4904 Cytometry data using non-parametric clustering and segmented-regression-based
4905 change point detection.")
4906 (license license:artistic2.0)))
4908 (define-public r-flowsom
4915 (uri (bioconductor-uri "FlowSOM" version))
4918 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
4919 (properties `((upstream-name . "FlowSOM")))
4920 (build-system r-build-system)
4922 `(("r-biocgenerics" ,r-biocgenerics)
4923 ("r-consensusclusterplus" ,r-consensusclusterplus)
4924 ("r-flowcore" ,r-flowcore)
4925 ("r-flowutils" ,r-flowutils)
4926 ("r-igraph" ,r-igraph)
4929 (home-page "https://bioconductor.org/packages/FlowSOM/")
4930 (synopsis "Visualize and interpret cytometry data")
4932 "FlowSOM offers visualization options for cytometry data, by using
4933 self-organizing map clustering and minimal spanning trees.")
4934 (license license:gpl2+)))