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)))
838 (define-public r-abadata
844 ;; We cannot use bioconductor-uri here because this tarball is
845 ;; located under "data/experiment/" instead of "bioc/".
846 (uri (string-append "https://www.bioconductor.org/packages/"
847 "release/data/experiment/src/contrib/"
848 "ABAData_" version ".tar.gz"))
851 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
853 `((upstream-name . "ABAData")))
854 (build-system r-build-system)
856 `(("r-annotationdbi" ,r-annotationdbi)))
857 (home-page "https://www.bioconductor.org/packages/ABAData/")
858 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
860 "This package provides the data for the gene expression enrichment
861 analysis conducted in the package ABAEnrichment. The package includes three
862 datasets which are derived from the Allen Brain Atlas:
865 @item Gene expression data from Human Brain (adults) averaged across donors,
866 @item Gene expression data from the Developing Human Brain pooled into five
867 age categories and averaged across donors, and
868 @item a developmental effect score based on the Developing Human Brain
872 All datasets are restricted to protein coding genes.")
873 (license license:gpl2+)))
875 (define-public r-arrmdata
881 ;; We cannot use bioconductor-uri here because this tarball is
882 ;; located under "data/experiment/" instead of "bioc/".
883 (uri (string-append "https://www.bioconductor.org/packages/"
884 "release/data/experiment/src/contrib/"
885 "ARRmData_" version ".tar.gz"))
888 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
890 `((upstream-name . "ARRmData")))
891 (build-system r-build-system)
892 (home-page "https://www.bioconductor.org/packages/ARRmData/")
893 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
895 "This package provides raw beta values from 36 samples across 3 groups
896 from Illumina 450k methylation arrays.")
897 (license license:artistic2.0)))
899 (define-public r-hsmmsinglecell
901 (name "r-hsmmsinglecell")
905 ;; We cannot use bioconductor-uri here because this tarball is
906 ;; located under "data/experiment/" instead of "bioc/".
907 (uri (string-append "https://www.bioconductor.org/packages/"
908 "release/data/experiment/src/contrib/"
909 "HSMMSingleCell_" version ".tar.gz"))
912 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
914 `((upstream-name . "HSMMSingleCell")))
915 (build-system r-build-system)
916 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
917 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
919 "Skeletal myoblasts undergo a well-characterized sequence of
920 morphological and transcriptional changes during differentiation. In this
921 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
922 under high mitogen conditions (GM) and then differentiated by switching to
923 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
924 hundred cells taken over a time-course of serum-induced differentiation.
925 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
926 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
927 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
928 which were then sequenced to a depth of ~4 million reads per library,
929 resulting in a complete gene expression profile for each cell.")
930 (license license:artistic2.0)))
938 ;; We cannot use bioconductor-uri here because this tarball is
939 ;; located under "data/experiment/" instead of "bioc/".
940 (uri (string-append "https://www.bioconductor.org/packages/"
941 "release/data/experiment/src/contrib/"
942 "ALL_" version ".tar.gz"))
945 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
946 (properties `((upstream-name . "ALL")))
947 (build-system r-build-system)
949 `(("r-biobase" ,r-biobase)))
950 (home-page "https://bioconductor.org/packages/ALL")
951 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
953 "The data consist of microarrays from 128 different individuals with
954 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
955 are available. The data have been normalized (using rma) and it is the
956 jointly normalized data that are available here. The data are presented in
957 the form of an @code{exprSet} object.")
958 (license license:artistic2.0)))
960 (define-public r-affydata
967 (uri (bioconductor-uri "affydata" version 'experiment))
970 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
971 (properties `((upstream-name . "affydata")))
972 (build-system r-build-system)
974 `(("r-affy" ,r-affy)))
975 (home-page "https://bioconductor.org/packages/affydata/")
976 (synopsis "Affymetrix data for demonstration purposes")
978 "This package provides example datasets that represent 'real world
979 examples' of Affymetrix data, unlike the artificial examples included in the
980 package @code{affy}.")
981 (license license:gpl2+)))
986 (define-public r-biocgenerics
988 (name "r-biocgenerics")
992 (uri (bioconductor-uri "BiocGenerics" version))
995 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
997 `((upstream-name . "BiocGenerics")))
998 (build-system r-build-system)
999 (home-page "https://bioconductor.org/packages/BiocGenerics")
1000 (synopsis "S4 generic functions for Bioconductor")
1002 "This package provides S4 generic functions needed by many Bioconductor
1004 (license license:artistic2.0)))
1006 (define-public r-affycomp
1013 (uri (bioconductor-uri "affycomp" version))
1016 "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
1017 (properties `((upstream-name . "affycomp")))
1018 (build-system r-build-system)
1019 (propagated-inputs `(("r-biobase" ,r-biobase)))
1020 (home-page "https://bioconductor.org/packages/affycomp/")
1021 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1023 "The package contains functions that can be used to compare expression
1024 measures for Affymetrix Oligonucleotide Arrays.")
1025 (license license:gpl2+)))
1027 (define-public r-affycompatible
1029 (name "r-affycompatible")
1034 (uri (bioconductor-uri "AffyCompatible" version))
1037 "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
1039 `((upstream-name . "AffyCompatible")))
1040 (build-system r-build-system)
1042 `(("r-biostrings" ,r-biostrings)
1043 ("r-rcurl" ,r-rcurl)
1045 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1046 (synopsis "Work with Affymetrix GeneChip files")
1048 "This package provides an interface to Affymetrix chip annotation and
1049 sample attribute files. The package allows an easy way for users to download
1050 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1051 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1052 Command Console} (AGCC)-compatible sample annotation files.")
1053 (license license:artistic2.0)))
1055 (define-public r-affycontam
1057 (name "r-affycontam")
1062 (uri (bioconductor-uri "affyContam" version))
1065 "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
1066 (properties `((upstream-name . "affyContam")))
1067 (build-system r-build-system)
1069 `(("r-affy" ,r-affy)
1070 ("r-affydata" ,r-affydata)
1071 ("r-biobase" ,r-biobase)))
1072 (home-page "https://bioconductor.org/packages/affyContam/")
1073 (synopsis "Structured corruption of Affymetrix CEL file data")
1075 "Microarray quality assessment is a major concern of microarray analysts.
1076 This package provides some simple approaches to in silico creation of quality
1077 problems in CEL-level data to help evaluate performance of quality metrics.")
1078 (license license:artistic2.0)))
1080 (define-public r-annotate
1087 (uri (bioconductor-uri "annotate" version))
1090 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
1091 (build-system r-build-system)
1093 `(("r-annotationdbi" ,r-annotationdbi)
1094 ("r-biobase" ,r-biobase)
1095 ("r-biocgenerics" ,r-biocgenerics)
1097 ("r-rcurl" ,r-rcurl)
1099 ("r-xtable" ,r-xtable)))
1101 "https://bioconductor.org/packages/annotate")
1102 (synopsis "Annotation for microarrays")
1103 (description "This package provides R environments for the annotation of
1105 (license license:artistic2.0)))
1107 (define-public r-hpar
1114 (uri (bioconductor-uri "hpar" version))
1117 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
1118 (build-system r-build-system)
1119 (home-page "https://bioconductor.org/packages/hpar/")
1120 (synopsis "Human Protein Atlas in R")
1121 (description "This package provides a simple interface to and data from
1122 the Human Protein Atlas project.")
1123 (license license:artistic2.0)))
1125 (define-public r-regioner
1132 (uri (bioconductor-uri "regioneR" version))
1135 "0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760"))))
1136 (properties `((upstream-name . "regioneR")))
1137 (build-system r-build-system)
1139 `(("r-biostrings" ,r-biostrings)
1140 ("r-bsgenome" ,r-bsgenome)
1141 ("r-genomeinfodb" ,r-genomeinfodb)
1142 ("r-genomicranges" ,r-genomicranges)
1143 ("r-iranges" ,r-iranges)
1144 ("r-memoise" ,r-memoise)
1145 ("r-rtracklayer" ,r-rtracklayer)
1146 ("r-s4vectors" ,r-s4vectors)))
1147 (home-page "https://bioconductor.org/packages/regioneR/")
1148 (synopsis "Association analysis of genomic regions")
1149 (description "This package offers a statistical framework based on
1150 customizable permutation tests to assess the association between genomic
1151 region sets and other genomic features.")
1152 (license license:artistic2.0)))
1154 (define-public r-reportingtools
1156 (name "r-reportingtools")
1161 (uri (bioconductor-uri "ReportingTools" version))
1164 "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
1166 `((upstream-name . "ReportingTools")))
1167 (build-system r-build-system)
1169 `(("r-annotate" ,r-annotate)
1170 ("r-annotationdbi" ,r-annotationdbi)
1171 ("r-biobase" ,r-biobase)
1172 ("r-biocgenerics" ,r-biocgenerics)
1173 ("r-category" ,r-category)
1174 ("r-deseq2" ,r-deseq2)
1175 ("r-edger" ,r-edger)
1176 ("r-ggbio" ,r-ggbio)
1177 ("r-ggplot2" ,r-ggplot2)
1178 ("r-gostats" ,r-gostats)
1179 ("r-gseabase" ,r-gseabase)
1180 ("r-hwriter" ,r-hwriter)
1181 ("r-iranges" ,r-iranges)
1182 ("r-knitr" ,r-knitr)
1183 ("r-lattice" ,r-lattice)
1184 ("r-limma" ,r-limma)
1185 ("r-pfam-db" ,r-pfam-db)
1186 ("r-r-utils" ,r-r-utils)
1188 (home-page "https://bioconductor.org/packages/ReportingTools/")
1189 (synopsis "Tools for making reports in various formats")
1191 "The ReportingTools package enables users to easily display reports of
1192 analysis results generated from sources such as microarray and sequencing
1193 data. The package allows users to create HTML pages that may be viewed on a
1194 web browser, or in other formats. Users can generate tables with sortable and
1195 filterable columns, make and display plots, and link table entries to other
1196 data sources such as NCBI or larger plots within the HTML page. Using the
1197 package, users can also produce a table of contents page to link various
1198 reports together for a particular project that can be viewed in a web
1200 (license license:artistic2.0)))
1202 (define-public r-geneplotter
1204 (name "r-geneplotter")
1209 (uri (bioconductor-uri "geneplotter" version))
1212 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1213 (build-system r-build-system)
1215 `(("r-annotate" ,r-annotate)
1216 ("r-annotationdbi" ,r-annotationdbi)
1217 ("r-biobase" ,r-biobase)
1218 ("r-biocgenerics" ,r-biocgenerics)
1219 ("r-lattice" ,r-lattice)
1220 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1221 (home-page "https://bioconductor.org/packages/geneplotter")
1222 (synopsis "Graphics functions for genomic data")
1224 "This package provides functions for plotting genomic data.")
1225 (license license:artistic2.0)))
1227 (define-public r-qvalue
1234 (uri (bioconductor-uri "qvalue" version))
1237 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1238 (build-system r-build-system)
1240 `(("r-ggplot2" ,r-ggplot2)
1241 ("r-reshape2" ,r-reshape2)))
1242 (home-page "http://github.com/jdstorey/qvalue")
1243 (synopsis "Q-value estimation for false discovery rate control")
1245 "This package takes a list of p-values resulting from the simultaneous
1246 testing of many hypotheses and estimates their q-values and local @dfn{false
1247 discovery rate} (FDR) values. The q-value of a test measures the proportion
1248 of false positives incurred when that particular test is called significant.
1249 The local FDR measures the posterior probability the null hypothesis is true
1250 given the test's p-value. Various plots are automatically generated, allowing
1251 one to make sensible significance cut-offs. The software can be applied to
1252 problems in genomics, brain imaging, astrophysics, and data mining.")
1253 ;; Any version of the LGPL.
1254 (license license:lgpl3+)))
1256 (define-public r-diffbind
1263 (uri (bioconductor-uri "DiffBind" version))
1266 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1267 (properties `((upstream-name . "DiffBind")))
1268 (build-system r-build-system)
1272 `(("r-amap" ,r-amap)
1273 ("r-biocparallel" ,r-biocparallel)
1274 ("r-deseq2" ,r-deseq2)
1275 ("r-dplyr" ,r-dplyr)
1276 ("r-edger" ,r-edger)
1277 ("r-genomicalignments" ,r-genomicalignments)
1278 ("r-genomicranges" ,r-genomicranges)
1279 ("r-ggplot2" ,r-ggplot2)
1280 ("r-ggrepel" ,r-ggrepel)
1281 ("r-gplots" ,r-gplots)
1282 ("r-iranges" ,r-iranges)
1283 ("r-lattice" ,r-lattice)
1284 ("r-limma" ,r-limma)
1285 ("r-locfit" ,r-locfit)
1286 ("r-rcolorbrewer" , r-rcolorbrewer)
1288 ("r-rhtslib" ,r-rhtslib)
1289 ("r-rsamtools" ,r-rsamtools)
1290 ("r-s4vectors" ,r-s4vectors)
1291 ("r-summarizedexperiment" ,r-summarizedexperiment)
1292 ("r-systempiper" ,r-systempiper)))
1293 (home-page "http://bioconductor.org/packages/DiffBind")
1294 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1296 "This package computes differentially bound sites from multiple
1297 ChIP-seq experiments using affinity (quantitative) data. Also enables
1298 occupancy (overlap) analysis and plotting functions.")
1299 (license license:artistic2.0)))
1301 (define-public r-ripseeker
1303 (name "r-ripseeker")
1308 (uri (bioconductor-uri "RIPSeeker" version))
1311 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1312 (properties `((upstream-name . "RIPSeeker")))
1313 (build-system r-build-system)
1315 `(("r-s4vectors" ,r-s4vectors)
1316 ("r-iranges" ,r-iranges)
1317 ("r-genomicranges" ,r-genomicranges)
1318 ("r-summarizedexperiment" ,r-summarizedexperiment)
1319 ("r-rsamtools" ,r-rsamtools)
1320 ("r-genomicalignments" ,r-genomicalignments)
1321 ("r-rtracklayer" ,r-rtracklayer)))
1322 (home-page "http://bioconductor.org/packages/RIPSeeker")
1324 "Identifying protein-associated transcripts from RIP-seq experiments")
1326 "This package infers and discriminates RIP peaks from RIP-seq alignments
1327 using two-state HMM with negative binomial emission probability. While
1328 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1329 a suite of bioinformatics tools integrated within this self-contained software
1330 package comprehensively addressing issues ranging from post-alignments
1331 processing to visualization and annotation.")
1332 (license license:gpl2)))
1334 (define-public r-multtest
1341 (uri (bioconductor-uri "multtest" version))
1344 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1345 (build-system r-build-system)
1347 `(("r-survival" ,r-survival)
1348 ("r-biocgenerics" ,r-biocgenerics)
1349 ("r-biobase" ,r-biobase)
1350 ("r-mass" ,r-mass)))
1351 (home-page "http://bioconductor.org/packages/multtest")
1352 (synopsis "Resampling-based multiple hypothesis testing")
1354 "This package can do non-parametric bootstrap and permutation
1355 resampling-based multiple testing procedures (including empirical Bayes
1356 methods) for controlling the family-wise error rate (FWER), generalized
1357 family-wise error rate (gFWER), tail probability of the proportion of
1358 false positives (TPPFP), and false discovery rate (FDR). Several choices
1359 of bootstrap-based null distribution are implemented (centered, centered
1360 and scaled, quantile-transformed). Single-step and step-wise methods are
1361 available. Tests based on a variety of T- and F-statistics (including
1362 T-statistics based on regression parameters from linear and survival models
1363 as well as those based on correlation parameters) are included. When probing
1364 hypotheses with T-statistics, users may also select a potentially faster null
1365 distribution which is multivariate normal with mean zero and variance
1366 covariance matrix derived from the vector influence function. Results are
1367 reported in terms of adjusted P-values, confidence regions and test statistic
1368 cutoffs. The procedures are directly applicable to identifying differentially
1369 expressed genes in DNA microarray experiments.")
1370 (license license:lgpl3)))
1372 (define-public r-graph
1378 (uri (bioconductor-uri "graph" version))
1381 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1382 (build-system r-build-system)
1384 `(("r-biocgenerics" ,r-biocgenerics)))
1385 (home-page "https://bioconductor.org/packages/graph")
1386 (synopsis "Handle graph data structures in R")
1388 "This package implements some simple graph handling capabilities for R.")
1389 (license license:artistic2.0)))
1391 (define-public r-codedepends
1393 (name "r-codedepends")
1398 (uri (cran-uri "CodeDepends" version))
1401 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1402 (properties `((upstream-name . "CodeDepends")))
1403 (build-system r-build-system)
1405 `(("r-codetools" ,r-codetools)
1406 ("r-graph" ,r-graph)
1408 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1409 (synopsis "Analysis of R code for reproducible research and code comprehension")
1411 "This package provides tools for analyzing R expressions or blocks of
1412 code and determining the dependencies between them. It focuses on R scripts,
1413 but can be used on the bodies of functions. There are many facilities
1414 including the ability to summarize or get a high-level view of code,
1415 determining dependencies between variables, code improvement suggestions.")
1416 ;; Any version of the GPL
1417 (license (list license:gpl2+ license:gpl3+))))
1419 (define-public r-chippeakanno
1421 (name "r-chippeakanno")
1426 (uri (bioconductor-uri "ChIPpeakAnno" version))
1429 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1430 (properties `((upstream-name . "ChIPpeakAnno")))
1431 (build-system r-build-system)
1433 `(("r-annotationdbi" ,r-annotationdbi)
1434 ("r-biobase" ,r-biobase)
1435 ("r-biocgenerics" ,r-biocgenerics)
1436 ("r-biocmanager" ,r-biocmanager)
1437 ("r-biomart" ,r-biomart)
1438 ("r-biostrings" ,r-biostrings)
1439 ("r-bsgenome" ,r-bsgenome)
1441 ("r-delayedarray" ,r-delayedarray)
1442 ("r-ensembldb" ,r-ensembldb)
1443 ("r-genomeinfodb" ,r-genomeinfodb)
1444 ("r-genomicalignments" ,r-genomicalignments)
1445 ("r-genomicfeatures" ,r-genomicfeatures)
1446 ("r-genomicranges" ,r-genomicranges)
1447 ("r-go-db" ,r-go-db)
1448 ("r-graph" ,r-graph)
1450 ("r-iranges" ,r-iranges)
1451 ("r-limma" ,r-limma)
1452 ("r-matrixstats" ,r-matrixstats)
1453 ("r-multtest" ,r-multtest)
1455 ("r-regioner" ,r-regioner)
1456 ("r-rsamtools" ,r-rsamtools)
1457 ("r-rtracklayer" ,r-rtracklayer)
1458 ("r-s4vectors" ,r-s4vectors)
1459 ("r-seqinr" ,r-seqinr)
1460 ("r-summarizedexperiment" ,r-summarizedexperiment)
1461 ("r-venndiagram" ,r-venndiagram)))
1462 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1463 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1465 "The package includes functions to retrieve the sequences around the peak,
1466 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1467 custom features such as most conserved elements and other transcription factor
1468 binding sites supplied by users. Starting 2.0.5, new functions have been added
1469 for finding the peaks with bi-directional promoters with summary statistics
1470 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1471 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1472 enrichedGO (addGeneIDs).")
1473 (license license:gpl2+)))
1475 (define-public r-marray
1481 (uri (bioconductor-uri "marray" version))
1483 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1484 (build-system r-build-system)
1486 `(("r-limma" ,r-limma)))
1487 (home-page "http://bioconductor.org/packages/marray")
1488 (synopsis "Exploratory analysis for two-color spotted microarray data")
1489 (description "This package contains class definitions for two-color spotted
1490 microarray data. It also includes functions for data input, diagnostic plots,
1491 normalization and quality checking.")
1492 (license license:lgpl2.0+)))
1494 (define-public r-cghbase
1500 (uri (bioconductor-uri "CGHbase" version))
1502 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1503 (properties `((upstream-name . "CGHbase")))
1504 (build-system r-build-system)
1506 `(("r-biobase" ,r-biobase)
1507 ("r-marray" ,r-marray)))
1508 (home-page "http://bioconductor.org/packages/CGHbase")
1509 (synopsis "Base functions and classes for arrayCGH data analysis")
1510 (description "This package contains functions and classes that are needed by
1511 the @code{arrayCGH} packages.")
1512 (license license:gpl2+)))
1514 (define-public r-cghcall
1520 (uri (bioconductor-uri "CGHcall" version))
1522 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1523 (properties `((upstream-name . "CGHcall")))
1524 (build-system r-build-system)
1526 `(("r-biobase" ,r-biobase)
1527 ("r-cghbase" ,r-cghbase)
1528 ("r-impute" ,r-impute)
1529 ("r-dnacopy" ,r-dnacopy)
1530 ("r-snowfall" ,r-snowfall)))
1531 (home-page "http://bioconductor.org/packages/CGHcall")
1532 (synopsis "Base functions and classes for arrayCGH data analysis")
1533 (description "This package contains functions and classes that are needed by
1534 @code{arrayCGH} packages.")
1535 (license license:gpl2+)))
1537 (define-public r-qdnaseq
1543 (uri (bioconductor-uri "QDNAseq" version))
1545 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1546 (properties `((upstream-name . "QDNAseq")))
1547 (build-system r-build-system)
1549 `(("r-biobase" ,r-biobase)
1550 ("r-biocparallel" ,r-biocparallel)
1551 ("r-cghbase" ,r-cghbase)
1552 ("r-cghcall" ,r-cghcall)
1553 ("r-dnacopy" ,r-dnacopy)
1554 ("r-genomicranges" ,r-genomicranges)
1555 ("r-iranges" ,r-iranges)
1556 ("r-matrixstats" ,r-matrixstats)
1557 ("r-r-utils" ,r-r-utils)
1558 ("r-rsamtools" ,r-rsamtools)))
1559 (home-page "http://bioconductor.org/packages/QDNAseq")
1560 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1561 (description "The genome is divided into non-overlapping fixed-sized bins,
1562 number of sequence reads in each counted, adjusted with a simultaneous
1563 two-dimensional loess correction for sequence mappability and GC content, and
1564 filtered to remove spurious regions in the genome. Downstream steps of
1565 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1567 (license license:gpl2+)))
1569 (define-public r-bayseq
1576 (uri (bioconductor-uri "baySeq" version))
1579 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1580 (properties `((upstream-name . "baySeq")))
1581 (build-system r-build-system)
1583 `(("r-abind" ,r-abind)
1584 ("r-edger" ,r-edger)
1585 ("r-genomicranges" ,r-genomicranges)))
1586 (home-page "https://bioconductor.org/packages/baySeq/")
1587 (synopsis "Bayesian analysis of differential expression patterns in count data")
1589 "This package identifies differential expression in high-throughput count
1590 data, such as that derived from next-generation sequencing machines,
1591 calculating estimated posterior likelihoods of differential expression (or
1592 more complex hypotheses) via empirical Bayesian methods.")
1593 (license license:gpl3)))
1595 (define-public r-chipcomp
1602 (uri (bioconductor-uri "ChIPComp" version))
1605 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1606 (properties `((upstream-name . "ChIPComp")))
1607 (build-system r-build-system)
1609 `(("r-biocgenerics" ,r-biocgenerics)
1610 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1611 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1612 ("r-genomeinfodb" ,r-genomeinfodb)
1613 ("r-genomicranges" ,r-genomicranges)
1614 ("r-iranges" ,r-iranges)
1615 ("r-limma" ,r-limma)
1616 ("r-rsamtools" ,r-rsamtools)
1617 ("r-rtracklayer" ,r-rtracklayer)
1618 ("r-s4vectors" ,r-s4vectors)))
1619 (home-page "https://bioconductor.org/packages/ChIPComp")
1620 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1622 "ChIPComp implements a statistical method for quantitative comparison of
1623 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1624 sites across multiple conditions considering matching control in ChIP-seq
1626 ;; Any version of the GPL.
1627 (license license:gpl3+)))
1629 (define-public r-riboprofiling
1631 (name "r-riboprofiling")
1636 (uri (bioconductor-uri "RiboProfiling" version))
1639 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1640 (properties `((upstream-name . "RiboProfiling")))
1641 (build-system r-build-system)
1643 `(("r-biocgenerics" ,r-biocgenerics)
1644 ("r-biostrings" ,r-biostrings)
1645 ("r-data-table" ,r-data-table)
1646 ("r-genomeinfodb" ,r-genomeinfodb)
1647 ("r-genomicalignments" ,r-genomicalignments)
1648 ("r-genomicfeatures" ,r-genomicfeatures)
1649 ("r-genomicranges" ,r-genomicranges)
1650 ("r-ggbio" ,r-ggbio)
1651 ("r-ggplot2" ,r-ggplot2)
1652 ("r-iranges" ,r-iranges)
1654 ("r-reshape2" ,r-reshape2)
1655 ("r-rsamtools" ,r-rsamtools)
1656 ("r-rtracklayer" ,r-rtracklayer)
1657 ("r-s4vectors" ,r-s4vectors)
1658 ("r-sqldf" ,r-sqldf)))
1659 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1660 (synopsis "Ribosome profiling data analysis")
1661 (description "Starting with a BAM file, this package provides the
1662 necessary functions for quality assessment, read start position recalibration,
1663 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1664 of count data: pairs, log fold-change, codon frequency and coverage
1665 assessment, principal component analysis on codon coverage.")
1666 (license license:gpl3)))
1668 (define-public r-riboseqr
1675 (uri (bioconductor-uri "riboSeqR" version))
1678 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1679 (properties `((upstream-name . "riboSeqR")))
1680 (build-system r-build-system)
1682 `(("r-abind" ,r-abind)
1683 ("r-bayseq" ,r-bayseq)
1684 ("r-genomeinfodb" ,r-genomeinfodb)
1685 ("r-genomicranges" ,r-genomicranges)
1686 ("r-iranges" ,r-iranges)
1687 ("r-rsamtools" ,r-rsamtools)
1688 ("r-seqlogo" ,r-seqlogo)))
1689 (home-page "https://bioconductor.org/packages/riboSeqR/")
1690 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1692 "This package provides plotting functions, frameshift detection and
1693 parsing of genetic sequencing data from ribosome profiling experiments.")
1694 (license license:gpl3)))
1696 (define-public r-interactionset
1698 (name "r-interactionset")
1703 (uri (bioconductor-uri "InteractionSet" version))
1706 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1708 `((upstream-name . "InteractionSet")))
1709 (build-system r-build-system)
1711 `(("r-biocgenerics" ,r-biocgenerics)
1712 ("r-genomeinfodb" ,r-genomeinfodb)
1713 ("r-genomicranges" ,r-genomicranges)
1714 ("r-iranges" ,r-iranges)
1715 ("r-matrix" ,r-matrix)
1717 ("r-s4vectors" ,r-s4vectors)
1718 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1719 (home-page "https://bioconductor.org/packages/InteractionSet")
1720 (synopsis "Base classes for storing genomic interaction data")
1722 "This package provides the @code{GInteractions},
1723 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1724 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1726 (license license:gpl3)))
1728 (define-public r-genomicinteractions
1730 (name "r-genomicinteractions")
1735 (uri (bioconductor-uri "GenomicInteractions" version))
1738 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1740 `((upstream-name . "GenomicInteractions")))
1741 (build-system r-build-system)
1743 `(("r-biobase" ,r-biobase)
1744 ("r-biocgenerics" ,r-biocgenerics)
1745 ("r-data-table" ,r-data-table)
1746 ("r-dplyr" ,r-dplyr)
1747 ("r-genomeinfodb" ,r-genomeinfodb)
1748 ("r-genomicranges" ,r-genomicranges)
1749 ("r-ggplot2" ,r-ggplot2)
1750 ("r-gridextra" ,r-gridextra)
1752 ("r-igraph" ,r-igraph)
1753 ("r-interactionset" ,r-interactionset)
1754 ("r-iranges" ,r-iranges)
1755 ("r-rsamtools" ,r-rsamtools)
1756 ("r-rtracklayer" ,r-rtracklayer)
1757 ("r-s4vectors" ,r-s4vectors)
1758 ("r-stringr" ,r-stringr)))
1759 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1760 (synopsis "R package for handling genomic interaction data")
1762 "This R package provides tools for handling genomic interaction data,
1763 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1764 information and producing various plots and statistics.")
1765 (license license:gpl3)))
1767 (define-public r-ctc
1774 (uri (bioconductor-uri "ctc" version))
1777 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1778 (build-system r-build-system)
1779 (propagated-inputs `(("r-amap" ,r-amap)))
1780 (home-page "https://bioconductor.org/packages/ctc/")
1781 (synopsis "Cluster and tree conversion")
1783 "This package provides tools for exporting and importing classification
1784 trees and clusters to other programs.")
1785 (license license:gpl2)))
1787 (define-public r-goseq
1794 (uri (bioconductor-uri "goseq" version))
1797 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1798 (build-system r-build-system)
1800 `(("r-annotationdbi" ,r-annotationdbi)
1801 ("r-biasedurn" ,r-biasedurn)
1802 ("r-biocgenerics" ,r-biocgenerics)
1803 ("r-genelendatabase" ,r-genelendatabase)
1804 ("r-go-db" ,r-go-db)
1805 ("r-mgcv" ,r-mgcv)))
1806 (home-page "https://bioconductor.org/packages/goseq/")
1807 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1809 "This package provides tools to detect Gene Ontology and/or other user
1810 defined categories which are over/under represented in RNA-seq data.")
1811 (license license:lgpl2.0+)))
1813 (define-public r-glimma
1820 (uri (bioconductor-uri "Glimma" version))
1823 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1824 (properties `((upstream-name . "Glimma")))
1825 (build-system r-build-system)
1827 `(("r-edger" ,r-edger)
1828 ("r-jsonlite" ,r-jsonlite)
1829 ("r-s4vectors" ,r-s4vectors)))
1830 (home-page "https://github.com/Shians/Glimma")
1831 (synopsis "Interactive HTML graphics")
1833 "This package generates interactive visualisations for analysis of
1834 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1835 HTML page. The interactions are built on top of the popular static
1836 representations of analysis results in order to provide additional
1838 (license license:lgpl3)))
1840 (define-public r-rots
1847 (uri (bioconductor-uri "ROTS" version))
1850 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1851 (properties `((upstream-name . "ROTS")))
1852 (build-system r-build-system)
1854 `(("r-biobase" ,r-biobase)
1855 ("r-rcpp" ,r-rcpp)))
1856 (home-page "https://bioconductor.org/packages/ROTS/")
1857 (synopsis "Reproducibility-Optimized Test Statistic")
1859 "This package provides tools for calculating the
1860 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1862 (license license:gpl2+)))
1864 (define-public r-plgem
1871 (uri (bioconductor-uri "plgem" version))
1874 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1875 (build-system r-build-system)
1877 `(("r-biobase" ,r-biobase)
1878 ("r-mass" ,r-mass)))
1879 (home-page "http://www.genopolis.it")
1880 (synopsis "Detect differential expression in microarray and proteomics datasets")
1882 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1883 model the variance-versus-mean dependence that exists in a variety of
1884 genome-wide datasets, including microarray and proteomics data. The use of
1885 PLGEM has been shown to improve the detection of differentially expressed
1886 genes or proteins in these datasets.")
1887 (license license:gpl2)))
1889 (define-public r-inspect
1896 (uri (bioconductor-uri "INSPEcT" version))
1899 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1900 (properties `((upstream-name . "INSPEcT")))
1901 (build-system r-build-system)
1903 `(("r-biobase" ,r-biobase)
1904 ("r-biocgenerics" ,r-biocgenerics)
1905 ("r-biocparallel" ,r-biocparallel)
1906 ("r-deseq2" ,r-deseq2)
1907 ("r-desolve" ,r-desolve)
1908 ("r-genomicalignments" ,r-genomicalignments)
1909 ("r-genomicfeatures" ,r-genomicfeatures)
1910 ("r-genomicranges" ,r-genomicranges)
1911 ("r-iranges" ,r-iranges)
1912 ("r-plgem" ,r-plgem)
1913 ("r-preprocesscore" ,r-preprocesscore)
1915 ("r-rootsolve" ,r-rootsolve)
1916 ("r-rsamtools" ,r-rsamtools)
1917 ("r-s4vectors" ,r-s4vectors)
1918 ("r-shiny" ,r-shiny)
1919 ("r-summarizedexperiment" ,r-summarizedexperiment)
1920 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1921 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1922 (home-page "https://bioconductor.org/packages/INSPEcT")
1923 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1925 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1926 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1927 order to evaluate synthesis, processing and degradation rates and assess via
1928 modeling the rates that determines changes in mature mRNA levels.")
1929 (license license:gpl2)))
1931 (define-public r-dnabarcodes
1933 (name "r-dnabarcodes")
1938 (uri (bioconductor-uri "DNABarcodes" version))
1941 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1942 (properties `((upstream-name . "DNABarcodes")))
1943 (build-system r-build-system)
1946 ("r-matrix" ,r-matrix)
1947 ("r-rcpp" ,r-rcpp)))
1948 (home-page "https://bioconductor.org/packages/DNABarcodes")
1949 (synopsis "Create and analyze DNA barcodes")
1951 "This package offers tools to create DNA barcode sets capable of
1952 correcting insertion, deletion, and substitution errors. Existing barcodes
1953 can be analyzed regarding their minimal, maximal and average distances between
1954 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1955 demultiplexed, i.e. assigned to their original reference barcode.")
1956 (license license:gpl2)))
1958 (define-public r-ruvseq
1965 (uri (bioconductor-uri "RUVSeq" version))
1968 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
1969 (properties `((upstream-name . "RUVSeq")))
1970 (build-system r-build-system)
1972 `(("r-biobase" ,r-biobase)
1973 ("r-edaseq" ,r-edaseq)
1974 ("r-edger" ,r-edger)
1975 ("r-mass" ,r-mass)))
1976 (home-page "https://github.com/drisso/RUVSeq")
1977 (synopsis "Remove unwanted variation from RNA-Seq data")
1979 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1980 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1982 (license license:artistic2.0)))
1984 (define-public r-biocneighbors
1986 (name "r-biocneighbors")
1991 (uri (bioconductor-uri "BiocNeighbors" version))
1994 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
1995 (properties `((upstream-name . "BiocNeighbors")))
1996 (build-system r-build-system)
1998 `(("r-biocgenerics" ,r-biocgenerics)
1999 ("r-biocparallel" ,r-biocparallel)
2001 ("r-rcppannoy" ,r-rcppannoy)
2002 ("r-rcpphnsw" ,r-rcpphnsw)
2003 ("r-s4vectors" ,r-s4vectors)))
2004 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2005 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2007 "This package implements exact and approximate methods for nearest
2008 neighbor detection, in a framework that allows them to be easily switched
2009 within Bioconductor packages or workflows. The exact algorithm is implemented
2010 using pre-clustering with the k-means algorithm. Functions are also provided
2011 to search for all neighbors within a given distance. Parallelization is
2012 achieved for all methods using the BiocParallel framework.")
2013 (license license:gpl3)))
2015 (define-public r-biocsingular
2017 (name "r-biocsingular")
2022 (uri (bioconductor-uri "BiocSingular" version))
2025 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
2026 (properties `((upstream-name . "BiocSingular")))
2027 (build-system r-build-system)
2029 `(("r-beachmat" ,r-beachmat)
2030 ("r-biocgenerics" ,r-biocgenerics)
2031 ("r-biocparallel" ,r-biocparallel)
2032 ("r-delayedarray" ,r-delayedarray)
2033 ("r-irlba" ,r-irlba)
2034 ("r-matrix" ,r-matrix)
2037 ("r-s4vectors" ,r-s4vectors)))
2038 (home-page "https://github.com/LTLA/BiocSingular")
2039 (synopsis "Singular value decomposition for Bioconductor packages")
2041 "This package implements exact and approximate methods for singular value
2042 decomposition and principal components analysis, in a framework that allows
2043 them to be easily switched within Bioconductor packages or workflows. Where
2044 possible, parallelization is achieved using the BiocParallel framework.")
2045 (license license:gpl3)))
2047 (define-public r-destiny
2054 (uri (bioconductor-uri "destiny" version))
2057 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
2058 (build-system r-build-system)
2060 `(("r-biobase" ,r-biobase)
2061 ("r-biocgenerics" ,r-biocgenerics)
2062 ("r-ggplot2" ,r-ggplot2)
2063 ("r-ggthemes" ,r-ggthemes)
2064 ("r-igraph" ,r-igraph)
2065 ("r-matrix" ,r-matrix)
2066 ("r-proxy" ,r-proxy)
2068 ("r-rcppeigen" ,r-rcppeigen)
2069 ("r-scales" ,r-scales)
2070 ("r-scatterplot3d" ,r-scatterplot3d)
2071 ("r-smoother" ,r-smoother)
2072 ("r-summarizedexperiment" ,r-summarizedexperiment)
2074 (home-page "https://bioconductor.org/packages/destiny/")
2075 (synopsis "Create and plot diffusion maps")
2076 (description "This package provides tools to create and plot diffusion
2078 ;; Any version of the GPL
2079 (license license:gpl3+)))
2081 (define-public r-savr
2088 (uri (bioconductor-uri "savR" version))
2091 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
2092 (properties `((upstream-name . "savR")))
2093 (build-system r-build-system)
2095 `(("r-ggplot2" ,r-ggplot2)
2096 ("r-gridextra" ,r-gridextra)
2097 ("r-reshape2" ,r-reshape2)
2098 ("r-scales" ,r-scales)
2100 (home-page "https://github.com/bcalder/savR")
2101 (synopsis "Parse and analyze Illumina SAV files")
2103 "This package provides tools to parse Illumina Sequence Analysis
2104 Viewer (SAV) files, access data, and generate QC plots.")
2105 (license license:agpl3+)))
2107 (define-public r-chipexoqual
2109 (name "r-chipexoqual")
2114 (uri (bioconductor-uri "ChIPexoQual" version))
2117 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
2118 (properties `((upstream-name . "ChIPexoQual")))
2119 (build-system r-build-system)
2121 `(("r-biocparallel" ,r-biocparallel)
2122 ("r-biovizbase" ,r-biovizbase)
2123 ("r-broom" ,r-broom)
2124 ("r-data-table" ,r-data-table)
2125 ("r-dplyr" ,r-dplyr)
2126 ("r-genomeinfodb" ,r-genomeinfodb)
2127 ("r-genomicalignments" ,r-genomicalignments)
2128 ("r-genomicranges" ,r-genomicranges)
2129 ("r-ggplot2" ,r-ggplot2)
2130 ("r-hexbin" ,r-hexbin)
2131 ("r-iranges" ,r-iranges)
2132 ("r-rcolorbrewer" ,r-rcolorbrewer)
2133 ("r-rmarkdown" ,r-rmarkdown)
2134 ("r-rsamtools" ,r-rsamtools)
2135 ("r-s4vectors" ,r-s4vectors)
2136 ("r-scales" ,r-scales)
2137 ("r-viridis" ,r-viridis)))
2138 (home-page "https://github.com/keleslab/ChIPexoQual")
2139 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2141 "This package provides a quality control pipeline for ChIP-exo/nexus
2143 (license license:gpl2+)))
2145 (define-public r-copynumber
2147 (name "r-copynumber")
2151 (uri (bioconductor-uri "copynumber" version))
2154 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
2155 (build-system r-build-system)
2157 `(("r-s4vectors" ,r-s4vectors)
2158 ("r-iranges" ,r-iranges)
2159 ("r-genomicranges" ,r-genomicranges)
2160 ("r-biocgenerics" ,r-biocgenerics)))
2161 (home-page "https://bioconductor.org/packages/copynumber")
2162 (synopsis "Segmentation of single- and multi-track copy number data")
2164 "This package segments single- and multi-track copy number data by a
2165 penalized least squares regression method.")
2166 (license license:artistic2.0)))
2168 (define-public r-dnacopy
2175 (uri (bioconductor-uri "DNAcopy" version))
2178 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2179 (properties `((upstream-name . "DNAcopy")))
2180 (build-system r-build-system)
2181 (native-inputs `(("gfortran" ,gfortran)))
2182 (home-page "https://bioconductor.org/packages/DNAcopy")
2183 (synopsis "DNA copy number data analysis")
2185 "This package implements the @dfn{circular binary segmentation} (CBS)
2186 algorithm to segment DNA copy number data and identify genomic regions with
2187 abnormal copy number.")
2188 (license license:gpl2+)))
2190 ;; This is a CRAN package, but it uncharacteristically depends on a
2191 ;; Bioconductor package.
2192 (define-public r-htscluster
2194 (name "r-htscluster")
2199 (uri (cran-uri "HTSCluster" version))
2202 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2203 (properties `((upstream-name . "HTSCluster")))
2204 (build-system r-build-system)
2206 `(("r-capushe" ,r-capushe)
2207 ("r-edger" ,r-edger)
2208 ("r-plotrix" ,r-plotrix)))
2209 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2210 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2212 "This package provides a Poisson mixture model is implemented to cluster
2213 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2214 estimation is performed using either the EM or CEM algorithm, and the slope
2215 heuristics are used for model selection (i.e., to choose the number of
2217 (license license:gpl3+)))
2219 (define-public r-deds
2226 (uri (bioconductor-uri "DEDS" version))
2229 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2230 (properties `((upstream-name . "DEDS")))
2231 (build-system r-build-system)
2232 (home-page "https://bioconductor.org/packages/DEDS/")
2233 (synopsis "Differential expression via distance summary for microarray data")
2235 "This library contains functions that calculate various statistics of
2236 differential expression for microarray data, including t statistics, fold
2237 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2238 also implements a new methodology called DEDS (Differential Expression via
2239 Distance Summary), which selects differentially expressed genes by integrating
2240 and summarizing a set of statistics using a weighted distance approach.")
2241 ;; Any version of the LGPL.
2242 (license license:lgpl3+)))
2244 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2246 (define-public r-nbpseq
2253 (uri (cran-uri "NBPSeq" version))
2256 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2257 (properties `((upstream-name . "NBPSeq")))
2258 (build-system r-build-system)
2260 `(("r-qvalue" ,r-qvalue)))
2261 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2262 (synopsis "Negative binomial models for RNA-Seq data")
2264 "This package provides negative binomial models for two-group comparisons
2265 and regression inferences from RNA-sequencing data.")
2266 (license license:gpl2)))
2268 (define-public r-ebseq
2275 (uri (bioconductor-uri "EBSeq" version))
2278 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2279 (properties `((upstream-name . "EBSeq")))
2280 (build-system r-build-system)
2282 `(("r-blockmodeling" ,r-blockmodeling)
2283 ("r-gplots" ,r-gplots)
2284 ("r-testthat" ,r-testthat)))
2285 (home-page "https://bioconductor.org/packages/EBSeq")
2286 (synopsis "Differential expression analysis of RNA-seq data")
2288 "This package provides tools for differential expression analysis at both
2289 gene and isoform level using RNA-seq data")
2290 (license license:artistic2.0)))
2292 (define-public r-lpsymphony
2294 (name "r-lpsymphony")
2299 (uri (bioconductor-uri "lpsymphony" version))
2302 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2303 (build-system r-build-system)
2305 `(("gfortran" ,gfortran)
2308 `(("pkg-config" ,pkg-config)))
2309 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2310 (synopsis "Symphony integer linear programming solver in R")
2312 "This package was derived from Rsymphony. The package provides an R
2313 interface to SYMPHONY, a linear programming solver written in C++. The main
2314 difference between this package and Rsymphony is that it includes the solver
2315 source code, while Rsymphony expects to find header and library files on the
2316 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2317 to install interface to SYMPHONY.")
2318 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2319 ;; lpsimphony is released under the same terms.
2320 (license license:epl1.0)))
2322 (define-public r-ihw
2329 (uri (bioconductor-uri "IHW" version))
2332 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2333 (properties `((upstream-name . "IHW")))
2334 (build-system r-build-system)
2336 `(("r-biocgenerics" ,r-biocgenerics)
2337 ("r-fdrtool" ,r-fdrtool)
2338 ("r-lpsymphony" ,r-lpsymphony)
2339 ("r-slam" ,r-slam)))
2340 (home-page "https://bioconductor.org/packages/IHW")
2341 (synopsis "Independent hypothesis weighting")
2343 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2344 procedure that increases power compared to the method of Benjamini and
2345 Hochberg by assigning data-driven weights to each hypothesis. The input to
2346 IHW is a two-column table of p-values and covariates. The covariate can be
2347 any continuous-valued or categorical variable that is thought to be
2348 informative on the statistical properties of each hypothesis test, while it is
2349 independent of the p-value under the null hypothesis.")
2350 (license license:artistic2.0)))
2352 (define-public r-icobra
2359 (uri (bioconductor-uri "iCOBRA" version))
2362 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2363 (properties `((upstream-name . "iCOBRA")))
2364 (build-system r-build-system)
2366 `(("r-dplyr" ,r-dplyr)
2368 ("r-ggplot2" ,r-ggplot2)
2369 ("r-limma" ,r-limma)
2370 ("r-reshape2" ,r-reshape2)
2372 ("r-scales" ,r-scales)
2373 ("r-shiny" ,r-shiny)
2374 ("r-shinybs" ,r-shinybs)
2375 ("r-shinydashboard" ,r-shinydashboard)
2376 ("r-upsetr" ,r-upsetr)))
2377 (home-page "https://bioconductor.org/packages/iCOBRA")
2378 (synopsis "Comparison and visualization of ranking and assignment methods")
2380 "This package provides functions for calculation and visualization of
2381 performance metrics for evaluation of ranking and binary
2382 classification (assignment) methods. It also contains a Shiny application for
2383 interactive exploration of results.")
2384 (license license:gpl2+)))
2386 (define-public r-mast
2393 (uri (bioconductor-uri "MAST" version))
2396 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2397 (properties `((upstream-name . "MAST")))
2398 (build-system r-build-system)
2400 `(("r-abind" ,r-abind)
2402 ("r-biobase" ,r-biobase)
2403 ("r-biocgenerics" ,r-biocgenerics)
2404 ("r-data-table" ,r-data-table)
2405 ("r-ggplot2" ,r-ggplot2)
2407 ("r-progress" ,r-progress)
2408 ("r-reshape2" ,r-reshape2)
2409 ("r-s4vectors" ,r-s4vectors)
2410 ("r-singlecellexperiment" ,r-singlecellexperiment)
2411 ("r-stringr" ,r-stringr)
2412 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2413 (home-page "https://github.com/RGLab/MAST/")
2414 (synopsis "Model-based analysis of single cell transcriptomics")
2416 "This package provides methods and models for handling zero-inflated
2417 single cell assay data.")
2418 (license license:gpl2+)))
2420 (define-public r-monocle
2427 (uri (bioconductor-uri "monocle" version))
2430 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2431 (build-system r-build-system)
2433 `(("r-biobase" ,r-biobase)
2434 ("r-biocgenerics" ,r-biocgenerics)
2435 ("r-biocviews" ,r-biocviews)
2436 ("r-cluster" ,r-cluster)
2437 ("r-combinat" ,r-combinat)
2438 ("r-ddrtree" ,r-ddrtree)
2439 ("r-densityclust" ,r-densityclust)
2440 ("r-dplyr" ,r-dplyr)
2441 ("r-fastica" ,r-fastica)
2442 ("r-ggplot2" ,r-ggplot2)
2443 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2444 ("r-igraph" ,r-igraph)
2445 ("r-irlba" ,r-irlba)
2446 ("r-limma" ,r-limma)
2448 ("r-matrix" ,r-matrix)
2449 ("r-matrixstats" ,r-matrixstats)
2450 ("r-pheatmap" ,r-pheatmap)
2452 ("r-proxy" ,r-proxy)
2453 ("r-qlcmatrix" ,r-qlcmatrix)
2456 ("r-reshape2" ,r-reshape2)
2457 ("r-rtsne" ,r-rtsne)
2459 ("r-stringr" ,r-stringr)
2460 ("r-tibble" ,r-tibble)
2462 ("r-viridis" ,r-viridis)))
2463 (home-page "https://bioconductor.org/packages/monocle")
2464 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2466 "Monocle performs differential expression and time-series analysis for
2467 single-cell expression experiments. It orders individual cells according to
2468 progress through a biological process, without knowing ahead of time which
2469 genes define progress through that process. Monocle also performs
2470 differential expression analysis, clustering, visualization, and other useful
2471 tasks on single cell expression data. It is designed to work with RNA-Seq and
2472 qPCR data, but could be used with other types as well.")
2473 (license license:artistic2.0)))
2475 (define-public r-monocle3
2483 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2485 (file-name (git-file-name name version))
2488 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2489 (build-system r-build-system)
2491 `(("r-biobase" ,r-biobase)
2492 ("r-biocgenerics" ,r-biocgenerics)
2493 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2494 ("r-dplyr" ,r-dplyr)
2495 ("r-ggplot2" ,r-ggplot2)
2496 ("r-ggrepel" ,r-ggrepel)
2498 ("r-htmlwidgets" ,r-htmlwidgets)
2499 ("r-igraph" ,r-igraph)
2500 ("r-irlba" ,r-irlba)
2501 ("r-limma" ,r-limma)
2502 ("r-lmtest" ,r-lmtest)
2504 ("r-matrix" ,r-matrix)
2505 ("r-matrix-utils" ,r-matrix-utils)
2506 ("r-pbapply" ,r-pbapply)
2507 ("r-pbmcapply" ,r-pbmcapply)
2508 ("r-pheatmap" ,r-pheatmap)
2509 ("r-plotly" ,r-plotly)
2511 ("r-proxy" ,r-proxy)
2513 ("r-purrr" ,r-purrr)
2516 ("r-rcppparallel" ,r-rcppparallel)
2517 ("r-reshape2" ,r-reshape2)
2518 ("r-reticulate" ,r-reticulate)
2519 ("r-rhpcblasctl" ,r-rhpcblasctl)
2520 ("r-rtsne" ,r-rtsne)
2521 ("r-shiny" ,r-shiny)
2523 ("r-spdep" ,r-spdep)
2524 ("r-speedglm" ,r-speedglm)
2525 ("r-stringr" ,r-stringr)
2526 ("r-singlecellexperiment" ,r-singlecellexperiment)
2527 ("r-tibble" ,r-tibble)
2528 ("r-tidyr" ,r-tidyr)
2530 ("r-viridis" ,r-viridis)))
2531 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2532 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2534 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2535 (license license:expat)))
2537 (define-public r-noiseq
2544 (uri (bioconductor-uri "NOISeq" version))
2547 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2548 (properties `((upstream-name . "NOISeq")))
2549 (build-system r-build-system)
2551 `(("r-biobase" ,r-biobase)
2552 ("r-matrix" ,r-matrix)))
2553 (home-page "https://bioconductor.org/packages/NOISeq")
2554 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2556 "This package provides tools to support the analysis of RNA-seq
2557 expression data or other similar kind of data. It provides exploratory plots
2558 to evaluate saturation, count distribution, expression per chromosome, type of
2559 detected features, features length, etc. It also supports the analysis of
2560 differential expression between two experimental conditions with no parametric
2562 (license license:artistic2.0)))
2564 (define-public r-scdd
2571 (uri (bioconductor-uri "scDD" version))
2574 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2575 (properties `((upstream-name . "scDD")))
2576 (build-system r-build-system)
2579 ("r-biocparallel" ,r-biocparallel)
2580 ("r-ebseq" ,r-ebseq)
2581 ("r-fields" ,r-fields)
2582 ("r-ggplot2" ,r-ggplot2)
2583 ("r-mclust" ,r-mclust)
2584 ("r-outliers" ,r-outliers)
2585 ("r-s4vectors" ,r-s4vectors)
2586 ("r-scran" ,r-scran)
2587 ("r-singlecellexperiment" ,r-singlecellexperiment)
2588 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2589 (home-page "https://github.com/kdkorthauer/scDD")
2590 (synopsis "Mixture modeling of single-cell RNA-seq data")
2592 "This package implements a method to analyze single-cell RNA-seq data
2593 utilizing flexible Dirichlet Process mixture models. Genes with differential
2594 distributions of expression are classified into several interesting patterns
2595 of differences between two conditions. The package also includes functions
2596 for simulating data with these patterns from negative binomial
2598 (license license:gpl2)))
2600 (define-public r-scone
2607 (uri (bioconductor-uri "scone" version))
2610 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2611 (build-system r-build-system)
2613 `(("r-aroma-light" ,r-aroma-light)
2614 ("r-biocparallel" ,r-biocparallel)
2616 ("r-class" ,r-class)
2617 ("r-cluster" ,r-cluster)
2618 ("r-compositions" ,r-compositions)
2619 ("r-diptest" ,r-diptest)
2620 ("r-edger" ,r-edger)
2622 ("r-gplots" ,r-gplots)
2623 ("r-hexbin" ,r-hexbin)
2624 ("r-limma" ,r-limma)
2625 ("r-matrixstats" ,r-matrixstats)
2626 ("r-mixtools" ,r-mixtools)
2627 ("r-rarpack" ,r-rarpack)
2628 ("r-rcolorbrewer" ,r-rcolorbrewer)
2629 ("r-rhdf5" ,r-rhdf5)
2630 ("r-ruvseq" ,r-ruvseq)
2631 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2632 (home-page "https://bioconductor.org/packages/scone")
2633 (synopsis "Single cell overview of normalized expression data")
2635 "SCONE is an R package for comparing and ranking the performance of
2636 different normalization schemes for single-cell RNA-seq and other
2637 high-throughput analyses.")
2638 (license license:artistic2.0)))
2640 (define-public r-geoquery
2647 (uri (bioconductor-uri "GEOquery" version))
2650 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2651 (properties `((upstream-name . "GEOquery")))
2652 (build-system r-build-system)
2654 `(("r-biobase" ,r-biobase)
2655 ("r-dplyr" ,r-dplyr)
2657 ("r-limma" ,r-limma)
2658 ("r-magrittr" ,r-magrittr)
2659 ("r-readr" ,r-readr)
2660 ("r-tidyr" ,r-tidyr)
2661 ("r-xml2" ,r-xml2)))
2662 (home-page "https://github.com/seandavi/GEOquery/")
2663 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2665 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2666 microarray data. Given the rich and varied nature of this resource, it is
2667 only natural to want to apply BioConductor tools to these data. GEOquery is
2668 the bridge between GEO and BioConductor.")
2669 (license license:gpl2)))
2671 (define-public r-illuminaio
2673 (name "r-illuminaio")
2678 (uri (bioconductor-uri "illuminaio" version))
2681 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2682 (build-system r-build-system)
2684 `(("r-base64" ,r-base64)))
2685 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2686 (synopsis "Parse Illumina microarray output files")
2688 "This package provides tools for parsing Illumina's microarray output
2689 files, including IDAT.")
2690 (license license:gpl2)))
2692 (define-public r-siggenes
2699 (uri (bioconductor-uri "siggenes" version))
2702 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2703 (build-system r-build-system)
2705 `(("r-biobase" ,r-biobase)
2706 ("r-multtest" ,r-multtest)
2707 ("r-scrime" ,r-scrime)))
2708 (home-page "https://bioconductor.org/packages/siggenes/")
2710 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2712 "This package provides tools for the identification of differentially
2713 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2714 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2715 Bayes Analyses of Microarrays} (EBAM).")
2716 (license license:lgpl2.0+)))
2718 (define-public r-bumphunter
2720 (name "r-bumphunter")
2725 (uri (bioconductor-uri "bumphunter" version))
2728 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2729 (build-system r-build-system)
2731 `(("r-annotationdbi" ,r-annotationdbi)
2732 ("r-biocgenerics" ,r-biocgenerics)
2733 ("r-dorng" ,r-dorng)
2734 ("r-foreach" ,r-foreach)
2735 ("r-genomeinfodb" ,r-genomeinfodb)
2736 ("r-genomicfeatures" ,r-genomicfeatures)
2737 ("r-genomicranges" ,r-genomicranges)
2738 ("r-iranges" ,r-iranges)
2739 ("r-iterators" ,r-iterators)
2740 ("r-limma" ,r-limma)
2741 ("r-locfit" ,r-locfit)
2742 ("r-matrixstats" ,r-matrixstats)
2743 ("r-s4vectors" ,r-s4vectors)))
2744 (home-page "https://github.com/ririzarr/bumphunter")
2745 (synopsis "Find bumps in genomic data")
2747 "This package provides tools for finding bumps in genomic data in order
2748 to identify differentially methylated regions in epigenetic epidemiology
2750 (license license:artistic2.0)))
2752 (define-public r-minfi
2759 (uri (bioconductor-uri "minfi" version))
2762 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2763 (build-system r-build-system)
2765 `(("r-beanplot" ,r-beanplot)
2766 ("r-biobase" ,r-biobase)
2767 ("r-biocgenerics" ,r-biocgenerics)
2768 ("r-biocparallel" ,r-biocparallel)
2769 ("r-biostrings" ,r-biostrings)
2770 ("r-bumphunter" ,r-bumphunter)
2771 ("r-data-table" ,r-data-table)
2772 ("r-delayedarray" ,r-delayedarray)
2773 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2774 ("r-genefilter" ,r-genefilter)
2775 ("r-genomeinfodb" ,r-genomeinfodb)
2776 ("r-genomicranges" ,r-genomicranges)
2777 ("r-geoquery" ,r-geoquery)
2778 ("r-hdf5array" ,r-hdf5array)
2779 ("r-illuminaio" ,r-illuminaio)
2780 ("r-iranges" ,r-iranges)
2781 ("r-lattice" ,r-lattice)
2782 ("r-limma" ,r-limma)
2784 ("r-mclust" ,r-mclust)
2786 ("r-nor1mix" ,r-nor1mix)
2787 ("r-preprocesscore" ,r-preprocesscore)
2788 ("r-quadprog" ,r-quadprog)
2789 ("r-rcolorbrewer" ,r-rcolorbrewer)
2790 ("r-reshape" ,r-reshape)
2791 ("r-s4vectors" ,r-s4vectors)
2792 ("r-siggenes" ,r-siggenes)
2793 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2794 (home-page "https://github.com/hansenlab/minfi")
2795 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2797 "This package provides tools to analyze and visualize Illumina Infinium
2798 methylation arrays.")
2799 (license license:artistic2.0)))
2801 (define-public r-methylumi
2803 (name "r-methylumi")
2808 (uri (bioconductor-uri "methylumi" version))
2811 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2812 (build-system r-build-system)
2814 `(("r-annotate" ,r-annotate)
2815 ("r-annotationdbi" ,r-annotationdbi)
2816 ("r-biobase" ,r-biobase)
2817 ("r-biocgenerics" ,r-biocgenerics)
2818 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2819 ("r-genefilter" ,r-genefilter)
2820 ("r-genomeinfodb" ,r-genomeinfodb)
2821 ("r-genomicranges" ,r-genomicranges)
2822 ("r-ggplot2" ,r-ggplot2)
2823 ("r-illuminaio" ,r-illuminaio)
2824 ("r-iranges" ,r-iranges)
2825 ("r-lattice" ,r-lattice)
2826 ("r-matrixstats" ,r-matrixstats)
2827 ("r-minfi" ,r-minfi)
2828 ("r-reshape2" ,r-reshape2)
2829 ("r-s4vectors" ,r-s4vectors)
2830 ("r-scales" ,r-scales)
2831 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2832 (home-page "https://bioconductor.org/packages/methylumi")
2833 (synopsis "Handle Illumina methylation data")
2835 "This package provides classes for holding and manipulating Illumina
2836 methylation data. Based on eSet, it can contain MIAME information, sample
2837 information, feature information, and multiple matrices of data. An
2838 \"intelligent\" import function, methylumiR can read the Illumina text files
2839 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2840 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2841 background correction, and quality control features for GoldenGate, Infinium,
2842 and Infinium HD arrays are also included.")
2843 (license license:gpl2)))
2845 (define-public r-lumi
2852 (uri (bioconductor-uri "lumi" version))
2855 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2856 (build-system r-build-system)
2858 `(("r-affy" ,r-affy)
2859 ("r-annotate" ,r-annotate)
2860 ("r-annotationdbi" ,r-annotationdbi)
2861 ("r-biobase" ,r-biobase)
2863 ("r-genomicfeatures" ,r-genomicfeatures)
2864 ("r-genomicranges" ,r-genomicranges)
2865 ("r-kernsmooth" ,r-kernsmooth)
2866 ("r-lattice" ,r-lattice)
2868 ("r-methylumi" ,r-methylumi)
2870 ("r-nleqslv" ,r-nleqslv)
2871 ("r-preprocesscore" ,r-preprocesscore)
2872 ("r-rsqlite" ,r-rsqlite)))
2873 (home-page "https://bioconductor.org/packages/lumi")
2874 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2876 "The lumi package provides an integrated solution for the Illumina
2877 microarray data analysis. It includes functions of Illumina
2878 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2879 variance stabilization, normalization and gene annotation at the probe level.
2880 It also includes the functions of processing Illumina methylation microarrays,
2881 especially Illumina Infinium methylation microarrays.")
2882 (license license:lgpl2.0+)))
2884 (define-public r-linnorm
2891 (uri (bioconductor-uri "Linnorm" version))
2894 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2895 (properties `((upstream-name . "Linnorm")))
2896 (build-system r-build-system)
2898 `(("r-amap" ,r-amap)
2899 ("r-apcluster" ,r-apcluster)
2900 ("r-ellipse" ,r-ellipse)
2901 ("r-fastcluster" ,r-fastcluster)
2903 ("r-ggdendro" ,r-ggdendro)
2904 ("r-ggplot2" ,r-ggplot2)
2905 ("r-gmodels" ,r-gmodels)
2906 ("r-igraph" ,r-igraph)
2907 ("r-limma" ,r-limma)
2909 ("r-mclust" ,r-mclust)
2911 ("r-rcpparmadillo" ,r-rcpparmadillo)
2912 ("r-rtsne" ,r-rtsne)
2913 ("r-statmod" ,r-statmod)
2914 ("r-vegan" ,r-vegan)
2916 (home-page "http://www.jjwanglab.org/Linnorm/")
2917 (synopsis "Linear model and normality based transformation method")
2919 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2920 count data or any large scale count data. It transforms such datasets for
2921 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2922 the following pipelines are implemented:
2925 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2926 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2927 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2928 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2929 @item Differential expression analysis or differential peak detection using
2930 limma (@code{Linnorm.limma})
2931 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2932 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2933 @item Stable gene selection for scRNA-seq data; for users without or who do
2934 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2935 @item Data imputation (@code{Linnorm.DataImput}).
2938 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2939 @code{RnaXSim} function is included for simulating RNA-seq data for the
2940 evaluation of DEG analysis methods.")
2941 (license license:expat)))
2943 (define-public r-ioniser
2950 (uri (bioconductor-uri "IONiseR" version))
2953 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2954 (properties `((upstream-name . "IONiseR")))
2955 (build-system r-build-system)
2957 `(("r-biocgenerics" ,r-biocgenerics)
2958 ("r-biocparallel" ,r-biocparallel)
2959 ("r-biostrings" ,r-biostrings)
2960 ("r-bit64" ,r-bit64)
2961 ("r-dplyr" ,r-dplyr)
2962 ("r-ggplot2" ,r-ggplot2)
2963 ("r-magrittr" ,r-magrittr)
2964 ("r-rhdf5" ,r-rhdf5)
2965 ("r-shortread" ,r-shortread)
2966 ("r-stringr" ,r-stringr)
2967 ("r-tibble" ,r-tibble)
2968 ("r-tidyr" ,r-tidyr)
2969 ("r-xvector" ,r-xvector)))
2970 (home-page "https://bioconductor.org/packages/IONiseR/")
2971 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2973 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2974 MinION data. It extracts summary statistics from a set of fast5 files and can
2975 be used either before or after base calling. In addition to standard
2976 summaries of the read-types produced, it provides a number of plots for
2977 visualising metrics relative to experiment run time or spatially over the
2978 surface of a flowcell.")
2979 (license license:expat)))
2981 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2982 (define-public r-gkmsvm
2989 (uri (cran-uri "gkmSVM" version))
2992 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2993 (properties `((upstream-name . "gkmSVM")))
2994 (build-system r-build-system)
2996 `(("r-biocgenerics" ,r-biocgenerics)
2997 ("r-biostrings" ,r-biostrings)
2998 ("r-genomeinfodb" ,r-genomeinfodb)
2999 ("r-genomicranges" ,r-genomicranges)
3000 ("r-iranges" ,r-iranges)
3001 ("r-kernlab" ,r-kernlab)
3004 ("r-rtracklayer" ,r-rtracklayer)
3005 ("r-s4vectors" ,r-s4vectors)
3006 ("r-seqinr" ,r-seqinr)))
3007 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3008 (synopsis "Gapped-kmer support vector machine")
3010 "This R package provides tools for training gapped-kmer SVM classifiers
3011 for DNA and protein sequences. This package supports several sequence
3012 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3013 (license license:gpl2+)))
3015 (define-public r-triform
3022 (uri (bioconductor-uri "triform" version))
3025 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
3026 (build-system r-build-system)
3028 `(("r-biocgenerics" ,r-biocgenerics)
3029 ("r-iranges" ,r-iranges)
3030 ("r-yaml" ,r-yaml)))
3031 (home-page "https://bioconductor.org/packages/triform/")
3032 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3034 "The Triform algorithm uses model-free statistics to identify peak-like
3035 distributions of TF ChIP sequencing reads, taking advantage of an improved
3036 peak definition in combination with known profile characteristics.")
3037 (license license:gpl2)))
3039 (define-public r-varianttools
3041 (name "r-varianttools")
3046 (uri (bioconductor-uri "VariantTools" version))
3049 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
3050 (properties `((upstream-name . "VariantTools")))
3051 (build-system r-build-system)
3053 `(("r-biobase" ,r-biobase)
3054 ("r-biocgenerics" ,r-biocgenerics)
3055 ("r-biocparallel" ,r-biocparallel)
3056 ("r-biostrings" ,r-biostrings)
3057 ("r-bsgenome" ,r-bsgenome)
3058 ("r-genomeinfodb" ,r-genomeinfodb)
3059 ("r-genomicfeatures" ,r-genomicfeatures)
3060 ("r-genomicranges" ,r-genomicranges)
3061 ("r-iranges" ,r-iranges)
3062 ("r-matrix" ,r-matrix)
3063 ("r-rsamtools" ,r-rsamtools)
3064 ("r-rtracklayer" ,r-rtracklayer)
3065 ("r-s4vectors" ,r-s4vectors)
3066 ("r-variantannotation" ,r-variantannotation)))
3067 (home-page "https://bioconductor.org/packages/VariantTools/")
3068 (synopsis "Tools for exploratory analysis of variant calls")
3070 "Explore, diagnose, and compare variant calls using filters. The
3071 VariantTools package supports a workflow for loading data, calling single
3072 sample variants and tumor-specific somatic mutations or other sample-specific
3073 variant types (e.g., RNA editing). Most of the functions operate on
3074 alignments (BAM files) or datasets of called variants. The user is expected
3075 to have already aligned the reads with a separate tool, e.g., GSNAP via
3077 (license license:artistic2.0)))
3079 (define-public r-heatplus
3086 (uri (bioconductor-uri "Heatplus" version))
3089 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
3090 (properties `((upstream-name . "Heatplus")))
3091 (build-system r-build-system)
3093 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3094 (home-page "https://github.com/alexploner/Heatplus")
3095 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3097 "This package provides tools to display a rectangular heatmap (intensity
3098 plot) of a data matrix. By default, both samples (columns) and features (row)
3099 of the matrix are sorted according to a hierarchical clustering, and the
3100 corresponding dendrogram is plotted. Optionally, panels with additional
3101 information about samples and features can be added to the plot.")
3102 (license license:gpl2+)))
3104 (define-public r-gosemsim
3111 (uri (bioconductor-uri "GOSemSim" version))
3114 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
3115 (properties `((upstream-name . "GOSemSim")))
3116 (build-system r-build-system)
3118 `(("r-annotationdbi" ,r-annotationdbi)
3119 ("r-go-db" ,r-go-db)
3120 ("r-rcpp" ,r-rcpp)))
3121 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3122 (synopsis "GO-terms semantic similarity measures")
3124 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3125 quantitative ways to compute similarities between genes and gene groups, and
3126 have became important basis for many bioinformatics analysis approaches.
3127 GOSemSim is an R package for semantic similarity computation among GO terms,
3128 sets of GO terms, gene products and gene clusters.")
3129 (license license:artistic2.0)))
3131 (define-public r-anota
3138 (uri (bioconductor-uri "anota" version))
3141 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
3142 (build-system r-build-system)
3144 `(("r-multtest" ,r-multtest)
3145 ("r-qvalue" ,r-qvalue)))
3146 (home-page "https://bioconductor.org/packages/anota/")
3147 (synopsis "Analysis of translational activity")
3149 "Genome wide studies of translational control is emerging as a tool to
3150 study various biological conditions. The output from such analysis is both
3151 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3152 involved in translation (the actively translating mRNA level) for each mRNA.
3153 The standard analysis of such data strives towards identifying differential
3154 translational between two or more sample classes - i.e. differences in
3155 actively translated mRNA levels that are independent of underlying differences
3156 in cytosolic mRNA levels. This package allows for such analysis using partial
3157 variances and the random variance model. As 10s of thousands of mRNAs are
3158 analyzed in parallel the library performs a number of tests to assure that
3159 the data set is suitable for such analysis.")
3160 (license license:gpl3)))
3162 (define-public r-sigpathway
3164 (name "r-sigpathway")
3169 (uri (bioconductor-uri "sigPathway" version))
3172 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3173 (properties `((upstream-name . "sigPathway")))
3174 (build-system r-build-system)
3175 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3176 (synopsis "Pathway analysis")
3178 "This package is used to conduct pathway analysis by calculating the NT_k
3179 and NE_k statistics in a statistical framework for determining whether a
3180 specified group of genes for a pathway has a coordinated association with a
3181 phenotype of interest.")
3182 (license license:gpl2)))
3184 (define-public r-fgsea
3191 (uri (bioconductor-uri "fgsea" version))
3194 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3195 (build-system r-build-system)
3198 ("r-biocparallel" ,r-biocparallel)
3199 ("r-data-table" ,r-data-table)
3200 ("r-fastmatch" ,r-fastmatch)
3201 ("r-ggplot2" ,r-ggplot2)
3202 ("r-gridextra" ,r-gridextra)
3203 ("r-matrix" ,r-matrix)
3204 ("r-rcpp" ,r-rcpp)))
3205 (home-page "https://github.com/ctlab/fgsea/")
3206 (synopsis "Fast gene set enrichment analysis")
3208 "The package implements an algorithm for fast gene set enrichment
3209 analysis. Using the fast algorithm allows to make more permutations and get
3210 more fine grained p-values, which allows to use accurate stantard approaches
3211 to multiple hypothesis correction.")
3212 (license license:expat)))
3214 (define-public r-dose
3221 (uri (bioconductor-uri "DOSE" version))
3224 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3225 (properties `((upstream-name . "DOSE")))
3226 (build-system r-build-system)
3228 `(("r-annotationdbi" ,r-annotationdbi)
3229 ("r-biocparallel" ,r-biocparallel)
3230 ("r-do-db" ,r-do-db)
3231 ("r-fgsea" ,r-fgsea)
3232 ("r-ggplot2" ,r-ggplot2)
3233 ("r-gosemsim" ,r-gosemsim)
3234 ("r-qvalue" ,r-qvalue)
3235 ("r-reshape2" ,r-reshape2)
3236 ("r-s4vectors" ,r-s4vectors)))
3237 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3238 (synopsis "Disease ontology semantic and enrichment analysis")
3240 "This package implements five methods proposed by Resnik, Schlicker,
3241 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3242 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3243 including hypergeometric model and gene set enrichment analysis are also
3244 implemented for discovering disease associations of high-throughput biological
3246 (license license:artistic2.0)))
3248 (define-public r-enrichplot
3250 (name "r-enrichplot")
3255 (uri (bioconductor-uri "enrichplot" version))
3258 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3259 (build-system r-build-system)
3261 `(("r-annotationdbi" ,r-annotationdbi)
3262 ("r-cowplot" ,r-cowplot)
3264 ("r-europepmc" ,r-europepmc)
3265 ("r-ggplot2" ,r-ggplot2)
3266 ("r-ggplotify" ,r-ggplotify)
3267 ("r-ggraph" ,r-ggraph)
3268 ("r-ggridges" ,r-ggridges)
3269 ("r-gosemsim" ,r-gosemsim)
3270 ("r-gridextra" ,r-gridextra)
3271 ("r-igraph" ,r-igraph)
3272 ("r-purrr" ,r-purrr)
3273 ("r-rcolorbrewer" ,r-rcolorbrewer)
3274 ("r-reshape2" ,r-reshape2)
3275 ("r-upsetr" ,r-upsetr)))
3276 (home-page "https://github.com/GuangchuangYu/enrichplot")
3277 (synopsis "Visualization of functional enrichment result")
3279 "The enrichplot package implements several visualization methods for
3280 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3281 All the visualization methods are developed based on ggplot2 graphics.")
3282 (license license:artistic2.0)))
3284 (define-public r-clusterprofiler
3286 (name "r-clusterprofiler")
3291 (uri (bioconductor-uri "clusterProfiler" version))
3294 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3296 `((upstream-name . "clusterProfiler")))
3297 (build-system r-build-system)
3299 `(("r-annotationdbi" ,r-annotationdbi)
3301 ("r-enrichplot" ,r-enrichplot)
3302 ("r-ggplot2" ,r-ggplot2)
3303 ("r-go-db" ,r-go-db)
3304 ("r-gosemsim" ,r-gosemsim)
3305 ("r-magrittr" ,r-magrittr)
3307 ("r-qvalue" ,r-qvalue)
3308 ("r-rvcheck" ,r-rvcheck)
3309 ("r-tidyr" ,r-tidyr)))
3310 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3311 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3313 "This package implements methods to analyze and visualize functional
3314 profiles (GO and KEGG) of gene and gene clusters.")
3315 (license license:artistic2.0)))
3317 (define-public r-mlinterfaces
3319 (name "r-mlinterfaces")
3324 (uri (bioconductor-uri "MLInterfaces" version))
3327 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
3328 (properties `((upstream-name . "MLInterfaces")))
3329 (build-system r-build-system)
3331 `(("r-annotate" ,r-annotate)
3332 ("r-biobase" ,r-biobase)
3333 ("r-biocgenerics" ,r-biocgenerics)
3334 ("r-cluster" ,r-cluster)
3337 ("r-gdata" ,r-gdata)
3338 ("r-genefilter" ,r-genefilter)
3339 ("r-ggvis" ,r-ggvis)
3340 ("r-hwriter" ,r-hwriter)
3342 ("r-mlbench" ,r-mlbench)
3344 ("r-rcolorbrewer" ,r-rcolorbrewer)
3346 ("r-rpart" ,r-rpart)
3347 ("r-sfsmisc" ,r-sfsmisc)
3348 ("r-shiny" ,r-shiny)
3349 ("r-threejs" ,r-threejs)))
3350 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3351 (synopsis "Interfaces to R machine learning procedures")
3353 "This package provides uniform interfaces to machine learning code for
3354 data in R and Bioconductor containers.")
3355 ;; Any version of the LGPL.
3356 (license license:lgpl2.1+)))
3358 (define-public r-annaffy
3365 (uri (bioconductor-uri "annaffy" version))
3368 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3369 (build-system r-build-system)
3372 (modify-phases %standard-phases
3373 (add-after 'unpack 'remove-reference-to-non-free-data
3375 (substitute* "DESCRIPTION"
3379 `(("r-annotationdbi" ,r-annotationdbi)
3380 ("r-biobase" ,r-biobase)
3382 ("r-go-db" ,r-go-db)))
3383 (home-page "https://bioconductor.org/packages/annaffy/")
3384 (synopsis "Annotation tools for Affymetrix biological metadata")
3386 "This package provides functions for handling data from Bioconductor
3387 Affymetrix annotation data packages. It produces compact HTML and text
3388 reports including experimental data and URL links to many online databases.
3389 It allows searching of biological metadata using various criteria.")
3390 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3391 ;; the LGPL 2.1 is included.
3392 (license license:lgpl2.1+)))
3394 (define-public r-a4core
3401 (uri (bioconductor-uri "a4Core" version))
3404 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3405 (properties `((upstream-name . "a4Core")))
3406 (build-system r-build-system)
3408 `(("r-biobase" ,r-biobase)
3409 ("r-glmnet" ,r-glmnet)))
3410 (home-page "https://bioconductor.org/packages/a4Core")
3411 (synopsis "Automated Affymetrix array analysis core package")
3413 "This is the core package for the automated analysis of Affymetrix
3415 (license license:gpl3)))
3417 (define-public r-a4classif
3419 (name "r-a4classif")
3424 (uri (bioconductor-uri "a4Classif" version))
3427 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3428 (properties `((upstream-name . "a4Classif")))
3429 (build-system r-build-system)
3431 `(("r-a4core" ,r-a4core)
3432 ("r-a4preproc" ,r-a4preproc)
3433 ("r-glmnet" ,r-glmnet)
3434 ("r-mlinterfaces" ,r-mlinterfaces)
3437 ("r-varselrf" ,r-varselrf)))
3438 (home-page "https://bioconductor.org/packages/a4Classif/")
3439 (synopsis "Automated Affymetrix array analysis classification package")
3441 "This is the classification package for the automated analysis of
3442 Affymetrix arrays.")
3443 (license license:gpl3)))
3445 (define-public r-a4preproc
3447 (name "r-a4preproc")
3452 (uri (bioconductor-uri "a4Preproc" version))
3455 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3456 (properties `((upstream-name . "a4Preproc")))
3457 (build-system r-build-system)
3459 `(("r-annotationdbi" ,r-annotationdbi)))
3460 (home-page "https://bioconductor.org/packages/a4Preproc/")
3461 (synopsis "Automated Affymetrix array analysis preprocessing package")
3463 "This is a package for the automated analysis of Affymetrix arrays. It
3464 is used for preprocessing the arrays.")
3465 (license license:gpl3)))
3467 (define-public r-a4reporting
3469 (name "r-a4reporting")
3474 (uri (bioconductor-uri "a4Reporting" version))
3477 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3478 (properties `((upstream-name . "a4Reporting")))
3479 (build-system r-build-system)
3481 `(("r-annaffy" ,r-annaffy)
3482 ("r-xtable" ,r-xtable)))
3483 (home-page "https://bioconductor.org/packages/a4Reporting/")
3484 (synopsis "Automated Affymetrix array analysis reporting package")
3486 "This is a package for the automated analysis of Affymetrix arrays. It
3487 provides reporting features.")
3488 (license license:gpl3)))
3490 (define-public r-a4base
3497 (uri (bioconductor-uri "a4Base" version))
3500 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3501 (properties `((upstream-name . "a4Base")))
3502 (build-system r-build-system)
3504 `(("r-a4core" ,r-a4core)
3505 ("r-a4preproc" ,r-a4preproc)
3506 ("r-annaffy" ,r-annaffy)
3507 ("r-annotationdbi" ,r-annotationdbi)
3508 ("r-biobase" ,r-biobase)
3509 ("r-genefilter" ,r-genefilter)
3510 ("r-glmnet" ,r-glmnet)
3511 ("r-gplots" ,r-gplots)
3512 ("r-limma" ,r-limma)
3514 ("r-multtest" ,r-multtest)))
3515 (home-page "https://bioconductor.org/packages/a4Base/")
3516 (synopsis "Automated Affymetrix array analysis base package")
3518 "This package provides basic features for the automated analysis of
3519 Affymetrix arrays.")
3520 (license license:gpl3)))
3529 (uri (bioconductor-uri "a4" version))
3532 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3533 (build-system r-build-system)
3535 `(("r-a4base" ,r-a4base)
3536 ("r-a4classif" ,r-a4classif)
3537 ("r-a4core" ,r-a4core)
3538 ("r-a4preproc" ,r-a4preproc)
3539 ("r-a4reporting" ,r-a4reporting)))
3540 (home-page "https://bioconductor.org/packages/a4/")
3541 (synopsis "Automated Affymetrix array analysis umbrella package")
3543 "This package provides a software suite for the automated analysis of
3544 Affymetrix arrays.")
3545 (license license:gpl3)))
3547 (define-public r-abseqr
3554 (uri (bioconductor-uri "abseqR" version))
3557 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3558 (properties `((upstream-name . "abseqR")))
3559 (build-system r-build-system)
3561 `(("pandoc" ,ghc-pandoc)))
3563 `(("r-biocparallel" ,r-biocparallel)
3564 ("r-biocstyle" ,r-biocstyle)
3565 ("r-circlize" ,r-circlize)
3566 ("r-flexdashboard" ,r-flexdashboard)
3567 ("r-ggcorrplot" ,r-ggcorrplot)
3568 ("r-ggdendro" ,r-ggdendro)
3569 ("r-ggplot2" ,r-ggplot2)
3570 ("r-gridextra" ,r-gridextra)
3571 ("r-knitr" ,r-knitr)
3572 ("r-plotly" ,r-plotly)
3575 ("r-rcolorbrewer" ,r-rcolorbrewer)
3576 ("r-reshape2" ,r-reshape2)
3577 ("r-rmarkdown" ,r-rmarkdown)
3578 ("r-stringr" ,r-stringr)
3579 ("r-vegan" ,r-vegan)
3580 ("r-venndiagram" ,r-venndiagram)))
3581 (home-page "https://github.com/malhamdoosh/abseqR")
3582 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3584 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3585 sequencing datasets generated from antibody libraries and abseqR is one of its
3586 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3587 capabilities and allows them to generate interactive HTML reports for the
3588 convenience of viewing and sharing with other researchers. Additionally,
3589 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3590 further downstream analysis on its output.")
3591 (license license:gpl3)))
3593 (define-public r-bacon
3600 (uri (bioconductor-uri "bacon" version))
3603 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3604 (build-system r-build-system)
3606 `(("r-biocparallel" ,r-biocparallel)
3607 ("r-ellipse" ,r-ellipse)
3608 ("r-ggplot2" ,r-ggplot2)))
3609 (home-page "https://bioconductor.org/packages/bacon/")
3610 (synopsis "Controlling bias and inflation in association studies")
3612 "Bacon can be used to remove inflation and bias often observed in
3613 epigenome- and transcriptome-wide association studies. To this end bacon
3614 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3615 fitting a three-component normal mixture on z-scores.")
3616 (license license:gpl2+)))
3618 (define-public r-rgadem
3625 (uri (bioconductor-uri "rGADEM" version))
3628 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3629 (properties `((upstream-name . "rGADEM")))
3630 (build-system r-build-system)
3632 `(("r-biostrings" ,r-biostrings)
3633 ("r-bsgenome" ,r-bsgenome)
3634 ("r-iranges" ,r-iranges)
3635 ("r-seqlogo" ,r-seqlogo)))
3636 (home-page "https://bioconductor.org/packages/rGADEM/")
3637 (synopsis "De novo sequence motif discovery")
3639 "rGADEM is an efficient de novo motif discovery tool for large-scale
3640 genomic sequence data.")
3641 (license license:artistic2.0)))
3643 (define-public r-motiv
3650 (uri (bioconductor-uri "MotIV" version))
3653 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3654 (properties `((upstream-name . "MotIV")))
3655 (build-system r-build-system)
3659 `(("r-biocgenerics" ,r-biocgenerics)
3660 ("r-biostrings" ,r-biostrings)
3661 ("r-iranges" ,r-iranges)
3662 ("r-lattice" ,r-lattice)
3663 ("r-rgadem" ,r-rgadem)
3664 ("r-s4vectors" ,r-s4vectors)))
3665 (home-page "https://bioconductor.org/packages/MotIV/")
3666 (synopsis "Motif identification and validation")
3668 "This package is used for the identification and validation of sequence
3669 motifs. It makes use of STAMP for comparing a set of motifs to a given
3670 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3671 distributions, modules and filter motifs.")
3672 (license license:gpl2)))
3674 (define-public r-motifstack
3676 (name "r-motifstack")
3681 (uri (bioconductor-uri "motifStack" version))
3684 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3685 (properties `((upstream-name . "motifStack")))
3686 (build-system r-build-system)
3688 `(("r-ade4" ,r-ade4)
3689 ("r-biostrings" ,r-biostrings)
3690 ("r-grimport2" ,r-grimport2)
3691 ("r-htmlwidgets" ,r-htmlwidgets)
3692 ("r-motiv" ,r-motiv)
3693 ("r-scales" ,r-scales)
3695 (home-page "https://bioconductor.org/packages/motifStack/")
3696 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3698 "The motifStack package is designed for graphic representation of
3699 multiple motifs with different similarity scores. It works with both DNA/RNA
3700 sequence motifs and amino acid sequence motifs. In addition, it provides the
3701 flexibility for users to customize the graphic parameters such as the font
3702 type and symbol colors.")
3703 (license license:gpl2+)))
3705 (define-public r-genomicscores
3707 (name "r-genomicscores")
3712 (uri (bioconductor-uri "GenomicScores" version))
3715 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3716 (properties `((upstream-name . "GenomicScores")))
3717 (build-system r-build-system)
3719 `(("r-annotationhub" ,r-annotationhub)
3720 ("r-biobase" ,r-biobase)
3721 ("r-biocgenerics" ,r-biocgenerics)
3722 ("r-biostrings" ,r-biostrings)
3723 ("r-bsgenome" ,r-bsgenome)
3724 ("r-genomeinfodb" ,r-genomeinfodb)
3725 ("r-genomicranges" ,r-genomicranges)
3726 ("r-iranges" ,r-iranges)
3727 ("r-s4vectors" ,r-s4vectors)
3729 (home-page "https://github.com/rcastelo/GenomicScores/")
3730 (synopsis "Work with genome-wide position-specific scores")
3732 "This package provides infrastructure to store and access genome-wide
3733 position-specific scores within R and Bioconductor.")
3734 (license license:artistic2.0)))
3736 (define-public r-atacseqqc
3738 (name "r-atacseqqc")
3743 (uri (bioconductor-uri "ATACseqQC" version))
3746 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3747 (properties `((upstream-name . "ATACseqQC")))
3748 (build-system r-build-system)
3750 `(("r-biocgenerics" ,r-biocgenerics)
3751 ("r-biostrings" ,r-biostrings)
3752 ("r-bsgenome" ,r-bsgenome)
3753 ("r-chippeakanno" ,r-chippeakanno)
3754 ("r-edger" ,r-edger)
3755 ("r-genomeinfodb" ,r-genomeinfodb)
3756 ("r-genomicalignments" ,r-genomicalignments)
3757 ("r-genomicranges" ,r-genomicranges)
3758 ("r-genomicscores" ,r-genomicscores)
3759 ("r-iranges" ,r-iranges)
3760 ("r-kernsmooth" ,r-kernsmooth)
3761 ("r-limma" ,r-limma)
3762 ("r-motifstack" ,r-motifstack)
3763 ("r-preseqr" ,r-preseqr)
3764 ("r-randomforest" ,r-randomforest)
3765 ("r-rsamtools" ,r-rsamtools)
3766 ("r-rtracklayer" ,r-rtracklayer)
3767 ("r-s4vectors" ,r-s4vectors)))
3768 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3769 (synopsis "ATAC-seq quality control")
3771 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3772 sequencing, is a rapid and sensitive method for chromatin accessibility
3773 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3774 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3775 assess whether their ATAC-seq experiment is successful. It includes
3776 diagnostic plots of fragment size distribution, proportion of mitochondria
3777 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3779 (license license:gpl2+)))
3781 (define-public r-gofuncr
3788 (uri (bioconductor-uri "GOfuncR" version))
3791 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3792 (properties `((upstream-name . "GOfuncR")))
3793 (build-system r-build-system)
3795 `(("r-annotationdbi" ,r-annotationdbi)
3796 ("r-genomicranges" ,r-genomicranges)
3797 ("r-gtools" ,r-gtools)
3798 ("r-iranges" ,r-iranges)
3799 ("r-mapplots" ,r-mapplots)
3801 ("r-vioplot" ,r-vioplot)))
3802 (home-page "https://bioconductor.org/packages/GOfuncR/")
3803 (synopsis "Gene ontology enrichment using FUNC")
3805 "GOfuncR performs a gene ontology enrichment analysis based on the
3806 ontology enrichment software FUNC. GO-annotations are obtained from
3807 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3808 included in the package and updated regularly. GOfuncR provides the standard
3809 candidate vs background enrichment analysis using the hypergeometric test, as
3810 well as three additional tests:
3813 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3814 @item a binomial test that is used when genes are associated with two counts,
3816 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3817 associated with four counts.
3820 To correct for multiple testing and interdependency of the tests, family-wise
3821 error rates are computed based on random permutations of the gene-associated
3822 variables. GOfuncR also provides tools for exploring the ontology graph and
3823 the annotations, and options to take gene-length or spatial clustering of
3824 genes into account. It is also possible to provide custom gene coordinates,
3825 annotations and ontologies.")
3826 (license license:gpl2+)))
3828 (define-public r-abaenrichment
3830 (name "r-abaenrichment")
3835 (uri (bioconductor-uri "ABAEnrichment" version))
3838 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
3839 (properties `((upstream-name . "ABAEnrichment")))
3840 (build-system r-build-system)
3842 `(("r-abadata" ,r-abadata)
3843 ("r-data-table" ,r-data-table)
3844 ("r-gofuncr" ,r-gofuncr)
3845 ("r-gplots" ,r-gplots)
3846 ("r-gtools" ,r-gtools)
3847 ("r-rcpp" ,r-rcpp)))
3848 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3849 (synopsis "Gene expression enrichment in human brain regions")
3851 "The package ABAEnrichment is designed to test for enrichment of user
3852 defined candidate genes in the set of expressed genes in different human brain
3853 regions. The core function @code{aba_enrich} integrates the expression of the
3854 candidate gene set (averaged across donors) and the structural information of
3855 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3856 (license license:gpl2+)))
3858 (define-public r-annotationfuncs
3860 (name "r-annotationfuncs")
3865 (uri (bioconductor-uri "AnnotationFuncs" version))
3868 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3870 `((upstream-name . "AnnotationFuncs")))
3871 (build-system r-build-system)
3873 `(("r-annotationdbi" ,r-annotationdbi)
3875 (home-page "https://www.iysik.com/r/annotationfuncs")
3876 (synopsis "Annotation translation functions")
3878 "This package provides functions for handling translating between
3879 different identifieres using the Biocore Data Team data-packages (e.g.
3880 @code{org.Bt.eg.db}).")
3881 (license license:gpl2)))
3883 (define-public r-annotationtools
3885 (name "r-annotationtools")
3890 (uri (bioconductor-uri "annotationTools" version))
3893 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3895 `((upstream-name . "annotationTools")))
3896 (build-system r-build-system)
3897 (propagated-inputs `(("r-biobase" ,r-biobase)))
3898 (home-page "https://bioconductor.org/packages/annotationTools/")
3899 (synopsis "Annotate microarrays and perform gene expression analyses")
3901 "This package provides functions to annotate microarrays, find orthologs,
3902 and integrate heterogeneous gene expression profiles using annotation and
3903 other molecular biology information available as flat file database (plain
3905 ;; Any version of the GPL.
3906 (license (list license:gpl2+))))
3908 (define-public r-allelicimbalance
3910 (name "r-allelicimbalance")
3915 (uri (bioconductor-uri "AllelicImbalance" version))
3918 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3920 `((upstream-name . "AllelicImbalance")))
3921 (build-system r-build-system)
3923 `(("r-annotationdbi" ,r-annotationdbi)
3924 ("r-biocgenerics" ,r-biocgenerics)
3925 ("r-biostrings" ,r-biostrings)
3926 ("r-bsgenome" ,r-bsgenome)
3927 ("r-genomeinfodb" ,r-genomeinfodb)
3928 ("r-genomicalignments" ,r-genomicalignments)
3929 ("r-genomicfeatures" ,r-genomicfeatures)
3930 ("r-genomicranges" ,r-genomicranges)
3931 ("r-gridextra" ,r-gridextra)
3933 ("r-iranges" ,r-iranges)
3934 ("r-lattice" ,r-lattice)
3935 ("r-latticeextra" ,r-latticeextra)
3937 ("r-rsamtools" ,r-rsamtools)
3938 ("r-s4vectors" ,r-s4vectors)
3939 ("r-seqinr" ,r-seqinr)
3940 ("r-summarizedexperiment" ,r-summarizedexperiment)
3941 ("r-variantannotation" ,r-variantannotation)))
3942 (home-page "https://github.com/pappewaio/AllelicImbalance")
3943 (synopsis "Investigate allele-specific expression")
3945 "This package provides a framework for allele-specific expression
3946 investigation using RNA-seq data.")
3947 (license license:gpl3)))
3949 (define-public r-aucell
3956 (uri (bioconductor-uri "AUCell" version))
3959 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
3960 (properties `((upstream-name . "AUCell")))
3961 (build-system r-build-system)
3963 `(("r-data-table" ,r-data-table)
3964 ("r-gseabase" ,r-gseabase)
3965 ("r-mixtools" ,r-mixtools)
3966 ("r-r-utils" ,r-r-utils)
3967 ("r-shiny" ,r-shiny)
3968 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3969 (home-page "https://bioconductor.org/packages/AUCell/")
3970 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3972 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3973 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3974 Under the Curve} (AUC) to calculate whether a critical subset of the input
3975 gene set is enriched within the expressed genes for each cell. The
3976 distribution of AUC scores across all the cells allows exploring the relative
3977 expression of the signature. Since the scoring method is ranking-based,
3978 AUCell is independent of the gene expression units and the normalization
3979 procedure. In addition, since the cells are evaluated individually, it can
3980 easily be applied to bigger datasets, subsetting the expression matrix if
3982 (license license:gpl3)))
3984 (define-public r-ebimage
3991 (uri (bioconductor-uri "EBImage" version))
3994 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
3995 (properties `((upstream-name . "EBImage")))
3996 (build-system r-build-system)
3998 `(("r-abind" ,r-abind)
3999 ("r-biocgenerics" ,r-biocgenerics)
4000 ("r-fftwtools" ,r-fftwtools)
4001 ("r-htmltools" ,r-htmltools)
4002 ("r-htmlwidgets" ,r-htmlwidgets)
4004 ("r-locfit" ,r-locfit)
4006 ("r-rcurl" ,r-rcurl)
4007 ("r-tiff" ,r-tiff)))
4009 `(("r-knitr" ,r-knitr))) ; for vignettes
4010 (home-page "https://github.com/aoles/EBImage")
4011 (synopsis "Image processing and analysis toolbox for R")
4013 "EBImage provides general purpose functionality for image processing and
4014 analysis. In the context of (high-throughput) microscopy-based cellular
4015 assays, EBImage offers tools to segment cells and extract quantitative
4016 cellular descriptors. This allows the automation of such tasks using the R
4017 programming language and facilitates the use of other tools in the R
4018 environment for signal processing, statistical modeling, machine learning and
4019 visualization with image data.")
4020 ;; Any version of the LGPL.
4021 (license license:lgpl2.1+)))
4023 (define-public r-yamss
4030 (uri (bioconductor-uri "yamss" version))
4033 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
4034 (build-system r-build-system)
4036 `(("r-biocgenerics" ,r-biocgenerics)
4037 ("r-data-table" ,r-data-table)
4038 ("r-ebimage" ,r-ebimage)
4039 ("r-iranges" ,r-iranges)
4040 ("r-limma" ,r-limma)
4041 ("r-matrix" ,r-matrix)
4043 ("r-s4vectors" ,r-s4vectors)
4044 ("r-summarizedexperiment"
4045 ,r-summarizedexperiment)))
4046 (home-page "https://github.com/hansenlab/yamss")
4047 (synopsis "Tools for high-throughput metabolomics")
4049 "This package provides tools to analyze and visualize high-throughput
4050 metabolomics data acquired using chromatography-mass spectrometry. These tools
4051 preprocess data in a way that enables reliable and powerful differential
4053 (license license:artistic2.0)))
4055 (define-public r-gtrellis
4062 (uri (bioconductor-uri "gtrellis" version))
4065 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
4066 (build-system r-build-system)
4068 `(("r-circlize" ,r-circlize)
4069 ("r-genomicranges" ,r-genomicranges)
4070 ("r-getoptlong" ,r-getoptlong)
4071 ("r-iranges" ,r-iranges)))
4072 (home-page "https://github.com/jokergoo/gtrellis")
4073 (synopsis "Genome level Trellis layout")
4075 "Genome level Trellis graph visualizes genomic data conditioned by
4076 genomic categories (e.g. chromosomes). For each genomic category, multiple
4077 dimensional data which are represented as tracks describe different features
4078 from different aspects. This package provides high flexibility to arrange
4079 genomic categories and to add self-defined graphics in the plot.")
4080 (license license:expat)))
4082 (define-public r-somaticsignatures
4084 (name "r-somaticsignatures")
4089 (uri (bioconductor-uri "SomaticSignatures" version))
4092 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
4094 `((upstream-name . "SomaticSignatures")))
4095 (build-system r-build-system)
4097 `(("r-biobase" ,r-biobase)
4098 ("r-biostrings" ,r-biostrings)
4099 ("r-genomeinfodb" ,r-genomeinfodb)
4100 ("r-genomicranges" ,r-genomicranges)
4101 ("r-ggbio" ,r-ggbio)
4102 ("r-ggplot2" ,r-ggplot2)
4103 ("r-iranges" ,r-iranges)
4105 ("r-pcamethods" ,r-pcamethods)
4106 ("r-proxy" ,r-proxy)
4107 ("r-reshape2" ,r-reshape2)
4108 ("r-s4vectors" ,r-s4vectors)
4109 ("r-variantannotation" ,r-variantannotation)))
4110 (home-page "https://github.com/juliangehring/SomaticSignatures")
4111 (synopsis "Somatic signatures")
4113 "This package identifies mutational signatures of @dfn{single nucleotide
4114 variants} (SNVs). It provides a infrastructure related to the methodology
4115 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4116 decomposition algorithms.")
4117 (license license:expat)))
4119 (define-public r-yapsa
4126 (uri (bioconductor-uri "YAPSA" version))
4129 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
4130 (properties `((upstream-name . "YAPSA")))
4131 (build-system r-build-system)
4133 `(("r-circlize" ,r-circlize)
4134 ("r-complexheatmap" ,r-complexheatmap)
4135 ("r-corrplot" ,r-corrplot)
4136 ("r-dendextend" ,r-dendextend)
4137 ("r-genomeinfodb" ,r-genomeinfodb)
4138 ("r-genomicranges" ,r-genomicranges)
4139 ("r-getoptlong" ,r-getoptlong)
4140 ("r-ggplot2" ,r-ggplot2)
4141 ("r-gridextra" ,r-gridextra)
4142 ("r-gtrellis" ,r-gtrellis)
4143 ("r-keggrest" ,r-keggrest)
4145 ("r-pmcmr" ,r-pmcmr)
4146 ("r-reshape2" ,r-reshape2)
4147 ("r-somaticsignatures" ,r-somaticsignatures)
4148 ("r-variantannotation" ,r-variantannotation)))
4149 (home-page "https://bioconductor.org/packages/YAPSA/")
4150 (synopsis "Yet another package for signature analysis")
4152 "This package provides functions and routines useful in the analysis of
4153 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4154 functions to perform a signature analysis with known signatures and a
4155 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4157 (license license:gpl3)))
4159 (define-public r-gcrma
4166 (uri (bioconductor-uri "gcrma" version))
4169 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4170 (build-system r-build-system)
4172 `(("r-affy" ,r-affy)
4173 ("r-affyio" ,r-affyio)
4174 ("r-biobase" ,r-biobase)
4175 ("r-biocmanager" ,r-biocmanager)
4176 ("r-biostrings" ,r-biostrings)
4177 ("r-xvector" ,r-xvector)))
4178 (home-page "https://bioconductor.org/packages/gcrma/")
4179 (synopsis "Background adjustment using sequence information")
4181 "Gcrma adjusts for background intensities in Affymetrix array data which
4182 include optical noise and @dfn{non-specific binding} (NSB). The main function
4183 @code{gcrma} converts background adjusted probe intensities to expression
4184 measures using the same normalization and summarization methods as a
4185 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4186 to estimate probe affinity to NSB. The sequence information is summarized in
4187 a more complex way than the simple GC content. Instead, the base types (A, T,
4188 G or C) at each position along the probe determine the affinity of each probe.
4189 The parameters of the position-specific base contributions to the probe
4190 affinity is estimated in an NSB experiment in which only NSB but no
4191 gene-specific bidning is expected.")
4192 ;; Any version of the LGPL
4193 (license license:lgpl2.1+)))
4195 (define-public r-simpleaffy
4197 (name "r-simpleaffy")
4202 (uri (bioconductor-uri "simpleaffy" version))
4205 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4206 (build-system r-build-system)
4208 `(("r-affy" ,r-affy)
4209 ("r-biobase" ,r-biobase)
4210 ("r-biocgenerics" ,r-biocgenerics)
4211 ("r-gcrma" ,r-gcrma)
4212 ("r-genefilter" ,r-genefilter)))
4213 (home-page "https://bioconductor.org/packages/simpleaffy/")
4214 (synopsis "Very simple high level analysis of Affymetrix data")
4216 "This package provides high level functions for reading Affy @file{.CEL}
4217 files, phenotypic data, and then computing simple things with it, such as
4218 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4219 library. It also has some basic scatter plot functions and mechanisms for
4220 generating high resolution journal figures.")
4221 (license license:gpl2+)))
4223 (define-public r-yaqcaffy
4230 (uri (bioconductor-uri "yaqcaffy" version))
4233 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4234 (build-system r-build-system)
4236 `(("r-simpleaffy" ,r-simpleaffy)))
4237 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4238 (synopsis "Affymetrix quality control and reproducibility analysis")
4240 "This is a package that can be used for quality control of Affymetrix
4241 GeneChip expression data and reproducibility analysis of human whole genome
4242 chips with the MAQC reference datasets.")
4243 (license license:artistic2.0)))
4245 (define-public r-quantro
4252 (uri (bioconductor-uri "quantro" version))
4255 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4256 (build-system r-build-system)
4258 `(("r-biobase" ,r-biobase)
4259 ("r-doparallel" ,r-doparallel)
4260 ("r-foreach" ,r-foreach)
4261 ("r-ggplot2" ,r-ggplot2)
4262 ("r-iterators" ,r-iterators)
4263 ("r-minfi" ,r-minfi)
4264 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4265 (home-page "https://bioconductor.org/packages/quantro/")
4266 (synopsis "Test for when to use quantile normalization")
4268 "This package provides a data-driven test for the assumptions of quantile
4269 normalization using raw data such as objects that inherit eSets (e.g.
4270 ExpressionSet, MethylSet). Group level information about each sample (such as
4271 Tumor / Normal status) must also be provided because the test assesses if
4272 there are global differences in the distributions between the user-defined
4274 (license license:gpl3+)))
4276 (define-public r-yarn
4283 (uri (bioconductor-uri "yarn" version))
4286 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4287 (build-system r-build-system)
4289 `(("r-biobase" ,r-biobase)
4290 ("r-biomart" ,r-biomart)
4291 ("r-downloader" ,r-downloader)
4292 ("r-edger" ,r-edger)
4293 ("r-gplots" ,r-gplots)
4294 ("r-limma" ,r-limma)
4295 ("r-matrixstats" ,r-matrixstats)
4296 ("r-preprocesscore" ,r-preprocesscore)
4297 ("r-quantro" ,r-quantro)
4298 ("r-rcolorbrewer" ,r-rcolorbrewer)
4299 ("r-readr" ,r-readr)))
4300 (home-page "https://bioconductor.org/packages/yarn/")
4301 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4303 "Expedite large RNA-Seq analyses using a combination of previously
4304 developed tools. YARN is meant to make it easier for the user in performing
4305 basic mis-annotation quality control, filtering, and condition-aware
4306 normalization. YARN leverages many Bioconductor tools and statistical
4307 techniques to account for the large heterogeneity and sparsity found in very
4308 large RNA-seq experiments.")
4309 (license license:artistic2.0)))
4311 (define-public r-roar
4318 (uri (bioconductor-uri "roar" version))
4321 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4322 (build-system r-build-system)
4324 `(("r-biocgenerics" ,r-biocgenerics)
4325 ("r-genomeinfodb" ,r-genomeinfodb)
4326 ("r-genomicalignments" ,r-genomicalignments)
4327 ("r-genomicranges" ,r-genomicranges)
4328 ("r-iranges" ,r-iranges)
4329 ("r-rtracklayer" ,r-rtracklayer)
4330 ("r-s4vectors" ,r-s4vectors)
4331 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4332 (home-page "https://github.com/vodkatad/roar/")
4333 (synopsis "Identify differential APA usage from RNA-seq alignments")
4335 "This package provides tools for identifying preferential usage of APA
4336 sites, comparing two biological conditions, starting from known alternative
4337 sites and alignments obtained from standard RNA-seq experiments.")
4338 (license license:gpl3)))
4340 (define-public r-xbseq
4347 (uri (bioconductor-uri "XBSeq" version))
4350 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4351 (properties `((upstream-name . "XBSeq")))
4352 (build-system r-build-system)
4354 `(("r-biobase" ,r-biobase)
4355 ("r-deseq2" ,r-deseq2)
4356 ("r-dplyr" ,r-dplyr)
4357 ("r-ggplot2" ,r-ggplot2)
4358 ("r-locfit" ,r-locfit)
4359 ("r-magrittr" ,r-magrittr)
4360 ("r-matrixstats" ,r-matrixstats)
4361 ("r-pracma" ,r-pracma)
4362 ("r-roar" ,r-roar)))
4363 (home-page "https://github.com/Liuy12/XBSeq")
4364 (synopsis "Test for differential expression for RNA-seq data")
4366 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4367 expression} (DE), where a statistical model was established based on the
4368 assumption that observed signals are the convolution of true expression
4369 signals and sequencing noises. The mapped reads in non-exonic regions are
4370 considered as sequencing noises, which follows a Poisson distribution. Given
4371 measurable observed signal and background noise from RNA-seq data, true
4372 expression signals, assuming governed by the negative binomial distribution,
4373 can be delineated and thus the accurate detection of differential expressed
4375 (license license:gpl3+)))
4377 (define-public r-massspecwavelet
4379 (name "r-massspecwavelet")
4384 (uri (bioconductor-uri "MassSpecWavelet" version))
4387 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4389 `((upstream-name . "MassSpecWavelet")))
4390 (build-system r-build-system)
4392 `(("r-waveslim" ,r-waveslim)))
4393 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4394 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4396 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4397 data mainly through the use of wavelet transforms. It supports peak detection
4398 based on @dfn{Continuous Wavelet Transform} (CWT).")
4399 (license license:lgpl2.0+)))
4401 (define-public r-xcms
4408 (uri (bioconductor-uri "xcms" version))
4411 "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
4412 (build-system r-build-system)
4414 `(("r-biobase" ,r-biobase)
4415 ("r-biocgenerics" ,r-biocgenerics)
4416 ("r-biocparallel" ,r-biocparallel)
4417 ("r-lattice" ,r-lattice)
4418 ("r-massspecwavelet" ,r-massspecwavelet)
4419 ("r-msnbase" ,r-msnbase)
4420 ("r-multtest" ,r-multtest)
4423 ("r-protgenerics" ,r-protgenerics)
4425 ("r-rcolorbrewer" ,r-rcolorbrewer)
4426 ("r-robustbase" ,r-robustbase)
4427 ("r-s4vectors" ,r-s4vectors)))
4428 (home-page "https://bioconductor.org/packages/xcms/")
4429 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4431 "This package provides a framework for processing and visualization of
4432 chromatographically separated and single-spectra mass spectral data. It
4433 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4434 data for high-throughput, untargeted analyte profiling.")
4435 (license license:gpl2+)))
4437 (define-public r-wrench
4444 (uri (bioconductor-uri "Wrench" version))
4447 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4448 (properties `((upstream-name . "Wrench")))
4449 (build-system r-build-system)
4451 `(("r-limma" ,r-limma)
4452 ("r-locfit" ,r-locfit)
4453 ("r-matrixstats" ,r-matrixstats)))
4454 (home-page "https://github.com/HCBravoLab/Wrench")
4455 (synopsis "Wrench normalization for sparse count data")
4457 "Wrench is a package for normalization sparse genomic count data, like
4458 that arising from 16s metagenomic surveys.")
4459 (license license:artistic2.0)))
4461 (define-public r-wiggleplotr
4463 (name "r-wiggleplotr")
4468 (uri (bioconductor-uri "wiggleplotr" version))
4471 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4472 (build-system r-build-system)
4474 `(("r-assertthat" ,r-assertthat)
4475 ("r-cowplot" ,r-cowplot)
4476 ("r-dplyr" ,r-dplyr)
4477 ("r-genomeinfodb" ,r-genomeinfodb)
4478 ("r-genomicranges" ,r-genomicranges)
4479 ("r-ggplot2" ,r-ggplot2)
4480 ("r-iranges" ,r-iranges)
4481 ("r-purrr" ,r-purrr)
4482 ("r-rtracklayer" ,r-rtracklayer)
4483 ("r-s4vectors" ,r-s4vectors)))
4484 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4485 (synopsis "Make read coverage plots from BigWig files")
4487 "This package provides tools to visualize read coverage from sequencing
4488 experiments together with genomic annotations (genes, transcripts, peaks).
4489 Introns of long transcripts can be rescaled to a fixed length for better
4490 visualization of exonic read coverage.")
4491 (license license:asl2.0)))
4493 (define-public r-widgettools
4495 (name "r-widgettools")
4500 (uri (bioconductor-uri "widgetTools" version))
4503 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4504 (properties `((upstream-name . "widgetTools")))
4505 (build-system r-build-system)
4506 (home-page "https://bioconductor.org/packages/widgetTools/")
4507 (synopsis "Tools for creating interactive tcltk widgets")
4509 "This package contains tools to support the construction of tcltk
4511 ;; Any version of the LGPL.
4512 (license license:lgpl3+)))
4514 (define-public r-webbioc
4521 (uri (bioconductor-uri "webbioc" version))
4524 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4525 (build-system r-build-system)
4527 `(("netpbm" ,netpbm)
4530 `(("r-affy" ,r-affy)
4531 ("r-annaffy" ,r-annaffy)
4532 ("r-biobase" ,r-biobase)
4533 ("r-biocmanager" ,r-biocmanager)
4534 ("r-gcrma" ,r-gcrma)
4535 ("r-multtest" ,r-multtest)
4536 ("r-qvalue" ,r-qvalue)
4538 (home-page "https://www.bioconductor.org/")
4539 (synopsis "Bioconductor web interface")
4541 "This package provides an integrated web interface for doing microarray
4542 analysis using several of the Bioconductor packages. It is intended to be
4543 deployed as a centralized bioinformatics resource for use by many users.
4544 Currently only Affymetrix oligonucleotide analysis is supported.")
4545 (license license:gpl2+)))
4547 (define-public r-zfpkm
4554 (uri (bioconductor-uri "zFPKM" version))
4557 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4558 (properties `((upstream-name . "zFPKM")))
4559 (build-system r-build-system)
4561 `(("r-checkmate" ,r-checkmate)
4562 ("r-dplyr" ,r-dplyr)
4563 ("r-ggplot2" ,r-ggplot2)
4564 ("r-summarizedexperiment" ,r-summarizedexperiment)
4565 ("r-tidyr" ,r-tidyr)))
4566 (home-page "https://github.com/ronammar/zFPKM/")
4567 (synopsis "Functions to facilitate zFPKM transformations")
4569 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4570 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4572 (license license:gpl3)))
4574 (define-public r-rbowtie2
4581 (uri (bioconductor-uri "Rbowtie2" version))
4584 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4585 (properties `((upstream-name . "Rbowtie2")))
4586 (build-system r-build-system)
4589 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4590 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4592 "This package provides an R wrapper of the popular @code{bowtie2}
4593 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4594 rapid adapter trimming, identification, and read merging.")
4595 (license license:gpl3+)))
4597 (define-public r-progeny
4604 (uri (bioconductor-uri "progeny" version))
4607 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4608 (build-system r-build-system)
4609 (propagated-inputs `(("r-biobase" ,r-biobase)))
4610 (home-page "https://github.com/saezlab/progeny")
4611 (synopsis "Pathway responsive gene activity inference")
4613 "This package provides a function to infer pathway activity from gene
4614 expression. It contains the linear model inferred in the publication
4615 \"Perturbation-response genes reveal signaling footprints in cancer gene
4617 (license license:asl2.0)))
4619 (define-public r-arrmnormalization
4621 (name "r-arrmnormalization")
4626 (uri (bioconductor-uri "ARRmNormalization" version))
4629 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4631 `((upstream-name . "ARRmNormalization")))
4632 (build-system r-build-system)
4633 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4634 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4635 (synopsis "Adaptive robust regression normalization for methylation data")
4637 "This is a package to perform the @dfn{Adaptive Robust Regression
4638 method} (ARRm) for the normalization of methylation data from the Illumina
4639 Infinium HumanMethylation 450k assay.")
4640 (license license:artistic2.0)))
4642 (define-public r-biocfilecache
4644 (name "r-biocfilecache")
4649 (uri (bioconductor-uri "BiocFileCache" version))
4652 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4653 (properties `((upstream-name . "BiocFileCache")))
4654 (build-system r-build-system)
4656 `(("r-curl" ,r-curl)
4658 ("r-dbplyr" ,r-dbplyr)
4659 ("r-dplyr" ,r-dplyr)
4661 ("r-rappdirs" ,r-rappdirs)
4662 ("r-rsqlite" ,r-rsqlite)))
4663 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4664 (synopsis "Manage files across sessions")
4666 "This package creates a persistent on-disk cache of files that the user
4667 can add, update, and retrieve. It is useful for managing resources (such as
4668 custom Txdb objects) that are costly or difficult to create, web resources,
4669 and data files used across sessions.")
4670 (license license:artistic2.0)))
4672 (define-public r-iclusterplus
4674 (name "r-iclusterplus")
4679 (uri (bioconductor-uri "iClusterPlus" version))
4682 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4683 (properties `((upstream-name . "iClusterPlus")))
4684 (build-system r-build-system)
4685 (native-inputs `(("gfortran" ,gfortran)))
4686 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4687 (synopsis "Integrative clustering of multi-type genomic data")
4689 "iClusterPlus is developed for integrative clustering analysis of
4690 multi-type genomic data and is an enhanced version of iCluster proposed and
4691 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4692 from the experiments where biological samples (e.g. tumor samples) are
4693 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4694 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4695 on. In the iClusterPlus model, binary observations such as somatic mutation
4696 are modeled as Binomial processes; categorical observations such as copy
4697 number states are realizations of Multinomial random variables; counts are
4698 modeled as Poisson random processes; and continuous measures are modeled by
4699 Gaussian distributions.")
4700 (license license:gpl2+)))
4702 (define-public r-rbowtie
4709 (uri (bioconductor-uri "Rbowtie" version))
4712 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4713 (properties `((upstream-name . "Rbowtie")))
4714 (build-system r-build-system)
4717 (home-page "https://bioconductor.org/packages/Rbowtie/")
4718 (synopsis "R bowtie wrapper")
4720 "This package provides an R wrapper around the popular bowtie short read
4721 aligner and around SpliceMap, a de novo splice junction discovery and
4723 (license license:artistic2.0)))
4725 (define-public r-sgseq
4732 (uri (bioconductor-uri "SGSeq" version))
4735 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4736 (properties `((upstream-name . "SGSeq")))
4737 (build-system r-build-system)
4739 `(("r-annotationdbi" ,r-annotationdbi)
4740 ("r-biocgenerics" ,r-biocgenerics)
4741 ("r-biostrings" ,r-biostrings)
4742 ("r-genomeinfodb" ,r-genomeinfodb)
4743 ("r-genomicalignments" ,r-genomicalignments)
4744 ("r-genomicfeatures" ,r-genomicfeatures)
4745 ("r-genomicranges" ,r-genomicranges)
4746 ("r-igraph" ,r-igraph)
4747 ("r-iranges" ,r-iranges)
4748 ("r-rsamtools" ,r-rsamtools)
4749 ("r-rtracklayer" ,r-rtracklayer)
4750 ("r-runit" ,r-runit)
4751 ("r-s4vectors" ,r-s4vectors)
4752 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4753 (home-page "https://bioconductor.org/packages/SGSeq/")
4754 (synopsis "Splice event prediction and quantification from RNA-seq data")
4756 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4757 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4758 represented as a splice graph, which can be obtained from existing annotation
4759 or predicted from the mapped sequence reads. Splice events are identified
4760 from the graph and are quantified locally using structurally compatible reads
4761 at the start or end of each splice variant. The software includes functions
4762 for splice event prediction, quantification, visualization and
4764 (license license:artistic2.0)))
4766 (define-public r-rhisat2
4773 (uri (bioconductor-uri "Rhisat2" version))
4776 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4777 (properties `((upstream-name . "Rhisat2")))
4778 (build-system r-build-system)
4780 `(("which" ,which)))
4782 `(("r-genomicfeatures" ,r-genomicfeatures)
4783 ("r-genomicranges" ,r-genomicranges)
4784 ("r-sgseq" ,r-sgseq)))
4785 (home-page "https://github.com/fmicompbio/Rhisat2")
4786 (synopsis "R Wrapper for HISAT2 sequence aligner")
4788 "This package provides an R interface to the HISAT2 spliced short-read
4789 aligner by Kim et al. (2015). The package contains wrapper functions to
4790 create a genome index and to perform the read alignment to the generated
4792 (license license:gpl3)))
4794 (define-public r-quasr
4801 (uri (bioconductor-uri "QuasR" version))
4804 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4805 (properties `((upstream-name . "QuasR")))
4806 (build-system r-build-system)
4810 `(("r-annotationdbi" ,r-annotationdbi)
4811 ("r-biobase" ,r-biobase)
4812 ("r-biocgenerics" ,r-biocgenerics)
4813 ("r-biocmanager" ,r-biocmanager)
4814 ("r-biocparallel" ,r-biocparallel)
4815 ("r-biostrings" ,r-biostrings)
4816 ("r-bsgenome" ,r-bsgenome)
4817 ("r-genomeinfodb" ,r-genomeinfodb)
4818 ("r-genomicalignments" ,r-genomicalignments)
4819 ("r-genomicfeatures" ,r-genomicfeatures)
4820 ("r-genomicfiles" ,r-genomicfiles)
4821 ("r-genomicranges" ,r-genomicranges)
4822 ("r-iranges" ,r-iranges)
4823 ("r-rbowtie" ,r-rbowtie)
4824 ("r-rhisat2" ,r-rhisat2)
4825 ("r-rhtslib" ,r-rhtslib)
4826 ("r-rsamtools" ,r-rsamtools)
4827 ("r-rtracklayer" ,r-rtracklayer)
4828 ("r-s4vectors" ,r-s4vectors)
4829 ("r-shortread" ,r-shortread)))
4830 (home-page "https://bioconductor.org/packages/QuasR/")
4831 (synopsis "Quantify and annotate short reads in R")
4833 "This package provides a framework for the quantification and analysis of
4834 short genomic reads. It covers a complete workflow starting from raw sequence
4835 reads, over creation of alignments and quality control plots, to the
4836 quantification of genomic regions of interest.")
4837 (license license:gpl2)))
4839 (define-public r-rqc
4846 (uri (bioconductor-uri "Rqc" version))
4849 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4850 (properties `((upstream-name . "Rqc")))
4851 (build-system r-build-system)
4853 `(("r-biocgenerics" ,r-biocgenerics)
4854 ("r-biocparallel" ,r-biocparallel)
4855 ("r-biocstyle" ,r-biocstyle)
4856 ("r-biostrings" ,r-biostrings)
4857 ("r-biovizbase" ,r-biovizbase)
4858 ("r-genomicalignments" ,r-genomicalignments)
4859 ("r-genomicfiles" ,r-genomicfiles)
4860 ("r-ggplot2" ,r-ggplot2)
4861 ("r-iranges" ,r-iranges)
4862 ("r-knitr" ,r-knitr)
4863 ("r-markdown" ,r-markdown)
4866 ("r-reshape2" ,r-reshape2)
4867 ("r-rsamtools" ,r-rsamtools)
4868 ("r-s4vectors" ,r-s4vectors)
4869 ("r-shiny" ,r-shiny)
4870 ("r-shortread" ,r-shortread)))
4871 (home-page "https://github.com/labbcb/Rqc")
4872 (synopsis "Quality control tool for high-throughput sequencing data")
4874 "Rqc is an optimized tool designed for quality control and assessment of
4875 high-throughput sequencing data. It performs parallel processing of entire
4876 files and produces a report which contains a set of high-resolution
4878 (license license:gpl2+)))
4880 (define-public r-birewire
4887 (uri (bioconductor-uri "BiRewire" version))
4890 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
4891 (properties `((upstream-name . "BiRewire")))
4892 (build-system r-build-system)
4894 `(("r-igraph" ,r-igraph)
4895 ("r-matrix" ,r-matrix)
4897 ("r-tsne" ,r-tsne)))
4898 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
4899 (synopsis "Tools for randomization of bipartite graphs")
4901 "This package provides functions for bipartite network rewiring through N
4902 consecutive switching steps and for the computation of the minimal number of
4903 switching steps to be performed in order to maximise the dissimilarity with
4904 respect to the original network. It includes functions for the analysis of
4905 the introduced randomness across the switching steps and several other
4906 routines to analyse the resulting networks and their natural projections.")
4907 (license license:gpl3)))
4909 (define-public r-birta
4916 (uri (bioconductor-uri "birta" version))
4919 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
4920 (build-system r-build-system)
4922 `(("r-biobase" ,r-biobase)
4923 ("r-limma" ,r-limma)
4924 ("r-mass" ,r-mass)))
4925 (home-page "https://bioconductor.org/packages/birta")
4926 (synopsis "Bayesian inference of regulation of transcriptional activity")
4928 "Expression levels of mRNA molecules are regulated by different
4929 processes, comprising inhibition or activation by transcription factors and
4930 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
4931 Inference of Regulation of Transcriptional Activity) uses the regulatory
4932 networks of transcription factors and miRNAs together with mRNA and miRNA
4933 expression data to predict switches in regulatory activity between two
4934 conditions. A Bayesian network is used to model the regulatory structure and
4935 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
4936 (license license:gpl2+)))
4938 (define-public r-ropls
4945 (uri (bioconductor-uri "ropls" version))
4948 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
4949 (build-system r-build-system)
4950 (propagated-inputs `(("r-biobase" ,r-biobase)))
4952 `(("r-knitr" ,r-knitr))) ; for vignettes
4953 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
4954 (synopsis "Multivariate analysis and feature selection of omics data")
4956 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
4957 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
4958 regression, classification, and feature selection of omics data where the
4959 number of variables exceeds the number of samples and with multicollinearity
4960 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
4961 separately model the variation correlated (predictive) to the factor of
4962 interest and the uncorrelated (orthogonal) variation. While performing
4963 similarly to PLS, OPLS facilitates interpretation.
4965 This package provides imlementations of PCA, PLS, and OPLS for multivariate
4966 analysis and feature selection of omics data. In addition to scores, loadings
4967 and weights plots, the package provides metrics and graphics to determine the
4968 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
4969 validity of the model by permutation testing, detect outliers, and perform
4970 feature selection (e.g. with Variable Importance in Projection or regression
4972 (license license:cecill)))
4974 (define-public r-biosigner
4976 (name "r-biosigner")
4981 (uri (bioconductor-uri "biosigner" version))
4984 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
4985 (build-system r-build-system)
4987 `(("r-biobase" ,r-biobase)
4988 ("r-e1071" ,r-e1071)
4989 ("r-randomforest" ,r-randomforest)
4990 ("r-ropls" ,r-ropls)))
4992 `(("r-knitr" ,r-knitr)
4993 ("r-rmarkdown" ,r-rmarkdown)
4994 ("pandoc" ,ghc-pandoc)
4995 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
4996 (home-page "https://bioconductor.org/packages/biosigner/")
4997 (synopsis "Signature discovery from omics data")
4999 "Feature selection is critical in omics data analysis to extract
5000 restricted and meaningful molecular signatures from complex and high-dimension
5001 data, and to build robust classifiers. This package implements a method to
5002 assess the relevance of the variables for the prediction performances of the
5003 classifier. The approach can be run in parallel with the PLS-DA, Random
5004 Forest, and SVM binary classifiers. The signatures and the corresponding
5005 'restricted' models are returned, enabling future predictions on new
5007 (license license:cecill)))
5009 (define-public r-annotatr
5016 (uri (bioconductor-uri "annotatr" version))
5019 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
5020 (build-system r-build-system)
5022 `(("r-annotationdbi" ,r-annotationdbi)
5023 ("r-annotationhub" ,r-annotationhub)
5024 ("r-dplyr" ,r-dplyr)
5025 ("r-genomeinfodb" ,r-genomeinfodb)
5026 ("r-genomicfeatures" ,r-genomicfeatures)
5027 ("r-genomicranges" ,r-genomicranges)
5028 ("r-ggplot2" ,r-ggplot2)
5029 ("r-iranges" ,r-iranges)
5030 ("r-readr" ,r-readr)
5031 ("r-regioner" ,r-regioner)
5032 ("r-reshape2" ,r-reshape2)
5033 ("r-rtracklayer" ,r-rtracklayer)
5034 ("r-s4vectors" ,r-s4vectors)))
5035 (home-page "https://bioconductor.org/packages/annotatr/")
5036 (synopsis "Annotation of genomic regions to genomic annotations")
5038 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5039 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5040 to investigate the intersecting genomic annotations. Such annotations include
5041 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5042 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5043 enhancers. The annotatr package provides an easy way to summarize and
5044 visualize the intersection of genomic sites/regions with genomic
5046 (license license:gpl3)))
5048 (define-public r-rsubread
5055 (uri (bioconductor-uri "Rsubread" version))
5058 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
5059 (properties `((upstream-name . "Rsubread")))
5060 (build-system r-build-system)
5061 (inputs `(("zlib" ,zlib)))
5062 (home-page "https://bioconductor.org/packages/Rsubread/")
5063 (synopsis "Subread sequence alignment and counting for R")
5065 "This package provides tools for alignment, quantification and analysis
5066 of second and third generation sequencing data. It includes functionality for
5067 read mapping, read counting, SNP calling, structural variant detection and
5068 gene fusion discovery. It can be applied to all major sequencing techologies
5069 and to both short and long sequence reads.")
5070 (license license:gpl3)))
5072 (define-public r-flowutils
5074 (name "r-flowutils")
5079 (uri (bioconductor-uri "flowUtils" version))
5082 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
5083 (properties `((upstream-name . "flowUtils")))
5084 (build-system r-build-system)
5086 `(("r-biobase" ,r-biobase)
5087 ("r-corpcor" ,r-corpcor)
5088 ("r-flowcore" ,r-flowcore)
5089 ("r-graph" ,r-graph)
5090 ("r-runit" ,r-runit)
5092 (home-page "https://github.com/jspidlen/flowUtils")
5093 (synopsis "Utilities for flow cytometry")
5095 "This package provides utilities for flow cytometry data.")
5096 (license license:artistic2.0)))
5098 (define-public r-consensusclusterplus
5100 (name "r-consensusclusterplus")
5105 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5108 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
5110 `((upstream-name . "ConsensusClusterPlus")))
5111 (build-system r-build-system)
5114 ("r-biobase" ,r-biobase)
5115 ("r-cluster" ,r-cluster)))
5116 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5117 (synopsis "Clustering algorithm")
5119 "This package provides an implementation of an algorithm for determining
5120 cluster count and membership by stability evidence in unsupervised analysis.")
5121 (license license:gpl2)))
5123 (define-public r-flowcore
5130 (uri (bioconductor-uri "flowCore" version))
5133 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
5134 (properties `((upstream-name . "flowCore")))
5135 (build-system r-build-system)
5138 ("r-biobase" ,r-biobase)
5139 ("r-biocgenerics" ,r-biocgenerics)
5140 ("r-corpcor" ,r-corpcor)
5141 ("r-graph" ,r-graph)
5143 ("r-matrixstats" ,r-matrixstats)
5145 ("r-rrcov" ,r-rrcov)))
5146 (home-page "https://bioconductor.org/packages/flowCore")
5147 (synopsis "Basic structures for flow cytometry data")
5149 "This package provides S4 data structures and basic functions to deal
5150 with flow cytometry data.")
5151 (license license:artistic2.0)))
5153 (define-public r-flowmeans
5155 (name "r-flowmeans")
5160 (uri (bioconductor-uri "flowMeans" version))
5163 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
5164 (properties `((upstream-name . "flowMeans")))
5165 (build-system r-build-system)
5167 `(("r-biobase" ,r-biobase)
5168 ("r-feature" ,r-feature)
5169 ("r-flowcore" ,r-flowcore)
5170 ("r-rrcov" ,r-rrcov)))
5171 (home-page "https://bioconductor.org/packages/flowMeans")
5172 (synopsis "Non-parametric flow cytometry data gating")
5174 "This package provides tools to identify cell populations in Flow
5175 Cytometry data using non-parametric clustering and segmented-regression-based
5176 change point detection.")
5177 (license license:artistic2.0)))
5179 (define-public r-flowsom
5186 (uri (bioconductor-uri "FlowSOM" version))
5189 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5190 (properties `((upstream-name . "FlowSOM")))
5191 (build-system r-build-system)
5193 `(("r-biocgenerics" ,r-biocgenerics)
5194 ("r-consensusclusterplus" ,r-consensusclusterplus)
5195 ("r-flowcore" ,r-flowcore)
5196 ("r-flowutils" ,r-flowutils)
5197 ("r-igraph" ,r-igraph)
5200 (home-page "https://bioconductor.org/packages/FlowSOM/")
5201 (synopsis "Visualize and interpret cytometry data")
5203 "FlowSOM offers visualization options for cytometry data, by using
5204 self-organizing map clustering and minimal spanning trees.")
5205 (license license:gpl2+)))
5207 (define-public r-mixomics
5214 (uri (bioconductor-uri "mixOmics" version))
5217 "0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg"))))
5218 (properties `((upstream-name . "mixOmics")))
5219 (build-system r-build-system)
5221 `(("r-corpcor" ,r-corpcor)
5222 ("r-dplyr" ,r-dplyr)
5223 ("r-ellipse" ,r-ellipse)
5224 ("r-ggplot2" ,r-ggplot2)
5225 ("r-gridextra" ,r-gridextra)
5226 ("r-igraph" ,r-igraph)
5227 ("r-lattice" ,r-lattice)
5229 ("r-matrixstats" ,r-matrixstats)
5230 ("r-rarpack" ,r-rarpack)
5231 ("r-rcolorbrewer" ,r-rcolorbrewer)
5232 ("r-reshape2" ,r-reshape2)
5233 ("r-tidyr" ,r-tidyr)))
5234 (home-page "http://www.mixOmics.org")
5235 (synopsis "Multivariate methods for exploration of biological datasets")
5237 "mixOmics offers a wide range of multivariate methods for the exploration
5238 and integration of biological datasets with a particular focus on variable
5239 selection. The package proposes several sparse multivariate models we have
5240 developed to identify the key variables that are highly correlated, and/or
5241 explain the biological outcome of interest. The data that can be analysed
5242 with mixOmics may come from high throughput sequencing technologies, such as
5243 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5244 also beyond the realm of omics (e.g. spectral imaging). The methods
5245 implemented in mixOmics can also handle missing values without having to
5246 delete entire rows with missing data.")
5247 (license license:gpl2+)))
5249 (define-public r-depecher
5256 (uri (bioconductor-uri "DepecheR" version))
5259 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5260 (properties `((upstream-name . "DepecheR")))
5261 (build-system r-build-system)
5264 (modify-phases %standard-phases
5265 (add-after 'unpack 'fix-syntax-error
5267 (substitute* "src/Makevars"
5271 `(("r-beanplot" ,r-beanplot)
5272 ("r-biocparallel" ,r-biocparallel)
5273 ("r-dosnow" ,r-dosnow)
5274 ("r-dplyr" ,r-dplyr)
5275 ("r-foreach" ,r-foreach)
5276 ("r-ggplot2" ,r-ggplot2)
5277 ("r-gplots" ,r-gplots)
5279 ("r-matrixstats" ,r-matrixstats)
5280 ("r-mixomics" ,r-mixomics)
5281 ("r-moments" ,r-moments)
5283 ("r-rcppeigen" ,r-rcppeigen)
5284 ("r-reshape2" ,r-reshape2)
5285 ("r-viridis" ,r-viridis)))
5286 (home-page "https://bioconductor.org/packages/DepecheR/")
5287 (synopsis "Identify traits of clusters in high-dimensional entities")
5289 "The purpose of this package is to identify traits in a dataset that can
5290 separate groups. This is done on two levels. First, clustering is performed,
5291 using an implementation of sparse K-means. Secondly, the generated clusters
5292 are used to predict outcomes of groups of individuals based on their
5293 distribution of observations in the different clusters. As certain clusters
5294 with separating information will be identified, and these clusters are defined
5295 by a sparse number of variables, this method can reduce the complexity of
5296 data, to only emphasize the data that actually matters.")
5297 (license license:expat)))
5299 (define-public r-rcistarget
5301 (name "r-rcistarget")
5306 (uri (bioconductor-uri "RcisTarget" version))
5309 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5310 (properties `((upstream-name . "RcisTarget")))
5311 (build-system r-build-system)
5313 `(("r-aucell" ,r-aucell)
5314 ("r-biocgenerics" ,r-biocgenerics)
5315 ("r-data-table" ,r-data-table)
5316 ("r-feather" ,r-feather)
5317 ("r-gseabase" ,r-gseabase)
5318 ("r-r-utils" ,r-r-utils)
5319 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5320 (home-page "https://aertslab.org/#scenic")
5321 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5323 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5324 over-represented on a gene list. In a first step, RcisTarget selects DNA
5325 motifs that are significantly over-represented in the surroundings of the
5326 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5327 achieved by using a database that contains genome-wide cross-species rankings
5328 for each motif. The motifs that are then annotated to TFs and those that have
5329 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5330 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5331 genes in the gene-set that are ranked above the leading edge).")
5332 (license license:gpl3)))
5334 (define-public r-cicero
5341 (uri (bioconductor-uri "cicero" version))
5344 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5345 (build-system r-build-system)
5347 `(("r-assertthat" ,r-assertthat)
5348 ("r-biobase" ,r-biobase)
5349 ("r-biocgenerics" ,r-biocgenerics)
5350 ("r-data-table" ,r-data-table)
5351 ("r-dplyr" ,r-dplyr)
5353 ("r-genomicranges" ,r-genomicranges)
5354 ("r-ggplot2" ,r-ggplot2)
5355 ("r-glasso" ,r-glasso)
5357 ("r-igraph" ,r-igraph)
5358 ("r-iranges" ,r-iranges)
5359 ("r-matrix" ,r-matrix)
5360 ("r-monocle" ,r-monocle)
5362 ("r-reshape2" ,r-reshape2)
5363 ("r-s4vectors" ,r-s4vectors)
5364 ("r-stringr" ,r-stringr)
5365 ("r-tibble" ,r-tibble)
5366 ("r-vgam" ,r-vgam)))
5367 (home-page "https://bioconductor.org/packages/cicero/")
5368 (synopsis "Predict cis-co-accessibility from single-cell data")
5370 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5371 accessibility data. It also extends the monocle package for use in chromatin
5372 accessibility data.")
5373 (license license:expat)))
5375 ;; This is the latest commit on the "monocle3" branch.
5376 (define-public r-cicero-monocle3
5377 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5379 (package (inherit r-cicero)
5380 (name "r-cicero-monocle3")
5381 (version (git-version "1.3.2" revision commit))
5386 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5388 (file-name (git-file-name name version))
5391 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5393 `(("r-monocle3" ,r-monocle3)
5394 ,@(alist-delete "r-monocle"
5395 (package-propagated-inputs r-cicero)))))))
5397 (define-public r-cistopic
5398 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5402 (version (git-version "0.2.1" revision commit))
5407 (url "https://github.com/aertslab/cisTopic.git")
5409 (file-name (git-file-name name version))
5412 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5413 (build-system r-build-system)
5415 `(("r-aucell" ,r-aucell)
5416 ("r-data-table" ,r-data-table)
5417 ("r-dplyr" ,r-dplyr)
5418 ("r-dosnow" ,r-dosnow)
5420 ("r-feather" ,r-feather)
5421 ("r-fitdistrplus" ,r-fitdistrplus)
5422 ("r-genomicranges" ,r-genomicranges)
5423 ("r-ggplot2" ,r-ggplot2)
5425 ("r-matrix" ,r-matrix)
5427 ("r-rcistarget" ,r-rcistarget)
5428 ("r-rtracklayer" ,r-rtracklayer)
5429 ("r-s4vectors" ,r-s4vectors)))
5430 (home-page "https://github.com/aertslab/cisTopic")
5431 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5433 "The sparse nature of single cell epigenomics data can be overruled using
5434 probabilistic modelling methods such as @dfn{Latent Dirichlet
5435 Allocation} (LDA). This package allows the probabilistic modelling of
5436 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5437 includes functionalities to identify cell states based on the contribution of
5438 cisTopics and explore the nature and regulatory proteins driving them.")
5439 (license license:gpl3))))
5441 (define-public r-genie3
5448 (uri (bioconductor-uri "GENIE3" version))
5451 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5452 (properties `((upstream-name . "GENIE3")))
5453 (build-system r-build-system)
5454 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5455 (home-page "https://bioconductor.org/packages/GENIE3")
5456 (synopsis "Gene network inference with ensemble of trees")
5458 "This package implements the GENIE3 algorithm for inferring gene
5459 regulatory networks from expression data.")
5460 (license license:gpl2+)))
5462 (define-public r-roc
5469 (uri (bioconductor-uri "ROC" version))
5472 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5473 (properties `((upstream-name . "ROC")))
5474 (build-system r-build-system)
5475 (home-page "https://www.bioconductor.org/packages/ROC/")
5476 (synopsis "Utilities for ROC curves")
5478 "This package provides utilities for @dfn{Receiver Operating
5479 Characteristic} (ROC) curves, with a focus on micro arrays.")
5480 (license license:artistic2.0)))
5482 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5484 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5489 (uri (bioconductor-uri
5490 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5491 version 'annotation))
5494 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5497 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5498 (build-system r-build-system)
5499 (propagated-inputs `(("r-minfi" ,r-minfi)))
5501 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5502 (synopsis "Annotation for Illumina's 450k methylation arrays")
5504 "This package provides manifests and annotation for Illumina's 450k array
5506 (license license:artistic2.0)))
5508 (define-public r-watermelon
5510 (name "r-watermelon")
5515 (uri (bioconductor-uri "wateRmelon" version))
5518 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
5519 (properties `((upstream-name . "wateRmelon")))
5520 (build-system r-build-system)
5522 `(("r-biobase" ,r-biobase)
5523 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
5524 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
5525 ("r-illuminaio" ,r-illuminaio)
5526 ("r-limma" ,r-limma)
5528 ("r-matrixstats" ,r-matrixstats)
5529 ("r-methylumi" ,r-methylumi)
5531 (home-page "https://bioconductor.org/packages/wateRmelon/")
5532 (synopsis "Illumina 450 methylation array normalization and metrics")
5534 "The standard index of DNA methylation (beta) is computed from methylated
5535 and unmethylated signal intensities. Betas calculated from raw signal
5536 intensities perform well, but using 11 methylomic datasets we demonstrate that
5537 quantile normalization methods produce marked improvement. The commonly used
5538 procedure of normalizing betas is inferior to the separate normalization of M
5539 and U, and it is also advantageous to normalize Type I and Type II assays
5540 separately. This package provides 15 flavours of betas and three performance
5541 metrics, with methods for objects produced by the @code{methylumi} and
5542 @code{minfi} packages.")
5543 (license license:gpl3)))
5545 (define-public r-gdsfmt
5552 (uri (bioconductor-uri "gdsfmt" version))
5555 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
5556 (modules '((guix build utils)))
5557 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
5558 ;; them and link with system libraries instead.
5561 (for-each delete-file-recursively
5565 (substitute* "src/Makevars"
5566 (("all: \\$\\(SHLIB\\)") "all:")
5567 (("\\$\\(SHLIB\\): liblzma.a") "")
5568 (("(ZLIB|LZ4)/.*") "")
5569 (("CoreArray/dVLIntGDS.cpp.*")
5570 "CoreArray/dVLIntGDS.cpp")
5571 (("CoreArray/dVLIntGDS.o.*")
5572 "CoreArray/dVLIntGDS.o")
5573 (("PKG_LIBS = ./liblzma.a")
5574 "PKG_LIBS = -llz4"))
5575 (substitute* "src/CoreArray/dStream.h"
5576 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
5577 (string-append "include <" header ">")))
5579 (properties `((upstream-name . "gdsfmt")))
5580 (build-system r-build-system)
5585 (home-page "http://corearray.sourceforge.net/")
5587 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
5589 "This package provides a high-level R interface to CoreArray @dfn{Genomic
5590 Data Structure} (GDS) data files, which are portable across platforms with
5591 hierarchical structure to store multiple scalable array-oriented data sets
5592 with metadata information. It is suited for large-scale datasets, especially
5593 for data which are much larger than the available random-access memory. The
5594 @code{gdsfmt} package offers efficient operations specifically designed for
5595 integers of less than 8 bits, since a diploid genotype, like
5596 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
5597 byte. Data compression and decompression are available with relatively
5598 efficient random access. It is also allowed to read a GDS file in parallel
5599 with multiple R processes supported by the package @code{parallel}.")
5600 (license license:lgpl3)))
5602 (define-public r-bigmelon
5609 (uri (bioconductor-uri "bigmelon" version))
5612 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
5613 (properties `((upstream-name . "bigmelon")))
5614 (build-system r-build-system)
5616 `(("r-biobase" ,r-biobase)
5617 ("r-biocgenerics" ,r-biocgenerics)
5618 ("r-gdsfmt" ,r-gdsfmt)
5619 ("r-geoquery" ,r-geoquery)
5620 ("r-methylumi" ,r-methylumi)
5621 ("r-minfi" ,r-minfi)
5622 ("r-watermelon" ,r-watermelon)))
5623 (home-page "https://bioconductor.org/packages/bigmelon/")
5624 (synopsis "Illumina methylation array analysis for large experiments")
5626 "This package provides methods for working with Illumina arrays using the
5627 @code{gdsfmt} package.")
5628 (license license:gpl3)))
5630 (define-public r-wavcluster
5632 (name "r-wavcluster")
5637 (uri (bioconductor-uri "wavClusteR" version))
5640 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
5641 (properties `((upstream-name . "wavClusteR")))
5642 (build-system r-build-system)
5644 `(("r-biocgenerics" ,r-biocgenerics)
5645 ("r-biostrings" ,r-biostrings)
5646 ("r-foreach" ,r-foreach)
5647 ("r-genomicfeatures" ,r-genomicfeatures)
5648 ("r-genomicranges" ,r-genomicranges)
5649 ("r-ggplot2" ,r-ggplot2)
5650 ("r-hmisc" ,r-hmisc)
5651 ("r-iranges" ,r-iranges)
5652 ("r-mclust" ,r-mclust)
5653 ("r-rsamtools" ,r-rsamtools)
5654 ("r-rtracklayer" ,r-rtracklayer)
5655 ("r-s4vectors" ,r-s4vectors)
5656 ("r-seqinr" ,r-seqinr)
5657 ("r-stringr" ,r-stringr)
5658 ("r-wmtsa" ,r-wmtsa)))
5659 (home-page "https://bioconductor.org/packages/wavClusteR/")
5660 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
5662 "This package provides an integrated pipeline for the analysis of
5663 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
5664 sequencing errors, SNPs and additional non-experimental sources by a non-
5665 parametric mixture model. The protein binding sites (clusters) are then
5666 resolved at high resolution and cluster statistics are estimated using a
5667 rigorous Bayesian framework. Post-processing of the results, data export for
5668 UCSC genome browser visualization and motif search analysis are provided. In
5669 addition, the package allows to integrate RNA-Seq data to estimate the False
5670 Discovery Rate of cluster detection. Key functions support parallel multicore
5671 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
5672 be applied to the analysis of other NGS data obtained from experimental
5673 procedures that induce nucleotide substitutions (e.g. BisSeq).")
5674 (license license:gpl2)))
5676 (define-public r-timeseriesexperiment
5678 (name "r-timeseriesexperiment")
5683 (uri (bioconductor-uri "TimeSeriesExperiment" version))
5686 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
5688 `((upstream-name . "TimeSeriesExperiment")))
5689 (build-system r-build-system)
5691 `(("r-deseq2" ,r-deseq2)
5692 ("r-dplyr" ,r-dplyr)
5693 ("r-dynamictreecut" ,r-dynamictreecut)
5694 ("r-edger" ,r-edger)
5695 ("r-ggplot2" ,r-ggplot2)
5696 ("r-hmisc" ,r-hmisc)
5697 ("r-limma" ,r-limma)
5698 ("r-magrittr" ,r-magrittr)
5699 ("r-proxy" ,r-proxy)
5700 ("r-s4vectors" ,r-s4vectors)
5701 ("r-summarizedexperiment" ,r-summarizedexperiment)
5702 ("r-tibble" ,r-tibble)
5703 ("r-tidyr" ,r-tidyr)
5704 ("r-vegan" ,r-vegan)
5705 ("r-viridis" ,r-viridis)))
5706 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
5707 (synopsis "Analysis for short time-series data")
5709 "This package is a visualization and analysis toolbox for short time
5710 course data which includes dimensionality reduction, clustering, two-sample
5711 differential expression testing and gene ranking techniques. The package also
5712 provides methods for retrieving enriched pathways.")
5713 (license license:lgpl3+)))