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)))
816 (define-public r-abadata
822 ;; We cannot use bioconductor-uri here because this tarball is
823 ;; located under "data/experiment/" instead of "bioc/".
824 (uri (string-append "https://www.bioconductor.org/packages/"
825 "release/data/experiment/src/contrib/"
826 "ABAData_" version ".tar.gz"))
829 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
831 `((upstream-name . "ABAData")))
832 (build-system r-build-system)
834 `(("r-annotationdbi" ,r-annotationdbi)))
835 (home-page "https://www.bioconductor.org/packages/ABAData/")
836 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
838 "This package provides the data for the gene expression enrichment
839 analysis conducted in the package ABAEnrichment. The package includes three
840 datasets which are derived from the Allen Brain Atlas:
843 @item Gene expression data from Human Brain (adults) averaged across donors,
844 @item Gene expression data from the Developing Human Brain pooled into five
845 age categories and averaged across donors, and
846 @item a developmental effect score based on the Developing Human Brain
850 All datasets are restricted to protein coding genes.")
851 (license license:gpl2+)))
853 (define-public r-arrmdata
859 ;; We cannot use bioconductor-uri here because this tarball is
860 ;; located under "data/experiment/" instead of "bioc/".
861 (uri (string-append "https://www.bioconductor.org/packages/"
862 "release/data/experiment/src/contrib/"
863 "ARRmData_" version ".tar.gz"))
866 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
868 `((upstream-name . "ARRmData")))
869 (build-system r-build-system)
870 (home-page "https://www.bioconductor.org/packages/ARRmData/")
871 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
873 "This package provides raw beta values from 36 samples across 3 groups
874 from Illumina 450k methylation arrays.")
875 (license license:artistic2.0)))
877 (define-public r-hsmmsinglecell
879 (name "r-hsmmsinglecell")
883 ;; We cannot use bioconductor-uri here because this tarball is
884 ;; located under "data/experiment/" instead of "bioc/".
885 (uri (string-append "https://www.bioconductor.org/packages/"
886 "release/data/experiment/src/contrib/"
887 "HSMMSingleCell_" version ".tar.gz"))
890 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
892 `((upstream-name . "HSMMSingleCell")))
893 (build-system r-build-system)
894 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
895 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
897 "Skeletal myoblasts undergo a well-characterized sequence of
898 morphological and transcriptional changes during differentiation. In this
899 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
900 under high mitogen conditions (GM) and then differentiated by switching to
901 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
902 hundred cells taken over a time-course of serum-induced differentiation.
903 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
904 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
905 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
906 which were then sequenced to a depth of ~4 million reads per library,
907 resulting in a complete gene expression profile for each cell.")
908 (license license:artistic2.0)))
916 ;; We cannot use bioconductor-uri here because this tarball is
917 ;; located under "data/experiment/" instead of "bioc/".
918 (uri (string-append "https://www.bioconductor.org/packages/"
919 "release/data/experiment/src/contrib/"
920 "ALL_" version ".tar.gz"))
923 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
924 (properties `((upstream-name . "ALL")))
925 (build-system r-build-system)
927 `(("r-biobase" ,r-biobase)))
928 (home-page "https://bioconductor.org/packages/ALL")
929 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
931 "The data consist of microarrays from 128 different individuals with
932 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
933 are available. The data have been normalized (using rma) and it is the
934 jointly normalized data that are available here. The data are presented in
935 the form of an @code{exprSet} object.")
936 (license license:artistic2.0)))
941 (define-public r-biocgenerics
943 (name "r-biocgenerics")
947 (uri (bioconductor-uri "BiocGenerics" version))
950 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
952 `((upstream-name . "BiocGenerics")))
953 (build-system r-build-system)
954 (home-page "https://bioconductor.org/packages/BiocGenerics")
955 (synopsis "S4 generic functions for Bioconductor")
957 "This package provides S4 generic functions needed by many Bioconductor
959 (license license:artistic2.0)))
961 (define-public r-annotate
968 (uri (bioconductor-uri "annotate" version))
971 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
972 (build-system r-build-system)
974 `(("r-annotationdbi" ,r-annotationdbi)
975 ("r-biobase" ,r-biobase)
976 ("r-biocgenerics" ,r-biocgenerics)
980 ("r-xtable" ,r-xtable)))
982 "https://bioconductor.org/packages/annotate")
983 (synopsis "Annotation for microarrays")
984 (description "This package provides R environments for the annotation of
986 (license license:artistic2.0)))
988 (define-public r-hpar
995 (uri (bioconductor-uri "hpar" version))
998 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
999 (build-system r-build-system)
1000 (home-page "https://bioconductor.org/packages/hpar/")
1001 (synopsis "Human Protein Atlas in R")
1002 (description "This package provides a simple interface to and data from
1003 the Human Protein Atlas project.")
1004 (license license:artistic2.0)))
1006 (define-public r-regioner
1013 (uri (bioconductor-uri "regioneR" version))
1016 "0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760"))))
1017 (properties `((upstream-name . "regioneR")))
1018 (build-system r-build-system)
1020 `(("r-biostrings" ,r-biostrings)
1021 ("r-bsgenome" ,r-bsgenome)
1022 ("r-genomeinfodb" ,r-genomeinfodb)
1023 ("r-genomicranges" ,r-genomicranges)
1024 ("r-iranges" ,r-iranges)
1025 ("r-memoise" ,r-memoise)
1026 ("r-rtracklayer" ,r-rtracklayer)
1027 ("r-s4vectors" ,r-s4vectors)))
1028 (home-page "https://bioconductor.org/packages/regioneR/")
1029 (synopsis "Association analysis of genomic regions")
1030 (description "This package offers a statistical framework based on
1031 customizable permutation tests to assess the association between genomic
1032 region sets and other genomic features.")
1033 (license license:artistic2.0)))
1035 (define-public r-geneplotter
1037 (name "r-geneplotter")
1042 (uri (bioconductor-uri "geneplotter" version))
1045 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1046 (build-system r-build-system)
1048 `(("r-annotate" ,r-annotate)
1049 ("r-annotationdbi" ,r-annotationdbi)
1050 ("r-biobase" ,r-biobase)
1051 ("r-biocgenerics" ,r-biocgenerics)
1052 ("r-lattice" ,r-lattice)
1053 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1054 (home-page "https://bioconductor.org/packages/geneplotter")
1055 (synopsis "Graphics functions for genomic data")
1057 "This package provides functions for plotting genomic data.")
1058 (license license:artistic2.0)))
1060 (define-public r-qvalue
1067 (uri (bioconductor-uri "qvalue" version))
1070 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1071 (build-system r-build-system)
1073 `(("r-ggplot2" ,r-ggplot2)
1074 ("r-reshape2" ,r-reshape2)))
1075 (home-page "http://github.com/jdstorey/qvalue")
1076 (synopsis "Q-value estimation for false discovery rate control")
1078 "This package takes a list of p-values resulting from the simultaneous
1079 testing of many hypotheses and estimates their q-values and local @dfn{false
1080 discovery rate} (FDR) values. The q-value of a test measures the proportion
1081 of false positives incurred when that particular test is called significant.
1082 The local FDR measures the posterior probability the null hypothesis is true
1083 given the test's p-value. Various plots are automatically generated, allowing
1084 one to make sensible significance cut-offs. The software can be applied to
1085 problems in genomics, brain imaging, astrophysics, and data mining.")
1086 ;; Any version of the LGPL.
1087 (license license:lgpl3+)))
1089 (define-public r-diffbind
1096 (uri (bioconductor-uri "DiffBind" version))
1099 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1100 (properties `((upstream-name . "DiffBind")))
1101 (build-system r-build-system)
1105 `(("r-amap" ,r-amap)
1106 ("r-biocparallel" ,r-biocparallel)
1107 ("r-deseq2" ,r-deseq2)
1108 ("r-dplyr" ,r-dplyr)
1109 ("r-edger" ,r-edger)
1110 ("r-genomicalignments" ,r-genomicalignments)
1111 ("r-genomicranges" ,r-genomicranges)
1112 ("r-ggplot2" ,r-ggplot2)
1113 ("r-ggrepel" ,r-ggrepel)
1114 ("r-gplots" ,r-gplots)
1115 ("r-iranges" ,r-iranges)
1116 ("r-lattice" ,r-lattice)
1117 ("r-limma" ,r-limma)
1118 ("r-locfit" ,r-locfit)
1119 ("r-rcolorbrewer" , r-rcolorbrewer)
1121 ("r-rhtslib" ,r-rhtslib)
1122 ("r-rsamtools" ,r-rsamtools)
1123 ("r-s4vectors" ,r-s4vectors)
1124 ("r-summarizedexperiment" ,r-summarizedexperiment)
1125 ("r-systempiper" ,r-systempiper)))
1126 (home-page "http://bioconductor.org/packages/DiffBind")
1127 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1129 "This package computes differentially bound sites from multiple
1130 ChIP-seq experiments using affinity (quantitative) data. Also enables
1131 occupancy (overlap) analysis and plotting functions.")
1132 (license license:artistic2.0)))
1134 (define-public r-ripseeker
1136 (name "r-ripseeker")
1141 (uri (bioconductor-uri "RIPSeeker" version))
1144 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1145 (properties `((upstream-name . "RIPSeeker")))
1146 (build-system r-build-system)
1148 `(("r-s4vectors" ,r-s4vectors)
1149 ("r-iranges" ,r-iranges)
1150 ("r-genomicranges" ,r-genomicranges)
1151 ("r-summarizedexperiment" ,r-summarizedexperiment)
1152 ("r-rsamtools" ,r-rsamtools)
1153 ("r-genomicalignments" ,r-genomicalignments)
1154 ("r-rtracklayer" ,r-rtracklayer)))
1155 (home-page "http://bioconductor.org/packages/RIPSeeker")
1157 "Identifying protein-associated transcripts from RIP-seq experiments")
1159 "This package infers and discriminates RIP peaks from RIP-seq alignments
1160 using two-state HMM with negative binomial emission probability. While
1161 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1162 a suite of bioinformatics tools integrated within this self-contained software
1163 package comprehensively addressing issues ranging from post-alignments
1164 processing to visualization and annotation.")
1165 (license license:gpl2)))
1167 (define-public r-multtest
1174 (uri (bioconductor-uri "multtest" version))
1177 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1178 (build-system r-build-system)
1180 `(("r-survival" ,r-survival)
1181 ("r-biocgenerics" ,r-biocgenerics)
1182 ("r-biobase" ,r-biobase)
1183 ("r-mass" ,r-mass)))
1184 (home-page "http://bioconductor.org/packages/multtest")
1185 (synopsis "Resampling-based multiple hypothesis testing")
1187 "This package can do non-parametric bootstrap and permutation
1188 resampling-based multiple testing procedures (including empirical Bayes
1189 methods) for controlling the family-wise error rate (FWER), generalized
1190 family-wise error rate (gFWER), tail probability of the proportion of
1191 false positives (TPPFP), and false discovery rate (FDR). Several choices
1192 of bootstrap-based null distribution are implemented (centered, centered
1193 and scaled, quantile-transformed). Single-step and step-wise methods are
1194 available. Tests based on a variety of T- and F-statistics (including
1195 T-statistics based on regression parameters from linear and survival models
1196 as well as those based on correlation parameters) are included. When probing
1197 hypotheses with T-statistics, users may also select a potentially faster null
1198 distribution which is multivariate normal with mean zero and variance
1199 covariance matrix derived from the vector influence function. Results are
1200 reported in terms of adjusted P-values, confidence regions and test statistic
1201 cutoffs. The procedures are directly applicable to identifying differentially
1202 expressed genes in DNA microarray experiments.")
1203 (license license:lgpl3)))
1205 (define-public r-graph
1211 (uri (bioconductor-uri "graph" version))
1214 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1215 (build-system r-build-system)
1217 `(("r-biocgenerics" ,r-biocgenerics)))
1218 (home-page "https://bioconductor.org/packages/graph")
1219 (synopsis "Handle graph data structures in R")
1221 "This package implements some simple graph handling capabilities for R.")
1222 (license license:artistic2.0)))
1224 (define-public r-codedepends
1226 (name "r-codedepends")
1231 (uri (cran-uri "CodeDepends" version))
1234 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1235 (properties `((upstream-name . "CodeDepends")))
1236 (build-system r-build-system)
1238 `(("r-codetools" ,r-codetools)
1239 ("r-graph" ,r-graph)
1241 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1242 (synopsis "Analysis of R code for reproducible research and code comprehension")
1244 "This package provides tools for analyzing R expressions or blocks of
1245 code and determining the dependencies between them. It focuses on R scripts,
1246 but can be used on the bodies of functions. There are many facilities
1247 including the ability to summarize or get a high-level view of code,
1248 determining dependencies between variables, code improvement suggestions.")
1249 ;; Any version of the GPL
1250 (license (list license:gpl2+ license:gpl3+))))
1252 (define-public r-chippeakanno
1254 (name "r-chippeakanno")
1259 (uri (bioconductor-uri "ChIPpeakAnno" version))
1262 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1263 (properties `((upstream-name . "ChIPpeakAnno")))
1264 (build-system r-build-system)
1266 `(("r-annotationdbi" ,r-annotationdbi)
1267 ("r-biobase" ,r-biobase)
1268 ("r-biocgenerics" ,r-biocgenerics)
1269 ("r-biocmanager" ,r-biocmanager)
1270 ("r-biomart" ,r-biomart)
1271 ("r-biostrings" ,r-biostrings)
1272 ("r-bsgenome" ,r-bsgenome)
1274 ("r-delayedarray" ,r-delayedarray)
1275 ("r-ensembldb" ,r-ensembldb)
1276 ("r-genomeinfodb" ,r-genomeinfodb)
1277 ("r-genomicalignments" ,r-genomicalignments)
1278 ("r-genomicfeatures" ,r-genomicfeatures)
1279 ("r-genomicranges" ,r-genomicranges)
1280 ("r-go-db" ,r-go-db)
1281 ("r-graph" ,r-graph)
1283 ("r-iranges" ,r-iranges)
1284 ("r-limma" ,r-limma)
1285 ("r-matrixstats" ,r-matrixstats)
1286 ("r-multtest" ,r-multtest)
1288 ("r-regioner" ,r-regioner)
1289 ("r-rsamtools" ,r-rsamtools)
1290 ("r-rtracklayer" ,r-rtracklayer)
1291 ("r-s4vectors" ,r-s4vectors)
1292 ("r-seqinr" ,r-seqinr)
1293 ("r-summarizedexperiment" ,r-summarizedexperiment)
1294 ("r-venndiagram" ,r-venndiagram)))
1295 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1296 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1298 "The package includes functions to retrieve the sequences around the peak,
1299 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1300 custom features such as most conserved elements and other transcription factor
1301 binding sites supplied by users. Starting 2.0.5, new functions have been added
1302 for finding the peaks with bi-directional promoters with summary statistics
1303 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1304 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1305 enrichedGO (addGeneIDs).")
1306 (license license:gpl2+)))
1308 (define-public r-marray
1314 (uri (bioconductor-uri "marray" version))
1316 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1317 (build-system r-build-system)
1319 `(("r-limma" ,r-limma)))
1320 (home-page "http://bioconductor.org/packages/marray")
1321 (synopsis "Exploratory analysis for two-color spotted microarray data")
1322 (description "This package contains class definitions for two-color spotted
1323 microarray data. It also includes functions for data input, diagnostic plots,
1324 normalization and quality checking.")
1325 (license license:lgpl2.0+)))
1327 (define-public r-cghbase
1333 (uri (bioconductor-uri "CGHbase" version))
1335 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1336 (properties `((upstream-name . "CGHbase")))
1337 (build-system r-build-system)
1339 `(("r-biobase" ,r-biobase)
1340 ("r-marray" ,r-marray)))
1341 (home-page "http://bioconductor.org/packages/CGHbase")
1342 (synopsis "Base functions and classes for arrayCGH data analysis")
1343 (description "This package contains functions and classes that are needed by
1344 the @code{arrayCGH} packages.")
1345 (license license:gpl2+)))
1347 (define-public r-cghcall
1353 (uri (bioconductor-uri "CGHcall" version))
1355 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1356 (properties `((upstream-name . "CGHcall")))
1357 (build-system r-build-system)
1359 `(("r-biobase" ,r-biobase)
1360 ("r-cghbase" ,r-cghbase)
1361 ("r-impute" ,r-impute)
1362 ("r-dnacopy" ,r-dnacopy)
1363 ("r-snowfall" ,r-snowfall)))
1364 (home-page "http://bioconductor.org/packages/CGHcall")
1365 (synopsis "Base functions and classes for arrayCGH data analysis")
1366 (description "This package contains functions and classes that are needed by
1367 @code{arrayCGH} packages.")
1368 (license license:gpl2+)))
1370 (define-public r-qdnaseq
1376 (uri (bioconductor-uri "QDNAseq" version))
1378 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1379 (properties `((upstream-name . "QDNAseq")))
1380 (build-system r-build-system)
1382 `(("r-biobase" ,r-biobase)
1383 ("r-biocparallel" ,r-biocparallel)
1384 ("r-cghbase" ,r-cghbase)
1385 ("r-cghcall" ,r-cghcall)
1386 ("r-dnacopy" ,r-dnacopy)
1387 ("r-genomicranges" ,r-genomicranges)
1388 ("r-iranges" ,r-iranges)
1389 ("r-matrixstats" ,r-matrixstats)
1390 ("r-r-utils" ,r-r-utils)
1391 ("r-rsamtools" ,r-rsamtools)))
1392 (home-page "http://bioconductor.org/packages/QDNAseq")
1393 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1394 (description "The genome is divided into non-overlapping fixed-sized bins,
1395 number of sequence reads in each counted, adjusted with a simultaneous
1396 two-dimensional loess correction for sequence mappability and GC content, and
1397 filtered to remove spurious regions in the genome. Downstream steps of
1398 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1400 (license license:gpl2+)))
1402 (define-public r-bayseq
1409 (uri (bioconductor-uri "baySeq" version))
1412 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1413 (properties `((upstream-name . "baySeq")))
1414 (build-system r-build-system)
1416 `(("r-abind" ,r-abind)
1417 ("r-edger" ,r-edger)
1418 ("r-genomicranges" ,r-genomicranges)))
1419 (home-page "https://bioconductor.org/packages/baySeq/")
1420 (synopsis "Bayesian analysis of differential expression patterns in count data")
1422 "This package identifies differential expression in high-throughput count
1423 data, such as that derived from next-generation sequencing machines,
1424 calculating estimated posterior likelihoods of differential expression (or
1425 more complex hypotheses) via empirical Bayesian methods.")
1426 (license license:gpl3)))
1428 (define-public r-chipcomp
1435 (uri (bioconductor-uri "ChIPComp" version))
1438 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1439 (properties `((upstream-name . "ChIPComp")))
1440 (build-system r-build-system)
1442 `(("r-biocgenerics" ,r-biocgenerics)
1443 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1444 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1445 ("r-genomeinfodb" ,r-genomeinfodb)
1446 ("r-genomicranges" ,r-genomicranges)
1447 ("r-iranges" ,r-iranges)
1448 ("r-limma" ,r-limma)
1449 ("r-rsamtools" ,r-rsamtools)
1450 ("r-rtracklayer" ,r-rtracklayer)
1451 ("r-s4vectors" ,r-s4vectors)))
1452 (home-page "https://bioconductor.org/packages/ChIPComp")
1453 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1455 "ChIPComp implements a statistical method for quantitative comparison of
1456 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1457 sites across multiple conditions considering matching control in ChIP-seq
1459 ;; Any version of the GPL.
1460 (license license:gpl3+)))
1462 (define-public r-riboprofiling
1464 (name "r-riboprofiling")
1469 (uri (bioconductor-uri "RiboProfiling" version))
1472 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1473 (properties `((upstream-name . "RiboProfiling")))
1474 (build-system r-build-system)
1476 `(("r-biocgenerics" ,r-biocgenerics)
1477 ("r-biostrings" ,r-biostrings)
1478 ("r-data-table" ,r-data-table)
1479 ("r-genomeinfodb" ,r-genomeinfodb)
1480 ("r-genomicalignments" ,r-genomicalignments)
1481 ("r-genomicfeatures" ,r-genomicfeatures)
1482 ("r-genomicranges" ,r-genomicranges)
1483 ("r-ggbio" ,r-ggbio)
1484 ("r-ggplot2" ,r-ggplot2)
1485 ("r-iranges" ,r-iranges)
1487 ("r-reshape2" ,r-reshape2)
1488 ("r-rsamtools" ,r-rsamtools)
1489 ("r-rtracklayer" ,r-rtracklayer)
1490 ("r-s4vectors" ,r-s4vectors)
1491 ("r-sqldf" ,r-sqldf)))
1492 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1493 (synopsis "Ribosome profiling data analysis")
1494 (description "Starting with a BAM file, this package provides the
1495 necessary functions for quality assessment, read start position recalibration,
1496 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1497 of count data: pairs, log fold-change, codon frequency and coverage
1498 assessment, principal component analysis on codon coverage.")
1499 (license license:gpl3)))
1501 (define-public r-riboseqr
1508 (uri (bioconductor-uri "riboSeqR" version))
1511 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1512 (properties `((upstream-name . "riboSeqR")))
1513 (build-system r-build-system)
1515 `(("r-abind" ,r-abind)
1516 ("r-bayseq" ,r-bayseq)
1517 ("r-genomeinfodb" ,r-genomeinfodb)
1518 ("r-genomicranges" ,r-genomicranges)
1519 ("r-iranges" ,r-iranges)
1520 ("r-rsamtools" ,r-rsamtools)
1521 ("r-seqlogo" ,r-seqlogo)))
1522 (home-page "https://bioconductor.org/packages/riboSeqR/")
1523 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1525 "This package provides plotting functions, frameshift detection and
1526 parsing of genetic sequencing data from ribosome profiling experiments.")
1527 (license license:gpl3)))
1529 (define-public r-interactionset
1531 (name "r-interactionset")
1536 (uri (bioconductor-uri "InteractionSet" version))
1539 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1541 `((upstream-name . "InteractionSet")))
1542 (build-system r-build-system)
1544 `(("r-biocgenerics" ,r-biocgenerics)
1545 ("r-genomeinfodb" ,r-genomeinfodb)
1546 ("r-genomicranges" ,r-genomicranges)
1547 ("r-iranges" ,r-iranges)
1548 ("r-matrix" ,r-matrix)
1550 ("r-s4vectors" ,r-s4vectors)
1551 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1552 (home-page "https://bioconductor.org/packages/InteractionSet")
1553 (synopsis "Base classes for storing genomic interaction data")
1555 "This package provides the @code{GInteractions},
1556 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1557 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1559 (license license:gpl3)))
1561 (define-public r-genomicinteractions
1563 (name "r-genomicinteractions")
1568 (uri (bioconductor-uri "GenomicInteractions" version))
1571 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1573 `((upstream-name . "GenomicInteractions")))
1574 (build-system r-build-system)
1576 `(("r-biobase" ,r-biobase)
1577 ("r-biocgenerics" ,r-biocgenerics)
1578 ("r-data-table" ,r-data-table)
1579 ("r-dplyr" ,r-dplyr)
1580 ("r-genomeinfodb" ,r-genomeinfodb)
1581 ("r-genomicranges" ,r-genomicranges)
1582 ("r-ggplot2" ,r-ggplot2)
1583 ("r-gridextra" ,r-gridextra)
1585 ("r-igraph" ,r-igraph)
1586 ("r-interactionset" ,r-interactionset)
1587 ("r-iranges" ,r-iranges)
1588 ("r-rsamtools" ,r-rsamtools)
1589 ("r-rtracklayer" ,r-rtracklayer)
1590 ("r-s4vectors" ,r-s4vectors)
1591 ("r-stringr" ,r-stringr)))
1592 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1593 (synopsis "R package for handling genomic interaction data")
1595 "This R package provides tools for handling genomic interaction data,
1596 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1597 information and producing various plots and statistics.")
1598 (license license:gpl3)))
1600 (define-public r-ctc
1607 (uri (bioconductor-uri "ctc" version))
1610 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1611 (build-system r-build-system)
1612 (propagated-inputs `(("r-amap" ,r-amap)))
1613 (home-page "https://bioconductor.org/packages/ctc/")
1614 (synopsis "Cluster and tree conversion")
1616 "This package provides tools for exporting and importing classification
1617 trees and clusters to other programs.")
1618 (license license:gpl2)))
1620 (define-public r-goseq
1627 (uri (bioconductor-uri "goseq" version))
1630 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1631 (build-system r-build-system)
1633 `(("r-annotationdbi" ,r-annotationdbi)
1634 ("r-biasedurn" ,r-biasedurn)
1635 ("r-biocgenerics" ,r-biocgenerics)
1636 ("r-genelendatabase" ,r-genelendatabase)
1637 ("r-go-db" ,r-go-db)
1638 ("r-mgcv" ,r-mgcv)))
1639 (home-page "https://bioconductor.org/packages/goseq/")
1640 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1642 "This package provides tools to detect Gene Ontology and/or other user
1643 defined categories which are over/under represented in RNA-seq data.")
1644 (license license:lgpl2.0+)))
1646 (define-public r-glimma
1653 (uri (bioconductor-uri "Glimma" version))
1656 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1657 (properties `((upstream-name . "Glimma")))
1658 (build-system r-build-system)
1660 `(("r-edger" ,r-edger)
1661 ("r-jsonlite" ,r-jsonlite)
1662 ("r-s4vectors" ,r-s4vectors)))
1663 (home-page "https://github.com/Shians/Glimma")
1664 (synopsis "Interactive HTML graphics")
1666 "This package generates interactive visualisations for analysis of
1667 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1668 HTML page. The interactions are built on top of the popular static
1669 representations of analysis results in order to provide additional
1671 (license license:lgpl3)))
1673 (define-public r-rots
1680 (uri (bioconductor-uri "ROTS" version))
1683 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1684 (properties `((upstream-name . "ROTS")))
1685 (build-system r-build-system)
1687 `(("r-biobase" ,r-biobase)
1688 ("r-rcpp" ,r-rcpp)))
1689 (home-page "https://bioconductor.org/packages/ROTS/")
1690 (synopsis "Reproducibility-Optimized Test Statistic")
1692 "This package provides tools for calculating the
1693 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1695 (license license:gpl2+)))
1697 (define-public r-plgem
1704 (uri (bioconductor-uri "plgem" version))
1707 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1708 (build-system r-build-system)
1710 `(("r-biobase" ,r-biobase)
1711 ("r-mass" ,r-mass)))
1712 (home-page "http://www.genopolis.it")
1713 (synopsis "Detect differential expression in microarray and proteomics datasets")
1715 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1716 model the variance-versus-mean dependence that exists in a variety of
1717 genome-wide datasets, including microarray and proteomics data. The use of
1718 PLGEM has been shown to improve the detection of differentially expressed
1719 genes or proteins in these datasets.")
1720 (license license:gpl2)))
1722 (define-public r-inspect
1729 (uri (bioconductor-uri "INSPEcT" version))
1732 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1733 (properties `((upstream-name . "INSPEcT")))
1734 (build-system r-build-system)
1736 `(("r-biobase" ,r-biobase)
1737 ("r-biocgenerics" ,r-biocgenerics)
1738 ("r-biocparallel" ,r-biocparallel)
1739 ("r-deseq2" ,r-deseq2)
1740 ("r-desolve" ,r-desolve)
1741 ("r-genomicalignments" ,r-genomicalignments)
1742 ("r-genomicfeatures" ,r-genomicfeatures)
1743 ("r-genomicranges" ,r-genomicranges)
1744 ("r-iranges" ,r-iranges)
1745 ("r-plgem" ,r-plgem)
1746 ("r-preprocesscore" ,r-preprocesscore)
1748 ("r-rootsolve" ,r-rootsolve)
1749 ("r-rsamtools" ,r-rsamtools)
1750 ("r-s4vectors" ,r-s4vectors)
1751 ("r-shiny" ,r-shiny)
1752 ("r-summarizedexperiment" ,r-summarizedexperiment)
1753 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1754 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1755 (home-page "https://bioconductor.org/packages/INSPEcT")
1756 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1758 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1759 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1760 order to evaluate synthesis, processing and degradation rates and assess via
1761 modeling the rates that determines changes in mature mRNA levels.")
1762 (license license:gpl2)))
1764 (define-public r-dnabarcodes
1766 (name "r-dnabarcodes")
1771 (uri (bioconductor-uri "DNABarcodes" version))
1774 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1775 (properties `((upstream-name . "DNABarcodes")))
1776 (build-system r-build-system)
1779 ("r-matrix" ,r-matrix)
1780 ("r-rcpp" ,r-rcpp)))
1781 (home-page "https://bioconductor.org/packages/DNABarcodes")
1782 (synopsis "Create and analyze DNA barcodes")
1784 "This package offers tools to create DNA barcode sets capable of
1785 correcting insertion, deletion, and substitution errors. Existing barcodes
1786 can be analyzed regarding their minimal, maximal and average distances between
1787 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1788 demultiplexed, i.e. assigned to their original reference barcode.")
1789 (license license:gpl2)))
1791 (define-public r-ruvseq
1798 (uri (bioconductor-uri "RUVSeq" version))
1801 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
1802 (properties `((upstream-name . "RUVSeq")))
1803 (build-system r-build-system)
1805 `(("r-biobase" ,r-biobase)
1806 ("r-edaseq" ,r-edaseq)
1807 ("r-edger" ,r-edger)
1808 ("r-mass" ,r-mass)))
1809 (home-page "https://github.com/drisso/RUVSeq")
1810 (synopsis "Remove unwanted variation from RNA-Seq data")
1812 "This package implements methods to @dfn{remove unwanted variation} (RUV)
1813 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1815 (license license:artistic2.0)))
1817 (define-public r-biocneighbors
1819 (name "r-biocneighbors")
1824 (uri (bioconductor-uri "BiocNeighbors" version))
1827 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
1828 (properties `((upstream-name . "BiocNeighbors")))
1829 (build-system r-build-system)
1831 `(("r-biocgenerics" ,r-biocgenerics)
1832 ("r-biocparallel" ,r-biocparallel)
1834 ("r-rcppannoy" ,r-rcppannoy)
1835 ("r-rcpphnsw" ,r-rcpphnsw)
1836 ("r-s4vectors" ,r-s4vectors)))
1837 (home-page "https://bioconductor.org/packages/BiocNeighbors")
1838 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1840 "This package implements exact and approximate methods for nearest
1841 neighbor detection, in a framework that allows them to be easily switched
1842 within Bioconductor packages or workflows. The exact algorithm is implemented
1843 using pre-clustering with the k-means algorithm. Functions are also provided
1844 to search for all neighbors within a given distance. Parallelization is
1845 achieved for all methods using the BiocParallel framework.")
1846 (license license:gpl3)))
1848 (define-public r-biocsingular
1850 (name "r-biocsingular")
1855 (uri (bioconductor-uri "BiocSingular" version))
1858 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
1859 (properties `((upstream-name . "BiocSingular")))
1860 (build-system r-build-system)
1862 `(("r-beachmat" ,r-beachmat)
1863 ("r-biocgenerics" ,r-biocgenerics)
1864 ("r-biocparallel" ,r-biocparallel)
1865 ("r-delayedarray" ,r-delayedarray)
1866 ("r-irlba" ,r-irlba)
1867 ("r-matrix" ,r-matrix)
1870 ("r-s4vectors" ,r-s4vectors)))
1871 (home-page "https://github.com/LTLA/BiocSingular")
1872 (synopsis "Singular value decomposition for Bioconductor packages")
1874 "This package implements exact and approximate methods for singular value
1875 decomposition and principal components analysis, in a framework that allows
1876 them to be easily switched within Bioconductor packages or workflows. Where
1877 possible, parallelization is achieved using the BiocParallel framework.")
1878 (license license:gpl3)))
1880 (define-public r-destiny
1887 (uri (bioconductor-uri "destiny" version))
1890 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
1891 (build-system r-build-system)
1893 `(("r-biobase" ,r-biobase)
1894 ("r-biocgenerics" ,r-biocgenerics)
1895 ("r-ggplot2" ,r-ggplot2)
1896 ("r-ggthemes" ,r-ggthemes)
1897 ("r-igraph" ,r-igraph)
1898 ("r-matrix" ,r-matrix)
1899 ("r-proxy" ,r-proxy)
1901 ("r-rcppeigen" ,r-rcppeigen)
1902 ("r-scales" ,r-scales)
1903 ("r-scatterplot3d" ,r-scatterplot3d)
1904 ("r-smoother" ,r-smoother)
1905 ("r-summarizedexperiment" ,r-summarizedexperiment)
1907 (home-page "https://bioconductor.org/packages/destiny/")
1908 (synopsis "Create and plot diffusion maps")
1909 (description "This package provides tools to create and plot diffusion
1911 ;; Any version of the GPL
1912 (license license:gpl3+)))
1914 (define-public r-savr
1921 (uri (bioconductor-uri "savR" version))
1924 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
1925 (properties `((upstream-name . "savR")))
1926 (build-system r-build-system)
1928 `(("r-ggplot2" ,r-ggplot2)
1929 ("r-gridextra" ,r-gridextra)
1930 ("r-reshape2" ,r-reshape2)
1931 ("r-scales" ,r-scales)
1933 (home-page "https://github.com/bcalder/savR")
1934 (synopsis "Parse and analyze Illumina SAV files")
1936 "This package provides tools to parse Illumina Sequence Analysis
1937 Viewer (SAV) files, access data, and generate QC plots.")
1938 (license license:agpl3+)))
1940 (define-public r-chipexoqual
1942 (name "r-chipexoqual")
1947 (uri (bioconductor-uri "ChIPexoQual" version))
1950 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
1951 (properties `((upstream-name . "ChIPexoQual")))
1952 (build-system r-build-system)
1954 `(("r-biocparallel" ,r-biocparallel)
1955 ("r-biovizbase" ,r-biovizbase)
1956 ("r-broom" ,r-broom)
1957 ("r-data-table" ,r-data-table)
1958 ("r-dplyr" ,r-dplyr)
1959 ("r-genomeinfodb" ,r-genomeinfodb)
1960 ("r-genomicalignments" ,r-genomicalignments)
1961 ("r-genomicranges" ,r-genomicranges)
1962 ("r-ggplot2" ,r-ggplot2)
1963 ("r-hexbin" ,r-hexbin)
1964 ("r-iranges" ,r-iranges)
1965 ("r-rcolorbrewer" ,r-rcolorbrewer)
1966 ("r-rmarkdown" ,r-rmarkdown)
1967 ("r-rsamtools" ,r-rsamtools)
1968 ("r-s4vectors" ,r-s4vectors)
1969 ("r-scales" ,r-scales)
1970 ("r-viridis" ,r-viridis)))
1971 (home-page "https://github.com/keleslab/ChIPexoQual")
1972 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1974 "This package provides a quality control pipeline for ChIP-exo/nexus
1976 (license license:gpl2+)))
1978 (define-public r-copynumber
1980 (name "r-copynumber")
1984 (uri (bioconductor-uri "copynumber" version))
1987 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
1988 (build-system r-build-system)
1990 `(("r-s4vectors" ,r-s4vectors)
1991 ("r-iranges" ,r-iranges)
1992 ("r-genomicranges" ,r-genomicranges)
1993 ("r-biocgenerics" ,r-biocgenerics)))
1994 (home-page "https://bioconductor.org/packages/copynumber")
1995 (synopsis "Segmentation of single- and multi-track copy number data")
1997 "This package segments single- and multi-track copy number data by a
1998 penalized least squares regression method.")
1999 (license license:artistic2.0)))
2001 (define-public r-dnacopy
2008 (uri (bioconductor-uri "DNAcopy" version))
2011 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2012 (properties `((upstream-name . "DNAcopy")))
2013 (build-system r-build-system)
2014 (native-inputs `(("gfortran" ,gfortran)))
2015 (home-page "https://bioconductor.org/packages/DNAcopy")
2016 (synopsis "DNA copy number data analysis")
2018 "This package implements the @dfn{circular binary segmentation} (CBS)
2019 algorithm to segment DNA copy number data and identify genomic regions with
2020 abnormal copy number.")
2021 (license license:gpl2+)))
2023 ;; This is a CRAN package, but it uncharacteristically depends on a
2024 ;; Bioconductor package.
2025 (define-public r-htscluster
2027 (name "r-htscluster")
2032 (uri (cran-uri "HTSCluster" version))
2035 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2036 (properties `((upstream-name . "HTSCluster")))
2037 (build-system r-build-system)
2039 `(("r-capushe" ,r-capushe)
2040 ("r-edger" ,r-edger)
2041 ("r-plotrix" ,r-plotrix)))
2042 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2043 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2045 "This package provides a Poisson mixture model is implemented to cluster
2046 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2047 estimation is performed using either the EM or CEM algorithm, and the slope
2048 heuristics are used for model selection (i.e., to choose the number of
2050 (license license:gpl3+)))
2052 (define-public r-deds
2059 (uri (bioconductor-uri "DEDS" version))
2062 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2063 (properties `((upstream-name . "DEDS")))
2064 (build-system r-build-system)
2065 (home-page "https://bioconductor.org/packages/DEDS/")
2066 (synopsis "Differential expression via distance summary for microarray data")
2068 "This library contains functions that calculate various statistics of
2069 differential expression for microarray data, including t statistics, fold
2070 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2071 also implements a new methodology called DEDS (Differential Expression via
2072 Distance Summary), which selects differentially expressed genes by integrating
2073 and summarizing a set of statistics using a weighted distance approach.")
2074 ;; Any version of the LGPL.
2075 (license license:lgpl3+)))
2077 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2079 (define-public r-nbpseq
2086 (uri (cran-uri "NBPSeq" version))
2089 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2090 (properties `((upstream-name . "NBPSeq")))
2091 (build-system r-build-system)
2093 `(("r-qvalue" ,r-qvalue)))
2094 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2095 (synopsis "Negative binomial models for RNA-Seq data")
2097 "This package provides negative binomial models for two-group comparisons
2098 and regression inferences from RNA-sequencing data.")
2099 (license license:gpl2)))
2101 (define-public r-ebseq
2108 (uri (bioconductor-uri "EBSeq" version))
2111 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2112 (properties `((upstream-name . "EBSeq")))
2113 (build-system r-build-system)
2115 `(("r-blockmodeling" ,r-blockmodeling)
2116 ("r-gplots" ,r-gplots)
2117 ("r-testthat" ,r-testthat)))
2118 (home-page "https://bioconductor.org/packages/EBSeq")
2119 (synopsis "Differential expression analysis of RNA-seq data")
2121 "This package provides tools for differential expression analysis at both
2122 gene and isoform level using RNA-seq data")
2123 (license license:artistic2.0)))
2125 (define-public r-lpsymphony
2127 (name "r-lpsymphony")
2132 (uri (bioconductor-uri "lpsymphony" version))
2135 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2136 (build-system r-build-system)
2138 `(("gfortran" ,gfortran)
2141 `(("pkg-config" ,pkg-config)))
2142 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2143 (synopsis "Symphony integer linear programming solver in R")
2145 "This package was derived from Rsymphony. The package provides an R
2146 interface to SYMPHONY, a linear programming solver written in C++. The main
2147 difference between this package and Rsymphony is that it includes the solver
2148 source code, while Rsymphony expects to find header and library files on the
2149 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2150 to install interface to SYMPHONY.")
2151 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2152 ;; lpsimphony is released under the same terms.
2153 (license license:epl1.0)))
2155 (define-public r-ihw
2162 (uri (bioconductor-uri "IHW" version))
2165 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2166 (properties `((upstream-name . "IHW")))
2167 (build-system r-build-system)
2169 `(("r-biocgenerics" ,r-biocgenerics)
2170 ("r-fdrtool" ,r-fdrtool)
2171 ("r-lpsymphony" ,r-lpsymphony)
2172 ("r-slam" ,r-slam)))
2173 (home-page "https://bioconductor.org/packages/IHW")
2174 (synopsis "Independent hypothesis weighting")
2176 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2177 procedure that increases power compared to the method of Benjamini and
2178 Hochberg by assigning data-driven weights to each hypothesis. The input to
2179 IHW is a two-column table of p-values and covariates. The covariate can be
2180 any continuous-valued or categorical variable that is thought to be
2181 informative on the statistical properties of each hypothesis test, while it is
2182 independent of the p-value under the null hypothesis.")
2183 (license license:artistic2.0)))
2185 (define-public r-icobra
2192 (uri (bioconductor-uri "iCOBRA" version))
2195 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2196 (properties `((upstream-name . "iCOBRA")))
2197 (build-system r-build-system)
2199 `(("r-dplyr" ,r-dplyr)
2201 ("r-ggplot2" ,r-ggplot2)
2202 ("r-limma" ,r-limma)
2203 ("r-reshape2" ,r-reshape2)
2205 ("r-scales" ,r-scales)
2206 ("r-shiny" ,r-shiny)
2207 ("r-shinybs" ,r-shinybs)
2208 ("r-shinydashboard" ,r-shinydashboard)
2209 ("r-upsetr" ,r-upsetr)))
2210 (home-page "https://bioconductor.org/packages/iCOBRA")
2211 (synopsis "Comparison and visualization of ranking and assignment methods")
2213 "This package provides functions for calculation and visualization of
2214 performance metrics for evaluation of ranking and binary
2215 classification (assignment) methods. It also contains a Shiny application for
2216 interactive exploration of results.")
2217 (license license:gpl2+)))
2219 (define-public r-mast
2226 (uri (bioconductor-uri "MAST" version))
2229 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2230 (properties `((upstream-name . "MAST")))
2231 (build-system r-build-system)
2233 `(("r-abind" ,r-abind)
2235 ("r-biobase" ,r-biobase)
2236 ("r-biocgenerics" ,r-biocgenerics)
2237 ("r-data-table" ,r-data-table)
2238 ("r-ggplot2" ,r-ggplot2)
2240 ("r-progress" ,r-progress)
2241 ("r-reshape2" ,r-reshape2)
2242 ("r-s4vectors" ,r-s4vectors)
2243 ("r-singlecellexperiment" ,r-singlecellexperiment)
2244 ("r-stringr" ,r-stringr)
2245 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2246 (home-page "https://github.com/RGLab/MAST/")
2247 (synopsis "Model-based analysis of single cell transcriptomics")
2249 "This package provides methods and models for handling zero-inflated
2250 single cell assay data.")
2251 (license license:gpl2+)))
2253 (define-public r-monocle
2260 (uri (bioconductor-uri "monocle" version))
2263 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2264 (build-system r-build-system)
2266 `(("r-biobase" ,r-biobase)
2267 ("r-biocgenerics" ,r-biocgenerics)
2268 ("r-biocviews" ,r-biocviews)
2269 ("r-cluster" ,r-cluster)
2270 ("r-combinat" ,r-combinat)
2271 ("r-ddrtree" ,r-ddrtree)
2272 ("r-densityclust" ,r-densityclust)
2273 ("r-dplyr" ,r-dplyr)
2274 ("r-fastica" ,r-fastica)
2275 ("r-ggplot2" ,r-ggplot2)
2276 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2277 ("r-igraph" ,r-igraph)
2278 ("r-irlba" ,r-irlba)
2279 ("r-limma" ,r-limma)
2281 ("r-matrix" ,r-matrix)
2282 ("r-matrixstats" ,r-matrixstats)
2283 ("r-pheatmap" ,r-pheatmap)
2285 ("r-proxy" ,r-proxy)
2286 ("r-qlcmatrix" ,r-qlcmatrix)
2289 ("r-reshape2" ,r-reshape2)
2290 ("r-rtsne" ,r-rtsne)
2292 ("r-stringr" ,r-stringr)
2293 ("r-tibble" ,r-tibble)
2295 ("r-viridis" ,r-viridis)))
2296 (home-page "https://bioconductor.org/packages/monocle")
2297 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2299 "Monocle performs differential expression and time-series analysis for
2300 single-cell expression experiments. It orders individual cells according to
2301 progress through a biological process, without knowing ahead of time which
2302 genes define progress through that process. Monocle also performs
2303 differential expression analysis, clustering, visualization, and other useful
2304 tasks on single cell expression data. It is designed to work with RNA-Seq and
2305 qPCR data, but could be used with other types as well.")
2306 (license license:artistic2.0)))
2308 (define-public r-monocle3
2316 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2318 (file-name (git-file-name name version))
2321 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2322 (build-system r-build-system)
2324 `(("r-biobase" ,r-biobase)
2325 ("r-biocgenerics" ,r-biocgenerics)
2326 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2327 ("r-dplyr" ,r-dplyr)
2328 ("r-ggplot2" ,r-ggplot2)
2329 ("r-ggrepel" ,r-ggrepel)
2331 ("r-htmlwidgets" ,r-htmlwidgets)
2332 ("r-igraph" ,r-igraph)
2333 ("r-irlba" ,r-irlba)
2334 ("r-limma" ,r-limma)
2335 ("r-lmtest" ,r-lmtest)
2337 ("r-matrix" ,r-matrix)
2338 ("r-matrix-utils" ,r-matrix-utils)
2339 ("r-pbapply" ,r-pbapply)
2340 ("r-pbmcapply" ,r-pbmcapply)
2341 ("r-pheatmap" ,r-pheatmap)
2342 ("r-plotly" ,r-plotly)
2344 ("r-proxy" ,r-proxy)
2346 ("r-purrr" ,r-purrr)
2349 ("r-rcppparallel" ,r-rcppparallel)
2350 ("r-reshape2" ,r-reshape2)
2351 ("r-reticulate" ,r-reticulate)
2352 ("r-rhpcblasctl" ,r-rhpcblasctl)
2353 ("r-rtsne" ,r-rtsne)
2354 ("r-shiny" ,r-shiny)
2356 ("r-spdep" ,r-spdep)
2357 ("r-speedglm" ,r-speedglm)
2358 ("r-stringr" ,r-stringr)
2359 ("r-singlecellexperiment" ,r-singlecellexperiment)
2360 ("r-tibble" ,r-tibble)
2361 ("r-tidyr" ,r-tidyr)
2363 ("r-viridis" ,r-viridis)))
2364 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2365 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2367 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2368 (license license:expat)))
2370 (define-public r-noiseq
2377 (uri (bioconductor-uri "NOISeq" version))
2380 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2381 (properties `((upstream-name . "NOISeq")))
2382 (build-system r-build-system)
2384 `(("r-biobase" ,r-biobase)
2385 ("r-matrix" ,r-matrix)))
2386 (home-page "https://bioconductor.org/packages/NOISeq")
2387 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2389 "This package provides tools to support the analysis of RNA-seq
2390 expression data or other similar kind of data. It provides exploratory plots
2391 to evaluate saturation, count distribution, expression per chromosome, type of
2392 detected features, features length, etc. It also supports the analysis of
2393 differential expression between two experimental conditions with no parametric
2395 (license license:artistic2.0)))
2397 (define-public r-scdd
2404 (uri (bioconductor-uri "scDD" version))
2407 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2408 (properties `((upstream-name . "scDD")))
2409 (build-system r-build-system)
2412 ("r-biocparallel" ,r-biocparallel)
2413 ("r-ebseq" ,r-ebseq)
2414 ("r-fields" ,r-fields)
2415 ("r-ggplot2" ,r-ggplot2)
2416 ("r-mclust" ,r-mclust)
2417 ("r-outliers" ,r-outliers)
2418 ("r-s4vectors" ,r-s4vectors)
2419 ("r-scran" ,r-scran)
2420 ("r-singlecellexperiment" ,r-singlecellexperiment)
2421 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2422 (home-page "https://github.com/kdkorthauer/scDD")
2423 (synopsis "Mixture modeling of single-cell RNA-seq data")
2425 "This package implements a method to analyze single-cell RNA-seq data
2426 utilizing flexible Dirichlet Process mixture models. Genes with differential
2427 distributions of expression are classified into several interesting patterns
2428 of differences between two conditions. The package also includes functions
2429 for simulating data with these patterns from negative binomial
2431 (license license:gpl2)))
2433 (define-public r-scone
2440 (uri (bioconductor-uri "scone" version))
2443 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2444 (build-system r-build-system)
2446 `(("r-aroma-light" ,r-aroma-light)
2447 ("r-biocparallel" ,r-biocparallel)
2449 ("r-class" ,r-class)
2450 ("r-cluster" ,r-cluster)
2451 ("r-compositions" ,r-compositions)
2452 ("r-diptest" ,r-diptest)
2453 ("r-edger" ,r-edger)
2455 ("r-gplots" ,r-gplots)
2456 ("r-hexbin" ,r-hexbin)
2457 ("r-limma" ,r-limma)
2458 ("r-matrixstats" ,r-matrixstats)
2459 ("r-mixtools" ,r-mixtools)
2460 ("r-rarpack" ,r-rarpack)
2461 ("r-rcolorbrewer" ,r-rcolorbrewer)
2462 ("r-rhdf5" ,r-rhdf5)
2463 ("r-ruvseq" ,r-ruvseq)
2464 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2465 (home-page "https://bioconductor.org/packages/scone")
2466 (synopsis "Single cell overview of normalized expression data")
2468 "SCONE is an R package for comparing and ranking the performance of
2469 different normalization schemes for single-cell RNA-seq and other
2470 high-throughput analyses.")
2471 (license license:artistic2.0)))
2473 (define-public r-geoquery
2480 (uri (bioconductor-uri "GEOquery" version))
2483 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2484 (properties `((upstream-name . "GEOquery")))
2485 (build-system r-build-system)
2487 `(("r-biobase" ,r-biobase)
2488 ("r-dplyr" ,r-dplyr)
2490 ("r-limma" ,r-limma)
2491 ("r-magrittr" ,r-magrittr)
2492 ("r-readr" ,r-readr)
2493 ("r-tidyr" ,r-tidyr)
2494 ("r-xml2" ,r-xml2)))
2495 (home-page "https://github.com/seandavi/GEOquery/")
2496 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2498 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2499 microarray data. Given the rich and varied nature of this resource, it is
2500 only natural to want to apply BioConductor tools to these data. GEOquery is
2501 the bridge between GEO and BioConductor.")
2502 (license license:gpl2)))
2504 (define-public r-illuminaio
2506 (name "r-illuminaio")
2511 (uri (bioconductor-uri "illuminaio" version))
2514 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2515 (build-system r-build-system)
2517 `(("r-base64" ,r-base64)))
2518 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2519 (synopsis "Parse Illumina microarray output files")
2521 "This package provides tools for parsing Illumina's microarray output
2522 files, including IDAT.")
2523 (license license:gpl2)))
2525 (define-public r-siggenes
2532 (uri (bioconductor-uri "siggenes" version))
2535 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2536 (build-system r-build-system)
2538 `(("r-biobase" ,r-biobase)
2539 ("r-multtest" ,r-multtest)
2540 ("r-scrime" ,r-scrime)))
2541 (home-page "https://bioconductor.org/packages/siggenes/")
2543 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2545 "This package provides tools for the identification of differentially
2546 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2547 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2548 Bayes Analyses of Microarrays} (EBAM).")
2549 (license license:lgpl2.0+)))
2551 (define-public r-bumphunter
2553 (name "r-bumphunter")
2558 (uri (bioconductor-uri "bumphunter" version))
2561 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2562 (build-system r-build-system)
2564 `(("r-annotationdbi" ,r-annotationdbi)
2565 ("r-biocgenerics" ,r-biocgenerics)
2566 ("r-dorng" ,r-dorng)
2567 ("r-foreach" ,r-foreach)
2568 ("r-genomeinfodb" ,r-genomeinfodb)
2569 ("r-genomicfeatures" ,r-genomicfeatures)
2570 ("r-genomicranges" ,r-genomicranges)
2571 ("r-iranges" ,r-iranges)
2572 ("r-iterators" ,r-iterators)
2573 ("r-limma" ,r-limma)
2574 ("r-locfit" ,r-locfit)
2575 ("r-matrixstats" ,r-matrixstats)
2576 ("r-s4vectors" ,r-s4vectors)))
2577 (home-page "https://github.com/ririzarr/bumphunter")
2578 (synopsis "Find bumps in genomic data")
2580 "This package provides tools for finding bumps in genomic data in order
2581 to identify differentially methylated regions in epigenetic epidemiology
2583 (license license:artistic2.0)))
2585 (define-public r-minfi
2592 (uri (bioconductor-uri "minfi" version))
2595 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2596 (build-system r-build-system)
2598 `(("r-beanplot" ,r-beanplot)
2599 ("r-biobase" ,r-biobase)
2600 ("r-biocgenerics" ,r-biocgenerics)
2601 ("r-biocparallel" ,r-biocparallel)
2602 ("r-biostrings" ,r-biostrings)
2603 ("r-bumphunter" ,r-bumphunter)
2604 ("r-data-table" ,r-data-table)
2605 ("r-delayedarray" ,r-delayedarray)
2606 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2607 ("r-genefilter" ,r-genefilter)
2608 ("r-genomeinfodb" ,r-genomeinfodb)
2609 ("r-genomicranges" ,r-genomicranges)
2610 ("r-geoquery" ,r-geoquery)
2611 ("r-hdf5array" ,r-hdf5array)
2612 ("r-illuminaio" ,r-illuminaio)
2613 ("r-iranges" ,r-iranges)
2614 ("r-lattice" ,r-lattice)
2615 ("r-limma" ,r-limma)
2617 ("r-mclust" ,r-mclust)
2619 ("r-nor1mix" ,r-nor1mix)
2620 ("r-preprocesscore" ,r-preprocesscore)
2621 ("r-quadprog" ,r-quadprog)
2622 ("r-rcolorbrewer" ,r-rcolorbrewer)
2623 ("r-reshape" ,r-reshape)
2624 ("r-s4vectors" ,r-s4vectors)
2625 ("r-siggenes" ,r-siggenes)
2626 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2627 (home-page "https://github.com/hansenlab/minfi")
2628 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2630 "This package provides tools to analyze and visualize Illumina Infinium
2631 methylation arrays.")
2632 (license license:artistic2.0)))
2634 (define-public r-methylumi
2636 (name "r-methylumi")
2641 (uri (bioconductor-uri "methylumi" version))
2644 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2645 (build-system r-build-system)
2647 `(("r-annotate" ,r-annotate)
2648 ("r-annotationdbi" ,r-annotationdbi)
2649 ("r-biobase" ,r-biobase)
2650 ("r-biocgenerics" ,r-biocgenerics)
2651 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2652 ("r-genefilter" ,r-genefilter)
2653 ("r-genomeinfodb" ,r-genomeinfodb)
2654 ("r-genomicranges" ,r-genomicranges)
2655 ("r-ggplot2" ,r-ggplot2)
2656 ("r-illuminaio" ,r-illuminaio)
2657 ("r-iranges" ,r-iranges)
2658 ("r-lattice" ,r-lattice)
2659 ("r-matrixstats" ,r-matrixstats)
2660 ("r-minfi" ,r-minfi)
2661 ("r-reshape2" ,r-reshape2)
2662 ("r-s4vectors" ,r-s4vectors)
2663 ("r-scales" ,r-scales)
2664 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2665 (home-page "https://bioconductor.org/packages/methylumi")
2666 (synopsis "Handle Illumina methylation data")
2668 "This package provides classes for holding and manipulating Illumina
2669 methylation data. Based on eSet, it can contain MIAME information, sample
2670 information, feature information, and multiple matrices of data. An
2671 \"intelligent\" import function, methylumiR can read the Illumina text files
2672 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2673 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2674 background correction, and quality control features for GoldenGate, Infinium,
2675 and Infinium HD arrays are also included.")
2676 (license license:gpl2)))
2678 (define-public r-lumi
2685 (uri (bioconductor-uri "lumi" version))
2688 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2689 (build-system r-build-system)
2691 `(("r-affy" ,r-affy)
2692 ("r-annotate" ,r-annotate)
2693 ("r-annotationdbi" ,r-annotationdbi)
2694 ("r-biobase" ,r-biobase)
2696 ("r-genomicfeatures" ,r-genomicfeatures)
2697 ("r-genomicranges" ,r-genomicranges)
2698 ("r-kernsmooth" ,r-kernsmooth)
2699 ("r-lattice" ,r-lattice)
2701 ("r-methylumi" ,r-methylumi)
2703 ("r-nleqslv" ,r-nleqslv)
2704 ("r-preprocesscore" ,r-preprocesscore)
2705 ("r-rsqlite" ,r-rsqlite)))
2706 (home-page "https://bioconductor.org/packages/lumi")
2707 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2709 "The lumi package provides an integrated solution for the Illumina
2710 microarray data analysis. It includes functions of Illumina
2711 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2712 variance stabilization, normalization and gene annotation at the probe level.
2713 It also includes the functions of processing Illumina methylation microarrays,
2714 especially Illumina Infinium methylation microarrays.")
2715 (license license:lgpl2.0+)))
2717 (define-public r-linnorm
2724 (uri (bioconductor-uri "Linnorm" version))
2727 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2728 (properties `((upstream-name . "Linnorm")))
2729 (build-system r-build-system)
2731 `(("r-amap" ,r-amap)
2732 ("r-apcluster" ,r-apcluster)
2733 ("r-ellipse" ,r-ellipse)
2734 ("r-fastcluster" ,r-fastcluster)
2736 ("r-ggdendro" ,r-ggdendro)
2737 ("r-ggplot2" ,r-ggplot2)
2738 ("r-gmodels" ,r-gmodels)
2739 ("r-igraph" ,r-igraph)
2740 ("r-limma" ,r-limma)
2742 ("r-mclust" ,r-mclust)
2744 ("r-rcpparmadillo" ,r-rcpparmadillo)
2745 ("r-rtsne" ,r-rtsne)
2746 ("r-statmod" ,r-statmod)
2747 ("r-vegan" ,r-vegan)
2749 (home-page "http://www.jjwanglab.org/Linnorm/")
2750 (synopsis "Linear model and normality based transformation method")
2752 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2753 count data or any large scale count data. It transforms such datasets for
2754 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2755 the following pipelines are implemented:
2758 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2759 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2760 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2761 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2762 @item Differential expression analysis or differential peak detection using
2763 limma (@code{Linnorm.limma})
2764 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2765 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2766 @item Stable gene selection for scRNA-seq data; for users without or who do
2767 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2768 @item Data imputation (@code{Linnorm.DataImput}).
2771 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2772 @code{RnaXSim} function is included for simulating RNA-seq data for the
2773 evaluation of DEG analysis methods.")
2774 (license license:expat)))
2776 (define-public r-ioniser
2783 (uri (bioconductor-uri "IONiseR" version))
2786 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2787 (properties `((upstream-name . "IONiseR")))
2788 (build-system r-build-system)
2790 `(("r-biocgenerics" ,r-biocgenerics)
2791 ("r-biocparallel" ,r-biocparallel)
2792 ("r-biostrings" ,r-biostrings)
2793 ("r-bit64" ,r-bit64)
2794 ("r-dplyr" ,r-dplyr)
2795 ("r-ggplot2" ,r-ggplot2)
2796 ("r-magrittr" ,r-magrittr)
2797 ("r-rhdf5" ,r-rhdf5)
2798 ("r-shortread" ,r-shortread)
2799 ("r-stringr" ,r-stringr)
2800 ("r-tibble" ,r-tibble)
2801 ("r-tidyr" ,r-tidyr)
2802 ("r-xvector" ,r-xvector)))
2803 (home-page "https://bioconductor.org/packages/IONiseR/")
2804 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
2806 "IONiseR provides tools for the quality assessment of Oxford Nanopore
2807 MinION data. It extracts summary statistics from a set of fast5 files and can
2808 be used either before or after base calling. In addition to standard
2809 summaries of the read-types produced, it provides a number of plots for
2810 visualising metrics relative to experiment run time or spatially over the
2811 surface of a flowcell.")
2812 (license license:expat)))
2814 ;; This is a CRAN package, but it depends on packages from Bioconductor.
2815 (define-public r-gkmsvm
2822 (uri (cran-uri "gkmSVM" version))
2825 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
2826 (properties `((upstream-name . "gkmSVM")))
2827 (build-system r-build-system)
2829 `(("r-biocgenerics" ,r-biocgenerics)
2830 ("r-biostrings" ,r-biostrings)
2831 ("r-genomeinfodb" ,r-genomeinfodb)
2832 ("r-genomicranges" ,r-genomicranges)
2833 ("r-iranges" ,r-iranges)
2834 ("r-kernlab" ,r-kernlab)
2837 ("r-rtracklayer" ,r-rtracklayer)
2838 ("r-s4vectors" ,r-s4vectors)
2839 ("r-seqinr" ,r-seqinr)))
2840 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
2841 (synopsis "Gapped-kmer support vector machine")
2843 "This R package provides tools for training gapped-kmer SVM classifiers
2844 for DNA and protein sequences. This package supports several sequence
2845 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
2846 (license license:gpl2+)))
2848 (define-public r-triform
2855 (uri (bioconductor-uri "triform" version))
2858 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
2859 (build-system r-build-system)
2861 `(("r-biocgenerics" ,r-biocgenerics)
2862 ("r-iranges" ,r-iranges)
2863 ("r-yaml" ,r-yaml)))
2864 (home-page "https://bioconductor.org/packages/triform/")
2865 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
2867 "The Triform algorithm uses model-free statistics to identify peak-like
2868 distributions of TF ChIP sequencing reads, taking advantage of an improved
2869 peak definition in combination with known profile characteristics.")
2870 (license license:gpl2)))
2872 (define-public r-varianttools
2874 (name "r-varianttools")
2879 (uri (bioconductor-uri "VariantTools" version))
2882 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
2883 (properties `((upstream-name . "VariantTools")))
2884 (build-system r-build-system)
2886 `(("r-biobase" ,r-biobase)
2887 ("r-biocgenerics" ,r-biocgenerics)
2888 ("r-biocparallel" ,r-biocparallel)
2889 ("r-biostrings" ,r-biostrings)
2890 ("r-bsgenome" ,r-bsgenome)
2891 ("r-genomeinfodb" ,r-genomeinfodb)
2892 ("r-genomicfeatures" ,r-genomicfeatures)
2893 ("r-genomicranges" ,r-genomicranges)
2894 ("r-iranges" ,r-iranges)
2895 ("r-matrix" ,r-matrix)
2896 ("r-rsamtools" ,r-rsamtools)
2897 ("r-rtracklayer" ,r-rtracklayer)
2898 ("r-s4vectors" ,r-s4vectors)
2899 ("r-variantannotation" ,r-variantannotation)))
2900 (home-page "https://bioconductor.org/packages/VariantTools/")
2901 (synopsis "Tools for exploratory analysis of variant calls")
2903 "Explore, diagnose, and compare variant calls using filters. The
2904 VariantTools package supports a workflow for loading data, calling single
2905 sample variants and tumor-specific somatic mutations or other sample-specific
2906 variant types (e.g., RNA editing). Most of the functions operate on
2907 alignments (BAM files) or datasets of called variants. The user is expected
2908 to have already aligned the reads with a separate tool, e.g., GSNAP via
2910 (license license:artistic2.0)))
2912 (define-public r-heatplus
2919 (uri (bioconductor-uri "Heatplus" version))
2922 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
2923 (properties `((upstream-name . "Heatplus")))
2924 (build-system r-build-system)
2926 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
2927 (home-page "https://github.com/alexploner/Heatplus")
2928 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
2930 "This package provides tools to display a rectangular heatmap (intensity
2931 plot) of a data matrix. By default, both samples (columns) and features (row)
2932 of the matrix are sorted according to a hierarchical clustering, and the
2933 corresponding dendrogram is plotted. Optionally, panels with additional
2934 information about samples and features can be added to the plot.")
2935 (license license:gpl2+)))
2937 (define-public r-gosemsim
2944 (uri (bioconductor-uri "GOSemSim" version))
2947 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
2948 (properties `((upstream-name . "GOSemSim")))
2949 (build-system r-build-system)
2951 `(("r-annotationdbi" ,r-annotationdbi)
2952 ("r-go-db" ,r-go-db)
2953 ("r-rcpp" ,r-rcpp)))
2954 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
2955 (synopsis "GO-terms semantic similarity measures")
2957 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
2958 quantitative ways to compute similarities between genes and gene groups, and
2959 have became important basis for many bioinformatics analysis approaches.
2960 GOSemSim is an R package for semantic similarity computation among GO terms,
2961 sets of GO terms, gene products and gene clusters.")
2962 (license license:artistic2.0)))
2964 (define-public r-anota
2971 (uri (bioconductor-uri "anota" version))
2974 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
2975 (build-system r-build-system)
2977 `(("r-multtest" ,r-multtest)
2978 ("r-qvalue" ,r-qvalue)))
2979 (home-page "https://bioconductor.org/packages/anota/")
2980 (synopsis "Analysis of translational activity")
2982 "Genome wide studies of translational control is emerging as a tool to
2983 study various biological conditions. The output from such analysis is both
2984 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
2985 involved in translation (the actively translating mRNA level) for each mRNA.
2986 The standard analysis of such data strives towards identifying differential
2987 translational between two or more sample classes - i.e. differences in
2988 actively translated mRNA levels that are independent of underlying differences
2989 in cytosolic mRNA levels. This package allows for such analysis using partial
2990 variances and the random variance model. As 10s of thousands of mRNAs are
2991 analyzed in parallel the library performs a number of tests to assure that
2992 the data set is suitable for such analysis.")
2993 (license license:gpl3)))
2995 (define-public r-sigpathway
2997 (name "r-sigpathway")
3002 (uri (bioconductor-uri "sigPathway" version))
3005 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3006 (properties `((upstream-name . "sigPathway")))
3007 (build-system r-build-system)
3008 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3009 (synopsis "Pathway analysis")
3011 "This package is used to conduct pathway analysis by calculating the NT_k
3012 and NE_k statistics in a statistical framework for determining whether a
3013 specified group of genes for a pathway has a coordinated association with a
3014 phenotype of interest.")
3015 (license license:gpl2)))
3017 (define-public r-fgsea
3024 (uri (bioconductor-uri "fgsea" version))
3027 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3028 (build-system r-build-system)
3031 ("r-biocparallel" ,r-biocparallel)
3032 ("r-data-table" ,r-data-table)
3033 ("r-fastmatch" ,r-fastmatch)
3034 ("r-ggplot2" ,r-ggplot2)
3035 ("r-gridextra" ,r-gridextra)
3036 ("r-matrix" ,r-matrix)
3037 ("r-rcpp" ,r-rcpp)))
3038 (home-page "https://github.com/ctlab/fgsea/")
3039 (synopsis "Fast gene set enrichment analysis")
3041 "The package implements an algorithm for fast gene set enrichment
3042 analysis. Using the fast algorithm allows to make more permutations and get
3043 more fine grained p-values, which allows to use accurate stantard approaches
3044 to multiple hypothesis correction.")
3045 (license license:expat)))
3047 (define-public r-dose
3054 (uri (bioconductor-uri "DOSE" version))
3057 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3058 (properties `((upstream-name . "DOSE")))
3059 (build-system r-build-system)
3061 `(("r-annotationdbi" ,r-annotationdbi)
3062 ("r-biocparallel" ,r-biocparallel)
3063 ("r-do-db" ,r-do-db)
3064 ("r-fgsea" ,r-fgsea)
3065 ("r-ggplot2" ,r-ggplot2)
3066 ("r-gosemsim" ,r-gosemsim)
3067 ("r-qvalue" ,r-qvalue)
3068 ("r-reshape2" ,r-reshape2)
3069 ("r-s4vectors" ,r-s4vectors)))
3070 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3071 (synopsis "Disease ontology semantic and enrichment analysis")
3073 "This package implements five methods proposed by Resnik, Schlicker,
3074 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3075 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3076 including hypergeometric model and gene set enrichment analysis are also
3077 implemented for discovering disease associations of high-throughput biological
3079 (license license:artistic2.0)))
3081 (define-public r-enrichplot
3083 (name "r-enrichplot")
3088 (uri (bioconductor-uri "enrichplot" version))
3091 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3092 (build-system r-build-system)
3094 `(("r-annotationdbi" ,r-annotationdbi)
3095 ("r-cowplot" ,r-cowplot)
3097 ("r-europepmc" ,r-europepmc)
3098 ("r-ggplot2" ,r-ggplot2)
3099 ("r-ggplotify" ,r-ggplotify)
3100 ("r-ggraph" ,r-ggraph)
3101 ("r-ggridges" ,r-ggridges)
3102 ("r-gosemsim" ,r-gosemsim)
3103 ("r-gridextra" ,r-gridextra)
3104 ("r-igraph" ,r-igraph)
3105 ("r-purrr" ,r-purrr)
3106 ("r-rcolorbrewer" ,r-rcolorbrewer)
3107 ("r-reshape2" ,r-reshape2)
3108 ("r-upsetr" ,r-upsetr)))
3109 (home-page "https://github.com/GuangchuangYu/enrichplot")
3110 (synopsis "Visualization of functional enrichment result")
3112 "The enrichplot package implements several visualization methods for
3113 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3114 All the visualization methods are developed based on ggplot2 graphics.")
3115 (license license:artistic2.0)))
3117 (define-public r-clusterprofiler
3119 (name "r-clusterprofiler")
3124 (uri (bioconductor-uri "clusterProfiler" version))
3127 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3129 `((upstream-name . "clusterProfiler")))
3130 (build-system r-build-system)
3132 `(("r-annotationdbi" ,r-annotationdbi)
3134 ("r-enrichplot" ,r-enrichplot)
3135 ("r-ggplot2" ,r-ggplot2)
3136 ("r-go-db" ,r-go-db)
3137 ("r-gosemsim" ,r-gosemsim)
3138 ("r-magrittr" ,r-magrittr)
3140 ("r-qvalue" ,r-qvalue)
3141 ("r-rvcheck" ,r-rvcheck)
3142 ("r-tidyr" ,r-tidyr)))
3143 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3144 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3146 "This package implements methods to analyze and visualize functional
3147 profiles (GO and KEGG) of gene and gene clusters.")
3148 (license license:artistic2.0)))
3150 (define-public r-mlinterfaces
3152 (name "r-mlinterfaces")
3157 (uri (bioconductor-uri "MLInterfaces" version))
3160 "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j"))))
3161 (properties `((upstream-name . "MLInterfaces")))
3162 (build-system r-build-system)
3164 `(("r-annotate" ,r-annotate)
3165 ("r-biobase" ,r-biobase)
3166 ("r-biocgenerics" ,r-biocgenerics)
3167 ("r-cluster" ,r-cluster)
3170 ("r-gdata" ,r-gdata)
3171 ("r-genefilter" ,r-genefilter)
3172 ("r-ggvis" ,r-ggvis)
3173 ("r-hwriter" ,r-hwriter)
3175 ("r-mlbench" ,r-mlbench)
3177 ("r-rcolorbrewer" ,r-rcolorbrewer)
3179 ("r-rpart" ,r-rpart)
3180 ("r-sfsmisc" ,r-sfsmisc)
3181 ("r-shiny" ,r-shiny)
3182 ("r-threejs" ,r-threejs)))
3183 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3184 (synopsis "Interfaces to R machine learning procedures")
3186 "This package provides uniform interfaces to machine learning code for
3187 data in R and Bioconductor containers.")
3188 ;; Any version of the LGPL.
3189 (license license:lgpl2.1+)))
3191 (define-public r-annaffy
3198 (uri (bioconductor-uri "annaffy" version))
3201 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3202 (build-system r-build-system)
3205 (modify-phases %standard-phases
3206 (add-after 'unpack 'remove-reference-to-non-free-data
3208 (substitute* "DESCRIPTION"
3212 `(("r-annotationdbi" ,r-annotationdbi)
3213 ("r-biobase" ,r-biobase)
3215 ("r-go-db" ,r-go-db)))
3216 (home-page "https://bioconductor.org/packages/annaffy/")
3217 (synopsis "Annotation tools for Affymetrix biological metadata")
3219 "This package provides functions for handling data from Bioconductor
3220 Affymetrix annotation data packages. It produces compact HTML and text
3221 reports including experimental data and URL links to many online databases.
3222 It allows searching of biological metadata using various criteria.")
3223 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3224 ;; the LGPL 2.1 is included.
3225 (license license:lgpl2.1+)))
3227 (define-public r-a4core
3234 (uri (bioconductor-uri "a4Core" version))
3237 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3238 (properties `((upstream-name . "a4Core")))
3239 (build-system r-build-system)
3241 `(("r-biobase" ,r-biobase)
3242 ("r-glmnet" ,r-glmnet)))
3243 (home-page "https://bioconductor.org/packages/a4Core")
3244 (synopsis "Automated Affymetrix array analysis core package")
3246 "This is the core package for the automated analysis of Affymetrix
3248 (license license:gpl3)))
3250 (define-public r-a4classif
3252 (name "r-a4classif")
3257 (uri (bioconductor-uri "a4Classif" version))
3260 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3261 (properties `((upstream-name . "a4Classif")))
3262 (build-system r-build-system)
3264 `(("r-a4core" ,r-a4core)
3265 ("r-a4preproc" ,r-a4preproc)
3266 ("r-glmnet" ,r-glmnet)
3267 ("r-mlinterfaces" ,r-mlinterfaces)
3270 ("r-varselrf" ,r-varselrf)))
3271 (home-page "https://bioconductor.org/packages/a4Classif/")
3272 (synopsis "Automated Affymetrix array analysis classification package")
3274 "This is the classification package for the automated analysis of
3275 Affymetrix arrays.")
3276 (license license:gpl3)))
3278 (define-public r-a4preproc
3280 (name "r-a4preproc")
3285 (uri (bioconductor-uri "a4Preproc" version))
3288 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3289 (properties `((upstream-name . "a4Preproc")))
3290 (build-system r-build-system)
3292 `(("r-annotationdbi" ,r-annotationdbi)))
3293 (home-page "https://bioconductor.org/packages/a4Preproc/")
3294 (synopsis "Automated Affymetrix array analysis preprocessing package")
3296 "This is a package for the automated analysis of Affymetrix arrays. It
3297 is used for preprocessing the arrays.")
3298 (license license:gpl3)))
3300 (define-public r-a4reporting
3302 (name "r-a4reporting")
3307 (uri (bioconductor-uri "a4Reporting" version))
3310 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3311 (properties `((upstream-name . "a4Reporting")))
3312 (build-system r-build-system)
3314 `(("r-annaffy" ,r-annaffy)
3315 ("r-xtable" ,r-xtable)))
3316 (home-page "https://bioconductor.org/packages/a4Reporting/")
3317 (synopsis "Automated Affymetrix array analysis reporting package")
3319 "This is a package for the automated analysis of Affymetrix arrays. It
3320 provides reporting features.")
3321 (license license:gpl3)))
3323 (define-public r-a4base
3330 (uri (bioconductor-uri "a4Base" version))
3333 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3334 (properties `((upstream-name . "a4Base")))
3335 (build-system r-build-system)
3337 `(("r-a4core" ,r-a4core)
3338 ("r-a4preproc" ,r-a4preproc)
3339 ("r-annaffy" ,r-annaffy)
3340 ("r-annotationdbi" ,r-annotationdbi)
3341 ("r-biobase" ,r-biobase)
3342 ("r-genefilter" ,r-genefilter)
3343 ("r-glmnet" ,r-glmnet)
3344 ("r-gplots" ,r-gplots)
3345 ("r-limma" ,r-limma)
3347 ("r-multtest" ,r-multtest)))
3348 (home-page "https://bioconductor.org/packages/a4Base/")
3349 (synopsis "Automated Affymetrix array analysis base package")
3351 "This package provides basic features for the automated analysis of
3352 Affymetrix arrays.")
3353 (license license:gpl3)))
3362 (uri (bioconductor-uri "a4" version))
3365 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3366 (build-system r-build-system)
3368 `(("r-a4base" ,r-a4base)
3369 ("r-a4classif" ,r-a4classif)
3370 ("r-a4core" ,r-a4core)
3371 ("r-a4preproc" ,r-a4preproc)
3372 ("r-a4reporting" ,r-a4reporting)))
3373 (home-page "https://bioconductor.org/packages/a4/")
3374 (synopsis "Automated Affymetrix array analysis umbrella package")
3376 "This package provides a software suite for the automated analysis of
3377 Affymetrix arrays.")
3378 (license license:gpl3)))
3380 (define-public r-abseqr
3387 (uri (bioconductor-uri "abseqR" version))
3390 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3391 (properties `((upstream-name . "abseqR")))
3392 (build-system r-build-system)
3394 `(("pandoc" ,ghc-pandoc)))
3396 `(("r-biocparallel" ,r-biocparallel)
3397 ("r-biocstyle" ,r-biocstyle)
3398 ("r-circlize" ,r-circlize)
3399 ("r-flexdashboard" ,r-flexdashboard)
3400 ("r-ggcorrplot" ,r-ggcorrplot)
3401 ("r-ggdendro" ,r-ggdendro)
3402 ("r-ggplot2" ,r-ggplot2)
3403 ("r-gridextra" ,r-gridextra)
3404 ("r-knitr" ,r-knitr)
3405 ("r-plotly" ,r-plotly)
3408 ("r-rcolorbrewer" ,r-rcolorbrewer)
3409 ("r-reshape2" ,r-reshape2)
3410 ("r-rmarkdown" ,r-rmarkdown)
3411 ("r-stringr" ,r-stringr)
3412 ("r-vegan" ,r-vegan)
3413 ("r-venndiagram" ,r-venndiagram)))
3414 (home-page "https://github.com/malhamdoosh/abseqR")
3415 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3417 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3418 sequencing datasets generated from antibody libraries and abseqR is one of its
3419 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3420 capabilities and allows them to generate interactive HTML reports for the
3421 convenience of viewing and sharing with other researchers. Additionally,
3422 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3423 further downstream analysis on its output.")
3424 (license license:gpl3)))
3426 (define-public r-bacon
3433 (uri (bioconductor-uri "bacon" version))
3436 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3437 (build-system r-build-system)
3439 `(("r-biocparallel" ,r-biocparallel)
3440 ("r-ellipse" ,r-ellipse)
3441 ("r-ggplot2" ,r-ggplot2)))
3442 (home-page "https://bioconductor.org/packages/bacon/")
3443 (synopsis "Controlling bias and inflation in association studies")
3445 "Bacon can be used to remove inflation and bias often observed in
3446 epigenome- and transcriptome-wide association studies. To this end bacon
3447 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3448 fitting a three-component normal mixture on z-scores.")
3449 (license license:gpl2+)))
3451 (define-public r-rgadem
3458 (uri (bioconductor-uri "rGADEM" version))
3461 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3462 (properties `((upstream-name . "rGADEM")))
3463 (build-system r-build-system)
3465 `(("r-biostrings" ,r-biostrings)
3466 ("r-bsgenome" ,r-bsgenome)
3467 ("r-iranges" ,r-iranges)
3468 ("r-seqlogo" ,r-seqlogo)))
3469 (home-page "https://bioconductor.org/packages/rGADEM/")
3470 (synopsis "De novo sequence motif discovery")
3472 "rGADEM is an efficient de novo motif discovery tool for large-scale
3473 genomic sequence data.")
3474 (license license:artistic2.0)))
3476 (define-public r-motiv
3483 (uri (bioconductor-uri "MotIV" version))
3486 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3487 (properties `((upstream-name . "MotIV")))
3488 (build-system r-build-system)
3492 `(("r-biocgenerics" ,r-biocgenerics)
3493 ("r-biostrings" ,r-biostrings)
3494 ("r-iranges" ,r-iranges)
3495 ("r-lattice" ,r-lattice)
3496 ("r-rgadem" ,r-rgadem)
3497 ("r-s4vectors" ,r-s4vectors)))
3498 (home-page "https://bioconductor.org/packages/MotIV/")
3499 (synopsis "Motif identification and validation")
3501 "This package is used for the identification and validation of sequence
3502 motifs. It makes use of STAMP for comparing a set of motifs to a given
3503 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3504 distributions, modules and filter motifs.")
3505 (license license:gpl2)))
3507 (define-public r-motifstack
3509 (name "r-motifstack")
3514 (uri (bioconductor-uri "motifStack" version))
3517 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3518 (properties `((upstream-name . "motifStack")))
3519 (build-system r-build-system)
3521 `(("r-ade4" ,r-ade4)
3522 ("r-biostrings" ,r-biostrings)
3523 ("r-grimport2" ,r-grimport2)
3524 ("r-htmlwidgets" ,r-htmlwidgets)
3525 ("r-motiv" ,r-motiv)
3526 ("r-scales" ,r-scales)
3528 (home-page "https://bioconductor.org/packages/motifStack/")
3529 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3531 "The motifStack package is designed for graphic representation of
3532 multiple motifs with different similarity scores. It works with both DNA/RNA
3533 sequence motifs and amino acid sequence motifs. In addition, it provides the
3534 flexibility for users to customize the graphic parameters such as the font
3535 type and symbol colors.")
3536 (license license:gpl2+)))
3538 (define-public r-genomicscores
3540 (name "r-genomicscores")
3545 (uri (bioconductor-uri "GenomicScores" version))
3548 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3549 (properties `((upstream-name . "GenomicScores")))
3550 (build-system r-build-system)
3552 `(("r-annotationhub" ,r-annotationhub)
3553 ("r-biobase" ,r-biobase)
3554 ("r-biocgenerics" ,r-biocgenerics)
3555 ("r-biostrings" ,r-biostrings)
3556 ("r-bsgenome" ,r-bsgenome)
3557 ("r-genomeinfodb" ,r-genomeinfodb)
3558 ("r-genomicranges" ,r-genomicranges)
3559 ("r-iranges" ,r-iranges)
3560 ("r-s4vectors" ,r-s4vectors)
3562 (home-page "https://github.com/rcastelo/GenomicScores/")
3563 (synopsis "Work with genome-wide position-specific scores")
3565 "This package provides infrastructure to store and access genome-wide
3566 position-specific scores within R and Bioconductor.")
3567 (license license:artistic2.0)))
3569 (define-public r-atacseqqc
3571 (name "r-atacseqqc")
3576 (uri (bioconductor-uri "ATACseqQC" version))
3579 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3580 (properties `((upstream-name . "ATACseqQC")))
3581 (build-system r-build-system)
3583 `(("r-biocgenerics" ,r-biocgenerics)
3584 ("r-biostrings" ,r-biostrings)
3585 ("r-bsgenome" ,r-bsgenome)
3586 ("r-chippeakanno" ,r-chippeakanno)
3587 ("r-edger" ,r-edger)
3588 ("r-genomeinfodb" ,r-genomeinfodb)
3589 ("r-genomicalignments" ,r-genomicalignments)
3590 ("r-genomicranges" ,r-genomicranges)
3591 ("r-genomicscores" ,r-genomicscores)
3592 ("r-iranges" ,r-iranges)
3593 ("r-kernsmooth" ,r-kernsmooth)
3594 ("r-limma" ,r-limma)
3595 ("r-motifstack" ,r-motifstack)
3596 ("r-preseqr" ,r-preseqr)
3597 ("r-randomforest" ,r-randomforest)
3598 ("r-rsamtools" ,r-rsamtools)
3599 ("r-rtracklayer" ,r-rtracklayer)
3600 ("r-s4vectors" ,r-s4vectors)))
3601 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3602 (synopsis "ATAC-seq quality control")
3604 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3605 sequencing, is a rapid and sensitive method for chromatin accessibility
3606 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3607 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3608 assess whether their ATAC-seq experiment is successful. It includes
3609 diagnostic plots of fragment size distribution, proportion of mitochondria
3610 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3612 (license license:gpl2+)))
3614 (define-public r-gofuncr
3621 (uri (bioconductor-uri "GOfuncR" version))
3624 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3625 (properties `((upstream-name . "GOfuncR")))
3626 (build-system r-build-system)
3628 `(("r-annotationdbi" ,r-annotationdbi)
3629 ("r-genomicranges" ,r-genomicranges)
3630 ("r-gtools" ,r-gtools)
3631 ("r-iranges" ,r-iranges)
3632 ("r-mapplots" ,r-mapplots)
3634 ("r-vioplot" ,r-vioplot)))
3635 (home-page "https://bioconductor.org/packages/GOfuncR/")
3636 (synopsis "Gene ontology enrichment using FUNC")
3638 "GOfuncR performs a gene ontology enrichment analysis based on the
3639 ontology enrichment software FUNC. GO-annotations are obtained from
3640 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3641 included in the package and updated regularly. GOfuncR provides the standard
3642 candidate vs background enrichment analysis using the hypergeometric test, as
3643 well as three additional tests:
3646 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3647 @item a binomial test that is used when genes are associated with two counts,
3649 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3650 associated with four counts.
3653 To correct for multiple testing and interdependency of the tests, family-wise
3654 error rates are computed based on random permutations of the gene-associated
3655 variables. GOfuncR also provides tools for exploring the ontology graph and
3656 the annotations, and options to take gene-length or spatial clustering of
3657 genes into account. It is also possible to provide custom gene coordinates,
3658 annotations and ontologies.")
3659 (license license:gpl2+)))
3661 (define-public r-abaenrichment
3663 (name "r-abaenrichment")
3668 (uri (bioconductor-uri "ABAEnrichment" version))
3671 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
3672 (properties `((upstream-name . "ABAEnrichment")))
3673 (build-system r-build-system)
3675 `(("r-abadata" ,r-abadata)
3676 ("r-data-table" ,r-data-table)
3677 ("r-gofuncr" ,r-gofuncr)
3678 ("r-gplots" ,r-gplots)
3679 ("r-gtools" ,r-gtools)
3680 ("r-rcpp" ,r-rcpp)))
3681 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3682 (synopsis "Gene expression enrichment in human brain regions")
3684 "The package ABAEnrichment is designed to test for enrichment of user
3685 defined candidate genes in the set of expressed genes in different human brain
3686 regions. The core function @code{aba_enrich} integrates the expression of the
3687 candidate gene set (averaged across donors) and the structural information of
3688 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3689 (license license:gpl2+)))
3691 (define-public r-annotationfuncs
3693 (name "r-annotationfuncs")
3698 (uri (bioconductor-uri "AnnotationFuncs" version))
3701 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3703 `((upstream-name . "AnnotationFuncs")))
3704 (build-system r-build-system)
3706 `(("r-annotationdbi" ,r-annotationdbi)
3708 (home-page "https://www.iysik.com/r/annotationfuncs")
3709 (synopsis "Annotation translation functions")
3711 "This package provides functions for handling translating between
3712 different identifieres using the Biocore Data Team data-packages (e.g.
3713 @code{org.Bt.eg.db}).")
3714 (license license:gpl2)))
3716 (define-public r-annotationtools
3718 (name "r-annotationtools")
3723 (uri (bioconductor-uri "annotationTools" version))
3726 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3728 `((upstream-name . "annotationTools")))
3729 (build-system r-build-system)
3730 (propagated-inputs `(("r-biobase" ,r-biobase)))
3731 (home-page "https://bioconductor.org/packages/annotationTools/")
3732 (synopsis "Annotate microarrays and perform gene expression analyses")
3734 "This package provides functions to annotate microarrays, find orthologs,
3735 and integrate heterogeneous gene expression profiles using annotation and
3736 other molecular biology information available as flat file database (plain
3738 ;; Any version of the GPL.
3739 (license (list license:gpl2+))))
3741 (define-public r-allelicimbalance
3743 (name "r-allelicimbalance")
3748 (uri (bioconductor-uri "AllelicImbalance" version))
3751 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3753 `((upstream-name . "AllelicImbalance")))
3754 (build-system r-build-system)
3756 `(("r-annotationdbi" ,r-annotationdbi)
3757 ("r-biocgenerics" ,r-biocgenerics)
3758 ("r-biostrings" ,r-biostrings)
3759 ("r-bsgenome" ,r-bsgenome)
3760 ("r-genomeinfodb" ,r-genomeinfodb)
3761 ("r-genomicalignments" ,r-genomicalignments)
3762 ("r-genomicfeatures" ,r-genomicfeatures)
3763 ("r-genomicranges" ,r-genomicranges)
3764 ("r-gridextra" ,r-gridextra)
3766 ("r-iranges" ,r-iranges)
3767 ("r-lattice" ,r-lattice)
3768 ("r-latticeextra" ,r-latticeextra)
3770 ("r-rsamtools" ,r-rsamtools)
3771 ("r-s4vectors" ,r-s4vectors)
3772 ("r-seqinr" ,r-seqinr)
3773 ("r-summarizedexperiment" ,r-summarizedexperiment)
3774 ("r-variantannotation" ,r-variantannotation)))
3775 (home-page "https://github.com/pappewaio/AllelicImbalance")
3776 (synopsis "Investigate allele-specific expression")
3778 "This package provides a framework for allele-specific expression
3779 investigation using RNA-seq data.")
3780 (license license:gpl3)))
3782 (define-public r-aucell
3789 (uri (bioconductor-uri "AUCell" version))
3792 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
3793 (properties `((upstream-name . "AUCell")))
3794 (build-system r-build-system)
3796 `(("r-data-table" ,r-data-table)
3797 ("r-gseabase" ,r-gseabase)
3798 ("r-mixtools" ,r-mixtools)
3799 ("r-r-utils" ,r-r-utils)
3800 ("r-shiny" ,r-shiny)
3801 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3802 (home-page "https://bioconductor.org/packages/AUCell/")
3803 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
3805 "AUCell allows to identify cells with active gene sets (e.g. signatures,
3806 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
3807 Under the Curve} (AUC) to calculate whether a critical subset of the input
3808 gene set is enriched within the expressed genes for each cell. The
3809 distribution of AUC scores across all the cells allows exploring the relative
3810 expression of the signature. Since the scoring method is ranking-based,
3811 AUCell is independent of the gene expression units and the normalization
3812 procedure. In addition, since the cells are evaluated individually, it can
3813 easily be applied to bigger datasets, subsetting the expression matrix if
3815 (license license:gpl3)))
3817 (define-public r-ebimage
3824 (uri (bioconductor-uri "EBImage" version))
3827 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
3828 (properties `((upstream-name . "EBImage")))
3829 (build-system r-build-system)
3831 `(("r-abind" ,r-abind)
3832 ("r-biocgenerics" ,r-biocgenerics)
3833 ("r-fftwtools" ,r-fftwtools)
3834 ("r-htmltools" ,r-htmltools)
3835 ("r-htmlwidgets" ,r-htmlwidgets)
3837 ("r-locfit" ,r-locfit)
3839 ("r-rcurl" ,r-rcurl)
3840 ("r-tiff" ,r-tiff)))
3842 `(("r-knitr" ,r-knitr))) ; for vignettes
3843 (home-page "https://github.com/aoles/EBImage")
3844 (synopsis "Image processing and analysis toolbox for R")
3846 "EBImage provides general purpose functionality for image processing and
3847 analysis. In the context of (high-throughput) microscopy-based cellular
3848 assays, EBImage offers tools to segment cells and extract quantitative
3849 cellular descriptors. This allows the automation of such tasks using the R
3850 programming language and facilitates the use of other tools in the R
3851 environment for signal processing, statistical modeling, machine learning and
3852 visualization with image data.")
3853 ;; Any version of the LGPL.
3854 (license license:lgpl2.1+)))
3856 (define-public r-yamss
3863 (uri (bioconductor-uri "yamss" version))
3866 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
3867 (build-system r-build-system)
3869 `(("r-biocgenerics" ,r-biocgenerics)
3870 ("r-data-table" ,r-data-table)
3871 ("r-ebimage" ,r-ebimage)
3872 ("r-iranges" ,r-iranges)
3873 ("r-limma" ,r-limma)
3874 ("r-matrix" ,r-matrix)
3876 ("r-s4vectors" ,r-s4vectors)
3877 ("r-summarizedexperiment"
3878 ,r-summarizedexperiment)))
3879 (home-page "https://github.com/hansenlab/yamss")
3880 (synopsis "Tools for high-throughput metabolomics")
3882 "This package provides tools to analyze and visualize high-throughput
3883 metabolomics data acquired using chromatography-mass spectrometry. These tools
3884 preprocess data in a way that enables reliable and powerful differential
3886 (license license:artistic2.0)))
3888 (define-public r-gtrellis
3895 (uri (bioconductor-uri "gtrellis" version))
3898 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
3899 (build-system r-build-system)
3901 `(("r-circlize" ,r-circlize)
3902 ("r-genomicranges" ,r-genomicranges)
3903 ("r-getoptlong" ,r-getoptlong)
3904 ("r-iranges" ,r-iranges)))
3905 (home-page "https://github.com/jokergoo/gtrellis")
3906 (synopsis "Genome level Trellis layout")
3908 "Genome level Trellis graph visualizes genomic data conditioned by
3909 genomic categories (e.g. chromosomes). For each genomic category, multiple
3910 dimensional data which are represented as tracks describe different features
3911 from different aspects. This package provides high flexibility to arrange
3912 genomic categories and to add self-defined graphics in the plot.")
3913 (license license:expat)))
3915 (define-public r-somaticsignatures
3917 (name "r-somaticsignatures")
3922 (uri (bioconductor-uri "SomaticSignatures" version))
3925 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
3927 `((upstream-name . "SomaticSignatures")))
3928 (build-system r-build-system)
3930 `(("r-biobase" ,r-biobase)
3931 ("r-biostrings" ,r-biostrings)
3932 ("r-genomeinfodb" ,r-genomeinfodb)
3933 ("r-genomicranges" ,r-genomicranges)
3934 ("r-ggbio" ,r-ggbio)
3935 ("r-ggplot2" ,r-ggplot2)
3936 ("r-iranges" ,r-iranges)
3938 ("r-pcamethods" ,r-pcamethods)
3939 ("r-proxy" ,r-proxy)
3940 ("r-reshape2" ,r-reshape2)
3941 ("r-s4vectors" ,r-s4vectors)
3942 ("r-variantannotation" ,r-variantannotation)))
3943 (home-page "https://github.com/juliangehring/SomaticSignatures")
3944 (synopsis "Somatic signatures")
3946 "This package identifies mutational signatures of @dfn{single nucleotide
3947 variants} (SNVs). It provides a infrastructure related to the methodology
3948 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
3949 decomposition algorithms.")
3950 (license license:expat)))
3952 (define-public r-yapsa
3959 (uri (bioconductor-uri "YAPSA" version))
3962 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
3963 (properties `((upstream-name . "YAPSA")))
3964 (build-system r-build-system)
3966 `(("r-circlize" ,r-circlize)
3967 ("r-complexheatmap" ,r-complexheatmap)
3968 ("r-corrplot" ,r-corrplot)
3969 ("r-dendextend" ,r-dendextend)
3970 ("r-genomeinfodb" ,r-genomeinfodb)
3971 ("r-genomicranges" ,r-genomicranges)
3972 ("r-getoptlong" ,r-getoptlong)
3973 ("r-ggplot2" ,r-ggplot2)
3974 ("r-gridextra" ,r-gridextra)
3975 ("r-gtrellis" ,r-gtrellis)
3976 ("r-keggrest" ,r-keggrest)
3978 ("r-pmcmr" ,r-pmcmr)
3979 ("r-reshape2" ,r-reshape2)
3980 ("r-somaticsignatures" ,r-somaticsignatures)
3981 ("r-variantannotation" ,r-variantannotation)))
3982 (home-page "https://bioconductor.org/packages/YAPSA/")
3983 (synopsis "Yet another package for signature analysis")
3985 "This package provides functions and routines useful in the analysis of
3986 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
3987 functions to perform a signature analysis with known signatures and a
3988 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
3990 (license license:gpl3)))
3992 (define-public r-gcrma
3999 (uri (bioconductor-uri "gcrma" version))
4002 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4003 (build-system r-build-system)
4005 `(("r-affy" ,r-affy)
4006 ("r-affyio" ,r-affyio)
4007 ("r-biobase" ,r-biobase)
4008 ("r-biocmanager" ,r-biocmanager)
4009 ("r-biostrings" ,r-biostrings)
4010 ("r-xvector" ,r-xvector)))
4011 (home-page "https://bioconductor.org/packages/gcrma/")
4012 (synopsis "Background adjustment using sequence information")
4014 "Gcrma adjusts for background intensities in Affymetrix array data which
4015 include optical noise and @dfn{non-specific binding} (NSB). The main function
4016 @code{gcrma} converts background adjusted probe intensities to expression
4017 measures using the same normalization and summarization methods as a
4018 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4019 to estimate probe affinity to NSB. The sequence information is summarized in
4020 a more complex way than the simple GC content. Instead, the base types (A, T,
4021 G or C) at each position along the probe determine the affinity of each probe.
4022 The parameters of the position-specific base contributions to the probe
4023 affinity is estimated in an NSB experiment in which only NSB but no
4024 gene-specific bidning is expected.")
4025 ;; Any version of the LGPL
4026 (license license:lgpl2.1+)))
4028 (define-public r-simpleaffy
4030 (name "r-simpleaffy")
4035 (uri (bioconductor-uri "simpleaffy" version))
4038 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4039 (build-system r-build-system)
4041 `(("r-affy" ,r-affy)
4042 ("r-biobase" ,r-biobase)
4043 ("r-biocgenerics" ,r-biocgenerics)
4044 ("r-gcrma" ,r-gcrma)
4045 ("r-genefilter" ,r-genefilter)))
4046 (home-page "https://bioconductor.org/packages/simpleaffy/")
4047 (synopsis "Very simple high level analysis of Affymetrix data")
4049 "This package provides high level functions for reading Affy @file{.CEL}
4050 files, phenotypic data, and then computing simple things with it, such as
4051 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4052 library. It also has some basic scatter plot functions and mechanisms for
4053 generating high resolution journal figures.")
4054 (license license:gpl2+)))
4056 (define-public r-yaqcaffy
4063 (uri (bioconductor-uri "yaqcaffy" version))
4066 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4067 (build-system r-build-system)
4069 `(("r-simpleaffy" ,r-simpleaffy)))
4070 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4071 (synopsis "Affymetrix quality control and reproducibility analysis")
4073 "This is a package that can be used for quality control of Affymetrix
4074 GeneChip expression data and reproducibility analysis of human whole genome
4075 chips with the MAQC reference datasets.")
4076 (license license:artistic2.0)))
4078 (define-public r-quantro
4085 (uri (bioconductor-uri "quantro" version))
4088 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4089 (build-system r-build-system)
4091 `(("r-biobase" ,r-biobase)
4092 ("r-doparallel" ,r-doparallel)
4093 ("r-foreach" ,r-foreach)
4094 ("r-ggplot2" ,r-ggplot2)
4095 ("r-iterators" ,r-iterators)
4096 ("r-minfi" ,r-minfi)
4097 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4098 (home-page "https://bioconductor.org/packages/quantro/")
4099 (synopsis "Test for when to use quantile normalization")
4101 "This package provides a data-driven test for the assumptions of quantile
4102 normalization using raw data such as objects that inherit eSets (e.g.
4103 ExpressionSet, MethylSet). Group level information about each sample (such as
4104 Tumor / Normal status) must also be provided because the test assesses if
4105 there are global differences in the distributions between the user-defined
4107 (license license:gpl3+)))
4109 (define-public r-yarn
4116 (uri (bioconductor-uri "yarn" version))
4119 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4120 (build-system r-build-system)
4122 `(("r-biobase" ,r-biobase)
4123 ("r-biomart" ,r-biomart)
4124 ("r-downloader" ,r-downloader)
4125 ("r-edger" ,r-edger)
4126 ("r-gplots" ,r-gplots)
4127 ("r-limma" ,r-limma)
4128 ("r-matrixstats" ,r-matrixstats)
4129 ("r-preprocesscore" ,r-preprocesscore)
4130 ("r-quantro" ,r-quantro)
4131 ("r-rcolorbrewer" ,r-rcolorbrewer)
4132 ("r-readr" ,r-readr)))
4133 (home-page "https://bioconductor.org/packages/yarn/")
4134 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4136 "Expedite large RNA-Seq analyses using a combination of previously
4137 developed tools. YARN is meant to make it easier for the user in performing
4138 basic mis-annotation quality control, filtering, and condition-aware
4139 normalization. YARN leverages many Bioconductor tools and statistical
4140 techniques to account for the large heterogeneity and sparsity found in very
4141 large RNA-seq experiments.")
4142 (license license:artistic2.0)))
4144 (define-public r-roar
4151 (uri (bioconductor-uri "roar" version))
4154 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4155 (build-system r-build-system)
4157 `(("r-biocgenerics" ,r-biocgenerics)
4158 ("r-genomeinfodb" ,r-genomeinfodb)
4159 ("r-genomicalignments" ,r-genomicalignments)
4160 ("r-genomicranges" ,r-genomicranges)
4161 ("r-iranges" ,r-iranges)
4162 ("r-rtracklayer" ,r-rtracklayer)
4163 ("r-s4vectors" ,r-s4vectors)
4164 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4165 (home-page "https://github.com/vodkatad/roar/")
4166 (synopsis "Identify differential APA usage from RNA-seq alignments")
4168 "This package provides tools for identifying preferential usage of APA
4169 sites, comparing two biological conditions, starting from known alternative
4170 sites and alignments obtained from standard RNA-seq experiments.")
4171 (license license:gpl3)))
4173 (define-public r-xbseq
4180 (uri (bioconductor-uri "XBSeq" version))
4183 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4184 (properties `((upstream-name . "XBSeq")))
4185 (build-system r-build-system)
4187 `(("r-biobase" ,r-biobase)
4188 ("r-deseq2" ,r-deseq2)
4189 ("r-dplyr" ,r-dplyr)
4190 ("r-ggplot2" ,r-ggplot2)
4191 ("r-locfit" ,r-locfit)
4192 ("r-magrittr" ,r-magrittr)
4193 ("r-matrixstats" ,r-matrixstats)
4194 ("r-pracma" ,r-pracma)
4195 ("r-roar" ,r-roar)))
4196 (home-page "https://github.com/Liuy12/XBSeq")
4197 (synopsis "Test for differential expression for RNA-seq data")
4199 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4200 expression} (DE), where a statistical model was established based on the
4201 assumption that observed signals are the convolution of true expression
4202 signals and sequencing noises. The mapped reads in non-exonic regions are
4203 considered as sequencing noises, which follows a Poisson distribution. Given
4204 measurable observed signal and background noise from RNA-seq data, true
4205 expression signals, assuming governed by the negative binomial distribution,
4206 can be delineated and thus the accurate detection of differential expressed
4208 (license license:gpl3+)))
4210 (define-public r-massspecwavelet
4212 (name "r-massspecwavelet")
4217 (uri (bioconductor-uri "MassSpecWavelet" version))
4220 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4222 `((upstream-name . "MassSpecWavelet")))
4223 (build-system r-build-system)
4225 `(("r-waveslim" ,r-waveslim)))
4226 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4227 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4229 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4230 data mainly through the use of wavelet transforms. It supports peak detection
4231 based on @dfn{Continuous Wavelet Transform} (CWT).")
4232 (license license:lgpl2.0+)))
4234 (define-public r-xcms
4241 (uri (bioconductor-uri "xcms" version))
4244 "06vhqvvzlkc5bslswagrapmn5ag3x84xg9gxk0fhlmgwapqwki1g"))))
4245 (build-system r-build-system)
4247 `(("r-biobase" ,r-biobase)
4248 ("r-biocgenerics" ,r-biocgenerics)
4249 ("r-biocparallel" ,r-biocparallel)
4250 ("r-lattice" ,r-lattice)
4251 ("r-massspecwavelet" ,r-massspecwavelet)
4252 ("r-msnbase" ,r-msnbase)
4253 ("r-multtest" ,r-multtest)
4256 ("r-protgenerics" ,r-protgenerics)
4258 ("r-rcolorbrewer" ,r-rcolorbrewer)
4259 ("r-robustbase" ,r-robustbase)
4260 ("r-s4vectors" ,r-s4vectors)))
4261 (home-page "https://bioconductor.org/packages/xcms/")
4262 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4264 "This package provides a framework for processing and visualization of
4265 chromatographically separated and single-spectra mass spectral data. It
4266 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4267 data for high-throughput, untargeted analyte profiling.")
4268 (license license:gpl2+)))
4270 (define-public r-wrench
4277 (uri (bioconductor-uri "Wrench" version))
4280 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4281 (properties `((upstream-name . "Wrench")))
4282 (build-system r-build-system)
4284 `(("r-limma" ,r-limma)
4285 ("r-locfit" ,r-locfit)
4286 ("r-matrixstats" ,r-matrixstats)))
4287 (home-page "https://github.com/HCBravoLab/Wrench")
4288 (synopsis "Wrench normalization for sparse count data")
4290 "Wrench is a package for normalization sparse genomic count data, like
4291 that arising from 16s metagenomic surveys.")
4292 (license license:artistic2.0)))
4294 (define-public r-wiggleplotr
4296 (name "r-wiggleplotr")
4301 (uri (bioconductor-uri "wiggleplotr" version))
4304 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4305 (build-system r-build-system)
4307 `(("r-assertthat" ,r-assertthat)
4308 ("r-cowplot" ,r-cowplot)
4309 ("r-dplyr" ,r-dplyr)
4310 ("r-genomeinfodb" ,r-genomeinfodb)
4311 ("r-genomicranges" ,r-genomicranges)
4312 ("r-ggplot2" ,r-ggplot2)
4313 ("r-iranges" ,r-iranges)
4314 ("r-purrr" ,r-purrr)
4315 ("r-rtracklayer" ,r-rtracklayer)
4316 ("r-s4vectors" ,r-s4vectors)))
4317 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4318 (synopsis "Make read coverage plots from BigWig files")
4320 "This package provides tools to visualize read coverage from sequencing
4321 experiments together with genomic annotations (genes, transcripts, peaks).
4322 Introns of long transcripts can be rescaled to a fixed length for better
4323 visualization of exonic read coverage.")
4324 (license license:asl2.0)))
4326 (define-public r-widgettools
4328 (name "r-widgettools")
4333 (uri (bioconductor-uri "widgetTools" version))
4336 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4337 (properties `((upstream-name . "widgetTools")))
4338 (build-system r-build-system)
4339 (home-page "https://bioconductor.org/packages/widgetTools/")
4340 (synopsis "Tools for creating interactive tcltk widgets")
4342 "This package contains tools to support the construction of tcltk
4344 ;; Any version of the LGPL.
4345 (license license:lgpl3+)))
4347 (define-public r-webbioc
4354 (uri (bioconductor-uri "webbioc" version))
4357 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4358 (build-system r-build-system)
4360 `(("netpbm" ,netpbm)
4363 `(("r-affy" ,r-affy)
4364 ("r-annaffy" ,r-annaffy)
4365 ("r-biobase" ,r-biobase)
4366 ("r-biocmanager" ,r-biocmanager)
4367 ("r-gcrma" ,r-gcrma)
4368 ("r-multtest" ,r-multtest)
4369 ("r-qvalue" ,r-qvalue)
4371 (home-page "https://www.bioconductor.org/")
4372 (synopsis "Bioconductor web interface")
4374 "This package provides an integrated web interface for doing microarray
4375 analysis using several of the Bioconductor packages. It is intended to be
4376 deployed as a centralized bioinformatics resource for use by many users.
4377 Currently only Affymetrix oligonucleotide analysis is supported.")
4378 (license license:gpl2+)))
4380 (define-public r-zfpkm
4387 (uri (bioconductor-uri "zFPKM" version))
4390 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4391 (properties `((upstream-name . "zFPKM")))
4392 (build-system r-build-system)
4394 `(("r-checkmate" ,r-checkmate)
4395 ("r-dplyr" ,r-dplyr)
4396 ("r-ggplot2" ,r-ggplot2)
4397 ("r-summarizedexperiment" ,r-summarizedexperiment)
4398 ("r-tidyr" ,r-tidyr)))
4399 (home-page "https://github.com/ronammar/zFPKM/")
4400 (synopsis "Functions to facilitate zFPKM transformations")
4402 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4403 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4405 (license license:gpl3)))
4407 (define-public r-rbowtie2
4414 (uri (bioconductor-uri "Rbowtie2" version))
4417 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4418 (properties `((upstream-name . "Rbowtie2")))
4419 (build-system r-build-system)
4422 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4423 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4425 "This package provides an R wrapper of the popular @code{bowtie2}
4426 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4427 rapid adapter trimming, identification, and read merging.")
4428 (license license:gpl3+)))
4430 (define-public r-progeny
4437 (uri (bioconductor-uri "progeny" version))
4440 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4441 (build-system r-build-system)
4442 (propagated-inputs `(("r-biobase" ,r-biobase)))
4443 (home-page "https://github.com/saezlab/progeny")
4444 (synopsis "Pathway responsive gene activity inference")
4446 "This package provides a function to infer pathway activity from gene
4447 expression. It contains the linear model inferred in the publication
4448 \"Perturbation-response genes reveal signaling footprints in cancer gene
4450 (license license:asl2.0)))
4452 (define-public r-arrmnormalization
4454 (name "r-arrmnormalization")
4459 (uri (bioconductor-uri "ARRmNormalization" version))
4462 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4464 `((upstream-name . "ARRmNormalization")))
4465 (build-system r-build-system)
4466 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4467 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4468 (synopsis "Adaptive robust regression normalization for methylation data")
4470 "This is a package to perform the @dfn{Adaptive Robust Regression
4471 method} (ARRm) for the normalization of methylation data from the Illumina
4472 Infinium HumanMethylation 450k assay.")
4473 (license license:artistic2.0)))
4475 (define-public r-biocfilecache
4477 (name "r-biocfilecache")
4482 (uri (bioconductor-uri "BiocFileCache" version))
4485 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4486 (properties `((upstream-name . "BiocFileCache")))
4487 (build-system r-build-system)
4489 `(("r-curl" ,r-curl)
4491 ("r-dbplyr" ,r-dbplyr)
4492 ("r-dplyr" ,r-dplyr)
4494 ("r-rappdirs" ,r-rappdirs)
4495 ("r-rsqlite" ,r-rsqlite)))
4496 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4497 (synopsis "Manage files across sessions")
4499 "This package creates a persistent on-disk cache of files that the user
4500 can add, update, and retrieve. It is useful for managing resources (such as
4501 custom Txdb objects) that are costly or difficult to create, web resources,
4502 and data files used across sessions.")
4503 (license license:artistic2.0)))
4505 (define-public r-iclusterplus
4507 (name "r-iclusterplus")
4512 (uri (bioconductor-uri "iClusterPlus" version))
4515 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4516 (properties `((upstream-name . "iClusterPlus")))
4517 (build-system r-build-system)
4518 (native-inputs `(("gfortran" ,gfortran)))
4519 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4520 (synopsis "Integrative clustering of multi-type genomic data")
4522 "iClusterPlus is developed for integrative clustering analysis of
4523 multi-type genomic data and is an enhanced version of iCluster proposed and
4524 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4525 from the experiments where biological samples (e.g. tumor samples) are
4526 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4527 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4528 on. In the iClusterPlus model, binary observations such as somatic mutation
4529 are modeled as Binomial processes; categorical observations such as copy
4530 number states are realizations of Multinomial random variables; counts are
4531 modeled as Poisson random processes; and continuous measures are modeled by
4532 Gaussian distributions.")
4533 (license license:gpl2+)))
4535 (define-public r-rbowtie
4542 (uri (bioconductor-uri "Rbowtie" version))
4545 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4546 (properties `((upstream-name . "Rbowtie")))
4547 (build-system r-build-system)
4550 (home-page "https://bioconductor.org/packages/Rbowtie/")
4551 (synopsis "R bowtie wrapper")
4553 "This package provides an R wrapper around the popular bowtie short read
4554 aligner and around SpliceMap, a de novo splice junction discovery and
4556 (license license:artistic2.0)))
4558 (define-public r-sgseq
4565 (uri (bioconductor-uri "SGSeq" version))
4568 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4569 (properties `((upstream-name . "SGSeq")))
4570 (build-system r-build-system)
4572 `(("r-annotationdbi" ,r-annotationdbi)
4573 ("r-biocgenerics" ,r-biocgenerics)
4574 ("r-biostrings" ,r-biostrings)
4575 ("r-genomeinfodb" ,r-genomeinfodb)
4576 ("r-genomicalignments" ,r-genomicalignments)
4577 ("r-genomicfeatures" ,r-genomicfeatures)
4578 ("r-genomicranges" ,r-genomicranges)
4579 ("r-igraph" ,r-igraph)
4580 ("r-iranges" ,r-iranges)
4581 ("r-rsamtools" ,r-rsamtools)
4582 ("r-rtracklayer" ,r-rtracklayer)
4583 ("r-runit" ,r-runit)
4584 ("r-s4vectors" ,r-s4vectors)
4585 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4586 (home-page "https://bioconductor.org/packages/SGSeq/")
4587 (synopsis "Splice event prediction and quantification from RNA-seq data")
4589 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4590 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4591 represented as a splice graph, which can be obtained from existing annotation
4592 or predicted from the mapped sequence reads. Splice events are identified
4593 from the graph and are quantified locally using structurally compatible reads
4594 at the start or end of each splice variant. The software includes functions
4595 for splice event prediction, quantification, visualization and
4597 (license license:artistic2.0)))
4599 (define-public r-rhisat2
4606 (uri (bioconductor-uri "Rhisat2" version))
4609 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4610 (properties `((upstream-name . "Rhisat2")))
4611 (build-system r-build-system)
4613 `(("which" ,which)))
4615 `(("r-genomicfeatures" ,r-genomicfeatures)
4616 ("r-genomicranges" ,r-genomicranges)
4617 ("r-sgseq" ,r-sgseq)))
4618 (home-page "https://github.com/fmicompbio/Rhisat2")
4619 (synopsis "R Wrapper for HISAT2 sequence aligner")
4621 "This package provides an R interface to the HISAT2 spliced short-read
4622 aligner by Kim et al. (2015). The package contains wrapper functions to
4623 create a genome index and to perform the read alignment to the generated
4625 (license license:gpl3)))
4627 (define-public r-quasr
4634 (uri (bioconductor-uri "QuasR" version))
4637 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4638 (properties `((upstream-name . "QuasR")))
4639 (build-system r-build-system)
4643 `(("r-annotationdbi" ,r-annotationdbi)
4644 ("r-biobase" ,r-biobase)
4645 ("r-biocgenerics" ,r-biocgenerics)
4646 ("r-biocmanager" ,r-biocmanager)
4647 ("r-biocparallel" ,r-biocparallel)
4648 ("r-biostrings" ,r-biostrings)
4649 ("r-bsgenome" ,r-bsgenome)
4650 ("r-genomeinfodb" ,r-genomeinfodb)
4651 ("r-genomicalignments" ,r-genomicalignments)
4652 ("r-genomicfeatures" ,r-genomicfeatures)
4653 ("r-genomicfiles" ,r-genomicfiles)
4654 ("r-genomicranges" ,r-genomicranges)
4655 ("r-iranges" ,r-iranges)
4656 ("r-rbowtie" ,r-rbowtie)
4657 ("r-rhisat2" ,r-rhisat2)
4658 ("r-rhtslib" ,r-rhtslib)
4659 ("r-rsamtools" ,r-rsamtools)
4660 ("r-rtracklayer" ,r-rtracklayer)
4661 ("r-s4vectors" ,r-s4vectors)
4662 ("r-shortread" ,r-shortread)))
4663 (home-page "https://bioconductor.org/packages/QuasR/")
4664 (synopsis "Quantify and annotate short reads in R")
4666 "This package provides a framework for the quantification and analysis of
4667 short genomic reads. It covers a complete workflow starting from raw sequence
4668 reads, over creation of alignments and quality control plots, to the
4669 quantification of genomic regions of interest.")
4670 (license license:gpl2)))
4672 (define-public r-rqc
4679 (uri (bioconductor-uri "Rqc" version))
4682 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4683 (properties `((upstream-name . "Rqc")))
4684 (build-system r-build-system)
4686 `(("r-biocgenerics" ,r-biocgenerics)
4687 ("r-biocparallel" ,r-biocparallel)
4688 ("r-biocstyle" ,r-biocstyle)
4689 ("r-biostrings" ,r-biostrings)
4690 ("r-biovizbase" ,r-biovizbase)
4691 ("r-genomicalignments" ,r-genomicalignments)
4692 ("r-genomicfiles" ,r-genomicfiles)
4693 ("r-ggplot2" ,r-ggplot2)
4694 ("r-iranges" ,r-iranges)
4695 ("r-knitr" ,r-knitr)
4696 ("r-markdown" ,r-markdown)
4699 ("r-reshape2" ,r-reshape2)
4700 ("r-rsamtools" ,r-rsamtools)
4701 ("r-s4vectors" ,r-s4vectors)
4702 ("r-shiny" ,r-shiny)
4703 ("r-shortread" ,r-shortread)))
4704 (home-page "https://github.com/labbcb/Rqc")
4705 (synopsis "Quality control tool for high-throughput sequencing data")
4707 "Rqc is an optimized tool designed for quality control and assessment of
4708 high-throughput sequencing data. It performs parallel processing of entire
4709 files and produces a report which contains a set of high-resolution
4711 (license license:gpl2+)))
4713 (define-public r-birewire
4720 (uri (bioconductor-uri "BiRewire" version))
4723 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
4724 (properties `((upstream-name . "BiRewire")))
4725 (build-system r-build-system)
4727 `(("r-igraph" ,r-igraph)
4728 ("r-matrix" ,r-matrix)
4730 ("r-tsne" ,r-tsne)))
4731 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
4732 (synopsis "Tools for randomization of bipartite graphs")
4734 "This package provides functions for bipartite network rewiring through N
4735 consecutive switching steps and for the computation of the minimal number of
4736 switching steps to be performed in order to maximise the dissimilarity with
4737 respect to the original network. It includes functions for the analysis of
4738 the introduced randomness across the switching steps and several other
4739 routines to analyse the resulting networks and their natural projections.")
4740 (license license:gpl3)))
4742 (define-public r-birta
4749 (uri (bioconductor-uri "birta" version))
4752 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
4753 (build-system r-build-system)
4755 `(("r-biobase" ,r-biobase)
4756 ("r-limma" ,r-limma)
4757 ("r-mass" ,r-mass)))
4758 (home-page "https://bioconductor.org/packages/birta")
4759 (synopsis "Bayesian inference of regulation of transcriptional activity")
4761 "Expression levels of mRNA molecules are regulated by different
4762 processes, comprising inhibition or activation by transcription factors and
4763 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
4764 Inference of Regulation of Transcriptional Activity) uses the regulatory
4765 networks of transcription factors and miRNAs together with mRNA and miRNA
4766 expression data to predict switches in regulatory activity between two
4767 conditions. A Bayesian network is used to model the regulatory structure and
4768 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
4769 (license license:gpl2+)))
4771 (define-public r-ropls
4778 (uri (bioconductor-uri "ropls" version))
4781 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
4782 (build-system r-build-system)
4783 (propagated-inputs `(("r-biobase" ,r-biobase)))
4785 `(("r-knitr" ,r-knitr))) ; for vignettes
4786 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
4787 (synopsis "Multivariate analysis and feature selection of omics data")
4789 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
4790 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
4791 regression, classification, and feature selection of omics data where the
4792 number of variables exceeds the number of samples and with multicollinearity
4793 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
4794 separately model the variation correlated (predictive) to the factor of
4795 interest and the uncorrelated (orthogonal) variation. While performing
4796 similarly to PLS, OPLS facilitates interpretation.
4798 This package provides imlementations of PCA, PLS, and OPLS for multivariate
4799 analysis and feature selection of omics data. In addition to scores, loadings
4800 and weights plots, the package provides metrics and graphics to determine the
4801 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
4802 validity of the model by permutation testing, detect outliers, and perform
4803 feature selection (e.g. with Variable Importance in Projection or regression
4805 (license license:cecill)))
4807 (define-public r-biosigner
4809 (name "r-biosigner")
4814 (uri (bioconductor-uri "biosigner" version))
4817 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
4818 (build-system r-build-system)
4820 `(("r-biobase" ,r-biobase)
4821 ("r-e1071" ,r-e1071)
4822 ("r-randomforest" ,r-randomforest)
4823 ("r-ropls" ,r-ropls)))
4825 `(("r-knitr" ,r-knitr)
4826 ("r-rmarkdown" ,r-rmarkdown)
4827 ("pandoc" ,ghc-pandoc)
4828 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
4829 (home-page "https://bioconductor.org/packages/biosigner/")
4830 (synopsis "Signature discovery from omics data")
4832 "Feature selection is critical in omics data analysis to extract
4833 restricted and meaningful molecular signatures from complex and high-dimension
4834 data, and to build robust classifiers. This package implements a method to
4835 assess the relevance of the variables for the prediction performances of the
4836 classifier. The approach can be run in parallel with the PLS-DA, Random
4837 Forest, and SVM binary classifiers. The signatures and the corresponding
4838 'restricted' models are returned, enabling future predictions on new
4840 (license license:cecill)))
4842 (define-public r-annotatr
4849 (uri (bioconductor-uri "annotatr" version))
4852 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
4853 (build-system r-build-system)
4855 `(("r-annotationdbi" ,r-annotationdbi)
4856 ("r-annotationhub" ,r-annotationhub)
4857 ("r-dplyr" ,r-dplyr)
4858 ("r-genomeinfodb" ,r-genomeinfodb)
4859 ("r-genomicfeatures" ,r-genomicfeatures)
4860 ("r-genomicranges" ,r-genomicranges)
4861 ("r-ggplot2" ,r-ggplot2)
4862 ("r-iranges" ,r-iranges)
4863 ("r-readr" ,r-readr)
4864 ("r-regioner" ,r-regioner)
4865 ("r-reshape2" ,r-reshape2)
4866 ("r-rtracklayer" ,r-rtracklayer)
4867 ("r-s4vectors" ,r-s4vectors)))
4868 (home-page "https://bioconductor.org/packages/annotatr/")
4869 (synopsis "Annotation of genomic regions to genomic annotations")
4871 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
4872 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
4873 to investigate the intersecting genomic annotations. Such annotations include
4874 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
4875 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
4876 enhancers. The annotatr package provides an easy way to summarize and
4877 visualize the intersection of genomic sites/regions with genomic
4879 (license license:gpl3)))
4881 (define-public r-rsubread
4888 (uri (bioconductor-uri "Rsubread" version))
4891 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
4892 (properties `((upstream-name . "Rsubread")))
4893 (build-system r-build-system)
4894 (inputs `(("zlib" ,zlib)))
4895 (home-page "https://bioconductor.org/packages/Rsubread/")
4896 (synopsis "Subread sequence alignment and counting for R")
4898 "This package provides tools for alignment, quantification and analysis
4899 of second and third generation sequencing data. It includes functionality for
4900 read mapping, read counting, SNP calling, structural variant detection and
4901 gene fusion discovery. It can be applied to all major sequencing techologies
4902 and to both short and long sequence reads.")
4903 (license license:gpl3)))
4905 (define-public r-flowutils
4907 (name "r-flowutils")
4912 (uri (bioconductor-uri "flowUtils" version))
4915 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
4916 (properties `((upstream-name . "flowUtils")))
4917 (build-system r-build-system)
4919 `(("r-biobase" ,r-biobase)
4920 ("r-corpcor" ,r-corpcor)
4921 ("r-flowcore" ,r-flowcore)
4922 ("r-graph" ,r-graph)
4923 ("r-runit" ,r-runit)
4925 (home-page "https://github.com/jspidlen/flowUtils")
4926 (synopsis "Utilities for flow cytometry")
4928 "This package provides utilities for flow cytometry data.")
4929 (license license:artistic2.0)))
4931 (define-public r-consensusclusterplus
4933 (name "r-consensusclusterplus")
4938 (uri (bioconductor-uri "ConsensusClusterPlus" version))
4941 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
4943 `((upstream-name . "ConsensusClusterPlus")))
4944 (build-system r-build-system)
4947 ("r-biobase" ,r-biobase)
4948 ("r-cluster" ,r-cluster)))
4949 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
4950 (synopsis "Clustering algorithm")
4952 "This package provides an implementation of an algorithm for determining
4953 cluster count and membership by stability evidence in unsupervised analysis.")
4954 (license license:gpl2)))
4956 (define-public r-flowcore
4963 (uri (bioconductor-uri "flowCore" version))
4966 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
4967 (properties `((upstream-name . "flowCore")))
4968 (build-system r-build-system)
4971 ("r-biobase" ,r-biobase)
4972 ("r-biocgenerics" ,r-biocgenerics)
4973 ("r-corpcor" ,r-corpcor)
4974 ("r-graph" ,r-graph)
4976 ("r-matrixstats" ,r-matrixstats)
4978 ("r-rrcov" ,r-rrcov)))
4979 (home-page "https://bioconductor.org/packages/flowCore")
4980 (synopsis "Basic structures for flow cytometry data")
4982 "This package provides S4 data structures and basic functions to deal
4983 with flow cytometry data.")
4984 (license license:artistic2.0)))
4986 (define-public r-flowmeans
4988 (name "r-flowmeans")
4993 (uri (bioconductor-uri "flowMeans" version))
4996 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
4997 (properties `((upstream-name . "flowMeans")))
4998 (build-system r-build-system)
5000 `(("r-biobase" ,r-biobase)
5001 ("r-feature" ,r-feature)
5002 ("r-flowcore" ,r-flowcore)
5003 ("r-rrcov" ,r-rrcov)))
5004 (home-page "https://bioconductor.org/packages/flowMeans")
5005 (synopsis "Non-parametric flow cytometry data gating")
5007 "This package provides tools to identify cell populations in Flow
5008 Cytometry data using non-parametric clustering and segmented-regression-based
5009 change point detection.")
5010 (license license:artistic2.0)))
5012 (define-public r-flowsom
5019 (uri (bioconductor-uri "FlowSOM" version))
5022 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5023 (properties `((upstream-name . "FlowSOM")))
5024 (build-system r-build-system)
5026 `(("r-biocgenerics" ,r-biocgenerics)
5027 ("r-consensusclusterplus" ,r-consensusclusterplus)
5028 ("r-flowcore" ,r-flowcore)
5029 ("r-flowutils" ,r-flowutils)
5030 ("r-igraph" ,r-igraph)
5033 (home-page "https://bioconductor.org/packages/FlowSOM/")
5034 (synopsis "Visualize and interpret cytometry data")
5036 "FlowSOM offers visualization options for cytometry data, by using
5037 self-organizing map clustering and minimal spanning trees.")
5038 (license license:gpl2+)))
5040 (define-public r-mixomics
5047 (uri (bioconductor-uri "mixOmics" version))
5050 "0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg"))))
5051 (properties `((upstream-name . "mixOmics")))
5052 (build-system r-build-system)
5054 `(("r-corpcor" ,r-corpcor)
5055 ("r-dplyr" ,r-dplyr)
5056 ("r-ellipse" ,r-ellipse)
5057 ("r-ggplot2" ,r-ggplot2)
5058 ("r-gridextra" ,r-gridextra)
5059 ("r-igraph" ,r-igraph)
5060 ("r-lattice" ,r-lattice)
5062 ("r-matrixstats" ,r-matrixstats)
5063 ("r-rarpack" ,r-rarpack)
5064 ("r-rcolorbrewer" ,r-rcolorbrewer)
5065 ("r-reshape2" ,r-reshape2)
5066 ("r-tidyr" ,r-tidyr)))
5067 (home-page "http://www.mixOmics.org")
5068 (synopsis "Multivariate methods for exploration of biological datasets")
5070 "mixOmics offers a wide range of multivariate methods for the exploration
5071 and integration of biological datasets with a particular focus on variable
5072 selection. The package proposes several sparse multivariate models we have
5073 developed to identify the key variables that are highly correlated, and/or
5074 explain the biological outcome of interest. The data that can be analysed
5075 with mixOmics may come from high throughput sequencing technologies, such as
5076 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5077 also beyond the realm of omics (e.g. spectral imaging). The methods
5078 implemented in mixOmics can also handle missing values without having to
5079 delete entire rows with missing data.")
5080 (license license:gpl2+)))
5082 (define-public r-depecher
5089 (uri (bioconductor-uri "DepecheR" version))
5092 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5093 (properties `((upstream-name . "DepecheR")))
5094 (build-system r-build-system)
5097 (modify-phases %standard-phases
5098 (add-after 'unpack 'fix-syntax-error
5100 (substitute* "src/Makevars"
5104 `(("r-beanplot" ,r-beanplot)
5105 ("r-biocparallel" ,r-biocparallel)
5106 ("r-dosnow" ,r-dosnow)
5107 ("r-dplyr" ,r-dplyr)
5108 ("r-foreach" ,r-foreach)
5109 ("r-ggplot2" ,r-ggplot2)
5110 ("r-gplots" ,r-gplots)
5112 ("r-matrixstats" ,r-matrixstats)
5113 ("r-mixomics" ,r-mixomics)
5114 ("r-moments" ,r-moments)
5116 ("r-rcppeigen" ,r-rcppeigen)
5117 ("r-reshape2" ,r-reshape2)
5118 ("r-viridis" ,r-viridis)))
5119 (home-page "https://bioconductor.org/packages/DepecheR/")
5120 (synopsis "Identify traits of clusters in high-dimensional entities")
5122 "The purpose of this package is to identify traits in a dataset that can
5123 separate groups. This is done on two levels. First, clustering is performed,
5124 using an implementation of sparse K-means. Secondly, the generated clusters
5125 are used to predict outcomes of groups of individuals based on their
5126 distribution of observations in the different clusters. As certain clusters
5127 with separating information will be identified, and these clusters are defined
5128 by a sparse number of variables, this method can reduce the complexity of
5129 data, to only emphasize the data that actually matters.")
5130 (license license:expat)))
5132 (define-public r-rcistarget
5134 (name "r-rcistarget")
5139 (uri (bioconductor-uri "RcisTarget" version))
5142 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5143 (properties `((upstream-name . "RcisTarget")))
5144 (build-system r-build-system)
5146 `(("r-aucell" ,r-aucell)
5147 ("r-biocgenerics" ,r-biocgenerics)
5148 ("r-data-table" ,r-data-table)
5149 ("r-feather" ,r-feather)
5150 ("r-gseabase" ,r-gseabase)
5151 ("r-r-utils" ,r-r-utils)
5152 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5153 (home-page "https://aertslab.org/#scenic")
5154 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5156 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5157 over-represented on a gene list. In a first step, RcisTarget selects DNA
5158 motifs that are significantly over-represented in the surroundings of the
5159 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5160 achieved by using a database that contains genome-wide cross-species rankings
5161 for each motif. The motifs that are then annotated to TFs and those that have
5162 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5163 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5164 genes in the gene-set that are ranked above the leading edge).")
5165 (license license:gpl3)))
5167 (define-public r-cicero
5174 (uri (bioconductor-uri "cicero" version))
5177 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5178 (build-system r-build-system)
5180 `(("r-assertthat" ,r-assertthat)
5181 ("r-biobase" ,r-biobase)
5182 ("r-biocgenerics" ,r-biocgenerics)
5183 ("r-data-table" ,r-data-table)
5184 ("r-dplyr" ,r-dplyr)
5186 ("r-genomicranges" ,r-genomicranges)
5187 ("r-ggplot2" ,r-ggplot2)
5188 ("r-glasso" ,r-glasso)
5190 ("r-igraph" ,r-igraph)
5191 ("r-iranges" ,r-iranges)
5192 ("r-matrix" ,r-matrix)
5193 ("r-monocle" ,r-monocle)
5195 ("r-reshape2" ,r-reshape2)
5196 ("r-s4vectors" ,r-s4vectors)
5197 ("r-stringr" ,r-stringr)
5198 ("r-tibble" ,r-tibble)
5199 ("r-vgam" ,r-vgam)))
5200 (home-page "https://bioconductor.org/packages/cicero/")
5201 (synopsis "Predict cis-co-accessibility from single-cell data")
5203 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5204 accessibility data. It also extends the monocle package for use in chromatin
5205 accessibility data.")
5206 (license license:expat)))
5208 ;; This is the latest commit on the "monocle3" branch.
5209 (define-public r-cicero-monocle3
5210 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5212 (package (inherit r-cicero)
5213 (name "r-cicero-monocle3")
5214 (version (git-version "1.3.2" revision commit))
5219 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5221 (file-name (git-file-name name version))
5224 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5226 `(("r-monocle3" ,r-monocle3)
5227 ,@(alist-delete "r-monocle"
5228 (package-propagated-inputs r-cicero)))))))
5230 (define-public r-cistopic
5231 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5235 (version (git-version "0.2.1" revision commit))
5240 (url "https://github.com/aertslab/cisTopic.git")
5242 (file-name (git-file-name name version))
5245 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5246 (build-system r-build-system)
5248 `(("r-aucell" ,r-aucell)
5249 ("r-data-table" ,r-data-table)
5250 ("r-dplyr" ,r-dplyr)
5251 ("r-dosnow" ,r-dosnow)
5253 ("r-feather" ,r-feather)
5254 ("r-fitdistrplus" ,r-fitdistrplus)
5255 ("r-genomicranges" ,r-genomicranges)
5256 ("r-ggplot2" ,r-ggplot2)
5258 ("r-matrix" ,r-matrix)
5260 ("r-rcistarget" ,r-rcistarget)
5261 ("r-rtracklayer" ,r-rtracklayer)
5262 ("r-s4vectors" ,r-s4vectors)))
5263 (home-page "https://github.com/aertslab/cisTopic")
5264 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5266 "The sparse nature of single cell epigenomics data can be overruled using
5267 probabilistic modelling methods such as @dfn{Latent Dirichlet
5268 Allocation} (LDA). This package allows the probabilistic modelling of
5269 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5270 includes functionalities to identify cell states based on the contribution of
5271 cisTopics and explore the nature and regulatory proteins driving them.")
5272 (license license:gpl3))))
5274 (define-public r-genie3
5281 (uri (bioconductor-uri "GENIE3" version))
5284 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5285 (properties `((upstream-name . "GENIE3")))
5286 (build-system r-build-system)
5287 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5288 (home-page "https://bioconductor.org/packages/GENIE3")
5289 (synopsis "Gene network inference with ensemble of trees")
5291 "This package implements the GENIE3 algorithm for inferring gene
5292 regulatory networks from expression data.")
5293 (license license:gpl2+)))
5295 (define-public r-roc
5302 (uri (bioconductor-uri "ROC" version))
5305 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5306 (properties `((upstream-name . "ROC")))
5307 (build-system r-build-system)
5308 (home-page "https://www.bioconductor.org/packages/ROC/")
5309 (synopsis "Utilities for ROC curves")
5311 "This package provides utilities for @dfn{Receiver Operating
5312 Characteristic} (ROC) curves, with a focus on micro arrays.")
5313 (license license:artistic2.0)))
5315 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5317 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5322 (uri (bioconductor-uri
5323 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5324 version 'annotation))
5327 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5330 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5331 (build-system r-build-system)
5332 (propagated-inputs `(("r-minfi" ,r-minfi)))
5334 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5335 (synopsis "Annotation for Illumina's 450k methylation arrays")
5337 "This package provides manifests and annotation for Illumina's 450k array
5339 (license license:artistic2.0)))
5341 (define-public r-watermelon
5343 (name "r-watermelon")
5348 (uri (bioconductor-uri "wateRmelon" version))
5351 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
5352 (properties `((upstream-name . "wateRmelon")))
5353 (build-system r-build-system)
5355 `(("r-biobase" ,r-biobase)
5356 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
5357 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
5358 ("r-illuminaio" ,r-illuminaio)
5359 ("r-limma" ,r-limma)
5361 ("r-matrixstats" ,r-matrixstats)
5362 ("r-methylumi" ,r-methylumi)
5364 (home-page "https://bioconductor.org/packages/wateRmelon/")
5365 (synopsis "Illumina 450 methylation array normalization and metrics")
5367 "The standard index of DNA methylation (beta) is computed from methylated
5368 and unmethylated signal intensities. Betas calculated from raw signal
5369 intensities perform well, but using 11 methylomic datasets we demonstrate that
5370 quantile normalization methods produce marked improvement. The commonly used
5371 procedure of normalizing betas is inferior to the separate normalization of M
5372 and U, and it is also advantageous to normalize Type I and Type II assays
5373 separately. This package provides 15 flavours of betas and three performance
5374 metrics, with methods for objects produced by the @code{methylumi} and
5375 @code{minfi} packages.")
5376 (license license:gpl3)))
5378 (define-public r-gdsfmt
5385 (uri (bioconductor-uri "gdsfmt" version))
5388 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
5389 (modules '((guix build utils)))
5390 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
5391 ;; them and link with system libraries instead.
5394 (for-each delete-file-recursively
5398 (substitute* "src/Makevars"
5399 (("all: \\$\\(SHLIB\\)") "all:")
5400 (("\\$\\(SHLIB\\): liblzma.a") "")
5401 (("(ZLIB|LZ4)/.*") "")
5402 (("CoreArray/dVLIntGDS.cpp.*")
5403 "CoreArray/dVLIntGDS.cpp")
5404 (("CoreArray/dVLIntGDS.o.*")
5405 "CoreArray/dVLIntGDS.o")
5406 (("PKG_LIBS = ./liblzma.a")
5407 "PKG_LIBS = -llz4"))
5408 (substitute* "src/CoreArray/dStream.h"
5409 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
5410 (string-append "include <" header ">")))
5412 (properties `((upstream-name . "gdsfmt")))
5413 (build-system r-build-system)
5418 (home-page "http://corearray.sourceforge.net/")
5420 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
5422 "This package provides a high-level R interface to CoreArray @dfn{Genomic
5423 Data Structure} (GDS) data files, which are portable across platforms with
5424 hierarchical structure to store multiple scalable array-oriented data sets
5425 with metadata information. It is suited for large-scale datasets, especially
5426 for data which are much larger than the available random-access memory. The
5427 @code{gdsfmt} package offers efficient operations specifically designed for
5428 integers of less than 8 bits, since a diploid genotype, like
5429 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
5430 byte. Data compression and decompression are available with relatively
5431 efficient random access. It is also allowed to read a GDS file in parallel
5432 with multiple R processes supported by the package @code{parallel}.")
5433 (license license:lgpl3)))
5435 (define-public r-bigmelon
5442 (uri (bioconductor-uri "bigmelon" version))
5445 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
5446 (properties `((upstream-name . "bigmelon")))
5447 (build-system r-build-system)
5449 `(("r-biobase" ,r-biobase)
5450 ("r-biocgenerics" ,r-biocgenerics)
5451 ("r-gdsfmt" ,r-gdsfmt)
5452 ("r-geoquery" ,r-geoquery)
5453 ("r-methylumi" ,r-methylumi)
5454 ("r-minfi" ,r-minfi)
5455 ("r-watermelon" ,r-watermelon)))
5456 (home-page "https://bioconductor.org/packages/bigmelon/")
5457 (synopsis "Illumina methylation array analysis for large experiments")
5459 "This package provides methods for working with Illumina arrays using the
5460 @code{gdsfmt} package.")
5461 (license license:gpl3)))
5463 (define-public r-wavcluster
5465 (name "r-wavcluster")
5470 (uri (bioconductor-uri "wavClusteR" version))
5473 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
5474 (properties `((upstream-name . "wavClusteR")))
5475 (build-system r-build-system)
5477 `(("r-biocgenerics" ,r-biocgenerics)
5478 ("r-biostrings" ,r-biostrings)
5479 ("r-foreach" ,r-foreach)
5480 ("r-genomicfeatures" ,r-genomicfeatures)
5481 ("r-genomicranges" ,r-genomicranges)
5482 ("r-ggplot2" ,r-ggplot2)
5483 ("r-hmisc" ,r-hmisc)
5484 ("r-iranges" ,r-iranges)
5485 ("r-mclust" ,r-mclust)
5486 ("r-rsamtools" ,r-rsamtools)
5487 ("r-rtracklayer" ,r-rtracklayer)
5488 ("r-s4vectors" ,r-s4vectors)
5489 ("r-seqinr" ,r-seqinr)
5490 ("r-stringr" ,r-stringr)
5491 ("r-wmtsa" ,r-wmtsa)))
5492 (home-page "https://bioconductor.org/packages/wavClusteR/")
5493 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
5495 "This package provides an integrated pipeline for the analysis of
5496 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
5497 sequencing errors, SNPs and additional non-experimental sources by a non-
5498 parametric mixture model. The protein binding sites (clusters) are then
5499 resolved at high resolution and cluster statistics are estimated using a
5500 rigorous Bayesian framework. Post-processing of the results, data export for
5501 UCSC genome browser visualization and motif search analysis are provided. In
5502 addition, the package allows to integrate RNA-Seq data to estimate the False
5503 Discovery Rate of cluster detection. Key functions support parallel multicore
5504 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
5505 be applied to the analysis of other NGS data obtained from experimental
5506 procedures that induce nucleotide substitutions (e.g. BisSeq).")
5507 (license license:gpl2)))
5509 (define-public r-timeseriesexperiment
5511 (name "r-timeseriesexperiment")
5516 (uri (bioconductor-uri "TimeSeriesExperiment" version))
5519 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
5521 `((upstream-name . "TimeSeriesExperiment")))
5522 (build-system r-build-system)
5524 `(("r-deseq2" ,r-deseq2)
5525 ("r-dplyr" ,r-dplyr)
5526 ("r-dynamictreecut" ,r-dynamictreecut)
5527 ("r-edger" ,r-edger)
5528 ("r-ggplot2" ,r-ggplot2)
5529 ("r-hmisc" ,r-hmisc)
5530 ("r-limma" ,r-limma)
5531 ("r-magrittr" ,r-magrittr)
5532 ("r-proxy" ,r-proxy)
5533 ("r-s4vectors" ,r-s4vectors)
5534 ("r-summarizedexperiment" ,r-summarizedexperiment)
5535 ("r-tibble" ,r-tibble)
5536 ("r-tidyr" ,r-tidyr)
5537 ("r-vegan" ,r-vegan)
5538 ("r-viridis" ,r-viridis)))
5539 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
5540 (synopsis "Analysis for short time-series data")
5542 "This package is a visualization and analysis toolbox for short time
5543 course data which includes dimensionality reduction, clustering, two-sample
5544 differential expression testing and gene ranking techniques. The package also
5545 provides methods for retrieving enriched pathways.")
5546 (license license:lgpl3+)))