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)))
871 (define-public r-biocgenerics
873 (name "r-biocgenerics")
877 (uri (bioconductor-uri "BiocGenerics" version))
880 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
882 `((upstream-name . "BiocGenerics")))
883 (build-system r-build-system)
884 (home-page "https://bioconductor.org/packages/BiocGenerics")
885 (synopsis "S4 generic functions for Bioconductor")
887 "This package provides S4 generic functions needed by many Bioconductor
889 (license license:artistic2.0)))
891 (define-public r-annotate
898 (uri (bioconductor-uri "annotate" version))
901 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
902 (build-system r-build-system)
904 `(("r-annotationdbi" ,r-annotationdbi)
905 ("r-biobase" ,r-biobase)
906 ("r-biocgenerics" ,r-biocgenerics)
910 ("r-xtable" ,r-xtable)))
912 "https://bioconductor.org/packages/annotate")
913 (synopsis "Annotation for microarrays")
914 (description "This package provides R environments for the annotation of
916 (license license:artistic2.0)))
918 (define-public r-hpar
925 (uri (bioconductor-uri "hpar" version))
928 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
929 (build-system r-build-system)
930 (home-page "https://bioconductor.org/packages/hpar/")
931 (synopsis "Human Protein Atlas in R")
932 (description "This package provides a simple interface to and data from
933 the Human Protein Atlas project.")
934 (license license:artistic2.0)))
936 (define-public r-regioner
943 (uri (bioconductor-uri "regioneR" version))
946 "1b8ybx4wcxlqw9nvajawsf0lqaqn9v89rxcawg4g3dbzlfssfc5q"))))
947 (properties `((upstream-name . "regioneR")))
948 (build-system r-build-system)
950 `(("r-biostrings" ,r-biostrings)
951 ("r-bsgenome" ,r-bsgenome)
952 ("r-genomeinfodb" ,r-genomeinfodb)
953 ("r-genomicranges" ,r-genomicranges)
954 ("r-iranges" ,r-iranges)
955 ("r-memoise" ,r-memoise)
956 ("r-rtracklayer" ,r-rtracklayer)
957 ("r-s4vectors" ,r-s4vectors)))
958 (home-page "https://bioconductor.org/packages/regioneR/")
959 (synopsis "Association analysis of genomic regions")
960 (description "This package offers a statistical framework based on
961 customizable permutation tests to assess the association between genomic
962 region sets and other genomic features.")
963 (license license:artistic2.0)))
965 (define-public r-geneplotter
967 (name "r-geneplotter")
972 (uri (bioconductor-uri "geneplotter" version))
975 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
976 (build-system r-build-system)
978 `(("r-annotate" ,r-annotate)
979 ("r-annotationdbi" ,r-annotationdbi)
980 ("r-biobase" ,r-biobase)
981 ("r-biocgenerics" ,r-biocgenerics)
982 ("r-lattice" ,r-lattice)
983 ("r-rcolorbrewer" ,r-rcolorbrewer)))
984 (home-page "https://bioconductor.org/packages/geneplotter")
985 (synopsis "Graphics functions for genomic data")
987 "This package provides functions for plotting genomic data.")
988 (license license:artistic2.0)))
990 (define-public r-qvalue
997 (uri (bioconductor-uri "qvalue" version))
1000 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1001 (build-system r-build-system)
1003 `(("r-ggplot2" ,r-ggplot2)
1004 ("r-reshape2" ,r-reshape2)))
1005 (home-page "http://github.com/jdstorey/qvalue")
1006 (synopsis "Q-value estimation for false discovery rate control")
1008 "This package takes a list of p-values resulting from the simultaneous
1009 testing of many hypotheses and estimates their q-values and local @dfn{false
1010 discovery rate} (FDR) values. The q-value of a test measures the proportion
1011 of false positives incurred when that particular test is called significant.
1012 The local FDR measures the posterior probability the null hypothesis is true
1013 given the test's p-value. Various plots are automatically generated, allowing
1014 one to make sensible significance cut-offs. The software can be applied to
1015 problems in genomics, brain imaging, astrophysics, and data mining.")
1016 ;; Any version of the LGPL.
1017 (license license:lgpl3+)))
1019 (define-public r-diffbind
1026 (uri (bioconductor-uri "DiffBind" version))
1029 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1030 (properties `((upstream-name . "DiffBind")))
1031 (build-system r-build-system)
1035 `(("r-amap" ,r-amap)
1036 ("r-biocparallel" ,r-biocparallel)
1037 ("r-deseq2" ,r-deseq2)
1038 ("r-dplyr" ,r-dplyr)
1039 ("r-edger" ,r-edger)
1040 ("r-genomicalignments" ,r-genomicalignments)
1041 ("r-genomicranges" ,r-genomicranges)
1042 ("r-ggplot2" ,r-ggplot2)
1043 ("r-ggrepel" ,r-ggrepel)
1044 ("r-gplots" ,r-gplots)
1045 ("r-iranges" ,r-iranges)
1046 ("r-lattice" ,r-lattice)
1047 ("r-limma" ,r-limma)
1048 ("r-locfit" ,r-locfit)
1049 ("r-rcolorbrewer" , r-rcolorbrewer)
1051 ("r-rhtslib" ,r-rhtslib)
1052 ("r-rsamtools" ,r-rsamtools)
1053 ("r-s4vectors" ,r-s4vectors)
1054 ("r-summarizedexperiment" ,r-summarizedexperiment)
1055 ("r-systempiper" ,r-systempiper)))
1056 (home-page "http://bioconductor.org/packages/DiffBind")
1057 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1059 "This package computes differentially bound sites from multiple
1060 ChIP-seq experiments using affinity (quantitative) data. Also enables
1061 occupancy (overlap) analysis and plotting functions.")
1062 (license license:artistic2.0)))
1064 (define-public r-ripseeker
1066 (name "r-ripseeker")
1071 (uri (bioconductor-uri "RIPSeeker" version))
1074 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1075 (properties `((upstream-name . "RIPSeeker")))
1076 (build-system r-build-system)
1078 `(("r-s4vectors" ,r-s4vectors)
1079 ("r-iranges" ,r-iranges)
1080 ("r-genomicranges" ,r-genomicranges)
1081 ("r-summarizedexperiment" ,r-summarizedexperiment)
1082 ("r-rsamtools" ,r-rsamtools)
1083 ("r-genomicalignments" ,r-genomicalignments)
1084 ("r-rtracklayer" ,r-rtracklayer)))
1085 (home-page "http://bioconductor.org/packages/RIPSeeker")
1087 "Identifying protein-associated transcripts from RIP-seq experiments")
1089 "This package infers and discriminates RIP peaks from RIP-seq alignments
1090 using two-state HMM with negative binomial emission probability. While
1091 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1092 a suite of bioinformatics tools integrated within this self-contained software
1093 package comprehensively addressing issues ranging from post-alignments
1094 processing to visualization and annotation.")
1095 (license license:gpl2)))
1097 (define-public r-multtest
1104 (uri (bioconductor-uri "multtest" version))
1107 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1108 (build-system r-build-system)
1110 `(("r-survival" ,r-survival)
1111 ("r-biocgenerics" ,r-biocgenerics)
1112 ("r-biobase" ,r-biobase)
1113 ("r-mass" ,r-mass)))
1114 (home-page "http://bioconductor.org/packages/multtest")
1115 (synopsis "Resampling-based multiple hypothesis testing")
1117 "This package can do non-parametric bootstrap and permutation
1118 resampling-based multiple testing procedures (including empirical Bayes
1119 methods) for controlling the family-wise error rate (FWER), generalized
1120 family-wise error rate (gFWER), tail probability of the proportion of
1121 false positives (TPPFP), and false discovery rate (FDR). Several choices
1122 of bootstrap-based null distribution are implemented (centered, centered
1123 and scaled, quantile-transformed). Single-step and step-wise methods are
1124 available. Tests based on a variety of T- and F-statistics (including
1125 T-statistics based on regression parameters from linear and survival models
1126 as well as those based on correlation parameters) are included. When probing
1127 hypotheses with T-statistics, users may also select a potentially faster null
1128 distribution which is multivariate normal with mean zero and variance
1129 covariance matrix derived from the vector influence function. Results are
1130 reported in terms of adjusted P-values, confidence regions and test statistic
1131 cutoffs. The procedures are directly applicable to identifying differentially
1132 expressed genes in DNA microarray experiments.")
1133 (license license:lgpl3)))
1135 (define-public r-graph
1141 (uri (bioconductor-uri "graph" version))
1144 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1145 (build-system r-build-system)
1147 `(("r-biocgenerics" ,r-biocgenerics)))
1148 (home-page "https://bioconductor.org/packages/graph")
1149 (synopsis "Handle graph data structures in R")
1151 "This package implements some simple graph handling capabilities for R.")
1152 (license license:artistic2.0)))
1154 (define-public r-codedepends
1156 (name "r-codedepends")
1161 (uri (cran-uri "CodeDepends" version))
1164 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1165 (properties `((upstream-name . "CodeDepends")))
1166 (build-system r-build-system)
1168 `(("r-codetools" ,r-codetools)
1169 ("r-graph" ,r-graph)
1171 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1172 (synopsis "Analysis of R code for reproducible research and code comprehension")
1174 "This package provides tools for analyzing R expressions or blocks of
1175 code and determining the dependencies between them. It focuses on R scripts,
1176 but can be used on the bodies of functions. There are many facilities
1177 including the ability to summarize or get a high-level view of code,
1178 determining dependencies between variables, code improvement suggestions.")
1179 ;; Any version of the GPL
1180 (license (list license:gpl2+ license:gpl3+))))
1182 (define-public r-chippeakanno
1184 (name "r-chippeakanno")
1189 (uri (bioconductor-uri "ChIPpeakAnno" version))
1192 "1mwi5s600c3jxy8f1azfrndc3g06qvhbmrp9wqac9nwjbfx1kfji"))))
1193 (properties `((upstream-name . "ChIPpeakAnno")))
1194 (build-system r-build-system)
1196 `(("r-annotationdbi" ,r-annotationdbi)
1197 ("r-biobase" ,r-biobase)
1198 ("r-biocgenerics" ,r-biocgenerics)
1199 ("r-biocmanager" ,r-biocmanager)
1200 ("r-biomart" ,r-biomart)
1201 ("r-biostrings" ,r-biostrings)
1202 ("r-bsgenome" ,r-bsgenome)
1204 ("r-delayedarray" ,r-delayedarray)
1205 ("r-ensembldb" ,r-ensembldb)
1206 ("r-genomeinfodb" ,r-genomeinfodb)
1207 ("r-genomicalignments" ,r-genomicalignments)
1208 ("r-genomicfeatures" ,r-genomicfeatures)
1209 ("r-genomicranges" ,r-genomicranges)
1210 ("r-go-db" ,r-go-db)
1211 ("r-graph" ,r-graph)
1213 ("r-iranges" ,r-iranges)
1214 ("r-limma" ,r-limma)
1215 ("r-matrixstats" ,r-matrixstats)
1216 ("r-multtest" ,r-multtest)
1218 ("r-regioner" ,r-regioner)
1219 ("r-rsamtools" ,r-rsamtools)
1220 ("r-rtracklayer" ,r-rtracklayer)
1221 ("r-s4vectors" ,r-s4vectors)
1222 ("r-seqinr" ,r-seqinr)
1223 ("r-summarizedexperiment" ,r-summarizedexperiment)
1224 ("r-venndiagram" ,r-venndiagram)))
1225 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1226 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1228 "The package includes functions to retrieve the sequences around the peak,
1229 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1230 custom features such as most conserved elements and other transcription factor
1231 binding sites supplied by users. Starting 2.0.5, new functions have been added
1232 for finding the peaks with bi-directional promoters with summary statistics
1233 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1234 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1235 enrichedGO (addGeneIDs).")
1236 (license license:gpl2+)))
1238 (define-public r-marray
1244 (uri (bioconductor-uri "marray" version))
1246 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1247 (build-system r-build-system)
1249 `(("r-limma" ,r-limma)))
1250 (home-page "http://bioconductor.org/packages/marray")
1251 (synopsis "Exploratory analysis for two-color spotted microarray data")
1252 (description "This package contains class definitions for two-color spotted
1253 microarray data. It also includes functions for data input, diagnostic plots,
1254 normalization and quality checking.")
1255 (license license:lgpl2.0+)))
1257 (define-public r-cghbase
1263 (uri (bioconductor-uri "CGHbase" version))
1265 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1266 (properties `((upstream-name . "CGHbase")))
1267 (build-system r-build-system)
1269 `(("r-biobase" ,r-biobase)
1270 ("r-marray" ,r-marray)))
1271 (home-page "http://bioconductor.org/packages/CGHbase")
1272 (synopsis "Base functions and classes for arrayCGH data analysis")
1273 (description "This package contains functions and classes that are needed by
1274 the @code{arrayCGH} packages.")
1275 (license license:gpl2+)))
1277 (define-public r-cghcall
1283 (uri (bioconductor-uri "CGHcall" version))
1285 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1286 (properties `((upstream-name . "CGHcall")))
1287 (build-system r-build-system)
1289 `(("r-biobase" ,r-biobase)
1290 ("r-cghbase" ,r-cghbase)
1291 ("r-impute" ,r-impute)
1292 ("r-dnacopy" ,r-dnacopy)
1293 ("r-snowfall" ,r-snowfall)))
1294 (home-page "http://bioconductor.org/packages/CGHcall")
1295 (synopsis "Base functions and classes for arrayCGH data analysis")
1296 (description "This package contains functions and classes that are needed by
1297 @code{arrayCGH} packages.")
1298 (license license:gpl2+)))
1300 (define-public r-qdnaseq
1306 (uri (bioconductor-uri "QDNAseq" version))
1308 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1309 (properties `((upstream-name . "QDNAseq")))
1310 (build-system r-build-system)
1312 `(("r-biobase" ,r-biobase)
1313 ("r-biocparallel" ,r-biocparallel)
1314 ("r-cghbase" ,r-cghbase)
1315 ("r-cghcall" ,r-cghcall)
1316 ("r-dnacopy" ,r-dnacopy)
1317 ("r-genomicranges" ,r-genomicranges)
1318 ("r-iranges" ,r-iranges)
1319 ("r-matrixstats" ,r-matrixstats)
1320 ("r-r-utils" ,r-r-utils)
1321 ("r-rsamtools" ,r-rsamtools)))
1322 (home-page "http://bioconductor.org/packages/QDNAseq")
1323 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1324 (description "The genome is divided into non-overlapping fixed-sized bins,
1325 number of sequence reads in each counted, adjusted with a simultaneous
1326 two-dimensional loess correction for sequence mappability and GC content, and
1327 filtered to remove spurious regions in the genome. Downstream steps of
1328 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1330 (license license:gpl2+)))
1332 (define-public r-bayseq
1339 (uri (bioconductor-uri "baySeq" version))
1342 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1343 (properties `((upstream-name . "baySeq")))
1344 (build-system r-build-system)
1346 `(("r-abind" ,r-abind)
1347 ("r-edger" ,r-edger)
1348 ("r-genomicranges" ,r-genomicranges)))
1349 (home-page "https://bioconductor.org/packages/baySeq/")
1350 (synopsis "Bayesian analysis of differential expression patterns in count data")
1352 "This package identifies differential expression in high-throughput count
1353 data, such as that derived from next-generation sequencing machines,
1354 calculating estimated posterior likelihoods of differential expression (or
1355 more complex hypotheses) via empirical Bayesian methods.")
1356 (license license:gpl3)))
1358 (define-public r-chipcomp
1365 (uri (bioconductor-uri "ChIPComp" version))
1368 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1369 (properties `((upstream-name . "ChIPComp")))
1370 (build-system r-build-system)
1372 `(("r-biocgenerics" ,r-biocgenerics)
1373 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1374 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1375 ("r-genomeinfodb" ,r-genomeinfodb)
1376 ("r-genomicranges" ,r-genomicranges)
1377 ("r-iranges" ,r-iranges)
1378 ("r-limma" ,r-limma)
1379 ("r-rsamtools" ,r-rsamtools)
1380 ("r-rtracklayer" ,r-rtracklayer)
1381 ("r-s4vectors" ,r-s4vectors)))
1382 (home-page "https://bioconductor.org/packages/ChIPComp")
1383 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1385 "ChIPComp implements a statistical method for quantitative comparison of
1386 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1387 sites across multiple conditions considering matching control in ChIP-seq
1389 ;; Any version of the GPL.
1390 (license license:gpl3+)))
1392 (define-public r-riboprofiling
1394 (name "r-riboprofiling")
1399 (uri (bioconductor-uri "RiboProfiling" version))
1402 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1403 (properties `((upstream-name . "RiboProfiling")))
1404 (build-system r-build-system)
1406 `(("r-biocgenerics" ,r-biocgenerics)
1407 ("r-biostrings" ,r-biostrings)
1408 ("r-data-table" ,r-data-table)
1409 ("r-genomeinfodb" ,r-genomeinfodb)
1410 ("r-genomicalignments" ,r-genomicalignments)
1411 ("r-genomicfeatures" ,r-genomicfeatures)
1412 ("r-genomicranges" ,r-genomicranges)
1413 ("r-ggbio" ,r-ggbio)
1414 ("r-ggplot2" ,r-ggplot2)
1415 ("r-iranges" ,r-iranges)
1417 ("r-reshape2" ,r-reshape2)
1418 ("r-rsamtools" ,r-rsamtools)
1419 ("r-rtracklayer" ,r-rtracklayer)
1420 ("r-s4vectors" ,r-s4vectors)
1421 ("r-sqldf" ,r-sqldf)))
1422 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1423 (synopsis "Ribosome profiling data analysis")
1424 (description "Starting with a BAM file, this package provides the
1425 necessary functions for quality assessment, read start position recalibration,
1426 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1427 of count data: pairs, log fold-change, codon frequency and coverage
1428 assessment, principal component analysis on codon coverage.")
1429 (license license:gpl3)))
1431 (define-public r-riboseqr
1438 (uri (bioconductor-uri "riboSeqR" version))
1441 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1442 (properties `((upstream-name . "riboSeqR")))
1443 (build-system r-build-system)
1445 `(("r-abind" ,r-abind)
1446 ("r-bayseq" ,r-bayseq)
1447 ("r-genomeinfodb" ,r-genomeinfodb)
1448 ("r-genomicranges" ,r-genomicranges)
1449 ("r-iranges" ,r-iranges)
1450 ("r-rsamtools" ,r-rsamtools)
1451 ("r-seqlogo" ,r-seqlogo)))
1452 (home-page "https://bioconductor.org/packages/riboSeqR/")
1453 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1455 "This package provides plotting functions, frameshift detection and
1456 parsing of genetic sequencing data from ribosome profiling experiments.")
1457 (license license:gpl3)))
1459 (define-public r-interactionset
1461 (name "r-interactionset")
1466 (uri (bioconductor-uri "InteractionSet" version))
1469 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1471 `((upstream-name . "InteractionSet")))
1472 (build-system r-build-system)
1474 `(("r-biocgenerics" ,r-biocgenerics)
1475 ("r-genomeinfodb" ,r-genomeinfodb)
1476 ("r-genomicranges" ,r-genomicranges)
1477 ("r-iranges" ,r-iranges)
1478 ("r-matrix" ,r-matrix)
1480 ("r-s4vectors" ,r-s4vectors)
1481 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1482 (home-page "https://bioconductor.org/packages/InteractionSet")
1483 (synopsis "Base classes for storing genomic interaction data")
1485 "This package provides the @code{GInteractions},
1486 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1487 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1489 (license license:gpl3)))
1491 (define-public r-genomicinteractions
1493 (name "r-genomicinteractions")
1498 (uri (bioconductor-uri "GenomicInteractions" version))
1501 "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b"))))
1503 `((upstream-name . "GenomicInteractions")))
1504 (build-system r-build-system)
1506 `(("r-biobase" ,r-biobase)
1507 ("r-biocgenerics" ,r-biocgenerics)
1508 ("r-data-table" ,r-data-table)
1509 ("r-dplyr" ,r-dplyr)
1510 ("r-genomeinfodb" ,r-genomeinfodb)
1511 ("r-genomicranges" ,r-genomicranges)
1512 ("r-ggplot2" ,r-ggplot2)
1513 ("r-gridextra" ,r-gridextra)
1515 ("r-igraph" ,r-igraph)
1516 ("r-interactionset" ,r-interactionset)
1517 ("r-iranges" ,r-iranges)
1518 ("r-rsamtools" ,r-rsamtools)
1519 ("r-rtracklayer" ,r-rtracklayer)
1520 ("r-s4vectors" ,r-s4vectors)
1521 ("r-stringr" ,r-stringr)))
1522 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1523 (synopsis "R package for handling genomic interaction data")
1525 "This R package provides tools for handling genomic interaction data,
1526 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1527 information and producing various plots and statistics.")
1528 (license license:gpl3)))
1530 (define-public r-ctc
1537 (uri (bioconductor-uri "ctc" version))
1540 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1541 (build-system r-build-system)
1542 (propagated-inputs `(("r-amap" ,r-amap)))
1543 (home-page "https://bioconductor.org/packages/ctc/")
1544 (synopsis "Cluster and tree conversion")
1546 "This package provides tools for exporting and importing classification
1547 trees and clusters to other programs.")
1548 (license license:gpl2)))
1550 (define-public r-goseq
1557 (uri (bioconductor-uri "goseq" version))
1560 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1561 (build-system r-build-system)
1563 `(("r-annotationdbi" ,r-annotationdbi)
1564 ("r-biasedurn" ,r-biasedurn)
1565 ("r-biocgenerics" ,r-biocgenerics)
1566 ("r-genelendatabase" ,r-genelendatabase)
1567 ("r-go-db" ,r-go-db)
1568 ("r-mgcv" ,r-mgcv)))
1569 (home-page "https://bioconductor.org/packages/goseq/")
1570 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1572 "This package provides tools to detect Gene Ontology and/or other user
1573 defined categories which are over/under represented in RNA-seq data.")
1574 (license license:lgpl2.0+)))
1576 (define-public r-glimma
1583 (uri (bioconductor-uri "Glimma" version))
1586 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1587 (properties `((upstream-name . "Glimma")))
1588 (build-system r-build-system)
1590 `(("r-edger" ,r-edger)
1591 ("r-jsonlite" ,r-jsonlite)
1592 ("r-s4vectors" ,r-s4vectors)))
1593 (home-page "https://github.com/Shians/Glimma")
1594 (synopsis "Interactive HTML graphics")
1596 "This package generates interactive visualisations for analysis of
1597 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1598 HTML page. The interactions are built on top of the popular static
1599 representations of analysis results in order to provide additional
1601 (license license:lgpl3)))
1603 (define-public r-rots
1610 (uri (bioconductor-uri "ROTS" version))
1613 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1614 (properties `((upstream-name . "ROTS")))
1615 (build-system r-build-system)
1617 `(("r-biobase" ,r-biobase)
1618 ("r-rcpp" ,r-rcpp)))
1619 (home-page "https://bioconductor.org/packages/ROTS/")
1620 (synopsis "Reproducibility-Optimized Test Statistic")
1622 "This package provides tools for calculating the
1623 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1625 (license license:gpl2+)))
1627 (define-public r-plgem
1634 (uri (bioconductor-uri "plgem" version))
1637 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1638 (build-system r-build-system)
1640 `(("r-biobase" ,r-biobase)
1641 ("r-mass" ,r-mass)))
1642 (home-page "http://www.genopolis.it")
1643 (synopsis "Detect differential expression in microarray and proteomics datasets")
1645 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1646 model the variance-versus-mean dependence that exists in a variety of
1647 genome-wide datasets, including microarray and proteomics data. The use of
1648 PLGEM has been shown to improve the detection of differentially expressed
1649 genes or proteins in these datasets.")
1650 (license license:gpl2)))
1652 (define-public r-inspect
1659 (uri (bioconductor-uri "INSPEcT" version))
1662 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1663 (properties `((upstream-name . "INSPEcT")))
1664 (build-system r-build-system)
1666 `(("r-biobase" ,r-biobase)
1667 ("r-biocgenerics" ,r-biocgenerics)
1668 ("r-biocparallel" ,r-biocparallel)
1669 ("r-deseq2" ,r-deseq2)
1670 ("r-desolve" ,r-desolve)
1671 ("r-genomicalignments" ,r-genomicalignments)
1672 ("r-genomicfeatures" ,r-genomicfeatures)
1673 ("r-genomicranges" ,r-genomicranges)
1674 ("r-iranges" ,r-iranges)
1675 ("r-plgem" ,r-plgem)
1676 ("r-preprocesscore" ,r-preprocesscore)
1678 ("r-rootsolve" ,r-rootsolve)
1679 ("r-rsamtools" ,r-rsamtools)
1680 ("r-s4vectors" ,r-s4vectors)
1681 ("r-shiny" ,r-shiny)
1682 ("r-summarizedexperiment" ,r-summarizedexperiment)
1683 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1684 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1685 (home-page "https://bioconductor.org/packages/INSPEcT")
1686 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1688 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1689 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1690 order to evaluate synthesis, processing and degradation rates and assess via
1691 modeling the rates that determines changes in mature mRNA levels.")
1692 (license license:gpl2)))
1694 (define-public r-dnabarcodes
1696 (name "r-dnabarcodes")
1701 (uri (bioconductor-uri "DNABarcodes" version))
1704 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1705 (properties `((upstream-name . "DNABarcodes")))
1706 (build-system r-build-system)
1709 ("r-matrix" ,r-matrix)
1710 ("r-rcpp" ,r-rcpp)))
1711 (home-page "https://bioconductor.org/packages/DNABarcodes")
1712 (synopsis "Create and analyze DNA barcodes")
1714 "This package offers tools to create DNA barcode sets capable of
1715 correcting insertion, deletion, and substitution errors. Existing barcodes
1716 can be analyzed regarding their minimal, maximal and average distances between
1717 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1718 demultiplexed, i.e. assigned to their original reference barcode.")
1719 (license license:gpl2)))
1721 (define-public r-ruvseq
1728 (uri (bioconductor-uri "RUVSeq" version))
1731 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
1732 (properties `((upstream-name . "RUVSeq")))
1733 (build-system r-build-system)
1735 `(("r-biobase" ,r-biobase)
1736 ("r-edaseq" ,r-edaseq)
1737 ("r-edger" ,r-edger)
1738 ("r-mass" ,r-mass)))
1739 (home-page "https://github.com/drisso/RUVSeq")
1740 (synopsis "Remove unwanted variation from RNA-Seq data")
1742 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1743 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1745 (license license:artistic2.0)))
1747 (define-public r-biocneighbors
1749 (name "r-biocneighbors")
1754 (uri (bioconductor-uri "BiocNeighbors" version))
1757 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
1758 (properties `((upstream-name . "BiocNeighbors")))
1759 (build-system r-build-system)
1761 `(("r-biocgenerics" ,r-biocgenerics)
1762 ("r-biocparallel" ,r-biocparallel)
1764 ("r-rcppannoy" ,r-rcppannoy)
1765 ("r-rcpphnsw" ,r-rcpphnsw)
1766 ("r-s4vectors" ,r-s4vectors)))
1767 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1768 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1770 "This package implements exact and approximate methods for nearest
1771 neighbor detection, in a framework that allows them to be easily switched
1772 within Bioconductor packages or workflows. The exact algorithm is implemented
1773 using pre-clustering with the k-means algorithm. Functions are also provided
1774 to search for all neighbors within a given distance. Parallelization is
1775 achieved for all methods using the BiocParallel framework.")
1776 (license license:gpl3)))
1778 (define-public r-biocsingular
1780 (name "r-biocsingular")
1785 (uri (bioconductor-uri "BiocSingular" version))
1788 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
1789 (properties `((upstream-name . "BiocSingular")))
1790 (build-system r-build-system)
1792 `(("r-beachmat" ,r-beachmat)
1793 ("r-biocgenerics" ,r-biocgenerics)
1794 ("r-biocparallel" ,r-biocparallel)
1795 ("r-delayedarray" ,r-delayedarray)
1796 ("r-irlba" ,r-irlba)
1797 ("r-matrix" ,r-matrix)
1800 ("r-s4vectors" ,r-s4vectors)))
1801 (home-page "https://github.com/LTLA/BiocSingular")
1802 (synopsis "Singular value decomposition for Bioconductor packages")
1804 "This package implements exact and approximate methods for singular value
1805 decomposition and principal components analysis, in a framework that allows
1806 them to be easily switched within Bioconductor packages or workflows. Where
1807 possible, parallelization is achieved using the BiocParallel framework.")
1808 (license license:gpl3)))
1810 (define-public r-destiny
1817 (uri (bioconductor-uri "destiny" version))
1820 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
1821 (build-system r-build-system)
1823 `(("r-biobase" ,r-biobase)
1824 ("r-biocgenerics" ,r-biocgenerics)
1825 ("r-ggplot2" ,r-ggplot2)
1826 ("r-ggthemes" ,r-ggthemes)
1827 ("r-igraph" ,r-igraph)
1828 ("r-matrix" ,r-matrix)
1829 ("r-proxy" ,r-proxy)
1831 ("r-rcppeigen" ,r-rcppeigen)
1832 ("r-scales" ,r-scales)
1833 ("r-scatterplot3d" ,r-scatterplot3d)
1834 ("r-smoother" ,r-smoother)
1835 ("r-summarizedexperiment" ,r-summarizedexperiment)
1837 (home-page "https://bioconductor.org/packages/destiny/")
1838 (synopsis "Create and plot diffusion maps")
1839 (description "This package provides tools to create and plot diffusion
1841 ;; Any version of the GPL
1842 (license license:gpl3+)))
1844 (define-public r-savr
1851 (uri (bioconductor-uri "savR" version))
1854 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
1855 (properties `((upstream-name . "savR")))
1856 (build-system r-build-system)
1858 `(("r-ggplot2" ,r-ggplot2)
1859 ("r-gridextra" ,r-gridextra)
1860 ("r-reshape2" ,r-reshape2)
1861 ("r-scales" ,r-scales)
1863 (home-page "https://github.com/bcalder/savR")
1864 (synopsis "Parse and analyze Illumina SAV files")
1866 "This package provides tools to parse Illumina Sequence Analysis
1867 Viewer (SAV) files, access data, and generate QC plots.")
1868 (license license:agpl3+)))
1870 (define-public r-chipexoqual
1872 (name "r-chipexoqual")
1877 (uri (bioconductor-uri "ChIPexoQual" version))
1880 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
1881 (properties `((upstream-name . "ChIPexoQual")))
1882 (build-system r-build-system)
1884 `(("r-biocparallel" ,r-biocparallel)
1885 ("r-biovizbase" ,r-biovizbase)
1886 ("r-broom" ,r-broom)
1887 ("r-data-table" ,r-data-table)
1888 ("r-dplyr" ,r-dplyr)
1889 ("r-genomeinfodb" ,r-genomeinfodb)
1890 ("r-genomicalignments" ,r-genomicalignments)
1891 ("r-genomicranges" ,r-genomicranges)
1892 ("r-ggplot2" ,r-ggplot2)
1893 ("r-hexbin" ,r-hexbin)
1894 ("r-iranges" ,r-iranges)
1895 ("r-rcolorbrewer" ,r-rcolorbrewer)
1896 ("r-rmarkdown" ,r-rmarkdown)
1897 ("r-rsamtools" ,r-rsamtools)
1898 ("r-s4vectors" ,r-s4vectors)
1899 ("r-scales" ,r-scales)
1900 ("r-viridis" ,r-viridis)))
1901 (home-page "https://github.com/keleslab/ChIPexoQual")
1902 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1904 "This package provides a quality control pipeline for ChIP-exo/nexus
1906 (license license:gpl2+)))
1908 (define-public r-copynumber
1910 (name "r-copynumber")
1914 (uri (bioconductor-uri "copynumber" version))
1917 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
1918 (build-system r-build-system)
1920 `(("r-s4vectors" ,r-s4vectors)
1921 ("r-iranges" ,r-iranges)
1922 ("r-genomicranges" ,r-genomicranges)
1923 ("r-biocgenerics" ,r-biocgenerics)))
1924 (home-page "https://bioconductor.org/packages/copynumber")
1925 (synopsis "Segmentation of single- and multi-track copy number data")
1927 "This package segments single- and multi-track copy number data by a
1928 penalized least squares regression method.")
1929 (license license:artistic2.0)))
1931 (define-public r-dnacopy
1938 (uri (bioconductor-uri "DNAcopy" version))
1941 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
1942 (properties `((upstream-name . "DNAcopy")))
1943 (build-system r-build-system)
1944 (native-inputs `(("gfortran" ,gfortran)))
1945 (home-page "https://bioconductor.org/packages/DNAcopy")
1946 (synopsis "DNA copy number data analysis")
1948 "This package implements the @dfn{circular binary segmentation} (CBS)
1949 algorithm to segment DNA copy number data and identify genomic regions with
1950 abnormal copy number.")
1951 (license license:gpl2+)))
1953 ;; This is a CRAN package, but it uncharacteristically depends on a
1954 ;; Bioconductor package.
1955 (define-public r-htscluster
1957 (name "r-htscluster")
1962 (uri (cran-uri "HTSCluster" version))
1965 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1966 (properties `((upstream-name . "HTSCluster")))
1967 (build-system r-build-system)
1969 `(("r-capushe" ,r-capushe)
1970 ("r-edger" ,r-edger)
1971 ("r-plotrix" ,r-plotrix)))
1972 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1973 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1975 "This package provides a Poisson mixture model is implemented to cluster
1976 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1977 estimation is performed using either the EM or CEM algorithm, and the slope
1978 heuristics are used for model selection (i.e., to choose the number of
1980 (license license:gpl3+)))
1982 (define-public r-deds
1989 (uri (bioconductor-uri "DEDS" version))
1992 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
1993 (properties `((upstream-name . "DEDS")))
1994 (build-system r-build-system)
1995 (home-page "https://bioconductor.org/packages/DEDS/")
1996 (synopsis "Differential expression via distance summary for microarray data")
1998 "This library contains functions that calculate various statistics of
1999 differential expression for microarray data, including t statistics, fold
2000 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2001 also implements a new methodology called DEDS (Differential Expression via
2002 Distance Summary), which selects differentially expressed genes by integrating
2003 and summarizing a set of statistics using a weighted distance approach.")
2004 ;; Any version of the LGPL.
2005 (license license:lgpl3+)))
2007 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2009 (define-public r-nbpseq
2016 (uri (cran-uri "NBPSeq" version))
2019 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2020 (properties `((upstream-name . "NBPSeq")))
2021 (build-system r-build-system)
2023 `(("r-qvalue" ,r-qvalue)))
2024 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2025 (synopsis "Negative binomial models for RNA-Seq data")
2027 "This package provides negative binomial models for two-group comparisons
2028 and regression inferences from RNA-sequencing data.")
2029 (license license:gpl2)))
2031 (define-public r-ebseq
2038 (uri (bioconductor-uri "EBSeq" version))
2041 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2042 (properties `((upstream-name . "EBSeq")))
2043 (build-system r-build-system)
2045 `(("r-blockmodeling" ,r-blockmodeling)
2046 ("r-gplots" ,r-gplots)
2047 ("r-testthat" ,r-testthat)))
2048 (home-page "https://bioconductor.org/packages/EBSeq")
2049 (synopsis "Differential expression analysis of RNA-seq data")
2051 "This package provides tools for differential expression analysis at both
2052 gene and isoform level using RNA-seq data")
2053 (license license:artistic2.0)))
2055 (define-public r-lpsymphony
2057 (name "r-lpsymphony")
2062 (uri (bioconductor-uri "lpsymphony" version))
2065 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2066 (build-system r-build-system)
2068 `(("gfortran" ,gfortran)
2071 `(("pkg-config" ,pkg-config)))
2072 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2073 (synopsis "Symphony integer linear programming solver in R")
2075 "This package was derived from Rsymphony. The package provides an R
2076 interface to SYMPHONY, a linear programming solver written in C++. The main
2077 difference between this package and Rsymphony is that it includes the solver
2078 source code, while Rsymphony expects to find header and library files on the
2079 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2080 to install interface to SYMPHONY.")
2081 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2082 ;; lpsimphony is released under the same terms.
2083 (license license:epl1.0)))
2085 (define-public r-ihw
2092 (uri (bioconductor-uri "IHW" version))
2095 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2096 (properties `((upstream-name . "IHW")))
2097 (build-system r-build-system)
2099 `(("r-biocgenerics" ,r-biocgenerics)
2100 ("r-fdrtool" ,r-fdrtool)
2101 ("r-lpsymphony" ,r-lpsymphony)
2102 ("r-slam" ,r-slam)))
2103 (home-page "https://bioconductor.org/packages/IHW")
2104 (synopsis "Independent hypothesis weighting")
2106 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2107 procedure that increases power compared to the method of Benjamini and
2108 Hochberg by assigning data-driven weights to each hypothesis. The input to
2109 IHW is a two-column table of p-values and covariates. The covariate can be
2110 any continuous-valued or categorical variable that is thought to be
2111 informative on the statistical properties of each hypothesis test, while it is
2112 independent of the p-value under the null hypothesis.")
2113 (license license:artistic2.0)))
2115 (define-public r-icobra
2122 (uri (bioconductor-uri "iCOBRA" version))
2125 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2126 (properties `((upstream-name . "iCOBRA")))
2127 (build-system r-build-system)
2129 `(("r-dplyr" ,r-dplyr)
2131 ("r-ggplot2" ,r-ggplot2)
2132 ("r-limma" ,r-limma)
2133 ("r-reshape2" ,r-reshape2)
2135 ("r-scales" ,r-scales)
2136 ("r-shiny" ,r-shiny)
2137 ("r-shinybs" ,r-shinybs)
2138 ("r-shinydashboard" ,r-shinydashboard)
2139 ("r-upsetr" ,r-upsetr)))
2140 (home-page "https://bioconductor.org/packages/iCOBRA")
2141 (synopsis "Comparison and visualization of ranking and assignment methods")
2143 "This package provides functions for calculation and visualization of
2144 performance metrics for evaluation of ranking and binary
2145 classification (assignment) methods. It also contains a Shiny application for
2146 interactive exploration of results.")
2147 (license license:gpl2+)))
2149 (define-public r-mast
2156 (uri (bioconductor-uri "MAST" version))
2159 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2160 (properties `((upstream-name . "MAST")))
2161 (build-system r-build-system)
2163 `(("r-abind" ,r-abind)
2165 ("r-biobase" ,r-biobase)
2166 ("r-biocgenerics" ,r-biocgenerics)
2167 ("r-data-table" ,r-data-table)
2168 ("r-ggplot2" ,r-ggplot2)
2170 ("r-progress" ,r-progress)
2171 ("r-reshape2" ,r-reshape2)
2172 ("r-s4vectors" ,r-s4vectors)
2173 ("r-singlecellexperiment" ,r-singlecellexperiment)
2174 ("r-stringr" ,r-stringr)
2175 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2176 (home-page "https://github.com/RGLab/MAST/")
2177 (synopsis "Model-based analysis of single cell transcriptomics")
2179 "This package provides methods and models for handling zero-inflated
2180 single cell assay data.")
2181 (license license:gpl2+)))
2183 (define-public r-monocle
2190 (uri (bioconductor-uri "monocle" version))
2193 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2194 (build-system r-build-system)
2196 `(("r-biobase" ,r-biobase)
2197 ("r-biocgenerics" ,r-biocgenerics)
2198 ("r-biocviews" ,r-biocviews)
2199 ("r-cluster" ,r-cluster)
2200 ("r-combinat" ,r-combinat)
2201 ("r-ddrtree" ,r-ddrtree)
2202 ("r-densityclust" ,r-densityclust)
2203 ("r-dplyr" ,r-dplyr)
2204 ("r-fastica" ,r-fastica)
2205 ("r-ggplot2" ,r-ggplot2)
2206 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2207 ("r-igraph" ,r-igraph)
2208 ("r-irlba" ,r-irlba)
2209 ("r-limma" ,r-limma)
2211 ("r-matrix" ,r-matrix)
2212 ("r-matrixstats" ,r-matrixstats)
2213 ("r-pheatmap" ,r-pheatmap)
2215 ("r-proxy" ,r-proxy)
2216 ("r-qlcmatrix" ,r-qlcmatrix)
2219 ("r-reshape2" ,r-reshape2)
2220 ("r-rtsne" ,r-rtsne)
2222 ("r-stringr" ,r-stringr)
2223 ("r-tibble" ,r-tibble)
2225 ("r-viridis" ,r-viridis)))
2226 (home-page "https://bioconductor.org/packages/monocle")
2227 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2229 "Monocle performs differential expression and time-series analysis for
2230 single-cell expression experiments. It orders individual cells according to
2231 progress through a biological process, without knowing ahead of time which
2232 genes define progress through that process. Monocle also performs
2233 differential expression analysis, clustering, visualization, and other useful
2234 tasks on single cell expression data. It is designed to work with RNA-Seq and
2235 qPCR data, but could be used with other types as well.")
2236 (license license:artistic2.0)))
2238 (define-public r-noiseq
2245 (uri (bioconductor-uri "NOISeq" version))
2248 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2249 (properties `((upstream-name . "NOISeq")))
2250 (build-system r-build-system)
2252 `(("r-biobase" ,r-biobase)
2253 ("r-matrix" ,r-matrix)))
2254 (home-page "https://bioconductor.org/packages/NOISeq")
2255 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2257 "This package provides tools to support the analysis of RNA-seq
2258 expression data or other similar kind of data. It provides exploratory plots
2259 to evaluate saturation, count distribution, expression per chromosome, type of
2260 detected features, features length, etc. It also supports the analysis of
2261 differential expression between two experimental conditions with no parametric
2263 (license license:artistic2.0)))
2265 (define-public r-scdd
2272 (uri (bioconductor-uri "scDD" version))
2275 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2276 (properties `((upstream-name . "scDD")))
2277 (build-system r-build-system)
2280 ("r-biocparallel" ,r-biocparallel)
2281 ("r-ebseq" ,r-ebseq)
2282 ("r-fields" ,r-fields)
2283 ("r-ggplot2" ,r-ggplot2)
2284 ("r-mclust" ,r-mclust)
2285 ("r-outliers" ,r-outliers)
2286 ("r-s4vectors" ,r-s4vectors)
2287 ("r-scran" ,r-scran)
2288 ("r-singlecellexperiment" ,r-singlecellexperiment)
2289 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2290 (home-page "https://github.com/kdkorthauer/scDD")
2291 (synopsis "Mixture modeling of single-cell RNA-seq data")
2293 "This package implements a method to analyze single-cell RNA-seq data
2294 utilizing flexible Dirichlet Process mixture models. Genes with differential
2295 distributions of expression are classified into several interesting patterns
2296 of differences between two conditions. The package also includes functions
2297 for simulating data with these patterns from negative binomial
2299 (license license:gpl2)))
2301 (define-public r-scone
2308 (uri (bioconductor-uri "scone" version))
2311 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2312 (build-system r-build-system)
2314 `(("r-aroma-light" ,r-aroma-light)
2315 ("r-biocparallel" ,r-biocparallel)
2317 ("r-class" ,r-class)
2318 ("r-cluster" ,r-cluster)
2319 ("r-compositions" ,r-compositions)
2320 ("r-diptest" ,r-diptest)
2321 ("r-edger" ,r-edger)
2323 ("r-gplots" ,r-gplots)
2324 ("r-hexbin" ,r-hexbin)
2325 ("r-limma" ,r-limma)
2326 ("r-matrixstats" ,r-matrixstats)
2327 ("r-mixtools" ,r-mixtools)
2328 ("r-rarpack" ,r-rarpack)
2329 ("r-rcolorbrewer" ,r-rcolorbrewer)
2330 ("r-rhdf5" ,r-rhdf5)
2331 ("r-ruvseq" ,r-ruvseq)
2332 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2333 (home-page "https://bioconductor.org/packages/scone")
2334 (synopsis "Single cell overview of normalized expression data")
2336 "SCONE is an R package for comparing and ranking the performance of
2337 different normalization schemes for single-cell RNA-seq and other
2338 high-throughput analyses.")
2339 (license license:artistic2.0)))
2341 (define-public r-geoquery
2348 (uri (bioconductor-uri "GEOquery" version))
2351 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2352 (properties `((upstream-name . "GEOquery")))
2353 (build-system r-build-system)
2355 `(("r-biobase" ,r-biobase)
2356 ("r-dplyr" ,r-dplyr)
2358 ("r-limma" ,r-limma)
2359 ("r-magrittr" ,r-magrittr)
2360 ("r-readr" ,r-readr)
2361 ("r-tidyr" ,r-tidyr)
2362 ("r-xml2" ,r-xml2)))
2363 (home-page "https://github.com/seandavi/GEOquery/")
2364 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2366 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2367 microarray data. Given the rich and varied nature of this resource, it is
2368 only natural to want to apply BioConductor tools to these data. GEOquery is
2369 the bridge between GEO and BioConductor.")
2370 (license license:gpl2)))
2372 (define-public r-illuminaio
2374 (name "r-illuminaio")
2379 (uri (bioconductor-uri "illuminaio" version))
2382 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2383 (build-system r-build-system)
2385 `(("r-base64" ,r-base64)))
2386 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2387 (synopsis "Parse Illumina microarray output files")
2389 "This package provides tools for parsing Illumina's microarray output
2390 files, including IDAT.")
2391 (license license:gpl2)))
2393 (define-public r-siggenes
2400 (uri (bioconductor-uri "siggenes" version))
2403 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2404 (build-system r-build-system)
2406 `(("r-biobase" ,r-biobase)
2407 ("r-multtest" ,r-multtest)
2408 ("r-scrime" ,r-scrime)))
2409 (home-page "https://bioconductor.org/packages/siggenes/")
2411 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2413 "This package provides tools for the identification of differentially
2414 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2415 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2416 Bayes Analyses of Microarrays} (EBAM).")
2417 (license license:lgpl2.0+)))
2419 (define-public r-bumphunter
2421 (name "r-bumphunter")
2426 (uri (bioconductor-uri "bumphunter" version))
2429 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2430 (build-system r-build-system)
2432 `(("r-annotationdbi" ,r-annotationdbi)
2433 ("r-biocgenerics" ,r-biocgenerics)
2434 ("r-dorng" ,r-dorng)
2435 ("r-foreach" ,r-foreach)
2436 ("r-genomeinfodb" ,r-genomeinfodb)
2437 ("r-genomicfeatures" ,r-genomicfeatures)
2438 ("r-genomicranges" ,r-genomicranges)
2439 ("r-iranges" ,r-iranges)
2440 ("r-iterators" ,r-iterators)
2441 ("r-limma" ,r-limma)
2442 ("r-locfit" ,r-locfit)
2443 ("r-matrixstats" ,r-matrixstats)
2444 ("r-s4vectors" ,r-s4vectors)))
2445 (home-page "https://github.com/ririzarr/bumphunter")
2446 (synopsis "Find bumps in genomic data")
2448 "This package provides tools for finding bumps in genomic data in order
2449 to identify differentially methylated regions in epigenetic epidemiology
2451 (license license:artistic2.0)))
2453 (define-public r-minfi
2460 (uri (bioconductor-uri "minfi" version))
2463 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2464 (build-system r-build-system)
2466 `(("r-beanplot" ,r-beanplot)
2467 ("r-biobase" ,r-biobase)
2468 ("r-biocgenerics" ,r-biocgenerics)
2469 ("r-biocparallel" ,r-biocparallel)
2470 ("r-biostrings" ,r-biostrings)
2471 ("r-bumphunter" ,r-bumphunter)
2472 ("r-data-table" ,r-data-table)
2473 ("r-delayedarray" ,r-delayedarray)
2474 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2475 ("r-genefilter" ,r-genefilter)
2476 ("r-genomeinfodb" ,r-genomeinfodb)
2477 ("r-genomicranges" ,r-genomicranges)
2478 ("r-geoquery" ,r-geoquery)
2479 ("r-hdf5array" ,r-hdf5array)
2480 ("r-illuminaio" ,r-illuminaio)
2481 ("r-iranges" ,r-iranges)
2482 ("r-lattice" ,r-lattice)
2483 ("r-limma" ,r-limma)
2485 ("r-mclust" ,r-mclust)
2487 ("r-nor1mix" ,r-nor1mix)
2488 ("r-preprocesscore" ,r-preprocesscore)
2489 ("r-quadprog" ,r-quadprog)
2490 ("r-rcolorbrewer" ,r-rcolorbrewer)
2491 ("r-reshape" ,r-reshape)
2492 ("r-s4vectors" ,r-s4vectors)
2493 ("r-siggenes" ,r-siggenes)
2494 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2495 (home-page "https://github.com/hansenlab/minfi")
2496 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2498 "This package provides tools to analyze and visualize Illumina Infinium
2499 methylation arrays.")
2500 (license license:artistic2.0)))
2502 (define-public r-methylumi
2504 (name "r-methylumi")
2509 (uri (bioconductor-uri "methylumi" version))
2512 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2513 (build-system r-build-system)
2515 `(("r-annotate" ,r-annotate)
2516 ("r-annotationdbi" ,r-annotationdbi)
2517 ("r-biobase" ,r-biobase)
2518 ("r-biocgenerics" ,r-biocgenerics)
2519 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2520 ("r-genefilter" ,r-genefilter)
2521 ("r-genomeinfodb" ,r-genomeinfodb)
2522 ("r-genomicranges" ,r-genomicranges)
2523 ("r-ggplot2" ,r-ggplot2)
2524 ("r-illuminaio" ,r-illuminaio)
2525 ("r-iranges" ,r-iranges)
2526 ("r-lattice" ,r-lattice)
2527 ("r-matrixstats" ,r-matrixstats)
2528 ("r-minfi" ,r-minfi)
2529 ("r-reshape2" ,r-reshape2)
2530 ("r-s4vectors" ,r-s4vectors)
2531 ("r-scales" ,r-scales)
2532 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2533 (home-page "https://bioconductor.org/packages/methylumi")
2534 (synopsis "Handle Illumina methylation data")
2536 "This package provides classes for holding and manipulating Illumina
2537 methylation data. Based on eSet, it can contain MIAME information, sample
2538 information, feature information, and multiple matrices of data. An
2539 \"intelligent\" import function, methylumiR can read the Illumina text files
2540 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2541 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2542 background correction, and quality control features for GoldenGate, Infinium,
2543 and Infinium HD arrays are also included.")
2544 (license license:gpl2)))
2546 (define-public r-lumi
2553 (uri (bioconductor-uri "lumi" version))
2556 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2557 (build-system r-build-system)
2559 `(("r-affy" ,r-affy)
2560 ("r-annotate" ,r-annotate)
2561 ("r-annotationdbi" ,r-annotationdbi)
2562 ("r-biobase" ,r-biobase)
2564 ("r-genomicfeatures" ,r-genomicfeatures)
2565 ("r-genomicranges" ,r-genomicranges)
2566 ("r-kernsmooth" ,r-kernsmooth)
2567 ("r-lattice" ,r-lattice)
2569 ("r-methylumi" ,r-methylumi)
2571 ("r-nleqslv" ,r-nleqslv)
2572 ("r-preprocesscore" ,r-preprocesscore)
2573 ("r-rsqlite" ,r-rsqlite)))
2574 (home-page "https://bioconductor.org/packages/lumi")
2575 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2577 "The lumi package provides an integrated solution for the Illumina
2578 microarray data analysis. It includes functions of Illumina
2579 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2580 variance stabilization, normalization and gene annotation at the probe level.
2581 It also includes the functions of processing Illumina methylation microarrays,
2582 especially Illumina Infinium methylation microarrays.")
2583 (license license:lgpl2.0+)))
2585 (define-public r-linnorm
2592 (uri (bioconductor-uri "Linnorm" version))
2595 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2596 (properties `((upstream-name . "Linnorm")))
2597 (build-system r-build-system)
2599 `(("r-amap" ,r-amap)
2600 ("r-apcluster" ,r-apcluster)
2601 ("r-ellipse" ,r-ellipse)
2602 ("r-fastcluster" ,r-fastcluster)
2604 ("r-ggdendro" ,r-ggdendro)
2605 ("r-ggplot2" ,r-ggplot2)
2606 ("r-gmodels" ,r-gmodels)
2607 ("r-igraph" ,r-igraph)
2608 ("r-limma" ,r-limma)
2610 ("r-mclust" ,r-mclust)
2612 ("r-rcpparmadillo" ,r-rcpparmadillo)
2613 ("r-rtsne" ,r-rtsne)
2614 ("r-statmod" ,r-statmod)
2615 ("r-vegan" ,r-vegan)
2617 (home-page "http://www.jjwanglab.org/Linnorm/")
2618 (synopsis "Linear model and normality based transformation method")
2620 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2621 count data or any large scale count data. It transforms such datasets for
2622 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2623 the following pipelines are implemented:
2626 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2627 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2628 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2629 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2630 @item Differential expression analysis or differential peak detection using
2631 limma (@code{Linnorm.limma})
2632 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2633 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2634 @item Stable gene selection for scRNA-seq data; for users without or who do
2635 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2636 @item Data imputation (@code{Linnorm.DataImput}).
2639 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2640 @code{RnaXSim} function is included for simulating RNA-seq data for the
2641 evaluation of DEG analysis methods.")
2642 (license license:expat)))
2644 (define-public r-ioniser
2651 (uri (bioconductor-uri "IONiseR" version))
2654 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2655 (properties `((upstream-name . "IONiseR")))
2656 (build-system r-build-system)
2658 `(("r-biocgenerics" ,r-biocgenerics)
2659 ("r-biocparallel" ,r-biocparallel)
2660 ("r-biostrings" ,r-biostrings)
2661 ("r-bit64" ,r-bit64)
2662 ("r-dplyr" ,r-dplyr)
2663 ("r-ggplot2" ,r-ggplot2)
2664 ("r-magrittr" ,r-magrittr)
2665 ("r-rhdf5" ,r-rhdf5)
2666 ("r-shortread" ,r-shortread)
2667 ("r-stringr" ,r-stringr)
2668 ("r-tibble" ,r-tibble)
2669 ("r-tidyr" ,r-tidyr)
2670 ("r-xvector" ,r-xvector)))
2671 (home-page "https://bioconductor.org/packages/IONiseR/")
2672 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2674 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2675 MinION data. It extracts summary statistics from a set of fast5 files and can
2676 be used either before or after base calling. In addition to standard
2677 summaries of the read-types produced, it provides a number of plots for
2678 visualising metrics relative to experiment run time or spatially over the
2679 surface of a flowcell.")
2680 (license license:expat)))
2682 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2683 (define-public r-gkmsvm
2690 (uri (cran-uri "gkmSVM" version))
2693 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2694 (properties `((upstream-name . "gkmSVM")))
2695 (build-system r-build-system)
2697 `(("r-biocgenerics" ,r-biocgenerics)
2698 ("r-biostrings" ,r-biostrings)
2699 ("r-genomeinfodb" ,r-genomeinfodb)
2700 ("r-genomicranges" ,r-genomicranges)
2701 ("r-iranges" ,r-iranges)
2702 ("r-kernlab" ,r-kernlab)
2705 ("r-rtracklayer" ,r-rtracklayer)
2706 ("r-s4vectors" ,r-s4vectors)
2707 ("r-seqinr" ,r-seqinr)))
2708 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2709 (synopsis "Gapped-kmer support vector machine")
2711 "This R package provides tools for training gapped-kmer SVM classifiers
2712 for DNA and protein sequences. This package supports several sequence
2713 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2714 (license license:gpl2+)))
2716 (define-public r-triform
2723 (uri (bioconductor-uri "triform" version))
2726 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
2727 (build-system r-build-system)
2729 `(("r-biocgenerics" ,r-biocgenerics)
2730 ("r-iranges" ,r-iranges)
2731 ("r-yaml" ,r-yaml)))
2732 (home-page "https://bioconductor.org/packages/triform/")
2733 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2735 "The Triform algorithm uses model-free statistics to identify peak-like
2736 distributions of TF ChIP sequencing reads, taking advantage of an improved
2737 peak definition in combination with known profile characteristics.")
2738 (license license:gpl2)))
2740 (define-public r-varianttools
2742 (name "r-varianttools")
2747 (uri (bioconductor-uri "VariantTools" version))
2750 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
2751 (properties `((upstream-name . "VariantTools")))
2752 (build-system r-build-system)
2754 `(("r-biobase" ,r-biobase)
2755 ("r-biocgenerics" ,r-biocgenerics)
2756 ("r-biocparallel" ,r-biocparallel)
2757 ("r-biostrings" ,r-biostrings)
2758 ("r-bsgenome" ,r-bsgenome)
2759 ("r-genomeinfodb" ,r-genomeinfodb)
2760 ("r-genomicfeatures" ,r-genomicfeatures)
2761 ("r-genomicranges" ,r-genomicranges)
2762 ("r-iranges" ,r-iranges)
2763 ("r-matrix" ,r-matrix)
2764 ("r-rsamtools" ,r-rsamtools)
2765 ("r-rtracklayer" ,r-rtracklayer)
2766 ("r-s4vectors" ,r-s4vectors)
2767 ("r-variantannotation" ,r-variantannotation)))
2768 (home-page "https://bioconductor.org/packages/VariantTools/")
2769 (synopsis "Tools for exploratory analysis of variant calls")
2771 "Explore, diagnose, and compare variant calls using filters. The
2772 VariantTools package supports a workflow for loading data, calling single
2773 sample variants and tumor-specific somatic mutations or other sample-specific
2774 variant types (e.g., RNA editing). Most of the functions operate on
2775 alignments (BAM files) or datasets of called variants. The user is expected
2776 to have already aligned the reads with a separate tool, e.g., GSNAP via
2778 (license license:artistic2.0)))
2780 (define-public r-heatplus
2787 (uri (bioconductor-uri "Heatplus" version))
2790 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
2791 (properties `((upstream-name . "Heatplus")))
2792 (build-system r-build-system)
2794 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2795 (home-page "https://github.com/alexploner/Heatplus")
2796 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2798 "This package provides tools to display a rectangular heatmap (intensity
2799 plot) of a data matrix. By default, both samples (columns) and features (row)
2800 of the matrix are sorted according to a hierarchical clustering, and the
2801 corresponding dendrogram is plotted. Optionally, panels with additional
2802 information about samples and features can be added to the plot.")
2803 (license license:gpl2+)))
2805 (define-public r-gosemsim
2812 (uri (bioconductor-uri "GOSemSim" version))
2815 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
2816 (properties `((upstream-name . "GOSemSim")))
2817 (build-system r-build-system)
2819 `(("r-annotationdbi" ,r-annotationdbi)
2820 ("r-go-db" ,r-go-db)
2821 ("r-rcpp" ,r-rcpp)))
2822 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2823 (synopsis "GO-terms semantic similarity measures")
2825 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2826 quantitative ways to compute similarities between genes and gene groups, and
2827 have became important basis for many bioinformatics analysis approaches.
2828 GOSemSim is an R package for semantic similarity computation among GO terms,
2829 sets of GO terms, gene products and gene clusters.")
2830 (license license:artistic2.0)))
2832 (define-public r-anota
2839 (uri (bioconductor-uri "anota" version))
2842 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
2843 (build-system r-build-system)
2845 `(("r-multtest" ,r-multtest)
2846 ("r-qvalue" ,r-qvalue)))
2847 (home-page "https://bioconductor.org/packages/anota/")
2848 (synopsis "Analysis of translational activity")
2850 "Genome wide studies of translational control is emerging as a tool to
2851 study various biological conditions. The output from such analysis is both
2852 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2853 involved in translation (the actively translating mRNA level) for each mRNA.
2854 The standard analysis of such data strives towards identifying differential
2855 translational between two or more sample classes - i.e. differences in
2856 actively translated mRNA levels that are independent of underlying differences
2857 in cytosolic mRNA levels. This package allows for such analysis using partial
2858 variances and the random variance model. As 10s of thousands of mRNAs are
2859 analyzed in parallel the library performs a number of tests to assure that
2860 the data set is suitable for such analysis.")
2861 (license license:gpl3)))
2863 (define-public r-sigpathway
2865 (name "r-sigpathway")
2870 (uri (bioconductor-uri "sigPathway" version))
2873 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
2874 (properties `((upstream-name . "sigPathway")))
2875 (build-system r-build-system)
2876 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
2877 (synopsis "Pathway analysis")
2879 "This package is used to conduct pathway analysis by calculating the NT_k
2880 and NE_k statistics in a statistical framework for determining whether a
2881 specified group of genes for a pathway has a coordinated association with a
2882 phenotype of interest.")
2883 (license license:gpl2)))
2885 (define-public r-fgsea
2892 (uri (bioconductor-uri "fgsea" version))
2895 "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c"))))
2896 (build-system r-build-system)
2899 ("r-biocparallel" ,r-biocparallel)
2900 ("r-data-table" ,r-data-table)
2901 ("r-fastmatch" ,r-fastmatch)
2902 ("r-ggplot2" ,r-ggplot2)
2903 ("r-gridextra" ,r-gridextra)
2904 ("r-matrix" ,r-matrix)
2905 ("r-rcpp" ,r-rcpp)))
2906 (home-page "https://github.com/ctlab/fgsea/")
2907 (synopsis "Fast gene set enrichment analysis")
2909 "The package implements an algorithm for fast gene set enrichment
2910 analysis. Using the fast algorithm allows to make more permutations and get
2911 more fine grained p-values, which allows to use accurate stantard approaches
2912 to multiple hypothesis correction.")
2913 (license license:expat)))
2915 (define-public r-dose
2922 (uri (bioconductor-uri "DOSE" version))
2925 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
2926 (properties `((upstream-name . "DOSE")))
2927 (build-system r-build-system)
2929 `(("r-annotationdbi" ,r-annotationdbi)
2930 ("r-biocparallel" ,r-biocparallel)
2931 ("r-do-db" ,r-do-db)
2932 ("r-fgsea" ,r-fgsea)
2933 ("r-ggplot2" ,r-ggplot2)
2934 ("r-gosemsim" ,r-gosemsim)
2935 ("r-qvalue" ,r-qvalue)
2936 ("r-reshape2" ,r-reshape2)
2937 ("r-s4vectors" ,r-s4vectors)))
2938 (home-page "https://guangchuangyu.github.io/software/DOSE/")
2939 (synopsis "Disease ontology semantic and enrichment analysis")
2941 "This package implements five methods proposed by Resnik, Schlicker,
2942 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
2943 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
2944 including hypergeometric model and gene set enrichment analysis are also
2945 implemented for discovering disease associations of high-throughput biological
2947 (license license:artistic2.0)))
2949 (define-public r-enrichplot
2951 (name "r-enrichplot")
2956 (uri (bioconductor-uri "enrichplot" version))
2959 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
2960 (build-system r-build-system)
2962 `(("r-annotationdbi" ,r-annotationdbi)
2963 ("r-cowplot" ,r-cowplot)
2965 ("r-europepmc" ,r-europepmc)
2966 ("r-ggplot2" ,r-ggplot2)
2967 ("r-ggplotify" ,r-ggplotify)
2968 ("r-ggraph" ,r-ggraph)
2969 ("r-ggridges" ,r-ggridges)
2970 ("r-gosemsim" ,r-gosemsim)
2971 ("r-gridextra" ,r-gridextra)
2972 ("r-igraph" ,r-igraph)
2973 ("r-purrr" ,r-purrr)
2974 ("r-rcolorbrewer" ,r-rcolorbrewer)
2975 ("r-reshape2" ,r-reshape2)
2976 ("r-upsetr" ,r-upsetr)))
2977 (home-page "https://github.com/GuangchuangYu/enrichplot")
2978 (synopsis "Visualization of functional enrichment result")
2980 "The enrichplot package implements several visualization methods for
2981 interpreting functional enrichment results obtained from ORA or GSEA analyses.
2982 All the visualization methods are developed based on ggplot2 graphics.")
2983 (license license:artistic2.0)))
2985 (define-public r-clusterprofiler
2987 (name "r-clusterprofiler")
2992 (uri (bioconductor-uri "clusterProfiler" version))
2995 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
2997 `((upstream-name . "clusterProfiler")))
2998 (build-system r-build-system)
3000 `(("r-annotationdbi" ,r-annotationdbi)
3002 ("r-enrichplot" ,r-enrichplot)
3003 ("r-ggplot2" ,r-ggplot2)
3004 ("r-go-db" ,r-go-db)
3005 ("r-gosemsim" ,r-gosemsim)
3006 ("r-magrittr" ,r-magrittr)
3008 ("r-qvalue" ,r-qvalue)
3009 ("r-rvcheck" ,r-rvcheck)
3010 ("r-tidyr" ,r-tidyr)))
3011 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3012 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3014 "This package implements methods to analyze and visualize functional
3015 profiles (GO and KEGG) of gene and gene clusters.")
3016 (license license:artistic2.0)))
3018 (define-public r-mlinterfaces
3020 (name "r-mlinterfaces")
3025 (uri (bioconductor-uri "MLInterfaces" version))
3028 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
3029 (properties `((upstream-name . "MLInterfaces")))
3030 (build-system r-build-system)
3032 `(("r-annotate" ,r-annotate)
3033 ("r-biobase" ,r-biobase)
3034 ("r-biocgenerics" ,r-biocgenerics)
3035 ("r-cluster" ,r-cluster)
3038 ("r-gdata" ,r-gdata)
3039 ("r-genefilter" ,r-genefilter)
3040 ("r-ggvis" ,r-ggvis)
3041 ("r-hwriter" ,r-hwriter)
3043 ("r-mlbench" ,r-mlbench)
3045 ("r-rcolorbrewer" ,r-rcolorbrewer)
3047 ("r-rpart" ,r-rpart)
3048 ("r-sfsmisc" ,r-sfsmisc)
3049 ("r-shiny" ,r-shiny)
3050 ("r-threejs" ,r-threejs)))
3051 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3052 (synopsis "Interfaces to R machine learning procedures")
3054 "This package provides uniform interfaces to machine learning code for
3055 data in R and Bioconductor containers.")
3056 ;; Any version of the LGPL.
3057 (license license:lgpl2.1+)))
3059 (define-public r-annaffy
3066 (uri (bioconductor-uri "annaffy" version))
3069 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3070 (build-system r-build-system)
3073 (modify-phases %standard-phases
3074 (add-after 'unpack 'remove-reference-to-non-free-data
3076 (substitute* "DESCRIPTION"
3080 `(("r-annotationdbi" ,r-annotationdbi)
3081 ("r-biobase" ,r-biobase)
3083 ("r-go-db" ,r-go-db)))
3084 (home-page "https://bioconductor.org/packages/annaffy/")
3085 (synopsis "Annotation tools for Affymetrix biological metadata")
3087 "This package provides functions for handling data from Bioconductor
3088 Affymetrix annotation data packages. It produces compact HTML and text
3089 reports including experimental data and URL links to many online databases.
3090 It allows searching of biological metadata using various criteria.")
3091 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3092 ;; the LGPL 2.1 is included.
3093 (license license:lgpl2.1+)))
3095 (define-public r-a4core
3102 (uri (bioconductor-uri "a4Core" version))
3105 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3106 (properties `((upstream-name . "a4Core")))
3107 (build-system r-build-system)
3109 `(("r-biobase" ,r-biobase)
3110 ("r-glmnet" ,r-glmnet)))
3111 (home-page "https://bioconductor.org/packages/a4Core")
3112 (synopsis "Automated Affymetrix array analysis core package")
3114 "This is the core package for the automated analysis of Affymetrix
3116 (license license:gpl3)))
3118 (define-public r-a4classif
3120 (name "r-a4classif")
3125 (uri (bioconductor-uri "a4Classif" version))
3128 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3129 (properties `((upstream-name . "a4Classif")))
3130 (build-system r-build-system)
3132 `(("r-a4core" ,r-a4core)
3133 ("r-a4preproc" ,r-a4preproc)
3134 ("r-glmnet" ,r-glmnet)
3135 ("r-mlinterfaces" ,r-mlinterfaces)
3138 ("r-varselrf" ,r-varselrf)))
3139 (home-page "https://bioconductor.org/packages/a4Classif/")
3140 (synopsis "Automated Affymetrix array analysis classification package")
3142 "This is the classification package for the automated analysis of
3143 Affymetrix arrays.")
3144 (license license:gpl3)))
3146 (define-public r-a4preproc
3148 (name "r-a4preproc")
3153 (uri (bioconductor-uri "a4Preproc" version))
3156 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3157 (properties `((upstream-name . "a4Preproc")))
3158 (build-system r-build-system)
3160 `(("r-annotationdbi" ,r-annotationdbi)))
3161 (home-page "https://bioconductor.org/packages/a4Preproc/")
3162 (synopsis "Automated Affymetrix array analysis preprocessing package")
3164 "This is a package for the automated analysis of Affymetrix arrays. It
3165 is used for preprocessing the arrays.")
3166 (license license:gpl3)))
3168 (define-public r-a4reporting
3170 (name "r-a4reporting")
3175 (uri (bioconductor-uri "a4Reporting" version))
3178 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3179 (properties `((upstream-name . "a4Reporting")))
3180 (build-system r-build-system)
3182 `(("r-annaffy" ,r-annaffy)
3183 ("r-xtable" ,r-xtable)))
3184 (home-page "https://bioconductor.org/packages/a4Reporting/")
3185 (synopsis "Automated Affymetrix array analysis reporting package")
3187 "This is a package for the automated analysis of Affymetrix arrays. It
3188 provides reporting features.")
3189 (license license:gpl3)))
3191 (define-public r-a4base
3198 (uri (bioconductor-uri "a4Base" version))
3201 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3202 (properties `((upstream-name . "a4Base")))
3203 (build-system r-build-system)
3205 `(("r-a4core" ,r-a4core)
3206 ("r-a4preproc" ,r-a4preproc)
3207 ("r-annaffy" ,r-annaffy)
3208 ("r-annotationdbi" ,r-annotationdbi)
3209 ("r-biobase" ,r-biobase)
3210 ("r-genefilter" ,r-genefilter)
3211 ("r-glmnet" ,r-glmnet)
3212 ("r-gplots" ,r-gplots)
3213 ("r-limma" ,r-limma)
3215 ("r-multtest" ,r-multtest)))
3216 (home-page "https://bioconductor.org/packages/a4Base/")
3217 (synopsis "Automated Affymetrix array analysis base package")
3219 "This package provides basic features for the automated analysis of
3220 Affymetrix arrays.")
3221 (license license:gpl3)))
3230 (uri (bioconductor-uri "a4" version))
3233 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3234 (build-system r-build-system)
3236 `(("r-a4base" ,r-a4base)
3237 ("r-a4classif" ,r-a4classif)
3238 ("r-a4core" ,r-a4core)
3239 ("r-a4preproc" ,r-a4preproc)
3240 ("r-a4reporting" ,r-a4reporting)))
3241 (home-page "https://bioconductor.org/packages/a4/")
3242 (synopsis "Automated Affymetrix array analysis umbrella package")
3244 "This package provides a software suite for the automated analysis of
3245 Affymetrix arrays.")
3246 (license license:gpl3)))
3248 (define-public r-abseqr
3255 (uri (bioconductor-uri "abseqR" version))
3258 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3259 (properties `((upstream-name . "abseqR")))
3260 (build-system r-build-system)
3262 `(("pandoc" ,ghc-pandoc)))
3264 `(("r-biocparallel" ,r-biocparallel)
3265 ("r-biocstyle" ,r-biocstyle)
3266 ("r-circlize" ,r-circlize)
3267 ("r-flexdashboard" ,r-flexdashboard)
3268 ("r-ggcorrplot" ,r-ggcorrplot)
3269 ("r-ggdendro" ,r-ggdendro)
3270 ("r-ggplot2" ,r-ggplot2)
3271 ("r-gridextra" ,r-gridextra)
3272 ("r-knitr" ,r-knitr)
3273 ("r-plotly" ,r-plotly)
3276 ("r-rcolorbrewer" ,r-rcolorbrewer)
3277 ("r-reshape2" ,r-reshape2)
3278 ("r-rmarkdown" ,r-rmarkdown)
3279 ("r-stringr" ,r-stringr)
3280 ("r-vegan" ,r-vegan)
3281 ("r-venndiagram" ,r-venndiagram)))
3282 (home-page "https://github.com/malhamdoosh/abseqR")
3283 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3285 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3286 sequencing datasets generated from antibody libraries and abseqR is one of its
3287 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3288 capabilities and allows them to generate interactive HTML reports for the
3289 convenience of viewing and sharing with other researchers. Additionally,
3290 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3291 further downstream analysis on its output.")
3292 (license license:gpl3)))
3294 (define-public r-bacon
3301 (uri (bioconductor-uri "bacon" version))
3304 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3305 (build-system r-build-system)
3307 `(("r-biocparallel" ,r-biocparallel)
3308 ("r-ellipse" ,r-ellipse)
3309 ("r-ggplot2" ,r-ggplot2)))
3310 (home-page "https://bioconductor.org/packages/bacon/")
3311 (synopsis "Controlling bias and inflation in association studies")
3313 "Bacon can be used to remove inflation and bias often observed in
3314 epigenome- and transcriptome-wide association studies. To this end bacon
3315 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3316 fitting a three-component normal mixture on z-scores.")
3317 (license license:gpl2+)))
3319 (define-public r-rgadem
3326 (uri (bioconductor-uri "rGADEM" version))
3329 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3330 (properties `((upstream-name . "rGADEM")))
3331 (build-system r-build-system)
3333 `(("r-biostrings" ,r-biostrings)
3334 ("r-bsgenome" ,r-bsgenome)
3335 ("r-iranges" ,r-iranges)
3336 ("r-seqlogo" ,r-seqlogo)))
3337 (home-page "https://bioconductor.org/packages/rGADEM/")
3338 (synopsis "De novo sequence motif discovery")
3340 "rGADEM is an efficient de novo motif discovery tool for large-scale
3341 genomic sequence data.")
3342 (license license:artistic2.0)))
3344 (define-public r-motiv
3351 (uri (bioconductor-uri "MotIV" version))
3354 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3355 (properties `((upstream-name . "MotIV")))
3356 (build-system r-build-system)
3360 `(("r-biocgenerics" ,r-biocgenerics)
3361 ("r-biostrings" ,r-biostrings)
3362 ("r-iranges" ,r-iranges)
3363 ("r-lattice" ,r-lattice)
3364 ("r-rgadem" ,r-rgadem)
3365 ("r-s4vectors" ,r-s4vectors)))
3366 (home-page "https://bioconductor.org/packages/MotIV/")
3367 (synopsis "Motif identification and validation")
3369 "This package is used for the identification and validation of sequence
3370 motifs. It makes use of STAMP for comparing a set of motifs to a given
3371 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3372 distributions, modules and filter motifs.")
3373 (license license:gpl2)))
3375 (define-public r-motifstack
3377 (name "r-motifstack")
3382 (uri (bioconductor-uri "motifStack" version))
3385 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3386 (properties `((upstream-name . "motifStack")))
3387 (build-system r-build-system)
3389 `(("r-ade4" ,r-ade4)
3390 ("r-biostrings" ,r-biostrings)
3391 ("r-grimport2" ,r-grimport2)
3392 ("r-htmlwidgets" ,r-htmlwidgets)
3393 ("r-motiv" ,r-motiv)
3394 ("r-scales" ,r-scales)
3396 (home-page "https://bioconductor.org/packages/motifStack/")
3397 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3399 "The motifStack package is designed for graphic representation of
3400 multiple motifs with different similarity scores. It works with both DNA/RNA
3401 sequence motifs and amino acid sequence motifs. In addition, it provides the
3402 flexibility for users to customize the graphic parameters such as the font
3403 type and symbol colors.")
3404 (license license:gpl2+)))
3406 (define-public r-genomicscores
3408 (name "r-genomicscores")
3413 (uri (bioconductor-uri "GenomicScores" version))
3416 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3417 (properties `((upstream-name . "GenomicScores")))
3418 (build-system r-build-system)
3420 `(("r-annotationhub" ,r-annotationhub)
3421 ("r-biobase" ,r-biobase)
3422 ("r-biocgenerics" ,r-biocgenerics)
3423 ("r-biostrings" ,r-biostrings)
3424 ("r-bsgenome" ,r-bsgenome)
3425 ("r-genomeinfodb" ,r-genomeinfodb)
3426 ("r-genomicranges" ,r-genomicranges)
3427 ("r-iranges" ,r-iranges)
3428 ("r-s4vectors" ,r-s4vectors)
3430 (home-page "https://github.com/rcastelo/GenomicScores/")
3431 (synopsis "Work with genome-wide position-specific scores")
3433 "This package provides infrastructure to store and access genome-wide
3434 position-specific scores within R and Bioconductor.")
3435 (license license:artistic2.0)))
3437 (define-public r-atacseqqc
3439 (name "r-atacseqqc")
3444 (uri (bioconductor-uri "ATACseqQC" version))
3447 "0h5j3724hnd86w22vy3whqx6gkf0nf2dxd2clgzdvjzblbcd5s69"))))
3448 (properties `((upstream-name . "ATACseqQC")))
3449 (build-system r-build-system)
3451 `(("r-biocgenerics" ,r-biocgenerics)
3452 ("r-biostrings" ,r-biostrings)
3453 ("r-bsgenome" ,r-bsgenome)
3454 ("r-chippeakanno" ,r-chippeakanno)
3455 ("r-edger" ,r-edger)
3456 ("r-genomeinfodb" ,r-genomeinfodb)
3457 ("r-genomicalignments" ,r-genomicalignments)
3458 ("r-genomicranges" ,r-genomicranges)
3459 ("r-genomicscores" ,r-genomicscores)
3460 ("r-iranges" ,r-iranges)
3461 ("r-kernsmooth" ,r-kernsmooth)
3462 ("r-limma" ,r-limma)
3463 ("r-motifstack" ,r-motifstack)
3464 ("r-preseqr" ,r-preseqr)
3465 ("r-randomforest" ,r-randomforest)
3466 ("r-rsamtools" ,r-rsamtools)
3467 ("r-rtracklayer" ,r-rtracklayer)
3468 ("r-s4vectors" ,r-s4vectors)))
3469 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3470 (synopsis "ATAC-seq quality control")
3472 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3473 sequencing, is a rapid and sensitive method for chromatin accessibility
3474 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3475 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3476 assess whether their ATAC-seq experiment is successful. It includes
3477 diagnostic plots of fragment size distribution, proportion of mitochondria
3478 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3480 (license license:gpl2+)))
3482 (define-public r-gofuncr
3489 (uri (bioconductor-uri "GOfuncR" version))
3492 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3493 (properties `((upstream-name . "GOfuncR")))
3494 (build-system r-build-system)
3496 `(("r-annotationdbi" ,r-annotationdbi)
3497 ("r-genomicranges" ,r-genomicranges)
3498 ("r-gtools" ,r-gtools)
3499 ("r-iranges" ,r-iranges)
3500 ("r-mapplots" ,r-mapplots)
3502 ("r-vioplot" ,r-vioplot)))
3503 (home-page "https://bioconductor.org/packages/GOfuncR/")
3504 (synopsis "Gene ontology enrichment using FUNC")
3506 "GOfuncR performs a gene ontology enrichment analysis based on the
3507 ontology enrichment software FUNC. GO-annotations are obtained from
3508 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3509 included in the package and updated regularly. GOfuncR provides the standard
3510 candidate vs background enrichment analysis using the hypergeometric test, as
3511 well as three additional tests:
3514 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3515 @item a binomial test that is used when genes are associated with two counts,
3517 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3518 associated with four counts.
3521 To correct for multiple testing and interdependency of the tests, family-wise
3522 error rates are computed based on random permutations of the gene-associated
3523 variables. GOfuncR also provides tools for exploring the ontology graph and
3524 the annotations, and options to take gene-length or spatial clustering of
3525 genes into account. It is also possible to provide custom gene coordinates,
3526 annotations and ontologies.")
3527 (license license:gpl2+)))
3529 (define-public r-abaenrichment
3531 (name "r-abaenrichment")
3536 (uri (bioconductor-uri "ABAEnrichment" version))
3539 "0av1dysk7qa8c4a0pp7yq89k8c4y40d2gyvsb8f27slvv2i3aad2"))))
3540 (properties `((upstream-name . "ABAEnrichment")))
3541 (build-system r-build-system)
3543 `(("r-abadata" ,r-abadata)
3544 ("r-data-table" ,r-data-table)
3545 ("r-gofuncr" ,r-gofuncr)
3546 ("r-gplots" ,r-gplots)
3547 ("r-gtools" ,r-gtools)
3548 ("r-rcpp" ,r-rcpp)))
3549 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3550 (synopsis "Gene expression enrichment in human brain regions")
3552 "The package ABAEnrichment is designed to test for enrichment of user
3553 defined candidate genes in the set of expressed genes in different human brain
3554 regions. The core function @code{aba_enrich} integrates the expression of the
3555 candidate gene set (averaged across donors) and the structural information of
3556 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3557 (license license:gpl2+)))
3559 (define-public r-annotationfuncs
3561 (name "r-annotationfuncs")
3566 (uri (bioconductor-uri "AnnotationFuncs" version))
3569 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3571 `((upstream-name . "AnnotationFuncs")))
3572 (build-system r-build-system)
3574 `(("r-annotationdbi" ,r-annotationdbi)
3576 (home-page "https://www.iysik.com/r/annotationfuncs")
3577 (synopsis "Annotation translation functions")
3579 "This package provides functions for handling translating between
3580 different identifieres using the Biocore Data Team data-packages (e.g.
3581 @code{org.Bt.eg.db}).")
3582 (license license:gpl2)))
3584 (define-public r-annotationtools
3586 (name "r-annotationtools")
3591 (uri (bioconductor-uri "annotationTools" version))
3594 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3596 `((upstream-name . "annotationTools")))
3597 (build-system r-build-system)
3598 (propagated-inputs `(("r-biobase" ,r-biobase)))
3599 (home-page "https://bioconductor.org/packages/annotationTools/")
3600 (synopsis "Annotate microarrays and perform gene expression analyses")
3602 "This package provides functions to annotate microarrays, find orthologs,
3603 and integrate heterogeneous gene expression profiles using annotation and
3604 other molecular biology information available as flat file database (plain
3606 ;; Any version of the GPL.
3607 (license (list license:gpl2+))))
3609 (define-public r-allelicimbalance
3611 (name "r-allelicimbalance")
3616 (uri (bioconductor-uri "AllelicImbalance" version))
3619 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3621 `((upstream-name . "AllelicImbalance")))
3622 (build-system r-build-system)
3624 `(("r-annotationdbi" ,r-annotationdbi)
3625 ("r-biocgenerics" ,r-biocgenerics)
3626 ("r-biostrings" ,r-biostrings)
3627 ("r-bsgenome" ,r-bsgenome)
3628 ("r-genomeinfodb" ,r-genomeinfodb)
3629 ("r-genomicalignments" ,r-genomicalignments)
3630 ("r-genomicfeatures" ,r-genomicfeatures)
3631 ("r-genomicranges" ,r-genomicranges)
3632 ("r-gridextra" ,r-gridextra)
3634 ("r-iranges" ,r-iranges)
3635 ("r-lattice" ,r-lattice)
3636 ("r-latticeextra" ,r-latticeextra)
3638 ("r-rsamtools" ,r-rsamtools)
3639 ("r-s4vectors" ,r-s4vectors)
3640 ("r-seqinr" ,r-seqinr)
3641 ("r-summarizedexperiment" ,r-summarizedexperiment)
3642 ("r-variantannotation" ,r-variantannotation)))
3643 (home-page "https://github.com/pappewaio/AllelicImbalance")
3644 (synopsis "Investigate allele-specific expression")
3646 "This package provides a framework for allele-specific expression
3647 investigation using RNA-seq data.")
3648 (license license:gpl3)))
3650 (define-public r-aucell
3657 (uri (bioconductor-uri "AUCell" version))
3660 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
3661 (properties `((upstream-name . "AUCell")))
3662 (build-system r-build-system)
3664 `(("r-data-table" ,r-data-table)
3665 ("r-gseabase" ,r-gseabase)
3666 ("r-mixtools" ,r-mixtools)
3667 ("r-r-utils" ,r-r-utils)
3668 ("r-shiny" ,r-shiny)
3669 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3670 (home-page "https://bioconductor.org/packages/AUCell/")
3671 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3673 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3674 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3675 Under the Curve} (AUC) to calculate whether a critical subset of the input
3676 gene set is enriched within the expressed genes for each cell. The
3677 distribution of AUC scores across all the cells allows exploring the relative
3678 expression of the signature. Since the scoring method is ranking-based,
3679 AUCell is independent of the gene expression units and the normalization
3680 procedure. In addition, since the cells are evaluated individually, it can
3681 easily be applied to bigger datasets, subsetting the expression matrix if
3683 (license license:gpl3)))
3685 (define-public r-ebimage
3692 (uri (bioconductor-uri "EBImage" version))
3695 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
3696 (properties `((upstream-name . "EBImage")))
3697 (build-system r-build-system)
3699 `(("r-abind" ,r-abind)
3700 ("r-biocgenerics" ,r-biocgenerics)
3701 ("r-fftwtools" ,r-fftwtools)
3702 ("r-htmltools" ,r-htmltools)
3703 ("r-htmlwidgets" ,r-htmlwidgets)
3705 ("r-locfit" ,r-locfit)
3707 ("r-rcurl" ,r-rcurl)
3708 ("r-tiff" ,r-tiff)))
3710 `(("r-knitr" ,r-knitr))) ; for vignettes
3711 (home-page "https://github.com/aoles/EBImage")
3712 (synopsis "Image processing and analysis toolbox for R")
3714 "EBImage provides general purpose functionality for image processing and
3715 analysis. In the context of (high-throughput) microscopy-based cellular
3716 assays, EBImage offers tools to segment cells and extract quantitative
3717 cellular descriptors. This allows the automation of such tasks using the R
3718 programming language and facilitates the use of other tools in the R
3719 environment for signal processing, statistical modeling, machine learning and
3720 visualization with image data.")
3721 ;; Any version of the LGPL.
3722 (license license:lgpl2.1+)))
3724 (define-public r-yamss
3731 (uri (bioconductor-uri "yamss" version))
3734 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
3735 (build-system r-build-system)
3737 `(("r-biocgenerics" ,r-biocgenerics)
3738 ("r-data-table" ,r-data-table)
3739 ("r-ebimage" ,r-ebimage)
3740 ("r-iranges" ,r-iranges)
3741 ("r-limma" ,r-limma)
3742 ("r-matrix" ,r-matrix)
3744 ("r-s4vectors" ,r-s4vectors)
3745 ("r-summarizedexperiment"
3746 ,r-summarizedexperiment)))
3747 (home-page "https://github.com/hansenlab/yamss")
3748 (synopsis "Tools for high-throughput metabolomics")
3750 "This package provides tools to analyze and visualize high-throughput
3751 metabolomics data acquired using chromatography-mass spectrometry. These tools
3752 preprocess data in a way that enables reliable and powerful differential
3754 (license license:artistic2.0)))
3756 (define-public r-gtrellis
3763 (uri (bioconductor-uri "gtrellis" version))
3766 "00d5swg3brnx8ryzpg7hp3mg9hx3vz4yd1lv2chlp2pj2rhsir1y"))))
3767 (build-system r-build-system)
3769 `(("r-circlize" ,r-circlize)
3770 ("r-genomicranges" ,r-genomicranges)
3771 ("r-getoptlong" ,r-getoptlong)
3772 ("r-iranges" ,r-iranges)))
3773 (home-page "https://github.com/jokergoo/gtrellis")
3774 (synopsis "Genome level Trellis layout")
3776 "Genome level Trellis graph visualizes genomic data conditioned by
3777 genomic categories (e.g. chromosomes). For each genomic category, multiple
3778 dimensional data which are represented as tracks describe different features
3779 from different aspects. This package provides high flexibility to arrange
3780 genomic categories and to add self-defined graphics in the plot.")
3781 (license license:expat)))
3783 (define-public r-somaticsignatures
3785 (name "r-somaticsignatures")
3790 (uri (bioconductor-uri "SomaticSignatures" version))
3793 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
3795 `((upstream-name . "SomaticSignatures")))
3796 (build-system r-build-system)
3798 `(("r-biobase" ,r-biobase)
3799 ("r-biostrings" ,r-biostrings)
3800 ("r-genomeinfodb" ,r-genomeinfodb)
3801 ("r-genomicranges" ,r-genomicranges)
3802 ("r-ggbio" ,r-ggbio)
3803 ("r-ggplot2" ,r-ggplot2)
3804 ("r-iranges" ,r-iranges)
3806 ("r-pcamethods" ,r-pcamethods)
3807 ("r-proxy" ,r-proxy)
3808 ("r-reshape2" ,r-reshape2)
3809 ("r-s4vectors" ,r-s4vectors)
3810 ("r-variantannotation" ,r-variantannotation)))
3811 (home-page "https://github.com/juliangehring/SomaticSignatures")
3812 (synopsis "Somatic signatures")
3814 "This package identifies mutational signatures of @dfn{single nucleotide
3815 variants} (SNVs). It provides a infrastructure related to the methodology
3816 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3817 decomposition algorithms.")
3818 (license license:expat)))
3820 (define-public r-yapsa
3827 (uri (bioconductor-uri "YAPSA" version))
3830 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
3831 (properties `((upstream-name . "YAPSA")))
3832 (build-system r-build-system)
3834 `(("r-circlize" ,r-circlize)
3835 ("r-complexheatmap" ,r-complexheatmap)
3836 ("r-corrplot" ,r-corrplot)
3837 ("r-dendextend" ,r-dendextend)
3838 ("r-genomeinfodb" ,r-genomeinfodb)
3839 ("r-genomicranges" ,r-genomicranges)
3840 ("r-getoptlong" ,r-getoptlong)
3841 ("r-ggplot2" ,r-ggplot2)
3842 ("r-gridextra" ,r-gridextra)
3843 ("r-gtrellis" ,r-gtrellis)
3844 ("r-keggrest" ,r-keggrest)
3846 ("r-pmcmr" ,r-pmcmr)
3847 ("r-reshape2" ,r-reshape2)
3848 ("r-somaticsignatures" ,r-somaticsignatures)
3849 ("r-variantannotation" ,r-variantannotation)))
3850 (home-page "https://bioconductor.org/packages/YAPSA/")
3851 (synopsis "Yet another package for signature analysis")
3853 "This package provides functions and routines useful in the analysis of
3854 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3855 functions to perform a signature analysis with known signatures and a
3856 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3858 (license license:gpl3)))
3860 (define-public r-gcrma
3867 (uri (bioconductor-uri "gcrma" version))
3870 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
3871 (build-system r-build-system)
3873 `(("r-affy" ,r-affy)
3874 ("r-affyio" ,r-affyio)
3875 ("r-biobase" ,r-biobase)
3876 ("r-biocmanager" ,r-biocmanager)
3877 ("r-biostrings" ,r-biostrings)
3878 ("r-xvector" ,r-xvector)))
3879 (home-page "https://bioconductor.org/packages/gcrma/")
3880 (synopsis "Background adjustment using sequence information")
3882 "Gcrma adjusts for background intensities in Affymetrix array data which
3883 include optical noise and @dfn{non-specific binding} (NSB). The main function
3884 @code{gcrma} converts background adjusted probe intensities to expression
3885 measures using the same normalization and summarization methods as a
3886 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
3887 to estimate probe affinity to NSB. The sequence information is summarized in
3888 a more complex way than the simple GC content. Instead, the base types (A, T,
3889 G or C) at each position along the probe determine the affinity of each probe.
3890 The parameters of the position-specific base contributions to the probe
3891 affinity is estimated in an NSB experiment in which only NSB but no
3892 gene-specific bidning is expected.")
3893 ;; Any version of the LGPL
3894 (license license:lgpl2.1+)))
3896 (define-public r-simpleaffy
3898 (name "r-simpleaffy")
3903 (uri (bioconductor-uri "simpleaffy" version))
3906 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
3907 (build-system r-build-system)
3909 `(("r-affy" ,r-affy)
3910 ("r-biobase" ,r-biobase)
3911 ("r-biocgenerics" ,r-biocgenerics)
3912 ("r-gcrma" ,r-gcrma)
3913 ("r-genefilter" ,r-genefilter)))
3914 (home-page "https://bioconductor.org/packages/simpleaffy/")
3915 (synopsis "Very simple high level analysis of Affymetrix data")
3917 "This package provides high level functions for reading Affy @file{.CEL}
3918 files, phenotypic data, and then computing simple things with it, such as
3919 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
3920 library. It also has some basic scatter plot functions and mechanisms for
3921 generating high resolution journal figures.")
3922 (license license:gpl2+)))
3924 (define-public r-yaqcaffy
3931 (uri (bioconductor-uri "yaqcaffy" version))
3934 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
3935 (build-system r-build-system)
3937 `(("r-simpleaffy" ,r-simpleaffy)))
3938 (home-page "https://bioconductor.org/packages/yaqcaffy/")
3939 (synopsis "Affymetrix quality control and reproducibility analysis")
3941 "This is a package that can be used for quality control of Affymetrix
3942 GeneChip expression data and reproducibility analysis of human whole genome
3943 chips with the MAQC reference datasets.")
3944 (license license:artistic2.0)))
3946 (define-public r-quantro
3953 (uri (bioconductor-uri "quantro" version))
3956 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
3957 (build-system r-build-system)
3959 `(("r-biobase" ,r-biobase)
3960 ("r-doparallel" ,r-doparallel)
3961 ("r-foreach" ,r-foreach)
3962 ("r-ggplot2" ,r-ggplot2)
3963 ("r-iterators" ,r-iterators)
3964 ("r-minfi" ,r-minfi)
3965 ("r-rcolorbrewer" ,r-rcolorbrewer)))
3966 (home-page "https://bioconductor.org/packages/quantro/")
3967 (synopsis "Test for when to use quantile normalization")
3969 "This package provides a data-driven test for the assumptions of quantile
3970 normalization using raw data such as objects that inherit eSets (e.g.
3971 ExpressionSet, MethylSet). Group level information about each sample (such as
3972 Tumor / Normal status) must also be provided because the test assesses if
3973 there are global differences in the distributions between the user-defined
3975 (license license:gpl3+)))
3977 (define-public r-yarn
3984 (uri (bioconductor-uri "yarn" version))
3987 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
3988 (build-system r-build-system)
3990 `(("r-biobase" ,r-biobase)
3991 ("r-biomart" ,r-biomart)
3992 ("r-downloader" ,r-downloader)
3993 ("r-edger" ,r-edger)
3994 ("r-gplots" ,r-gplots)
3995 ("r-limma" ,r-limma)
3996 ("r-matrixstats" ,r-matrixstats)
3997 ("r-preprocesscore" ,r-preprocesscore)
3998 ("r-quantro" ,r-quantro)
3999 ("r-rcolorbrewer" ,r-rcolorbrewer)
4000 ("r-readr" ,r-readr)))
4001 (home-page "https://bioconductor.org/packages/yarn/")
4002 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4004 "Expedite large RNA-Seq analyses using a combination of previously
4005 developed tools. YARN is meant to make it easier for the user in performing
4006 basic mis-annotation quality control, filtering, and condition-aware
4007 normalization. YARN leverages many Bioconductor tools and statistical
4008 techniques to account for the large heterogeneity and sparsity found in very
4009 large RNA-seq experiments.")
4010 (license license:artistic2.0)))
4012 (define-public r-roar
4019 (uri (bioconductor-uri "roar" version))
4022 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4023 (build-system r-build-system)
4025 `(("r-biocgenerics" ,r-biocgenerics)
4026 ("r-genomeinfodb" ,r-genomeinfodb)
4027 ("r-genomicalignments" ,r-genomicalignments)
4028 ("r-genomicranges" ,r-genomicranges)
4029 ("r-iranges" ,r-iranges)
4030 ("r-rtracklayer" ,r-rtracklayer)
4031 ("r-s4vectors" ,r-s4vectors)
4032 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4033 (home-page "https://github.com/vodkatad/roar/")
4034 (synopsis "Identify differential APA usage from RNA-seq alignments")
4036 "This package provides tools for identifying preferential usage of APA
4037 sites, comparing two biological conditions, starting from known alternative
4038 sites and alignments obtained from standard RNA-seq experiments.")
4039 (license license:gpl3)))
4041 (define-public r-xbseq
4048 (uri (bioconductor-uri "XBSeq" version))
4051 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4052 (properties `((upstream-name . "XBSeq")))
4053 (build-system r-build-system)
4055 `(("r-biobase" ,r-biobase)
4056 ("r-deseq2" ,r-deseq2)
4057 ("r-dplyr" ,r-dplyr)
4058 ("r-ggplot2" ,r-ggplot2)
4059 ("r-locfit" ,r-locfit)
4060 ("r-magrittr" ,r-magrittr)
4061 ("r-matrixstats" ,r-matrixstats)
4062 ("r-pracma" ,r-pracma)
4063 ("r-roar" ,r-roar)))
4064 (home-page "https://github.com/Liuy12/XBSeq")
4065 (synopsis "Test for differential expression for RNA-seq data")
4067 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4068 expression} (DE), where a statistical model was established based on the
4069 assumption that observed signals are the convolution of true expression
4070 signals and sequencing noises. The mapped reads in non-exonic regions are
4071 considered as sequencing noises, which follows a Poisson distribution. Given
4072 measurable observed signal and background noise from RNA-seq data, true
4073 expression signals, assuming governed by the negative binomial distribution,
4074 can be delineated and thus the accurate detection of differential expressed
4076 (license license:gpl3+)))
4078 (define-public r-massspecwavelet
4080 (name "r-massspecwavelet")
4085 (uri (bioconductor-uri "MassSpecWavelet" version))
4088 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4090 `((upstream-name . "MassSpecWavelet")))
4091 (build-system r-build-system)
4093 `(("r-waveslim" ,r-waveslim)))
4094 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4095 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4097 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4098 data mainly through the use of wavelet transforms. It supports peak detection
4099 based on @dfn{Continuous Wavelet Transform} (CWT).")
4100 (license license:lgpl2.0+)))
4102 (define-public r-xcms
4109 (uri (bioconductor-uri "xcms" version))
4112 "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
4113 (build-system r-build-system)
4115 `(("r-biobase" ,r-biobase)
4116 ("r-biocgenerics" ,r-biocgenerics)
4117 ("r-biocparallel" ,r-biocparallel)
4118 ("r-lattice" ,r-lattice)
4119 ("r-massspecwavelet" ,r-massspecwavelet)
4120 ("r-msnbase" ,r-msnbase)
4121 ("r-multtest" ,r-multtest)
4124 ("r-protgenerics" ,r-protgenerics)
4126 ("r-rcolorbrewer" ,r-rcolorbrewer)
4127 ("r-robustbase" ,r-robustbase)
4128 ("r-s4vectors" ,r-s4vectors)))
4129 (home-page "https://bioconductor.org/packages/xcms/")
4130 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4132 "This package provides a framework for processing and visualization of
4133 chromatographically separated and single-spectra mass spectral data. It
4134 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4135 data for high-throughput, untargeted analyte profiling.")
4136 (license license:gpl2+)))
4138 (define-public r-wrench
4145 (uri (bioconductor-uri "Wrench" version))
4148 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4149 (properties `((upstream-name . "Wrench")))
4150 (build-system r-build-system)
4152 `(("r-limma" ,r-limma)
4153 ("r-locfit" ,r-locfit)
4154 ("r-matrixstats" ,r-matrixstats)))
4155 (home-page "https://github.com/HCBravoLab/Wrench")
4156 (synopsis "Wrench normalization for sparse count data")
4158 "Wrench is a package for normalization sparse genomic count data, like
4159 that arising from 16s metagenomic surveys.")
4160 (license license:artistic2.0)))
4162 (define-public r-wiggleplotr
4164 (name "r-wiggleplotr")
4169 (uri (bioconductor-uri "wiggleplotr" version))
4172 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4173 (build-system r-build-system)
4175 `(("r-assertthat" ,r-assertthat)
4176 ("r-cowplot" ,r-cowplot)
4177 ("r-dplyr" ,r-dplyr)
4178 ("r-genomeinfodb" ,r-genomeinfodb)
4179 ("r-genomicranges" ,r-genomicranges)
4180 ("r-ggplot2" ,r-ggplot2)
4181 ("r-iranges" ,r-iranges)
4182 ("r-purrr" ,r-purrr)
4183 ("r-rtracklayer" ,r-rtracklayer)
4184 ("r-s4vectors" ,r-s4vectors)))
4185 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4186 (synopsis "Make read coverage plots from BigWig files")
4188 "This package provides tools to visualize read coverage from sequencing
4189 experiments together with genomic annotations (genes, transcripts, peaks).
4190 Introns of long transcripts can be rescaled to a fixed length for better
4191 visualization of exonic read coverage.")
4192 (license license:asl2.0)))
4194 (define-public r-widgettools
4196 (name "r-widgettools")
4201 (uri (bioconductor-uri "widgetTools" version))
4204 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4205 (properties `((upstream-name . "widgetTools")))
4206 (build-system r-build-system)
4207 (home-page "https://bioconductor.org/packages/widgetTools/")
4208 (synopsis "Tools for creating interactive tcltk widgets")
4210 "This package contains tools to support the construction of tcltk
4212 ;; Any version of the LGPL.
4213 (license license:lgpl3+)))
4215 (define-public r-webbioc
4222 (uri (bioconductor-uri "webbioc" version))
4225 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4226 (build-system r-build-system)
4228 `(("netpbm" ,netpbm)
4231 `(("r-affy" ,r-affy)
4232 ("r-annaffy" ,r-annaffy)
4233 ("r-biobase" ,r-biobase)
4234 ("r-biocmanager" ,r-biocmanager)
4235 ("r-gcrma" ,r-gcrma)
4236 ("r-multtest" ,r-multtest)
4237 ("r-qvalue" ,r-qvalue)
4239 (home-page "https://www.bioconductor.org/")
4240 (synopsis "Bioconductor web interface")
4242 "This package provides an integrated web interface for doing microarray
4243 analysis using several of the Bioconductor packages. It is intended to be
4244 deployed as a centralized bioinformatics resource for use by many users.
4245 Currently only Affymetrix oligonucleotide analysis is supported.")
4246 (license license:gpl2+)))
4248 (define-public r-zfpkm
4255 (uri (bioconductor-uri "zFPKM" version))
4258 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4259 (properties `((upstream-name . "zFPKM")))
4260 (build-system r-build-system)
4262 `(("r-checkmate" ,r-checkmate)
4263 ("r-dplyr" ,r-dplyr)
4264 ("r-ggplot2" ,r-ggplot2)
4265 ("r-summarizedexperiment" ,r-summarizedexperiment)
4266 ("r-tidyr" ,r-tidyr)))
4267 (home-page "https://github.com/ronammar/zFPKM/")
4268 (synopsis "Functions to facilitate zFPKM transformations")
4270 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4271 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4273 (license license:gpl3)))
4275 (define-public r-rbowtie2
4282 (uri (bioconductor-uri "Rbowtie2" version))
4285 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4286 (properties `((upstream-name . "Rbowtie2")))
4287 (build-system r-build-system)
4290 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4291 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4293 "This package provides an R wrapper of the popular @code{bowtie2}
4294 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4295 rapid adapter trimming, identification, and read merging.")
4296 (license license:gpl3+)))
4298 (define-public r-progeny
4305 (uri (bioconductor-uri "progeny" version))
4308 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4309 (build-system r-build-system)
4310 (propagated-inputs `(("r-biobase" ,r-biobase)))
4311 (home-page "https://github.com/saezlab/progeny")
4312 (synopsis "Pathway responsive gene activity inference")
4314 "This package provides a function to infer pathway activity from gene
4315 expression. It contains the linear model inferred in the publication
4316 \"Perturbation-response genes reveal signaling footprints in cancer gene
4318 (license license:asl2.0)))
4320 (define-public r-arrmnormalization
4322 (name "r-arrmnormalization")
4327 (uri (bioconductor-uri "ARRmNormalization" version))
4330 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4332 `((upstream-name . "ARRmNormalization")))
4333 (build-system r-build-system)
4334 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4335 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4336 (synopsis "Adaptive robust regression normalization for methylation data")
4338 "This is a package to perform the @dfn{Adaptive Robust Regression
4339 method} (ARRm) for the normalization of methylation data from the Illumina
4340 Infinium HumanMethylation 450k assay.")
4341 (license license:artistic2.0)))
4343 (define-public r-biocfilecache
4345 (name "r-biocfilecache")
4350 (uri (bioconductor-uri "BiocFileCache" version))
4353 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4354 (properties `((upstream-name . "BiocFileCache")))
4355 (build-system r-build-system)
4357 `(("r-curl" ,r-curl)
4359 ("r-dbplyr" ,r-dbplyr)
4360 ("r-dplyr" ,r-dplyr)
4362 ("r-rappdirs" ,r-rappdirs)
4363 ("r-rsqlite" ,r-rsqlite)))
4364 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4365 (synopsis "Manage files across sessions")
4367 "This package creates a persistent on-disk cache of files that the user
4368 can add, update, and retrieve. It is useful for managing resources (such as
4369 custom Txdb objects) that are costly or difficult to create, web resources,
4370 and data files used across sessions.")
4371 (license license:artistic2.0)))
4373 (define-public r-iclusterplus
4375 (name "r-iclusterplus")
4380 (uri (bioconductor-uri "iClusterPlus" version))
4383 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4384 (properties `((upstream-name . "iClusterPlus")))
4385 (build-system r-build-system)
4386 (native-inputs `(("gfortran" ,gfortran)))
4387 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4388 (synopsis "Integrative clustering of multi-type genomic data")
4390 "iClusterPlus is developed for integrative clustering analysis of
4391 multi-type genomic data and is an enhanced version of iCluster proposed and
4392 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4393 from the experiments where biological samples (e.g. tumor samples) are
4394 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4395 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4396 on. In the iClusterPlus model, binary observations such as somatic mutation
4397 are modeled as Binomial processes; categorical observations such as copy
4398 number states are realizations of Multinomial random variables; counts are
4399 modeled as Poisson random processes; and continuous measures are modeled by
4400 Gaussian distributions.")
4401 (license license:gpl2+)))
4403 (define-public r-rbowtie
4410 (uri (bioconductor-uri "Rbowtie" version))
4413 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4414 (properties `((upstream-name . "Rbowtie")))
4415 (build-system r-build-system)
4418 (home-page "https://bioconductor.org/packages/Rbowtie/")
4419 (synopsis "R bowtie wrapper")
4421 "This package provides an R wrapper around the popular bowtie short read
4422 aligner and around SpliceMap, a de novo splice junction discovery and
4424 (license license:artistic2.0)))
4426 (define-public r-sgseq
4433 (uri (bioconductor-uri "SGSeq" version))
4436 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4437 (properties `((upstream-name . "SGSeq")))
4438 (build-system r-build-system)
4440 `(("r-annotationdbi" ,r-annotationdbi)
4441 ("r-biocgenerics" ,r-biocgenerics)
4442 ("r-biostrings" ,r-biostrings)
4443 ("r-genomeinfodb" ,r-genomeinfodb)
4444 ("r-genomicalignments" ,r-genomicalignments)
4445 ("r-genomicfeatures" ,r-genomicfeatures)
4446 ("r-genomicranges" ,r-genomicranges)
4447 ("r-igraph" ,r-igraph)
4448 ("r-iranges" ,r-iranges)
4449 ("r-rsamtools" ,r-rsamtools)
4450 ("r-rtracklayer" ,r-rtracklayer)
4451 ("r-runit" ,r-runit)
4452 ("r-s4vectors" ,r-s4vectors)
4453 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4454 (home-page "https://bioconductor.org/packages/SGSeq/")
4455 (synopsis "Splice event prediction and quantification from RNA-seq data")
4457 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4458 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4459 represented as a splice graph, which can be obtained from existing annotation
4460 or predicted from the mapped sequence reads. Splice events are identified
4461 from the graph and are quantified locally using structurally compatible reads
4462 at the start or end of each splice variant. The software includes functions
4463 for splice event prediction, quantification, visualization and
4465 (license license:artistic2.0)))
4467 (define-public r-rhisat2
4474 (uri (bioconductor-uri "Rhisat2" version))
4477 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4478 (properties `((upstream-name . "Rhisat2")))
4479 (build-system r-build-system)
4481 `(("which" ,which)))
4483 `(("r-genomicfeatures" ,r-genomicfeatures)
4484 ("r-genomicranges" ,r-genomicranges)
4485 ("r-sgseq" ,r-sgseq)))
4486 (home-page "https://github.com/fmicompbio/Rhisat2")
4487 (synopsis "R Wrapper for HISAT2 sequence aligner")
4489 "This package provides an R interface to the HISAT2 spliced short-read
4490 aligner by Kim et al. (2015). The package contains wrapper functions to
4491 create a genome index and to perform the read alignment to the generated
4493 (license license:gpl3)))
4495 (define-public r-quasr
4502 (uri (bioconductor-uri "QuasR" version))
4505 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4506 (properties `((upstream-name . "QuasR")))
4507 (build-system r-build-system)
4511 `(("r-annotationdbi" ,r-annotationdbi)
4512 ("r-biobase" ,r-biobase)
4513 ("r-biocgenerics" ,r-biocgenerics)
4514 ("r-biocmanager" ,r-biocmanager)
4515 ("r-biocparallel" ,r-biocparallel)
4516 ("r-biostrings" ,r-biostrings)
4517 ("r-bsgenome" ,r-bsgenome)
4518 ("r-genomeinfodb" ,r-genomeinfodb)
4519 ("r-genomicalignments" ,r-genomicalignments)
4520 ("r-genomicfeatures" ,r-genomicfeatures)
4521 ("r-genomicfiles" ,r-genomicfiles)
4522 ("r-genomicranges" ,r-genomicranges)
4523 ("r-iranges" ,r-iranges)
4524 ("r-rbowtie" ,r-rbowtie)
4525 ("r-rhisat2" ,r-rhisat2)
4526 ("r-rhtslib" ,r-rhtslib)
4527 ("r-rsamtools" ,r-rsamtools)
4528 ("r-rtracklayer" ,r-rtracklayer)
4529 ("r-s4vectors" ,r-s4vectors)
4530 ("r-shortread" ,r-shortread)))
4531 (home-page "https://bioconductor.org/packages/QuasR/")
4532 (synopsis "Quantify and annotate short reads in R")
4534 "This package provides a framework for the quantification and analysis of
4535 short genomic reads. It covers a complete workflow starting from raw sequence
4536 reads, over creation of alignments and quality control plots, to the
4537 quantification of genomic regions of interest.")
4538 (license license:gpl2)))
4540 (define-public r-rqc
4547 (uri (bioconductor-uri "Rqc" version))
4550 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4551 (properties `((upstream-name . "Rqc")))
4552 (build-system r-build-system)
4554 `(("r-biocgenerics" ,r-biocgenerics)
4555 ("r-biocparallel" ,r-biocparallel)
4556 ("r-biocstyle" ,r-biocstyle)
4557 ("r-biostrings" ,r-biostrings)
4558 ("r-biovizbase" ,r-biovizbase)
4559 ("r-genomicalignments" ,r-genomicalignments)
4560 ("r-genomicfiles" ,r-genomicfiles)
4561 ("r-ggplot2" ,r-ggplot2)
4562 ("r-iranges" ,r-iranges)
4563 ("r-knitr" ,r-knitr)
4564 ("r-markdown" ,r-markdown)
4567 ("r-reshape2" ,r-reshape2)
4568 ("r-rsamtools" ,r-rsamtools)
4569 ("r-s4vectors" ,r-s4vectors)
4570 ("r-shiny" ,r-shiny)
4571 ("r-shortread" ,r-shortread)))
4572 (home-page "https://github.com/labbcb/Rqc")
4573 (synopsis "Quality control tool for high-throughput sequencing data")
4575 "Rqc is an optimized tool designed for quality control and assessment of
4576 high-throughput sequencing data. It performs parallel processing of entire
4577 files and produces a report which contains a set of high-resolution
4579 (license license:gpl2+)))
4581 (define-public r-birewire
4588 (uri (bioconductor-uri "BiRewire" version))
4591 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
4592 (properties `((upstream-name . "BiRewire")))
4593 (build-system r-build-system)
4595 `(("r-igraph" ,r-igraph)
4596 ("r-matrix" ,r-matrix)
4598 ("r-tsne" ,r-tsne)))
4599 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
4600 (synopsis "Tools for randomization of bipartite graphs")
4602 "This package provides functions for bipartite network rewiring through N
4603 consecutive switching steps and for the computation of the minimal number of
4604 switching steps to be performed in order to maximise the dissimilarity with
4605 respect to the original network. It includes functions for the analysis of
4606 the introduced randomness across the switching steps and several other
4607 routines to analyse the resulting networks and their natural projections.")
4608 (license license:gpl3)))
4610 (define-public r-birta
4617 (uri (bioconductor-uri "birta" version))
4620 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
4621 (build-system r-build-system)
4623 `(("r-biobase" ,r-biobase)
4624 ("r-limma" ,r-limma)
4625 ("r-mass" ,r-mass)))
4626 (home-page "https://bioconductor.org/packages/birta")
4627 (synopsis "Bayesian inference of regulation of transcriptional activity")
4629 "Expression levels of mRNA molecules are regulated by different
4630 processes, comprising inhibition or activation by transcription factors and
4631 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
4632 Inference of Regulation of Transcriptional Activity) uses the regulatory
4633 networks of transcription factors and miRNAs together with mRNA and miRNA
4634 expression data to predict switches in regulatory activity between two
4635 conditions. A Bayesian network is used to model the regulatory structure and
4636 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
4637 (license license:gpl2+)))
4639 (define-public r-ropls
4646 (uri (bioconductor-uri "ropls" version))
4649 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
4650 (build-system r-build-system)
4651 (propagated-inputs `(("r-biobase" ,r-biobase)))
4653 `(("r-knitr" ,r-knitr))) ; for vignettes
4654 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
4655 (synopsis "Multivariate analysis and feature selection of omics data")
4657 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
4658 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
4659 regression, classification, and feature selection of omics data where the
4660 number of variables exceeds the number of samples and with multicollinearity
4661 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
4662 separately model the variation correlated (predictive) to the factor of
4663 interest and the uncorrelated (orthogonal) variation. While performing
4664 similarly to PLS, OPLS facilitates interpretation.
4666 This package provides imlementations of PCA, PLS, and OPLS for multivariate
4667 analysis and feature selection of omics data. In addition to scores, loadings
4668 and weights plots, the package provides metrics and graphics to determine the
4669 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
4670 validity of the model by permutation testing, detect outliers, and perform
4671 feature selection (e.g. with Variable Importance in Projection or regression
4673 (license license:cecill)))
4675 (define-public r-biosigner
4677 (name "r-biosigner")
4682 (uri (bioconductor-uri "biosigner" version))
4685 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
4686 (build-system r-build-system)
4688 `(("r-biobase" ,r-biobase)
4689 ("r-e1071" ,r-e1071)
4690 ("r-randomforest" ,r-randomforest)
4691 ("r-ropls" ,r-ropls)))
4693 `(("r-knitr" ,r-knitr)
4694 ("r-rmarkdown" ,r-rmarkdown)
4695 ("pandoc" ,ghc-pandoc)
4696 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
4697 (home-page "https://bioconductor.org/packages/biosigner/")
4698 (synopsis "Signature discovery from omics data")
4700 "Feature selection is critical in omics data analysis to extract
4701 restricted and meaningful molecular signatures from complex and high-dimension
4702 data, and to build robust classifiers. This package implements a method to
4703 assess the relevance of the variables for the prediction performances of the
4704 classifier. The approach can be run in parallel with the PLS-DA, Random
4705 Forest, and SVM binary classifiers. The signatures and the corresponding
4706 'restricted' models are returned, enabling future predictions on new
4708 (license license:cecill)))
4710 (define-public r-annotatr
4717 (uri (bioconductor-uri "annotatr" version))
4720 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
4721 (build-system r-build-system)
4723 `(("r-annotationdbi" ,r-annotationdbi)
4724 ("r-annotationhub" ,r-annotationhub)
4725 ("r-dplyr" ,r-dplyr)
4726 ("r-genomeinfodb" ,r-genomeinfodb)
4727 ("r-genomicfeatures" ,r-genomicfeatures)
4728 ("r-genomicranges" ,r-genomicranges)
4729 ("r-ggplot2" ,r-ggplot2)
4730 ("r-iranges" ,r-iranges)
4731 ("r-readr" ,r-readr)
4732 ("r-regioner" ,r-regioner)
4733 ("r-reshape2" ,r-reshape2)
4734 ("r-rtracklayer" ,r-rtracklayer)
4735 ("r-s4vectors" ,r-s4vectors)))
4736 (home-page "https://bioconductor.org/packages/annotatr/")
4737 (synopsis "Annotation of genomic regions to genomic annotations")
4739 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
4740 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
4741 to investigate the intersecting genomic annotations. Such annotations include
4742 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
4743 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
4744 enhancers. The annotatr package provides an easy way to summarize and
4745 visualize the intersection of genomic sites/regions with genomic
4747 (license license:gpl3)))
4749 (define-public r-rsubread
4756 (uri (bioconductor-uri "Rsubread" version))
4759 "1230p8nsakifmpsqfiaj8rpm7npa8ab903mfjmayfa71n6yzvcbs"))))
4760 (properties `((upstream-name . "Rsubread")))
4761 (build-system r-build-system)
4762 (inputs `(("zlib" ,zlib)))
4763 (home-page "https://bioconductor.org/packages/Rsubread/")
4764 (synopsis "Subread sequence alignment and counting for R")
4766 "This package provides tools for alignment, quantification and analysis
4767 of second and third generation sequencing data. It includes functionality for
4768 read mapping, read counting, SNP calling, structural variant detection and
4769 gene fusion discovery. It can be applied to all major sequencing techologies
4770 and to both short and long sequence reads.")
4771 (license license:gpl3)))