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>
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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 (gnu packages xml)
44 #:use-module (srfi srfi-1))
49 (define-public r-bsgenome-celegans-ucsc-ce6
51 (name "r-bsgenome-celegans-ucsc-ce6")
55 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
59 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
61 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
62 (build-system r-build-system)
64 `(("r-bsgenome" ,r-bsgenome)))
66 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
67 (synopsis "Full genome sequences for Worm")
69 "This package provides full genome sequences for Caenorhabditis
70 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
72 (license license:artistic2.0)))
74 (define-public r-bsgenome-celegans-ucsc-ce10
76 (name "r-bsgenome-celegans-ucsc-ce10")
80 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
84 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
86 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
87 (build-system r-build-system)
89 `(("r-bsgenome" ,r-bsgenome)))
91 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
92 (synopsis "Full genome sequences for Worm")
94 "This package provides full genome sequences for Caenorhabditis
95 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
97 (license license:artistic2.0)))
99 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
101 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
105 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
106 version 'annotation))
109 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
111 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
112 (build-system r-build-system)
114 `(("r-bsgenome" ,r-bsgenome)))
116 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
117 (synopsis "Full genome sequences for Fly")
119 "This package provides full genome sequences for Drosophila
120 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
122 (license license:artistic2.0)))
124 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
126 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
130 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
131 version 'annotation))
134 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
136 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
137 (build-system r-build-system)
139 `(("r-bsgenome" ,r-bsgenome)))
141 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
142 (synopsis "Full genome sequences for Fly")
144 "This package provides full genome sequences for Drosophila
145 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
146 Biostrings objects.")
147 (license license:artistic2.0)))
149 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
151 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
155 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
156 version 'annotation))
159 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
161 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
162 (build-system r-build-system)
164 `(("r-bsgenome" ,r-bsgenome)
165 ("r-bsgenome-dmelanogaster-ucsc-dm3"
166 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
167 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
168 (synopsis "Full masked genome sequences for Fly")
170 "This package provides full masked genome sequences for Drosophila
171 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
172 Biostrings objects. The sequences are the same as in
173 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
174 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
175 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
176 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
177 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
178 (license license:artistic2.0)))
180 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
182 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
186 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
187 version 'annotation))
190 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
192 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
193 (build-system r-build-system)
195 `(("r-bsgenome" ,r-bsgenome)))
197 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
198 (synopsis "Full genome sequences for Homo sapiens")
200 "This package provides full genome sequences for Homo sapiens from
201 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
202 (license license:artistic2.0)))
204 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
206 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
210 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
211 version 'annotation))
214 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
216 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
217 (build-system r-build-system)
219 `(("r-bsgenome" ,r-bsgenome)
220 ("r-bsgenome-hsapiens-ucsc-hg19"
221 ,r-bsgenome-hsapiens-ucsc-hg19)))
222 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
223 (synopsis "Full masked genome sequences for Homo sapiens")
225 "This package provides full genome sequences for Homo sapiens (Human) as
226 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
227 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
228 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
229 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
230 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
231 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
233 (license license:artistic2.0)))
235 (define-public r-bsgenome-mmusculus-ucsc-mm9
237 (name "r-bsgenome-mmusculus-ucsc-mm9")
241 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
242 version 'annotation))
245 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
247 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
248 (build-system r-build-system)
250 `(("r-bsgenome" ,r-bsgenome)))
252 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
253 (synopsis "Full genome sequences for Mouse")
255 "This package provides full genome sequences for Mus musculus (Mouse) as
256 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
257 (license license:artistic2.0)))
259 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
261 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
265 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
266 version 'annotation))
269 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
271 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
272 (build-system r-build-system)
274 `(("r-bsgenome" ,r-bsgenome)
275 ("r-bsgenome-mmusculus-ucsc-mm9"
276 ,r-bsgenome-mmusculus-ucsc-mm9)))
277 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
278 (synopsis "Full masked genome sequences for Mouse")
280 "This package provides full genome sequences for Mus musculus (Mouse) as
281 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
282 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
283 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
284 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
285 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
286 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
288 (license license:artistic2.0)))
290 (define-public r-bsgenome-mmusculus-ucsc-mm10
292 (name "r-bsgenome-mmusculus-ucsc-mm10")
296 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
297 version 'annotation))
300 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
302 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
303 (build-system r-build-system)
305 `(("r-bsgenome" ,r-bsgenome)))
307 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
308 (synopsis "Full genome sequences for Mouse")
310 "This package provides full genome sequences for Mus
311 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
312 in Biostrings objects.")
313 (license license:artistic2.0)))
315 (define-public r-org-ce-eg-db
317 (name "r-org-ce-eg-db")
321 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
324 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
326 `((upstream-name . "org.Ce.eg.db")))
327 (build-system r-build-system)
329 `(("r-annotationdbi" ,r-annotationdbi)))
330 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
331 (synopsis "Genome wide annotation for Worm")
333 "This package provides mappings from Entrez gene identifiers to various
334 annotations for the genome of the model worm Caenorhabditis elegans.")
335 (license license:artistic2.0)))
337 (define-public r-org-dm-eg-db
339 (name "r-org-dm-eg-db")
343 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
346 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
348 `((upstream-name . "org.Dm.eg.db")))
349 (build-system r-build-system)
351 `(("r-annotationdbi" ,r-annotationdbi)))
352 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
353 (synopsis "Genome wide annotation for Fly")
355 "This package provides mappings from Entrez gene identifiers to various
356 annotations for the genome of the model fruit fly Drosophila melanogaster.")
357 (license license:artistic2.0)))
359 (define-public r-org-dr-eg-db
361 (name "r-org-dr-eg-db")
365 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
368 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
370 `((upstream-name . "org.Dr.eg.db")))
371 (build-system r-build-system)
373 `(("r-annotationdbi" ,r-annotationdbi)))
374 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
375 (synopsis "Annotation for Zebrafish")
377 "This package provides genome wide annotations for Zebrafish, primarily
378 based on mapping using Entrez Gene identifiers.")
379 (license license:artistic2.0)))
381 (define-public r-org-hs-eg-db
383 (name "r-org-hs-eg-db")
387 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
390 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
392 `((upstream-name . "org.Hs.eg.db")))
393 (build-system r-build-system)
395 `(("r-annotationdbi" ,r-annotationdbi)))
396 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
397 (synopsis "Genome wide annotation for Human")
399 "This package contains genome-wide annotations for Human, primarily based
400 on mapping using Entrez Gene identifiers.")
401 (license license:artistic2.0)))
403 (define-public r-org-mm-eg-db
405 (name "r-org-mm-eg-db")
409 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
412 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
414 `((upstream-name . "org.Mm.eg.db")))
415 (build-system r-build-system)
417 `(("r-annotationdbi" ,r-annotationdbi)))
418 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
419 (synopsis "Genome wide annotation for Mouse")
421 "This package provides mappings from Entrez gene identifiers to various
422 annotations for the genome of the model mouse Mus musculus.")
423 (license license:artistic2.0)))
425 (define-public r-bsgenome-hsapiens-ucsc-hg19
427 (name "r-bsgenome-hsapiens-ucsc-hg19")
431 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
432 version 'annotation))
435 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
437 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
438 (build-system r-build-system)
440 `(("r-bsgenome" ,r-bsgenome)))
442 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
443 (synopsis "Full genome sequences for Homo sapiens")
445 "This package provides full genome sequences for Homo sapiens as provided
446 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
447 (license license:artistic2.0)))
449 (define-public r-ensdb-hsapiens-v75
451 (name "r-ensdb-hsapiens-v75")
456 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
459 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
461 `((upstream-name . "EnsDb.Hsapiens.v75")))
462 (build-system r-build-system)
464 `(("r-ensembldb" ,r-ensembldb)))
465 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
466 (synopsis "Ensembl based annotation package")
468 "This package exposes an annotation database generated from Ensembl.")
469 (license license:artistic2.0)))
471 (define-public r-genelendatabase
473 (name "r-genelendatabase")
478 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
481 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
483 `((upstream-name . "geneLenDataBase")))
484 (build-system r-build-system)
486 `(("r-rtracklayer" ,r-rtracklayer)
487 ("r-genomicfeatures" ,r-genomicfeatures)))
488 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
489 (synopsis "Lengths of mRNA transcripts for a number of genomes")
491 "This package provides the lengths of mRNA transcripts for a number of
492 genomes and gene ID formats, largely based on the UCSC table browser.")
493 (license license:lgpl2.0+)))
495 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
497 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
501 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
502 version 'annotation))
505 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
507 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
508 (build-system r-build-system)
510 `(("r-genomicfeatures" ,r-genomicfeatures)))
512 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
513 (synopsis "Annotation package for human genome in TxDb format")
515 "This package provides an annotation database of Homo sapiens genome
516 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
517 track. The database is exposed as a @code{TxDb} object.")
518 (license license:artistic2.0)))
520 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
522 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
526 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
527 version 'annotation))
530 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
532 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
533 (build-system r-build-system)
535 `(("r-genomicfeatures" ,r-genomicfeatures)))
537 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
538 (synopsis "Annotation package for human genome in TxDb format")
540 "This package provides an annotation database of Homo sapiens genome
541 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
542 track. The database is exposed as a @code{TxDb} object.")
543 (license license:artistic2.0)))
545 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
547 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
551 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
552 version 'annotation))
555 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
557 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
558 (build-system r-build-system)
560 `(("r-genomicfeatures" ,r-genomicfeatures)
561 ("r-annotationdbi" ,r-annotationdbi)))
563 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
564 (synopsis "Annotation package for mouse genome in TxDb format")
566 "This package provides an annotation database of Mouse genome data. It
567 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
568 database is exposed as a @code{TxDb} object.")
569 (license license:artistic2.0)))
571 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
573 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
577 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
578 version 'annotation))
581 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
583 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
584 (build-system r-build-system)
586 `(("r-bsgenome" ,r-bsgenome)
587 ("r-genomicfeatures" ,r-genomicfeatures)
588 ("r-annotationdbi" ,r-annotationdbi)))
590 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
591 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
593 "This package loads a TxDb object, which is an R interface to
594 prefabricated databases contained in this package. This package provides
595 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
596 based on the knownGene track.")
597 (license license:artistic2.0)))
599 (define-public r-txdb-celegans-ucsc-ce6-ensgene
601 (name "r-txdb-celegans-ucsc-ce6-ensgene")
606 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
607 version 'annotation))
610 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
612 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
613 (build-system r-build-system)
615 `(("r-annotationdbi" ,r-annotationdbi)
616 ("r-genomicfeatures" ,r-genomicfeatures)))
617 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
618 (synopsis "Annotation package for C elegans TxDb objects")
620 "This package exposes a C elegans annotation database generated from UCSC
621 by exposing these as TxDb objects.")
622 (license license:artistic2.0)))
624 (define-public r-fdb-infiniummethylation-hg19
626 (name "r-fdb-infiniummethylation-hg19")
630 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
631 version 'annotation))
634 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
636 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
637 (build-system r-build-system)
639 `(("r-biostrings" ,r-biostrings)
640 ("r-genomicfeatures" ,r-genomicfeatures)
641 ("r-annotationdbi" ,r-annotationdbi)
642 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
643 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
644 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
645 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
647 "This is an annotation package for Illumina Infinium DNA methylation
648 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
650 (license license:artistic2.0)))
652 (define-public r-illuminahumanmethylationepicmanifest
654 (name "r-illuminahumanmethylationepicmanifest")
658 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
659 version 'annotation))
662 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
664 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
665 (build-system r-build-system)
667 `(("r-minfi" ,r-minfi)))
668 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
669 (synopsis "Manifest for Illumina's EPIC methylation arrays")
671 "This is a manifest package for Illumina's EPIC methylation arrays.")
672 (license license:artistic2.0)))
674 (define-public r-do-db
680 (uri (bioconductor-uri "DO.db" version 'annotation))
683 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
685 `((upstream-name . "DO.db")))
686 (build-system r-build-system)
688 `(("r-annotationdbi" ,r-annotationdbi)))
689 (home-page "https://www.bioconductor.org/packages/DO.db/")
690 (synopsis "Annotation maps describing the entire Disease Ontology")
692 "This package provides a set of annotation maps describing the entire
694 (license license:artistic2.0)))
696 (define-public r-pfam-db
703 (uri (bioconductor-uri "PFAM.db" version 'annotation))
706 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
707 (properties `((upstream-name . "PFAM.db")))
708 (build-system r-build-system)
710 `(("r-annotationdbi" ,r-annotationdbi)))
711 (home-page "https://bioconductor.org/packages/PFAM.db")
712 (synopsis "Set of protein ID mappings for PFAM")
714 "This package provides a set of protein ID mappings for PFAM, assembled
715 using data from public repositories.")
716 (license license:artistic2.0)))
718 (define-public r-phastcons100way-ucsc-hg19
720 (name "r-phastcons100way-ucsc-hg19")
725 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
726 version 'annotation))
729 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
731 `((upstream-name . "phastCons100way.UCSC.hg19")))
732 (build-system r-build-system)
734 `(("r-bsgenome" ,r-bsgenome)
735 ("r-genomeinfodb" ,r-genomeinfodb)
736 ("r-genomicranges" ,r-genomicranges)
737 ("r-genomicscores" ,r-genomicscores)
738 ("r-iranges" ,r-iranges)
739 ("r-s4vectors" ,r-s4vectors)))
740 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
741 (synopsis "UCSC phastCons conservation scores for hg19")
743 "This package provides UCSC phastCons conservation scores for the human
744 genome (hg19) calculated from multiple alignments with other 99 vertebrate
746 (license license:artistic2.0)))
751 (define-public r-abadata
757 (uri (bioconductor-uri "ABAData" version 'experiment))
760 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
762 `((upstream-name . "ABAData")))
763 (build-system r-build-system)
765 `(("r-annotationdbi" ,r-annotationdbi)))
766 (home-page "https://www.bioconductor.org/packages/ABAData/")
767 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
769 "This package provides the data for the gene expression enrichment
770 analysis conducted in the package ABAEnrichment. The package includes three
771 datasets which are derived from the Allen Brain Atlas:
774 @item Gene expression data from Human Brain (adults) averaged across donors,
775 @item Gene expression data from the Developing Human Brain pooled into five
776 age categories and averaged across donors, and
777 @item a developmental effect score based on the Developing Human Brain
781 All datasets are restricted to protein coding genes.")
782 (license license:gpl2+)))
784 (define-public r-arrmdata
790 (uri (bioconductor-uri "ARRmData" version 'experiment))
793 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
795 `((upstream-name . "ARRmData")))
796 (build-system r-build-system)
797 (home-page "https://www.bioconductor.org/packages/ARRmData/")
798 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
800 "This package provides raw beta values from 36 samples across 3 groups
801 from Illumina 450k methylation arrays.")
802 (license license:artistic2.0)))
804 (define-public r-hsmmsinglecell
806 (name "r-hsmmsinglecell")
810 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
813 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
815 `((upstream-name . "HSMMSingleCell")))
816 (build-system r-build-system)
817 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
818 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
820 "Skeletal myoblasts undergo a well-characterized sequence of
821 morphological and transcriptional changes during differentiation. In this
822 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
823 under high mitogen conditions (GM) and then differentiated by switching to
824 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
825 hundred cells taken over a time-course of serum-induced differentiation.
826 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
827 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
828 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
829 which were then sequenced to a depth of ~4 million reads per library,
830 resulting in a complete gene expression profile for each cell.")
831 (license license:artistic2.0)))
839 (uri (bioconductor-uri "ALL" version 'experiment))
842 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
843 (properties `((upstream-name . "ALL")))
844 (build-system r-build-system)
846 `(("r-biobase" ,r-biobase)))
847 (home-page "https://bioconductor.org/packages/ALL")
848 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
850 "The data consist of microarrays from 128 different individuals with
851 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
852 are available. The data have been normalized (using rma) and it is the
853 jointly normalized data that are available here. The data are presented in
854 the form of an @code{exprSet} object.")
855 (license license:artistic2.0)))
857 (define-public r-affydata
864 (uri (bioconductor-uri "affydata" version 'experiment))
867 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
868 (properties `((upstream-name . "affydata")))
869 (build-system r-build-system)
871 `(("r-affy" ,r-affy)))
872 (home-page "https://bioconductor.org/packages/affydata/")
873 (synopsis "Affymetrix data for demonstration purposes")
875 "This package provides example datasets that represent 'real world
876 examples' of Affymetrix data, unlike the artificial examples included in the
877 package @code{affy}.")
878 (license license:gpl2+)))
883 (define-public r-biocversion
885 (name "r-biocversion")
890 (uri (bioconductor-uri "BiocVersion" version))
893 "0mfqjqfvrwwglldq3g7nbic5hf3nwzv02nbfxnl2cfvf9gznlh5f"))))
894 (properties `((upstream-name . "BiocVersion")))
895 (build-system r-build-system)
896 (home-page "https://bioconductor.org/packages/BiocVersion/")
897 (synopsis "Set the appropriate version of Bioconductor packages")
899 "This package provides repository information for the appropriate version
901 (license license:artistic2.0)))
903 (define-public r-biocgenerics
905 (name "r-biocgenerics")
909 (uri (bioconductor-uri "BiocGenerics" version))
912 "1np8y442zyakm4axpinbw1qsgc6wd3zjsnirbhc8lcii4ky9j0rn"))))
914 `((upstream-name . "BiocGenerics")))
915 (build-system r-build-system)
916 (home-page "https://bioconductor.org/packages/BiocGenerics")
917 (synopsis "S4 generic functions for Bioconductor")
919 "This package provides S4 generic functions needed by many Bioconductor
921 (license license:artistic2.0)))
923 (define-public r-affycomp
930 (uri (bioconductor-uri "affycomp" version))
933 "0cl7c3m2lz2w8g2k7z7wjd0dyj0dkssvms99qpg8a1v3hx1xs6js"))))
934 (properties `((upstream-name . "affycomp")))
935 (build-system r-build-system)
936 (propagated-inputs `(("r-biobase" ,r-biobase)))
937 (home-page "https://bioconductor.org/packages/affycomp/")
938 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
940 "The package contains functions that can be used to compare expression
941 measures for Affymetrix Oligonucleotide Arrays.")
942 (license license:gpl2+)))
944 (define-public r-affycompatible
946 (name "r-affycompatible")
951 (uri (bioconductor-uri "AffyCompatible" version))
954 "10ahrdlifp1i7rd58zb10w75y5bnigs7xp5gv4fhb5y7p7dvb0ks"))))
956 `((upstream-name . "AffyCompatible")))
957 (build-system r-build-system)
959 `(("r-biostrings" ,r-biostrings)
962 (home-page "https://bioconductor.org/packages/AffyCompatible/")
963 (synopsis "Work with Affymetrix GeneChip files")
965 "This package provides an interface to Affymetrix chip annotation and
966 sample attribute files. The package allows an easy way for users to download
967 and manage local data bases of Affynmetrix NetAffx annotation files. It also
968 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
969 Command Console} (AGCC)-compatible sample annotation files.")
970 (license license:artistic2.0)))
972 (define-public r-affycontam
974 (name "r-affycontam")
979 (uri (bioconductor-uri "affyContam" version))
982 "0yd1prgv5zfkg22ski73mvg96qknwz8v6ji6s4qy8p4wrqyj7b7l"))))
983 (properties `((upstream-name . "affyContam")))
984 (build-system r-build-system)
987 ("r-affydata" ,r-affydata)
988 ("r-biobase" ,r-biobase)))
989 (home-page "https://bioconductor.org/packages/affyContam/")
990 (synopsis "Structured corruption of Affymetrix CEL file data")
992 "Microarray quality assessment is a major concern of microarray analysts.
993 This package provides some simple approaches to in silico creation of quality
994 problems in CEL-level data to help evaluate performance of quality metrics.")
995 (license license:artistic2.0)))
997 (define-public r-affycoretools
999 (name "r-affycoretools")
1004 (uri (bioconductor-uri "affycoretools" version))
1007 "0cgy9phwdk4x9lr11xh6zs7v8r5xq959fmsmzwrpnd50dr7hzkvd"))))
1008 (properties `((upstream-name . "affycoretools")))
1009 (build-system r-build-system)
1011 `(("r-affy" ,r-affy)
1012 ("r-annotationdbi" ,r-annotationdbi)
1013 ("r-biobase" ,r-biobase)
1014 ("r-biocgenerics" ,r-biocgenerics)
1016 ("r-edger" ,r-edger)
1017 ("r-gcrma" ,r-gcrma)
1018 ("r-ggplot2" ,r-ggplot2)
1019 ("r-gostats" ,r-gostats)
1020 ("r-gplots" ,r-gplots)
1021 ("r-hwriter" ,r-hwriter)
1022 ("r-lattice" ,r-lattice)
1023 ("r-limma" ,r-limma)
1024 ("r-oligoclasses" ,r-oligoclasses)
1025 ("r-reportingtools" ,r-reportingtools)
1026 ("r-rsqlite" ,r-rsqlite)
1027 ("r-s4vectors" ,r-s4vectors)
1028 ("r-xtable" ,r-xtable)))
1029 (home-page "https://bioconductor.org/packages/affycoretools/")
1030 (synopsis "Functions for analyses with Affymetrix GeneChips")
1032 "This package provides various wrapper functions that have been written
1033 to streamline the more common analyses that a Biostatistician might see.")
1034 (license license:artistic2.0)))
1036 (define-public r-affxparser
1038 (name "r-affxparser")
1043 (uri (bioconductor-uri "affxparser" version))
1046 "03h4lxr48p84f6i7zb2rm10ma3k4d1nmvdw5yhxcmzqbmd12lk40"))))
1047 (properties `((upstream-name . "affxparser")))
1048 (build-system r-build-system)
1049 (home-page "https://github.com/HenrikBengtsson/affxparser")
1050 (synopsis "Affymetrix File Parsing SDK")
1052 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1053 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1054 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1055 are supported. Currently, there are methods for reading @dfn{chip definition
1056 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1057 either in full or in part. For example, probe signals from a few probesets
1058 can be extracted very quickly from a set of CEL files into a convenient list
1060 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1062 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1064 (define-public r-annotate
1071 (uri (bioconductor-uri "annotate" version))
1074 "0rcmdy6hs6m4d6wxgi52c0bhdsbf2sm9f155qbcb05sn0nh8pxwy"))))
1075 (build-system r-build-system)
1077 `(("r-annotationdbi" ,r-annotationdbi)
1078 ("r-biobase" ,r-biobase)
1079 ("r-biocgenerics" ,r-biocgenerics)
1081 ("r-rcurl" ,r-rcurl)
1083 ("r-xtable" ,r-xtable)))
1085 "https://bioconductor.org/packages/annotate")
1086 (synopsis "Annotation for microarrays")
1087 (description "This package provides R environments for the annotation of
1089 (license license:artistic2.0)))
1091 (define-public r-hpar
1098 (uri (bioconductor-uri "hpar" version))
1101 "1yhay1ryrgj9cqa1x136cw40ca93afyvg0sarm30jsbj8nc1rm5m"))))
1102 (build-system r-build-system)
1103 (home-page "https://bioconductor.org/packages/hpar/")
1104 (synopsis "Human Protein Atlas in R")
1105 (description "This package provides a simple interface to and data from
1106 the Human Protein Atlas project.")
1107 (license license:artistic2.0)))
1109 (define-public r-regioner
1116 (uri (bioconductor-uri "regioneR" version))
1119 "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya"))))
1120 (properties `((upstream-name . "regioneR")))
1121 (build-system r-build-system)
1123 `(("r-biostrings" ,r-biostrings)
1124 ("r-bsgenome" ,r-bsgenome)
1125 ("r-genomeinfodb" ,r-genomeinfodb)
1126 ("r-genomicranges" ,r-genomicranges)
1127 ("r-iranges" ,r-iranges)
1128 ("r-memoise" ,r-memoise)
1129 ("r-rtracklayer" ,r-rtracklayer)
1130 ("r-s4vectors" ,r-s4vectors)))
1131 (home-page "https://bioconductor.org/packages/regioneR/")
1132 (synopsis "Association analysis of genomic regions")
1133 (description "This package offers a statistical framework based on
1134 customizable permutation tests to assess the association between genomic
1135 region sets and other genomic features.")
1136 (license license:artistic2.0)))
1138 (define-public r-reportingtools
1140 (name "r-reportingtools")
1145 (uri (bioconductor-uri "ReportingTools" version))
1148 "0wmi2219wydyzc07rz3azsrksa7wiacfh9pr5x2fsmj9f0w3n15w"))))
1150 `((upstream-name . "ReportingTools")))
1151 (build-system r-build-system)
1153 `(("r-annotate" ,r-annotate)
1154 ("r-annotationdbi" ,r-annotationdbi)
1155 ("r-biobase" ,r-biobase)
1156 ("r-biocgenerics" ,r-biocgenerics)
1157 ("r-category" ,r-category)
1158 ("r-deseq2" ,r-deseq2)
1159 ("r-edger" ,r-edger)
1160 ("r-ggbio" ,r-ggbio)
1161 ("r-ggplot2" ,r-ggplot2)
1162 ("r-gostats" ,r-gostats)
1163 ("r-gseabase" ,r-gseabase)
1164 ("r-hwriter" ,r-hwriter)
1165 ("r-iranges" ,r-iranges)
1166 ("r-knitr" ,r-knitr)
1167 ("r-lattice" ,r-lattice)
1168 ("r-limma" ,r-limma)
1169 ("r-pfam-db" ,r-pfam-db)
1170 ("r-r-utils" ,r-r-utils)
1172 (home-page "https://bioconductor.org/packages/ReportingTools/")
1173 (synopsis "Tools for making reports in various formats")
1175 "The ReportingTools package enables users to easily display reports of
1176 analysis results generated from sources such as microarray and sequencing
1177 data. The package allows users to create HTML pages that may be viewed on a
1178 web browser, or in other formats. Users can generate tables with sortable and
1179 filterable columns, make and display plots, and link table entries to other
1180 data sources such as NCBI or larger plots within the HTML page. Using the
1181 package, users can also produce a table of contents page to link various
1182 reports together for a particular project that can be viewed in a web
1184 (license license:artistic2.0)))
1186 (define-public r-geneplotter
1188 (name "r-geneplotter")
1193 (uri (bioconductor-uri "geneplotter" version))
1196 "1k6780fn1kkghpm1prhhsyw621441a3bmnqfl9ns0zbc1zdq39nx"))))
1197 (build-system r-build-system)
1199 `(("r-annotate" ,r-annotate)
1200 ("r-annotationdbi" ,r-annotationdbi)
1201 ("r-biobase" ,r-biobase)
1202 ("r-biocgenerics" ,r-biocgenerics)
1203 ("r-lattice" ,r-lattice)
1204 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1205 (home-page "https://bioconductor.org/packages/geneplotter")
1206 (synopsis "Graphics functions for genomic data")
1208 "This package provides functions for plotting genomic data.")
1209 (license license:artistic2.0)))
1211 (define-public r-oligoclasses
1213 (name "r-oligoclasses")
1218 (uri (bioconductor-uri "oligoClasses" version))
1221 "02m1m3dkiyywalphw3i5n6y3bs8zp24xh59v9cz6jgjpah811skf"))))
1222 (properties `((upstream-name . "oligoClasses")))
1223 (build-system r-build-system)
1225 `(("r-affyio" ,r-affyio)
1226 ("r-biobase" ,r-biobase)
1227 ("r-biocgenerics" ,r-biocgenerics)
1228 ("r-biocmanager" ,r-biocmanager)
1229 ("r-biostrings" ,r-biostrings)
1232 ("r-foreach" ,r-foreach)
1233 ("r-genomicranges" ,r-genomicranges)
1234 ("r-iranges" ,r-iranges)
1235 ("r-rsqlite" ,r-rsqlite)
1236 ("r-s4vectors" ,r-s4vectors)
1237 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1238 (home-page "https://bioconductor.org/packages/oligoClasses/")
1239 (synopsis "Classes for high-throughput arrays")
1241 "This package contains class definitions, validity checks, and
1242 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1244 (license license:gpl2+)))
1246 (define-public r-oligo
1253 (uri (bioconductor-uri "oligo" version))
1256 "01icfyy82f9k0m7ngrppz1ckq3wpq7zp6kgf8ppc55j6582c5jh3"))))
1257 (properties `((upstream-name . "oligo")))
1258 (build-system r-build-system)
1259 (inputs `(("zlib" ,zlib)))
1261 `(("r-affxparser" ,r-affxparser)
1262 ("r-affyio" ,r-affyio)
1263 ("r-biobase" ,r-biobase)
1264 ("r-biocgenerics" ,r-biocgenerics)
1265 ("r-biostrings" ,r-biostrings)
1268 ("r-oligoclasses" ,r-oligoclasses)
1269 ("r-preprocesscore" ,r-preprocesscore)
1270 ("r-rsqlite" ,r-rsqlite)
1271 ("r-zlibbioc" ,r-zlibbioc)))
1272 (home-page "https://bioconductor.org/packages/oligo/")
1273 (synopsis "Preprocessing tools for oligonucleotide arrays")
1275 "This package provides a package to analyze oligonucleotide
1276 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1277 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1278 (license license:lgpl2.0+)))
1280 (define-public r-qvalue
1287 (uri (bioconductor-uri "qvalue" version))
1290 "0njnidyncm3g3712mnp77cs4kghn596ss1pz6fhp1cr0wxcayp6j"))))
1291 (build-system r-build-system)
1293 `(("r-ggplot2" ,r-ggplot2)
1294 ("r-reshape2" ,r-reshape2)))
1295 (home-page "http://github.com/jdstorey/qvalue")
1296 (synopsis "Q-value estimation for false discovery rate control")
1298 "This package takes a list of p-values resulting from the simultaneous
1299 testing of many hypotheses and estimates their q-values and local @dfn{false
1300 discovery rate} (FDR) values. The q-value of a test measures the proportion
1301 of false positives incurred when that particular test is called significant.
1302 The local FDR measures the posterior probability the null hypothesis is true
1303 given the test's p-value. Various plots are automatically generated, allowing
1304 one to make sensible significance cut-offs. The software can be applied to
1305 problems in genomics, brain imaging, astrophysics, and data mining.")
1306 ;; Any version of the LGPL.
1307 (license license:lgpl3+)))
1309 (define-public r-diffbind
1316 (uri (bioconductor-uri "DiffBind" version))
1319 "1729wyi2l4480yrkp5wg3ryirrmlk0j3njqs1qyckq3c8bjk12h2"))))
1320 (properties `((upstream-name . "DiffBind")))
1321 (build-system r-build-system)
1325 `(("r-amap" ,r-amap)
1326 ("r-biocparallel" ,r-biocparallel)
1327 ("r-deseq2" ,r-deseq2)
1328 ("r-dplyr" ,r-dplyr)
1329 ("r-edger" ,r-edger)
1330 ("r-genomicalignments" ,r-genomicalignments)
1331 ("r-genomicranges" ,r-genomicranges)
1332 ("r-ggplot2" ,r-ggplot2)
1333 ("r-ggrepel" ,r-ggrepel)
1334 ("r-gplots" ,r-gplots)
1335 ("r-iranges" ,r-iranges)
1336 ("r-lattice" ,r-lattice)
1337 ("r-limma" ,r-limma)
1338 ("r-locfit" ,r-locfit)
1339 ("r-rcolorbrewer" , r-rcolorbrewer)
1341 ("r-rhtslib" ,r-rhtslib)
1342 ("r-rsamtools" ,r-rsamtools)
1343 ("r-s4vectors" ,r-s4vectors)
1344 ("r-summarizedexperiment" ,r-summarizedexperiment)
1345 ("r-systempiper" ,r-systempiper)))
1346 (home-page "http://bioconductor.org/packages/DiffBind")
1347 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1349 "This package computes differentially bound sites from multiple
1350 ChIP-seq experiments using affinity (quantitative) data. Also enables
1351 occupancy (overlap) analysis and plotting functions.")
1352 (license license:artistic2.0)))
1354 (define-public r-ripseeker
1356 (name "r-ripseeker")
1361 (uri (bioconductor-uri "RIPSeeker" version))
1364 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1365 (properties `((upstream-name . "RIPSeeker")))
1366 (build-system r-build-system)
1368 `(("r-s4vectors" ,r-s4vectors)
1369 ("r-iranges" ,r-iranges)
1370 ("r-genomicranges" ,r-genomicranges)
1371 ("r-summarizedexperiment" ,r-summarizedexperiment)
1372 ("r-rsamtools" ,r-rsamtools)
1373 ("r-genomicalignments" ,r-genomicalignments)
1374 ("r-rtracklayer" ,r-rtracklayer)))
1375 (home-page "http://bioconductor.org/packages/RIPSeeker")
1377 "Identifying protein-associated transcripts from RIP-seq experiments")
1379 "This package infers and discriminates RIP peaks from RIP-seq alignments
1380 using two-state HMM with negative binomial emission probability. While
1381 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1382 a suite of bioinformatics tools integrated within this self-contained software
1383 package comprehensively addressing issues ranging from post-alignments
1384 processing to visualization and annotation.")
1385 (license license:gpl2)))
1387 (define-public r-multtest
1394 (uri (bioconductor-uri "multtest" version))
1397 "0qna9lx76ldsfy8qf5xmhl4ymqfkj29m1gdqhph06s470c8mwari"))))
1398 (build-system r-build-system)
1400 `(("r-survival" ,r-survival)
1401 ("r-biocgenerics" ,r-biocgenerics)
1402 ("r-biobase" ,r-biobase)
1403 ("r-mass" ,r-mass)))
1404 (home-page "http://bioconductor.org/packages/multtest")
1405 (synopsis "Resampling-based multiple hypothesis testing")
1407 "This package can do non-parametric bootstrap and permutation
1408 resampling-based multiple testing procedures (including empirical Bayes
1409 methods) for controlling the family-wise error rate (FWER), generalized
1410 family-wise error rate (gFWER), tail probability of the proportion of
1411 false positives (TPPFP), and false discovery rate (FDR). Several choices
1412 of bootstrap-based null distribution are implemented (centered, centered
1413 and scaled, quantile-transformed). Single-step and step-wise methods are
1414 available. Tests based on a variety of T- and F-statistics (including
1415 T-statistics based on regression parameters from linear and survival models
1416 as well as those based on correlation parameters) are included. When probing
1417 hypotheses with T-statistics, users may also select a potentially faster null
1418 distribution which is multivariate normal with mean zero and variance
1419 covariance matrix derived from the vector influence function. Results are
1420 reported in terms of adjusted P-values, confidence regions and test statistic
1421 cutoffs. The procedures are directly applicable to identifying differentially
1422 expressed genes in DNA microarray experiments.")
1423 (license license:lgpl3)))
1425 (define-public r-graph
1431 (uri (bioconductor-uri "graph" version))
1434 "1ivf59k7k552m7zd8g3wwazd71dq3xmgmhcq435738i02h0fqnyc"))))
1435 (build-system r-build-system)
1437 `(("r-biocgenerics" ,r-biocgenerics)))
1438 (home-page "https://bioconductor.org/packages/graph")
1439 (synopsis "Handle graph data structures in R")
1441 "This package implements some simple graph handling capabilities for R.")
1442 (license license:artistic2.0)))
1444 (define-public r-codedepends
1446 (name "r-codedepends")
1451 (uri (cran-uri "CodeDepends" version))
1454 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1455 (properties `((upstream-name . "CodeDepends")))
1456 (build-system r-build-system)
1458 `(("r-codetools" ,r-codetools)
1459 ("r-graph" ,r-graph)
1461 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1462 (synopsis "Analysis of R code for reproducible research and code comprehension")
1464 "This package provides tools for analyzing R expressions or blocks of
1465 code and determining the dependencies between them. It focuses on R scripts,
1466 but can be used on the bodies of functions. There are many facilities
1467 including the ability to summarize or get a high-level view of code,
1468 determining dependencies between variables, code improvement suggestions.")
1469 ;; Any version of the GPL
1470 (license (list license:gpl2+ license:gpl3+))))
1472 (define-public r-chippeakanno
1474 (name "r-chippeakanno")
1479 (uri (bioconductor-uri "ChIPpeakAnno" version))
1482 "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa"))))
1483 (properties `((upstream-name . "ChIPpeakAnno")))
1484 (build-system r-build-system)
1486 `(("r-annotationdbi" ,r-annotationdbi)
1487 ("r-biobase" ,r-biobase)
1488 ("r-biocgenerics" ,r-biocgenerics)
1489 ("r-biocmanager" ,r-biocmanager)
1490 ("r-biomart" ,r-biomart)
1491 ("r-biostrings" ,r-biostrings)
1492 ("r-bsgenome" ,r-bsgenome)
1494 ("r-delayedarray" ,r-delayedarray)
1495 ("r-ensembldb" ,r-ensembldb)
1496 ("r-genomeinfodb" ,r-genomeinfodb)
1497 ("r-genomicalignments" ,r-genomicalignments)
1498 ("r-genomicfeatures" ,r-genomicfeatures)
1499 ("r-genomicranges" ,r-genomicranges)
1500 ("r-go-db" ,r-go-db)
1501 ("r-graph" ,r-graph)
1503 ("r-iranges" ,r-iranges)
1504 ("r-limma" ,r-limma)
1505 ("r-matrixstats" ,r-matrixstats)
1506 ("r-multtest" ,r-multtest)
1508 ("r-regioner" ,r-regioner)
1509 ("r-rsamtools" ,r-rsamtools)
1510 ("r-rtracklayer" ,r-rtracklayer)
1511 ("r-s4vectors" ,r-s4vectors)
1512 ("r-seqinr" ,r-seqinr)
1513 ("r-summarizedexperiment" ,r-summarizedexperiment)
1514 ("r-venndiagram" ,r-venndiagram)))
1515 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1516 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1518 "The package includes functions to retrieve the sequences around the peak,
1519 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1520 custom features such as most conserved elements and other transcription factor
1521 binding sites supplied by users. Starting 2.0.5, new functions have been added
1522 for finding the peaks with bi-directional promoters with summary statistics
1523 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1524 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1525 enrichedGO (addGeneIDs).")
1526 (license license:gpl2+)))
1528 (define-public r-marray
1534 (uri (bioconductor-uri "marray" version))
1536 (base32 "1mbs9rk279hnm9yz34za3xz3hb88ll1d0abw4m2pgjgbh4kkhdrl"))))
1537 (build-system r-build-system)
1539 `(("r-limma" ,r-limma)))
1540 (home-page "http://bioconductor.org/packages/marray")
1541 (synopsis "Exploratory analysis for two-color spotted microarray data")
1542 (description "This package contains class definitions for two-color spotted
1543 microarray data. It also includes functions for data input, diagnostic plots,
1544 normalization and quality checking.")
1545 (license license:lgpl2.0+)))
1547 (define-public r-cghbase
1553 (uri (bioconductor-uri "CGHbase" version))
1555 (base32 "0136pk6pfwpiiy9vca4pgg4wh74jfb5ssglpdszzhamljpvg765x"))))
1556 (properties `((upstream-name . "CGHbase")))
1557 (build-system r-build-system)
1559 `(("r-biobase" ,r-biobase)
1560 ("r-marray" ,r-marray)))
1561 (home-page "http://bioconductor.org/packages/CGHbase")
1562 (synopsis "Base functions and classes for arrayCGH data analysis")
1563 (description "This package contains functions and classes that are needed by
1564 the @code{arrayCGH} packages.")
1565 (license license:gpl2+)))
1567 (define-public r-cghcall
1573 (uri (bioconductor-uri "CGHcall" version))
1575 (base32 "1x8pz7zhw2nabik1vgdhlivndqvil3s7vnl5070k493v6gza0p3s"))))
1576 (properties `((upstream-name . "CGHcall")))
1577 (build-system r-build-system)
1579 `(("r-biobase" ,r-biobase)
1580 ("r-cghbase" ,r-cghbase)
1581 ("r-impute" ,r-impute)
1582 ("r-dnacopy" ,r-dnacopy)
1583 ("r-snowfall" ,r-snowfall)))
1584 (home-page "http://bioconductor.org/packages/CGHcall")
1585 (synopsis "Base functions and classes for arrayCGH data analysis")
1586 (description "This package contains functions and classes that are needed by
1587 @code{arrayCGH} packages.")
1588 (license license:gpl2+)))
1590 (define-public r-qdnaseq
1596 (uri (bioconductor-uri "QDNAseq" version))
1598 (base32 "0xcqdpv9a47zpxx0q9sif5y4s1yzx3pig0kywy961kh5xgl5bcrq"))))
1599 (properties `((upstream-name . "QDNAseq")))
1600 (build-system r-build-system)
1602 `(("r-biobase" ,r-biobase)
1603 ("r-cghbase" ,r-cghbase)
1604 ("r-cghcall" ,r-cghcall)
1605 ("r-dnacopy" ,r-dnacopy)
1606 ("r-future" ,r-future)
1607 ("r-future-apply" ,r-future-apply)
1608 ("r-genomicranges" ,r-genomicranges)
1609 ("r-iranges" ,r-iranges)
1610 ("r-matrixstats" ,r-matrixstats)
1611 ("r-r-utils" ,r-r-utils)
1612 ("r-rsamtools" ,r-rsamtools)))
1613 (home-page "http://bioconductor.org/packages/QDNAseq")
1614 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1615 (description "The genome is divided into non-overlapping fixed-sized bins,
1616 number of sequence reads in each counted, adjusted with a simultaneous
1617 two-dimensional loess correction for sequence mappability and GC content, and
1618 filtered to remove spurious regions in the genome. Downstream steps of
1619 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1621 (license license:gpl2+)))
1623 (define-public r-bayseq
1630 (uri (bioconductor-uri "baySeq" version))
1633 "040s1d3756spyzblkyx2vcy7bn3vf87mhsp3is35yxkj55n3myjk"))))
1634 (properties `((upstream-name . "baySeq")))
1635 (build-system r-build-system)
1637 `(("r-abind" ,r-abind)
1638 ("r-edger" ,r-edger)
1639 ("r-genomicranges" ,r-genomicranges)))
1640 (home-page "https://bioconductor.org/packages/baySeq/")
1641 (synopsis "Bayesian analysis of differential expression patterns in count data")
1643 "This package identifies differential expression in high-throughput count
1644 data, such as that derived from next-generation sequencing machines,
1645 calculating estimated posterior likelihoods of differential expression (or
1646 more complex hypotheses) via empirical Bayesian methods.")
1647 (license license:gpl3)))
1649 (define-public r-chipcomp
1656 (uri (bioconductor-uri "ChIPComp" version))
1659 "0wk0vvg6dk9wk60lzbadrnqar75dppvyr4hiwrhv9rhhah2mg2mg"))))
1660 (properties `((upstream-name . "ChIPComp")))
1661 (build-system r-build-system)
1663 `(("r-biocgenerics" ,r-biocgenerics)
1664 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1665 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1666 ("r-genomeinfodb" ,r-genomeinfodb)
1667 ("r-genomicranges" ,r-genomicranges)
1668 ("r-iranges" ,r-iranges)
1669 ("r-limma" ,r-limma)
1670 ("r-rsamtools" ,r-rsamtools)
1671 ("r-rtracklayer" ,r-rtracklayer)
1672 ("r-s4vectors" ,r-s4vectors)))
1673 (home-page "https://bioconductor.org/packages/ChIPComp")
1674 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1676 "ChIPComp implements a statistical method for quantitative comparison of
1677 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1678 sites across multiple conditions considering matching control in ChIP-seq
1680 ;; Any version of the GPL.
1681 (license license:gpl3+)))
1683 (define-public r-riboprofiling
1685 (name "r-riboprofiling")
1690 (uri (bioconductor-uri "RiboProfiling" version))
1693 "0nfzyiq7cd6fs5agzl1zyfg8s631wi7kjngiyvd3vxlhi8wsjicx"))))
1694 (properties `((upstream-name . "RiboProfiling")))
1695 (build-system r-build-system)
1697 `(("r-biocgenerics" ,r-biocgenerics)
1698 ("r-biostrings" ,r-biostrings)
1699 ("r-data-table" ,r-data-table)
1700 ("r-genomeinfodb" ,r-genomeinfodb)
1701 ("r-genomicalignments" ,r-genomicalignments)
1702 ("r-genomicfeatures" ,r-genomicfeatures)
1703 ("r-genomicranges" ,r-genomicranges)
1704 ("r-ggbio" ,r-ggbio)
1705 ("r-ggplot2" ,r-ggplot2)
1706 ("r-iranges" ,r-iranges)
1708 ("r-reshape2" ,r-reshape2)
1709 ("r-rsamtools" ,r-rsamtools)
1710 ("r-rtracklayer" ,r-rtracklayer)
1711 ("r-s4vectors" ,r-s4vectors)
1712 ("r-sqldf" ,r-sqldf)))
1713 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1714 (synopsis "Ribosome profiling data analysis")
1715 (description "Starting with a BAM file, this package provides the
1716 necessary functions for quality assessment, read start position recalibration,
1717 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1718 of count data: pairs, log fold-change, codon frequency and coverage
1719 assessment, principal component analysis on codon coverage.")
1720 (license license:gpl3)))
1722 (define-public r-riboseqr
1729 (uri (bioconductor-uri "riboSeqR" version))
1732 "1jr7h64hyhyf9gf15lah6iqwyljfc8mraf9kya4lql6lcjjkjiqm"))))
1733 (properties `((upstream-name . "riboSeqR")))
1734 (build-system r-build-system)
1736 `(("r-abind" ,r-abind)
1737 ("r-bayseq" ,r-bayseq)
1738 ("r-genomeinfodb" ,r-genomeinfodb)
1739 ("r-genomicranges" ,r-genomicranges)
1740 ("r-iranges" ,r-iranges)
1741 ("r-rsamtools" ,r-rsamtools)
1742 ("r-seqlogo" ,r-seqlogo)))
1743 (home-page "https://bioconductor.org/packages/riboSeqR/")
1744 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1746 "This package provides plotting functions, frameshift detection and
1747 parsing of genetic sequencing data from ribosome profiling experiments.")
1748 (license license:gpl3)))
1750 (define-public r-interactionset
1752 (name "r-interactionset")
1757 (uri (bioconductor-uri "InteractionSet" version))
1760 "0n2l95h56x5g68p10cap8p4x3a6vaph2hjlk09vmi3j48lrzb2kh"))))
1762 `((upstream-name . "InteractionSet")))
1763 (build-system r-build-system)
1765 `(("r-biocgenerics" ,r-biocgenerics)
1766 ("r-genomeinfodb" ,r-genomeinfodb)
1767 ("r-genomicranges" ,r-genomicranges)
1768 ("r-iranges" ,r-iranges)
1769 ("r-matrix" ,r-matrix)
1771 ("r-s4vectors" ,r-s4vectors)
1772 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1773 (home-page "https://bioconductor.org/packages/InteractionSet")
1774 (synopsis "Base classes for storing genomic interaction data")
1776 "This package provides the @code{GInteractions},
1777 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1778 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1780 (license license:gpl3)))
1782 (define-public r-genomicinteractions
1784 (name "r-genomicinteractions")
1789 (uri (bioconductor-uri "GenomicInteractions" version))
1792 "10kwb70c9aq0bfqpq48h186lsbwgrg18m14r9z8x6n8l7cds5azc"))))
1794 `((upstream-name . "GenomicInteractions")))
1795 (build-system r-build-system)
1797 `(("r-biobase" ,r-biobase)
1798 ("r-biocgenerics" ,r-biocgenerics)
1799 ("r-data-table" ,r-data-table)
1800 ("r-dplyr" ,r-dplyr)
1801 ("r-genomeinfodb" ,r-genomeinfodb)
1802 ("r-genomicranges" ,r-genomicranges)
1803 ("r-ggplot2" ,r-ggplot2)
1804 ("r-gridextra" ,r-gridextra)
1806 ("r-igraph" ,r-igraph)
1807 ("r-interactionset" ,r-interactionset)
1808 ("r-iranges" ,r-iranges)
1809 ("r-rsamtools" ,r-rsamtools)
1810 ("r-rtracklayer" ,r-rtracklayer)
1811 ("r-s4vectors" ,r-s4vectors)
1812 ("r-stringr" ,r-stringr)))
1813 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1814 (synopsis "R package for handling genomic interaction data")
1816 "This R package provides tools for handling genomic interaction data,
1817 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1818 information and producing various plots and statistics.")
1819 (license license:gpl3)))
1821 (define-public r-ctc
1828 (uri (bioconductor-uri "ctc" version))
1831 "0wh27izkyr1j26nznisw654mb5c94xpwjjkx7r6bhwg9ihxxcl6d"))))
1832 (build-system r-build-system)
1833 (propagated-inputs `(("r-amap" ,r-amap)))
1834 (home-page "https://bioconductor.org/packages/ctc/")
1835 (synopsis "Cluster and tree conversion")
1837 "This package provides tools for exporting and importing classification
1838 trees and clusters to other programs.")
1839 (license license:gpl2)))
1841 (define-public r-goseq
1848 (uri (bioconductor-uri "goseq" version))
1851 "11ypa41qv1nx3cncxlwlbhdxqlwq95rb9byv2z3crrf9nfp24byv"))))
1852 (build-system r-build-system)
1854 `(("r-annotationdbi" ,r-annotationdbi)
1855 ("r-biasedurn" ,r-biasedurn)
1856 ("r-biocgenerics" ,r-biocgenerics)
1857 ("r-genelendatabase" ,r-genelendatabase)
1858 ("r-go-db" ,r-go-db)
1859 ("r-mgcv" ,r-mgcv)))
1860 (home-page "https://bioconductor.org/packages/goseq/")
1861 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1863 "This package provides tools to detect Gene Ontology and/or other user
1864 defined categories which are over/under represented in RNA-seq data.")
1865 (license license:lgpl2.0+)))
1867 (define-public r-glimma
1874 (uri (bioconductor-uri "Glimma" version))
1877 "1rjrqgl96iz4b3xqpc174wgz7bqmc8gbm9ljag0y27kz29fwng8r"))))
1878 (properties `((upstream-name . "Glimma")))
1879 (build-system r-build-system)
1881 `(("r-edger" ,r-edger)
1882 ("r-jsonlite" ,r-jsonlite)
1883 ("r-s4vectors" ,r-s4vectors)))
1884 (home-page "https://github.com/Shians/Glimma")
1885 (synopsis "Interactive HTML graphics")
1887 "This package generates interactive visualisations for analysis of
1888 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1889 HTML page. The interactions are built on top of the popular static
1890 representations of analysis results in order to provide additional
1892 (license license:lgpl3)))
1894 (define-public r-rots
1901 (uri (bioconductor-uri "ROTS" version))
1904 "08mwlb0lpprys2b7vif8aj5bnprmn09mm79zz158gbhrv9j9d1qm"))))
1905 (properties `((upstream-name . "ROTS")))
1906 (build-system r-build-system)
1908 `(("r-biobase" ,r-biobase)
1909 ("r-rcpp" ,r-rcpp)))
1910 (home-page "https://bioconductor.org/packages/ROTS/")
1911 (synopsis "Reproducibility-Optimized Test Statistic")
1913 "This package provides tools for calculating the
1914 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1916 (license license:gpl2+)))
1918 (define-public r-plgem
1925 (uri (bioconductor-uri "plgem" version))
1928 "0fkyvcw2qxp4g527s9rzia45yapi0r6gbij7svisil8rbgfdp45v"))))
1929 (build-system r-build-system)
1931 `(("r-biobase" ,r-biobase)
1932 ("r-mass" ,r-mass)))
1933 (home-page "http://www.genopolis.it")
1934 (synopsis "Detect differential expression in microarray and proteomics datasets")
1936 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1937 model the variance-versus-mean dependence that exists in a variety of
1938 genome-wide datasets, including microarray and proteomics data. The use of
1939 PLGEM has been shown to improve the detection of differentially expressed
1940 genes or proteins in these datasets.")
1941 (license license:gpl2)))
1943 (define-public r-inspect
1950 (uri (bioconductor-uri "INSPEcT" version))
1953 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1954 (properties `((upstream-name . "INSPEcT")))
1955 (build-system r-build-system)
1957 `(("r-biobase" ,r-biobase)
1958 ("r-biocgenerics" ,r-biocgenerics)
1959 ("r-biocparallel" ,r-biocparallel)
1960 ("r-deseq2" ,r-deseq2)
1961 ("r-desolve" ,r-desolve)
1962 ("r-genomicalignments" ,r-genomicalignments)
1963 ("r-genomicfeatures" ,r-genomicfeatures)
1964 ("r-genomicranges" ,r-genomicranges)
1965 ("r-iranges" ,r-iranges)
1966 ("r-plgem" ,r-plgem)
1967 ("r-preprocesscore" ,r-preprocesscore)
1969 ("r-rootsolve" ,r-rootsolve)
1970 ("r-rsamtools" ,r-rsamtools)
1971 ("r-s4vectors" ,r-s4vectors)
1972 ("r-shiny" ,r-shiny)
1973 ("r-summarizedexperiment" ,r-summarizedexperiment)
1974 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1975 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1976 (home-page "https://bioconductor.org/packages/INSPEcT")
1977 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1979 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1980 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1981 order to evaluate synthesis, processing and degradation rates and assess via
1982 modeling the rates that determines changes in mature mRNA levels.")
1983 (license license:gpl2)))
1985 (define-public r-dnabarcodes
1987 (name "r-dnabarcodes")
1992 (uri (bioconductor-uri "DNABarcodes" version))
1995 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1996 (properties `((upstream-name . "DNABarcodes")))
1997 (build-system r-build-system)
2000 ("r-matrix" ,r-matrix)
2001 ("r-rcpp" ,r-rcpp)))
2002 (home-page "https://bioconductor.org/packages/DNABarcodes")
2003 (synopsis "Create and analyze DNA barcodes")
2005 "This package offers tools to create DNA barcode sets capable of
2006 correcting insertion, deletion, and substitution errors. Existing barcodes
2007 can be analyzed regarding their minimal, maximal and average distances between
2008 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2009 demultiplexed, i.e. assigned to their original reference barcode.")
2010 (license license:gpl2)))
2012 (define-public r-ruvseq
2019 (uri (bioconductor-uri "RUVSeq" version))
2022 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
2023 (properties `((upstream-name . "RUVSeq")))
2024 (build-system r-build-system)
2026 `(("r-biobase" ,r-biobase)
2027 ("r-edaseq" ,r-edaseq)
2028 ("r-edger" ,r-edger)
2029 ("r-mass" ,r-mass)))
2030 (home-page "https://github.com/drisso/RUVSeq")
2031 (synopsis "Remove unwanted variation from RNA-Seq data")
2033 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2034 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2036 (license license:artistic2.0)))
2038 (define-public r-biocneighbors
2040 (name "r-biocneighbors")
2045 (uri (bioconductor-uri "BiocNeighbors" version))
2048 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
2049 (properties `((upstream-name . "BiocNeighbors")))
2050 (build-system r-build-system)
2052 `(("r-biocgenerics" ,r-biocgenerics)
2053 ("r-biocparallel" ,r-biocparallel)
2055 ("r-rcppannoy" ,r-rcppannoy)
2056 ("r-rcpphnsw" ,r-rcpphnsw)
2057 ("r-s4vectors" ,r-s4vectors)))
2058 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2059 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2061 "This package implements exact and approximate methods for nearest
2062 neighbor detection, in a framework that allows them to be easily switched
2063 within Bioconductor packages or workflows. The exact algorithm is implemented
2064 using pre-clustering with the k-means algorithm. Functions are also provided
2065 to search for all neighbors within a given distance. Parallelization is
2066 achieved for all methods using the BiocParallel framework.")
2067 (license license:gpl3)))
2069 (define-public r-biocsingular
2071 (name "r-biocsingular")
2076 (uri (bioconductor-uri "BiocSingular" version))
2079 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
2080 (properties `((upstream-name . "BiocSingular")))
2081 (build-system r-build-system)
2083 `(("r-beachmat" ,r-beachmat)
2084 ("r-biocgenerics" ,r-biocgenerics)
2085 ("r-biocparallel" ,r-biocparallel)
2086 ("r-delayedarray" ,r-delayedarray)
2087 ("r-irlba" ,r-irlba)
2088 ("r-matrix" ,r-matrix)
2091 ("r-s4vectors" ,r-s4vectors)))
2092 (home-page "https://github.com/LTLA/BiocSingular")
2093 (synopsis "Singular value decomposition for Bioconductor packages")
2095 "This package implements exact and approximate methods for singular value
2096 decomposition and principal components analysis, in a framework that allows
2097 them to be easily switched within Bioconductor packages or workflows. Where
2098 possible, parallelization is achieved using the BiocParallel framework.")
2099 (license license:gpl3)))
2101 (define-public r-destiny
2108 (uri (bioconductor-uri "destiny" version))
2111 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
2112 (build-system r-build-system)
2114 `(("r-biobase" ,r-biobase)
2115 ("r-biocgenerics" ,r-biocgenerics)
2116 ("r-ggplot2" ,r-ggplot2)
2117 ("r-ggthemes" ,r-ggthemes)
2118 ("r-igraph" ,r-igraph)
2119 ("r-matrix" ,r-matrix)
2120 ("r-proxy" ,r-proxy)
2122 ("r-rcppeigen" ,r-rcppeigen)
2123 ("r-scales" ,r-scales)
2124 ("r-scatterplot3d" ,r-scatterplot3d)
2125 ("r-smoother" ,r-smoother)
2126 ("r-summarizedexperiment" ,r-summarizedexperiment)
2128 (home-page "https://bioconductor.org/packages/destiny/")
2129 (synopsis "Create and plot diffusion maps")
2130 (description "This package provides tools to create and plot diffusion
2132 ;; Any version of the GPL
2133 (license license:gpl3+)))
2135 (define-public r-savr
2142 (uri (bioconductor-uri "savR" version))
2145 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
2146 (properties `((upstream-name . "savR")))
2147 (build-system r-build-system)
2149 `(("r-ggplot2" ,r-ggplot2)
2150 ("r-gridextra" ,r-gridextra)
2151 ("r-reshape2" ,r-reshape2)
2152 ("r-scales" ,r-scales)
2154 (home-page "https://github.com/bcalder/savR")
2155 (synopsis "Parse and analyze Illumina SAV files")
2157 "This package provides tools to parse Illumina Sequence Analysis
2158 Viewer (SAV) files, access data, and generate QC plots.")
2159 (license license:agpl3+)))
2161 (define-public r-chipexoqual
2163 (name "r-chipexoqual")
2168 (uri (bioconductor-uri "ChIPexoQual" version))
2171 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
2172 (properties `((upstream-name . "ChIPexoQual")))
2173 (build-system r-build-system)
2175 `(("r-biocparallel" ,r-biocparallel)
2176 ("r-biovizbase" ,r-biovizbase)
2177 ("r-broom" ,r-broom)
2178 ("r-data-table" ,r-data-table)
2179 ("r-dplyr" ,r-dplyr)
2180 ("r-genomeinfodb" ,r-genomeinfodb)
2181 ("r-genomicalignments" ,r-genomicalignments)
2182 ("r-genomicranges" ,r-genomicranges)
2183 ("r-ggplot2" ,r-ggplot2)
2184 ("r-hexbin" ,r-hexbin)
2185 ("r-iranges" ,r-iranges)
2186 ("r-rcolorbrewer" ,r-rcolorbrewer)
2187 ("r-rmarkdown" ,r-rmarkdown)
2188 ("r-rsamtools" ,r-rsamtools)
2189 ("r-s4vectors" ,r-s4vectors)
2190 ("r-scales" ,r-scales)
2191 ("r-viridis" ,r-viridis)))
2192 (home-page "https://github.com/keleslab/ChIPexoQual")
2193 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2195 "This package provides a quality control pipeline for ChIP-exo/nexus
2197 (license license:gpl2+)))
2199 (define-public r-copynumber
2201 (name "r-copynumber")
2205 (uri (bioconductor-uri "copynumber" version))
2208 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
2209 (build-system r-build-system)
2211 `(("r-s4vectors" ,r-s4vectors)
2212 ("r-iranges" ,r-iranges)
2213 ("r-genomicranges" ,r-genomicranges)
2214 ("r-biocgenerics" ,r-biocgenerics)))
2215 (home-page "https://bioconductor.org/packages/copynumber")
2216 (synopsis "Segmentation of single- and multi-track copy number data")
2218 "This package segments single- and multi-track copy number data by a
2219 penalized least squares regression method.")
2220 (license license:artistic2.0)))
2222 (define-public r-dnacopy
2229 (uri (bioconductor-uri "DNAcopy" version))
2232 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2233 (properties `((upstream-name . "DNAcopy")))
2234 (build-system r-build-system)
2235 (native-inputs `(("gfortran" ,gfortran)))
2236 (home-page "https://bioconductor.org/packages/DNAcopy")
2237 (synopsis "DNA copy number data analysis")
2239 "This package implements the @dfn{circular binary segmentation} (CBS)
2240 algorithm to segment DNA copy number data and identify genomic regions with
2241 abnormal copy number.")
2242 (license license:gpl2+)))
2244 ;; This is a CRAN package, but it uncharacteristically depends on a
2245 ;; Bioconductor package.
2246 (define-public r-htscluster
2248 (name "r-htscluster")
2253 (uri (cran-uri "HTSCluster" version))
2256 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2257 (properties `((upstream-name . "HTSCluster")))
2258 (build-system r-build-system)
2260 `(("r-capushe" ,r-capushe)
2261 ("r-edger" ,r-edger)
2262 ("r-plotrix" ,r-plotrix)))
2263 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2264 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2266 "This package provides a Poisson mixture model is implemented to cluster
2267 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2268 estimation is performed using either the EM or CEM algorithm, and the slope
2269 heuristics are used for model selection (i.e., to choose the number of
2271 (license license:gpl3+)))
2273 (define-public r-deds
2280 (uri (bioconductor-uri "DEDS" version))
2283 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2284 (properties `((upstream-name . "DEDS")))
2285 (build-system r-build-system)
2286 (home-page "https://bioconductor.org/packages/DEDS/")
2287 (synopsis "Differential expression via distance summary for microarray data")
2289 "This library contains functions that calculate various statistics of
2290 differential expression for microarray data, including t statistics, fold
2291 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2292 also implements a new methodology called DEDS (Differential Expression via
2293 Distance Summary), which selects differentially expressed genes by integrating
2294 and summarizing a set of statistics using a weighted distance approach.")
2295 ;; Any version of the LGPL.
2296 (license license:lgpl3+)))
2298 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2300 (define-public r-nbpseq
2307 (uri (cran-uri "NBPSeq" version))
2310 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2311 (properties `((upstream-name . "NBPSeq")))
2312 (build-system r-build-system)
2314 `(("r-qvalue" ,r-qvalue)))
2315 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2316 (synopsis "Negative binomial models for RNA-Seq data")
2318 "This package provides negative binomial models for two-group comparisons
2319 and regression inferences from RNA-sequencing data.")
2320 (license license:gpl2)))
2322 (define-public r-ebseq
2329 (uri (bioconductor-uri "EBSeq" version))
2332 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2333 (properties `((upstream-name . "EBSeq")))
2334 (build-system r-build-system)
2336 `(("r-blockmodeling" ,r-blockmodeling)
2337 ("r-gplots" ,r-gplots)
2338 ("r-testthat" ,r-testthat)))
2339 (home-page "https://bioconductor.org/packages/EBSeq")
2340 (synopsis "Differential expression analysis of RNA-seq data")
2342 "This package provides tools for differential expression analysis at both
2343 gene and isoform level using RNA-seq data")
2344 (license license:artistic2.0)))
2346 (define-public r-lpsymphony
2348 (name "r-lpsymphony")
2353 (uri (bioconductor-uri "lpsymphony" version))
2356 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2357 (build-system r-build-system)
2359 `(("gfortran" ,gfortran)
2362 `(("pkg-config" ,pkg-config)))
2363 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2364 (synopsis "Symphony integer linear programming solver in R")
2366 "This package was derived from Rsymphony. The package provides an R
2367 interface to SYMPHONY, a linear programming solver written in C++. The main
2368 difference between this package and Rsymphony is that it includes the solver
2369 source code, while Rsymphony expects to find header and library files on the
2370 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2371 to install interface to SYMPHONY.")
2372 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2373 ;; lpsimphony is released under the same terms.
2374 (license license:epl1.0)))
2376 (define-public r-ihw
2383 (uri (bioconductor-uri "IHW" version))
2386 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2387 (properties `((upstream-name . "IHW")))
2388 (build-system r-build-system)
2390 `(("r-biocgenerics" ,r-biocgenerics)
2391 ("r-fdrtool" ,r-fdrtool)
2392 ("r-lpsymphony" ,r-lpsymphony)
2393 ("r-slam" ,r-slam)))
2394 (home-page "https://bioconductor.org/packages/IHW")
2395 (synopsis "Independent hypothesis weighting")
2397 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2398 procedure that increases power compared to the method of Benjamini and
2399 Hochberg by assigning data-driven weights to each hypothesis. The input to
2400 IHW is a two-column table of p-values and covariates. The covariate can be
2401 any continuous-valued or categorical variable that is thought to be
2402 informative on the statistical properties of each hypothesis test, while it is
2403 independent of the p-value under the null hypothesis.")
2404 (license license:artistic2.0)))
2406 (define-public r-icobra
2413 (uri (bioconductor-uri "iCOBRA" version))
2416 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2417 (properties `((upstream-name . "iCOBRA")))
2418 (build-system r-build-system)
2420 `(("r-dplyr" ,r-dplyr)
2422 ("r-ggplot2" ,r-ggplot2)
2423 ("r-limma" ,r-limma)
2424 ("r-reshape2" ,r-reshape2)
2426 ("r-scales" ,r-scales)
2427 ("r-shiny" ,r-shiny)
2428 ("r-shinybs" ,r-shinybs)
2429 ("r-shinydashboard" ,r-shinydashboard)
2430 ("r-upsetr" ,r-upsetr)))
2431 (home-page "https://bioconductor.org/packages/iCOBRA")
2432 (synopsis "Comparison and visualization of ranking and assignment methods")
2434 "This package provides functions for calculation and visualization of
2435 performance metrics for evaluation of ranking and binary
2436 classification (assignment) methods. It also contains a Shiny application for
2437 interactive exploration of results.")
2438 (license license:gpl2+)))
2440 (define-public r-mast
2447 (uri (bioconductor-uri "MAST" version))
2450 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2451 (properties `((upstream-name . "MAST")))
2452 (build-system r-build-system)
2454 `(("r-abind" ,r-abind)
2456 ("r-biobase" ,r-biobase)
2457 ("r-biocgenerics" ,r-biocgenerics)
2458 ("r-data-table" ,r-data-table)
2459 ("r-ggplot2" ,r-ggplot2)
2461 ("r-progress" ,r-progress)
2462 ("r-reshape2" ,r-reshape2)
2463 ("r-s4vectors" ,r-s4vectors)
2464 ("r-singlecellexperiment" ,r-singlecellexperiment)
2465 ("r-stringr" ,r-stringr)
2466 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2467 (home-page "https://github.com/RGLab/MAST/")
2468 (synopsis "Model-based analysis of single cell transcriptomics")
2470 "This package provides methods and models for handling zero-inflated
2471 single cell assay data.")
2472 (license license:gpl2+)))
2474 (define-public r-monocle
2481 (uri (bioconductor-uri "monocle" version))
2484 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2485 (build-system r-build-system)
2487 `(("r-biobase" ,r-biobase)
2488 ("r-biocgenerics" ,r-biocgenerics)
2489 ("r-biocviews" ,r-biocviews)
2490 ("r-cluster" ,r-cluster)
2491 ("r-combinat" ,r-combinat)
2492 ("r-ddrtree" ,r-ddrtree)
2493 ("r-densityclust" ,r-densityclust)
2494 ("r-dplyr" ,r-dplyr)
2495 ("r-fastica" ,r-fastica)
2496 ("r-ggplot2" ,r-ggplot2)
2497 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2498 ("r-igraph" ,r-igraph)
2499 ("r-irlba" ,r-irlba)
2500 ("r-limma" ,r-limma)
2502 ("r-matrix" ,r-matrix)
2503 ("r-matrixstats" ,r-matrixstats)
2504 ("r-pheatmap" ,r-pheatmap)
2506 ("r-proxy" ,r-proxy)
2507 ("r-qlcmatrix" ,r-qlcmatrix)
2510 ("r-reshape2" ,r-reshape2)
2511 ("r-rtsne" ,r-rtsne)
2513 ("r-stringr" ,r-stringr)
2514 ("r-tibble" ,r-tibble)
2516 ("r-viridis" ,r-viridis)))
2517 (home-page "https://bioconductor.org/packages/monocle")
2518 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2520 "Monocle performs differential expression and time-series analysis for
2521 single-cell expression experiments. It orders individual cells according to
2522 progress through a biological process, without knowing ahead of time which
2523 genes define progress through that process. Monocle also performs
2524 differential expression analysis, clustering, visualization, and other useful
2525 tasks on single cell expression data. It is designed to work with RNA-Seq and
2526 qPCR data, but could be used with other types as well.")
2527 (license license:artistic2.0)))
2529 (define-public r-monocle3
2537 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2539 (file-name (git-file-name name version))
2542 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2543 (build-system r-build-system)
2545 `(("r-biobase" ,r-biobase)
2546 ("r-biocgenerics" ,r-biocgenerics)
2547 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2548 ("r-dplyr" ,r-dplyr)
2549 ("r-ggplot2" ,r-ggplot2)
2550 ("r-ggrepel" ,r-ggrepel)
2552 ("r-htmlwidgets" ,r-htmlwidgets)
2553 ("r-igraph" ,r-igraph)
2554 ("r-irlba" ,r-irlba)
2555 ("r-limma" ,r-limma)
2556 ("r-lmtest" ,r-lmtest)
2558 ("r-matrix" ,r-matrix)
2559 ("r-matrix-utils" ,r-matrix-utils)
2560 ("r-pbapply" ,r-pbapply)
2561 ("r-pbmcapply" ,r-pbmcapply)
2562 ("r-pheatmap" ,r-pheatmap)
2563 ("r-plotly" ,r-plotly)
2565 ("r-proxy" ,r-proxy)
2567 ("r-purrr" ,r-purrr)
2570 ("r-rcppparallel" ,r-rcppparallel)
2571 ("r-reshape2" ,r-reshape2)
2572 ("r-reticulate" ,r-reticulate)
2573 ("r-rhpcblasctl" ,r-rhpcblasctl)
2574 ("r-rtsne" ,r-rtsne)
2575 ("r-shiny" ,r-shiny)
2577 ("r-spdep" ,r-spdep)
2578 ("r-speedglm" ,r-speedglm)
2579 ("r-stringr" ,r-stringr)
2580 ("r-singlecellexperiment" ,r-singlecellexperiment)
2581 ("r-tibble" ,r-tibble)
2582 ("r-tidyr" ,r-tidyr)
2584 ("r-viridis" ,r-viridis)))
2585 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2586 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2588 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2589 (license license:expat)))
2591 (define-public r-noiseq
2598 (uri (bioconductor-uri "NOISeq" version))
2601 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2602 (properties `((upstream-name . "NOISeq")))
2603 (build-system r-build-system)
2605 `(("r-biobase" ,r-biobase)
2606 ("r-matrix" ,r-matrix)))
2607 (home-page "https://bioconductor.org/packages/NOISeq")
2608 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2610 "This package provides tools to support the analysis of RNA-seq
2611 expression data or other similar kind of data. It provides exploratory plots
2612 to evaluate saturation, count distribution, expression per chromosome, type of
2613 detected features, features length, etc. It also supports the analysis of
2614 differential expression between two experimental conditions with no parametric
2616 (license license:artistic2.0)))
2618 (define-public r-scdd
2625 (uri (bioconductor-uri "scDD" version))
2628 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2629 (properties `((upstream-name . "scDD")))
2630 (build-system r-build-system)
2633 ("r-biocparallel" ,r-biocparallel)
2634 ("r-ebseq" ,r-ebseq)
2635 ("r-fields" ,r-fields)
2636 ("r-ggplot2" ,r-ggplot2)
2637 ("r-mclust" ,r-mclust)
2638 ("r-outliers" ,r-outliers)
2639 ("r-s4vectors" ,r-s4vectors)
2640 ("r-scran" ,r-scran)
2641 ("r-singlecellexperiment" ,r-singlecellexperiment)
2642 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2643 (home-page "https://github.com/kdkorthauer/scDD")
2644 (synopsis "Mixture modeling of single-cell RNA-seq data")
2646 "This package implements a method to analyze single-cell RNA-seq data
2647 utilizing flexible Dirichlet Process mixture models. Genes with differential
2648 distributions of expression are classified into several interesting patterns
2649 of differences between two conditions. The package also includes functions
2650 for simulating data with these patterns from negative binomial
2652 (license license:gpl2)))
2654 (define-public r-scone
2661 (uri (bioconductor-uri "scone" version))
2664 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2665 (build-system r-build-system)
2667 `(("r-aroma-light" ,r-aroma-light)
2668 ("r-biocparallel" ,r-biocparallel)
2670 ("r-class" ,r-class)
2671 ("r-cluster" ,r-cluster)
2672 ("r-compositions" ,r-compositions)
2673 ("r-diptest" ,r-diptest)
2674 ("r-edger" ,r-edger)
2676 ("r-gplots" ,r-gplots)
2677 ("r-hexbin" ,r-hexbin)
2678 ("r-limma" ,r-limma)
2679 ("r-matrixstats" ,r-matrixstats)
2680 ("r-mixtools" ,r-mixtools)
2681 ("r-rarpack" ,r-rarpack)
2682 ("r-rcolorbrewer" ,r-rcolorbrewer)
2683 ("r-rhdf5" ,r-rhdf5)
2684 ("r-ruvseq" ,r-ruvseq)
2685 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2686 (home-page "https://bioconductor.org/packages/scone")
2687 (synopsis "Single cell overview of normalized expression data")
2689 "SCONE is an R package for comparing and ranking the performance of
2690 different normalization schemes for single-cell RNA-seq and other
2691 high-throughput analyses.")
2692 (license license:artistic2.0)))
2694 (define-public r-geoquery
2701 (uri (bioconductor-uri "GEOquery" version))
2704 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2705 (properties `((upstream-name . "GEOquery")))
2706 (build-system r-build-system)
2708 `(("r-biobase" ,r-biobase)
2709 ("r-dplyr" ,r-dplyr)
2711 ("r-limma" ,r-limma)
2712 ("r-magrittr" ,r-magrittr)
2713 ("r-readr" ,r-readr)
2714 ("r-tidyr" ,r-tidyr)
2715 ("r-xml2" ,r-xml2)))
2716 (home-page "https://github.com/seandavi/GEOquery/")
2717 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2719 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2720 microarray data. Given the rich and varied nature of this resource, it is
2721 only natural to want to apply BioConductor tools to these data. GEOquery is
2722 the bridge between GEO and BioConductor.")
2723 (license license:gpl2)))
2725 (define-public r-illuminaio
2727 (name "r-illuminaio")
2732 (uri (bioconductor-uri "illuminaio" version))
2735 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2736 (build-system r-build-system)
2738 `(("r-base64" ,r-base64)))
2739 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2740 (synopsis "Parse Illumina microarray output files")
2742 "This package provides tools for parsing Illumina's microarray output
2743 files, including IDAT.")
2744 (license license:gpl2)))
2746 (define-public r-siggenes
2753 (uri (bioconductor-uri "siggenes" version))
2756 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2757 (build-system r-build-system)
2759 `(("r-biobase" ,r-biobase)
2760 ("r-multtest" ,r-multtest)
2761 ("r-scrime" ,r-scrime)))
2762 (home-page "https://bioconductor.org/packages/siggenes/")
2764 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2766 "This package provides tools for the identification of differentially
2767 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2768 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2769 Bayes Analyses of Microarrays} (EBAM).")
2770 (license license:lgpl2.0+)))
2772 (define-public r-bumphunter
2774 (name "r-bumphunter")
2779 (uri (bioconductor-uri "bumphunter" version))
2782 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2783 (build-system r-build-system)
2785 `(("r-annotationdbi" ,r-annotationdbi)
2786 ("r-biocgenerics" ,r-biocgenerics)
2787 ("r-dorng" ,r-dorng)
2788 ("r-foreach" ,r-foreach)
2789 ("r-genomeinfodb" ,r-genomeinfodb)
2790 ("r-genomicfeatures" ,r-genomicfeatures)
2791 ("r-genomicranges" ,r-genomicranges)
2792 ("r-iranges" ,r-iranges)
2793 ("r-iterators" ,r-iterators)
2794 ("r-limma" ,r-limma)
2795 ("r-locfit" ,r-locfit)
2796 ("r-matrixstats" ,r-matrixstats)
2797 ("r-s4vectors" ,r-s4vectors)))
2798 (home-page "https://github.com/ririzarr/bumphunter")
2799 (synopsis "Find bumps in genomic data")
2801 "This package provides tools for finding bumps in genomic data in order
2802 to identify differentially methylated regions in epigenetic epidemiology
2804 (license license:artistic2.0)))
2806 (define-public r-minfi
2813 (uri (bioconductor-uri "minfi" version))
2816 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2817 (build-system r-build-system)
2819 `(("r-beanplot" ,r-beanplot)
2820 ("r-biobase" ,r-biobase)
2821 ("r-biocgenerics" ,r-biocgenerics)
2822 ("r-biocparallel" ,r-biocparallel)
2823 ("r-biostrings" ,r-biostrings)
2824 ("r-bumphunter" ,r-bumphunter)
2825 ("r-data-table" ,r-data-table)
2826 ("r-delayedarray" ,r-delayedarray)
2827 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2828 ("r-genefilter" ,r-genefilter)
2829 ("r-genomeinfodb" ,r-genomeinfodb)
2830 ("r-genomicranges" ,r-genomicranges)
2831 ("r-geoquery" ,r-geoquery)
2832 ("r-hdf5array" ,r-hdf5array)
2833 ("r-illuminaio" ,r-illuminaio)
2834 ("r-iranges" ,r-iranges)
2835 ("r-lattice" ,r-lattice)
2836 ("r-limma" ,r-limma)
2838 ("r-mclust" ,r-mclust)
2840 ("r-nor1mix" ,r-nor1mix)
2841 ("r-preprocesscore" ,r-preprocesscore)
2842 ("r-quadprog" ,r-quadprog)
2843 ("r-rcolorbrewer" ,r-rcolorbrewer)
2844 ("r-reshape" ,r-reshape)
2845 ("r-s4vectors" ,r-s4vectors)
2846 ("r-siggenes" ,r-siggenes)
2847 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2848 (home-page "https://github.com/hansenlab/minfi")
2849 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2851 "This package provides tools to analyze and visualize Illumina Infinium
2852 methylation arrays.")
2853 (license license:artistic2.0)))
2855 (define-public r-methylumi
2857 (name "r-methylumi")
2862 (uri (bioconductor-uri "methylumi" version))
2865 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2866 (build-system r-build-system)
2868 `(("r-annotate" ,r-annotate)
2869 ("r-annotationdbi" ,r-annotationdbi)
2870 ("r-biobase" ,r-biobase)
2871 ("r-biocgenerics" ,r-biocgenerics)
2872 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2873 ("r-genefilter" ,r-genefilter)
2874 ("r-genomeinfodb" ,r-genomeinfodb)
2875 ("r-genomicranges" ,r-genomicranges)
2876 ("r-ggplot2" ,r-ggplot2)
2877 ("r-illuminaio" ,r-illuminaio)
2878 ("r-iranges" ,r-iranges)
2879 ("r-lattice" ,r-lattice)
2880 ("r-matrixstats" ,r-matrixstats)
2881 ("r-minfi" ,r-minfi)
2882 ("r-reshape2" ,r-reshape2)
2883 ("r-s4vectors" ,r-s4vectors)
2884 ("r-scales" ,r-scales)
2885 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2886 (home-page "https://bioconductor.org/packages/methylumi")
2887 (synopsis "Handle Illumina methylation data")
2889 "This package provides classes for holding and manipulating Illumina
2890 methylation data. Based on eSet, it can contain MIAME information, sample
2891 information, feature information, and multiple matrices of data. An
2892 \"intelligent\" import function, methylumiR can read the Illumina text files
2893 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2894 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2895 background correction, and quality control features for GoldenGate, Infinium,
2896 and Infinium HD arrays are also included.")
2897 (license license:gpl2)))
2899 (define-public r-lumi
2906 (uri (bioconductor-uri "lumi" version))
2909 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2910 (build-system r-build-system)
2912 `(("r-affy" ,r-affy)
2913 ("r-annotate" ,r-annotate)
2914 ("r-annotationdbi" ,r-annotationdbi)
2915 ("r-biobase" ,r-biobase)
2917 ("r-genomicfeatures" ,r-genomicfeatures)
2918 ("r-genomicranges" ,r-genomicranges)
2919 ("r-kernsmooth" ,r-kernsmooth)
2920 ("r-lattice" ,r-lattice)
2922 ("r-methylumi" ,r-methylumi)
2924 ("r-nleqslv" ,r-nleqslv)
2925 ("r-preprocesscore" ,r-preprocesscore)
2926 ("r-rsqlite" ,r-rsqlite)))
2927 (home-page "https://bioconductor.org/packages/lumi")
2928 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2930 "The lumi package provides an integrated solution for the Illumina
2931 microarray data analysis. It includes functions of Illumina
2932 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2933 variance stabilization, normalization and gene annotation at the probe level.
2934 It also includes the functions of processing Illumina methylation microarrays,
2935 especially Illumina Infinium methylation microarrays.")
2936 (license license:lgpl2.0+)))
2938 (define-public r-linnorm
2945 (uri (bioconductor-uri "Linnorm" version))
2948 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2949 (properties `((upstream-name . "Linnorm")))
2950 (build-system r-build-system)
2952 `(("r-amap" ,r-amap)
2953 ("r-apcluster" ,r-apcluster)
2954 ("r-ellipse" ,r-ellipse)
2955 ("r-fastcluster" ,r-fastcluster)
2957 ("r-ggdendro" ,r-ggdendro)
2958 ("r-ggplot2" ,r-ggplot2)
2959 ("r-gmodels" ,r-gmodels)
2960 ("r-igraph" ,r-igraph)
2961 ("r-limma" ,r-limma)
2963 ("r-mclust" ,r-mclust)
2965 ("r-rcpparmadillo" ,r-rcpparmadillo)
2966 ("r-rtsne" ,r-rtsne)
2967 ("r-statmod" ,r-statmod)
2968 ("r-vegan" ,r-vegan)
2970 (home-page "http://www.jjwanglab.org/Linnorm/")
2971 (synopsis "Linear model and normality based transformation method")
2973 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2974 count data or any large scale count data. It transforms such datasets for
2975 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2976 the following pipelines are implemented:
2979 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2980 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2981 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2982 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2983 @item Differential expression analysis or differential peak detection using
2984 limma (@code{Linnorm.limma})
2985 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2986 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2987 @item Stable gene selection for scRNA-seq data; for users without or who do
2988 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2989 @item Data imputation (@code{Linnorm.DataImput}).
2992 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2993 @code{RnaXSim} function is included for simulating RNA-seq data for the
2994 evaluation of DEG analysis methods.")
2995 (license license:expat)))
2997 (define-public r-ioniser
3004 (uri (bioconductor-uri "IONiseR" version))
3007 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
3008 (properties `((upstream-name . "IONiseR")))
3009 (build-system r-build-system)
3011 `(("r-biocgenerics" ,r-biocgenerics)
3012 ("r-biocparallel" ,r-biocparallel)
3013 ("r-biostrings" ,r-biostrings)
3014 ("r-bit64" ,r-bit64)
3015 ("r-dplyr" ,r-dplyr)
3016 ("r-ggplot2" ,r-ggplot2)
3017 ("r-magrittr" ,r-magrittr)
3018 ("r-rhdf5" ,r-rhdf5)
3019 ("r-shortread" ,r-shortread)
3020 ("r-stringr" ,r-stringr)
3021 ("r-tibble" ,r-tibble)
3022 ("r-tidyr" ,r-tidyr)
3023 ("r-xvector" ,r-xvector)))
3024 (home-page "https://bioconductor.org/packages/IONiseR/")
3025 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3027 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3028 MinION data. It extracts summary statistics from a set of fast5 files and can
3029 be used either before or after base calling. In addition to standard
3030 summaries of the read-types produced, it provides a number of plots for
3031 visualising metrics relative to experiment run time or spatially over the
3032 surface of a flowcell.")
3033 (license license:expat)))
3035 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3036 (define-public r-gkmsvm
3043 (uri (cran-uri "gkmSVM" version))
3046 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3047 (properties `((upstream-name . "gkmSVM")))
3048 (build-system r-build-system)
3050 `(("r-biocgenerics" ,r-biocgenerics)
3051 ("r-biostrings" ,r-biostrings)
3052 ("r-genomeinfodb" ,r-genomeinfodb)
3053 ("r-genomicranges" ,r-genomicranges)
3054 ("r-iranges" ,r-iranges)
3055 ("r-kernlab" ,r-kernlab)
3058 ("r-rtracklayer" ,r-rtracklayer)
3059 ("r-s4vectors" ,r-s4vectors)
3060 ("r-seqinr" ,r-seqinr)))
3061 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3062 (synopsis "Gapped-kmer support vector machine")
3064 "This R package provides tools for training gapped-kmer SVM classifiers
3065 for DNA and protein sequences. This package supports several sequence
3066 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3067 (license license:gpl2+)))
3069 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3070 (define-public r-mutoss
3077 (uri (cran-uri "mutoss" version))
3080 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3081 (properties `((upstream-name . "mutoss")))
3082 (build-system r-build-system)
3084 `(("r-multcomp" ,r-multcomp)
3085 ("r-multtest" ,r-multtest)
3086 ("r-mvtnorm" ,r-mvtnorm)
3087 ("r-plotrix" ,r-plotrix)))
3088 (home-page "https://github.com/kornl/mutoss/")
3089 (synopsis "Unified multiple testing procedures")
3091 "This package is designed to ease the application and comparison of
3092 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3093 are standardized and usable by the accompanying mutossGUI package.")
3094 ;; Any version of the GPL.
3095 (license (list license:gpl2+ license:gpl3+))))
3097 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3098 ;; from Bioconductor, so we put it here.
3099 (define-public r-metap
3106 (uri (cran-uri "metap" version))
3109 "0pfbcixjrzx81l9wqhlp55khg9k63zf8pvg2n39c19akr4ppzhvf"))))
3110 (build-system r-build-system)
3112 `(("r-lattice" ,r-lattice)
3113 ("r-mutoss" ,r-mutoss)
3114 ("r-rdpack" ,r-rdpack)
3115 ("r-tfisher" ,r-tfisher)))
3116 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3117 (synopsis "Meta-analysis of significance values")
3119 "The canonical way to perform meta-analysis involves using effect sizes.
3120 When they are not available this package provides a number of methods for
3121 meta-analysis of significance values including the methods of Edgington,
3122 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3123 published results; and a routine for graphical display.")
3124 (license license:gpl2)))
3126 (define-public r-triform
3133 (uri (bioconductor-uri "triform" version))
3136 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
3137 (build-system r-build-system)
3139 `(("r-biocgenerics" ,r-biocgenerics)
3140 ("r-iranges" ,r-iranges)
3141 ("r-yaml" ,r-yaml)))
3142 (home-page "https://bioconductor.org/packages/triform/")
3143 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3145 "The Triform algorithm uses model-free statistics to identify peak-like
3146 distributions of TF ChIP sequencing reads, taking advantage of an improved
3147 peak definition in combination with known profile characteristics.")
3148 (license license:gpl2)))
3150 (define-public r-varianttools
3152 (name "r-varianttools")
3157 (uri (bioconductor-uri "VariantTools" version))
3160 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
3161 (properties `((upstream-name . "VariantTools")))
3162 (build-system r-build-system)
3164 `(("r-biobase" ,r-biobase)
3165 ("r-biocgenerics" ,r-biocgenerics)
3166 ("r-biocparallel" ,r-biocparallel)
3167 ("r-biostrings" ,r-biostrings)
3168 ("r-bsgenome" ,r-bsgenome)
3169 ("r-genomeinfodb" ,r-genomeinfodb)
3170 ("r-genomicfeatures" ,r-genomicfeatures)
3171 ("r-genomicranges" ,r-genomicranges)
3172 ("r-iranges" ,r-iranges)
3173 ("r-matrix" ,r-matrix)
3174 ("r-rsamtools" ,r-rsamtools)
3175 ("r-rtracklayer" ,r-rtracklayer)
3176 ("r-s4vectors" ,r-s4vectors)
3177 ("r-variantannotation" ,r-variantannotation)))
3178 (home-page "https://bioconductor.org/packages/VariantTools/")
3179 (synopsis "Tools for exploratory analysis of variant calls")
3181 "Explore, diagnose, and compare variant calls using filters. The
3182 VariantTools package supports a workflow for loading data, calling single
3183 sample variants and tumor-specific somatic mutations or other sample-specific
3184 variant types (e.g., RNA editing). Most of the functions operate on
3185 alignments (BAM files) or datasets of called variants. The user is expected
3186 to have already aligned the reads with a separate tool, e.g., GSNAP via
3188 (license license:artistic2.0)))
3190 (define-public r-heatplus
3197 (uri (bioconductor-uri "Heatplus" version))
3200 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
3201 (properties `((upstream-name . "Heatplus")))
3202 (build-system r-build-system)
3204 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3205 (home-page "https://github.com/alexploner/Heatplus")
3206 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3208 "This package provides tools to display a rectangular heatmap (intensity
3209 plot) of a data matrix. By default, both samples (columns) and features (row)
3210 of the matrix are sorted according to a hierarchical clustering, and the
3211 corresponding dendrogram is plotted. Optionally, panels with additional
3212 information about samples and features can be added to the plot.")
3213 (license license:gpl2+)))
3215 (define-public r-gosemsim
3222 (uri (bioconductor-uri "GOSemSim" version))
3225 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
3226 (properties `((upstream-name . "GOSemSim")))
3227 (build-system r-build-system)
3229 `(("r-annotationdbi" ,r-annotationdbi)
3230 ("r-go-db" ,r-go-db)
3231 ("r-rcpp" ,r-rcpp)))
3232 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3233 (synopsis "GO-terms semantic similarity measures")
3235 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3236 quantitative ways to compute similarities between genes and gene groups, and
3237 have became important basis for many bioinformatics analysis approaches.
3238 GOSemSim is an R package for semantic similarity computation among GO terms,
3239 sets of GO terms, gene products and gene clusters.")
3240 (license license:artistic2.0)))
3242 (define-public r-anota
3249 (uri (bioconductor-uri "anota" version))
3252 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
3253 (build-system r-build-system)
3255 `(("r-multtest" ,r-multtest)
3256 ("r-qvalue" ,r-qvalue)))
3257 (home-page "https://bioconductor.org/packages/anota/")
3258 (synopsis "Analysis of translational activity")
3260 "Genome wide studies of translational control is emerging as a tool to
3261 study various biological conditions. The output from such analysis is both
3262 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3263 involved in translation (the actively translating mRNA level) for each mRNA.
3264 The standard analysis of such data strives towards identifying differential
3265 translational between two or more sample classes - i.e. differences in
3266 actively translated mRNA levels that are independent of underlying differences
3267 in cytosolic mRNA levels. This package allows for such analysis using partial
3268 variances and the random variance model. As 10s of thousands of mRNAs are
3269 analyzed in parallel the library performs a number of tests to assure that
3270 the data set is suitable for such analysis.")
3271 (license license:gpl3)))
3273 (define-public r-sigpathway
3275 (name "r-sigpathway")
3280 (uri (bioconductor-uri "sigPathway" version))
3283 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3284 (properties `((upstream-name . "sigPathway")))
3285 (build-system r-build-system)
3286 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3287 (synopsis "Pathway analysis")
3289 "This package is used to conduct pathway analysis by calculating the NT_k
3290 and NE_k statistics in a statistical framework for determining whether a
3291 specified group of genes for a pathway has a coordinated association with a
3292 phenotype of interest.")
3293 (license license:gpl2)))
3295 (define-public r-fgsea
3302 (uri (bioconductor-uri "fgsea" version))
3305 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3306 (build-system r-build-system)
3309 ("r-biocparallel" ,r-biocparallel)
3310 ("r-data-table" ,r-data-table)
3311 ("r-fastmatch" ,r-fastmatch)
3312 ("r-ggplot2" ,r-ggplot2)
3313 ("r-gridextra" ,r-gridextra)
3314 ("r-matrix" ,r-matrix)
3315 ("r-rcpp" ,r-rcpp)))
3316 (home-page "https://github.com/ctlab/fgsea/")
3317 (synopsis "Fast gene set enrichment analysis")
3319 "The package implements an algorithm for fast gene set enrichment
3320 analysis. Using the fast algorithm allows to make more permutations and get
3321 more fine grained p-values, which allows to use accurate stantard approaches
3322 to multiple hypothesis correction.")
3323 (license license:expat)))
3325 (define-public r-dose
3332 (uri (bioconductor-uri "DOSE" version))
3335 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3336 (properties `((upstream-name . "DOSE")))
3337 (build-system r-build-system)
3339 `(("r-annotationdbi" ,r-annotationdbi)
3340 ("r-biocparallel" ,r-biocparallel)
3341 ("r-do-db" ,r-do-db)
3342 ("r-fgsea" ,r-fgsea)
3343 ("r-ggplot2" ,r-ggplot2)
3344 ("r-gosemsim" ,r-gosemsim)
3345 ("r-qvalue" ,r-qvalue)
3346 ("r-reshape2" ,r-reshape2)
3347 ("r-s4vectors" ,r-s4vectors)))
3348 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3349 (synopsis "Disease ontology semantic and enrichment analysis")
3351 "This package implements five methods proposed by Resnik, Schlicker,
3352 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3353 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3354 including hypergeometric model and gene set enrichment analysis are also
3355 implemented for discovering disease associations of high-throughput biological
3357 (license license:artistic2.0)))
3359 (define-public r-enrichplot
3361 (name "r-enrichplot")
3366 (uri (bioconductor-uri "enrichplot" version))
3369 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3370 (build-system r-build-system)
3372 `(("r-annotationdbi" ,r-annotationdbi)
3373 ("r-cowplot" ,r-cowplot)
3375 ("r-europepmc" ,r-europepmc)
3376 ("r-ggplot2" ,r-ggplot2)
3377 ("r-ggplotify" ,r-ggplotify)
3378 ("r-ggraph" ,r-ggraph)
3379 ("r-ggridges" ,r-ggridges)
3380 ("r-gosemsim" ,r-gosemsim)
3381 ("r-gridextra" ,r-gridextra)
3382 ("r-igraph" ,r-igraph)
3383 ("r-purrr" ,r-purrr)
3384 ("r-rcolorbrewer" ,r-rcolorbrewer)
3385 ("r-reshape2" ,r-reshape2)
3386 ("r-upsetr" ,r-upsetr)))
3387 (home-page "https://github.com/GuangchuangYu/enrichplot")
3388 (synopsis "Visualization of functional enrichment result")
3390 "The enrichplot package implements several visualization methods for
3391 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3392 All the visualization methods are developed based on ggplot2 graphics.")
3393 (license license:artistic2.0)))
3395 (define-public r-clusterprofiler
3397 (name "r-clusterprofiler")
3402 (uri (bioconductor-uri "clusterProfiler" version))
3405 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3407 `((upstream-name . "clusterProfiler")))
3408 (build-system r-build-system)
3410 `(("r-annotationdbi" ,r-annotationdbi)
3412 ("r-enrichplot" ,r-enrichplot)
3413 ("r-ggplot2" ,r-ggplot2)
3414 ("r-go-db" ,r-go-db)
3415 ("r-gosemsim" ,r-gosemsim)
3416 ("r-magrittr" ,r-magrittr)
3418 ("r-qvalue" ,r-qvalue)
3419 ("r-rvcheck" ,r-rvcheck)
3420 ("r-tidyr" ,r-tidyr)))
3421 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3422 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3424 "This package implements methods to analyze and visualize functional
3425 profiles (GO and KEGG) of gene and gene clusters.")
3426 (license license:artistic2.0)))
3428 (define-public r-mlinterfaces
3430 (name "r-mlinterfaces")
3435 (uri (bioconductor-uri "MLInterfaces" version))
3438 "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh"))))
3439 (properties `((upstream-name . "MLInterfaces")))
3440 (build-system r-build-system)
3442 `(("r-annotate" ,r-annotate)
3443 ("r-biobase" ,r-biobase)
3444 ("r-biocgenerics" ,r-biocgenerics)
3445 ("r-cluster" ,r-cluster)
3448 ("r-gdata" ,r-gdata)
3449 ("r-genefilter" ,r-genefilter)
3450 ("r-ggvis" ,r-ggvis)
3451 ("r-hwriter" ,r-hwriter)
3453 ("r-mlbench" ,r-mlbench)
3455 ("r-rcolorbrewer" ,r-rcolorbrewer)
3457 ("r-rpart" ,r-rpart)
3458 ("r-sfsmisc" ,r-sfsmisc)
3459 ("r-shiny" ,r-shiny)
3460 ("r-threejs" ,r-threejs)))
3461 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3462 (synopsis "Interfaces to R machine learning procedures")
3464 "This package provides uniform interfaces to machine learning code for
3465 data in R and Bioconductor containers.")
3466 ;; Any version of the LGPL.
3467 (license license:lgpl2.1+)))
3469 (define-public r-annaffy
3476 (uri (bioconductor-uri "annaffy" version))
3479 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3480 (build-system r-build-system)
3483 (modify-phases %standard-phases
3484 (add-after 'unpack 'remove-reference-to-non-free-data
3486 (substitute* "DESCRIPTION"
3490 `(("r-annotationdbi" ,r-annotationdbi)
3491 ("r-biobase" ,r-biobase)
3493 ("r-go-db" ,r-go-db)))
3494 (home-page "https://bioconductor.org/packages/annaffy/")
3495 (synopsis "Annotation tools for Affymetrix biological metadata")
3497 "This package provides functions for handling data from Bioconductor
3498 Affymetrix annotation data packages. It produces compact HTML and text
3499 reports including experimental data and URL links to many online databases.
3500 It allows searching of biological metadata using various criteria.")
3501 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3502 ;; the LGPL 2.1 is included.
3503 (license license:lgpl2.1+)))
3505 (define-public r-a4core
3512 (uri (bioconductor-uri "a4Core" version))
3515 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3516 (properties `((upstream-name . "a4Core")))
3517 (build-system r-build-system)
3519 `(("r-biobase" ,r-biobase)
3520 ("r-glmnet" ,r-glmnet)))
3521 (home-page "https://bioconductor.org/packages/a4Core")
3522 (synopsis "Automated Affymetrix array analysis core package")
3524 "This is the core package for the automated analysis of Affymetrix
3526 (license license:gpl3)))
3528 (define-public r-a4classif
3530 (name "r-a4classif")
3535 (uri (bioconductor-uri "a4Classif" version))
3538 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3539 (properties `((upstream-name . "a4Classif")))
3540 (build-system r-build-system)
3542 `(("r-a4core" ,r-a4core)
3543 ("r-a4preproc" ,r-a4preproc)
3544 ("r-glmnet" ,r-glmnet)
3545 ("r-mlinterfaces" ,r-mlinterfaces)
3548 ("r-varselrf" ,r-varselrf)))
3549 (home-page "https://bioconductor.org/packages/a4Classif/")
3550 (synopsis "Automated Affymetrix array analysis classification package")
3552 "This is the classification package for the automated analysis of
3553 Affymetrix arrays.")
3554 (license license:gpl3)))
3556 (define-public r-a4preproc
3558 (name "r-a4preproc")
3563 (uri (bioconductor-uri "a4Preproc" version))
3566 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3567 (properties `((upstream-name . "a4Preproc")))
3568 (build-system r-build-system)
3570 `(("r-annotationdbi" ,r-annotationdbi)))
3571 (home-page "https://bioconductor.org/packages/a4Preproc/")
3572 (synopsis "Automated Affymetrix array analysis preprocessing package")
3574 "This is a package for the automated analysis of Affymetrix arrays. It
3575 is used for preprocessing the arrays.")
3576 (license license:gpl3)))
3578 (define-public r-a4reporting
3580 (name "r-a4reporting")
3585 (uri (bioconductor-uri "a4Reporting" version))
3588 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3589 (properties `((upstream-name . "a4Reporting")))
3590 (build-system r-build-system)
3592 `(("r-annaffy" ,r-annaffy)
3593 ("r-xtable" ,r-xtable)))
3594 (home-page "https://bioconductor.org/packages/a4Reporting/")
3595 (synopsis "Automated Affymetrix array analysis reporting package")
3597 "This is a package for the automated analysis of Affymetrix arrays. It
3598 provides reporting features.")
3599 (license license:gpl3)))
3601 (define-public r-a4base
3608 (uri (bioconductor-uri "a4Base" version))
3611 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3612 (properties `((upstream-name . "a4Base")))
3613 (build-system r-build-system)
3615 `(("r-a4core" ,r-a4core)
3616 ("r-a4preproc" ,r-a4preproc)
3617 ("r-annaffy" ,r-annaffy)
3618 ("r-annotationdbi" ,r-annotationdbi)
3619 ("r-biobase" ,r-biobase)
3620 ("r-genefilter" ,r-genefilter)
3621 ("r-glmnet" ,r-glmnet)
3622 ("r-gplots" ,r-gplots)
3623 ("r-limma" ,r-limma)
3625 ("r-multtest" ,r-multtest)))
3626 (home-page "https://bioconductor.org/packages/a4Base/")
3627 (synopsis "Automated Affymetrix array analysis base package")
3629 "This package provides basic features for the automated analysis of
3630 Affymetrix arrays.")
3631 (license license:gpl3)))
3640 (uri (bioconductor-uri "a4" version))
3643 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3644 (build-system r-build-system)
3646 `(("r-a4base" ,r-a4base)
3647 ("r-a4classif" ,r-a4classif)
3648 ("r-a4core" ,r-a4core)
3649 ("r-a4preproc" ,r-a4preproc)
3650 ("r-a4reporting" ,r-a4reporting)))
3651 (home-page "https://bioconductor.org/packages/a4/")
3652 (synopsis "Automated Affymetrix array analysis umbrella package")
3654 "This package provides a software suite for the automated analysis of
3655 Affymetrix arrays.")
3656 (license license:gpl3)))
3658 (define-public r-abseqr
3665 (uri (bioconductor-uri "abseqR" version))
3668 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3669 (properties `((upstream-name . "abseqR")))
3670 (build-system r-build-system)
3672 `(("pandoc" ,ghc-pandoc)))
3674 `(("r-biocparallel" ,r-biocparallel)
3675 ("r-biocstyle" ,r-biocstyle)
3676 ("r-circlize" ,r-circlize)
3677 ("r-flexdashboard" ,r-flexdashboard)
3678 ("r-ggcorrplot" ,r-ggcorrplot)
3679 ("r-ggdendro" ,r-ggdendro)
3680 ("r-ggplot2" ,r-ggplot2)
3681 ("r-gridextra" ,r-gridextra)
3682 ("r-knitr" ,r-knitr)
3683 ("r-plotly" ,r-plotly)
3686 ("r-rcolorbrewer" ,r-rcolorbrewer)
3687 ("r-reshape2" ,r-reshape2)
3688 ("r-rmarkdown" ,r-rmarkdown)
3689 ("r-stringr" ,r-stringr)
3690 ("r-vegan" ,r-vegan)
3691 ("r-venndiagram" ,r-venndiagram)))
3692 (home-page "https://github.com/malhamdoosh/abseqR")
3693 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3695 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3696 sequencing datasets generated from antibody libraries and abseqR is one of its
3697 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3698 capabilities and allows them to generate interactive HTML reports for the
3699 convenience of viewing and sharing with other researchers. Additionally,
3700 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3701 further downstream analysis on its output.")
3702 (license license:gpl3)))
3704 (define-public r-bacon
3711 (uri (bioconductor-uri "bacon" version))
3714 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3715 (build-system r-build-system)
3717 `(("r-biocparallel" ,r-biocparallel)
3718 ("r-ellipse" ,r-ellipse)
3719 ("r-ggplot2" ,r-ggplot2)))
3720 (home-page "https://bioconductor.org/packages/bacon/")
3721 (synopsis "Controlling bias and inflation in association studies")
3723 "Bacon can be used to remove inflation and bias often observed in
3724 epigenome- and transcriptome-wide association studies. To this end bacon
3725 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3726 fitting a three-component normal mixture on z-scores.")
3727 (license license:gpl2+)))
3729 (define-public r-rgadem
3736 (uri (bioconductor-uri "rGADEM" version))
3739 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3740 (properties `((upstream-name . "rGADEM")))
3741 (build-system r-build-system)
3743 `(("r-biostrings" ,r-biostrings)
3744 ("r-bsgenome" ,r-bsgenome)
3745 ("r-iranges" ,r-iranges)
3746 ("r-seqlogo" ,r-seqlogo)))
3747 (home-page "https://bioconductor.org/packages/rGADEM/")
3748 (synopsis "De novo sequence motif discovery")
3750 "rGADEM is an efficient de novo motif discovery tool for large-scale
3751 genomic sequence data.")
3752 (license license:artistic2.0)))
3754 (define-public r-motiv
3761 (uri (bioconductor-uri "MotIV" version))
3764 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3765 (properties `((upstream-name . "MotIV")))
3766 (build-system r-build-system)
3770 `(("r-biocgenerics" ,r-biocgenerics)
3771 ("r-biostrings" ,r-biostrings)
3772 ("r-iranges" ,r-iranges)
3773 ("r-lattice" ,r-lattice)
3774 ("r-rgadem" ,r-rgadem)
3775 ("r-s4vectors" ,r-s4vectors)))
3776 (home-page "https://bioconductor.org/packages/MotIV/")
3777 (synopsis "Motif identification and validation")
3779 "This package is used for the identification and validation of sequence
3780 motifs. It makes use of STAMP for comparing a set of motifs to a given
3781 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3782 distributions, modules and filter motifs.")
3783 (license license:gpl2)))
3785 (define-public r-motifstack
3787 (name "r-motifstack")
3792 (uri (bioconductor-uri "motifStack" version))
3795 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3796 (properties `((upstream-name . "motifStack")))
3797 (build-system r-build-system)
3799 `(("r-ade4" ,r-ade4)
3800 ("r-biostrings" ,r-biostrings)
3801 ("r-grimport2" ,r-grimport2)
3802 ("r-htmlwidgets" ,r-htmlwidgets)
3803 ("r-motiv" ,r-motiv)
3804 ("r-scales" ,r-scales)
3806 (home-page "https://bioconductor.org/packages/motifStack/")
3807 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3809 "The motifStack package is designed for graphic representation of
3810 multiple motifs with different similarity scores. It works with both DNA/RNA
3811 sequence motifs and amino acid sequence motifs. In addition, it provides the
3812 flexibility for users to customize the graphic parameters such as the font
3813 type and symbol colors.")
3814 (license license:gpl2+)))
3816 (define-public r-genomicscores
3818 (name "r-genomicscores")
3823 (uri (bioconductor-uri "GenomicScores" version))
3826 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3827 (properties `((upstream-name . "GenomicScores")))
3828 (build-system r-build-system)
3830 `(("r-annotationhub" ,r-annotationhub)
3831 ("r-biobase" ,r-biobase)
3832 ("r-biocgenerics" ,r-biocgenerics)
3833 ("r-biostrings" ,r-biostrings)
3834 ("r-bsgenome" ,r-bsgenome)
3835 ("r-genomeinfodb" ,r-genomeinfodb)
3836 ("r-genomicranges" ,r-genomicranges)
3837 ("r-iranges" ,r-iranges)
3838 ("r-s4vectors" ,r-s4vectors)
3840 (home-page "https://github.com/rcastelo/GenomicScores/")
3841 (synopsis "Work with genome-wide position-specific scores")
3843 "This package provides infrastructure to store and access genome-wide
3844 position-specific scores within R and Bioconductor.")
3845 (license license:artistic2.0)))
3847 (define-public r-atacseqqc
3849 (name "r-atacseqqc")
3854 (uri (bioconductor-uri "ATACseqQC" version))
3857 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3858 (properties `((upstream-name . "ATACseqQC")))
3859 (build-system r-build-system)
3861 `(("r-biocgenerics" ,r-biocgenerics)
3862 ("r-biostrings" ,r-biostrings)
3863 ("r-bsgenome" ,r-bsgenome)
3864 ("r-chippeakanno" ,r-chippeakanno)
3865 ("r-edger" ,r-edger)
3866 ("r-genomeinfodb" ,r-genomeinfodb)
3867 ("r-genomicalignments" ,r-genomicalignments)
3868 ("r-genomicranges" ,r-genomicranges)
3869 ("r-genomicscores" ,r-genomicscores)
3870 ("r-iranges" ,r-iranges)
3871 ("r-kernsmooth" ,r-kernsmooth)
3872 ("r-limma" ,r-limma)
3873 ("r-motifstack" ,r-motifstack)
3874 ("r-preseqr" ,r-preseqr)
3875 ("r-randomforest" ,r-randomforest)
3876 ("r-rsamtools" ,r-rsamtools)
3877 ("r-rtracklayer" ,r-rtracklayer)
3878 ("r-s4vectors" ,r-s4vectors)))
3879 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3880 (synopsis "ATAC-seq quality control")
3882 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3883 sequencing, is a rapid and sensitive method for chromatin accessibility
3884 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3885 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3886 assess whether their ATAC-seq experiment is successful. It includes
3887 diagnostic plots of fragment size distribution, proportion of mitochondria
3888 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3890 (license license:gpl2+)))
3892 (define-public r-gofuncr
3899 (uri (bioconductor-uri "GOfuncR" version))
3902 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3903 (properties `((upstream-name . "GOfuncR")))
3904 (build-system r-build-system)
3906 `(("r-annotationdbi" ,r-annotationdbi)
3907 ("r-genomicranges" ,r-genomicranges)
3908 ("r-gtools" ,r-gtools)
3909 ("r-iranges" ,r-iranges)
3910 ("r-mapplots" ,r-mapplots)
3912 ("r-vioplot" ,r-vioplot)))
3913 (home-page "https://bioconductor.org/packages/GOfuncR/")
3914 (synopsis "Gene ontology enrichment using FUNC")
3916 "GOfuncR performs a gene ontology enrichment analysis based on the
3917 ontology enrichment software FUNC. GO-annotations are obtained from
3918 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3919 included in the package and updated regularly. GOfuncR provides the standard
3920 candidate vs background enrichment analysis using the hypergeometric test, as
3921 well as three additional tests:
3924 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3925 @item a binomial test that is used when genes are associated with two counts,
3927 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3928 associated with four counts.
3931 To correct for multiple testing and interdependency of the tests, family-wise
3932 error rates are computed based on random permutations of the gene-associated
3933 variables. GOfuncR also provides tools for exploring the ontology graph and
3934 the annotations, and options to take gene-length or spatial clustering of
3935 genes into account. It is also possible to provide custom gene coordinates,
3936 annotations and ontologies.")
3937 (license license:gpl2+)))
3939 (define-public r-abaenrichment
3941 (name "r-abaenrichment")
3946 (uri (bioconductor-uri "ABAEnrichment" version))
3949 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
3950 (properties `((upstream-name . "ABAEnrichment")))
3951 (build-system r-build-system)
3953 `(("r-abadata" ,r-abadata)
3954 ("r-data-table" ,r-data-table)
3955 ("r-gofuncr" ,r-gofuncr)
3956 ("r-gplots" ,r-gplots)
3957 ("r-gtools" ,r-gtools)
3958 ("r-rcpp" ,r-rcpp)))
3959 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3960 (synopsis "Gene expression enrichment in human brain regions")
3962 "The package ABAEnrichment is designed to test for enrichment of user
3963 defined candidate genes in the set of expressed genes in different human brain
3964 regions. The core function @code{aba_enrich} integrates the expression of the
3965 candidate gene set (averaged across donors) and the structural information of
3966 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3967 (license license:gpl2+)))
3969 (define-public r-annotationfuncs
3971 (name "r-annotationfuncs")
3976 (uri (bioconductor-uri "AnnotationFuncs" version))
3979 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3981 `((upstream-name . "AnnotationFuncs")))
3982 (build-system r-build-system)
3984 `(("r-annotationdbi" ,r-annotationdbi)
3986 (home-page "https://www.iysik.com/r/annotationfuncs")
3987 (synopsis "Annotation translation functions")
3989 "This package provides functions for handling translating between
3990 different identifieres using the Biocore Data Team data-packages (e.g.
3991 @code{org.Bt.eg.db}).")
3992 (license license:gpl2)))
3994 (define-public r-annotationtools
3996 (name "r-annotationtools")
4001 (uri (bioconductor-uri "annotationTools" version))
4004 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
4006 `((upstream-name . "annotationTools")))
4007 (build-system r-build-system)
4008 (propagated-inputs `(("r-biobase" ,r-biobase)))
4009 (home-page "https://bioconductor.org/packages/annotationTools/")
4010 (synopsis "Annotate microarrays and perform gene expression analyses")
4012 "This package provides functions to annotate microarrays, find orthologs,
4013 and integrate heterogeneous gene expression profiles using annotation and
4014 other molecular biology information available as flat file database (plain
4016 ;; Any version of the GPL.
4017 (license (list license:gpl2+))))
4019 (define-public r-allelicimbalance
4021 (name "r-allelicimbalance")
4026 (uri (bioconductor-uri "AllelicImbalance" version))
4029 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
4031 `((upstream-name . "AllelicImbalance")))
4032 (build-system r-build-system)
4034 `(("r-annotationdbi" ,r-annotationdbi)
4035 ("r-biocgenerics" ,r-biocgenerics)
4036 ("r-biostrings" ,r-biostrings)
4037 ("r-bsgenome" ,r-bsgenome)
4038 ("r-genomeinfodb" ,r-genomeinfodb)
4039 ("r-genomicalignments" ,r-genomicalignments)
4040 ("r-genomicfeatures" ,r-genomicfeatures)
4041 ("r-genomicranges" ,r-genomicranges)
4042 ("r-gridextra" ,r-gridextra)
4044 ("r-iranges" ,r-iranges)
4045 ("r-lattice" ,r-lattice)
4046 ("r-latticeextra" ,r-latticeextra)
4048 ("r-rsamtools" ,r-rsamtools)
4049 ("r-s4vectors" ,r-s4vectors)
4050 ("r-seqinr" ,r-seqinr)
4051 ("r-summarizedexperiment" ,r-summarizedexperiment)
4052 ("r-variantannotation" ,r-variantannotation)))
4053 (home-page "https://github.com/pappewaio/AllelicImbalance")
4054 (synopsis "Investigate allele-specific expression")
4056 "This package provides a framework for allele-specific expression
4057 investigation using RNA-seq data.")
4058 (license license:gpl3)))
4060 (define-public r-aucell
4067 (uri (bioconductor-uri "AUCell" version))
4070 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
4071 (properties `((upstream-name . "AUCell")))
4072 (build-system r-build-system)
4074 `(("r-data-table" ,r-data-table)
4075 ("r-gseabase" ,r-gseabase)
4076 ("r-mixtools" ,r-mixtools)
4077 ("r-r-utils" ,r-r-utils)
4078 ("r-shiny" ,r-shiny)
4079 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4080 (home-page "https://bioconductor.org/packages/AUCell/")
4081 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4083 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4084 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4085 Under the Curve} (AUC) to calculate whether a critical subset of the input
4086 gene set is enriched within the expressed genes for each cell. The
4087 distribution of AUC scores across all the cells allows exploring the relative
4088 expression of the signature. Since the scoring method is ranking-based,
4089 AUCell is independent of the gene expression units and the normalization
4090 procedure. In addition, since the cells are evaluated individually, it can
4091 easily be applied to bigger datasets, subsetting the expression matrix if
4093 (license license:gpl3)))
4095 (define-public r-ebimage
4102 (uri (bioconductor-uri "EBImage" version))
4105 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
4106 (properties `((upstream-name . "EBImage")))
4107 (build-system r-build-system)
4109 `(("r-abind" ,r-abind)
4110 ("r-biocgenerics" ,r-biocgenerics)
4111 ("r-fftwtools" ,r-fftwtools)
4112 ("r-htmltools" ,r-htmltools)
4113 ("r-htmlwidgets" ,r-htmlwidgets)
4115 ("r-locfit" ,r-locfit)
4117 ("r-rcurl" ,r-rcurl)
4118 ("r-tiff" ,r-tiff)))
4120 `(("r-knitr" ,r-knitr))) ; for vignettes
4121 (home-page "https://github.com/aoles/EBImage")
4122 (synopsis "Image processing and analysis toolbox for R")
4124 "EBImage provides general purpose functionality for image processing and
4125 analysis. In the context of (high-throughput) microscopy-based cellular
4126 assays, EBImage offers tools to segment cells and extract quantitative
4127 cellular descriptors. This allows the automation of such tasks using the R
4128 programming language and facilitates the use of other tools in the R
4129 environment for signal processing, statistical modeling, machine learning and
4130 visualization with image data.")
4131 ;; Any version of the LGPL.
4132 (license license:lgpl2.1+)))
4134 (define-public r-yamss
4141 (uri (bioconductor-uri "yamss" version))
4144 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
4145 (build-system r-build-system)
4147 `(("r-biocgenerics" ,r-biocgenerics)
4148 ("r-data-table" ,r-data-table)
4149 ("r-ebimage" ,r-ebimage)
4150 ("r-iranges" ,r-iranges)
4151 ("r-limma" ,r-limma)
4152 ("r-matrix" ,r-matrix)
4154 ("r-s4vectors" ,r-s4vectors)
4155 ("r-summarizedexperiment"
4156 ,r-summarizedexperiment)))
4157 (home-page "https://github.com/hansenlab/yamss")
4158 (synopsis "Tools for high-throughput metabolomics")
4160 "This package provides tools to analyze and visualize high-throughput
4161 metabolomics data acquired using chromatography-mass spectrometry. These tools
4162 preprocess data in a way that enables reliable and powerful differential
4164 (license license:artistic2.0)))
4166 (define-public r-gtrellis
4173 (uri (bioconductor-uri "gtrellis" version))
4176 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
4177 (build-system r-build-system)
4179 `(("r-circlize" ,r-circlize)
4180 ("r-genomicranges" ,r-genomicranges)
4181 ("r-getoptlong" ,r-getoptlong)
4182 ("r-iranges" ,r-iranges)))
4183 (home-page "https://github.com/jokergoo/gtrellis")
4184 (synopsis "Genome level Trellis layout")
4186 "Genome level Trellis graph visualizes genomic data conditioned by
4187 genomic categories (e.g. chromosomes). For each genomic category, multiple
4188 dimensional data which are represented as tracks describe different features
4189 from different aspects. This package provides high flexibility to arrange
4190 genomic categories and to add self-defined graphics in the plot.")
4191 (license license:expat)))
4193 (define-public r-somaticsignatures
4195 (name "r-somaticsignatures")
4200 (uri (bioconductor-uri "SomaticSignatures" version))
4203 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
4205 `((upstream-name . "SomaticSignatures")))
4206 (build-system r-build-system)
4208 `(("r-biobase" ,r-biobase)
4209 ("r-biostrings" ,r-biostrings)
4210 ("r-genomeinfodb" ,r-genomeinfodb)
4211 ("r-genomicranges" ,r-genomicranges)
4212 ("r-ggbio" ,r-ggbio)
4213 ("r-ggplot2" ,r-ggplot2)
4214 ("r-iranges" ,r-iranges)
4216 ("r-pcamethods" ,r-pcamethods)
4217 ("r-proxy" ,r-proxy)
4218 ("r-reshape2" ,r-reshape2)
4219 ("r-s4vectors" ,r-s4vectors)
4220 ("r-variantannotation" ,r-variantannotation)))
4221 (home-page "https://github.com/juliangehring/SomaticSignatures")
4222 (synopsis "Somatic signatures")
4224 "This package identifies mutational signatures of @dfn{single nucleotide
4225 variants} (SNVs). It provides a infrastructure related to the methodology
4226 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4227 decomposition algorithms.")
4228 (license license:expat)))
4230 (define-public r-yapsa
4237 (uri (bioconductor-uri "YAPSA" version))
4240 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
4241 (properties `((upstream-name . "YAPSA")))
4242 (build-system r-build-system)
4244 `(("r-circlize" ,r-circlize)
4245 ("r-complexheatmap" ,r-complexheatmap)
4246 ("r-corrplot" ,r-corrplot)
4247 ("r-dendextend" ,r-dendextend)
4248 ("r-genomeinfodb" ,r-genomeinfodb)
4249 ("r-genomicranges" ,r-genomicranges)
4250 ("r-getoptlong" ,r-getoptlong)
4251 ("r-ggplot2" ,r-ggplot2)
4252 ("r-gridextra" ,r-gridextra)
4253 ("r-gtrellis" ,r-gtrellis)
4254 ("r-keggrest" ,r-keggrest)
4256 ("r-pmcmr" ,r-pmcmr)
4257 ("r-reshape2" ,r-reshape2)
4258 ("r-somaticsignatures" ,r-somaticsignatures)
4259 ("r-variantannotation" ,r-variantannotation)))
4260 (home-page "https://bioconductor.org/packages/YAPSA/")
4261 (synopsis "Yet another package for signature analysis")
4263 "This package provides functions and routines useful in the analysis of
4264 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4265 functions to perform a signature analysis with known signatures and a
4266 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4268 (license license:gpl3)))
4270 (define-public r-gcrma
4277 (uri (bioconductor-uri "gcrma" version))
4280 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4281 (build-system r-build-system)
4283 `(("r-affy" ,r-affy)
4284 ("r-affyio" ,r-affyio)
4285 ("r-biobase" ,r-biobase)
4286 ("r-biocmanager" ,r-biocmanager)
4287 ("r-biostrings" ,r-biostrings)
4288 ("r-xvector" ,r-xvector)))
4289 (home-page "https://bioconductor.org/packages/gcrma/")
4290 (synopsis "Background adjustment using sequence information")
4292 "Gcrma adjusts for background intensities in Affymetrix array data which
4293 include optical noise and @dfn{non-specific binding} (NSB). The main function
4294 @code{gcrma} converts background adjusted probe intensities to expression
4295 measures using the same normalization and summarization methods as a
4296 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4297 to estimate probe affinity to NSB. The sequence information is summarized in
4298 a more complex way than the simple GC content. Instead, the base types (A, T,
4299 G or C) at each position along the probe determine the affinity of each probe.
4300 The parameters of the position-specific base contributions to the probe
4301 affinity is estimated in an NSB experiment in which only NSB but no
4302 gene-specific bidning is expected.")
4303 ;; Any version of the LGPL
4304 (license license:lgpl2.1+)))
4306 (define-public r-simpleaffy
4308 (name "r-simpleaffy")
4313 (uri (bioconductor-uri "simpleaffy" version))
4316 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4317 (build-system r-build-system)
4319 `(("r-affy" ,r-affy)
4320 ("r-biobase" ,r-biobase)
4321 ("r-biocgenerics" ,r-biocgenerics)
4322 ("r-gcrma" ,r-gcrma)
4323 ("r-genefilter" ,r-genefilter)))
4324 (home-page "https://bioconductor.org/packages/simpleaffy/")
4325 (synopsis "Very simple high level analysis of Affymetrix data")
4327 "This package provides high level functions for reading Affy @file{.CEL}
4328 files, phenotypic data, and then computing simple things with it, such as
4329 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4330 library. It also has some basic scatter plot functions and mechanisms for
4331 generating high resolution journal figures.")
4332 (license license:gpl2+)))
4334 (define-public r-yaqcaffy
4341 (uri (bioconductor-uri "yaqcaffy" version))
4344 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4345 (build-system r-build-system)
4347 `(("r-simpleaffy" ,r-simpleaffy)))
4348 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4349 (synopsis "Affymetrix quality control and reproducibility analysis")
4351 "This is a package that can be used for quality control of Affymetrix
4352 GeneChip expression data and reproducibility analysis of human whole genome
4353 chips with the MAQC reference datasets.")
4354 (license license:artistic2.0)))
4356 (define-public r-quantro
4363 (uri (bioconductor-uri "quantro" version))
4366 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4367 (build-system r-build-system)
4369 `(("r-biobase" ,r-biobase)
4370 ("r-doparallel" ,r-doparallel)
4371 ("r-foreach" ,r-foreach)
4372 ("r-ggplot2" ,r-ggplot2)
4373 ("r-iterators" ,r-iterators)
4374 ("r-minfi" ,r-minfi)
4375 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4376 (home-page "https://bioconductor.org/packages/quantro/")
4377 (synopsis "Test for when to use quantile normalization")
4379 "This package provides a data-driven test for the assumptions of quantile
4380 normalization using raw data such as objects that inherit eSets (e.g.
4381 ExpressionSet, MethylSet). Group level information about each sample (such as
4382 Tumor / Normal status) must also be provided because the test assesses if
4383 there are global differences in the distributions between the user-defined
4385 (license license:gpl3+)))
4387 (define-public r-yarn
4394 (uri (bioconductor-uri "yarn" version))
4397 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4398 (build-system r-build-system)
4400 `(("r-biobase" ,r-biobase)
4401 ("r-biomart" ,r-biomart)
4402 ("r-downloader" ,r-downloader)
4403 ("r-edger" ,r-edger)
4404 ("r-gplots" ,r-gplots)
4405 ("r-limma" ,r-limma)
4406 ("r-matrixstats" ,r-matrixstats)
4407 ("r-preprocesscore" ,r-preprocesscore)
4408 ("r-quantro" ,r-quantro)
4409 ("r-rcolorbrewer" ,r-rcolorbrewer)
4410 ("r-readr" ,r-readr)))
4411 (home-page "https://bioconductor.org/packages/yarn/")
4412 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4414 "Expedite large RNA-Seq analyses using a combination of previously
4415 developed tools. YARN is meant to make it easier for the user in performing
4416 basic mis-annotation quality control, filtering, and condition-aware
4417 normalization. YARN leverages many Bioconductor tools and statistical
4418 techniques to account for the large heterogeneity and sparsity found in very
4419 large RNA-seq experiments.")
4420 (license license:artistic2.0)))
4422 (define-public r-roar
4429 (uri (bioconductor-uri "roar" version))
4432 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4433 (build-system r-build-system)
4435 `(("r-biocgenerics" ,r-biocgenerics)
4436 ("r-genomeinfodb" ,r-genomeinfodb)
4437 ("r-genomicalignments" ,r-genomicalignments)
4438 ("r-genomicranges" ,r-genomicranges)
4439 ("r-iranges" ,r-iranges)
4440 ("r-rtracklayer" ,r-rtracklayer)
4441 ("r-s4vectors" ,r-s4vectors)
4442 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4443 (home-page "https://github.com/vodkatad/roar/")
4444 (synopsis "Identify differential APA usage from RNA-seq alignments")
4446 "This package provides tools for identifying preferential usage of APA
4447 sites, comparing two biological conditions, starting from known alternative
4448 sites and alignments obtained from standard RNA-seq experiments.")
4449 (license license:gpl3)))
4451 (define-public r-xbseq
4458 (uri (bioconductor-uri "XBSeq" version))
4461 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4462 (properties `((upstream-name . "XBSeq")))
4463 (build-system r-build-system)
4465 `(("r-biobase" ,r-biobase)
4466 ("r-deseq2" ,r-deseq2)
4467 ("r-dplyr" ,r-dplyr)
4468 ("r-ggplot2" ,r-ggplot2)
4469 ("r-locfit" ,r-locfit)
4470 ("r-magrittr" ,r-magrittr)
4471 ("r-matrixstats" ,r-matrixstats)
4472 ("r-pracma" ,r-pracma)
4473 ("r-roar" ,r-roar)))
4474 (home-page "https://github.com/Liuy12/XBSeq")
4475 (synopsis "Test for differential expression for RNA-seq data")
4477 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4478 expression} (DE), where a statistical model was established based on the
4479 assumption that observed signals are the convolution of true expression
4480 signals and sequencing noises. The mapped reads in non-exonic regions are
4481 considered as sequencing noises, which follows a Poisson distribution. Given
4482 measurable observed signal and background noise from RNA-seq data, true
4483 expression signals, assuming governed by the negative binomial distribution,
4484 can be delineated and thus the accurate detection of differential expressed
4486 (license license:gpl3+)))
4488 (define-public r-massspecwavelet
4490 (name "r-massspecwavelet")
4495 (uri (bioconductor-uri "MassSpecWavelet" version))
4498 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4500 `((upstream-name . "MassSpecWavelet")))
4501 (build-system r-build-system)
4503 `(("r-waveslim" ,r-waveslim)))
4504 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4505 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4507 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4508 data mainly through the use of wavelet transforms. It supports peak detection
4509 based on @dfn{Continuous Wavelet Transform} (CWT).")
4510 (license license:lgpl2.0+)))
4512 (define-public r-xcms
4519 (uri (bioconductor-uri "xcms" version))
4522 "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v"))))
4523 (build-system r-build-system)
4525 `(("r-biobase" ,r-biobase)
4526 ("r-biocgenerics" ,r-biocgenerics)
4527 ("r-biocparallel" ,r-biocparallel)
4528 ("r-lattice" ,r-lattice)
4529 ("r-massspecwavelet" ,r-massspecwavelet)
4530 ("r-msnbase" ,r-msnbase)
4531 ("r-multtest" ,r-multtest)
4534 ("r-protgenerics" ,r-protgenerics)
4536 ("r-rcolorbrewer" ,r-rcolorbrewer)
4537 ("r-robustbase" ,r-robustbase)
4538 ("r-s4vectors" ,r-s4vectors)))
4539 (home-page "https://bioconductor.org/packages/xcms/")
4540 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4542 "This package provides a framework for processing and visualization of
4543 chromatographically separated and single-spectra mass spectral data. It
4544 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4545 data for high-throughput, untargeted analyte profiling.")
4546 (license license:gpl2+)))
4548 (define-public r-wrench
4555 (uri (bioconductor-uri "Wrench" version))
4558 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4559 (properties `((upstream-name . "Wrench")))
4560 (build-system r-build-system)
4562 `(("r-limma" ,r-limma)
4563 ("r-locfit" ,r-locfit)
4564 ("r-matrixstats" ,r-matrixstats)))
4565 (home-page "https://github.com/HCBravoLab/Wrench")
4566 (synopsis "Wrench normalization for sparse count data")
4568 "Wrench is a package for normalization sparse genomic count data, like
4569 that arising from 16s metagenomic surveys.")
4570 (license license:artistic2.0)))
4572 (define-public r-wiggleplotr
4574 (name "r-wiggleplotr")
4579 (uri (bioconductor-uri "wiggleplotr" version))
4582 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4583 (build-system r-build-system)
4585 `(("r-assertthat" ,r-assertthat)
4586 ("r-cowplot" ,r-cowplot)
4587 ("r-dplyr" ,r-dplyr)
4588 ("r-genomeinfodb" ,r-genomeinfodb)
4589 ("r-genomicranges" ,r-genomicranges)
4590 ("r-ggplot2" ,r-ggplot2)
4591 ("r-iranges" ,r-iranges)
4592 ("r-purrr" ,r-purrr)
4593 ("r-rtracklayer" ,r-rtracklayer)
4594 ("r-s4vectors" ,r-s4vectors)))
4595 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4596 (synopsis "Make read coverage plots from BigWig files")
4598 "This package provides tools to visualize read coverage from sequencing
4599 experiments together with genomic annotations (genes, transcripts, peaks).
4600 Introns of long transcripts can be rescaled to a fixed length for better
4601 visualization of exonic read coverage.")
4602 (license license:asl2.0)))
4604 (define-public r-widgettools
4606 (name "r-widgettools")
4611 (uri (bioconductor-uri "widgetTools" version))
4614 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4615 (properties `((upstream-name . "widgetTools")))
4616 (build-system r-build-system)
4617 (home-page "https://bioconductor.org/packages/widgetTools/")
4618 (synopsis "Tools for creating interactive tcltk widgets")
4620 "This package contains tools to support the construction of tcltk
4622 ;; Any version of the LGPL.
4623 (license license:lgpl3+)))
4625 (define-public r-webbioc
4632 (uri (bioconductor-uri "webbioc" version))
4635 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4636 (build-system r-build-system)
4638 `(("netpbm" ,netpbm)
4641 `(("r-affy" ,r-affy)
4642 ("r-annaffy" ,r-annaffy)
4643 ("r-biobase" ,r-biobase)
4644 ("r-biocmanager" ,r-biocmanager)
4645 ("r-gcrma" ,r-gcrma)
4646 ("r-multtest" ,r-multtest)
4647 ("r-qvalue" ,r-qvalue)
4649 (home-page "https://www.bioconductor.org/")
4650 (synopsis "Bioconductor web interface")
4652 "This package provides an integrated web interface for doing microarray
4653 analysis using several of the Bioconductor packages. It is intended to be
4654 deployed as a centralized bioinformatics resource for use by many users.
4655 Currently only Affymetrix oligonucleotide analysis is supported.")
4656 (license license:gpl2+)))
4658 (define-public r-zfpkm
4665 (uri (bioconductor-uri "zFPKM" version))
4668 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4669 (properties `((upstream-name . "zFPKM")))
4670 (build-system r-build-system)
4672 `(("r-checkmate" ,r-checkmate)
4673 ("r-dplyr" ,r-dplyr)
4674 ("r-ggplot2" ,r-ggplot2)
4675 ("r-summarizedexperiment" ,r-summarizedexperiment)
4676 ("r-tidyr" ,r-tidyr)))
4677 (home-page "https://github.com/ronammar/zFPKM/")
4678 (synopsis "Functions to facilitate zFPKM transformations")
4680 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4681 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4683 (license license:gpl3)))
4685 (define-public r-rbowtie2
4692 (uri (bioconductor-uri "Rbowtie2" version))
4695 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4696 (properties `((upstream-name . "Rbowtie2")))
4697 (build-system r-build-system)
4700 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4701 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4703 "This package provides an R wrapper of the popular @code{bowtie2}
4704 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4705 rapid adapter trimming, identification, and read merging.")
4706 (license license:gpl3+)))
4708 (define-public r-progeny
4715 (uri (bioconductor-uri "progeny" version))
4718 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4719 (build-system r-build-system)
4720 (propagated-inputs `(("r-biobase" ,r-biobase)))
4721 (home-page "https://github.com/saezlab/progeny")
4722 (synopsis "Pathway responsive gene activity inference")
4724 "This package provides a function to infer pathway activity from gene
4725 expression. It contains the linear model inferred in the publication
4726 \"Perturbation-response genes reveal signaling footprints in cancer gene
4728 (license license:asl2.0)))
4730 (define-public r-arrmnormalization
4732 (name "r-arrmnormalization")
4737 (uri (bioconductor-uri "ARRmNormalization" version))
4740 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4742 `((upstream-name . "ARRmNormalization")))
4743 (build-system r-build-system)
4744 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4745 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4746 (synopsis "Adaptive robust regression normalization for methylation data")
4748 "This is a package to perform the @dfn{Adaptive Robust Regression
4749 method} (ARRm) for the normalization of methylation data from the Illumina
4750 Infinium HumanMethylation 450k assay.")
4751 (license license:artistic2.0)))
4753 (define-public r-biocfilecache
4755 (name "r-biocfilecache")
4760 (uri (bioconductor-uri "BiocFileCache" version))
4763 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4764 (properties `((upstream-name . "BiocFileCache")))
4765 (build-system r-build-system)
4767 `(("r-curl" ,r-curl)
4769 ("r-dbplyr" ,r-dbplyr)
4770 ("r-dplyr" ,r-dplyr)
4772 ("r-rappdirs" ,r-rappdirs)
4773 ("r-rsqlite" ,r-rsqlite)))
4774 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4775 (synopsis "Manage files across sessions")
4777 "This package creates a persistent on-disk cache of files that the user
4778 can add, update, and retrieve. It is useful for managing resources (such as
4779 custom Txdb objects) that are costly or difficult to create, web resources,
4780 and data files used across sessions.")
4781 (license license:artistic2.0)))
4783 (define-public r-iclusterplus
4785 (name "r-iclusterplus")
4790 (uri (bioconductor-uri "iClusterPlus" version))
4793 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4794 (properties `((upstream-name . "iClusterPlus")))
4795 (build-system r-build-system)
4796 (native-inputs `(("gfortran" ,gfortran)))
4797 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4798 (synopsis "Integrative clustering of multi-type genomic data")
4800 "iClusterPlus is developed for integrative clustering analysis of
4801 multi-type genomic data and is an enhanced version of iCluster proposed and
4802 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4803 from the experiments where biological samples (e.g. tumor samples) are
4804 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4805 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4806 on. In the iClusterPlus model, binary observations such as somatic mutation
4807 are modeled as Binomial processes; categorical observations such as copy
4808 number states are realizations of Multinomial random variables; counts are
4809 modeled as Poisson random processes; and continuous measures are modeled by
4810 Gaussian distributions.")
4811 (license license:gpl2+)))
4813 (define-public r-rbowtie
4820 (uri (bioconductor-uri "Rbowtie" version))
4823 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4824 (properties `((upstream-name . "Rbowtie")))
4825 (build-system r-build-system)
4828 (home-page "https://bioconductor.org/packages/Rbowtie/")
4829 (synopsis "R bowtie wrapper")
4831 "This package provides an R wrapper around the popular bowtie short read
4832 aligner and around SpliceMap, a de novo splice junction discovery and
4834 (license license:artistic2.0)))
4836 (define-public r-sgseq
4843 (uri (bioconductor-uri "SGSeq" version))
4846 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4847 (properties `((upstream-name . "SGSeq")))
4848 (build-system r-build-system)
4850 `(("r-annotationdbi" ,r-annotationdbi)
4851 ("r-biocgenerics" ,r-biocgenerics)
4852 ("r-biostrings" ,r-biostrings)
4853 ("r-genomeinfodb" ,r-genomeinfodb)
4854 ("r-genomicalignments" ,r-genomicalignments)
4855 ("r-genomicfeatures" ,r-genomicfeatures)
4856 ("r-genomicranges" ,r-genomicranges)
4857 ("r-igraph" ,r-igraph)
4858 ("r-iranges" ,r-iranges)
4859 ("r-rsamtools" ,r-rsamtools)
4860 ("r-rtracklayer" ,r-rtracklayer)
4861 ("r-runit" ,r-runit)
4862 ("r-s4vectors" ,r-s4vectors)
4863 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4864 (home-page "https://bioconductor.org/packages/SGSeq/")
4865 (synopsis "Splice event prediction and quantification from RNA-seq data")
4867 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4868 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4869 represented as a splice graph, which can be obtained from existing annotation
4870 or predicted from the mapped sequence reads. Splice events are identified
4871 from the graph and are quantified locally using structurally compatible reads
4872 at the start or end of each splice variant. The software includes functions
4873 for splice event prediction, quantification, visualization and
4875 (license license:artistic2.0)))
4877 (define-public r-rhisat2
4884 (uri (bioconductor-uri "Rhisat2" version))
4887 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4888 (properties `((upstream-name . "Rhisat2")))
4889 (build-system r-build-system)
4891 `(("which" ,which)))
4893 `(("r-genomicfeatures" ,r-genomicfeatures)
4894 ("r-genomicranges" ,r-genomicranges)
4895 ("r-sgseq" ,r-sgseq)))
4896 (home-page "https://github.com/fmicompbio/Rhisat2")
4897 (synopsis "R Wrapper for HISAT2 sequence aligner")
4899 "This package provides an R interface to the HISAT2 spliced short-read
4900 aligner by Kim et al. (2015). The package contains wrapper functions to
4901 create a genome index and to perform the read alignment to the generated
4903 (license license:gpl3)))
4905 (define-public r-quasr
4912 (uri (bioconductor-uri "QuasR" version))
4915 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4916 (properties `((upstream-name . "QuasR")))
4917 (build-system r-build-system)
4921 `(("r-annotationdbi" ,r-annotationdbi)
4922 ("r-biobase" ,r-biobase)
4923 ("r-biocgenerics" ,r-biocgenerics)
4924 ("r-biocmanager" ,r-biocmanager)
4925 ("r-biocparallel" ,r-biocparallel)
4926 ("r-biostrings" ,r-biostrings)
4927 ("r-bsgenome" ,r-bsgenome)
4928 ("r-genomeinfodb" ,r-genomeinfodb)
4929 ("r-genomicalignments" ,r-genomicalignments)
4930 ("r-genomicfeatures" ,r-genomicfeatures)
4931 ("r-genomicfiles" ,r-genomicfiles)
4932 ("r-genomicranges" ,r-genomicranges)
4933 ("r-iranges" ,r-iranges)
4934 ("r-rbowtie" ,r-rbowtie)
4935 ("r-rhisat2" ,r-rhisat2)
4936 ("r-rhtslib" ,r-rhtslib)
4937 ("r-rsamtools" ,r-rsamtools)
4938 ("r-rtracklayer" ,r-rtracklayer)
4939 ("r-s4vectors" ,r-s4vectors)
4940 ("r-shortread" ,r-shortread)))
4941 (home-page "https://bioconductor.org/packages/QuasR/")
4942 (synopsis "Quantify and annotate short reads in R")
4944 "This package provides a framework for the quantification and analysis of
4945 short genomic reads. It covers a complete workflow starting from raw sequence
4946 reads, over creation of alignments and quality control plots, to the
4947 quantification of genomic regions of interest.")
4948 (license license:gpl2)))
4950 (define-public r-rqc
4957 (uri (bioconductor-uri "Rqc" version))
4960 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4961 (properties `((upstream-name . "Rqc")))
4962 (build-system r-build-system)
4964 `(("r-biocgenerics" ,r-biocgenerics)
4965 ("r-biocparallel" ,r-biocparallel)
4966 ("r-biocstyle" ,r-biocstyle)
4967 ("r-biostrings" ,r-biostrings)
4968 ("r-biovizbase" ,r-biovizbase)
4969 ("r-genomicalignments" ,r-genomicalignments)
4970 ("r-genomicfiles" ,r-genomicfiles)
4971 ("r-ggplot2" ,r-ggplot2)
4972 ("r-iranges" ,r-iranges)
4973 ("r-knitr" ,r-knitr)
4974 ("r-markdown" ,r-markdown)
4977 ("r-reshape2" ,r-reshape2)
4978 ("r-rsamtools" ,r-rsamtools)
4979 ("r-s4vectors" ,r-s4vectors)
4980 ("r-shiny" ,r-shiny)
4981 ("r-shortread" ,r-shortread)))
4982 (home-page "https://github.com/labbcb/Rqc")
4983 (synopsis "Quality control tool for high-throughput sequencing data")
4985 "Rqc is an optimized tool designed for quality control and assessment of
4986 high-throughput sequencing data. It performs parallel processing of entire
4987 files and produces a report which contains a set of high-resolution
4989 (license license:gpl2+)))
4991 (define-public r-birewire
4998 (uri (bioconductor-uri "BiRewire" version))
5001 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
5002 (properties `((upstream-name . "BiRewire")))
5003 (build-system r-build-system)
5005 `(("r-igraph" ,r-igraph)
5006 ("r-matrix" ,r-matrix)
5008 ("r-tsne" ,r-tsne)))
5009 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5010 (synopsis "Tools for randomization of bipartite graphs")
5012 "This package provides functions for bipartite network rewiring through N
5013 consecutive switching steps and for the computation of the minimal number of
5014 switching steps to be performed in order to maximise the dissimilarity with
5015 respect to the original network. It includes functions for the analysis of
5016 the introduced randomness across the switching steps and several other
5017 routines to analyse the resulting networks and their natural projections.")
5018 (license license:gpl3)))
5020 (define-public r-birta
5027 (uri (bioconductor-uri "birta" version))
5030 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
5031 (build-system r-build-system)
5033 `(("r-biobase" ,r-biobase)
5034 ("r-limma" ,r-limma)
5035 ("r-mass" ,r-mass)))
5036 (home-page "https://bioconductor.org/packages/birta")
5037 (synopsis "Bayesian inference of regulation of transcriptional activity")
5039 "Expression levels of mRNA molecules are regulated by different
5040 processes, comprising inhibition or activation by transcription factors and
5041 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5042 Inference of Regulation of Transcriptional Activity) uses the regulatory
5043 networks of transcription factors and miRNAs together with mRNA and miRNA
5044 expression data to predict switches in regulatory activity between two
5045 conditions. A Bayesian network is used to model the regulatory structure and
5046 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5047 (license license:gpl2+)))
5049 (define-public r-multidataset
5051 (name "r-multidataset")
5056 (uri (bioconductor-uri "MultiDataSet" version))
5059 "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj"))))
5060 (properties `((upstream-name . "MultiDataSet")))
5061 (build-system r-build-system)
5063 `(("r-biobase" ,r-biobase)
5064 ("r-biocgenerics" ,r-biocgenerics)
5065 ("r-genomicranges" ,r-genomicranges)
5066 ("r-ggplot2" ,r-ggplot2)
5067 ("r-ggrepel" ,r-ggrepel)
5068 ("r-iranges" ,r-iranges)
5069 ("r-limma" ,r-limma)
5070 ("r-qqman" ,r-qqman)
5071 ("r-s4vectors" ,r-s4vectors)
5072 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5073 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5074 (synopsis "Implementation of MultiDataSet and ResultSet")
5076 "This package provides an implementation of the BRGE's (Bioinformatic
5077 Research Group in Epidemiology from Center for Research in Environmental
5078 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5079 integrating multi omics data sets and ResultSet is a container for omics
5080 results. This package contains base classes for MEAL and rexposome
5082 (license license:expat)))
5084 (define-public r-ropls
5091 (uri (bioconductor-uri "ropls" version))
5094 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
5095 (build-system r-build-system)
5096 (propagated-inputs `(("r-biobase" ,r-biobase)))
5098 `(("r-knitr" ,r-knitr))) ; for vignettes
5099 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5100 (synopsis "Multivariate analysis and feature selection of omics data")
5102 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5103 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5104 regression, classification, and feature selection of omics data where the
5105 number of variables exceeds the number of samples and with multicollinearity
5106 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5107 separately model the variation correlated (predictive) to the factor of
5108 interest and the uncorrelated (orthogonal) variation. While performing
5109 similarly to PLS, OPLS facilitates interpretation.
5111 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5112 analysis and feature selection of omics data. In addition to scores, loadings
5113 and weights plots, the package provides metrics and graphics to determine the
5114 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5115 validity of the model by permutation testing, detect outliers, and perform
5116 feature selection (e.g. with Variable Importance in Projection or regression
5118 (license license:cecill)))
5120 (define-public r-biosigner
5122 (name "r-biosigner")
5127 (uri (bioconductor-uri "biosigner" version))
5130 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
5131 (build-system r-build-system)
5133 `(("r-biobase" ,r-biobase)
5134 ("r-e1071" ,r-e1071)
5135 ("r-randomforest" ,r-randomforest)
5136 ("r-ropls" ,r-ropls)))
5138 `(("r-knitr" ,r-knitr)
5139 ("r-rmarkdown" ,r-rmarkdown)
5140 ("pandoc" ,ghc-pandoc)
5141 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5142 (home-page "https://bioconductor.org/packages/biosigner/")
5143 (synopsis "Signature discovery from omics data")
5145 "Feature selection is critical in omics data analysis to extract
5146 restricted and meaningful molecular signatures from complex and high-dimension
5147 data, and to build robust classifiers. This package implements a method to
5148 assess the relevance of the variables for the prediction performances of the
5149 classifier. The approach can be run in parallel with the PLS-DA, Random
5150 Forest, and SVM binary classifiers. The signatures and the corresponding
5151 'restricted' models are returned, enabling future predictions on new
5153 (license license:cecill)))
5155 (define-public r-annotatr
5162 (uri (bioconductor-uri "annotatr" version))
5165 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
5166 (build-system r-build-system)
5168 `(("r-annotationdbi" ,r-annotationdbi)
5169 ("r-annotationhub" ,r-annotationhub)
5170 ("r-dplyr" ,r-dplyr)
5171 ("r-genomeinfodb" ,r-genomeinfodb)
5172 ("r-genomicfeatures" ,r-genomicfeatures)
5173 ("r-genomicranges" ,r-genomicranges)
5174 ("r-ggplot2" ,r-ggplot2)
5175 ("r-iranges" ,r-iranges)
5176 ("r-readr" ,r-readr)
5177 ("r-regioner" ,r-regioner)
5178 ("r-reshape2" ,r-reshape2)
5179 ("r-rtracklayer" ,r-rtracklayer)
5180 ("r-s4vectors" ,r-s4vectors)))
5181 (home-page "https://bioconductor.org/packages/annotatr/")
5182 (synopsis "Annotation of genomic regions to genomic annotations")
5184 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5185 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5186 to investigate the intersecting genomic annotations. Such annotations include
5187 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5188 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5189 enhancers. The annotatr package provides an easy way to summarize and
5190 visualize the intersection of genomic sites/regions with genomic
5192 (license license:gpl3)))
5194 (define-public r-rsubread
5201 (uri (bioconductor-uri "Rsubread" version))
5204 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
5205 (properties `((upstream-name . "Rsubread")))
5206 (build-system r-build-system)
5207 (inputs `(("zlib" ,zlib)))
5208 (home-page "https://bioconductor.org/packages/Rsubread/")
5209 (synopsis "Subread sequence alignment and counting for R")
5211 "This package provides tools for alignment, quantification and analysis
5212 of second and third generation sequencing data. It includes functionality for
5213 read mapping, read counting, SNP calling, structural variant detection and
5214 gene fusion discovery. It can be applied to all major sequencing techologies
5215 and to both short and long sequence reads.")
5216 (license license:gpl3)))
5218 (define-public r-flowutils
5220 (name "r-flowutils")
5225 (uri (bioconductor-uri "flowUtils" version))
5228 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
5229 (properties `((upstream-name . "flowUtils")))
5230 (build-system r-build-system)
5232 `(("r-biobase" ,r-biobase)
5233 ("r-corpcor" ,r-corpcor)
5234 ("r-flowcore" ,r-flowcore)
5235 ("r-graph" ,r-graph)
5236 ("r-runit" ,r-runit)
5238 (home-page "https://github.com/jspidlen/flowUtils")
5239 (synopsis "Utilities for flow cytometry")
5241 "This package provides utilities for flow cytometry data.")
5242 (license license:artistic2.0)))
5244 (define-public r-consensusclusterplus
5246 (name "r-consensusclusterplus")
5251 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5254 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
5256 `((upstream-name . "ConsensusClusterPlus")))
5257 (build-system r-build-system)
5260 ("r-biobase" ,r-biobase)
5261 ("r-cluster" ,r-cluster)))
5262 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5263 (synopsis "Clustering algorithm")
5265 "This package provides an implementation of an algorithm for determining
5266 cluster count and membership by stability evidence in unsupervised analysis.")
5267 (license license:gpl2)))
5269 (define-public r-cytolib
5276 (uri (bioconductor-uri "cytolib" version))
5279 "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9"))))
5280 (properties `((upstream-name . "cytolib")))
5281 (build-system r-build-system)
5282 (home-page "https://bioconductor.org/packages/cytolib/")
5283 (synopsis "C++ infrastructure for working with gated cytometry")
5285 "This package provides the core data structure and API to represent and
5286 interact with gated cytometry data.")
5287 (license license:artistic2.0)))
5289 (define-public r-flowcore
5296 (uri (bioconductor-uri "flowCore" version))
5299 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
5300 (properties `((upstream-name . "flowCore")))
5301 (build-system r-build-system)
5304 ("r-biobase" ,r-biobase)
5305 ("r-biocgenerics" ,r-biocgenerics)
5306 ("r-corpcor" ,r-corpcor)
5307 ("r-graph" ,r-graph)
5309 ("r-matrixstats" ,r-matrixstats)
5311 ("r-rrcov" ,r-rrcov)))
5312 (home-page "https://bioconductor.org/packages/flowCore")
5313 (synopsis "Basic structures for flow cytometry data")
5315 "This package provides S4 data structures and basic functions to deal
5316 with flow cytometry data.")
5317 (license license:artistic2.0)))
5319 (define-public r-flowmeans
5321 (name "r-flowmeans")
5326 (uri (bioconductor-uri "flowMeans" version))
5329 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
5330 (properties `((upstream-name . "flowMeans")))
5331 (build-system r-build-system)
5333 `(("r-biobase" ,r-biobase)
5334 ("r-feature" ,r-feature)
5335 ("r-flowcore" ,r-flowcore)
5336 ("r-rrcov" ,r-rrcov)))
5337 (home-page "https://bioconductor.org/packages/flowMeans")
5338 (synopsis "Non-parametric flow cytometry data gating")
5340 "This package provides tools to identify cell populations in Flow
5341 Cytometry data using non-parametric clustering and segmented-regression-based
5342 change point detection.")
5343 (license license:artistic2.0)))
5345 (define-public r-ncdfflow
5352 (uri (bioconductor-uri "ncdfFlow" version))
5355 "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i"))))
5356 (properties `((upstream-name . "ncdfFlow")))
5357 (build-system r-build-system)
5362 ("r-biobase" ,r-biobase)
5363 ("r-biocgenerics" ,r-biocgenerics)
5364 ("r-flowcore" ,r-flowcore)
5366 ("r-rcpparmadillo" ,r-rcpparmadillo)
5367 ("r-rhdf5lib" ,r-rhdf5lib)
5368 ("r-zlibbioc" ,r-zlibbioc)))
5369 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5370 (synopsis "HDF5 based storage for flow cytometry data")
5372 "This package provides HDF5 storage based methods and functions for
5373 manipulation of flow cytometry data.")
5374 (license license:artistic2.0)))
5376 (define-public r-ggcyto
5383 (uri (bioconductor-uri "ggcyto" version))
5386 "165qszvy5z176h1l3dnjb5dcm279b6bjl5n5gzz8wfn4xpn8anc8"))))
5387 (properties `((upstream-name . "ggcyto")))
5388 (build-system r-build-system)
5390 `(("r-data-table" ,r-data-table)
5391 ("r-flowcore" ,r-flowcore)
5392 ("r-flowworkspace" ,r-flowworkspace)
5393 ("r-ggplot2" ,r-ggplot2)
5394 ("r-gridextra" ,r-gridextra)
5395 ("r-ncdfflow" ,r-ncdfflow)
5397 ("r-rcolorbrewer" ,r-rcolorbrewer)
5398 ("r-rlang" ,r-rlang)
5399 ("r-scales" ,r-scales)))
5400 (home-page "https://github.com/RGLab/ggcyto/issues")
5401 (synopsis "Visualize Cytometry data with ggplot")
5403 "With the dedicated fortify method implemented for @code{flowSet},
5404 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
5405 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
5406 and some custom layers also make it easy to add gates and population
5407 statistics to the plot.")
5408 (license license:artistic2.0)))
5410 (define-public r-flowviz
5417 (uri (bioconductor-uri "flowViz" version))
5420 "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7"))))
5421 (properties `((upstream-name . "flowViz")))
5422 (build-system r-build-system)
5424 `(("r-biobase" ,r-biobase)
5425 ("r-flowcore" ,r-flowcore)
5426 ("r-hexbin" ,r-hexbin)
5427 ("r-idpmisc" ,r-idpmisc)
5428 ("r-kernsmooth" ,r-kernsmooth)
5429 ("r-lattice" ,r-lattice)
5430 ("r-latticeextra" ,r-latticeextra)
5432 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5433 (home-page "https://bioconductor.org/packages/flowViz/")
5434 (synopsis "Visualization for flow cytometry")
5436 "This package provides visualization tools for flow cytometry data.")
5437 (license license:artistic2.0)))
5439 (define-public r-flowclust
5441 (name "r-flowclust")
5446 (uri (bioconductor-uri "flowClust" version))
5449 "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s"))))
5450 (properties `((upstream-name . "flowClust")))
5451 (build-system r-build-system)
5454 (list "--configure-args=--enable-bundled-gsl=no")))
5456 `(("r-biobase" ,r-biobase)
5457 ("r-biocgenerics" ,r-biocgenerics)
5459 ("r-corpcor" ,r-corpcor)
5460 ("r-ellipse" ,r-ellipse)
5461 ("r-flowcore" ,r-flowcore)
5462 ("r-flowviz" ,r-flowviz)
5463 ("r-graph" ,r-graph)
5464 ("r-mnormt" ,r-mnormt)))
5468 `(("pkg-config" ,pkg-config)))
5469 (home-page "https://bioconductor.org/packages/flowClust")
5470 (synopsis "Clustering for flow cytometry")
5472 "This package provides robust model-based clustering using a t-mixture
5473 model with Box-Cox transformation.")
5474 (license license:artistic2.0)))
5476 ;; TODO: this package bundles an old version of protobuf. It's not easy to
5477 ;; make it use our protobuf package instead.
5478 (define-public r-rprotobuflib
5480 (name "r-rprotobuflib")
5485 (uri (bioconductor-uri "RProtoBufLib" version))
5488 "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm"))))
5489 (properties `((upstream-name . "RProtoBufLib")))
5490 (build-system r-build-system)
5493 (modify-phases %standard-phases
5494 (add-after 'unpack 'unpack-bundled-sources
5496 (with-directory-excursion "src"
5497 (invoke "tar" "xf" "protobuf-2.6.0.tgz"))
5499 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
5500 (synopsis "C++ headers and static libraries of Protocol buffers")
5502 "This package provides the headers and static library of Protocol buffers
5503 for other R packages to compile and link against.")
5504 (license license:bsd-3)))
5506 (define-public r-flowworkspace
5508 (name "r-flowworkspace")
5513 (uri (bioconductor-uri "flowWorkspace" version))
5516 "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762"))))
5517 (properties `((upstream-name . "flowWorkspace")))
5518 (build-system r-build-system)
5521 ("r-biobase" ,r-biobase)
5522 ("r-biocgenerics" ,r-biocgenerics)
5523 ("r-cytolib" ,r-cytolib)
5524 ("r-data-table" ,r-data-table)
5525 ("r-digest" ,r-digest)
5526 ("r-dplyr" ,r-dplyr)
5527 ("r-flowcore" ,r-flowcore)
5528 ("r-flowviz" ,r-flowviz)
5529 ("r-graph" ,r-graph)
5530 ("r-gridextra" ,r-gridextra)
5531 ("r-lattice" ,r-lattice)
5532 ("r-latticeextra" ,r-latticeextra)
5533 ("r-matrixstats" ,r-matrixstats)
5534 ("r-ncdfflow" ,r-ncdfflow)
5536 ("r-rcolorbrewer" ,r-rcolorbrewer)
5538 ("r-rcppparallel" ,r-rcppparallel)
5539 ("r-rgraphviz" ,r-rgraphviz)
5540 ("r-rprotobuflib" ,r-rprotobuflib)
5541 ("r-scales" ,r-scales)
5542 ("r-stringr" ,r-stringr)))
5543 (home-page "https://bioconductor.org/packages/flowWorkspace/")
5544 (synopsis "Infrastructure for working with cytometry data")
5546 "This package is designed to facilitate comparison of automated gating
5547 methods against manual gating done in flowJo. This package allows you to
5548 import basic flowJo workspaces into BioConductor and replicate the gating from
5549 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
5550 samples, compensation, and transformation are performed so that the output
5551 matches the flowJo analysis.")
5552 (license license:artistic2.0)))
5554 (define-public r-flowstats
5556 (name "r-flowstats")
5561 (uri (bioconductor-uri "flowStats" version))
5564 "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w"))))
5565 (properties `((upstream-name . "flowStats")))
5566 (build-system r-build-system)
5568 `(("r-biobase" ,r-biobase)
5569 ("r-biocgenerics" ,r-biocgenerics)
5570 ("r-cluster" ,r-cluster)
5572 ("r-flowcore" ,r-flowcore)
5573 ("r-flowviz" ,r-flowviz)
5574 ("r-flowworkspace" ,r-flowworkspace)
5575 ("r-kernsmooth" ,r-kernsmooth)
5577 ("r-lattice" ,r-lattice)
5579 ("r-ncdfflow" ,r-ncdfflow)
5580 ("r-rcolorbrewer" ,r-rcolorbrewer)
5581 ("r-rrcov" ,r-rrcov)))
5582 (home-page "http://www.github.com/RGLab/flowStats")
5583 (synopsis "Statistical methods for the analysis of flow cytometry data")
5585 "This package provides methods and functionality to analyze flow data
5586 that is beyond the basic infrastructure provided by the @code{flowCore}
5588 (license license:artistic2.0)))
5590 (define-public r-opencyto
5597 (uri (bioconductor-uri "openCyto" version))
5600 "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb"))))
5601 (properties `((upstream-name . "openCyto")))
5602 (build-system r-build-system)
5604 `(("r-biobase" ,r-biobase)
5605 ("r-biocgenerics" ,r-biocgenerics)
5607 ("r-data-table" ,r-data-table)
5608 ("r-flowclust" ,r-flowclust)
5609 ("r-flowcore" ,r-flowcore)
5610 ("r-flowstats" ,r-flowstats)
5611 ("r-flowviz" ,r-flowviz)
5612 ("r-flowworkspace" ,r-flowworkspace)
5613 ("r-graph" ,r-graph)
5614 ("r-gtools" ,r-gtools)
5616 ("r-lattice" ,r-lattice)
5618 ("r-ncdfflow" ,r-ncdfflow)
5620 ("r-r-utils" ,r-r-utils)
5622 ("r-rcolorbrewer" ,r-rcolorbrewer)
5624 ("r-rrcov" ,r-rrcov)))
5625 (home-page "https://bioconductor.org/packages/openCyto")
5626 (synopsis "Hierarchical gating pipeline for flow cytometry data")
5628 "This package is designed to facilitate the automated gating methods in a
5629 sequential way to mimic the manual gating strategy.")
5630 (license license:artistic2.0)))
5632 (define-public r-cytoml
5639 (uri (bioconductor-uri "CytoML" version))
5642 "0m8x18wkvis85cawv7j07pk59w76wnzy93ia99gd24j82z4h97p1"))))
5643 (properties `((upstream-name . "CytoML")))
5644 (build-system r-build-system)
5646 `(("libxml2" ,libxml2)))
5648 `(("r-base64enc" ,r-base64enc)
5650 ("r-biobase" ,r-biobase)
5651 ("r-corpcor" ,r-corpcor)
5652 ("r-cytolib" ,r-cytolib)
5653 ("r-data-table" ,r-data-table)
5654 ("r-dplyr" ,r-dplyr)
5655 ("r-flowcore" ,r-flowcore)
5656 ("r-flowworkspace" ,r-flowworkspace)
5657 ("r-ggcyto" ,r-ggcyto)
5658 ("r-graph" ,r-graph)
5659 ("r-jsonlite" ,r-jsonlite)
5660 ("r-lattice" ,r-lattice)
5661 ("r-ncdfflow" ,r-ncdfflow)
5662 ("r-opencyto" ,r-opencyto)
5666 ("r-rcppparallel" ,r-rcppparallel)
5667 ("r-rgraphviz" ,r-rgraphviz)
5668 ("r-rprotobuflib" ,r-rprotobuflib)
5669 ("r-runit" ,r-runit)
5671 ("r-yaml" ,r-yaml)))
5672 (home-page "https://github.com/RGLab/CytoML")
5673 (synopsis "GatingML interface for cross platform cytometry data sharing")
5675 "This package provides an interface to implementations of the GatingML2.0
5676 standard to exchange gated cytometry data with other software platforms.")
5677 (license license:artistic2.0)))
5679 (define-public r-flowsom
5686 (uri (bioconductor-uri "FlowSOM" version))
5689 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5690 (properties `((upstream-name . "FlowSOM")))
5691 (build-system r-build-system)
5693 `(("r-biocgenerics" ,r-biocgenerics)
5694 ("r-consensusclusterplus" ,r-consensusclusterplus)
5695 ("r-flowcore" ,r-flowcore)
5696 ("r-flowutils" ,r-flowutils)
5697 ("r-igraph" ,r-igraph)
5700 (home-page "https://bioconductor.org/packages/FlowSOM/")
5701 (synopsis "Visualize and interpret cytometry data")
5703 "FlowSOM offers visualization options for cytometry data, by using
5704 self-organizing map clustering and minimal spanning trees.")
5705 (license license:gpl2+)))
5707 (define-public r-mixomics
5714 (uri (bioconductor-uri "mixOmics" version))
5717 "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
5718 (properties `((upstream-name . "mixOmics")))
5719 (build-system r-build-system)
5721 `(("r-corpcor" ,r-corpcor)
5722 ("r-dplyr" ,r-dplyr)
5723 ("r-ellipse" ,r-ellipse)
5724 ("r-ggplot2" ,r-ggplot2)
5725 ("r-gridextra" ,r-gridextra)
5726 ("r-igraph" ,r-igraph)
5727 ("r-lattice" ,r-lattice)
5729 ("r-matrixstats" ,r-matrixstats)
5730 ("r-rarpack" ,r-rarpack)
5731 ("r-rcolorbrewer" ,r-rcolorbrewer)
5732 ("r-reshape2" ,r-reshape2)
5733 ("r-tidyr" ,r-tidyr)))
5734 (home-page "http://www.mixOmics.org")
5735 (synopsis "Multivariate methods for exploration of biological datasets")
5737 "mixOmics offers a wide range of multivariate methods for the exploration
5738 and integration of biological datasets with a particular focus on variable
5739 selection. The package proposes several sparse multivariate models we have
5740 developed to identify the key variables that are highly correlated, and/or
5741 explain the biological outcome of interest. The data that can be analysed
5742 with mixOmics may come from high throughput sequencing technologies, such as
5743 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5744 also beyond the realm of omics (e.g. spectral imaging). The methods
5745 implemented in mixOmics can also handle missing values without having to
5746 delete entire rows with missing data.")
5747 (license license:gpl2+)))
5749 (define-public r-depecher
5756 (uri (bioconductor-uri "DepecheR" version))
5759 "1f6zbc0fq7xjflh3mkjx1n83mpppw663dj22rlpxzwp1kpmf6wm5"))))
5760 (properties `((upstream-name . "DepecheR")))
5761 (build-system r-build-system)
5763 `(("r-beanplot" ,r-beanplot)
5764 ("r-dosnow" ,r-dosnow)
5765 ("r-dplyr" ,r-dplyr)
5767 ("r-foreach" ,r-foreach)
5768 ("r-ggplot2" ,r-ggplot2)
5769 ("r-gplots" ,r-gplots)
5771 ("r-matrixstats" ,r-matrixstats)
5772 ("r-mixomics" ,r-mixomics)
5773 ("r-moments" ,r-moments)
5775 ("r-rcppeigen" ,r-rcppeigen)
5776 ("r-reshape2" ,r-reshape2)
5777 ("r-robustbase" ,r-robustbase)
5778 ("r-viridis" ,r-viridis)))
5779 (home-page "https://bioconductor.org/packages/DepecheR/")
5780 (synopsis "Identify traits of clusters in high-dimensional entities")
5782 "The purpose of this package is to identify traits in a dataset that can
5783 separate groups. This is done on two levels. First, clustering is performed,
5784 using an implementation of sparse K-means. Secondly, the generated clusters
5785 are used to predict outcomes of groups of individuals based on their
5786 distribution of observations in the different clusters. As certain clusters
5787 with separating information will be identified, and these clusters are defined
5788 by a sparse number of variables, this method can reduce the complexity of
5789 data, to only emphasize the data that actually matters.")
5790 (license license:expat)))
5792 (define-public r-rcistarget
5794 (name "r-rcistarget")
5799 (uri (bioconductor-uri "RcisTarget" version))
5802 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5803 (properties `((upstream-name . "RcisTarget")))
5804 (build-system r-build-system)
5806 `(("r-aucell" ,r-aucell)
5807 ("r-biocgenerics" ,r-biocgenerics)
5808 ("r-data-table" ,r-data-table)
5809 ("r-feather" ,r-feather)
5810 ("r-gseabase" ,r-gseabase)
5811 ("r-r-utils" ,r-r-utils)
5812 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5813 (home-page "https://aertslab.org/#scenic")
5814 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5816 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5817 over-represented on a gene list. In a first step, RcisTarget selects DNA
5818 motifs that are significantly over-represented in the surroundings of the
5819 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5820 achieved by using a database that contains genome-wide cross-species rankings
5821 for each motif. The motifs that are then annotated to TFs and those that have
5822 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5823 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5824 genes in the gene-set that are ranked above the leading edge).")
5825 (license license:gpl3)))
5827 (define-public r-cicero
5834 (uri (bioconductor-uri "cicero" version))
5837 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5838 (build-system r-build-system)
5840 `(("r-assertthat" ,r-assertthat)
5841 ("r-biobase" ,r-biobase)
5842 ("r-biocgenerics" ,r-biocgenerics)
5843 ("r-data-table" ,r-data-table)
5844 ("r-dplyr" ,r-dplyr)
5846 ("r-genomicranges" ,r-genomicranges)
5847 ("r-ggplot2" ,r-ggplot2)
5848 ("r-glasso" ,r-glasso)
5850 ("r-igraph" ,r-igraph)
5851 ("r-iranges" ,r-iranges)
5852 ("r-matrix" ,r-matrix)
5853 ("r-monocle" ,r-monocle)
5855 ("r-reshape2" ,r-reshape2)
5856 ("r-s4vectors" ,r-s4vectors)
5857 ("r-stringr" ,r-stringr)
5858 ("r-tibble" ,r-tibble)
5859 ("r-vgam" ,r-vgam)))
5860 (home-page "https://bioconductor.org/packages/cicero/")
5861 (synopsis "Predict cis-co-accessibility from single-cell data")
5863 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5864 accessibility data. It also extends the monocle package for use in chromatin
5865 accessibility data.")
5866 (license license:expat)))
5868 ;; This is the latest commit on the "monocle3" branch.
5869 (define-public r-cicero-monocle3
5870 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5872 (package (inherit r-cicero)
5873 (name "r-cicero-monocle3")
5874 (version (git-version "1.3.2" revision commit))
5879 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5881 (file-name (git-file-name name version))
5884 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5886 `(("r-monocle3" ,r-monocle3)
5887 ,@(alist-delete "r-monocle"
5888 (package-propagated-inputs r-cicero)))))))
5890 (define-public r-cistopic
5891 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5895 (version (git-version "0.2.1" revision commit))
5900 (url "https://github.com/aertslab/cisTopic.git")
5902 (file-name (git-file-name name version))
5905 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5906 (build-system r-build-system)
5908 `(("r-aucell" ,r-aucell)
5909 ("r-data-table" ,r-data-table)
5910 ("r-dplyr" ,r-dplyr)
5911 ("r-dosnow" ,r-dosnow)
5913 ("r-feather" ,r-feather)
5914 ("r-fitdistrplus" ,r-fitdistrplus)
5915 ("r-genomicranges" ,r-genomicranges)
5916 ("r-ggplot2" ,r-ggplot2)
5918 ("r-matrix" ,r-matrix)
5920 ("r-rcistarget" ,r-rcistarget)
5921 ("r-rtracklayer" ,r-rtracklayer)
5922 ("r-s4vectors" ,r-s4vectors)))
5923 (home-page "https://github.com/aertslab/cisTopic")
5924 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5926 "The sparse nature of single cell epigenomics data can be overruled using
5927 probabilistic modelling methods such as @dfn{Latent Dirichlet
5928 Allocation} (LDA). This package allows the probabilistic modelling of
5929 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5930 includes functionalities to identify cell states based on the contribution of
5931 cisTopics and explore the nature and regulatory proteins driving them.")
5932 (license license:gpl3))))
5934 (define-public r-genie3
5941 (uri (bioconductor-uri "GENIE3" version))
5944 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5945 (properties `((upstream-name . "GENIE3")))
5946 (build-system r-build-system)
5947 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5948 (home-page "https://bioconductor.org/packages/GENIE3")
5949 (synopsis "Gene network inference with ensemble of trees")
5951 "This package implements the GENIE3 algorithm for inferring gene
5952 regulatory networks from expression data.")
5953 (license license:gpl2+)))
5955 (define-public r-roc
5962 (uri (bioconductor-uri "ROC" version))
5965 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5966 (properties `((upstream-name . "ROC")))
5967 (build-system r-build-system)
5968 (home-page "https://www.bioconductor.org/packages/ROC/")
5969 (synopsis "Utilities for ROC curves")
5971 "This package provides utilities for @dfn{Receiver Operating
5972 Characteristic} (ROC) curves, with a focus on micro arrays.")
5973 (license license:artistic2.0)))
5975 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5977 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5982 (uri (bioconductor-uri
5983 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5984 version 'annotation))
5987 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5990 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5991 (build-system r-build-system)
5992 (propagated-inputs `(("r-minfi" ,r-minfi)))
5994 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5995 (synopsis "Annotation for Illumina's 450k methylation arrays")
5997 "This package provides manifests and annotation for Illumina's 450k array
5999 (license license:artistic2.0)))
6001 (define-public r-watermelon
6003 (name "r-watermelon")
6008 (uri (bioconductor-uri "wateRmelon" version))
6011 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
6012 (properties `((upstream-name . "wateRmelon")))
6013 (build-system r-build-system)
6015 `(("r-biobase" ,r-biobase)
6016 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6017 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6018 ("r-illuminaio" ,r-illuminaio)
6019 ("r-limma" ,r-limma)
6021 ("r-matrixstats" ,r-matrixstats)
6022 ("r-methylumi" ,r-methylumi)
6024 (home-page "https://bioconductor.org/packages/wateRmelon/")
6025 (synopsis "Illumina 450 methylation array normalization and metrics")
6027 "The standard index of DNA methylation (beta) is computed from methylated
6028 and unmethylated signal intensities. Betas calculated from raw signal
6029 intensities perform well, but using 11 methylomic datasets we demonstrate that
6030 quantile normalization methods produce marked improvement. The commonly used
6031 procedure of normalizing betas is inferior to the separate normalization of M
6032 and U, and it is also advantageous to normalize Type I and Type II assays
6033 separately. This package provides 15 flavours of betas and three performance
6034 metrics, with methods for objects produced by the @code{methylumi} and
6035 @code{minfi} packages.")
6036 (license license:gpl3)))
6038 (define-public r-gdsfmt
6045 (uri (bioconductor-uri "gdsfmt" version))
6048 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
6049 (modules '((guix build utils)))
6050 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6051 ;; them and link with system libraries instead.
6054 (for-each delete-file-recursively
6058 (substitute* "src/Makevars"
6059 (("all: \\$\\(SHLIB\\)") "all:")
6060 (("\\$\\(SHLIB\\): liblzma.a") "")
6061 (("(ZLIB|LZ4)/.*") "")
6062 (("CoreArray/dVLIntGDS.cpp.*")
6063 "CoreArray/dVLIntGDS.cpp")
6064 (("CoreArray/dVLIntGDS.o.*")
6065 "CoreArray/dVLIntGDS.o")
6066 (("PKG_LIBS = ./liblzma.a")
6067 "PKG_LIBS = -llz4"))
6068 (substitute* "src/CoreArray/dStream.h"
6069 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6070 (string-append "include <" header ">")))
6072 (properties `((upstream-name . "gdsfmt")))
6073 (build-system r-build-system)
6078 (home-page "http://corearray.sourceforge.net/")
6080 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6082 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6083 Data Structure} (GDS) data files, which are portable across platforms with
6084 hierarchical structure to store multiple scalable array-oriented data sets
6085 with metadata information. It is suited for large-scale datasets, especially
6086 for data which are much larger than the available random-access memory. The
6087 @code{gdsfmt} package offers efficient operations specifically designed for
6088 integers of less than 8 bits, since a diploid genotype, like
6089 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6090 byte. Data compression and decompression are available with relatively
6091 efficient random access. It is also allowed to read a GDS file in parallel
6092 with multiple R processes supported by the package @code{parallel}.")
6093 (license license:lgpl3)))
6095 (define-public r-bigmelon
6102 (uri (bioconductor-uri "bigmelon" version))
6105 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
6106 (properties `((upstream-name . "bigmelon")))
6107 (build-system r-build-system)
6109 `(("r-biobase" ,r-biobase)
6110 ("r-biocgenerics" ,r-biocgenerics)
6111 ("r-gdsfmt" ,r-gdsfmt)
6112 ("r-geoquery" ,r-geoquery)
6113 ("r-methylumi" ,r-methylumi)
6114 ("r-minfi" ,r-minfi)
6115 ("r-watermelon" ,r-watermelon)))
6116 (home-page "https://bioconductor.org/packages/bigmelon/")
6117 (synopsis "Illumina methylation array analysis for large experiments")
6119 "This package provides methods for working with Illumina arrays using the
6120 @code{gdsfmt} package.")
6121 (license license:gpl3)))
6123 (define-public r-seqbias
6130 (uri (bioconductor-uri "seqbias" version))
6133 "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
6134 (properties `((upstream-name . "seqbias")))
6135 (build-system r-build-system)
6137 `(("r-biostrings" ,r-biostrings)
6138 ("r-genomicranges" ,r-genomicranges)
6139 ("r-rhtslib" ,r-rhtslib)))
6141 `(("zlib" ,zlib))) ; This comes from rhtslib.
6142 (home-page "https://bioconductor.org/packages/seqbias/")
6143 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6145 "This package implements a model of per-position sequencing bias in
6146 high-throughput sequencing data using a simple Bayesian network, the structure
6147 and parameters of which are trained on a set of aligned reads and a reference
6149 (license license:lgpl3)))
6151 (define-public r-reqon
6158 (uri (bioconductor-uri "ReQON" version))
6161 "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
6162 (properties `((upstream-name . "ReQON")))
6163 (build-system r-build-system)
6165 `(("r-rjava" ,r-rjava)
6166 ("r-rsamtools" ,r-rsamtools)
6167 ("r-seqbias" ,r-seqbias)))
6168 (home-page "https://bioconductor.org/packages/ReQON/")
6169 (synopsis "Recalibrating quality of nucleotides")
6171 "This package provides an implementation of an algorithm for
6172 recalibrating the base quality scores for aligned sequencing data in BAM
6174 (license license:gpl2)))
6176 (define-public r-wavcluster
6178 (name "r-wavcluster")
6183 (uri (bioconductor-uri "wavClusteR" version))
6186 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
6187 (properties `((upstream-name . "wavClusteR")))
6188 (build-system r-build-system)
6190 `(("r-biocgenerics" ,r-biocgenerics)
6191 ("r-biostrings" ,r-biostrings)
6192 ("r-foreach" ,r-foreach)
6193 ("r-genomicfeatures" ,r-genomicfeatures)
6194 ("r-genomicranges" ,r-genomicranges)
6195 ("r-ggplot2" ,r-ggplot2)
6196 ("r-hmisc" ,r-hmisc)
6197 ("r-iranges" ,r-iranges)
6198 ("r-mclust" ,r-mclust)
6199 ("r-rsamtools" ,r-rsamtools)
6200 ("r-rtracklayer" ,r-rtracklayer)
6201 ("r-s4vectors" ,r-s4vectors)
6202 ("r-seqinr" ,r-seqinr)
6203 ("r-stringr" ,r-stringr)
6204 ("r-wmtsa" ,r-wmtsa)))
6205 (home-page "https://bioconductor.org/packages/wavClusteR/")
6206 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6208 "This package provides an integrated pipeline for the analysis of
6209 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6210 sequencing errors, SNPs and additional non-experimental sources by a non-
6211 parametric mixture model. The protein binding sites (clusters) are then
6212 resolved at high resolution and cluster statistics are estimated using a
6213 rigorous Bayesian framework. Post-processing of the results, data export for
6214 UCSC genome browser visualization and motif search analysis are provided. In
6215 addition, the package allows to integrate RNA-Seq data to estimate the False
6216 Discovery Rate of cluster detection. Key functions support parallel multicore
6217 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6218 be applied to the analysis of other NGS data obtained from experimental
6219 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6220 (license license:gpl2)))
6222 (define-public r-timeseriesexperiment
6224 (name "r-timeseriesexperiment")
6229 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6232 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
6234 `((upstream-name . "TimeSeriesExperiment")))
6235 (build-system r-build-system)
6237 `(("r-deseq2" ,r-deseq2)
6238 ("r-dplyr" ,r-dplyr)
6239 ("r-dynamictreecut" ,r-dynamictreecut)
6240 ("r-edger" ,r-edger)
6241 ("r-ggplot2" ,r-ggplot2)
6242 ("r-hmisc" ,r-hmisc)
6243 ("r-limma" ,r-limma)
6244 ("r-magrittr" ,r-magrittr)
6245 ("r-proxy" ,r-proxy)
6246 ("r-s4vectors" ,r-s4vectors)
6247 ("r-summarizedexperiment" ,r-summarizedexperiment)
6248 ("r-tibble" ,r-tibble)
6249 ("r-tidyr" ,r-tidyr)
6250 ("r-vegan" ,r-vegan)
6251 ("r-viridis" ,r-viridis)))
6252 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6253 (synopsis "Analysis for short time-series data")
6255 "This package is a visualization and analysis toolbox for short time
6256 course data which includes dimensionality reduction, clustering, two-sample
6257 differential expression testing and gene ranking techniques. The package also
6258 provides methods for retrieving enriched pathways.")
6259 (license license:lgpl3+)))
6261 (define-public r-variantfiltering
6263 (name "r-variantfiltering")
6268 (uri (bioconductor-uri "VariantFiltering" version))
6271 "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
6273 `((upstream-name . "VariantFiltering")))
6274 (build-system r-build-system)
6276 `(("r-annotationdbi" ,r-annotationdbi)
6277 ("r-biobase" ,r-biobase)
6278 ("r-biocgenerics" ,r-biocgenerics)
6279 ("r-biocparallel" ,r-biocparallel)
6280 ("r-biostrings" ,r-biostrings)
6281 ("r-bsgenome" ,r-bsgenome)
6283 ("r-genomeinfodb" ,r-genomeinfodb)
6284 ("r-genomicfeatures" ,r-genomicfeatures)
6285 ("r-genomicranges" ,r-genomicranges)
6286 ("r-genomicscores" ,r-genomicscores)
6287 ("r-graph" ,r-graph)
6289 ("r-iranges" ,r-iranges)
6291 ("r-rsamtools" ,r-rsamtools)
6292 ("r-s4vectors" ,r-s4vectors)
6293 ("r-shiny" ,r-shiny)
6294 ("r-shinyjs" ,r-shinyjs)
6295 ("r-shinythemes" ,r-shinythemes)
6296 ("r-shinytree" ,r-shinytree)
6297 ("r-summarizedexperiment" ,r-summarizedexperiment)
6298 ("r-variantannotation" ,r-variantannotation)
6299 ("r-xvector" ,r-xvector)))
6300 (home-page "https://github.com/rcastelo/VariantFiltering")
6301 (synopsis "Filtering of coding and non-coding genetic variants")
6303 "Filter genetic variants using different criteria such as inheritance
6304 model, amino acid change consequence, minor allele frequencies across human
6305 populations, splice site strength, conservation, etc.")
6306 (license license:artistic2.0)))
6308 (define-public r-genomegraphs
6310 (name "r-genomegraphs")
6315 (uri (bioconductor-uri "GenomeGraphs" version))
6318 "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd"))))
6319 (properties `((upstream-name . "GenomeGraphs")))
6320 (build-system r-build-system)
6322 `(("r-biomart" ,r-biomart)))
6323 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
6324 (synopsis "Plotting genomic information from Ensembl")
6326 "Genomic data analyses requires integrated visualization of known genomic
6327 information and new experimental data. GenomeGraphs uses the biomaRt package
6328 to perform live annotation queries to Ensembl and translates this to e.g.
6329 gene/transcript structures in viewports of the grid graphics package. This
6330 results in genomic information plotted together with your data. Another
6331 strength of GenomeGraphs is to plot different data types such as array CGH,
6332 gene expression, sequencing and other data, together in one plot using the
6333 same genome coordinate system.")
6334 (license license:artistic2.0)))
6336 (define-public r-wavetiling
6338 (name "r-wavetiling")
6343 (uri (bioconductor-uri "waveTiling" version))
6346 "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir"))))
6347 (properties `((upstream-name . "waveTiling")))
6348 (build-system r-build-system)
6350 `(("r-affy" ,r-affy)
6351 ("r-biobase" ,r-biobase)
6352 ("r-biostrings" ,r-biostrings)
6353 ("r-genomegraphs" ,r-genomegraphs)
6354 ("r-genomicranges" ,r-genomicranges)
6355 ("r-iranges" ,r-iranges)
6356 ("r-oligo" ,r-oligo)
6357 ("r-oligoclasses" ,r-oligoclasses)
6358 ("r-preprocesscore" ,r-preprocesscore)
6359 ("r-waveslim" ,r-waveslim)))
6360 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
6361 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
6363 "This package is designed to conduct transcriptome analysis for tiling
6364 arrays based on fast wavelet-based functional models.")
6365 (license license:gpl2+)))
6367 (define-public r-variancepartition
6369 (name "r-variancepartition")
6374 (uri (bioconductor-uri "variancePartition" version))
6377 "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
6379 `((upstream-name . "variancePartition")))
6380 (build-system r-build-system)
6382 `(("r-biobase" ,r-biobase)
6383 ("r-biocparallel" ,r-biocparallel)
6384 ("r-colorramps" ,r-colorramps)
6385 ("r-doparallel" ,r-doparallel)
6386 ("r-foreach" ,r-foreach)
6387 ("r-ggplot2" ,r-ggplot2)
6388 ("r-gplots" ,r-gplots)
6389 ("r-iterators" ,r-iterators)
6390 ("r-limma" ,r-limma)
6392 ("r-lmertest" ,r-lmertest)
6394 ("r-pbkrtest" ,r-pbkrtest)
6395 ("r-progress" ,r-progress)
6396 ("r-reshape2" ,r-reshape2)
6397 ("r-scales" ,r-scales)))
6398 (home-page "https://bioconductor.org/packages/variancePartition/")
6399 (synopsis "Analyze variation in gene expression experiments")
6401 "This is a package providing tools to quantify and interpret multiple
6402 sources of biological and technical variation in gene expression experiments.
6403 It uses a linear mixed model to quantify variation in gene expression
6404 attributable to individual, tissue, time point, or technical variables. The
6405 package includes dream differential expression analysis for repeated
6407 (license license:gpl2+)))
6409 (define-public r-htqpcr
6416 (uri (bioconductor-uri "HTqPCR" version))
6419 "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
6420 (properties `((upstream-name . "HTqPCR")))
6421 (build-system r-build-system)
6423 `(("r-affy" ,r-affy)
6424 ("r-biobase" ,r-biobase)
6425 ("r-gplots" ,r-gplots)
6426 ("r-limma" ,r-limma)
6427 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6428 (home-page "http://www.ebi.ac.uk/bertone/software")
6429 (synopsis "Automated analysis of high-throughput qPCR data")
6431 "Analysis of Ct values from high throughput quantitative real-time
6432 PCR (qPCR) assays across multiple conditions or replicates. The input data
6433 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
6434 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
6435 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
6436 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
6437 loading, quality assessment, normalization, visualization and parametric or
6438 non-parametric testing for statistical significance in Ct values between
6439 features (e.g. genes, microRNAs).")
6440 (license license:artistic2.0)))
6442 (define-public r-unifiedwmwqpcr
6444 (name "r-unifiedwmwqpcr")
6449 (uri (bioconductor-uri "unifiedWMWqPCR" version))
6452 "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
6454 `((upstream-name . "unifiedWMWqPCR")))
6455 (build-system r-build-system)
6457 `(("r-biocgenerics" ,r-biocgenerics)
6458 ("r-htqpcr" ,r-htqpcr)))
6459 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6460 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6462 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6463 data. This modified test allows for testing differential expression in qPCR
6465 (license license:gpl2+)))
6467 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6469 (define-public r-activedriverwgs
6471 (name "r-activedriverwgs")
6476 (uri (cran-uri "ActiveDriverWGS" version))
6479 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
6481 `((upstream-name . "ActiveDriverWGS")))
6482 (build-system r-build-system)
6484 `(("r-biostrings" ,r-biostrings)
6485 ("r-bsgenome" ,r-bsgenome)
6486 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
6487 ("r-genomeinfodb" ,r-genomeinfodb)
6488 ("r-genomicranges" ,r-genomicranges)
6489 ("r-iranges" ,r-iranges)
6491 ("r-s4vectors" ,r-s4vectors)))
6492 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
6493 (synopsis "Driver discovery tool for cancer whole genomes")
6495 "This package provides a method for finding an enrichment of cancer
6496 simple somatic mutations (SNVs and Indels) in functional elements across the
6497 human genome. ActiveDriverWGS detects coding and noncoding driver elements
6498 using whole genome sequencing data.")
6499 (license license:gpl3)))
6501 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
6503 (define-public r-activepathways
6505 (name "r-activepathways")
6510 (uri (cran-uri "ActivePathways" version))
6513 "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20"))))
6515 `((upstream-name . "ActivePathways")))
6516 (build-system r-build-system)
6518 `(("r-data-table" ,r-data-table)
6519 ("r-ggplot2" ,r-ggplot2)
6520 ("r-metap" ,r-metap)))
6521 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
6522 (synopsis "Multivariate pathway enrichment analysis")
6524 "This package represents an integrative method of analyzing multi omics
6525 data that conducts enrichment analysis of annotated gene sets. ActivePathways
6526 uses a statistical data fusion approach, rationalizes contributing evidence
6527 and highlights associated genes, improving systems-level understanding of
6528 cellular organization in health and disease.")
6529 (license license:gpl3)))