1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020 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>
6 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
8 ;;; This file is part of GNU Guix.
10 ;;; GNU Guix is free software; you can redistribute it and/or modify it
11 ;;; under the terms of the GNU General Public License as published by
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13 ;;; your option) any later version.
15 ;;; GNU Guix is distributed in the hope that it will be useful, but
16 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
17 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 ;;; GNU General Public License for more details.
20 ;;; You should have received a copy of the GNU General Public License
21 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
23 (define-module (gnu packages bioconductor)
24 #:use-module ((guix licenses) #:prefix license:)
25 #:use-module (guix packages)
26 #:use-module (guix download)
27 #:use-module (guix git-download)
28 #:use-module (guix build-system r)
29 #:use-module (gnu packages)
30 #:use-module (gnu packages base)
31 #:use-module (gnu packages bioinformatics)
32 #:use-module (gnu packages cran)
33 #:use-module (gnu packages compression)
34 #:use-module (gnu packages gcc)
35 #:use-module (gnu packages graph)
36 #:use-module (gnu packages graphviz)
37 #:use-module (gnu packages haskell-xyz)
38 #:use-module (gnu packages image)
39 #:use-module (gnu packages maths)
40 #:use-module (gnu packages netpbm)
41 #:use-module (gnu packages perl)
42 #:use-module (gnu packages pkg-config)
43 #:use-module (gnu packages statistics)
44 #:use-module (gnu packages web)
45 #:use-module (gnu packages xml)
46 #:use-module (srfi srfi-1))
51 (define-public r-reactome-db
53 (name "r-reactome-db")
58 (uri (bioconductor-uri "reactome.db" version 'annotation))
61 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
62 (properties `((upstream-name . "reactome.db")))
63 (build-system r-build-system)
65 `(("r-annotationdbi" ,r-annotationdbi)))
66 (home-page "https://bioconductor.org/packages/reactome.db/")
67 (synopsis "Annotation maps for reactome")
69 "This package provides a set of annotation maps for the REACTOME
70 database, assembled using data from REACTOME.")
71 (license license:cc-by4.0)))
73 (define-public r-bsgenome-celegans-ucsc-ce6
75 (name "r-bsgenome-celegans-ucsc-ce6")
79 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
83 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
85 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
86 (build-system r-build-system)
88 `(("r-bsgenome" ,r-bsgenome)))
90 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
91 (synopsis "Full genome sequences for Worm")
93 "This package provides full genome sequences for Caenorhabditis
94 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
96 (license license:artistic2.0)))
98 (define-public r-bsgenome-celegans-ucsc-ce10
100 (name "r-bsgenome-celegans-ucsc-ce10")
104 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
105 version 'annotation))
108 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
110 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
111 (build-system r-build-system)
113 `(("r-bsgenome" ,r-bsgenome)))
115 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
116 (synopsis "Full genome sequences for Worm")
118 "This package provides full genome sequences for Caenorhabditis
119 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
121 (license license:artistic2.0)))
123 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
125 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
129 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
130 version 'annotation))
133 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
135 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
136 (build-system r-build-system)
138 `(("r-bsgenome" ,r-bsgenome)))
140 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
141 (synopsis "Full genome sequences for Fly")
143 "This package provides full genome sequences for Drosophila
144 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
146 (license license:artistic2.0)))
148 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
150 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
154 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
155 version 'annotation))
158 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
160 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
161 (build-system r-build-system)
163 `(("r-bsgenome" ,r-bsgenome)))
165 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
166 (synopsis "Full genome sequences for Fly")
168 "This package provides full genome sequences for Drosophila
169 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
170 Biostrings objects.")
171 (license license:artistic2.0)))
173 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
175 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
179 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
180 version 'annotation))
183 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
185 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
186 (build-system r-build-system)
188 `(("r-bsgenome" ,r-bsgenome)
189 ("r-bsgenome-dmelanogaster-ucsc-dm3"
190 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
191 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
192 (synopsis "Full masked genome sequences for Fly")
194 "This package provides full masked genome sequences for Drosophila
195 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
196 Biostrings objects. The sequences are the same as in
197 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
198 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
199 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
200 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
201 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
202 (license license:artistic2.0)))
204 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
206 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
210 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
211 version 'annotation))
214 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
216 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
217 (build-system r-build-system)
219 `(("r-bsgenome" ,r-bsgenome)))
221 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
222 (synopsis "Full genome sequences for Homo sapiens")
224 "This package provides full genome sequences for Homo sapiens from
225 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
226 (license license:artistic2.0)))
228 (define-public r-bsgenome-hsapiens-ncbi-grch38
230 (name "r-bsgenome-hsapiens-ncbi-grch38")
235 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
236 version 'annotation))
239 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
240 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
241 (build-system r-build-system)
242 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
244 "https://bioconductor.org/packages/release/data/annotation/html/\
245 BSgenome.Hsapiens.NCBI.GRCh38.html")
246 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
248 "This package provides full genome sequences for Homo sapiens (Human) as
249 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
250 (license license:artistic2.0)))
252 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
254 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
258 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
259 version 'annotation))
262 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
264 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
265 (build-system r-build-system)
267 `(("r-bsgenome" ,r-bsgenome)
268 ("r-bsgenome-hsapiens-ucsc-hg19"
269 ,r-bsgenome-hsapiens-ucsc-hg19)))
270 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
271 (synopsis "Full masked genome sequences for Homo sapiens")
273 "This package provides full genome sequences for Homo sapiens (Human) as
274 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
275 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
276 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
277 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
278 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
279 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
281 (license license:artistic2.0)))
283 (define-public r-bsgenome-mmusculus-ucsc-mm9
285 (name "r-bsgenome-mmusculus-ucsc-mm9")
289 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
290 version 'annotation))
293 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
295 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
296 (build-system r-build-system)
298 `(("r-bsgenome" ,r-bsgenome)))
300 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
301 (synopsis "Full genome sequences for Mouse")
303 "This package provides full genome sequences for Mus musculus (Mouse) as
304 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
305 (license license:artistic2.0)))
307 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
309 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
313 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
314 version 'annotation))
317 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
319 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
320 (build-system r-build-system)
322 `(("r-bsgenome" ,r-bsgenome)
323 ("r-bsgenome-mmusculus-ucsc-mm9"
324 ,r-bsgenome-mmusculus-ucsc-mm9)))
325 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
326 (synopsis "Full masked genome sequences for Mouse")
328 "This package provides full genome sequences for Mus musculus (Mouse) as
329 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
330 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
331 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
332 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
333 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
334 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
336 (license license:artistic2.0)))
338 (define-public r-bsgenome-mmusculus-ucsc-mm10
340 (name "r-bsgenome-mmusculus-ucsc-mm10")
344 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
345 version 'annotation))
348 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
350 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
351 (build-system r-build-system)
353 `(("r-bsgenome" ,r-bsgenome)))
355 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
356 (synopsis "Full genome sequences for Mouse")
358 "This package provides full genome sequences for Mus
359 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
360 in Biostrings objects.")
361 (license license:artistic2.0)))
363 (define-public r-org-ce-eg-db
365 (name "r-org-ce-eg-db")
369 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
372 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
374 `((upstream-name . "org.Ce.eg.db")))
375 (build-system r-build-system)
377 `(("r-annotationdbi" ,r-annotationdbi)))
378 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
379 (synopsis "Genome wide annotation for Worm")
381 "This package provides mappings from Entrez gene identifiers to various
382 annotations for the genome of the model worm Caenorhabditis elegans.")
383 (license license:artistic2.0)))
385 (define-public r-org-dm-eg-db
387 (name "r-org-dm-eg-db")
391 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
394 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
396 `((upstream-name . "org.Dm.eg.db")))
397 (build-system r-build-system)
399 `(("r-annotationdbi" ,r-annotationdbi)))
400 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
401 (synopsis "Genome wide annotation for Fly")
403 "This package provides mappings from Entrez gene identifiers to various
404 annotations for the genome of the model fruit fly Drosophila melanogaster.")
405 (license license:artistic2.0)))
407 (define-public r-org-dr-eg-db
409 (name "r-org-dr-eg-db")
413 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
416 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
418 `((upstream-name . "org.Dr.eg.db")))
419 (build-system r-build-system)
421 `(("r-annotationdbi" ,r-annotationdbi)))
422 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
423 (synopsis "Annotation for Zebrafish")
425 "This package provides genome wide annotations for Zebrafish, primarily
426 based on mapping using Entrez Gene identifiers.")
427 (license license:artistic2.0)))
429 (define-public r-org-hs-eg-db
431 (name "r-org-hs-eg-db")
435 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
438 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
440 `((upstream-name . "org.Hs.eg.db")))
441 (build-system r-build-system)
443 `(("r-annotationdbi" ,r-annotationdbi)))
444 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
445 (synopsis "Genome wide annotation for Human")
447 "This package contains genome-wide annotations for Human, primarily based
448 on mapping using Entrez Gene identifiers.")
449 (license license:artistic2.0)))
451 (define-public r-org-mm-eg-db
453 (name "r-org-mm-eg-db")
457 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
460 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
462 `((upstream-name . "org.Mm.eg.db")))
463 (build-system r-build-system)
465 `(("r-annotationdbi" ,r-annotationdbi)))
466 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
467 (synopsis "Genome wide annotation for Mouse")
469 "This package provides mappings from Entrez gene identifiers to various
470 annotations for the genome of the model mouse Mus musculus.")
471 (license license:artistic2.0)))
473 (define-public r-bsgenome-hsapiens-ucsc-hg19
475 (name "r-bsgenome-hsapiens-ucsc-hg19")
479 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
480 version 'annotation))
483 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
485 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
486 (build-system r-build-system)
488 `(("r-bsgenome" ,r-bsgenome)))
490 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
491 (synopsis "Full genome sequences for Homo sapiens")
493 "This package provides full genome sequences for Homo sapiens as provided
494 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
495 (license license:artistic2.0)))
497 (define-public r-bsgenome-hsapiens-ucsc-hg38
499 (name "r-bsgenome-hsapiens-ucsc-hg38")
503 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
504 version 'annotation))
507 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
509 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
510 (build-system r-build-system)
512 `(("r-bsgenome" ,r-bsgenome)))
514 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
515 (synopsis "Full genome sequences for Homo sapiens")
517 "This package provides full genome sequences for Homo sapiens (Human)
518 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
519 (license license:artistic2.0)))
521 (define-public r-ensdb-hsapiens-v75
523 (name "r-ensdb-hsapiens-v75")
528 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
531 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
533 `((upstream-name . "EnsDb.Hsapiens.v75")))
534 (build-system r-build-system)
536 `(("r-ensembldb" ,r-ensembldb)))
537 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
538 (synopsis "Ensembl based annotation package")
540 "This package exposes an annotation database generated from Ensembl.")
541 (license license:artistic2.0)))
543 (define-public r-genelendatabase
545 (name "r-genelendatabase")
550 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
553 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
555 `((upstream-name . "geneLenDataBase")))
556 (build-system r-build-system)
558 `(("r-rtracklayer" ,r-rtracklayer)
559 ("r-genomicfeatures" ,r-genomicfeatures)))
560 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
561 (synopsis "Lengths of mRNA transcripts for a number of genomes")
563 "This package provides the lengths of mRNA transcripts for a number of
564 genomes and gene ID formats, largely based on the UCSC table browser.")
565 (license license:lgpl2.0+)))
567 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
569 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
573 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
574 version 'annotation))
577 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
579 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
580 (build-system r-build-system)
582 `(("r-genomicfeatures" ,r-genomicfeatures)))
584 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
585 (synopsis "Annotation package for human genome in TxDb format")
587 "This package provides an annotation database of Homo sapiens genome
588 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
589 track. The database is exposed as a @code{TxDb} object.")
590 (license license:artistic2.0)))
592 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
594 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
598 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
599 version 'annotation))
602 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
604 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
605 (build-system r-build-system)
607 `(("r-genomicfeatures" ,r-genomicfeatures)))
609 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
610 (synopsis "Annotation package for human genome in TxDb format")
612 "This package provides an annotation database of Homo sapiens genome
613 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
614 track. The database is exposed as a @code{TxDb} object.")
615 (license license:artistic2.0)))
617 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
619 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
623 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
624 version 'annotation))
627 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
629 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
630 (build-system r-build-system)
632 `(("r-genomicfeatures" ,r-genomicfeatures)
633 ("r-annotationdbi" ,r-annotationdbi)))
635 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
636 (synopsis "Annotation package for mouse genome in TxDb format")
638 "This package provides an annotation database of Mouse genome data. It
639 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
640 database is exposed as a @code{TxDb} object.")
641 (license license:artistic2.0)))
643 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
645 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
649 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
650 version 'annotation))
653 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
655 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
656 (build-system r-build-system)
658 `(("r-bsgenome" ,r-bsgenome)
659 ("r-genomicfeatures" ,r-genomicfeatures)
660 ("r-annotationdbi" ,r-annotationdbi)))
662 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
663 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
665 "This package loads a TxDb object, which is an R interface to
666 prefabricated databases contained in this package. This package provides
667 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
668 based on the knownGene track.")
669 (license license:artistic2.0)))
671 (define-public r-txdb-celegans-ucsc-ce6-ensgene
673 (name "r-txdb-celegans-ucsc-ce6-ensgene")
678 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
679 version 'annotation))
682 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
684 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
685 (build-system r-build-system)
687 `(("r-annotationdbi" ,r-annotationdbi)
688 ("r-genomicfeatures" ,r-genomicfeatures)))
689 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
690 (synopsis "Annotation package for C elegans TxDb objects")
692 "This package exposes a C elegans annotation database generated from UCSC
693 by exposing these as TxDb objects.")
694 (license license:artistic2.0)))
696 (define-public r-fdb-infiniummethylation-hg19
698 (name "r-fdb-infiniummethylation-hg19")
702 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
703 version 'annotation))
706 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
708 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
709 (build-system r-build-system)
711 `(("r-biostrings" ,r-biostrings)
712 ("r-genomicfeatures" ,r-genomicfeatures)
713 ("r-annotationdbi" ,r-annotationdbi)
714 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
715 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
716 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
717 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
719 "This is an annotation package for Illumina Infinium DNA methylation
720 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
722 (license license:artistic2.0)))
724 (define-public r-illuminahumanmethylationepicmanifest
726 (name "r-illuminahumanmethylationepicmanifest")
730 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
731 version 'annotation))
734 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
736 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
737 (build-system r-build-system)
739 `(("r-minfi" ,r-minfi)))
740 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
741 (synopsis "Manifest for Illumina's EPIC methylation arrays")
743 "This is a manifest package for Illumina's EPIC methylation arrays.")
744 (license license:artistic2.0)))
746 (define-public r-ideoviz
752 (uri (bioconductor-uri "IdeoViz" version))
755 "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50"))))
756 (build-system r-build-system)
758 `(("r-biobase" ,r-biobase)
759 ("r-iranges" ,r-iranges)
760 ("r-genomicranges" ,r-genomicranges)
761 ("r-rcolorbrewer" ,r-rcolorbrewer)
762 ("r-rtracklayer" ,r-rtracklayer)
763 ("r-genomeinfodb" ,r-genomeinfodb)))
764 (home-page "https://bioconductor.org/packages/IdeoViz/")
765 (synopsis "Plots data along a chromosomal ideogram")
766 (description "This package provides functions to plot data associated with
767 arbitrary genomic intervals along chromosomal ideogram.")
768 (license license:gpl2)))
770 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
771 ;; from Bioconductor.
772 (define-public r-deconstructsigs
774 (name "r-deconstructsigs")
778 (uri (cran-uri "deconstructSigs" version))
781 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
783 `((upstream-name . "deconstructSigs")))
784 (build-system r-build-system)
786 `(("r-bsgenome" ,r-bsgenome)
787 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
788 ("r-genomeinfodb" ,r-genomeinfodb)
789 ("r-reshape2" ,r-reshape2)))
790 (home-page "https://github.com/raerose01/deconstructSigs")
791 (synopsis "Identifies signatures present in a tumor sample")
792 (description "This package takes sample information in the form of the
793 fraction of mutations in each of 96 trinucleotide contexts and identifies
794 the weighted combination of published signatures that, when summed, most
795 closely reconstructs the mutational profile.")
796 (license license:gpl2+)))
798 ;; This is a CRAN package, but it depends on Bioconductor packages.
806 (uri (cran-uri "NMF" version))
809 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
810 (properties `((upstream-name . "NMF")))
811 (build-system r-build-system)
813 `(("r-cluster" ,r-cluster)
814 ("r-biobase" ,r-biobase)
815 ("r-biocmanager" ,r-biocmanager)
816 ("r-bigmemory" ,r-bigmemory) ; suggested
817 ("r-synchronicity" ,r-synchronicity) ; suggested
818 ("r-colorspace" ,r-colorspace)
819 ("r-digest" ,r-digest)
820 ("r-doparallel" ,r-doparallel)
821 ("r-foreach" ,r-foreach)
822 ("r-ggplot2" ,r-ggplot2)
823 ("r-gridbase" ,r-gridbase)
824 ("r-pkgmaker" ,r-pkgmaker)
825 ("r-rcolorbrewer" ,r-rcolorbrewer)
826 ("r-registry" ,r-registry)
827 ("r-reshape2" ,r-reshape2)
828 ("r-rngtools" ,r-rngtools)
829 ("r-stringr" ,r-stringr)))
831 `(("r-knitr" ,r-knitr)))
832 (home-page "http://renozao.github.io/NMF")
833 (synopsis "Algorithms and framework for nonnegative matrix factorization")
835 "This package provides a framework to perform Non-negative Matrix
836 Factorization (NMF). The package implements a set of already published
837 algorithms and seeding methods, and provides a framework to test, develop and
838 plug new or custom algorithms. Most of the built-in algorithms have been
839 optimized in C++, and the main interface function provides an easy way of
840 performing parallel computations on multicore machines.")
841 (license license:gpl2+)))
843 (define-public r-do-db
849 (uri (bioconductor-uri "DO.db" version 'annotation))
852 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
854 `((upstream-name . "DO.db")))
855 (build-system r-build-system)
857 `(("r-annotationdbi" ,r-annotationdbi)))
858 (home-page "https://www.bioconductor.org/packages/DO.db/")
859 (synopsis "Annotation maps describing the entire Disease Ontology")
861 "This package provides a set of annotation maps describing the entire
863 (license license:artistic2.0)))
865 (define-public r-pasilla
872 "http://bioconductor.org/packages/release/data/experiment"
873 "/src/contrib/pasilla_" version ".tar.gz"))
876 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
877 (build-system r-build-system)
879 `(("r-biocstyle" ,r-biocstyle)
880 ("r-dexseq" ,r-dexseq)
882 ("r-rmarkdown" ,r-rmarkdown)))
883 (home-page "https://www.bioconductor.org/packages/pasilla/")
884 (synopsis "Data package with per-exon and per-gene read counts")
885 (description "This package provides per-exon and per-gene read counts
886 computed for selected genes from RNA-seq data that were presented in the
887 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
888 by Brooks et al., Genome Research 2011.")
889 (license license:lgpl2.1+)))
891 (define-public r-pfam-db
898 (uri (bioconductor-uri "PFAM.db" version 'annotation))
901 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
902 (properties `((upstream-name . "PFAM.db")))
903 (build-system r-build-system)
905 `(("r-annotationdbi" ,r-annotationdbi)))
906 (home-page "https://bioconductor.org/packages/PFAM.db")
907 (synopsis "Set of protein ID mappings for PFAM")
909 "This package provides a set of protein ID mappings for PFAM, assembled
910 using data from public repositories.")
911 (license license:artistic2.0)))
913 (define-public r-phastcons100way-ucsc-hg19
915 (name "r-phastcons100way-ucsc-hg19")
920 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
921 version 'annotation))
924 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
926 `((upstream-name . "phastCons100way.UCSC.hg19")))
927 (build-system r-build-system)
929 `(("r-bsgenome" ,r-bsgenome)
930 ("r-genomeinfodb" ,r-genomeinfodb)
931 ("r-genomicranges" ,r-genomicranges)
932 ("r-genomicscores" ,r-genomicscores)
933 ("r-iranges" ,r-iranges)
934 ("r-s4vectors" ,r-s4vectors)))
935 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
936 (synopsis "UCSC phastCons conservation scores for hg19")
938 "This package provides UCSC phastCons conservation scores for the human
939 genome (hg19) calculated from multiple alignments with other 99 vertebrate
941 (license license:artistic2.0)))
946 (define-public r-abadata
952 (uri (bioconductor-uri "ABAData" version 'experiment))
955 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
957 `((upstream-name . "ABAData")))
958 (build-system r-build-system)
960 `(("r-annotationdbi" ,r-annotationdbi)))
961 (home-page "https://www.bioconductor.org/packages/ABAData/")
962 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
964 "This package provides the data for the gene expression enrichment
965 analysis conducted in the package ABAEnrichment. The package includes three
966 datasets which are derived from the Allen Brain Atlas:
969 @item Gene expression data from Human Brain (adults) averaged across donors,
970 @item Gene expression data from the Developing Human Brain pooled into five
971 age categories and averaged across donors, and
972 @item a developmental effect score based on the Developing Human Brain
976 All datasets are restricted to protein coding genes.")
977 (license license:gpl2+)))
979 (define-public r-arrmdata
985 (uri (bioconductor-uri "ARRmData" version 'experiment))
988 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
990 `((upstream-name . "ARRmData")))
991 (build-system r-build-system)
992 (home-page "https://www.bioconductor.org/packages/ARRmData/")
993 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
995 "This package provides raw beta values from 36 samples across 3 groups
996 from Illumina 450k methylation arrays.")
997 (license license:artistic2.0)))
999 (define-public r-hsmmsinglecell
1001 (name "r-hsmmsinglecell")
1005 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1008 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1010 `((upstream-name . "HSMMSingleCell")))
1011 (build-system r-build-system)
1012 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1013 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1015 "Skeletal myoblasts undergo a well-characterized sequence of
1016 morphological and transcriptional changes during differentiation. In this
1017 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1018 under high mitogen conditions (GM) and then differentiated by switching to
1019 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1020 hundred cells taken over a time-course of serum-induced differentiation.
1021 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1022 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1023 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1024 which were then sequenced to a depth of ~4 million reads per library,
1025 resulting in a complete gene expression profile for each cell.")
1026 (license license:artistic2.0)))
1028 (define-public r-all
1034 (uri (bioconductor-uri "ALL" version 'experiment))
1037 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1038 (properties `((upstream-name . "ALL")))
1039 (build-system r-build-system)
1041 `(("r-biobase" ,r-biobase)))
1042 (home-page "https://bioconductor.org/packages/ALL")
1043 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1045 "The data consist of microarrays from 128 different individuals with
1046 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1047 are available. The data have been normalized (using rma) and it is the
1048 jointly normalized data that are available here. The data are presented in
1049 the form of an @code{exprSet} object.")
1050 (license license:artistic2.0)))
1052 (define-public r-affydata
1059 (uri (bioconductor-uri "affydata" version 'experiment))
1062 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1063 (properties `((upstream-name . "affydata")))
1064 (build-system r-build-system)
1066 `(("r-affy" ,r-affy)))
1067 (home-page "https://bioconductor.org/packages/affydata/")
1068 (synopsis "Affymetrix data for demonstration purposes")
1070 "This package provides example datasets that represent 'real world
1071 examples' of Affymetrix data, unlike the artificial examples included in the
1072 package @code{affy}.")
1073 (license license:gpl2+)))
1075 (define-public r-coverageview
1077 (name "r-coverageview")
1081 (uri (bioconductor-uri "CoverageView" version))
1084 "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj"))))
1085 (build-system r-build-system)
1087 `(("r-s4vectors" ,r-s4vectors)
1088 ("r-iranges" ,r-iranges)
1089 ("r-genomicranges" ,r-genomicranges)
1090 ("r-genomicalignments" ,r-genomicalignments)
1091 ("r-rtracklayer" ,r-rtracklayer)
1092 ("r-rsamtools" ,r-rsamtools)))
1093 (home-page "https://bioconductor.org/packages/CoverageView/")
1094 (synopsis "Coverage visualization package for R")
1095 (description "This package provides a framework for the visualization of
1096 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1097 be also used for genome-wide nucleosome positioning experiments or other
1098 experiment types where it is important to have a framework in order to inspect
1099 how the coverage distributed across the genome.")
1100 (license license:artistic2.0)))
1102 (define-public r-cummerbund
1104 (name "r-cummerbund")
1108 (uri (bioconductor-uri "cummeRbund" version))
1111 "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc"))))
1112 (build-system r-build-system)
1114 `(("r-biobase" ,r-biobase)
1115 ("r-biocgenerics" ,r-biocgenerics)
1116 ("r-fastcluster", r-fastcluster)
1117 ("r-ggplot2" ,r-ggplot2)
1120 ("r-reshape2" ,r-reshape2)
1121 ("r-rsqlite" ,r-rsqlite)
1122 ("r-rtracklayer" ,r-rtracklayer)
1123 ("r-s4vectors" ,r-s4vectors)))
1124 (home-page "https://bioconductor.org/packages/cummeRbund/")
1125 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1126 (description "This package allows for persistent storage, access,
1127 exploration, and manipulation of Cufflinks high-throughput sequencing
1128 data. In addition, provides numerous plotting functions for commonly
1129 used visualizations.")
1130 (license license:artistic2.0)))
1132 (define-public r-curatedtcgadata
1134 (name "r-curatedtcgadata")
1139 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1142 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1144 `((upstream-name . "curatedTCGAData")))
1145 (build-system r-build-system)
1147 `(("r-annotationhub" ,r-annotationhub)
1148 ("r-experimenthub" ,r-experimenthub)
1149 ("r-hdf5array" ,r-hdf5array)
1150 ("r-multiassayexperiment" ,r-multiassayexperiment)
1151 ("r-s4vectors" ,r-s4vectors)
1152 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1153 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1154 (synopsis "Curated data from The Cancer Genome Atlas")
1156 "This package provides publicly available data from The Cancer Genome
1157 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1158 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1159 number, mutation, microRNA, protein, and others) with clinical / pathological
1160 data. It also links assay barcodes with patient identifiers, enabling
1161 harmonized subsetting of rows (features) and columns (patients / samples)
1162 across the entire multi-'omics experiment.")
1163 (license license:artistic2.0)))
1168 (define-public r-biocversion
1170 (name "r-biocversion")
1175 (uri (bioconductor-uri "BiocVersion" version))
1178 "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz"))))
1179 (properties `((upstream-name . "BiocVersion")))
1180 (build-system r-build-system)
1181 (home-page "https://bioconductor.org/packages/BiocVersion/")
1182 (synopsis "Set the appropriate version of Bioconductor packages")
1184 "This package provides repository information for the appropriate version
1186 (license license:artistic2.0)))
1188 (define-public r-biocgenerics
1190 (name "r-biocgenerics")
1194 (uri (bioconductor-uri "BiocGenerics" version))
1197 "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk"))))
1199 `((upstream-name . "BiocGenerics")))
1200 (build-system r-build-system)
1201 (home-page "https://bioconductor.org/packages/BiocGenerics")
1202 (synopsis "S4 generic functions for Bioconductor")
1204 "This package provides S4 generic functions needed by many Bioconductor
1206 (license license:artistic2.0)))
1208 (define-public r-affycomp
1215 (uri (bioconductor-uri "affycomp" version))
1218 "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0"))))
1219 (properties `((upstream-name . "affycomp")))
1220 (build-system r-build-system)
1221 (propagated-inputs `(("r-biobase" ,r-biobase)))
1222 (home-page "https://bioconductor.org/packages/affycomp/")
1223 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1225 "The package contains functions that can be used to compare expression
1226 measures for Affymetrix Oligonucleotide Arrays.")
1227 (license license:gpl2+)))
1229 (define-public r-affycompatible
1231 (name "r-affycompatible")
1236 (uri (bioconductor-uri "AffyCompatible" version))
1239 "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd"))))
1241 `((upstream-name . "AffyCompatible")))
1242 (build-system r-build-system)
1244 `(("r-biostrings" ,r-biostrings)
1245 ("r-rcurl" ,r-rcurl)
1247 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1248 (synopsis "Work with Affymetrix GeneChip files")
1250 "This package provides an interface to Affymetrix chip annotation and
1251 sample attribute files. The package allows an easy way for users to download
1252 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1253 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1254 Command Console} (AGCC)-compatible sample annotation files.")
1255 (license license:artistic2.0)))
1257 (define-public r-affycontam
1259 (name "r-affycontam")
1264 (uri (bioconductor-uri "affyContam" version))
1267 "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i"))))
1268 (properties `((upstream-name . "affyContam")))
1269 (build-system r-build-system)
1271 `(("r-affy" ,r-affy)
1272 ("r-affydata" ,r-affydata)
1273 ("r-biobase" ,r-biobase)))
1274 (home-page "https://bioconductor.org/packages/affyContam/")
1275 (synopsis "Structured corruption of Affymetrix CEL file data")
1277 "Microarray quality assessment is a major concern of microarray analysts.
1278 This package provides some simple approaches to in silico creation of quality
1279 problems in CEL-level data to help evaluate performance of quality metrics.")
1280 (license license:artistic2.0)))
1282 (define-public r-affycoretools
1284 (name "r-affycoretools")
1289 (uri (bioconductor-uri "affycoretools" version))
1292 "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s"))))
1293 (properties `((upstream-name . "affycoretools")))
1294 (build-system r-build-system)
1296 `(("r-affy" ,r-affy)
1297 ("r-annotationdbi" ,r-annotationdbi)
1298 ("r-biobase" ,r-biobase)
1299 ("r-biocgenerics" ,r-biocgenerics)
1301 ("r-edger" ,r-edger)
1302 ("r-gcrma" ,r-gcrma)
1303 ("r-glimma" ,r-glimma)
1304 ("r-ggplot2" ,r-ggplot2)
1305 ("r-gostats" ,r-gostats)
1306 ("r-gplots" ,r-gplots)
1307 ("r-hwriter" ,r-hwriter)
1308 ("r-lattice" ,r-lattice)
1309 ("r-limma" ,r-limma)
1310 ("r-oligoclasses" ,r-oligoclasses)
1311 ("r-reportingtools" ,r-reportingtools)
1312 ("r-rsqlite" ,r-rsqlite)
1313 ("r-s4vectors" ,r-s4vectors)
1314 ("r-xtable" ,r-xtable)))
1316 `(("r-knitr" ,r-knitr)))
1317 (home-page "https://bioconductor.org/packages/affycoretools/")
1318 (synopsis "Functions for analyses with Affymetrix GeneChips")
1320 "This package provides various wrapper functions that have been written
1321 to streamline the more common analyses that a Biostatistician might see.")
1322 (license license:artistic2.0)))
1324 (define-public r-affxparser
1326 (name "r-affxparser")
1331 (uri (bioconductor-uri "affxparser" version))
1334 "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq"))))
1335 (properties `((upstream-name . "affxparser")))
1336 (build-system r-build-system)
1337 (home-page "https://github.com/HenrikBengtsson/affxparser")
1338 (synopsis "Affymetrix File Parsing SDK")
1340 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1341 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1342 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1343 are supported. Currently, there are methods for reading @dfn{chip definition
1344 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1345 either in full or in part. For example, probe signals from a few probesets
1346 can be extracted very quickly from a set of CEL files into a convenient list
1348 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1350 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1352 (define-public r-annotate
1359 (uri (bioconductor-uri "annotate" version))
1362 "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w"))))
1363 (build-system r-build-system)
1365 `(("r-annotationdbi" ,r-annotationdbi)
1366 ("r-biobase" ,r-biobase)
1367 ("r-biocgenerics" ,r-biocgenerics)
1369 ("r-rcurl" ,r-rcurl)
1371 ("r-xtable" ,r-xtable)))
1373 "https://bioconductor.org/packages/annotate")
1374 (synopsis "Annotation for microarrays")
1375 (description "This package provides R environments for the annotation of
1377 (license license:artistic2.0)))
1379 (define-public r-hpar
1386 (uri (bioconductor-uri "hpar" version))
1389 "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9"))))
1390 (build-system r-build-system)
1392 `(("r-knitr" ,r-knitr)))
1393 (home-page "https://bioconductor.org/packages/hpar/")
1394 (synopsis "Human Protein Atlas in R")
1395 (description "This package provides a simple interface to and data from
1396 the Human Protein Atlas project.")
1397 (license license:artistic2.0)))
1399 (define-public r-regioner
1406 (uri (bioconductor-uri "regioneR" version))
1409 "0bzjwzj5mvb49wgvs3gd3jfpm7s0zfkca763i65i7m994lgvz33c"))))
1410 (properties `((upstream-name . "regioneR")))
1411 (build-system r-build-system)
1413 `(("r-biostrings" ,r-biostrings)
1414 ("r-bsgenome" ,r-bsgenome)
1415 ("r-genomeinfodb" ,r-genomeinfodb)
1416 ("r-genomicranges" ,r-genomicranges)
1417 ("r-iranges" ,r-iranges)
1418 ("r-memoise" ,r-memoise)
1419 ("r-rtracklayer" ,r-rtracklayer)
1420 ("r-s4vectors" ,r-s4vectors)))
1422 `(("r-knitr" ,r-knitr)))
1423 (home-page "https://bioconductor.org/packages/regioneR/")
1424 (synopsis "Association analysis of genomic regions")
1425 (description "This package offers a statistical framework based on
1426 customizable permutation tests to assess the association between genomic
1427 region sets and other genomic features.")
1428 (license license:artistic2.0)))
1430 (define-public r-reportingtools
1432 (name "r-reportingtools")
1437 (uri (bioconductor-uri "ReportingTools" version))
1440 "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx"))))
1442 `((upstream-name . "ReportingTools")))
1443 (build-system r-build-system)
1445 `(("r-annotate" ,r-annotate)
1446 ("r-annotationdbi" ,r-annotationdbi)
1447 ("r-biobase" ,r-biobase)
1448 ("r-biocgenerics" ,r-biocgenerics)
1449 ("r-category" ,r-category)
1450 ("r-deseq2" ,r-deseq2)
1451 ("r-edger" ,r-edger)
1452 ("r-ggbio" ,r-ggbio)
1453 ("r-ggplot2" ,r-ggplot2)
1454 ("r-gostats" ,r-gostats)
1455 ("r-gseabase" ,r-gseabase)
1456 ("r-hwriter" ,r-hwriter)
1457 ("r-iranges" ,r-iranges)
1458 ("r-knitr" ,r-knitr)
1459 ("r-lattice" ,r-lattice)
1460 ("r-limma" ,r-limma)
1461 ("r-pfam-db" ,r-pfam-db)
1462 ("r-r-utils" ,r-r-utils)
1465 `(("r-knitr" ,r-knitr)))
1466 (home-page "https://bioconductor.org/packages/ReportingTools/")
1467 (synopsis "Tools for making reports in various formats")
1469 "The ReportingTools package enables users to easily display reports of
1470 analysis results generated from sources such as microarray and sequencing
1471 data. The package allows users to create HTML pages that may be viewed on a
1472 web browser, or in other formats. Users can generate tables with sortable and
1473 filterable columns, make and display plots, and link table entries to other
1474 data sources such as NCBI or larger plots within the HTML page. Using the
1475 package, users can also produce a table of contents page to link various
1476 reports together for a particular project that can be viewed in a web
1478 (license license:artistic2.0)))
1480 (define-public r-geneplotter
1482 (name "r-geneplotter")
1487 (uri (bioconductor-uri "geneplotter" version))
1490 "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5"))))
1491 (build-system r-build-system)
1493 `(("r-annotate" ,r-annotate)
1494 ("r-annotationdbi" ,r-annotationdbi)
1495 ("r-biobase" ,r-biobase)
1496 ("r-biocgenerics" ,r-biocgenerics)
1497 ("r-lattice" ,r-lattice)
1498 ("r-rcolorbrewer" ,r-rcolorbrewer)))
1499 (home-page "https://bioconductor.org/packages/geneplotter")
1500 (synopsis "Graphics functions for genomic data")
1502 "This package provides functions for plotting genomic data.")
1503 (license license:artistic2.0)))
1505 (define-public r-oligoclasses
1507 (name "r-oligoclasses")
1512 (uri (bioconductor-uri "oligoClasses" version))
1515 "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
1516 (properties `((upstream-name . "oligoClasses")))
1517 (build-system r-build-system)
1519 `(("r-affyio" ,r-affyio)
1520 ("r-biobase" ,r-biobase)
1521 ("r-biocgenerics" ,r-biocgenerics)
1522 ("r-biocmanager" ,r-biocmanager)
1523 ("r-biostrings" ,r-biostrings)
1526 ("r-foreach" ,r-foreach)
1527 ("r-genomicranges" ,r-genomicranges)
1528 ("r-iranges" ,r-iranges)
1529 ("r-rsqlite" ,r-rsqlite)
1530 ("r-s4vectors" ,r-s4vectors)
1531 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1532 (home-page "https://bioconductor.org/packages/oligoClasses/")
1533 (synopsis "Classes for high-throughput arrays")
1535 "This package contains class definitions, validity checks, and
1536 initialization methods for classes used by the @code{oligo} and @code{crlmm}
1538 (license license:gpl2+)))
1540 (define-public r-oligo
1547 (uri (bioconductor-uri "oligo" version))
1550 "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
1551 (properties `((upstream-name . "oligo")))
1552 (build-system r-build-system)
1553 (inputs `(("zlib" ,zlib)))
1555 `(("r-affxparser" ,r-affxparser)
1556 ("r-affyio" ,r-affyio)
1557 ("r-biobase" ,r-biobase)
1558 ("r-biocgenerics" ,r-biocgenerics)
1559 ("r-biostrings" ,r-biostrings)
1562 ("r-oligoclasses" ,r-oligoclasses)
1563 ("r-preprocesscore" ,r-preprocesscore)
1564 ("r-rsqlite" ,r-rsqlite)
1565 ("r-zlibbioc" ,r-zlibbioc)))
1567 `(("r-knitr" ,r-knitr)))
1568 (home-page "https://bioconductor.org/packages/oligo/")
1569 (synopsis "Preprocessing tools for oligonucleotide arrays")
1571 "This package provides a package to analyze oligonucleotide
1572 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
1573 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
1574 (license license:lgpl2.0+)))
1576 (define-public r-qvalue
1583 (uri (bioconductor-uri "qvalue" version))
1586 "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f"))))
1587 (build-system r-build-system)
1589 `(("r-ggplot2" ,r-ggplot2)
1590 ("r-reshape2" ,r-reshape2)))
1592 `(("r-knitr" ,r-knitr)))
1593 (home-page "https://github.com/StoreyLab/qvalue")
1594 (synopsis "Q-value estimation for false discovery rate control")
1596 "This package takes a list of p-values resulting from the simultaneous
1597 testing of many hypotheses and estimates their q-values and local @dfn{false
1598 discovery rate} (FDR) values. The q-value of a test measures the proportion
1599 of false positives incurred when that particular test is called significant.
1600 The local FDR measures the posterior probability the null hypothesis is true
1601 given the test's p-value. Various plots are automatically generated, allowing
1602 one to make sensible significance cut-offs. The software can be applied to
1603 problems in genomics, brain imaging, astrophysics, and data mining.")
1604 ;; Any version of the LGPL.
1605 (license license:lgpl3+)))
1607 (define-public r-diffbind
1614 (uri (bioconductor-uri "DiffBind" version))
1617 "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5"))))
1618 (properties `((upstream-name . "DiffBind")))
1619 (build-system r-build-system)
1623 `(("r-amap" ,r-amap)
1624 ("r-biocparallel" ,r-biocparallel)
1625 ("r-deseq2" ,r-deseq2)
1626 ("r-dplyr" ,r-dplyr)
1627 ("r-edger" ,r-edger)
1628 ("r-genomicalignments" ,r-genomicalignments)
1629 ("r-genomicranges" ,r-genomicranges)
1630 ("r-ggplot2" ,r-ggplot2)
1631 ("r-ggrepel" ,r-ggrepel)
1632 ("r-gplots" ,r-gplots)
1633 ("r-iranges" ,r-iranges)
1634 ("r-lattice" ,r-lattice)
1635 ("r-limma" ,r-limma)
1636 ("r-locfit" ,r-locfit)
1637 ("r-rcolorbrewer" , r-rcolorbrewer)
1639 ("r-rhtslib" ,r-rhtslib)
1640 ("r-rsamtools" ,r-rsamtools)
1641 ("r-s4vectors" ,r-s4vectors)
1642 ("r-summarizedexperiment" ,r-summarizedexperiment)
1643 ("r-systempiper" ,r-systempiper)))
1644 (home-page "https://bioconductor.org/packages/DiffBind")
1645 (synopsis "Differential binding analysis of ChIP-Seq peak data")
1647 "This package computes differentially bound sites from multiple
1648 ChIP-seq experiments using affinity (quantitative) data. Also enables
1649 occupancy (overlap) analysis and plotting functions.")
1650 (license license:artistic2.0)))
1652 (define-public r-ripseeker
1654 (name "r-ripseeker")
1659 (uri (bioconductor-uri "RIPSeeker" version))
1662 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
1663 (properties `((upstream-name . "RIPSeeker")))
1664 (build-system r-build-system)
1666 `(("r-s4vectors" ,r-s4vectors)
1667 ("r-iranges" ,r-iranges)
1668 ("r-genomicranges" ,r-genomicranges)
1669 ("r-summarizedexperiment" ,r-summarizedexperiment)
1670 ("r-rsamtools" ,r-rsamtools)
1671 ("r-genomicalignments" ,r-genomicalignments)
1672 ("r-rtracklayer" ,r-rtracklayer)))
1673 (home-page "https://bioconductor.org/packages/RIPSeeker")
1675 "Identifying protein-associated transcripts from RIP-seq experiments")
1677 "This package infers and discriminates RIP peaks from RIP-seq alignments
1678 using two-state HMM with negative binomial emission probability. While
1679 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
1680 a suite of bioinformatics tools integrated within this self-contained software
1681 package comprehensively addressing issues ranging from post-alignments
1682 processing to visualization and annotation.")
1683 (license license:gpl2)))
1685 (define-public r-multtest
1692 (uri (bioconductor-uri "multtest" version))
1695 "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2"))))
1696 (build-system r-build-system)
1698 `(("r-survival" ,r-survival)
1699 ("r-biocgenerics" ,r-biocgenerics)
1700 ("r-biobase" ,r-biobase)
1701 ("r-mass" ,r-mass)))
1702 (home-page "https://bioconductor.org/packages/multtest")
1703 (synopsis "Resampling-based multiple hypothesis testing")
1705 "This package can do non-parametric bootstrap and permutation
1706 resampling-based multiple testing procedures (including empirical Bayes
1707 methods) for controlling the family-wise error rate (FWER), generalized
1708 family-wise error rate (gFWER), tail probability of the proportion of
1709 false positives (TPPFP), and false discovery rate (FDR). Several choices
1710 of bootstrap-based null distribution are implemented (centered, centered
1711 and scaled, quantile-transformed). Single-step and step-wise methods are
1712 available. Tests based on a variety of T- and F-statistics (including
1713 T-statistics based on regression parameters from linear and survival models
1714 as well as those based on correlation parameters) are included. When probing
1715 hypotheses with T-statistics, users may also select a potentially faster null
1716 distribution which is multivariate normal with mean zero and variance
1717 covariance matrix derived from the vector influence function. Results are
1718 reported in terms of adjusted P-values, confidence regions and test statistic
1719 cutoffs. The procedures are directly applicable to identifying differentially
1720 expressed genes in DNA microarray experiments.")
1721 (license license:lgpl3)))
1723 (define-public r-graph
1729 (uri (bioconductor-uri "graph" version))
1732 "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g"))))
1733 (build-system r-build-system)
1735 `(("r-biocgenerics" ,r-biocgenerics)))
1736 (home-page "https://bioconductor.org/packages/graph")
1737 (synopsis "Handle graph data structures in R")
1739 "This package implements some simple graph handling capabilities for R.")
1740 (license license:artistic2.0)))
1742 ;; This is a CRAN package, but it depends on a Bioconductor package.
1743 (define-public r-ggm
1750 (uri (cran-uri "ggm" version))
1753 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
1754 (properties `((upstream-name . "ggm")))
1755 (build-system r-build-system)
1757 `(("r-graph" ,r-graph)
1758 ("r-igraph" ,r-igraph)))
1759 (home-page "https://cran.r-project.org/package=ggm")
1760 (synopsis "Functions for graphical Markov models")
1762 "This package provides functions and datasets for maximum likelihood
1763 fitting of some classes of graphical Markov models.")
1764 (license license:gpl2+)))
1766 (define-public r-codedepends
1768 (name "r-codedepends")
1773 (uri (cran-uri "CodeDepends" version))
1776 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1777 (properties `((upstream-name . "CodeDepends")))
1778 (build-system r-build-system)
1780 `(("r-codetools" ,r-codetools)
1781 ("r-graph" ,r-graph)
1783 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1784 (synopsis "Analysis of R code for reproducible research and code comprehension")
1786 "This package provides tools for analyzing R expressions or blocks of
1787 code and determining the dependencies between them. It focuses on R scripts,
1788 but can be used on the bodies of functions. There are many facilities
1789 including the ability to summarize or get a high-level view of code,
1790 determining dependencies between variables, code improvement suggestions.")
1791 ;; Any version of the GPL
1792 (license (list license:gpl2+ license:gpl3+))))
1794 (define-public r-chippeakanno
1796 (name "r-chippeakanno")
1801 (uri (bioconductor-uri "ChIPpeakAnno" version))
1804 "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
1805 (properties `((upstream-name . "ChIPpeakAnno")))
1806 (build-system r-build-system)
1808 `(("r-annotationdbi" ,r-annotationdbi)
1809 ("r-biobase" ,r-biobase)
1810 ("r-biocgenerics" ,r-biocgenerics)
1811 ("r-biocmanager" ,r-biocmanager)
1812 ("r-biomart" ,r-biomart)
1813 ("r-biostrings" ,r-biostrings)
1814 ("r-bsgenome" ,r-bsgenome)
1816 ("r-delayedarray" ,r-delayedarray)
1817 ("r-ensembldb" ,r-ensembldb)
1818 ("r-genomeinfodb" ,r-genomeinfodb)
1819 ("r-genomicalignments" ,r-genomicalignments)
1820 ("r-genomicfeatures" ,r-genomicfeatures)
1821 ("r-genomicranges" ,r-genomicranges)
1822 ("r-go-db" ,r-go-db)
1823 ("r-graph" ,r-graph)
1825 ("r-iranges" ,r-iranges)
1826 ("r-limma" ,r-limma)
1827 ("r-matrixstats" ,r-matrixstats)
1828 ("r-multtest" ,r-multtest)
1830 ("r-regioner" ,r-regioner)
1831 ("r-rsamtools" ,r-rsamtools)
1832 ("r-rtracklayer" ,r-rtracklayer)
1833 ("r-s4vectors" ,r-s4vectors)
1834 ("r-seqinr" ,r-seqinr)
1835 ("r-summarizedexperiment" ,r-summarizedexperiment)
1836 ("r-venndiagram" ,r-venndiagram)))
1838 `(("r-knitr" ,r-knitr)))
1839 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1840 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1842 "The package includes functions to retrieve the sequences around the peak,
1843 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1844 custom features such as most conserved elements and other transcription factor
1845 binding sites supplied by users. Starting 2.0.5, new functions have been added
1846 for finding the peaks with bi-directional promoters with summary statistics
1847 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1848 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1849 enrichedGO (addGeneIDs).")
1850 (license license:gpl2+)))
1852 (define-public r-marray
1858 (uri (bioconductor-uri "marray" version))
1860 (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
1861 (build-system r-build-system)
1863 `(("r-limma" ,r-limma)))
1864 (home-page "https://bioconductor.org/packages/marray")
1865 (synopsis "Exploratory analysis for two-color spotted microarray data")
1866 (description "This package contains class definitions for two-color spotted
1867 microarray data. It also includes functions for data input, diagnostic plots,
1868 normalization and quality checking.")
1869 (license license:lgpl2.0+)))
1871 (define-public r-cghbase
1877 (uri (bioconductor-uri "CGHbase" version))
1879 (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
1880 (properties `((upstream-name . "CGHbase")))
1881 (build-system r-build-system)
1883 `(("r-biobase" ,r-biobase)
1884 ("r-marray" ,r-marray)))
1885 (home-page "https://bioconductor.org/packages/CGHbase")
1886 (synopsis "Base functions and classes for arrayCGH data analysis")
1887 (description "This package contains functions and classes that are needed by
1888 the @code{arrayCGH} packages.")
1889 (license license:gpl2+)))
1891 (define-public r-cghcall
1897 (uri (bioconductor-uri "CGHcall" version))
1899 (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
1900 (properties `((upstream-name . "CGHcall")))
1901 (build-system r-build-system)
1903 `(("r-biobase" ,r-biobase)
1904 ("r-cghbase" ,r-cghbase)
1905 ("r-impute" ,r-impute)
1906 ("r-dnacopy" ,r-dnacopy)
1907 ("r-snowfall" ,r-snowfall)))
1908 (home-page "https://bioconductor.org/packages/CGHcall")
1909 (synopsis "Base functions and classes for arrayCGH data analysis")
1910 (description "This package contains functions and classes that are needed by
1911 @code{arrayCGH} packages.")
1912 (license license:gpl2+)))
1914 (define-public r-qdnaseq
1920 (uri (bioconductor-uri "QDNAseq" version))
1922 (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
1923 (properties `((upstream-name . "QDNAseq")))
1924 (build-system r-build-system)
1926 `(("r-biobase" ,r-biobase)
1927 ("r-cghbase" ,r-cghbase)
1928 ("r-cghcall" ,r-cghcall)
1929 ("r-dnacopy" ,r-dnacopy)
1930 ("r-future" ,r-future)
1931 ("r-future-apply" ,r-future-apply)
1932 ("r-genomicranges" ,r-genomicranges)
1933 ("r-iranges" ,r-iranges)
1934 ("r-matrixstats" ,r-matrixstats)
1935 ("r-r-utils" ,r-r-utils)
1936 ("r-rsamtools" ,r-rsamtools)))
1937 (home-page "https://bioconductor.org/packages/QDNAseq")
1938 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1939 (description "The genome is divided into non-overlapping fixed-sized bins,
1940 number of sequence reads in each counted, adjusted with a simultaneous
1941 two-dimensional loess correction for sequence mappability and GC content, and
1942 filtered to remove spurious regions in the genome. Downstream steps of
1943 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1945 (license license:gpl2+)))
1947 (define-public r-bayseq
1954 (uri (bioconductor-uri "baySeq" version))
1957 "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
1958 (properties `((upstream-name . "baySeq")))
1959 (build-system r-build-system)
1961 `(("r-abind" ,r-abind)
1962 ("r-edger" ,r-edger)
1963 ("r-genomicranges" ,r-genomicranges)))
1964 (home-page "https://bioconductor.org/packages/baySeq/")
1965 (synopsis "Bayesian analysis of differential expression patterns in count data")
1967 "This package identifies differential expression in high-throughput count
1968 data, such as that derived from next-generation sequencing machines,
1969 calculating estimated posterior likelihoods of differential expression (or
1970 more complex hypotheses) via empirical Bayesian methods.")
1971 (license license:gpl3)))
1973 (define-public r-chipcomp
1980 (uri (bioconductor-uri "ChIPComp" version))
1983 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
1984 (properties `((upstream-name . "ChIPComp")))
1985 (build-system r-build-system)
1987 `(("r-biocgenerics" ,r-biocgenerics)
1988 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1989 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1990 ("r-genomeinfodb" ,r-genomeinfodb)
1991 ("r-genomicranges" ,r-genomicranges)
1992 ("r-iranges" ,r-iranges)
1993 ("r-limma" ,r-limma)
1994 ("r-rsamtools" ,r-rsamtools)
1995 ("r-rtracklayer" ,r-rtracklayer)
1996 ("r-s4vectors" ,r-s4vectors)))
1997 (home-page "https://bioconductor.org/packages/ChIPComp")
1998 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2000 "ChIPComp implements a statistical method for quantitative comparison of
2001 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2002 sites across multiple conditions considering matching control in ChIP-seq
2004 ;; Any version of the GPL.
2005 (license license:gpl3+)))
2007 (define-public r-riboprofiling
2009 (name "r-riboprofiling")
2014 (uri (bioconductor-uri "RiboProfiling" version))
2017 "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
2018 (properties `((upstream-name . "RiboProfiling")))
2019 (build-system r-build-system)
2021 `(("r-biocgenerics" ,r-biocgenerics)
2022 ("r-biostrings" ,r-biostrings)
2023 ("r-data-table" ,r-data-table)
2024 ("r-genomeinfodb" ,r-genomeinfodb)
2025 ("r-genomicalignments" ,r-genomicalignments)
2026 ("r-genomicfeatures" ,r-genomicfeatures)
2027 ("r-genomicranges" ,r-genomicranges)
2028 ("r-ggbio" ,r-ggbio)
2029 ("r-ggplot2" ,r-ggplot2)
2030 ("r-iranges" ,r-iranges)
2032 ("r-reshape2" ,r-reshape2)
2033 ("r-rsamtools" ,r-rsamtools)
2034 ("r-rtracklayer" ,r-rtracklayer)
2035 ("r-s4vectors" ,r-s4vectors)
2036 ("r-sqldf" ,r-sqldf)))
2038 `(("r-knitr" ,r-knitr)))
2039 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2040 (synopsis "Ribosome profiling data analysis")
2041 (description "Starting with a BAM file, this package provides the
2042 necessary functions for quality assessment, read start position recalibration,
2043 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2044 of count data: pairs, log fold-change, codon frequency and coverage
2045 assessment, principal component analysis on codon coverage.")
2046 (license license:gpl3)))
2048 (define-public r-riboseqr
2055 (uri (bioconductor-uri "riboSeqR" version))
2058 "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
2059 (properties `((upstream-name . "riboSeqR")))
2060 (build-system r-build-system)
2062 `(("r-abind" ,r-abind)
2063 ("r-bayseq" ,r-bayseq)
2064 ("r-genomeinfodb" ,r-genomeinfodb)
2065 ("r-genomicranges" ,r-genomicranges)
2066 ("r-iranges" ,r-iranges)
2067 ("r-rsamtools" ,r-rsamtools)
2068 ("r-seqlogo" ,r-seqlogo)))
2069 (home-page "https://bioconductor.org/packages/riboSeqR/")
2070 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2072 "This package provides plotting functions, frameshift detection and
2073 parsing of genetic sequencing data from ribosome profiling experiments.")
2074 (license license:gpl3)))
2076 (define-public r-interactionset
2078 (name "r-interactionset")
2083 (uri (bioconductor-uri "InteractionSet" version))
2086 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
2088 `((upstream-name . "InteractionSet")))
2089 (build-system r-build-system)
2091 `(("r-biocgenerics" ,r-biocgenerics)
2092 ("r-genomeinfodb" ,r-genomeinfodb)
2093 ("r-genomicranges" ,r-genomicranges)
2094 ("r-iranges" ,r-iranges)
2095 ("r-matrix" ,r-matrix)
2097 ("r-s4vectors" ,r-s4vectors)
2098 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2100 `(("r-knitr" ,r-knitr)))
2101 (home-page "https://bioconductor.org/packages/InteractionSet")
2102 (synopsis "Base classes for storing genomic interaction data")
2104 "This package provides the @code{GInteractions},
2105 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2106 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2108 (license license:gpl3)))
2110 (define-public r-genomicinteractions
2112 (name "r-genomicinteractions")
2117 (uri (bioconductor-uri "GenomicInteractions" version))
2120 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
2122 `((upstream-name . "GenomicInteractions")))
2123 (build-system r-build-system)
2125 `(("r-biobase" ,r-biobase)
2126 ("r-biocgenerics" ,r-biocgenerics)
2127 ("r-data-table" ,r-data-table)
2128 ("r-dplyr" ,r-dplyr)
2129 ("r-genomeinfodb" ,r-genomeinfodb)
2130 ("r-genomicranges" ,r-genomicranges)
2131 ("r-ggplot2" ,r-ggplot2)
2132 ("r-gridextra" ,r-gridextra)
2134 ("r-igraph" ,r-igraph)
2135 ("r-interactionset" ,r-interactionset)
2136 ("r-iranges" ,r-iranges)
2137 ("r-rsamtools" ,r-rsamtools)
2138 ("r-rtracklayer" ,r-rtracklayer)
2139 ("r-s4vectors" ,r-s4vectors)
2140 ("r-stringr" ,r-stringr)))
2142 `(("r-knitr" ,r-knitr)))
2143 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2144 (synopsis "R package for handling genomic interaction data")
2146 "This R package provides tools for handling genomic interaction data,
2147 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2148 information and producing various plots and statistics.")
2149 (license license:gpl3)))
2151 (define-public r-ctc
2158 (uri (bioconductor-uri "ctc" version))
2161 "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
2162 (build-system r-build-system)
2163 (propagated-inputs `(("r-amap" ,r-amap)))
2164 (home-page "https://bioconductor.org/packages/ctc/")
2165 (synopsis "Cluster and tree conversion")
2167 "This package provides tools for exporting and importing classification
2168 trees and clusters to other programs.")
2169 (license license:gpl2)))
2171 (define-public r-goseq
2178 (uri (bioconductor-uri "goseq" version))
2181 "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
2182 (build-system r-build-system)
2184 `(("r-annotationdbi" ,r-annotationdbi)
2185 ("r-biasedurn" ,r-biasedurn)
2186 ("r-biocgenerics" ,r-biocgenerics)
2187 ("r-genelendatabase" ,r-genelendatabase)
2188 ("r-go-db" ,r-go-db)
2189 ("r-mgcv" ,r-mgcv)))
2190 (home-page "https://bioconductor.org/packages/goseq/")
2191 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2193 "This package provides tools to detect Gene Ontology and/or other user
2194 defined categories which are over/under represented in RNA-seq data.")
2195 (license license:lgpl2.0+)))
2197 (define-public r-glimma
2204 (uri (bioconductor-uri "Glimma" version))
2207 "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
2208 (properties `((upstream-name . "Glimma")))
2209 (build-system r-build-system)
2211 `(("r-edger" ,r-edger)
2212 ("r-jsonlite" ,r-jsonlite)
2213 ("r-s4vectors" ,r-s4vectors)))
2215 `(("r-knitr" ,r-knitr)))
2216 (home-page "https://github.com/Shians/Glimma")
2217 (synopsis "Interactive HTML graphics")
2219 "This package generates interactive visualisations for analysis of
2220 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2221 HTML page. The interactions are built on top of the popular static
2222 representations of analysis results in order to provide additional
2224 (license license:lgpl3)))
2226 (define-public r-rots
2233 (uri (bioconductor-uri "ROTS" version))
2236 "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
2237 (properties `((upstream-name . "ROTS")))
2238 (build-system r-build-system)
2240 `(("r-biobase" ,r-biobase)
2241 ("r-rcpp" ,r-rcpp)))
2242 (home-page "https://bioconductor.org/packages/ROTS/")
2243 (synopsis "Reproducibility-Optimized Test Statistic")
2245 "This package provides tools for calculating the
2246 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2248 (license license:gpl2+)))
2250 (define-public r-plgem
2257 (uri (bioconductor-uri "plgem" version))
2260 "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
2261 (build-system r-build-system)
2263 `(("r-biobase" ,r-biobase)
2264 ("r-mass" ,r-mass)))
2265 (home-page "http://www.genopolis.it")
2266 (synopsis "Detect differential expression in microarray and proteomics datasets")
2268 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2269 model the variance-versus-mean dependence that exists in a variety of
2270 genome-wide datasets, including microarray and proteomics data. The use of
2271 PLGEM has been shown to improve the detection of differentially expressed
2272 genes or proteins in these datasets.")
2273 (license license:gpl2)))
2275 (define-public r-inspect
2282 (uri (bioconductor-uri "INSPEcT" version))
2285 "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z"))))
2286 (properties `((upstream-name . "INSPEcT")))
2287 (build-system r-build-system)
2289 `(("r-biobase" ,r-biobase)
2290 ("r-biocgenerics" ,r-biocgenerics)
2291 ("r-biocparallel" ,r-biocparallel)
2292 ("r-deseq2" ,r-deseq2)
2293 ("r-desolve" ,r-desolve)
2294 ("r-gdata" ,r-gdata)
2295 ("r-genomeinfodb" ,r-genomeinfodb)
2296 ("r-genomicalignments" ,r-genomicalignments)
2297 ("r-genomicfeatures" ,r-genomicfeatures)
2298 ("r-genomicranges" ,r-genomicranges)
2299 ("r-iranges" ,r-iranges)
2300 ("r-kernsmooth" ,r-kernsmooth)
2301 ("r-plgem" ,r-plgem)
2303 ("r-rootsolve" ,r-rootsolve)
2304 ("r-rsamtools" ,r-rsamtools)
2305 ("r-rtracklayer" ,r-rtracklayer)
2306 ("r-s4vectors" ,r-s4vectors)
2307 ("r-shiny" ,r-shiny)
2308 ("r-summarizedexperiment" ,r-summarizedexperiment)
2309 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2310 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2312 `(("r-knitr" ,r-knitr)))
2313 (home-page "https://bioconductor.org/packages/INSPEcT")
2314 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2316 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2317 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2318 order to evaluate synthesis, processing and degradation rates and assess via
2319 modeling the rates that determines changes in mature mRNA levels.")
2320 (license license:gpl2)))
2322 (define-public r-dnabarcodes
2324 (name "r-dnabarcodes")
2329 (uri (bioconductor-uri "DNABarcodes" version))
2332 "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7"))))
2333 (properties `((upstream-name . "DNABarcodes")))
2334 (build-system r-build-system)
2337 ("r-matrix" ,r-matrix)
2338 ("r-rcpp" ,r-rcpp)))
2340 `(("r-knitr" ,r-knitr)))
2341 (home-page "https://bioconductor.org/packages/DNABarcodes")
2342 (synopsis "Create and analyze DNA barcodes")
2344 "This package offers tools to create DNA barcode sets capable of
2345 correcting insertion, deletion, and substitution errors. Existing barcodes
2346 can be analyzed regarding their minimal, maximal and average distances between
2347 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2348 demultiplexed, i.e. assigned to their original reference barcode.")
2349 (license license:gpl2)))
2351 (define-public r-ruvseq
2358 (uri (bioconductor-uri "RUVSeq" version))
2361 "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x"))))
2362 (properties `((upstream-name . "RUVSeq")))
2363 (build-system r-build-system)
2365 `(("r-biobase" ,r-biobase)
2366 ("r-edaseq" ,r-edaseq)
2367 ("r-edger" ,r-edger)
2368 ("r-mass" ,r-mass)))
2370 `(("r-knitr" ,r-knitr)))
2371 (home-page "https://github.com/drisso/RUVSeq")
2372 (synopsis "Remove unwanted variation from RNA-Seq data")
2374 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2375 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2377 (license license:artistic2.0)))
2379 (define-public r-biocneighbors
2381 (name "r-biocneighbors")
2386 (uri (bioconductor-uri "BiocNeighbors" version))
2389 "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy"))))
2390 (properties `((upstream-name . "BiocNeighbors")))
2391 (build-system r-build-system)
2393 `(("r-biocparallel" ,r-biocparallel)
2394 ("r-matrix" ,r-matrix)
2396 ("r-rcppannoy" ,r-rcppannoy)
2397 ("r-rcpphnsw" ,r-rcpphnsw)
2398 ("r-s4vectors" ,r-s4vectors)))
2400 `(("r-knitr" ,r-knitr)))
2401 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2402 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2404 "This package implements exact and approximate methods for nearest
2405 neighbor detection, in a framework that allows them to be easily switched
2406 within Bioconductor packages or workflows. The exact algorithm is implemented
2407 using pre-clustering with the k-means algorithm. Functions are also provided
2408 to search for all neighbors within a given distance. Parallelization is
2409 achieved for all methods using the BiocParallel framework.")
2410 (license license:gpl3)))
2412 (define-public r-biocsingular
2414 (name "r-biocsingular")
2419 (uri (bioconductor-uri "BiocSingular" version))
2422 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
2423 (properties `((upstream-name . "BiocSingular")))
2424 (build-system r-build-system)
2426 `(("r-beachmat" ,r-beachmat)
2427 ("r-biocgenerics" ,r-biocgenerics)
2428 ("r-biocparallel" ,r-biocparallel)
2429 ("r-delayedarray" ,r-delayedarray)
2430 ("r-irlba" ,r-irlba)
2431 ("r-matrix" ,r-matrix)
2434 ("r-s4vectors" ,r-s4vectors)))
2436 `(("r-knitr" ,r-knitr)))
2437 (home-page "https://github.com/LTLA/BiocSingular")
2438 (synopsis "Singular value decomposition for Bioconductor packages")
2440 "This package implements exact and approximate methods for singular value
2441 decomposition and principal components analysis, in a framework that allows
2442 them to be easily switched within Bioconductor packages or workflows. Where
2443 possible, parallelization is achieved using the BiocParallel framework.")
2444 (license license:gpl3)))
2446 (define-public r-destiny
2453 (uri (bioconductor-uri "destiny" version))
2456 "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n"))))
2457 (build-system r-build-system)
2459 `(("r-biobase" ,r-biobase)
2460 ("r-biocgenerics" ,r-biocgenerics)
2461 ("r-ggplot-multistats" ,r-ggplot-multistats)
2462 ("r-ggplot2" ,r-ggplot2)
2463 ("r-ggthemes" ,r-ggthemes)
2464 ("r-irlba" ,r-irlba)
2465 ("r-knn-covertree" ,r-knn-covertree)
2466 ("r-matrix" ,r-matrix)
2467 ("r-nbconvertr" ,r-nbconvertr)
2468 ("r-pcamethods" ,r-pcamethods)
2469 ("r-proxy" ,r-proxy)
2471 ("r-rcppeigen" ,r-rcppeigen)
2472 ("r-rcpphnsw" ,r-rcpphnsw)
2473 ("r-rspectra" ,r-rspectra)
2474 ("r-scales" ,r-scales)
2475 ("r-scatterplot3d" ,r-scatterplot3d)
2476 ("r-singlecellexperiment" ,r-singlecellexperiment)
2477 ("r-smoother" ,r-smoother)
2478 ("r-summarizedexperiment" ,r-summarizedexperiment)
2479 ("r-tidyr" ,r-tidyr)
2480 ("r-tidyselect" ,r-tidyselect)
2483 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2484 (home-page "https://bioconductor.org/packages/destiny/")
2485 (synopsis "Create and plot diffusion maps")
2486 (description "This package provides tools to create and plot diffusion
2488 ;; Any version of the GPL
2489 (license license:gpl3+)))
2491 (define-public r-savr
2498 (uri (bioconductor-uri "savR" version))
2501 "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a"))))
2502 (properties `((upstream-name . "savR")))
2503 (build-system r-build-system)
2505 `(("r-ggplot2" ,r-ggplot2)
2506 ("r-gridextra" ,r-gridextra)
2507 ("r-reshape2" ,r-reshape2)
2508 ("r-scales" ,r-scales)
2510 (home-page "https://github.com/bcalder/savR")
2511 (synopsis "Parse and analyze Illumina SAV files")
2513 "This package provides tools to parse Illumina Sequence Analysis
2514 Viewer (SAV) files, access data, and generate QC plots.")
2515 (license license:agpl3+)))
2517 (define-public r-chipexoqual
2519 (name "r-chipexoqual")
2524 (uri (bioconductor-uri "ChIPexoQual" version))
2527 "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp"))))
2528 (properties `((upstream-name . "ChIPexoQual")))
2529 (build-system r-build-system)
2531 `(("r-biocparallel" ,r-biocparallel)
2532 ("r-biovizbase" ,r-biovizbase)
2533 ("r-broom" ,r-broom)
2534 ("r-data-table" ,r-data-table)
2535 ("r-dplyr" ,r-dplyr)
2536 ("r-genomeinfodb" ,r-genomeinfodb)
2537 ("r-genomicalignments" ,r-genomicalignments)
2538 ("r-genomicranges" ,r-genomicranges)
2539 ("r-ggplot2" ,r-ggplot2)
2540 ("r-hexbin" ,r-hexbin)
2541 ("r-iranges" ,r-iranges)
2542 ("r-rcolorbrewer" ,r-rcolorbrewer)
2543 ("r-rmarkdown" ,r-rmarkdown)
2544 ("r-rsamtools" ,r-rsamtools)
2545 ("r-s4vectors" ,r-s4vectors)
2546 ("r-scales" ,r-scales)
2547 ("r-viridis" ,r-viridis)))
2549 `(("r-knitr" ,r-knitr)))
2550 (home-page "https://github.com/keleslab/ChIPexoQual")
2551 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2553 "This package provides a quality control pipeline for ChIP-exo/nexus
2555 (license license:gpl2+)))
2557 (define-public r-copynumber
2559 (name "r-copynumber")
2563 (uri (bioconductor-uri "copynumber" version))
2566 "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my"))))
2567 (build-system r-build-system)
2569 `(("r-s4vectors" ,r-s4vectors)
2570 ("r-iranges" ,r-iranges)
2571 ("r-genomicranges" ,r-genomicranges)
2572 ("r-biocgenerics" ,r-biocgenerics)))
2573 (home-page "https://bioconductor.org/packages/copynumber")
2574 (synopsis "Segmentation of single- and multi-track copy number data")
2576 "This package segments single- and multi-track copy number data by a
2577 penalized least squares regression method.")
2578 (license license:artistic2.0)))
2580 (define-public r-dnacopy
2587 (uri (bioconductor-uri "DNAcopy" version))
2590 "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza"))))
2591 (properties `((upstream-name . "DNAcopy")))
2592 (build-system r-build-system)
2593 (native-inputs `(("gfortran" ,gfortran)))
2594 (home-page "https://bioconductor.org/packages/DNAcopy")
2595 (synopsis "DNA copy number data analysis")
2597 "This package implements the @dfn{circular binary segmentation} (CBS)
2598 algorithm to segment DNA copy number data and identify genomic regions with
2599 abnormal copy number.")
2600 (license license:gpl2+)))
2602 ;; This is a CRAN package, but it uncharacteristically depends on a
2603 ;; Bioconductor package.
2604 (define-public r-htscluster
2606 (name "r-htscluster")
2611 (uri (cran-uri "HTSCluster" version))
2614 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2615 (properties `((upstream-name . "HTSCluster")))
2616 (build-system r-build-system)
2618 `(("r-capushe" ,r-capushe)
2619 ("r-edger" ,r-edger)
2620 ("r-plotrix" ,r-plotrix)))
2621 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2622 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2624 "This package provides a Poisson mixture model is implemented to cluster
2625 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2626 estimation is performed using either the EM or CEM algorithm, and the slope
2627 heuristics are used for model selection (i.e., to choose the number of
2629 (license license:gpl3+)))
2631 (define-public r-deds
2638 (uri (bioconductor-uri "DEDS" version))
2641 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2642 (properties `((upstream-name . "DEDS")))
2643 (build-system r-build-system)
2644 (home-page "https://bioconductor.org/packages/DEDS/")
2645 (synopsis "Differential expression via distance summary for microarray data")
2647 "This library contains functions that calculate various statistics of
2648 differential expression for microarray data, including t statistics, fold
2649 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2650 also implements a new methodology called DEDS (Differential Expression via
2651 Distance Summary), which selects differentially expressed genes by integrating
2652 and summarizing a set of statistics using a weighted distance approach.")
2653 ;; Any version of the LGPL.
2654 (license license:lgpl3+)))
2656 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2658 (define-public r-nbpseq
2665 (uri (cran-uri "NBPSeq" version))
2668 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2669 (properties `((upstream-name . "NBPSeq")))
2670 (build-system r-build-system)
2672 `(("r-qvalue" ,r-qvalue)))
2673 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2674 (synopsis "Negative binomial models for RNA-Seq data")
2676 "This package provides negative binomial models for two-group comparisons
2677 and regression inferences from RNA-sequencing data.")
2678 (license license:gpl2)))
2680 (define-public r-ebseq
2687 (uri (bioconductor-uri "EBSeq" version))
2690 "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f"))))
2691 (properties `((upstream-name . "EBSeq")))
2692 (build-system r-build-system)
2694 `(("r-blockmodeling" ,r-blockmodeling)
2695 ("r-gplots" ,r-gplots)
2696 ("r-testthat" ,r-testthat)))
2697 (home-page "https://bioconductor.org/packages/EBSeq")
2698 (synopsis "Differential expression analysis of RNA-seq data")
2700 "This package provides tools for differential expression analysis at both
2701 gene and isoform level using RNA-seq data")
2702 (license license:artistic2.0)))
2704 (define-public r-karyoploter
2706 (name "r-karyoploter")
2710 (uri (bioconductor-uri "karyoploteR" version))
2713 "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
2714 (build-system r-build-system)
2716 `(("r-annotationdbi" ,r-annotationdbi)
2717 ("r-bamsignals" ,r-bamsignals)
2718 ("r-bezier" ,r-bezier)
2719 ("r-biovizbase" ,r-biovizbase)
2720 ("r-digest" ,r-digest)
2721 ("r-genomeinfodb" ,r-genomeinfodb)
2722 ("r-genomicfeatures" ,r-genomicfeatures)
2723 ("r-genomicranges" ,r-genomicranges)
2724 ("r-iranges" ,r-iranges)
2725 ("r-memoise" ,r-memoise)
2726 ("r-regioner" ,r-regioner)
2727 ("r-rsamtools" ,r-rsamtools)
2728 ("r-rtracklayer" ,r-rtracklayer)
2729 ("r-s4vectors" ,r-s4vectors)
2730 ("r-variantannotation" ,r-variantannotation)))
2732 `(("r-knitr" ,r-knitr)))
2733 (home-page "https://bioconductor.org/packages/karyoploteR/")
2734 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2735 (description "This package creates karyotype plots of arbitrary genomes and
2736 offers a complete set of functions to plot arbitrary data on them. It mimicks
2737 many R base graphics functions coupling them with a coordinate change function
2738 automatically mapping the chromosome and data coordinates into the plot
2740 (license license:artistic2.0)))
2742 (define-public r-lpsymphony
2744 (name "r-lpsymphony")
2749 (uri (bioconductor-uri "lpsymphony" version))
2752 "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4"))))
2753 (build-system r-build-system)
2757 `(("pkg-config" ,pkg-config)
2758 ("r-knitr" ,r-knitr)))
2759 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2760 (synopsis "Symphony integer linear programming solver in R")
2762 "This package was derived from Rsymphony. The package provides an R
2763 interface to SYMPHONY, a linear programming solver written in C++. The main
2764 difference between this package and Rsymphony is that it includes the solver
2765 source code, while Rsymphony expects to find header and library files on the
2766 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2767 to install interface to SYMPHONY.")
2768 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2769 ;; lpsimphony is released under the same terms.
2770 (license license:epl1.0)))
2772 (define-public r-ihw
2779 (uri (bioconductor-uri "IHW" version))
2782 "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j"))))
2783 (properties `((upstream-name . "IHW")))
2784 (build-system r-build-system)
2786 `(("r-biocgenerics" ,r-biocgenerics)
2787 ("r-fdrtool" ,r-fdrtool)
2788 ("r-lpsymphony" ,r-lpsymphony)
2789 ("r-slam" ,r-slam)))
2791 `(("r-knitr" ,r-knitr)))
2792 (home-page "https://bioconductor.org/packages/IHW")
2793 (synopsis "Independent hypothesis weighting")
2795 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2796 procedure that increases power compared to the method of Benjamini and
2797 Hochberg by assigning data-driven weights to each hypothesis. The input to
2798 IHW is a two-column table of p-values and covariates. The covariate can be
2799 any continuous-valued or categorical variable that is thought to be
2800 informative on the statistical properties of each hypothesis test, while it is
2801 independent of the p-value under the null hypothesis.")
2802 (license license:artistic2.0)))
2804 (define-public r-icobra
2811 (uri (bioconductor-uri "iCOBRA" version))
2814 "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1"))))
2815 (properties `((upstream-name . "iCOBRA")))
2816 (build-system r-build-system)
2818 `(("r-dplyr" ,r-dplyr)
2820 ("r-ggplot2" ,r-ggplot2)
2821 ("r-limma" ,r-limma)
2822 ("r-reshape2" ,r-reshape2)
2824 ("r-scales" ,r-scales)
2825 ("r-shiny" ,r-shiny)
2826 ("r-shinybs" ,r-shinybs)
2827 ("r-shinydashboard" ,r-shinydashboard)
2828 ("r-upsetr" ,r-upsetr)))
2830 `(("r-knitr" ,r-knitr)))
2831 (home-page "https://bioconductor.org/packages/iCOBRA")
2832 (synopsis "Comparison and visualization of ranking and assignment methods")
2834 "This package provides functions for calculation and visualization of
2835 performance metrics for evaluation of ranking and binary
2836 classification (assignment) methods. It also contains a Shiny application for
2837 interactive exploration of results.")
2838 (license license:gpl2+)))
2840 (define-public r-mast
2847 (uri (bioconductor-uri "MAST" version))
2850 "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr"))))
2851 (properties `((upstream-name . "MAST")))
2852 (build-system r-build-system)
2854 `(("r-abind" ,r-abind)
2855 ("r-biobase" ,r-biobase)
2856 ("r-biocgenerics" ,r-biocgenerics)
2857 ("r-data-table" ,r-data-table)
2858 ("r-ggplot2" ,r-ggplot2)
2860 ("r-progress" ,r-progress)
2861 ("r-reshape2" ,r-reshape2)
2862 ("r-s4vectors" ,r-s4vectors)
2863 ("r-singlecellexperiment" ,r-singlecellexperiment)
2864 ("r-stringr" ,r-stringr)
2865 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2867 `(("r-knitr" ,r-knitr)))
2868 (home-page "https://github.com/RGLab/MAST/")
2869 (synopsis "Model-based analysis of single cell transcriptomics")
2871 "This package provides methods and models for handling zero-inflated
2872 single cell assay data.")
2873 (license license:gpl2+)))
2875 (define-public r-monocle
2882 (uri (bioconductor-uri "monocle" version))
2885 "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd"))))
2886 (build-system r-build-system)
2888 `(("r-biobase" ,r-biobase)
2889 ("r-biocgenerics" ,r-biocgenerics)
2890 ("r-biocviews" ,r-biocviews)
2891 ("r-cluster" ,r-cluster)
2892 ("r-combinat" ,r-combinat)
2893 ("r-ddrtree" ,r-ddrtree)
2894 ("r-densityclust" ,r-densityclust)
2895 ("r-dplyr" ,r-dplyr)
2896 ("r-fastica" ,r-fastica)
2897 ("r-ggplot2" ,r-ggplot2)
2898 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2899 ("r-igraph" ,r-igraph)
2900 ("r-irlba" ,r-irlba)
2901 ("r-limma" ,r-limma)
2903 ("r-matrix" ,r-matrix)
2904 ("r-matrixstats" ,r-matrixstats)
2905 ("r-pheatmap" ,r-pheatmap)
2907 ("r-proxy" ,r-proxy)
2908 ("r-qlcmatrix" ,r-qlcmatrix)
2911 ("r-reshape2" ,r-reshape2)
2912 ("r-rtsne" ,r-rtsne)
2914 ("r-stringr" ,r-stringr)
2915 ("r-tibble" ,r-tibble)
2917 ("r-viridis" ,r-viridis)))
2919 `(("r-knitr" ,r-knitr)))
2920 (home-page "https://bioconductor.org/packages/monocle")
2921 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2923 "Monocle performs differential expression and time-series analysis for
2924 single-cell expression experiments. It orders individual cells according to
2925 progress through a biological process, without knowing ahead of time which
2926 genes define progress through that process. Monocle also performs
2927 differential expression analysis, clustering, visualization, and other useful
2928 tasks on single cell expression data. It is designed to work with RNA-Seq and
2929 qPCR data, but could be used with other types as well.")
2930 (license license:artistic2.0)))
2932 (define-public r-monocle3
2940 (url "https://github.com/cole-trapnell-lab/monocle3")
2942 (file-name (git-file-name name version))
2945 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2946 (build-system r-build-system)
2948 `(("r-biobase" ,r-biobase)
2949 ("r-biocgenerics" ,r-biocgenerics)
2950 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2951 ("r-dplyr" ,r-dplyr)
2952 ("r-ggplot2" ,r-ggplot2)
2953 ("r-ggrepel" ,r-ggrepel)
2955 ("r-htmlwidgets" ,r-htmlwidgets)
2956 ("r-igraph" ,r-igraph)
2957 ("r-irlba" ,r-irlba)
2958 ("r-limma" ,r-limma)
2959 ("r-lmtest" ,r-lmtest)
2961 ("r-matrix" ,r-matrix)
2962 ("r-matrix-utils" ,r-matrix-utils)
2963 ("r-pbapply" ,r-pbapply)
2964 ("r-pbmcapply" ,r-pbmcapply)
2965 ("r-pheatmap" ,r-pheatmap)
2966 ("r-plotly" ,r-plotly)
2968 ("r-proxy" ,r-proxy)
2970 ("r-purrr" ,r-purrr)
2973 ("r-rcppparallel" ,r-rcppparallel)
2974 ("r-reshape2" ,r-reshape2)
2975 ("r-reticulate" ,r-reticulate)
2976 ("r-rhpcblasctl" ,r-rhpcblasctl)
2977 ("r-rtsne" ,r-rtsne)
2978 ("r-shiny" ,r-shiny)
2980 ("r-spdep" ,r-spdep)
2981 ("r-speedglm" ,r-speedglm)
2982 ("r-stringr" ,r-stringr)
2983 ("r-singlecellexperiment" ,r-singlecellexperiment)
2984 ("r-tibble" ,r-tibble)
2985 ("r-tidyr" ,r-tidyr)
2987 ("r-viridis" ,r-viridis)))
2988 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2989 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2991 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2992 (license license:expat)))
2994 (define-public r-noiseq
3001 (uri (bioconductor-uri "NOISeq" version))
3004 "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33"))))
3005 (properties `((upstream-name . "NOISeq")))
3006 (build-system r-build-system)
3008 `(("r-biobase" ,r-biobase)
3009 ("r-matrix" ,r-matrix)))
3010 (home-page "https://bioconductor.org/packages/NOISeq")
3011 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3013 "This package provides tools to support the analysis of RNA-seq
3014 expression data or other similar kind of data. It provides exploratory plots
3015 to evaluate saturation, count distribution, expression per chromosome, type of
3016 detected features, features length, etc. It also supports the analysis of
3017 differential expression between two experimental conditions with no parametric
3019 (license license:artistic2.0)))
3021 (define-public r-scdd
3028 (uri (bioconductor-uri "scDD" version))
3031 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
3032 (properties `((upstream-name . "scDD")))
3033 (build-system r-build-system)
3036 ("r-biocparallel" ,r-biocparallel)
3037 ("r-ebseq" ,r-ebseq)
3038 ("r-fields" ,r-fields)
3039 ("r-ggplot2" ,r-ggplot2)
3040 ("r-mclust" ,r-mclust)
3041 ("r-outliers" ,r-outliers)
3042 ("r-s4vectors" ,r-s4vectors)
3043 ("r-scran" ,r-scran)
3044 ("r-singlecellexperiment" ,r-singlecellexperiment)
3045 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3047 `(("r-knitr" ,r-knitr)))
3048 (home-page "https://github.com/kdkorthauer/scDD")
3049 (synopsis "Mixture modeling of single-cell RNA-seq data")
3051 "This package implements a method to analyze single-cell RNA-seq data
3052 utilizing flexible Dirichlet Process mixture models. Genes with differential
3053 distributions of expression are classified into several interesting patterns
3054 of differences between two conditions. The package also includes functions
3055 for simulating data with these patterns from negative binomial
3057 (license license:gpl2)))
3059 (define-public r-scone
3066 (uri (bioconductor-uri "scone" version))
3069 "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g"))))
3070 (build-system r-build-system)
3072 `(("r-aroma-light" ,r-aroma-light)
3073 ("r-biocparallel" ,r-biocparallel)
3075 ("r-class" ,r-class)
3076 ("r-cluster" ,r-cluster)
3077 ("r-compositions" ,r-compositions)
3078 ("r-diptest" ,r-diptest)
3079 ("r-edger" ,r-edger)
3081 ("r-gplots" ,r-gplots)
3082 ("r-hexbin" ,r-hexbin)
3083 ("r-limma" ,r-limma)
3084 ("r-matrixstats" ,r-matrixstats)
3085 ("r-mixtools" ,r-mixtools)
3086 ("r-rarpack" ,r-rarpack)
3087 ("r-rcolorbrewer" ,r-rcolorbrewer)
3088 ("r-rhdf5" ,r-rhdf5)
3089 ("r-ruvseq" ,r-ruvseq)
3090 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3092 `(("r-knitr" ,r-knitr)))
3093 (home-page "https://bioconductor.org/packages/scone")
3094 (synopsis "Single cell overview of normalized expression data")
3096 "SCONE is an R package for comparing and ranking the performance of
3097 different normalization schemes for single-cell RNA-seq and other
3098 high-throughput analyses.")
3099 (license license:artistic2.0)))
3101 (define-public r-geoquery
3108 (uri (bioconductor-uri "GEOquery" version))
3111 "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m"))))
3112 (properties `((upstream-name . "GEOquery")))
3113 (build-system r-build-system)
3115 `(("r-biobase" ,r-biobase)
3116 ("r-dplyr" ,r-dplyr)
3118 ("r-limma" ,r-limma)
3119 ("r-magrittr" ,r-magrittr)
3120 ("r-readr" ,r-readr)
3121 ("r-tidyr" ,r-tidyr)
3122 ("r-xml2" ,r-xml2)))
3124 `(("r-knitr" ,r-knitr)))
3125 (home-page "https://github.com/seandavi/GEOquery/")
3126 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3128 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3129 microarray data. Given the rich and varied nature of this resource, it is
3130 only natural to want to apply BioConductor tools to these data. GEOquery is
3131 the bridge between GEO and BioConductor.")
3132 (license license:gpl2)))
3134 (define-public r-illuminaio
3136 (name "r-illuminaio")
3141 (uri (bioconductor-uri "illuminaio" version))
3144 "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c"))))
3145 (build-system r-build-system)
3147 `(("r-base64" ,r-base64)))
3148 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3149 (synopsis "Parse Illumina microarray output files")
3151 "This package provides tools for parsing Illumina's microarray output
3152 files, including IDAT.")
3153 (license license:gpl2)))
3155 (define-public r-siggenes
3162 (uri (bioconductor-uri "siggenes" version))
3165 "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy"))))
3166 (build-system r-build-system)
3168 `(("r-biobase" ,r-biobase)
3169 ("r-multtest" ,r-multtest)
3170 ("r-scrime" ,r-scrime)))
3171 (home-page "https://bioconductor.org/packages/siggenes/")
3173 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3175 "This package provides tools for the identification of differentially
3176 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3177 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3178 Bayes Analyses of Microarrays} (EBAM).")
3179 (license license:lgpl2.0+)))
3181 (define-public r-bumphunter
3183 (name "r-bumphunter")
3188 (uri (bioconductor-uri "bumphunter" version))
3191 "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq"))))
3192 (build-system r-build-system)
3194 `(("r-annotationdbi" ,r-annotationdbi)
3195 ("r-biocgenerics" ,r-biocgenerics)
3196 ("r-dorng" ,r-dorng)
3197 ("r-foreach" ,r-foreach)
3198 ("r-genomeinfodb" ,r-genomeinfodb)
3199 ("r-genomicfeatures" ,r-genomicfeatures)
3200 ("r-genomicranges" ,r-genomicranges)
3201 ("r-iranges" ,r-iranges)
3202 ("r-iterators" ,r-iterators)
3203 ("r-limma" ,r-limma)
3204 ("r-locfit" ,r-locfit)
3205 ("r-matrixstats" ,r-matrixstats)
3206 ("r-s4vectors" ,r-s4vectors)))
3207 (home-page "https://github.com/ririzarr/bumphunter")
3208 (synopsis "Find bumps in genomic data")
3210 "This package provides tools for finding bumps in genomic data in order
3211 to identify differentially methylated regions in epigenetic epidemiology
3213 (license license:artistic2.0)))
3215 (define-public r-minfi
3222 (uri (bioconductor-uri "minfi" version))
3225 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
3226 (build-system r-build-system)
3228 `(("r-beanplot" ,r-beanplot)
3229 ("r-biobase" ,r-biobase)
3230 ("r-biocgenerics" ,r-biocgenerics)
3231 ("r-biocparallel" ,r-biocparallel)
3232 ("r-biostrings" ,r-biostrings)
3233 ("r-bumphunter" ,r-bumphunter)
3234 ("r-data-table" ,r-data-table)
3235 ("r-delayedarray" ,r-delayedarray)
3236 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3237 ("r-genefilter" ,r-genefilter)
3238 ("r-genomeinfodb" ,r-genomeinfodb)
3239 ("r-genomicranges" ,r-genomicranges)
3240 ("r-geoquery" ,r-geoquery)
3241 ("r-hdf5array" ,r-hdf5array)
3242 ("r-illuminaio" ,r-illuminaio)
3243 ("r-iranges" ,r-iranges)
3244 ("r-lattice" ,r-lattice)
3245 ("r-limma" ,r-limma)
3247 ("r-mclust" ,r-mclust)
3249 ("r-nor1mix" ,r-nor1mix)
3250 ("r-preprocesscore" ,r-preprocesscore)
3251 ("r-quadprog" ,r-quadprog)
3252 ("r-rcolorbrewer" ,r-rcolorbrewer)
3253 ("r-reshape" ,r-reshape)
3254 ("r-s4vectors" ,r-s4vectors)
3255 ("r-siggenes" ,r-siggenes)
3256 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3258 `(("r-knitr" ,r-knitr)))
3259 (home-page "https://github.com/hansenlab/minfi")
3260 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3262 "This package provides tools to analyze and visualize Illumina Infinium
3263 methylation arrays.")
3264 (license license:artistic2.0)))
3266 (define-public r-methylumi
3268 (name "r-methylumi")
3273 (uri (bioconductor-uri "methylumi" version))
3276 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
3277 (build-system r-build-system)
3279 `(("r-annotate" ,r-annotate)
3280 ("r-annotationdbi" ,r-annotationdbi)
3281 ("r-biobase" ,r-biobase)
3282 ("r-biocgenerics" ,r-biocgenerics)
3283 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3284 ("r-genefilter" ,r-genefilter)
3285 ("r-genomeinfodb" ,r-genomeinfodb)
3286 ("r-genomicranges" ,r-genomicranges)
3287 ("r-ggplot2" ,r-ggplot2)
3288 ("r-illuminaio" ,r-illuminaio)
3289 ("r-iranges" ,r-iranges)
3290 ("r-lattice" ,r-lattice)
3291 ("r-matrixstats" ,r-matrixstats)
3292 ("r-minfi" ,r-minfi)
3293 ("r-reshape2" ,r-reshape2)
3294 ("r-s4vectors" ,r-s4vectors)
3295 ("r-scales" ,r-scales)
3296 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3298 `(("r-knitr" ,r-knitr)))
3299 (home-page "https://bioconductor.org/packages/methylumi")
3300 (synopsis "Handle Illumina methylation data")
3302 "This package provides classes for holding and manipulating Illumina
3303 methylation data. Based on eSet, it can contain MIAME information, sample
3304 information, feature information, and multiple matrices of data. An
3305 \"intelligent\" import function, methylumiR can read the Illumina text files
3306 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3307 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3308 background correction, and quality control features for GoldenGate, Infinium,
3309 and Infinium HD arrays are also included.")
3310 (license license:gpl2)))
3312 (define-public r-lumi
3319 (uri (bioconductor-uri "lumi" version))
3322 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
3323 (build-system r-build-system)
3325 `(("r-affy" ,r-affy)
3326 ("r-annotate" ,r-annotate)
3327 ("r-annotationdbi" ,r-annotationdbi)
3328 ("r-biobase" ,r-biobase)
3330 ("r-genomicfeatures" ,r-genomicfeatures)
3331 ("r-genomicranges" ,r-genomicranges)
3332 ("r-kernsmooth" ,r-kernsmooth)
3333 ("r-lattice" ,r-lattice)
3335 ("r-methylumi" ,r-methylumi)
3337 ("r-nleqslv" ,r-nleqslv)
3338 ("r-preprocesscore" ,r-preprocesscore)
3339 ("r-rsqlite" ,r-rsqlite)))
3340 (home-page "https://bioconductor.org/packages/lumi")
3341 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3343 "The lumi package provides an integrated solution for the Illumina
3344 microarray data analysis. It includes functions of Illumina
3345 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3346 variance stabilization, normalization and gene annotation at the probe level.
3347 It also includes the functions of processing Illumina methylation microarrays,
3348 especially Illumina Infinium methylation microarrays.")
3349 (license license:lgpl2.0+)))
3351 (define-public r-linnorm
3358 (uri (bioconductor-uri "Linnorm" version))
3361 "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp"))))
3362 (properties `((upstream-name . "Linnorm")))
3363 (build-system r-build-system)
3365 `(("r-amap" ,r-amap)
3366 ("r-apcluster" ,r-apcluster)
3367 ("r-ellipse" ,r-ellipse)
3368 ("r-fastcluster" ,r-fastcluster)
3370 ("r-ggdendro" ,r-ggdendro)
3371 ("r-ggplot2" ,r-ggplot2)
3372 ("r-gmodels" ,r-gmodels)
3373 ("r-igraph" ,r-igraph)
3374 ("r-limma" ,r-limma)
3376 ("r-mclust" ,r-mclust)
3378 ("r-rcpparmadillo" ,r-rcpparmadillo)
3379 ("r-rtsne" ,r-rtsne)
3380 ("r-statmod" ,r-statmod)
3381 ("r-vegan" ,r-vegan)
3384 `(("r-knitr" ,r-knitr)))
3385 (home-page "http://www.jjwanglab.org/Linnorm/")
3386 (synopsis "Linear model and normality based transformation method")
3388 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3389 count data or any large scale count data. It transforms such datasets for
3390 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3391 the following pipelines are implemented:
3394 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3395 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3396 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3397 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3398 @item Differential expression analysis or differential peak detection using
3399 limma (@code{Linnorm.limma})
3400 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3401 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3402 @item Stable gene selection for scRNA-seq data; for users without or who do
3403 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3404 @item Data imputation (@code{Linnorm.DataImput}).
3407 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3408 @code{RnaXSim} function is included for simulating RNA-seq data for the
3409 evaluation of DEG analysis methods.")
3410 (license license:expat)))
3412 (define-public r-ioniser
3419 (uri (bioconductor-uri "IONiseR" version))
3422 "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w"))))
3423 (properties `((upstream-name . "IONiseR")))
3424 (build-system r-build-system)
3426 `(("r-biocgenerics" ,r-biocgenerics)
3427 ("r-biocparallel" ,r-biocparallel)
3428 ("r-biostrings" ,r-biostrings)
3429 ("r-bit64" ,r-bit64)
3430 ("r-dplyr" ,r-dplyr)
3431 ("r-ggplot2" ,r-ggplot2)
3432 ("r-magrittr" ,r-magrittr)
3433 ("r-rhdf5" ,r-rhdf5)
3434 ("r-shortread" ,r-shortread)
3435 ("r-stringr" ,r-stringr)
3436 ("r-tibble" ,r-tibble)
3437 ("r-tidyr" ,r-tidyr)
3438 ("r-xvector" ,r-xvector)))
3440 `(("r-knitr" ,r-knitr)))
3441 (home-page "https://bioconductor.org/packages/IONiseR/")
3442 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3444 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3445 MinION data. It extracts summary statistics from a set of fast5 files and can
3446 be used either before or after base calling. In addition to standard
3447 summaries of the read-types produced, it provides a number of plots for
3448 visualising metrics relative to experiment run time or spatially over the
3449 surface of a flowcell.")
3450 (license license:expat)))
3452 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3453 (define-public r-gkmsvm
3460 (uri (cran-uri "gkmSVM" version))
3463 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3464 (properties `((upstream-name . "gkmSVM")))
3465 (build-system r-build-system)
3467 `(("r-kernlab" ,r-kernlab)
3470 ("r-seqinr" ,r-seqinr)))
3471 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3472 (synopsis "Gapped-kmer support vector machine")
3474 "This R package provides tools for training gapped-kmer SVM classifiers
3475 for DNA and protein sequences. This package supports several sequence
3476 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3477 (license license:gpl2+)))
3479 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3480 (define-public r-mutoss
3487 (uri (cran-uri "mutoss" version))
3490 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3491 (properties `((upstream-name . "mutoss")))
3492 (build-system r-build-system)
3494 `(("r-multcomp" ,r-multcomp)
3495 ("r-multtest" ,r-multtest)
3496 ("r-mvtnorm" ,r-mvtnorm)
3497 ("r-plotrix" ,r-plotrix)))
3498 (home-page "https://github.com/kornl/mutoss/")
3499 (synopsis "Unified multiple testing procedures")
3501 "This package is designed to ease the application and comparison of
3502 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3503 are standardized and usable by the accompanying mutossGUI package.")
3504 ;; Any version of the GPL.
3505 (license (list license:gpl2+ license:gpl3+))))
3507 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3508 ;; from Bioconductor, so we put it here.
3509 (define-public r-metap
3516 (uri (cran-uri "metap" version))
3519 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3520 (build-system r-build-system)
3522 `(("r-lattice" ,r-lattice)
3523 ("r-mutoss" ,r-mutoss)
3524 ("r-rdpack" ,r-rdpack)
3525 ("r-tfisher" ,r-tfisher)))
3526 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3527 (synopsis "Meta-analysis of significance values")
3529 "The canonical way to perform meta-analysis involves using effect sizes.
3530 When they are not available this package provides a number of methods for
3531 meta-analysis of significance values including the methods of Edgington,
3532 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3533 published results; and a routine for graphical display.")
3534 (license license:gpl2)))
3536 (define-public r-triform
3543 (uri (bioconductor-uri "triform" version))
3546 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3547 (build-system r-build-system)
3549 `(("r-biocgenerics" ,r-biocgenerics)
3550 ("r-iranges" ,r-iranges)
3551 ("r-yaml" ,r-yaml)))
3552 (home-page "https://bioconductor.org/packages/triform/")
3553 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3555 "The Triform algorithm uses model-free statistics to identify peak-like
3556 distributions of TF ChIP sequencing reads, taking advantage of an improved
3557 peak definition in combination with known profile characteristics.")
3558 (license license:gpl2)))
3560 (define-public r-varianttools
3562 (name "r-varianttools")
3567 (uri (bioconductor-uri "VariantTools" version))
3570 "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx"))))
3571 (properties `((upstream-name . "VariantTools")))
3572 (build-system r-build-system)
3574 `(("r-biobase" ,r-biobase)
3575 ("r-biocgenerics" ,r-biocgenerics)
3576 ("r-biocparallel" ,r-biocparallel)
3577 ("r-biostrings" ,r-biostrings)
3578 ("r-bsgenome" ,r-bsgenome)
3579 ("r-genomeinfodb" ,r-genomeinfodb)
3580 ("r-genomicfeatures" ,r-genomicfeatures)
3581 ("r-genomicranges" ,r-genomicranges)
3582 ("r-iranges" ,r-iranges)
3583 ("r-matrix" ,r-matrix)
3584 ("r-rsamtools" ,r-rsamtools)
3585 ("r-rtracklayer" ,r-rtracklayer)
3586 ("r-s4vectors" ,r-s4vectors)
3587 ("r-variantannotation" ,r-variantannotation)))
3588 (home-page "https://bioconductor.org/packages/VariantTools/")
3589 (synopsis "Tools for exploratory analysis of variant calls")
3591 "Explore, diagnose, and compare variant calls using filters. The
3592 VariantTools package supports a workflow for loading data, calling single
3593 sample variants and tumor-specific somatic mutations or other sample-specific
3594 variant types (e.g., RNA editing). Most of the functions operate on
3595 alignments (BAM files) or datasets of called variants. The user is expected
3596 to have already aligned the reads with a separate tool, e.g., GSNAP via
3598 (license license:artistic2.0)))
3600 (define-public r-heatplus
3607 (uri (bioconductor-uri "Heatplus" version))
3610 "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw"))))
3611 (properties `((upstream-name . "Heatplus")))
3612 (build-system r-build-system)
3614 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3615 (home-page "https://github.com/alexploner/Heatplus")
3616 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3618 "This package provides tools to display a rectangular heatmap (intensity
3619 plot) of a data matrix. By default, both samples (columns) and features (row)
3620 of the matrix are sorted according to a hierarchical clustering, and the
3621 corresponding dendrogram is plotted. Optionally, panels with additional
3622 information about samples and features can be added to the plot.")
3623 (license license:gpl2+)))
3625 (define-public r-gosemsim
3632 (uri (bioconductor-uri "GOSemSim" version))
3635 "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
3636 (properties `((upstream-name . "GOSemSim")))
3637 (build-system r-build-system)
3639 `(("r-annotationdbi" ,r-annotationdbi)
3640 ("r-go-db" ,r-go-db)
3641 ("r-rcpp" ,r-rcpp)))
3643 `(("r-knitr" ,r-knitr)))
3644 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3645 (synopsis "GO-terms semantic similarity measures")
3647 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3648 quantitative ways to compute similarities between genes and gene groups, and
3649 have became important basis for many bioinformatics analysis approaches.
3650 GOSemSim is an R package for semantic similarity computation among GO terms,
3651 sets of GO terms, gene products and gene clusters.")
3652 (license license:artistic2.0)))
3654 (define-public r-anota
3661 (uri (bioconductor-uri "anota" version))
3664 "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm"))))
3665 (build-system r-build-system)
3667 `(("r-multtest" ,r-multtest)
3668 ("r-qvalue" ,r-qvalue)))
3669 (home-page "https://bioconductor.org/packages/anota/")
3670 (synopsis "Analysis of translational activity")
3672 "Genome wide studies of translational control is emerging as a tool to
3673 study various biological conditions. The output from such analysis is both
3674 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3675 involved in translation (the actively translating mRNA level) for each mRNA.
3676 The standard analysis of such data strives towards identifying differential
3677 translational between two or more sample classes - i.e. differences in
3678 actively translated mRNA levels that are independent of underlying differences
3679 in cytosolic mRNA levels. This package allows for such analysis using partial
3680 variances and the random variance model. As 10s of thousands of mRNAs are
3681 analyzed in parallel the library performs a number of tests to assure that
3682 the data set is suitable for such analysis.")
3683 (license license:gpl3)))
3685 (define-public r-sigpathway
3687 (name "r-sigpathway")
3692 (uri (bioconductor-uri "sigPathway" version))
3695 "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5"))))
3696 (properties `((upstream-name . "sigPathway")))
3697 (build-system r-build-system)
3698 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3699 (synopsis "Pathway analysis")
3701 "This package is used to conduct pathway analysis by calculating the NT_k
3702 and NE_k statistics in a statistical framework for determining whether a
3703 specified group of genes for a pathway has a coordinated association with a
3704 phenotype of interest.")
3705 (license license:gpl2)))
3707 (define-public r-fgsea
3714 (uri (bioconductor-uri "fgsea" version))
3717 "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc"))))
3718 (build-system r-build-system)
3721 ("r-biocparallel" ,r-biocparallel)
3722 ("r-data-table" ,r-data-table)
3723 ("r-fastmatch" ,r-fastmatch)
3724 ("r-ggplot2" ,r-ggplot2)
3725 ("r-gridextra" ,r-gridextra)
3726 ("r-matrix" ,r-matrix)
3727 ("r-rcpp" ,r-rcpp)))
3729 `(("r-knitr" ,r-knitr)))
3730 (home-page "https://github.com/ctlab/fgsea/")
3731 (synopsis "Fast gene set enrichment analysis")
3733 "The package implements an algorithm for fast gene set enrichment
3734 analysis. Using the fast algorithm makes more permutations and gets
3735 more fine grained p-values, which allows using accurate standard approaches
3736 to multiple hypothesis correction.")
3737 (license license:expat)))
3739 (define-public r-dose
3746 (uri (bioconductor-uri "DOSE" version))
3749 "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8"))))
3750 (properties `((upstream-name . "DOSE")))
3751 (build-system r-build-system)
3753 `(("r-annotationdbi" ,r-annotationdbi)
3754 ("r-biocparallel" ,r-biocparallel)
3755 ("r-do-db" ,r-do-db)
3756 ("r-fgsea" ,r-fgsea)
3757 ("r-ggplot2" ,r-ggplot2)
3758 ("r-gosemsim" ,r-gosemsim)
3759 ("r-qvalue" ,r-qvalue)
3760 ("r-reshape2" ,r-reshape2)))
3762 `(("r-knitr" ,r-knitr)))
3763 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3764 (synopsis "Disease ontology semantic and enrichment analysis")
3766 "This package implements five methods proposed by Resnik, Schlicker,
3767 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3768 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3769 including hypergeometric model and gene set enrichment analysis are also
3770 implemented for discovering disease associations of high-throughput biological
3772 (license license:artistic2.0)))
3774 (define-public r-enrichplot
3776 (name "r-enrichplot")
3781 (uri (bioconductor-uri "enrichplot" version))
3784 "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7"))))
3785 (build-system r-build-system)
3787 `(("r-annotationdbi" ,r-annotationdbi)
3788 ("r-cowplot" ,r-cowplot)
3790 ("r-europepmc" ,r-europepmc)
3791 ("r-ggplot2" ,r-ggplot2)
3792 ("r-ggplotify" ,r-ggplotify)
3793 ("r-ggraph" ,r-ggraph)
3794 ("r-ggridges" ,r-ggridges)
3795 ("r-gosemsim" ,r-gosemsim)
3796 ("r-gridextra" ,r-gridextra)
3797 ("r-igraph" ,r-igraph)
3799 ("r-purrr" ,r-purrr)
3800 ("r-rcolorbrewer" ,r-rcolorbrewer)
3801 ("r-reshape2" ,r-reshape2)
3802 ("r-scatterpie" ,r-scatterpie)))
3804 `(("r-knitr" ,r-knitr)))
3805 (home-page "https://github.com/GuangchuangYu/enrichplot")
3806 (synopsis "Visualization of functional enrichment result")
3808 "The enrichplot package implements several visualization methods for
3809 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3810 All the visualization methods are developed based on ggplot2 graphics.")
3811 (license license:artistic2.0)))
3813 (define-public r-clusterprofiler
3815 (name "r-clusterprofiler")
3820 (uri (bioconductor-uri "clusterProfiler" version))
3823 "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
3825 `((upstream-name . "clusterProfiler")))
3826 (build-system r-build-system)
3828 `(("r-annotationdbi" ,r-annotationdbi)
3830 ("r-downloader" ,r-downloader)
3831 ("r-dplyr" ,r-dplyr)
3832 ("r-enrichplot" ,r-enrichplot)
3833 ("r-go-db" ,r-go-db)
3834 ("r-gosemsim" ,r-gosemsim)
3835 ("r-magrittr" ,r-magrittr)
3837 ("r-qvalue" ,r-qvalue)
3838 ("r-rlang" ,r-rlang)
3839 ("r-rvcheck" ,r-rvcheck)
3840 ("r-tidyr" ,r-tidyr)))
3842 `(("r-knitr" ,r-knitr)))
3843 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3844 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3846 "This package implements methods to analyze and visualize functional
3847 profiles (GO and KEGG) of gene and gene clusters.")
3848 (license license:artistic2.0)))
3850 (define-public r-mlinterfaces
3852 (name "r-mlinterfaces")
3857 (uri (bioconductor-uri "MLInterfaces" version))
3860 "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq"))))
3861 (properties `((upstream-name . "MLInterfaces")))
3862 (build-system r-build-system)
3864 `(("r-annotate" ,r-annotate)
3865 ("r-biobase" ,r-biobase)
3866 ("r-biocgenerics" ,r-biocgenerics)
3867 ("r-cluster" ,r-cluster)
3870 ("r-gdata" ,r-gdata)
3871 ("r-genefilter" ,r-genefilter)
3872 ("r-ggvis" ,r-ggvis)
3873 ("r-hwriter" ,r-hwriter)
3875 ("r-mlbench" ,r-mlbench)
3877 ("r-rcolorbrewer" ,r-rcolorbrewer)
3879 ("r-rpart" ,r-rpart)
3880 ("r-sfsmisc" ,r-sfsmisc)
3881 ("r-shiny" ,r-shiny)
3882 ("r-threejs" ,r-threejs)))
3883 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3884 (synopsis "Interfaces to R machine learning procedures")
3886 "This package provides uniform interfaces to machine learning code for
3887 data in R and Bioconductor containers.")
3888 ;; Any version of the LGPL.
3889 (license license:lgpl2.1+)))
3891 (define-public r-annaffy
3898 (uri (bioconductor-uri "annaffy" version))
3901 "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
3902 (build-system r-build-system)
3905 (modify-phases %standard-phases
3906 (add-after 'unpack 'remove-reference-to-non-free-data
3908 (substitute* "DESCRIPTION"
3912 `(("r-annotationdbi" ,r-annotationdbi)
3913 ("r-biobase" ,r-biobase)
3915 ("r-go-db" ,r-go-db)))
3916 (home-page "https://bioconductor.org/packages/annaffy/")
3917 (synopsis "Annotation tools for Affymetrix biological metadata")
3919 "This package provides functions for handling data from Bioconductor
3920 Affymetrix annotation data packages. It produces compact HTML and text
3921 reports including experimental data and URL links to many online databases.
3922 It allows searching of biological metadata using various criteria.")
3923 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3924 ;; the LGPL 2.1 is included.
3925 (license license:lgpl2.1+)))
3927 (define-public r-a4core
3934 (uri (bioconductor-uri "a4Core" version))
3937 "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp"))))
3938 (properties `((upstream-name . "a4Core")))
3939 (build-system r-build-system)
3941 `(("r-biobase" ,r-biobase)
3942 ("r-glmnet" ,r-glmnet)))
3943 (home-page "https://bioconductor.org/packages/a4Core")
3944 (synopsis "Automated Affymetrix array analysis core package")
3946 "This is the core package for the automated analysis of Affymetrix
3948 (license license:gpl3)))
3950 (define-public r-a4classif
3952 (name "r-a4classif")
3957 (uri (bioconductor-uri "a4Classif" version))
3960 "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr"))))
3961 (properties `((upstream-name . "a4Classif")))
3962 (build-system r-build-system)
3964 `(("r-a4core" ,r-a4core)
3965 ("r-a4preproc" ,r-a4preproc)
3966 ("r-glmnet" ,r-glmnet)
3967 ("r-mlinterfaces" ,r-mlinterfaces)
3970 ("r-varselrf" ,r-varselrf)))
3971 (home-page "https://bioconductor.org/packages/a4Classif/")
3972 (synopsis "Automated Affymetrix array analysis classification package")
3974 "This is the classification package for the automated analysis of
3975 Affymetrix arrays.")
3976 (license license:gpl3)))
3978 (define-public r-a4preproc
3980 (name "r-a4preproc")
3985 (uri (bioconductor-uri "a4Preproc" version))
3988 "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8"))))
3989 (properties `((upstream-name . "a4Preproc")))
3990 (build-system r-build-system)
3992 `(("r-annotationdbi" ,r-annotationdbi)))
3993 (home-page "https://bioconductor.org/packages/a4Preproc/")
3994 (synopsis "Automated Affymetrix array analysis preprocessing package")
3996 "This is a package for the automated analysis of Affymetrix arrays. It
3997 is used for preprocessing the arrays.")
3998 (license license:gpl3)))
4000 (define-public r-a4reporting
4002 (name "r-a4reporting")
4007 (uri (bioconductor-uri "a4Reporting" version))
4010 "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f"))))
4011 (properties `((upstream-name . "a4Reporting")))
4012 (build-system r-build-system)
4014 `(("r-annaffy" ,r-annaffy)
4015 ("r-xtable" ,r-xtable)))
4016 (home-page "https://bioconductor.org/packages/a4Reporting/")
4017 (synopsis "Automated Affymetrix array analysis reporting package")
4019 "This is a package for the automated analysis of Affymetrix arrays. It
4020 provides reporting features.")
4021 (license license:gpl3)))
4023 (define-public r-a4base
4030 (uri (bioconductor-uri "a4Base" version))
4033 "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02"))))
4034 (properties `((upstream-name . "a4Base")))
4035 (build-system r-build-system)
4037 `(("r-a4core" ,r-a4core)
4038 ("r-a4preproc" ,r-a4preproc)
4039 ("r-annaffy" ,r-annaffy)
4040 ("r-annotationdbi" ,r-annotationdbi)
4041 ("r-biobase" ,r-biobase)
4042 ("r-genefilter" ,r-genefilter)
4043 ("r-glmnet" ,r-glmnet)
4044 ("r-gplots" ,r-gplots)
4045 ("r-limma" ,r-limma)
4047 ("r-multtest" ,r-multtest)))
4048 (home-page "https://bioconductor.org/packages/a4Base/")
4049 (synopsis "Automated Affymetrix array analysis base package")
4051 "This package provides basic features for the automated analysis of
4052 Affymetrix arrays.")
4053 (license license:gpl3)))
4062 (uri (bioconductor-uri "a4" version))
4065 "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7"))))
4066 (build-system r-build-system)
4068 `(("r-a4base" ,r-a4base)
4069 ("r-a4classif" ,r-a4classif)
4070 ("r-a4core" ,r-a4core)
4071 ("r-a4preproc" ,r-a4preproc)
4072 ("r-a4reporting" ,r-a4reporting)))
4073 (home-page "https://bioconductor.org/packages/a4/")
4074 (synopsis "Automated Affymetrix array analysis umbrella package")
4076 "This package provides a software suite for the automated analysis of
4077 Affymetrix arrays.")
4078 (license license:gpl3)))
4080 (define-public r-abseqr
4087 (uri (bioconductor-uri "abseqR" version))
4090 "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5"))))
4091 (properties `((upstream-name . "abseqR")))
4092 (build-system r-build-system)
4094 `(("pandoc" ,pandoc)
4095 ("pandoc-citeproc" ,pandoc-citeproc)))
4097 `(("r-biocparallel" ,r-biocparallel)
4098 ("r-biocstyle" ,r-biocstyle)
4099 ("r-circlize" ,r-circlize)
4100 ("r-flexdashboard" ,r-flexdashboard)
4101 ("r-ggcorrplot" ,r-ggcorrplot)
4102 ("r-ggdendro" ,r-ggdendro)
4103 ("r-ggplot2" ,r-ggplot2)
4104 ("r-gridextra" ,r-gridextra)
4105 ("r-knitr" ,r-knitr)
4106 ("r-plotly" ,r-plotly)
4109 ("r-rcolorbrewer" ,r-rcolorbrewer)
4110 ("r-reshape2" ,r-reshape2)
4111 ("r-rmarkdown" ,r-rmarkdown)
4112 ("r-stringr" ,r-stringr)
4113 ("r-vegan" ,r-vegan)
4114 ("r-venndiagram" ,r-venndiagram)))
4116 `(("r-knitr" ,r-knitr)))
4117 (home-page "https://github.com/malhamdoosh/abseqR")
4118 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4120 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4121 sequencing datasets generated from antibody libraries and abseqR is one of its
4122 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4123 capabilities and allows them to generate interactive HTML reports for the
4124 convenience of viewing and sharing with other researchers. Additionally,
4125 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4126 further downstream analysis on its output.")
4127 (license license:gpl3)))
4129 (define-public r-bacon
4136 (uri (bioconductor-uri "bacon" version))
4139 "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl"))))
4140 (build-system r-build-system)
4142 `(("r-biocparallel" ,r-biocparallel)
4143 ("r-ellipse" ,r-ellipse)
4144 ("r-ggplot2" ,r-ggplot2)))
4146 `(("r-knitr" ,r-knitr)))
4147 (home-page "https://bioconductor.org/packages/bacon/")
4148 (synopsis "Controlling bias and inflation in association studies")
4150 "Bacon can be used to remove inflation and bias often observed in
4151 epigenome- and transcriptome-wide association studies. To this end bacon
4152 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4153 fitting a three-component normal mixture on z-scores.")
4154 (license license:gpl2+)))
4156 (define-public r-rgadem
4163 (uri (bioconductor-uri "rGADEM" version))
4166 "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8"))))
4167 (properties `((upstream-name . "rGADEM")))
4168 (build-system r-build-system)
4170 `(("r-biostrings" ,r-biostrings)
4171 ("r-bsgenome" ,r-bsgenome)
4172 ("r-genomicranges" ,r-genomicranges)
4173 ("r-iranges" ,r-iranges)
4174 ("r-seqlogo" ,r-seqlogo)))
4175 (home-page "https://bioconductor.org/packages/rGADEM/")
4176 (synopsis "De novo sequence motif discovery")
4178 "rGADEM is an efficient de novo motif discovery tool for large-scale
4179 genomic sequence data.")
4180 (license license:artistic2.0)))
4182 (define-public r-motiv
4189 (uri (bioconductor-uri "MotIV" version))
4192 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4193 (properties `((upstream-name . "MotIV")))
4194 (build-system r-build-system)
4198 `(("r-biocgenerics" ,r-biocgenerics)
4199 ("r-biostrings" ,r-biostrings)
4200 ("r-genomicranges" ,r-genomicranges)
4201 ("r-iranges" ,r-iranges)
4202 ("r-lattice" ,r-lattice)
4203 ("r-rgadem" ,r-rgadem)
4204 ("r-s4vectors" ,r-s4vectors)))
4205 (home-page "https://bioconductor.org/packages/MotIV/")
4206 (synopsis "Motif identification and validation")
4208 "This package is used for the identification and validation of sequence
4209 motifs. It makes use of STAMP for comparing a set of motifs to a given
4210 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4211 distributions, modules and filter motifs.")
4212 (license license:gpl2)))
4214 (define-public r-motifdb
4220 (uri (bioconductor-uri "MotifDb" version))
4222 (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm"))))
4223 (properties `((upstream-name . "MotifDb")))
4224 (build-system r-build-system)
4226 `(("r-biocgenerics" ,r-biocgenerics)
4227 ("r-biostrings" ,r-biostrings)
4228 ("r-genomicranges" ,r-genomicranges)
4229 ("r-iranges" ,r-iranges)
4230 ("r-rtracklayer" ,r-rtracklayer)
4231 ("r-s4vectors" ,r-s4vectors)
4232 ("r-splitstackshape" ,r-splitstackshape)))
4234 `(("r-knitr" ,r-knitr)))
4235 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4236 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4237 (description "This package provides more than 2000 annotated position
4238 frequency matrices from nine public sources, for multiple organisms.")
4239 (license license:artistic2.0)))
4241 (define-public r-motifbreakr
4243 (name "r-motifbreakr")
4247 (uri (bioconductor-uri "motifbreakR" version))
4249 (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm"))))
4250 (properties `((upstream-name . "motifbreakR")))
4251 (build-system r-build-system)
4253 `(("r-biocgenerics" ,r-biocgenerics)
4254 ("r-biocparallel" ,r-biocparallel)
4255 ("r-biostrings" ,r-biostrings)
4256 ("r-bsgenome" ,r-bsgenome)
4257 ("r-genomeinfodb" ,r-genomeinfodb)
4258 ("r-genomicranges" ,r-genomicranges)
4259 ("r-grimport" ,r-grimport)
4261 ("r-iranges" ,r-iranges)
4262 ("r-matrixstats" ,r-matrixstats)
4263 ("r-motifdb" ,r-motifdb)
4264 ("r-motifstack" ,r-motifstack)
4265 ("r-rtracklayer" ,r-rtracklayer)
4266 ("r-s4vectors" ,r-s4vectors)
4267 ("r-stringr" ,r-stringr)
4268 ("r-summarizedexperiment" ,r-summarizedexperiment)
4269 ("r-tfmpvalue" ,r-tfmpvalue)
4270 ("r-variantannotation" ,r-variantannotation)))
4272 `(("r-knitr" ,r-knitr)))
4273 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4274 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4275 (description "This package allows biologists to judge in the first place
4276 whether the sequence surrounding the polymorphism is a good match, and in
4277 the second place how much information is gained or lost in one allele of
4278 the polymorphism relative to another. This package gives a choice of
4279 algorithms for interrogation of genomes with motifs from public sources:
4281 @item a weighted-sum probability matrix;
4282 @item log-probabilities;
4283 @item weighted by relative entropy.
4286 This package can predict effects for novel or previously described variants in
4287 public databases, making it suitable for tasks beyond the scope of its original
4288 design. Lastly, it can be used to interrogate any genome curated within
4290 (license license:gpl2+)))
4292 (define-public r-motifstack
4294 (name "r-motifstack")
4299 (uri (bioconductor-uri "motifStack" version))
4302 "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
4303 (properties `((upstream-name . "motifStack")))
4304 (build-system r-build-system)
4306 `(("r-ade4" ,r-ade4)
4307 ("r-biostrings" ,r-biostrings)
4308 ("r-ggplot2" ,r-ggplot2)
4309 ("r-grimport2" ,r-grimport2)
4310 ("r-htmlwidgets" ,r-htmlwidgets)
4311 ("r-motiv" ,r-motiv)
4312 ("r-scales" ,r-scales)
4315 `(("r-knitr" ,r-knitr)))
4316 (home-page "https://bioconductor.org/packages/motifStack/")
4317 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4319 "The motifStack package is designed for graphic representation of
4320 multiple motifs with different similarity scores. It works with both DNA/RNA
4321 sequence motifs and amino acid sequence motifs. In addition, it provides the
4322 flexibility for users to customize the graphic parameters such as the font
4323 type and symbol colors.")
4324 (license license:gpl2+)))
4326 (define-public r-genomicscores
4328 (name "r-genomicscores")
4333 (uri (bioconductor-uri "GenomicScores" version))
4336 "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb"))))
4337 (properties `((upstream-name . "GenomicScores")))
4338 (build-system r-build-system)
4340 `(("r-annotationhub" ,r-annotationhub)
4341 ("r-biobase" ,r-biobase)
4342 ("r-biocgenerics" ,r-biocgenerics)
4343 ("r-biostrings" ,r-biostrings)
4344 ("r-delayedarray" ,r-delayedarray)
4345 ("r-genomeinfodb" ,r-genomeinfodb)
4346 ("r-genomicranges" ,r-genomicranges)
4347 ("r-hdf5array" ,r-hdf5array)
4348 ("r-iranges" ,r-iranges)
4349 ("r-rhdf5" ,r-rhdf5)
4350 ("r-s4vectors" ,r-s4vectors)
4353 `(("r-knitr" ,r-knitr)))
4354 (home-page "https://github.com/rcastelo/GenomicScores/")
4355 (synopsis "Work with genome-wide position-specific scores")
4357 "This package provides infrastructure to store and access genome-wide
4358 position-specific scores within R and Bioconductor.")
4359 (license license:artistic2.0)))
4361 (define-public r-atacseqqc
4363 (name "r-atacseqqc")
4368 (uri (bioconductor-uri "ATACseqQC" version))
4371 "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
4372 (properties `((upstream-name . "ATACseqQC")))
4373 (build-system r-build-system)
4375 `(("r-biocgenerics" ,r-biocgenerics)
4376 ("r-biostrings" ,r-biostrings)
4377 ("r-bsgenome" ,r-bsgenome)
4378 ("r-chippeakanno" ,r-chippeakanno)
4379 ("r-edger" ,r-edger)
4380 ("r-genomeinfodb" ,r-genomeinfodb)
4381 ("r-genomicalignments" ,r-genomicalignments)
4382 ("r-genomicranges" ,r-genomicranges)
4383 ("r-genomicscores" ,r-genomicscores)
4384 ("r-iranges" ,r-iranges)
4385 ("r-kernsmooth" ,r-kernsmooth)
4386 ("r-limma" ,r-limma)
4387 ("r-motifstack" ,r-motifstack)
4388 ("r-preseqr" ,r-preseqr)
4389 ("r-randomforest" ,r-randomforest)
4390 ("r-rsamtools" ,r-rsamtools)
4391 ("r-rtracklayer" ,r-rtracklayer)
4392 ("r-s4vectors" ,r-s4vectors)))
4394 `(("r-knitr" ,r-knitr)))
4395 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4396 (synopsis "ATAC-seq quality control")
4398 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4399 sequencing, is a rapid and sensitive method for chromatin accessibility
4400 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4401 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4402 assess whether their ATAC-seq experiment is successful. It includes
4403 diagnostic plots of fragment size distribution, proportion of mitochondria
4404 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4406 (license license:gpl2+)))
4408 (define-public r-gofuncr
4415 (uri (bioconductor-uri "GOfuncR" version))
4418 "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1"))))
4419 (properties `((upstream-name . "GOfuncR")))
4420 (build-system r-build-system)
4422 `(("r-annotationdbi" ,r-annotationdbi)
4423 ("r-genomicranges" ,r-genomicranges)
4424 ("r-gtools" ,r-gtools)
4425 ("r-iranges" ,r-iranges)
4426 ("r-mapplots" ,r-mapplots)
4428 ("r-vioplot" ,r-vioplot)))
4430 `(("r-knitr" ,r-knitr)))
4431 (home-page "https://bioconductor.org/packages/GOfuncR/")
4432 (synopsis "Gene ontology enrichment using FUNC")
4434 "GOfuncR performs a gene ontology enrichment analysis based on the
4435 ontology enrichment software FUNC. GO-annotations are obtained from
4436 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4437 included in the package and updated regularly. GOfuncR provides the standard
4438 candidate vs background enrichment analysis using the hypergeometric test, as
4439 well as three additional tests:
4442 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4443 @item a binomial test that is used when genes are associated with two counts,
4445 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4446 associated with four counts.
4449 To correct for multiple testing and interdependency of the tests, family-wise
4450 error rates are computed based on random permutations of the gene-associated
4451 variables. GOfuncR also provides tools for exploring the ontology graph and
4452 the annotations, and options to take gene-length or spatial clustering of
4453 genes into account. It is also possible to provide custom gene coordinates,
4454 annotations and ontologies.")
4455 (license license:gpl2+)))
4457 (define-public r-abaenrichment
4459 (name "r-abaenrichment")
4464 (uri (bioconductor-uri "ABAEnrichment" version))
4467 "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw"))))
4468 (properties `((upstream-name . "ABAEnrichment")))
4469 (build-system r-build-system)
4471 `(("r-abadata" ,r-abadata)
4472 ("r-data-table" ,r-data-table)
4473 ("r-gofuncr" ,r-gofuncr)
4474 ("r-gplots" ,r-gplots)
4475 ("r-gtools" ,r-gtools)
4476 ("r-rcpp" ,r-rcpp)))
4478 `(("r-knitr" ,r-knitr)))
4479 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4480 (synopsis "Gene expression enrichment in human brain regions")
4482 "The package ABAEnrichment is designed to test for enrichment of user
4483 defined candidate genes in the set of expressed genes in different human brain
4484 regions. The core function @code{aba_enrich} integrates the expression of the
4485 candidate gene set (averaged across donors) and the structural information of
4486 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4487 (license license:gpl2+)))
4489 (define-public r-annotationfuncs
4491 (name "r-annotationfuncs")
4496 (uri (bioconductor-uri "AnnotationFuncs" version))
4499 "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d"))))
4501 `((upstream-name . "AnnotationFuncs")))
4502 (build-system r-build-system)
4504 `(("r-annotationdbi" ,r-annotationdbi)
4506 (home-page "https://www.iysik.com/r/annotationfuncs")
4507 (synopsis "Annotation translation functions")
4509 "This package provides functions for handling translating between
4510 different identifieres using the Biocore Data Team data-packages (e.g.
4511 @code{org.Bt.eg.db}).")
4512 (license license:gpl2)))
4514 (define-public r-annotationtools
4516 (name "r-annotationtools")
4521 (uri (bioconductor-uri "annotationTools" version))
4524 "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk"))))
4526 `((upstream-name . "annotationTools")))
4527 (build-system r-build-system)
4528 (propagated-inputs `(("r-biobase" ,r-biobase)))
4529 (home-page "https://bioconductor.org/packages/annotationTools/")
4530 (synopsis "Annotate microarrays and perform gene expression analyses")
4532 "This package provides functions to annotate microarrays, find orthologs,
4533 and integrate heterogeneous gene expression profiles using annotation and
4534 other molecular biology information available as flat file database (plain
4536 ;; Any version of the GPL.
4537 (license (list license:gpl2+))))
4539 (define-public r-allelicimbalance
4541 (name "r-allelicimbalance")
4546 (uri (bioconductor-uri "AllelicImbalance" version))
4549 "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr"))))
4551 `((upstream-name . "AllelicImbalance")))
4552 (build-system r-build-system)
4554 `(("r-annotationdbi" ,r-annotationdbi)
4555 ("r-biocgenerics" ,r-biocgenerics)
4556 ("r-biostrings" ,r-biostrings)
4557 ("r-bsgenome" ,r-bsgenome)
4558 ("r-genomeinfodb" ,r-genomeinfodb)
4559 ("r-genomicalignments" ,r-genomicalignments)
4560 ("r-genomicfeatures" ,r-genomicfeatures)
4561 ("r-genomicranges" ,r-genomicranges)
4562 ("r-gridextra" ,r-gridextra)
4564 ("r-iranges" ,r-iranges)
4565 ("r-lattice" ,r-lattice)
4566 ("r-latticeextra" ,r-latticeextra)
4568 ("r-rsamtools" ,r-rsamtools)
4569 ("r-s4vectors" ,r-s4vectors)
4570 ("r-seqinr" ,r-seqinr)
4571 ("r-summarizedexperiment" ,r-summarizedexperiment)
4572 ("r-variantannotation" ,r-variantannotation)))
4574 `(("r-knitr" ,r-knitr)))
4575 (home-page "https://github.com/pappewaio/AllelicImbalance")
4576 (synopsis "Investigate allele-specific expression")
4578 "This package provides a framework for allele-specific expression
4579 investigation using RNA-seq data.")
4580 (license license:gpl3)))
4582 (define-public r-aucell
4589 (uri (bioconductor-uri "AUCell" version))
4592 "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns"))))
4593 (properties `((upstream-name . "AUCell")))
4594 (build-system r-build-system)
4596 `(("r-biocgenerics" ,r-biocgenerics)
4597 ("r-data-table" ,r-data-table)
4598 ("r-gseabase" ,r-gseabase)
4599 ("r-mixtools" ,r-mixtools)
4600 ("r-r-utils" ,r-r-utils)
4601 ("r-s4vectors" ,r-s4vectors)
4602 ("r-shiny" ,r-shiny)
4603 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4605 `(("r-knitr" ,r-knitr)))
4606 (home-page "https://bioconductor.org/packages/AUCell/")
4607 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4609 "AUCell identifies cells with active gene sets (e.g. signatures,
4610 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4611 Under the Curve} (AUC) to calculate whether a critical subset of the input
4612 gene set is enriched within the expressed genes for each cell. The
4613 distribution of AUC scores across all the cells allows exploring the relative
4614 expression of the signature. Since the scoring method is ranking-based,
4615 AUCell is independent of the gene expression units and the normalization
4616 procedure. In addition, since the cells are evaluated individually, it can
4617 easily be applied to bigger datasets, subsetting the expression matrix if
4619 (license license:gpl3)))
4621 (define-public r-ebimage
4628 (uri (bioconductor-uri "EBImage" version))
4631 "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v"))))
4632 (properties `((upstream-name . "EBImage")))
4633 (build-system r-build-system)
4635 `(("r-abind" ,r-abind)
4636 ("r-biocgenerics" ,r-biocgenerics)
4637 ("r-fftwtools" ,r-fftwtools)
4638 ("r-htmltools" ,r-htmltools)
4639 ("r-htmlwidgets" ,r-htmlwidgets)
4641 ("r-locfit" ,r-locfit)
4643 ("r-rcurl" ,r-rcurl)
4644 ("r-tiff" ,r-tiff)))
4646 `(("r-knitr" ,r-knitr))) ; for vignettes
4647 (home-page "https://github.com/aoles/EBImage")
4648 (synopsis "Image processing and analysis toolbox for R")
4650 "EBImage provides general purpose functionality for image processing and
4651 analysis. In the context of (high-throughput) microscopy-based cellular
4652 assays, EBImage offers tools to segment cells and extract quantitative
4653 cellular descriptors. This allows the automation of such tasks using the R
4654 programming language and facilitates the use of other tools in the R
4655 environment for signal processing, statistical modeling, machine learning and
4656 visualization with image data.")
4657 ;; Any version of the LGPL.
4658 (license license:lgpl2.1+)))
4660 (define-public r-yamss
4667 (uri (bioconductor-uri "yamss" version))
4670 "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c"))))
4671 (build-system r-build-system)
4673 `(("r-biocgenerics" ,r-biocgenerics)
4674 ("r-data-table" ,r-data-table)
4675 ("r-ebimage" ,r-ebimage)
4676 ("r-iranges" ,r-iranges)
4677 ("r-limma" ,r-limma)
4678 ("r-matrix" ,r-matrix)
4680 ("r-s4vectors" ,r-s4vectors)
4681 ("r-summarizedexperiment"
4682 ,r-summarizedexperiment)))
4684 `(("r-knitr" ,r-knitr)))
4685 (home-page "https://github.com/hansenlab/yamss")
4686 (synopsis "Tools for high-throughput metabolomics")
4688 "This package provides tools to analyze and visualize high-throughput
4689 metabolomics data acquired using chromatography-mass spectrometry. These tools
4690 preprocess data in a way that enables reliable and powerful differential
4692 (license license:artistic2.0)))
4694 (define-public r-gtrellis
4701 (uri (bioconductor-uri "gtrellis" version))
4704 "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1"))))
4705 (build-system r-build-system)
4707 `(("r-circlize" ,r-circlize)
4708 ("r-genomicranges" ,r-genomicranges)
4709 ("r-getoptlong" ,r-getoptlong)
4710 ("r-iranges" ,r-iranges)))
4712 `(("r-knitr" ,r-knitr)))
4713 (home-page "https://github.com/jokergoo/gtrellis")
4714 (synopsis "Genome level Trellis layout")
4716 "Genome level Trellis graph visualizes genomic data conditioned by
4717 genomic categories (e.g. chromosomes). For each genomic category, multiple
4718 dimensional data which are represented as tracks describe different features
4719 from different aspects. This package provides high flexibility to arrange
4720 genomic categories and to add self-defined graphics in the plot.")
4721 (license license:expat)))
4723 (define-public r-somaticsignatures
4725 (name "r-somaticsignatures")
4730 (uri (bioconductor-uri "SomaticSignatures" version))
4733 "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1"))))
4735 `((upstream-name . "SomaticSignatures")))
4736 (build-system r-build-system)
4738 `(("r-biobase" ,r-biobase)
4739 ("r-biostrings" ,r-biostrings)
4740 ("r-genomeinfodb" ,r-genomeinfodb)
4741 ("r-genomicranges" ,r-genomicranges)
4742 ("r-ggbio" ,r-ggbio)
4743 ("r-ggplot2" ,r-ggplot2)
4744 ("r-iranges" ,r-iranges)
4746 ("r-pcamethods" ,r-pcamethods)
4747 ("r-proxy" ,r-proxy)
4748 ("r-reshape2" ,r-reshape2)
4749 ("r-s4vectors" ,r-s4vectors)
4750 ("r-variantannotation" ,r-variantannotation)))
4752 `(("r-knitr" ,r-knitr)))
4753 (home-page "https://github.com/juliangehring/SomaticSignatures")
4754 (synopsis "Somatic signatures")
4756 "This package identifies mutational signatures of @dfn{single nucleotide
4757 variants} (SNVs). It provides a infrastructure related to the methodology
4758 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4759 decomposition algorithms.")
4760 (license license:expat)))
4762 (define-public r-yapsa
4769 (uri (bioconductor-uri "YAPSA" version))
4772 "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
4773 (properties `((upstream-name . "YAPSA")))
4774 (build-system r-build-system)
4776 `(("r-biostrings" ,r-biostrings)
4777 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4778 ("r-circlize" ,r-circlize)
4779 ("r-complexheatmap" ,r-complexheatmap)
4780 ("r-corrplot" ,r-corrplot)
4781 ("r-dendextend" ,r-dendextend)
4782 ("r-doparallel" ,r-doparallel)
4783 ("r-dplyr" ,r-dplyr)
4784 ("r-genomeinfodb" ,r-genomeinfodb)
4785 ("r-genomicranges" ,r-genomicranges)
4786 ("r-getoptlong" ,r-getoptlong)
4787 ("r-ggbeeswarm" ,r-ggbeeswarm)
4788 ("r-ggplot2" ,r-ggplot2)
4789 ("r-gridextra" ,r-gridextra)
4790 ("r-gtrellis" ,r-gtrellis)
4791 ("r-keggrest" ,r-keggrest)
4793 ("r-magrittr" ,r-magrittr)
4794 ("r-pmcmr" ,r-pmcmr)
4795 ("r-pracma" ,r-pracma)
4796 ("r-reshape2" ,r-reshape2)
4797 ("r-somaticsignatures" ,r-somaticsignatures)
4798 ("r-variantannotation" ,r-variantannotation)))
4800 `(("r-knitr" ,r-knitr)))
4801 (home-page "https://bioconductor.org/packages/YAPSA/")
4802 (synopsis "Yet another package for signature analysis")
4804 "This package provides functions and routines useful in the analysis of
4805 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4806 functions to perform a signature analysis with known signatures and a
4807 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4809 (license license:gpl3)))
4811 (define-public r-gcrma
4818 (uri (bioconductor-uri "gcrma" version))
4821 "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g"))))
4822 (build-system r-build-system)
4824 `(("r-affy" ,r-affy)
4825 ("r-affyio" ,r-affyio)
4826 ("r-biobase" ,r-biobase)
4827 ("r-biocmanager" ,r-biocmanager)
4828 ("r-biostrings" ,r-biostrings)
4829 ("r-xvector" ,r-xvector)))
4830 (home-page "https://bioconductor.org/packages/gcrma/")
4831 (synopsis "Background adjustment using sequence information")
4833 "Gcrma adjusts for background intensities in Affymetrix array data which
4834 include optical noise and @dfn{non-specific binding} (NSB). The main function
4835 @code{gcrma} converts background adjusted probe intensities to expression
4836 measures using the same normalization and summarization methods as a
4837 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4838 to estimate probe affinity to NSB. The sequence information is summarized in
4839 a more complex way than the simple GC content. Instead, the base types (A, T,
4840 G or C) at each position along the probe determine the affinity of each probe.
4841 The parameters of the position-specific base contributions to the probe
4842 affinity is estimated in an NSB experiment in which only NSB but no
4843 gene-specific bidning is expected.")
4844 ;; Any version of the LGPL
4845 (license license:lgpl2.1+)))
4847 (define-public r-simpleaffy
4849 (name "r-simpleaffy")
4854 (uri (bioconductor-uri "simpleaffy" version))
4857 "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7"))))
4858 (build-system r-build-system)
4860 `(("r-affy" ,r-affy)
4861 ("r-biobase" ,r-biobase)
4862 ("r-biocgenerics" ,r-biocgenerics)
4863 ("r-gcrma" ,r-gcrma)
4864 ("r-genefilter" ,r-genefilter)))
4865 (home-page "https://bioconductor.org/packages/simpleaffy/")
4866 (synopsis "Very simple high level analysis of Affymetrix data")
4868 "This package provides high level functions for reading Affy @file{.CEL}
4869 files, phenotypic data, and then computing simple things with it, such as
4870 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4871 library. It also has some basic scatter plot functions and mechanisms for
4872 generating high resolution journal figures.")
4873 (license license:gpl2+)))
4875 (define-public r-yaqcaffy
4882 (uri (bioconductor-uri "yaqcaffy" version))
4885 "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0"))))
4886 (build-system r-build-system)
4888 `(("r-simpleaffy" ,r-simpleaffy)))
4889 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4890 (synopsis "Affymetrix quality control and reproducibility analysis")
4892 "This is a package that can be used for quality control of Affymetrix
4893 GeneChip expression data and reproducibility analysis of human whole genome
4894 chips with the MAQC reference datasets.")
4895 (license license:artistic2.0)))
4897 (define-public r-quantro
4904 (uri (bioconductor-uri "quantro" version))
4907 "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
4908 (build-system r-build-system)
4910 `(("r-biobase" ,r-biobase)
4911 ("r-doparallel" ,r-doparallel)
4912 ("r-foreach" ,r-foreach)
4913 ("r-ggplot2" ,r-ggplot2)
4914 ("r-iterators" ,r-iterators)
4915 ("r-minfi" ,r-minfi)
4916 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4918 `(("r-knitr" ,r-knitr)))
4919 (home-page "https://bioconductor.org/packages/quantro/")
4920 (synopsis "Test for when to use quantile normalization")
4922 "This package provides a data-driven test for the assumptions of quantile
4923 normalization using raw data such as objects that inherit eSets (e.g.
4924 ExpressionSet, MethylSet). Group level information about each sample (such as
4925 Tumor / Normal status) must also be provided because the test assesses if
4926 there are global differences in the distributions between the user-defined
4928 (license license:gpl3+)))
4930 (define-public r-yarn
4937 (uri (bioconductor-uri "yarn" version))
4940 "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
4941 (build-system r-build-system)
4943 `(("r-biobase" ,r-biobase)
4944 ("r-biomart" ,r-biomart)
4945 ("r-downloader" ,r-downloader)
4946 ("r-edger" ,r-edger)
4947 ("r-gplots" ,r-gplots)
4948 ("r-limma" ,r-limma)
4949 ("r-matrixstats" ,r-matrixstats)
4950 ("r-preprocesscore" ,r-preprocesscore)
4951 ("r-quantro" ,r-quantro)
4952 ("r-rcolorbrewer" ,r-rcolorbrewer)
4953 ("r-readr" ,r-readr)))
4955 `(("r-knitr" ,r-knitr)))
4956 (home-page "https://bioconductor.org/packages/yarn/")
4957 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4959 "Expedite large RNA-Seq analyses using a combination of previously
4960 developed tools. YARN is meant to make it easier for the user in performing
4961 basic mis-annotation quality control, filtering, and condition-aware
4962 normalization. YARN leverages many Bioconductor tools and statistical
4963 techniques to account for the large heterogeneity and sparsity found in very
4964 large RNA-seq experiments.")
4965 (license license:artistic2.0)))
4967 (define-public r-roar
4974 (uri (bioconductor-uri "roar" version))
4977 "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f"))))
4978 (build-system r-build-system)
4980 `(("r-biocgenerics" ,r-biocgenerics)
4981 ("r-genomeinfodb" ,r-genomeinfodb)
4982 ("r-genomicalignments" ,r-genomicalignments)
4983 ("r-genomicranges" ,r-genomicranges)
4984 ("r-iranges" ,r-iranges)
4985 ("r-rtracklayer" ,r-rtracklayer)
4986 ("r-s4vectors" ,r-s4vectors)
4987 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4988 (home-page "https://github.com/vodkatad/roar/")
4989 (synopsis "Identify differential APA usage from RNA-seq alignments")
4991 "This package provides tools for identifying preferential usage of APA
4992 sites, comparing two biological conditions, starting from known alternative
4993 sites and alignments obtained from standard RNA-seq experiments.")
4994 (license license:gpl3)))
4996 (define-public r-xbseq
5003 (uri (bioconductor-uri "XBSeq" version))
5006 "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0"))))
5007 (properties `((upstream-name . "XBSeq")))
5008 (build-system r-build-system)
5010 `(("r-biobase" ,r-biobase)
5011 ("r-deseq2" ,r-deseq2)
5012 ("r-dplyr" ,r-dplyr)
5013 ("r-ggplot2" ,r-ggplot2)
5014 ("r-locfit" ,r-locfit)
5015 ("r-magrittr" ,r-magrittr)
5016 ("r-matrixstats" ,r-matrixstats)
5017 ("r-pracma" ,r-pracma)
5018 ("r-roar" ,r-roar)))
5020 `(("r-knitr" ,r-knitr)))
5021 (home-page "https://github.com/Liuy12/XBSeq")
5022 (synopsis "Test for differential expression for RNA-seq data")
5024 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5025 expression} (DE), where a statistical model was established based on the
5026 assumption that observed signals are the convolution of true expression
5027 signals and sequencing noises. The mapped reads in non-exonic regions are
5028 considered as sequencing noises, which follows a Poisson distribution. Given
5029 measurable observed signal and background noise from RNA-seq data, true
5030 expression signals, assuming governed by the negative binomial distribution,
5031 can be delineated and thus the accurate detection of differential expressed
5033 (license license:gpl3+)))
5035 (define-public r-massspecwavelet
5037 (name "r-massspecwavelet")
5042 (uri (bioconductor-uri "MassSpecWavelet" version))
5045 "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq"))))
5047 `((upstream-name . "MassSpecWavelet")))
5048 (build-system r-build-system)
5050 `(("r-waveslim" ,r-waveslim)))
5051 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5052 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5054 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5055 data mainly through the use of wavelet transforms. It supports peak detection
5056 based on @dfn{Continuous Wavelet Transform} (CWT).")
5057 (license license:lgpl2.0+)))
5059 (define-public r-xcms
5066 (uri (bioconductor-uri "xcms" version))
5069 "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn"))))
5070 (build-system r-build-system)
5072 `(("r-biobase" ,r-biobase)
5073 ("r-biocgenerics" ,r-biocgenerics)
5074 ("r-biocparallel" ,r-biocparallel)
5075 ("r-iranges" ,r-iranges)
5076 ("r-lattice" ,r-lattice)
5077 ("r-massspecwavelet" ,r-massspecwavelet)
5078 ("r-msnbase" ,r-msnbase)
5081 ("r-protgenerics" ,r-protgenerics)
5083 ("r-rcolorbrewer" ,r-rcolorbrewer)
5084 ("r-robustbase" ,r-robustbase)
5085 ("r-s4vectors" ,r-s4vectors)
5086 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5088 `(("r-knitr" ,r-knitr)))
5089 (home-page "https://bioconductor.org/packages/xcms/")
5090 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5092 "This package provides a framework for processing and visualization of
5093 chromatographically separated and single-spectra mass spectral data. It
5094 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5095 data for high-throughput, untargeted analyte profiling.")
5096 (license license:gpl2+)))
5098 (define-public r-wrench
5105 (uri (bioconductor-uri "Wrench" version))
5108 "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6"))))
5109 (properties `((upstream-name . "Wrench")))
5110 (build-system r-build-system)
5112 `(("r-limma" ,r-limma)
5113 ("r-locfit" ,r-locfit)
5114 ("r-matrixstats" ,r-matrixstats)))
5116 `(("r-knitr" ,r-knitr)))
5117 (home-page "https://github.com/HCBravoLab/Wrench")
5118 (synopsis "Wrench normalization for sparse count data")
5120 "Wrench is a package for normalization sparse genomic count data, like
5121 that arising from 16s metagenomic surveys.")
5122 (license license:artistic2.0)))
5124 (define-public r-wiggleplotr
5126 (name "r-wiggleplotr")
5131 (uri (bioconductor-uri "wiggleplotr" version))
5134 "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
5135 (build-system r-build-system)
5137 `(("r-assertthat" ,r-assertthat)
5138 ("r-cowplot" ,r-cowplot)
5139 ("r-dplyr" ,r-dplyr)
5140 ("r-genomeinfodb" ,r-genomeinfodb)
5141 ("r-genomicranges" ,r-genomicranges)
5142 ("r-ggplot2" ,r-ggplot2)
5143 ("r-iranges" ,r-iranges)
5144 ("r-purrr" ,r-purrr)
5145 ("r-rtracklayer" ,r-rtracklayer)
5146 ("r-s4vectors" ,r-s4vectors)))
5148 `(("r-knitr" ,r-knitr)))
5149 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5150 (synopsis "Make read coverage plots from BigWig files")
5152 "This package provides tools to visualize read coverage from sequencing
5153 experiments together with genomic annotations (genes, transcripts, peaks).
5154 Introns of long transcripts can be rescaled to a fixed length for better
5155 visualization of exonic read coverage.")
5156 (license license:asl2.0)))
5158 (define-public r-widgettools
5160 (name "r-widgettools")
5165 (uri (bioconductor-uri "widgetTools" version))
5168 "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx"))))
5169 (properties `((upstream-name . "widgetTools")))
5170 (build-system r-build-system)
5171 (home-page "https://bioconductor.org/packages/widgetTools/")
5172 (synopsis "Tools for creating interactive tcltk widgets")
5174 "This package contains tools to support the construction of tcltk
5176 ;; Any version of the LGPL.
5177 (license license:lgpl3+)))
5179 (define-public r-webbioc
5186 (uri (bioconductor-uri "webbioc" version))
5189 "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f"))))
5190 (build-system r-build-system)
5192 `(("netpbm" ,netpbm)
5195 `(("r-affy" ,r-affy)
5196 ("r-annaffy" ,r-annaffy)
5197 ("r-biobase" ,r-biobase)
5198 ("r-biocmanager" ,r-biocmanager)
5199 ("r-gcrma" ,r-gcrma)
5200 ("r-multtest" ,r-multtest)
5201 ("r-qvalue" ,r-qvalue)
5203 (home-page "https://www.bioconductor.org/")
5204 (synopsis "Bioconductor web interface")
5206 "This package provides an integrated web interface for doing microarray
5207 analysis using several of the Bioconductor packages. It is intended to be
5208 deployed as a centralized bioinformatics resource for use by many users.
5209 Currently only Affymetrix oligonucleotide analysis is supported.")
5210 (license license:gpl2+)))
5212 (define-public r-zfpkm
5219 (uri (bioconductor-uri "zFPKM" version))
5222 "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys"))))
5223 (properties `((upstream-name . "zFPKM")))
5224 (build-system r-build-system)
5226 `(("r-checkmate" ,r-checkmate)
5227 ("r-dplyr" ,r-dplyr)
5228 ("r-ggplot2" ,r-ggplot2)
5229 ("r-summarizedexperiment" ,r-summarizedexperiment)
5230 ("r-tidyr" ,r-tidyr)))
5232 `(("r-knitr" ,r-knitr)))
5233 (home-page "https://github.com/ronammar/zFPKM/")
5234 (synopsis "Functions to facilitate zFPKM transformations")
5236 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5237 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5239 (license license:gpl3)))
5241 (define-public r-rbowtie2
5248 (uri (bioconductor-uri "Rbowtie2" version))
5251 "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
5252 (properties `((upstream-name . "Rbowtie2")))
5253 (build-system r-build-system)
5257 `(("r-knitr" ,r-knitr)))
5258 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5259 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5261 "This package provides an R wrapper of the popular @code{bowtie2}
5262 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5263 rapid adapter trimming, identification, and read merging.")
5264 (license license:gpl3+)))
5266 (define-public r-progeny
5273 (uri (bioconductor-uri "progeny" version))
5276 "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh"))))
5277 (build-system r-build-system)
5279 `(("r-biobase" ,r-biobase)
5280 ("r-dplyr" ,r-dplyr)
5281 ("r-ggplot2" ,r-ggplot2)
5282 ("r-ggrepel" ,r-ggrepel)
5283 ("r-gridextra" ,r-gridextra)
5284 ("r-tidyr" ,r-tidyr)))
5286 `(("r-knitr" ,r-knitr)))
5287 (home-page "https://github.com/saezlab/progeny")
5288 (synopsis "Pathway responsive gene activity inference")
5290 "This package provides a function to infer pathway activity from gene
5291 expression. It contains the linear model inferred in the publication
5292 \"Perturbation-response genes reveal signaling footprints in cancer gene
5294 (license license:asl2.0)))
5296 (define-public r-arrmnormalization
5298 (name "r-arrmnormalization")
5303 (uri (bioconductor-uri "ARRmNormalization" version))
5306 "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv"))))
5308 `((upstream-name . "ARRmNormalization")))
5309 (build-system r-build-system)
5310 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5311 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5312 (synopsis "Adaptive robust regression normalization for methylation data")
5314 "This is a package to perform the @dfn{Adaptive Robust Regression
5315 method} (ARRm) for the normalization of methylation data from the Illumina
5316 Infinium HumanMethylation 450k assay.")
5317 (license license:artistic2.0)))
5319 (define-public r-biocfilecache
5321 (name "r-biocfilecache")
5326 (uri (bioconductor-uri "BiocFileCache" version))
5329 "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
5330 (properties `((upstream-name . "BiocFileCache")))
5331 (build-system r-build-system)
5333 `(("r-curl" ,r-curl)
5335 ("r-dbplyr" ,r-dbplyr)
5336 ("r-dplyr" ,r-dplyr)
5338 ("r-rappdirs" ,r-rappdirs)
5339 ("r-rsqlite" ,r-rsqlite)))
5341 `(("r-knitr" ,r-knitr)))
5342 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5343 (synopsis "Manage files across sessions")
5345 "This package creates a persistent on-disk cache of files that the user
5346 can add, update, and retrieve. It is useful for managing resources (such as
5347 custom Txdb objects) that are costly or difficult to create, web resources,
5348 and data files used across sessions.")
5349 (license license:artistic2.0)))
5351 (define-public r-iclusterplus
5353 (name "r-iclusterplus")
5358 (uri (bioconductor-uri "iClusterPlus" version))
5361 "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w"))))
5362 (properties `((upstream-name . "iClusterPlus")))
5363 (build-system r-build-system)
5364 (native-inputs `(("gfortran" ,gfortran)))
5365 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5366 (synopsis "Integrative clustering of multi-type genomic data")
5368 "iClusterPlus is developed for integrative clustering analysis of
5369 multi-type genomic data and is an enhanced version of iCluster proposed and
5370 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5371 from the experiments where biological samples (e.g. tumor samples) are
5372 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5373 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5374 on. In the iClusterPlus model, binary observations such as somatic mutation
5375 are modeled as Binomial processes; categorical observations such as copy
5376 number states are realizations of Multinomial random variables; counts are
5377 modeled as Poisson random processes; and continuous measures are modeled by
5378 Gaussian distributions.")
5379 (license license:gpl2+)))
5381 (define-public r-rbowtie
5388 (uri (bioconductor-uri "Rbowtie" version))
5391 "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
5392 (properties `((upstream-name . "Rbowtie")))
5393 (build-system r-build-system)
5397 `(("r-knitr" ,r-knitr)))
5398 (home-page "https://bioconductor.org/packages/Rbowtie/")
5399 (synopsis "R bowtie wrapper")
5401 "This package provides an R wrapper around the popular bowtie short read
5402 aligner and around SpliceMap, a de novo splice junction discovery and
5404 (license license:artistic2.0)))
5406 (define-public r-sgseq
5413 (uri (bioconductor-uri "SGSeq" version))
5416 "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c"))))
5417 (properties `((upstream-name . "SGSeq")))
5418 (build-system r-build-system)
5420 `(("r-annotationdbi" ,r-annotationdbi)
5421 ("r-biocgenerics" ,r-biocgenerics)
5422 ("r-biostrings" ,r-biostrings)
5423 ("r-genomeinfodb" ,r-genomeinfodb)
5424 ("r-genomicalignments" ,r-genomicalignments)
5425 ("r-genomicfeatures" ,r-genomicfeatures)
5426 ("r-genomicranges" ,r-genomicranges)
5427 ("r-igraph" ,r-igraph)
5428 ("r-iranges" ,r-iranges)
5429 ("r-rsamtools" ,r-rsamtools)
5430 ("r-rtracklayer" ,r-rtracklayer)
5431 ("r-runit" ,r-runit)
5432 ("r-s4vectors" ,r-s4vectors)
5433 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5435 `(("r-knitr" ,r-knitr)))
5436 (home-page "https://bioconductor.org/packages/SGSeq/")
5437 (synopsis "Splice event prediction and quantification from RNA-seq data")
5439 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5440 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5441 represented as a splice graph, which can be obtained from existing annotation
5442 or predicted from the mapped sequence reads. Splice events are identified
5443 from the graph and are quantified locally using structurally compatible reads
5444 at the start or end of each splice variant. The software includes functions
5445 for splice event prediction, quantification, visualization and
5447 (license license:artistic2.0)))
5449 (define-public r-rhisat2
5456 (uri (bioconductor-uri "Rhisat2" version))
5459 "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a"))))
5460 (properties `((upstream-name . "Rhisat2")))
5461 (build-system r-build-system)
5464 (modify-phases %standard-phases
5465 (add-after 'unpack 'make-reproducible
5467 (substitute* "src/Makefile"
5468 (("`hostname`") "guix")
5470 ;; Avoid shelling out to "which".
5471 (("^CC =.*") (which "gcc"))
5472 (("^CPP =.*") (which "g++")))
5475 `(("r-genomicfeatures" ,r-genomicfeatures)
5476 ("r-genomicranges" ,r-genomicranges)
5477 ("r-sgseq" ,r-sgseq)))
5479 `(("r-knitr" ,r-knitr)))
5480 (home-page "https://github.com/fmicompbio/Rhisat2")
5481 (synopsis "R Wrapper for HISAT2 sequence aligner")
5483 "This package provides an R interface to the HISAT2 spliced short-read
5484 aligner by Kim et al. (2015). The package contains wrapper functions to
5485 create a genome index and to perform the read alignment to the generated
5487 (license license:gpl3)))
5489 (define-public r-quasr
5496 (uri (bioconductor-uri "QuasR" version))
5499 "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8"))))
5500 (properties `((upstream-name . "QuasR")))
5501 (build-system r-build-system)
5505 `(("r-annotationdbi" ,r-annotationdbi)
5506 ("r-biobase" ,r-biobase)
5507 ("r-biocgenerics" ,r-biocgenerics)
5508 ("r-biocmanager" ,r-biocmanager)
5509 ("r-biocparallel" ,r-biocparallel)
5510 ("r-biostrings" ,r-biostrings)
5511 ("r-bsgenome" ,r-bsgenome)
5512 ("r-genomeinfodb" ,r-genomeinfodb)
5513 ("r-genomicalignments" ,r-genomicalignments)
5514 ("r-genomicfeatures" ,r-genomicfeatures)
5515 ("r-genomicfiles" ,r-genomicfiles)
5516 ("r-genomicranges" ,r-genomicranges)
5517 ("r-iranges" ,r-iranges)
5518 ("r-rbowtie" ,r-rbowtie)
5519 ("r-rhisat2" ,r-rhisat2)
5520 ("r-rhtslib" ,r-rhtslib)
5521 ("r-rsamtools" ,r-rsamtools)
5522 ("r-rtracklayer" ,r-rtracklayer)
5523 ("r-s4vectors" ,r-s4vectors)
5524 ("r-shortread" ,r-shortread)))
5526 `(("r-knitr" ,r-knitr)))
5527 (home-page "https://bioconductor.org/packages/QuasR/")
5528 (synopsis "Quantify and annotate short reads in R")
5530 "This package provides a framework for the quantification and analysis of
5531 short genomic reads. It covers a complete workflow starting from raw sequence
5532 reads, over creation of alignments and quality control plots, to the
5533 quantification of genomic regions of interest.")
5534 (license license:gpl2)))
5536 (define-public r-rqc
5543 (uri (bioconductor-uri "Rqc" version))
5546 "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3"))))
5547 (properties `((upstream-name . "Rqc")))
5548 (build-system r-build-system)
5550 `(("r-biocgenerics" ,r-biocgenerics)
5551 ("r-biocparallel" ,r-biocparallel)
5552 ("r-biocstyle" ,r-biocstyle)
5553 ("r-biostrings" ,r-biostrings)
5554 ("r-biovizbase" ,r-biovizbase)
5555 ("r-genomicalignments" ,r-genomicalignments)
5556 ("r-genomicfiles" ,r-genomicfiles)
5557 ("r-ggplot2" ,r-ggplot2)
5558 ("r-iranges" ,r-iranges)
5559 ("r-knitr" ,r-knitr)
5560 ("r-markdown" ,r-markdown)
5563 ("r-reshape2" ,r-reshape2)
5564 ("r-rsamtools" ,r-rsamtools)
5565 ("r-s4vectors" ,r-s4vectors)
5566 ("r-shiny" ,r-shiny)
5567 ("r-shortread" ,r-shortread)))
5569 `(("r-knitr" ,r-knitr)))
5570 (home-page "https://github.com/labbcb/Rqc")
5571 (synopsis "Quality control tool for high-throughput sequencing data")
5573 "Rqc is an optimized tool designed for quality control and assessment of
5574 high-throughput sequencing data. It performs parallel processing of entire
5575 files and produces a report which contains a set of high-resolution
5577 (license license:gpl2+)))
5579 (define-public r-birewire
5586 (uri (bioconductor-uri "BiRewire" version))
5589 "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g"))))
5590 (properties `((upstream-name . "BiRewire")))
5591 (build-system r-build-system)
5593 `(("r-igraph" ,r-igraph)
5594 ("r-matrix" ,r-matrix)
5596 ("r-tsne" ,r-tsne)))
5597 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5598 (synopsis "Tools for randomization of bipartite graphs")
5600 "This package provides functions for bipartite network rewiring through N
5601 consecutive switching steps and for the computation of the minimal number of
5602 switching steps to be performed in order to maximise the dissimilarity with
5603 respect to the original network. It includes functions for the analysis of
5604 the introduced randomness across the switching steps and several other
5605 routines to analyse the resulting networks and their natural projections.")
5606 (license license:gpl3)))
5608 (define-public r-birta
5615 (uri (bioconductor-uri "birta" version))
5618 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5619 (build-system r-build-system)
5621 `(("r-biobase" ,r-biobase)
5622 ("r-limma" ,r-limma)
5623 ("r-mass" ,r-mass)))
5624 (home-page "https://bioconductor.org/packages/birta")
5625 (synopsis "Bayesian inference of regulation of transcriptional activity")
5627 "Expression levels of mRNA molecules are regulated by different
5628 processes, comprising inhibition or activation by transcription factors and
5629 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5630 Inference of Regulation of Transcriptional Activity) uses the regulatory
5631 networks of transcription factors and miRNAs together with mRNA and miRNA
5632 expression data to predict switches in regulatory activity between two
5633 conditions. A Bayesian network is used to model the regulatory structure and
5634 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5635 (license license:gpl2+)))
5637 (define-public r-multidataset
5639 (name "r-multidataset")
5644 (uri (bioconductor-uri "MultiDataSet" version))
5647 "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39"))))
5648 (properties `((upstream-name . "MultiDataSet")))
5649 (build-system r-build-system)
5651 `(("r-biobase" ,r-biobase)
5652 ("r-biocgenerics" ,r-biocgenerics)
5653 ("r-genomicranges" ,r-genomicranges)
5654 ("r-ggplot2" ,r-ggplot2)
5655 ("r-ggrepel" ,r-ggrepel)
5656 ("r-iranges" ,r-iranges)
5657 ("r-limma" ,r-limma)
5658 ("r-qqman" ,r-qqman)
5659 ("r-s4vectors" ,r-s4vectors)
5660 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5662 `(("r-knitr" ,r-knitr)))
5663 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5664 (synopsis "Implementation of MultiDataSet and ResultSet")
5666 "This package provides an implementation of the BRGE's (Bioinformatic
5667 Research Group in Epidemiology from Center for Research in Environmental
5668 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5669 integrating multi omics data sets and ResultSet is a container for omics
5670 results. This package contains base classes for MEAL and rexposome
5672 (license license:expat)))
5674 (define-public r-ropls
5681 (uri (bioconductor-uri "ropls" version))
5684 "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx"))))
5685 (build-system r-build-system)
5687 `(("r-biobase" ,r-biobase)
5688 ("r-multidataset" ,r-multidataset)))
5690 `(("r-knitr" ,r-knitr))) ; for vignettes
5691 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5692 (synopsis "Multivariate analysis and feature selection of omics data")
5694 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5695 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5696 regression, classification, and feature selection of omics data where the
5697 number of variables exceeds the number of samples and with multicollinearity
5698 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5699 separately model the variation correlated (predictive) to the factor of
5700 interest and the uncorrelated (orthogonal) variation. While performing
5701 similarly to PLS, OPLS facilitates interpretation.
5703 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5704 analysis and feature selection of omics data. In addition to scores, loadings
5705 and weights plots, the package provides metrics and graphics to determine the
5706 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5707 validity of the model by permutation testing, detect outliers, and perform
5708 feature selection (e.g. with Variable Importance in Projection or regression
5710 (license license:cecill)))
5712 (define-public r-biosigner
5714 (name "r-biosigner")
5719 (uri (bioconductor-uri "biosigner" version))
5722 "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06"))))
5723 (build-system r-build-system)
5725 `(("r-biobase" ,r-biobase)
5726 ("r-e1071" ,r-e1071)
5727 ("r-multidataset" ,r-multidataset)
5728 ("r-randomforest" ,r-randomforest)
5729 ("r-ropls" ,r-ropls)))
5731 `(("r-knitr" ,r-knitr)))
5732 (home-page "https://bioconductor.org/packages/biosigner/")
5733 (synopsis "Signature discovery from omics data")
5735 "Feature selection is critical in omics data analysis to extract
5736 restricted and meaningful molecular signatures from complex and high-dimension
5737 data, and to build robust classifiers. This package implements a method to
5738 assess the relevance of the variables for the prediction performances of the
5739 classifier. The approach can be run in parallel with the PLS-DA, Random
5740 Forest, and SVM binary classifiers. The signatures and the corresponding
5741 'restricted' models are returned, enabling future predictions on new
5743 (license license:cecill)))
5745 (define-public r-annotatr
5752 (uri (bioconductor-uri "annotatr" version))
5755 "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl"))))
5756 (build-system r-build-system)
5758 `(("r-annotationdbi" ,r-annotationdbi)
5759 ("r-annotationhub" ,r-annotationhub)
5760 ("r-dplyr" ,r-dplyr)
5761 ("r-genomeinfodb" ,r-genomeinfodb)
5762 ("r-genomicfeatures" ,r-genomicfeatures)
5763 ("r-genomicranges" ,r-genomicranges)
5764 ("r-ggplot2" ,r-ggplot2)
5765 ("r-iranges" ,r-iranges)
5766 ("r-readr" ,r-readr)
5767 ("r-regioner" ,r-regioner)
5768 ("r-reshape2" ,r-reshape2)
5769 ("r-rtracklayer" ,r-rtracklayer)
5770 ("r-s4vectors" ,r-s4vectors)))
5772 `(("r-knitr" ,r-knitr)))
5773 (home-page "https://bioconductor.org/packages/annotatr/")
5774 (synopsis "Annotation of genomic regions to genomic annotations")
5776 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5777 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5778 to investigate the intersecting genomic annotations. Such annotations include
5779 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5780 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5781 enhancers. The annotatr package provides an easy way to summarize and
5782 visualize the intersection of genomic sites/regions with genomic
5784 (license license:gpl3)))
5786 (define-public r-rsubread
5793 (uri (bioconductor-uri "Rsubread" version))
5796 "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
5797 (properties `((upstream-name . "Rsubread")))
5798 (build-system r-build-system)
5799 (inputs `(("zlib" ,zlib)))
5801 `(("r-matrix" ,r-matrix)))
5802 (home-page "https://bioconductor.org/packages/Rsubread/")
5803 (synopsis "Subread sequence alignment and counting for R")
5805 "This package provides tools for alignment, quantification and analysis
5806 of second and third generation sequencing data. It includes functionality for
5807 read mapping, read counting, SNP calling, structural variant detection and
5808 gene fusion discovery. It can be applied to all major sequencing techologies
5809 and to both short and long sequence reads.")
5810 (license license:gpl3)))
5812 (define-public r-flowutils
5814 (name "r-flowutils")
5819 (uri (bioconductor-uri "flowUtils" version))
5822 "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4"))))
5823 (properties `((upstream-name . "flowUtils")))
5824 (build-system r-build-system)
5826 `(("r-biobase" ,r-biobase)
5827 ("r-corpcor" ,r-corpcor)
5828 ("r-flowcore" ,r-flowcore)
5829 ("r-graph" ,r-graph)
5830 ("r-runit" ,r-runit)
5832 (home-page "https://github.com/jspidlen/flowUtils")
5833 (synopsis "Utilities for flow cytometry")
5835 "This package provides utilities for flow cytometry data.")
5836 (license license:artistic2.0)))
5838 (define-public r-consensusclusterplus
5840 (name "r-consensusclusterplus")
5845 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5848 "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq"))))
5850 `((upstream-name . "ConsensusClusterPlus")))
5851 (build-system r-build-system)
5854 ("r-biobase" ,r-biobase)
5855 ("r-cluster" ,r-cluster)))
5856 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5857 (synopsis "Clustering algorithm")
5859 "This package provides an implementation of an algorithm for determining
5860 cluster count and membership by stability evidence in unsupervised analysis.")
5861 (license license:gpl2)))
5863 (define-public r-cytolib
5870 (uri (bioconductor-uri "cytolib" version))
5873 "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj"))))
5874 (properties `((upstream-name . "cytolib")))
5875 (build-system r-build-system)
5879 `(("r-knitr" ,r-knitr)))
5883 ("r-rcpparmadillo" ,r-rcpparmadillo)
5884 ("r-rcppparallel" ,r-rcppparallel)
5885 ("r-rhdf5lib" ,r-rhdf5lib)
5886 ("r-rprotobuflib" ,r-rprotobuflib)))
5887 (home-page "https://bioconductor.org/packages/cytolib/")
5888 (synopsis "C++ infrastructure for working with gated cytometry")
5890 "This package provides the core data structure and API to represent and
5891 interact with gated cytometry data.")
5892 (license license:artistic2.0)))
5894 (define-public r-flowcore
5901 (uri (bioconductor-uri "flowCore" version))
5904 "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p"))))
5905 (properties `((upstream-name . "flowCore")))
5906 (build-system r-build-system)
5909 ("r-biobase" ,r-biobase)
5910 ("r-biocgenerics" ,r-biocgenerics)
5911 ("r-cytolib" ,r-cytolib)
5912 ("r-matrixstats" ,r-matrixstats)
5914 ("r-rcpparmadillo" ,r-rcpparmadillo)
5915 ("r-rprotobuflib" ,r-rprotobuflib)))
5917 `(("r-knitr" ,r-knitr)))
5918 (home-page "https://bioconductor.org/packages/flowCore")
5919 (synopsis "Basic structures for flow cytometry data")
5921 "This package provides S4 data structures and basic functions to deal
5922 with flow cytometry data.")
5923 (license license:artistic2.0)))
5925 (define-public r-flowmeans
5927 (name "r-flowmeans")
5932 (uri (bioconductor-uri "flowMeans" version))
5935 "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7"))))
5936 (properties `((upstream-name . "flowMeans")))
5937 (build-system r-build-system)
5939 `(("r-biobase" ,r-biobase)
5940 ("r-feature" ,r-feature)
5941 ("r-flowcore" ,r-flowcore)
5942 ("r-rrcov" ,r-rrcov)))
5943 (home-page "https://bioconductor.org/packages/flowMeans")
5944 (synopsis "Non-parametric flow cytometry data gating")
5946 "This package provides tools to identify cell populations in Flow
5947 Cytometry data using non-parametric clustering and segmented-regression-based
5948 change point detection.")
5949 (license license:artistic2.0)))
5951 (define-public r-ncdfflow
5958 (uri (bioconductor-uri "ncdfFlow" version))
5961 "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f"))))
5962 (properties `((upstream-name . "ncdfFlow")))
5963 (build-system r-build-system)
5968 ("r-biobase" ,r-biobase)
5969 ("r-biocgenerics" ,r-biocgenerics)
5970 ("r-flowcore" ,r-flowcore)
5972 ("r-rcpparmadillo" ,r-rcpparmadillo)
5973 ("r-rhdf5lib" ,r-rhdf5lib)
5974 ("r-zlibbioc" ,r-zlibbioc)))
5976 `(("r-knitr" ,r-knitr)))
5977 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5978 (synopsis "HDF5 based storage for flow cytometry data")
5980 "This package provides HDF5 storage based methods and functions for
5981 manipulation of flow cytometry data.")
5982 (license license:artistic2.0)))
5984 (define-public r-ggcyto
5991 (uri (bioconductor-uri "ggcyto" version))
5994 "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
5995 (properties `((upstream-name . "ggcyto")))
5996 (build-system r-build-system)
5998 `(("r-data-table" ,r-data-table)
5999 ("r-flowcore" ,r-flowcore)
6000 ("r-flowworkspace" ,r-flowworkspace)
6001 ("r-ggplot2" ,r-ggplot2)
6002 ("r-gridextra" ,r-gridextra)
6003 ("r-hexbin" ,r-hexbin)
6004 ("r-ncdfflow" ,r-ncdfflow)
6006 ("r-rcolorbrewer" ,r-rcolorbrewer)
6007 ("r-rlang" ,r-rlang)
6008 ("r-scales" ,r-scales)))
6010 `(("r-knitr" ,r-knitr)))
6011 (home-page "https://github.com/RGLab/ggcyto/issues")
6012 (synopsis "Visualize Cytometry data with ggplot")
6014 "With the dedicated fortify method implemented for @code{flowSet},
6015 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6016 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6017 and some custom layers also make it easy to add gates and population
6018 statistics to the plot.")
6019 (license license:artistic2.0)))
6021 (define-public r-flowviz
6028 (uri (bioconductor-uri "flowViz" version))
6031 "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq"))))
6032 (properties `((upstream-name . "flowViz")))
6033 (build-system r-build-system)
6035 `(("r-biobase" ,r-biobase)
6036 ("r-flowcore" ,r-flowcore)
6037 ("r-hexbin" ,r-hexbin)
6038 ("r-idpmisc" ,r-idpmisc)
6039 ("r-kernsmooth" ,r-kernsmooth)
6040 ("r-lattice" ,r-lattice)
6041 ("r-latticeextra" ,r-latticeextra)
6043 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6045 `(("r-knitr" ,r-knitr)))
6046 (home-page "https://bioconductor.org/packages/flowViz/")
6047 (synopsis "Visualization for flow cytometry")
6049 "This package provides visualization tools for flow cytometry data.")
6050 (license license:artistic2.0)))
6052 (define-public r-flowclust
6054 (name "r-flowclust")
6059 (uri (bioconductor-uri "flowClust" version))
6062 "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b"))))
6063 (properties `((upstream-name . "flowClust")))
6064 (build-system r-build-system)
6067 (list "--configure-args=--enable-bundled-gsl=no")))
6069 `(("r-biobase" ,r-biobase)
6070 ("r-biocgenerics" ,r-biocgenerics)
6072 ("r-corpcor" ,r-corpcor)
6073 ("r-ellipse" ,r-ellipse)
6074 ("r-flowcore" ,r-flowcore)
6075 ("r-flowviz" ,r-flowviz)
6076 ("r-graph" ,r-graph)
6077 ("r-mnormt" ,r-mnormt)))
6081 `(("pkg-config" ,pkg-config)
6082 ("r-knitr" ,r-knitr)))
6083 (home-page "https://bioconductor.org/packages/flowClust")
6084 (synopsis "Clustering for flow cytometry")
6086 "This package provides robust model-based clustering using a t-mixture
6087 model with Box-Cox transformation.")
6088 (license license:artistic2.0)))
6090 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6091 ;; make it use our protobuf package instead.
6092 (define-public r-rprotobuflib
6094 (name "r-rprotobuflib")
6099 (uri (bioconductor-uri "RProtoBufLib" version))
6102 "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
6103 (properties `((upstream-name . "RProtoBufLib")))
6104 (build-system r-build-system)
6107 (modify-phases %standard-phases
6108 (add-after 'unpack 'unpack-bundled-sources
6110 (with-directory-excursion "src"
6111 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6114 `(("r-knitr" ,r-knitr)))
6115 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6116 (synopsis "C++ headers and static libraries of Protocol buffers")
6118 "This package provides the headers and static library of Protocol buffers
6119 for other R packages to compile and link against.")
6120 (license license:bsd-3)))
6122 (define-public r-flowworkspace
6124 (name "r-flowworkspace")
6129 (uri (bioconductor-uri "flowWorkspace" version))
6132 "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
6133 (properties `((upstream-name . "flowWorkspace")))
6134 (build-system r-build-system)
6137 ("r-biobase" ,r-biobase)
6138 ("r-biocgenerics" ,r-biocgenerics)
6139 ("r-cytolib" ,r-cytolib)
6140 ("r-data-table" ,r-data-table)
6141 ("r-digest" ,r-digest)
6142 ("r-dplyr" ,r-dplyr)
6143 ("r-flowcore" ,r-flowcore)
6144 ("r-ggplot2" ,r-ggplot2)
6145 ("r-graph" ,r-graph)
6146 ("r-lattice" ,r-lattice)
6147 ("r-latticeextra" ,r-latticeextra)
6148 ("r-matrixstats" ,r-matrixstats)
6149 ("r-ncdfflow" ,r-ncdfflow)
6152 ("r-rcpparmadillo" ,r-rcpparmadillo)
6153 ("r-rcppparallel" ,r-rcppparallel)
6154 ("r-rgraphviz" ,r-rgraphviz)
6155 ("r-rhdf5lib" ,r-rhdf5lib)
6156 ("r-rprotobuflib" ,r-rprotobuflib)
6157 ("r-scales" ,r-scales)
6158 ("r-stringr" ,r-stringr)
6161 `(("r-knitr" ,r-knitr)))
6162 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6163 (synopsis "Infrastructure for working with cytometry data")
6165 "This package is designed to facilitate comparison of automated gating
6166 methods against manual gating done in flowJo. This package allows you to
6167 import basic flowJo workspaces into BioConductor and replicate the gating from
6168 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6169 samples, compensation, and transformation are performed so that the output
6170 matches the flowJo analysis.")
6171 (license license:artistic2.0)))
6173 (define-public r-flowstats
6175 (name "r-flowstats")
6180 (uri (bioconductor-uri "flowStats" version))
6183 "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
6184 (properties `((upstream-name . "flowStats")))
6185 (build-system r-build-system)
6187 `(("r-biobase" ,r-biobase)
6188 ("r-biocgenerics" ,r-biocgenerics)
6189 ("r-cluster" ,r-cluster)
6191 ("r-flowcore" ,r-flowcore)
6192 ("r-flowviz" ,r-flowviz)
6193 ("r-flowworkspace" ,r-flowworkspace)
6194 ("r-kernsmooth" ,r-kernsmooth)
6196 ("r-lattice" ,r-lattice)
6198 ("r-ncdfflow" ,r-ncdfflow)
6199 ("r-rcolorbrewer" ,r-rcolorbrewer)
6200 ("r-rrcov" ,r-rrcov)))
6201 (home-page "http://www.github.com/RGLab/flowStats")
6202 (synopsis "Statistical methods for the analysis of flow cytometry data")
6204 "This package provides methods and functionality to analyze flow data
6205 that is beyond the basic infrastructure provided by the @code{flowCore}
6207 (license license:artistic2.0)))
6209 (define-public r-opencyto
6216 (uri (bioconductor-uri "openCyto" version))
6219 "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
6220 (properties `((upstream-name . "openCyto")))
6221 (build-system r-build-system)
6223 `(("r-biobase" ,r-biobase)
6224 ("r-biocgenerics" ,r-biocgenerics)
6226 ("r-data-table" ,r-data-table)
6227 ("r-flowclust" ,r-flowclust)
6228 ("r-flowcore" ,r-flowcore)
6229 ("r-flowstats" ,r-flowstats)
6230 ("r-flowviz" ,r-flowviz)
6231 ("r-flowworkspace" ,r-flowworkspace)
6232 ("r-graph" ,r-graph)
6233 ("r-gtools" ,r-gtools)
6235 ("r-lattice" ,r-lattice)
6237 ("r-ncdfflow" ,r-ncdfflow)
6239 ("r-r-utils" ,r-r-utils)
6241 ("r-rcolorbrewer" ,r-rcolorbrewer)
6243 ("r-rrcov" ,r-rrcov)))
6245 `(("r-knitr" ,r-knitr)))
6246 (home-page "https://bioconductor.org/packages/openCyto")
6247 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6249 "This package is designed to facilitate the automated gating methods in a
6250 sequential way to mimic the manual gating strategy.")
6251 (license license:artistic2.0)))
6253 (define-public r-cytoml
6260 (uri (bioconductor-uri "CytoML" version))
6263 "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
6264 (properties `((upstream-name . "CytoML")))
6265 (build-system r-build-system)
6267 `(("libxml2" ,libxml2)))
6269 `(("r-base64enc" ,r-base64enc)
6271 ("r-biobase" ,r-biobase)
6272 ("r-corpcor" ,r-corpcor)
6273 ("r-cytolib" ,r-cytolib)
6274 ("r-data-table" ,r-data-table)
6275 ("r-dplyr" ,r-dplyr)
6276 ("r-flowcore" ,r-flowcore)
6277 ("r-flowworkspace" ,r-flowworkspace)
6278 ("r-ggcyto" ,r-ggcyto)
6279 ("r-graph" ,r-graph)
6280 ("r-jsonlite" ,r-jsonlite)
6281 ("r-lattice" ,r-lattice)
6282 ("r-opencyto" ,r-opencyto)
6286 ("r-rcpparmadillo" ,r-rcpparmadillo)
6287 ("r-rcppparallel" ,r-rcppparallel)
6288 ("r-rgraphviz" ,r-rgraphviz)
6289 ("r-rhdf5lib" ,r-rhdf5lib)
6290 ("r-rprotobuflib" ,r-rprotobuflib)
6291 ("r-runit" ,r-runit)
6292 ("r-tibble" ,r-tibble)
6295 ("r-yaml" ,r-yaml)))
6297 `(("r-knitr" ,r-knitr)))
6298 (home-page "https://github.com/RGLab/CytoML")
6299 (synopsis "GatingML interface for cross platform cytometry data sharing")
6301 "This package provides an interface to implementations of the GatingML2.0
6302 standard to exchange gated cytometry data with other software platforms.")
6303 (license license:artistic2.0)))
6305 (define-public r-flowsom
6312 (uri (bioconductor-uri "FlowSOM" version))
6315 "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
6316 (properties `((upstream-name . "FlowSOM")))
6317 (build-system r-build-system)
6319 `(("r-biocgenerics" ,r-biocgenerics)
6320 ("r-consensusclusterplus" ,r-consensusclusterplus)
6321 ("r-cytoml" ,r-cytoml)
6322 ("r-flowcore" ,r-flowcore)
6323 ("r-flowworkspace" ,r-flowworkspace)
6324 ("r-igraph" ,r-igraph)
6325 ("r-rcolorbrewer" ,r-rcolorbrewer)
6328 (home-page "https://bioconductor.org/packages/FlowSOM/")
6329 (synopsis "Visualize and interpret cytometry data")
6331 "FlowSOM offers visualization options for cytometry data, by using
6332 self-organizing map clustering and minimal spanning trees.")
6333 (license license:gpl2+)))
6335 (define-public r-mixomics
6342 (uri (bioconductor-uri "mixOmics" version))
6345 "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
6346 (properties `((upstream-name . "mixOmics")))
6347 (build-system r-build-system)
6349 `(("r-corpcor" ,r-corpcor)
6350 ("r-dplyr" ,r-dplyr)
6351 ("r-ellipse" ,r-ellipse)
6352 ("r-ggplot2" ,r-ggplot2)
6353 ("r-gridextra" ,r-gridextra)
6354 ("r-igraph" ,r-igraph)
6355 ("r-lattice" ,r-lattice)
6357 ("r-matrixstats" ,r-matrixstats)
6358 ("r-rarpack" ,r-rarpack)
6359 ("r-rcolorbrewer" ,r-rcolorbrewer)
6360 ("r-reshape2" ,r-reshape2)
6361 ("r-tidyr" ,r-tidyr)))
6363 `(("r-knitr" ,r-knitr)))
6364 (home-page "http://www.mixOmics.org")
6365 (synopsis "Multivariate methods for exploration of biological datasets")
6367 "mixOmics offers a wide range of multivariate methods for the exploration
6368 and integration of biological datasets with a particular focus on variable
6369 selection. The package proposes several sparse multivariate models we have
6370 developed to identify the key variables that are highly correlated, and/or
6371 explain the biological outcome of interest. The data that can be analysed
6372 with mixOmics may come from high throughput sequencing technologies, such as
6373 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6374 also beyond the realm of omics (e.g. spectral imaging). The methods
6375 implemented in mixOmics can also handle missing values without having to
6376 delete entire rows with missing data.")
6377 (license license:gpl2+)))
6379 (define-public r-depecher
6386 (uri (bioconductor-uri "DepecheR" version))
6389 "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
6390 (properties `((upstream-name . "DepecheR")))
6391 (build-system r-build-system)
6393 `(("r-beanplot" ,r-beanplot)
6394 ("r-dosnow" ,r-dosnow)
6395 ("r-dplyr" ,r-dplyr)
6397 ("r-foreach" ,r-foreach)
6398 ("r-ggplot2" ,r-ggplot2)
6399 ("r-gplots" ,r-gplots)
6401 ("r-matrixstats" ,r-matrixstats)
6402 ("r-mixomics" ,r-mixomics)
6403 ("r-moments" ,r-moments)
6405 ("r-rcppeigen" ,r-rcppeigen)
6406 ("r-reshape2" ,r-reshape2)
6407 ("r-robustbase" ,r-robustbase)
6408 ("r-viridis" ,r-viridis)))
6410 `(("r-knitr" ,r-knitr)))
6411 (home-page "https://bioconductor.org/packages/DepecheR/")
6412 (synopsis "Identify traits of clusters in high-dimensional entities")
6414 "The purpose of this package is to identify traits in a dataset that can
6415 separate groups. This is done on two levels. First, clustering is performed,
6416 using an implementation of sparse K-means. Secondly, the generated clusters
6417 are used to predict outcomes of groups of individuals based on their
6418 distribution of observations in the different clusters. As certain clusters
6419 with separating information will be identified, and these clusters are defined
6420 by a sparse number of variables, this method can reduce the complexity of
6421 data, to only emphasize the data that actually matters.")
6422 (license license:expat)))
6424 (define-public r-rcistarget
6426 (name "r-rcistarget")
6431 (uri (bioconductor-uri "RcisTarget" version))
6434 "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
6435 (properties `((upstream-name . "RcisTarget")))
6436 (build-system r-build-system)
6438 `(("r-aucell" ,r-aucell)
6439 ("r-biocgenerics" ,r-biocgenerics)
6440 ("r-data-table" ,r-data-table)
6441 ("r-feather" ,r-feather)
6442 ("r-gseabase" ,r-gseabase)
6443 ("r-r-utils" ,r-r-utils)
6444 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6446 `(("r-knitr" ,r-knitr)))
6447 (home-page "https://aertslab.org/#scenic")
6448 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6450 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6451 over-represented on a gene list. In a first step, RcisTarget selects DNA
6452 motifs that are significantly over-represented in the surroundings of the
6453 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6454 achieved by using a database that contains genome-wide cross-species rankings
6455 for each motif. The motifs that are then annotated to TFs and those that have
6456 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6457 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6458 genes in the gene-set that are ranked above the leading edge).")
6459 (license license:gpl3)))
6461 (define-public r-cicero
6468 (uri (bioconductor-uri "cicero" version))
6471 "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
6472 (build-system r-build-system)
6474 `(("r-assertthat" ,r-assertthat)
6475 ("r-biobase" ,r-biobase)
6476 ("r-biocgenerics" ,r-biocgenerics)
6477 ("r-data-table" ,r-data-table)
6478 ("r-dplyr" ,r-dplyr)
6480 ("r-genomicranges" ,r-genomicranges)
6481 ("r-ggplot2" ,r-ggplot2)
6482 ("r-glasso" ,r-glasso)
6484 ("r-igraph" ,r-igraph)
6485 ("r-iranges" ,r-iranges)
6486 ("r-matrix" ,r-matrix)
6487 ("r-monocle" ,r-monocle)
6489 ("r-reshape2" ,r-reshape2)
6490 ("r-s4vectors" ,r-s4vectors)
6491 ("r-stringi" ,r-stringi)
6492 ("r-stringr" ,r-stringr)
6493 ("r-tibble" ,r-tibble)
6494 ("r-tidyr" ,r-tidyr)
6495 ("r-vgam" ,r-vgam)))
6497 `(("r-knitr" ,r-knitr)))
6498 (home-page "https://bioconductor.org/packages/cicero/")
6499 (synopsis "Predict cis-co-accessibility from single-cell data")
6501 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6502 accessibility data. It also extends the monocle package for use in chromatin
6503 accessibility data.")
6504 (license license:expat)))
6506 ;; This is the latest commit on the "monocle3" branch.
6507 (define-public r-cicero-monocle3
6508 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6510 (package (inherit r-cicero)
6511 (name "r-cicero-monocle3")
6512 (version (git-version "1.3.2" revision commit))
6517 (url "https://github.com/cole-trapnell-lab/cicero-release")
6519 (file-name (git-file-name name version))
6522 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6524 `(("r-monocle3" ,r-monocle3)
6525 ,@(alist-delete "r-monocle"
6526 (package-propagated-inputs r-cicero)))))))
6528 (define-public r-cistopic
6529 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6533 (version (git-version "0.2.1" revision commit))
6538 (url "https://github.com/aertslab/cisTopic")
6540 (file-name (git-file-name name version))
6543 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6544 (build-system r-build-system)
6546 `(("r-aucell" ,r-aucell)
6547 ("r-data-table" ,r-data-table)
6548 ("r-dplyr" ,r-dplyr)
6549 ("r-dosnow" ,r-dosnow)
6551 ("r-feather" ,r-feather)
6552 ("r-fitdistrplus" ,r-fitdistrplus)
6553 ("r-genomicranges" ,r-genomicranges)
6554 ("r-ggplot2" ,r-ggplot2)
6556 ("r-matrix" ,r-matrix)
6558 ("r-rcistarget" ,r-rcistarget)
6559 ("r-rtracklayer" ,r-rtracklayer)
6560 ("r-s4vectors" ,r-s4vectors)))
6561 (home-page "https://github.com/aertslab/cisTopic")
6562 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6564 "The sparse nature of single cell epigenomics data can be overruled using
6565 probabilistic modelling methods such as @dfn{Latent Dirichlet
6566 Allocation} (LDA). This package allows the probabilistic modelling of
6567 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6568 includes functionalities to identify cell states based on the contribution of
6569 cisTopics and explore the nature and regulatory proteins driving them.")
6570 (license license:gpl3))))
6572 (define-public r-genie3
6579 (uri (bioconductor-uri "GENIE3" version))
6582 "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
6583 (properties `((upstream-name . "GENIE3")))
6584 (build-system r-build-system)
6585 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6587 `(("r-knitr" ,r-knitr)))
6588 (home-page "https://bioconductor.org/packages/GENIE3")
6589 (synopsis "Gene network inference with ensemble of trees")
6591 "This package implements the GENIE3 algorithm for inferring gene
6592 regulatory networks from expression data.")
6593 (license license:gpl2+)))
6595 (define-public r-roc
6602 (uri (bioconductor-uri "ROC" version))
6605 "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
6606 (properties `((upstream-name . "ROC")))
6607 (build-system r-build-system)
6609 `(("r-knitr" ,r-knitr)))
6610 (home-page "https://www.bioconductor.org/packages/ROC/")
6611 (synopsis "Utilities for ROC curves")
6613 "This package provides utilities for @dfn{Receiver Operating
6614 Characteristic} (ROC) curves, with a focus on micro arrays.")
6615 (license license:artistic2.0)))
6617 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6619 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6624 (uri (bioconductor-uri
6625 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6626 version 'annotation))
6629 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6632 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6633 (build-system r-build-system)
6634 (propagated-inputs `(("r-minfi" ,r-minfi)))
6636 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6637 (synopsis "Annotation for Illumina's 450k methylation arrays")
6639 "This package provides manifests and annotation for Illumina's 450k array
6641 (license license:artistic2.0)))
6643 (define-public r-watermelon
6645 (name "r-watermelon")
6650 (uri (bioconductor-uri "wateRmelon" version))
6653 "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
6654 (properties `((upstream-name . "wateRmelon")))
6655 (build-system r-build-system)
6657 `(("r-biobase" ,r-biobase)
6658 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6659 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6660 ("r-illuminaio" ,r-illuminaio)
6661 ("r-limma" ,r-limma)
6663 ("r-matrixstats" ,r-matrixstats)
6664 ("r-methylumi" ,r-methylumi)
6666 (home-page "https://bioconductor.org/packages/wateRmelon/")
6667 (synopsis "Illumina 450 methylation array normalization and metrics")
6669 "The standard index of DNA methylation (beta) is computed from methylated
6670 and unmethylated signal intensities. Betas calculated from raw signal
6671 intensities perform well, but using 11 methylomic datasets we demonstrate that
6672 quantile normalization methods produce marked improvement. The commonly used
6673 procedure of normalizing betas is inferior to the separate normalization of M
6674 and U, and it is also advantageous to normalize Type I and Type II assays
6675 separately. This package provides 15 flavours of betas and three performance
6676 metrics, with methods for objects produced by the @code{methylumi} and
6677 @code{minfi} packages.")
6678 (license license:gpl3)))
6680 (define-public r-gdsfmt
6687 (uri (bioconductor-uri "gdsfmt" version))
6690 "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
6691 (modules '((guix build utils)))
6692 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6693 ;; them and link with system libraries instead.
6696 (for-each delete-file-recursively
6700 (substitute* "src/Makevars"
6701 (("all: \\$\\(SHLIB\\)") "all:")
6702 (("\\$\\(SHLIB\\): liblzma.a") "")
6703 (("(ZLIB|LZ4)/.*") "")
6704 (("CoreArray/dVLIntGDS.cpp.*")
6705 "CoreArray/dVLIntGDS.cpp")
6706 (("CoreArray/dVLIntGDS.o.*")
6707 "CoreArray/dVLIntGDS.o")
6708 (("PKG_LIBS = ./liblzma.a")
6709 "PKG_LIBS = -llz4"))
6710 (substitute* "src/CoreArray/dStream.h"
6711 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6712 (string-append "include <" header ">")))
6714 (properties `((upstream-name . "gdsfmt")))
6715 (build-system r-build-system)
6721 `(("r-knitr" ,r-knitr)))
6722 (home-page "http://corearray.sourceforge.net/")
6724 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6726 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6727 Data Structure} (GDS) data files, which are portable across platforms with
6728 hierarchical structure to store multiple scalable array-oriented data sets
6729 with metadata information. It is suited for large-scale datasets, especially
6730 for data which are much larger than the available random-access memory. The
6731 @code{gdsfmt} package offers efficient operations specifically designed for
6732 integers of less than 8 bits, since a diploid genotype, like
6733 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6734 byte. Data compression and decompression are available with relatively
6735 efficient random access. It is also allowed to read a GDS file in parallel
6736 with multiple R processes supported by the package @code{parallel}.")
6737 (license license:lgpl3)))
6739 (define-public r-bigmelon
6746 (uri (bioconductor-uri "bigmelon" version))
6749 "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
6750 (properties `((upstream-name . "bigmelon")))
6751 (build-system r-build-system)
6753 `(("r-biobase" ,r-biobase)
6754 ("r-biocgenerics" ,r-biocgenerics)
6755 ("r-gdsfmt" ,r-gdsfmt)
6756 ("r-geoquery" ,r-geoquery)
6757 ("r-methylumi" ,r-methylumi)
6758 ("r-minfi" ,r-minfi)
6759 ("r-watermelon" ,r-watermelon)))
6760 (home-page "https://bioconductor.org/packages/bigmelon/")
6761 (synopsis "Illumina methylation array analysis for large experiments")
6763 "This package provides methods for working with Illumina arrays using the
6764 @code{gdsfmt} package.")
6765 (license license:gpl3)))
6767 (define-public r-seqbias
6774 (uri (bioconductor-uri "seqbias" version))
6777 "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
6778 (properties `((upstream-name . "seqbias")))
6779 (build-system r-build-system)
6781 `(("r-biostrings" ,r-biostrings)
6782 ("r-genomicranges" ,r-genomicranges)
6783 ("r-rhtslib" ,r-rhtslib)))
6785 `(("zlib" ,zlib))) ; This comes from rhtslib.
6786 (home-page "https://bioconductor.org/packages/seqbias/")
6787 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6789 "This package implements a model of per-position sequencing bias in
6790 high-throughput sequencing data using a simple Bayesian network, the structure
6791 and parameters of which are trained on a set of aligned reads and a reference
6793 (license license:lgpl3)))
6795 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6797 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6801 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6802 version 'annotation))
6805 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6806 (build-system r-build-system)
6807 ;; As this package provides little more than a very large data file it
6808 ;; doesn't make sense to build substitutes.
6809 (arguments `(#:substitutable? #f))
6811 `(("r-biocgenerics" ,r-biocgenerics)
6812 ("r-s4vectors" ,r-s4vectors)
6813 ("r-iranges" ,r-iranges)
6814 ("r-genomeinfodb" ,r-genomeinfodb)
6815 ("r-genomicranges" ,r-genomicranges)
6816 ("r-bsgenome" ,r-bsgenome)
6817 ("r-biostrings" ,r-biostrings)))
6819 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6820 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6821 (description "This package provides SNP locations and alleles for Homo
6822 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6823 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6824 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6825 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6826 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6827 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6828 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6829 correct position but this injection will exclude chrM (i.e. nothing will be
6830 injected in that sequence).")
6831 (license license:artistic2.0)))
6833 (define-public r-reqon
6840 (uri (bioconductor-uri "ReQON" version))
6843 "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
6844 (properties `((upstream-name . "ReQON")))
6845 (build-system r-build-system)
6847 `(("r-rjava" ,r-rjava)
6848 ("r-rsamtools" ,r-rsamtools)
6849 ("r-seqbias" ,r-seqbias)))
6850 (home-page "https://bioconductor.org/packages/ReQON/")
6851 (synopsis "Recalibrating quality of nucleotides")
6853 "This package provides an implementation of an algorithm for
6854 recalibrating the base quality scores for aligned sequencing data in BAM
6856 (license license:gpl2)))
6858 (define-public r-wavcluster
6860 (name "r-wavcluster")
6865 (uri (bioconductor-uri "wavClusteR" version))
6868 "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
6869 (properties `((upstream-name . "wavClusteR")))
6870 (build-system r-build-system)
6872 `(("r-biocgenerics" ,r-biocgenerics)
6873 ("r-biostrings" ,r-biostrings)
6874 ("r-foreach" ,r-foreach)
6875 ("r-genomicfeatures" ,r-genomicfeatures)
6876 ("r-genomicranges" ,r-genomicranges)
6877 ("r-ggplot2" ,r-ggplot2)
6878 ("r-hmisc" ,r-hmisc)
6879 ("r-iranges" ,r-iranges)
6880 ("r-mclust" ,r-mclust)
6881 ("r-rsamtools" ,r-rsamtools)
6882 ("r-rtracklayer" ,r-rtracklayer)
6883 ("r-s4vectors" ,r-s4vectors)
6884 ("r-seqinr" ,r-seqinr)
6885 ("r-stringr" ,r-stringr)
6886 ("r-wmtsa" ,r-wmtsa)))
6888 `(("r-knitr" ,r-knitr)))
6889 (home-page "https://bioconductor.org/packages/wavClusteR/")
6890 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6892 "This package provides an integrated pipeline for the analysis of
6893 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6894 sequencing errors, SNPs and additional non-experimental sources by a non-
6895 parametric mixture model. The protein binding sites (clusters) are then
6896 resolved at high resolution and cluster statistics are estimated using a
6897 rigorous Bayesian framework. Post-processing of the results, data export for
6898 UCSC genome browser visualization and motif search analysis are provided. In
6899 addition, the package integrates RNA-Seq data to estimate the False
6900 Discovery Rate of cluster detection. Key functions support parallel multicore
6901 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6902 be applied to the analysis of other NGS data obtained from experimental
6903 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6904 (license license:gpl2)))
6906 (define-public r-timeseriesexperiment
6908 (name "r-timeseriesexperiment")
6913 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6916 "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
6918 `((upstream-name . "TimeSeriesExperiment")))
6919 (build-system r-build-system)
6921 `(("r-deseq2" ,r-deseq2)
6922 ("r-dplyr" ,r-dplyr)
6923 ("r-dynamictreecut" ,r-dynamictreecut)
6924 ("r-edger" ,r-edger)
6925 ("r-ggplot2" ,r-ggplot2)
6926 ("r-hmisc" ,r-hmisc)
6927 ("r-limma" ,r-limma)
6928 ("r-magrittr" ,r-magrittr)
6929 ("r-proxy" ,r-proxy)
6930 ("r-s4vectors" ,r-s4vectors)
6931 ("r-summarizedexperiment" ,r-summarizedexperiment)
6932 ("r-tibble" ,r-tibble)
6933 ("r-tidyr" ,r-tidyr)
6934 ("r-vegan" ,r-vegan)
6935 ("r-viridis" ,r-viridis)))
6937 `(("r-knitr" ,r-knitr)))
6938 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6939 (synopsis "Analysis for short time-series data")
6941 "This package is a visualization and analysis toolbox for short time
6942 course data which includes dimensionality reduction, clustering, two-sample
6943 differential expression testing and gene ranking techniques. The package also
6944 provides methods for retrieving enriched pathways.")
6945 (license license:lgpl3+)))
6947 (define-public r-variantfiltering
6949 (name "r-variantfiltering")
6954 (uri (bioconductor-uri "VariantFiltering" version))
6957 "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
6959 `((upstream-name . "VariantFiltering")))
6960 (build-system r-build-system)
6962 `(("r-annotationdbi" ,r-annotationdbi)
6963 ("r-biobase" ,r-biobase)
6964 ("r-biocgenerics" ,r-biocgenerics)
6965 ("r-biocparallel" ,r-biocparallel)
6966 ("r-biostrings" ,r-biostrings)
6967 ("r-bsgenome" ,r-bsgenome)
6969 ("r-genomeinfodb" ,r-genomeinfodb)
6970 ("r-genomicfeatures" ,r-genomicfeatures)
6971 ("r-genomicranges" ,r-genomicranges)
6972 ("r-genomicscores" ,r-genomicscores)
6973 ("r-graph" ,r-graph)
6975 ("r-iranges" ,r-iranges)
6977 ("r-rsamtools" ,r-rsamtools)
6978 ("r-s4vectors" ,r-s4vectors)
6979 ("r-shiny" ,r-shiny)
6980 ("r-shinyjs" ,r-shinyjs)
6981 ("r-shinythemes" ,r-shinythemes)
6982 ("r-shinytree" ,r-shinytree)
6983 ("r-summarizedexperiment" ,r-summarizedexperiment)
6984 ("r-variantannotation" ,r-variantannotation)
6985 ("r-xvector" ,r-xvector)))
6986 (home-page "https://github.com/rcastelo/VariantFiltering")
6987 (synopsis "Filtering of coding and non-coding genetic variants")
6989 "Filter genetic variants using different criteria such as inheritance
6990 model, amino acid change consequence, minor allele frequencies across human
6991 populations, splice site strength, conservation, etc.")
6992 (license license:artistic2.0)))
6994 (define-public r-genomegraphs
6996 (name "r-genomegraphs")
7001 (uri (bioconductor-uri "GenomeGraphs" version))
7004 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7005 (properties `((upstream-name . "GenomeGraphs")))
7006 (build-system r-build-system)
7008 `(("r-biomart" ,r-biomart)))
7009 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7010 (synopsis "Plotting genomic information from Ensembl")
7012 "Genomic data analyses requires integrated visualization of known genomic
7013 information and new experimental data. GenomeGraphs uses the biomaRt package
7014 to perform live annotation queries to Ensembl and translates this to e.g.
7015 gene/transcript structures in viewports of the grid graphics package. This
7016 results in genomic information plotted together with your data. Another
7017 strength of GenomeGraphs is to plot different data types such as array CGH,
7018 gene expression, sequencing and other data, together in one plot using the
7019 same genome coordinate system.")
7020 (license license:artistic2.0)))
7022 (define-public r-wavetiling
7024 (name "r-wavetiling")
7029 (uri (bioconductor-uri "waveTiling" version))
7032 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7033 (properties `((upstream-name . "waveTiling")))
7034 (build-system r-build-system)
7036 `(("r-affy" ,r-affy)
7037 ("r-biobase" ,r-biobase)
7038 ("r-biostrings" ,r-biostrings)
7039 ("r-genomegraphs" ,r-genomegraphs)
7040 ("r-genomicranges" ,r-genomicranges)
7041 ("r-iranges" ,r-iranges)
7042 ("r-oligo" ,r-oligo)
7043 ("r-oligoclasses" ,r-oligoclasses)
7044 ("r-preprocesscore" ,r-preprocesscore)
7045 ("r-waveslim" ,r-waveslim)))
7046 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7047 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7049 "This package is designed to conduct transcriptome analysis for tiling
7050 arrays based on fast wavelet-based functional models.")
7051 (license license:gpl2+)))
7053 (define-public r-variancepartition
7055 (name "r-variancepartition")
7060 (uri (bioconductor-uri "variancePartition" version))
7063 "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
7065 `((upstream-name . "variancePartition")))
7066 (build-system r-build-system)
7068 `(("r-biobase" ,r-biobase)
7069 ("r-biocparallel" ,r-biocparallel)
7070 ("r-colorramps" ,r-colorramps)
7071 ("r-doparallel" ,r-doparallel)
7072 ("r-foreach" ,r-foreach)
7073 ("r-ggplot2" ,r-ggplot2)
7074 ("r-gplots" ,r-gplots)
7075 ("r-iterators" ,r-iterators)
7076 ("r-limma" ,r-limma)
7078 ("r-lmertest" ,r-lmertest)
7080 ("r-pbkrtest" ,r-pbkrtest)
7081 ("r-progress" ,r-progress)
7082 ("r-reshape2" ,r-reshape2)
7083 ("r-scales" ,r-scales)))
7085 `(("r-knitr" ,r-knitr)))
7086 (home-page "https://bioconductor.org/packages/variancePartition/")
7087 (synopsis "Analyze variation in gene expression experiments")
7089 "This is a package providing tools to quantify and interpret multiple
7090 sources of biological and technical variation in gene expression experiments.
7091 It uses a linear mixed model to quantify variation in gene expression
7092 attributable to individual, tissue, time point, or technical variables. The
7093 package includes dream differential expression analysis for repeated
7095 (license license:gpl2+)))
7097 (define-public r-htqpcr
7104 (uri (bioconductor-uri "HTqPCR" version))
7107 "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
7108 (properties `((upstream-name . "HTqPCR")))
7109 (build-system r-build-system)
7111 `(("r-affy" ,r-affy)
7112 ("r-biobase" ,r-biobase)
7113 ("r-gplots" ,r-gplots)
7114 ("r-limma" ,r-limma)
7115 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7116 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7117 "groups/bertone/software/HTqPCR.pdf"))
7118 (synopsis "Automated analysis of high-throughput qPCR data")
7120 "Analysis of Ct values from high throughput quantitative real-time
7121 PCR (qPCR) assays across multiple conditions or replicates. The input data
7122 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7123 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7124 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7125 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7126 loading, quality assessment, normalization, visualization and parametric or
7127 non-parametric testing for statistical significance in Ct values between
7128 features (e.g. genes, microRNAs).")
7129 (license license:artistic2.0)))
7131 (define-public r-unifiedwmwqpcr
7133 (name "r-unifiedwmwqpcr")
7138 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7141 "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
7143 `((upstream-name . "unifiedWMWqPCR")))
7144 (build-system r-build-system)
7146 `(("r-biocgenerics" ,r-biocgenerics)
7147 ("r-htqpcr" ,r-htqpcr)))
7148 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7149 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7151 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7152 data. This modified test allows for testing differential expression in qPCR
7154 (license license:gpl2+)))
7156 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7158 (define-public r-activedriverwgs
7160 (name "r-activedriverwgs")
7165 (uri (cran-uri "ActiveDriverWGS" version))
7168 "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1"))))
7170 `((upstream-name . "ActiveDriverWGS")))
7171 (build-system r-build-system)
7173 `(("r-biostrings" ,r-biostrings)
7174 ("r-bsgenome" ,r-bsgenome)
7175 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7176 ("r-genomeinfodb" ,r-genomeinfodb)
7177 ("r-genomicranges" ,r-genomicranges)
7178 ("r-iranges" ,r-iranges)
7180 ("r-s4vectors" ,r-s4vectors)))
7181 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7182 (synopsis "Driver discovery tool for cancer whole genomes")
7184 "This package provides a method for finding an enrichment of cancer
7185 simple somatic mutations (SNVs and Indels) in functional elements across the
7186 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7187 using whole genome sequencing data.")
7188 (license license:gpl3)))
7190 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7192 (define-public r-activepathways
7194 (name "r-activepathways")
7199 (uri (cran-uri "ActivePathways" version))
7202 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7204 `((upstream-name . "ActivePathways")))
7205 (build-system r-build-system)
7207 `(("r-data-table" ,r-data-table)
7208 ("r-ggplot2" ,r-ggplot2)))
7210 `(("r-knitr" ,r-knitr)))
7211 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7212 (synopsis "Multivariate pathway enrichment analysis")
7214 "This package represents an integrative method of analyzing multi omics
7215 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7216 uses a statistical data fusion approach, rationalizes contributing evidence
7217 and highlights associated genes, improving systems-level understanding of
7218 cellular organization in health and disease.")
7219 (license license:gpl3)))
7221 (define-public r-bgmix
7228 (uri (bioconductor-uri "BGmix" version))
7231 "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
7232 (properties `((upstream-name . "BGmix")))
7233 (build-system r-build-system)
7235 `(("r-kernsmooth" ,r-kernsmooth)))
7236 (home-page "https://bioconductor.org/packages/BGmix/")
7237 (synopsis "Bayesian models for differential gene expression")
7239 "This package provides fully Bayesian mixture models for differential
7241 (license license:gpl2)))
7243 (define-public r-bgx
7250 (uri (bioconductor-uri "bgx" version))
7253 "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
7254 (properties `((upstream-name . "bgx")))
7255 (build-system r-build-system)
7257 `(("r-affy" ,r-affy)
7258 ("r-biobase" ,r-biobase)
7259 ("r-gcrma" ,r-gcrma)
7260 ("r-rcpp" ,r-rcpp)))
7261 (home-page "https://bioconductor.org/packages/bgx/")
7262 (synopsis "Bayesian gene expression")
7264 "This package provides tools for Bayesian integrated analysis of
7265 Affymetrix GeneChips.")
7266 (license license:gpl2)))
7268 (define-public r-bhc
7275 (uri (bioconductor-uri "BHC" version))
7278 "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
7279 (properties `((upstream-name . "BHC")))
7280 (build-system r-build-system)
7281 (home-page "https://bioconductor.org/packages/BHC/")
7282 (synopsis "Bayesian hierarchical clustering")
7284 "The method implemented in this package performs bottom-up hierarchical
7285 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7286 in the data and Bayesian model selection to decide at each step which clusters
7287 to merge. This avoids several limitations of traditional methods, for example
7288 how many clusters there should be and how to choose a principled distance
7289 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7290 categories) or time-series data. This version also includes a randomised
7291 algorithm which is more efficient for larger data sets.")
7292 (license license:gpl3)))
7294 (define-public r-bicare
7301 (uri (bioconductor-uri "BicARE" version))
7304 "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
7305 (properties `((upstream-name . "BicARE")))
7306 (build-system r-build-system)
7308 `(("r-biobase" ,r-biobase)
7309 ("r-gseabase" ,r-gseabase)
7310 ("r-multtest" ,r-multtest)))
7311 (home-page "http://bioinfo.curie.fr")
7312 (synopsis "Biclustering analysis and results exploration")
7314 "This is a package for biclustering analysis and exploration of
7316 (license license:gpl2)))
7318 (define-public r-bifet
7325 (uri (bioconductor-uri "BiFET" version))
7328 "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
7329 (properties `((upstream-name . "BiFET")))
7330 (build-system r-build-system)
7332 `(("r-genomicranges" ,r-genomicranges)
7333 ("r-poibin" ,r-poibin)))
7335 `(("r-knitr" ,r-knitr)))
7336 (home-page "https://bioconductor.org/packages/BiFET")
7337 (synopsis "Bias-free footprint enrichment test")
7339 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7340 over-represented in target regions compared to background regions after
7341 correcting for the bias arising from the imbalance in read counts and GC
7342 contents between the target and background regions. For a given TF k, BiFET
7343 tests the null hypothesis that the target regions have the same probability of
7344 having footprints for the TF k as the background regions while correcting for
7345 the read count and GC content bias.")
7346 (license license:gpl3)))
7348 (define-public r-rsbml
7355 (uri (bioconductor-uri "rsbml" version))
7358 "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
7359 (properties `((upstream-name . "rsbml")))
7360 (build-system r-build-system)
7362 `(("libsbml" ,libsbml)
7365 `(("r-biocgenerics" ,r-biocgenerics)
7366 ("r-graph" ,r-graph)))
7368 `(("pkg-config" ,pkg-config)))
7369 (home-page "http://www.sbml.org")
7370 (synopsis "R support for SBML")
7372 "This package provides an R interface to libsbml for SBML parsing,
7373 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7374 (license license:artistic2.0)))
7376 (define-public r-hypergraph
7378 (name "r-hypergraph")
7383 (uri (bioconductor-uri "hypergraph" version))
7386 "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
7387 (properties `((upstream-name . "hypergraph")))
7388 (build-system r-build-system)
7390 `(("r-graph" ,r-graph)))
7391 (home-page "https://bioconductor.org/packages/hypergraph")
7392 (synopsis "Hypergraph data structures")
7394 "This package implements some simple capabilities for representing and
7395 manipulating hypergraphs.")
7396 (license license:artistic2.0)))
7398 (define-public r-hyperdraw
7400 (name "r-hyperdraw")
7405 (uri (bioconductor-uri "hyperdraw" version))
7408 "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
7409 (properties `((upstream-name . "hyperdraw")))
7410 (build-system r-build-system)
7411 (inputs `(("graphviz" ,graphviz)))
7413 `(("r-graph" ,r-graph)
7414 ("r-hypergraph" ,r-hypergraph)
7415 ("r-rgraphviz" ,r-rgraphviz)))
7416 (home-page "https://bioconductor.org/packages/hyperdraw")
7417 (synopsis "Visualizing hypergraphs")
7419 "This package provides functions for visualizing hypergraphs.")
7420 (license license:gpl2+)))
7422 (define-public r-biggr
7429 (uri (bioconductor-uri "BiGGR" version))
7432 "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
7433 (properties `((upstream-name . "BiGGR")))
7434 (build-system r-build-system)
7436 `(("r-hyperdraw" ,r-hyperdraw)
7437 ("r-hypergraph" ,r-hypergraph)
7439 ("r-limsolve" ,r-limsolve)
7440 ("r-rsbml" ,r-rsbml)
7441 ("r-stringr" ,r-stringr)))
7442 (home-page "https://bioconductor.org/packages/BiGGR/")
7443 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7445 "This package provides an interface to simulate metabolic reconstruction
7446 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7447 reconstruction databases. The package facilitates @dfn{flux balance
7448 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7449 networks and estimated fluxes can be visualized with hypergraphs.")
7450 (license license:gpl3+)))
7452 (define-public r-bigmemoryextras
7454 (name "r-bigmemoryextras")
7459 (uri (bioconductor-uri "bigmemoryExtras" version))
7462 "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
7464 `((upstream-name . "bigmemoryExtras")))
7465 (build-system r-build-system)
7467 `(("r-bigmemory" ,r-bigmemory)))
7469 `(("r-knitr" ,r-knitr)))
7470 (home-page "https://github.com/phaverty/bigmemoryExtras")
7471 (synopsis "Extension of the bigmemory package")
7473 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7474 safety and convenience features to the @code{filebacked.big.matrix} class from
7475 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7476 monitoring and gracefully restoring the connection to on-disk data and it also
7477 protects against accidental data modification with a filesystem-based
7478 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7479 classes as @code{assayData} matrices within the @code{Biobase} package's
7480 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7481 related to attaching to, and indexing into, file-backed matrices with
7482 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7483 a file-backed matrix with factor properties.")
7484 (license license:artistic2.0)))
7486 (define-public r-bigpint
7493 (uri (bioconductor-uri "bigPint" version))
7496 "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
7497 (properties `((upstream-name . "bigPint")))
7498 (build-system r-build-system)
7500 `(("r-delayedarray" ,r-delayedarray)
7501 ("r-dplyr" ,r-dplyr)
7502 ("r-ggally" ,r-ggally)
7503 ("r-ggplot2" ,r-ggplot2)
7504 ("r-gridextra" ,r-gridextra)
7505 ("r-hexbin" ,r-hexbin)
7506 ("r-hmisc" ,r-hmisc)
7507 ("r-htmlwidgets" ,r-htmlwidgets)
7508 ("r-plotly" ,r-plotly)
7510 ("r-rcolorbrewer" ,r-rcolorbrewer)
7511 ("r-reshape" ,r-reshape)
7512 ("r-shiny" ,r-shiny)
7513 ("r-shinycssloaders" ,r-shinycssloaders)
7514 ("r-shinydashboard" ,r-shinydashboard)
7515 ("r-stringr" ,r-stringr)
7516 ("r-summarizedexperiment" ,r-summarizedexperiment)
7517 ("r-tidyr" ,r-tidyr)))
7519 `(("r-knitr" ,r-knitr)))
7520 (home-page "https://github.com/lindsayrutter/bigPint")
7521 (synopsis "Big multivariate data plotted interactively")
7523 "This package provides methods for visualizing large multivariate
7524 datasets using static and interactive scatterplot matrices, parallel
7525 coordinate plots, volcano plots, and litre plots. It includes examples for
7526 visualizing RNA-sequencing datasets and differentially expressed genes.")
7527 (license license:gpl3)))
7529 (define-public r-chemminer
7531 (name "r-chemminer")
7536 (uri (bioconductor-uri "ChemmineR" version))
7539 "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
7540 (properties `((upstream-name . "ChemmineR")))
7541 (build-system r-build-system)
7543 `(("r-base64enc" ,r-base64enc)
7545 ("r-biocgenerics" ,r-biocgenerics)
7547 ("r-digest" ,r-digest)
7549 ("r-ggplot2" ,r-ggplot2)
7550 ("r-gridextra" ,r-gridextra)
7553 ("r-rcurl" ,r-rcurl)
7554 ("r-rjson" ,r-rjson)
7555 ("r-rsvg" ,r-rsvg)))
7557 `(("r-knitr" ,r-knitr)))
7558 (home-page "https://github.com/girke-lab/ChemmineR")
7559 (synopsis "Cheminformatics toolkit for R")
7561 "ChemmineR is a cheminformatics package for analyzing drug-like small
7562 molecule data in R. It contains functions for efficient processing of large
7563 numbers of molecules, physicochemical/structural property predictions,
7564 structural similarity searching, classification and clustering of compound
7565 libraries with a wide spectrum of algorithms. In addition, it offers
7566 visualization functions for compound clustering results and chemical
7568 (license license:artistic2.0)))
7570 (define-public r-bioassayr
7572 (name "r-bioassayr")
7577 (uri (bioconductor-uri "bioassayR" version))
7580 "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
7581 (properties `((upstream-name . "bioassayR")))
7582 (build-system r-build-system)
7584 `(("r-biocgenerics" ,r-biocgenerics)
7585 ("r-chemminer" ,r-chemminer)
7587 ("r-matrix" ,r-matrix)
7588 ("r-rjson" ,r-rjson)
7589 ("r-rsqlite" ,r-rsqlite)
7592 `(("r-knitr" ,r-knitr)))
7593 (home-page "https://github.com/TylerBackman/bioassayR")
7594 (synopsis "Cross-target analysis of small molecule bioactivity")
7596 "bioassayR is a computational tool that enables simultaneous analysis of
7597 thousands of bioassay experiments performed over a diverse set of compounds
7598 and biological targets. Unique features include support for large-scale
7599 cross-target analyses of both public and custom bioassays, generation of
7600 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7601 preloaded database that provides access to a substantial portion of publicly
7602 available bioactivity data.")
7603 (license license:artistic2.0)))
7605 (define-public r-biobroom
7612 (uri (bioconductor-uri "biobroom" version))
7615 "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
7616 (properties `((upstream-name . "biobroom")))
7617 (build-system r-build-system)
7619 `(("r-biobase" ,r-biobase)
7620 ("r-broom" ,r-broom)
7621 ("r-dplyr" ,r-dplyr)
7622 ("r-tidyr" ,r-tidyr)))
7624 `(("r-knitr" ,r-knitr)))
7625 (home-page "https://github.com/StoreyLab/biobroom")
7626 (synopsis "Turn Bioconductor objects into tidy data frames")
7628 "This package contains methods for converting standard objects
7629 constructed by bioinformatics packages, especially those in Bioconductor, and
7630 converting them to @code{tidy} data. It thus serves as a complement to the
7631 @code{broom} package, and follows the same tidy, augment, glance division of
7632 tidying methods. Tidying data makes it easy to recombine, reshape and
7633 visualize bioinformatics analyses.")
7634 ;; Any version of the LGPL.
7635 (license license:lgpl3+)))
7637 (define-public r-graphite
7644 (uri (bioconductor-uri "graphite" version))
7647 "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
7648 (properties `((upstream-name . "graphite")))
7649 (build-system r-build-system)
7651 `(("r-annotationdbi" ,r-annotationdbi)
7652 ("r-checkmate" ,r-checkmate)
7653 ("r-graph" ,r-graph)
7655 ("r-rappdirs" ,r-rappdirs)))
7656 (home-page "https://bioconductor.org/packages/graphite/")
7657 (synopsis "Networks from pathway databases")
7659 "Graphite provides networks derived from eight public pathway databases,
7660 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7662 (license license:agpl3+)))
7664 (define-public r-reactomepa
7666 (name "r-reactomepa")
7671 (uri (bioconductor-uri "ReactomePA" version))
7674 "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
7675 (properties `((upstream-name . "ReactomePA")))
7676 (build-system r-build-system)
7678 `(("r-annotationdbi" ,r-annotationdbi)
7680 ("r-enrichplot" ,r-enrichplot)
7681 ("r-ggplot2" ,r-ggplot2)
7682 ("r-ggraph" ,r-ggraph)
7683 ("r-graphite" ,r-graphite)
7684 ("r-igraph" ,r-igraph)
7685 ("r-reactome-db" ,r-reactome-db)))
7687 `(("r-knitr" ,r-knitr)))
7688 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7689 (synopsis "Reactome pathway analysis")
7691 "This package provides functions for pathway analysis based on the
7692 REACTOME pathway database. It implements enrichment analysis, gene set
7693 enrichment analysis and several functions for visualization.")
7694 (license license:gpl2)))
7696 (define-public r-ebarrays
7703 (uri (bioconductor-uri "EBarrays" version))
7706 "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
7707 (properties `((upstream-name . "EBarrays")))
7708 (build-system r-build-system)
7710 `(("r-biobase" ,r-biobase)
7711 ("r-cluster" ,r-cluster)
7712 ("r-lattice" ,r-lattice)))
7713 (home-page "https://bioconductor.org/packages/EBarrays/")
7714 (synopsis "Gene clustering and differential expression identification")
7716 "EBarrays provides tools for the analysis of replicated/unreplicated
7718 (license license:gpl2+)))
7720 (define-public r-bioccasestudies
7722 (name "r-bioccasestudies")
7727 (uri (bioconductor-uri "BiocCaseStudies" version))
7730 "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
7732 `((upstream-name . "BiocCaseStudies")))
7733 (build-system r-build-system)
7734 (propagated-inputs `(("r-biobase" ,r-biobase)))
7735 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7736 (synopsis "Support for the case studies monograph")
7738 "This package provides software and data to support the case studies
7740 (license license:artistic2.0)))
7742 (define-public r-biocgraph
7744 (name "r-biocgraph")
7749 (uri (bioconductor-uri "biocGraph" version))
7752 "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
7753 (properties `((upstream-name . "biocGraph")))
7754 (build-system r-build-system)
7756 `(("r-biocgenerics" ,r-biocgenerics)
7757 ("r-geneplotter" ,r-geneplotter)
7758 ("r-graph" ,r-graph)
7759 ("r-rgraphviz" ,r-rgraphviz)))
7760 (home-page "https://bioconductor.org/packages/biocGraph/")
7761 (synopsis "Graph examples and use cases in Bioinformatics")
7763 "This package provides examples and code that make use of the
7764 different graph related packages produced by Bioconductor.")
7765 (license license:artistic2.0)))
7767 (define-public r-experimenthub
7769 (name "r-experimenthub")
7774 (uri (bioconductor-uri "ExperimentHub" version))
7777 "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
7778 (properties `((upstream-name . "ExperimentHub")))
7779 (build-system r-build-system)
7781 `(("r-annotationhub" ,r-annotationhub)
7782 ("r-biocfilecache" ,r-biocfilecache)
7783 ("r-biocgenerics" ,r-biocgenerics)
7784 ("r-biocmanager" ,r-biocmanager)
7786 ("r-rappdirs" ,r-rappdirs)
7787 ("r-s4vectors" ,r-s4vectors)))
7789 `(("r-knitr" ,r-knitr)))
7790 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7791 (synopsis "Client to access ExperimentHub resources")
7793 "This package provides a client for the Bioconductor ExperimentHub web
7794 resource. ExperimentHub provides a central location where curated data from
7795 experiments, publications or training courses can be accessed. Each resource
7796 has associated metadata, tags and date of modification. The client creates
7797 and manages a local cache of files retrieved enabling quick and reproducible
7799 (license license:artistic2.0)))
7801 (define-public r-multiassayexperiment
7803 (name "r-multiassayexperiment")
7808 (uri (bioconductor-uri "MultiAssayExperiment" version))
7811 "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
7813 `((upstream-name . "MultiAssayExperiment")))
7814 (build-system r-build-system)
7816 `(("r-biobase" ,r-biobase)
7817 ("r-biocgenerics" ,r-biocgenerics)
7818 ("r-genomicranges" ,r-genomicranges)
7819 ("r-iranges" ,r-iranges)
7820 ("r-s4vectors" ,r-s4vectors)
7821 ("r-summarizedexperiment" ,r-summarizedexperiment)
7822 ("r-tidyr" ,r-tidyr)))
7824 `(("r-knitr" ,r-knitr)))
7825 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7826 (synopsis "Integration of multi-omics experiments in Bioconductor")
7828 "MultiAssayExperiment harmonizes data management of multiple assays
7829 performed on an overlapping set of specimens. It provides a familiar
7830 Bioconductor user experience by extending concepts from
7831 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7832 classes for individual assays, and allowing subsetting by genomic ranges or
7834 (license license:artistic2.0)))
7836 (define-public r-bioconcotk
7838 (name "r-bioconcotk")
7843 (uri (bioconductor-uri "BiocOncoTK" version))
7846 "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
7847 (properties `((upstream-name . "BiocOncoTK")))
7848 (build-system r-build-system)
7850 `(("r-bigrquery" ,r-bigrquery)
7852 ("r-complexheatmap" ,r-complexheatmap)
7853 ("r-curatedtcgadata" ,r-curatedtcgadata)
7855 ("r-dplyr" ,r-dplyr)
7857 ("r-genomicfeatures" ,r-genomicfeatures)
7858 ("r-genomicranges" ,r-genomicranges)
7859 ("r-ggplot2" ,r-ggplot2)
7860 ("r-ggpubr" ,r-ggpubr)
7861 ("r-graph" ,r-graph)
7863 ("r-iranges" ,r-iranges)
7864 ("r-magrittr" ,r-magrittr)
7866 ("r-rgraphviz" ,r-rgraphviz)
7867 ("r-rjson" ,r-rjson)
7868 ("r-s4vectors" ,r-s4vectors)
7869 ("r-scales" ,r-scales)
7870 ("r-shiny" ,r-shiny)
7871 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7873 `(("r-knitr" ,r-knitr)))
7874 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7875 (synopsis "Bioconductor components for general cancer genomics")
7877 "The purpose of this package is to provide a central interface to various
7878 tools for genome-scale analysis of cancer studies.")
7879 (license license:artistic2.0)))
7881 (define-public r-biocor
7888 (uri (bioconductor-uri "BioCor" version))
7891 "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
7892 (properties `((upstream-name . "BioCor")))
7893 (build-system r-build-system)
7895 `(("r-biocparallel" ,r-biocparallel)
7896 ("r-gseabase" ,r-gseabase)
7897 ("r-matrix" ,r-matrix)))
7899 `(("r-knitr" ,r-knitr)))
7900 (home-page "https://llrs.github.io/BioCor/")
7901 (synopsis "Functional similarities")
7903 "This package provides tools to calculate functional similarities based
7904 on the pathways described on KEGG and REACTOME or in gene sets. These
7905 similarities can be calculated for pathways or gene sets, genes, or clusters
7906 and combined with other similarities. They can be used to improve networks,
7907 gene selection, testing relationships, and so on.")
7908 (license license:expat)))
7910 (define-public r-biocpkgtools
7912 (name "r-biocpkgtools")
7917 (uri (bioconductor-uri "BiocPkgTools" version))
7920 "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
7921 (properties `((upstream-name . "BiocPkgTools")))
7922 (build-system r-build-system)
7924 `(("r-biocfilecache" ,r-biocfilecache)
7925 ("r-biocmanager" ,r-biocmanager)
7926 ("r-biocviews" ,r-biocviews)
7927 ("r-dplyr" ,r-dplyr)
7930 ("r-graph" ,r-graph)
7931 ("r-htmltools" ,r-htmltools)
7932 ("r-htmlwidgets" ,r-htmlwidgets)
7934 ("r-igraph" ,r-igraph)
7935 ("r-jsonlite" ,r-jsonlite)
7936 ("r-magrittr" ,r-magrittr)
7937 ("r-rappdirs" ,r-rappdirs)
7939 ("r-readr" ,r-readr)
7941 ("r-rlang" ,r-rlang)
7942 ("r-rvest" ,r-rvest)
7943 ("r-stringr" ,r-stringr)
7944 ("r-tibble" ,r-tibble)
7945 ("r-tidyr" ,r-tidyr)
7946 ("r-tidyselect" ,r-tidyselect)
7947 ("r-xml2" ,r-xml2)))
7949 `(("r-knitr" ,r-knitr)))
7950 (home-page "https://github.com/seandavi/BiocPkgTools")
7951 (synopsis "Collection of tools for learning about Bioconductor packages")
7953 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7954 and build status. This package is a simple collection of functions to access
7955 that metadata from R. The goal is to expose metadata for data mining and
7956 value-added functionality such as package searching, text mining, and
7957 analytics on packages.")
7958 (license license:expat)))
7960 (define-public r-biocset
7967 (uri (bioconductor-uri "BiocSet" version))
7970 "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
7971 (properties `((upstream-name . "BiocSet")))
7972 (build-system r-build-system)
7974 `(("r-annotationdbi" ,r-annotationdbi)
7975 ("r-dplyr" ,r-dplyr)
7976 ("r-keggrest" ,r-keggrest)
7978 ("r-rlang" ,r-rlang)
7979 ("r-rtracklayer" ,r-rtracklayer)
7980 ("r-tibble" ,r-tibble)))
7982 `(("r-knitr" ,r-knitr)))
7984 "https://bioconductor.org/packages/BiocSet")
7986 "Representing Different Biological Sets")
7988 "BiocSet displays different biological sets in a triple tibble format.
7989 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7990 The user has the ability to activate one of these three tibbles to perform
7991 common functions from the @code{dplyr} package. Mapping functionality and
7992 accessing web references for elements/sets are also available in BiocSet.")
7993 (license license:artistic2.0)))
7995 (define-public r-biocworkflowtools
7997 (name "r-biocworkflowtools")
8002 (uri (bioconductor-uri "BiocWorkflowTools" version))
8005 "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
8007 `((upstream-name . "BiocWorkflowTools")))
8008 (build-system r-build-system)
8010 `(("r-biocstyle" ,r-biocstyle)
8011 ("r-bookdown" ,r-bookdown)
8012 ("r-git2r" ,r-git2r)
8014 ("r-knitr" ,r-knitr)
8015 ("r-rmarkdown" ,r-rmarkdown)
8016 ("r-rstudioapi" ,r-rstudioapi)
8017 ("r-stringr" ,r-stringr)
8018 ("r-usethis" ,r-usethis)))
8020 `(("r-knitr" ,r-knitr)))
8021 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8022 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8024 "This package provides functions to ease the transition between
8025 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8026 (license license:expat)))
8028 (define-public r-biodist
8035 (uri (bioconductor-uri "bioDist" version))
8038 "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
8039 (properties `((upstream-name . "bioDist")))
8040 (build-system r-build-system)
8042 `(("r-biobase" ,r-biobase)
8043 ("r-kernsmooth" ,r-kernsmooth)))
8044 (home-page "https://bioconductor.org/packages/bioDist/")
8045 (synopsis "Different distance measures")
8047 "This package provides a collection of software tools for calculating
8048 distance measures.")
8049 (license license:artistic2.0)))
8051 (define-public r-pcatools
8058 (uri (bioconductor-uri "PCAtools" version))
8061 "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
8062 (properties `((upstream-name . "PCAtools")))
8063 (build-system r-build-system)
8065 `(("r-beachmat" ,r-beachmat)
8067 ("r-biocparallel" ,r-biocparallel)
8068 ("r-biocsingular" ,r-biocsingular)
8069 ("r-cowplot" ,r-cowplot)
8070 ("r-delayedarray" ,r-delayedarray)
8071 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8072 ("r-dqrng" ,r-dqrng)
8073 ("r-ggplot2" ,r-ggplot2)
8074 ("r-ggrepel" ,r-ggrepel)
8075 ("r-lattice" ,r-lattice)
8076 ("r-matrix" ,r-matrix)
8078 ("r-reshape2" ,r-reshape2)))
8079 (native-inputs `(("r-knitr" ,r-knitr)))
8080 (home-page "https://github.com/kevinblighe/PCAtools")
8081 (synopsis "PCAtools: everything Principal Components Analysis")
8083 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8084 structure of the data without the need to build any model to represent it.
8085 This \"summary\" of the data is arrived at through a process of reduction that
8086 can transform the large number of variables into a lesser number that are
8087 uncorrelated (i.e. the 'principal components'), while at the same time being
8088 capable of easy interpretation on the original data. PCAtools provides
8089 functions for data exploration via PCA, and allows the user to generate
8090 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8091 can also identify an optimal number of principal components via different
8092 metrics, such as the elbow method and Horn's parallel analysis, which has
8093 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8094 dimensional mass cytometry data.")
8095 (license license:gpl3)))
8097 (define-public r-rgreat
8104 (uri (bioconductor-uri "rGREAT" version))
8107 "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
8108 (properties `((upstream-name . "rGREAT")))
8109 (build-system r-build-system)
8111 `(("r-genomicranges" ,r-genomicranges)
8112 ("r-getoptlong" ,r-getoptlong)
8113 ("r-iranges" ,r-iranges)
8114 ("r-rcurl" ,r-rcurl)
8115 ("r-rjson" ,r-rjson)))
8116 (native-inputs `(("r-knitr" ,r-knitr)))
8117 (home-page "https://github.com/jokergoo/rGREAT")
8118 (synopsis "Client for GREAT analysis")
8120 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8121 Tool) analysis automatic by constructing a HTTP POST request according to
8122 user's input and automatically retrieving results from GREAT web server.")
8123 (license license:expat)))
8125 (define-public r-m3c
8132 (uri (bioconductor-uri "M3C" version))
8135 "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
8136 (properties `((upstream-name . "M3C")))
8137 (build-system r-build-system)
8139 `(("r-cluster" ,r-cluster)
8140 ("r-corpcor" ,r-corpcor)
8141 ("r-doparallel" ,r-doparallel)
8142 ("r-dosnow" ,r-dosnow)
8143 ("r-foreach" ,r-foreach)
8144 ("r-ggplot2" ,r-ggplot2)
8145 ("r-matrix" ,r-matrix)
8146 ("r-matrixcalc" ,r-matrixcalc)
8147 ("r-rtsne" ,r-rtsne)
8148 ("r-umap" ,r-umap)))
8149 (native-inputs `(("r-knitr" ,r-knitr)))
8150 (home-page "https://bioconductor.org/packages/M3C")
8151 (synopsis "Monte Carlo reference-based consensus clustering")
8153 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8154 simulation to eliminate overestimation of @code{K} and can reject the null
8155 hypothesis @code{K=1}.")
8156 (license license:agpl3+)))
8158 (define-public r-icens
8165 (uri (bioconductor-uri "Icens" version))
8168 "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
8169 (properties `((upstream-name . "Icens")))
8170 (build-system r-build-system)
8172 `(("r-survival" ,r-survival)))
8173 (home-page "https://bioconductor.org/packages/Icens")
8174 (synopsis "NPMLE for censored and truncated data")
8176 "This package provides many functions for computing the
8177 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8179 (license license:artistic2.0)))
8181 ;; This is a CRAN package but it depends on r-icens, which is published on
8183 (define-public r-interval
8190 (uri (cran-uri "interval" version))
8193 "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
8194 (properties `((upstream-name . "interval")))
8195 (build-system r-build-system)
8197 `(("r-icens" ,r-icens)
8198 ("r-mlecens" ,r-mlecens)
8200 ("r-survival" ,r-survival)))
8201 (home-page "https://cran.r-project.org/web/packages/interval/")
8202 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8204 "This package provides functions to fit nonparametric survival curves,
8205 plot them, and perform logrank or Wilcoxon type tests.")
8206 (license license:gpl2+)))