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 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 bioinformatics)
28 #:use-module (gnu packages cran)
29 #:use-module (gnu packages compression)
30 #:use-module (gnu packages gcc)
31 #:use-module (gnu packages graph)
32 #:use-module (gnu packages maths)
33 #:use-module (gnu packages pkg-config)
34 #:use-module (gnu packages statistics)
35 #:use-module (gnu packages web))
40 (define-public r-bsgenome-celegans-ucsc-ce6
42 (name "r-bsgenome-celegans-ucsc-ce6")
46 ;; We cannot use bioconductor-uri here because this tarball is
47 ;; located under "data/annotation/" instead of "bioc/".
48 (uri (string-append "https://www.bioconductor.org/packages/"
49 "release/data/annotation/src/contrib/"
50 "BSgenome.Celegans.UCSC.ce6_"
54 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
56 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
57 (build-system r-build-system)
58 ;; As this package provides little more than a very large data file it
59 ;; doesn't make sense to build substitutes.
60 (arguments `(#:substitutable? #f))
62 `(("r-bsgenome" ,r-bsgenome)))
64 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
65 (synopsis "Full genome sequences for Worm")
67 "This package provides full genome sequences for Caenorhabditis
68 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
70 (license license:artistic2.0)))
72 (define-public r-bsgenome-celegans-ucsc-ce10
74 (name "r-bsgenome-celegans-ucsc-ce10")
78 ;; We cannot use bioconductor-uri here because this tarball is
79 ;; located under "data/annotation/" instead of "bioc/".
80 (uri (string-append "https://www.bioconductor.org/packages/"
81 "release/data/annotation/src/contrib/"
82 "BSgenome.Celegans.UCSC.ce10_"
86 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
88 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
89 (build-system r-build-system)
90 ;; As this package provides little more than a very large data file it
91 ;; doesn't make sense to build substitutes.
92 (arguments `(#:substitutable? #f))
94 `(("r-bsgenome" ,r-bsgenome)))
96 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
97 (synopsis "Full genome sequences for Worm")
99 "This package provides full genome sequences for Caenorhabditis
100 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
102 (license license:artistic2.0)))
104 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
106 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
110 ;; We cannot use bioconductor-uri here because this tarball is
111 ;; located under "data/annotation/" instead of "bioc/".
112 (uri (string-append "https://www.bioconductor.org/packages/"
113 "release/data/annotation/src/contrib/"
114 "BSgenome.Dmelanogaster.UCSC.dm6_"
118 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
120 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
121 (build-system r-build-system)
122 ;; As this package provides little more than a very large data file it
123 ;; doesn't make sense to build substitutes.
124 (arguments `(#:substitutable? #f))
126 `(("r-bsgenome" ,r-bsgenome)))
128 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
129 (synopsis "Full genome sequences for Fly")
131 "This package provides full genome sequences for Drosophila
132 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
134 (license license:artistic2.0)))
136 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
138 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
142 ;; We cannot use bioconductor-uri here because this tarball is
143 ;; located under "data/annotation/" instead of "bioc/".
144 (uri (string-append "https://www.bioconductor.org/packages/"
145 "release/data/annotation/src/contrib/"
146 "BSgenome.Dmelanogaster.UCSC.dm3_"
150 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
152 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
153 (build-system r-build-system)
154 ;; As this package provides little more than a very large data file it
155 ;; doesn't make sense to build substitutes.
156 (arguments `(#:substitutable? #f))
158 `(("r-bsgenome" ,r-bsgenome)))
160 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
161 (synopsis "Full genome sequences for Fly")
163 "This package provides full genome sequences for Drosophila
164 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
165 Biostrings objects.")
166 (license license:artistic2.0)))
168 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
170 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
174 ;; We cannot use bioconductor-uri here because this tarball is
175 ;; located under "data/annotation/" instead of "bioc/".
176 (uri (string-append "http://www.bioconductor.org/packages/"
177 "release/data/annotation/src/contrib/"
178 "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
182 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
184 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
185 (build-system r-build-system)
187 `(("r-bsgenome" ,r-bsgenome)
188 ("r-bsgenome-dmelanogaster-ucsc-dm3"
189 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
190 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
191 (synopsis "Full masked genome sequences for Fly")
193 "This package provides full masked genome sequences for Drosophila
194 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
195 Biostrings objects. The sequences are the same as in
196 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
197 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
198 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
199 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
200 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
205 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
209 ;; We cannot use bioconductor-uri here because this tarball is
210 ;; located under "data/annotation/" instead of "bioc/".
211 (uri (string-append "https://www.bioconductor.org/packages/"
212 "release/data/annotation/src/contrib/"
213 "BSgenome.Hsapiens.1000genomes.hs37d5_"
217 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
219 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
220 (build-system r-build-system)
221 ;; As this package provides little more than a very large data file it
222 ;; doesn't make sense to build substitutes.
223 (arguments `(#:substitutable? #f))
225 `(("r-bsgenome" ,r-bsgenome)))
227 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
228 (synopsis "Full genome sequences for Homo sapiens")
230 "This package provides full genome sequences for Homo sapiens from
231 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
232 (license license:artistic2.0)))
234 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
236 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
240 ;; We cannot use bioconductor-uri here because this tarball is
241 ;; located under "data/annotation/" instead of "bioc/".
242 (uri (string-append "http://www.bioconductor.org/packages/"
243 "release/data/annotation/src/contrib/"
244 "BSgenome.Hsapiens.UCSC.hg19.masked_"
248 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
250 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
251 (build-system r-build-system)
253 `(("r-bsgenome" ,r-bsgenome)
254 ("r-bsgenome-hsapiens-ucsc-hg19"
255 ,r-bsgenome-hsapiens-ucsc-hg19)))
256 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
257 (synopsis "Full masked genome sequences for Homo sapiens")
259 "This package provides full genome sequences for Homo sapiens (Human) as
260 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
261 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
262 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
263 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
264 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
265 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
267 (license license:artistic2.0)))
269 (define-public r-bsgenome-mmusculus-ucsc-mm9
271 (name "r-bsgenome-mmusculus-ucsc-mm9")
275 ;; We cannot use bioconductor-uri here because this tarball is
276 ;; located under "data/annotation/" instead of "bioc/".
277 (uri (string-append "https://www.bioconductor.org/packages/"
278 "release/data/annotation/src/contrib/"
279 "BSgenome.Mmusculus.UCSC.mm9_"
283 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
285 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
286 (build-system r-build-system)
287 ;; As this package provides little more than a very large data file it
288 ;; doesn't make sense to build substitutes.
289 (arguments `(#:substitutable? #f))
291 `(("r-bsgenome" ,r-bsgenome)))
293 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
294 (synopsis "Full genome sequences for Mouse")
296 "This package provides full genome sequences for Mus musculus (Mouse) as
297 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
298 (license license:artistic2.0)))
300 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
302 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
306 ;; We cannot use bioconductor-uri here because this tarball is
307 ;; located under "data/annotation/" instead of "bioc/".
308 (uri (string-append "http://www.bioconductor.org/packages/"
309 "release/data/annotation/src/contrib/"
310 "BSgenome.Mmusculus.UCSC.mm9.masked_"
314 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
316 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
317 (build-system r-build-system)
319 `(("r-bsgenome" ,r-bsgenome)
320 ("r-bsgenome-mmusculus-ucsc-mm9"
321 ,r-bsgenome-mmusculus-ucsc-mm9)))
322 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
323 (synopsis "Full masked genome sequences for Mouse")
325 "This package provides full genome sequences for Mus musculus (Mouse) as
326 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
327 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
328 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
329 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
330 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
331 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
333 (license license:artistic2.0)))
335 (define-public r-bsgenome-mmusculus-ucsc-mm10
337 (name "r-bsgenome-mmusculus-ucsc-mm10")
341 ;; We cannot use bioconductor-uri here because this tarball is
342 ;; located under "data/annotation/" instead of "bioc/".
343 (uri (string-append "https://www.bioconductor.org/packages/"
344 "release/data/annotation/src/contrib/"
345 "BSgenome.Mmusculus.UCSC.mm10_"
349 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
351 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
352 (build-system r-build-system)
353 ;; As this package provides little more than a very large data file it
354 ;; doesn't make sense to build substitutes.
355 (arguments `(#:substitutable? #f))
357 `(("r-bsgenome" ,r-bsgenome)))
359 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
360 (synopsis "Full genome sequences for Mouse")
362 "This package provides full genome sequences for Mus
363 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
364 in Biostrings objects.")
365 (license license:artistic2.0)))
367 (define-public r-org-ce-eg-db
369 (name "r-org-ce-eg-db")
373 ;; We cannot use bioconductor-uri here because this tarball is
374 ;; located under "data/annotation/" instead of "bioc/".
375 (uri (string-append "https://www.bioconductor.org/packages/"
376 "release/data/annotation/src/contrib/"
377 "org.Ce.eg.db_" version ".tar.gz"))
380 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
382 `((upstream-name . "org.Ce.eg.db")))
383 (build-system r-build-system)
385 `(("r-annotationdbi" ,r-annotationdbi)))
386 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
387 (synopsis "Genome wide annotation for Worm")
389 "This package provides mappings from Entrez gene identifiers to various
390 annotations for the genome of the model worm Caenorhabditis elegans.")
391 (license license:artistic2.0)))
393 (define-public r-org-dm-eg-db
395 (name "r-org-dm-eg-db")
399 ;; We cannot use bioconductor-uri here because this tarball is
400 ;; located under "data/annotation/" instead of "bioc/".
401 (uri (string-append "https://www.bioconductor.org/packages/"
402 "release/data/annotation/src/contrib/"
403 "org.Dm.eg.db_" version ".tar.gz"))
406 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
408 `((upstream-name . "org.Dm.eg.db")))
409 (build-system r-build-system)
411 `(("r-annotationdbi" ,r-annotationdbi)))
412 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
413 (synopsis "Genome wide annotation for Fly")
415 "This package provides mappings from Entrez gene identifiers to various
416 annotations for the genome of the model fruit fly Drosophila melanogaster.")
417 (license license:artistic2.0)))
419 (define-public r-org-dr-eg-db
421 (name "r-org-dr-eg-db")
425 ;; We cannot use bioconductor-uri here because this tarball is
426 ;; located under "data/annotation/" instead of "bioc/".
427 (uri (string-append "https://www.bioconductor.org/packages/"
428 "release/data/annotation/src/contrib/"
429 "org.Dr.eg.db_" version ".tar.gz"))
432 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
434 `((upstream-name . "org.Dr.eg.db")))
435 (build-system r-build-system)
437 `(("r-annotationdbi" ,r-annotationdbi)))
438 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
439 (synopsis "Annotation for Zebrafish")
441 "This package provides genome wide annotations for Zebrafish, primarily
442 based on mapping using Entrez Gene identifiers.")
443 (license license:artistic2.0)))
445 (define-public r-org-hs-eg-db
447 (name "r-org-hs-eg-db")
451 ;; We cannot use bioconductor-uri here because this tarball is
452 ;; located under "data/annotation/" instead of "bioc/".
453 (uri (string-append "https://www.bioconductor.org/packages/"
454 "release/data/annotation/src/contrib/"
455 "org.Hs.eg.db_" version ".tar.gz"))
458 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
460 `((upstream-name . "org.Hs.eg.db")))
461 (build-system r-build-system)
463 `(("r-annotationdbi" ,r-annotationdbi)))
464 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
465 (synopsis "Genome wide annotation for Human")
467 "This package contains genome-wide annotations for Human, primarily based
468 on mapping using Entrez Gene identifiers.")
469 (license license:artistic2.0)))
471 (define-public r-org-mm-eg-db
473 (name "r-org-mm-eg-db")
477 ;; We cannot use bioconductor-uri here because this tarball is
478 ;; located under "data/annotation/" instead of "bioc/".
479 (uri (string-append "https://www.bioconductor.org/packages/"
480 "release/data/annotation/src/contrib/"
481 "org.Mm.eg.db_" version ".tar.gz"))
484 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
486 `((upstream-name . "org.Mm.eg.db")))
487 (build-system r-build-system)
489 `(("r-annotationdbi" ,r-annotationdbi)))
490 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
491 (synopsis "Genome wide annotation for Mouse")
493 "This package provides mappings from Entrez gene identifiers to various
494 annotations for the genome of the model mouse Mus musculus.")
495 (license license:artistic2.0)))
497 (define-public r-bsgenome-hsapiens-ucsc-hg19
499 (name "r-bsgenome-hsapiens-ucsc-hg19")
503 ;; We cannot use bioconductor-uri here because this tarball is
504 ;; located under "data/annotation/" instead of "bioc/".
505 (uri (string-append "https://www.bioconductor.org/packages/"
506 "release/data/annotation/src/contrib/"
507 "BSgenome.Hsapiens.UCSC.hg19_"
511 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
513 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
514 (build-system r-build-system)
515 ;; As this package provides little more than a very large data file it
516 ;; doesn't make sense to build substitutes.
517 (arguments `(#:substitutable? #f))
519 `(("r-bsgenome" ,r-bsgenome)))
521 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
522 (synopsis "Full genome sequences for Homo sapiens")
524 "This package provides full genome sequences for Homo sapiens as provided
525 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
526 (license license:artistic2.0)))
528 (define-public r-genelendatabase
530 (name "r-genelendatabase")
535 ;; We cannot use bioconductor-uri here because this tarball is
536 ;; located under "data/experiment/" instead of "bioc/".
537 (uri (string-append "https://bioconductor.org/packages/"
538 "release/data/experiment/src/contrib"
539 "/geneLenDataBase_" version ".tar.gz"))
542 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
544 `((upstream-name . "geneLenDataBase")))
545 (build-system r-build-system)
547 `(("r-rtracklayer" ,r-rtracklayer)
548 ("r-genomicfeatures" ,r-genomicfeatures)))
549 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
550 (synopsis "Lengths of mRNA transcripts for a number of genomes")
552 "This package provides the lengths of mRNA transcripts for a number of
553 genomes and gene ID formats, largely based on the UCSC table browser.")
554 (license license:lgpl2.0+)))
556 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
558 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
562 ;; We cannot use bioconductor-uri here because this tarball is
563 ;; located under "data/annotation/" instead of "bioc/".
564 (uri (string-append "https://bioconductor.org/packages/"
565 "release/data/annotation/src/contrib"
566 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
570 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
572 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
573 (build-system r-build-system)
574 ;; As this package provides little more than a very large data file it
575 ;; doesn't make sense to build substitutes.
576 (arguments `(#:substitutable? #f))
578 `(("r-genomicfeatures" ,r-genomicfeatures)))
580 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
581 (synopsis "Annotation package for human genome in TxDb format")
583 "This package provides an annotation database of Homo sapiens genome
584 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
585 track. The database is exposed as a @code{TxDb} object.")
586 (license license:artistic2.0)))
588 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
590 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
594 ;; We cannot use bioconductor-uri here because this tarball is
595 ;; located under "data/annotation/" instead of "bioc/".
596 (uri (string-append "https://bioconductor.org/packages/"
597 "release/data/annotation/src/contrib"
598 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
602 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
604 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
605 (build-system r-build-system)
607 `(("r-genomicfeatures" ,r-genomicfeatures)
608 ("r-annotationdbi" ,r-annotationdbi)))
610 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
611 (synopsis "Annotation package for mouse genome in TxDb format")
613 "This package provides an annotation database of Mouse genome data. It
614 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
615 database is exposed as a @code{TxDb} object.")
616 (license license:artistic2.0)))
618 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
620 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
624 ;; We cannot use bioconductor-uri here because this tarball is
625 ;; located under "data/annotation/" instead of "bioc/".
626 (uri (string-append "https://www.bioconductor.org/packages/"
627 "release/data/annotation/src/contrib/"
628 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
632 "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39"))))
634 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
635 (build-system r-build-system)
636 ;; As this package provides little more than a very large data file it
637 ;; doesn't make sense to build substitutes.
638 (arguments `(#:substitutable? #f))
640 `(("r-bsgenome" ,r-bsgenome)
641 ("r-genomicfeatures" ,r-genomicfeatures)
642 ("r-annotationdbi" ,r-annotationdbi)))
644 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
645 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
647 "This package loads a TxDb object, which is an R interface to
648 prefabricated databases contained in this package. This package provides
649 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
650 based on the knownGene track.")
651 (license license:artistic2.0)))
656 (define-public r-hsmmsinglecell
658 (name "r-hsmmsinglecell")
662 ;; We cannot use bioconductor-uri here because this tarball is
663 ;; located under "data/experiment/" instead of "bioc/".
664 (uri (string-append "https://www.bioconductor.org/packages/"
665 "release/data/experiment/src/contrib/"
666 "HSMMSingleCell_" version ".tar.gz"))
669 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
671 `((upstream-name . "HSMMSingleCell")))
672 (build-system r-build-system)
673 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
674 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
676 "Skeletal myoblasts undergo a well-characterized sequence of
677 morphological and transcriptional changes during differentiation. In this
678 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
679 under high mitogen conditions (GM) and then differentiated by switching to
680 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
681 hundred cells taken over a time-course of serum-induced differentiation.
682 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
683 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
684 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
685 which were then sequenced to a depth of ~4 million reads per library,
686 resulting in a complete gene expression profile for each cell.")
687 (license license:artistic2.0)))
692 (define-public r-biocgenerics
694 (name "r-biocgenerics")
698 (uri (bioconductor-uri "BiocGenerics" version))
701 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
703 `((upstream-name . "BiocGenerics")))
704 (build-system r-build-system)
705 (home-page "https://bioconductor.org/packages/BiocGenerics")
706 (synopsis "S4 generic functions for Bioconductor")
708 "This package provides S4 generic functions needed by many Bioconductor
710 (license license:artistic2.0)))
712 (define-public r-annotate
719 (uri (bioconductor-uri "annotate" version))
722 "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
723 (build-system r-build-system)
725 `(("r-annotationdbi" ,r-annotationdbi)
726 ("r-biobase" ,r-biobase)
727 ("r-biocgenerics" ,r-biocgenerics)
731 ("r-xtable" ,r-xtable)))
733 "https://bioconductor.org/packages/annotate")
734 (synopsis "Annotation for microarrays")
735 (description "This package provides R environments for the annotation of
737 (license license:artistic2.0)))
739 (define-public r-hpar
746 (uri (bioconductor-uri "hpar" version))
749 "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
750 (build-system r-build-system)
751 (home-page "https://bioconductor.org/packages/hpar/")
752 (synopsis "Human Protein Atlas in R")
753 (description "This package provides a simple interface to and data from
754 the Human Protein Atlas project.")
755 (license license:artistic2.0)))
757 (define-public r-regioner
764 (uri (bioconductor-uri "regioneR" version))
767 "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
768 (properties `((upstream-name . "regioneR")))
769 (build-system r-build-system)
771 `(("r-biostrings" ,r-biostrings)
772 ("r-bsgenome" ,r-bsgenome)
773 ("r-genomeinfodb" ,r-genomeinfodb)
774 ("r-genomicranges" ,r-genomicranges)
775 ("r-iranges" ,r-iranges)
776 ("r-memoise" ,r-memoise)
777 ("r-rtracklayer" ,r-rtracklayer)
778 ("r-s4vectors" ,r-s4vectors)))
779 (home-page "https://bioconductor.org/packages/regioneR/")
780 (synopsis "Association analysis of genomic regions")
781 (description "This package offers a statistical framework based on
782 customizable permutation tests to assess the association between genomic
783 region sets and other genomic features.")
784 (license license:artistic2.0)))
786 (define-public r-geneplotter
788 (name "r-geneplotter")
793 (uri (bioconductor-uri "geneplotter" version))
796 "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"))))
797 (build-system r-build-system)
799 `(("r-annotate" ,r-annotate)
800 ("r-annotationdbi" ,r-annotationdbi)
801 ("r-biobase" ,r-biobase)
802 ("r-biocgenerics" ,r-biocgenerics)
803 ("r-lattice" ,r-lattice)
804 ("r-rcolorbrewer" ,r-rcolorbrewer)))
805 (home-page "https://bioconductor.org/packages/geneplotter")
806 (synopsis "Graphics functions for genomic data")
808 "This package provides functions for plotting genomic data.")
809 (license license:artistic2.0)))
811 (define-public r-qvalue
818 (uri (bioconductor-uri "qvalue" version))
821 "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc"))))
822 (build-system r-build-system)
824 `(("r-ggplot2" ,r-ggplot2)
825 ("r-reshape2" ,r-reshape2)))
826 (home-page "http://github.com/jdstorey/qvalue")
827 (synopsis "Q-value estimation for false discovery rate control")
829 "This package takes a list of p-values resulting from the simultaneous
830 testing of many hypotheses and estimates their q-values and local @dfn{false
831 discovery rate} (FDR) values. The q-value of a test measures the proportion
832 of false positives incurred when that particular test is called significant.
833 The local FDR measures the posterior probability the null hypothesis is true
834 given the test's p-value. Various plots are automatically generated, allowing
835 one to make sensible significance cut-offs. The software can be applied to
836 problems in genomics, brain imaging, astrophysics, and data mining.")
837 ;; Any version of the LGPL.
838 (license license:lgpl3+)))
840 (define-public r-diffbind
847 (uri (bioconductor-uri "DiffBind" version))
850 "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
851 (properties `((upstream-name . "DiffBind")))
852 (build-system r-build-system)
857 ("r-biocparallel" ,r-biocparallel)
858 ("r-deseq2" ,r-deseq2)
861 ("r-genomicalignments" ,r-genomicalignments)
862 ("r-genomicranges" ,r-genomicranges)
863 ("r-ggplot2" ,r-ggplot2)
864 ("r-ggrepel" ,r-ggrepel)
865 ("r-gplots" ,r-gplots)
866 ("r-iranges" ,r-iranges)
867 ("r-lattice" ,r-lattice)
869 ("r-locfit" ,r-locfit)
870 ("r-rcolorbrewer" , r-rcolorbrewer)
872 ("r-rsamtools" ,r-rsamtools)
873 ("r-s4vectors" ,r-s4vectors)
874 ("r-summarizedexperiment" ,r-summarizedexperiment)
875 ("r-systempiper" ,r-systempiper)
876 ("r-zlibbioc" ,r-zlibbioc)))
877 (home-page "http://bioconductor.org/packages/DiffBind")
878 (synopsis "Differential binding analysis of ChIP-Seq peak data")
880 "This package computes differentially bound sites from multiple
881 ChIP-seq experiments using affinity (quantitative) data. Also enables
882 occupancy (overlap) analysis and plotting functions.")
883 (license license:artistic2.0)))
885 (define-public r-ripseeker
892 (uri (bioconductor-uri "RIPSeeker" version))
895 "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
896 (properties `((upstream-name . "RIPSeeker")))
897 (build-system r-build-system)
899 `(("r-s4vectors" ,r-s4vectors)
900 ("r-iranges" ,r-iranges)
901 ("r-genomicranges" ,r-genomicranges)
902 ("r-summarizedexperiment" ,r-summarizedexperiment)
903 ("r-rsamtools" ,r-rsamtools)
904 ("r-genomicalignments" ,r-genomicalignments)
905 ("r-rtracklayer" ,r-rtracklayer)))
906 (home-page "http://bioconductor.org/packages/RIPSeeker")
908 "Identifying protein-associated transcripts from RIP-seq experiments")
910 "This package infers and discriminates RIP peaks from RIP-seq alignments
911 using two-state HMM with negative binomial emission probability. While
912 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
913 a suite of bioinformatics tools integrated within this self-contained software
914 package comprehensively addressing issues ranging from post-alignments
915 processing to visualization and annotation.")
916 (license license:gpl2)))
918 (define-public r-multtest
925 (uri (bioconductor-uri "multtest" version))
928 "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
929 (build-system r-build-system)
931 `(("r-survival" ,r-survival)
932 ("r-biocgenerics" ,r-biocgenerics)
933 ("r-biobase" ,r-biobase)
935 (home-page "http://bioconductor.org/packages/multtest")
936 (synopsis "Resampling-based multiple hypothesis testing")
938 "This package can do non-parametric bootstrap and permutation
939 resampling-based multiple testing procedures (including empirical Bayes
940 methods) for controlling the family-wise error rate (FWER), generalized
941 family-wise error rate (gFWER), tail probability of the proportion of
942 false positives (TPPFP), and false discovery rate (FDR). Several choices
943 of bootstrap-based null distribution are implemented (centered, centered
944 and scaled, quantile-transformed). Single-step and step-wise methods are
945 available. Tests based on a variety of T- and F-statistics (including
946 T-statistics based on regression parameters from linear and survival models
947 as well as those based on correlation parameters) are included. When probing
948 hypotheses with T-statistics, users may also select a potentially faster null
949 distribution which is multivariate normal with mean zero and variance
950 covariance matrix derived from the vector influence function. Results are
951 reported in terms of adjusted P-values, confidence regions and test statistic
952 cutoffs. The procedures are directly applicable to identifying differentially
953 expressed genes in DNA microarray experiments.")
954 (license license:lgpl3)))
956 (define-public r-graph
962 (uri (bioconductor-uri "graph" version))
965 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
966 (build-system r-build-system)
968 `(("r-biocgenerics" ,r-biocgenerics)))
969 (home-page "https://bioconductor.org/packages/graph")
970 (synopsis "Handle graph data structures in R")
972 "This package implements some simple graph handling capabilities for R.")
973 (license license:artistic2.0)))
975 (define-public r-codedepends
977 (name "r-codedepends")
982 (uri (cran-uri "CodeDepends" version))
985 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
986 (properties `((upstream-name . "CodeDepends")))
987 (build-system r-build-system)
989 `(("r-codetools" ,r-codetools)
992 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
993 (synopsis "Analysis of R code for reproducible research and code comprehension")
995 "This package provides tools for analyzing R expressions or blocks of
996 code and determining the dependencies between them. It focuses on R scripts,
997 but can be used on the bodies of functions. There are many facilities
998 including the ability to summarize or get a high-level view of code,
999 determining dependencies between variables, code improvement suggestions.")
1000 ;; Any version of the GPL
1001 (license (list license:gpl2+ license:gpl3+))))
1003 (define-public r-chippeakanno
1005 (name "r-chippeakanno")
1010 (uri (bioconductor-uri "ChIPpeakAnno" version))
1013 "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
1014 (properties `((upstream-name . "ChIPpeakAnno")))
1015 (build-system r-build-system)
1017 `(("r-biocgenerics" ,r-biocgenerics)
1018 ("r-biocmanager" ,r-biocmanager)
1019 ("r-biostrings" ,r-biostrings)
1020 ("r-delayedarray" ,r-delayedarray)
1021 ("r-go-db" ,r-go-db)
1022 ("r-biomart" ,r-biomart)
1023 ("r-bsgenome" ,r-bsgenome)
1024 ("r-genomicfeatures" ,r-genomicfeatures)
1025 ("r-genomicranges" ,r-genomicranges)
1026 ("r-genomeinfodb" ,r-genomeinfodb)
1027 ("r-iranges" ,r-iranges)
1028 ("r-matrixstats" ,r-matrixstats)
1029 ("r-annotationdbi" ,r-annotationdbi)
1030 ("r-limma" ,r-limma)
1031 ("r-multtest" ,r-multtest)
1033 ("r-graph" ,r-graph)
1034 ("r-regioner" ,r-regioner)
1036 ("r-ensembldb" ,r-ensembldb)
1037 ("r-biobase" ,r-biobase)
1038 ("r-s4vectors" ,r-s4vectors)
1039 ("r-seqinr" ,r-seqinr)
1041 ("r-genomicalignments" ,r-genomicalignments)
1042 ("r-summarizedexperiment" ,r-summarizedexperiment)
1043 ("r-rsamtools" ,r-rsamtools)
1044 ("r-venndiagram" ,r-venndiagram)))
1045 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1046 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1048 "The package includes functions to retrieve the sequences around the peak,
1049 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1050 custom features such as most conserved elements and other transcription factor
1051 binding sites supplied by users. Starting 2.0.5, new functions have been added
1052 for finding the peaks with bi-directional promoters with summary statistics
1053 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1054 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1055 enrichedGO (addGeneIDs).")
1056 (license license:gpl2+)))
1058 (define-public r-marray
1064 (uri (bioconductor-uri "marray" version))
1066 (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
1067 (build-system r-build-system)
1069 `(("r-limma" ,r-limma)))
1070 (home-page "http://bioconductor.org/packages/marray")
1071 (synopsis "Exploratory analysis for two-color spotted microarray data")
1072 (description "This package contains class definitions for two-color spotted
1073 microarray data. It also includes fuctions for data input, diagnostic plots,
1074 normalization and quality checking.")
1075 (license license:lgpl2.0+)))
1077 (define-public r-cghbase
1083 (uri (bioconductor-uri "CGHbase" version))
1085 (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
1086 (properties `((upstream-name . "CGHbase")))
1087 (build-system r-build-system)
1089 `(("r-biobase" ,r-biobase)
1090 ("r-marray" ,r-marray)))
1091 (home-page "http://bioconductor.org/packages/CGHbase")
1092 (synopsis "Base functions and classes for arrayCGH data analysis")
1093 (description "This package contains functions and classes that are needed by
1094 the @code{arrayCGH} packages.")
1095 (license license:gpl2+)))
1097 (define-public r-cghcall
1103 (uri (bioconductor-uri "CGHcall" version))
1105 (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
1106 (properties `((upstream-name . "CGHcall")))
1107 (build-system r-build-system)
1109 `(("r-biobase" ,r-biobase)
1110 ("r-cghbase" ,r-cghbase)
1111 ("r-impute" ,r-impute)
1112 ("r-dnacopy" ,r-dnacopy)
1113 ("r-snowfall" ,r-snowfall)))
1114 (home-page "http://bioconductor.org/packages/CGHcall")
1115 (synopsis "Base functions and classes for arrayCGH data analysis")
1116 (description "This package contains functions and classes that are needed by
1117 @code{arrayCGH} packages.")
1118 (license license:gpl2+)))
1120 (define-public r-qdnaseq
1126 (uri (bioconductor-uri "QDNAseq" version))
1128 (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
1129 (properties `((upstream-name . "QDNAseq")))
1130 (build-system r-build-system)
1132 `(("r-biobase" ,r-biobase)
1133 ("r-biocparallel" ,r-biocparallel)
1134 ("r-cghbase" ,r-cghbase)
1135 ("r-cghcall" ,r-cghcall)
1136 ("r-dnacopy" ,r-dnacopy)
1137 ("r-genomicranges" ,r-genomicranges)
1138 ("r-iranges" ,r-iranges)
1139 ("r-matrixstats" ,r-matrixstats)
1140 ("r-r-utils" ,r-r-utils)
1141 ("r-rsamtools" ,r-rsamtools)))
1142 (home-page "http://bioconductor.org/packages/QDNAseq")
1143 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1144 (description "The genome is divided into non-overlapping fixed-sized bins,
1145 number of sequence reads in each counted, adjusted with a simultaneous
1146 two-dimensional loess correction for sequence mappability and GC content, and
1147 filtered to remove spurious regions in the genome. Downstream steps of
1148 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1150 (license license:gpl2+)))
1152 (define-public r-bayseq
1159 (uri (bioconductor-uri "baySeq" version))
1162 "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
1163 (properties `((upstream-name . "baySeq")))
1164 (build-system r-build-system)
1166 `(("r-abind" ,r-abind)
1167 ("r-edger" ,r-edger)
1168 ("r-genomicranges" ,r-genomicranges)))
1169 (home-page "https://bioconductor.org/packages/baySeq/")
1170 (synopsis "Bayesian analysis of differential expression patterns in count data")
1172 "This package identifies differential expression in high-throughput count
1173 data, such as that derived from next-generation sequencing machines,
1174 calculating estimated posterior likelihoods of differential expression (or
1175 more complex hypotheses) via empirical Bayesian methods.")
1176 (license license:gpl3)))
1178 (define-public r-chipcomp
1185 (uri (bioconductor-uri "ChIPComp" version))
1188 "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
1189 (properties `((upstream-name . "ChIPComp")))
1190 (build-system r-build-system)
1192 `(("r-biocgenerics" ,r-biocgenerics)
1193 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1194 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1195 ("r-genomeinfodb" ,r-genomeinfodb)
1196 ("r-genomicranges" ,r-genomicranges)
1197 ("r-iranges" ,r-iranges)
1198 ("r-limma" ,r-limma)
1199 ("r-rsamtools" ,r-rsamtools)
1200 ("r-rtracklayer" ,r-rtracklayer)
1201 ("r-s4vectors" ,r-s4vectors)))
1202 (home-page "https://bioconductor.org/packages/ChIPComp")
1203 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1205 "ChIPComp implements a statistical method for quantitative comparison of
1206 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1207 sites across multiple conditions considering matching control in ChIP-seq
1209 ;; Any version of the GPL.
1210 (license license:gpl3+)))
1212 (define-public r-riboprofiling
1214 (name "r-riboprofiling")
1219 (uri (bioconductor-uri "RiboProfiling" version))
1222 "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
1223 (properties `((upstream-name . "RiboProfiling")))
1224 (build-system r-build-system)
1226 `(("r-biocgenerics" ,r-biocgenerics)
1227 ("r-biostrings" ,r-biostrings)
1228 ("r-data-table" ,r-data-table)
1229 ("r-genomeinfodb" ,r-genomeinfodb)
1230 ("r-genomicalignments" ,r-genomicalignments)
1231 ("r-genomicfeatures" ,r-genomicfeatures)
1232 ("r-genomicranges" ,r-genomicranges)
1233 ("r-ggbio" ,r-ggbio)
1234 ("r-ggplot2" ,r-ggplot2)
1235 ("r-iranges" ,r-iranges)
1237 ("r-reshape2" ,r-reshape2)
1238 ("r-rsamtools" ,r-rsamtools)
1239 ("r-rtracklayer" ,r-rtracklayer)
1240 ("r-s4vectors" ,r-s4vectors)
1241 ("r-sqldf" ,r-sqldf)))
1242 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1243 (synopsis "Ribosome profiling data analysis")
1244 (description "Starting with a BAM file, this package provides the
1245 necessary functions for quality assessment, read start position recalibration,
1246 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1247 of count data: pairs, log fold-change, codon frequency and coverage
1248 assessment, principal component analysis on codon coverage.")
1249 (license license:gpl3)))
1251 (define-public r-riboseqr
1258 (uri (bioconductor-uri "riboSeqR" version))
1261 "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
1262 (properties `((upstream-name . "riboSeqR")))
1263 (build-system r-build-system)
1265 `(("r-abind" ,r-abind)
1266 ("r-bayseq" ,r-bayseq)
1267 ("r-genomeinfodb" ,r-genomeinfodb)
1268 ("r-genomicranges" ,r-genomicranges)
1269 ("r-iranges" ,r-iranges)
1270 ("r-rsamtools" ,r-rsamtools)
1271 ("r-seqlogo" ,r-seqlogo)))
1272 (home-page "https://bioconductor.org/packages/riboSeqR/")
1273 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1275 "This package provides plotting functions, frameshift detection and
1276 parsing of genetic sequencing data from ribosome profiling experiments.")
1277 (license license:gpl3)))
1279 (define-public r-interactionset
1281 (name "r-interactionset")
1286 (uri (bioconductor-uri "InteractionSet" version))
1289 "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
1291 `((upstream-name . "InteractionSet")))
1292 (build-system r-build-system)
1294 `(("r-biocgenerics" ,r-biocgenerics)
1295 ("r-genomeinfodb" ,r-genomeinfodb)
1296 ("r-genomicranges" ,r-genomicranges)
1297 ("r-iranges" ,r-iranges)
1298 ("r-matrix" ,r-matrix)
1300 ("r-s4vectors" ,r-s4vectors)
1301 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1302 (home-page "https://bioconductor.org/packages/InteractionSet")
1303 (synopsis "Base classes for storing genomic interaction data")
1305 "This packages provides the @code{GInteractions},
1306 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1307 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1309 (license license:gpl3)))
1311 (define-public r-genomicinteractions
1313 (name "r-genomicinteractions")
1318 (uri (bioconductor-uri "GenomicInteractions" version))
1321 "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
1323 `((upstream-name . "GenomicInteractions")))
1324 (build-system r-build-system)
1326 `(("r-biobase" ,r-biobase)
1327 ("r-biocgenerics" ,r-biocgenerics)
1328 ("r-data-table" ,r-data-table)
1329 ("r-dplyr" ,r-dplyr)
1330 ("r-genomeinfodb" ,r-genomeinfodb)
1331 ("r-genomicranges" ,r-genomicranges)
1332 ("r-ggplot2" ,r-ggplot2)
1333 ("r-gridextra" ,r-gridextra)
1335 ("r-igraph" ,r-igraph)
1336 ("r-interactionset" ,r-interactionset)
1337 ("r-iranges" ,r-iranges)
1338 ("r-rsamtools" ,r-rsamtools)
1339 ("r-rtracklayer" ,r-rtracklayer)
1340 ("r-s4vectors" ,r-s4vectors)
1341 ("r-stringr" ,r-stringr)))
1342 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1343 (synopsis "R package for handling genomic interaction data")
1345 "This R package provides tools for handling genomic interaction data,
1346 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1347 information and producing various plots and statistics.")
1348 (license license:gpl3)))
1350 (define-public r-ctc
1357 (uri (bioconductor-uri "ctc" version))
1360 "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
1361 (build-system r-build-system)
1362 (propagated-inputs `(("r-amap" ,r-amap)))
1363 (home-page "https://bioconductor.org/packages/ctc/")
1364 (synopsis "Cluster and tree conversion")
1366 "This package provides tools for exporting and importing classification
1367 trees and clusters to other programs.")
1368 (license license:gpl2)))
1370 (define-public r-goseq
1377 (uri (bioconductor-uri "goseq" version))
1380 "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
1381 (build-system r-build-system)
1383 `(("r-annotationdbi" ,r-annotationdbi)
1384 ("r-biasedurn" ,r-biasedurn)
1385 ("r-biocgenerics" ,r-biocgenerics)
1386 ("r-genelendatabase" ,r-genelendatabase)
1387 ("r-go-db" ,r-go-db)
1388 ("r-mgcv" ,r-mgcv)))
1389 (home-page "https://bioconductor.org/packages/goseq/")
1390 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1392 "This package provides tools to detect Gene Ontology and/or other user
1393 defined categories which are over/under represented in RNA-seq data.")
1394 (license license:lgpl2.0+)))
1396 (define-public r-glimma
1403 (uri (bioconductor-uri "Glimma" version))
1406 "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
1407 (properties `((upstream-name . "Glimma")))
1408 (build-system r-build-system)
1410 `(("r-edger" ,r-edger)
1411 ("r-jsonlite" ,r-jsonlite)
1412 ("r-s4vectors" ,r-s4vectors)))
1413 (home-page "https://github.com/Shians/Glimma")
1414 (synopsis "Interactive HTML graphics")
1416 "This package generates interactive visualisations for analysis of
1417 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1418 HTML page. The interactions are built on top of the popular static
1419 representations of analysis results in order to provide additional
1421 (license license:lgpl3)))
1423 (define-public r-rots
1430 (uri (bioconductor-uri "ROTS" version))
1433 "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
1434 (properties `((upstream-name . "ROTS")))
1435 (build-system r-build-system)
1437 `(("r-biobase" ,r-biobase)
1438 ("r-rcpp" ,r-rcpp)))
1439 (home-page "https://bioconductor.org/packages/ROTS/")
1440 (synopsis "Reproducibility-Optimized Test Statistic")
1442 "This package provides tools for calculating the
1443 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1445 (license license:gpl2+)))
1447 (define-public r-plgem
1454 (uri (bioconductor-uri "plgem" version))
1457 "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
1458 (build-system r-build-system)
1460 `(("r-biobase" ,r-biobase)
1461 ("r-mass" ,r-mass)))
1462 (home-page "http://www.genopolis.it")
1463 (synopsis "Detect differential expression in microarray and proteomics datasets")
1465 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1466 model the variance-versus-mean dependence that exists in a variety of
1467 genome-wide datasets, including microarray and proteomics data. The use of
1468 PLGEM has been shown to improve the detection of differentially expressed
1469 genes or proteins in these datasets.")
1470 (license license:gpl2)))
1472 (define-public r-inspect
1479 (uri (bioconductor-uri "INSPEcT" version))
1482 "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
1483 (properties `((upstream-name . "INSPEcT")))
1484 (build-system r-build-system)
1486 `(("r-biobase" ,r-biobase)
1487 ("r-biocgenerics" ,r-biocgenerics)
1488 ("r-biocparallel" ,r-biocparallel)
1489 ("r-deseq2" ,r-deseq2)
1490 ("r-desolve" ,r-desolve)
1491 ("r-genomicalignments" ,r-genomicalignments)
1492 ("r-genomicfeatures" ,r-genomicfeatures)
1493 ("r-genomicranges" ,r-genomicranges)
1494 ("r-iranges" ,r-iranges)
1495 ("r-plgem" ,r-plgem)
1496 ("r-preprocesscore" ,r-preprocesscore)
1498 ("r-rootsolve" ,r-rootsolve)
1499 ("r-rsamtools" ,r-rsamtools)
1500 ("r-s4vectors" ,r-s4vectors)
1501 ("r-shiny" ,r-shiny)
1502 ("r-summarizedexperiment" ,r-summarizedexperiment)
1503 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1504 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1505 (home-page "https://bioconductor.org/packages/INSPEcT")
1506 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1508 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1509 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1510 order to evaluate synthesis, processing and degradation rates and assess via
1511 modeling the rates that determines changes in mature mRNA levels.")
1512 (license license:gpl2)))
1514 (define-public r-dnabarcodes
1516 (name "r-dnabarcodes")
1521 (uri (bioconductor-uri "DNABarcodes" version))
1524 "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
1525 (properties `((upstream-name . "DNABarcodes")))
1526 (build-system r-build-system)
1529 ("r-matrix" ,r-matrix)
1530 ("r-rcpp" ,r-rcpp)))
1531 (home-page "https://bioconductor.org/packages/DNABarcodes")
1532 (synopsis "Create and analyze DNA barcodes")
1534 "This package offers tools to create DNA barcode sets capable of
1535 correcting insertion, deletion, and substitution errors. Existing barcodes
1536 can be analyzed regarding their minimal, maximal and average distances between
1537 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1538 demultiplexed, i.e. assigned to their original reference barcode.")
1539 (license license:gpl2)))
1541 (define-public r-ruvseq
1548 (uri (bioconductor-uri "RUVSeq" version))
1551 "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
1552 (properties `((upstream-name . "RUVSeq")))
1553 (build-system r-build-system)
1555 `(("r-biobase" ,r-biobase)
1556 ("r-edaseq" ,r-edaseq)
1557 ("r-edger" ,r-edger)
1558 ("r-mass" ,r-mass)))
1559 (home-page "https://github.com/drisso/RUVSeq")
1560 (synopsis "Remove unwanted variation from RNA-Seq data")
1562 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1563 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1565 (license license:artistic2.0)))
1567 (define-public r-biocneighbors
1569 (name "r-biocneighbors")
1574 (uri (bioconductor-uri "BiocNeighbors" version))
1577 "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1578 (properties `((upstream-name . "BiocNeighbors")))
1579 (build-system r-build-system)
1581 `(("r-biocparallel" ,r-biocparallel)
1583 ("r-rcppannoy" ,r-rcppannoy)
1584 ("r-s4vectors" ,r-s4vectors)))
1585 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1586 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1588 "This package implements exact and approximate methods for nearest
1589 neighbor detection, in a framework that allows them to be easily switched
1590 within Bioconductor packages or workflows. The exact algorithm is implemented
1591 using pre-clustering with the k-means algorithm. Functions are also provided
1592 to search for all neighbors within a given distance. Parallelization is
1593 achieved for all methods using the BiocParallel framework.")
1594 (license license:gpl3)))
1596 (define-public r-destiny
1603 (uri (bioconductor-uri "destiny" version))
1606 "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1607 (build-system r-build-system)
1609 `(("r-biobase" ,r-biobase)
1610 ("r-biocgenerics" ,r-biocgenerics)
1612 ("r-ggthemes" ,r-ggthemes)
1613 ("r-hmisc" ,r-hmisc)
1614 ("r-igraph" ,r-igraph)
1615 ("r-matrix" ,r-matrix)
1616 ("r-proxy" ,r-proxy)
1618 ("r-rcppeigen" ,r-rcppeigen)
1619 ("r-scales" ,r-scales)
1620 ("r-scatterplot3d" ,r-scatterplot3d)
1621 ("r-smoother" ,r-smoother)
1622 ("r-summarizedexperiment" ,r-summarizedexperiment)
1624 (home-page "https://bioconductor.org/packages/destiny/")
1625 (synopsis "Create and plot diffusion maps")
1626 (description "This package provides tools to create and plot diffusion
1628 ;; Any version of the GPL
1629 (license license:gpl3+)))
1631 (define-public r-savr
1638 (uri (bioconductor-uri "savR" version))
1641 "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1642 (properties `((upstream-name . "savR")))
1643 (build-system r-build-system)
1645 `(("r-ggplot2" ,r-ggplot2)
1646 ("r-gridextra" ,r-gridextra)
1647 ("r-reshape2" ,r-reshape2)
1648 ("r-scales" ,r-scales)
1650 (home-page "https://github.com/bcalder/savR")
1651 (synopsis "Parse and analyze Illumina SAV files")
1653 "This package provides tools to parse Illumina Sequence Analysis
1654 Viewer (SAV) files, access data, and generate QC plots.")
1655 (license license:agpl3+)))
1657 (define-public r-chipexoqual
1659 (name "r-chipexoqual")
1664 (uri (bioconductor-uri "ChIPexoQual" version))
1667 "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1668 (properties `((upstream-name . "ChIPexoQual")))
1669 (build-system r-build-system)
1671 `(("r-biocparallel" ,r-biocparallel)
1672 ("r-biovizbase" ,r-biovizbase)
1673 ("r-broom" ,r-broom)
1674 ("r-data-table" ,r-data-table)
1675 ("r-dplyr" ,r-dplyr)
1676 ("r-genomeinfodb" ,r-genomeinfodb)
1677 ("r-genomicalignments" ,r-genomicalignments)
1678 ("r-genomicranges" ,r-genomicranges)
1679 ("r-ggplot2" ,r-ggplot2)
1680 ("r-hexbin" ,r-hexbin)
1681 ("r-iranges" ,r-iranges)
1682 ("r-rcolorbrewer" ,r-rcolorbrewer)
1683 ("r-rmarkdown" ,r-rmarkdown)
1684 ("r-rsamtools" ,r-rsamtools)
1685 ("r-s4vectors" ,r-s4vectors)
1686 ("r-scales" ,r-scales)
1687 ("r-viridis" ,r-viridis)))
1688 (home-page "https://github.com/keleslab/ChIPexoQual")
1689 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1691 "This package provides a quality control pipeline for ChIP-exo/nexus
1693 (license license:gpl2+)))
1695 (define-public r-copynumber
1697 (name "r-copynumber")
1701 (uri (bioconductor-uri "copynumber" version))
1704 "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"))))
1705 (build-system r-build-system)
1707 `(("r-s4vectors" ,r-s4vectors)
1708 ("r-iranges" ,r-iranges)
1709 ("r-genomicranges" ,r-genomicranges)
1710 ("r-biocgenerics" ,r-biocgenerics)))
1711 (home-page "https://bioconductor.org/packages/copynumber")
1712 (synopsis "Segmentation of single- and multi-track copy number data")
1714 "This package segments single- and multi-track copy number data by a
1715 penalized least squares regression method.")
1716 (license license:artistic2.0)))
1718 (define-public r-dnacopy
1725 (uri (bioconductor-uri "DNAcopy" version))
1728 "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1729 (properties `((upstream-name . "DNAcopy")))
1730 (build-system r-build-system)
1731 (native-inputs `(("gfortran" ,gfortran)))
1732 (home-page "https://bioconductor.org/packages/DNAcopy")
1733 (synopsis "DNA copy number data analysis")
1735 "This package implements the @dfn{circular binary segmentation} (CBS)
1736 algorithm to segment DNA copy number data and identify genomic regions with
1737 abnormal copy number.")
1738 (license license:gpl2+)))
1740 ;; This is a CRAN package, but it uncharacteristically depends on a
1741 ;; Bioconductor package.
1742 (define-public r-htscluster
1744 (name "r-htscluster")
1749 (uri (cran-uri "HTSCluster" version))
1752 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1753 (properties `((upstream-name . "HTSCluster")))
1754 (build-system r-build-system)
1756 `(("r-capushe" ,r-capushe)
1757 ("r-edger" ,r-edger)
1758 ("r-plotrix" ,r-plotrix)))
1759 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1760 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1762 "This package provides a Poisson mixture model is implemented to cluster
1763 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
1764 estimation is performed using either the EM or CEM algorithm, and the slope
1765 heuristics are used for model selection (i.e., to choose the number of
1767 (license license:gpl3+)))
1769 (define-public r-deds
1776 (uri (bioconductor-uri "DEDS" version))
1779 "1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"))))
1780 (properties `((upstream-name . "DEDS")))
1781 (build-system r-build-system)
1782 (home-page "https://bioconductor.org/packages/DEDS/")
1783 (synopsis "Differential expression via distance summary for microarray data")
1785 "This library contains functions that calculate various statistics of
1786 differential expression for microarray data, including t statistics, fold
1787 change, F statistics, SAM, moderated t and F statistics and B statistics. It
1788 also implements a new methodology called DEDS (Differential Expression via
1789 Distance Summary), which selects differentially expressed genes by integrating
1790 and summarizing a set of statistics using a weighted distance approach.")
1791 ;; Any version of the LGPL.
1792 (license license:lgpl3+)))
1794 ;; This is a CRAN package, but since it depends on a Bioconductor package we
1796 (define-public r-nbpseq
1803 (uri (cran-uri "NBPSeq" version))
1806 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
1807 (properties `((upstream-name . "NBPSeq")))
1808 (build-system r-build-system)
1810 `(("r-qvalue" ,r-qvalue)))
1811 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
1812 (synopsis "Negative binomial models for RNA-Seq data")
1814 "This package provides negative binomial models for two-group comparisons
1815 and regression inferences from RNA-sequencing data.")
1816 (license license:gpl2)))
1818 (define-public r-ebseq
1825 (uri (bioconductor-uri "EBSeq" version))
1828 "1gzbk1hbwdan0j131ah88yryfvsiq0wqjnb09qbr4qaczpgvbad0"))))
1829 (properties `((upstream-name . "EBSeq")))
1830 (build-system r-build-system)
1832 `(("r-blockmodeling" ,r-blockmodeling)
1833 ("r-gplots" ,r-gplots)
1834 ("r-testthat" ,r-testthat)))
1835 (home-page "https://bioconductor.org/packages/EBSeq")
1836 (synopsis "Differential expression analysis of RNA-seq data")
1838 "This package provides tools for differential expression analysis at both
1839 gene and isoform level using RNA-seq data")
1840 (license license:artistic2.0)))
1842 (define-public r-lpsymphony
1844 (name "r-lpsymphony")
1849 (uri (bioconductor-uri "lpsymphony" version))
1852 "0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"))))
1853 (build-system r-build-system)
1855 `(("gfortran" ,gfortran)
1858 `(("pkg-config" ,pkg-config)))
1859 (home-page "http://r-forge.r-project.org/projects/rsymphony")
1860 (synopsis "Symphony integer linear programming solver in R")
1862 "This package was derived from Rsymphony. The package provides an R
1863 interface to SYMPHONY, a linear programming solver written in C++. The main
1864 difference between this package and Rsymphony is that it includes the solver
1865 source code, while Rsymphony expects to find header and library files on the
1866 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
1867 to install interface to SYMPHONY.")
1868 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
1869 ;; lpsimphony is released under the same terms.
1870 (license license:epl1.0)))
1872 (define-public r-ihw
1879 (uri (bioconductor-uri "IHW" version))
1882 "10wqasl8k2j3y5qvak3xr2xj6symk656xww1y5n2l22nz832j19n"))))
1883 (properties `((upstream-name . "IHW")))
1884 (build-system r-build-system)
1886 `(("r-biocgenerics" ,r-biocgenerics)
1887 ("r-fdrtool" ,r-fdrtool)
1888 ("r-lpsymphony" ,r-lpsymphony)
1889 ("r-slam" ,r-slam)))
1890 (home-page "https://bioconductor.org/packages/IHW")
1891 (synopsis "Independent hypothesis weighting")
1893 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
1894 procedure that increases power compared to the method of Benjamini and
1895 Hochberg by assigning data-driven weights to each hypothesis. The input to
1896 IHW is a two-column table of p-values and covariates. The covariate can be
1897 any continuous-valued or categorical variable that is thought to be
1898 informative on the statistical properties of each hypothesis test, while it is
1899 independent of the p-value under the null hypothesis.")
1900 (license license:artistic2.0)))
1902 (define-public r-icobra
1909 (uri (bioconductor-uri "iCOBRA" version))
1912 "0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"))))
1913 (properties `((upstream-name . "iCOBRA")))
1914 (build-system r-build-system)
1916 `(("r-dplyr" ,r-dplyr)
1918 ("r-ggplot2" ,r-ggplot2)
1919 ("r-limma" ,r-limma)
1920 ("r-reshape2" ,r-reshape2)
1922 ("r-scales" ,r-scales)
1923 ("r-shiny" ,r-shiny)
1924 ("r-shinybs" ,r-shinybs)
1925 ("r-shinydashboard" ,r-shinydashboard)
1926 ("r-upsetr" ,r-upsetr)))
1927 (home-page "https://bioconductor.org/packages/iCOBRA")
1928 (synopsis "Comparison and visualization of ranking and assignment methods")
1930 "This package provides functions for calculation and visualization of
1931 performance metrics for evaluation of ranking and binary
1932 classification (assignment) methods. It also contains a Shiny application for
1933 interactive exploration of results.")
1934 (license license:gpl2+)))
1936 (define-public r-mast
1943 (uri (bioconductor-uri "MAST" version))
1946 "0rhx655dza0m6yg9jcfz2nmxqahvxx2l91kqgyp7qai0bzz9d9ix"))))
1947 (properties `((upstream-name . "MAST")))
1948 (build-system r-build-system)
1950 `(("r-abind" ,r-abind)
1951 ("r-biobase" ,r-biobase)
1952 ("r-biocgenerics" ,r-biocgenerics)
1953 ("r-data-table" ,r-data-table)
1954 ("r-ggplot2" ,r-ggplot2)
1956 ("r-progress" ,r-progress)
1957 ("r-reshape2" ,r-reshape2)
1958 ("r-s4vectors" ,r-s4vectors)
1959 ("r-singlecellexperiment" ,r-singlecellexperiment)
1960 ("r-stringr" ,r-stringr)
1961 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1962 (home-page "https://github.com/RGLab/MAST/")
1963 (synopsis "Model-based analysis of single cell transcriptomics")
1965 "This package provides methods and models for handling zero-inflated
1966 single cell assay data.")
1967 (license license:gpl2+)))
1969 (define-public r-monocle
1976 (uri (bioconductor-uri "monocle" version))
1979 "0shwkgqs93j2l5h36yyvb1lf724107cfjrmzp5fxfj1lqc0y61lf"))))
1980 (build-system r-build-system)
1982 `(("r-biobase" ,r-biobase)
1983 ("r-biocgenerics" ,r-biocgenerics)
1984 ("r-biocviews" ,r-biocviews)
1985 ("r-cluster" ,r-cluster)
1986 ("r-combinat" ,r-combinat)
1987 ("r-ddrtree" ,r-ddrtree)
1988 ("r-densityclust" ,r-densityclust)
1989 ("r-dplyr" ,r-dplyr)
1990 ("r-fastica" ,r-fastica)
1991 ("r-ggplot2" ,r-ggplot2)
1992 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
1993 ("r-igraph" ,r-igraph)
1994 ("r-irlba" ,r-irlba)
1995 ("r-limma" ,r-limma)
1997 ("r-matrix" ,r-matrix)
1998 ("r-matrixstats" ,r-matrixstats)
1999 ("r-pheatmap" ,r-pheatmap)
2001 ("r-proxy" ,r-proxy)
2002 ("r-qlcmatrix" ,r-qlcmatrix)
2005 ("r-reshape2" ,r-reshape2)
2006 ("r-rtsne" ,r-rtsne)
2008 ("r-stringr" ,r-stringr)
2009 ("r-tibble" ,r-tibble)
2011 ("r-viridis" ,r-viridis)))
2012 (home-page "https://bioconductor.org/packages/monocle")
2013 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2015 "Monocle performs differential expression and time-series analysis for
2016 single-cell expression experiments. It orders individual cells according to
2017 progress through a biological process, without knowing ahead of time which
2018 genes define progress through that process. Monocle also performs
2019 differential expression analysis, clustering, visualization, and other useful
2020 tasks on single cell expression data. It is designed to work with RNA-Seq and
2021 qPCR data, but could be used with other types as well.")
2022 (license license:artistic2.0)))
2024 (define-public r-noiseq
2031 (uri (bioconductor-uri "NOISeq" version))
2034 "1wyhhi9ydlbjlz427093mdp5ppby77n37w5c2iyxlpsdk2m2nqsn"))))
2035 (properties `((upstream-name . "NOISeq")))
2036 (build-system r-build-system)
2038 `(("r-biobase" ,r-biobase)
2039 ("r-matrix" ,r-matrix)))
2040 (home-page "https://bioconductor.org/packages/NOISeq")
2041 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2043 "This package provides tools to support the analysis of RNA-seq
2044 expression data or other similar kind of data. It provides exploratory plots
2045 to evaluate saturation, count distribution, expression per chromosome, type of
2046 detected features, features length, etc. It also supports the analysis of
2047 differential expression between two experimental conditions with no parametric
2049 (license license:artistic2.0)))