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 (srfi srfi-1))
48 (define-public r-bsgenome-celegans-ucsc-ce6
50 (name "r-bsgenome-celegans-ucsc-ce6")
54 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
58 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
60 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
61 (build-system r-build-system)
63 `(("r-bsgenome" ,r-bsgenome)))
65 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
66 (synopsis "Full genome sequences for Worm")
68 "This package provides full genome sequences for Caenorhabditis
69 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
71 (license license:artistic2.0)))
73 (define-public r-bsgenome-celegans-ucsc-ce10
75 (name "r-bsgenome-celegans-ucsc-ce10")
79 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
83 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
85 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
86 (build-system r-build-system)
88 `(("r-bsgenome" ,r-bsgenome)))
90 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
91 (synopsis "Full genome sequences for Worm")
93 "This package provides full genome sequences for Caenorhabditis
94 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
96 (license license:artistic2.0)))
98 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
100 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
104 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
105 version 'annotation))
108 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
110 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
111 (build-system r-build-system)
113 `(("r-bsgenome" ,r-bsgenome)))
115 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
116 (synopsis "Full genome sequences for Fly")
118 "This package provides full genome sequences for Drosophila
119 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
121 (license license:artistic2.0)))
123 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
125 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
129 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
130 version 'annotation))
133 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
135 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
136 (build-system r-build-system)
138 `(("r-bsgenome" ,r-bsgenome)))
140 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
141 (synopsis "Full genome sequences for Fly")
143 "This package provides full genome sequences for Drosophila
144 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
145 Biostrings objects.")
146 (license license:artistic2.0)))
148 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
150 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
154 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
155 version 'annotation))
158 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
160 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
161 (build-system r-build-system)
163 `(("r-bsgenome" ,r-bsgenome)
164 ("r-bsgenome-dmelanogaster-ucsc-dm3"
165 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
166 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
167 (synopsis "Full masked genome sequences for Fly")
169 "This package provides full masked genome sequences for Drosophila
170 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
171 Biostrings objects. The sequences are the same as in
172 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
173 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
174 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
175 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
176 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
177 (license license:artistic2.0)))
179 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
181 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
185 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
186 version 'annotation))
189 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
191 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
192 (build-system r-build-system)
194 `(("r-bsgenome" ,r-bsgenome)))
196 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
197 (synopsis "Full genome sequences for Homo sapiens")
199 "This package provides full genome sequences for Homo sapiens from
200 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
201 (license license:artistic2.0)))
203 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
205 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
209 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
210 version 'annotation))
213 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
215 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
216 (build-system r-build-system)
218 `(("r-bsgenome" ,r-bsgenome)
219 ("r-bsgenome-hsapiens-ucsc-hg19"
220 ,r-bsgenome-hsapiens-ucsc-hg19)))
221 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
222 (synopsis "Full masked genome sequences for Homo sapiens")
224 "This package provides full genome sequences for Homo sapiens (Human) as
225 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
226 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
227 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
228 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
229 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
230 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
232 (license license:artistic2.0)))
234 (define-public r-bsgenome-mmusculus-ucsc-mm9
236 (name "r-bsgenome-mmusculus-ucsc-mm9")
240 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
241 version 'annotation))
244 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
246 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
247 (build-system r-build-system)
249 `(("r-bsgenome" ,r-bsgenome)))
251 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
252 (synopsis "Full genome sequences for Mouse")
254 "This package provides full genome sequences for Mus musculus (Mouse) as
255 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
256 (license license:artistic2.0)))
258 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
260 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
264 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
265 version 'annotation))
268 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
270 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
271 (build-system r-build-system)
273 `(("r-bsgenome" ,r-bsgenome)
274 ("r-bsgenome-mmusculus-ucsc-mm9"
275 ,r-bsgenome-mmusculus-ucsc-mm9)))
276 (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
277 (synopsis "Full masked genome sequences for Mouse")
279 "This package provides full genome sequences for Mus musculus (Mouse) as
280 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
281 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
282 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
283 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
284 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
285 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
287 (license license:artistic2.0)))
289 (define-public r-bsgenome-mmusculus-ucsc-mm10
291 (name "r-bsgenome-mmusculus-ucsc-mm10")
295 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
296 version 'annotation))
299 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
301 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
302 (build-system r-build-system)
304 `(("r-bsgenome" ,r-bsgenome)))
306 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
307 (synopsis "Full genome sequences for Mouse")
309 "This package provides full genome sequences for Mus
310 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
311 in Biostrings objects.")
312 (license license:artistic2.0)))
314 (define-public r-org-ce-eg-db
316 (name "r-org-ce-eg-db")
320 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
323 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
325 `((upstream-name . "org.Ce.eg.db")))
326 (build-system r-build-system)
328 `(("r-annotationdbi" ,r-annotationdbi)))
329 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
330 (synopsis "Genome wide annotation for Worm")
332 "This package provides mappings from Entrez gene identifiers to various
333 annotations for the genome of the model worm Caenorhabditis elegans.")
334 (license license:artistic2.0)))
336 (define-public r-org-dm-eg-db
338 (name "r-org-dm-eg-db")
342 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
345 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
347 `((upstream-name . "org.Dm.eg.db")))
348 (build-system r-build-system)
350 `(("r-annotationdbi" ,r-annotationdbi)))
351 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
352 (synopsis "Genome wide annotation for Fly")
354 "This package provides mappings from Entrez gene identifiers to various
355 annotations for the genome of the model fruit fly Drosophila melanogaster.")
356 (license license:artistic2.0)))
358 (define-public r-org-dr-eg-db
360 (name "r-org-dr-eg-db")
364 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
367 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
369 `((upstream-name . "org.Dr.eg.db")))
370 (build-system r-build-system)
372 `(("r-annotationdbi" ,r-annotationdbi)))
373 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
374 (synopsis "Annotation for Zebrafish")
376 "This package provides genome wide annotations for Zebrafish, primarily
377 based on mapping using Entrez Gene identifiers.")
378 (license license:artistic2.0)))
380 (define-public r-org-hs-eg-db
382 (name "r-org-hs-eg-db")
386 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
389 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
391 `((upstream-name . "org.Hs.eg.db")))
392 (build-system r-build-system)
394 `(("r-annotationdbi" ,r-annotationdbi)))
395 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
396 (synopsis "Genome wide annotation for Human")
398 "This package contains genome-wide annotations for Human, primarily based
399 on mapping using Entrez Gene identifiers.")
400 (license license:artistic2.0)))
402 (define-public r-org-mm-eg-db
404 (name "r-org-mm-eg-db")
408 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
411 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
413 `((upstream-name . "org.Mm.eg.db")))
414 (build-system r-build-system)
416 `(("r-annotationdbi" ,r-annotationdbi)))
417 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
418 (synopsis "Genome wide annotation for Mouse")
420 "This package provides mappings from Entrez gene identifiers to various
421 annotations for the genome of the model mouse Mus musculus.")
422 (license license:artistic2.0)))
424 (define-public r-bsgenome-hsapiens-ucsc-hg19
426 (name "r-bsgenome-hsapiens-ucsc-hg19")
430 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
431 version 'annotation))
434 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
436 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
437 (build-system r-build-system)
439 `(("r-bsgenome" ,r-bsgenome)))
441 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
442 (synopsis "Full genome sequences for Homo sapiens")
444 "This package provides full genome sequences for Homo sapiens as provided
445 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
446 (license license:artistic2.0)))
448 (define-public r-ensdb-hsapiens-v75
450 (name "r-ensdb-hsapiens-v75")
455 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
458 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
460 `((upstream-name . "EnsDb.Hsapiens.v75")))
461 (build-system r-build-system)
463 `(("r-ensembldb" ,r-ensembldb)))
464 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
465 (synopsis "Ensembl based annotation package")
467 "This package exposes an annotation database generated from Ensembl.")
468 (license license:artistic2.0)))
470 (define-public r-genelendatabase
472 (name "r-genelendatabase")
477 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
480 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
482 `((upstream-name . "geneLenDataBase")))
483 (build-system r-build-system)
485 `(("r-rtracklayer" ,r-rtracklayer)
486 ("r-genomicfeatures" ,r-genomicfeatures)))
487 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
488 (synopsis "Lengths of mRNA transcripts for a number of genomes")
490 "This package provides the lengths of mRNA transcripts for a number of
491 genomes and gene ID formats, largely based on the UCSC table browser.")
492 (license license:lgpl2.0+)))
494 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
496 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
500 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
501 version 'annotation))
504 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
506 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
507 (build-system r-build-system)
509 `(("r-genomicfeatures" ,r-genomicfeatures)))
511 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
512 (synopsis "Annotation package for human genome in TxDb format")
514 "This package provides an annotation database of Homo sapiens genome
515 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
516 track. The database is exposed as a @code{TxDb} object.")
517 (license license:artistic2.0)))
519 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
521 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
525 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
526 version 'annotation))
529 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
531 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
532 (build-system r-build-system)
534 `(("r-genomicfeatures" ,r-genomicfeatures)))
536 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
537 (synopsis "Annotation package for human genome in TxDb format")
539 "This package provides an annotation database of Homo sapiens genome
540 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
541 track. The database is exposed as a @code{TxDb} object.")
542 (license license:artistic2.0)))
544 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
546 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
550 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
551 version 'annotation))
554 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
556 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
557 (build-system r-build-system)
559 `(("r-genomicfeatures" ,r-genomicfeatures)
560 ("r-annotationdbi" ,r-annotationdbi)))
562 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
563 (synopsis "Annotation package for mouse genome in TxDb format")
565 "This package provides an annotation database of Mouse genome data. It
566 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
567 database is exposed as a @code{TxDb} object.")
568 (license license:artistic2.0)))
570 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
572 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
576 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
577 version 'annotation))
580 "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b"))))
582 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
583 (build-system r-build-system)
585 `(("r-bsgenome" ,r-bsgenome)
586 ("r-genomicfeatures" ,r-genomicfeatures)
587 ("r-annotationdbi" ,r-annotationdbi)))
589 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
590 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
592 "This package loads a TxDb object, which is an R interface to
593 prefabricated databases contained in this package. This package provides
594 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
595 based on the knownGene track.")
596 (license license:artistic2.0)))
598 (define-public r-txdb-celegans-ucsc-ce6-ensgene
600 (name "r-txdb-celegans-ucsc-ce6-ensgene")
605 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
606 version 'annotation))
609 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
611 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
612 (build-system r-build-system)
614 `(("r-annotationdbi" ,r-annotationdbi)
615 ("r-genomicfeatures" ,r-genomicfeatures)))
616 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
617 (synopsis "Annotation package for C elegans TxDb objects")
619 "This package exposes a C elegans annotation database generated from UCSC
620 by exposing these as TxDb objects.")
621 (license license:artistic2.0)))
623 (define-public r-fdb-infiniummethylation-hg19
625 (name "r-fdb-infiniummethylation-hg19")
629 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
630 version 'annotation))
633 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
635 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
636 (build-system r-build-system)
638 `(("r-biostrings" ,r-biostrings)
639 ("r-genomicfeatures" ,r-genomicfeatures)
640 ("r-annotationdbi" ,r-annotationdbi)
641 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
642 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
643 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
644 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
646 "This is an annotation package for Illumina Infinium DNA methylation
647 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
649 (license license:artistic2.0)))
651 (define-public r-illuminahumanmethylationepicmanifest
653 (name "r-illuminahumanmethylationepicmanifest")
657 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
658 version 'annotation))
661 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
663 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
664 (build-system r-build-system)
666 `(("r-minfi" ,r-minfi)))
667 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
668 (synopsis "Manifest for Illumina's EPIC methylation arrays")
670 "This is a manifest package for Illumina's EPIC methylation arrays.")
671 (license license:artistic2.0)))
673 (define-public r-do-db
679 (uri (bioconductor-uri "DO.db" version 'annotation))
682 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
684 `((upstream-name . "DO.db")))
685 (build-system r-build-system)
687 `(("r-annotationdbi" ,r-annotationdbi)))
688 (home-page "https://www.bioconductor.org/packages/DO.db/")
689 (synopsis "Annotation maps describing the entire Disease Ontology")
691 "This package provides a set of annotation maps describing the entire
693 (license license:artistic2.0)))
695 (define-public r-pfam-db
702 (uri (bioconductor-uri "PFAM.db" version 'annotation))
705 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
706 (properties `((upstream-name . "PFAM.db")))
707 (build-system r-build-system)
709 `(("r-annotationdbi" ,r-annotationdbi)))
710 (home-page "https://bioconductor.org/packages/PFAM.db")
711 (synopsis "Set of protein ID mappings for PFAM")
713 "This package provides a set of protein ID mappings for PFAM, assembled
714 using data from public repositories.")
715 (license license:artistic2.0)))
717 (define-public r-phastcons100way-ucsc-hg19
719 (name "r-phastcons100way-ucsc-hg19")
724 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
725 version 'annotation))
728 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
730 `((upstream-name . "phastCons100way.UCSC.hg19")))
731 (build-system r-build-system)
733 `(("r-bsgenome" ,r-bsgenome)
734 ("r-genomeinfodb" ,r-genomeinfodb)
735 ("r-genomicranges" ,r-genomicranges)
736 ("r-genomicscores" ,r-genomicscores)
737 ("r-iranges" ,r-iranges)
738 ("r-s4vectors" ,r-s4vectors)))
739 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
740 (synopsis "UCSC phastCons conservation scores for hg19")
742 "This package provides UCSC phastCons conservation scores for the human
743 genome (hg19) calculated from multiple alignments with other 99 vertebrate
745 (license license:artistic2.0)))
750 (define-public r-abadata
756 (uri (bioconductor-uri "ABAData" version 'experiment))
759 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
761 `((upstream-name . "ABAData")))
762 (build-system r-build-system)
764 `(("r-annotationdbi" ,r-annotationdbi)))
765 (home-page "https://www.bioconductor.org/packages/ABAData/")
766 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
768 "This package provides the data for the gene expression enrichment
769 analysis conducted in the package ABAEnrichment. The package includes three
770 datasets which are derived from the Allen Brain Atlas:
773 @item Gene expression data from Human Brain (adults) averaged across donors,
774 @item Gene expression data from the Developing Human Brain pooled into five
775 age categories and averaged across donors, and
776 @item a developmental effect score based on the Developing Human Brain
780 All datasets are restricted to protein coding genes.")
781 (license license:gpl2+)))
783 (define-public r-arrmdata
789 (uri (bioconductor-uri "ARRmData" version 'experiment))
792 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
794 `((upstream-name . "ARRmData")))
795 (build-system r-build-system)
796 (home-page "https://www.bioconductor.org/packages/ARRmData/")
797 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
799 "This package provides raw beta values from 36 samples across 3 groups
800 from Illumina 450k methylation arrays.")
801 (license license:artistic2.0)))
803 (define-public r-hsmmsinglecell
805 (name "r-hsmmsinglecell")
809 ;; We cannot use bioconductor-uri here because this tarball is
810 ;; located under "data/experiment/" instead of "bioc/".
811 (uri (string-append "https://www.bioconductor.org/packages/"
812 "release/data/experiment/src/contrib/"
813 "HSMMSingleCell_" version ".tar.gz"))
816 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
818 `((upstream-name . "HSMMSingleCell")))
819 (build-system r-build-system)
820 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
821 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
823 "Skeletal myoblasts undergo a well-characterized sequence of
824 morphological and transcriptional changes during differentiation. In this
825 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
826 under high mitogen conditions (GM) and then differentiated by switching to
827 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
828 hundred cells taken over a time-course of serum-induced differentiation.
829 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
830 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
831 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
832 which were then sequenced to a depth of ~4 million reads per library,
833 resulting in a complete gene expression profile for each cell.")
834 (license license:artistic2.0)))
842 ;; We cannot use bioconductor-uri here because this tarball is
843 ;; located under "data/experiment/" instead of "bioc/".
844 (uri (string-append "https://www.bioconductor.org/packages/"
845 "release/data/experiment/src/contrib/"
846 "ALL_" version ".tar.gz"))
849 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
850 (properties `((upstream-name . "ALL")))
851 (build-system r-build-system)
853 `(("r-biobase" ,r-biobase)))
854 (home-page "https://bioconductor.org/packages/ALL")
855 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
857 "The data consist of microarrays from 128 different individuals with
858 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
859 are available. The data have been normalized (using rma) and it is the
860 jointly normalized data that are available here. The data are presented in
861 the form of an @code{exprSet} object.")
862 (license license:artistic2.0)))
864 (define-public r-affydata
871 (uri (bioconductor-uri "affydata" version 'experiment))
874 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
875 (properties `((upstream-name . "affydata")))
876 (build-system r-build-system)
878 `(("r-affy" ,r-affy)))
879 (home-page "https://bioconductor.org/packages/affydata/")
880 (synopsis "Affymetrix data for demonstration purposes")
882 "This package provides example datasets that represent 'real world
883 examples' of Affymetrix data, unlike the artificial examples included in the
884 package @code{affy}.")
885 (license license:gpl2+)))
890 (define-public r-biocgenerics
892 (name "r-biocgenerics")
896 (uri (bioconductor-uri "BiocGenerics" version))
899 "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f"))))
901 `((upstream-name . "BiocGenerics")))
902 (build-system r-build-system)
903 (home-page "https://bioconductor.org/packages/BiocGenerics")
904 (synopsis "S4 generic functions for Bioconductor")
906 "This package provides S4 generic functions needed by many Bioconductor
908 (license license:artistic2.0)))
910 (define-public r-affycomp
917 (uri (bioconductor-uri "affycomp" version))
920 "1nijqljg5r3qj1y6an0i58sby76hqacj3a3nvainxic4n5wlzh0n"))))
921 (properties `((upstream-name . "affycomp")))
922 (build-system r-build-system)
923 (propagated-inputs `(("r-biobase" ,r-biobase)))
924 (home-page "https://bioconductor.org/packages/affycomp/")
925 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
927 "The package contains functions that can be used to compare expression
928 measures for Affymetrix Oligonucleotide Arrays.")
929 (license license:gpl2+)))
931 (define-public r-affycompatible
933 (name "r-affycompatible")
938 (uri (bioconductor-uri "AffyCompatible" version))
941 "1zi96qa6vkgwvvy5cn6c3p1kbfsaz74zsw2kjxarz5qs744f0xvs"))))
943 `((upstream-name . "AffyCompatible")))
944 (build-system r-build-system)
946 `(("r-biostrings" ,r-biostrings)
949 (home-page "https://bioconductor.org/packages/AffyCompatible/")
950 (synopsis "Work with Affymetrix GeneChip files")
952 "This package provides an interface to Affymetrix chip annotation and
953 sample attribute files. The package allows an easy way for users to download
954 and manage local data bases of Affynmetrix NetAffx annotation files. It also
955 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
956 Command Console} (AGCC)-compatible sample annotation files.")
957 (license license:artistic2.0)))
959 (define-public r-affycontam
961 (name "r-affycontam")
966 (uri (bioconductor-uri "affyContam" version))
969 "0nzk1cm26rhmym753wyhn35hqnz5lvavi3i5qfgdvhxgjy3m1jgp"))))
970 (properties `((upstream-name . "affyContam")))
971 (build-system r-build-system)
974 ("r-affydata" ,r-affydata)
975 ("r-biobase" ,r-biobase)))
976 (home-page "https://bioconductor.org/packages/affyContam/")
977 (synopsis "Structured corruption of Affymetrix CEL file data")
979 "Microarray quality assessment is a major concern of microarray analysts.
980 This package provides some simple approaches to in silico creation of quality
981 problems in CEL-level data to help evaluate performance of quality metrics.")
982 (license license:artistic2.0)))
984 (define-public r-affycoretools
986 (name "r-affycoretools")
991 (uri (bioconductor-uri "affycoretools" version))
994 "17dxpzhwwdwnxkdpmyjwdnacg41hw60mlc71w4nzlvs28sfsy09s"))))
995 (properties `((upstream-name . "affycoretools")))
996 (build-system r-build-system)
999 ("r-annotationdbi" ,r-annotationdbi)
1000 ("r-biobase" ,r-biobase)
1001 ("r-biocgenerics" ,r-biocgenerics)
1003 ("r-edger" ,r-edger)
1004 ("r-gcrma" ,r-gcrma)
1005 ("r-ggplot2" ,r-ggplot2)
1006 ("r-gostats" ,r-gostats)
1007 ("r-gplots" ,r-gplots)
1008 ("r-hwriter" ,r-hwriter)
1009 ("r-lattice" ,r-lattice)
1010 ("r-limma" ,r-limma)
1011 ("r-oligoclasses" ,r-oligoclasses)
1012 ("r-reportingtools" ,r-reportingtools)
1013 ("r-rsqlite" ,r-rsqlite)
1014 ("r-s4vectors" ,r-s4vectors)
1015 ("r-xtable" ,r-xtable)))
1016 (home-page "https://bioconductor.org/packages/affycoretools/")
1017 (synopsis "Functions for analyses with Affymetrix GeneChips")
1019 "This package provides various wrapper functions that have been written
1020 to streamline the more common analyses that a Biostatistician might see.")
1021 (license license:artistic2.0)))
1023 (define-public r-affxparser
1025 (name "r-affxparser")
1030 (uri (bioconductor-uri "affxparser" version))
1033 "1jv7k9pn4c7szi3ma2f2xsd58pkrkvjpk5wra73r6kc607qgrv33"))))
1034 (properties `((upstream-name . "affxparser")))
1035 (build-system r-build-system)
1036 (home-page "https://github.com/HenrikBengtsson/affxparser")
1037 (synopsis "Affymetrix File Parsing SDK")
1039 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1040 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1041 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1042 are supported. Currently, there are methods for reading @dfn{chip definition
1043 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1044 either in full or in part. For example, probe signals from a few probesets
1045 can be extracted very quickly from a set of CEL files into a convenient list
1047 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1049 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1051 (define-public r-annotate
1058 (uri (bioconductor-uri "annotate" version))
1061 "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs"))))
1062 (build-system r-build-system)
1064 `(("r-annotationdbi" ,r-annotationdbi)
1065 ("r-biobase" ,r-biobase)
1066 ("r-biocgenerics" ,r-biocgenerics)
1068 ("r-rcurl" ,r-rcurl)
1070 ("r-xtable" ,r-xtable)))
1072 "https://bioconductor.org/packages/annotate")
1073 (synopsis "Annotation for microarrays")
1074 (description "This package provides R environments for the annotation of
1076 (license license:artistic2.0)))
1078 (define-public r-hpar
1085 (uri (bioconductor-uri "hpar" version))
1088 "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5"))))
1089 (build-system r-build-system)
1090 (home-page "https://bioconductor.org/packages/hpar/")
1091 (synopsis "Human Protein Atlas in R")
1092 (description "This package provides a simple interface to and data from
1093 the Human Protein Atlas project.")
1094 (license license:artistic2.0)))
1096 (define-public r-regioner
1103 (uri (bioconductor-uri "regioneR" version))
1106 "12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
1107 (properties `((upstream-name . "regioneR")))
1108 (build-system r-build-system)
1110 `(("r-biostrings" ,r-biostrings)
1111 ("r-bsgenome" ,r-bsgenome)
1112 ("r-genomeinfodb" ,r-genomeinfodb)
1113 ("r-genomicranges" ,r-genomicranges)
1114 ("r-iranges" ,r-iranges)
1115 ("r-memoise" ,r-memoise)
1116 ("r-rtracklayer" ,r-rtracklayer)
1117 ("r-s4vectors" ,r-s4vectors)))
1118 (home-page "https://bioconductor.org/packages/regioneR/")
1119 (synopsis "Association analysis of genomic regions")
1120 (description "This package offers a statistical framework based on
1121 customizable permutation tests to assess the association between genomic
1122 region sets and other genomic features.")
1123 (license license:artistic2.0)))
1125 (define-public r-reportingtools
1127 (name "r-reportingtools")
1132 (uri (bioconductor-uri "ReportingTools" version))
1135 "16ska7mlacka0xi8x2icy8v42vaxccb3a1x73szmfvcrwr592qsc"))))
1137 `((upstream-name . "ReportingTools")))
1138 (build-system r-build-system)
1140 `(("r-annotate" ,r-annotate)
1141 ("r-annotationdbi" ,r-annotationdbi)
1142 ("r-biobase" ,r-biobase)
1143 ("r-biocgenerics" ,r-biocgenerics)
1144 ("r-category" ,r-category)
1145 ("r-deseq2" ,r-deseq2)
1146 ("r-edger" ,r-edger)
1147 ("r-ggbio" ,r-ggbio)
1148 ("r-ggplot2" ,r-ggplot2)
1149 ("r-gostats" ,r-gostats)
1150 ("r-gseabase" ,r-gseabase)
1151 ("r-hwriter" ,r-hwriter)
1152 ("r-iranges" ,r-iranges)
1153 ("r-knitr" ,r-knitr)
1154 ("r-lattice" ,r-lattice)
1155 ("r-limma" ,r-limma)
1156 ("r-pfam-db" ,r-pfam-db)
1157 ("r-r-utils" ,r-r-utils)
1159 (home-page "https://bioconductor.org/packages/ReportingTools/")
1160 (synopsis "Tools for making reports in various formats")
1162 "The ReportingTools package enables users to easily display reports of
1163 analysis results generated from sources such as microarray and sequencing
1164 data. The package allows users to create HTML pages that may be viewed on a
1165 web browser, or in other formats. Users can generate tables with sortable and
1166 filterable columns, make and display plots, and link table entries to other
1167 data sources such as NCBI or larger plots within the HTML page. Using the
1168 package, users can also produce a table of contents page to link various
1169 reports together for a particular project that can be viewed in a web
1171 (license license:artistic2.0)))
1173 (define-public r-geneplotter
1175 (name "r-geneplotter")
1180 (uri (bioconductor-uri "geneplotter" version))
1183 "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb"))))
1184 (build-system r-build-system)
1186 `(("r-annotate" ,r-annotate)
1187 ("r-annotationdbi" ,r-annotationdbi)
1188 ("r-biobase" ,r-biobase)
1189 ("r-biocgenerics" ,r-biocgenerics)
1190 ("r-lattice" ,r-lattice)
1191 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1192 (home-page "https://bioconductor.org/packages/geneplotter")
1193 (synopsis "Graphics functions for genomic data")
1195 "This package provides functions for plotting genomic data.")
1196 (license license:artistic2.0)))
1198 (define-public r-oligoclasses
1200 (name "r-oligoclasses")
1205 (uri (bioconductor-uri "oligoClasses" version))
1208 "0z86zrmn80kcy6fgb9i9zs82vhim73n8hlkqy7y8sbb2jwksdr72"))))
1209 (properties `((upstream-name . "oligoClasses")))
1210 (build-system r-build-system)
1212 `(("r-affyio" ,r-affyio)
1213 ("r-biobase" ,r-biobase)
1214 ("r-biocgenerics" ,r-biocgenerics)
1215 ("r-biocmanager" ,r-biocmanager)
1216 ("r-biostrings" ,r-biostrings)
1219 ("r-foreach" ,r-foreach)
1220 ("r-genomicranges" ,r-genomicranges)
1221 ("r-iranges" ,r-iranges)
1222 ("r-rsqlite" ,r-rsqlite)
1223 ("r-s4vectors" ,r-s4vectors)
1224 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1225 (home-page "https://bioconductor.org/packages/oligoClasses/")
1226 (synopsis "Classes for high-throughput arrays")
1228 "This package contains class definitions, validity checks, and
1229 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1231 (license license:gpl2+)))
1233 (define-public r-oligo
1240 (uri (bioconductor-uri "oligo" version))
1243 "0qkyz65zvry0syibjkvkshwijccna18jy0hlib0n5x4c8x9zs5df"))))
1244 (properties `((upstream-name . "oligo")))
1245 (build-system r-build-system)
1246 (inputs `(("zlib" ,zlib)))
1248 `(("r-affxparser" ,r-affxparser)
1249 ("r-affyio" ,r-affyio)
1250 ("r-biobase" ,r-biobase)
1251 ("r-biocgenerics" ,r-biocgenerics)
1252 ("r-biostrings" ,r-biostrings)
1255 ("r-oligoclasses" ,r-oligoclasses)
1256 ("r-preprocesscore" ,r-preprocesscore)
1257 ("r-rsqlite" ,r-rsqlite)
1258 ("r-zlibbioc" ,r-zlibbioc)))
1259 (home-page "https://bioconductor.org/packages/oligo/")
1260 (synopsis "Preprocessing tools for oligonucleotide arrays")
1262 "This package provides a package to analyze oligonucleotide
1263 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1264 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1265 (license license:lgpl2.0+)))
1267 (define-public r-qvalue
1274 (uri (bioconductor-uri "qvalue" version))
1277 "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5"))))
1278 (build-system r-build-system)
1280 `(("r-ggplot2" ,r-ggplot2)
1281 ("r-reshape2" ,r-reshape2)))
1282 (home-page "http://github.com/jdstorey/qvalue")
1283 (synopsis "Q-value estimation for false discovery rate control")
1285 "This package takes a list of p-values resulting from the simultaneous
1286 testing of many hypotheses and estimates their q-values and local @dfn{false
1287 discovery rate} (FDR) values. The q-value of a test measures the proportion
1288 of false positives incurred when that particular test is called significant.
1289 The local FDR measures the posterior probability the null hypothesis is true
1290 given the test's p-value. Various plots are automatically generated, allowing
1291 one to make sensible significance cut-offs. The software can be applied to
1292 problems in genomics, brain imaging, astrophysics, and data mining.")
1293 ;; Any version of the LGPL.
1294 (license license:lgpl3+)))
1296 (define-public r-diffbind
1303 (uri (bioconductor-uri "DiffBind" version))
1306 "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich"))))
1307 (properties `((upstream-name . "DiffBind")))
1308 (build-system r-build-system)
1312 `(("r-amap" ,r-amap)
1313 ("r-biocparallel" ,r-biocparallel)
1314 ("r-deseq2" ,r-deseq2)
1315 ("r-dplyr" ,r-dplyr)
1316 ("r-edger" ,r-edger)
1317 ("r-genomicalignments" ,r-genomicalignments)
1318 ("r-genomicranges" ,r-genomicranges)
1319 ("r-ggplot2" ,r-ggplot2)
1320 ("r-ggrepel" ,r-ggrepel)
1321 ("r-gplots" ,r-gplots)
1322 ("r-iranges" ,r-iranges)
1323 ("r-lattice" ,r-lattice)
1324 ("r-limma" ,r-limma)
1325 ("r-locfit" ,r-locfit)
1326 ("r-rcolorbrewer" , r-rcolorbrewer)
1328 ("r-rhtslib" ,r-rhtslib)
1329 ("r-rsamtools" ,r-rsamtools)
1330 ("r-s4vectors" ,r-s4vectors)
1331 ("r-summarizedexperiment" ,r-summarizedexperiment)
1332 ("r-systempiper" ,r-systempiper)))
1333 (home-page "http://bioconductor.org/packages/DiffBind")
1334 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1336 "This package computes differentially bound sites from multiple
1337 ChIP-seq experiments using affinity (quantitative) data. Also enables
1338 occupancy (overlap) analysis and plotting functions.")
1339 (license license:artistic2.0)))
1341 (define-public r-ripseeker
1343 (name "r-ripseeker")
1348 (uri (bioconductor-uri "RIPSeeker" version))
1351 "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43"))))
1352 (properties `((upstream-name . "RIPSeeker")))
1353 (build-system r-build-system)
1355 `(("r-s4vectors" ,r-s4vectors)
1356 ("r-iranges" ,r-iranges)
1357 ("r-genomicranges" ,r-genomicranges)
1358 ("r-summarizedexperiment" ,r-summarizedexperiment)
1359 ("r-rsamtools" ,r-rsamtools)
1360 ("r-genomicalignments" ,r-genomicalignments)
1361 ("r-rtracklayer" ,r-rtracklayer)))
1362 (home-page "http://bioconductor.org/packages/RIPSeeker")
1364 "Identifying protein-associated transcripts from RIP-seq experiments")
1366 "This package infers and discriminates RIP peaks from RIP-seq alignments
1367 using two-state HMM with negative binomial emission probability. While
1368 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1369 a suite of bioinformatics tools integrated within this self-contained software
1370 package comprehensively addressing issues ranging from post-alignments
1371 processing to visualization and annotation.")
1372 (license license:gpl2)))
1374 (define-public r-multtest
1381 (uri (bioconductor-uri "multtest" version))
1384 "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv"))))
1385 (build-system r-build-system)
1387 `(("r-survival" ,r-survival)
1388 ("r-biocgenerics" ,r-biocgenerics)
1389 ("r-biobase" ,r-biobase)
1390 ("r-mass" ,r-mass)))
1391 (home-page "http://bioconductor.org/packages/multtest")
1392 (synopsis "Resampling-based multiple hypothesis testing")
1394 "This package can do non-parametric bootstrap and permutation
1395 resampling-based multiple testing procedures (including empirical Bayes
1396 methods) for controlling the family-wise error rate (FWER), generalized
1397 family-wise error rate (gFWER), tail probability of the proportion of
1398 false positives (TPPFP), and false discovery rate (FDR). Several choices
1399 of bootstrap-based null distribution are implemented (centered, centered
1400 and scaled, quantile-transformed). Single-step and step-wise methods are
1401 available. Tests based on a variety of T- and F-statistics (including
1402 T-statistics based on regression parameters from linear and survival models
1403 as well as those based on correlation parameters) are included. When probing
1404 hypotheses with T-statistics, users may also select a potentially faster null
1405 distribution which is multivariate normal with mean zero and variance
1406 covariance matrix derived from the vector influence function. Results are
1407 reported in terms of adjusted P-values, confidence regions and test statistic
1408 cutoffs. The procedures are directly applicable to identifying differentially
1409 expressed genes in DNA microarray experiments.")
1410 (license license:lgpl3)))
1412 (define-public r-graph
1418 (uri (bioconductor-uri "graph" version))
1421 "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w"))))
1422 (build-system r-build-system)
1424 `(("r-biocgenerics" ,r-biocgenerics)))
1425 (home-page "https://bioconductor.org/packages/graph")
1426 (synopsis "Handle graph data structures in R")
1428 "This package implements some simple graph handling capabilities for R.")
1429 (license license:artistic2.0)))
1431 (define-public r-codedepends
1433 (name "r-codedepends")
1438 (uri (cran-uri "CodeDepends" version))
1441 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1442 (properties `((upstream-name . "CodeDepends")))
1443 (build-system r-build-system)
1445 `(("r-codetools" ,r-codetools)
1446 ("r-graph" ,r-graph)
1448 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
1449 (synopsis "Analysis of R code for reproducible research and code comprehension")
1451 "This package provides tools for analyzing R expressions or blocks of
1452 code and determining the dependencies between them. It focuses on R scripts,
1453 but can be used on the bodies of functions. There are many facilities
1454 including the ability to summarize or get a high-level view of code,
1455 determining dependencies between variables, code improvement suggestions.")
1456 ;; Any version of the GPL
1457 (license (list license:gpl2+ license:gpl3+))))
1459 (define-public r-chippeakanno
1461 (name "r-chippeakanno")
1466 (uri (bioconductor-uri "ChIPpeakAnno" version))
1469 "0wzwdxvvr7wknz5jnan0wsp81c1gv4d2qx0mrb1yybqf4z068779"))))
1470 (properties `((upstream-name . "ChIPpeakAnno")))
1471 (build-system r-build-system)
1473 `(("r-annotationdbi" ,r-annotationdbi)
1474 ("r-biobase" ,r-biobase)
1475 ("r-biocgenerics" ,r-biocgenerics)
1476 ("r-biocmanager" ,r-biocmanager)
1477 ("r-biomart" ,r-biomart)
1478 ("r-biostrings" ,r-biostrings)
1479 ("r-bsgenome" ,r-bsgenome)
1481 ("r-delayedarray" ,r-delayedarray)
1482 ("r-ensembldb" ,r-ensembldb)
1483 ("r-genomeinfodb" ,r-genomeinfodb)
1484 ("r-genomicalignments" ,r-genomicalignments)
1485 ("r-genomicfeatures" ,r-genomicfeatures)
1486 ("r-genomicranges" ,r-genomicranges)
1487 ("r-go-db" ,r-go-db)
1488 ("r-graph" ,r-graph)
1490 ("r-iranges" ,r-iranges)
1491 ("r-limma" ,r-limma)
1492 ("r-matrixstats" ,r-matrixstats)
1493 ("r-multtest" ,r-multtest)
1495 ("r-regioner" ,r-regioner)
1496 ("r-rsamtools" ,r-rsamtools)
1497 ("r-rtracklayer" ,r-rtracklayer)
1498 ("r-s4vectors" ,r-s4vectors)
1499 ("r-seqinr" ,r-seqinr)
1500 ("r-summarizedexperiment" ,r-summarizedexperiment)
1501 ("r-venndiagram" ,r-venndiagram)))
1502 (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
1503 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1505 "The package includes functions to retrieve the sequences around the peak,
1506 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1507 custom features such as most conserved elements and other transcription factor
1508 binding sites supplied by users. Starting 2.0.5, new functions have been added
1509 for finding the peaks with bi-directional promoters with summary statistics
1510 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1511 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1512 enrichedGO (addGeneIDs).")
1513 (license license:gpl2+)))
1515 (define-public r-marray
1521 (uri (bioconductor-uri "marray" version))
1523 (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz"))))
1524 (build-system r-build-system)
1526 `(("r-limma" ,r-limma)))
1527 (home-page "http://bioconductor.org/packages/marray")
1528 (synopsis "Exploratory analysis for two-color spotted microarray data")
1529 (description "This package contains class definitions for two-color spotted
1530 microarray data. It also includes functions for data input, diagnostic plots,
1531 normalization and quality checking.")
1532 (license license:lgpl2.0+)))
1534 (define-public r-cghbase
1540 (uri (bioconductor-uri "CGHbase" version))
1542 (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm"))))
1543 (properties `((upstream-name . "CGHbase")))
1544 (build-system r-build-system)
1546 `(("r-biobase" ,r-biobase)
1547 ("r-marray" ,r-marray)))
1548 (home-page "http://bioconductor.org/packages/CGHbase")
1549 (synopsis "Base functions and classes for arrayCGH data analysis")
1550 (description "This package contains functions and classes that are needed by
1551 the @code{arrayCGH} packages.")
1552 (license license:gpl2+)))
1554 (define-public r-cghcall
1560 (uri (bioconductor-uri "CGHcall" version))
1562 (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93"))))
1563 (properties `((upstream-name . "CGHcall")))
1564 (build-system r-build-system)
1566 `(("r-biobase" ,r-biobase)
1567 ("r-cghbase" ,r-cghbase)
1568 ("r-impute" ,r-impute)
1569 ("r-dnacopy" ,r-dnacopy)
1570 ("r-snowfall" ,r-snowfall)))
1571 (home-page "http://bioconductor.org/packages/CGHcall")
1572 (synopsis "Base functions and classes for arrayCGH data analysis")
1573 (description "This package contains functions and classes that are needed by
1574 @code{arrayCGH} packages.")
1575 (license license:gpl2+)))
1577 (define-public r-qdnaseq
1583 (uri (bioconductor-uri "QDNAseq" version))
1585 (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz"))))
1586 (properties `((upstream-name . "QDNAseq")))
1587 (build-system r-build-system)
1589 `(("r-biobase" ,r-biobase)
1590 ("r-biocparallel" ,r-biocparallel)
1591 ("r-cghbase" ,r-cghbase)
1592 ("r-cghcall" ,r-cghcall)
1593 ("r-dnacopy" ,r-dnacopy)
1594 ("r-genomicranges" ,r-genomicranges)
1595 ("r-iranges" ,r-iranges)
1596 ("r-matrixstats" ,r-matrixstats)
1597 ("r-r-utils" ,r-r-utils)
1598 ("r-rsamtools" ,r-rsamtools)))
1599 (home-page "http://bioconductor.org/packages/QDNAseq")
1600 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1601 (description "The genome is divided into non-overlapping fixed-sized bins,
1602 number of sequence reads in each counted, adjusted with a simultaneous
1603 two-dimensional loess correction for sequence mappability and GC content, and
1604 filtered to remove spurious regions in the genome. Downstream steps of
1605 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1607 (license license:gpl2+)))
1609 (define-public r-bayseq
1616 (uri (bioconductor-uri "baySeq" version))
1619 "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w"))))
1620 (properties `((upstream-name . "baySeq")))
1621 (build-system r-build-system)
1623 `(("r-abind" ,r-abind)
1624 ("r-edger" ,r-edger)
1625 ("r-genomicranges" ,r-genomicranges)))
1626 (home-page "https://bioconductor.org/packages/baySeq/")
1627 (synopsis "Bayesian analysis of differential expression patterns in count data")
1629 "This package identifies differential expression in high-throughput count
1630 data, such as that derived from next-generation sequencing machines,
1631 calculating estimated posterior likelihoods of differential expression (or
1632 more complex hypotheses) via empirical Bayesian methods.")
1633 (license license:gpl3)))
1635 (define-public r-chipcomp
1642 (uri (bioconductor-uri "ChIPComp" version))
1645 "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y"))))
1646 (properties `((upstream-name . "ChIPComp")))
1647 (build-system r-build-system)
1649 `(("r-biocgenerics" ,r-biocgenerics)
1650 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1651 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1652 ("r-genomeinfodb" ,r-genomeinfodb)
1653 ("r-genomicranges" ,r-genomicranges)
1654 ("r-iranges" ,r-iranges)
1655 ("r-limma" ,r-limma)
1656 ("r-rsamtools" ,r-rsamtools)
1657 ("r-rtracklayer" ,r-rtracklayer)
1658 ("r-s4vectors" ,r-s4vectors)))
1659 (home-page "https://bioconductor.org/packages/ChIPComp")
1660 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
1662 "ChIPComp implements a statistical method for quantitative comparison of
1663 multiple ChIP-seq datasets. It detects differentially bound sharp binding
1664 sites across multiple conditions considering matching control in ChIP-seq
1666 ;; Any version of the GPL.
1667 (license license:gpl3+)))
1669 (define-public r-riboprofiling
1671 (name "r-riboprofiling")
1676 (uri (bioconductor-uri "RiboProfiling" version))
1679 "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9"))))
1680 (properties `((upstream-name . "RiboProfiling")))
1681 (build-system r-build-system)
1683 `(("r-biocgenerics" ,r-biocgenerics)
1684 ("r-biostrings" ,r-biostrings)
1685 ("r-data-table" ,r-data-table)
1686 ("r-genomeinfodb" ,r-genomeinfodb)
1687 ("r-genomicalignments" ,r-genomicalignments)
1688 ("r-genomicfeatures" ,r-genomicfeatures)
1689 ("r-genomicranges" ,r-genomicranges)
1690 ("r-ggbio" ,r-ggbio)
1691 ("r-ggplot2" ,r-ggplot2)
1692 ("r-iranges" ,r-iranges)
1694 ("r-reshape2" ,r-reshape2)
1695 ("r-rsamtools" ,r-rsamtools)
1696 ("r-rtracklayer" ,r-rtracklayer)
1697 ("r-s4vectors" ,r-s4vectors)
1698 ("r-sqldf" ,r-sqldf)))
1699 (home-page "https://bioconductor.org/packages/RiboProfiling/")
1700 (synopsis "Ribosome profiling data analysis")
1701 (description "Starting with a BAM file, this package provides the
1702 necessary functions for quality assessment, read start position recalibration,
1703 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
1704 of count data: pairs, log fold-change, codon frequency and coverage
1705 assessment, principal component analysis on codon coverage.")
1706 (license license:gpl3)))
1708 (define-public r-riboseqr
1715 (uri (bioconductor-uri "riboSeqR" version))
1718 "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga"))))
1719 (properties `((upstream-name . "riboSeqR")))
1720 (build-system r-build-system)
1722 `(("r-abind" ,r-abind)
1723 ("r-bayseq" ,r-bayseq)
1724 ("r-genomeinfodb" ,r-genomeinfodb)
1725 ("r-genomicranges" ,r-genomicranges)
1726 ("r-iranges" ,r-iranges)
1727 ("r-rsamtools" ,r-rsamtools)
1728 ("r-seqlogo" ,r-seqlogo)))
1729 (home-page "https://bioconductor.org/packages/riboSeqR/")
1730 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
1732 "This package provides plotting functions, frameshift detection and
1733 parsing of genetic sequencing data from ribosome profiling experiments.")
1734 (license license:gpl3)))
1736 (define-public r-interactionset
1738 (name "r-interactionset")
1743 (uri (bioconductor-uri "InteractionSet" version))
1746 "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6"))))
1748 `((upstream-name . "InteractionSet")))
1749 (build-system r-build-system)
1751 `(("r-biocgenerics" ,r-biocgenerics)
1752 ("r-genomeinfodb" ,r-genomeinfodb)
1753 ("r-genomicranges" ,r-genomicranges)
1754 ("r-iranges" ,r-iranges)
1755 ("r-matrix" ,r-matrix)
1757 ("r-s4vectors" ,r-s4vectors)
1758 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1759 (home-page "https://bioconductor.org/packages/InteractionSet")
1760 (synopsis "Base classes for storing genomic interaction data")
1762 "This package provides the @code{GInteractions},
1763 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
1764 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
1766 (license license:gpl3)))
1768 (define-public r-genomicinteractions
1770 (name "r-genomicinteractions")
1775 (uri (bioconductor-uri "GenomicInteractions" version))
1778 "0hq2n5yfr9h2ayn10dy9lz08gd2q0awrm5cy2kqdmz4d8ss4r94p"))))
1780 `((upstream-name . "GenomicInteractions")))
1781 (build-system r-build-system)
1783 `(("r-biobase" ,r-biobase)
1784 ("r-biocgenerics" ,r-biocgenerics)
1785 ("r-data-table" ,r-data-table)
1786 ("r-dplyr" ,r-dplyr)
1787 ("r-genomeinfodb" ,r-genomeinfodb)
1788 ("r-genomicranges" ,r-genomicranges)
1789 ("r-ggplot2" ,r-ggplot2)
1790 ("r-gridextra" ,r-gridextra)
1792 ("r-igraph" ,r-igraph)
1793 ("r-interactionset" ,r-interactionset)
1794 ("r-iranges" ,r-iranges)
1795 ("r-rsamtools" ,r-rsamtools)
1796 ("r-rtracklayer" ,r-rtracklayer)
1797 ("r-s4vectors" ,r-s4vectors)
1798 ("r-stringr" ,r-stringr)))
1799 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
1800 (synopsis "R package for handling genomic interaction data")
1802 "This R package provides tools for handling genomic interaction data,
1803 such as ChIA-PET/Hi-C, annotating genomic features with interaction
1804 information and producing various plots and statistics.")
1805 (license license:gpl3)))
1807 (define-public r-ctc
1814 (uri (bioconductor-uri "ctc" version))
1817 "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am"))))
1818 (build-system r-build-system)
1819 (propagated-inputs `(("r-amap" ,r-amap)))
1820 (home-page "https://bioconductor.org/packages/ctc/")
1821 (synopsis "Cluster and tree conversion")
1823 "This package provides tools for exporting and importing classification
1824 trees and clusters to other programs.")
1825 (license license:gpl2)))
1827 (define-public r-goseq
1834 (uri (bioconductor-uri "goseq" version))
1837 "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw"))))
1838 (build-system r-build-system)
1840 `(("r-annotationdbi" ,r-annotationdbi)
1841 ("r-biasedurn" ,r-biasedurn)
1842 ("r-biocgenerics" ,r-biocgenerics)
1843 ("r-genelendatabase" ,r-genelendatabase)
1844 ("r-go-db" ,r-go-db)
1845 ("r-mgcv" ,r-mgcv)))
1846 (home-page "https://bioconductor.org/packages/goseq/")
1847 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
1849 "This package provides tools to detect Gene Ontology and/or other user
1850 defined categories which are over/under represented in RNA-seq data.")
1851 (license license:lgpl2.0+)))
1853 (define-public r-glimma
1860 (uri (bioconductor-uri "Glimma" version))
1863 "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x"))))
1864 (properties `((upstream-name . "Glimma")))
1865 (build-system r-build-system)
1867 `(("r-edger" ,r-edger)
1868 ("r-jsonlite" ,r-jsonlite)
1869 ("r-s4vectors" ,r-s4vectors)))
1870 (home-page "https://github.com/Shians/Glimma")
1871 (synopsis "Interactive HTML graphics")
1873 "This package generates interactive visualisations for analysis of
1874 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
1875 HTML page. The interactions are built on top of the popular static
1876 representations of analysis results in order to provide additional
1878 (license license:lgpl3)))
1880 (define-public r-rots
1887 (uri (bioconductor-uri "ROTS" version))
1890 "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77"))))
1891 (properties `((upstream-name . "ROTS")))
1892 (build-system r-build-system)
1894 `(("r-biobase" ,r-biobase)
1895 ("r-rcpp" ,r-rcpp)))
1896 (home-page "https://bioconductor.org/packages/ROTS/")
1897 (synopsis "Reproducibility-Optimized Test Statistic")
1899 "This package provides tools for calculating the
1900 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
1902 (license license:gpl2+)))
1904 (define-public r-plgem
1911 (uri (bioconductor-uri "plgem" version))
1914 "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp"))))
1915 (build-system r-build-system)
1917 `(("r-biobase" ,r-biobase)
1918 ("r-mass" ,r-mass)))
1919 (home-page "http://www.genopolis.it")
1920 (synopsis "Detect differential expression in microarray and proteomics datasets")
1922 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
1923 model the variance-versus-mean dependence that exists in a variety of
1924 genome-wide datasets, including microarray and proteomics data. The use of
1925 PLGEM has been shown to improve the detection of differentially expressed
1926 genes or proteins in these datasets.")
1927 (license license:gpl2)))
1929 (define-public r-inspect
1936 (uri (bioconductor-uri "INSPEcT" version))
1939 "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r"))))
1940 (properties `((upstream-name . "INSPEcT")))
1941 (build-system r-build-system)
1943 `(("r-biobase" ,r-biobase)
1944 ("r-biocgenerics" ,r-biocgenerics)
1945 ("r-biocparallel" ,r-biocparallel)
1946 ("r-deseq2" ,r-deseq2)
1947 ("r-desolve" ,r-desolve)
1948 ("r-genomicalignments" ,r-genomicalignments)
1949 ("r-genomicfeatures" ,r-genomicfeatures)
1950 ("r-genomicranges" ,r-genomicranges)
1951 ("r-iranges" ,r-iranges)
1952 ("r-plgem" ,r-plgem)
1953 ("r-preprocesscore" ,r-preprocesscore)
1955 ("r-rootsolve" ,r-rootsolve)
1956 ("r-rsamtools" ,r-rsamtools)
1957 ("r-s4vectors" ,r-s4vectors)
1958 ("r-shiny" ,r-shiny)
1959 ("r-summarizedexperiment" ,r-summarizedexperiment)
1960 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
1961 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
1962 (home-page "https://bioconductor.org/packages/INSPEcT")
1963 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
1965 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
1966 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
1967 order to evaluate synthesis, processing and degradation rates and assess via
1968 modeling the rates that determines changes in mature mRNA levels.")
1969 (license license:gpl2)))
1971 (define-public r-dnabarcodes
1973 (name "r-dnabarcodes")
1978 (uri (bioconductor-uri "DNABarcodes" version))
1981 "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0"))))
1982 (properties `((upstream-name . "DNABarcodes")))
1983 (build-system r-build-system)
1986 ("r-matrix" ,r-matrix)
1987 ("r-rcpp" ,r-rcpp)))
1988 (home-page "https://bioconductor.org/packages/DNABarcodes")
1989 (synopsis "Create and analyze DNA barcodes")
1991 "This package offers tools to create DNA barcode sets capable of
1992 correcting insertion, deletion, and substitution errors. Existing barcodes
1993 can be analyzed regarding their minimal, maximal and average distances between
1994 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
1995 demultiplexed, i.e. assigned to their original reference barcode.")
1996 (license license:gpl2)))
1998 (define-public r-ruvseq
2005 (uri (bioconductor-uri "RUVSeq" version))
2008 "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33"))))
2009 (properties `((upstream-name . "RUVSeq")))
2010 (build-system r-build-system)
2012 `(("r-biobase" ,r-biobase)
2013 ("r-edaseq" ,r-edaseq)
2014 ("r-edger" ,r-edger)
2015 ("r-mass" ,r-mass)))
2016 (home-page "https://github.com/drisso/RUVSeq")
2017 (synopsis "Remove unwanted variation from RNA-Seq data")
2019 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2020 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2022 (license license:artistic2.0)))
2024 (define-public r-biocneighbors
2026 (name "r-biocneighbors")
2031 (uri (bioconductor-uri "BiocNeighbors" version))
2034 "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg"))))
2035 (properties `((upstream-name . "BiocNeighbors")))
2036 (build-system r-build-system)
2038 `(("r-biocgenerics" ,r-biocgenerics)
2039 ("r-biocparallel" ,r-biocparallel)
2041 ("r-rcppannoy" ,r-rcppannoy)
2042 ("r-rcpphnsw" ,r-rcpphnsw)
2043 ("r-s4vectors" ,r-s4vectors)))
2044 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2045 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2047 "This package implements exact and approximate methods for nearest
2048 neighbor detection, in a framework that allows them to be easily switched
2049 within Bioconductor packages or workflows. The exact algorithm is implemented
2050 using pre-clustering with the k-means algorithm. Functions are also provided
2051 to search for all neighbors within a given distance. Parallelization is
2052 achieved for all methods using the BiocParallel framework.")
2053 (license license:gpl3)))
2055 (define-public r-biocsingular
2057 (name "r-biocsingular")
2062 (uri (bioconductor-uri "BiocSingular" version))
2065 "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5"))))
2066 (properties `((upstream-name . "BiocSingular")))
2067 (build-system r-build-system)
2069 `(("r-beachmat" ,r-beachmat)
2070 ("r-biocgenerics" ,r-biocgenerics)
2071 ("r-biocparallel" ,r-biocparallel)
2072 ("r-delayedarray" ,r-delayedarray)
2073 ("r-irlba" ,r-irlba)
2074 ("r-matrix" ,r-matrix)
2077 ("r-s4vectors" ,r-s4vectors)))
2078 (home-page "https://github.com/LTLA/BiocSingular")
2079 (synopsis "Singular value decomposition for Bioconductor packages")
2081 "This package implements exact and approximate methods for singular value
2082 decomposition and principal components analysis, in a framework that allows
2083 them to be easily switched within Bioconductor packages or workflows. Where
2084 possible, parallelization is achieved using the BiocParallel framework.")
2085 (license license:gpl3)))
2087 (define-public r-destiny
2094 (uri (bioconductor-uri "destiny" version))
2097 "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3"))))
2098 (build-system r-build-system)
2100 `(("r-biobase" ,r-biobase)
2101 ("r-biocgenerics" ,r-biocgenerics)
2102 ("r-ggplot2" ,r-ggplot2)
2103 ("r-ggthemes" ,r-ggthemes)
2104 ("r-igraph" ,r-igraph)
2105 ("r-matrix" ,r-matrix)
2106 ("r-proxy" ,r-proxy)
2108 ("r-rcppeigen" ,r-rcppeigen)
2109 ("r-scales" ,r-scales)
2110 ("r-scatterplot3d" ,r-scatterplot3d)
2111 ("r-smoother" ,r-smoother)
2112 ("r-summarizedexperiment" ,r-summarizedexperiment)
2114 (home-page "https://bioconductor.org/packages/destiny/")
2115 (synopsis "Create and plot diffusion maps")
2116 (description "This package provides tools to create and plot diffusion
2118 ;; Any version of the GPL
2119 (license license:gpl3+)))
2121 (define-public r-savr
2128 (uri (bioconductor-uri "savR" version))
2131 "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h"))))
2132 (properties `((upstream-name . "savR")))
2133 (build-system r-build-system)
2135 `(("r-ggplot2" ,r-ggplot2)
2136 ("r-gridextra" ,r-gridextra)
2137 ("r-reshape2" ,r-reshape2)
2138 ("r-scales" ,r-scales)
2140 (home-page "https://github.com/bcalder/savR")
2141 (synopsis "Parse and analyze Illumina SAV files")
2143 "This package provides tools to parse Illumina Sequence Analysis
2144 Viewer (SAV) files, access data, and generate QC plots.")
2145 (license license:agpl3+)))
2147 (define-public r-chipexoqual
2149 (name "r-chipexoqual")
2154 (uri (bioconductor-uri "ChIPexoQual" version))
2157 "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj"))))
2158 (properties `((upstream-name . "ChIPexoQual")))
2159 (build-system r-build-system)
2161 `(("r-biocparallel" ,r-biocparallel)
2162 ("r-biovizbase" ,r-biovizbase)
2163 ("r-broom" ,r-broom)
2164 ("r-data-table" ,r-data-table)
2165 ("r-dplyr" ,r-dplyr)
2166 ("r-genomeinfodb" ,r-genomeinfodb)
2167 ("r-genomicalignments" ,r-genomicalignments)
2168 ("r-genomicranges" ,r-genomicranges)
2169 ("r-ggplot2" ,r-ggplot2)
2170 ("r-hexbin" ,r-hexbin)
2171 ("r-iranges" ,r-iranges)
2172 ("r-rcolorbrewer" ,r-rcolorbrewer)
2173 ("r-rmarkdown" ,r-rmarkdown)
2174 ("r-rsamtools" ,r-rsamtools)
2175 ("r-s4vectors" ,r-s4vectors)
2176 ("r-scales" ,r-scales)
2177 ("r-viridis" ,r-viridis)))
2178 (home-page "https://github.com/keleslab/ChIPexoQual")
2179 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2181 "This package provides a quality control pipeline for ChIP-exo/nexus
2183 (license license:gpl2+)))
2185 (define-public r-copynumber
2187 (name "r-copynumber")
2191 (uri (bioconductor-uri "copynumber" version))
2194 "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp"))))
2195 (build-system r-build-system)
2197 `(("r-s4vectors" ,r-s4vectors)
2198 ("r-iranges" ,r-iranges)
2199 ("r-genomicranges" ,r-genomicranges)
2200 ("r-biocgenerics" ,r-biocgenerics)))
2201 (home-page "https://bioconductor.org/packages/copynumber")
2202 (synopsis "Segmentation of single- and multi-track copy number data")
2204 "This package segments single- and multi-track copy number data by a
2205 penalized least squares regression method.")
2206 (license license:artistic2.0)))
2208 (define-public r-dnacopy
2215 (uri (bioconductor-uri "DNAcopy" version))
2218 "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa"))))
2219 (properties `((upstream-name . "DNAcopy")))
2220 (build-system r-build-system)
2221 (native-inputs `(("gfortran" ,gfortran)))
2222 (home-page "https://bioconductor.org/packages/DNAcopy")
2223 (synopsis "DNA copy number data analysis")
2225 "This package implements the @dfn{circular binary segmentation} (CBS)
2226 algorithm to segment DNA copy number data and identify genomic regions with
2227 abnormal copy number.")
2228 (license license:gpl2+)))
2230 ;; This is a CRAN package, but it uncharacteristically depends on a
2231 ;; Bioconductor package.
2232 (define-public r-htscluster
2234 (name "r-htscluster")
2239 (uri (cran-uri "HTSCluster" version))
2242 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2243 (properties `((upstream-name . "HTSCluster")))
2244 (build-system r-build-system)
2246 `(("r-capushe" ,r-capushe)
2247 ("r-edger" ,r-edger)
2248 ("r-plotrix" ,r-plotrix)))
2249 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2250 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2252 "This package provides a Poisson mixture model is implemented to cluster
2253 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2254 estimation is performed using either the EM or CEM algorithm, and the slope
2255 heuristics are used for model selection (i.e., to choose the number of
2257 (license license:gpl3+)))
2259 (define-public r-deds
2266 (uri (bioconductor-uri "DEDS" version))
2269 "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs"))))
2270 (properties `((upstream-name . "DEDS")))
2271 (build-system r-build-system)
2272 (home-page "https://bioconductor.org/packages/DEDS/")
2273 (synopsis "Differential expression via distance summary for microarray data")
2275 "This library contains functions that calculate various statistics of
2276 differential expression for microarray data, including t statistics, fold
2277 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2278 also implements a new methodology called DEDS (Differential Expression via
2279 Distance Summary), which selects differentially expressed genes by integrating
2280 and summarizing a set of statistics using a weighted distance approach.")
2281 ;; Any version of the LGPL.
2282 (license license:lgpl3+)))
2284 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2286 (define-public r-nbpseq
2293 (uri (cran-uri "NBPSeq" version))
2296 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2297 (properties `((upstream-name . "NBPSeq")))
2298 (build-system r-build-system)
2300 `(("r-qvalue" ,r-qvalue)))
2301 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2302 (synopsis "Negative binomial models for RNA-Seq data")
2304 "This package provides negative binomial models for two-group comparisons
2305 and regression inferences from RNA-sequencing data.")
2306 (license license:gpl2)))
2308 (define-public r-ebseq
2315 (uri (bioconductor-uri "EBSeq" version))
2318 "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83"))))
2319 (properties `((upstream-name . "EBSeq")))
2320 (build-system r-build-system)
2322 `(("r-blockmodeling" ,r-blockmodeling)
2323 ("r-gplots" ,r-gplots)
2324 ("r-testthat" ,r-testthat)))
2325 (home-page "https://bioconductor.org/packages/EBSeq")
2326 (synopsis "Differential expression analysis of RNA-seq data")
2328 "This package provides tools for differential expression analysis at both
2329 gene and isoform level using RNA-seq data")
2330 (license license:artistic2.0)))
2332 (define-public r-lpsymphony
2334 (name "r-lpsymphony")
2339 (uri (bioconductor-uri "lpsymphony" version))
2342 "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv"))))
2343 (build-system r-build-system)
2345 `(("gfortran" ,gfortran)
2348 `(("pkg-config" ,pkg-config)))
2349 (home-page "http://r-forge.r-project.org/projects/rsymphony")
2350 (synopsis "Symphony integer linear programming solver in R")
2352 "This package was derived from Rsymphony. The package provides an R
2353 interface to SYMPHONY, a linear programming solver written in C++. The main
2354 difference between this package and Rsymphony is that it includes the solver
2355 source code, while Rsymphony expects to find header and library files on the
2356 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2357 to install interface to SYMPHONY.")
2358 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2359 ;; lpsimphony is released under the same terms.
2360 (license license:epl1.0)))
2362 (define-public r-ihw
2369 (uri (bioconductor-uri "IHW" version))
2372 "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz"))))
2373 (properties `((upstream-name . "IHW")))
2374 (build-system r-build-system)
2376 `(("r-biocgenerics" ,r-biocgenerics)
2377 ("r-fdrtool" ,r-fdrtool)
2378 ("r-lpsymphony" ,r-lpsymphony)
2379 ("r-slam" ,r-slam)))
2380 (home-page "https://bioconductor.org/packages/IHW")
2381 (synopsis "Independent hypothesis weighting")
2383 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2384 procedure that increases power compared to the method of Benjamini and
2385 Hochberg by assigning data-driven weights to each hypothesis. The input to
2386 IHW is a two-column table of p-values and covariates. The covariate can be
2387 any continuous-valued or categorical variable that is thought to be
2388 informative on the statistical properties of each hypothesis test, while it is
2389 independent of the p-value under the null hypothesis.")
2390 (license license:artistic2.0)))
2392 (define-public r-icobra
2399 (uri (bioconductor-uri "iCOBRA" version))
2402 "1wj0vqyb6h4rddmn4va3182yap9bv4m1r1jlzyjfyrqxhl2sqb1q"))))
2403 (properties `((upstream-name . "iCOBRA")))
2404 (build-system r-build-system)
2406 `(("r-dplyr" ,r-dplyr)
2408 ("r-ggplot2" ,r-ggplot2)
2409 ("r-limma" ,r-limma)
2410 ("r-reshape2" ,r-reshape2)
2412 ("r-scales" ,r-scales)
2413 ("r-shiny" ,r-shiny)
2414 ("r-shinybs" ,r-shinybs)
2415 ("r-shinydashboard" ,r-shinydashboard)
2416 ("r-upsetr" ,r-upsetr)))
2417 (home-page "https://bioconductor.org/packages/iCOBRA")
2418 (synopsis "Comparison and visualization of ranking and assignment methods")
2420 "This package provides functions for calculation and visualization of
2421 performance metrics for evaluation of ranking and binary
2422 classification (assignment) methods. It also contains a Shiny application for
2423 interactive exploration of results.")
2424 (license license:gpl2+)))
2426 (define-public r-mast
2433 (uri (bioconductor-uri "MAST" version))
2436 "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx"))))
2437 (properties `((upstream-name . "MAST")))
2438 (build-system r-build-system)
2440 `(("r-abind" ,r-abind)
2442 ("r-biobase" ,r-biobase)
2443 ("r-biocgenerics" ,r-biocgenerics)
2444 ("r-data-table" ,r-data-table)
2445 ("r-ggplot2" ,r-ggplot2)
2447 ("r-progress" ,r-progress)
2448 ("r-reshape2" ,r-reshape2)
2449 ("r-s4vectors" ,r-s4vectors)
2450 ("r-singlecellexperiment" ,r-singlecellexperiment)
2451 ("r-stringr" ,r-stringr)
2452 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2453 (home-page "https://github.com/RGLab/MAST/")
2454 (synopsis "Model-based analysis of single cell transcriptomics")
2456 "This package provides methods and models for handling zero-inflated
2457 single cell assay data.")
2458 (license license:gpl2+)))
2460 (define-public r-monocle
2467 (uri (bioconductor-uri "monocle" version))
2470 "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z"))))
2471 (build-system r-build-system)
2473 `(("r-biobase" ,r-biobase)
2474 ("r-biocgenerics" ,r-biocgenerics)
2475 ("r-biocviews" ,r-biocviews)
2476 ("r-cluster" ,r-cluster)
2477 ("r-combinat" ,r-combinat)
2478 ("r-ddrtree" ,r-ddrtree)
2479 ("r-densityclust" ,r-densityclust)
2480 ("r-dplyr" ,r-dplyr)
2481 ("r-fastica" ,r-fastica)
2482 ("r-ggplot2" ,r-ggplot2)
2483 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2484 ("r-igraph" ,r-igraph)
2485 ("r-irlba" ,r-irlba)
2486 ("r-limma" ,r-limma)
2488 ("r-matrix" ,r-matrix)
2489 ("r-matrixstats" ,r-matrixstats)
2490 ("r-pheatmap" ,r-pheatmap)
2492 ("r-proxy" ,r-proxy)
2493 ("r-qlcmatrix" ,r-qlcmatrix)
2496 ("r-reshape2" ,r-reshape2)
2497 ("r-rtsne" ,r-rtsne)
2499 ("r-stringr" ,r-stringr)
2500 ("r-tibble" ,r-tibble)
2502 ("r-viridis" ,r-viridis)))
2503 (home-page "https://bioconductor.org/packages/monocle")
2504 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2506 "Monocle performs differential expression and time-series analysis for
2507 single-cell expression experiments. It orders individual cells according to
2508 progress through a biological process, without knowing ahead of time which
2509 genes define progress through that process. Monocle also performs
2510 differential expression analysis, clustering, visualization, and other useful
2511 tasks on single cell expression data. It is designed to work with RNA-Seq and
2512 qPCR data, but could be used with other types as well.")
2513 (license license:artistic2.0)))
2515 (define-public r-monocle3
2523 (url "https://github.com/cole-trapnell-lab/monocle3.git")
2525 (file-name (git-file-name name version))
2528 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2529 (build-system r-build-system)
2531 `(("r-biobase" ,r-biobase)
2532 ("r-biocgenerics" ,r-biocgenerics)
2533 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2534 ("r-dplyr" ,r-dplyr)
2535 ("r-ggplot2" ,r-ggplot2)
2536 ("r-ggrepel" ,r-ggrepel)
2538 ("r-htmlwidgets" ,r-htmlwidgets)
2539 ("r-igraph" ,r-igraph)
2540 ("r-irlba" ,r-irlba)
2541 ("r-limma" ,r-limma)
2542 ("r-lmtest" ,r-lmtest)
2544 ("r-matrix" ,r-matrix)
2545 ("r-matrix-utils" ,r-matrix-utils)
2546 ("r-pbapply" ,r-pbapply)
2547 ("r-pbmcapply" ,r-pbmcapply)
2548 ("r-pheatmap" ,r-pheatmap)
2549 ("r-plotly" ,r-plotly)
2551 ("r-proxy" ,r-proxy)
2553 ("r-purrr" ,r-purrr)
2556 ("r-rcppparallel" ,r-rcppparallel)
2557 ("r-reshape2" ,r-reshape2)
2558 ("r-reticulate" ,r-reticulate)
2559 ("r-rhpcblasctl" ,r-rhpcblasctl)
2560 ("r-rtsne" ,r-rtsne)
2561 ("r-shiny" ,r-shiny)
2563 ("r-spdep" ,r-spdep)
2564 ("r-speedglm" ,r-speedglm)
2565 ("r-stringr" ,r-stringr)
2566 ("r-singlecellexperiment" ,r-singlecellexperiment)
2567 ("r-tibble" ,r-tibble)
2568 ("r-tidyr" ,r-tidyr)
2570 ("r-viridis" ,r-viridis)))
2571 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2572 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2574 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2575 (license license:expat)))
2577 (define-public r-noiseq
2584 (uri (bioconductor-uri "NOISeq" version))
2587 "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j"))))
2588 (properties `((upstream-name . "NOISeq")))
2589 (build-system r-build-system)
2591 `(("r-biobase" ,r-biobase)
2592 ("r-matrix" ,r-matrix)))
2593 (home-page "https://bioconductor.org/packages/NOISeq")
2594 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
2596 "This package provides tools to support the analysis of RNA-seq
2597 expression data or other similar kind of data. It provides exploratory plots
2598 to evaluate saturation, count distribution, expression per chromosome, type of
2599 detected features, features length, etc. It also supports the analysis of
2600 differential expression between two experimental conditions with no parametric
2602 (license license:artistic2.0)))
2604 (define-public r-scdd
2611 (uri (bioconductor-uri "scDD" version))
2614 "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf"))))
2615 (properties `((upstream-name . "scDD")))
2616 (build-system r-build-system)
2619 ("r-biocparallel" ,r-biocparallel)
2620 ("r-ebseq" ,r-ebseq)
2621 ("r-fields" ,r-fields)
2622 ("r-ggplot2" ,r-ggplot2)
2623 ("r-mclust" ,r-mclust)
2624 ("r-outliers" ,r-outliers)
2625 ("r-s4vectors" ,r-s4vectors)
2626 ("r-scran" ,r-scran)
2627 ("r-singlecellexperiment" ,r-singlecellexperiment)
2628 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2629 (home-page "https://github.com/kdkorthauer/scDD")
2630 (synopsis "Mixture modeling of single-cell RNA-seq data")
2632 "This package implements a method to analyze single-cell RNA-seq data
2633 utilizing flexible Dirichlet Process mixture models. Genes with differential
2634 distributions of expression are classified into several interesting patterns
2635 of differences between two conditions. The package also includes functions
2636 for simulating data with these patterns from negative binomial
2638 (license license:gpl2)))
2640 (define-public r-scone
2647 (uri (bioconductor-uri "scone" version))
2650 "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck"))))
2651 (build-system r-build-system)
2653 `(("r-aroma-light" ,r-aroma-light)
2654 ("r-biocparallel" ,r-biocparallel)
2656 ("r-class" ,r-class)
2657 ("r-cluster" ,r-cluster)
2658 ("r-compositions" ,r-compositions)
2659 ("r-diptest" ,r-diptest)
2660 ("r-edger" ,r-edger)
2662 ("r-gplots" ,r-gplots)
2663 ("r-hexbin" ,r-hexbin)
2664 ("r-limma" ,r-limma)
2665 ("r-matrixstats" ,r-matrixstats)
2666 ("r-mixtools" ,r-mixtools)
2667 ("r-rarpack" ,r-rarpack)
2668 ("r-rcolorbrewer" ,r-rcolorbrewer)
2669 ("r-rhdf5" ,r-rhdf5)
2670 ("r-ruvseq" ,r-ruvseq)
2671 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2672 (home-page "https://bioconductor.org/packages/scone")
2673 (synopsis "Single cell overview of normalized expression data")
2675 "SCONE is an R package for comparing and ranking the performance of
2676 different normalization schemes for single-cell RNA-seq and other
2677 high-throughput analyses.")
2678 (license license:artistic2.0)))
2680 (define-public r-geoquery
2687 (uri (bioconductor-uri "GEOquery" version))
2690 "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr"))))
2691 (properties `((upstream-name . "GEOquery")))
2692 (build-system r-build-system)
2694 `(("r-biobase" ,r-biobase)
2695 ("r-dplyr" ,r-dplyr)
2697 ("r-limma" ,r-limma)
2698 ("r-magrittr" ,r-magrittr)
2699 ("r-readr" ,r-readr)
2700 ("r-tidyr" ,r-tidyr)
2701 ("r-xml2" ,r-xml2)))
2702 (home-page "https://github.com/seandavi/GEOquery/")
2703 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
2705 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
2706 microarray data. Given the rich and varied nature of this resource, it is
2707 only natural to want to apply BioConductor tools to these data. GEOquery is
2708 the bridge between GEO and BioConductor.")
2709 (license license:gpl2)))
2711 (define-public r-illuminaio
2713 (name "r-illuminaio")
2718 (uri (bioconductor-uri "illuminaio" version))
2721 "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8"))))
2722 (build-system r-build-system)
2724 `(("r-base64" ,r-base64)))
2725 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
2726 (synopsis "Parse Illumina microarray output files")
2728 "This package provides tools for parsing Illumina's microarray output
2729 files, including IDAT.")
2730 (license license:gpl2)))
2732 (define-public r-siggenes
2739 (uri (bioconductor-uri "siggenes" version))
2742 "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib"))))
2743 (build-system r-build-system)
2745 `(("r-biobase" ,r-biobase)
2746 ("r-multtest" ,r-multtest)
2747 ("r-scrime" ,r-scrime)))
2748 (home-page "https://bioconductor.org/packages/siggenes/")
2750 "Multiple testing using SAM and Efron's empirical Bayes approaches")
2752 "This package provides tools for the identification of differentially
2753 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
2754 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
2755 Bayes Analyses of Microarrays} (EBAM).")
2756 (license license:lgpl2.0+)))
2758 (define-public r-bumphunter
2760 (name "r-bumphunter")
2765 (uri (bioconductor-uri "bumphunter" version))
2768 "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx"))))
2769 (build-system r-build-system)
2771 `(("r-annotationdbi" ,r-annotationdbi)
2772 ("r-biocgenerics" ,r-biocgenerics)
2773 ("r-dorng" ,r-dorng)
2774 ("r-foreach" ,r-foreach)
2775 ("r-genomeinfodb" ,r-genomeinfodb)
2776 ("r-genomicfeatures" ,r-genomicfeatures)
2777 ("r-genomicranges" ,r-genomicranges)
2778 ("r-iranges" ,r-iranges)
2779 ("r-iterators" ,r-iterators)
2780 ("r-limma" ,r-limma)
2781 ("r-locfit" ,r-locfit)
2782 ("r-matrixstats" ,r-matrixstats)
2783 ("r-s4vectors" ,r-s4vectors)))
2784 (home-page "https://github.com/ririzarr/bumphunter")
2785 (synopsis "Find bumps in genomic data")
2787 "This package provides tools for finding bumps in genomic data in order
2788 to identify differentially methylated regions in epigenetic epidemiology
2790 (license license:artistic2.0)))
2792 (define-public r-minfi
2799 (uri (bioconductor-uri "minfi" version))
2802 "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd"))))
2803 (build-system r-build-system)
2805 `(("r-beanplot" ,r-beanplot)
2806 ("r-biobase" ,r-biobase)
2807 ("r-biocgenerics" ,r-biocgenerics)
2808 ("r-biocparallel" ,r-biocparallel)
2809 ("r-biostrings" ,r-biostrings)
2810 ("r-bumphunter" ,r-bumphunter)
2811 ("r-data-table" ,r-data-table)
2812 ("r-delayedarray" ,r-delayedarray)
2813 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2814 ("r-genefilter" ,r-genefilter)
2815 ("r-genomeinfodb" ,r-genomeinfodb)
2816 ("r-genomicranges" ,r-genomicranges)
2817 ("r-geoquery" ,r-geoquery)
2818 ("r-hdf5array" ,r-hdf5array)
2819 ("r-illuminaio" ,r-illuminaio)
2820 ("r-iranges" ,r-iranges)
2821 ("r-lattice" ,r-lattice)
2822 ("r-limma" ,r-limma)
2824 ("r-mclust" ,r-mclust)
2826 ("r-nor1mix" ,r-nor1mix)
2827 ("r-preprocesscore" ,r-preprocesscore)
2828 ("r-quadprog" ,r-quadprog)
2829 ("r-rcolorbrewer" ,r-rcolorbrewer)
2830 ("r-reshape" ,r-reshape)
2831 ("r-s4vectors" ,r-s4vectors)
2832 ("r-siggenes" ,r-siggenes)
2833 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2834 (home-page "https://github.com/hansenlab/minfi")
2835 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
2837 "This package provides tools to analyze and visualize Illumina Infinium
2838 methylation arrays.")
2839 (license license:artistic2.0)))
2841 (define-public r-methylumi
2843 (name "r-methylumi")
2848 (uri (bioconductor-uri "methylumi" version))
2851 "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f"))))
2852 (build-system r-build-system)
2854 `(("r-annotate" ,r-annotate)
2855 ("r-annotationdbi" ,r-annotationdbi)
2856 ("r-biobase" ,r-biobase)
2857 ("r-biocgenerics" ,r-biocgenerics)
2858 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
2859 ("r-genefilter" ,r-genefilter)
2860 ("r-genomeinfodb" ,r-genomeinfodb)
2861 ("r-genomicranges" ,r-genomicranges)
2862 ("r-ggplot2" ,r-ggplot2)
2863 ("r-illuminaio" ,r-illuminaio)
2864 ("r-iranges" ,r-iranges)
2865 ("r-lattice" ,r-lattice)
2866 ("r-matrixstats" ,r-matrixstats)
2867 ("r-minfi" ,r-minfi)
2868 ("r-reshape2" ,r-reshape2)
2869 ("r-s4vectors" ,r-s4vectors)
2870 ("r-scales" ,r-scales)
2871 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2872 (home-page "https://bioconductor.org/packages/methylumi")
2873 (synopsis "Handle Illumina methylation data")
2875 "This package provides classes for holding and manipulating Illumina
2876 methylation data. Based on eSet, it can contain MIAME information, sample
2877 information, feature information, and multiple matrices of data. An
2878 \"intelligent\" import function, methylumiR can read the Illumina text files
2879 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
2880 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
2881 background correction, and quality control features for GoldenGate, Infinium,
2882 and Infinium HD arrays are also included.")
2883 (license license:gpl2)))
2885 (define-public r-lumi
2892 (uri (bioconductor-uri "lumi" version))
2895 "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba"))))
2896 (build-system r-build-system)
2898 `(("r-affy" ,r-affy)
2899 ("r-annotate" ,r-annotate)
2900 ("r-annotationdbi" ,r-annotationdbi)
2901 ("r-biobase" ,r-biobase)
2903 ("r-genomicfeatures" ,r-genomicfeatures)
2904 ("r-genomicranges" ,r-genomicranges)
2905 ("r-kernsmooth" ,r-kernsmooth)
2906 ("r-lattice" ,r-lattice)
2908 ("r-methylumi" ,r-methylumi)
2910 ("r-nleqslv" ,r-nleqslv)
2911 ("r-preprocesscore" ,r-preprocesscore)
2912 ("r-rsqlite" ,r-rsqlite)))
2913 (home-page "https://bioconductor.org/packages/lumi")
2914 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
2916 "The lumi package provides an integrated solution for the Illumina
2917 microarray data analysis. It includes functions of Illumina
2918 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
2919 variance stabilization, normalization and gene annotation at the probe level.
2920 It also includes the functions of processing Illumina methylation microarrays,
2921 especially Illumina Infinium methylation microarrays.")
2922 (license license:lgpl2.0+)))
2924 (define-public r-linnorm
2931 (uri (bioconductor-uri "Linnorm" version))
2934 "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5"))))
2935 (properties `((upstream-name . "Linnorm")))
2936 (build-system r-build-system)
2938 `(("r-amap" ,r-amap)
2939 ("r-apcluster" ,r-apcluster)
2940 ("r-ellipse" ,r-ellipse)
2941 ("r-fastcluster" ,r-fastcluster)
2943 ("r-ggdendro" ,r-ggdendro)
2944 ("r-ggplot2" ,r-ggplot2)
2945 ("r-gmodels" ,r-gmodels)
2946 ("r-igraph" ,r-igraph)
2947 ("r-limma" ,r-limma)
2949 ("r-mclust" ,r-mclust)
2951 ("r-rcpparmadillo" ,r-rcpparmadillo)
2952 ("r-rtsne" ,r-rtsne)
2953 ("r-statmod" ,r-statmod)
2954 ("r-vegan" ,r-vegan)
2956 (home-page "http://www.jjwanglab.org/Linnorm/")
2957 (synopsis "Linear model and normality based transformation method")
2959 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
2960 count data or any large scale count data. It transforms such datasets for
2961 parametric tests. In addition to the transformtion function (@code{Linnorm}),
2962 the following pipelines are implemented:
2965 @item Library size/batch effect normalization (@code{Linnorm.Norm})
2966 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
2967 clustering or hierarchical clustering (@code{Linnorm.tSNE},
2968 @code{Linnorm.PCA}, @code{Linnorm.HClust})
2969 @item Differential expression analysis or differential peak detection using
2970 limma (@code{Linnorm.limma})
2971 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
2972 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
2973 @item Stable gene selection for scRNA-seq data; for users without or who do
2974 not want to rely on spike-in genes (@code{Linnorm.SGenes})
2975 @item Data imputation (@code{Linnorm.DataImput}).
2978 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
2979 @code{RnaXSim} function is included for simulating RNA-seq data for the
2980 evaluation of DEG analysis methods.")
2981 (license license:expat)))
2983 (define-public r-ioniser
2990 (uri (bioconductor-uri "IONiseR" version))
2993 "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y"))))
2994 (properties `((upstream-name . "IONiseR")))
2995 (build-system r-build-system)
2997 `(("r-biocgenerics" ,r-biocgenerics)
2998 ("r-biocparallel" ,r-biocparallel)
2999 ("r-biostrings" ,r-biostrings)
3000 ("r-bit64" ,r-bit64)
3001 ("r-dplyr" ,r-dplyr)
3002 ("r-ggplot2" ,r-ggplot2)
3003 ("r-magrittr" ,r-magrittr)
3004 ("r-rhdf5" ,r-rhdf5)
3005 ("r-shortread" ,r-shortread)
3006 ("r-stringr" ,r-stringr)
3007 ("r-tibble" ,r-tibble)
3008 ("r-tidyr" ,r-tidyr)
3009 ("r-xvector" ,r-xvector)))
3010 (home-page "https://bioconductor.org/packages/IONiseR/")
3011 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3013 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3014 MinION data. It extracts summary statistics from a set of fast5 files and can
3015 be used either before or after base calling. In addition to standard
3016 summaries of the read-types produced, it provides a number of plots for
3017 visualising metrics relative to experiment run time or spatially over the
3018 surface of a flowcell.")
3019 (license license:expat)))
3021 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3022 (define-public r-gkmsvm
3029 (uri (cran-uri "gkmSVM" version))
3032 "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
3033 (properties `((upstream-name . "gkmSVM")))
3034 (build-system r-build-system)
3036 `(("r-biocgenerics" ,r-biocgenerics)
3037 ("r-biostrings" ,r-biostrings)
3038 ("r-genomeinfodb" ,r-genomeinfodb)
3039 ("r-genomicranges" ,r-genomicranges)
3040 ("r-iranges" ,r-iranges)
3041 ("r-kernlab" ,r-kernlab)
3044 ("r-rtracklayer" ,r-rtracklayer)
3045 ("r-s4vectors" ,r-s4vectors)
3046 ("r-seqinr" ,r-seqinr)))
3047 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3048 (synopsis "Gapped-kmer support vector machine")
3050 "This R package provides tools for training gapped-kmer SVM classifiers
3051 for DNA and protein sequences. This package supports several sequence
3052 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3053 (license license:gpl2+)))
3055 (define-public r-triform
3062 (uri (bioconductor-uri "triform" version))
3065 "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya"))))
3066 (build-system r-build-system)
3068 `(("r-biocgenerics" ,r-biocgenerics)
3069 ("r-iranges" ,r-iranges)
3070 ("r-yaml" ,r-yaml)))
3071 (home-page "https://bioconductor.org/packages/triform/")
3072 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3074 "The Triform algorithm uses model-free statistics to identify peak-like
3075 distributions of TF ChIP sequencing reads, taking advantage of an improved
3076 peak definition in combination with known profile characteristics.")
3077 (license license:gpl2)))
3079 (define-public r-varianttools
3081 (name "r-varianttools")
3086 (uri (bioconductor-uri "VariantTools" version))
3089 "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql"))))
3090 (properties `((upstream-name . "VariantTools")))
3091 (build-system r-build-system)
3093 `(("r-biobase" ,r-biobase)
3094 ("r-biocgenerics" ,r-biocgenerics)
3095 ("r-biocparallel" ,r-biocparallel)
3096 ("r-biostrings" ,r-biostrings)
3097 ("r-bsgenome" ,r-bsgenome)
3098 ("r-genomeinfodb" ,r-genomeinfodb)
3099 ("r-genomicfeatures" ,r-genomicfeatures)
3100 ("r-genomicranges" ,r-genomicranges)
3101 ("r-iranges" ,r-iranges)
3102 ("r-matrix" ,r-matrix)
3103 ("r-rsamtools" ,r-rsamtools)
3104 ("r-rtracklayer" ,r-rtracklayer)
3105 ("r-s4vectors" ,r-s4vectors)
3106 ("r-variantannotation" ,r-variantannotation)))
3107 (home-page "https://bioconductor.org/packages/VariantTools/")
3108 (synopsis "Tools for exploratory analysis of variant calls")
3110 "Explore, diagnose, and compare variant calls using filters. The
3111 VariantTools package supports a workflow for loading data, calling single
3112 sample variants and tumor-specific somatic mutations or other sample-specific
3113 variant types (e.g., RNA editing). Most of the functions operate on
3114 alignments (BAM files) or datasets of called variants. The user is expected
3115 to have already aligned the reads with a separate tool, e.g., GSNAP via
3117 (license license:artistic2.0)))
3119 (define-public r-heatplus
3126 (uri (bioconductor-uri "Heatplus" version))
3129 "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6"))))
3130 (properties `((upstream-name . "Heatplus")))
3131 (build-system r-build-system)
3133 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3134 (home-page "https://github.com/alexploner/Heatplus")
3135 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3137 "This package provides tools to display a rectangular heatmap (intensity
3138 plot) of a data matrix. By default, both samples (columns) and features (row)
3139 of the matrix are sorted according to a hierarchical clustering, and the
3140 corresponding dendrogram is plotted. Optionally, panels with additional
3141 information about samples and features can be added to the plot.")
3142 (license license:gpl2+)))
3144 (define-public r-gosemsim
3151 (uri (bioconductor-uri "GOSemSim" version))
3154 "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg"))))
3155 (properties `((upstream-name . "GOSemSim")))
3156 (build-system r-build-system)
3158 `(("r-annotationdbi" ,r-annotationdbi)
3159 ("r-go-db" ,r-go-db)
3160 ("r-rcpp" ,r-rcpp)))
3161 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3162 (synopsis "GO-terms semantic similarity measures")
3164 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3165 quantitative ways to compute similarities between genes and gene groups, and
3166 have became important basis for many bioinformatics analysis approaches.
3167 GOSemSim is an R package for semantic similarity computation among GO terms,
3168 sets of GO terms, gene products and gene clusters.")
3169 (license license:artistic2.0)))
3171 (define-public r-anota
3178 (uri (bioconductor-uri "anota" version))
3181 "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c"))))
3182 (build-system r-build-system)
3184 `(("r-multtest" ,r-multtest)
3185 ("r-qvalue" ,r-qvalue)))
3186 (home-page "https://bioconductor.org/packages/anota/")
3187 (synopsis "Analysis of translational activity")
3189 "Genome wide studies of translational control is emerging as a tool to
3190 study various biological conditions. The output from such analysis is both
3191 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3192 involved in translation (the actively translating mRNA level) for each mRNA.
3193 The standard analysis of such data strives towards identifying differential
3194 translational between two or more sample classes - i.e. differences in
3195 actively translated mRNA levels that are independent of underlying differences
3196 in cytosolic mRNA levels. This package allows for such analysis using partial
3197 variances and the random variance model. As 10s of thousands of mRNAs are
3198 analyzed in parallel the library performs a number of tests to assure that
3199 the data set is suitable for such analysis.")
3200 (license license:gpl3)))
3202 (define-public r-sigpathway
3204 (name "r-sigpathway")
3209 (uri (bioconductor-uri "sigPathway" version))
3212 "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7"))))
3213 (properties `((upstream-name . "sigPathway")))
3214 (build-system r-build-system)
3215 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3216 (synopsis "Pathway analysis")
3218 "This package is used to conduct pathway analysis by calculating the NT_k
3219 and NE_k statistics in a statistical framework for determining whether a
3220 specified group of genes for a pathway has a coordinated association with a
3221 phenotype of interest.")
3222 (license license:gpl2)))
3224 (define-public r-fgsea
3231 (uri (bioconductor-uri "fgsea" version))
3234 "1k2f9hkp1mvc9fpqzhbf08jd0yg4xaa312v9vy37fxd9pyrwp5a6"))))
3235 (build-system r-build-system)
3238 ("r-biocparallel" ,r-biocparallel)
3239 ("r-data-table" ,r-data-table)
3240 ("r-fastmatch" ,r-fastmatch)
3241 ("r-ggplot2" ,r-ggplot2)
3242 ("r-gridextra" ,r-gridextra)
3243 ("r-matrix" ,r-matrix)
3244 ("r-rcpp" ,r-rcpp)))
3245 (home-page "https://github.com/ctlab/fgsea/")
3246 (synopsis "Fast gene set enrichment analysis")
3248 "The package implements an algorithm for fast gene set enrichment
3249 analysis. Using the fast algorithm allows to make more permutations and get
3250 more fine grained p-values, which allows to use accurate stantard approaches
3251 to multiple hypothesis correction.")
3252 (license license:expat)))
3254 (define-public r-dose
3261 (uri (bioconductor-uri "DOSE" version))
3264 "06jm1mnfd92s84f21562vsmj6jfkravfqf4lcxx2lk7s4ll66znj"))))
3265 (properties `((upstream-name . "DOSE")))
3266 (build-system r-build-system)
3268 `(("r-annotationdbi" ,r-annotationdbi)
3269 ("r-biocparallel" ,r-biocparallel)
3270 ("r-do-db" ,r-do-db)
3271 ("r-fgsea" ,r-fgsea)
3272 ("r-ggplot2" ,r-ggplot2)
3273 ("r-gosemsim" ,r-gosemsim)
3274 ("r-qvalue" ,r-qvalue)
3275 ("r-reshape2" ,r-reshape2)
3276 ("r-s4vectors" ,r-s4vectors)))
3277 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3278 (synopsis "Disease ontology semantic and enrichment analysis")
3280 "This package implements five methods proposed by Resnik, Schlicker,
3281 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3282 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3283 including hypergeometric model and gene set enrichment analysis are also
3284 implemented for discovering disease associations of high-throughput biological
3286 (license license:artistic2.0)))
3288 (define-public r-enrichplot
3290 (name "r-enrichplot")
3295 (uri (bioconductor-uri "enrichplot" version))
3298 "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h"))))
3299 (build-system r-build-system)
3301 `(("r-annotationdbi" ,r-annotationdbi)
3302 ("r-cowplot" ,r-cowplot)
3304 ("r-europepmc" ,r-europepmc)
3305 ("r-ggplot2" ,r-ggplot2)
3306 ("r-ggplotify" ,r-ggplotify)
3307 ("r-ggraph" ,r-ggraph)
3308 ("r-ggridges" ,r-ggridges)
3309 ("r-gosemsim" ,r-gosemsim)
3310 ("r-gridextra" ,r-gridextra)
3311 ("r-igraph" ,r-igraph)
3312 ("r-purrr" ,r-purrr)
3313 ("r-rcolorbrewer" ,r-rcolorbrewer)
3314 ("r-reshape2" ,r-reshape2)
3315 ("r-upsetr" ,r-upsetr)))
3316 (home-page "https://github.com/GuangchuangYu/enrichplot")
3317 (synopsis "Visualization of functional enrichment result")
3319 "The enrichplot package implements several visualization methods for
3320 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3321 All the visualization methods are developed based on ggplot2 graphics.")
3322 (license license:artistic2.0)))
3324 (define-public r-clusterprofiler
3326 (name "r-clusterprofiler")
3331 (uri (bioconductor-uri "clusterProfiler" version))
3334 "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq"))))
3336 `((upstream-name . "clusterProfiler")))
3337 (build-system r-build-system)
3339 `(("r-annotationdbi" ,r-annotationdbi)
3341 ("r-enrichplot" ,r-enrichplot)
3342 ("r-ggplot2" ,r-ggplot2)
3343 ("r-go-db" ,r-go-db)
3344 ("r-gosemsim" ,r-gosemsim)
3345 ("r-magrittr" ,r-magrittr)
3347 ("r-qvalue" ,r-qvalue)
3348 ("r-rvcheck" ,r-rvcheck)
3349 ("r-tidyr" ,r-tidyr)))
3350 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3351 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3353 "This package implements methods to analyze and visualize functional
3354 profiles (GO and KEGG) of gene and gene clusters.")
3355 (license license:artistic2.0)))
3357 (define-public r-mlinterfaces
3359 (name "r-mlinterfaces")
3364 (uri (bioconductor-uri "MLInterfaces" version))
3367 "1c1hciwy37zpr5bzdjj2xxx2r4jdfmr5w0zmg010lm2985z41gqh"))))
3368 (properties `((upstream-name . "MLInterfaces")))
3369 (build-system r-build-system)
3371 `(("r-annotate" ,r-annotate)
3372 ("r-biobase" ,r-biobase)
3373 ("r-biocgenerics" ,r-biocgenerics)
3374 ("r-cluster" ,r-cluster)
3377 ("r-gdata" ,r-gdata)
3378 ("r-genefilter" ,r-genefilter)
3379 ("r-ggvis" ,r-ggvis)
3380 ("r-hwriter" ,r-hwriter)
3382 ("r-mlbench" ,r-mlbench)
3384 ("r-rcolorbrewer" ,r-rcolorbrewer)
3386 ("r-rpart" ,r-rpart)
3387 ("r-sfsmisc" ,r-sfsmisc)
3388 ("r-shiny" ,r-shiny)
3389 ("r-threejs" ,r-threejs)))
3390 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3391 (synopsis "Interfaces to R machine learning procedures")
3393 "This package provides uniform interfaces to machine learning code for
3394 data in R and Bioconductor containers.")
3395 ;; Any version of the LGPL.
3396 (license license:lgpl2.1+)))
3398 (define-public r-annaffy
3405 (uri (bioconductor-uri "annaffy" version))
3408 "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9"))))
3409 (build-system r-build-system)
3412 (modify-phases %standard-phases
3413 (add-after 'unpack 'remove-reference-to-non-free-data
3415 (substitute* "DESCRIPTION"
3419 `(("r-annotationdbi" ,r-annotationdbi)
3420 ("r-biobase" ,r-biobase)
3422 ("r-go-db" ,r-go-db)))
3423 (home-page "https://bioconductor.org/packages/annaffy/")
3424 (synopsis "Annotation tools for Affymetrix biological metadata")
3426 "This package provides functions for handling data from Bioconductor
3427 Affymetrix annotation data packages. It produces compact HTML and text
3428 reports including experimental data and URL links to many online databases.
3429 It allows searching of biological metadata using various criteria.")
3430 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3431 ;; the LGPL 2.1 is included.
3432 (license license:lgpl2.1+)))
3434 (define-public r-a4core
3441 (uri (bioconductor-uri "a4Core" version))
3444 "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7"))))
3445 (properties `((upstream-name . "a4Core")))
3446 (build-system r-build-system)
3448 `(("r-biobase" ,r-biobase)
3449 ("r-glmnet" ,r-glmnet)))
3450 (home-page "https://bioconductor.org/packages/a4Core")
3451 (synopsis "Automated Affymetrix array analysis core package")
3453 "This is the core package for the automated analysis of Affymetrix
3455 (license license:gpl3)))
3457 (define-public r-a4classif
3459 (name "r-a4classif")
3464 (uri (bioconductor-uri "a4Classif" version))
3467 "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0"))))
3468 (properties `((upstream-name . "a4Classif")))
3469 (build-system r-build-system)
3471 `(("r-a4core" ,r-a4core)
3472 ("r-a4preproc" ,r-a4preproc)
3473 ("r-glmnet" ,r-glmnet)
3474 ("r-mlinterfaces" ,r-mlinterfaces)
3477 ("r-varselrf" ,r-varselrf)))
3478 (home-page "https://bioconductor.org/packages/a4Classif/")
3479 (synopsis "Automated Affymetrix array analysis classification package")
3481 "This is the classification package for the automated analysis of
3482 Affymetrix arrays.")
3483 (license license:gpl3)))
3485 (define-public r-a4preproc
3487 (name "r-a4preproc")
3492 (uri (bioconductor-uri "a4Preproc" version))
3495 "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr"))))
3496 (properties `((upstream-name . "a4Preproc")))
3497 (build-system r-build-system)
3499 `(("r-annotationdbi" ,r-annotationdbi)))
3500 (home-page "https://bioconductor.org/packages/a4Preproc/")
3501 (synopsis "Automated Affymetrix array analysis preprocessing package")
3503 "This is a package for the automated analysis of Affymetrix arrays. It
3504 is used for preprocessing the arrays.")
3505 (license license:gpl3)))
3507 (define-public r-a4reporting
3509 (name "r-a4reporting")
3514 (uri (bioconductor-uri "a4Reporting" version))
3517 "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj"))))
3518 (properties `((upstream-name . "a4Reporting")))
3519 (build-system r-build-system)
3521 `(("r-annaffy" ,r-annaffy)
3522 ("r-xtable" ,r-xtable)))
3523 (home-page "https://bioconductor.org/packages/a4Reporting/")
3524 (synopsis "Automated Affymetrix array analysis reporting package")
3526 "This is a package for the automated analysis of Affymetrix arrays. It
3527 provides reporting features.")
3528 (license license:gpl3)))
3530 (define-public r-a4base
3537 (uri (bioconductor-uri "a4Base" version))
3540 "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1"))))
3541 (properties `((upstream-name . "a4Base")))
3542 (build-system r-build-system)
3544 `(("r-a4core" ,r-a4core)
3545 ("r-a4preproc" ,r-a4preproc)
3546 ("r-annaffy" ,r-annaffy)
3547 ("r-annotationdbi" ,r-annotationdbi)
3548 ("r-biobase" ,r-biobase)
3549 ("r-genefilter" ,r-genefilter)
3550 ("r-glmnet" ,r-glmnet)
3551 ("r-gplots" ,r-gplots)
3552 ("r-limma" ,r-limma)
3554 ("r-multtest" ,r-multtest)))
3555 (home-page "https://bioconductor.org/packages/a4Base/")
3556 (synopsis "Automated Affymetrix array analysis base package")
3558 "This package provides basic features for the automated analysis of
3559 Affymetrix arrays.")
3560 (license license:gpl3)))
3569 (uri (bioconductor-uri "a4" version))
3572 "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy"))))
3573 (build-system r-build-system)
3575 `(("r-a4base" ,r-a4base)
3576 ("r-a4classif" ,r-a4classif)
3577 ("r-a4core" ,r-a4core)
3578 ("r-a4preproc" ,r-a4preproc)
3579 ("r-a4reporting" ,r-a4reporting)))
3580 (home-page "https://bioconductor.org/packages/a4/")
3581 (synopsis "Automated Affymetrix array analysis umbrella package")
3583 "This package provides a software suite for the automated analysis of
3584 Affymetrix arrays.")
3585 (license license:gpl3)))
3587 (define-public r-abseqr
3594 (uri (bioconductor-uri "abseqR" version))
3597 "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r"))))
3598 (properties `((upstream-name . "abseqR")))
3599 (build-system r-build-system)
3601 `(("pandoc" ,ghc-pandoc)))
3603 `(("r-biocparallel" ,r-biocparallel)
3604 ("r-biocstyle" ,r-biocstyle)
3605 ("r-circlize" ,r-circlize)
3606 ("r-flexdashboard" ,r-flexdashboard)
3607 ("r-ggcorrplot" ,r-ggcorrplot)
3608 ("r-ggdendro" ,r-ggdendro)
3609 ("r-ggplot2" ,r-ggplot2)
3610 ("r-gridextra" ,r-gridextra)
3611 ("r-knitr" ,r-knitr)
3612 ("r-plotly" ,r-plotly)
3615 ("r-rcolorbrewer" ,r-rcolorbrewer)
3616 ("r-reshape2" ,r-reshape2)
3617 ("r-rmarkdown" ,r-rmarkdown)
3618 ("r-stringr" ,r-stringr)
3619 ("r-vegan" ,r-vegan)
3620 ("r-venndiagram" ,r-venndiagram)))
3621 (home-page "https://github.com/malhamdoosh/abseqR")
3622 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
3624 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
3625 sequencing datasets generated from antibody libraries and abseqR is one of its
3626 packages. AbseqR empowers the users of abseqPy with plotting and reporting
3627 capabilities and allows them to generate interactive HTML reports for the
3628 convenience of viewing and sharing with other researchers. Additionally,
3629 abseqR extends abseqPy to compare multiple repertoire analyses and perform
3630 further downstream analysis on its output.")
3631 (license license:gpl3)))
3633 (define-public r-bacon
3640 (uri (bioconductor-uri "bacon" version))
3643 "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q"))))
3644 (build-system r-build-system)
3646 `(("r-biocparallel" ,r-biocparallel)
3647 ("r-ellipse" ,r-ellipse)
3648 ("r-ggplot2" ,r-ggplot2)))
3649 (home-page "https://bioconductor.org/packages/bacon/")
3650 (synopsis "Controlling bias and inflation in association studies")
3652 "Bacon can be used to remove inflation and bias often observed in
3653 epigenome- and transcriptome-wide association studies. To this end bacon
3654 constructs an empirical null distribution using a Gibbs Sampling algorithm by
3655 fitting a three-component normal mixture on z-scores.")
3656 (license license:gpl2+)))
3658 (define-public r-rgadem
3665 (uri (bioconductor-uri "rGADEM" version))
3668 "1zf8ayllf1i79wc39vyln2hii1bgg88sw6h1hngkqx4phyvl9q18"))))
3669 (properties `((upstream-name . "rGADEM")))
3670 (build-system r-build-system)
3672 `(("r-biostrings" ,r-biostrings)
3673 ("r-bsgenome" ,r-bsgenome)
3674 ("r-iranges" ,r-iranges)
3675 ("r-seqlogo" ,r-seqlogo)))
3676 (home-page "https://bioconductor.org/packages/rGADEM/")
3677 (synopsis "De novo sequence motif discovery")
3679 "rGADEM is an efficient de novo motif discovery tool for large-scale
3680 genomic sequence data.")
3681 (license license:artistic2.0)))
3683 (define-public r-motiv
3690 (uri (bioconductor-uri "MotIV" version))
3693 "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf"))))
3694 (properties `((upstream-name . "MotIV")))
3695 (build-system r-build-system)
3699 `(("r-biocgenerics" ,r-biocgenerics)
3700 ("r-biostrings" ,r-biostrings)
3701 ("r-iranges" ,r-iranges)
3702 ("r-lattice" ,r-lattice)
3703 ("r-rgadem" ,r-rgadem)
3704 ("r-s4vectors" ,r-s4vectors)))
3705 (home-page "https://bioconductor.org/packages/MotIV/")
3706 (synopsis "Motif identification and validation")
3708 "This package is used for the identification and validation of sequence
3709 motifs. It makes use of STAMP for comparing a set of motifs to a given
3710 database (e.g. JASPAR). It can also be used to visualize motifs, motif
3711 distributions, modules and filter motifs.")
3712 (license license:gpl2)))
3714 (define-public r-motifstack
3716 (name "r-motifstack")
3721 (uri (bioconductor-uri "motifStack" version))
3724 "0qbv5pvn1g9xfn221vqjmp9vfxpkda1wxkn0kyn2nqyb80d4jf9f"))))
3725 (properties `((upstream-name . "motifStack")))
3726 (build-system r-build-system)
3728 `(("r-ade4" ,r-ade4)
3729 ("r-biostrings" ,r-biostrings)
3730 ("r-grimport2" ,r-grimport2)
3731 ("r-htmlwidgets" ,r-htmlwidgets)
3732 ("r-motiv" ,r-motiv)
3733 ("r-scales" ,r-scales)
3735 (home-page "https://bioconductor.org/packages/motifStack/")
3736 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
3738 "The motifStack package is designed for graphic representation of
3739 multiple motifs with different similarity scores. It works with both DNA/RNA
3740 sequence motifs and amino acid sequence motifs. In addition, it provides the
3741 flexibility for users to customize the graphic parameters such as the font
3742 type and symbol colors.")
3743 (license license:gpl2+)))
3745 (define-public r-genomicscores
3747 (name "r-genomicscores")
3752 (uri (bioconductor-uri "GenomicScores" version))
3755 "0xgv5h6hwr4p2p05z8vzhivy97gfirm4rj1ihb5c8fhgc5vp85dy"))))
3756 (properties `((upstream-name . "GenomicScores")))
3757 (build-system r-build-system)
3759 `(("r-annotationhub" ,r-annotationhub)
3760 ("r-biobase" ,r-biobase)
3761 ("r-biocgenerics" ,r-biocgenerics)
3762 ("r-biostrings" ,r-biostrings)
3763 ("r-bsgenome" ,r-bsgenome)
3764 ("r-genomeinfodb" ,r-genomeinfodb)
3765 ("r-genomicranges" ,r-genomicranges)
3766 ("r-iranges" ,r-iranges)
3767 ("r-s4vectors" ,r-s4vectors)
3769 (home-page "https://github.com/rcastelo/GenomicScores/")
3770 (synopsis "Work with genome-wide position-specific scores")
3772 "This package provides infrastructure to store and access genome-wide
3773 position-specific scores within R and Bioconductor.")
3774 (license license:artistic2.0)))
3776 (define-public r-atacseqqc
3778 (name "r-atacseqqc")
3783 (uri (bioconductor-uri "ATACseqQC" version))
3786 "1i8f0vs0z4jbc2yvj1diay7jhcmb1a82zv96xllk771f25nvmmxp"))))
3787 (properties `((upstream-name . "ATACseqQC")))
3788 (build-system r-build-system)
3790 `(("r-biocgenerics" ,r-biocgenerics)
3791 ("r-biostrings" ,r-biostrings)
3792 ("r-bsgenome" ,r-bsgenome)
3793 ("r-chippeakanno" ,r-chippeakanno)
3794 ("r-edger" ,r-edger)
3795 ("r-genomeinfodb" ,r-genomeinfodb)
3796 ("r-genomicalignments" ,r-genomicalignments)
3797 ("r-genomicranges" ,r-genomicranges)
3798 ("r-genomicscores" ,r-genomicscores)
3799 ("r-iranges" ,r-iranges)
3800 ("r-kernsmooth" ,r-kernsmooth)
3801 ("r-limma" ,r-limma)
3802 ("r-motifstack" ,r-motifstack)
3803 ("r-preseqr" ,r-preseqr)
3804 ("r-randomforest" ,r-randomforest)
3805 ("r-rsamtools" ,r-rsamtools)
3806 ("r-rtracklayer" ,r-rtracklayer)
3807 ("r-s4vectors" ,r-s4vectors)))
3808 (home-page "https://bioconductor.org/packages/ATACseqQC/")
3809 (synopsis "ATAC-seq quality control")
3811 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
3812 sequencing, is a rapid and sensitive method for chromatin accessibility
3813 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
3814 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
3815 assess whether their ATAC-seq experiment is successful. It includes
3816 diagnostic plots of fragment size distribution, proportion of mitochondria
3817 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
3819 (license license:gpl2+)))
3821 (define-public r-gofuncr
3828 (uri (bioconductor-uri "GOfuncR" version))
3831 "1znnkh96yyv6rkbjxx2942nixw4ixdll1f72v92wzsxdcbwkgqdm"))))
3832 (properties `((upstream-name . "GOfuncR")))
3833 (build-system r-build-system)
3835 `(("r-annotationdbi" ,r-annotationdbi)
3836 ("r-genomicranges" ,r-genomicranges)
3837 ("r-gtools" ,r-gtools)
3838 ("r-iranges" ,r-iranges)
3839 ("r-mapplots" ,r-mapplots)
3841 ("r-vioplot" ,r-vioplot)))
3842 (home-page "https://bioconductor.org/packages/GOfuncR/")
3843 (synopsis "Gene ontology enrichment using FUNC")
3845 "GOfuncR performs a gene ontology enrichment analysis based on the
3846 ontology enrichment software FUNC. GO-annotations are obtained from
3847 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
3848 included in the package and updated regularly. GOfuncR provides the standard
3849 candidate vs background enrichment analysis using the hypergeometric test, as
3850 well as three additional tests:
3853 @item the Wilcoxon rank-sum test that is used when genes are ranked,
3854 @item a binomial test that is used when genes are associated with two counts,
3856 @item a Chi-square or Fisher's exact test that is used in cases when genes are
3857 associated with four counts.
3860 To correct for multiple testing and interdependency of the tests, family-wise
3861 error rates are computed based on random permutations of the gene-associated
3862 variables. GOfuncR also provides tools for exploring the ontology graph and
3863 the annotations, and options to take gene-length or spatial clustering of
3864 genes into account. It is also possible to provide custom gene coordinates,
3865 annotations and ontologies.")
3866 (license license:gpl2+)))
3868 (define-public r-abaenrichment
3870 (name "r-abaenrichment")
3875 (uri (bioconductor-uri "ABAEnrichment" version))
3878 "1w322wsp6bd3gyfwzgdf088cvfmpq774knr57d0dj420ljf4xn48"))))
3879 (properties `((upstream-name . "ABAEnrichment")))
3880 (build-system r-build-system)
3882 `(("r-abadata" ,r-abadata)
3883 ("r-data-table" ,r-data-table)
3884 ("r-gofuncr" ,r-gofuncr)
3885 ("r-gplots" ,r-gplots)
3886 ("r-gtools" ,r-gtools)
3887 ("r-rcpp" ,r-rcpp)))
3888 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
3889 (synopsis "Gene expression enrichment in human brain regions")
3891 "The package ABAEnrichment is designed to test for enrichment of user
3892 defined candidate genes in the set of expressed genes in different human brain
3893 regions. The core function @code{aba_enrich} integrates the expression of the
3894 candidate gene set (averaged across donors) and the structural information of
3895 the brain using an ontology, both provided by the Allen Brain Atlas project.")
3896 (license license:gpl2+)))
3898 (define-public r-annotationfuncs
3900 (name "r-annotationfuncs")
3905 (uri (bioconductor-uri "AnnotationFuncs" version))
3908 "12vh07x8s9y74h65q1pnjlma752pz29bmyyhlnqaiy83gsg26hm3"))))
3910 `((upstream-name . "AnnotationFuncs")))
3911 (build-system r-build-system)
3913 `(("r-annotationdbi" ,r-annotationdbi)
3915 (home-page "https://www.iysik.com/r/annotationfuncs")
3916 (synopsis "Annotation translation functions")
3918 "This package provides functions for handling translating between
3919 different identifieres using the Biocore Data Team data-packages (e.g.
3920 @code{org.Bt.eg.db}).")
3921 (license license:gpl2)))
3923 (define-public r-annotationtools
3925 (name "r-annotationtools")
3930 (uri (bioconductor-uri "annotationTools" version))
3933 "148fi8bv1m0y81psm0jv1nqvjhvr461drnl0krqd7skcf0mb0fc1"))))
3935 `((upstream-name . "annotationTools")))
3936 (build-system r-build-system)
3937 (propagated-inputs `(("r-biobase" ,r-biobase)))
3938 (home-page "https://bioconductor.org/packages/annotationTools/")
3939 (synopsis "Annotate microarrays and perform gene expression analyses")
3941 "This package provides functions to annotate microarrays, find orthologs,
3942 and integrate heterogeneous gene expression profiles using annotation and
3943 other molecular biology information available as flat file database (plain
3945 ;; Any version of the GPL.
3946 (license (list license:gpl2+))))
3948 (define-public r-allelicimbalance
3950 (name "r-allelicimbalance")
3955 (uri (bioconductor-uri "AllelicImbalance" version))
3958 "1f51y8zjgz0wdd33qbs1gpnadbprixr4wcfvff6v3s09rmnr8fng"))))
3960 `((upstream-name . "AllelicImbalance")))
3961 (build-system r-build-system)
3963 `(("r-annotationdbi" ,r-annotationdbi)
3964 ("r-biocgenerics" ,r-biocgenerics)
3965 ("r-biostrings" ,r-biostrings)
3966 ("r-bsgenome" ,r-bsgenome)
3967 ("r-genomeinfodb" ,r-genomeinfodb)
3968 ("r-genomicalignments" ,r-genomicalignments)
3969 ("r-genomicfeatures" ,r-genomicfeatures)
3970 ("r-genomicranges" ,r-genomicranges)
3971 ("r-gridextra" ,r-gridextra)
3973 ("r-iranges" ,r-iranges)
3974 ("r-lattice" ,r-lattice)
3975 ("r-latticeextra" ,r-latticeextra)
3977 ("r-rsamtools" ,r-rsamtools)
3978 ("r-s4vectors" ,r-s4vectors)
3979 ("r-seqinr" ,r-seqinr)
3980 ("r-summarizedexperiment" ,r-summarizedexperiment)
3981 ("r-variantannotation" ,r-variantannotation)))
3982 (home-page "https://github.com/pappewaio/AllelicImbalance")
3983 (synopsis "Investigate allele-specific expression")
3985 "This package provides a framework for allele-specific expression
3986 investigation using RNA-seq data.")
3987 (license license:gpl3)))
3989 (define-public r-aucell
3996 (uri (bioconductor-uri "AUCell" version))
3999 "1vd8w6dygn1b5bwlha09mm6fbwyj07pmawpv53agcg1y7jlxs31b"))))
4000 (properties `((upstream-name . "AUCell")))
4001 (build-system r-build-system)
4003 `(("r-data-table" ,r-data-table)
4004 ("r-gseabase" ,r-gseabase)
4005 ("r-mixtools" ,r-mixtools)
4006 ("r-r-utils" ,r-r-utils)
4007 ("r-shiny" ,r-shiny)
4008 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4009 (home-page "https://bioconductor.org/packages/AUCell/")
4010 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4012 "AUCell allows to identify cells with active gene sets (e.g. signatures,
4013 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4014 Under the Curve} (AUC) to calculate whether a critical subset of the input
4015 gene set is enriched within the expressed genes for each cell. The
4016 distribution of AUC scores across all the cells allows exploring the relative
4017 expression of the signature. Since the scoring method is ranking-based,
4018 AUCell is independent of the gene expression units and the normalization
4019 procedure. In addition, since the cells are evaluated individually, it can
4020 easily be applied to bigger datasets, subsetting the expression matrix if
4022 (license license:gpl3)))
4024 (define-public r-ebimage
4031 (uri (bioconductor-uri "EBImage" version))
4034 "0c8rfi40959rbpbizpiizkq21az3lfwf2azlj55yz5m61qp7mgsq"))))
4035 (properties `((upstream-name . "EBImage")))
4036 (build-system r-build-system)
4038 `(("r-abind" ,r-abind)
4039 ("r-biocgenerics" ,r-biocgenerics)
4040 ("r-fftwtools" ,r-fftwtools)
4041 ("r-htmltools" ,r-htmltools)
4042 ("r-htmlwidgets" ,r-htmlwidgets)
4044 ("r-locfit" ,r-locfit)
4046 ("r-rcurl" ,r-rcurl)
4047 ("r-tiff" ,r-tiff)))
4049 `(("r-knitr" ,r-knitr))) ; for vignettes
4050 (home-page "https://github.com/aoles/EBImage")
4051 (synopsis "Image processing and analysis toolbox for R")
4053 "EBImage provides general purpose functionality for image processing and
4054 analysis. In the context of (high-throughput) microscopy-based cellular
4055 assays, EBImage offers tools to segment cells and extract quantitative
4056 cellular descriptors. This allows the automation of such tasks using the R
4057 programming language and facilitates the use of other tools in the R
4058 environment for signal processing, statistical modeling, machine learning and
4059 visualization with image data.")
4060 ;; Any version of the LGPL.
4061 (license license:lgpl2.1+)))
4063 (define-public r-yamss
4070 (uri (bioconductor-uri "yamss" version))
4073 "00756szrmfm1jdayl90jgblydn6sick9nagdf77pn7wzh6wlaj23"))))
4074 (build-system r-build-system)
4076 `(("r-biocgenerics" ,r-biocgenerics)
4077 ("r-data-table" ,r-data-table)
4078 ("r-ebimage" ,r-ebimage)
4079 ("r-iranges" ,r-iranges)
4080 ("r-limma" ,r-limma)
4081 ("r-matrix" ,r-matrix)
4083 ("r-s4vectors" ,r-s4vectors)
4084 ("r-summarizedexperiment"
4085 ,r-summarizedexperiment)))
4086 (home-page "https://github.com/hansenlab/yamss")
4087 (synopsis "Tools for high-throughput metabolomics")
4089 "This package provides tools to analyze and visualize high-throughput
4090 metabolomics data acquired using chromatography-mass spectrometry. These tools
4091 preprocess data in a way that enables reliable and powerful differential
4093 (license license:artistic2.0)))
4095 (define-public r-gtrellis
4102 (uri (bioconductor-uri "gtrellis" version))
4105 "069hln9vflyxic24bxrlmdmz9h3jdd2qaqy898rgk5bn0gqwcjix"))))
4106 (build-system r-build-system)
4108 `(("r-circlize" ,r-circlize)
4109 ("r-genomicranges" ,r-genomicranges)
4110 ("r-getoptlong" ,r-getoptlong)
4111 ("r-iranges" ,r-iranges)))
4112 (home-page "https://github.com/jokergoo/gtrellis")
4113 (synopsis "Genome level Trellis layout")
4115 "Genome level Trellis graph visualizes genomic data conditioned by
4116 genomic categories (e.g. chromosomes). For each genomic category, multiple
4117 dimensional data which are represented as tracks describe different features
4118 from different aspects. This package provides high flexibility to arrange
4119 genomic categories and to add self-defined graphics in the plot.")
4120 (license license:expat)))
4122 (define-public r-somaticsignatures
4124 (name "r-somaticsignatures")
4129 (uri (bioconductor-uri "SomaticSignatures" version))
4132 "0wc4ddwngvkc9jhihzaxx8yazqncl1kbgkx8vqn5gd4w2hx0h5bx"))))
4134 `((upstream-name . "SomaticSignatures")))
4135 (build-system r-build-system)
4137 `(("r-biobase" ,r-biobase)
4138 ("r-biostrings" ,r-biostrings)
4139 ("r-genomeinfodb" ,r-genomeinfodb)
4140 ("r-genomicranges" ,r-genomicranges)
4141 ("r-ggbio" ,r-ggbio)
4142 ("r-ggplot2" ,r-ggplot2)
4143 ("r-iranges" ,r-iranges)
4145 ("r-pcamethods" ,r-pcamethods)
4146 ("r-proxy" ,r-proxy)
4147 ("r-reshape2" ,r-reshape2)
4148 ("r-s4vectors" ,r-s4vectors)
4149 ("r-variantannotation" ,r-variantannotation)))
4150 (home-page "https://github.com/juliangehring/SomaticSignatures")
4151 (synopsis "Somatic signatures")
4153 "This package identifies mutational signatures of @dfn{single nucleotide
4154 variants} (SNVs). It provides a infrastructure related to the methodology
4155 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4156 decomposition algorithms.")
4157 (license license:expat)))
4159 (define-public r-yapsa
4166 (uri (bioconductor-uri "YAPSA" version))
4169 "0rfjn2x6hsqiigd53bnl7z5ix5s2mbpr9glsyihsa7i6iazh3n1q"))))
4170 (properties `((upstream-name . "YAPSA")))
4171 (build-system r-build-system)
4173 `(("r-circlize" ,r-circlize)
4174 ("r-complexheatmap" ,r-complexheatmap)
4175 ("r-corrplot" ,r-corrplot)
4176 ("r-dendextend" ,r-dendextend)
4177 ("r-genomeinfodb" ,r-genomeinfodb)
4178 ("r-genomicranges" ,r-genomicranges)
4179 ("r-getoptlong" ,r-getoptlong)
4180 ("r-ggplot2" ,r-ggplot2)
4181 ("r-gridextra" ,r-gridextra)
4182 ("r-gtrellis" ,r-gtrellis)
4183 ("r-keggrest" ,r-keggrest)
4185 ("r-pmcmr" ,r-pmcmr)
4186 ("r-reshape2" ,r-reshape2)
4187 ("r-somaticsignatures" ,r-somaticsignatures)
4188 ("r-variantannotation" ,r-variantannotation)))
4189 (home-page "https://bioconductor.org/packages/YAPSA/")
4190 (synopsis "Yet another package for signature analysis")
4192 "This package provides functions and routines useful in the analysis of
4193 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4194 functions to perform a signature analysis with known signatures and a
4195 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4197 (license license:gpl3)))
4199 (define-public r-gcrma
4206 (uri (bioconductor-uri "gcrma" version))
4209 "1wazr3f4hwzpd0cjs2nlnzifr2g1r8a692pxap9xnmrw66zq94s4"))))
4210 (build-system r-build-system)
4212 `(("r-affy" ,r-affy)
4213 ("r-affyio" ,r-affyio)
4214 ("r-biobase" ,r-biobase)
4215 ("r-biocmanager" ,r-biocmanager)
4216 ("r-biostrings" ,r-biostrings)
4217 ("r-xvector" ,r-xvector)))
4218 (home-page "https://bioconductor.org/packages/gcrma/")
4219 (synopsis "Background adjustment using sequence information")
4221 "Gcrma adjusts for background intensities in Affymetrix array data which
4222 include optical noise and @dfn{non-specific binding} (NSB). The main function
4223 @code{gcrma} converts background adjusted probe intensities to expression
4224 measures using the same normalization and summarization methods as a
4225 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4226 to estimate probe affinity to NSB. The sequence information is summarized in
4227 a more complex way than the simple GC content. Instead, the base types (A, T,
4228 G or C) at each position along the probe determine the affinity of each probe.
4229 The parameters of the position-specific base contributions to the probe
4230 affinity is estimated in an NSB experiment in which only NSB but no
4231 gene-specific bidning is expected.")
4232 ;; Any version of the LGPL
4233 (license license:lgpl2.1+)))
4235 (define-public r-simpleaffy
4237 (name "r-simpleaffy")
4242 (uri (bioconductor-uri "simpleaffy" version))
4245 "0zjpbjkk27w56mrxsxynkqc298xxsarsnzbd7injg6zakhlmhy6a"))))
4246 (build-system r-build-system)
4248 `(("r-affy" ,r-affy)
4249 ("r-biobase" ,r-biobase)
4250 ("r-biocgenerics" ,r-biocgenerics)
4251 ("r-gcrma" ,r-gcrma)
4252 ("r-genefilter" ,r-genefilter)))
4253 (home-page "https://bioconductor.org/packages/simpleaffy/")
4254 (synopsis "Very simple high level analysis of Affymetrix data")
4256 "This package provides high level functions for reading Affy @file{.CEL}
4257 files, phenotypic data, and then computing simple things with it, such as
4258 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4259 library. It also has some basic scatter plot functions and mechanisms for
4260 generating high resolution journal figures.")
4261 (license license:gpl2+)))
4263 (define-public r-yaqcaffy
4270 (uri (bioconductor-uri "yaqcaffy" version))
4273 "1v12mbai6gf7wpxbyz4clvr7w1mlbv3scjf4kydfin8wwrrzq670"))))
4274 (build-system r-build-system)
4276 `(("r-simpleaffy" ,r-simpleaffy)))
4277 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4278 (synopsis "Affymetrix quality control and reproducibility analysis")
4280 "This is a package that can be used for quality control of Affymetrix
4281 GeneChip expression data and reproducibility analysis of human whole genome
4282 chips with the MAQC reference datasets.")
4283 (license license:artistic2.0)))
4285 (define-public r-quantro
4292 (uri (bioconductor-uri "quantro" version))
4295 "0zfb2s410ijp0didapnq7q4gn2d26wy785cygxyvg8sq6mlw2cab"))))
4296 (build-system r-build-system)
4298 `(("r-biobase" ,r-biobase)
4299 ("r-doparallel" ,r-doparallel)
4300 ("r-foreach" ,r-foreach)
4301 ("r-ggplot2" ,r-ggplot2)
4302 ("r-iterators" ,r-iterators)
4303 ("r-minfi" ,r-minfi)
4304 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4305 (home-page "https://bioconductor.org/packages/quantro/")
4306 (synopsis "Test for when to use quantile normalization")
4308 "This package provides a data-driven test for the assumptions of quantile
4309 normalization using raw data such as objects that inherit eSets (e.g.
4310 ExpressionSet, MethylSet). Group level information about each sample (such as
4311 Tumor / Normal status) must also be provided because the test assesses if
4312 there are global differences in the distributions between the user-defined
4314 (license license:gpl3+)))
4316 (define-public r-yarn
4323 (uri (bioconductor-uri "yarn" version))
4326 "00gmwylpdmssz8xpd91d8fsiyglr7f9vc9bdalpa7w5vg4c6d2f6"))))
4327 (build-system r-build-system)
4329 `(("r-biobase" ,r-biobase)
4330 ("r-biomart" ,r-biomart)
4331 ("r-downloader" ,r-downloader)
4332 ("r-edger" ,r-edger)
4333 ("r-gplots" ,r-gplots)
4334 ("r-limma" ,r-limma)
4335 ("r-matrixstats" ,r-matrixstats)
4336 ("r-preprocesscore" ,r-preprocesscore)
4337 ("r-quantro" ,r-quantro)
4338 ("r-rcolorbrewer" ,r-rcolorbrewer)
4339 ("r-readr" ,r-readr)))
4340 (home-page "https://bioconductor.org/packages/yarn/")
4341 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4343 "Expedite large RNA-Seq analyses using a combination of previously
4344 developed tools. YARN is meant to make it easier for the user in performing
4345 basic mis-annotation quality control, filtering, and condition-aware
4346 normalization. YARN leverages many Bioconductor tools and statistical
4347 techniques to account for the large heterogeneity and sparsity found in very
4348 large RNA-seq experiments.")
4349 (license license:artistic2.0)))
4351 (define-public r-roar
4358 (uri (bioconductor-uri "roar" version))
4361 "11ib5vr2vrrqsqcikph528c56bp52myyfdlwkklp8m0r15kwpxr7"))))
4362 (build-system r-build-system)
4364 `(("r-biocgenerics" ,r-biocgenerics)
4365 ("r-genomeinfodb" ,r-genomeinfodb)
4366 ("r-genomicalignments" ,r-genomicalignments)
4367 ("r-genomicranges" ,r-genomicranges)
4368 ("r-iranges" ,r-iranges)
4369 ("r-rtracklayer" ,r-rtracklayer)
4370 ("r-s4vectors" ,r-s4vectors)
4371 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4372 (home-page "https://github.com/vodkatad/roar/")
4373 (synopsis "Identify differential APA usage from RNA-seq alignments")
4375 "This package provides tools for identifying preferential usage of APA
4376 sites, comparing two biological conditions, starting from known alternative
4377 sites and alignments obtained from standard RNA-seq experiments.")
4378 (license license:gpl3)))
4380 (define-public r-xbseq
4387 (uri (bioconductor-uri "XBSeq" version))
4390 "12l5qnkg6iahwyfmcsf18hys2i9cjn486sacvsqqfcjj3m88w1gy"))))
4391 (properties `((upstream-name . "XBSeq")))
4392 (build-system r-build-system)
4394 `(("r-biobase" ,r-biobase)
4395 ("r-deseq2" ,r-deseq2)
4396 ("r-dplyr" ,r-dplyr)
4397 ("r-ggplot2" ,r-ggplot2)
4398 ("r-locfit" ,r-locfit)
4399 ("r-magrittr" ,r-magrittr)
4400 ("r-matrixstats" ,r-matrixstats)
4401 ("r-pracma" ,r-pracma)
4402 ("r-roar" ,r-roar)))
4403 (home-page "https://github.com/Liuy12/XBSeq")
4404 (synopsis "Test for differential expression for RNA-seq data")
4406 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
4407 expression} (DE), where a statistical model was established based on the
4408 assumption that observed signals are the convolution of true expression
4409 signals and sequencing noises. The mapped reads in non-exonic regions are
4410 considered as sequencing noises, which follows a Poisson distribution. Given
4411 measurable observed signal and background noise from RNA-seq data, true
4412 expression signals, assuming governed by the negative binomial distribution,
4413 can be delineated and thus the accurate detection of differential expressed
4415 (license license:gpl3+)))
4417 (define-public r-massspecwavelet
4419 (name "r-massspecwavelet")
4424 (uri (bioconductor-uri "MassSpecWavelet" version))
4427 "1qg73qv69fvf2al7znkh9lmyx5qmkqv2mpl33lahdwzkm0lh6n72"))))
4429 `((upstream-name . "MassSpecWavelet")))
4430 (build-system r-build-system)
4432 `(("r-waveslim" ,r-waveslim)))
4433 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
4434 (synopsis "Mass spectrum processing by wavelet-based algorithms")
4436 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
4437 data mainly through the use of wavelet transforms. It supports peak detection
4438 based on @dfn{Continuous Wavelet Transform} (CWT).")
4439 (license license:lgpl2.0+)))
4441 (define-public r-xcms
4448 (uri (bioconductor-uri "xcms" version))
4451 "0icww3f1kahyk96mc07yhsbyiranzm2614n509as09jf8bdhq23v"))))
4452 (build-system r-build-system)
4454 `(("r-biobase" ,r-biobase)
4455 ("r-biocgenerics" ,r-biocgenerics)
4456 ("r-biocparallel" ,r-biocparallel)
4457 ("r-lattice" ,r-lattice)
4458 ("r-massspecwavelet" ,r-massspecwavelet)
4459 ("r-msnbase" ,r-msnbase)
4460 ("r-multtest" ,r-multtest)
4463 ("r-protgenerics" ,r-protgenerics)
4465 ("r-rcolorbrewer" ,r-rcolorbrewer)
4466 ("r-robustbase" ,r-robustbase)
4467 ("r-s4vectors" ,r-s4vectors)))
4468 (home-page "https://bioconductor.org/packages/xcms/")
4469 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
4471 "This package provides a framework for processing and visualization of
4472 chromatographically separated and single-spectra mass spectral data. It
4473 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
4474 data for high-throughput, untargeted analyte profiling.")
4475 (license license:gpl2+)))
4477 (define-public r-wrench
4484 (uri (bioconductor-uri "Wrench" version))
4487 "1js4dsgpgwq552r4ay78awd5vhzlmva0v8xvn3dy9v18y4j9k94i"))))
4488 (properties `((upstream-name . "Wrench")))
4489 (build-system r-build-system)
4491 `(("r-limma" ,r-limma)
4492 ("r-locfit" ,r-locfit)
4493 ("r-matrixstats" ,r-matrixstats)))
4494 (home-page "https://github.com/HCBravoLab/Wrench")
4495 (synopsis "Wrench normalization for sparse count data")
4497 "Wrench is a package for normalization sparse genomic count data, like
4498 that arising from 16s metagenomic surveys.")
4499 (license license:artistic2.0)))
4501 (define-public r-wiggleplotr
4503 (name "r-wiggleplotr")
4508 (uri (bioconductor-uri "wiggleplotr" version))
4511 "0yl3ymsk5iijbypjg7lf6mkjgb54893vml2v5aqp2q4l8q0ld7l0"))))
4512 (build-system r-build-system)
4514 `(("r-assertthat" ,r-assertthat)
4515 ("r-cowplot" ,r-cowplot)
4516 ("r-dplyr" ,r-dplyr)
4517 ("r-genomeinfodb" ,r-genomeinfodb)
4518 ("r-genomicranges" ,r-genomicranges)
4519 ("r-ggplot2" ,r-ggplot2)
4520 ("r-iranges" ,r-iranges)
4521 ("r-purrr" ,r-purrr)
4522 ("r-rtracklayer" ,r-rtracklayer)
4523 ("r-s4vectors" ,r-s4vectors)))
4524 (home-page "https://bioconductor.org/packages/wiggleplotr/")
4525 (synopsis "Make read coverage plots from BigWig files")
4527 "This package provides tools to visualize read coverage from sequencing
4528 experiments together with genomic annotations (genes, transcripts, peaks).
4529 Introns of long transcripts can be rescaled to a fixed length for better
4530 visualization of exonic read coverage.")
4531 (license license:asl2.0)))
4533 (define-public r-widgettools
4535 (name "r-widgettools")
4540 (uri (bioconductor-uri "widgetTools" version))
4543 "021b4s5vcy68p95p8rrcz8a8b1gyk4k8zq06snn32k2dqr91xi1a"))))
4544 (properties `((upstream-name . "widgetTools")))
4545 (build-system r-build-system)
4546 (home-page "https://bioconductor.org/packages/widgetTools/")
4547 (synopsis "Tools for creating interactive tcltk widgets")
4549 "This package contains tools to support the construction of tcltk
4551 ;; Any version of the LGPL.
4552 (license license:lgpl3+)))
4554 (define-public r-webbioc
4561 (uri (bioconductor-uri "webbioc" version))
4564 "0ilrwzbk0v41p6hwng7jmr3hwwb4skdcjqml1mc3xmh99lcvw8hz"))))
4565 (build-system r-build-system)
4567 `(("netpbm" ,netpbm)
4570 `(("r-affy" ,r-affy)
4571 ("r-annaffy" ,r-annaffy)
4572 ("r-biobase" ,r-biobase)
4573 ("r-biocmanager" ,r-biocmanager)
4574 ("r-gcrma" ,r-gcrma)
4575 ("r-multtest" ,r-multtest)
4576 ("r-qvalue" ,r-qvalue)
4578 (home-page "https://www.bioconductor.org/")
4579 (synopsis "Bioconductor web interface")
4581 "This package provides an integrated web interface for doing microarray
4582 analysis using several of the Bioconductor packages. It is intended to be
4583 deployed as a centralized bioinformatics resource for use by many users.
4584 Currently only Affymetrix oligonucleotide analysis is supported.")
4585 (license license:gpl2+)))
4587 (define-public r-zfpkm
4594 (uri (bioconductor-uri "zFPKM" version))
4597 "14knxp8cjjp9fhc6py66c7hrckf112jamz3gl1v60l1f2l1hmfvz"))))
4598 (properties `((upstream-name . "zFPKM")))
4599 (build-system r-build-system)
4601 `(("r-checkmate" ,r-checkmate)
4602 ("r-dplyr" ,r-dplyr)
4603 ("r-ggplot2" ,r-ggplot2)
4604 ("r-summarizedexperiment" ,r-summarizedexperiment)
4605 ("r-tidyr" ,r-tidyr)))
4606 (home-page "https://github.com/ronammar/zFPKM/")
4607 (synopsis "Functions to facilitate zFPKM transformations")
4609 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
4610 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
4612 (license license:gpl3)))
4614 (define-public r-rbowtie2
4621 (uri (bioconductor-uri "Rbowtie2" version))
4624 "1yphnrk5j52gzvy9g6mw05dzh9sm8xxvhyja59ak68nrs1bh3lq4"))))
4625 (properties `((upstream-name . "Rbowtie2")))
4626 (build-system r-build-system)
4629 (home-page "https://bioconductor.org/packages/Rbowtie2/")
4630 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
4632 "This package provides an R wrapper of the popular @code{bowtie2}
4633 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
4634 rapid adapter trimming, identification, and read merging.")
4635 (license license:gpl3+)))
4637 (define-public r-progeny
4644 (uri (bioconductor-uri "progeny" version))
4647 "03rm90vfb9ivxhapvs3h5yggfazf8bf5vh1krknvb3xyw27br9dw"))))
4648 (build-system r-build-system)
4649 (propagated-inputs `(("r-biobase" ,r-biobase)))
4650 (home-page "https://github.com/saezlab/progeny")
4651 (synopsis "Pathway responsive gene activity inference")
4653 "This package provides a function to infer pathway activity from gene
4654 expression. It contains the linear model inferred in the publication
4655 \"Perturbation-response genes reveal signaling footprints in cancer gene
4657 (license license:asl2.0)))
4659 (define-public r-arrmnormalization
4661 (name "r-arrmnormalization")
4666 (uri (bioconductor-uri "ARRmNormalization" version))
4669 "05m7hy1qd4lr1ylb0ld30dirdl9jfp1zhvifl6wvj40x74b6h2d1"))))
4671 `((upstream-name . "ARRmNormalization")))
4672 (build-system r-build-system)
4673 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
4674 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
4675 (synopsis "Adaptive robust regression normalization for methylation data")
4677 "This is a package to perform the @dfn{Adaptive Robust Regression
4678 method} (ARRm) for the normalization of methylation data from the Illumina
4679 Infinium HumanMethylation 450k assay.")
4680 (license license:artistic2.0)))
4682 (define-public r-biocfilecache
4684 (name "r-biocfilecache")
4689 (uri (bioconductor-uri "BiocFileCache" version))
4692 "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb"))))
4693 (properties `((upstream-name . "BiocFileCache")))
4694 (build-system r-build-system)
4696 `(("r-curl" ,r-curl)
4698 ("r-dbplyr" ,r-dbplyr)
4699 ("r-dplyr" ,r-dplyr)
4701 ("r-rappdirs" ,r-rappdirs)
4702 ("r-rsqlite" ,r-rsqlite)))
4703 (home-page "https://bioconductor.org/packages/BiocFileCache/")
4704 (synopsis "Manage files across sessions")
4706 "This package creates a persistent on-disk cache of files that the user
4707 can add, update, and retrieve. It is useful for managing resources (such as
4708 custom Txdb objects) that are costly or difficult to create, web resources,
4709 and data files used across sessions.")
4710 (license license:artistic2.0)))
4712 (define-public r-iclusterplus
4714 (name "r-iclusterplus")
4719 (uri (bioconductor-uri "iClusterPlus" version))
4722 "14x43jjhbp4zwb4dv9rwrm5l5p7h76bc1zkdbiikqip9bzph0viq"))))
4723 (properties `((upstream-name . "iClusterPlus")))
4724 (build-system r-build-system)
4725 (native-inputs `(("gfortran" ,gfortran)))
4726 (home-page "https://bioconductor.org/packages/iClusterPlus/")
4727 (synopsis "Integrative clustering of multi-type genomic data")
4729 "iClusterPlus is developed for integrative clustering analysis of
4730 multi-type genomic data and is an enhanced version of iCluster proposed and
4731 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
4732 from the experiments where biological samples (e.g. tumor samples) are
4733 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
4734 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
4735 on. In the iClusterPlus model, binary observations such as somatic mutation
4736 are modeled as Binomial processes; categorical observations such as copy
4737 number states are realizations of Multinomial random variables; counts are
4738 modeled as Poisson random processes; and continuous measures are modeled by
4739 Gaussian distributions.")
4740 (license license:gpl2+)))
4742 (define-public r-rbowtie
4749 (uri (bioconductor-uri "Rbowtie" version))
4752 "1p8gbd2zn677lq8d009p2cplg1jm2jhn81lppipj638i9ynjh44f"))))
4753 (properties `((upstream-name . "Rbowtie")))
4754 (build-system r-build-system)
4757 (home-page "https://bioconductor.org/packages/Rbowtie/")
4758 (synopsis "R bowtie wrapper")
4760 "This package provides an R wrapper around the popular bowtie short read
4761 aligner and around SpliceMap, a de novo splice junction discovery and
4763 (license license:artistic2.0)))
4765 (define-public r-sgseq
4772 (uri (bioconductor-uri "SGSeq" version))
4775 "09c0hv74pl310wahyyp4x50g6sz30bvrg24p2j9h7glla5dh2z4s"))))
4776 (properties `((upstream-name . "SGSeq")))
4777 (build-system r-build-system)
4779 `(("r-annotationdbi" ,r-annotationdbi)
4780 ("r-biocgenerics" ,r-biocgenerics)
4781 ("r-biostrings" ,r-biostrings)
4782 ("r-genomeinfodb" ,r-genomeinfodb)
4783 ("r-genomicalignments" ,r-genomicalignments)
4784 ("r-genomicfeatures" ,r-genomicfeatures)
4785 ("r-genomicranges" ,r-genomicranges)
4786 ("r-igraph" ,r-igraph)
4787 ("r-iranges" ,r-iranges)
4788 ("r-rsamtools" ,r-rsamtools)
4789 ("r-rtracklayer" ,r-rtracklayer)
4790 ("r-runit" ,r-runit)
4791 ("r-s4vectors" ,r-s4vectors)
4792 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4793 (home-page "https://bioconductor.org/packages/SGSeq/")
4794 (synopsis "Splice event prediction and quantification from RNA-seq data")
4796 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
4797 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
4798 represented as a splice graph, which can be obtained from existing annotation
4799 or predicted from the mapped sequence reads. Splice events are identified
4800 from the graph and are quantified locally using structurally compatible reads
4801 at the start or end of each splice variant. The software includes functions
4802 for splice event prediction, quantification, visualization and
4804 (license license:artistic2.0)))
4806 (define-public r-rhisat2
4813 (uri (bioconductor-uri "Rhisat2" version))
4816 "02ig9qci18n93vmya7q6bijrqsbfh69fyg8iqysf89ym2vd3x3c5"))))
4817 (properties `((upstream-name . "Rhisat2")))
4818 (build-system r-build-system)
4820 `(("which" ,which)))
4822 `(("r-genomicfeatures" ,r-genomicfeatures)
4823 ("r-genomicranges" ,r-genomicranges)
4824 ("r-sgseq" ,r-sgseq)))
4825 (home-page "https://github.com/fmicompbio/Rhisat2")
4826 (synopsis "R Wrapper for HISAT2 sequence aligner")
4828 "This package provides an R interface to the HISAT2 spliced short-read
4829 aligner by Kim et al. (2015). The package contains wrapper functions to
4830 create a genome index and to perform the read alignment to the generated
4832 (license license:gpl3)))
4834 (define-public r-quasr
4841 (uri (bioconductor-uri "QuasR" version))
4844 "1pshm41iba9nfq2pigk4dyldn5434w83rhgj99cdjnd0rszj7ajx"))))
4845 (properties `((upstream-name . "QuasR")))
4846 (build-system r-build-system)
4850 `(("r-annotationdbi" ,r-annotationdbi)
4851 ("r-biobase" ,r-biobase)
4852 ("r-biocgenerics" ,r-biocgenerics)
4853 ("r-biocmanager" ,r-biocmanager)
4854 ("r-biocparallel" ,r-biocparallel)
4855 ("r-biostrings" ,r-biostrings)
4856 ("r-bsgenome" ,r-bsgenome)
4857 ("r-genomeinfodb" ,r-genomeinfodb)
4858 ("r-genomicalignments" ,r-genomicalignments)
4859 ("r-genomicfeatures" ,r-genomicfeatures)
4860 ("r-genomicfiles" ,r-genomicfiles)
4861 ("r-genomicranges" ,r-genomicranges)
4862 ("r-iranges" ,r-iranges)
4863 ("r-rbowtie" ,r-rbowtie)
4864 ("r-rhisat2" ,r-rhisat2)
4865 ("r-rhtslib" ,r-rhtslib)
4866 ("r-rsamtools" ,r-rsamtools)
4867 ("r-rtracklayer" ,r-rtracklayer)
4868 ("r-s4vectors" ,r-s4vectors)
4869 ("r-shortread" ,r-shortread)))
4870 (home-page "https://bioconductor.org/packages/QuasR/")
4871 (synopsis "Quantify and annotate short reads in R")
4873 "This package provides a framework for the quantification and analysis of
4874 short genomic reads. It covers a complete workflow starting from raw sequence
4875 reads, over creation of alignments and quality control plots, to the
4876 quantification of genomic regions of interest.")
4877 (license license:gpl2)))
4879 (define-public r-rqc
4886 (uri (bioconductor-uri "Rqc" version))
4889 "09kyn5nc2fqfdm3q07h0x2jyh24vsq5sxxm63ir1lvv250lmal4g"))))
4890 (properties `((upstream-name . "Rqc")))
4891 (build-system r-build-system)
4893 `(("r-biocgenerics" ,r-biocgenerics)
4894 ("r-biocparallel" ,r-biocparallel)
4895 ("r-biocstyle" ,r-biocstyle)
4896 ("r-biostrings" ,r-biostrings)
4897 ("r-biovizbase" ,r-biovizbase)
4898 ("r-genomicalignments" ,r-genomicalignments)
4899 ("r-genomicfiles" ,r-genomicfiles)
4900 ("r-ggplot2" ,r-ggplot2)
4901 ("r-iranges" ,r-iranges)
4902 ("r-knitr" ,r-knitr)
4903 ("r-markdown" ,r-markdown)
4906 ("r-reshape2" ,r-reshape2)
4907 ("r-rsamtools" ,r-rsamtools)
4908 ("r-s4vectors" ,r-s4vectors)
4909 ("r-shiny" ,r-shiny)
4910 ("r-shortread" ,r-shortread)))
4911 (home-page "https://github.com/labbcb/Rqc")
4912 (synopsis "Quality control tool for high-throughput sequencing data")
4914 "Rqc is an optimized tool designed for quality control and assessment of
4915 high-throughput sequencing data. It performs parallel processing of entire
4916 files and produces a report which contains a set of high-resolution
4918 (license license:gpl2+)))
4920 (define-public r-birewire
4927 (uri (bioconductor-uri "BiRewire" version))
4930 "1gjb18l3gq3w8zl6r5d49hw0r1kfh9f7ghv9hz6y86aniprvb518"))))
4931 (properties `((upstream-name . "BiRewire")))
4932 (build-system r-build-system)
4934 `(("r-igraph" ,r-igraph)
4935 ("r-matrix" ,r-matrix)
4937 ("r-tsne" ,r-tsne)))
4938 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
4939 (synopsis "Tools for randomization of bipartite graphs")
4941 "This package provides functions for bipartite network rewiring through N
4942 consecutive switching steps and for the computation of the minimal number of
4943 switching steps to be performed in order to maximise the dissimilarity with
4944 respect to the original network. It includes functions for the analysis of
4945 the introduced randomness across the switching steps and several other
4946 routines to analyse the resulting networks and their natural projections.")
4947 (license license:gpl3)))
4949 (define-public r-birta
4956 (uri (bioconductor-uri "birta" version))
4959 "12xjyvgmh4h0b7hi4qg50kcpb9003gnh2xyfgncb8l9mzvsbkxc2"))))
4960 (build-system r-build-system)
4962 `(("r-biobase" ,r-biobase)
4963 ("r-limma" ,r-limma)
4964 ("r-mass" ,r-mass)))
4965 (home-page "https://bioconductor.org/packages/birta")
4966 (synopsis "Bayesian inference of regulation of transcriptional activity")
4968 "Expression levels of mRNA molecules are regulated by different
4969 processes, comprising inhibition or activation by transcription factors and
4970 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
4971 Inference of Regulation of Transcriptional Activity) uses the regulatory
4972 networks of transcription factors and miRNAs together with mRNA and miRNA
4973 expression data to predict switches in regulatory activity between two
4974 conditions. A Bayesian network is used to model the regulatory structure and
4975 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
4976 (license license:gpl2+)))
4978 (define-public r-ropls
4985 (uri (bioconductor-uri "ropls" version))
4988 "099nv9dgmw3avkxv7cd27r16yj56svjlp5q4i389yp1n0r5zhyl2"))))
4989 (build-system r-build-system)
4990 (propagated-inputs `(("r-biobase" ,r-biobase)))
4992 `(("r-knitr" ,r-knitr))) ; for vignettes
4993 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
4994 (synopsis "Multivariate analysis and feature selection of omics data")
4996 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
4997 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
4998 regression, classification, and feature selection of omics data where the
4999 number of variables exceeds the number of samples and with multicollinearity
5000 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5001 separately model the variation correlated (predictive) to the factor of
5002 interest and the uncorrelated (orthogonal) variation. While performing
5003 similarly to PLS, OPLS facilitates interpretation.
5005 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5006 analysis and feature selection of omics data. In addition to scores, loadings
5007 and weights plots, the package provides metrics and graphics to determine the
5008 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5009 validity of the model by permutation testing, detect outliers, and perform
5010 feature selection (e.g. with Variable Importance in Projection or regression
5012 (license license:cecill)))
5014 (define-public r-biosigner
5016 (name "r-biosigner")
5021 (uri (bioconductor-uri "biosigner" version))
5024 "1643iya40v6whb7lw7y34w5sanbasvj4yhvcygbip667yhphyv5b"))))
5025 (build-system r-build-system)
5027 `(("r-biobase" ,r-biobase)
5028 ("r-e1071" ,r-e1071)
5029 ("r-randomforest" ,r-randomforest)
5030 ("r-ropls" ,r-ropls)))
5032 `(("r-knitr" ,r-knitr)
5033 ("r-rmarkdown" ,r-rmarkdown)
5034 ("pandoc" ,ghc-pandoc)
5035 ("pandoc-citeproc" ,ghc-pandoc-citeproc))) ; all for vignettes
5036 (home-page "https://bioconductor.org/packages/biosigner/")
5037 (synopsis "Signature discovery from omics data")
5039 "Feature selection is critical in omics data analysis to extract
5040 restricted and meaningful molecular signatures from complex and high-dimension
5041 data, and to build robust classifiers. This package implements a method to
5042 assess the relevance of the variables for the prediction performances of the
5043 classifier. The approach can be run in parallel with the PLS-DA, Random
5044 Forest, and SVM binary classifiers. The signatures and the corresponding
5045 'restricted' models are returned, enabling future predictions on new
5047 (license license:cecill)))
5049 (define-public r-annotatr
5056 (uri (bioconductor-uri "annotatr" version))
5059 "1zlhy6swfgqjhhcqn8c6akxd4c4z8p85swfh095imji7hxnlhh1f"))))
5060 (build-system r-build-system)
5062 `(("r-annotationdbi" ,r-annotationdbi)
5063 ("r-annotationhub" ,r-annotationhub)
5064 ("r-dplyr" ,r-dplyr)
5065 ("r-genomeinfodb" ,r-genomeinfodb)
5066 ("r-genomicfeatures" ,r-genomicfeatures)
5067 ("r-genomicranges" ,r-genomicranges)
5068 ("r-ggplot2" ,r-ggplot2)
5069 ("r-iranges" ,r-iranges)
5070 ("r-readr" ,r-readr)
5071 ("r-regioner" ,r-regioner)
5072 ("r-reshape2" ,r-reshape2)
5073 ("r-rtracklayer" ,r-rtracklayer)
5074 ("r-s4vectors" ,r-s4vectors)))
5075 (home-page "https://bioconductor.org/packages/annotatr/")
5076 (synopsis "Annotation of genomic regions to genomic annotations")
5078 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5079 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5080 to investigate the intersecting genomic annotations. Such annotations include
5081 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5082 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5083 enhancers. The annotatr package provides an easy way to summarize and
5084 visualize the intersection of genomic sites/regions with genomic
5086 (license license:gpl3)))
5088 (define-public r-rsubread
5095 (uri (bioconductor-uri "Rsubread" version))
5098 "0z4ydk9296bp76ah5y6a7za5jyn4h238xngb789zragly902x83y"))))
5099 (properties `((upstream-name . "Rsubread")))
5100 (build-system r-build-system)
5101 (inputs `(("zlib" ,zlib)))
5102 (home-page "https://bioconductor.org/packages/Rsubread/")
5103 (synopsis "Subread sequence alignment and counting for R")
5105 "This package provides tools for alignment, quantification and analysis
5106 of second and third generation sequencing data. It includes functionality for
5107 read mapping, read counting, SNP calling, structural variant detection and
5108 gene fusion discovery. It can be applied to all major sequencing techologies
5109 and to both short and long sequence reads.")
5110 (license license:gpl3)))
5112 (define-public r-flowutils
5114 (name "r-flowutils")
5119 (uri (bioconductor-uri "flowUtils" version))
5122 "1r7b0rszdzjq7jphh65p5m4x5ps0zbbagxl26gn2mapbjdyb47rm"))))
5123 (properties `((upstream-name . "flowUtils")))
5124 (build-system r-build-system)
5126 `(("r-biobase" ,r-biobase)
5127 ("r-corpcor" ,r-corpcor)
5128 ("r-flowcore" ,r-flowcore)
5129 ("r-graph" ,r-graph)
5130 ("r-runit" ,r-runit)
5132 (home-page "https://github.com/jspidlen/flowUtils")
5133 (synopsis "Utilities for flow cytometry")
5135 "This package provides utilities for flow cytometry data.")
5136 (license license:artistic2.0)))
5138 (define-public r-consensusclusterplus
5140 (name "r-consensusclusterplus")
5145 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5148 "1mlcm3wq5n8s0gxs35j0ph9576fhbrbrrsj2xy84fy20prcfs4w8"))))
5150 `((upstream-name . "ConsensusClusterPlus")))
5151 (build-system r-build-system)
5154 ("r-biobase" ,r-biobase)
5155 ("r-cluster" ,r-cluster)))
5156 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5157 (synopsis "Clustering algorithm")
5159 "This package provides an implementation of an algorithm for determining
5160 cluster count and membership by stability evidence in unsupervised analysis.")
5161 (license license:gpl2)))
5163 (define-public r-flowcore
5170 (uri (bioconductor-uri "flowCore" version))
5173 "0pvcyzycsmgc8iw60q9xnhllfan6ihwpz3gvk8h1n9jmhpxzylan"))))
5174 (properties `((upstream-name . "flowCore")))
5175 (build-system r-build-system)
5178 ("r-biobase" ,r-biobase)
5179 ("r-biocgenerics" ,r-biocgenerics)
5180 ("r-corpcor" ,r-corpcor)
5181 ("r-graph" ,r-graph)
5183 ("r-matrixstats" ,r-matrixstats)
5185 ("r-rrcov" ,r-rrcov)))
5186 (home-page "https://bioconductor.org/packages/flowCore")
5187 (synopsis "Basic structures for flow cytometry data")
5189 "This package provides S4 data structures and basic functions to deal
5190 with flow cytometry data.")
5191 (license license:artistic2.0)))
5193 (define-public r-flowmeans
5195 (name "r-flowmeans")
5200 (uri (bioconductor-uri "flowMeans" version))
5203 "0yp6y3mq5h4nf1d7ybqnriigwfmwanrqavpj3ry482sgiaip1hp2"))))
5204 (properties `((upstream-name . "flowMeans")))
5205 (build-system r-build-system)
5207 `(("r-biobase" ,r-biobase)
5208 ("r-feature" ,r-feature)
5209 ("r-flowcore" ,r-flowcore)
5210 ("r-rrcov" ,r-rrcov)))
5211 (home-page "https://bioconductor.org/packages/flowMeans")
5212 (synopsis "Non-parametric flow cytometry data gating")
5214 "This package provides tools to identify cell populations in Flow
5215 Cytometry data using non-parametric clustering and segmented-regression-based
5216 change point detection.")
5217 (license license:artistic2.0)))
5219 (define-public r-flowsom
5226 (uri (bioconductor-uri "FlowSOM" version))
5229 "03wl3xk7g7vajc4kkrqa0gsbjfxlqr918qi849h5nir31963398l"))))
5230 (properties `((upstream-name . "FlowSOM")))
5231 (build-system r-build-system)
5233 `(("r-biocgenerics" ,r-biocgenerics)
5234 ("r-consensusclusterplus" ,r-consensusclusterplus)
5235 ("r-flowcore" ,r-flowcore)
5236 ("r-flowutils" ,r-flowutils)
5237 ("r-igraph" ,r-igraph)
5240 (home-page "https://bioconductor.org/packages/FlowSOM/")
5241 (synopsis "Visualize and interpret cytometry data")
5243 "FlowSOM offers visualization options for cytometry data, by using
5244 self-organizing map clustering and minimal spanning trees.")
5245 (license license:gpl2+)))
5247 (define-public r-mixomics
5254 (uri (bioconductor-uri "mixOmics" version))
5257 "0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
5258 (properties `((upstream-name . "mixOmics")))
5259 (build-system r-build-system)
5261 `(("r-corpcor" ,r-corpcor)
5262 ("r-dplyr" ,r-dplyr)
5263 ("r-ellipse" ,r-ellipse)
5264 ("r-ggplot2" ,r-ggplot2)
5265 ("r-gridextra" ,r-gridextra)
5266 ("r-igraph" ,r-igraph)
5267 ("r-lattice" ,r-lattice)
5269 ("r-matrixstats" ,r-matrixstats)
5270 ("r-rarpack" ,r-rarpack)
5271 ("r-rcolorbrewer" ,r-rcolorbrewer)
5272 ("r-reshape2" ,r-reshape2)
5273 ("r-tidyr" ,r-tidyr)))
5274 (home-page "http://www.mixOmics.org")
5275 (synopsis "Multivariate methods for exploration of biological datasets")
5277 "mixOmics offers a wide range of multivariate methods for the exploration
5278 and integration of biological datasets with a particular focus on variable
5279 selection. The package proposes several sparse multivariate models we have
5280 developed to identify the key variables that are highly correlated, and/or
5281 explain the biological outcome of interest. The data that can be analysed
5282 with mixOmics may come from high throughput sequencing technologies, such as
5283 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
5284 also beyond the realm of omics (e.g. spectral imaging). The methods
5285 implemented in mixOmics can also handle missing values without having to
5286 delete entire rows with missing data.")
5287 (license license:gpl2+)))
5289 (define-public r-depecher
5296 (uri (bioconductor-uri "DepecheR" version))
5299 "0qj2h2a50fncppvi2phh0mbivxkn1mv702mqpi9mvvkf3bzq8m0h"))))
5300 (properties `((upstream-name . "DepecheR")))
5301 (build-system r-build-system)
5304 (modify-phases %standard-phases
5305 (add-after 'unpack 'fix-syntax-error
5307 (substitute* "src/Makevars"
5311 `(("r-beanplot" ,r-beanplot)
5312 ("r-biocparallel" ,r-biocparallel)
5313 ("r-dosnow" ,r-dosnow)
5314 ("r-dplyr" ,r-dplyr)
5315 ("r-foreach" ,r-foreach)
5316 ("r-ggplot2" ,r-ggplot2)
5317 ("r-gplots" ,r-gplots)
5319 ("r-matrixstats" ,r-matrixstats)
5320 ("r-mixomics" ,r-mixomics)
5321 ("r-moments" ,r-moments)
5323 ("r-rcppeigen" ,r-rcppeigen)
5324 ("r-reshape2" ,r-reshape2)
5325 ("r-viridis" ,r-viridis)))
5326 (home-page "https://bioconductor.org/packages/DepecheR/")
5327 (synopsis "Identify traits of clusters in high-dimensional entities")
5329 "The purpose of this package is to identify traits in a dataset that can
5330 separate groups. This is done on two levels. First, clustering is performed,
5331 using an implementation of sparse K-means. Secondly, the generated clusters
5332 are used to predict outcomes of groups of individuals based on their
5333 distribution of observations in the different clusters. As certain clusters
5334 with separating information will be identified, and these clusters are defined
5335 by a sparse number of variables, this method can reduce the complexity of
5336 data, to only emphasize the data that actually matters.")
5337 (license license:expat)))
5339 (define-public r-rcistarget
5341 (name "r-rcistarget")
5346 (uri (bioconductor-uri "RcisTarget" version))
5349 "133x2vr86ifbk82q08x1c8q19zsk5za7b6qrzz77dhsyf4bhcvpd"))))
5350 (properties `((upstream-name . "RcisTarget")))
5351 (build-system r-build-system)
5353 `(("r-aucell" ,r-aucell)
5354 ("r-biocgenerics" ,r-biocgenerics)
5355 ("r-data-table" ,r-data-table)
5356 ("r-feather" ,r-feather)
5357 ("r-gseabase" ,r-gseabase)
5358 ("r-r-utils" ,r-r-utils)
5359 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5360 (home-page "https://aertslab.org/#scenic")
5361 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
5363 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
5364 over-represented on a gene list. In a first step, RcisTarget selects DNA
5365 motifs that are significantly over-represented in the surroundings of the
5366 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
5367 achieved by using a database that contains genome-wide cross-species rankings
5368 for each motif. The motifs that are then annotated to TFs and those that have
5369 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
5370 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
5371 genes in the gene-set that are ranked above the leading edge).")
5372 (license license:gpl3)))
5374 (define-public r-cicero
5381 (uri (bioconductor-uri "cicero" version))
5384 "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr"))))
5385 (build-system r-build-system)
5387 `(("r-assertthat" ,r-assertthat)
5388 ("r-biobase" ,r-biobase)
5389 ("r-biocgenerics" ,r-biocgenerics)
5390 ("r-data-table" ,r-data-table)
5391 ("r-dplyr" ,r-dplyr)
5393 ("r-genomicranges" ,r-genomicranges)
5394 ("r-ggplot2" ,r-ggplot2)
5395 ("r-glasso" ,r-glasso)
5397 ("r-igraph" ,r-igraph)
5398 ("r-iranges" ,r-iranges)
5399 ("r-matrix" ,r-matrix)
5400 ("r-monocle" ,r-monocle)
5402 ("r-reshape2" ,r-reshape2)
5403 ("r-s4vectors" ,r-s4vectors)
5404 ("r-stringr" ,r-stringr)
5405 ("r-tibble" ,r-tibble)
5406 ("r-vgam" ,r-vgam)))
5407 (home-page "https://bioconductor.org/packages/cicero/")
5408 (synopsis "Predict cis-co-accessibility from single-cell data")
5410 "Cicero computes putative cis-regulatory maps from single-cell chromatin
5411 accessibility data. It also extends the monocle package for use in chromatin
5412 accessibility data.")
5413 (license license:expat)))
5415 ;; This is the latest commit on the "monocle3" branch.
5416 (define-public r-cicero-monocle3
5417 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
5419 (package (inherit r-cicero)
5420 (name "r-cicero-monocle3")
5421 (version (git-version "1.3.2" revision commit))
5426 (url "https://github.com/cole-trapnell-lab/cicero-release.git")
5428 (file-name (git-file-name name version))
5431 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
5433 `(("r-monocle3" ,r-monocle3)
5434 ,@(alist-delete "r-monocle"
5435 (package-propagated-inputs r-cicero)))))))
5437 (define-public r-cistopic
5438 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
5442 (version (git-version "0.2.1" revision commit))
5447 (url "https://github.com/aertslab/cisTopic.git")
5449 (file-name (git-file-name name version))
5452 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
5453 (build-system r-build-system)
5455 `(("r-aucell" ,r-aucell)
5456 ("r-data-table" ,r-data-table)
5457 ("r-dplyr" ,r-dplyr)
5458 ("r-dosnow" ,r-dosnow)
5460 ("r-feather" ,r-feather)
5461 ("r-fitdistrplus" ,r-fitdistrplus)
5462 ("r-genomicranges" ,r-genomicranges)
5463 ("r-ggplot2" ,r-ggplot2)
5465 ("r-matrix" ,r-matrix)
5467 ("r-rcistarget" ,r-rcistarget)
5468 ("r-rtracklayer" ,r-rtracklayer)
5469 ("r-s4vectors" ,r-s4vectors)))
5470 (home-page "https://github.com/aertslab/cisTopic")
5471 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
5473 "The sparse nature of single cell epigenomics data can be overruled using
5474 probabilistic modelling methods such as @dfn{Latent Dirichlet
5475 Allocation} (LDA). This package allows the probabilistic modelling of
5476 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
5477 includes functionalities to identify cell states based on the contribution of
5478 cisTopics and explore the nature and regulatory proteins driving them.")
5479 (license license:gpl3))))
5481 (define-public r-genie3
5488 (uri (bioconductor-uri "GENIE3" version))
5491 "0lvrpw4xn7xyinmn13f65i0vkzfzwdj5y8gsa8vyy8kcn83d28fx"))))
5492 (properties `((upstream-name . "GENIE3")))
5493 (build-system r-build-system)
5494 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
5495 (home-page "https://bioconductor.org/packages/GENIE3")
5496 (synopsis "Gene network inference with ensemble of trees")
5498 "This package implements the GENIE3 algorithm for inferring gene
5499 regulatory networks from expression data.")
5500 (license license:gpl2+)))
5502 (define-public r-roc
5509 (uri (bioconductor-uri "ROC" version))
5512 "1sapnl8kyaldgvdc657wqcmyjb24nvrnaw7v94bbs8yf5pmfm71c"))))
5513 (properties `((upstream-name . "ROC")))
5514 (build-system r-build-system)
5515 (home-page "https://www.bioconductor.org/packages/ROC/")
5516 (synopsis "Utilities for ROC curves")
5518 "This package provides utilities for @dfn{Receiver Operating
5519 Characteristic} (ROC) curves, with a focus on micro arrays.")
5520 (license license:artistic2.0)))
5522 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
5524 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
5529 (uri (bioconductor-uri
5530 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
5531 version 'annotation))
5534 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
5537 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
5538 (build-system r-build-system)
5539 (propagated-inputs `(("r-minfi" ,r-minfi)))
5541 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
5542 (synopsis "Annotation for Illumina's 450k methylation arrays")
5544 "This package provides manifests and annotation for Illumina's 450k array
5546 (license license:artistic2.0)))
5548 (define-public r-watermelon
5550 (name "r-watermelon")
5555 (uri (bioconductor-uri "wateRmelon" version))
5558 "0354ahmfvhqw3yfp17rmz35vlgjp262n4q3hr8qyccyrnk2dz17z"))))
5559 (properties `((upstream-name . "wateRmelon")))
5560 (build-system r-build-system)
5562 `(("r-biobase" ,r-biobase)
5563 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
5564 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
5565 ("r-illuminaio" ,r-illuminaio)
5566 ("r-limma" ,r-limma)
5568 ("r-matrixstats" ,r-matrixstats)
5569 ("r-methylumi" ,r-methylumi)
5571 (home-page "https://bioconductor.org/packages/wateRmelon/")
5572 (synopsis "Illumina 450 methylation array normalization and metrics")
5574 "The standard index of DNA methylation (beta) is computed from methylated
5575 and unmethylated signal intensities. Betas calculated from raw signal
5576 intensities perform well, but using 11 methylomic datasets we demonstrate that
5577 quantile normalization methods produce marked improvement. The commonly used
5578 procedure of normalizing betas is inferior to the separate normalization of M
5579 and U, and it is also advantageous to normalize Type I and Type II assays
5580 separately. This package provides 15 flavours of betas and three performance
5581 metrics, with methods for objects produced by the @code{methylumi} and
5582 @code{minfi} packages.")
5583 (license license:gpl3)))
5585 (define-public r-gdsfmt
5592 (uri (bioconductor-uri "gdsfmt" version))
5595 "0h3hgwxq26dg09fyxqg545v9dg1dizsj58cf05rncr3jj4f8g0xy"))
5596 (modules '((guix build utils)))
5597 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
5598 ;; them and link with system libraries instead.
5601 (for-each delete-file-recursively
5605 (substitute* "src/Makevars"
5606 (("all: \\$\\(SHLIB\\)") "all:")
5607 (("\\$\\(SHLIB\\): liblzma.a") "")
5608 (("(ZLIB|LZ4)/.*") "")
5609 (("CoreArray/dVLIntGDS.cpp.*")
5610 "CoreArray/dVLIntGDS.cpp")
5611 (("CoreArray/dVLIntGDS.o.*")
5612 "CoreArray/dVLIntGDS.o")
5613 (("PKG_LIBS = ./liblzma.a")
5614 "PKG_LIBS = -llz4"))
5615 (substitute* "src/CoreArray/dStream.h"
5616 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
5617 (string-append "include <" header ">")))
5619 (properties `((upstream-name . "gdsfmt")))
5620 (build-system r-build-system)
5625 (home-page "http://corearray.sourceforge.net/")
5627 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
5629 "This package provides a high-level R interface to CoreArray @dfn{Genomic
5630 Data Structure} (GDS) data files, which are portable across platforms with
5631 hierarchical structure to store multiple scalable array-oriented data sets
5632 with metadata information. It is suited for large-scale datasets, especially
5633 for data which are much larger than the available random-access memory. The
5634 @code{gdsfmt} package offers efficient operations specifically designed for
5635 integers of less than 8 bits, since a diploid genotype, like
5636 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
5637 byte. Data compression and decompression are available with relatively
5638 efficient random access. It is also allowed to read a GDS file in parallel
5639 with multiple R processes supported by the package @code{parallel}.")
5640 (license license:lgpl3)))
5642 (define-public r-bigmelon
5649 (uri (bioconductor-uri "bigmelon" version))
5652 "0269kf3d34dbng3swk7pclpk02vy4k3askygmzi5my3fqyfzdkj9"))))
5653 (properties `((upstream-name . "bigmelon")))
5654 (build-system r-build-system)
5656 `(("r-biobase" ,r-biobase)
5657 ("r-biocgenerics" ,r-biocgenerics)
5658 ("r-gdsfmt" ,r-gdsfmt)
5659 ("r-geoquery" ,r-geoquery)
5660 ("r-methylumi" ,r-methylumi)
5661 ("r-minfi" ,r-minfi)
5662 ("r-watermelon" ,r-watermelon)))
5663 (home-page "https://bioconductor.org/packages/bigmelon/")
5664 (synopsis "Illumina methylation array analysis for large experiments")
5666 "This package provides methods for working with Illumina arrays using the
5667 @code{gdsfmt} package.")
5668 (license license:gpl3)))
5670 (define-public r-seqbias
5677 (uri (bioconductor-uri "seqbias" version))
5680 "1pk97jsq0rxijsdm5wnmlw79mhy19skdq1h3mmfbdjh560md47lw"))))
5681 (properties `((upstream-name . "seqbias")))
5682 (build-system r-build-system)
5684 `(("r-biostrings" ,r-biostrings)
5685 ("r-genomicranges" ,r-genomicranges)
5686 ("r-rhtslib" ,r-rhtslib)))
5688 `(("zlib" ,zlib))) ; This comes from rhtslib.
5689 (home-page "https://bioconductor.org/packages/seqbias/")
5690 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
5692 "This package implements a model of per-position sequencing bias in
5693 high-throughput sequencing data using a simple Bayesian network, the structure
5694 and parameters of which are trained on a set of aligned reads and a reference
5696 (license license:lgpl3)))
5698 (define-public r-reqon
5705 (uri (bioconductor-uri "ReQON" version))
5708 "04bljr8vgb9z9800d9v8w7a4rvjkwq48zd8n5divq30zj9k2na7a"))))
5709 (properties `((upstream-name . "ReQON")))
5710 (build-system r-build-system)
5712 `(("r-rjava" ,r-rjava)
5713 ("r-rsamtools" ,r-rsamtools)
5714 ("r-seqbias" ,r-seqbias)))
5715 (home-page "https://bioconductor.org/packages/ReQON/")
5716 (synopsis "Recalibrating quality of nucleotides")
5718 "This package provides an implementation of an algorithm for
5719 recalibrating the base quality scores for aligned sequencing data in BAM
5721 (license license:gpl2)))
5723 (define-public r-wavcluster
5725 (name "r-wavcluster")
5730 (uri (bioconductor-uri "wavClusteR" version))
5733 "02i53dskirzr9nls3dsmv7dqhvy3vikkpx7247zpy2qd9r5yvhy2"))))
5734 (properties `((upstream-name . "wavClusteR")))
5735 (build-system r-build-system)
5737 `(("r-biocgenerics" ,r-biocgenerics)
5738 ("r-biostrings" ,r-biostrings)
5739 ("r-foreach" ,r-foreach)
5740 ("r-genomicfeatures" ,r-genomicfeatures)
5741 ("r-genomicranges" ,r-genomicranges)
5742 ("r-ggplot2" ,r-ggplot2)
5743 ("r-hmisc" ,r-hmisc)
5744 ("r-iranges" ,r-iranges)
5745 ("r-mclust" ,r-mclust)
5746 ("r-rsamtools" ,r-rsamtools)
5747 ("r-rtracklayer" ,r-rtracklayer)
5748 ("r-s4vectors" ,r-s4vectors)
5749 ("r-seqinr" ,r-seqinr)
5750 ("r-stringr" ,r-stringr)
5751 ("r-wmtsa" ,r-wmtsa)))
5752 (home-page "https://bioconductor.org/packages/wavClusteR/")
5753 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
5755 "This package provides an integrated pipeline for the analysis of
5756 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
5757 sequencing errors, SNPs and additional non-experimental sources by a non-
5758 parametric mixture model. The protein binding sites (clusters) are then
5759 resolved at high resolution and cluster statistics are estimated using a
5760 rigorous Bayesian framework. Post-processing of the results, data export for
5761 UCSC genome browser visualization and motif search analysis are provided. In
5762 addition, the package allows to integrate RNA-Seq data to estimate the False
5763 Discovery Rate of cluster detection. Key functions support parallel multicore
5764 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
5765 be applied to the analysis of other NGS data obtained from experimental
5766 procedures that induce nucleotide substitutions (e.g. BisSeq).")
5767 (license license:gpl2)))
5769 (define-public r-timeseriesexperiment
5771 (name "r-timeseriesexperiment")
5776 (uri (bioconductor-uri "TimeSeriesExperiment" version))
5779 "1j11g7a2p0yk38fx6wd6152l1xynghj01pfxihalw601jwf1bl0y"))))
5781 `((upstream-name . "TimeSeriesExperiment")))
5782 (build-system r-build-system)
5784 `(("r-deseq2" ,r-deseq2)
5785 ("r-dplyr" ,r-dplyr)
5786 ("r-dynamictreecut" ,r-dynamictreecut)
5787 ("r-edger" ,r-edger)
5788 ("r-ggplot2" ,r-ggplot2)
5789 ("r-hmisc" ,r-hmisc)
5790 ("r-limma" ,r-limma)
5791 ("r-magrittr" ,r-magrittr)
5792 ("r-proxy" ,r-proxy)
5793 ("r-s4vectors" ,r-s4vectors)
5794 ("r-summarizedexperiment" ,r-summarizedexperiment)
5795 ("r-tibble" ,r-tibble)
5796 ("r-tidyr" ,r-tidyr)
5797 ("r-vegan" ,r-vegan)
5798 ("r-viridis" ,r-viridis)))
5799 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
5800 (synopsis "Analysis for short time-series data")
5802 "This package is a visualization and analysis toolbox for short time
5803 course data which includes dimensionality reduction, clustering, two-sample
5804 differential expression testing and gene ranking techniques. The package also
5805 provides methods for retrieving enriched pathways.")
5806 (license license:lgpl3+)))
5808 (define-public r-variantfiltering
5810 (name "r-variantfiltering")
5815 (uri (bioconductor-uri "VariantFiltering" version))
5818 "0vpghxacqcbaxx2scb5gfhcmfpw1lkls7h6qnbwbnmjwy01q2p17"))))
5820 `((upstream-name . "VariantFiltering")))
5821 (build-system r-build-system)
5823 `(("r-annotationdbi" ,r-annotationdbi)
5824 ("r-biobase" ,r-biobase)
5825 ("r-biocgenerics" ,r-biocgenerics)
5826 ("r-biocparallel" ,r-biocparallel)
5827 ("r-biostrings" ,r-biostrings)
5828 ("r-bsgenome" ,r-bsgenome)
5830 ("r-genomeinfodb" ,r-genomeinfodb)
5831 ("r-genomicfeatures" ,r-genomicfeatures)
5832 ("r-genomicranges" ,r-genomicranges)
5833 ("r-genomicscores" ,r-genomicscores)
5834 ("r-graph" ,r-graph)
5836 ("r-iranges" ,r-iranges)
5838 ("r-rsamtools" ,r-rsamtools)
5839 ("r-s4vectors" ,r-s4vectors)
5840 ("r-shiny" ,r-shiny)
5841 ("r-shinyjs" ,r-shinyjs)
5842 ("r-shinythemes" ,r-shinythemes)
5843 ("r-shinytree" ,r-shinytree)
5844 ("r-summarizedexperiment" ,r-summarizedexperiment)
5845 ("r-variantannotation" ,r-variantannotation)
5846 ("r-xvector" ,r-xvector)))
5847 (home-page "https://github.com/rcastelo/VariantFiltering")
5848 (synopsis "Filtering of coding and non-coding genetic variants")
5850 "Filter genetic variants using different criteria such as inheritance
5851 model, amino acid change consequence, minor allele frequencies across human
5852 populations, splice site strength, conservation, etc.")
5853 (license license:artistic2.0)))
5855 (define-public r-genomegraphs
5857 (name "r-genomegraphs")
5862 (uri (bioconductor-uri "GenomeGraphs" version))
5865 "026skcn2cqchlzaqsnk11gb8d8aq1rz7lrnx4mmsba234mh4j7kd"))))
5866 (properties `((upstream-name . "GenomeGraphs")))
5867 (build-system r-build-system)
5869 `(("r-biomart" ,r-biomart)))
5870 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
5871 (synopsis "Plotting genomic information from Ensembl")
5873 "Genomic data analyses requires integrated visualization of known genomic
5874 information and new experimental data. GenomeGraphs uses the biomaRt package
5875 to perform live annotation queries to Ensembl and translates this to e.g.
5876 gene/transcript structures in viewports of the grid graphics package. This
5877 results in genomic information plotted together with your data. Another
5878 strength of GenomeGraphs is to plot different data types such as array CGH,
5879 gene expression, sequencing and other data, together in one plot using the
5880 same genome coordinate system.")
5881 (license license:artistic2.0)))
5883 (define-public r-wavetiling
5885 (name "r-wavetiling")
5890 (uri (bioconductor-uri "waveTiling" version))
5893 "0l0saa0myabpq2rl9dq70zff8jpxr3mkanxlj65hc41f0m5xllir"))))
5894 (properties `((upstream-name . "waveTiling")))
5895 (build-system r-build-system)
5897 `(("r-affy" ,r-affy)
5898 ("r-biobase" ,r-biobase)
5899 ("r-biostrings" ,r-biostrings)
5900 ("r-genomegraphs" ,r-genomegraphs)
5901 ("r-genomicranges" ,r-genomicranges)
5902 ("r-iranges" ,r-iranges)
5903 ("r-oligo" ,r-oligo)
5904 ("r-oligoclasses" ,r-oligoclasses)
5905 ("r-preprocesscore" ,r-preprocesscore)
5906 ("r-waveslim" ,r-waveslim)))
5907 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
5908 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
5910 "This package is designed to conduct transcriptome analysis for tiling
5911 arrays based on fast wavelet-based functional models.")
5912 (license license:gpl2+)))
5914 (define-public r-variancepartition
5916 (name "r-variancepartition")
5921 (uri (bioconductor-uri "variancePartition" version))
5924 "0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
5926 `((upstream-name . "variancePartition")))
5927 (build-system r-build-system)
5929 `(("r-biobase" ,r-biobase)
5930 ("r-biocparallel" ,r-biocparallel)
5931 ("r-colorramps" ,r-colorramps)
5932 ("r-doparallel" ,r-doparallel)
5933 ("r-foreach" ,r-foreach)
5934 ("r-ggplot2" ,r-ggplot2)
5935 ("r-gplots" ,r-gplots)
5936 ("r-iterators" ,r-iterators)
5937 ("r-limma" ,r-limma)
5939 ("r-lmertest" ,r-lmertest)
5941 ("r-pbkrtest" ,r-pbkrtest)
5942 ("r-progress" ,r-progress)
5943 ("r-reshape2" ,r-reshape2)
5944 ("r-scales" ,r-scales)))
5945 (home-page "https://bioconductor.org/packages/variancePartition/")
5946 (synopsis "Analyze variation in gene expression experiments")
5948 "This is a package providing tools to quantify and interpret multiple
5949 sources of biological and technical variation in gene expression experiments.
5950 It uses a linear mixed model to quantify variation in gene expression
5951 attributable to individual, tissue, time point, or technical variables. The
5952 package includes dream differential expression analysis for repeated
5954 (license license:gpl2+)))
5956 (define-public r-htqpcr
5963 (uri (bioconductor-uri "HTqPCR" version))
5966 "09xgj797f0qsbm4jswxw7ijjwa4jxg06bfkq66xfhbvascyyrhg7"))))
5967 (properties `((upstream-name . "HTqPCR")))
5968 (build-system r-build-system)
5970 `(("r-affy" ,r-affy)
5971 ("r-biobase" ,r-biobase)
5972 ("r-gplots" ,r-gplots)
5973 ("r-limma" ,r-limma)
5974 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5975 (home-page "http://www.ebi.ac.uk/bertone/software")
5976 (synopsis "Automated analysis of high-throughput qPCR data")
5978 "Analysis of Ct values from high throughput quantitative real-time
5979 PCR (qPCR) assays across multiple conditions or replicates. The input data
5980 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
5981 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
5982 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
5983 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
5984 loading, quality assessment, normalization, visualization and parametric or
5985 non-parametric testing for statistical significance in Ct values between
5986 features (e.g. genes, microRNAs).")
5987 (license license:artistic2.0)))
5989 (define-public r-unifiedwmwqpcr
5991 (name "r-unifiedwmwqpcr")
5996 (uri (bioconductor-uri "unifiedWMWqPCR" version))
5999 "10j70bp5y1x2prz2iagqmwf04y79yqinq08wz4ilh8wggb9f7l8a"))))
6001 `((upstream-name . "unifiedWMWqPCR")))
6002 (build-system r-build-system)
6004 `(("r-biocgenerics" ,r-biocgenerics)
6005 ("r-htqpcr" ,r-htqpcr)))
6006 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
6007 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
6009 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
6010 data. This modified test allows for testing differential expression in qPCR
6012 (license license:gpl2+)))