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>
5 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
7 ;;; This file is part of GNU Guix.
9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
10 ;;; under the terms of the GNU General Public License as published by
11 ;;; the Free Software Foundation; either version 3 of the License, or (at
12 ;;; your option) any later version.
14 ;;; GNU Guix is distributed in the hope that it will be useful, but
15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 ;;; GNU General Public License for more details.
19 ;;; You should have received a copy of the GNU General Public License
20 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
22 (define-module (gnu packages bioconductor)
23 #:use-module ((guix licenses) #:prefix license:)
24 #:use-module (guix packages)
25 #:use-module (guix download)
26 #:use-module (guix git-download)
27 #:use-module (guix build-system r)
28 #:use-module (gnu packages)
29 #:use-module (gnu packages base)
30 #:use-module (gnu packages bioinformatics)
31 #:use-module (gnu packages cran)
32 #:use-module (gnu packages compression)
33 #:use-module (gnu packages gcc)
34 #:use-module (gnu packages graph)
35 #:use-module (gnu packages haskell-xyz)
36 #:use-module (gnu packages image)
37 #:use-module (gnu packages maths)
38 #:use-module (gnu packages netpbm)
39 #:use-module (gnu packages perl)
40 #:use-module (gnu packages pkg-config)
41 #:use-module (gnu packages statistics)
42 #:use-module (gnu packages web)
43 #:use-module (srfi srfi-1))
48 (define-public r-bsgenome-celegans-ucsc-ce6
50 (name "r-bsgenome-celegans-ucsc-ce6")
54 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
58 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
60 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
61 (build-system r-build-system)
63 `(("r-bsgenome" ,r-bsgenome)))
65 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
66 (synopsis "Full genome sequences for Worm")
68 "This package provides full genome sequences for Caenorhabditis
69 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
71 (license license:artistic2.0)))
73 (define-public r-bsgenome-celegans-ucsc-ce10
75 (name "r-bsgenome-celegans-ucsc-ce10")
79 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
83 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
85 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
86 (build-system r-build-system)
88 `(("r-bsgenome" ,r-bsgenome)))
90 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
91 (synopsis "Full genome sequences for Worm")
93 "This package provides full genome sequences for Caenorhabditis
94 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
96 (license license:artistic2.0)))
98 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
100 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
104 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
105 version 'annotation))
108 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
110 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
111 (build-system r-build-system)
113 `(("r-bsgenome" ,r-bsgenome)))
115 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
116 (synopsis "Full genome sequences for Fly")
118 "This package provides full genome sequences for Drosophila
119 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
121 (license license:artistic2.0)))
123 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
125 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
129 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
130 version 'annotation))
133 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
135 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
136 (build-system r-build-system)
138 `(("r-bsgenome" ,r-bsgenome)))
140 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
141 (synopsis "Full genome sequences for Fly")
143 "This package provides full genome sequences for Drosophila
144 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
145 Biostrings objects.")
146 (license license:artistic2.0)))
148 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
150 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
154 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
155 version 'annotation))
158 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
160 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
161 (build-system r-build-system)
163 `(("r-bsgenome" ,r-bsgenome)
164 ("r-bsgenome-dmelanogaster-ucsc-dm3"
165 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
166 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
167 (synopsis "Full masked genome sequences for Fly")
169 "This package provides full masked genome sequences for Drosophila
170 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
171 Biostrings objects. The sequences are the same as in
172 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
173 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
174 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
175 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
176 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
177 (license license:artistic2.0)))
179 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
181 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
185 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
186 version 'annotation))
189 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
191 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
192 (build-system r-build-system)
194 `(("r-bsgenome" ,r-bsgenome)))
196 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
197 (synopsis "Full genome sequences for Homo sapiens")
199 "This package provides full genome sequences for Homo sapiens from
200 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
205 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
209 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
210 version 'annotation))
213 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
215 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
216 (build-system r-build-system)
218 `(("r-bsgenome" ,r-bsgenome)
219 ("r-bsgenome-hsapiens-ucsc-hg19"
220 ,r-bsgenome-hsapiens-ucsc-hg19)))
221 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
222 (synopsis "Full masked genome sequences for Homo sapiens")
224 "This package provides full genome sequences for Homo sapiens (Human) as
225 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
226 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
227 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
228 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
229 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
230 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
232 (license license:artistic2.0)))
234 (define-public r-bsgenome-mmusculus-ucsc-mm9
236 (name "r-bsgenome-mmusculus-ucsc-mm9")
240 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
241 version 'annotation))
244 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
246 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
247 (build-system r-build-system)
249 `(("r-bsgenome" ,r-bsgenome)))
251 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
252 (synopsis "Full genome sequences for Mouse")
254 "This package provides full genome sequences for Mus musculus (Mouse) as
255 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
256 (license license:artistic2.0)))
258 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
260 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
264 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
265 version 'annotation))
268 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
270 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
271 (build-system r-build-system)
273 `(("r-bsgenome" ,r-bsgenome)
274 ("r-bsgenome-mmusculus-ucsc-mm9"
275 ,r-bsgenome-mmusculus-ucsc-mm9)))
276 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
277 (synopsis "Full masked genome sequences for Mouse")
279 "This package provides full genome sequences for Mus musculus (Mouse) as
280 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
281 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
282 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
283 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
284 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
285 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
287 (license license:artistic2.0)))
289 (define-public r-bsgenome-mmusculus-ucsc-mm10
291 (name "r-bsgenome-mmusculus-ucsc-mm10")
295 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
296 version 'annotation))
299 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
301 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
302 (build-system r-build-system)
304 `(("r-bsgenome" ,r-bsgenome)))
306 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
307 (synopsis "Full genome sequences for Mouse")
309 "This package provides full genome sequences for Mus
310 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
311 in Biostrings objects.")
312 (license license:artistic2.0)))
314 (define-public r-org-ce-eg-db
316 (name "r-org-ce-eg-db")
320 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
323 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
325 `((upstream-name . "org.Ce.eg.db")))
326 (build-system r-build-system)
328 `(("r-annotationdbi" ,r-annotationdbi)))
329 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
330 (synopsis "Genome wide annotation for Worm")
332 "This package provides mappings from Entrez gene identifiers to various
333 annotations for the genome of the model worm Caenorhabditis elegans.")
334 (license license:artistic2.0)))
336 (define-public r-org-dm-eg-db
338 (name "r-org-dm-eg-db")
342 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
345 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
347 `((upstream-name . "org.Dm.eg.db")))
348 (build-system r-build-system)
350 `(("r-annotationdbi" ,r-annotationdbi)))
351 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
352 (synopsis "Genome wide annotation for Fly")
354 "This package provides mappings from Entrez gene identifiers to various
355 annotations for the genome of the model fruit fly Drosophila melanogaster.")
356 (license license:artistic2.0)))
358 (define-public r-org-dr-eg-db
360 (name "r-org-dr-eg-db")
364 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
367 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
369 `((upstream-name . "org.Dr.eg.db")))
370 (build-system r-build-system)
372 `(("r-annotationdbi" ,r-annotationdbi)))
373 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
374 (synopsis "Annotation for Zebrafish")
376 "This package provides genome wide annotations for Zebrafish, primarily
377 based on mapping using Entrez Gene identifiers.")
378 (license license:artistic2.0)))
380 (define-public r-org-hs-eg-db
382 (name "r-org-hs-eg-db")
386 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
389 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
391 `((upstream-name . "org.Hs.eg.db")))
392 (build-system r-build-system)
394 `(("r-annotationdbi" ,r-annotationdbi)))
395 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
396 (synopsis "Genome wide annotation for Human")
398 "This package contains genome-wide annotations for Human, primarily based
399 on mapping using Entrez Gene identifiers.")
400 (license license:artistic2.0)))
402 (define-public r-org-mm-eg-db
404 (name "r-org-mm-eg-db")
408 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
411 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
413 `((upstream-name . "org.Mm.eg.db")))
414 (build-system r-build-system)
416 `(("r-annotationdbi" ,r-annotationdbi)))
417 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
418 (synopsis "Genome wide annotation for Mouse")
420 "This package provides mappings from Entrez gene identifiers to various
421 annotations for the genome of the model mouse Mus musculus.")
422 (license license:artistic2.0)))
424 (define-public r-bsgenome-hsapiens-ucsc-hg19
426 (name "r-bsgenome-hsapiens-ucsc-hg19")
430 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
431 version 'annotation))
434 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
436 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
437 (build-system r-build-system)
439 `(("r-bsgenome" ,r-bsgenome)))
441 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
442 (synopsis "Full genome sequences for Homo sapiens")
444 "This package provides full genome sequences for Homo sapiens as provided
445 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
446 (license license:artistic2.0)))
448 (define-public r-ensdb-hsapiens-v75
450 (name "r-ensdb-hsapiens-v75")
455 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
458 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
460 `((upstream-name . "EnsDb.Hsapiens.v75")))
461 (build-system r-build-system)
463 `(("r-ensembldb" ,r-ensembldb)))
464 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
465 (synopsis "Ensembl based annotation package")
467 "This package exposes an annotation database generated from Ensembl.")
468 (license license:artistic2.0)))
470 (define-public r-genelendatabase
472 (name "r-genelendatabase")
477 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
480 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
482 `((upstream-name . "geneLenDataBase")))
483 (build-system r-build-system)
485 `(("r-rtracklayer" ,r-rtracklayer)
486 ("r-genomicfeatures" ,r-genomicfeatures)))
487 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
488 (synopsis "Lengths of mRNA transcripts for a number of genomes")
490 "This package provides the lengths of mRNA transcripts for a number of
491 genomes and gene ID formats, largely based on the UCSC table browser.")
492 (license license:lgpl2.0+)))
494 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
496 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
500 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
501 version 'annotation))
504 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
506 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
507 (build-system r-build-system)
509 `(("r-genomicfeatures" ,r-genomicfeatures)))
511 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
512 (synopsis "Annotation package for human genome in TxDb format")
514 "This package provides an annotation database of Homo sapiens genome
515 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
516 track. The database is exposed as a @code{TxDb} object.")
517 (license license:artistic2.0)))
519 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
521 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
525 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
526 version 'annotation))
529 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
531 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
532 (build-system r-build-system)
534 `(("r-genomicfeatures" ,r-genomicfeatures)))
536 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
537 (synopsis "Annotation package for human genome in TxDb format")
539 "This package provides an annotation database of Homo sapiens genome
540 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
541 track. The database is exposed as a @code{TxDb} object.")
542 (license license:artistic2.0)))
544 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
546 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
550 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
551 version 'annotation))
554 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
556 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
557 (build-system r-build-system)
559 `(("r-genomicfeatures" ,r-genomicfeatures)
560 ("r-annotationdbi" ,r-annotationdbi)))
562 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
563 (synopsis "Annotation package for mouse genome in TxDb format")
565 "This package provides an annotation database of Mouse genome data. It
566 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
567 database is exposed as a @code{TxDb} object.")
568 (license license:artistic2.0)))
570 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
572 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
576 ;; We cannot use bioconductor-uri here because this tarball is
577 ;; located under "data/annotation/" instead of "bioc/".
578 (uri (string-append "https://www.bioconductor.org/packages/"
579 "release/data/annotation/src/contrib/"
580 "TxDb.Mmusculus.UCSC.mm10.knownGene_"
584 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
586 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
587 (build-system r-build-system)
588 ;; As this package provides little more than a very large data file it
589 ;; doesn't make sense to build substitutes.
590 (arguments `(#:substitutable? #f))
592 `(("r-bsgenome" ,r-bsgenome)
593 ("r-genomicfeatures" ,r-genomicfeatures)
594 ("r-annotationdbi" ,r-annotationdbi)))
596 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
597 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
599 "This package loads a TxDb object, which is an R interface to
600 prefabricated databases contained in this package. This package provides
601 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
602 based on the knownGene track.")
603 (license license:artistic2.0)))
605 (define-public r-txdb-celegans-ucsc-ce6-ensgene
607 (name "r-txdb-celegans-ucsc-ce6-ensgene")
612 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
613 version 'annotation))
616 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
618 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
619 (build-system r-build-system)
621 `(("r-annotationdbi" ,r-annotationdbi)
622 ("r-genomicfeatures" ,r-genomicfeatures)))
623 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
624 (synopsis "Annotation package for C elegans TxDb objects")
626 "This package exposes a C elegans annotation database generated from UCSC
627 by exposing these as TxDb objects.")
628 (license license:artistic2.0)))
630 (define-public r-fdb-infiniummethylation-hg19
632 (name "r-fdb-infiniummethylation-hg19")
636 ;; We cannot use bioconductor-uri here because this tarball is
637 ;; located under "data/annotation/" instead of "bioc/".
638 (uri (string-append "https://www.bioconductor.org/packages/"
639 "release/data/annotation/src/contrib/"
640 "FDb.InfiniumMethylation.hg19_"
644 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
646 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
647 (build-system r-build-system)
649 `(("r-biostrings" ,r-biostrings)
650 ("r-genomicfeatures" ,r-genomicfeatures)
651 ("r-annotationdbi" ,r-annotationdbi)
652 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
653 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
654 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
655 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
657 "This is an annotation package for Illumina Infinium DNA methylation
658 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
660 (license license:artistic2.0)))
662 (define-public r-illuminahumanmethylationepicmanifest
664 (name "r-illuminahumanmethylationepicmanifest")
668 ;; We cannot use bioconductor-uri here because this tarball is
669 ;; located under "data/annotation/" instead of "bioc/".
670 (uri (string-append "https://www.bioconductor.org/packages/"
671 "release/data/annotation/src/contrib/"
672 "IlluminaHumanMethylationEPICmanifest_"
676 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
678 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
679 (build-system r-build-system)
681 `(("r-minfi" ,r-minfi)))
682 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
683 (synopsis "Manifest for Illumina's EPIC methylation arrays")
685 "This is a manifest package for Illumina's EPIC methylation arrays.")
686 (license license:artistic2.0)))
688 (define-public r-do-db
694 ;; We cannot use bioconductor-uri here because this tarball is
695 ;; located under "data/annotation/" instead of "bioc/".
696 (uri (string-append "https://www.bioconductor.org/packages/"
697 "release/data/annotation/src/contrib/"
698 "DO.db_" version ".tar.gz"))
701 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
703 `((upstream-name . "DO.db")))
704 (build-system r-build-system)
706 `(("r-annotationdbi" ,r-annotationdbi)))
707 (home-page "https://www.bioconductor.org/packages/DO.db/")
708 (synopsis "Annotation maps describing the entire Disease Ontology")
710 "This package provides a set of annotation maps describing the entire
712 (license license:artistic2.0)))
714 (define-public r-pfam-db
721 (uri (bioconductor-uri "PFAM.db" version 'annotation))
724 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
725 (properties `((upstream-name . "PFAM.db")))
726 (build-system r-build-system)
728 `(("r-annotationdbi" ,r-annotationdbi)))
729 (home-page "https://bioconductor.org/packages/PFAM.db")
730 (synopsis "Set of protein ID mappings for PFAM")
732 "This package provides a set of protein ID mappings for PFAM, assembled
733 using data from public repositories.")
734 (license license:artistic2.0)))
736 (define-public r-phastcons100way-ucsc-hg19
738 (name "r-phastcons100way-ucsc-hg19")
743 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
744 version 'annotation))
747 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
749 `((upstream-name . "phastCons100way.UCSC.hg19")))
750 (build-system r-build-system)
752 `(("r-bsgenome" ,r-bsgenome)
753 ("r-genomeinfodb" ,r-genomeinfodb)
754 ("r-genomicranges" ,r-genomicranges)
755 ("r-genomicscores" ,r-genomicscores)
756 ("r-iranges" ,r-iranges)
757 ("r-s4vectors" ,r-s4vectors)))
758 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
759 (synopsis "UCSC phastCons conservation scores for hg19")
761 "This package provides UCSC phastCons conservation scores for the human
762 genome (hg19) calculated from multiple alignments with other 99 vertebrate
764 (license license:artistic2.0)))
769 (define-public r-abadata
775 ;; We cannot use bioconductor-uri here because this tarball is
776 ;; located under "data/experiment/" instead of "bioc/".
777 (uri (string-append "https://www.bioconductor.org/packages/"
778 "release/data/experiment/src/contrib/"
779 "ABAData_" version ".tar.gz"))
782 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
784 `((upstream-name . "ABAData")))
785 (build-system r-build-system)
787 `(("r-annotationdbi" ,r-annotationdbi)))
788 (home-page "https://www.bioconductor.org/packages/ABAData/")
789 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
791 "This package provides the data for the gene expression enrichment
792 analysis conducted in the package ABAEnrichment. The package includes three
793 datasets which are derived from the Allen Brain Atlas:
796 @item Gene expression data from Human Brain (adults) averaged across donors,
797 @item Gene expression data from the Developing Human Brain pooled into five
798 age categories and averaged across donors, and
799 @item a developmental effect score based on the Developing Human Brain
803 All datasets are restricted to protein coding genes.")
804 (license license:gpl2+)))
806 (define-public r-arrmdata
812 ;; We cannot use bioconductor-uri here because this tarball is
813 ;; located under "data/experiment/" instead of "bioc/".
814 (uri (string-append "https://www.bioconductor.org/packages/"
815 "release/data/experiment/src/contrib/"
816 "ARRmData_" version ".tar.gz"))
819 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
821 `((upstream-name . "ARRmData")))
822 (build-system r-build-system)
823 (home-page "https://www.bioconductor.org/packages/ARRmData/")
824 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
826 "This package provides raw beta values from 36 samples across 3 groups
827 from Illumina 450k methylation arrays.")
828 (license license:artistic2.0)))
830 (define-public r-hsmmsinglecell
832 (name "r-hsmmsinglecell")
836 ;; We cannot use bioconductor-uri here because this tarball is
837 ;; located under "data/experiment/" instead of "bioc/".
838 (uri (string-append "https://www.bioconductor.org/packages/"
839 "release/data/experiment/src/contrib/"
840 "HSMMSingleCell_" version ".tar.gz"))
843 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
845 `((upstream-name . "HSMMSingleCell")))
846 (build-system r-build-system)
847 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
848 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
850 "Skeletal myoblasts undergo a well-characterized sequence of
851 morphological and transcriptional changes during differentiation. In this
852 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
853 under high mitogen conditions (GM) and then differentiated by switching to
854 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
855 hundred cells taken over a time-course of serum-induced differentiation.
856 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
857 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
858 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
859 which were then sequenced to a depth of ~4 million reads per library,
860 resulting in a complete gene expression profile for each cell.")
861 (license license:artistic2.0)))
869 ;; We cannot use bioconductor-uri here because this tarball is
870 ;; located under "data/experiment/" instead of "bioc/".
871 (uri (string-append "https://www.bioconductor.org/packages/"
872 "release/data/experiment/src/contrib/"
873 "ALL_" version ".tar.gz"))
876 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
877 (properties `((upstream-name . "ALL")))
878 (build-system r-build-system)
880 `(("r-biobase" ,r-biobase)))
881 (home-page "https://bioconductor.org/packages/ALL")
882 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
884 "The data consist of microarrays from 128 different individuals with
885 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
886 are available. The data have been normalized (using rma) and it is the
887 jointly normalized data that are available here. The data are presented in
888 the form of an @code{exprSet} object.")
889 (license license:artistic2.0)))
891 (define-public r-affydata
898 (uri (bioconductor-uri "affydata" version 'experiment))
901 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
902 (properties `((upstream-name . "affydata")))
903 (build-system r-build-system)
905 `(("r-affy" ,r-affy)))
906 (home-page "https://bioconductor.org/packages/affydata/")
907 (synopsis "Affymetrix data for demonstration purposes")
909 "This package provides example datasets that represent 'real world
910 examples' of Affymetrix data, unlike the artificial examples included in the
911 package @code{affy}.")
912 (license license:gpl2+)))
917 (define-public r-biocgenerics
919 (name "r-biocgenerics")
923 (uri (bioconductor-uri "BiocGenerics" version))
926 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
928 `((upstream-name . "BiocGenerics")))
929 (build-system r-build-system)
930 (home-page "https://bioconductor.org/packages/BiocGenerics")
931 (synopsis "S4 generic functions for Bioconductor")
933 "This package provides S4 generic functions needed by many Bioconductor
935 (license license:artistic2.0)))
937 (define-public r-affycomp
944 (uri (bioconductor-uri "affycomp" version))
947 "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
948 (properties `((upstream-name . "affycomp")))
949 (build-system r-build-system)
950 (propagated-inputs `(("r-biobase" ,r-biobase)))
951 (home-page "https://bioconductor.org/packages/affycomp/")
952 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
954 "The package contains functions that can be used to compare expression
955 measures for Affymetrix Oligonucleotide Arrays.")
956 (license license:gpl2+)))
958 (define-public r-affycompatible
960 (name "r-affycompatible")
965 (uri (bioconductor-uri "AffyCompatible" version))
968 "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
970 `((upstream-name . "AffyCompatible")))
971 (build-system r-build-system)
973 `(("r-biostrings" ,r-biostrings)
976 (home-page "https://bioconductor.org/packages/AffyCompatible/")
977 (synopsis "Work with Affymetrix GeneChip files")
979 "This package provides an interface to Affymetrix chip annotation and
980 sample attribute files. The package allows an easy way for users to download
981 and manage local data bases of Affynmetrix NetAffx annotation files. It also
982 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
983 Command Console} (AGCC)-compatible sample annotation files.")
984 (license license:artistic2.0)))
986 (define-public r-affycontam
988 (name "r-affycontam")
993 (uri (bioconductor-uri "affyContam" version))
996 "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
997 (properties `((upstream-name . "affyContam")))
998 (build-system r-build-system)
1000 `(("r-affy" ,r-affy)
1001 ("r-affydata" ,r-affydata)
1002 ("r-biobase" ,r-biobase)))
1003 (home-page "https://bioconductor.org/packages/affyContam/")
1004 (synopsis "Structured corruption of Affymetrix CEL file data")
1006 "Microarray quality assessment is a major concern of microarray analysts.
1007 This package provides some simple approaches to in silico creation of quality
1008 problems in CEL-level data to help evaluate performance of quality metrics.")
1009 (license license:artistic2.0)))
1011 (define-public r-affycoretools
1013 (name "r-affycoretools")
1018 (uri (bioconductor-uri "affycoretools" version))
1021 "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s"))))
1022 (properties `((upstream-name . "affycoretools")))
1023 (build-system r-build-system)
1025 `(("r-affy" ,r-affy)
1026 ("r-annotationdbi" ,r-annotationdbi)
1027 ("r-biobase" ,r-biobase)
1028 ("r-biocgenerics" ,r-biocgenerics)
1030 ("r-edger" ,r-edger)
1031 ("r-gcrma" ,r-gcrma)
1032 ("r-ggplot2" ,r-ggplot2)
1033 ("r-gostats" ,r-gostats)
1034 ("r-gplots" ,r-gplots)
1035 ("r-hwriter" ,r-hwriter)
1036 ("r-lattice" ,r-lattice)
1037 ("r-limma" ,r-limma)
1038 ("r-oligoclasses" ,r-oligoclasses)
1039 ("r-reportingtools" ,r-reportingtools)
1040 ("r-rsqlite" ,r-rsqlite)
1041 ("r-s4vectors" ,r-s4vectors)
1042 ("r-xtable" ,r-xtable)))
1043 (home-page "https://bioconductor.org/packages/affycoretools/")
1044 (synopsis "Functions for analyses with Affymetrix GeneChips")
1046 "This package provides various wrapper functions that have been written
1047 to streamline the more common analyses that a Biostatistician might see.")
1048 (license license:artistic2.0)))
1050 (define-public r-affxparser
1052 (name "r-affxparser")
1057 (uri (bioconductor-uri "affxparser" version))
1060 "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33"))))
1061 (properties `((upstream-name . "affxparser")))
1062 (build-system r-build-system)
1063 (home-page "https://github.com/HenrikBengtsson/affxparser")
1064 (synopsis "Affymetrix File Parsing SDK")
1066 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1067 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1068 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1069 are supported. Currently, there are methods for reading @dfn{chip definition
1070 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1071 either in full or in part. For example, probe signals from a few probesets
1072 can be extracted very quickly from a set of CEL files into a convenient list
1074 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1076 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1078 (define-public r-annotate
1085 (uri (bioconductor-uri "annotate" version))
1088 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
1089 (build-system r-build-system)
1091 `(("r-annotationdbi" ,r-annotationdbi)
1092 ("r-biobase" ,r-biobase)
1093 ("r-biocgenerics" ,r-biocgenerics)
1095 ("r-rcurl" ,r-rcurl)
1097 ("r-xtable" ,r-xtable)))
1099 "https://bioconductor.org/packages/annotate")
1100 (synopsis "Annotation for microarrays")
1101 (description "This package provides R environments for the annotation of
1103 (license license:artistic2.0)))
1105 (define-public r-hpar
1112 (uri (bioconductor-uri "hpar" version))
1115 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
1116 (build-system r-build-system)
1117 (home-page "https://bioconductor.org/packages/hpar/")
1118 (synopsis "Human Protein Atlas in R")
1119 (description "This package provides a simple interface to and data from
1120 the Human Protein Atlas project.")
1121 (license license:artistic2.0)))
1123 (define-public r-regioner
1130 (uri (bioconductor-uri "regioneR" version))
1133 "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
1134 (properties `((upstream-name . "regioneR")))
1135 (build-system r-build-system)
1137 `(("r-biostrings" ,r-biostrings)
1138 ("r-bsgenome" ,r-bsgenome)
1139 ("r-genomeinfodb" ,r-genomeinfodb)
1140 ("r-genomicranges" ,r-genomicranges)
1141 ("r-iranges" ,r-iranges)
1142 ("r-memoise" ,r-memoise)
1143 ("r-rtracklayer" ,r-rtracklayer)
1144 ("r-s4vectors" ,r-s4vectors)))
1145 (home-page "https://bioconductor.org/packages/regioneR/")
1146 (synopsis "Association analysis of genomic regions")
1147 (description "This package offers a statistical framework based on
1148 customizable permutation tests to assess the association between genomic
1149 region sets and other genomic features.")
1150 (license license:artistic2.0)))
1152 (define-public r-reportingtools
1154 (name "r-reportingtools")
1159 (uri (bioconductor-uri "ReportingTools" version))
1162 "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
1164 `((upstream-name . "ReportingTools")))
1165 (build-system r-build-system)
1167 `(("r-annotate" ,r-annotate)
1168 ("r-annotationdbi" ,r-annotationdbi)
1169 ("r-biobase" ,r-biobase)
1170 ("r-biocgenerics" ,r-biocgenerics)
1171 ("r-category" ,r-category)
1172 ("r-deseq2" ,r-deseq2)
1173 ("r-edger" ,r-edger)
1174 ("r-ggbio" ,r-ggbio)
1175 ("r-ggplot2" ,r-ggplot2)
1176 ("r-gostats" ,r-gostats)
1177 ("r-gseabase" ,r-gseabase)
1178 ("r-hwriter" ,r-hwriter)
1179 ("r-iranges" ,r-iranges)
1180 ("r-knitr" ,r-knitr)
1181 ("r-lattice" ,r-lattice)
1182 ("r-limma" ,r-limma)
1183 ("r-pfam-db" ,r-pfam-db)
1184 ("r-r-utils" ,r-r-utils)
1186 (home-page "https://bioconductor.org/packages/ReportingTools/")
1187 (synopsis "Tools for making reports in various formats")
1189 "The ReportingTools package enables users to easily display reports of
1190 analysis results generated from sources such as microarray and sequencing
1191 data. The package allows users to create HTML pages that may be viewed on a
1192 web browser, or in other formats. Users can generate tables with sortable and
1193 filterable columns, make and display plots, and link table entries to other
1194 data sources such as NCBI or larger plots within the HTML page. Using the
1195 package, users can also produce a table of contents page to link various
1196 reports together for a particular project that can be viewed in a web
1198 (license license:artistic2.0)))
1200 (define-public r-geneplotter
1202 (name "r-geneplotter")
1207 (uri (bioconductor-uri "geneplotter" version))
1210 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1211 (build-system r-build-system)
1213 `(("r-annotate" ,r-annotate)
1214 ("r-annotationdbi" ,r-annotationdbi)
1215 ("r-biobase" ,r-biobase)
1216 ("r-biocgenerics" ,r-biocgenerics)
1217 ("r-lattice" ,r-lattice)
1218 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1219 (home-page "https://bioconductor.org/packages/geneplotter")
1220 (synopsis "Graphics functions for genomic data")
1222 "This package provides functions for plotting genomic data.")
1223 (license license:artistic2.0)))
1225 (define-public r-oligoclasses
1227 (name "r-oligoclasses")
1232 (uri (bioconductor-uri "oligoClasses" version))
1235 "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72"))))
1236 (properties `((upstream-name . "oligoClasses")))
1237 (build-system r-build-system)
1239 `(("r-affyio" ,r-affyio)
1240 ("r-biobase" ,r-biobase)
1241 ("r-biocgenerics" ,r-biocgenerics)
1242 ("r-biocmanager" ,r-biocmanager)
1243 ("r-biostrings" ,r-biostrings)
1246 ("r-foreach" ,r-foreach)
1247 ("r-genomicranges" ,r-genomicranges)
1248 ("r-iranges" ,r-iranges)
1249 ("r-rsqlite" ,r-rsqlite)
1250 ("r-s4vectors" ,r-s4vectors)
1251 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1252 (home-page "https://bioconductor.org/packages/oligoClasses/")
1253 (synopsis "Classes for high-throughput arrays")
1255 "This package contains class definitions, validity checks, and
1256 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1258 (license license:gpl2+)))
1260 (define-public r-oligo
1267 (uri (bioconductor-uri "oligo" version))
1270 "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df"))))
1271 (properties `((upstream-name . "oligo")))
1272 (build-system r-build-system)
1273 (inputs `(("zlib" ,zlib)))
1275 `(("r-affxparser" ,r-affxparser)
1276 ("r-affyio" ,r-affyio)
1277 ("r-biobase" ,r-biobase)
1278 ("r-biocgenerics" ,r-biocgenerics)
1279 ("r-biostrings" ,r-biostrings)
1282 ("r-oligoclasses" ,r-oligoclasses)
1283 ("r-preprocesscore" ,r-preprocesscore)
1284 ("r-rsqlite" ,r-rsqlite)
1285 ("r-zlibbioc" ,r-zlibbioc)))
1286 (home-page "https://bioconductor.org/packages/oligo/")
1287 (synopsis "Preprocessing tools for oligonucleotide arrays")
1289 "This package provides a package to analyze oligonucleotide
1290 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1291 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1292 (license license:lgpl2.0+)))
1294 (define-public r-qvalue
1301 (uri (bioconductor-uri "qvalue" version))
1304 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1305 (build-system r-build-system)
1307 `(("r-ggplot2" ,r-ggplot2)
1308 ("r-reshape2" ,r-reshape2)))
1309 (home-page "http://github.com/jdstorey/qvalue")
1310 (synopsis "Q-value estimation for false discovery rate control")
1312 "This package takes a list of p-values resulting from the simultaneous
1313 testing of many hypotheses and estimates their q-values and local @dfn{false
1314 discovery rate} (FDR) values. The q-value of a test measures the proportion
1315 of false positives incurred when that particular test is called significant.
1316 The local FDR measures the posterior probability the null hypothesis is true
1317 given the test's p-value. Various plots are automatically generated, allowing
1318 one to make sensible significance cut-offs. The software can be applied to
1319 problems in genomics, brain imaging, astrophysics, and data mining.")
1320 ;; Any version of the LGPL.
1321 (license license:lgpl3+)))
1323 (define-public r-diffbind
1330 (uri (bioconductor-uri "DiffBind" version))
1333 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1334 (properties `((upstream-name . "DiffBind")))
1335 (build-system r-build-system)
1339 `(("r-amap" ,r-amap)
1340 ("r-biocparallel" ,r-biocparallel)
1341 ("r-deseq2" ,r-deseq2)
1342 ("r-dplyr" ,r-dplyr)
1343 ("r-edger" ,r-edger)
1344 ("r-genomicalignments" ,r-genomicalignments)
1345 ("r-genomicranges" ,r-genomicranges)
1346 ("r-ggplot2" ,r-ggplot2)
1347 ("r-ggrepel" ,r-ggrepel)
1348 ("r-gplots" ,r-gplots)
1349 ("r-iranges" ,r-iranges)
1350 ("r-lattice" ,r-lattice)
1351 ("r-limma" ,r-limma)
1352 ("r-locfit" ,r-locfit)
1353 ("r-rcolorbrewer" , r-rcolorbrewer)
1355 ("r-rhtslib" ,r-rhtslib)
1356 ("r-rsamtools" ,r-rsamtools)
1357 ("r-s4vectors" ,r-s4vectors)
1358 ("r-summarizedexperiment" ,r-summarizedexperiment)
1359 ("r-systempiper" ,r-systempiper)))
1360 (home-page "http://bioconductor.org/packages/DiffBind")
1361 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1363 "This package computes differentially bound sites from multiple
1364 ChIP-seq experiments using affinity (quantitative) data. Also enables
1365 occupancy (overlap) analysis and plotting functions.")
1366 (license license:artistic2.0)))
1368 (define-public r-ripseeker
1370 (name "r-ripseeker")
1375 (uri (bioconductor-uri "RIPSeeker" version))
1378 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1379 (properties `((upstream-name . "RIPSeeker")))
1380 (build-system r-build-system)
1382 `(("r-s4vectors" ,r-s4vectors)
1383 ("r-iranges" ,r-iranges)
1384 ("r-genomicranges" ,r-genomicranges)
1385 ("r-summarizedexperiment" ,r-summarizedexperiment)
1386 ("r-rsamtools" ,r-rsamtools)
1387 ("r-genomicalignments" ,r-genomicalignments)
1388 ("r-rtracklayer" ,r-rtracklayer)))
1389 (home-page "http://bioconductor.org/packages/RIPSeeker")
1391 "Identifying protein-associated transcripts from RIP-seq experiments")
1393 "This package infers and discriminates RIP peaks from RIP-seq alignments
1394 using two-state HMM with negative binomial emission probability. While
1395 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1396 a suite of bioinformatics tools integrated within this self-contained software
1397 package comprehensively addressing issues ranging from post-alignments
1398 processing to visualization and annotation.")
1399 (license license:gpl2)))
1401 (define-public r-multtest
1408 (uri (bioconductor-uri "multtest" version))
1411 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1412 (build-system r-build-system)
1414 `(("r-survival" ,r-survival)
1415 ("r-biocgenerics" ,r-biocgenerics)
1416 ("r-biobase" ,r-biobase)
1417 ("r-mass" ,r-mass)))
1418 (home-page "http://bioconductor.org/packages/multtest")
1419 (synopsis "Resampling-based multiple hypothesis testing")
1421 "This package can do non-parametric bootstrap and permutation
1422 resampling-based multiple testing procedures (including empirical Bayes
1423 methods) for controlling the family-wise error rate (FWER), generalized
1424 family-wise error rate (gFWER), tail probability of the proportion of
1425 false positives (TPPFP), and false discovery rate (FDR). Several choices
1426 of bootstrap-based null distribution are implemented (centered, centered
1427 and scaled, quantile-transformed). Single-step and step-wise methods are
1428 available. Tests based on a variety of T- and F-statistics (including
1429 T-statistics based on regression parameters from linear and survival models
1430 as well as those based on correlation parameters) are included. When probing
1431 hypotheses with T-statistics, users may also select a potentially faster null
1432 distribution which is multivariate normal with mean zero and variance
1433 covariance matrix derived from the vector influence function. Results are
1434 reported in terms of adjusted P-values, confidence regions and test statistic
1435 cutoffs. The procedures are directly applicable to identifying differentially
1436 expressed genes in DNA microarray experiments.")
1437 (license license:lgpl3)))
1439 (define-public r-graph
1445 (uri (bioconductor-uri "graph" version))
1448 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1449 (build-system r-build-system)
1451 `(("r-biocgenerics" ,r-biocgenerics)))
1452 (home-page "https://bioconductor.org/packages/graph")
1453 (synopsis "Handle graph data structures in R")
1455 "This package implements some simple graph handling capabilities for R.")
1456 (license license:artistic2.0)))
1458 (define-public r-codedepends
1460 (name "r-codedepends")
1465 (uri (cran-uri "CodeDepends" version))
1468 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1469 (properties `((upstream-name . "CodeDepends")))
1470 (build-system r-build-system)
1472 `(("r-codetools" ,r-codetools)
1473 ("r-graph" ,r-graph)
1475 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1476 (synopsis "Analysis of R code for reproducible research and code comprehension")
1478 "This package provides tools for analyzing R expressions or blocks of
1479 code and determining the dependencies between them. It focuses on R scripts,
1480 but can be used on the bodies of functions. There are many facilities
1481 including the ability to summarize or get a high-level view of code,
1482 determining dependencies between variables, code improvement suggestions.")
1483 ;; Any version of the GPL
1484 (license (list license:gpl2+ license:gpl3+))))
1486 (define-public r-chippeakanno
1488 (name "r-chippeakanno")
1493 (uri (bioconductor-uri "ChIPpeakAnno" version))
1496 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1497 (properties `((upstream-name . "ChIPpeakAnno")))
1498 (build-system r-build-system)
1500 `(("r-annotationdbi" ,r-annotationdbi)
1501 ("r-biobase" ,r-biobase)
1502 ("r-biocgenerics" ,r-biocgenerics)
1503 ("r-biocmanager" ,r-biocmanager)
1504 ("r-biomart" ,r-biomart)
1505 ("r-biostrings" ,r-biostrings)
1506 ("r-bsgenome" ,r-bsgenome)
1508 ("r-delayedarray" ,r-delayedarray)
1509 ("r-ensembldb" ,r-ensembldb)
1510 ("r-genomeinfodb" ,r-genomeinfodb)
1511 ("r-genomicalignments" ,r-genomicalignments)
1512 ("r-genomicfeatures" ,r-genomicfeatures)
1513 ("r-genomicranges" ,r-genomicranges)
1514 ("r-go-db" ,r-go-db)
1515 ("r-graph" ,r-graph)
1517 ("r-iranges" ,r-iranges)
1518 ("r-limma" ,r-limma)
1519 ("r-matrixstats" ,r-matrixstats)
1520 ("r-multtest" ,r-multtest)
1522 ("r-regioner" ,r-regioner)
1523 ("r-rsamtools" ,r-rsamtools)
1524 ("r-rtracklayer" ,r-rtracklayer)
1525 ("r-s4vectors" ,r-s4vectors)
1526 ("r-seqinr" ,r-seqinr)
1527 ("r-summarizedexperiment" ,r-summarizedexperiment)
1528 ("r-venndiagram" ,r-venndiagram)))
1529 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1530 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1532 "The package includes functions to retrieve the sequences around the peak,
1533 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1534 custom features such as most conserved elements and other transcription factor
1535 binding sites supplied by users. Starting 2.0.5, new functions have been added
1536 for finding the peaks with bi-directional promoters with summary statistics
1537 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1538 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1539 enrichedGO (addGeneIDs).")
1540 (license license:gpl2+)))
1542 (define-public r-marray
1548 (uri (bioconductor-uri "marray" version))
1550 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1551 (build-system r-build-system)
1553 `(("r-limma" ,r-limma)))
1554 (home-page "http://bioconductor.org/packages/marray")
1555 (synopsis "Exploratory analysis for two-color spotted microarray data")
1556 (description "This package contains class definitions for two-color spotted
1557 microarray data. It also includes functions for data input, diagnostic plots,
1558 normalization and quality checking.")
1559 (license license:lgpl2.0+)))
1561 (define-public r-cghbase
1567 (uri (bioconductor-uri "CGHbase" version))
1569 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1570 (properties `((upstream-name . "CGHbase")))
1571 (build-system r-build-system)
1573 `(("r-biobase" ,r-biobase)
1574 ("r-marray" ,r-marray)))
1575 (home-page "http://bioconductor.org/packages/CGHbase")
1576 (synopsis "Base functions and classes for arrayCGH data analysis")
1577 (description "This package contains functions and classes that are needed by
1578 the @code{arrayCGH} packages.")
1579 (license license:gpl2+)))
1581 (define-public r-cghcall
1587 (uri (bioconductor-uri "CGHcall" version))
1589 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1590 (properties `((upstream-name . "CGHcall")))
1591 (build-system r-build-system)
1593 `(("r-biobase" ,r-biobase)
1594 ("r-cghbase" ,r-cghbase)
1595 ("r-impute" ,r-impute)
1596 ("r-dnacopy" ,r-dnacopy)
1597 ("r-snowfall" ,r-snowfall)))
1598 (home-page "http://bioconductor.org/packages/CGHcall")
1599 (synopsis "Base functions and classes for arrayCGH data analysis")
1600 (description "This package contains functions and classes that are needed by
1601 @code{arrayCGH} packages.")
1602 (license license:gpl2+)))
1604 (define-public r-qdnaseq
1610 (uri (bioconductor-uri "QDNAseq" version))
1612 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1613 (properties `((upstream-name . "QDNAseq")))
1614 (build-system r-build-system)
1616 `(("r-biobase" ,r-biobase)
1617 ("r-biocparallel" ,r-biocparallel)
1618 ("r-cghbase" ,r-cghbase)
1619 ("r-cghcall" ,r-cghcall)
1620 ("r-dnacopy" ,r-dnacopy)
1621 ("r-genomicranges" ,r-genomicranges)
1622 ("r-iranges" ,r-iranges)
1623 ("r-matrixstats" ,r-matrixstats)
1624 ("r-r-utils" ,r-r-utils)
1625 ("r-rsamtools" ,r-rsamtools)))
1626 (home-page "http://bioconductor.org/packages/QDNAseq")
1627 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1628 (description "The genome is divided into non-overlapping fixed-sized bins,
1629 number of sequence reads in each counted, adjusted with a simultaneous
1630 two-dimensional loess correction for sequence mappability and GC content, and
1631 filtered to remove spurious regions in the genome. Downstream steps of
1632 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1634 (license license:gpl2+)))
1636 (define-public r-bayseq
1643 (uri (bioconductor-uri "baySeq" version))
1646 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1647 (properties `((upstream-name . "baySeq")))
1648 (build-system r-build-system)
1650 `(("r-abind" ,r-abind)
1651 ("r-edger" ,r-edger)
1652 ("r-genomicranges" ,r-genomicranges)))
1653 (home-page "https://bioconductor.org/packages/baySeq/")
1654 (synopsis "Bayesian analysis of differential expression patterns in count data")
1656 "This package identifies differential expression in high-throughput count
1657 data, such as that derived from next-generation sequencing machines,
1658 calculating estimated posterior likelihoods of differential expression (or
1659 more complex hypotheses) via empirical Bayesian methods.")
1660 (license license:gpl3)))
1662 (define-public r-chipcomp
1669 (uri (bioconductor-uri "ChIPComp" version))
1672 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1673 (properties `((upstream-name . "ChIPComp")))
1674 (build-system r-build-system)
1676 `(("r-biocgenerics" ,r-biocgenerics)
1677 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1678 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1679 ("r-genomeinfodb" ,r-genomeinfodb)
1680 ("r-genomicranges" ,r-genomicranges)
1681 ("r-iranges" ,r-iranges)
1682 ("r-limma" ,r-limma)
1683 ("r-rsamtools" ,r-rsamtools)
1684 ("r-rtracklayer" ,r-rtracklayer)
1685 ("r-s4vectors" ,r-s4vectors)))
1686 (home-page "https://bioconductor.org/packages/ChIPComp")
1687 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1689 "ChIPComp implements a statistical method for quantitative comparison of
1690 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1691 sites across multiple conditions considering matching control in ChIP-seq
1693 ;; Any version of the GPL.
1694 (license license:gpl3+)))
1696 (define-public r-riboprofiling
1698 (name "r-riboprofiling")
1703 (uri (bioconductor-uri "RiboProfiling" version))
1706 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1707 (properties `((upstream-name . "RiboProfiling")))
1708 (build-system r-build-system)
1710 `(("r-biocgenerics" ,r-biocgenerics)
1711 ("r-biostrings" ,r-biostrings)
1712 ("r-data-table" ,r-data-table)
1713 ("r-genomeinfodb" ,r-genomeinfodb)
1714 ("r-genomicalignments" ,r-genomicalignments)
1715 ("r-genomicfeatures" ,r-genomicfeatures)
1716 ("r-genomicranges" ,r-genomicranges)
1717 ("r-ggbio" ,r-ggbio)
1718 ("r-ggplot2" ,r-ggplot2)
1719 ("r-iranges" ,r-iranges)
1721 ("r-reshape2" ,r-reshape2)
1722 ("r-rsamtools" ,r-rsamtools)
1723 ("r-rtracklayer" ,r-rtracklayer)
1724 ("r-s4vectors" ,r-s4vectors)
1725 ("r-sqldf" ,r-sqldf)))
1726 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1727 (synopsis "Ribosome profiling data analysis")
1728 (description "Starting with a BAM file, this package provides the
1729 necessary functions for quality assessment, read start position recalibration,
1730 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1731 of count data: pairs, log fold-change, codon frequency and coverage
1732 assessment, principal component analysis on codon coverage.")
1733 (license license:gpl3)))
1735 (define-public r-riboseqr
1742 (uri (bioconductor-uri "riboSeqR" version))
1745 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1746 (properties `((upstream-name . "riboSeqR")))
1747 (build-system r-build-system)
1749 `(("r-abind" ,r-abind)
1750 ("r-bayseq" ,r-bayseq)
1751 ("r-genomeinfodb" ,r-genomeinfodb)
1752 ("r-genomicranges" ,r-genomicranges)
1753 ("r-iranges" ,r-iranges)
1754 ("r-rsamtools" ,r-rsamtools)
1755 ("r-seqlogo" ,r-seqlogo)))
1756 (home-page "https://bioconductor.org/packages/riboSeqR/")
1757 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1759 "This package provides plotting functions, frameshift detection and
1760 parsing of genetic sequencing data from ribosome profiling experiments.")
1761 (license license:gpl3)))
1763 (define-public r-interactionset
1765 (name "r-interactionset")
1770 (uri (bioconductor-uri "InteractionSet" version))
1773 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1775 `((upstream-name . "InteractionSet")))
1776 (build-system r-build-system)
1778 `(("r-biocgenerics" ,r-biocgenerics)
1779 ("r-genomeinfodb" ,r-genomeinfodb)
1780 ("r-genomicranges" ,r-genomicranges)
1781 ("r-iranges" ,r-iranges)
1782 ("r-matrix" ,r-matrix)
1784 ("r-s4vectors" ,r-s4vectors)
1785 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1786 (home-page "https://bioconductor.org/packages/InteractionSet")
1787 (synopsis "Base classes for storing genomic interaction data")
1789 "This package provides the @code{GInteractions},
1790 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1791 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1793 (license license:gpl3)))
1795 (define-public r-genomicinteractions
1797 (name "r-genomicinteractions")
1802 (uri (bioconductor-uri "GenomicInteractions" version))
1805 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1807 `((upstream-name . "GenomicInteractions")))
1808 (build-system r-build-system)
1810 `(("r-biobase" ,r-biobase)
1811 ("r-biocgenerics" ,r-biocgenerics)
1812 ("r-data-table" ,r-data-table)
1813 ("r-dplyr" ,r-dplyr)
1814 ("r-genomeinfodb" ,r-genomeinfodb)
1815 ("r-genomicranges" ,r-genomicranges)
1816 ("r-ggplot2" ,r-ggplot2)
1817 ("r-gridextra" ,r-gridextra)
1819 ("r-igraph" ,r-igraph)
1820 ("r-interactionset" ,r-interactionset)
1821 ("r-iranges" ,r-iranges)
1822 ("r-rsamtools" ,r-rsamtools)
1823 ("r-rtracklayer" ,r-rtracklayer)
1824 ("r-s4vectors" ,r-s4vectors)
1825 ("r-stringr" ,r-stringr)))
1826 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1827 (synopsis "R package for handling genomic interaction data")
1829 "This R package provides tools for handling genomic interaction data,
1830 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1831 information and producing various plots and statistics.")
1832 (license license:gpl3)))
1834 (define-public r-ctc
1841 (uri (bioconductor-uri "ctc" version))
1844 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1845 (build-system r-build-system)
1846 (propagated-inputs `(("r-amap" ,r-amap)))
1847 (home-page "https://bioconductor.org/packages/ctc/")
1848 (synopsis "Cluster and tree conversion")
1850 "This package provides tools for exporting and importing classification
1851 trees and clusters to other programs.")
1852 (license license:gpl2)))
1854 (define-public r-goseq
1861 (uri (bioconductor-uri "goseq" version))
1864 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1865 (build-system r-build-system)
1867 `(("r-annotationdbi" ,r-annotationdbi)
1868 ("r-biasedurn" ,r-biasedurn)
1869 ("r-biocgenerics" ,r-biocgenerics)
1870 ("r-genelendatabase" ,r-genelendatabase)
1871 ("r-go-db" ,r-go-db)
1872 ("r-mgcv" ,r-mgcv)))
1873 (home-page "https://bioconductor.org/packages/goseq/")
1874 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1876 "This package provides tools to detect Gene Ontology and/or other user
1877 defined categories which are over/under represented in RNA-seq data.")
1878 (license license:lgpl2.0+)))
1880 (define-public r-glimma
1887 (uri (bioconductor-uri "Glimma" version))
1890 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1891 (properties `((upstream-name . "Glimma")))
1892 (build-system r-build-system)
1894 `(("r-edger" ,r-edger)
1895 ("r-jsonlite" ,r-jsonlite)
1896 ("r-s4vectors" ,r-s4vectors)))
1897 (home-page "https://github.com/Shians/Glimma")
1898 (synopsis "Interactive HTML graphics")
1900 "This package generates interactive visualisations for analysis of
1901 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1902 HTML page. The interactions are built on top of the popular static
1903 representations of analysis results in order to provide additional
1905 (license license:lgpl3)))
1907 (define-public r-rots
1914 (uri (bioconductor-uri "ROTS" version))
1917 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1918 (properties `((upstream-name . "ROTS")))
1919 (build-system r-build-system)
1921 `(("r-biobase" ,r-biobase)
1922 ("r-rcpp" ,r-rcpp)))
1923 (home-page "https://bioconductor.org/packages/ROTS/")
1924 (synopsis "Reproducibility-Optimized Test Statistic")
1926 "This package provides tools for calculating the
1927 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1929 (license license:gpl2+)))
1931 (define-public r-plgem
1938 (uri (bioconductor-uri "plgem" version))
1941 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1942 (build-system r-build-system)
1944 `(("r-biobase" ,r-biobase)
1945 ("r-mass" ,r-mass)))
1946 (home-page "http://www.genopolis.it")
1947 (synopsis "Detect differential expression in microarray and proteomics datasets")
1949 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1950 model the variance-versus-mean dependence that exists in a variety of
1951 genome-wide datasets, including microarray and proteomics data. The use of
1952 PLGEM has been shown to improve the detection of differentially expressed
1953 genes or proteins in these datasets.")
1954 (license license:gpl2)))
1956 (define-public r-inspect
1963 (uri (bioconductor-uri "INSPEcT" version))
1966 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1967 (properties `((upstream-name . "INSPEcT")))
1968 (build-system r-build-system)
1970 `(("r-biobase" ,r-biobase)
1971 ("r-biocgenerics" ,r-biocgenerics)
1972 ("r-biocparallel" ,r-biocparallel)
1973 ("r-deseq2" ,r-deseq2)
1974 ("r-desolve" ,r-desolve)
1975 ("r-genomicalignments" ,r-genomicalignments)
1976 ("r-genomicfeatures" ,r-genomicfeatures)
1977 ("r-genomicranges" ,r-genomicranges)
1978 ("r-iranges" ,r-iranges)
1979 ("r-plgem" ,r-plgem)
1980 ("r-preprocesscore" ,r-preprocesscore)
1982 ("r-rootsolve" ,r-rootsolve)
1983 ("r-rsamtools" ,r-rsamtools)
1984 ("r-s4vectors" ,r-s4vectors)
1985 ("r-shiny" ,r-shiny)
1986 ("r-summarizedexperiment" ,r-summarizedexperiment)
1987 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1988 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1989 (home-page "https://bioconductor.org/packages/INSPEcT")
1990 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1992 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1993 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1994 order to evaluate synthesis, processing and degradation rates and assess via
1995 modeling the rates that determines changes in mature mRNA levels.")
1996 (license license:gpl2)))
1998 (define-public r-dnabarcodes
2000 (name "r-dnabarcodes")
2005 (uri (bioconductor-uri "DNABarcodes" version))
2008 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
2009 (properties `((upstream-name . "DNABarcodes")))
2010 (build-system r-build-system)
2013 ("r-matrix" ,r-matrix)
2014 ("r-rcpp" ,r-rcpp)))
2015 (home-page "https://bioconductor.org/packages/DNABarcodes")
2016 (synopsis "Create and analyze DNA barcodes")
2018 "This package offers tools to create DNA barcode sets capable of
2019 correcting insertion, deletion, and substitution errors. Existing barcodes
2020 can be analyzed regarding their minimal, maximal and average distances between
2021 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2022 demultiplexed, i.e. assigned to their original reference barcode.")
2023 (license license:gpl2)))
2025 (define-public r-ruvseq
2032 (uri (bioconductor-uri "RUVSeq" version))
2035 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
2036 (properties `((upstream-name . "RUVSeq")))
2037 (build-system r-build-system)
2039 `(("r-biobase" ,r-biobase)
2040 ("r-edaseq" ,r-edaseq)
2041 ("r-edger" ,r-edger)
2042 ("r-mass" ,r-mass)))
2043 (home-page "https://github.com/drisso/RUVSeq")
2044 (synopsis "Remove unwanted variation from RNA-Seq data")
2046 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2047 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2049 (license license:artistic2.0)))
2051 (define-public r-biocneighbors
2053 (name "r-biocneighbors")
2058 (uri (bioconductor-uri "BiocNeighbors" version))
2061 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
2062 (properties `((upstream-name . "BiocNeighbors")))
2063 (build-system r-build-system)
2065 `(("r-biocgenerics" ,r-biocgenerics)
2066 ("r-biocparallel" ,r-biocparallel)
2068 ("r-rcppannoy" ,r-rcppannoy)
2069 ("r-rcpphnsw" ,r-rcpphnsw)
2070 ("r-s4vectors" ,r-s4vectors)))
2071 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2072 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2074 "This package implements exact and approximate methods for nearest
2075 neighbor detection, in a framework that allows them to be easily switched
2076 within Bioconductor packages or workflows. The exact algorithm is implemented
2077 using pre-clustering with the k-means algorithm. Functions are also provided
2078 to search for all neighbors within a given distance. Parallelization is
2079 achieved for all methods using the BiocParallel framework.")
2080 (license license:gpl3)))
2082 (define-public r-biocsingular
2084 (name "r-biocsingular")
2089 (uri (bioconductor-uri "BiocSingular" version))
2092 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
2093 (properties `((upstream-name . "BiocSingular")))
2094 (build-system r-build-system)
2096 `(("r-beachmat" ,r-beachmat)
2097 ("r-biocgenerics" ,r-biocgenerics)
2098 ("r-biocparallel" ,r-biocparallel)
2099 ("r-delayedarray" ,r-delayedarray)
2100 ("r-irlba" ,r-irlba)
2101 ("r-matrix" ,r-matrix)
2104 ("r-s4vectors" ,r-s4vectors)))
2105 (home-page "https://github.com/LTLA/BiocSingular")
2106 (synopsis "Singular value decomposition for Bioconductor packages")
2108 "This package implements exact and approximate methods for singular value
2109 decomposition and principal components analysis, in a framework that allows
2110 them to be easily switched within Bioconductor packages or workflows. Where
2111 possible, parallelization is achieved using the BiocParallel framework.")
2112 (license license:gpl3)))
2114 (define-public r-destiny
2121 (uri (bioconductor-uri "destiny" version))
2124 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
2125 (build-system r-build-system)
2127 `(("r-biobase" ,r-biobase)
2128 ("r-biocgenerics" ,r-biocgenerics)
2129 ("r-ggplot2" ,r-ggplot2)
2130 ("r-ggthemes" ,r-ggthemes)
2131 ("r-igraph" ,r-igraph)
2132 ("r-matrix" ,r-matrix)
2133 ("r-proxy" ,r-proxy)
2135 ("r-rcppeigen" ,r-rcppeigen)
2136 ("r-scales" ,r-scales)
2137 ("r-scatterplot3d" ,r-scatterplot3d)
2138 ("r-smoother" ,r-smoother)
2139 ("r-summarizedexperiment" ,r-summarizedexperiment)
2141 (home-page "https://bioconductor.org/packages/destiny/")
2142 (synopsis "Create and plot diffusion maps")
2143 (description "This package provides tools to create and plot diffusion
2145 ;; Any version of the GPL
2146 (license license:gpl3+)))
2148 (define-public r-savr
2155 (uri (bioconductor-uri "savR" version))
2158 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
2159 (properties `((upstream-name . "savR")))
2160 (build-system r-build-system)
2162 `(("r-ggplot2" ,r-ggplot2)
2163 ("r-gridextra" ,r-gridextra)
2164 ("r-reshape2" ,r-reshape2)
2165 ("r-scales" ,r-scales)
2167 (home-page "https://github.com/bcalder/savR")
2168 (synopsis "Parse and analyze Illumina SAV files")
2170 "This package provides tools to parse Illumina Sequence Analysis
2171 Viewer (SAV) files, access data, and generate QC plots.")
2172 (license license:agpl3+)))
2174 (define-public r-chipexoqual
2176 (name "r-chipexoqual")
2181 (uri (bioconductor-uri "ChIPexoQual" version))
2184 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
2185 (properties `((upstream-name . "ChIPexoQual")))
2186 (build-system r-build-system)
2188 `(("r-biocparallel" ,r-biocparallel)
2189 ("r-biovizbase" ,r-biovizbase)
2190 ("r-broom" ,r-broom)
2191 ("r-data-table" ,r-data-table)
2192 ("r-dplyr" ,r-dplyr)
2193 ("r-genomeinfodb" ,r-genomeinfodb)
2194 ("r-genomicalignments" ,r-genomicalignments)
2195 ("r-genomicranges" ,r-genomicranges)
2196 ("r-ggplot2" ,r-ggplot2)
2197 ("r-hexbin" ,r-hexbin)
2198 ("r-iranges" ,r-iranges)
2199 ("r-rcolorbrewer" ,r-rcolorbrewer)
2200 ("r-rmarkdown" ,r-rmarkdown)
2201 ("r-rsamtools" ,r-rsamtools)
2202 ("r-s4vectors" ,r-s4vectors)
2203 ("r-scales" ,r-scales)
2204 ("r-viridis" ,r-viridis)))
2205 (home-page "https://github.com/keleslab/ChIPexoQual")
2206 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2208 "This package provides a quality control pipeline for ChIP-exo/nexus
2210 (license license:gpl2+)))
2212 (define-public r-copynumber
2214 (name "r-copynumber")
2218 (uri (bioconductor-uri "copynumber" version))
2221 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
2222 (build-system r-build-system)
2224 `(("r-s4vectors" ,r-s4vectors)
2225 ("r-iranges" ,r-iranges)
2226 ("r-genomicranges" ,r-genomicranges)
2227 ("r-biocgenerics" ,r-biocgenerics)))
2228 (home-page "https://bioconductor.org/packages/copynumber")
2229 (synopsis "Segmentation of single- and multi-track copy number data")
2231 "This package segments single- and multi-track copy number data by a
2232 penalized least squares regression method.")
2233 (license license:artistic2.0)))
2235 (define-public r-dnacopy
2242 (uri (bioconductor-uri "DNAcopy" version))
2245 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2246 (properties `((upstream-name . "DNAcopy")))
2247 (build-system r-build-system)
2248 (native-inputs `(("gfortran" ,gfortran)))
2249 (home-page "https://bioconductor.org/packages/DNAcopy")
2250 (synopsis "DNA copy number data analysis")
2252 "This package implements the @dfn{circular binary segmentation} (CBS)
2253 algorithm to segment DNA copy number data and identify genomic regions with
2254 abnormal copy number.")
2255 (license license:gpl2+)))
2257 ;; This is a CRAN package, but it uncharacteristically depends on a
2258 ;; Bioconductor package.
2259 (define-public r-htscluster
2261 (name "r-htscluster")
2266 (uri (cran-uri "HTSCluster" version))
2269 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2270 (properties `((upstream-name . "HTSCluster")))
2271 (build-system r-build-system)
2273 `(("r-capushe" ,r-capushe)
2274 ("r-edger" ,r-edger)
2275 ("r-plotrix" ,r-plotrix)))
2276 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2277 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2279 "This package provides a Poisson mixture model is implemented to cluster
2280 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2281 estimation is performed using either the EM or CEM algorithm, and the slope
2282 heuristics are used for model selection (i.e., to choose the number of
2284 (license license:gpl3+)))
2286 (define-public r-deds
2293 (uri (bioconductor-uri "DEDS" version))
2296 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2297 (properties `((upstream-name . "DEDS")))
2298 (build-system r-build-system)
2299 (home-page "https://bioconductor.org/packages/DEDS/")
2300 (synopsis "Differential expression via distance summary for microarray data")
2302 "This library contains functions that calculate various statistics of
2303 differential expression for microarray data, including t statistics, fold
2304 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2305 also implements a new methodology called DEDS (Differential Expression via
2306 Distance Summary), which selects differentially expressed genes by integrating
2307 and summarizing a set of statistics using a weighted distance approach.")
2308 ;; Any version of the LGPL.
2309 (license license:lgpl3+)))
2311 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2313 (define-public r-nbpseq
2320 (uri (cran-uri "NBPSeq" version))
2323 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2324 (properties `((upstream-name . "NBPSeq")))
2325 (build-system r-build-system)
2327 `(("r-qvalue" ,r-qvalue)))
2328 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2329 (synopsis "Negative binomial models for RNA-Seq data")
2331 "This package provides negative binomial models for two-group comparisons
2332 and regression inferences from RNA-sequencing data.")
2333 (license license:gpl2)))
2335 (define-public r-ebseq
2342 (uri (bioconductor-uri "EBSeq" version))
2345 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2346 (properties `((upstream-name . "EBSeq")))
2347 (build-system r-build-system)
2349 `(("r-blockmodeling" ,r-blockmodeling)
2350 ("r-gplots" ,r-gplots)
2351 ("r-testthat" ,r-testthat)))
2352 (home-page "https://bioconductor.org/packages/EBSeq")
2353 (synopsis "Differential expression analysis of RNA-seq data")
2355 "This package provides tools for differential expression analysis at both
2356 gene and isoform level using RNA-seq data")
2357 (license license:artistic2.0)))
2359 (define-public r-lpsymphony
2361 (name "r-lpsymphony")
2366 (uri (bioconductor-uri "lpsymphony" version))
2369 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2370 (build-system r-build-system)
2372 `(("gfortran" ,gfortran)
2375 `(("pkg-config" ,pkg-config)))
2376 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2377 (synopsis "Symphony integer linear programming solver in R")
2379 "This package was derived from Rsymphony. The package provides an R
2380 interface to SYMPHONY, a linear programming solver written in C++. The main
2381 difference between this package and Rsymphony is that it includes the solver
2382 source code, while Rsymphony expects to find header and library files on the
2383 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2384 to install interface to SYMPHONY.")
2385 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2386 ;; lpsimphony is released under the same terms.
2387 (license license:epl1.0)))
2389 (define-public r-ihw
2396 (uri (bioconductor-uri "IHW" version))
2399 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2400 (properties `((upstream-name . "IHW")))
2401 (build-system r-build-system)
2403 `(("r-biocgenerics" ,r-biocgenerics)
2404 ("r-fdrtool" ,r-fdrtool)
2405 ("r-lpsymphony" ,r-lpsymphony)
2406 ("r-slam" ,r-slam)))
2407 (home-page "https://bioconductor.org/packages/IHW")
2408 (synopsis "Independent hypothesis weighting")
2410 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2411 procedure that increases power compared to the method of Benjamini and
2412 Hochberg by assigning data-driven weights to each hypothesis. The input to
2413 IHW is a two-column table of p-values and covariates. The covariate can be
2414 any continuous-valued or categorical variable that is thought to be
2415 informative on the statistical properties of each hypothesis test, while it is
2416 independent of the p-value under the null hypothesis.")
2417 (license license:artistic2.0)))
2419 (define-public r-icobra
2426 (uri (bioconductor-uri "iCOBRA" version))
2429 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2430 (properties `((upstream-name . "iCOBRA")))
2431 (build-system r-build-system)
2433 `(("r-dplyr" ,r-dplyr)
2435 ("r-ggplot2" ,r-ggplot2)
2436 ("r-limma" ,r-limma)
2437 ("r-reshape2" ,r-reshape2)
2439 ("r-scales" ,r-scales)
2440 ("r-shiny" ,r-shiny)
2441 ("r-shinybs" ,r-shinybs)
2442 ("r-shinydashboard" ,r-shinydashboard)
2443 ("r-upsetr" ,r-upsetr)))
2444 (home-page "https://bioconductor.org/packages/iCOBRA")
2445 (synopsis "Comparison and visualization of ranking and assignment methods")
2447 "This package provides functions for calculation and visualization of
2448 performance metrics for evaluation of ranking and binary
2449 classification (assignment) methods. It also contains a Shiny application for
2450 interactive exploration of results.")
2451 (license license:gpl2+)))
2453 (define-public r-mast
2460 (uri (bioconductor-uri "MAST" version))
2463 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2464 (properties `((upstream-name . "MAST")))
2465 (build-system r-build-system)
2467 `(("r-abind" ,r-abind)
2469 ("r-biobase" ,r-biobase)
2470 ("r-biocgenerics" ,r-biocgenerics)
2471 ("r-data-table" ,r-data-table)
2472 ("r-ggplot2" ,r-ggplot2)
2474 ("r-progress" ,r-progress)
2475 ("r-reshape2" ,r-reshape2)
2476 ("r-s4vectors" ,r-s4vectors)
2477 ("r-singlecellexperiment" ,r-singlecellexperiment)
2478 ("r-stringr" ,r-stringr)
2479 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2480 (home-page "https://github.com/RGLab/MAST/")
2481 (synopsis "Model-based analysis of single cell transcriptomics")
2483 "This package provides methods and models for handling zero-inflated
2484 single cell assay data.")
2485 (license license:gpl2+)))
2487 (define-public r-monocle
2494 (uri (bioconductor-uri "monocle" version))
2497 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2498 (build-system r-build-system)
2500 `(("r-biobase" ,r-biobase)
2501 ("r-biocgenerics" ,r-biocgenerics)
2502 ("r-biocviews" ,r-biocviews)
2503 ("r-cluster" ,r-cluster)
2504 ("r-combinat" ,r-combinat)
2505 ("r-ddrtree" ,r-ddrtree)
2506 ("r-densityclust" ,r-densityclust)
2507 ("r-dplyr" ,r-dplyr)
2508 ("r-fastica" ,r-fastica)
2509 ("r-ggplot2" ,r-ggplot2)
2510 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2511 ("r-igraph" ,r-igraph)
2512 ("r-irlba" ,r-irlba)
2513 ("r-limma" ,r-limma)
2515 ("r-matrix" ,r-matrix)
2516 ("r-matrixstats" ,r-matrixstats)
2517 ("r-pheatmap" ,r-pheatmap)
2519 ("r-proxy" ,r-proxy)
2520 ("r-qlcmatrix" ,r-qlcmatrix)
2523 ("r-reshape2" ,r-reshape2)
2524 ("r-rtsne" ,r-rtsne)
2526 ("r-stringr" ,r-stringr)
2527 ("r-tibble" ,r-tibble)
2529 ("r-viridis" ,r-viridis)))
2530 (home-page "https://bioconductor.org/packages/monocle")
2531 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2533 "Monocle performs differential expression and time-series analysis for
2534 single-cell expression experiments. It orders individual cells according to
2535 progress through a biological process, without knowing ahead of time which
2536 genes define progress through that process. Monocle also performs
2537 differential expression analysis, clustering, visualization, and other useful
2538 tasks on single cell expression data. It is designed to work with RNA-Seq and
2539 qPCR data, but could be used with other types as well.")
2540 (license license:artistic2.0)))
2542 (define-public r-monocle3
2550 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2552 (file-name (git-file-name name version))
2555 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2556 (build-system r-build-system)
2558 `(("r-biobase" ,r-biobase)
2559 ("r-biocgenerics" ,r-biocgenerics)
2560 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2561 ("r-dplyr" ,r-dplyr)
2562 ("r-ggplot2" ,r-ggplot2)
2563 ("r-ggrepel" ,r-ggrepel)
2565 ("r-htmlwidgets" ,r-htmlwidgets)
2566 ("r-igraph" ,r-igraph)
2567 ("r-irlba" ,r-irlba)
2568 ("r-limma" ,r-limma)
2569 ("r-lmtest" ,r-lmtest)
2571 ("r-matrix" ,r-matrix)
2572 ("r-matrix-utils" ,r-matrix-utils)
2573 ("r-pbapply" ,r-pbapply)
2574 ("r-pbmcapply" ,r-pbmcapply)
2575 ("r-pheatmap" ,r-pheatmap)
2576 ("r-plotly" ,r-plotly)
2578 ("r-proxy" ,r-proxy)
2580 ("r-purrr" ,r-purrr)
2583 ("r-rcppparallel" ,r-rcppparallel)
2584 ("r-reshape2" ,r-reshape2)
2585 ("r-reticulate" ,r-reticulate)
2586 ("r-rhpcblasctl" ,r-rhpcblasctl)
2587 ("r-rtsne" ,r-rtsne)
2588 ("r-shiny" ,r-shiny)
2590 ("r-spdep" ,r-spdep)
2591 ("r-speedglm" ,r-speedglm)
2592 ("r-stringr" ,r-stringr)
2593 ("r-singlecellexperiment" ,r-singlecellexperiment)
2594 ("r-tibble" ,r-tibble)
2595 ("r-tidyr" ,r-tidyr)
2597 ("r-viridis" ,r-viridis)))
2598 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2599 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2601 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2602 (license license:expat)))
2604 (define-public r-noiseq
2611 (uri (bioconductor-uri "NOISeq" version))
2614 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2615 (properties `((upstream-name . "NOISeq")))
2616 (build-system r-build-system)
2618 `(("r-biobase" ,r-biobase)
2619 ("r-matrix" ,r-matrix)))
2620 (home-page "https://bioconductor.org/packages/NOISeq")
2621 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2623 "This package provides tools to support the analysis of RNA-seq
2624 expression data or other similar kind of data. It provides exploratory plots
2625 to evaluate saturation, count distribution, expression per chromosome, type of
2626 detected features, features length, etc. It also supports the analysis of
2627 differential expression between two experimental conditions with no parametric
2629 (license license:artistic2.0)))
2631 (define-public r-scdd
2638 (uri (bioconductor-uri "scDD" version))
2641 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2642 (properties `((upstream-name . "scDD")))
2643 (build-system r-build-system)
2646 ("r-biocparallel" ,r-biocparallel)
2647 ("r-ebseq" ,r-ebseq)
2648 ("r-fields" ,r-fields)
2649 ("r-ggplot2" ,r-ggplot2)
2650 ("r-mclust" ,r-mclust)
2651 ("r-outliers" ,r-outliers)
2652 ("r-s4vectors" ,r-s4vectors)
2653 ("r-scran" ,r-scran)
2654 ("r-singlecellexperiment" ,r-singlecellexperiment)
2655 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2656 (home-page "https://github.com/kdkorthauer/scDD")
2657 (synopsis "Mixture modeling of single-cell RNA-seq data")
2659 "This package implements a method to analyze single-cell RNA-seq data
2660 utilizing flexible Dirichlet Process mixture models. Genes with differential
2661 distributions of expression are classified into several interesting patterns
2662 of differences between two conditions. The package also includes functions
2663 for simulating data with these patterns from negative binomial
2665 (license license:gpl2)))
2667 (define-public r-scone
2674 (uri (bioconductor-uri "scone" version))
2677 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2678 (build-system r-build-system)
2680 `(("r-aroma-light" ,r-aroma-light)
2681 ("r-biocparallel" ,r-biocparallel)
2683 ("r-class" ,r-class)
2684 ("r-cluster" ,r-cluster)
2685 ("r-compositions" ,r-compositions)
2686 ("r-diptest" ,r-diptest)
2687 ("r-edger" ,r-edger)
2689 ("r-gplots" ,r-gplots)
2690 ("r-hexbin" ,r-hexbin)
2691 ("r-limma" ,r-limma)
2692 ("r-matrixstats" ,r-matrixstats)
2693 ("r-mixtools" ,r-mixtools)
2694 ("r-rarpack" ,r-rarpack)
2695 ("r-rcolorbrewer" ,r-rcolorbrewer)
2696 ("r-rhdf5" ,r-rhdf5)
2697 ("r-ruvseq" ,r-ruvseq)
2698 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2699 (home-page "https://bioconductor.org/packages/scone")
2700 (synopsis "Single cell overview of normalized expression data")
2702 "SCONE is an R package for comparing and ranking the performance of
2703 different normalization schemes for single-cell RNA-seq and other
2704 high-throughput analyses.")
2705 (license license:artistic2.0)))
2707 (define-public r-geoquery
2714 (uri (bioconductor-uri "GEOquery" version))
2717 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2718 (properties `((upstream-name . "GEOquery")))
2719 (build-system r-build-system)
2721 `(("r-biobase" ,r-biobase)
2722 ("r-dplyr" ,r-dplyr)
2724 ("r-limma" ,r-limma)
2725 ("r-magrittr" ,r-magrittr)
2726 ("r-readr" ,r-readr)
2727 ("r-tidyr" ,r-tidyr)
2728 ("r-xml2" ,r-xml2)))
2729 (home-page "https://github.com/seandavi/GEOquery/")
2730 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2732 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2733 microarray data. Given the rich and varied nature of this resource, it is
2734 only natural to want to apply BioConductor tools to these data. GEOquery is
2735 the bridge between GEO and BioConductor.")
2736 (license license:gpl2)))
2738 (define-public r-illuminaio
2740 (name "r-illuminaio")
2745 (uri (bioconductor-uri "illuminaio" version))
2748 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2749 (build-system r-build-system)
2751 `(("r-base64" ,r-base64)))
2752 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2753 (synopsis "Parse Illumina microarray output files")
2755 "This package provides tools for parsing Illumina's microarray output
2756 files, including IDAT.")
2757 (license license:gpl2)))
2759 (define-public r-siggenes
2766 (uri (bioconductor-uri "siggenes" version))
2769 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2770 (build-system r-build-system)
2772 `(("r-biobase" ,r-biobase)
2773 ("r-multtest" ,r-multtest)
2774 ("r-scrime" ,r-scrime)))
2775 (home-page "https://bioconductor.org/packages/siggenes/")
2777 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2779 "This package provides tools for the identification of differentially
2780 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2781 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2782 Bayes Analyses of Microarrays} (EBAM).")
2783 (license license:lgpl2.0+)))
2785 (define-public r-bumphunter
2787 (name "r-bumphunter")
2792 (uri (bioconductor-uri "bumphunter" version))
2795 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2796 (build-system r-build-system)
2798 `(("r-annotationdbi" ,r-annotationdbi)
2799 ("r-biocgenerics" ,r-biocgenerics)
2800 ("r-dorng" ,r-dorng)
2801 ("r-foreach" ,r-foreach)
2802 ("r-genomeinfodb" ,r-genomeinfodb)
2803 ("r-genomicfeatures" ,r-genomicfeatures)
2804 ("r-genomicranges" ,r-genomicranges)
2805 ("r-iranges" ,r-iranges)
2806 ("r-iterators" ,r-iterators)
2807 ("r-limma" ,r-limma)
2808 ("r-locfit" ,r-locfit)
2809 ("r-matrixstats" ,r-matrixstats)
2810 ("r-s4vectors" ,r-s4vectors)))
2811 (home-page "https://github.com/ririzarr/bumphunter")
2812 (synopsis "Find bumps in genomic data")
2814 "This package provides tools for finding bumps in genomic data in order
2815 to identify differentially methylated regions in epigenetic epidemiology
2817 (license license:artistic2.0)))
2819 (define-public r-minfi
2826 (uri (bioconductor-uri "minfi" version))
2829 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2830 (build-system r-build-system)
2832 `(("r-beanplot" ,r-beanplot)
2833 ("r-biobase" ,r-biobase)
2834 ("r-biocgenerics" ,r-biocgenerics)
2835 ("r-biocparallel" ,r-biocparallel)
2836 ("r-biostrings" ,r-biostrings)
2837 ("r-bumphunter" ,r-bumphunter)
2838 ("r-data-table" ,r-data-table)
2839 ("r-delayedarray" ,r-delayedarray)
2840 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2841 ("r-genefilter" ,r-genefilter)
2842 ("r-genomeinfodb" ,r-genomeinfodb)
2843 ("r-genomicranges" ,r-genomicranges)
2844 ("r-geoquery" ,r-geoquery)
2845 ("r-hdf5array" ,r-hdf5array)
2846 ("r-illuminaio" ,r-illuminaio)
2847 ("r-iranges" ,r-iranges)
2848 ("r-lattice" ,r-lattice)
2849 ("r-limma" ,r-limma)
2851 ("r-mclust" ,r-mclust)
2853 ("r-nor1mix" ,r-nor1mix)
2854 ("r-preprocesscore" ,r-preprocesscore)
2855 ("r-quadprog" ,r-quadprog)
2856 ("r-rcolorbrewer" ,r-rcolorbrewer)
2857 ("r-reshape" ,r-reshape)
2858 ("r-s4vectors" ,r-s4vectors)
2859 ("r-siggenes" ,r-siggenes)
2860 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2861 (home-page "https://github.com/hansenlab/minfi")
2862 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2864 "This package provides tools to analyze and visualize Illumina Infinium
2865 methylation arrays.")
2866 (license license:artistic2.0)))
2868 (define-public r-methylumi
2870 (name "r-methylumi")
2875 (uri (bioconductor-uri "methylumi" version))
2878 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2879 (build-system r-build-system)
2881 `(("r-annotate" ,r-annotate)
2882 ("r-annotationdbi" ,r-annotationdbi)
2883 ("r-biobase" ,r-biobase)
2884 ("r-biocgenerics" ,r-biocgenerics)
2885 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2886 ("r-genefilter" ,r-genefilter)
2887 ("r-genomeinfodb" ,r-genomeinfodb)
2888 ("r-genomicranges" ,r-genomicranges)
2889 ("r-ggplot2" ,r-ggplot2)
2890 ("r-illuminaio" ,r-illuminaio)
2891 ("r-iranges" ,r-iranges)
2892 ("r-lattice" ,r-lattice)
2893 ("r-matrixstats" ,r-matrixstats)
2894 ("r-minfi" ,r-minfi)
2895 ("r-reshape2" ,r-reshape2)
2896 ("r-s4vectors" ,r-s4vectors)
2897 ("r-scales" ,r-scales)
2898 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2899 (home-page "https://bioconductor.org/packages/methylumi")
2900 (synopsis "Handle Illumina methylation data")
2902 "This package provides classes for holding and manipulating Illumina
2903 methylation data. Based on eSet, it can contain MIAME information, sample
2904 information, feature information, and multiple matrices of data. An
2905 \"intelligent\" import function, methylumiR can read the Illumina text files
2906 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2907 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2908 background correction, and quality control features for GoldenGate, Infinium,
2909 and Infinium HD arrays are also included.")
2910 (license license:gpl2)))
2912 (define-public r-lumi
2919 (uri (bioconductor-uri "lumi" version))
2922 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2923 (build-system r-build-system)
2925 `(("r-affy" ,r-affy)
2926 ("r-annotate" ,r-annotate)
2927 ("r-annotationdbi" ,r-annotationdbi)
2928 ("r-biobase" ,r-biobase)
2930 ("r-genomicfeatures" ,r-genomicfeatures)
2931 ("r-genomicranges" ,r-genomicranges)
2932 ("r-kernsmooth" ,r-kernsmooth)
2933 ("r-lattice" ,r-lattice)
2935 ("r-methylumi" ,r-methylumi)
2937 ("r-nleqslv" ,r-nleqslv)
2938 ("r-preprocesscore" ,r-preprocesscore)
2939 ("r-rsqlite" ,r-rsqlite)))
2940 (home-page "https://bioconductor.org/packages/lumi")
2941 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2943 "The lumi package provides an integrated solution for the Illumina
2944 microarray data analysis. It includes functions of Illumina
2945 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2946 variance stabilization, normalization and gene annotation at the probe level.
2947 It also includes the functions of processing Illumina methylation microarrays,
2948 especially Illumina Infinium methylation microarrays.")
2949 (license license:lgpl2.0+)))
2951 (define-public r-linnorm
2958 (uri (bioconductor-uri "Linnorm" version))
2961 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2962 (properties `((upstream-name . "Linnorm")))
2963 (build-system r-build-system)
2965 `(("r-amap" ,r-amap)
2966 ("r-apcluster" ,r-apcluster)
2967 ("r-ellipse" ,r-ellipse)
2968 ("r-fastcluster" ,r-fastcluster)
2970 ("r-ggdendro" ,r-ggdendro)
2971 ("r-ggplot2" ,r-ggplot2)
2972 ("r-gmodels" ,r-gmodels)
2973 ("r-igraph" ,r-igraph)
2974 ("r-limma" ,r-limma)
2976 ("r-mclust" ,r-mclust)
2978 ("r-rcpparmadillo" ,r-rcpparmadillo)
2979 ("r-rtsne" ,r-rtsne)
2980 ("r-statmod" ,r-statmod)
2981 ("r-vegan" ,r-vegan)
2983 (home-page "http://www.jjwanglab.org/Linnorm/")
2984 (synopsis "Linear model and normality based transformation method")
2986 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2987 count data or any large scale count data. It transforms such datasets for
2988 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2989 the following pipelines are implemented:
2992 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2993 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2994 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2995 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2996 @item Differential expression analysis or differential peak detection using
2997 limma (@code{Linnorm.limma})
2998 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2999 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3000 @item Stable gene selection for scRNA-seq data; for users without or who do
3001 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3002 @item Data imputation (@code{Linnorm.DataImput}).
3005 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3006 @code{RnaXSim} function is included for simulating RNA-seq data for the
3007 evaluation of DEG analysis methods.")
3008 (license license:expat)))
3010 (define-public r-ioniser
3017 (uri (bioconductor-uri "IONiseR" version))
3020 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
3021 (properties `((upstream-name . "IONiseR")))
3022 (build-system r-build-system)
3024 `(("r-biocgenerics" ,r-biocgenerics)
3025 ("r-biocparallel" ,r-biocparallel)
3026 ("r-biostrings" ,r-biostrings)
3027 ("r-bit64" ,r-bit64)
3028 ("r-dplyr" ,r-dplyr)
3029 ("r-ggplot2" ,r-ggplot2)
3030 ("r-magrittr" ,r-magrittr)
3031 ("r-rhdf5" ,r-rhdf5)
3032 ("r-shortread" ,r-shortread)
3033 ("r-stringr" ,r-stringr)
3034 ("r-tibble" ,r-tibble)
3035 ("r-tidyr" ,r-tidyr)
3036 ("r-xvector" ,r-xvector)))
3037 (home-page "https://bioconductor.org/packages/IONiseR/")
3038 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3040 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3041 MinION data. It extracts summary statistics from a set of fast5 files and can
3042 be used either before or after base calling. In addition to standard
3043 summaries of the read-types produced, it provides a number of plots for
3044 visualising metrics relative to experiment run time or spatially over the
3045 surface of a flowcell.")
3046 (license license:expat)))
3048 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3049 (define-public r-gkmsvm
3056 (uri (cran-uri "gkmSVM" version))
3059 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3060 (properties `((upstream-name . "gkmSVM")))
3061 (build-system r-build-system)
3063 `(("r-biocgenerics" ,r-biocgenerics)
3064 ("r-biostrings" ,r-biostrings)
3065 ("r-genomeinfodb" ,r-genomeinfodb)
3066 ("r-genomicranges" ,r-genomicranges)
3067 ("r-iranges" ,r-iranges)
3068 ("r-kernlab" ,r-kernlab)
3071 ("r-rtracklayer" ,r-rtracklayer)
3072 ("r-s4vectors" ,r-s4vectors)
3073 ("r-seqinr" ,r-seqinr)))
3074 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3075 (synopsis "Gapped-kmer support vector machine")
3077 "This R package provides tools for training gapped-kmer SVM classifiers
3078 for DNA and protein sequences. This package supports several sequence
3079 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3080 (license license:gpl2+)))
3082 (define-public r-triform
3089 (uri (bioconductor-uri "triform" version))
3092 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
3093 (build-system r-build-system)
3095 `(("r-biocgenerics" ,r-biocgenerics)
3096 ("r-iranges" ,r-iranges)
3097 ("r-yaml" ,r-yaml)))
3098 (home-page "https://bioconductor.org/packages/triform/")
3099 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3101 "The Triform algorithm uses model-free statistics to identify peak-like
3102 distributions of TF ChIP sequencing reads, taking advantage of an improved
3103 peak definition in combination with known profile characteristics.")
3104 (license license:gpl2)))
3106 (define-public r-varianttools
3108 (name "r-varianttools")
3113 (uri (bioconductor-uri "VariantTools" version))
3116 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
3117 (properties `((upstream-name . "VariantTools")))
3118 (build-system r-build-system)
3120 `(("r-biobase" ,r-biobase)
3121 ("r-biocgenerics" ,r-biocgenerics)
3122 ("r-biocparallel" ,r-biocparallel)
3123 ("r-biostrings" ,r-biostrings)
3124 ("r-bsgenome" ,r-bsgenome)
3125 ("r-genomeinfodb" ,r-genomeinfodb)
3126 ("r-genomicfeatures" ,r-genomicfeatures)
3127 ("r-genomicranges" ,r-genomicranges)
3128 ("r-iranges" ,r-iranges)
3129 ("r-matrix" ,r-matrix)
3130 ("r-rsamtools" ,r-rsamtools)
3131 ("r-rtracklayer" ,r-rtracklayer)
3132 ("r-s4vectors" ,r-s4vectors)
3133 ("r-variantannotation" ,r-variantannotation)))
3134 (home-page "https://bioconductor.org/packages/VariantTools/")
3135 (synopsis "Tools for exploratory analysis of variant calls")
3137 "Explore, diagnose, and compare variant calls using filters. The
3138 VariantTools package supports a workflow for loading data, calling single
3139 sample variants and tumor-specific somatic mutations or other sample-specific
3140 variant types (e.g., RNA editing). Most of the functions operate on
3141 alignments (BAM files) or datasets of called variants. The user is expected
3142 to have already aligned the reads with a separate tool, e.g., GSNAP via
3144 (license license:artistic2.0)))
3146 (define-public r-heatplus
3153 (uri (bioconductor-uri "Heatplus" version))
3156 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
3157 (properties `((upstream-name . "Heatplus")))
3158 (build-system r-build-system)
3160 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3161 (home-page "https://github.com/alexploner/Heatplus")
3162 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3164 "This package provides tools to display a rectangular heatmap (intensity
3165 plot) of a data matrix. By default, both samples (columns) and features (row)
3166 of the matrix are sorted according to a hierarchical clustering, and the
3167 corresponding dendrogram is plotted. Optionally, panels with additional
3168 information about samples and features can be added to the plot.")
3169 (license license:gpl2+)))
3171 (define-public r-gosemsim
3178 (uri (bioconductor-uri "GOSemSim" version))
3181 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
3182 (properties `((upstream-name . "GOSemSim")))
3183 (build-system r-build-system)
3185 `(("r-annotationdbi" ,r-annotationdbi)
3186 ("r-go-db" ,r-go-db)
3187 ("r-rcpp" ,r-rcpp)))
3188 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3189 (synopsis "GO-terms semantic similarity measures")
3191 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3192 quantitative ways to compute similarities between genes and gene groups, and
3193 have became important basis for many bioinformatics analysis approaches.
3194 GOSemSim is an R package for semantic similarity computation among GO terms,
3195 sets of GO terms, gene products and gene clusters.")
3196 (license license:artistic2.0)))
3198 (define-public r-anota
3205 (uri (bioconductor-uri "anota" version))
3208 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
3209 (build-system r-build-system)
3211 `(("r-multtest" ,r-multtest)
3212 ("r-qvalue" ,r-qvalue)))
3213 (home-page "https://bioconductor.org/packages/anota/")
3214 (synopsis "Analysis of translational activity")
3216 "Genome wide studies of translational control is emerging as a tool to
3217 study various biological conditions. The output from such analysis is both
3218 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3219 involved in translation (the actively translating mRNA level) for each mRNA.
3220 The standard analysis of such data strives towards identifying differential
3221 translational between two or more sample classes - i.e. differences in
3222 actively translated mRNA levels that are independent of underlying differences
3223 in cytosolic mRNA levels. This package allows for such analysis using partial
3224 variances and the random variance model. As 10s of thousands of mRNAs are
3225 analyzed in parallel the library performs a number of tests to assure that
3226 the data set is suitable for such analysis.")
3227 (license license:gpl3)))
3229 (define-public r-sigpathway
3231 (name "r-sigpathway")
3236 (uri (bioconductor-uri "sigPathway" version))
3239 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3240 (properties `((upstream-name . "sigPathway")))
3241 (build-system r-build-system)
3242 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3243 (synopsis "Pathway analysis")
3245 "This package is used to conduct pathway analysis by calculating the NT_k
3246 and NE_k statistics in a statistical framework for determining whether a
3247 specified group of genes for a pathway has a coordinated association with a
3248 phenotype of interest.")
3249 (license license:gpl2)))
3251 (define-public r-fgsea
3258 (uri (bioconductor-uri "fgsea" version))
3261 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3262 (build-system r-build-system)
3265 ("r-biocparallel" ,r-biocparallel)
3266 ("r-data-table" ,r-data-table)
3267 ("r-fastmatch" ,r-fastmatch)
3268 ("r-ggplot2" ,r-ggplot2)
3269 ("r-gridextra" ,r-gridextra)
3270 ("r-matrix" ,r-matrix)
3271 ("r-rcpp" ,r-rcpp)))
3272 (home-page "https://github.com/ctlab/fgsea/")
3273 (synopsis "Fast gene set enrichment analysis")
3275 "The package implements an algorithm for fast gene set enrichment
3276 analysis. Using the fast algorithm allows to make more permutations and get
3277 more fine grained p-values, which allows to use accurate stantard approaches
3278 to multiple hypothesis correction.")
3279 (license license:expat)))
3281 (define-public r-dose
3288 (uri (bioconductor-uri "DOSE" version))
3291 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3292 (properties `((upstream-name . "DOSE")))
3293 (build-system r-build-system)
3295 `(("r-annotationdbi" ,r-annotationdbi)
3296 ("r-biocparallel" ,r-biocparallel)
3297 ("r-do-db" ,r-do-db)
3298 ("r-fgsea" ,r-fgsea)
3299 ("r-ggplot2" ,r-ggplot2)
3300 ("r-gosemsim" ,r-gosemsim)
3301 ("r-qvalue" ,r-qvalue)
3302 ("r-reshape2" ,r-reshape2)
3303 ("r-s4vectors" ,r-s4vectors)))
3304 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3305 (synopsis "Disease ontology semantic and enrichment analysis")
3307 "This package implements five methods proposed by Resnik, Schlicker,
3308 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3309 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3310 including hypergeometric model and gene set enrichment analysis are also
3311 implemented for discovering disease associations of high-throughput biological
3313 (license license:artistic2.0)))
3315 (define-public r-enrichplot
3317 (name "r-enrichplot")
3322 (uri (bioconductor-uri "enrichplot" version))
3325 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3326 (build-system r-build-system)
3328 `(("r-annotationdbi" ,r-annotationdbi)
3329 ("r-cowplot" ,r-cowplot)
3331 ("r-europepmc" ,r-europepmc)
3332 ("r-ggplot2" ,r-ggplot2)
3333 ("r-ggplotify" ,r-ggplotify)
3334 ("r-ggraph" ,r-ggraph)
3335 ("r-ggridges" ,r-ggridges)
3336 ("r-gosemsim" ,r-gosemsim)
3337 ("r-gridextra" ,r-gridextra)
3338 ("r-igraph" ,r-igraph)
3339 ("r-purrr" ,r-purrr)
3340 ("r-rcolorbrewer" ,r-rcolorbrewer)
3341 ("r-reshape2" ,r-reshape2)
3342 ("r-upsetr" ,r-upsetr)))
3343 (home-page "https://github.com/GuangchuangYu/enrichplot")
3344 (synopsis "Visualization of functional enrichment result")
3346 "The enrichplot package implements several visualization methods for
3347 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3348 All the visualization methods are developed based on ggplot2 graphics.")
3349 (license license:artistic2.0)))
3351 (define-public r-clusterprofiler
3353 (name "r-clusterprofiler")
3358 (uri (bioconductor-uri "clusterProfiler" version))
3361 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3363 `((upstream-name . "clusterProfiler")))
3364 (build-system r-build-system)
3366 `(("r-annotationdbi" ,r-annotationdbi)
3368 ("r-enrichplot" ,r-enrichplot)
3369 ("r-ggplot2" ,r-ggplot2)
3370 ("r-go-db" ,r-go-db)
3371 ("r-gosemsim" ,r-gosemsim)
3372 ("r-magrittr" ,r-magrittr)
3374 ("r-qvalue" ,r-qvalue)
3375 ("r-rvcheck" ,r-rvcheck)
3376 ("r-tidyr" ,r-tidyr)))
3377 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3378 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3380 "This package implements methods to analyze and visualize functional
3381 profiles (GO and KEGG) of gene and gene clusters.")
3382 (license license:artistic2.0)))
3384 (define-public r-mlinterfaces
3386 (name "r-mlinterfaces")
3391 (uri (bioconductor-uri "MLInterfaces" version))
3394 "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh"))))
3395 (properties `((upstream-name . "MLInterfaces")))
3396 (build-system r-build-system)
3398 `(("r-annotate" ,r-annotate)
3399 ("r-biobase" ,r-biobase)
3400 ("r-biocgenerics" ,r-biocgenerics)
3401 ("r-cluster" ,r-cluster)
3404 ("r-gdata" ,r-gdata)
3405 ("r-genefilter" ,r-genefilter)
3406 ("r-ggvis" ,r-ggvis)
3407 ("r-hwriter" ,r-hwriter)
3409 ("r-mlbench" ,r-mlbench)
3411 ("r-rcolorbrewer" ,r-rcolorbrewer)
3413 ("r-rpart" ,r-rpart)
3414 ("r-sfsmisc" ,r-sfsmisc)
3415 ("r-shiny" ,r-shiny)
3416 ("r-threejs" ,r-threejs)))
3417 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3418 (synopsis "Interfaces to R machine learning procedures")
3420 "This package provides uniform interfaces to machine learning code for
3421 data in R and Bioconductor containers.")
3422 ;; Any version of the LGPL.
3423 (license license:lgpl2.1+)))
3425 (define-public r-annaffy
3432 (uri (bioconductor-uri "annaffy" version))
3435 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3436 (build-system r-build-system)
3439 (modify-phases %standard-phases
3440 (add-after 'unpack 'remove-reference-to-non-free-data
3442 (substitute* "DESCRIPTION"
3446 `(("r-annotationdbi" ,r-annotationdbi)
3447 ("r-biobase" ,r-biobase)
3449 ("r-go-db" ,r-go-db)))
3450 (home-page "https://bioconductor.org/packages/annaffy/")
3451 (synopsis "Annotation tools for Affymetrix biological metadata")
3453 "This package provides functions for handling data from Bioconductor
3454 Affymetrix annotation data packages. It produces compact HTML and text
3455 reports including experimental data and URL links to many online databases.
3456 It allows searching of biological metadata using various criteria.")
3457 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3458 ;; the LGPL 2.1 is included.
3459 (license license:lgpl2.1+)))
3461 (define-public r-a4core
3468 (uri (bioconductor-uri "a4Core" version))
3471 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3472 (properties `((upstream-name . "a4Core")))
3473 (build-system r-build-system)
3475 `(("r-biobase" ,r-biobase)
3476 ("r-glmnet" ,r-glmnet)))
3477 (home-page "https://bioconductor.org/packages/a4Core")
3478 (synopsis "Automated Affymetrix array analysis core package")
3480 "This is the core package for the automated analysis of Affymetrix
3482 (license license:gpl3)))
3484 (define-public r-a4classif
3486 (name "r-a4classif")
3491 (uri (bioconductor-uri "a4Classif" version))
3494 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3495 (properties `((upstream-name . "a4Classif")))
3496 (build-system r-build-system)
3498 `(("r-a4core" ,r-a4core)
3499 ("r-a4preproc" ,r-a4preproc)
3500 ("r-glmnet" ,r-glmnet)
3501 ("r-mlinterfaces" ,r-mlinterfaces)
3504 ("r-varselrf" ,r-varselrf)))
3505 (home-page "https://bioconductor.org/packages/a4Classif/")
3506 (synopsis "Automated Affymetrix array analysis classification package")
3508 "This is the classification package for the automated analysis of
3509 Affymetrix arrays.")
3510 (license license:gpl3)))
3512 (define-public r-a4preproc
3514 (name "r-a4preproc")
3519 (uri (bioconductor-uri "a4Preproc" version))
3522 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3523 (properties `((upstream-name . "a4Preproc")))
3524 (build-system r-build-system)
3526 `(("r-annotationdbi" ,r-annotationdbi)))
3527 (home-page "https://bioconductor.org/packages/a4Preproc/")
3528 (synopsis "Automated Affymetrix array analysis preprocessing package")
3530 "This is a package for the automated analysis of Affymetrix arrays. It
3531 is used for preprocessing the arrays.")
3532 (license license:gpl3)))
3534 (define-public r-a4reporting
3536 (name "r-a4reporting")
3541 (uri (bioconductor-uri "a4Reporting" version))
3544 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3545 (properties `((upstream-name . "a4Reporting")))
3546 (build-system r-build-system)
3548 `(("r-annaffy" ,r-annaffy)
3549 ("r-xtable" ,r-xtable)))
3550 (home-page "https://bioconductor.org/packages/a4Reporting/")
3551 (synopsis "Automated Affymetrix array analysis reporting package")
3553 "This is a package for the automated analysis of Affymetrix arrays. It
3554 provides reporting features.")
3555 (license license:gpl3)))
3557 (define-public r-a4base
3564 (uri (bioconductor-uri "a4Base" version))
3567 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3568 (properties `((upstream-name . "a4Base")))
3569 (build-system r-build-system)
3571 `(("r-a4core" ,r-a4core)
3572 ("r-a4preproc" ,r-a4preproc)
3573 ("r-annaffy" ,r-annaffy)
3574 ("r-annotationdbi" ,r-annotationdbi)
3575 ("r-biobase" ,r-biobase)
3576 ("r-genefilter" ,r-genefilter)
3577 ("r-glmnet" ,r-glmnet)
3578 ("r-gplots" ,r-gplots)
3579 ("r-limma" ,r-limma)
3581 ("r-multtest" ,r-multtest)))
3582 (home-page "https://bioconductor.org/packages/a4Base/")
3583 (synopsis "Automated Affymetrix array analysis base package")
3585 "This package provides basic features for the automated analysis of
3586 Affymetrix arrays.")
3587 (license license:gpl3)))
3596 (uri (bioconductor-uri "a4" version))
3599 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3600 (build-system r-build-system)
3602 `(("r-a4base" ,r-a4base)
3603 ("r-a4classif" ,r-a4classif)
3604 ("r-a4core" ,r-a4core)
3605 ("r-a4preproc" ,r-a4preproc)
3606 ("r-a4reporting" ,r-a4reporting)))
3607 (home-page "https://bioconductor.org/packages/a4/")
3608 (synopsis "Automated Affymetrix array analysis umbrella package")
3610 "This package provides a software suite for the automated analysis of
3611 Affymetrix arrays.")
3612 (license license:gpl3)))
3614 (define-public r-abseqr
3621 (uri (bioconductor-uri "abseqR" version))
3624 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3625 (properties `((upstream-name . "abseqR")))
3626 (build-system r-build-system)
3628 `(("pandoc" ,ghc-pandoc)))
3630 `(("r-biocparallel" ,r-biocparallel)
3631 ("r-biocstyle" ,r-biocstyle)
3632 ("r-circlize" ,r-circlize)
3633 ("r-flexdashboard" ,r-flexdashboard)
3634 ("r-ggcorrplot" ,r-ggcorrplot)
3635 ("r-ggdendro" ,r-ggdendro)
3636 ("r-ggplot2" ,r-ggplot2)
3637 ("r-gridextra" ,r-gridextra)
3638 ("r-knitr" ,r-knitr)
3639 ("r-plotly" ,r-plotly)
3642 ("r-rcolorbrewer" ,r-rcolorbrewer)
3643 ("r-reshape2" ,r-reshape2)
3644 ("r-rmarkdown" ,r-rmarkdown)
3645 ("r-stringr" ,r-stringr)
3646 ("r-vegan" ,r-vegan)
3647 ("r-venndiagram" ,r-venndiagram)))
3648 (home-page "https://github.com/malhamdoosh/abseqR")
3649 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3651 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3652 sequencing datasets generated from antibody libraries and abseqR is one of its
3653 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3654 capabilities and allows them to generate interactive HTML reports for the
3655 convenience of viewing and sharing with other researchers. Additionally,
3656 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3657 further downstream analysis on its output.")
3658 (license license:gpl3)))
3660 (define-public r-bacon
3667 (uri (bioconductor-uri "bacon" version))
3670 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3671 (build-system r-build-system)
3673 `(("r-biocparallel" ,r-biocparallel)
3674 ("r-ellipse" ,r-ellipse)
3675 ("r-ggplot2" ,r-ggplot2)))
3676 (home-page "https://bioconductor.org/packages/bacon/")
3677 (synopsis "Controlling bias and inflation in association studies")
3679 "Bacon can be used to remove inflation and bias often observed in
3680 epigenome- and transcriptome-wide association studies. To this end bacon
3681 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3682 fitting a three-component normal mixture on z-scores.")
3683 (license license:gpl2+)))
3685 (define-public r-rgadem
3692 (uri (bioconductor-uri "rGADEM" version))
3695 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3696 (properties `((upstream-name . "rGADEM")))
3697 (build-system r-build-system)
3699 `(("r-biostrings" ,r-biostrings)
3700 ("r-bsgenome" ,r-bsgenome)
3701 ("r-iranges" ,r-iranges)
3702 ("r-seqlogo" ,r-seqlogo)))
3703 (home-page "https://bioconductor.org/packages/rGADEM/")
3704 (synopsis "De novo sequence motif discovery")
3706 "rGADEM is an efficient de novo motif discovery tool for large-scale
3707 genomic sequence data.")
3708 (license license:artistic2.0)))
3710 (define-public r-motiv
3717 (uri (bioconductor-uri "MotIV" version))
3720 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3721 (properties `((upstream-name . "MotIV")))
3722 (build-system r-build-system)
3726 `(("r-biocgenerics" ,r-biocgenerics)
3727 ("r-biostrings" ,r-biostrings)
3728 ("r-iranges" ,r-iranges)
3729 ("r-lattice" ,r-lattice)
3730 ("r-rgadem" ,r-rgadem)
3731 ("r-s4vectors" ,r-s4vectors)))
3732 (home-page "https://bioconductor.org/packages/MotIV/")
3733 (synopsis "Motif identification and validation")
3735 "This package is used for the identification and validation of sequence
3736 motifs. It makes use of STAMP for comparing a set of motifs to a given
3737 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3738 distributions, modules and filter motifs.")
3739 (license license:gpl2)))
3741 (define-public r-motifstack
3743 (name "r-motifstack")
3748 (uri (bioconductor-uri "motifStack" version))
3751 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3752 (properties `((upstream-name . "motifStack")))
3753 (build-system r-build-system)
3755 `(("r-ade4" ,r-ade4)
3756 ("r-biostrings" ,r-biostrings)
3757 ("r-grimport2" ,r-grimport2)
3758 ("r-htmlwidgets" ,r-htmlwidgets)
3759 ("r-motiv" ,r-motiv)
3760 ("r-scales" ,r-scales)
3762 (home-page "https://bioconductor.org/packages/motifStack/")
3763 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3765 "The motifStack package is designed for graphic representation of
3766 multiple motifs with different similarity scores. It works with both DNA/RNA
3767 sequence motifs and amino acid sequence motifs. In addition, it provides the
3768 flexibility for users to customize the graphic parameters such as the font
3769 type and symbol colors.")
3770 (license license:gpl2+)))
3772 (define-public r-genomicscores
3774 (name "r-genomicscores")
3779 (uri (bioconductor-uri "GenomicScores" version))
3782 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3783 (properties `((upstream-name . "GenomicScores")))
3784 (build-system r-build-system)
3786 `(("r-annotationhub" ,r-annotationhub)
3787 ("r-biobase" ,r-biobase)
3788 ("r-biocgenerics" ,r-biocgenerics)
3789 ("r-biostrings" ,r-biostrings)
3790 ("r-bsgenome" ,r-bsgenome)
3791 ("r-genomeinfodb" ,r-genomeinfodb)
3792 ("r-genomicranges" ,r-genomicranges)
3793 ("r-iranges" ,r-iranges)
3794 ("r-s4vectors" ,r-s4vectors)
3796 (home-page "https://github.com/rcastelo/GenomicScores/")
3797 (synopsis "Work with genome-wide position-specific scores")
3799 "This package provides infrastructure to store and access genome-wide
3800 position-specific scores within R and Bioconductor.")
3801 (license license:artistic2.0)))
3803 (define-public r-atacseqqc
3805 (name "r-atacseqqc")
3810 (uri (bioconductor-uri "ATACseqQC" version))
3813 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3814 (properties `((upstream-name . "ATACseqQC")))
3815 (build-system r-build-system)
3817 `(("r-biocgenerics" ,r-biocgenerics)
3818 ("r-biostrings" ,r-biostrings)
3819 ("r-bsgenome" ,r-bsgenome)
3820 ("r-chippeakanno" ,r-chippeakanno)
3821 ("r-edger" ,r-edger)
3822 ("r-genomeinfodb" ,r-genomeinfodb)
3823 ("r-genomicalignments" ,r-genomicalignments)
3824 ("r-genomicranges" ,r-genomicranges)
3825 ("r-genomicscores" ,r-genomicscores)
3826 ("r-iranges" ,r-iranges)
3827 ("r-kernsmooth" ,r-kernsmooth)
3828 ("r-limma" ,r-limma)
3829 ("r-motifstack" ,r-motifstack)
3830 ("r-preseqr" ,r-preseqr)
3831 ("r-randomforest" ,r-randomforest)
3832 ("r-rsamtools" ,r-rsamtools)
3833 ("r-rtracklayer" ,r-rtracklayer)
3834 ("r-s4vectors" ,r-s4vectors)))
3835 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3836 (synopsis "ATAC-seq quality control")
3838 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3839 sequencing, is a rapid and sensitive method for chromatin accessibility
3840 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3841 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3842 assess whether their ATAC-seq experiment is successful. It includes
3843 diagnostic plots of fragment size distribution, proportion of mitochondria
3844 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3846 (license license:gpl2+)))
3848 (define-public r-gofuncr
3855 (uri (bioconductor-uri "GOfuncR" version))
3858 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3859 (properties `((upstream-name . "GOfuncR")))
3860 (build-system r-build-system)
3862 `(("r-annotationdbi" ,r-annotationdbi)
3863 ("r-genomicranges" ,r-genomicranges)
3864 ("r-gtools" ,r-gtools)
3865 ("r-iranges" ,r-iranges)
3866 ("r-mapplots" ,r-mapplots)
3868 ("r-vioplot" ,r-vioplot)))
3869 (home-page "https://bioconductor.org/packages/GOfuncR/")
3870 (synopsis "Gene ontology enrichment using FUNC")
3872 "GOfuncR performs a gene ontology enrichment analysis based on the
3873 ontology enrichment software FUNC. GO-annotations are obtained from
3874 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3875 included in the package and updated regularly. GOfuncR provides the standard
3876 candidate vs background enrichment analysis using the hypergeometric test, as
3877 well as three additional tests:
3880 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3881 @item a binomial test that is used when genes are associated with two counts,
3883 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3884 associated with four counts.
3887 To correct for multiple testing and interdependency of the tests, family-wise
3888 error rates are computed based on random permutations of the gene-associated
3889 variables. GOfuncR also provides tools for exploring the ontology graph and
3890 the annotations, and options to take gene-length or spatial clustering of
3891 genes into account. It is also possible to provide custom gene coordinates,
3892 annotations and ontologies.")
3893 (license license:gpl2+)))
3895 (define-public r-abaenrichment
3897 (name "r-abaenrichment")
3902 (uri (bioconductor-uri "ABAEnrichment" version))
3905 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
3906 (properties `((upstream-name . "ABAEnrichment")))
3907 (build-system r-build-system)
3909 `(("r-abadata" ,r-abadata)
3910 ("r-data-table" ,r-data-table)
3911 ("r-gofuncr" ,r-gofuncr)
3912 ("r-gplots" ,r-gplots)
3913 ("r-gtools" ,r-gtools)
3914 ("r-rcpp" ,r-rcpp)))
3915 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3916 (synopsis "Gene expression enrichment in human brain regions")
3918 "The package ABAEnrichment is designed to test for enrichment of user
3919 defined candidate genes in the set of expressed genes in different human brain
3920 regions. The core function @code{aba_enrich} integrates the expression of the
3921 candidate gene set (averaged across donors) and the structural information of
3922 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3923 (license license:gpl2+)))
3925 (define-public r-annotationfuncs
3927 (name "r-annotationfuncs")
3932 (uri (bioconductor-uri "AnnotationFuncs" version))
3935 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3937 `((upstream-name . "AnnotationFuncs")))
3938 (build-system r-build-system)
3940 `(("r-annotationdbi" ,r-annotationdbi)
3942 (home-page "https://www.iysik.com/r/annotationfuncs")
3943 (synopsis "Annotation translation functions")
3945 "This package provides functions for handling translating between
3946 different identifieres using the Biocore Data Team data-packages (e.g.
3947 @code{org.Bt.eg.db}).")
3948 (license license:gpl2)))
3950 (define-public r-annotationtools
3952 (name "r-annotationtools")
3957 (uri (bioconductor-uri "annotationTools" version))
3960 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3962 `((upstream-name . "annotationTools")))
3963 (build-system r-build-system)
3964 (propagated-inputs `(("r-biobase" ,r-biobase)))
3965 (home-page "https://bioconductor.org/packages/annotationTools/")
3966 (synopsis "Annotate microarrays and perform gene expression analyses")
3968 "This package provides functions to annotate microarrays, find orthologs,
3969 and integrate heterogeneous gene expression profiles using annotation and
3970 other molecular biology information available as flat file database (plain
3972 ;; Any version of the GPL.
3973 (license (list license:gpl2+))))
3975 (define-public r-allelicimbalance
3977 (name "r-allelicimbalance")
3982 (uri (bioconductor-uri "AllelicImbalance" version))
3985 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3987 `((upstream-name . "AllelicImbalance")))
3988 (build-system r-build-system)
3990 `(("r-annotationdbi" ,r-annotationdbi)
3991 ("r-biocgenerics" ,r-biocgenerics)
3992 ("r-biostrings" ,r-biostrings)
3993 ("r-bsgenome" ,r-bsgenome)
3994 ("r-genomeinfodb" ,r-genomeinfodb)
3995 ("r-genomicalignments" ,r-genomicalignments)
3996 ("r-genomicfeatures" ,r-genomicfeatures)
3997 ("r-genomicranges" ,r-genomicranges)
3998 ("r-gridextra" ,r-gridextra)
4000 ("r-iranges" ,r-iranges)
4001 ("r-lattice" ,r-lattice)
4002 ("r-latticeextra" ,r-latticeextra)
4004 ("r-rsamtools" ,r-rsamtools)
4005 ("r-s4vectors" ,r-s4vectors)
4006 ("r-seqinr" ,r-seqinr)
4007 ("r-summarizedexperiment" ,r-summarizedexperiment)
4008 ("r-variantannotation" ,r-variantannotation)))
4009 (home-page "https://github.com/pappewaio/AllelicImbalance")
4010 (synopsis "Investigate allele-specific expression")
4012 "This package provides a framework for allele-specific expression
4013 investigation using RNA-seq data.")
4014 (license license:gpl3)))
4016 (define-public r-aucell
4023 (uri (bioconductor-uri "AUCell" version))
4026 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
4027 (properties `((upstream-name . "AUCell")))
4028 (build-system r-build-system)
4030 `(("r-data-table" ,r-data-table)
4031 ("r-gseabase" ,r-gseabase)
4032 ("r-mixtools" ,r-mixtools)
4033 ("r-r-utils" ,r-r-utils)
4034 ("r-shiny" ,r-shiny)
4035 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4036 (home-page "https://bioconductor.org/packages/AUCell/")
4037 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4039 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4040 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4041 Under the Curve} (AUC) to calculate whether a critical subset of the input
4042 gene set is enriched within the expressed genes for each cell. The
4043 distribution of AUC scores across all the cells allows exploring the relative
4044 expression of the signature. Since the scoring method is ranking-based,
4045 AUCell is independent of the gene expression units and the normalization
4046 procedure. In addition, since the cells are evaluated individually, it can
4047 easily be applied to bigger datasets, subsetting the expression matrix if
4049 (license license:gpl3)))
4051 (define-public r-ebimage
4058 (uri (bioconductor-uri "EBImage" version))
4061 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
4062 (properties `((upstream-name . "EBImage")))
4063 (build-system r-build-system)
4065 `(("r-abind" ,r-abind)
4066 ("r-biocgenerics" ,r-biocgenerics)
4067 ("r-fftwtools" ,r-fftwtools)
4068 ("r-htmltools" ,r-htmltools)
4069 ("r-htmlwidgets" ,r-htmlwidgets)
4071 ("r-locfit" ,r-locfit)
4073 ("r-rcurl" ,r-rcurl)
4074 ("r-tiff" ,r-tiff)))
4076 `(("r-knitr" ,r-knitr))) ; for vignettes
4077 (home-page "https://github.com/aoles/EBImage")
4078 (synopsis "Image processing and analysis toolbox for R")
4080 "EBImage provides general purpose functionality for image processing and
4081 analysis. In the context of (high-throughput) microscopy-based cellular
4082 assays, EBImage offers tools to segment cells and extract quantitative
4083 cellular descriptors. This allows the automation of such tasks using the R
4084 programming language and facilitates the use of other tools in the R
4085 environment for signal processing, statistical modeling, machine learning and
4086 visualization with image data.")
4087 ;; Any version of the LGPL.
4088 (license license:lgpl2.1+)))
4090 (define-public r-yamss
4097 (uri (bioconductor-uri "yamss" version))
4100 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
4101 (build-system r-build-system)
4103 `(("r-biocgenerics" ,r-biocgenerics)
4104 ("r-data-table" ,r-data-table)
4105 ("r-ebimage" ,r-ebimage)
4106 ("r-iranges" ,r-iranges)
4107 ("r-limma" ,r-limma)
4108 ("r-matrix" ,r-matrix)
4110 ("r-s4vectors" ,r-s4vectors)
4111 ("r-summarizedexperiment"
4112 ,r-summarizedexperiment)))
4113 (home-page "https://github.com/hansenlab/yamss")
4114 (synopsis "Tools for high-throughput metabolomics")
4116 "This package provides tools to analyze and visualize high-throughput
4117 metabolomics data acquired using chromatography-mass spectrometry. These tools
4118 preprocess data in a way that enables reliable and powerful differential
4120 (license license:artistic2.0)))
4122 (define-public r-gtrellis
4129 (uri (bioconductor-uri "gtrellis" version))
4132 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
4133 (build-system r-build-system)
4135 `(("r-circlize" ,r-circlize)
4136 ("r-genomicranges" ,r-genomicranges)
4137 ("r-getoptlong" ,r-getoptlong)
4138 ("r-iranges" ,r-iranges)))
4139 (home-page "https://github.com/jokergoo/gtrellis")
4140 (synopsis "Genome level Trellis layout")
4142 "Genome level Trellis graph visualizes genomic data conditioned by
4143 genomic categories (e.g. chromosomes). For each genomic category, multiple
4144 dimensional data which are represented as tracks describe different features
4145 from different aspects. This package provides high flexibility to arrange
4146 genomic categories and to add self-defined graphics in the plot.")
4147 (license license:expat)))
4149 (define-public r-somaticsignatures
4151 (name "r-somaticsignatures")
4156 (uri (bioconductor-uri "SomaticSignatures" version))
4159 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
4161 `((upstream-name . "SomaticSignatures")))
4162 (build-system r-build-system)
4164 `(("r-biobase" ,r-biobase)
4165 ("r-biostrings" ,r-biostrings)
4166 ("r-genomeinfodb" ,r-genomeinfodb)
4167 ("r-genomicranges" ,r-genomicranges)
4168 ("r-ggbio" ,r-ggbio)
4169 ("r-ggplot2" ,r-ggplot2)
4170 ("r-iranges" ,r-iranges)
4172 ("r-pcamethods" ,r-pcamethods)
4173 ("r-proxy" ,r-proxy)
4174 ("r-reshape2" ,r-reshape2)
4175 ("r-s4vectors" ,r-s4vectors)
4176 ("r-variantannotation" ,r-variantannotation)))
4177 (home-page "https://github.com/juliangehring/SomaticSignatures")
4178 (synopsis "Somatic signatures")
4180 "This package identifies mutational signatures of @dfn{single nucleotide
4181 variants} (SNVs). It provides a infrastructure related to the methodology
4182 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4183 decomposition algorithms.")
4184 (license license:expat)))
4186 (define-public r-yapsa
4193 (uri (bioconductor-uri "YAPSA" version))
4196 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
4197 (properties `((upstream-name . "YAPSA")))
4198 (build-system r-build-system)
4200 `(("r-circlize" ,r-circlize)
4201 ("r-complexheatmap" ,r-complexheatmap)
4202 ("r-corrplot" ,r-corrplot)
4203 ("r-dendextend" ,r-dendextend)
4204 ("r-genomeinfodb" ,r-genomeinfodb)
4205 ("r-genomicranges" ,r-genomicranges)
4206 ("r-getoptlong" ,r-getoptlong)
4207 ("r-ggplot2" ,r-ggplot2)
4208 ("r-gridextra" ,r-gridextra)
4209 ("r-gtrellis" ,r-gtrellis)
4210 ("r-keggrest" ,r-keggrest)
4212 ("r-pmcmr" ,r-pmcmr)
4213 ("r-reshape2" ,r-reshape2)
4214 ("r-somaticsignatures" ,r-somaticsignatures)
4215 ("r-variantannotation" ,r-variantannotation)))
4216 (home-page "https://bioconductor.org/packages/YAPSA/")
4217 (synopsis "Yet another package for signature analysis")
4219 "This package provides functions and routines useful in the analysis of
4220 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4221 functions to perform a signature analysis with known signatures and a
4222 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4224 (license license:gpl3)))
4226 (define-public r-gcrma
4233 (uri (bioconductor-uri "gcrma" version))
4236 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4237 (build-system r-build-system)
4239 `(("r-affy" ,r-affy)
4240 ("r-affyio" ,r-affyio)
4241 ("r-biobase" ,r-biobase)
4242 ("r-biocmanager" ,r-biocmanager)
4243 ("r-biostrings" ,r-biostrings)
4244 ("r-xvector" ,r-xvector)))
4245 (home-page "https://bioconductor.org/packages/gcrma/")
4246 (synopsis "Background adjustment using sequence information")
4248 "Gcrma adjusts for background intensities in Affymetrix array data which
4249 include optical noise and @dfn{non-specific binding} (NSB). The main function
4250 @code{gcrma} converts background adjusted probe intensities to expression
4251 measures using the same normalization and summarization methods as a
4252 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4253 to estimate probe affinity to NSB. The sequence information is summarized in
4254 a more complex way than the simple GC content. Instead, the base types (A, T,
4255 G or C) at each position along the probe determine the affinity of each probe.
4256 The parameters of the position-specific base contributions to the probe
4257 affinity is estimated in an NSB experiment in which only NSB but no
4258 gene-specific bidning is expected.")
4259 ;; Any version of the LGPL
4260 (license license:lgpl2.1+)))
4262 (define-public r-simpleaffy
4264 (name "r-simpleaffy")
4269 (uri (bioconductor-uri "simpleaffy" version))
4272 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4273 (build-system r-build-system)
4275 `(("r-affy" ,r-affy)
4276 ("r-biobase" ,r-biobase)
4277 ("r-biocgenerics" ,r-biocgenerics)
4278 ("r-gcrma" ,r-gcrma)
4279 ("r-genefilter" ,r-genefilter)))
4280 (home-page "https://bioconductor.org/packages/simpleaffy/")
4281 (synopsis "Very simple high level analysis of Affymetrix data")
4283 "This package provides high level functions for reading Affy @file{.CEL}
4284 files, phenotypic data, and then computing simple things with it, such as
4285 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4286 library. It also has some basic scatter plot functions and mechanisms for
4287 generating high resolution journal figures.")
4288 (license license:gpl2+)))
4290 (define-public r-yaqcaffy
4297 (uri (bioconductor-uri "yaqcaffy" version))
4300 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4301 (build-system r-build-system)
4303 `(("r-simpleaffy" ,r-simpleaffy)))
4304 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4305 (synopsis "Affymetrix quality control and reproducibility analysis")
4307 "This is a package that can be used for quality control of Affymetrix
4308 GeneChip expression data and reproducibility analysis of human whole genome
4309 chips with the MAQC reference datasets.")
4310 (license license:artistic2.0)))
4312 (define-public r-quantro
4319 (uri (bioconductor-uri "quantro" version))
4322 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4323 (build-system r-build-system)
4325 `(("r-biobase" ,r-biobase)
4326 ("r-doparallel" ,r-doparallel)
4327 ("r-foreach" ,r-foreach)
4328 ("r-ggplot2" ,r-ggplot2)
4329 ("r-iterators" ,r-iterators)
4330 ("r-minfi" ,r-minfi)
4331 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4332 (home-page "https://bioconductor.org/packages/quantro/")
4333 (synopsis "Test for when to use quantile normalization")
4335 "This package provides a data-driven test for the assumptions of quantile
4336 normalization using raw data such as objects that inherit eSets (e.g.
4337 ExpressionSet, MethylSet). Group level information about each sample (such as
4338 Tumor / Normal status) must also be provided because the test assesses if
4339 there are global differences in the distributions between the user-defined
4341 (license license:gpl3+)))
4343 (define-public r-yarn
4350 (uri (bioconductor-uri "yarn" version))
4353 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4354 (build-system r-build-system)
4356 `(("r-biobase" ,r-biobase)
4357 ("r-biomart" ,r-biomart)
4358 ("r-downloader" ,r-downloader)
4359 ("r-edger" ,r-edger)
4360 ("r-gplots" ,r-gplots)
4361 ("r-limma" ,r-limma)
4362 ("r-matrixstats" ,r-matrixstats)
4363 ("r-preprocesscore" ,r-preprocesscore)
4364 ("r-quantro" ,r-quantro)
4365 ("r-rcolorbrewer" ,r-rcolorbrewer)
4366 ("r-readr" ,r-readr)))
4367 (home-page "https://bioconductor.org/packages/yarn/")
4368 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4370 "Expedite large RNA-Seq analyses using a combination of previously
4371 developed tools. YARN is meant to make it easier for the user in performing
4372 basic mis-annotation quality control, filtering, and condition-aware
4373 normalization. YARN leverages many Bioconductor tools and statistical
4374 techniques to account for the large heterogeneity and sparsity found in very
4375 large RNA-seq experiments.")
4376 (license license:artistic2.0)))
4378 (define-public r-roar
4385 (uri (bioconductor-uri "roar" version))
4388 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4389 (build-system r-build-system)
4391 `(("r-biocgenerics" ,r-biocgenerics)
4392 ("r-genomeinfodb" ,r-genomeinfodb)
4393 ("r-genomicalignments" ,r-genomicalignments)
4394 ("r-genomicranges" ,r-genomicranges)
4395 ("r-iranges" ,r-iranges)
4396 ("r-rtracklayer" ,r-rtracklayer)
4397 ("r-s4vectors" ,r-s4vectors)
4398 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4399 (home-page "https://github.com/vodkatad/roar/")
4400 (synopsis "Identify differential APA usage from RNA-seq alignments")
4402 "This package provides tools for identifying preferential usage of APA
4403 sites, comparing two biological conditions, starting from known alternative
4404 sites and alignments obtained from standard RNA-seq experiments.")
4405 (license license:gpl3)))
4407 (define-public r-xbseq
4414 (uri (bioconductor-uri "XBSeq" version))
4417 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4418 (properties `((upstream-name . "XBSeq")))
4419 (build-system r-build-system)
4421 `(("r-biobase" ,r-biobase)
4422 ("r-deseq2" ,r-deseq2)
4423 ("r-dplyr" ,r-dplyr)
4424 ("r-ggplot2" ,r-ggplot2)
4425 ("r-locfit" ,r-locfit)
4426 ("r-magrittr" ,r-magrittr)
4427 ("r-matrixstats" ,r-matrixstats)
4428 ("r-pracma" ,r-pracma)
4429 ("r-roar" ,r-roar)))
4430 (home-page "https://github.com/Liuy12/XBSeq")
4431 (synopsis "Test for differential expression for RNA-seq data")
4433 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4434 expression} (DE), where a statistical model was established based on the
4435 assumption that observed signals are the convolution of true expression
4436 signals and sequencing noises. The mapped reads in non-exonic regions are
4437 considered as sequencing noises, which follows a Poisson distribution. Given
4438 measurable observed signal and background noise from RNA-seq data, true
4439 expression signals, assuming governed by the negative binomial distribution,
4440 can be delineated and thus the accurate detection of differential expressed
4442 (license license:gpl3+)))
4444 (define-public r-massspecwavelet
4446 (name "r-massspecwavelet")
4451 (uri (bioconductor-uri "MassSpecWavelet" version))
4454 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4456 `((upstream-name . "MassSpecWavelet")))
4457 (build-system r-build-system)
4459 `(("r-waveslim" ,r-waveslim)))
4460 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4461 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4463 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4464 data mainly through the use of wavelet transforms. It supports peak detection
4465 based on @dfn{Continuous Wavelet Transform} (CWT).")
4466 (license license:lgpl2.0+)))
4468 (define-public r-xcms
4475 (uri (bioconductor-uri "xcms" version))
4478 "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v"))))
4479 (build-system r-build-system)
4481 `(("r-biobase" ,r-biobase)
4482 ("r-biocgenerics" ,r-biocgenerics)
4483 ("r-biocparallel" ,r-biocparallel)
4484 ("r-lattice" ,r-lattice)
4485 ("r-massspecwavelet" ,r-massspecwavelet)
4486 ("r-msnbase" ,r-msnbase)
4487 ("r-multtest" ,r-multtest)
4490 ("r-protgenerics" ,r-protgenerics)
4492 ("r-rcolorbrewer" ,r-rcolorbrewer)
4493 ("r-robustbase" ,r-robustbase)
4494 ("r-s4vectors" ,r-s4vectors)))
4495 (home-page "https://bioconductor.org/packages/xcms/")
4496 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4498 "This package provides a framework for processing and visualization of
4499 chromatographically separated and single-spectra mass spectral data. It
4500 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4501 data for high-throughput, untargeted analyte profiling.")
4502 (license license:gpl2+)))
4504 (define-public r-wrench
4511 (uri (bioconductor-uri "Wrench" version))
4514 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4515 (properties `((upstream-name . "Wrench")))
4516 (build-system r-build-system)
4518 `(("r-limma" ,r-limma)
4519 ("r-locfit" ,r-locfit)
4520 ("r-matrixstats" ,r-matrixstats)))
4521 (home-page "https://github.com/HCBravoLab/Wrench")
4522 (synopsis "Wrench normalization for sparse count data")
4524 "Wrench is a package for normalization sparse genomic count data, like
4525 that arising from 16s metagenomic surveys.")
4526 (license license:artistic2.0)))
4528 (define-public r-wiggleplotr
4530 (name "r-wiggleplotr")
4535 (uri (bioconductor-uri "wiggleplotr" version))
4538 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4539 (build-system r-build-system)
4541 `(("r-assertthat" ,r-assertthat)
4542 ("r-cowplot" ,r-cowplot)
4543 ("r-dplyr" ,r-dplyr)
4544 ("r-genomeinfodb" ,r-genomeinfodb)
4545 ("r-genomicranges" ,r-genomicranges)
4546 ("r-ggplot2" ,r-ggplot2)
4547 ("r-iranges" ,r-iranges)
4548 ("r-purrr" ,r-purrr)
4549 ("r-rtracklayer" ,r-rtracklayer)
4550 ("r-s4vectors" ,r-s4vectors)))
4551 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4552 (synopsis "Make read coverage plots from BigWig files")
4554 "This package provides tools to visualize read coverage from sequencing
4555 experiments together with genomic annotations (genes, transcripts, peaks).
4556 Introns of long transcripts can be rescaled to a fixed length for better
4557 visualization of exonic read coverage.")
4558 (license license:asl2.0)))
4560 (define-public r-widgettools
4562 (name "r-widgettools")
4567 (uri (bioconductor-uri "widgetTools" version))
4570 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4571 (properties `((upstream-name . "widgetTools")))
4572 (build-system r-build-system)
4573 (home-page "https://bioconductor.org/packages/widgetTools/")
4574 (synopsis "Tools for creating interactive tcltk widgets")
4576 "This package contains tools to support the construction of tcltk
4578 ;; Any version of the LGPL.
4579 (license license:lgpl3+)))
4581 (define-public r-webbioc
4588 (uri (bioconductor-uri "webbioc" version))
4591 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4592 (build-system r-build-system)
4594 `(("netpbm" ,netpbm)
4597 `(("r-affy" ,r-affy)
4598 ("r-annaffy" ,r-annaffy)
4599 ("r-biobase" ,r-biobase)
4600 ("r-biocmanager" ,r-biocmanager)
4601 ("r-gcrma" ,r-gcrma)
4602 ("r-multtest" ,r-multtest)
4603 ("r-qvalue" ,r-qvalue)
4605 (home-page "https://www.bioconductor.org/")
4606 (synopsis "Bioconductor web interface")
4608 "This package provides an integrated web interface for doing microarray
4609 analysis using several of the Bioconductor packages. It is intended to be
4610 deployed as a centralized bioinformatics resource for use by many users.
4611 Currently only Affymetrix oligonucleotide analysis is supported.")
4612 (license license:gpl2+)))
4614 (define-public r-zfpkm
4621 (uri (bioconductor-uri "zFPKM" version))
4624 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4625 (properties `((upstream-name . "zFPKM")))
4626 (build-system r-build-system)
4628 `(("r-checkmate" ,r-checkmate)
4629 ("r-dplyr" ,r-dplyr)
4630 ("r-ggplot2" ,r-ggplot2)
4631 ("r-summarizedexperiment" ,r-summarizedexperiment)
4632 ("r-tidyr" ,r-tidyr)))
4633 (home-page "https://github.com/ronammar/zFPKM/")
4634 (synopsis "Functions to facilitate zFPKM transformations")
4636 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4637 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4639 (license license:gpl3)))
4641 (define-public r-rbowtie2
4648 (uri (bioconductor-uri "Rbowtie2" version))
4651 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4652 (properties `((upstream-name . "Rbowtie2")))
4653 (build-system r-build-system)
4656 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4657 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4659 "This package provides an R wrapper of the popular @code{bowtie2}
4660 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4661 rapid adapter trimming, identification, and read merging.")
4662 (license license:gpl3+)))
4664 (define-public r-progeny
4671 (uri (bioconductor-uri "progeny" version))
4674 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4675 (build-system r-build-system)
4676 (propagated-inputs `(("r-biobase" ,r-biobase)))
4677 (home-page "https://github.com/saezlab/progeny")
4678 (synopsis "Pathway responsive gene activity inference")
4680 "This package provides a function to infer pathway activity from gene
4681 expression. It contains the linear model inferred in the publication
4682 \"Perturbation-response genes reveal signaling footprints in cancer gene
4684 (license license:asl2.0)))
4686 (define-public r-arrmnormalization
4688 (name "r-arrmnormalization")
4693 (uri (bioconductor-uri "ARRmNormalization" version))
4696 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4698 `((upstream-name . "ARRmNormalization")))
4699 (build-system r-build-system)
4700 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4701 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4702 (synopsis "Adaptive robust regression normalization for methylation data")
4704 "This is a package to perform the @dfn{Adaptive Robust Regression
4705 method} (ARRm) for the normalization of methylation data from the Illumina
4706 Infinium HumanMethylation 450k assay.")
4707 (license license:artistic2.0)))
4709 (define-public r-biocfilecache
4711 (name "r-biocfilecache")
4716 (uri (bioconductor-uri "BiocFileCache" version))
4719 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4720 (properties `((upstream-name . "BiocFileCache")))
4721 (build-system r-build-system)
4723 `(("r-curl" ,r-curl)
4725 ("r-dbplyr" ,r-dbplyr)
4726 ("r-dplyr" ,r-dplyr)
4728 ("r-rappdirs" ,r-rappdirs)
4729 ("r-rsqlite" ,r-rsqlite)))
4730 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4731 (synopsis "Manage files across sessions")
4733 "This package creates a persistent on-disk cache of files that the user
4734 can add, update, and retrieve. It is useful for managing resources (such as
4735 custom Txdb objects) that are costly or difficult to create, web resources,
4736 and data files used across sessions.")
4737 (license license:artistic2.0)))
4739 (define-public r-iclusterplus
4741 (name "r-iclusterplus")
4746 (uri (bioconductor-uri "iClusterPlus" version))
4749 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4750 (properties `((upstream-name . "iClusterPlus")))
4751 (build-system r-build-system)
4752 (native-inputs `(("gfortran" ,gfortran)))
4753 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4754 (synopsis "Integrative clustering of multi-type genomic data")
4756 "iClusterPlus is developed for integrative clustering analysis of
4757 multi-type genomic data and is an enhanced version of iCluster proposed and
4758 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4759 from the experiments where biological samples (e.g. tumor samples) are
4760 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4761 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4762 on. In the iClusterPlus model, binary observations such as somatic mutation
4763 are modeled as Binomial processes; categorical observations such as copy
4764 number states are realizations of Multinomial random variables; counts are
4765 modeled as Poisson random processes; and continuous measures are modeled by
4766 Gaussian distributions.")
4767 (license license:gpl2+)))
4769 (define-public r-rbowtie
4776 (uri (bioconductor-uri "Rbowtie" version))
4779 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4780 (properties `((upstream-name . "Rbowtie")))
4781 (build-system r-build-system)
4784 (home-page "https://bioconductor.org/packages/Rbowtie/")
4785 (synopsis "R bowtie wrapper")
4787 "This package provides an R wrapper around the popular bowtie short read
4788 aligner and around SpliceMap, a de novo splice junction discovery and
4790 (license license:artistic2.0)))
4792 (define-public r-sgseq
4799 (uri (bioconductor-uri "SGSeq" version))
4802 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4803 (properties `((upstream-name . "SGSeq")))
4804 (build-system r-build-system)
4806 `(("r-annotationdbi" ,r-annotationdbi)
4807 ("r-biocgenerics" ,r-biocgenerics)
4808 ("r-biostrings" ,r-biostrings)
4809 ("r-genomeinfodb" ,r-genomeinfodb)
4810 ("r-genomicalignments" ,r-genomicalignments)
4811 ("r-genomicfeatures" ,r-genomicfeatures)
4812 ("r-genomicranges" ,r-genomicranges)
4813 ("r-igraph" ,r-igraph)
4814 ("r-iranges" ,r-iranges)
4815 ("r-rsamtools" ,r-rsamtools)
4816 ("r-rtracklayer" ,r-rtracklayer)
4817 ("r-runit" ,r-runit)
4818 ("r-s4vectors" ,r-s4vectors)
4819 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4820 (home-page "https://bioconductor.org/packages/SGSeq/")
4821 (synopsis "Splice event prediction and quantification from RNA-seq data")
4823 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4824 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4825 represented as a splice graph, which can be obtained from existing annotation
4826 or predicted from the mapped sequence reads. Splice events are identified
4827 from the graph and are quantified locally using structurally compatible reads
4828 at the start or end of each splice variant. The software includes functions
4829 for splice event prediction, quantification, visualization and
4831 (license license:artistic2.0)))
4833 (define-public r-rhisat2
4840 (uri (bioconductor-uri "Rhisat2" version))
4843 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4844 (properties `((upstream-name . "Rhisat2")))
4845 (build-system r-build-system)
4847 `(("which" ,which)))
4849 `(("r-genomicfeatures" ,r-genomicfeatures)
4850 ("r-genomicranges" ,r-genomicranges)
4851 ("r-sgseq" ,r-sgseq)))
4852 (home-page "https://github.com/fmicompbio/Rhisat2")
4853 (synopsis "R Wrapper for HISAT2 sequence aligner")
4855 "This package provides an R interface to the HISAT2 spliced short-read
4856 aligner by Kim et al. (2015). The package contains wrapper functions to
4857 create a genome index and to perform the read alignment to the generated
4859 (license license:gpl3)))
4861 (define-public r-quasr
4868 (uri (bioconductor-uri "QuasR" version))
4871 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4872 (properties `((upstream-name . "QuasR")))
4873 (build-system r-build-system)
4877 `(("r-annotationdbi" ,r-annotationdbi)
4878 ("r-biobase" ,r-biobase)
4879 ("r-biocgenerics" ,r-biocgenerics)
4880 ("r-biocmanager" ,r-biocmanager)
4881 ("r-biocparallel" ,r-biocparallel)
4882 ("r-biostrings" ,r-biostrings)
4883 ("r-bsgenome" ,r-bsgenome)
4884 ("r-genomeinfodb" ,r-genomeinfodb)
4885 ("r-genomicalignments" ,r-genomicalignments)
4886 ("r-genomicfeatures" ,r-genomicfeatures)
4887 ("r-genomicfiles" ,r-genomicfiles)
4888 ("r-genomicranges" ,r-genomicranges)
4889 ("r-iranges" ,r-iranges)
4890 ("r-rbowtie" ,r-rbowtie)
4891 ("r-rhisat2" ,r-rhisat2)
4892 ("r-rhtslib" ,r-rhtslib)
4893 ("r-rsamtools" ,r-rsamtools)
4894 ("r-rtracklayer" ,r-rtracklayer)
4895 ("r-s4vectors" ,r-s4vectors)
4896 ("r-shortread" ,r-shortread)))
4897 (home-page "https://bioconductor.org/packages/QuasR/")
4898 (synopsis "Quantify and annotate short reads in R")
4900 "This package provides a framework for the quantification and analysis of
4901 short genomic reads. It covers a complete workflow starting from raw sequence
4902 reads, over creation of alignments and quality control plots, to the
4903 quantification of genomic regions of interest.")
4904 (license license:gpl2)))
4906 (define-public r-rqc
4913 (uri (bioconductor-uri "Rqc" version))
4916 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4917 (properties `((upstream-name . "Rqc")))
4918 (build-system r-build-system)
4920 `(("r-biocgenerics" ,r-biocgenerics)
4921 ("r-biocparallel" ,r-biocparallel)
4922 ("r-biocstyle" ,r-biocstyle)
4923 ("r-biostrings" ,r-biostrings)
4924 ("r-biovizbase" ,r-biovizbase)
4925 ("r-genomicalignments" ,r-genomicalignments)
4926 ("r-genomicfiles" ,r-genomicfiles)
4927 ("r-ggplot2" ,r-ggplot2)
4928 ("r-iranges" ,r-iranges)
4929 ("r-knitr" ,r-knitr)
4930 ("r-markdown" ,r-markdown)
4933 ("r-reshape2" ,r-reshape2)
4934 ("r-rsamtools" ,r-rsamtools)
4935 ("r-s4vectors" ,r-s4vectors)
4936 ("r-shiny" ,r-shiny)
4937 ("r-shortread" ,r-shortread)))
4938 (home-page "https://github.com/labbcb/Rqc")
4939 (synopsis "Quality control tool for high-throughput sequencing data")
4941 "Rqc is an optimized tool designed for quality control and assessment of
4942 high-throughput sequencing data. It performs parallel processing of entire
4943 files and produces a report which contains a set of high-resolution
4945 (license license:gpl2+)))
4947 (define-public r-birewire
4954 (uri (bioconductor-uri "BiRewire" version))
4957 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
4958 (properties `((upstream-name . "BiRewire")))
4959 (build-system r-build-system)
4961 `(("r-igraph" ,r-igraph)
4962 ("r-matrix" ,r-matrix)
4964 ("r-tsne" ,r-tsne)))
4965 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
4966 (synopsis "Tools for randomization of bipartite graphs")
4968 "This package provides functions for bipartite network rewiring through N
4969 consecutive switching steps and for the computation of the minimal number of
4970 switching steps to be performed in order to maximise the dissimilarity with
4971 respect to the original network. It includes functions for the analysis of
4972 the introduced randomness across the switching steps and several other
4973 routines to analyse the resulting networks and their natural projections.")
4974 (license license:gpl3)))
4976 (define-public r-birta
4983 (uri (bioconductor-uri "birta" version))
4986 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
4987 (build-system r-build-system)
4989 `(("r-biobase" ,r-biobase)
4990 ("r-limma" ,r-limma)
4991 ("r-mass" ,r-mass)))
4992 (home-page "https://bioconductor.org/packages/birta")
4993 (synopsis "Bayesian inference of regulation of transcriptional activity")
4995 "Expression levels of mRNA molecules are regulated by different
4996 processes, comprising inhibition or activation by transcription factors and
4997 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
4998 Inference of Regulation of Transcriptional Activity) uses the regulatory
4999 networks of transcription factors and miRNAs together with mRNA and miRNA
5000 expression data to predict switches in regulatory activity between two
5001 conditions. A Bayesian network is used to model the regulatory structure and
5002 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5003 (license license:gpl2+)))
5005 (define-public r-ropls
5012 (uri (bioconductor-uri "ropls" version))
5015 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
5016 (build-system r-build-system)
5017 (propagated-inputs `(("r-biobase" ,r-biobase)))
5019 `(("r-knitr" ,r-knitr))) ; for vignettes
5020 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5021 (synopsis "Multivariate analysis and feature selection of omics data")
5023 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5024 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5025 regression, classification, and feature selection of omics data where the
5026 number of variables exceeds the number of samples and with multicollinearity
5027 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5028 separately model the variation correlated (predictive) to the factor of
5029 interest and the uncorrelated (orthogonal) variation. While performing
5030 similarly to PLS, OPLS facilitates interpretation.
5032 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5033 analysis and feature selection of omics data. In addition to scores, loadings
5034 and weights plots, the package provides metrics and graphics to determine the
5035 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5036 validity of the model by permutation testing, detect outliers, and perform
5037 feature selection (e.g. with Variable Importance in Projection or regression
5039 (license license:cecill)))
5041 (define-public r-biosigner
5043 (name "r-biosigner")
5048 (uri (bioconductor-uri "biosigner" version))
5051 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
5052 (build-system r-build-system)
5054 `(("r-biobase" ,r-biobase)
5055 ("r-e1071" ,r-e1071)
5056 ("r-randomforest" ,r-randomforest)
5057 ("r-ropls" ,r-ropls)))
5059 `(("r-knitr" ,r-knitr)
5060 ("r-rmarkdown" ,r-rmarkdown)
5061 ("pandoc" ,ghc-pandoc)
5062 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5063 (home-page "https://bioconductor.org/packages/biosigner/")
5064 (synopsis "Signature discovery from omics data")
5066 "Feature selection is critical in omics data analysis to extract
5067 restricted and meaningful molecular signatures from complex and high-dimension
5068 data, and to build robust classifiers. This package implements a method to
5069 assess the relevance of the variables for the prediction performances of the
5070 classifier. The approach can be run in parallel with the PLS-DA, Random
5071 Forest, and SVM binary classifiers. The signatures and the corresponding
5072 'restricted' models are returned, enabling future predictions on new
5074 (license license:cecill)))
5076 (define-public r-annotatr
5083 (uri (bioconductor-uri "annotatr" version))
5086 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
5087 (build-system r-build-system)
5089 `(("r-annotationdbi" ,r-annotationdbi)
5090 ("r-annotationhub" ,r-annotationhub)
5091 ("r-dplyr" ,r-dplyr)
5092 ("r-genomeinfodb" ,r-genomeinfodb)
5093 ("r-genomicfeatures" ,r-genomicfeatures)
5094 ("r-genomicranges" ,r-genomicranges)
5095 ("r-ggplot2" ,r-ggplot2)
5096 ("r-iranges" ,r-iranges)
5097 ("r-readr" ,r-readr)
5098 ("r-regioner" ,r-regioner)
5099 ("r-reshape2" ,r-reshape2)
5100 ("r-rtracklayer" ,r-rtracklayer)
5101 ("r-s4vectors" ,r-s4vectors)))
5102 (home-page "https://bioconductor.org/packages/annotatr/")
5103 (synopsis "Annotation of genomic regions to genomic annotations")
5105 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5106 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5107 to investigate the intersecting genomic annotations. Such annotations include
5108 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5109 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5110 enhancers. The annotatr package provides an easy way to summarize and
5111 visualize the intersection of genomic sites/regions with genomic
5113 (license license:gpl3)))
5115 (define-public r-rsubread
5122 (uri (bioconductor-uri "Rsubread" version))
5125 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
5126 (properties `((upstream-name . "Rsubread")))
5127 (build-system r-build-system)
5128 (inputs `(("zlib" ,zlib)))
5129 (home-page "https://bioconductor.org/packages/Rsubread/")
5130 (synopsis "Subread sequence alignment and counting for R")
5132 "This package provides tools for alignment, quantification and analysis
5133 of second and third generation sequencing data. It includes functionality for
5134 read mapping, read counting, SNP calling, structural variant detection and
5135 gene fusion discovery. It can be applied to all major sequencing techologies
5136 and to both short and long sequence reads.")
5137 (license license:gpl3)))
5139 (define-public r-flowutils
5141 (name "r-flowutils")
5146 (uri (bioconductor-uri "flowUtils" version))
5149 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
5150 (properties `((upstream-name . "flowUtils")))
5151 (build-system r-build-system)
5153 `(("r-biobase" ,r-biobase)
5154 ("r-corpcor" ,r-corpcor)
5155 ("r-flowcore" ,r-flowcore)
5156 ("r-graph" ,r-graph)
5157 ("r-runit" ,r-runit)
5159 (home-page "https://github.com/jspidlen/flowUtils")
5160 (synopsis "Utilities for flow cytometry")
5162 "This package provides utilities for flow cytometry data.")
5163 (license license:artistic2.0)))
5165 (define-public r-consensusclusterplus
5167 (name "r-consensusclusterplus")
5172 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5175 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
5177 `((upstream-name . "ConsensusClusterPlus")))
5178 (build-system r-build-system)
5181 ("r-biobase" ,r-biobase)
5182 ("r-cluster" ,r-cluster)))
5183 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5184 (synopsis "Clustering algorithm")
5186 "This package provides an implementation of an algorithm for determining
5187 cluster count and membership by stability evidence in unsupervised analysis.")
5188 (license license:gpl2)))
5190 (define-public r-flowcore
5197 (uri (bioconductor-uri "flowCore" version))
5200 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
5201 (properties `((upstream-name . "flowCore")))
5202 (build-system r-build-system)
5205 ("r-biobase" ,r-biobase)
5206 ("r-biocgenerics" ,r-biocgenerics)
5207 ("r-corpcor" ,r-corpcor)
5208 ("r-graph" ,r-graph)
5210 ("r-matrixstats" ,r-matrixstats)
5212 ("r-rrcov" ,r-rrcov)))
5213 (home-page "https://bioconductor.org/packages/flowCore")
5214 (synopsis "Basic structures for flow cytometry data")
5216 "This package provides S4 data structures and basic functions to deal
5217 with flow cytometry data.")
5218 (license license:artistic2.0)))
5220 (define-public r-flowmeans
5222 (name "r-flowmeans")
5227 (uri (bioconductor-uri "flowMeans" version))
5230 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
5231 (properties `((upstream-name . "flowMeans")))
5232 (build-system r-build-system)
5234 `(("r-biobase" ,r-biobase)
5235 ("r-feature" ,r-feature)
5236 ("r-flowcore" ,r-flowcore)
5237 ("r-rrcov" ,r-rrcov)))
5238 (home-page "https://bioconductor.org/packages/flowMeans")
5239 (synopsis "Non-parametric flow cytometry data gating")
5241 "This package provides tools to identify cell populations in Flow
5242 Cytometry data using non-parametric clustering and segmented-regression-based
5243 change point detection.")
5244 (license license:artistic2.0)))
5246 (define-public r-flowsom
5253 (uri (bioconductor-uri "FlowSOM" version))
5256 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5257 (properties `((upstream-name . "FlowSOM")))
5258 (build-system r-build-system)
5260 `(("r-biocgenerics" ,r-biocgenerics)
5261 ("r-consensusclusterplus" ,r-consensusclusterplus)
5262 ("r-flowcore" ,r-flowcore)
5263 ("r-flowutils" ,r-flowutils)
5264 ("r-igraph" ,r-igraph)
5267 (home-page "https://bioconductor.org/packages/FlowSOM/")
5268 (synopsis "Visualize and interpret cytometry data")
5270 "FlowSOM offers visualization options for cytometry data, by using
5271 self-organizing map clustering and minimal spanning trees.")
5272 (license license:gpl2+)))
5274 (define-public r-mixomics
5281 (uri (bioconductor-uri "mixOmics" version))
5284 "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
5285 (properties `((upstream-name . "mixOmics")))
5286 (build-system r-build-system)
5288 `(("r-corpcor" ,r-corpcor)
5289 ("r-dplyr" ,r-dplyr)
5290 ("r-ellipse" ,r-ellipse)
5291 ("r-ggplot2" ,r-ggplot2)
5292 ("r-gridextra" ,r-gridextra)
5293 ("r-igraph" ,r-igraph)
5294 ("r-lattice" ,r-lattice)
5296 ("r-matrixstats" ,r-matrixstats)
5297 ("r-rarpack" ,r-rarpack)
5298 ("r-rcolorbrewer" ,r-rcolorbrewer)
5299 ("r-reshape2" ,r-reshape2)
5300 ("r-tidyr" ,r-tidyr)))
5301 (home-page "http://www.mixOmics.org")
5302 (synopsis "Multivariate methods for exploration of biological datasets")
5304 "mixOmics offers a wide range of multivariate methods for the exploration
5305 and integration of biological datasets with a particular focus on variable
5306 selection. The package proposes several sparse multivariate models we have
5307 developed to identify the key variables that are highly correlated, and/or
5308 explain the biological outcome of interest. The data that can be analysed
5309 with mixOmics may come from high throughput sequencing technologies, such as
5310 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5311 also beyond the realm of omics (e.g. spectral imaging). The methods
5312 implemented in mixOmics can also handle missing values without having to
5313 delete entire rows with missing data.")
5314 (license license:gpl2+)))
5316 (define-public r-depecher
5323 (uri (bioconductor-uri "DepecheR" version))
5326 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5327 (properties `((upstream-name . "DepecheR")))
5328 (build-system r-build-system)
5331 (modify-phases %standard-phases
5332 (add-after 'unpack 'fix-syntax-error
5334 (substitute* "src/Makevars"
5338 `(("r-beanplot" ,r-beanplot)
5339 ("r-biocparallel" ,r-biocparallel)
5340 ("r-dosnow" ,r-dosnow)
5341 ("r-dplyr" ,r-dplyr)
5342 ("r-foreach" ,r-foreach)
5343 ("r-ggplot2" ,r-ggplot2)
5344 ("r-gplots" ,r-gplots)
5346 ("r-matrixstats" ,r-matrixstats)
5347 ("r-mixomics" ,r-mixomics)
5348 ("r-moments" ,r-moments)
5350 ("r-rcppeigen" ,r-rcppeigen)
5351 ("r-reshape2" ,r-reshape2)
5352 ("r-viridis" ,r-viridis)))
5353 (home-page "https://bioconductor.org/packages/DepecheR/")
5354 (synopsis "Identify traits of clusters in high-dimensional entities")
5356 "The purpose of this package is to identify traits in a dataset that can
5357 separate groups. This is done on two levels. First, clustering is performed,
5358 using an implementation of sparse K-means. Secondly, the generated clusters
5359 are used to predict outcomes of groups of individuals based on their
5360 distribution of observations in the different clusters. As certain clusters
5361 with separating information will be identified, and these clusters are defined
5362 by a sparse number of variables, this method can reduce the complexity of
5363 data, to only emphasize the data that actually matters.")
5364 (license license:expat)))
5366 (define-public r-rcistarget
5368 (name "r-rcistarget")
5373 (uri (bioconductor-uri "RcisTarget" version))
5376 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5377 (properties `((upstream-name . "RcisTarget")))
5378 (build-system r-build-system)
5380 `(("r-aucell" ,r-aucell)
5381 ("r-biocgenerics" ,r-biocgenerics)
5382 ("r-data-table" ,r-data-table)
5383 ("r-feather" ,r-feather)
5384 ("r-gseabase" ,r-gseabase)
5385 ("r-r-utils" ,r-r-utils)
5386 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5387 (home-page "https://aertslab.org/#scenic")
5388 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5390 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5391 over-represented on a gene list. In a first step, RcisTarget selects DNA
5392 motifs that are significantly over-represented in the surroundings of the
5393 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5394 achieved by using a database that contains genome-wide cross-species rankings
5395 for each motif. The motifs that are then annotated to TFs and those that have
5396 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5397 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5398 genes in the gene-set that are ranked above the leading edge).")
5399 (license license:gpl3)))
5401 (define-public r-cicero
5408 (uri (bioconductor-uri "cicero" version))
5411 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5412 (build-system r-build-system)
5414 `(("r-assertthat" ,r-assertthat)
5415 ("r-biobase" ,r-biobase)
5416 ("r-biocgenerics" ,r-biocgenerics)
5417 ("r-data-table" ,r-data-table)
5418 ("r-dplyr" ,r-dplyr)
5420 ("r-genomicranges" ,r-genomicranges)
5421 ("r-ggplot2" ,r-ggplot2)
5422 ("r-glasso" ,r-glasso)
5424 ("r-igraph" ,r-igraph)
5425 ("r-iranges" ,r-iranges)
5426 ("r-matrix" ,r-matrix)
5427 ("r-monocle" ,r-monocle)
5429 ("r-reshape2" ,r-reshape2)
5430 ("r-s4vectors" ,r-s4vectors)
5431 ("r-stringr" ,r-stringr)
5432 ("r-tibble" ,r-tibble)
5433 ("r-vgam" ,r-vgam)))
5434 (home-page "https://bioconductor.org/packages/cicero/")
5435 (synopsis "Predict cis-co-accessibility from single-cell data")
5437 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5438 accessibility data. It also extends the monocle package for use in chromatin
5439 accessibility data.")
5440 (license license:expat)))
5442 ;; This is the latest commit on the "monocle3" branch.
5443 (define-public r-cicero-monocle3
5444 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5446 (package (inherit r-cicero)
5447 (name "r-cicero-monocle3")
5448 (version (git-version "1.3.2" revision commit))
5453 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5455 (file-name (git-file-name name version))
5458 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5460 `(("r-monocle3" ,r-monocle3)
5461 ,@(alist-delete "r-monocle"
5462 (package-propagated-inputs r-cicero)))))))
5464 (define-public r-cistopic
5465 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5469 (version (git-version "0.2.1" revision commit))
5474 (url "https://github.com/aertslab/cisTopic.git")
5476 (file-name (git-file-name name version))
5479 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5480 (build-system r-build-system)
5482 `(("r-aucell" ,r-aucell)
5483 ("r-data-table" ,r-data-table)
5484 ("r-dplyr" ,r-dplyr)
5485 ("r-dosnow" ,r-dosnow)
5487 ("r-feather" ,r-feather)
5488 ("r-fitdistrplus" ,r-fitdistrplus)
5489 ("r-genomicranges" ,r-genomicranges)
5490 ("r-ggplot2" ,r-ggplot2)
5492 ("r-matrix" ,r-matrix)
5494 ("r-rcistarget" ,r-rcistarget)
5495 ("r-rtracklayer" ,r-rtracklayer)
5496 ("r-s4vectors" ,r-s4vectors)))
5497 (home-page "https://github.com/aertslab/cisTopic")
5498 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5500 "The sparse nature of single cell epigenomics data can be overruled using
5501 probabilistic modelling methods such as @dfn{Latent Dirichlet
5502 Allocation} (LDA). This package allows the probabilistic modelling of
5503 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5504 includes functionalities to identify cell states based on the contribution of
5505 cisTopics and explore the nature and regulatory proteins driving them.")
5506 (license license:gpl3))))
5508 (define-public r-genie3
5515 (uri (bioconductor-uri "GENIE3" version))
5518 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5519 (properties `((upstream-name . "GENIE3")))
5520 (build-system r-build-system)
5521 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5522 (home-page "https://bioconductor.org/packages/GENIE3")
5523 (synopsis "Gene network inference with ensemble of trees")
5525 "This package implements the GENIE3 algorithm for inferring gene
5526 regulatory networks from expression data.")
5527 (license license:gpl2+)))
5529 (define-public r-roc
5536 (uri (bioconductor-uri "ROC" version))
5539 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5540 (properties `((upstream-name . "ROC")))
5541 (build-system r-build-system)
5542 (home-page "https://www.bioconductor.org/packages/ROC/")
5543 (synopsis "Utilities for ROC curves")
5545 "This package provides utilities for @dfn{Receiver Operating
5546 Characteristic} (ROC) curves, with a focus on micro arrays.")
5547 (license license:artistic2.0)))
5549 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5551 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5556 (uri (bioconductor-uri
5557 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5558 version 'annotation))
5561 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5564 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5565 (build-system r-build-system)
5566 (propagated-inputs `(("r-minfi" ,r-minfi)))
5568 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5569 (synopsis "Annotation for Illumina's 450k methylation arrays")
5571 "This package provides manifests and annotation for Illumina's 450k array
5573 (license license:artistic2.0)))
5575 (define-public r-watermelon
5577 (name "r-watermelon")
5582 (uri (bioconductor-uri "wateRmelon" version))
5585 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
5586 (properties `((upstream-name . "wateRmelon")))
5587 (build-system r-build-system)
5589 `(("r-biobase" ,r-biobase)
5590 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
5591 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
5592 ("r-illuminaio" ,r-illuminaio)
5593 ("r-limma" ,r-limma)
5595 ("r-matrixstats" ,r-matrixstats)
5596 ("r-methylumi" ,r-methylumi)
5598 (home-page "https://bioconductor.org/packages/wateRmelon/")
5599 (synopsis "Illumina 450 methylation array normalization and metrics")
5601 "The standard index of DNA methylation (beta) is computed from methylated
5602 and unmethylated signal intensities. Betas calculated from raw signal
5603 intensities perform well, but using 11 methylomic datasets we demonstrate that
5604 quantile normalization methods produce marked improvement. The commonly used
5605 procedure of normalizing betas is inferior to the separate normalization of M
5606 and U, and it is also advantageous to normalize Type I and Type II assays
5607 separately. This package provides 15 flavours of betas and three performance
5608 metrics, with methods for objects produced by the @code{methylumi} and
5609 @code{minfi} packages.")
5610 (license license:gpl3)))
5612 (define-public r-gdsfmt
5619 (uri (bioconductor-uri "gdsfmt" version))
5622 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
5623 (modules '((guix build utils)))
5624 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
5625 ;; them and link with system libraries instead.
5628 (for-each delete-file-recursively
5632 (substitute* "src/Makevars"
5633 (("all: \\$\\(SHLIB\\)") "all:")
5634 (("\\$\\(SHLIB\\): liblzma.a") "")
5635 (("(ZLIB|LZ4)/.*") "")
5636 (("CoreArray/dVLIntGDS.cpp.*")
5637 "CoreArray/dVLIntGDS.cpp")
5638 (("CoreArray/dVLIntGDS.o.*")
5639 "CoreArray/dVLIntGDS.o")
5640 (("PKG_LIBS = ./liblzma.a")
5641 "PKG_LIBS = -llz4"))
5642 (substitute* "src/CoreArray/dStream.h"
5643 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
5644 (string-append "include <" header ">")))
5646 (properties `((upstream-name . "gdsfmt")))
5647 (build-system r-build-system)
5652 (home-page "http://corearray.sourceforge.net/")
5654 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
5656 "This package provides a high-level R interface to CoreArray @dfn{Genomic
5657 Data Structure} (GDS) data files, which are portable across platforms with
5658 hierarchical structure to store multiple scalable array-oriented data sets
5659 with metadata information. It is suited for large-scale datasets, especially
5660 for data which are much larger than the available random-access memory. The
5661 @code{gdsfmt} package offers efficient operations specifically designed for
5662 integers of less than 8 bits, since a diploid genotype, like
5663 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
5664 byte. Data compression and decompression are available with relatively
5665 efficient random access. It is also allowed to read a GDS file in parallel
5666 with multiple R processes supported by the package @code{parallel}.")
5667 (license license:lgpl3)))
5669 (define-public r-bigmelon
5676 (uri (bioconductor-uri "bigmelon" version))
5679 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
5680 (properties `((upstream-name . "bigmelon")))
5681 (build-system r-build-system)
5683 `(("r-biobase" ,r-biobase)
5684 ("r-biocgenerics" ,r-biocgenerics)
5685 ("r-gdsfmt" ,r-gdsfmt)
5686 ("r-geoquery" ,r-geoquery)
5687 ("r-methylumi" ,r-methylumi)
5688 ("r-minfi" ,r-minfi)
5689 ("r-watermelon" ,r-watermelon)))
5690 (home-page "https://bioconductor.org/packages/bigmelon/")
5691 (synopsis "Illumina methylation array analysis for large experiments")
5693 "This package provides methods for working with Illumina arrays using the
5694 @code{gdsfmt} package.")
5695 (license license:gpl3)))
5697 (define-public r-seqbias
5704 (uri (bioconductor-uri "seqbias" version))
5707 "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
5708 (properties `((upstream-name . "seqbias")))
5709 (build-system r-build-system)
5711 `(("r-biostrings" ,r-biostrings)
5712 ("r-genomicranges" ,r-genomicranges)
5713 ("r-rhtslib" ,r-rhtslib)))
5715 `(("zlib" ,zlib))) ; This comes from rhtslib.
5716 (home-page "https://bioconductor.org/packages/seqbias/")
5717 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
5719 "This package implements a model of per-position sequencing bias in
5720 high-throughput sequencing data using a simple Bayesian network, the structure
5721 and parameters of which are trained on a set of aligned reads and a reference
5723 (license license:lgpl3)))
5725 (define-public r-reqon
5732 (uri (bioconductor-uri "ReQON" version))
5735 "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
5736 (properties `((upstream-name . "ReQON")))
5737 (build-system r-build-system)
5739 `(("r-rjava" ,r-rjava)
5740 ("r-rsamtools" ,r-rsamtools)
5741 ("r-seqbias" ,r-seqbias)))
5742 (home-page "https://bioconductor.org/packages/ReQON/")
5743 (synopsis "Recalibrating quality of nucleotides")
5745 "This package provides an implementation of an algorithm for
5746 recalibrating the base quality scores for aligned sequencing data in BAM
5748 (license license:gpl2)))
5750 (define-public r-wavcluster
5752 (name "r-wavcluster")
5757 (uri (bioconductor-uri "wavClusteR" version))
5760 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
5761 (properties `((upstream-name . "wavClusteR")))
5762 (build-system r-build-system)
5764 `(("r-biocgenerics" ,r-biocgenerics)
5765 ("r-biostrings" ,r-biostrings)
5766 ("r-foreach" ,r-foreach)
5767 ("r-genomicfeatures" ,r-genomicfeatures)
5768 ("r-genomicranges" ,r-genomicranges)
5769 ("r-ggplot2" ,r-ggplot2)
5770 ("r-hmisc" ,r-hmisc)
5771 ("r-iranges" ,r-iranges)
5772 ("r-mclust" ,r-mclust)
5773 ("r-rsamtools" ,r-rsamtools)
5774 ("r-rtracklayer" ,r-rtracklayer)
5775 ("r-s4vectors" ,r-s4vectors)
5776 ("r-seqinr" ,r-seqinr)
5777 ("r-stringr" ,r-stringr)
5778 ("r-wmtsa" ,r-wmtsa)))
5779 (home-page "https://bioconductor.org/packages/wavClusteR/")
5780 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
5782 "This package provides an integrated pipeline for the analysis of
5783 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
5784 sequencing errors, SNPs and additional non-experimental sources by a non-
5785 parametric mixture model. The protein binding sites (clusters) are then
5786 resolved at high resolution and cluster statistics are estimated using a
5787 rigorous Bayesian framework. Post-processing of the results, data export for
5788 UCSC genome browser visualization and motif search analysis are provided. In
5789 addition, the package allows to integrate RNA-Seq data to estimate the False
5790 Discovery Rate of cluster detection. Key functions support parallel multicore
5791 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
5792 be applied to the analysis of other NGS data obtained from experimental
5793 procedures that induce nucleotide substitutions (e.g. BisSeq).")
5794 (license license:gpl2)))
5796 (define-public r-timeseriesexperiment
5798 (name "r-timeseriesexperiment")
5803 (uri (bioconductor-uri "TimeSeriesExperiment" version))
5806 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
5808 `((upstream-name . "TimeSeriesExperiment")))
5809 (build-system r-build-system)
5811 `(("r-deseq2" ,r-deseq2)
5812 ("r-dplyr" ,r-dplyr)
5813 ("r-dynamictreecut" ,r-dynamictreecut)
5814 ("r-edger" ,r-edger)
5815 ("r-ggplot2" ,r-ggplot2)
5816 ("r-hmisc" ,r-hmisc)
5817 ("r-limma" ,r-limma)
5818 ("r-magrittr" ,r-magrittr)
5819 ("r-proxy" ,r-proxy)
5820 ("r-s4vectors" ,r-s4vectors)
5821 ("r-summarizedexperiment" ,r-summarizedexperiment)
5822 ("r-tibble" ,r-tibble)
5823 ("r-tidyr" ,r-tidyr)
5824 ("r-vegan" ,r-vegan)
5825 ("r-viridis" ,r-viridis)))
5826 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
5827 (synopsis "Analysis for short time-series data")
5829 "This package is a visualization and analysis toolbox for short time
5830 course data which includes dimensionality reduction, clustering, two-sample
5831 differential expression testing and gene ranking techniques. The package also
5832 provides methods for retrieving enriched pathways.")
5833 (license license:lgpl3+)))
5835 (define-public r-variantfiltering
5837 (name "r-variantfiltering")
5842 (uri (bioconductor-uri "VariantFiltering" version))
5845 "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
5847 `((upstream-name . "VariantFiltering")))
5848 (build-system r-build-system)
5850 `(("r-annotationdbi" ,r-annotationdbi)
5851 ("r-biobase" ,r-biobase)
5852 ("r-biocgenerics" ,r-biocgenerics)
5853 ("r-biocparallel" ,r-biocparallel)
5854 ("r-biostrings" ,r-biostrings)
5855 ("r-bsgenome" ,r-bsgenome)
5857 ("r-genomeinfodb" ,r-genomeinfodb)
5858 ("r-genomicfeatures" ,r-genomicfeatures)
5859 ("r-genomicranges" ,r-genomicranges)
5860 ("r-genomicscores" ,r-genomicscores)
5861 ("r-graph" ,r-graph)
5863 ("r-iranges" ,r-iranges)
5865 ("r-rsamtools" ,r-rsamtools)
5866 ("r-s4vectors" ,r-s4vectors)
5867 ("r-shiny" ,r-shiny)
5868 ("r-shinyjs" ,r-shinyjs)
5869 ("r-shinythemes" ,r-shinythemes)
5870 ("r-shinytree" ,r-shinytree)
5871 ("r-summarizedexperiment" ,r-summarizedexperiment)
5872 ("r-variantannotation" ,r-variantannotation)
5873 ("r-xvector" ,r-xvector)))
5874 (home-page "https://github.com/rcastelo/VariantFiltering")
5875 (synopsis "Filtering of coding and non-coding genetic variants")
5877 "Filter genetic variants using different criteria such as inheritance
5878 model, amino acid change consequence, minor allele frequencies across human
5879 populations, splice site strength, conservation, etc.")
5880 (license license:artistic2.0)))
5882 (define-public r-genomegraphs
5884 (name "r-genomegraphs")
5889 (uri (bioconductor-uri "GenomeGraphs" version))
5892 "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd"))))
5893 (properties `((upstream-name . "GenomeGraphs")))
5894 (build-system r-build-system)
5896 `(("r-biomart" ,r-biomart)))
5897 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
5898 (synopsis "Plotting genomic information from Ensembl")
5900 "Genomic data analyses requires integrated visualization of known genomic
5901 information and new experimental data. GenomeGraphs uses the biomaRt package
5902 to perform live annotation queries to Ensembl and translates this to e.g.
5903 gene/transcript structures in viewports of the grid graphics package. This
5904 results in genomic information plotted together with your data. Another
5905 strength of GenomeGraphs is to plot different data types such as array CGH,
5906 gene expression, sequencing and other data, together in one plot using the
5907 same genome coordinate system.")
5908 (license license:artistic2.0)))
5910 (define-public r-wavetiling
5912 (name "r-wavetiling")
5917 (uri (bioconductor-uri "waveTiling" version))
5920 "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir"))))
5921 (properties `((upstream-name . "waveTiling")))
5922 (build-system r-build-system)
5924 `(("r-affy" ,r-affy)
5925 ("r-biobase" ,r-biobase)
5926 ("r-biostrings" ,r-biostrings)
5927 ("r-genomegraphs" ,r-genomegraphs)
5928 ("r-genomicranges" ,r-genomicranges)
5929 ("r-iranges" ,r-iranges)
5930 ("r-oligo" ,r-oligo)
5931 ("r-oligoclasses" ,r-oligoclasses)
5932 ("r-preprocesscore" ,r-preprocesscore)
5933 ("r-waveslim" ,r-waveslim)))
5934 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
5935 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
5937 "This package is designed to conduct transcriptome analysis for tiling
5938 arrays based on fast wavelet-based functional models.")
5939 (license license:gpl2+)))
5941 (define-public r-variancepartition
5943 (name "r-variancepartition")
5948 (uri (bioconductor-uri "variancePartition" version))
5951 "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
5953 `((upstream-name . "variancePartition")))
5954 (build-system r-build-system)
5956 `(("r-biobase" ,r-biobase)
5957 ("r-biocparallel" ,r-biocparallel)
5958 ("r-colorramps" ,r-colorramps)
5959 ("r-doparallel" ,r-doparallel)
5960 ("r-foreach" ,r-foreach)
5961 ("r-ggplot2" ,r-ggplot2)
5962 ("r-gplots" ,r-gplots)
5963 ("r-iterators" ,r-iterators)
5964 ("r-limma" ,r-limma)
5966 ("r-lmertest" ,r-lmertest)
5968 ("r-pbkrtest" ,r-pbkrtest)
5969 ("r-progress" ,r-progress)
5970 ("r-reshape2" ,r-reshape2)
5971 ("r-scales" ,r-scales)))
5972 (home-page "https://bioconductor.org/packages/variancePartition/")
5973 (synopsis "Analyze variation in gene expression experiments")
5975 "This is a package providing tools to quantify and interpret multiple
5976 sources of biological and technical variation in gene expression experiments.
5977 It uses a linear mixed model to quantify variation in gene expression
5978 attributable to individual, tissue, time point, or technical variables. The
5979 package includes dream differential expression analysis for repeated
5981 (license license:gpl2+)))
5983 (define-public r-htqpcr
5990 (uri (bioconductor-uri "HTqPCR" version))
5993 "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
5994 (properties `((upstream-name . "HTqPCR")))
5995 (build-system r-build-system)
5997 `(("r-affy" ,r-affy)
5998 ("r-biobase" ,r-biobase)
5999 ("r-gplots" ,r-gplots)
6000 ("r-limma" ,r-limma)
6001 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6002 (home-page "http://www.ebi.ac.uk/bertone/software")
6003 (synopsis "Automated analysis of high-throughput qPCR data")
6005 "Analysis of Ct values from high throughput quantitative real-time
6006 PCR (qPCR) assays across multiple conditions or replicates. The input data
6007 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6008 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6009 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6010 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6011 loading, quality assessment, normalization, visualization and parametric or
6012 non-parametric testing for statistical significance in Ct values between
6013 features (e.g. genes, microRNAs).")
6014 (license license:artistic2.0)))
6016 (define-public r-unifiedwmwqpcr
6018 (name "r-unifiedwmwqpcr")
6023 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6026 "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
6028 `((upstream-name . "unifiedWMWqPCR")))
6029 (build-system r-build-system)
6031 `(("r-biocgenerics" ,r-biocgenerics)
6032 ("r-htqpcr" ,r-htqpcr)))
6033 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6034 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6036 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6037 data. This modified test allows for testing differential expression in qPCR
6039 (license license:gpl2+)))