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 git-download)
26 #:use-module (guix build-system r)
27 #:use-module (gnu packages)
28 #:use-module (gnu packages base)
29 #:use-module (gnu packages bioinformatics)
30 #:use-module (gnu packages cran)
31 #:use-module (gnu packages compression)
32 #:use-module (gnu packages gcc)
33 #:use-module (gnu packages graph)
34 #:use-module (gnu packages haskell-xyz)
35 #:use-module (gnu packages image)
36 #:use-module (gnu packages maths)
37 #:use-module (gnu packages netpbm)
38 #:use-module (gnu packages perl)
39 #:use-module (gnu packages pkg-config)
40 #:use-module (gnu packages statistics)
41 #:use-module (gnu packages web)
42 #:use-module (srfi srfi-1))
47 (define-public r-bsgenome-celegans-ucsc-ce6
49 (name "r-bsgenome-celegans-ucsc-ce6")
53 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
57 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
59 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
60 (build-system r-build-system)
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-ensdb-hsapiens-v75
530 (name "r-ensdb-hsapiens-v75")
535 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
538 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
540 `((upstream-name . "EnsDb.Hsapiens.v75")))
541 (build-system r-build-system)
543 `(("r-ensembldb" ,r-ensembldb)))
544 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
545 (synopsis "Ensembl based annotation package")
547 "This package exposes an annotation database generated from Ensembl.")
548 (license license:artistic2.0)))
550 (define-public r-genelendatabase
552 (name "r-genelendatabase")
557 ;; We cannot use bioconductor-uri here because this tarball is
558 ;; located under "data/experiment/" instead of "bioc/".
559 (uri (string-append "https://bioconductor.org/packages/"
560 "release/data/experiment/src/contrib"
561 "/geneLenDataBase_" version ".tar.gz"))
564 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
566 `((upstream-name . "geneLenDataBase")))
567 (build-system r-build-system)
569 `(("r-rtracklayer" ,r-rtracklayer)
570 ("r-genomicfeatures" ,r-genomicfeatures)))
571 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
572 (synopsis "Lengths of mRNA transcripts for a number of genomes")
574 "This package provides the lengths of mRNA transcripts for a number of
575 genomes and gene ID formats, largely based on the UCSC table browser.")
576 (license license:lgpl2.0+)))
578 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
580 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
584 ;; We cannot use bioconductor-uri here because this tarball is
585 ;; located under "data/annotation/" instead of "bioc/".
586 (uri (string-append "https://bioconductor.org/packages/"
587 "release/data/annotation/src/contrib"
588 "/TxDb.Hsapiens.UCSC.hg19.knownGene_"
592 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
594 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
595 (build-system r-build-system)
596 ;; As this package provides little more than a very large data file it
597 ;; doesn't make sense to build substitutes.
598 (arguments `(#:substitutable? #f))
600 `(("r-genomicfeatures" ,r-genomicfeatures)))
602 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
603 (synopsis "Annotation package for human genome in TxDb format")
605 "This package provides an annotation database of Homo sapiens genome
606 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
607 track. The database is exposed as a @code{TxDb} object.")
608 (license license:artistic2.0)))
610 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
612 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
616 ;; We cannot use bioconductor-uri here because this tarball is
617 ;; located under "data/annotation/" instead of "bioc/".
618 (uri (string-append "https://bioconductor.org/packages/"
619 "release/data/annotation/src/contrib"
620 "/TxDb.Hsapiens.UCSC.hg38.knownGene_"
624 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
626 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
627 (build-system r-build-system)
629 `(("r-genomicfeatures" ,r-genomicfeatures)))
631 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
632 (synopsis "Annotation package for human genome in TxDb format")
634 "This package provides an annotation database of Homo sapiens genome
635 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
636 track. The database is exposed as a @code{TxDb} object.")
637 (license license:artistic2.0)))
639 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
641 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
645 ;; We cannot use bioconductor-uri here because this tarball is
646 ;; located under "data/annotation/" instead of "bioc/".
647 (uri (string-append "https://bioconductor.org/packages/"
648 "release/data/annotation/src/contrib"
649 "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
653 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
655 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
656 (build-system r-build-system)
658 `(("r-genomicfeatures" ,r-genomicfeatures)
659 ("r-annotationdbi" ,r-annotationdbi)))
661 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
662 (synopsis "Annotation package for mouse genome in TxDb format")
664 "This package provides an annotation database of Mouse genome data. It
665 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
666 database is exposed as a @code{TxDb} object.")
667 (license license:artistic2.0)))
669 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
671 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
675 ;; We cannot use bioconductor-uri here because this tarball is
676 ;; located under "data/annotation/" instead of "bioc/".
677 (uri (string-append "https://www.bioconductor.org/packages/"
678 "release/data/annotation/src/contrib/"
679 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
683 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
685 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
686 (build-system r-build-system)
687 ;; As this package provides little more than a very large data file it
688 ;; doesn't make sense to build substitutes.
689 (arguments `(#:substitutable? #f))
691 `(("r-bsgenome" ,r-bsgenome)
692 ("r-genomicfeatures" ,r-genomicfeatures)
693 ("r-annotationdbi" ,r-annotationdbi)))
695 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
696 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
698 "This package loads a TxDb object, which is an R interface to
699 prefabricated databases contained in this package. This package provides
700 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
701 based on the knownGene track.")
702 (license license:artistic2.0)))
704 (define-public r-txdb-celegans-ucsc-ce6-ensgene
706 (name "r-txdb-celegans-ucsc-ce6-ensgene")
711 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
712 version 'annotation))
715 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
717 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
718 (build-system r-build-system)
720 `(("r-annotationdbi" ,r-annotationdbi)
721 ("r-genomicfeatures" ,r-genomicfeatures)))
722 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
723 (synopsis "Annotation package for C elegans TxDb objects")
725 "This package exposes a C elegans annotation database generated from UCSC
726 by exposing these as TxDb objects.")
727 (license license:artistic2.0)))
729 (define-public r-fdb-infiniummethylation-hg19
731 (name "r-fdb-infiniummethylation-hg19")
735 ;; We cannot use bioconductor-uri here because this tarball is
736 ;; located under "data/annotation/" instead of "bioc/".
737 (uri (string-append "https://www.bioconductor.org/packages/"
738 "release/data/annotation/src/contrib/"
739 "FDb.InfiniumMethylation.hg19_"
743 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
745 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
746 (build-system r-build-system)
748 `(("r-biostrings" ,r-biostrings)
749 ("r-genomicfeatures" ,r-genomicfeatures)
750 ("r-annotationdbi" ,r-annotationdbi)
751 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
752 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
753 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
754 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
756 "This is an annotation package for Illumina Infinium DNA methylation
757 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
759 (license license:artistic2.0)))
761 (define-public r-illuminahumanmethylationepicmanifest
763 (name "r-illuminahumanmethylationepicmanifest")
767 ;; We cannot use bioconductor-uri here because this tarball is
768 ;; located under "data/annotation/" instead of "bioc/".
769 (uri (string-append "https://www.bioconductor.org/packages/"
770 "release/data/annotation/src/contrib/"
771 "IlluminaHumanMethylationEPICmanifest_"
775 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
777 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
778 (build-system r-build-system)
780 `(("r-minfi" ,r-minfi)))
781 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
782 (synopsis "Manifest for Illumina's EPIC methylation arrays")
784 "This is a manifest package for Illumina's EPIC methylation arrays.")
785 (license license:artistic2.0)))
787 (define-public r-do-db
793 ;; We cannot use bioconductor-uri here because this tarball is
794 ;; located under "data/annotation/" instead of "bioc/".
795 (uri (string-append "https://www.bioconductor.org/packages/"
796 "release/data/annotation/src/contrib/"
797 "DO.db_" version ".tar.gz"))
800 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
802 `((upstream-name . "DO.db")))
803 (build-system r-build-system)
805 `(("r-annotationdbi" ,r-annotationdbi)))
806 (home-page "https://www.bioconductor.org/packages/DO.db/")
807 (synopsis "Annotation maps describing the entire Disease Ontology")
809 "This package provides a set of annotation maps describing the entire
811 (license license:artistic2.0)))
813 (define-public r-pfam-db
820 (uri (bioconductor-uri "PFAM.db" version 'annotation))
823 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
824 (properties `((upstream-name . "PFAM.db")))
825 (build-system r-build-system)
827 `(("r-annotationdbi" ,r-annotationdbi)))
828 (home-page "https://bioconductor.org/packages/PFAM.db")
829 (synopsis "Set of protein ID mappings for PFAM")
831 "This package provides a set of protein ID mappings for PFAM, assembled
832 using data from public repositories.")
833 (license license:artistic2.0)))
835 (define-public r-phastcons100way-ucsc-hg19
837 (name "r-phastcons100way-ucsc-hg19")
842 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
843 version 'annotation))
846 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
848 `((upstream-name . "phastCons100way.UCSC.hg19")))
849 (build-system r-build-system)
851 `(("r-bsgenome" ,r-bsgenome)
852 ("r-genomeinfodb" ,r-genomeinfodb)
853 ("r-genomicranges" ,r-genomicranges)
854 ("r-genomicscores" ,r-genomicscores)
855 ("r-iranges" ,r-iranges)
856 ("r-s4vectors" ,r-s4vectors)))
857 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
858 (synopsis "UCSC phastCons conservation scores for hg19")
860 "This package provides UCSC phastCons conservation scores for the human
861 genome (hg19) calculated from multiple alignments with other 99 vertebrate
863 (license license:artistic2.0)))
868 (define-public r-abadata
874 ;; We cannot use bioconductor-uri here because this tarball is
875 ;; located under "data/experiment/" instead of "bioc/".
876 (uri (string-append "https://www.bioconductor.org/packages/"
877 "release/data/experiment/src/contrib/"
878 "ABAData_" version ".tar.gz"))
881 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
883 `((upstream-name . "ABAData")))
884 (build-system r-build-system)
886 `(("r-annotationdbi" ,r-annotationdbi)))
887 (home-page "https://www.bioconductor.org/packages/ABAData/")
888 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
890 "This package provides the data for the gene expression enrichment
891 analysis conducted in the package ABAEnrichment. The package includes three
892 datasets which are derived from the Allen Brain Atlas:
895 @item Gene expression data from Human Brain (adults) averaged across donors,
896 @item Gene expression data from the Developing Human Brain pooled into five
897 age categories and averaged across donors, and
898 @item a developmental effect score based on the Developing Human Brain
902 All datasets are restricted to protein coding genes.")
903 (license license:gpl2+)))
905 (define-public r-arrmdata
911 ;; We cannot use bioconductor-uri here because this tarball is
912 ;; located under "data/experiment/" instead of "bioc/".
913 (uri (string-append "https://www.bioconductor.org/packages/"
914 "release/data/experiment/src/contrib/"
915 "ARRmData_" version ".tar.gz"))
918 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
920 `((upstream-name . "ARRmData")))
921 (build-system r-build-system)
922 (home-page "https://www.bioconductor.org/packages/ARRmData/")
923 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
925 "This package provides raw beta values from 36 samples across 3 groups
926 from Illumina 450k methylation arrays.")
927 (license license:artistic2.0)))
929 (define-public r-hsmmsinglecell
931 (name "r-hsmmsinglecell")
935 ;; We cannot use bioconductor-uri here because this tarball is
936 ;; located under "data/experiment/" instead of "bioc/".
937 (uri (string-append "https://www.bioconductor.org/packages/"
938 "release/data/experiment/src/contrib/"
939 "HSMMSingleCell_" version ".tar.gz"))
942 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
944 `((upstream-name . "HSMMSingleCell")))
945 (build-system r-build-system)
946 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
947 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
949 "Skeletal myoblasts undergo a well-characterized sequence of
950 morphological and transcriptional changes during differentiation. In this
951 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
952 under high mitogen conditions (GM) and then differentiated by switching to
953 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
954 hundred cells taken over a time-course of serum-induced differentiation.
955 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
956 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
957 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
958 which were then sequenced to a depth of ~4 million reads per library,
959 resulting in a complete gene expression profile for each cell.")
960 (license license:artistic2.0)))
968 ;; We cannot use bioconductor-uri here because this tarball is
969 ;; located under "data/experiment/" instead of "bioc/".
970 (uri (string-append "https://www.bioconductor.org/packages/"
971 "release/data/experiment/src/contrib/"
972 "ALL_" version ".tar.gz"))
975 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
976 (properties `((upstream-name . "ALL")))
977 (build-system r-build-system)
979 `(("r-biobase" ,r-biobase)))
980 (home-page "https://bioconductor.org/packages/ALL")
981 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
983 "The data consist of microarrays from 128 different individuals with
984 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
985 are available. The data have been normalized (using rma) and it is the
986 jointly normalized data that are available here. The data are presented in
987 the form of an @code{exprSet} object.")
988 (license license:artistic2.0)))
990 (define-public r-affydata
997 (uri (bioconductor-uri "affydata" version 'experiment))
1000 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1001 (properties `((upstream-name . "affydata")))
1002 (build-system r-build-system)
1004 `(("r-affy" ,r-affy)))
1005 (home-page "https://bioconductor.org/packages/affydata/")
1006 (synopsis "Affymetrix data for demonstration purposes")
1008 "This package provides example datasets that represent 'real world
1009 examples' of Affymetrix data, unlike the artificial examples included in the
1010 package @code{affy}.")
1011 (license license:gpl2+)))
1016 (define-public r-biocgenerics
1018 (name "r-biocgenerics")
1022 (uri (bioconductor-uri "BiocGenerics" version))
1025 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
1027 `((upstream-name . "BiocGenerics")))
1028 (build-system r-build-system)
1029 (home-page "https://bioconductor.org/packages/BiocGenerics")
1030 (synopsis "S4 generic functions for Bioconductor")
1032 "This package provides S4 generic functions needed by many Bioconductor
1034 (license license:artistic2.0)))
1036 (define-public r-affycomp
1043 (uri (bioconductor-uri "affycomp" version))
1046 "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
1047 (properties `((upstream-name . "affycomp")))
1048 (build-system r-build-system)
1049 (propagated-inputs `(("r-biobase" ,r-biobase)))
1050 (home-page "https://bioconductor.org/packages/affycomp/")
1051 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1053 "The package contains functions that can be used to compare expression
1054 measures for Affymetrix Oligonucleotide Arrays.")
1055 (license license:gpl2+)))
1057 (define-public r-affycompatible
1059 (name "r-affycompatible")
1064 (uri (bioconductor-uri "AffyCompatible" version))
1067 "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
1069 `((upstream-name . "AffyCompatible")))
1070 (build-system r-build-system)
1072 `(("r-biostrings" ,r-biostrings)
1073 ("r-rcurl" ,r-rcurl)
1075 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1076 (synopsis "Work with Affymetrix GeneChip files")
1078 "This package provides an interface to Affymetrix chip annotation and
1079 sample attribute files. The package allows an easy way for users to download
1080 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1081 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1082 Command Console} (AGCC)-compatible sample annotation files.")
1083 (license license:artistic2.0)))
1085 (define-public r-affycontam
1087 (name "r-affycontam")
1092 (uri (bioconductor-uri "affyContam" version))
1095 "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
1096 (properties `((upstream-name . "affyContam")))
1097 (build-system r-build-system)
1099 `(("r-affy" ,r-affy)
1100 ("r-affydata" ,r-affydata)
1101 ("r-biobase" ,r-biobase)))
1102 (home-page "https://bioconductor.org/packages/affyContam/")
1103 (synopsis "Structured corruption of Affymetrix CEL file data")
1105 "Microarray quality assessment is a major concern of microarray analysts.
1106 This package provides some simple approaches to in silico creation of quality
1107 problems in CEL-level data to help evaluate performance of quality metrics.")
1108 (license license:artistic2.0)))
1110 (define-public r-affycoretools
1112 (name "r-affycoretools")
1117 (uri (bioconductor-uri "affycoretools" version))
1120 "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s"))))
1121 (properties `((upstream-name . "affycoretools")))
1122 (build-system r-build-system)
1124 `(("r-affy" ,r-affy)
1125 ("r-annotationdbi" ,r-annotationdbi)
1126 ("r-biobase" ,r-biobase)
1127 ("r-biocgenerics" ,r-biocgenerics)
1129 ("r-edger" ,r-edger)
1130 ("r-gcrma" ,r-gcrma)
1131 ("r-ggplot2" ,r-ggplot2)
1132 ("r-gostats" ,r-gostats)
1133 ("r-gplots" ,r-gplots)
1134 ("r-hwriter" ,r-hwriter)
1135 ("r-lattice" ,r-lattice)
1136 ("r-limma" ,r-limma)
1137 ("r-oligoclasses" ,r-oligoclasses)
1138 ("r-reportingtools" ,r-reportingtools)
1139 ("r-rsqlite" ,r-rsqlite)
1140 ("r-s4vectors" ,r-s4vectors)
1141 ("r-xtable" ,r-xtable)))
1142 (home-page "https://bioconductor.org/packages/affycoretools/")
1143 (synopsis "Functions for analyses with Affymetrix GeneChips")
1145 "This package provides various wrapper functions that have been written
1146 to streamline the more common analyses that a Biostatistician might see.")
1147 (license license:artistic2.0)))
1149 (define-public r-affxparser
1151 (name "r-affxparser")
1156 (uri (bioconductor-uri "affxparser" version))
1159 "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33"))))
1160 (properties `((upstream-name . "affxparser")))
1161 (build-system r-build-system)
1162 (home-page "https://github.com/HenrikBengtsson/affxparser")
1163 (synopsis "Affymetrix File Parsing SDK")
1165 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1166 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1167 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1168 are supported. Currently, there are methods for reading @dfn{chip definition
1169 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1170 either in full or in part. For example, probe signals from a few probesets
1171 can be extracted very quickly from a set of CEL files into a convenient list
1173 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1175 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1177 (define-public r-annotate
1184 (uri (bioconductor-uri "annotate" version))
1187 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
1188 (build-system r-build-system)
1190 `(("r-annotationdbi" ,r-annotationdbi)
1191 ("r-biobase" ,r-biobase)
1192 ("r-biocgenerics" ,r-biocgenerics)
1194 ("r-rcurl" ,r-rcurl)
1196 ("r-xtable" ,r-xtable)))
1198 "https://bioconductor.org/packages/annotate")
1199 (synopsis "Annotation for microarrays")
1200 (description "This package provides R environments for the annotation of
1202 (license license:artistic2.0)))
1204 (define-public r-hpar
1211 (uri (bioconductor-uri "hpar" version))
1214 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
1215 (build-system r-build-system)
1216 (home-page "https://bioconductor.org/packages/hpar/")
1217 (synopsis "Human Protein Atlas in R")
1218 (description "This package provides a simple interface to and data from
1219 the Human Protein Atlas project.")
1220 (license license:artistic2.0)))
1222 (define-public r-regioner
1229 (uri (bioconductor-uri "regioneR" version))
1232 "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
1233 (properties `((upstream-name . "regioneR")))
1234 (build-system r-build-system)
1236 `(("r-biostrings" ,r-biostrings)
1237 ("r-bsgenome" ,r-bsgenome)
1238 ("r-genomeinfodb" ,r-genomeinfodb)
1239 ("r-genomicranges" ,r-genomicranges)
1240 ("r-iranges" ,r-iranges)
1241 ("r-memoise" ,r-memoise)
1242 ("r-rtracklayer" ,r-rtracklayer)
1243 ("r-s4vectors" ,r-s4vectors)))
1244 (home-page "https://bioconductor.org/packages/regioneR/")
1245 (synopsis "Association analysis of genomic regions")
1246 (description "This package offers a statistical framework based on
1247 customizable permutation tests to assess the association between genomic
1248 region sets and other genomic features.")
1249 (license license:artistic2.0)))
1251 (define-public r-reportingtools
1253 (name "r-reportingtools")
1258 (uri (bioconductor-uri "ReportingTools" version))
1261 "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
1263 `((upstream-name . "ReportingTools")))
1264 (build-system r-build-system)
1266 `(("r-annotate" ,r-annotate)
1267 ("r-annotationdbi" ,r-annotationdbi)
1268 ("r-biobase" ,r-biobase)
1269 ("r-biocgenerics" ,r-biocgenerics)
1270 ("r-category" ,r-category)
1271 ("r-deseq2" ,r-deseq2)
1272 ("r-edger" ,r-edger)
1273 ("r-ggbio" ,r-ggbio)
1274 ("r-ggplot2" ,r-ggplot2)
1275 ("r-gostats" ,r-gostats)
1276 ("r-gseabase" ,r-gseabase)
1277 ("r-hwriter" ,r-hwriter)
1278 ("r-iranges" ,r-iranges)
1279 ("r-knitr" ,r-knitr)
1280 ("r-lattice" ,r-lattice)
1281 ("r-limma" ,r-limma)
1282 ("r-pfam-db" ,r-pfam-db)
1283 ("r-r-utils" ,r-r-utils)
1285 (home-page "https://bioconductor.org/packages/ReportingTools/")
1286 (synopsis "Tools for making reports in various formats")
1288 "The ReportingTools package enables users to easily display reports of
1289 analysis results generated from sources such as microarray and sequencing
1290 data. The package allows users to create HTML pages that may be viewed on a
1291 web browser, or in other formats. Users can generate tables with sortable and
1292 filterable columns, make and display plots, and link table entries to other
1293 data sources such as NCBI or larger plots within the HTML page. Using the
1294 package, users can also produce a table of contents page to link various
1295 reports together for a particular project that can be viewed in a web
1297 (license license:artistic2.0)))
1299 (define-public r-geneplotter
1301 (name "r-geneplotter")
1306 (uri (bioconductor-uri "geneplotter" version))
1309 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1310 (build-system r-build-system)
1312 `(("r-annotate" ,r-annotate)
1313 ("r-annotationdbi" ,r-annotationdbi)
1314 ("r-biobase" ,r-biobase)
1315 ("r-biocgenerics" ,r-biocgenerics)
1316 ("r-lattice" ,r-lattice)
1317 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1318 (home-page "https://bioconductor.org/packages/geneplotter")
1319 (synopsis "Graphics functions for genomic data")
1321 "This package provides functions for plotting genomic data.")
1322 (license license:artistic2.0)))
1324 (define-public r-oligoclasses
1326 (name "r-oligoclasses")
1331 (uri (bioconductor-uri "oligoClasses" version))
1334 "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72"))))
1335 (properties `((upstream-name . "oligoClasses")))
1336 (build-system r-build-system)
1338 `(("r-affyio" ,r-affyio)
1339 ("r-biobase" ,r-biobase)
1340 ("r-biocgenerics" ,r-biocgenerics)
1341 ("r-biocmanager" ,r-biocmanager)
1342 ("r-biostrings" ,r-biostrings)
1345 ("r-foreach" ,r-foreach)
1346 ("r-genomicranges" ,r-genomicranges)
1347 ("r-iranges" ,r-iranges)
1348 ("r-rsqlite" ,r-rsqlite)
1349 ("r-s4vectors" ,r-s4vectors)
1350 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1351 (home-page "https://bioconductor.org/packages/oligoClasses/")
1352 (synopsis "Classes for high-throughput arrays")
1354 "This package contains class definitions, validity checks, and
1355 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1357 (license license:gpl2+)))
1359 (define-public r-oligo
1366 (uri (bioconductor-uri "oligo" version))
1369 "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df"))))
1370 (properties `((upstream-name . "oligo")))
1371 (build-system r-build-system)
1372 (inputs `(("zlib" ,zlib)))
1374 `(("r-affxparser" ,r-affxparser)
1375 ("r-affyio" ,r-affyio)
1376 ("r-biobase" ,r-biobase)
1377 ("r-biocgenerics" ,r-biocgenerics)
1378 ("r-biostrings" ,r-biostrings)
1381 ("r-oligoclasses" ,r-oligoclasses)
1382 ("r-preprocesscore" ,r-preprocesscore)
1383 ("r-rsqlite" ,r-rsqlite)
1384 ("r-zlibbioc" ,r-zlibbioc)))
1385 (home-page "https://bioconductor.org/packages/oligo/")
1386 (synopsis "Preprocessing tools for oligonucleotide arrays")
1388 "This package provides a package to analyze oligonucleotide
1389 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1390 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1391 (license license:lgpl2.0+)))
1393 (define-public r-qvalue
1400 (uri (bioconductor-uri "qvalue" version))
1403 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1404 (build-system r-build-system)
1406 `(("r-ggplot2" ,r-ggplot2)
1407 ("r-reshape2" ,r-reshape2)))
1408 (home-page "http://github.com/jdstorey/qvalue")
1409 (synopsis "Q-value estimation for false discovery rate control")
1411 "This package takes a list of p-values resulting from the simultaneous
1412 testing of many hypotheses and estimates their q-values and local @dfn{false
1413 discovery rate} (FDR) values. The q-value of a test measures the proportion
1414 of false positives incurred when that particular test is called significant.
1415 The local FDR measures the posterior probability the null hypothesis is true
1416 given the test's p-value. Various plots are automatically generated, allowing
1417 one to make sensible significance cut-offs. The software can be applied to
1418 problems in genomics, brain imaging, astrophysics, and data mining.")
1419 ;; Any version of the LGPL.
1420 (license license:lgpl3+)))
1422 (define-public r-diffbind
1429 (uri (bioconductor-uri "DiffBind" version))
1432 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1433 (properties `((upstream-name . "DiffBind")))
1434 (build-system r-build-system)
1438 `(("r-amap" ,r-amap)
1439 ("r-biocparallel" ,r-biocparallel)
1440 ("r-deseq2" ,r-deseq2)
1441 ("r-dplyr" ,r-dplyr)
1442 ("r-edger" ,r-edger)
1443 ("r-genomicalignments" ,r-genomicalignments)
1444 ("r-genomicranges" ,r-genomicranges)
1445 ("r-ggplot2" ,r-ggplot2)
1446 ("r-ggrepel" ,r-ggrepel)
1447 ("r-gplots" ,r-gplots)
1448 ("r-iranges" ,r-iranges)
1449 ("r-lattice" ,r-lattice)
1450 ("r-limma" ,r-limma)
1451 ("r-locfit" ,r-locfit)
1452 ("r-rcolorbrewer" , r-rcolorbrewer)
1454 ("r-rhtslib" ,r-rhtslib)
1455 ("r-rsamtools" ,r-rsamtools)
1456 ("r-s4vectors" ,r-s4vectors)
1457 ("r-summarizedexperiment" ,r-summarizedexperiment)
1458 ("r-systempiper" ,r-systempiper)))
1459 (home-page "http://bioconductor.org/packages/DiffBind")
1460 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1462 "This package computes differentially bound sites from multiple
1463 ChIP-seq experiments using affinity (quantitative) data. Also enables
1464 occupancy (overlap) analysis and plotting functions.")
1465 (license license:artistic2.0)))
1467 (define-public r-ripseeker
1469 (name "r-ripseeker")
1474 (uri (bioconductor-uri "RIPSeeker" version))
1477 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1478 (properties `((upstream-name . "RIPSeeker")))
1479 (build-system r-build-system)
1481 `(("r-s4vectors" ,r-s4vectors)
1482 ("r-iranges" ,r-iranges)
1483 ("r-genomicranges" ,r-genomicranges)
1484 ("r-summarizedexperiment" ,r-summarizedexperiment)
1485 ("r-rsamtools" ,r-rsamtools)
1486 ("r-genomicalignments" ,r-genomicalignments)
1487 ("r-rtracklayer" ,r-rtracklayer)))
1488 (home-page "http://bioconductor.org/packages/RIPSeeker")
1490 "Identifying protein-associated transcripts from RIP-seq experiments")
1492 "This package infers and discriminates RIP peaks from RIP-seq alignments
1493 using two-state HMM with negative binomial emission probability. While
1494 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1495 a suite of bioinformatics tools integrated within this self-contained software
1496 package comprehensively addressing issues ranging from post-alignments
1497 processing to visualization and annotation.")
1498 (license license:gpl2)))
1500 (define-public r-multtest
1507 (uri (bioconductor-uri "multtest" version))
1510 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1511 (build-system r-build-system)
1513 `(("r-survival" ,r-survival)
1514 ("r-biocgenerics" ,r-biocgenerics)
1515 ("r-biobase" ,r-biobase)
1516 ("r-mass" ,r-mass)))
1517 (home-page "http://bioconductor.org/packages/multtest")
1518 (synopsis "Resampling-based multiple hypothesis testing")
1520 "This package can do non-parametric bootstrap and permutation
1521 resampling-based multiple testing procedures (including empirical Bayes
1522 methods) for controlling the family-wise error rate (FWER), generalized
1523 family-wise error rate (gFWER), tail probability of the proportion of
1524 false positives (TPPFP), and false discovery rate (FDR). Several choices
1525 of bootstrap-based null distribution are implemented (centered, centered
1526 and scaled, quantile-transformed). Single-step and step-wise methods are
1527 available. Tests based on a variety of T- and F-statistics (including
1528 T-statistics based on regression parameters from linear and survival models
1529 as well as those based on correlation parameters) are included. When probing
1530 hypotheses with T-statistics, users may also select a potentially faster null
1531 distribution which is multivariate normal with mean zero and variance
1532 covariance matrix derived from the vector influence function. Results are
1533 reported in terms of adjusted P-values, confidence regions and test statistic
1534 cutoffs. The procedures are directly applicable to identifying differentially
1535 expressed genes in DNA microarray experiments.")
1536 (license license:lgpl3)))
1538 (define-public r-graph
1544 (uri (bioconductor-uri "graph" version))
1547 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1548 (build-system r-build-system)
1550 `(("r-biocgenerics" ,r-biocgenerics)))
1551 (home-page "https://bioconductor.org/packages/graph")
1552 (synopsis "Handle graph data structures in R")
1554 "This package implements some simple graph handling capabilities for R.")
1555 (license license:artistic2.0)))
1557 (define-public r-codedepends
1559 (name "r-codedepends")
1564 (uri (cran-uri "CodeDepends" version))
1567 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1568 (properties `((upstream-name . "CodeDepends")))
1569 (build-system r-build-system)
1571 `(("r-codetools" ,r-codetools)
1572 ("r-graph" ,r-graph)
1574 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1575 (synopsis "Analysis of R code for reproducible research and code comprehension")
1577 "This package provides tools for analyzing R expressions or blocks of
1578 code and determining the dependencies between them. It focuses on R scripts,
1579 but can be used on the bodies of functions. There are many facilities
1580 including the ability to summarize or get a high-level view of code,
1581 determining dependencies between variables, code improvement suggestions.")
1582 ;; Any version of the GPL
1583 (license (list license:gpl2+ license:gpl3+))))
1585 (define-public r-chippeakanno
1587 (name "r-chippeakanno")
1592 (uri (bioconductor-uri "ChIPpeakAnno" version))
1595 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1596 (properties `((upstream-name . "ChIPpeakAnno")))
1597 (build-system r-build-system)
1599 `(("r-annotationdbi" ,r-annotationdbi)
1600 ("r-biobase" ,r-biobase)
1601 ("r-biocgenerics" ,r-biocgenerics)
1602 ("r-biocmanager" ,r-biocmanager)
1603 ("r-biomart" ,r-biomart)
1604 ("r-biostrings" ,r-biostrings)
1605 ("r-bsgenome" ,r-bsgenome)
1607 ("r-delayedarray" ,r-delayedarray)
1608 ("r-ensembldb" ,r-ensembldb)
1609 ("r-genomeinfodb" ,r-genomeinfodb)
1610 ("r-genomicalignments" ,r-genomicalignments)
1611 ("r-genomicfeatures" ,r-genomicfeatures)
1612 ("r-genomicranges" ,r-genomicranges)
1613 ("r-go-db" ,r-go-db)
1614 ("r-graph" ,r-graph)
1616 ("r-iranges" ,r-iranges)
1617 ("r-limma" ,r-limma)
1618 ("r-matrixstats" ,r-matrixstats)
1619 ("r-multtest" ,r-multtest)
1621 ("r-regioner" ,r-regioner)
1622 ("r-rsamtools" ,r-rsamtools)
1623 ("r-rtracklayer" ,r-rtracklayer)
1624 ("r-s4vectors" ,r-s4vectors)
1625 ("r-seqinr" ,r-seqinr)
1626 ("r-summarizedexperiment" ,r-summarizedexperiment)
1627 ("r-venndiagram" ,r-venndiagram)))
1628 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1629 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1631 "The package includes functions to retrieve the sequences around the peak,
1632 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1633 custom features such as most conserved elements and other transcription factor
1634 binding sites supplied by users. Starting 2.0.5, new functions have been added
1635 for finding the peaks with bi-directional promoters with summary statistics
1636 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1637 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1638 enrichedGO (addGeneIDs).")
1639 (license license:gpl2+)))
1641 (define-public r-marray
1647 (uri (bioconductor-uri "marray" version))
1649 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1650 (build-system r-build-system)
1652 `(("r-limma" ,r-limma)))
1653 (home-page "http://bioconductor.org/packages/marray")
1654 (synopsis "Exploratory analysis for two-color spotted microarray data")
1655 (description "This package contains class definitions for two-color spotted
1656 microarray data. It also includes functions for data input, diagnostic plots,
1657 normalization and quality checking.")
1658 (license license:lgpl2.0+)))
1660 (define-public r-cghbase
1666 (uri (bioconductor-uri "CGHbase" version))
1668 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1669 (properties `((upstream-name . "CGHbase")))
1670 (build-system r-build-system)
1672 `(("r-biobase" ,r-biobase)
1673 ("r-marray" ,r-marray)))
1674 (home-page "http://bioconductor.org/packages/CGHbase")
1675 (synopsis "Base functions and classes for arrayCGH data analysis")
1676 (description "This package contains functions and classes that are needed by
1677 the @code{arrayCGH} packages.")
1678 (license license:gpl2+)))
1680 (define-public r-cghcall
1686 (uri (bioconductor-uri "CGHcall" version))
1688 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1689 (properties `((upstream-name . "CGHcall")))
1690 (build-system r-build-system)
1692 `(("r-biobase" ,r-biobase)
1693 ("r-cghbase" ,r-cghbase)
1694 ("r-impute" ,r-impute)
1695 ("r-dnacopy" ,r-dnacopy)
1696 ("r-snowfall" ,r-snowfall)))
1697 (home-page "http://bioconductor.org/packages/CGHcall")
1698 (synopsis "Base functions and classes for arrayCGH data analysis")
1699 (description "This package contains functions and classes that are needed by
1700 @code{arrayCGH} packages.")
1701 (license license:gpl2+)))
1703 (define-public r-qdnaseq
1709 (uri (bioconductor-uri "QDNAseq" version))
1711 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1712 (properties `((upstream-name . "QDNAseq")))
1713 (build-system r-build-system)
1715 `(("r-biobase" ,r-biobase)
1716 ("r-biocparallel" ,r-biocparallel)
1717 ("r-cghbase" ,r-cghbase)
1718 ("r-cghcall" ,r-cghcall)
1719 ("r-dnacopy" ,r-dnacopy)
1720 ("r-genomicranges" ,r-genomicranges)
1721 ("r-iranges" ,r-iranges)
1722 ("r-matrixstats" ,r-matrixstats)
1723 ("r-r-utils" ,r-r-utils)
1724 ("r-rsamtools" ,r-rsamtools)))
1725 (home-page "http://bioconductor.org/packages/QDNAseq")
1726 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1727 (description "The genome is divided into non-overlapping fixed-sized bins,
1728 number of sequence reads in each counted, adjusted with a simultaneous
1729 two-dimensional loess correction for sequence mappability and GC content, and
1730 filtered to remove spurious regions in the genome. Downstream steps of
1731 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1733 (license license:gpl2+)))
1735 (define-public r-bayseq
1742 (uri (bioconductor-uri "baySeq" version))
1745 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1746 (properties `((upstream-name . "baySeq")))
1747 (build-system r-build-system)
1749 `(("r-abind" ,r-abind)
1750 ("r-edger" ,r-edger)
1751 ("r-genomicranges" ,r-genomicranges)))
1752 (home-page "https://bioconductor.org/packages/baySeq/")
1753 (synopsis "Bayesian analysis of differential expression patterns in count data")
1755 "This package identifies differential expression in high-throughput count
1756 data, such as that derived from next-generation sequencing machines,
1757 calculating estimated posterior likelihoods of differential expression (or
1758 more complex hypotheses) via empirical Bayesian methods.")
1759 (license license:gpl3)))
1761 (define-public r-chipcomp
1768 (uri (bioconductor-uri "ChIPComp" version))
1771 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1772 (properties `((upstream-name . "ChIPComp")))
1773 (build-system r-build-system)
1775 `(("r-biocgenerics" ,r-biocgenerics)
1776 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1777 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1778 ("r-genomeinfodb" ,r-genomeinfodb)
1779 ("r-genomicranges" ,r-genomicranges)
1780 ("r-iranges" ,r-iranges)
1781 ("r-limma" ,r-limma)
1782 ("r-rsamtools" ,r-rsamtools)
1783 ("r-rtracklayer" ,r-rtracklayer)
1784 ("r-s4vectors" ,r-s4vectors)))
1785 (home-page "https://bioconductor.org/packages/ChIPComp")
1786 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1788 "ChIPComp implements a statistical method for quantitative comparison of
1789 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1790 sites across multiple conditions considering matching control in ChIP-seq
1792 ;; Any version of the GPL.
1793 (license license:gpl3+)))
1795 (define-public r-riboprofiling
1797 (name "r-riboprofiling")
1802 (uri (bioconductor-uri "RiboProfiling" version))
1805 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1806 (properties `((upstream-name . "RiboProfiling")))
1807 (build-system r-build-system)
1809 `(("r-biocgenerics" ,r-biocgenerics)
1810 ("r-biostrings" ,r-biostrings)
1811 ("r-data-table" ,r-data-table)
1812 ("r-genomeinfodb" ,r-genomeinfodb)
1813 ("r-genomicalignments" ,r-genomicalignments)
1814 ("r-genomicfeatures" ,r-genomicfeatures)
1815 ("r-genomicranges" ,r-genomicranges)
1816 ("r-ggbio" ,r-ggbio)
1817 ("r-ggplot2" ,r-ggplot2)
1818 ("r-iranges" ,r-iranges)
1820 ("r-reshape2" ,r-reshape2)
1821 ("r-rsamtools" ,r-rsamtools)
1822 ("r-rtracklayer" ,r-rtracklayer)
1823 ("r-s4vectors" ,r-s4vectors)
1824 ("r-sqldf" ,r-sqldf)))
1825 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1826 (synopsis "Ribosome profiling data analysis")
1827 (description "Starting with a BAM file, this package provides the
1828 necessary functions for quality assessment, read start position recalibration,
1829 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1830 of count data: pairs, log fold-change, codon frequency and coverage
1831 assessment, principal component analysis on codon coverage.")
1832 (license license:gpl3)))
1834 (define-public r-riboseqr
1841 (uri (bioconductor-uri "riboSeqR" version))
1844 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1845 (properties `((upstream-name . "riboSeqR")))
1846 (build-system r-build-system)
1848 `(("r-abind" ,r-abind)
1849 ("r-bayseq" ,r-bayseq)
1850 ("r-genomeinfodb" ,r-genomeinfodb)
1851 ("r-genomicranges" ,r-genomicranges)
1852 ("r-iranges" ,r-iranges)
1853 ("r-rsamtools" ,r-rsamtools)
1854 ("r-seqlogo" ,r-seqlogo)))
1855 (home-page "https://bioconductor.org/packages/riboSeqR/")
1856 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1858 "This package provides plotting functions, frameshift detection and
1859 parsing of genetic sequencing data from ribosome profiling experiments.")
1860 (license license:gpl3)))
1862 (define-public r-interactionset
1864 (name "r-interactionset")
1869 (uri (bioconductor-uri "InteractionSet" version))
1872 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1874 `((upstream-name . "InteractionSet")))
1875 (build-system r-build-system)
1877 `(("r-biocgenerics" ,r-biocgenerics)
1878 ("r-genomeinfodb" ,r-genomeinfodb)
1879 ("r-genomicranges" ,r-genomicranges)
1880 ("r-iranges" ,r-iranges)
1881 ("r-matrix" ,r-matrix)
1883 ("r-s4vectors" ,r-s4vectors)
1884 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1885 (home-page "https://bioconductor.org/packages/InteractionSet")
1886 (synopsis "Base classes for storing genomic interaction data")
1888 "This package provides the @code{GInteractions},
1889 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1890 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1892 (license license:gpl3)))
1894 (define-public r-genomicinteractions
1896 (name "r-genomicinteractions")
1901 (uri (bioconductor-uri "GenomicInteractions" version))
1904 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1906 `((upstream-name . "GenomicInteractions")))
1907 (build-system r-build-system)
1909 `(("r-biobase" ,r-biobase)
1910 ("r-biocgenerics" ,r-biocgenerics)
1911 ("r-data-table" ,r-data-table)
1912 ("r-dplyr" ,r-dplyr)
1913 ("r-genomeinfodb" ,r-genomeinfodb)
1914 ("r-genomicranges" ,r-genomicranges)
1915 ("r-ggplot2" ,r-ggplot2)
1916 ("r-gridextra" ,r-gridextra)
1918 ("r-igraph" ,r-igraph)
1919 ("r-interactionset" ,r-interactionset)
1920 ("r-iranges" ,r-iranges)
1921 ("r-rsamtools" ,r-rsamtools)
1922 ("r-rtracklayer" ,r-rtracklayer)
1923 ("r-s4vectors" ,r-s4vectors)
1924 ("r-stringr" ,r-stringr)))
1925 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1926 (synopsis "R package for handling genomic interaction data")
1928 "This R package provides tools for handling genomic interaction data,
1929 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1930 information and producing various plots and statistics.")
1931 (license license:gpl3)))
1933 (define-public r-ctc
1940 (uri (bioconductor-uri "ctc" version))
1943 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1944 (build-system r-build-system)
1945 (propagated-inputs `(("r-amap" ,r-amap)))
1946 (home-page "https://bioconductor.org/packages/ctc/")
1947 (synopsis "Cluster and tree conversion")
1949 "This package provides tools for exporting and importing classification
1950 trees and clusters to other programs.")
1951 (license license:gpl2)))
1953 (define-public r-goseq
1960 (uri (bioconductor-uri "goseq" version))
1963 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1964 (build-system r-build-system)
1966 `(("r-annotationdbi" ,r-annotationdbi)
1967 ("r-biasedurn" ,r-biasedurn)
1968 ("r-biocgenerics" ,r-biocgenerics)
1969 ("r-genelendatabase" ,r-genelendatabase)
1970 ("r-go-db" ,r-go-db)
1971 ("r-mgcv" ,r-mgcv)))
1972 (home-page "https://bioconductor.org/packages/goseq/")
1973 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1975 "This package provides tools to detect Gene Ontology and/or other user
1976 defined categories which are over/under represented in RNA-seq data.")
1977 (license license:lgpl2.0+)))
1979 (define-public r-glimma
1986 (uri (bioconductor-uri "Glimma" version))
1989 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1990 (properties `((upstream-name . "Glimma")))
1991 (build-system r-build-system)
1993 `(("r-edger" ,r-edger)
1994 ("r-jsonlite" ,r-jsonlite)
1995 ("r-s4vectors" ,r-s4vectors)))
1996 (home-page "https://github.com/Shians/Glimma")
1997 (synopsis "Interactive HTML graphics")
1999 "This package generates interactive visualisations for analysis of
2000 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2001 HTML page. The interactions are built on top of the popular static
2002 representations of analysis results in order to provide additional
2004 (license license:lgpl3)))
2006 (define-public r-rots
2013 (uri (bioconductor-uri "ROTS" version))
2016 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
2017 (properties `((upstream-name . "ROTS")))
2018 (build-system r-build-system)
2020 `(("r-biobase" ,r-biobase)
2021 ("r-rcpp" ,r-rcpp)))
2022 (home-page "https://bioconductor.org/packages/ROTS/")
2023 (synopsis "Reproducibility-Optimized Test Statistic")
2025 "This package provides tools for calculating the
2026 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2028 (license license:gpl2+)))
2030 (define-public r-plgem
2037 (uri (bioconductor-uri "plgem" version))
2040 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
2041 (build-system r-build-system)
2043 `(("r-biobase" ,r-biobase)
2044 ("r-mass" ,r-mass)))
2045 (home-page "http://www.genopolis.it")
2046 (synopsis "Detect differential expression in microarray and proteomics datasets")
2048 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2049 model the variance-versus-mean dependence that exists in a variety of
2050 genome-wide datasets, including microarray and proteomics data. The use of
2051 PLGEM has been shown to improve the detection of differentially expressed
2052 genes or proteins in these datasets.")
2053 (license license:gpl2)))
2055 (define-public r-inspect
2062 (uri (bioconductor-uri "INSPEcT" version))
2065 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
2066 (properties `((upstream-name . "INSPEcT")))
2067 (build-system r-build-system)
2069 `(("r-biobase" ,r-biobase)
2070 ("r-biocgenerics" ,r-biocgenerics)
2071 ("r-biocparallel" ,r-biocparallel)
2072 ("r-deseq2" ,r-deseq2)
2073 ("r-desolve" ,r-desolve)
2074 ("r-genomicalignments" ,r-genomicalignments)
2075 ("r-genomicfeatures" ,r-genomicfeatures)
2076 ("r-genomicranges" ,r-genomicranges)
2077 ("r-iranges" ,r-iranges)
2078 ("r-plgem" ,r-plgem)
2079 ("r-preprocesscore" ,r-preprocesscore)
2081 ("r-rootsolve" ,r-rootsolve)
2082 ("r-rsamtools" ,r-rsamtools)
2083 ("r-s4vectors" ,r-s4vectors)
2084 ("r-shiny" ,r-shiny)
2085 ("r-summarizedexperiment" ,r-summarizedexperiment)
2086 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2087 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2088 (home-page "https://bioconductor.org/packages/INSPEcT")
2089 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2091 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2092 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2093 order to evaluate synthesis, processing and degradation rates and assess via
2094 modeling the rates that determines changes in mature mRNA levels.")
2095 (license license:gpl2)))
2097 (define-public r-dnabarcodes
2099 (name "r-dnabarcodes")
2104 (uri (bioconductor-uri "DNABarcodes" version))
2107 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
2108 (properties `((upstream-name . "DNABarcodes")))
2109 (build-system r-build-system)
2112 ("r-matrix" ,r-matrix)
2113 ("r-rcpp" ,r-rcpp)))
2114 (home-page "https://bioconductor.org/packages/DNABarcodes")
2115 (synopsis "Create and analyze DNA barcodes")
2117 "This package offers tools to create DNA barcode sets capable of
2118 correcting insertion, deletion, and substitution errors. Existing barcodes
2119 can be analyzed regarding their minimal, maximal and average distances between
2120 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2121 demultiplexed, i.e. assigned to their original reference barcode.")
2122 (license license:gpl2)))
2124 (define-public r-ruvseq
2131 (uri (bioconductor-uri "RUVSeq" version))
2134 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
2135 (properties `((upstream-name . "RUVSeq")))
2136 (build-system r-build-system)
2138 `(("r-biobase" ,r-biobase)
2139 ("r-edaseq" ,r-edaseq)
2140 ("r-edger" ,r-edger)
2141 ("r-mass" ,r-mass)))
2142 (home-page "https://github.com/drisso/RUVSeq")
2143 (synopsis "Remove unwanted variation from RNA-Seq data")
2145 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2146 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2148 (license license:artistic2.0)))
2150 (define-public r-biocneighbors
2152 (name "r-biocneighbors")
2157 (uri (bioconductor-uri "BiocNeighbors" version))
2160 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
2161 (properties `((upstream-name . "BiocNeighbors")))
2162 (build-system r-build-system)
2164 `(("r-biocgenerics" ,r-biocgenerics)
2165 ("r-biocparallel" ,r-biocparallel)
2167 ("r-rcppannoy" ,r-rcppannoy)
2168 ("r-rcpphnsw" ,r-rcpphnsw)
2169 ("r-s4vectors" ,r-s4vectors)))
2170 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2171 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2173 "This package implements exact and approximate methods for nearest
2174 neighbor detection, in a framework that allows them to be easily switched
2175 within Bioconductor packages or workflows. The exact algorithm is implemented
2176 using pre-clustering with the k-means algorithm. Functions are also provided
2177 to search for all neighbors within a given distance. Parallelization is
2178 achieved for all methods using the BiocParallel framework.")
2179 (license license:gpl3)))
2181 (define-public r-biocsingular
2183 (name "r-biocsingular")
2188 (uri (bioconductor-uri "BiocSingular" version))
2191 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
2192 (properties `((upstream-name . "BiocSingular")))
2193 (build-system r-build-system)
2195 `(("r-beachmat" ,r-beachmat)
2196 ("r-biocgenerics" ,r-biocgenerics)
2197 ("r-biocparallel" ,r-biocparallel)
2198 ("r-delayedarray" ,r-delayedarray)
2199 ("r-irlba" ,r-irlba)
2200 ("r-matrix" ,r-matrix)
2203 ("r-s4vectors" ,r-s4vectors)))
2204 (home-page "https://github.com/LTLA/BiocSingular")
2205 (synopsis "Singular value decomposition for Bioconductor packages")
2207 "This package implements exact and approximate methods for singular value
2208 decomposition and principal components analysis, in a framework that allows
2209 them to be easily switched within Bioconductor packages or workflows. Where
2210 possible, parallelization is achieved using the BiocParallel framework.")
2211 (license license:gpl3)))
2213 (define-public r-destiny
2220 (uri (bioconductor-uri "destiny" version))
2223 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
2224 (build-system r-build-system)
2226 `(("r-biobase" ,r-biobase)
2227 ("r-biocgenerics" ,r-biocgenerics)
2228 ("r-ggplot2" ,r-ggplot2)
2229 ("r-ggthemes" ,r-ggthemes)
2230 ("r-igraph" ,r-igraph)
2231 ("r-matrix" ,r-matrix)
2232 ("r-proxy" ,r-proxy)
2234 ("r-rcppeigen" ,r-rcppeigen)
2235 ("r-scales" ,r-scales)
2236 ("r-scatterplot3d" ,r-scatterplot3d)
2237 ("r-smoother" ,r-smoother)
2238 ("r-summarizedexperiment" ,r-summarizedexperiment)
2240 (home-page "https://bioconductor.org/packages/destiny/")
2241 (synopsis "Create and plot diffusion maps")
2242 (description "This package provides tools to create and plot diffusion
2244 ;; Any version of the GPL
2245 (license license:gpl3+)))
2247 (define-public r-savr
2254 (uri (bioconductor-uri "savR" version))
2257 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
2258 (properties `((upstream-name . "savR")))
2259 (build-system r-build-system)
2261 `(("r-ggplot2" ,r-ggplot2)
2262 ("r-gridextra" ,r-gridextra)
2263 ("r-reshape2" ,r-reshape2)
2264 ("r-scales" ,r-scales)
2266 (home-page "https://github.com/bcalder/savR")
2267 (synopsis "Parse and analyze Illumina SAV files")
2269 "This package provides tools to parse Illumina Sequence Analysis
2270 Viewer (SAV) files, access data, and generate QC plots.")
2271 (license license:agpl3+)))
2273 (define-public r-chipexoqual
2275 (name "r-chipexoqual")
2280 (uri (bioconductor-uri "ChIPexoQual" version))
2283 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
2284 (properties `((upstream-name . "ChIPexoQual")))
2285 (build-system r-build-system)
2287 `(("r-biocparallel" ,r-biocparallel)
2288 ("r-biovizbase" ,r-biovizbase)
2289 ("r-broom" ,r-broom)
2290 ("r-data-table" ,r-data-table)
2291 ("r-dplyr" ,r-dplyr)
2292 ("r-genomeinfodb" ,r-genomeinfodb)
2293 ("r-genomicalignments" ,r-genomicalignments)
2294 ("r-genomicranges" ,r-genomicranges)
2295 ("r-ggplot2" ,r-ggplot2)
2296 ("r-hexbin" ,r-hexbin)
2297 ("r-iranges" ,r-iranges)
2298 ("r-rcolorbrewer" ,r-rcolorbrewer)
2299 ("r-rmarkdown" ,r-rmarkdown)
2300 ("r-rsamtools" ,r-rsamtools)
2301 ("r-s4vectors" ,r-s4vectors)
2302 ("r-scales" ,r-scales)
2303 ("r-viridis" ,r-viridis)))
2304 (home-page "https://github.com/keleslab/ChIPexoQual")
2305 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2307 "This package provides a quality control pipeline for ChIP-exo/nexus
2309 (license license:gpl2+)))
2311 (define-public r-copynumber
2313 (name "r-copynumber")
2317 (uri (bioconductor-uri "copynumber" version))
2320 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
2321 (build-system r-build-system)
2323 `(("r-s4vectors" ,r-s4vectors)
2324 ("r-iranges" ,r-iranges)
2325 ("r-genomicranges" ,r-genomicranges)
2326 ("r-biocgenerics" ,r-biocgenerics)))
2327 (home-page "https://bioconductor.org/packages/copynumber")
2328 (synopsis "Segmentation of single- and multi-track copy number data")
2330 "This package segments single- and multi-track copy number data by a
2331 penalized least squares regression method.")
2332 (license license:artistic2.0)))
2334 (define-public r-dnacopy
2341 (uri (bioconductor-uri "DNAcopy" version))
2344 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2345 (properties `((upstream-name . "DNAcopy")))
2346 (build-system r-build-system)
2347 (native-inputs `(("gfortran" ,gfortran)))
2348 (home-page "https://bioconductor.org/packages/DNAcopy")
2349 (synopsis "DNA copy number data analysis")
2351 "This package implements the @dfn{circular binary segmentation} (CBS)
2352 algorithm to segment DNA copy number data and identify genomic regions with
2353 abnormal copy number.")
2354 (license license:gpl2+)))
2356 ;; This is a CRAN package, but it uncharacteristically depends on a
2357 ;; Bioconductor package.
2358 (define-public r-htscluster
2360 (name "r-htscluster")
2365 (uri (cran-uri "HTSCluster" version))
2368 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2369 (properties `((upstream-name . "HTSCluster")))
2370 (build-system r-build-system)
2372 `(("r-capushe" ,r-capushe)
2373 ("r-edger" ,r-edger)
2374 ("r-plotrix" ,r-plotrix)))
2375 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2376 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2378 "This package provides a Poisson mixture model is implemented to cluster
2379 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2380 estimation is performed using either the EM or CEM algorithm, and the slope
2381 heuristics are used for model selection (i.e., to choose the number of
2383 (license license:gpl3+)))
2385 (define-public r-deds
2392 (uri (bioconductor-uri "DEDS" version))
2395 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2396 (properties `((upstream-name . "DEDS")))
2397 (build-system r-build-system)
2398 (home-page "https://bioconductor.org/packages/DEDS/")
2399 (synopsis "Differential expression via distance summary for microarray data")
2401 "This library contains functions that calculate various statistics of
2402 differential expression for microarray data, including t statistics, fold
2403 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2404 also implements a new methodology called DEDS (Differential Expression via
2405 Distance Summary), which selects differentially expressed genes by integrating
2406 and summarizing a set of statistics using a weighted distance approach.")
2407 ;; Any version of the LGPL.
2408 (license license:lgpl3+)))
2410 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2412 (define-public r-nbpseq
2419 (uri (cran-uri "NBPSeq" version))
2422 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2423 (properties `((upstream-name . "NBPSeq")))
2424 (build-system r-build-system)
2426 `(("r-qvalue" ,r-qvalue)))
2427 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2428 (synopsis "Negative binomial models for RNA-Seq data")
2430 "This package provides negative binomial models for two-group comparisons
2431 and regression inferences from RNA-sequencing data.")
2432 (license license:gpl2)))
2434 (define-public r-ebseq
2441 (uri (bioconductor-uri "EBSeq" version))
2444 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2445 (properties `((upstream-name . "EBSeq")))
2446 (build-system r-build-system)
2448 `(("r-blockmodeling" ,r-blockmodeling)
2449 ("r-gplots" ,r-gplots)
2450 ("r-testthat" ,r-testthat)))
2451 (home-page "https://bioconductor.org/packages/EBSeq")
2452 (synopsis "Differential expression analysis of RNA-seq data")
2454 "This package provides tools for differential expression analysis at both
2455 gene and isoform level using RNA-seq data")
2456 (license license:artistic2.0)))
2458 (define-public r-lpsymphony
2460 (name "r-lpsymphony")
2465 (uri (bioconductor-uri "lpsymphony" version))
2468 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2469 (build-system r-build-system)
2471 `(("gfortran" ,gfortran)
2474 `(("pkg-config" ,pkg-config)))
2475 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2476 (synopsis "Symphony integer linear programming solver in R")
2478 "This package was derived from Rsymphony. The package provides an R
2479 interface to SYMPHONY, a linear programming solver written in C++. The main
2480 difference between this package and Rsymphony is that it includes the solver
2481 source code, while Rsymphony expects to find header and library files on the
2482 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2483 to install interface to SYMPHONY.")
2484 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2485 ;; lpsimphony is released under the same terms.
2486 (license license:epl1.0)))
2488 (define-public r-ihw
2495 (uri (bioconductor-uri "IHW" version))
2498 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2499 (properties `((upstream-name . "IHW")))
2500 (build-system r-build-system)
2502 `(("r-biocgenerics" ,r-biocgenerics)
2503 ("r-fdrtool" ,r-fdrtool)
2504 ("r-lpsymphony" ,r-lpsymphony)
2505 ("r-slam" ,r-slam)))
2506 (home-page "https://bioconductor.org/packages/IHW")
2507 (synopsis "Independent hypothesis weighting")
2509 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2510 procedure that increases power compared to the method of Benjamini and
2511 Hochberg by assigning data-driven weights to each hypothesis. The input to
2512 IHW is a two-column table of p-values and covariates. The covariate can be
2513 any continuous-valued or categorical variable that is thought to be
2514 informative on the statistical properties of each hypothesis test, while it is
2515 independent of the p-value under the null hypothesis.")
2516 (license license:artistic2.0)))
2518 (define-public r-icobra
2525 (uri (bioconductor-uri "iCOBRA" version))
2528 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2529 (properties `((upstream-name . "iCOBRA")))
2530 (build-system r-build-system)
2532 `(("r-dplyr" ,r-dplyr)
2534 ("r-ggplot2" ,r-ggplot2)
2535 ("r-limma" ,r-limma)
2536 ("r-reshape2" ,r-reshape2)
2538 ("r-scales" ,r-scales)
2539 ("r-shiny" ,r-shiny)
2540 ("r-shinybs" ,r-shinybs)
2541 ("r-shinydashboard" ,r-shinydashboard)
2542 ("r-upsetr" ,r-upsetr)))
2543 (home-page "https://bioconductor.org/packages/iCOBRA")
2544 (synopsis "Comparison and visualization of ranking and assignment methods")
2546 "This package provides functions for calculation and visualization of
2547 performance metrics for evaluation of ranking and binary
2548 classification (assignment) methods. It also contains a Shiny application for
2549 interactive exploration of results.")
2550 (license license:gpl2+)))
2552 (define-public r-mast
2559 (uri (bioconductor-uri "MAST" version))
2562 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2563 (properties `((upstream-name . "MAST")))
2564 (build-system r-build-system)
2566 `(("r-abind" ,r-abind)
2568 ("r-biobase" ,r-biobase)
2569 ("r-biocgenerics" ,r-biocgenerics)
2570 ("r-data-table" ,r-data-table)
2571 ("r-ggplot2" ,r-ggplot2)
2573 ("r-progress" ,r-progress)
2574 ("r-reshape2" ,r-reshape2)
2575 ("r-s4vectors" ,r-s4vectors)
2576 ("r-singlecellexperiment" ,r-singlecellexperiment)
2577 ("r-stringr" ,r-stringr)
2578 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2579 (home-page "https://github.com/RGLab/MAST/")
2580 (synopsis "Model-based analysis of single cell transcriptomics")
2582 "This package provides methods and models for handling zero-inflated
2583 single cell assay data.")
2584 (license license:gpl2+)))
2586 (define-public r-monocle
2593 (uri (bioconductor-uri "monocle" version))
2596 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2597 (build-system r-build-system)
2599 `(("r-biobase" ,r-biobase)
2600 ("r-biocgenerics" ,r-biocgenerics)
2601 ("r-biocviews" ,r-biocviews)
2602 ("r-cluster" ,r-cluster)
2603 ("r-combinat" ,r-combinat)
2604 ("r-ddrtree" ,r-ddrtree)
2605 ("r-densityclust" ,r-densityclust)
2606 ("r-dplyr" ,r-dplyr)
2607 ("r-fastica" ,r-fastica)
2608 ("r-ggplot2" ,r-ggplot2)
2609 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2610 ("r-igraph" ,r-igraph)
2611 ("r-irlba" ,r-irlba)
2612 ("r-limma" ,r-limma)
2614 ("r-matrix" ,r-matrix)
2615 ("r-matrixstats" ,r-matrixstats)
2616 ("r-pheatmap" ,r-pheatmap)
2618 ("r-proxy" ,r-proxy)
2619 ("r-qlcmatrix" ,r-qlcmatrix)
2622 ("r-reshape2" ,r-reshape2)
2623 ("r-rtsne" ,r-rtsne)
2625 ("r-stringr" ,r-stringr)
2626 ("r-tibble" ,r-tibble)
2628 ("r-viridis" ,r-viridis)))
2629 (home-page "https://bioconductor.org/packages/monocle")
2630 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2632 "Monocle performs differential expression and time-series analysis for
2633 single-cell expression experiments. It orders individual cells according to
2634 progress through a biological process, without knowing ahead of time which
2635 genes define progress through that process. Monocle also performs
2636 differential expression analysis, clustering, visualization, and other useful
2637 tasks on single cell expression data. It is designed to work with RNA-Seq and
2638 qPCR data, but could be used with other types as well.")
2639 (license license:artistic2.0)))
2641 (define-public r-monocle3
2649 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2651 (file-name (git-file-name name version))
2654 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2655 (build-system r-build-system)
2657 `(("r-biobase" ,r-biobase)
2658 ("r-biocgenerics" ,r-biocgenerics)
2659 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2660 ("r-dplyr" ,r-dplyr)
2661 ("r-ggplot2" ,r-ggplot2)
2662 ("r-ggrepel" ,r-ggrepel)
2664 ("r-htmlwidgets" ,r-htmlwidgets)
2665 ("r-igraph" ,r-igraph)
2666 ("r-irlba" ,r-irlba)
2667 ("r-limma" ,r-limma)
2668 ("r-lmtest" ,r-lmtest)
2670 ("r-matrix" ,r-matrix)
2671 ("r-matrix-utils" ,r-matrix-utils)
2672 ("r-pbapply" ,r-pbapply)
2673 ("r-pbmcapply" ,r-pbmcapply)
2674 ("r-pheatmap" ,r-pheatmap)
2675 ("r-plotly" ,r-plotly)
2677 ("r-proxy" ,r-proxy)
2679 ("r-purrr" ,r-purrr)
2682 ("r-rcppparallel" ,r-rcppparallel)
2683 ("r-reshape2" ,r-reshape2)
2684 ("r-reticulate" ,r-reticulate)
2685 ("r-rhpcblasctl" ,r-rhpcblasctl)
2686 ("r-rtsne" ,r-rtsne)
2687 ("r-shiny" ,r-shiny)
2689 ("r-spdep" ,r-spdep)
2690 ("r-speedglm" ,r-speedglm)
2691 ("r-stringr" ,r-stringr)
2692 ("r-singlecellexperiment" ,r-singlecellexperiment)
2693 ("r-tibble" ,r-tibble)
2694 ("r-tidyr" ,r-tidyr)
2696 ("r-viridis" ,r-viridis)))
2697 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2698 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2700 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2701 (license license:expat)))
2703 (define-public r-noiseq
2710 (uri (bioconductor-uri "NOISeq" version))
2713 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2714 (properties `((upstream-name . "NOISeq")))
2715 (build-system r-build-system)
2717 `(("r-biobase" ,r-biobase)
2718 ("r-matrix" ,r-matrix)))
2719 (home-page "https://bioconductor.org/packages/NOISeq")
2720 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2722 "This package provides tools to support the analysis of RNA-seq
2723 expression data or other similar kind of data. It provides exploratory plots
2724 to evaluate saturation, count distribution, expression per chromosome, type of
2725 detected features, features length, etc. It also supports the analysis of
2726 differential expression between two experimental conditions with no parametric
2728 (license license:artistic2.0)))
2730 (define-public r-scdd
2737 (uri (bioconductor-uri "scDD" version))
2740 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2741 (properties `((upstream-name . "scDD")))
2742 (build-system r-build-system)
2745 ("r-biocparallel" ,r-biocparallel)
2746 ("r-ebseq" ,r-ebseq)
2747 ("r-fields" ,r-fields)
2748 ("r-ggplot2" ,r-ggplot2)
2749 ("r-mclust" ,r-mclust)
2750 ("r-outliers" ,r-outliers)
2751 ("r-s4vectors" ,r-s4vectors)
2752 ("r-scran" ,r-scran)
2753 ("r-singlecellexperiment" ,r-singlecellexperiment)
2754 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2755 (home-page "https://github.com/kdkorthauer/scDD")
2756 (synopsis "Mixture modeling of single-cell RNA-seq data")
2758 "This package implements a method to analyze single-cell RNA-seq data
2759 utilizing flexible Dirichlet Process mixture models. Genes with differential
2760 distributions of expression are classified into several interesting patterns
2761 of differences between two conditions. The package also includes functions
2762 for simulating data with these patterns from negative binomial
2764 (license license:gpl2)))
2766 (define-public r-scone
2773 (uri (bioconductor-uri "scone" version))
2776 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2777 (build-system r-build-system)
2779 `(("r-aroma-light" ,r-aroma-light)
2780 ("r-biocparallel" ,r-biocparallel)
2782 ("r-class" ,r-class)
2783 ("r-cluster" ,r-cluster)
2784 ("r-compositions" ,r-compositions)
2785 ("r-diptest" ,r-diptest)
2786 ("r-edger" ,r-edger)
2788 ("r-gplots" ,r-gplots)
2789 ("r-hexbin" ,r-hexbin)
2790 ("r-limma" ,r-limma)
2791 ("r-matrixstats" ,r-matrixstats)
2792 ("r-mixtools" ,r-mixtools)
2793 ("r-rarpack" ,r-rarpack)
2794 ("r-rcolorbrewer" ,r-rcolorbrewer)
2795 ("r-rhdf5" ,r-rhdf5)
2796 ("r-ruvseq" ,r-ruvseq)
2797 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2798 (home-page "https://bioconductor.org/packages/scone")
2799 (synopsis "Single cell overview of normalized expression data")
2801 "SCONE is an R package for comparing and ranking the performance of
2802 different normalization schemes for single-cell RNA-seq and other
2803 high-throughput analyses.")
2804 (license license:artistic2.0)))
2806 (define-public r-geoquery
2813 (uri (bioconductor-uri "GEOquery" version))
2816 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2817 (properties `((upstream-name . "GEOquery")))
2818 (build-system r-build-system)
2820 `(("r-biobase" ,r-biobase)
2821 ("r-dplyr" ,r-dplyr)
2823 ("r-limma" ,r-limma)
2824 ("r-magrittr" ,r-magrittr)
2825 ("r-readr" ,r-readr)
2826 ("r-tidyr" ,r-tidyr)
2827 ("r-xml2" ,r-xml2)))
2828 (home-page "https://github.com/seandavi/GEOquery/")
2829 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2831 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2832 microarray data. Given the rich and varied nature of this resource, it is
2833 only natural to want to apply BioConductor tools to these data. GEOquery is
2834 the bridge between GEO and BioConductor.")
2835 (license license:gpl2)))
2837 (define-public r-illuminaio
2839 (name "r-illuminaio")
2844 (uri (bioconductor-uri "illuminaio" version))
2847 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2848 (build-system r-build-system)
2850 `(("r-base64" ,r-base64)))
2851 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2852 (synopsis "Parse Illumina microarray output files")
2854 "This package provides tools for parsing Illumina's microarray output
2855 files, including IDAT.")
2856 (license license:gpl2)))
2858 (define-public r-siggenes
2865 (uri (bioconductor-uri "siggenes" version))
2868 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2869 (build-system r-build-system)
2871 `(("r-biobase" ,r-biobase)
2872 ("r-multtest" ,r-multtest)
2873 ("r-scrime" ,r-scrime)))
2874 (home-page "https://bioconductor.org/packages/siggenes/")
2876 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2878 "This package provides tools for the identification of differentially
2879 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2880 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2881 Bayes Analyses of Microarrays} (EBAM).")
2882 (license license:lgpl2.0+)))
2884 (define-public r-bumphunter
2886 (name "r-bumphunter")
2891 (uri (bioconductor-uri "bumphunter" version))
2894 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2895 (build-system r-build-system)
2897 `(("r-annotationdbi" ,r-annotationdbi)
2898 ("r-biocgenerics" ,r-biocgenerics)
2899 ("r-dorng" ,r-dorng)
2900 ("r-foreach" ,r-foreach)
2901 ("r-genomeinfodb" ,r-genomeinfodb)
2902 ("r-genomicfeatures" ,r-genomicfeatures)
2903 ("r-genomicranges" ,r-genomicranges)
2904 ("r-iranges" ,r-iranges)
2905 ("r-iterators" ,r-iterators)
2906 ("r-limma" ,r-limma)
2907 ("r-locfit" ,r-locfit)
2908 ("r-matrixstats" ,r-matrixstats)
2909 ("r-s4vectors" ,r-s4vectors)))
2910 (home-page "https://github.com/ririzarr/bumphunter")
2911 (synopsis "Find bumps in genomic data")
2913 "This package provides tools for finding bumps in genomic data in order
2914 to identify differentially methylated regions in epigenetic epidemiology
2916 (license license:artistic2.0)))
2918 (define-public r-minfi
2925 (uri (bioconductor-uri "minfi" version))
2928 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2929 (build-system r-build-system)
2931 `(("r-beanplot" ,r-beanplot)
2932 ("r-biobase" ,r-biobase)
2933 ("r-biocgenerics" ,r-biocgenerics)
2934 ("r-biocparallel" ,r-biocparallel)
2935 ("r-biostrings" ,r-biostrings)
2936 ("r-bumphunter" ,r-bumphunter)
2937 ("r-data-table" ,r-data-table)
2938 ("r-delayedarray" ,r-delayedarray)
2939 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2940 ("r-genefilter" ,r-genefilter)
2941 ("r-genomeinfodb" ,r-genomeinfodb)
2942 ("r-genomicranges" ,r-genomicranges)
2943 ("r-geoquery" ,r-geoquery)
2944 ("r-hdf5array" ,r-hdf5array)
2945 ("r-illuminaio" ,r-illuminaio)
2946 ("r-iranges" ,r-iranges)
2947 ("r-lattice" ,r-lattice)
2948 ("r-limma" ,r-limma)
2950 ("r-mclust" ,r-mclust)
2952 ("r-nor1mix" ,r-nor1mix)
2953 ("r-preprocesscore" ,r-preprocesscore)
2954 ("r-quadprog" ,r-quadprog)
2955 ("r-rcolorbrewer" ,r-rcolorbrewer)
2956 ("r-reshape" ,r-reshape)
2957 ("r-s4vectors" ,r-s4vectors)
2958 ("r-siggenes" ,r-siggenes)
2959 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2960 (home-page "https://github.com/hansenlab/minfi")
2961 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2963 "This package provides tools to analyze and visualize Illumina Infinium
2964 methylation arrays.")
2965 (license license:artistic2.0)))
2967 (define-public r-methylumi
2969 (name "r-methylumi")
2974 (uri (bioconductor-uri "methylumi" version))
2977 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2978 (build-system r-build-system)
2980 `(("r-annotate" ,r-annotate)
2981 ("r-annotationdbi" ,r-annotationdbi)
2982 ("r-biobase" ,r-biobase)
2983 ("r-biocgenerics" ,r-biocgenerics)
2984 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2985 ("r-genefilter" ,r-genefilter)
2986 ("r-genomeinfodb" ,r-genomeinfodb)
2987 ("r-genomicranges" ,r-genomicranges)
2988 ("r-ggplot2" ,r-ggplot2)
2989 ("r-illuminaio" ,r-illuminaio)
2990 ("r-iranges" ,r-iranges)
2991 ("r-lattice" ,r-lattice)
2992 ("r-matrixstats" ,r-matrixstats)
2993 ("r-minfi" ,r-minfi)
2994 ("r-reshape2" ,r-reshape2)
2995 ("r-s4vectors" ,r-s4vectors)
2996 ("r-scales" ,r-scales)
2997 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2998 (home-page "https://bioconductor.org/packages/methylumi")
2999 (synopsis "Handle Illumina methylation data")
3001 "This package provides classes for holding and manipulating Illumina
3002 methylation data. Based on eSet, it can contain MIAME information, sample
3003 information, feature information, and multiple matrices of data. An
3004 \"intelligent\" import function, methylumiR can read the Illumina text files
3005 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3006 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3007 background correction, and quality control features for GoldenGate, Infinium,
3008 and Infinium HD arrays are also included.")
3009 (license license:gpl2)))
3011 (define-public r-lumi
3018 (uri (bioconductor-uri "lumi" version))
3021 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
3022 (build-system r-build-system)
3024 `(("r-affy" ,r-affy)
3025 ("r-annotate" ,r-annotate)
3026 ("r-annotationdbi" ,r-annotationdbi)
3027 ("r-biobase" ,r-biobase)
3029 ("r-genomicfeatures" ,r-genomicfeatures)
3030 ("r-genomicranges" ,r-genomicranges)
3031 ("r-kernsmooth" ,r-kernsmooth)
3032 ("r-lattice" ,r-lattice)
3034 ("r-methylumi" ,r-methylumi)
3036 ("r-nleqslv" ,r-nleqslv)
3037 ("r-preprocesscore" ,r-preprocesscore)
3038 ("r-rsqlite" ,r-rsqlite)))
3039 (home-page "https://bioconductor.org/packages/lumi")
3040 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3042 "The lumi package provides an integrated solution for the Illumina
3043 microarray data analysis. It includes functions of Illumina
3044 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3045 variance stabilization, normalization and gene annotation at the probe level.
3046 It also includes the functions of processing Illumina methylation microarrays,
3047 especially Illumina Infinium methylation microarrays.")
3048 (license license:lgpl2.0+)))
3050 (define-public r-linnorm
3057 (uri (bioconductor-uri "Linnorm" version))
3060 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
3061 (properties `((upstream-name . "Linnorm")))
3062 (build-system r-build-system)
3064 `(("r-amap" ,r-amap)
3065 ("r-apcluster" ,r-apcluster)
3066 ("r-ellipse" ,r-ellipse)
3067 ("r-fastcluster" ,r-fastcluster)
3069 ("r-ggdendro" ,r-ggdendro)
3070 ("r-ggplot2" ,r-ggplot2)
3071 ("r-gmodels" ,r-gmodels)
3072 ("r-igraph" ,r-igraph)
3073 ("r-limma" ,r-limma)
3075 ("r-mclust" ,r-mclust)
3077 ("r-rcpparmadillo" ,r-rcpparmadillo)
3078 ("r-rtsne" ,r-rtsne)
3079 ("r-statmod" ,r-statmod)
3080 ("r-vegan" ,r-vegan)
3082 (home-page "http://www.jjwanglab.org/Linnorm/")
3083 (synopsis "Linear model and normality based transformation method")
3085 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3086 count data or any large scale count data. It transforms such datasets for
3087 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3088 the following pipelines are implemented:
3091 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3092 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3093 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3094 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3095 @item Differential expression analysis or differential peak detection using
3096 limma (@code{Linnorm.limma})
3097 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3098 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3099 @item Stable gene selection for scRNA-seq data; for users without or who do
3100 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3101 @item Data imputation (@code{Linnorm.DataImput}).
3104 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3105 @code{RnaXSim} function is included for simulating RNA-seq data for the
3106 evaluation of DEG analysis methods.")
3107 (license license:expat)))
3109 (define-public r-ioniser
3116 (uri (bioconductor-uri "IONiseR" version))
3119 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
3120 (properties `((upstream-name . "IONiseR")))
3121 (build-system r-build-system)
3123 `(("r-biocgenerics" ,r-biocgenerics)
3124 ("r-biocparallel" ,r-biocparallel)
3125 ("r-biostrings" ,r-biostrings)
3126 ("r-bit64" ,r-bit64)
3127 ("r-dplyr" ,r-dplyr)
3128 ("r-ggplot2" ,r-ggplot2)
3129 ("r-magrittr" ,r-magrittr)
3130 ("r-rhdf5" ,r-rhdf5)
3131 ("r-shortread" ,r-shortread)
3132 ("r-stringr" ,r-stringr)
3133 ("r-tibble" ,r-tibble)
3134 ("r-tidyr" ,r-tidyr)
3135 ("r-xvector" ,r-xvector)))
3136 (home-page "https://bioconductor.org/packages/IONiseR/")
3137 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3139 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3140 MinION data. It extracts summary statistics from a set of fast5 files and can
3141 be used either before or after base calling. In addition to standard
3142 summaries of the read-types produced, it provides a number of plots for
3143 visualising metrics relative to experiment run time or spatially over the
3144 surface of a flowcell.")
3145 (license license:expat)))
3147 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3148 (define-public r-gkmsvm
3155 (uri (cran-uri "gkmSVM" version))
3158 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3159 (properties `((upstream-name . "gkmSVM")))
3160 (build-system r-build-system)
3162 `(("r-biocgenerics" ,r-biocgenerics)
3163 ("r-biostrings" ,r-biostrings)
3164 ("r-genomeinfodb" ,r-genomeinfodb)
3165 ("r-genomicranges" ,r-genomicranges)
3166 ("r-iranges" ,r-iranges)
3167 ("r-kernlab" ,r-kernlab)
3170 ("r-rtracklayer" ,r-rtracklayer)
3171 ("r-s4vectors" ,r-s4vectors)
3172 ("r-seqinr" ,r-seqinr)))
3173 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3174 (synopsis "Gapped-kmer support vector machine")
3176 "This R package provides tools for training gapped-kmer SVM classifiers
3177 for DNA and protein sequences. This package supports several sequence
3178 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3179 (license license:gpl2+)))
3181 (define-public r-triform
3188 (uri (bioconductor-uri "triform" version))
3191 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
3192 (build-system r-build-system)
3194 `(("r-biocgenerics" ,r-biocgenerics)
3195 ("r-iranges" ,r-iranges)
3196 ("r-yaml" ,r-yaml)))
3197 (home-page "https://bioconductor.org/packages/triform/")
3198 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3200 "The Triform algorithm uses model-free statistics to identify peak-like
3201 distributions of TF ChIP sequencing reads, taking advantage of an improved
3202 peak definition in combination with known profile characteristics.")
3203 (license license:gpl2)))
3205 (define-public r-varianttools
3207 (name "r-varianttools")
3212 (uri (bioconductor-uri "VariantTools" version))
3215 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
3216 (properties `((upstream-name . "VariantTools")))
3217 (build-system r-build-system)
3219 `(("r-biobase" ,r-biobase)
3220 ("r-biocgenerics" ,r-biocgenerics)
3221 ("r-biocparallel" ,r-biocparallel)
3222 ("r-biostrings" ,r-biostrings)
3223 ("r-bsgenome" ,r-bsgenome)
3224 ("r-genomeinfodb" ,r-genomeinfodb)
3225 ("r-genomicfeatures" ,r-genomicfeatures)
3226 ("r-genomicranges" ,r-genomicranges)
3227 ("r-iranges" ,r-iranges)
3228 ("r-matrix" ,r-matrix)
3229 ("r-rsamtools" ,r-rsamtools)
3230 ("r-rtracklayer" ,r-rtracklayer)
3231 ("r-s4vectors" ,r-s4vectors)
3232 ("r-variantannotation" ,r-variantannotation)))
3233 (home-page "https://bioconductor.org/packages/VariantTools/")
3234 (synopsis "Tools for exploratory analysis of variant calls")
3236 "Explore, diagnose, and compare variant calls using filters. The
3237 VariantTools package supports a workflow for loading data, calling single
3238 sample variants and tumor-specific somatic mutations or other sample-specific
3239 variant types (e.g., RNA editing). Most of the functions operate on
3240 alignments (BAM files) or datasets of called variants. The user is expected
3241 to have already aligned the reads with a separate tool, e.g., GSNAP via
3243 (license license:artistic2.0)))
3245 (define-public r-heatplus
3252 (uri (bioconductor-uri "Heatplus" version))
3255 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
3256 (properties `((upstream-name . "Heatplus")))
3257 (build-system r-build-system)
3259 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3260 (home-page "https://github.com/alexploner/Heatplus")
3261 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3263 "This package provides tools to display a rectangular heatmap (intensity
3264 plot) of a data matrix. By default, both samples (columns) and features (row)
3265 of the matrix are sorted according to a hierarchical clustering, and the
3266 corresponding dendrogram is plotted. Optionally, panels with additional
3267 information about samples and features can be added to the plot.")
3268 (license license:gpl2+)))
3270 (define-public r-gosemsim
3277 (uri (bioconductor-uri "GOSemSim" version))
3280 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
3281 (properties `((upstream-name . "GOSemSim")))
3282 (build-system r-build-system)
3284 `(("r-annotationdbi" ,r-annotationdbi)
3285 ("r-go-db" ,r-go-db)
3286 ("r-rcpp" ,r-rcpp)))
3287 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3288 (synopsis "GO-terms semantic similarity measures")
3290 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3291 quantitative ways to compute similarities between genes and gene groups, and
3292 have became important basis for many bioinformatics analysis approaches.
3293 GOSemSim is an R package for semantic similarity computation among GO terms,
3294 sets of GO terms, gene products and gene clusters.")
3295 (license license:artistic2.0)))
3297 (define-public r-anota
3304 (uri (bioconductor-uri "anota" version))
3307 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
3308 (build-system r-build-system)
3310 `(("r-multtest" ,r-multtest)
3311 ("r-qvalue" ,r-qvalue)))
3312 (home-page "https://bioconductor.org/packages/anota/")
3313 (synopsis "Analysis of translational activity")
3315 "Genome wide studies of translational control is emerging as a tool to
3316 study various biological conditions. The output from such analysis is both
3317 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3318 involved in translation (the actively translating mRNA level) for each mRNA.
3319 The standard analysis of such data strives towards identifying differential
3320 translational between two or more sample classes - i.e. differences in
3321 actively translated mRNA levels that are independent of underlying differences
3322 in cytosolic mRNA levels. This package allows for such analysis using partial
3323 variances and the random variance model. As 10s of thousands of mRNAs are
3324 analyzed in parallel the library performs a number of tests to assure that
3325 the data set is suitable for such analysis.")
3326 (license license:gpl3)))
3328 (define-public r-sigpathway
3330 (name "r-sigpathway")
3335 (uri (bioconductor-uri "sigPathway" version))
3338 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3339 (properties `((upstream-name . "sigPathway")))
3340 (build-system r-build-system)
3341 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3342 (synopsis "Pathway analysis")
3344 "This package is used to conduct pathway analysis by calculating the NT_k
3345 and NE_k statistics in a statistical framework for determining whether a
3346 specified group of genes for a pathway has a coordinated association with a
3347 phenotype of interest.")
3348 (license license:gpl2)))
3350 (define-public r-fgsea
3357 (uri (bioconductor-uri "fgsea" version))
3360 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3361 (build-system r-build-system)
3364 ("r-biocparallel" ,r-biocparallel)
3365 ("r-data-table" ,r-data-table)
3366 ("r-fastmatch" ,r-fastmatch)
3367 ("r-ggplot2" ,r-ggplot2)
3368 ("r-gridextra" ,r-gridextra)
3369 ("r-matrix" ,r-matrix)
3370 ("r-rcpp" ,r-rcpp)))
3371 (home-page "https://github.com/ctlab/fgsea/")
3372 (synopsis "Fast gene set enrichment analysis")
3374 "The package implements an algorithm for fast gene set enrichment
3375 analysis. Using the fast algorithm allows to make more permutations and get
3376 more fine grained p-values, which allows to use accurate stantard approaches
3377 to multiple hypothesis correction.")
3378 (license license:expat)))
3380 (define-public r-dose
3387 (uri (bioconductor-uri "DOSE" version))
3390 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3391 (properties `((upstream-name . "DOSE")))
3392 (build-system r-build-system)
3394 `(("r-annotationdbi" ,r-annotationdbi)
3395 ("r-biocparallel" ,r-biocparallel)
3396 ("r-do-db" ,r-do-db)
3397 ("r-fgsea" ,r-fgsea)
3398 ("r-ggplot2" ,r-ggplot2)
3399 ("r-gosemsim" ,r-gosemsim)
3400 ("r-qvalue" ,r-qvalue)
3401 ("r-reshape2" ,r-reshape2)
3402 ("r-s4vectors" ,r-s4vectors)))
3403 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3404 (synopsis "Disease ontology semantic and enrichment analysis")
3406 "This package implements five methods proposed by Resnik, Schlicker,
3407 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3408 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3409 including hypergeometric model and gene set enrichment analysis are also
3410 implemented for discovering disease associations of high-throughput biological
3412 (license license:artistic2.0)))
3414 (define-public r-enrichplot
3416 (name "r-enrichplot")
3421 (uri (bioconductor-uri "enrichplot" version))
3424 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3425 (build-system r-build-system)
3427 `(("r-annotationdbi" ,r-annotationdbi)
3428 ("r-cowplot" ,r-cowplot)
3430 ("r-europepmc" ,r-europepmc)
3431 ("r-ggplot2" ,r-ggplot2)
3432 ("r-ggplotify" ,r-ggplotify)
3433 ("r-ggraph" ,r-ggraph)
3434 ("r-ggridges" ,r-ggridges)
3435 ("r-gosemsim" ,r-gosemsim)
3436 ("r-gridextra" ,r-gridextra)
3437 ("r-igraph" ,r-igraph)
3438 ("r-purrr" ,r-purrr)
3439 ("r-rcolorbrewer" ,r-rcolorbrewer)
3440 ("r-reshape2" ,r-reshape2)
3441 ("r-upsetr" ,r-upsetr)))
3442 (home-page "https://github.com/GuangchuangYu/enrichplot")
3443 (synopsis "Visualization of functional enrichment result")
3445 "The enrichplot package implements several visualization methods for
3446 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3447 All the visualization methods are developed based on ggplot2 graphics.")
3448 (license license:artistic2.0)))
3450 (define-public r-clusterprofiler
3452 (name "r-clusterprofiler")
3457 (uri (bioconductor-uri "clusterProfiler" version))
3460 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3462 `((upstream-name . "clusterProfiler")))
3463 (build-system r-build-system)
3465 `(("r-annotationdbi" ,r-annotationdbi)
3467 ("r-enrichplot" ,r-enrichplot)
3468 ("r-ggplot2" ,r-ggplot2)
3469 ("r-go-db" ,r-go-db)
3470 ("r-gosemsim" ,r-gosemsim)
3471 ("r-magrittr" ,r-magrittr)
3473 ("r-qvalue" ,r-qvalue)
3474 ("r-rvcheck" ,r-rvcheck)
3475 ("r-tidyr" ,r-tidyr)))
3476 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3477 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3479 "This package implements methods to analyze and visualize functional
3480 profiles (GO and KEGG) of gene and gene clusters.")
3481 (license license:artistic2.0)))
3483 (define-public r-mlinterfaces
3485 (name "r-mlinterfaces")
3490 (uri (bioconductor-uri "MLInterfaces" version))
3493 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
3494 (properties `((upstream-name . "MLInterfaces")))
3495 (build-system r-build-system)
3497 `(("r-annotate" ,r-annotate)
3498 ("r-biobase" ,r-biobase)
3499 ("r-biocgenerics" ,r-biocgenerics)
3500 ("r-cluster" ,r-cluster)
3503 ("r-gdata" ,r-gdata)
3504 ("r-genefilter" ,r-genefilter)
3505 ("r-ggvis" ,r-ggvis)
3506 ("r-hwriter" ,r-hwriter)
3508 ("r-mlbench" ,r-mlbench)
3510 ("r-rcolorbrewer" ,r-rcolorbrewer)
3512 ("r-rpart" ,r-rpart)
3513 ("r-sfsmisc" ,r-sfsmisc)
3514 ("r-shiny" ,r-shiny)
3515 ("r-threejs" ,r-threejs)))
3516 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3517 (synopsis "Interfaces to R machine learning procedures")
3519 "This package provides uniform interfaces to machine learning code for
3520 data in R and Bioconductor containers.")
3521 ;; Any version of the LGPL.
3522 (license license:lgpl2.1+)))
3524 (define-public r-annaffy
3531 (uri (bioconductor-uri "annaffy" version))
3534 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3535 (build-system r-build-system)
3538 (modify-phases %standard-phases
3539 (add-after 'unpack 'remove-reference-to-non-free-data
3541 (substitute* "DESCRIPTION"
3545 `(("r-annotationdbi" ,r-annotationdbi)
3546 ("r-biobase" ,r-biobase)
3548 ("r-go-db" ,r-go-db)))
3549 (home-page "https://bioconductor.org/packages/annaffy/")
3550 (synopsis "Annotation tools for Affymetrix biological metadata")
3552 "This package provides functions for handling data from Bioconductor
3553 Affymetrix annotation data packages. It produces compact HTML and text
3554 reports including experimental data and URL links to many online databases.
3555 It allows searching of biological metadata using various criteria.")
3556 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3557 ;; the LGPL 2.1 is included.
3558 (license license:lgpl2.1+)))
3560 (define-public r-a4core
3567 (uri (bioconductor-uri "a4Core" version))
3570 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3571 (properties `((upstream-name . "a4Core")))
3572 (build-system r-build-system)
3574 `(("r-biobase" ,r-biobase)
3575 ("r-glmnet" ,r-glmnet)))
3576 (home-page "https://bioconductor.org/packages/a4Core")
3577 (synopsis "Automated Affymetrix array analysis core package")
3579 "This is the core package for the automated analysis of Affymetrix
3581 (license license:gpl3)))
3583 (define-public r-a4classif
3585 (name "r-a4classif")
3590 (uri (bioconductor-uri "a4Classif" version))
3593 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3594 (properties `((upstream-name . "a4Classif")))
3595 (build-system r-build-system)
3597 `(("r-a4core" ,r-a4core)
3598 ("r-a4preproc" ,r-a4preproc)
3599 ("r-glmnet" ,r-glmnet)
3600 ("r-mlinterfaces" ,r-mlinterfaces)
3603 ("r-varselrf" ,r-varselrf)))
3604 (home-page "https://bioconductor.org/packages/a4Classif/")
3605 (synopsis "Automated Affymetrix array analysis classification package")
3607 "This is the classification package for the automated analysis of
3608 Affymetrix arrays.")
3609 (license license:gpl3)))
3611 (define-public r-a4preproc
3613 (name "r-a4preproc")
3618 (uri (bioconductor-uri "a4Preproc" version))
3621 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3622 (properties `((upstream-name . "a4Preproc")))
3623 (build-system r-build-system)
3625 `(("r-annotationdbi" ,r-annotationdbi)))
3626 (home-page "https://bioconductor.org/packages/a4Preproc/")
3627 (synopsis "Automated Affymetrix array analysis preprocessing package")
3629 "This is a package for the automated analysis of Affymetrix arrays. It
3630 is used for preprocessing the arrays.")
3631 (license license:gpl3)))
3633 (define-public r-a4reporting
3635 (name "r-a4reporting")
3640 (uri (bioconductor-uri "a4Reporting" version))
3643 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3644 (properties `((upstream-name . "a4Reporting")))
3645 (build-system r-build-system)
3647 `(("r-annaffy" ,r-annaffy)
3648 ("r-xtable" ,r-xtable)))
3649 (home-page "https://bioconductor.org/packages/a4Reporting/")
3650 (synopsis "Automated Affymetrix array analysis reporting package")
3652 "This is a package for the automated analysis of Affymetrix arrays. It
3653 provides reporting features.")
3654 (license license:gpl3)))
3656 (define-public r-a4base
3663 (uri (bioconductor-uri "a4Base" version))
3666 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3667 (properties `((upstream-name . "a4Base")))
3668 (build-system r-build-system)
3670 `(("r-a4core" ,r-a4core)
3671 ("r-a4preproc" ,r-a4preproc)
3672 ("r-annaffy" ,r-annaffy)
3673 ("r-annotationdbi" ,r-annotationdbi)
3674 ("r-biobase" ,r-biobase)
3675 ("r-genefilter" ,r-genefilter)
3676 ("r-glmnet" ,r-glmnet)
3677 ("r-gplots" ,r-gplots)
3678 ("r-limma" ,r-limma)
3680 ("r-multtest" ,r-multtest)))
3681 (home-page "https://bioconductor.org/packages/a4Base/")
3682 (synopsis "Automated Affymetrix array analysis base package")
3684 "This package provides basic features for the automated analysis of
3685 Affymetrix arrays.")
3686 (license license:gpl3)))
3695 (uri (bioconductor-uri "a4" version))
3698 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3699 (build-system r-build-system)
3701 `(("r-a4base" ,r-a4base)
3702 ("r-a4classif" ,r-a4classif)
3703 ("r-a4core" ,r-a4core)
3704 ("r-a4preproc" ,r-a4preproc)
3705 ("r-a4reporting" ,r-a4reporting)))
3706 (home-page "https://bioconductor.org/packages/a4/")
3707 (synopsis "Automated Affymetrix array analysis umbrella package")
3709 "This package provides a software suite for the automated analysis of
3710 Affymetrix arrays.")
3711 (license license:gpl3)))
3713 (define-public r-abseqr
3720 (uri (bioconductor-uri "abseqR" version))
3723 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3724 (properties `((upstream-name . "abseqR")))
3725 (build-system r-build-system)
3727 `(("pandoc" ,ghc-pandoc)))
3729 `(("r-biocparallel" ,r-biocparallel)
3730 ("r-biocstyle" ,r-biocstyle)
3731 ("r-circlize" ,r-circlize)
3732 ("r-flexdashboard" ,r-flexdashboard)
3733 ("r-ggcorrplot" ,r-ggcorrplot)
3734 ("r-ggdendro" ,r-ggdendro)
3735 ("r-ggplot2" ,r-ggplot2)
3736 ("r-gridextra" ,r-gridextra)
3737 ("r-knitr" ,r-knitr)
3738 ("r-plotly" ,r-plotly)
3741 ("r-rcolorbrewer" ,r-rcolorbrewer)
3742 ("r-reshape2" ,r-reshape2)
3743 ("r-rmarkdown" ,r-rmarkdown)
3744 ("r-stringr" ,r-stringr)
3745 ("r-vegan" ,r-vegan)
3746 ("r-venndiagram" ,r-venndiagram)))
3747 (home-page "https://github.com/malhamdoosh/abseqR")
3748 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3750 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3751 sequencing datasets generated from antibody libraries and abseqR is one of its
3752 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3753 capabilities and allows them to generate interactive HTML reports for the
3754 convenience of viewing and sharing with other researchers. Additionally,
3755 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3756 further downstream analysis on its output.")
3757 (license license:gpl3)))
3759 (define-public r-bacon
3766 (uri (bioconductor-uri "bacon" version))
3769 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3770 (build-system r-build-system)
3772 `(("r-biocparallel" ,r-biocparallel)
3773 ("r-ellipse" ,r-ellipse)
3774 ("r-ggplot2" ,r-ggplot2)))
3775 (home-page "https://bioconductor.org/packages/bacon/")
3776 (synopsis "Controlling bias and inflation in association studies")
3778 "Bacon can be used to remove inflation and bias often observed in
3779 epigenome- and transcriptome-wide association studies. To this end bacon
3780 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3781 fitting a three-component normal mixture on z-scores.")
3782 (license license:gpl2+)))
3784 (define-public r-rgadem
3791 (uri (bioconductor-uri "rGADEM" version))
3794 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3795 (properties `((upstream-name . "rGADEM")))
3796 (build-system r-build-system)
3798 `(("r-biostrings" ,r-biostrings)
3799 ("r-bsgenome" ,r-bsgenome)
3800 ("r-iranges" ,r-iranges)
3801 ("r-seqlogo" ,r-seqlogo)))
3802 (home-page "https://bioconductor.org/packages/rGADEM/")
3803 (synopsis "De novo sequence motif discovery")
3805 "rGADEM is an efficient de novo motif discovery tool for large-scale
3806 genomic sequence data.")
3807 (license license:artistic2.0)))
3809 (define-public r-motiv
3816 (uri (bioconductor-uri "MotIV" version))
3819 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3820 (properties `((upstream-name . "MotIV")))
3821 (build-system r-build-system)
3825 `(("r-biocgenerics" ,r-biocgenerics)
3826 ("r-biostrings" ,r-biostrings)
3827 ("r-iranges" ,r-iranges)
3828 ("r-lattice" ,r-lattice)
3829 ("r-rgadem" ,r-rgadem)
3830 ("r-s4vectors" ,r-s4vectors)))
3831 (home-page "https://bioconductor.org/packages/MotIV/")
3832 (synopsis "Motif identification and validation")
3834 "This package is used for the identification and validation of sequence
3835 motifs. It makes use of STAMP for comparing a set of motifs to a given
3836 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3837 distributions, modules and filter motifs.")
3838 (license license:gpl2)))
3840 (define-public r-motifstack
3842 (name "r-motifstack")
3847 (uri (bioconductor-uri "motifStack" version))
3850 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3851 (properties `((upstream-name . "motifStack")))
3852 (build-system r-build-system)
3854 `(("r-ade4" ,r-ade4)
3855 ("r-biostrings" ,r-biostrings)
3856 ("r-grimport2" ,r-grimport2)
3857 ("r-htmlwidgets" ,r-htmlwidgets)
3858 ("r-motiv" ,r-motiv)
3859 ("r-scales" ,r-scales)
3861 (home-page "https://bioconductor.org/packages/motifStack/")
3862 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3864 "The motifStack package is designed for graphic representation of
3865 multiple motifs with different similarity scores. It works with both DNA/RNA
3866 sequence motifs and amino acid sequence motifs. In addition, it provides the
3867 flexibility for users to customize the graphic parameters such as the font
3868 type and symbol colors.")
3869 (license license:gpl2+)))
3871 (define-public r-genomicscores
3873 (name "r-genomicscores")
3878 (uri (bioconductor-uri "GenomicScores" version))
3881 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3882 (properties `((upstream-name . "GenomicScores")))
3883 (build-system r-build-system)
3885 `(("r-annotationhub" ,r-annotationhub)
3886 ("r-biobase" ,r-biobase)
3887 ("r-biocgenerics" ,r-biocgenerics)
3888 ("r-biostrings" ,r-biostrings)
3889 ("r-bsgenome" ,r-bsgenome)
3890 ("r-genomeinfodb" ,r-genomeinfodb)
3891 ("r-genomicranges" ,r-genomicranges)
3892 ("r-iranges" ,r-iranges)
3893 ("r-s4vectors" ,r-s4vectors)
3895 (home-page "https://github.com/rcastelo/GenomicScores/")
3896 (synopsis "Work with genome-wide position-specific scores")
3898 "This package provides infrastructure to store and access genome-wide
3899 position-specific scores within R and Bioconductor.")
3900 (license license:artistic2.0)))
3902 (define-public r-atacseqqc
3904 (name "r-atacseqqc")
3909 (uri (bioconductor-uri "ATACseqQC" version))
3912 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3913 (properties `((upstream-name . "ATACseqQC")))
3914 (build-system r-build-system)
3916 `(("r-biocgenerics" ,r-biocgenerics)
3917 ("r-biostrings" ,r-biostrings)
3918 ("r-bsgenome" ,r-bsgenome)
3919 ("r-chippeakanno" ,r-chippeakanno)
3920 ("r-edger" ,r-edger)
3921 ("r-genomeinfodb" ,r-genomeinfodb)
3922 ("r-genomicalignments" ,r-genomicalignments)
3923 ("r-genomicranges" ,r-genomicranges)
3924 ("r-genomicscores" ,r-genomicscores)
3925 ("r-iranges" ,r-iranges)
3926 ("r-kernsmooth" ,r-kernsmooth)
3927 ("r-limma" ,r-limma)
3928 ("r-motifstack" ,r-motifstack)
3929 ("r-preseqr" ,r-preseqr)
3930 ("r-randomforest" ,r-randomforest)
3931 ("r-rsamtools" ,r-rsamtools)
3932 ("r-rtracklayer" ,r-rtracklayer)
3933 ("r-s4vectors" ,r-s4vectors)))
3934 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3935 (synopsis "ATAC-seq quality control")
3937 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3938 sequencing, is a rapid and sensitive method for chromatin accessibility
3939 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3940 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3941 assess whether their ATAC-seq experiment is successful. It includes
3942 diagnostic plots of fragment size distribution, proportion of mitochondria
3943 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3945 (license license:gpl2+)))
3947 (define-public r-gofuncr
3954 (uri (bioconductor-uri "GOfuncR" version))
3957 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3958 (properties `((upstream-name . "GOfuncR")))
3959 (build-system r-build-system)
3961 `(("r-annotationdbi" ,r-annotationdbi)
3962 ("r-genomicranges" ,r-genomicranges)
3963 ("r-gtools" ,r-gtools)
3964 ("r-iranges" ,r-iranges)
3965 ("r-mapplots" ,r-mapplots)
3967 ("r-vioplot" ,r-vioplot)))
3968 (home-page "https://bioconductor.org/packages/GOfuncR/")
3969 (synopsis "Gene ontology enrichment using FUNC")
3971 "GOfuncR performs a gene ontology enrichment analysis based on the
3972 ontology enrichment software FUNC. GO-annotations are obtained from
3973 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3974 included in the package and updated regularly. GOfuncR provides the standard
3975 candidate vs background enrichment analysis using the hypergeometric test, as
3976 well as three additional tests:
3979 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3980 @item a binomial test that is used when genes are associated with two counts,
3982 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3983 associated with four counts.
3986 To correct for multiple testing and interdependency of the tests, family-wise
3987 error rates are computed based on random permutations of the gene-associated
3988 variables. GOfuncR also provides tools for exploring the ontology graph and
3989 the annotations, and options to take gene-length or spatial clustering of
3990 genes into account. It is also possible to provide custom gene coordinates,
3991 annotations and ontologies.")
3992 (license license:gpl2+)))
3994 (define-public r-abaenrichment
3996 (name "r-abaenrichment")
4001 (uri (bioconductor-uri "ABAEnrichment" version))
4004 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
4005 (properties `((upstream-name . "ABAEnrichment")))
4006 (build-system r-build-system)
4008 `(("r-abadata" ,r-abadata)
4009 ("r-data-table" ,r-data-table)
4010 ("r-gofuncr" ,r-gofuncr)
4011 ("r-gplots" ,r-gplots)
4012 ("r-gtools" ,r-gtools)
4013 ("r-rcpp" ,r-rcpp)))
4014 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4015 (synopsis "Gene expression enrichment in human brain regions")
4017 "The package ABAEnrichment is designed to test for enrichment of user
4018 defined candidate genes in the set of expressed genes in different human brain
4019 regions. The core function @code{aba_enrich} integrates the expression of the
4020 candidate gene set (averaged across donors) and the structural information of
4021 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4022 (license license:gpl2+)))
4024 (define-public r-annotationfuncs
4026 (name "r-annotationfuncs")
4031 (uri (bioconductor-uri "AnnotationFuncs" version))
4034 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
4036 `((upstream-name . "AnnotationFuncs")))
4037 (build-system r-build-system)
4039 `(("r-annotationdbi" ,r-annotationdbi)
4041 (home-page "https://www.iysik.com/r/annotationfuncs")
4042 (synopsis "Annotation translation functions")
4044 "This package provides functions for handling translating between
4045 different identifieres using the Biocore Data Team data-packages (e.g.
4046 @code{org.Bt.eg.db}).")
4047 (license license:gpl2)))
4049 (define-public r-annotationtools
4051 (name "r-annotationtools")
4056 (uri (bioconductor-uri "annotationTools" version))
4059 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
4061 `((upstream-name . "annotationTools")))
4062 (build-system r-build-system)
4063 (propagated-inputs `(("r-biobase" ,r-biobase)))
4064 (home-page "https://bioconductor.org/packages/annotationTools/")
4065 (synopsis "Annotate microarrays and perform gene expression analyses")
4067 "This package provides functions to annotate microarrays, find orthologs,
4068 and integrate heterogeneous gene expression profiles using annotation and
4069 other molecular biology information available as flat file database (plain
4071 ;; Any version of the GPL.
4072 (license (list license:gpl2+))))
4074 (define-public r-allelicimbalance
4076 (name "r-allelicimbalance")
4081 (uri (bioconductor-uri "AllelicImbalance" version))
4084 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
4086 `((upstream-name . "AllelicImbalance")))
4087 (build-system r-build-system)
4089 `(("r-annotationdbi" ,r-annotationdbi)
4090 ("r-biocgenerics" ,r-biocgenerics)
4091 ("r-biostrings" ,r-biostrings)
4092 ("r-bsgenome" ,r-bsgenome)
4093 ("r-genomeinfodb" ,r-genomeinfodb)
4094 ("r-genomicalignments" ,r-genomicalignments)
4095 ("r-genomicfeatures" ,r-genomicfeatures)
4096 ("r-genomicranges" ,r-genomicranges)
4097 ("r-gridextra" ,r-gridextra)
4099 ("r-iranges" ,r-iranges)
4100 ("r-lattice" ,r-lattice)
4101 ("r-latticeextra" ,r-latticeextra)
4103 ("r-rsamtools" ,r-rsamtools)
4104 ("r-s4vectors" ,r-s4vectors)
4105 ("r-seqinr" ,r-seqinr)
4106 ("r-summarizedexperiment" ,r-summarizedexperiment)
4107 ("r-variantannotation" ,r-variantannotation)))
4108 (home-page "https://github.com/pappewaio/AllelicImbalance")
4109 (synopsis "Investigate allele-specific expression")
4111 "This package provides a framework for allele-specific expression
4112 investigation using RNA-seq data.")
4113 (license license:gpl3)))
4115 (define-public r-aucell
4122 (uri (bioconductor-uri "AUCell" version))
4125 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
4126 (properties `((upstream-name . "AUCell")))
4127 (build-system r-build-system)
4129 `(("r-data-table" ,r-data-table)
4130 ("r-gseabase" ,r-gseabase)
4131 ("r-mixtools" ,r-mixtools)
4132 ("r-r-utils" ,r-r-utils)
4133 ("r-shiny" ,r-shiny)
4134 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4135 (home-page "https://bioconductor.org/packages/AUCell/")
4136 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4138 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4139 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4140 Under the Curve} (AUC) to calculate whether a critical subset of the input
4141 gene set is enriched within the expressed genes for each cell. The
4142 distribution of AUC scores across all the cells allows exploring the relative
4143 expression of the signature. Since the scoring method is ranking-based,
4144 AUCell is independent of the gene expression units and the normalization
4145 procedure. In addition, since the cells are evaluated individually, it can
4146 easily be applied to bigger datasets, subsetting the expression matrix if
4148 (license license:gpl3)))
4150 (define-public r-ebimage
4157 (uri (bioconductor-uri "EBImage" version))
4160 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
4161 (properties `((upstream-name . "EBImage")))
4162 (build-system r-build-system)
4164 `(("r-abind" ,r-abind)
4165 ("r-biocgenerics" ,r-biocgenerics)
4166 ("r-fftwtools" ,r-fftwtools)
4167 ("r-htmltools" ,r-htmltools)
4168 ("r-htmlwidgets" ,r-htmlwidgets)
4170 ("r-locfit" ,r-locfit)
4172 ("r-rcurl" ,r-rcurl)
4173 ("r-tiff" ,r-tiff)))
4175 `(("r-knitr" ,r-knitr))) ; for vignettes
4176 (home-page "https://github.com/aoles/EBImage")
4177 (synopsis "Image processing and analysis toolbox for R")
4179 "EBImage provides general purpose functionality for image processing and
4180 analysis. In the context of (high-throughput) microscopy-based cellular
4181 assays, EBImage offers tools to segment cells and extract quantitative
4182 cellular descriptors. This allows the automation of such tasks using the R
4183 programming language and facilitates the use of other tools in the R
4184 environment for signal processing, statistical modeling, machine learning and
4185 visualization with image data.")
4186 ;; Any version of the LGPL.
4187 (license license:lgpl2.1+)))
4189 (define-public r-yamss
4196 (uri (bioconductor-uri "yamss" version))
4199 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
4200 (build-system r-build-system)
4202 `(("r-biocgenerics" ,r-biocgenerics)
4203 ("r-data-table" ,r-data-table)
4204 ("r-ebimage" ,r-ebimage)
4205 ("r-iranges" ,r-iranges)
4206 ("r-limma" ,r-limma)
4207 ("r-matrix" ,r-matrix)
4209 ("r-s4vectors" ,r-s4vectors)
4210 ("r-summarizedexperiment"
4211 ,r-summarizedexperiment)))
4212 (home-page "https://github.com/hansenlab/yamss")
4213 (synopsis "Tools for high-throughput metabolomics")
4215 "This package provides tools to analyze and visualize high-throughput
4216 metabolomics data acquired using chromatography-mass spectrometry. These tools
4217 preprocess data in a way that enables reliable and powerful differential
4219 (license license:artistic2.0)))
4221 (define-public r-gtrellis
4228 (uri (bioconductor-uri "gtrellis" version))
4231 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
4232 (build-system r-build-system)
4234 `(("r-circlize" ,r-circlize)
4235 ("r-genomicranges" ,r-genomicranges)
4236 ("r-getoptlong" ,r-getoptlong)
4237 ("r-iranges" ,r-iranges)))
4238 (home-page "https://github.com/jokergoo/gtrellis")
4239 (synopsis "Genome level Trellis layout")
4241 "Genome level Trellis graph visualizes genomic data conditioned by
4242 genomic categories (e.g. chromosomes). For each genomic category, multiple
4243 dimensional data which are represented as tracks describe different features
4244 from different aspects. This package provides high flexibility to arrange
4245 genomic categories and to add self-defined graphics in the plot.")
4246 (license license:expat)))
4248 (define-public r-somaticsignatures
4250 (name "r-somaticsignatures")
4255 (uri (bioconductor-uri "SomaticSignatures" version))
4258 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
4260 `((upstream-name . "SomaticSignatures")))
4261 (build-system r-build-system)
4263 `(("r-biobase" ,r-biobase)
4264 ("r-biostrings" ,r-biostrings)
4265 ("r-genomeinfodb" ,r-genomeinfodb)
4266 ("r-genomicranges" ,r-genomicranges)
4267 ("r-ggbio" ,r-ggbio)
4268 ("r-ggplot2" ,r-ggplot2)
4269 ("r-iranges" ,r-iranges)
4271 ("r-pcamethods" ,r-pcamethods)
4272 ("r-proxy" ,r-proxy)
4273 ("r-reshape2" ,r-reshape2)
4274 ("r-s4vectors" ,r-s4vectors)
4275 ("r-variantannotation" ,r-variantannotation)))
4276 (home-page "https://github.com/juliangehring/SomaticSignatures")
4277 (synopsis "Somatic signatures")
4279 "This package identifies mutational signatures of @dfn{single nucleotide
4280 variants} (SNVs). It provides a infrastructure related to the methodology
4281 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4282 decomposition algorithms.")
4283 (license license:expat)))
4285 (define-public r-yapsa
4292 (uri (bioconductor-uri "YAPSA" version))
4295 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
4296 (properties `((upstream-name . "YAPSA")))
4297 (build-system r-build-system)
4299 `(("r-circlize" ,r-circlize)
4300 ("r-complexheatmap" ,r-complexheatmap)
4301 ("r-corrplot" ,r-corrplot)
4302 ("r-dendextend" ,r-dendextend)
4303 ("r-genomeinfodb" ,r-genomeinfodb)
4304 ("r-genomicranges" ,r-genomicranges)
4305 ("r-getoptlong" ,r-getoptlong)
4306 ("r-ggplot2" ,r-ggplot2)
4307 ("r-gridextra" ,r-gridextra)
4308 ("r-gtrellis" ,r-gtrellis)
4309 ("r-keggrest" ,r-keggrest)
4311 ("r-pmcmr" ,r-pmcmr)
4312 ("r-reshape2" ,r-reshape2)
4313 ("r-somaticsignatures" ,r-somaticsignatures)
4314 ("r-variantannotation" ,r-variantannotation)))
4315 (home-page "https://bioconductor.org/packages/YAPSA/")
4316 (synopsis "Yet another package for signature analysis")
4318 "This package provides functions and routines useful in the analysis of
4319 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4320 functions to perform a signature analysis with known signatures and a
4321 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4323 (license license:gpl3)))
4325 (define-public r-gcrma
4332 (uri (bioconductor-uri "gcrma" version))
4335 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4336 (build-system r-build-system)
4338 `(("r-affy" ,r-affy)
4339 ("r-affyio" ,r-affyio)
4340 ("r-biobase" ,r-biobase)
4341 ("r-biocmanager" ,r-biocmanager)
4342 ("r-biostrings" ,r-biostrings)
4343 ("r-xvector" ,r-xvector)))
4344 (home-page "https://bioconductor.org/packages/gcrma/")
4345 (synopsis "Background adjustment using sequence information")
4347 "Gcrma adjusts for background intensities in Affymetrix array data which
4348 include optical noise and @dfn{non-specific binding} (NSB). The main function
4349 @code{gcrma} converts background adjusted probe intensities to expression
4350 measures using the same normalization and summarization methods as a
4351 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4352 to estimate probe affinity to NSB. The sequence information is summarized in
4353 a more complex way than the simple GC content. Instead, the base types (A, T,
4354 G or C) at each position along the probe determine the affinity of each probe.
4355 The parameters of the position-specific base contributions to the probe
4356 affinity is estimated in an NSB experiment in which only NSB but no
4357 gene-specific bidning is expected.")
4358 ;; Any version of the LGPL
4359 (license license:lgpl2.1+)))
4361 (define-public r-simpleaffy
4363 (name "r-simpleaffy")
4368 (uri (bioconductor-uri "simpleaffy" version))
4371 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4372 (build-system r-build-system)
4374 `(("r-affy" ,r-affy)
4375 ("r-biobase" ,r-biobase)
4376 ("r-biocgenerics" ,r-biocgenerics)
4377 ("r-gcrma" ,r-gcrma)
4378 ("r-genefilter" ,r-genefilter)))
4379 (home-page "https://bioconductor.org/packages/simpleaffy/")
4380 (synopsis "Very simple high level analysis of Affymetrix data")
4382 "This package provides high level functions for reading Affy @file{.CEL}
4383 files, phenotypic data, and then computing simple things with it, such as
4384 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4385 library. It also has some basic scatter plot functions and mechanisms for
4386 generating high resolution journal figures.")
4387 (license license:gpl2+)))
4389 (define-public r-yaqcaffy
4396 (uri (bioconductor-uri "yaqcaffy" version))
4399 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4400 (build-system r-build-system)
4402 `(("r-simpleaffy" ,r-simpleaffy)))
4403 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4404 (synopsis "Affymetrix quality control and reproducibility analysis")
4406 "This is a package that can be used for quality control of Affymetrix
4407 GeneChip expression data and reproducibility analysis of human whole genome
4408 chips with the MAQC reference datasets.")
4409 (license license:artistic2.0)))
4411 (define-public r-quantro
4418 (uri (bioconductor-uri "quantro" version))
4421 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4422 (build-system r-build-system)
4424 `(("r-biobase" ,r-biobase)
4425 ("r-doparallel" ,r-doparallel)
4426 ("r-foreach" ,r-foreach)
4427 ("r-ggplot2" ,r-ggplot2)
4428 ("r-iterators" ,r-iterators)
4429 ("r-minfi" ,r-minfi)
4430 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4431 (home-page "https://bioconductor.org/packages/quantro/")
4432 (synopsis "Test for when to use quantile normalization")
4434 "This package provides a data-driven test for the assumptions of quantile
4435 normalization using raw data such as objects that inherit eSets (e.g.
4436 ExpressionSet, MethylSet). Group level information about each sample (such as
4437 Tumor / Normal status) must also be provided because the test assesses if
4438 there are global differences in the distributions between the user-defined
4440 (license license:gpl3+)))
4442 (define-public r-yarn
4449 (uri (bioconductor-uri "yarn" version))
4452 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4453 (build-system r-build-system)
4455 `(("r-biobase" ,r-biobase)
4456 ("r-biomart" ,r-biomart)
4457 ("r-downloader" ,r-downloader)
4458 ("r-edger" ,r-edger)
4459 ("r-gplots" ,r-gplots)
4460 ("r-limma" ,r-limma)
4461 ("r-matrixstats" ,r-matrixstats)
4462 ("r-preprocesscore" ,r-preprocesscore)
4463 ("r-quantro" ,r-quantro)
4464 ("r-rcolorbrewer" ,r-rcolorbrewer)
4465 ("r-readr" ,r-readr)))
4466 (home-page "https://bioconductor.org/packages/yarn/")
4467 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4469 "Expedite large RNA-Seq analyses using a combination of previously
4470 developed tools. YARN is meant to make it easier for the user in performing
4471 basic mis-annotation quality control, filtering, and condition-aware
4472 normalization. YARN leverages many Bioconductor tools and statistical
4473 techniques to account for the large heterogeneity and sparsity found in very
4474 large RNA-seq experiments.")
4475 (license license:artistic2.0)))
4477 (define-public r-roar
4484 (uri (bioconductor-uri "roar" version))
4487 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4488 (build-system r-build-system)
4490 `(("r-biocgenerics" ,r-biocgenerics)
4491 ("r-genomeinfodb" ,r-genomeinfodb)
4492 ("r-genomicalignments" ,r-genomicalignments)
4493 ("r-genomicranges" ,r-genomicranges)
4494 ("r-iranges" ,r-iranges)
4495 ("r-rtracklayer" ,r-rtracklayer)
4496 ("r-s4vectors" ,r-s4vectors)
4497 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4498 (home-page "https://github.com/vodkatad/roar/")
4499 (synopsis "Identify differential APA usage from RNA-seq alignments")
4501 "This package provides tools for identifying preferential usage of APA
4502 sites, comparing two biological conditions, starting from known alternative
4503 sites and alignments obtained from standard RNA-seq experiments.")
4504 (license license:gpl3)))
4506 (define-public r-xbseq
4513 (uri (bioconductor-uri "XBSeq" version))
4516 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4517 (properties `((upstream-name . "XBSeq")))
4518 (build-system r-build-system)
4520 `(("r-biobase" ,r-biobase)
4521 ("r-deseq2" ,r-deseq2)
4522 ("r-dplyr" ,r-dplyr)
4523 ("r-ggplot2" ,r-ggplot2)
4524 ("r-locfit" ,r-locfit)
4525 ("r-magrittr" ,r-magrittr)
4526 ("r-matrixstats" ,r-matrixstats)
4527 ("r-pracma" ,r-pracma)
4528 ("r-roar" ,r-roar)))
4529 (home-page "https://github.com/Liuy12/XBSeq")
4530 (synopsis "Test for differential expression for RNA-seq data")
4532 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4533 expression} (DE), where a statistical model was established based on the
4534 assumption that observed signals are the convolution of true expression
4535 signals and sequencing noises. The mapped reads in non-exonic regions are
4536 considered as sequencing noises, which follows a Poisson distribution. Given
4537 measurable observed signal and background noise from RNA-seq data, true
4538 expression signals, assuming governed by the negative binomial distribution,
4539 can be delineated and thus the accurate detection of differential expressed
4541 (license license:gpl3+)))
4543 (define-public r-massspecwavelet
4545 (name "r-massspecwavelet")
4550 (uri (bioconductor-uri "MassSpecWavelet" version))
4553 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4555 `((upstream-name . "MassSpecWavelet")))
4556 (build-system r-build-system)
4558 `(("r-waveslim" ,r-waveslim)))
4559 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4560 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4562 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4563 data mainly through the use of wavelet transforms. It supports peak detection
4564 based on @dfn{Continuous Wavelet Transform} (CWT).")
4565 (license license:lgpl2.0+)))
4567 (define-public r-xcms
4574 (uri (bioconductor-uri "xcms" version))
4577 "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
4578 (build-system r-build-system)
4580 `(("r-biobase" ,r-biobase)
4581 ("r-biocgenerics" ,r-biocgenerics)
4582 ("r-biocparallel" ,r-biocparallel)
4583 ("r-lattice" ,r-lattice)
4584 ("r-massspecwavelet" ,r-massspecwavelet)
4585 ("r-msnbase" ,r-msnbase)
4586 ("r-multtest" ,r-multtest)
4589 ("r-protgenerics" ,r-protgenerics)
4591 ("r-rcolorbrewer" ,r-rcolorbrewer)
4592 ("r-robustbase" ,r-robustbase)
4593 ("r-s4vectors" ,r-s4vectors)))
4594 (home-page "https://bioconductor.org/packages/xcms/")
4595 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4597 "This package provides a framework for processing and visualization of
4598 chromatographically separated and single-spectra mass spectral data. It
4599 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4600 data for high-throughput, untargeted analyte profiling.")
4601 (license license:gpl2+)))
4603 (define-public r-wrench
4610 (uri (bioconductor-uri "Wrench" version))
4613 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4614 (properties `((upstream-name . "Wrench")))
4615 (build-system r-build-system)
4617 `(("r-limma" ,r-limma)
4618 ("r-locfit" ,r-locfit)
4619 ("r-matrixstats" ,r-matrixstats)))
4620 (home-page "https://github.com/HCBravoLab/Wrench")
4621 (synopsis "Wrench normalization for sparse count data")
4623 "Wrench is a package for normalization sparse genomic count data, like
4624 that arising from 16s metagenomic surveys.")
4625 (license license:artistic2.0)))
4627 (define-public r-wiggleplotr
4629 (name "r-wiggleplotr")
4634 (uri (bioconductor-uri "wiggleplotr" version))
4637 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4638 (build-system r-build-system)
4640 `(("r-assertthat" ,r-assertthat)
4641 ("r-cowplot" ,r-cowplot)
4642 ("r-dplyr" ,r-dplyr)
4643 ("r-genomeinfodb" ,r-genomeinfodb)
4644 ("r-genomicranges" ,r-genomicranges)
4645 ("r-ggplot2" ,r-ggplot2)
4646 ("r-iranges" ,r-iranges)
4647 ("r-purrr" ,r-purrr)
4648 ("r-rtracklayer" ,r-rtracklayer)
4649 ("r-s4vectors" ,r-s4vectors)))
4650 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4651 (synopsis "Make read coverage plots from BigWig files")
4653 "This package provides tools to visualize read coverage from sequencing
4654 experiments together with genomic annotations (genes, transcripts, peaks).
4655 Introns of long transcripts can be rescaled to a fixed length for better
4656 visualization of exonic read coverage.")
4657 (license license:asl2.0)))
4659 (define-public r-widgettools
4661 (name "r-widgettools")
4666 (uri (bioconductor-uri "widgetTools" version))
4669 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4670 (properties `((upstream-name . "widgetTools")))
4671 (build-system r-build-system)
4672 (home-page "https://bioconductor.org/packages/widgetTools/")
4673 (synopsis "Tools for creating interactive tcltk widgets")
4675 "This package contains tools to support the construction of tcltk
4677 ;; Any version of the LGPL.
4678 (license license:lgpl3+)))
4680 (define-public r-webbioc
4687 (uri (bioconductor-uri "webbioc" version))
4690 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4691 (build-system r-build-system)
4693 `(("netpbm" ,netpbm)
4696 `(("r-affy" ,r-affy)
4697 ("r-annaffy" ,r-annaffy)
4698 ("r-biobase" ,r-biobase)
4699 ("r-biocmanager" ,r-biocmanager)
4700 ("r-gcrma" ,r-gcrma)
4701 ("r-multtest" ,r-multtest)
4702 ("r-qvalue" ,r-qvalue)
4704 (home-page "https://www.bioconductor.org/")
4705 (synopsis "Bioconductor web interface")
4707 "This package provides an integrated web interface for doing microarray
4708 analysis using several of the Bioconductor packages. It is intended to be
4709 deployed as a centralized bioinformatics resource for use by many users.
4710 Currently only Affymetrix oligonucleotide analysis is supported.")
4711 (license license:gpl2+)))
4713 (define-public r-zfpkm
4720 (uri (bioconductor-uri "zFPKM" version))
4723 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4724 (properties `((upstream-name . "zFPKM")))
4725 (build-system r-build-system)
4727 `(("r-checkmate" ,r-checkmate)
4728 ("r-dplyr" ,r-dplyr)
4729 ("r-ggplot2" ,r-ggplot2)
4730 ("r-summarizedexperiment" ,r-summarizedexperiment)
4731 ("r-tidyr" ,r-tidyr)))
4732 (home-page "https://github.com/ronammar/zFPKM/")
4733 (synopsis "Functions to facilitate zFPKM transformations")
4735 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4736 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4738 (license license:gpl3)))
4740 (define-public r-rbowtie2
4747 (uri (bioconductor-uri "Rbowtie2" version))
4750 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4751 (properties `((upstream-name . "Rbowtie2")))
4752 (build-system r-build-system)
4755 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4756 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4758 "This package provides an R wrapper of the popular @code{bowtie2}
4759 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4760 rapid adapter trimming, identification, and read merging.")
4761 (license license:gpl3+)))
4763 (define-public r-progeny
4770 (uri (bioconductor-uri "progeny" version))
4773 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4774 (build-system r-build-system)
4775 (propagated-inputs `(("r-biobase" ,r-biobase)))
4776 (home-page "https://github.com/saezlab/progeny")
4777 (synopsis "Pathway responsive gene activity inference")
4779 "This package provides a function to infer pathway activity from gene
4780 expression. It contains the linear model inferred in the publication
4781 \"Perturbation-response genes reveal signaling footprints in cancer gene
4783 (license license:asl2.0)))
4785 (define-public r-arrmnormalization
4787 (name "r-arrmnormalization")
4792 (uri (bioconductor-uri "ARRmNormalization" version))
4795 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4797 `((upstream-name . "ARRmNormalization")))
4798 (build-system r-build-system)
4799 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4800 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4801 (synopsis "Adaptive robust regression normalization for methylation data")
4803 "This is a package to perform the @dfn{Adaptive Robust Regression
4804 method} (ARRm) for the normalization of methylation data from the Illumina
4805 Infinium HumanMethylation 450k assay.")
4806 (license license:artistic2.0)))
4808 (define-public r-biocfilecache
4810 (name "r-biocfilecache")
4815 (uri (bioconductor-uri "BiocFileCache" version))
4818 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4819 (properties `((upstream-name . "BiocFileCache")))
4820 (build-system r-build-system)
4822 `(("r-curl" ,r-curl)
4824 ("r-dbplyr" ,r-dbplyr)
4825 ("r-dplyr" ,r-dplyr)
4827 ("r-rappdirs" ,r-rappdirs)
4828 ("r-rsqlite" ,r-rsqlite)))
4829 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4830 (synopsis "Manage files across sessions")
4832 "This package creates a persistent on-disk cache of files that the user
4833 can add, update, and retrieve. It is useful for managing resources (such as
4834 custom Txdb objects) that are costly or difficult to create, web resources,
4835 and data files used across sessions.")
4836 (license license:artistic2.0)))
4838 (define-public r-iclusterplus
4840 (name "r-iclusterplus")
4845 (uri (bioconductor-uri "iClusterPlus" version))
4848 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4849 (properties `((upstream-name . "iClusterPlus")))
4850 (build-system r-build-system)
4851 (native-inputs `(("gfortran" ,gfortran)))
4852 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4853 (synopsis "Integrative clustering of multi-type genomic data")
4855 "iClusterPlus is developed for integrative clustering analysis of
4856 multi-type genomic data and is an enhanced version of iCluster proposed and
4857 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4858 from the experiments where biological samples (e.g. tumor samples) are
4859 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4860 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4861 on. In the iClusterPlus model, binary observations such as somatic mutation
4862 are modeled as Binomial processes; categorical observations such as copy
4863 number states are realizations of Multinomial random variables; counts are
4864 modeled as Poisson random processes; and continuous measures are modeled by
4865 Gaussian distributions.")
4866 (license license:gpl2+)))
4868 (define-public r-rbowtie
4875 (uri (bioconductor-uri "Rbowtie" version))
4878 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4879 (properties `((upstream-name . "Rbowtie")))
4880 (build-system r-build-system)
4883 (home-page "https://bioconductor.org/packages/Rbowtie/")
4884 (synopsis "R bowtie wrapper")
4886 "This package provides an R wrapper around the popular bowtie short read
4887 aligner and around SpliceMap, a de novo splice junction discovery and
4889 (license license:artistic2.0)))
4891 (define-public r-sgseq
4898 (uri (bioconductor-uri "SGSeq" version))
4901 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4902 (properties `((upstream-name . "SGSeq")))
4903 (build-system r-build-system)
4905 `(("r-annotationdbi" ,r-annotationdbi)
4906 ("r-biocgenerics" ,r-biocgenerics)
4907 ("r-biostrings" ,r-biostrings)
4908 ("r-genomeinfodb" ,r-genomeinfodb)
4909 ("r-genomicalignments" ,r-genomicalignments)
4910 ("r-genomicfeatures" ,r-genomicfeatures)
4911 ("r-genomicranges" ,r-genomicranges)
4912 ("r-igraph" ,r-igraph)
4913 ("r-iranges" ,r-iranges)
4914 ("r-rsamtools" ,r-rsamtools)
4915 ("r-rtracklayer" ,r-rtracklayer)
4916 ("r-runit" ,r-runit)
4917 ("r-s4vectors" ,r-s4vectors)
4918 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4919 (home-page "https://bioconductor.org/packages/SGSeq/")
4920 (synopsis "Splice event prediction and quantification from RNA-seq data")
4922 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4923 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4924 represented as a splice graph, which can be obtained from existing annotation
4925 or predicted from the mapped sequence reads. Splice events are identified
4926 from the graph and are quantified locally using structurally compatible reads
4927 at the start or end of each splice variant. The software includes functions
4928 for splice event prediction, quantification, visualization and
4930 (license license:artistic2.0)))
4932 (define-public r-rhisat2
4939 (uri (bioconductor-uri "Rhisat2" version))
4942 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4943 (properties `((upstream-name . "Rhisat2")))
4944 (build-system r-build-system)
4946 `(("which" ,which)))
4948 `(("r-genomicfeatures" ,r-genomicfeatures)
4949 ("r-genomicranges" ,r-genomicranges)
4950 ("r-sgseq" ,r-sgseq)))
4951 (home-page "https://github.com/fmicompbio/Rhisat2")
4952 (synopsis "R Wrapper for HISAT2 sequence aligner")
4954 "This package provides an R interface to the HISAT2 spliced short-read
4955 aligner by Kim et al. (2015). The package contains wrapper functions to
4956 create a genome index and to perform the read alignment to the generated
4958 (license license:gpl3)))
4960 (define-public r-quasr
4967 (uri (bioconductor-uri "QuasR" version))
4970 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4971 (properties `((upstream-name . "QuasR")))
4972 (build-system r-build-system)
4976 `(("r-annotationdbi" ,r-annotationdbi)
4977 ("r-biobase" ,r-biobase)
4978 ("r-biocgenerics" ,r-biocgenerics)
4979 ("r-biocmanager" ,r-biocmanager)
4980 ("r-biocparallel" ,r-biocparallel)
4981 ("r-biostrings" ,r-biostrings)
4982 ("r-bsgenome" ,r-bsgenome)
4983 ("r-genomeinfodb" ,r-genomeinfodb)
4984 ("r-genomicalignments" ,r-genomicalignments)
4985 ("r-genomicfeatures" ,r-genomicfeatures)
4986 ("r-genomicfiles" ,r-genomicfiles)
4987 ("r-genomicranges" ,r-genomicranges)
4988 ("r-iranges" ,r-iranges)
4989 ("r-rbowtie" ,r-rbowtie)
4990 ("r-rhisat2" ,r-rhisat2)
4991 ("r-rhtslib" ,r-rhtslib)
4992 ("r-rsamtools" ,r-rsamtools)
4993 ("r-rtracklayer" ,r-rtracklayer)
4994 ("r-s4vectors" ,r-s4vectors)
4995 ("r-shortread" ,r-shortread)))
4996 (home-page "https://bioconductor.org/packages/QuasR/")
4997 (synopsis "Quantify and annotate short reads in R")
4999 "This package provides a framework for the quantification and analysis of
5000 short genomic reads. It covers a complete workflow starting from raw sequence
5001 reads, over creation of alignments and quality control plots, to the
5002 quantification of genomic regions of interest.")
5003 (license license:gpl2)))
5005 (define-public r-rqc
5012 (uri (bioconductor-uri "Rqc" version))
5015 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
5016 (properties `((upstream-name . "Rqc")))
5017 (build-system r-build-system)
5019 `(("r-biocgenerics" ,r-biocgenerics)
5020 ("r-biocparallel" ,r-biocparallel)
5021 ("r-biocstyle" ,r-biocstyle)
5022 ("r-biostrings" ,r-biostrings)
5023 ("r-biovizbase" ,r-biovizbase)
5024 ("r-genomicalignments" ,r-genomicalignments)
5025 ("r-genomicfiles" ,r-genomicfiles)
5026 ("r-ggplot2" ,r-ggplot2)
5027 ("r-iranges" ,r-iranges)
5028 ("r-knitr" ,r-knitr)
5029 ("r-markdown" ,r-markdown)
5032 ("r-reshape2" ,r-reshape2)
5033 ("r-rsamtools" ,r-rsamtools)
5034 ("r-s4vectors" ,r-s4vectors)
5035 ("r-shiny" ,r-shiny)
5036 ("r-shortread" ,r-shortread)))
5037 (home-page "https://github.com/labbcb/Rqc")
5038 (synopsis "Quality control tool for high-throughput sequencing data")
5040 "Rqc is an optimized tool designed for quality control and assessment of
5041 high-throughput sequencing data. It performs parallel processing of entire
5042 files and produces a report which contains a set of high-resolution
5044 (license license:gpl2+)))
5046 (define-public r-birewire
5053 (uri (bioconductor-uri "BiRewire" version))
5056 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
5057 (properties `((upstream-name . "BiRewire")))
5058 (build-system r-build-system)
5060 `(("r-igraph" ,r-igraph)
5061 ("r-matrix" ,r-matrix)
5063 ("r-tsne" ,r-tsne)))
5064 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5065 (synopsis "Tools for randomization of bipartite graphs")
5067 "This package provides functions for bipartite network rewiring through N
5068 consecutive switching steps and for the computation of the minimal number of
5069 switching steps to be performed in order to maximise the dissimilarity with
5070 respect to the original network. It includes functions for the analysis of
5071 the introduced randomness across the switching steps and several other
5072 routines to analyse the resulting networks and their natural projections.")
5073 (license license:gpl3)))
5075 (define-public r-birta
5082 (uri (bioconductor-uri "birta" version))
5085 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
5086 (build-system r-build-system)
5088 `(("r-biobase" ,r-biobase)
5089 ("r-limma" ,r-limma)
5090 ("r-mass" ,r-mass)))
5091 (home-page "https://bioconductor.org/packages/birta")
5092 (synopsis "Bayesian inference of regulation of transcriptional activity")
5094 "Expression levels of mRNA molecules are regulated by different
5095 processes, comprising inhibition or activation by transcription factors and
5096 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5097 Inference of Regulation of Transcriptional Activity) uses the regulatory
5098 networks of transcription factors and miRNAs together with mRNA and miRNA
5099 expression data to predict switches in regulatory activity between two
5100 conditions. A Bayesian network is used to model the regulatory structure and
5101 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5102 (license license:gpl2+)))
5104 (define-public r-ropls
5111 (uri (bioconductor-uri "ropls" version))
5114 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
5115 (build-system r-build-system)
5116 (propagated-inputs `(("r-biobase" ,r-biobase)))
5118 `(("r-knitr" ,r-knitr))) ; for vignettes
5119 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5120 (synopsis "Multivariate analysis and feature selection of omics data")
5122 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5123 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5124 regression, classification, and feature selection of omics data where the
5125 number of variables exceeds the number of samples and with multicollinearity
5126 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5127 separately model the variation correlated (predictive) to the factor of
5128 interest and the uncorrelated (orthogonal) variation. While performing
5129 similarly to PLS, OPLS facilitates interpretation.
5131 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5132 analysis and feature selection of omics data. In addition to scores, loadings
5133 and weights plots, the package provides metrics and graphics to determine the
5134 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5135 validity of the model by permutation testing, detect outliers, and perform
5136 feature selection (e.g. with Variable Importance in Projection or regression
5138 (license license:cecill)))
5140 (define-public r-biosigner
5142 (name "r-biosigner")
5147 (uri (bioconductor-uri "biosigner" version))
5150 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
5151 (build-system r-build-system)
5153 `(("r-biobase" ,r-biobase)
5154 ("r-e1071" ,r-e1071)
5155 ("r-randomforest" ,r-randomforest)
5156 ("r-ropls" ,r-ropls)))
5158 `(("r-knitr" ,r-knitr)
5159 ("r-rmarkdown" ,r-rmarkdown)
5160 ("pandoc" ,ghc-pandoc)
5161 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5162 (home-page "https://bioconductor.org/packages/biosigner/")
5163 (synopsis "Signature discovery from omics data")
5165 "Feature selection is critical in omics data analysis to extract
5166 restricted and meaningful molecular signatures from complex and high-dimension
5167 data, and to build robust classifiers. This package implements a method to
5168 assess the relevance of the variables for the prediction performances of the
5169 classifier. The approach can be run in parallel with the PLS-DA, Random
5170 Forest, and SVM binary classifiers. The signatures and the corresponding
5171 'restricted' models are returned, enabling future predictions on new
5173 (license license:cecill)))
5175 (define-public r-annotatr
5182 (uri (bioconductor-uri "annotatr" version))
5185 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
5186 (build-system r-build-system)
5188 `(("r-annotationdbi" ,r-annotationdbi)
5189 ("r-annotationhub" ,r-annotationhub)
5190 ("r-dplyr" ,r-dplyr)
5191 ("r-genomeinfodb" ,r-genomeinfodb)
5192 ("r-genomicfeatures" ,r-genomicfeatures)
5193 ("r-genomicranges" ,r-genomicranges)
5194 ("r-ggplot2" ,r-ggplot2)
5195 ("r-iranges" ,r-iranges)
5196 ("r-readr" ,r-readr)
5197 ("r-regioner" ,r-regioner)
5198 ("r-reshape2" ,r-reshape2)
5199 ("r-rtracklayer" ,r-rtracklayer)
5200 ("r-s4vectors" ,r-s4vectors)))
5201 (home-page "https://bioconductor.org/packages/annotatr/")
5202 (synopsis "Annotation of genomic regions to genomic annotations")
5204 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5205 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5206 to investigate the intersecting genomic annotations. Such annotations include
5207 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5208 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5209 enhancers. The annotatr package provides an easy way to summarize and
5210 visualize the intersection of genomic sites/regions with genomic
5212 (license license:gpl3)))
5214 (define-public r-rsubread
5221 (uri (bioconductor-uri "Rsubread" version))
5224 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
5225 (properties `((upstream-name . "Rsubread")))
5226 (build-system r-build-system)
5227 (inputs `(("zlib" ,zlib)))
5228 (home-page "https://bioconductor.org/packages/Rsubread/")
5229 (synopsis "Subread sequence alignment and counting for R")
5231 "This package provides tools for alignment, quantification and analysis
5232 of second and third generation sequencing data. It includes functionality for
5233 read mapping, read counting, SNP calling, structural variant detection and
5234 gene fusion discovery. It can be applied to all major sequencing techologies
5235 and to both short and long sequence reads.")
5236 (license license:gpl3)))
5238 (define-public r-flowutils
5240 (name "r-flowutils")
5245 (uri (bioconductor-uri "flowUtils" version))
5248 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
5249 (properties `((upstream-name . "flowUtils")))
5250 (build-system r-build-system)
5252 `(("r-biobase" ,r-biobase)
5253 ("r-corpcor" ,r-corpcor)
5254 ("r-flowcore" ,r-flowcore)
5255 ("r-graph" ,r-graph)
5256 ("r-runit" ,r-runit)
5258 (home-page "https://github.com/jspidlen/flowUtils")
5259 (synopsis "Utilities for flow cytometry")
5261 "This package provides utilities for flow cytometry data.")
5262 (license license:artistic2.0)))
5264 (define-public r-consensusclusterplus
5266 (name "r-consensusclusterplus")
5271 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5274 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
5276 `((upstream-name . "ConsensusClusterPlus")))
5277 (build-system r-build-system)
5280 ("r-biobase" ,r-biobase)
5281 ("r-cluster" ,r-cluster)))
5282 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5283 (synopsis "Clustering algorithm")
5285 "This package provides an implementation of an algorithm for determining
5286 cluster count and membership by stability evidence in unsupervised analysis.")
5287 (license license:gpl2)))
5289 (define-public r-flowcore
5296 (uri (bioconductor-uri "flowCore" version))
5299 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
5300 (properties `((upstream-name . "flowCore")))
5301 (build-system r-build-system)
5304 ("r-biobase" ,r-biobase)
5305 ("r-biocgenerics" ,r-biocgenerics)
5306 ("r-corpcor" ,r-corpcor)
5307 ("r-graph" ,r-graph)
5309 ("r-matrixstats" ,r-matrixstats)
5311 ("r-rrcov" ,r-rrcov)))
5312 (home-page "https://bioconductor.org/packages/flowCore")
5313 (synopsis "Basic structures for flow cytometry data")
5315 "This package provides S4 data structures and basic functions to deal
5316 with flow cytometry data.")
5317 (license license:artistic2.0)))
5319 (define-public r-flowmeans
5321 (name "r-flowmeans")
5326 (uri (bioconductor-uri "flowMeans" version))
5329 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
5330 (properties `((upstream-name . "flowMeans")))
5331 (build-system r-build-system)
5333 `(("r-biobase" ,r-biobase)
5334 ("r-feature" ,r-feature)
5335 ("r-flowcore" ,r-flowcore)
5336 ("r-rrcov" ,r-rrcov)))
5337 (home-page "https://bioconductor.org/packages/flowMeans")
5338 (synopsis "Non-parametric flow cytometry data gating")
5340 "This package provides tools to identify cell populations in Flow
5341 Cytometry data using non-parametric clustering and segmented-regression-based
5342 change point detection.")
5343 (license license:artistic2.0)))
5345 (define-public r-flowsom
5352 (uri (bioconductor-uri "FlowSOM" version))
5355 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5356 (properties `((upstream-name . "FlowSOM")))
5357 (build-system r-build-system)
5359 `(("r-biocgenerics" ,r-biocgenerics)
5360 ("r-consensusclusterplus" ,r-consensusclusterplus)
5361 ("r-flowcore" ,r-flowcore)
5362 ("r-flowutils" ,r-flowutils)
5363 ("r-igraph" ,r-igraph)
5366 (home-page "https://bioconductor.org/packages/FlowSOM/")
5367 (synopsis "Visualize and interpret cytometry data")
5369 "FlowSOM offers visualization options for cytometry data, by using
5370 self-organizing map clustering and minimal spanning trees.")
5371 (license license:gpl2+)))
5373 (define-public r-mixomics
5380 (uri (bioconductor-uri "mixOmics" version))
5383 "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
5384 (properties `((upstream-name . "mixOmics")))
5385 (build-system r-build-system)
5387 `(("r-corpcor" ,r-corpcor)
5388 ("r-dplyr" ,r-dplyr)
5389 ("r-ellipse" ,r-ellipse)
5390 ("r-ggplot2" ,r-ggplot2)
5391 ("r-gridextra" ,r-gridextra)
5392 ("r-igraph" ,r-igraph)
5393 ("r-lattice" ,r-lattice)
5395 ("r-matrixstats" ,r-matrixstats)
5396 ("r-rarpack" ,r-rarpack)
5397 ("r-rcolorbrewer" ,r-rcolorbrewer)
5398 ("r-reshape2" ,r-reshape2)
5399 ("r-tidyr" ,r-tidyr)))
5400 (home-page "http://www.mixOmics.org")
5401 (synopsis "Multivariate methods for exploration of biological datasets")
5403 "mixOmics offers a wide range of multivariate methods for the exploration
5404 and integration of biological datasets with a particular focus on variable
5405 selection. The package proposes several sparse multivariate models we have
5406 developed to identify the key variables that are highly correlated, and/or
5407 explain the biological outcome of interest. The data that can be analysed
5408 with mixOmics may come from high throughput sequencing technologies, such as
5409 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5410 also beyond the realm of omics (e.g. spectral imaging). The methods
5411 implemented in mixOmics can also handle missing values without having to
5412 delete entire rows with missing data.")
5413 (license license:gpl2+)))
5415 (define-public r-depecher
5422 (uri (bioconductor-uri "DepecheR" version))
5425 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5426 (properties `((upstream-name . "DepecheR")))
5427 (build-system r-build-system)
5430 (modify-phases %standard-phases
5431 (add-after 'unpack 'fix-syntax-error
5433 (substitute* "src/Makevars"
5437 `(("r-beanplot" ,r-beanplot)
5438 ("r-biocparallel" ,r-biocparallel)
5439 ("r-dosnow" ,r-dosnow)
5440 ("r-dplyr" ,r-dplyr)
5441 ("r-foreach" ,r-foreach)
5442 ("r-ggplot2" ,r-ggplot2)
5443 ("r-gplots" ,r-gplots)
5445 ("r-matrixstats" ,r-matrixstats)
5446 ("r-mixomics" ,r-mixomics)
5447 ("r-moments" ,r-moments)
5449 ("r-rcppeigen" ,r-rcppeigen)
5450 ("r-reshape2" ,r-reshape2)
5451 ("r-viridis" ,r-viridis)))
5452 (home-page "https://bioconductor.org/packages/DepecheR/")
5453 (synopsis "Identify traits of clusters in high-dimensional entities")
5455 "The purpose of this package is to identify traits in a dataset that can
5456 separate groups. This is done on two levels. First, clustering is performed,
5457 using an implementation of sparse K-means. Secondly, the generated clusters
5458 are used to predict outcomes of groups of individuals based on their
5459 distribution of observations in the different clusters. As certain clusters
5460 with separating information will be identified, and these clusters are defined
5461 by a sparse number of variables, this method can reduce the complexity of
5462 data, to only emphasize the data that actually matters.")
5463 (license license:expat)))
5465 (define-public r-rcistarget
5467 (name "r-rcistarget")
5472 (uri (bioconductor-uri "RcisTarget" version))
5475 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5476 (properties `((upstream-name . "RcisTarget")))
5477 (build-system r-build-system)
5479 `(("r-aucell" ,r-aucell)
5480 ("r-biocgenerics" ,r-biocgenerics)
5481 ("r-data-table" ,r-data-table)
5482 ("r-feather" ,r-feather)
5483 ("r-gseabase" ,r-gseabase)
5484 ("r-r-utils" ,r-r-utils)
5485 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5486 (home-page "https://aertslab.org/#scenic")
5487 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5489 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5490 over-represented on a gene list. In a first step, RcisTarget selects DNA
5491 motifs that are significantly over-represented in the surroundings of the
5492 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5493 achieved by using a database that contains genome-wide cross-species rankings
5494 for each motif. The motifs that are then annotated to TFs and those that have
5495 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5496 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5497 genes in the gene-set that are ranked above the leading edge).")
5498 (license license:gpl3)))
5500 (define-public r-cicero
5507 (uri (bioconductor-uri "cicero" version))
5510 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5511 (build-system r-build-system)
5513 `(("r-assertthat" ,r-assertthat)
5514 ("r-biobase" ,r-biobase)
5515 ("r-biocgenerics" ,r-biocgenerics)
5516 ("r-data-table" ,r-data-table)
5517 ("r-dplyr" ,r-dplyr)
5519 ("r-genomicranges" ,r-genomicranges)
5520 ("r-ggplot2" ,r-ggplot2)
5521 ("r-glasso" ,r-glasso)
5523 ("r-igraph" ,r-igraph)
5524 ("r-iranges" ,r-iranges)
5525 ("r-matrix" ,r-matrix)
5526 ("r-monocle" ,r-monocle)
5528 ("r-reshape2" ,r-reshape2)
5529 ("r-s4vectors" ,r-s4vectors)
5530 ("r-stringr" ,r-stringr)
5531 ("r-tibble" ,r-tibble)
5532 ("r-vgam" ,r-vgam)))
5533 (home-page "https://bioconductor.org/packages/cicero/")
5534 (synopsis "Predict cis-co-accessibility from single-cell data")
5536 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5537 accessibility data. It also extends the monocle package for use in chromatin
5538 accessibility data.")
5539 (license license:expat)))
5541 ;; This is the latest commit on the "monocle3" branch.
5542 (define-public r-cicero-monocle3
5543 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5545 (package (inherit r-cicero)
5546 (name "r-cicero-monocle3")
5547 (version (git-version "1.3.2" revision commit))
5552 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5554 (file-name (git-file-name name version))
5557 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5559 `(("r-monocle3" ,r-monocle3)
5560 ,@(alist-delete "r-monocle"
5561 (package-propagated-inputs r-cicero)))))))
5563 (define-public r-cistopic
5564 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5568 (version (git-version "0.2.1" revision commit))
5573 (url "https://github.com/aertslab/cisTopic.git")
5575 (file-name (git-file-name name version))
5578 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5579 (build-system r-build-system)
5581 `(("r-aucell" ,r-aucell)
5582 ("r-data-table" ,r-data-table)
5583 ("r-dplyr" ,r-dplyr)
5584 ("r-dosnow" ,r-dosnow)
5586 ("r-feather" ,r-feather)
5587 ("r-fitdistrplus" ,r-fitdistrplus)
5588 ("r-genomicranges" ,r-genomicranges)
5589 ("r-ggplot2" ,r-ggplot2)
5591 ("r-matrix" ,r-matrix)
5593 ("r-rcistarget" ,r-rcistarget)
5594 ("r-rtracklayer" ,r-rtracklayer)
5595 ("r-s4vectors" ,r-s4vectors)))
5596 (home-page "https://github.com/aertslab/cisTopic")
5597 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5599 "The sparse nature of single cell epigenomics data can be overruled using
5600 probabilistic modelling methods such as @dfn{Latent Dirichlet
5601 Allocation} (LDA). This package allows the probabilistic modelling of
5602 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5603 includes functionalities to identify cell states based on the contribution of
5604 cisTopics and explore the nature and regulatory proteins driving them.")
5605 (license license:gpl3))))
5607 (define-public r-genie3
5614 (uri (bioconductor-uri "GENIE3" version))
5617 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5618 (properties `((upstream-name . "GENIE3")))
5619 (build-system r-build-system)
5620 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5621 (home-page "https://bioconductor.org/packages/GENIE3")
5622 (synopsis "Gene network inference with ensemble of trees")
5624 "This package implements the GENIE3 algorithm for inferring gene
5625 regulatory networks from expression data.")
5626 (license license:gpl2+)))
5628 (define-public r-roc
5635 (uri (bioconductor-uri "ROC" version))
5638 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5639 (properties `((upstream-name . "ROC")))
5640 (build-system r-build-system)
5641 (home-page "https://www.bioconductor.org/packages/ROC/")
5642 (synopsis "Utilities for ROC curves")
5644 "This package provides utilities for @dfn{Receiver Operating
5645 Characteristic} (ROC) curves, with a focus on micro arrays.")
5646 (license license:artistic2.0)))
5648 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5650 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5655 (uri (bioconductor-uri
5656 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5657 version 'annotation))
5660 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5663 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5664 (build-system r-build-system)
5665 (propagated-inputs `(("r-minfi" ,r-minfi)))
5667 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5668 (synopsis "Annotation for Illumina's 450k methylation arrays")
5670 "This package provides manifests and annotation for Illumina's 450k array
5672 (license license:artistic2.0)))
5674 (define-public r-watermelon
5676 (name "r-watermelon")
5681 (uri (bioconductor-uri "wateRmelon" version))
5684 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
5685 (properties `((upstream-name . "wateRmelon")))
5686 (build-system r-build-system)
5688 `(("r-biobase" ,r-biobase)
5689 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
5690 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
5691 ("r-illuminaio" ,r-illuminaio)
5692 ("r-limma" ,r-limma)
5694 ("r-matrixstats" ,r-matrixstats)
5695 ("r-methylumi" ,r-methylumi)
5697 (home-page "https://bioconductor.org/packages/wateRmelon/")
5698 (synopsis "Illumina 450 methylation array normalization and metrics")
5700 "The standard index of DNA methylation (beta) is computed from methylated
5701 and unmethylated signal intensities. Betas calculated from raw signal
5702 intensities perform well, but using 11 methylomic datasets we demonstrate that
5703 quantile normalization methods produce marked improvement. The commonly used
5704 procedure of normalizing betas is inferior to the separate normalization of M
5705 and U, and it is also advantageous to normalize Type I and Type II assays
5706 separately. This package provides 15 flavours of betas and three performance
5707 metrics, with methods for objects produced by the @code{methylumi} and
5708 @code{minfi} packages.")
5709 (license license:gpl3)))
5711 (define-public r-gdsfmt
5718 (uri (bioconductor-uri "gdsfmt" version))
5721 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
5722 (modules '((guix build utils)))
5723 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
5724 ;; them and link with system libraries instead.
5727 (for-each delete-file-recursively
5731 (substitute* "src/Makevars"
5732 (("all: \\$\\(SHLIB\\)") "all:")
5733 (("\\$\\(SHLIB\\): liblzma.a") "")
5734 (("(ZLIB|LZ4)/.*") "")
5735 (("CoreArray/dVLIntGDS.cpp.*")
5736 "CoreArray/dVLIntGDS.cpp")
5737 (("CoreArray/dVLIntGDS.o.*")
5738 "CoreArray/dVLIntGDS.o")
5739 (("PKG_LIBS = ./liblzma.a")
5740 "PKG_LIBS = -llz4"))
5741 (substitute* "src/CoreArray/dStream.h"
5742 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
5743 (string-append "include <" header ">")))
5745 (properties `((upstream-name . "gdsfmt")))
5746 (build-system r-build-system)
5751 (home-page "http://corearray.sourceforge.net/")
5753 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
5755 "This package provides a high-level R interface to CoreArray @dfn{Genomic
5756 Data Structure} (GDS) data files, which are portable across platforms with
5757 hierarchical structure to store multiple scalable array-oriented data sets
5758 with metadata information. It is suited for large-scale datasets, especially
5759 for data which are much larger than the available random-access memory. The
5760 @code{gdsfmt} package offers efficient operations specifically designed for
5761 integers of less than 8 bits, since a diploid genotype, like
5762 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
5763 byte. Data compression and decompression are available with relatively
5764 efficient random access. It is also allowed to read a GDS file in parallel
5765 with multiple R processes supported by the package @code{parallel}.")
5766 (license license:lgpl3)))
5768 (define-public r-bigmelon
5775 (uri (bioconductor-uri "bigmelon" version))
5778 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
5779 (properties `((upstream-name . "bigmelon")))
5780 (build-system r-build-system)
5782 `(("r-biobase" ,r-biobase)
5783 ("r-biocgenerics" ,r-biocgenerics)
5784 ("r-gdsfmt" ,r-gdsfmt)
5785 ("r-geoquery" ,r-geoquery)
5786 ("r-methylumi" ,r-methylumi)
5787 ("r-minfi" ,r-minfi)
5788 ("r-watermelon" ,r-watermelon)))
5789 (home-page "https://bioconductor.org/packages/bigmelon/")
5790 (synopsis "Illumina methylation array analysis for large experiments")
5792 "This package provides methods for working with Illumina arrays using the
5793 @code{gdsfmt} package.")
5794 (license license:gpl3)))
5796 (define-public r-seqbias
5803 (uri (bioconductor-uri "seqbias" version))
5806 "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
5807 (properties `((upstream-name . "seqbias")))
5808 (build-system r-build-system)
5810 `(("r-biostrings" ,r-biostrings)
5811 ("r-genomicranges" ,r-genomicranges)
5812 ("r-rhtslib" ,r-rhtslib)))
5814 `(("zlib" ,zlib))) ; This comes from rhtslib.
5815 (home-page "https://bioconductor.org/packages/seqbias/")
5816 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
5818 "This package implements a model of per-position sequencing bias in
5819 high-throughput sequencing data using a simple Bayesian network, the structure
5820 and parameters of which are trained on a set of aligned reads and a reference
5822 (license license:lgpl3)))
5824 (define-public r-reqon
5831 (uri (bioconductor-uri "ReQON" version))
5834 "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
5835 (properties `((upstream-name . "ReQON")))
5836 (build-system r-build-system)
5838 `(("r-rjava" ,r-rjava)
5839 ("r-rsamtools" ,r-rsamtools)
5840 ("r-seqbias" ,r-seqbias)))
5841 (home-page "https://bioconductor.org/packages/ReQON/")
5842 (synopsis "Recalibrating quality of nucleotides")
5844 "This package provides an implementation of an algorithm for
5845 recalibrating the base quality scores for aligned sequencing data in BAM
5847 (license license:gpl2)))
5849 (define-public r-wavcluster
5851 (name "r-wavcluster")
5856 (uri (bioconductor-uri "wavClusteR" version))
5859 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
5860 (properties `((upstream-name . "wavClusteR")))
5861 (build-system r-build-system)
5863 `(("r-biocgenerics" ,r-biocgenerics)
5864 ("r-biostrings" ,r-biostrings)
5865 ("r-foreach" ,r-foreach)
5866 ("r-genomicfeatures" ,r-genomicfeatures)
5867 ("r-genomicranges" ,r-genomicranges)
5868 ("r-ggplot2" ,r-ggplot2)
5869 ("r-hmisc" ,r-hmisc)
5870 ("r-iranges" ,r-iranges)
5871 ("r-mclust" ,r-mclust)
5872 ("r-rsamtools" ,r-rsamtools)
5873 ("r-rtracklayer" ,r-rtracklayer)
5874 ("r-s4vectors" ,r-s4vectors)
5875 ("r-seqinr" ,r-seqinr)
5876 ("r-stringr" ,r-stringr)
5877 ("r-wmtsa" ,r-wmtsa)))
5878 (home-page "https://bioconductor.org/packages/wavClusteR/")
5879 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
5881 "This package provides an integrated pipeline for the analysis of
5882 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
5883 sequencing errors, SNPs and additional non-experimental sources by a non-
5884 parametric mixture model. The protein binding sites (clusters) are then
5885 resolved at high resolution and cluster statistics are estimated using a
5886 rigorous Bayesian framework. Post-processing of the results, data export for
5887 UCSC genome browser visualization and motif search analysis are provided. In
5888 addition, the package allows to integrate RNA-Seq data to estimate the False
5889 Discovery Rate of cluster detection. Key functions support parallel multicore
5890 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
5891 be applied to the analysis of other NGS data obtained from experimental
5892 procedures that induce nucleotide substitutions (e.g. BisSeq).")
5893 (license license:gpl2)))
5895 (define-public r-timeseriesexperiment
5897 (name "r-timeseriesexperiment")
5902 (uri (bioconductor-uri "TimeSeriesExperiment" version))
5905 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
5907 `((upstream-name . "TimeSeriesExperiment")))
5908 (build-system r-build-system)
5910 `(("r-deseq2" ,r-deseq2)
5911 ("r-dplyr" ,r-dplyr)
5912 ("r-dynamictreecut" ,r-dynamictreecut)
5913 ("r-edger" ,r-edger)
5914 ("r-ggplot2" ,r-ggplot2)
5915 ("r-hmisc" ,r-hmisc)
5916 ("r-limma" ,r-limma)
5917 ("r-magrittr" ,r-magrittr)
5918 ("r-proxy" ,r-proxy)
5919 ("r-s4vectors" ,r-s4vectors)
5920 ("r-summarizedexperiment" ,r-summarizedexperiment)
5921 ("r-tibble" ,r-tibble)
5922 ("r-tidyr" ,r-tidyr)
5923 ("r-vegan" ,r-vegan)
5924 ("r-viridis" ,r-viridis)))
5925 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
5926 (synopsis "Analysis for short time-series data")
5928 "This package is a visualization and analysis toolbox for short time
5929 course data which includes dimensionality reduction, clustering, two-sample
5930 differential expression testing and gene ranking techniques. The package also
5931 provides methods for retrieving enriched pathways.")
5932 (license license:lgpl3+)))
5934 (define-public r-variantfiltering
5936 (name "r-variantfiltering")
5941 (uri (bioconductor-uri "VariantFiltering" version))
5944 "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
5946 `((upstream-name . "VariantFiltering")))
5947 (build-system r-build-system)
5949 `(("r-annotationdbi" ,r-annotationdbi)
5950 ("r-biobase" ,r-biobase)
5951 ("r-biocgenerics" ,r-biocgenerics)
5952 ("r-biocparallel" ,r-biocparallel)
5953 ("r-biostrings" ,r-biostrings)
5954 ("r-bsgenome" ,r-bsgenome)
5956 ("r-genomeinfodb" ,r-genomeinfodb)
5957 ("r-genomicfeatures" ,r-genomicfeatures)
5958 ("r-genomicranges" ,r-genomicranges)
5959 ("r-genomicscores" ,r-genomicscores)
5960 ("r-graph" ,r-graph)
5962 ("r-iranges" ,r-iranges)
5964 ("r-rsamtools" ,r-rsamtools)
5965 ("r-s4vectors" ,r-s4vectors)
5966 ("r-shiny" ,r-shiny)
5967 ("r-shinyjs" ,r-shinyjs)
5968 ("r-shinythemes" ,r-shinythemes)
5969 ("r-shinytree" ,r-shinytree)
5970 ("r-summarizedexperiment" ,r-summarizedexperiment)
5971 ("r-variantannotation" ,r-variantannotation)
5972 ("r-xvector" ,r-xvector)))
5973 (home-page "https://github.com/rcastelo/VariantFiltering")
5974 (synopsis "Filtering of coding and non-coding genetic variants")
5976 "Filter genetic variants using different criteria such as inheritance
5977 model, amino acid change consequence, minor allele frequencies across human
5978 populations, splice site strength, conservation, etc.")
5979 (license license:artistic2.0)))
5981 (define-public r-genomegraphs
5983 (name "r-genomegraphs")
5988 (uri (bioconductor-uri "GenomeGraphs" version))
5991 "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd"))))
5992 (properties `((upstream-name . "GenomeGraphs")))
5993 (build-system r-build-system)
5995 `(("r-biomart" ,r-biomart)))
5996 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
5997 (synopsis "Plotting genomic information from Ensembl")
5999 "Genomic data analyses requires integrated visualization of known genomic
6000 information and new experimental data. GenomeGraphs uses the biomaRt package
6001 to perform live annotation queries to Ensembl and translates this to e.g.
6002 gene/transcript structures in viewports of the grid graphics package. This
6003 results in genomic information plotted together with your data. Another
6004 strength of GenomeGraphs is to plot different data types such as array CGH,
6005 gene expression, sequencing and other data, together in one plot using the
6006 same genome coordinate system.")
6007 (license license:artistic2.0)))
6009 (define-public r-wavetiling
6011 (name "r-wavetiling")
6016 (uri (bioconductor-uri "waveTiling" version))
6019 "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir"))))
6020 (properties `((upstream-name . "waveTiling")))
6021 (build-system r-build-system)
6023 `(("r-affy" ,r-affy)
6024 ("r-biobase" ,r-biobase)
6025 ("r-biostrings" ,r-biostrings)
6026 ("r-genomegraphs" ,r-genomegraphs)
6027 ("r-genomicranges" ,r-genomicranges)
6028 ("r-iranges" ,r-iranges)
6029 ("r-oligo" ,r-oligo)
6030 ("r-oligoclasses" ,r-oligoclasses)
6031 ("r-preprocesscore" ,r-preprocesscore)
6032 ("r-waveslim" ,r-waveslim)))
6033 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6034 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6036 "This package is designed to conduct transcriptome analysis for tiling
6037 arrays based on fast wavelet-based functional models.")
6038 (license license:gpl2+)))
6040 (define-public r-variancepartition
6042 (name "r-variancepartition")
6047 (uri (bioconductor-uri "variancePartition" version))
6050 "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
6052 `((upstream-name . "variancePartition")))
6053 (build-system r-build-system)
6055 `(("r-biobase" ,r-biobase)
6056 ("r-biocparallel" ,r-biocparallel)
6057 ("r-colorramps" ,r-colorramps)
6058 ("r-doparallel" ,r-doparallel)
6059 ("r-foreach" ,r-foreach)
6060 ("r-ggplot2" ,r-ggplot2)
6061 ("r-gplots" ,r-gplots)
6062 ("r-iterators" ,r-iterators)
6063 ("r-limma" ,r-limma)
6065 ("r-lmertest" ,r-lmertest)
6067 ("r-pbkrtest" ,r-pbkrtest)
6068 ("r-progress" ,r-progress)
6069 ("r-reshape2" ,r-reshape2)
6070 ("r-scales" ,r-scales)))
6071 (home-page "https://bioconductor.org/packages/variancePartition/")
6072 (synopsis "Analyze variation in gene expression experiments")
6074 "This is a package providing tools to quantify and interpret multiple
6075 sources of biological and technical variation in gene expression experiments.
6076 It uses a linear mixed model to quantify variation in gene expression
6077 attributable to individual, tissue, time point, or technical variables. The
6078 package includes dream differential expression analysis for repeated
6080 (license license:gpl2+)))