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 ;; This is a CRAN package, but it depends on a Bioconductor package.
1767 (define-public r-codedepends
1769 (name "r-codedepends")
1774 (uri (cran-uri "CodeDepends" version))
1777 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
1778 (properties `((upstream-name . "CodeDepends")))
1779 (build-system r-build-system)
1781 `(("r-codetools" ,r-codetools)
1782 ("r-graph" ,r-graph)
1784 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
1785 (synopsis "Analysis of R code for reproducible research and code comprehension")
1787 "This package provides tools for analyzing R expressions or blocks of
1788 code and determining the dependencies between them. It focuses on R scripts,
1789 but can be used on the bodies of functions. There are many facilities
1790 including the ability to summarize or get a high-level view of code,
1791 determining dependencies between variables, code improvement suggestions.")
1792 ;; Any version of the GPL
1793 (license (list license:gpl2+ license:gpl3+))))
1795 (define-public r-chippeakanno
1797 (name "r-chippeakanno")
1802 (uri (bioconductor-uri "ChIPpeakAnno" version))
1805 "0q3f55hh0a2hl96272js6gagmgps9cxs8s13pf6fii64rzaz5m7y"))))
1806 (properties `((upstream-name . "ChIPpeakAnno")))
1807 (build-system r-build-system)
1809 `(("r-annotationdbi" ,r-annotationdbi)
1810 ("r-biobase" ,r-biobase)
1811 ("r-biocgenerics" ,r-biocgenerics)
1812 ("r-biocmanager" ,r-biocmanager)
1813 ("r-biomart" ,r-biomart)
1814 ("r-biostrings" ,r-biostrings)
1815 ("r-bsgenome" ,r-bsgenome)
1817 ("r-delayedarray" ,r-delayedarray)
1818 ("r-ensembldb" ,r-ensembldb)
1819 ("r-genomeinfodb" ,r-genomeinfodb)
1820 ("r-genomicalignments" ,r-genomicalignments)
1821 ("r-genomicfeatures" ,r-genomicfeatures)
1822 ("r-genomicranges" ,r-genomicranges)
1823 ("r-go-db" ,r-go-db)
1824 ("r-graph" ,r-graph)
1826 ("r-iranges" ,r-iranges)
1827 ("r-limma" ,r-limma)
1828 ("r-matrixstats" ,r-matrixstats)
1829 ("r-multtest" ,r-multtest)
1831 ("r-regioner" ,r-regioner)
1832 ("r-rsamtools" ,r-rsamtools)
1833 ("r-rtracklayer" ,r-rtracklayer)
1834 ("r-s4vectors" ,r-s4vectors)
1835 ("r-seqinr" ,r-seqinr)
1836 ("r-summarizedexperiment" ,r-summarizedexperiment)
1837 ("r-venndiagram" ,r-venndiagram)))
1839 `(("r-knitr" ,r-knitr)))
1840 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
1841 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
1843 "The package includes functions to retrieve the sequences around the peak,
1844 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
1845 custom features such as most conserved elements and other transcription factor
1846 binding sites supplied by users. Starting 2.0.5, new functions have been added
1847 for finding the peaks with bi-directional promoters with summary statistics
1848 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
1849 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
1850 enrichedGO (addGeneIDs).")
1851 (license license:gpl2+)))
1853 (define-public r-marray
1859 (uri (bioconductor-uri "marray" version))
1861 (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd"))))
1862 (build-system r-build-system)
1864 `(("r-limma" ,r-limma)))
1865 (home-page "https://bioconductor.org/packages/marray")
1866 (synopsis "Exploratory analysis for two-color spotted microarray data")
1867 (description "This package contains class definitions for two-color spotted
1868 microarray data. It also includes functions for data input, diagnostic plots,
1869 normalization and quality checking.")
1870 (license license:lgpl2.0+)))
1872 (define-public r-cghbase
1878 (uri (bioconductor-uri "CGHbase" version))
1880 (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf"))))
1881 (properties `((upstream-name . "CGHbase")))
1882 (build-system r-build-system)
1884 `(("r-biobase" ,r-biobase)
1885 ("r-marray" ,r-marray)))
1886 (home-page "https://bioconductor.org/packages/CGHbase")
1887 (synopsis "Base functions and classes for arrayCGH data analysis")
1888 (description "This package contains functions and classes that are needed by
1889 the @code{arrayCGH} packages.")
1890 (license license:gpl2+)))
1892 (define-public r-cghcall
1898 (uri (bioconductor-uri "CGHcall" version))
1900 (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg"))))
1901 (properties `((upstream-name . "CGHcall")))
1902 (build-system r-build-system)
1904 `(("r-biobase" ,r-biobase)
1905 ("r-cghbase" ,r-cghbase)
1906 ("r-impute" ,r-impute)
1907 ("r-dnacopy" ,r-dnacopy)
1908 ("r-snowfall" ,r-snowfall)))
1909 (home-page "https://bioconductor.org/packages/CGHcall")
1910 (synopsis "Base functions and classes for arrayCGH data analysis")
1911 (description "This package contains functions and classes that are needed by
1912 @code{arrayCGH} packages.")
1913 (license license:gpl2+)))
1915 (define-public r-qdnaseq
1921 (uri (bioconductor-uri "QDNAseq" version))
1923 (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86"))))
1924 (properties `((upstream-name . "QDNAseq")))
1925 (build-system r-build-system)
1927 `(("r-biobase" ,r-biobase)
1928 ("r-cghbase" ,r-cghbase)
1929 ("r-cghcall" ,r-cghcall)
1930 ("r-dnacopy" ,r-dnacopy)
1931 ("r-future" ,r-future)
1932 ("r-future-apply" ,r-future-apply)
1933 ("r-genomicranges" ,r-genomicranges)
1934 ("r-iranges" ,r-iranges)
1935 ("r-matrixstats" ,r-matrixstats)
1936 ("r-r-utils" ,r-r-utils)
1937 ("r-rsamtools" ,r-rsamtools)))
1938 (home-page "https://bioconductor.org/packages/QDNAseq")
1939 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
1940 (description "The genome is divided into non-overlapping fixed-sized bins,
1941 number of sequence reads in each counted, adjusted with a simultaneous
1942 two-dimensional loess correction for sequence mappability and GC content, and
1943 filtered to remove spurious regions in the genome. Downstream steps of
1944 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
1946 (license license:gpl2+)))
1948 (define-public r-bayseq
1955 (uri (bioconductor-uri "baySeq" version))
1958 "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj"))))
1959 (properties `((upstream-name . "baySeq")))
1960 (build-system r-build-system)
1962 `(("r-abind" ,r-abind)
1963 ("r-edger" ,r-edger)
1964 ("r-genomicranges" ,r-genomicranges)))
1965 (home-page "https://bioconductor.org/packages/baySeq/")
1966 (synopsis "Bayesian analysis of differential expression patterns in count data")
1968 "This package identifies differential expression in high-throughput count
1969 data, such as that derived from next-generation sequencing machines,
1970 calculating estimated posterior likelihoods of differential expression (or
1971 more complex hypotheses) via empirical Bayesian methods.")
1972 (license license:gpl3)))
1974 (define-public r-chipcomp
1981 (uri (bioconductor-uri "ChIPComp" version))
1984 "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp"))))
1985 (properties `((upstream-name . "ChIPComp")))
1986 (build-system r-build-system)
1988 `(("r-biocgenerics" ,r-biocgenerics)
1989 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1990 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
1991 ("r-genomeinfodb" ,r-genomeinfodb)
1992 ("r-genomicranges" ,r-genomicranges)
1993 ("r-iranges" ,r-iranges)
1994 ("r-limma" ,r-limma)
1995 ("r-rsamtools" ,r-rsamtools)
1996 ("r-rtracklayer" ,r-rtracklayer)
1997 ("r-s4vectors" ,r-s4vectors)))
1998 (home-page "https://bioconductor.org/packages/ChIPComp")
1999 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2001 "ChIPComp implements a statistical method for quantitative comparison of
2002 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2003 sites across multiple conditions considering matching control in ChIP-seq
2005 ;; Any version of the GPL.
2006 (license license:gpl3+)))
2008 (define-public r-riboprofiling
2010 (name "r-riboprofiling")
2015 (uri (bioconductor-uri "RiboProfiling" version))
2018 "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha"))))
2019 (properties `((upstream-name . "RiboProfiling")))
2020 (build-system r-build-system)
2022 `(("r-biocgenerics" ,r-biocgenerics)
2023 ("r-biostrings" ,r-biostrings)
2024 ("r-data-table" ,r-data-table)
2025 ("r-genomeinfodb" ,r-genomeinfodb)
2026 ("r-genomicalignments" ,r-genomicalignments)
2027 ("r-genomicfeatures" ,r-genomicfeatures)
2028 ("r-genomicranges" ,r-genomicranges)
2029 ("r-ggbio" ,r-ggbio)
2030 ("r-ggplot2" ,r-ggplot2)
2031 ("r-iranges" ,r-iranges)
2033 ("r-reshape2" ,r-reshape2)
2034 ("r-rsamtools" ,r-rsamtools)
2035 ("r-rtracklayer" ,r-rtracklayer)
2036 ("r-s4vectors" ,r-s4vectors)
2037 ("r-sqldf" ,r-sqldf)))
2039 `(("r-knitr" ,r-knitr)))
2040 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2041 (synopsis "Ribosome profiling data analysis")
2042 (description "Starting with a BAM file, this package provides the
2043 necessary functions for quality assessment, read start position recalibration,
2044 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2045 of count data: pairs, log fold-change, codon frequency and coverage
2046 assessment, principal component analysis on codon coverage.")
2047 (license license:gpl3)))
2049 (define-public r-riboseqr
2056 (uri (bioconductor-uri "riboSeqR" version))
2059 "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk"))))
2060 (properties `((upstream-name . "riboSeqR")))
2061 (build-system r-build-system)
2063 `(("r-abind" ,r-abind)
2064 ("r-bayseq" ,r-bayseq)
2065 ("r-genomeinfodb" ,r-genomeinfodb)
2066 ("r-genomicranges" ,r-genomicranges)
2067 ("r-iranges" ,r-iranges)
2068 ("r-rsamtools" ,r-rsamtools)
2069 ("r-seqlogo" ,r-seqlogo)))
2070 (home-page "https://bioconductor.org/packages/riboSeqR/")
2071 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2073 "This package provides plotting functions, frameshift detection and
2074 parsing of genetic sequencing data from ribosome profiling experiments.")
2075 (license license:gpl3)))
2077 (define-public r-interactionset
2079 (name "r-interactionset")
2084 (uri (bioconductor-uri "InteractionSet" version))
2087 "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v"))))
2089 `((upstream-name . "InteractionSet")))
2090 (build-system r-build-system)
2092 `(("r-biocgenerics" ,r-biocgenerics)
2093 ("r-genomeinfodb" ,r-genomeinfodb)
2094 ("r-genomicranges" ,r-genomicranges)
2095 ("r-iranges" ,r-iranges)
2096 ("r-matrix" ,r-matrix)
2098 ("r-s4vectors" ,r-s4vectors)
2099 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2101 `(("r-knitr" ,r-knitr)))
2102 (home-page "https://bioconductor.org/packages/InteractionSet")
2103 (synopsis "Base classes for storing genomic interaction data")
2105 "This package provides the @code{GInteractions},
2106 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2107 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2109 (license license:gpl3)))
2111 (define-public r-genomicinteractions
2113 (name "r-genomicinteractions")
2118 (uri (bioconductor-uri "GenomicInteractions" version))
2121 "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy"))))
2123 `((upstream-name . "GenomicInteractions")))
2124 (build-system r-build-system)
2126 `(("r-biobase" ,r-biobase)
2127 ("r-biocgenerics" ,r-biocgenerics)
2128 ("r-data-table" ,r-data-table)
2129 ("r-dplyr" ,r-dplyr)
2130 ("r-genomeinfodb" ,r-genomeinfodb)
2131 ("r-genomicranges" ,r-genomicranges)
2132 ("r-ggplot2" ,r-ggplot2)
2133 ("r-gridextra" ,r-gridextra)
2135 ("r-igraph" ,r-igraph)
2136 ("r-interactionset" ,r-interactionset)
2137 ("r-iranges" ,r-iranges)
2138 ("r-rsamtools" ,r-rsamtools)
2139 ("r-rtracklayer" ,r-rtracklayer)
2140 ("r-s4vectors" ,r-s4vectors)
2141 ("r-stringr" ,r-stringr)))
2143 `(("r-knitr" ,r-knitr)))
2144 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2145 (synopsis "R package for handling genomic interaction data")
2147 "This R package provides tools for handling genomic interaction data,
2148 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2149 information and producing various plots and statistics.")
2150 (license license:gpl3)))
2152 (define-public r-ctc
2159 (uri (bioconductor-uri "ctc" version))
2162 "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6"))))
2163 (build-system r-build-system)
2164 (propagated-inputs `(("r-amap" ,r-amap)))
2165 (home-page "https://bioconductor.org/packages/ctc/")
2166 (synopsis "Cluster and tree conversion")
2168 "This package provides tools for exporting and importing classification
2169 trees and clusters to other programs.")
2170 (license license:gpl2)))
2172 (define-public r-goseq
2179 (uri (bioconductor-uri "goseq" version))
2182 "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym"))))
2183 (build-system r-build-system)
2185 `(("r-annotationdbi" ,r-annotationdbi)
2186 ("r-biasedurn" ,r-biasedurn)
2187 ("r-biocgenerics" ,r-biocgenerics)
2188 ("r-genelendatabase" ,r-genelendatabase)
2189 ("r-go-db" ,r-go-db)
2190 ("r-mgcv" ,r-mgcv)))
2191 (home-page "https://bioconductor.org/packages/goseq/")
2192 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2194 "This package provides tools to detect Gene Ontology and/or other user
2195 defined categories which are over/under represented in RNA-seq data.")
2196 (license license:lgpl2.0+)))
2198 (define-public r-glimma
2205 (uri (bioconductor-uri "Glimma" version))
2208 "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y"))))
2209 (properties `((upstream-name . "Glimma")))
2210 (build-system r-build-system)
2212 `(("r-edger" ,r-edger)
2213 ("r-jsonlite" ,r-jsonlite)
2214 ("r-s4vectors" ,r-s4vectors)))
2216 `(("r-knitr" ,r-knitr)))
2217 (home-page "https://github.com/Shians/Glimma")
2218 (synopsis "Interactive HTML graphics")
2220 "This package generates interactive visualisations for analysis of
2221 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2222 HTML page. The interactions are built on top of the popular static
2223 representations of analysis results in order to provide additional
2225 (license license:lgpl3)))
2227 (define-public r-rots
2234 (uri (bioconductor-uri "ROTS" version))
2237 "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm"))))
2238 (properties `((upstream-name . "ROTS")))
2239 (build-system r-build-system)
2241 `(("r-biobase" ,r-biobase)
2242 ("r-rcpp" ,r-rcpp)))
2243 (home-page "https://bioconductor.org/packages/ROTS/")
2244 (synopsis "Reproducibility-Optimized Test Statistic")
2246 "This package provides tools for calculating the
2247 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2249 (license license:gpl2+)))
2251 (define-public r-plgem
2258 (uri (bioconductor-uri "plgem" version))
2261 "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a"))))
2262 (build-system r-build-system)
2264 `(("r-biobase" ,r-biobase)
2265 ("r-mass" ,r-mass)))
2266 (home-page "http://www.genopolis.it")
2267 (synopsis "Detect differential expression in microarray and proteomics datasets")
2269 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
2270 model the variance-versus-mean dependence that exists in a variety of
2271 genome-wide datasets, including microarray and proteomics data. The use of
2272 PLGEM has been shown to improve the detection of differentially expressed
2273 genes or proteins in these datasets.")
2274 (license license:gpl2)))
2276 (define-public r-inspect
2283 (uri (bioconductor-uri "INSPEcT" version))
2286 "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z"))))
2287 (properties `((upstream-name . "INSPEcT")))
2288 (build-system r-build-system)
2290 `(("r-biobase" ,r-biobase)
2291 ("r-biocgenerics" ,r-biocgenerics)
2292 ("r-biocparallel" ,r-biocparallel)
2293 ("r-deseq2" ,r-deseq2)
2294 ("r-desolve" ,r-desolve)
2295 ("r-gdata" ,r-gdata)
2296 ("r-genomeinfodb" ,r-genomeinfodb)
2297 ("r-genomicalignments" ,r-genomicalignments)
2298 ("r-genomicfeatures" ,r-genomicfeatures)
2299 ("r-genomicranges" ,r-genomicranges)
2300 ("r-iranges" ,r-iranges)
2301 ("r-kernsmooth" ,r-kernsmooth)
2302 ("r-plgem" ,r-plgem)
2304 ("r-rootsolve" ,r-rootsolve)
2305 ("r-rsamtools" ,r-rsamtools)
2306 ("r-rtracklayer" ,r-rtracklayer)
2307 ("r-s4vectors" ,r-s4vectors)
2308 ("r-shiny" ,r-shiny)
2309 ("r-summarizedexperiment" ,r-summarizedexperiment)
2310 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
2311 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
2313 `(("r-knitr" ,r-knitr)))
2314 (home-page "https://bioconductor.org/packages/INSPEcT")
2315 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
2317 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
2318 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
2319 order to evaluate synthesis, processing and degradation rates and assess via
2320 modeling the rates that determines changes in mature mRNA levels.")
2321 (license license:gpl2)))
2323 (define-public r-dnabarcodes
2325 (name "r-dnabarcodes")
2330 (uri (bioconductor-uri "DNABarcodes" version))
2333 "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7"))))
2334 (properties `((upstream-name . "DNABarcodes")))
2335 (build-system r-build-system)
2338 ("r-matrix" ,r-matrix)
2339 ("r-rcpp" ,r-rcpp)))
2341 `(("r-knitr" ,r-knitr)))
2342 (home-page "https://bioconductor.org/packages/DNABarcodes")
2343 (synopsis "Create and analyze DNA barcodes")
2345 "This package offers tools to create DNA barcode sets capable of
2346 correcting insertion, deletion, and substitution errors. Existing barcodes
2347 can be analyzed regarding their minimal, maximal and average distances between
2348 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
2349 demultiplexed, i.e. assigned to their original reference barcode.")
2350 (license license:gpl2)))
2352 (define-public r-ruvseq
2359 (uri (bioconductor-uri "RUVSeq" version))
2362 "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x"))))
2363 (properties `((upstream-name . "RUVSeq")))
2364 (build-system r-build-system)
2366 `(("r-biobase" ,r-biobase)
2367 ("r-edaseq" ,r-edaseq)
2368 ("r-edger" ,r-edger)
2369 ("r-mass" ,r-mass)))
2371 `(("r-knitr" ,r-knitr)))
2372 (home-page "https://github.com/drisso/RUVSeq")
2373 (synopsis "Remove unwanted variation from RNA-Seq data")
2375 "This package implements methods to @dfn{remove unwanted variation} (RUV)
2376 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
2378 (license license:artistic2.0)))
2380 (define-public r-biocneighbors
2382 (name "r-biocneighbors")
2387 (uri (bioconductor-uri "BiocNeighbors" version))
2390 "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy"))))
2391 (properties `((upstream-name . "BiocNeighbors")))
2392 (build-system r-build-system)
2394 `(("r-biocparallel" ,r-biocparallel)
2395 ("r-matrix" ,r-matrix)
2397 ("r-rcppannoy" ,r-rcppannoy)
2398 ("r-rcpphnsw" ,r-rcpphnsw)
2399 ("r-s4vectors" ,r-s4vectors)))
2401 `(("r-knitr" ,r-knitr)))
2402 (home-page "https://bioconductor.org/packages/BiocNeighbors")
2403 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
2405 "This package implements exact and approximate methods for nearest
2406 neighbor detection, in a framework that allows them to be easily switched
2407 within Bioconductor packages or workflows. The exact algorithm is implemented
2408 using pre-clustering with the k-means algorithm. Functions are also provided
2409 to search for all neighbors within a given distance. Parallelization is
2410 achieved for all methods using the BiocParallel framework.")
2411 (license license:gpl3)))
2413 (define-public r-biocsingular
2415 (name "r-biocsingular")
2420 (uri (bioconductor-uri "BiocSingular" version))
2423 "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih"))))
2424 (properties `((upstream-name . "BiocSingular")))
2425 (build-system r-build-system)
2427 `(("r-beachmat" ,r-beachmat)
2428 ("r-biocgenerics" ,r-biocgenerics)
2429 ("r-biocparallel" ,r-biocparallel)
2430 ("r-delayedarray" ,r-delayedarray)
2431 ("r-irlba" ,r-irlba)
2432 ("r-matrix" ,r-matrix)
2435 ("r-s4vectors" ,r-s4vectors)))
2437 `(("r-knitr" ,r-knitr)))
2438 (home-page "https://github.com/LTLA/BiocSingular")
2439 (synopsis "Singular value decomposition for Bioconductor packages")
2441 "This package implements exact and approximate methods for singular value
2442 decomposition and principal components analysis, in a framework that allows
2443 them to be easily switched within Bioconductor packages or workflows. Where
2444 possible, parallelization is achieved using the BiocParallel framework.")
2445 (license license:gpl3)))
2447 (define-public r-destiny
2454 (uri (bioconductor-uri "destiny" version))
2457 "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n"))))
2458 (build-system r-build-system)
2460 `(("r-biobase" ,r-biobase)
2461 ("r-biocgenerics" ,r-biocgenerics)
2462 ("r-ggplot-multistats" ,r-ggplot-multistats)
2463 ("r-ggplot2" ,r-ggplot2)
2464 ("r-ggthemes" ,r-ggthemes)
2465 ("r-irlba" ,r-irlba)
2466 ("r-knn-covertree" ,r-knn-covertree)
2467 ("r-matrix" ,r-matrix)
2468 ("r-nbconvertr" ,r-nbconvertr)
2469 ("r-pcamethods" ,r-pcamethods)
2470 ("r-proxy" ,r-proxy)
2472 ("r-rcppeigen" ,r-rcppeigen)
2473 ("r-rcpphnsw" ,r-rcpphnsw)
2474 ("r-rspectra" ,r-rspectra)
2475 ("r-scales" ,r-scales)
2476 ("r-scatterplot3d" ,r-scatterplot3d)
2477 ("r-singlecellexperiment" ,r-singlecellexperiment)
2478 ("r-smoother" ,r-smoother)
2479 ("r-summarizedexperiment" ,r-summarizedexperiment)
2480 ("r-tidyr" ,r-tidyr)
2481 ("r-tidyselect" ,r-tidyselect)
2484 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
2485 (home-page "https://bioconductor.org/packages/destiny/")
2486 (synopsis "Create and plot diffusion maps")
2487 (description "This package provides tools to create and plot diffusion
2489 ;; Any version of the GPL
2490 (license license:gpl3+)))
2492 (define-public r-savr
2499 (uri (bioconductor-uri "savR" version))
2502 "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a"))))
2503 (properties `((upstream-name . "savR")))
2504 (build-system r-build-system)
2506 `(("r-ggplot2" ,r-ggplot2)
2507 ("r-gridextra" ,r-gridextra)
2508 ("r-reshape2" ,r-reshape2)
2509 ("r-scales" ,r-scales)
2511 (home-page "https://github.com/bcalder/savR")
2512 (synopsis "Parse and analyze Illumina SAV files")
2514 "This package provides tools to parse Illumina Sequence Analysis
2515 Viewer (SAV) files, access data, and generate QC plots.")
2516 (license license:agpl3+)))
2518 (define-public r-chipexoqual
2520 (name "r-chipexoqual")
2525 (uri (bioconductor-uri "ChIPexoQual" version))
2528 "02rsf1rvm0p6dn18zq2a4hpvpd9m2i5rziyi4zm8j43qvs8xhafp"))))
2529 (properties `((upstream-name . "ChIPexoQual")))
2530 (build-system r-build-system)
2532 `(("r-biocparallel" ,r-biocparallel)
2533 ("r-biovizbase" ,r-biovizbase)
2534 ("r-broom" ,r-broom)
2535 ("r-data-table" ,r-data-table)
2536 ("r-dplyr" ,r-dplyr)
2537 ("r-genomeinfodb" ,r-genomeinfodb)
2538 ("r-genomicalignments" ,r-genomicalignments)
2539 ("r-genomicranges" ,r-genomicranges)
2540 ("r-ggplot2" ,r-ggplot2)
2541 ("r-hexbin" ,r-hexbin)
2542 ("r-iranges" ,r-iranges)
2543 ("r-rcolorbrewer" ,r-rcolorbrewer)
2544 ("r-rmarkdown" ,r-rmarkdown)
2545 ("r-rsamtools" ,r-rsamtools)
2546 ("r-s4vectors" ,r-s4vectors)
2547 ("r-scales" ,r-scales)
2548 ("r-viridis" ,r-viridis)))
2550 `(("r-knitr" ,r-knitr)))
2551 (home-page "https://github.com/keleslab/ChIPexoQual")
2552 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
2554 "This package provides a quality control pipeline for ChIP-exo/nexus
2556 (license license:gpl2+)))
2558 (define-public r-copynumber
2560 (name "r-copynumber")
2564 (uri (bioconductor-uri "copynumber" version))
2567 "1b7v6xijpi2mir49cf83gpadhxm5pnbs6d8q8qga7y06hn9jx6my"))))
2568 (build-system r-build-system)
2570 `(("r-s4vectors" ,r-s4vectors)
2571 ("r-iranges" ,r-iranges)
2572 ("r-genomicranges" ,r-genomicranges)
2573 ("r-biocgenerics" ,r-biocgenerics)))
2574 (home-page "https://bioconductor.org/packages/copynumber")
2575 (synopsis "Segmentation of single- and multi-track copy number data")
2577 "This package segments single- and multi-track copy number data by a
2578 penalized least squares regression method.")
2579 (license license:artistic2.0)))
2581 (define-public r-dnacopy
2588 (uri (bioconductor-uri "DNAcopy" version))
2591 "0jg8lr83drzfs5h73c7mk7x99vj99a2p2s1sqjc4gicn927xvhza"))))
2592 (properties `((upstream-name . "DNAcopy")))
2593 (build-system r-build-system)
2594 (native-inputs `(("gfortran" ,gfortran)))
2595 (home-page "https://bioconductor.org/packages/DNAcopy")
2596 (synopsis "DNA copy number data analysis")
2598 "This package implements the @dfn{circular binary segmentation} (CBS)
2599 algorithm to segment DNA copy number data and identify genomic regions with
2600 abnormal copy number.")
2601 (license license:gpl2+)))
2603 ;; This is a CRAN package, but it uncharacteristically depends on a
2604 ;; Bioconductor package.
2605 (define-public r-htscluster
2607 (name "r-htscluster")
2612 (uri (cran-uri "HTSCluster" version))
2615 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
2616 (properties `((upstream-name . "HTSCluster")))
2617 (build-system r-build-system)
2619 `(("r-capushe" ,r-capushe)
2620 ("r-edger" ,r-edger)
2621 ("r-plotrix" ,r-plotrix)))
2622 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
2623 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
2625 "This package provides a Poisson mixture model is implemented to cluster
2626 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
2627 estimation is performed using either the EM or CEM algorithm, and the slope
2628 heuristics are used for model selection (i.e., to choose the number of
2630 (license license:gpl3+)))
2632 (define-public r-deds
2639 (uri (bioconductor-uri "DEDS" version))
2642 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
2643 (properties `((upstream-name . "DEDS")))
2644 (build-system r-build-system)
2645 (home-page "https://bioconductor.org/packages/DEDS/")
2646 (synopsis "Differential expression via distance summary for microarray data")
2648 "This library contains functions that calculate various statistics of
2649 differential expression for microarray data, including t statistics, fold
2650 change, F statistics, SAM, moderated t and F statistics and B statistics. It
2651 also implements a new methodology called DEDS (Differential Expression via
2652 Distance Summary), which selects differentially expressed genes by integrating
2653 and summarizing a set of statistics using a weighted distance approach.")
2654 ;; Any version of the LGPL.
2655 (license license:lgpl3+)))
2657 ;; This is a CRAN package, but since it depends on a Bioconductor package we
2659 (define-public r-nbpseq
2666 (uri (cran-uri "NBPSeq" version))
2669 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
2670 (properties `((upstream-name . "NBPSeq")))
2671 (build-system r-build-system)
2673 `(("r-qvalue" ,r-qvalue)))
2674 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
2675 (synopsis "Negative binomial models for RNA-Seq data")
2677 "This package provides negative binomial models for two-group comparisons
2678 and regression inferences from RNA-sequencing data.")
2679 (license license:gpl2)))
2681 (define-public r-ebseq
2688 (uri (bioconductor-uri "EBSeq" version))
2691 "0s9r1xxpfm5794ipjm5a5c8gfxicc6arma6f74aaz8zi5y5q9x5f"))))
2692 (properties `((upstream-name . "EBSeq")))
2693 (build-system r-build-system)
2695 `(("r-blockmodeling" ,r-blockmodeling)
2696 ("r-gplots" ,r-gplots)
2697 ("r-testthat" ,r-testthat)))
2698 (home-page "https://bioconductor.org/packages/EBSeq")
2699 (synopsis "Differential expression analysis of RNA-seq data")
2701 "This package provides tools for differential expression analysis at both
2702 gene and isoform level using RNA-seq data")
2703 (license license:artistic2.0)))
2705 (define-public r-karyoploter
2707 (name "r-karyoploter")
2711 (uri (bioconductor-uri "karyoploteR" version))
2714 "0h0gk4xd95k5phy6qcsv7j931d7gk3p24i2fg4mz5dsk110lpifs"))))
2715 (build-system r-build-system)
2717 `(("r-annotationdbi" ,r-annotationdbi)
2718 ("r-bamsignals" ,r-bamsignals)
2719 ("r-bezier" ,r-bezier)
2720 ("r-biovizbase" ,r-biovizbase)
2721 ("r-digest" ,r-digest)
2722 ("r-genomeinfodb" ,r-genomeinfodb)
2723 ("r-genomicfeatures" ,r-genomicfeatures)
2724 ("r-genomicranges" ,r-genomicranges)
2725 ("r-iranges" ,r-iranges)
2726 ("r-memoise" ,r-memoise)
2727 ("r-regioner" ,r-regioner)
2728 ("r-rsamtools" ,r-rsamtools)
2729 ("r-rtracklayer" ,r-rtracklayer)
2730 ("r-s4vectors" ,r-s4vectors)
2731 ("r-variantannotation" ,r-variantannotation)))
2733 `(("r-knitr" ,r-knitr)))
2734 (home-page "https://bioconductor.org/packages/karyoploteR/")
2735 (synopsis "Plot customizable linear genomes displaying arbitrary data")
2736 (description "This package creates karyotype plots of arbitrary genomes and
2737 offers a complete set of functions to plot arbitrary data on them. It mimicks
2738 many R base graphics functions coupling them with a coordinate change function
2739 automatically mapping the chromosome and data coordinates into the plot
2741 (license license:artistic2.0)))
2743 (define-public r-lpsymphony
2745 (name "r-lpsymphony")
2750 (uri (bioconductor-uri "lpsymphony" version))
2753 "072ikmd267n18hrj7dip4dp1vb5dinj82p3h95n2jaf04h9hwfn4"))))
2754 (build-system r-build-system)
2758 `(("pkg-config" ,pkg-config)
2759 ("r-knitr" ,r-knitr)))
2760 (home-page "https://r-forge.r-project.org/projects/rsymphony")
2761 (synopsis "Symphony integer linear programming solver in R")
2763 "This package was derived from Rsymphony. The package provides an R
2764 interface to SYMPHONY, a linear programming solver written in C++. The main
2765 difference between this package and Rsymphony is that it includes the solver
2766 source code, while Rsymphony expects to find header and library files on the
2767 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
2768 to install interface to SYMPHONY.")
2769 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
2770 ;; lpsimphony is released under the same terms.
2771 (license license:epl1.0)))
2773 (define-public r-ihw
2780 (uri (bioconductor-uri "IHW" version))
2783 "169ir0k1gygdh1wybwa0drdxnhrdrlyzzy0rkygi7jsirn69m74j"))))
2784 (properties `((upstream-name . "IHW")))
2785 (build-system r-build-system)
2787 `(("r-biocgenerics" ,r-biocgenerics)
2788 ("r-fdrtool" ,r-fdrtool)
2789 ("r-lpsymphony" ,r-lpsymphony)
2790 ("r-slam" ,r-slam)))
2792 `(("r-knitr" ,r-knitr)))
2793 (home-page "https://bioconductor.org/packages/IHW")
2794 (synopsis "Independent hypothesis weighting")
2796 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
2797 procedure that increases power compared to the method of Benjamini and
2798 Hochberg by assigning data-driven weights to each hypothesis. The input to
2799 IHW is a two-column table of p-values and covariates. The covariate can be
2800 any continuous-valued or categorical variable that is thought to be
2801 informative on the statistical properties of each hypothesis test, while it is
2802 independent of the p-value under the null hypothesis.")
2803 (license license:artistic2.0)))
2805 (define-public r-icobra
2812 (uri (bioconductor-uri "iCOBRA" version))
2815 "0cvklagby3i221dlhyb51cciv0b3ch4a8z0wpm67q5n6n3k0cil1"))))
2816 (properties `((upstream-name . "iCOBRA")))
2817 (build-system r-build-system)
2819 `(("r-dplyr" ,r-dplyr)
2821 ("r-ggplot2" ,r-ggplot2)
2822 ("r-limma" ,r-limma)
2823 ("r-reshape2" ,r-reshape2)
2825 ("r-scales" ,r-scales)
2826 ("r-shiny" ,r-shiny)
2827 ("r-shinybs" ,r-shinybs)
2828 ("r-shinydashboard" ,r-shinydashboard)
2829 ("r-upsetr" ,r-upsetr)))
2831 `(("r-knitr" ,r-knitr)))
2832 (home-page "https://bioconductor.org/packages/iCOBRA")
2833 (synopsis "Comparison and visualization of ranking and assignment methods")
2835 "This package provides functions for calculation and visualization of
2836 performance metrics for evaluation of ranking and binary
2837 classification (assignment) methods. It also contains a Shiny application for
2838 interactive exploration of results.")
2839 (license license:gpl2+)))
2841 (define-public r-mast
2848 (uri (bioconductor-uri "MAST" version))
2851 "12d0q2fbq9d5jgyccmfv0cghv282s0j86wjfbnjpdf73fdrp6brr"))))
2852 (properties `((upstream-name . "MAST")))
2853 (build-system r-build-system)
2855 `(("r-abind" ,r-abind)
2856 ("r-biobase" ,r-biobase)
2857 ("r-biocgenerics" ,r-biocgenerics)
2858 ("r-data-table" ,r-data-table)
2859 ("r-ggplot2" ,r-ggplot2)
2861 ("r-progress" ,r-progress)
2862 ("r-reshape2" ,r-reshape2)
2863 ("r-s4vectors" ,r-s4vectors)
2864 ("r-singlecellexperiment" ,r-singlecellexperiment)
2865 ("r-stringr" ,r-stringr)
2866 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2868 `(("r-knitr" ,r-knitr)))
2869 (home-page "https://github.com/RGLab/MAST/")
2870 (synopsis "Model-based analysis of single cell transcriptomics")
2872 "This package provides methods and models for handling zero-inflated
2873 single cell assay data.")
2874 (license license:gpl2+)))
2876 (define-public r-monocle
2883 (uri (bioconductor-uri "monocle" version))
2886 "1vziidavlyhixmx6j7lf29qx8xcjwrc9q3x2f63gcff41q3jf9xd"))))
2887 (build-system r-build-system)
2889 `(("r-biobase" ,r-biobase)
2890 ("r-biocgenerics" ,r-biocgenerics)
2891 ("r-biocviews" ,r-biocviews)
2892 ("r-cluster" ,r-cluster)
2893 ("r-combinat" ,r-combinat)
2894 ("r-ddrtree" ,r-ddrtree)
2895 ("r-densityclust" ,r-densityclust)
2896 ("r-dplyr" ,r-dplyr)
2897 ("r-fastica" ,r-fastica)
2898 ("r-ggplot2" ,r-ggplot2)
2899 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
2900 ("r-igraph" ,r-igraph)
2901 ("r-irlba" ,r-irlba)
2902 ("r-limma" ,r-limma)
2904 ("r-matrix" ,r-matrix)
2905 ("r-matrixstats" ,r-matrixstats)
2906 ("r-pheatmap" ,r-pheatmap)
2908 ("r-proxy" ,r-proxy)
2909 ("r-qlcmatrix" ,r-qlcmatrix)
2912 ("r-reshape2" ,r-reshape2)
2913 ("r-rtsne" ,r-rtsne)
2915 ("r-stringr" ,r-stringr)
2916 ("r-tibble" ,r-tibble)
2918 ("r-viridis" ,r-viridis)))
2920 `(("r-knitr" ,r-knitr)))
2921 (home-page "https://bioconductor.org/packages/monocle")
2922 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
2924 "Monocle performs differential expression and time-series analysis for
2925 single-cell expression experiments. It orders individual cells according to
2926 progress through a biological process, without knowing ahead of time which
2927 genes define progress through that process. Monocle also performs
2928 differential expression analysis, clustering, visualization, and other useful
2929 tasks on single cell expression data. It is designed to work with RNA-Seq and
2930 qPCR data, but could be used with other types as well.")
2931 (license license:artistic2.0)))
2933 (define-public r-monocle3
2941 (url "https://github.com/cole-trapnell-lab/monocle3")
2943 (file-name (git-file-name name version))
2946 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
2947 (build-system r-build-system)
2949 `(("r-biobase" ,r-biobase)
2950 ("r-biocgenerics" ,r-biocgenerics)
2951 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
2952 ("r-dplyr" ,r-dplyr)
2953 ("r-ggplot2" ,r-ggplot2)
2954 ("r-ggrepel" ,r-ggrepel)
2956 ("r-htmlwidgets" ,r-htmlwidgets)
2957 ("r-igraph" ,r-igraph)
2958 ("r-irlba" ,r-irlba)
2959 ("r-limma" ,r-limma)
2960 ("r-lmtest" ,r-lmtest)
2962 ("r-matrix" ,r-matrix)
2963 ("r-matrix-utils" ,r-matrix-utils)
2964 ("r-pbapply" ,r-pbapply)
2965 ("r-pbmcapply" ,r-pbmcapply)
2966 ("r-pheatmap" ,r-pheatmap)
2967 ("r-plotly" ,r-plotly)
2969 ("r-proxy" ,r-proxy)
2971 ("r-purrr" ,r-purrr)
2974 ("r-rcppparallel" ,r-rcppparallel)
2975 ("r-reshape2" ,r-reshape2)
2976 ("r-reticulate" ,r-reticulate)
2977 ("r-rhpcblasctl" ,r-rhpcblasctl)
2978 ("r-rtsne" ,r-rtsne)
2979 ("r-shiny" ,r-shiny)
2981 ("r-spdep" ,r-spdep)
2982 ("r-speedglm" ,r-speedglm)
2983 ("r-stringr" ,r-stringr)
2984 ("r-singlecellexperiment" ,r-singlecellexperiment)
2985 ("r-tibble" ,r-tibble)
2986 ("r-tidyr" ,r-tidyr)
2988 ("r-viridis" ,r-viridis)))
2989 (home-page "https://github.com/cole-trapnell-lab/monocle3")
2990 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
2992 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
2993 (license license:expat)))
2995 (define-public r-noiseq
3002 (uri (bioconductor-uri "NOISeq" version))
3005 "0lg3za0km6v9l6dxigbxx6nsx9y6m3dyzh9srngi53s8387vhj33"))))
3006 (properties `((upstream-name . "NOISeq")))
3007 (build-system r-build-system)
3009 `(("r-biobase" ,r-biobase)
3010 ("r-matrix" ,r-matrix)))
3011 (home-page "https://bioconductor.org/packages/NOISeq")
3012 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3014 "This package provides tools to support the analysis of RNA-seq
3015 expression data or other similar kind of data. It provides exploratory plots
3016 to evaluate saturation, count distribution, expression per chromosome, type of
3017 detected features, features length, etc. It also supports the analysis of
3018 differential expression between two experimental conditions with no parametric
3020 (license license:artistic2.0)))
3022 (define-public r-scdd
3029 (uri (bioconductor-uri "scDD" version))
3032 "19q01jksxpv4p26wp2c6faa4fffkjnqlbcds2x955pk35jkqknxx"))))
3033 (properties `((upstream-name . "scDD")))
3034 (build-system r-build-system)
3037 ("r-biocparallel" ,r-biocparallel)
3038 ("r-ebseq" ,r-ebseq)
3039 ("r-fields" ,r-fields)
3040 ("r-ggplot2" ,r-ggplot2)
3041 ("r-mclust" ,r-mclust)
3042 ("r-outliers" ,r-outliers)
3043 ("r-s4vectors" ,r-s4vectors)
3044 ("r-scran" ,r-scran)
3045 ("r-singlecellexperiment" ,r-singlecellexperiment)
3046 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3048 `(("r-knitr" ,r-knitr)))
3049 (home-page "https://github.com/kdkorthauer/scDD")
3050 (synopsis "Mixture modeling of single-cell RNA-seq data")
3052 "This package implements a method to analyze single-cell RNA-seq data
3053 utilizing flexible Dirichlet Process mixture models. Genes with differential
3054 distributions of expression are classified into several interesting patterns
3055 of differences between two conditions. The package also includes functions
3056 for simulating data with these patterns from negative binomial
3058 (license license:gpl2)))
3060 (define-public r-scone
3067 (uri (bioconductor-uri "scone" version))
3070 "12hcmbpncm0l1yxhm3sgkqqfri7s5qc46ikv5qcj8pw5a42rkx3g"))))
3071 (build-system r-build-system)
3073 `(("r-aroma-light" ,r-aroma-light)
3074 ("r-biocparallel" ,r-biocparallel)
3076 ("r-class" ,r-class)
3077 ("r-cluster" ,r-cluster)
3078 ("r-compositions" ,r-compositions)
3079 ("r-diptest" ,r-diptest)
3080 ("r-edger" ,r-edger)
3082 ("r-gplots" ,r-gplots)
3083 ("r-hexbin" ,r-hexbin)
3084 ("r-limma" ,r-limma)
3085 ("r-matrixstats" ,r-matrixstats)
3086 ("r-mixtools" ,r-mixtools)
3087 ("r-rarpack" ,r-rarpack)
3088 ("r-rcolorbrewer" ,r-rcolorbrewer)
3089 ("r-rhdf5" ,r-rhdf5)
3090 ("r-ruvseq" ,r-ruvseq)
3091 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3093 `(("r-knitr" ,r-knitr)))
3094 (home-page "https://bioconductor.org/packages/scone")
3095 (synopsis "Single cell overview of normalized expression data")
3097 "SCONE is an R package for comparing and ranking the performance of
3098 different normalization schemes for single-cell RNA-seq and other
3099 high-throughput analyses.")
3100 (license license:artistic2.0)))
3102 (define-public r-geoquery
3109 (uri (bioconductor-uri "GEOquery" version))
3112 "0sap1dsa3k3qpv5z5y3cimxyhbm8qai87gqn3g1w3hwlcqsss92m"))))
3113 (properties `((upstream-name . "GEOquery")))
3114 (build-system r-build-system)
3116 `(("r-biobase" ,r-biobase)
3117 ("r-dplyr" ,r-dplyr)
3119 ("r-limma" ,r-limma)
3120 ("r-magrittr" ,r-magrittr)
3121 ("r-readr" ,r-readr)
3122 ("r-tidyr" ,r-tidyr)
3123 ("r-xml2" ,r-xml2)))
3125 `(("r-knitr" ,r-knitr)))
3126 (home-page "https://github.com/seandavi/GEOquery/")
3127 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3129 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3130 microarray data. Given the rich and varied nature of this resource, it is
3131 only natural to want to apply BioConductor tools to these data. GEOquery is
3132 the bridge between GEO and BioConductor.")
3133 (license license:gpl2)))
3135 (define-public r-illuminaio
3137 (name "r-illuminaio")
3142 (uri (bioconductor-uri "illuminaio" version))
3145 "0i587r1v5aa25w0jm1zvh7spc1gqmvza49i2kv00g1qzj8whq67c"))))
3146 (build-system r-build-system)
3148 `(("r-base64" ,r-base64)))
3149 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3150 (synopsis "Parse Illumina microarray output files")
3152 "This package provides tools for parsing Illumina's microarray output
3153 files, including IDAT.")
3154 (license license:gpl2)))
3156 (define-public r-siggenes
3163 (uri (bioconductor-uri "siggenes" version))
3166 "0i4y1hgq1ljxkf6sypb6c8yp412a8q5v5z68cx1zrgxnccvp0mfy"))))
3167 (build-system r-build-system)
3169 `(("r-biobase" ,r-biobase)
3170 ("r-multtest" ,r-multtest)
3171 ("r-scrime" ,r-scrime)))
3172 (home-page "https://bioconductor.org/packages/siggenes/")
3174 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3176 "This package provides tools for the identification of differentially
3177 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3178 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3179 Bayes Analyses of Microarrays} (EBAM).")
3180 (license license:lgpl2.0+)))
3182 (define-public r-bumphunter
3184 (name "r-bumphunter")
3189 (uri (bioconductor-uri "bumphunter" version))
3192 "04y6spdx89j3bsq2xniqd3sbfmakwc0klbpzjlp1q2xs9kywr4dq"))))
3193 (build-system r-build-system)
3195 `(("r-annotationdbi" ,r-annotationdbi)
3196 ("r-biocgenerics" ,r-biocgenerics)
3197 ("r-dorng" ,r-dorng)
3198 ("r-foreach" ,r-foreach)
3199 ("r-genomeinfodb" ,r-genomeinfodb)
3200 ("r-genomicfeatures" ,r-genomicfeatures)
3201 ("r-genomicranges" ,r-genomicranges)
3202 ("r-iranges" ,r-iranges)
3203 ("r-iterators" ,r-iterators)
3204 ("r-limma" ,r-limma)
3205 ("r-locfit" ,r-locfit)
3206 ("r-matrixstats" ,r-matrixstats)
3207 ("r-s4vectors" ,r-s4vectors)))
3208 (home-page "https://github.com/ririzarr/bumphunter")
3209 (synopsis "Find bumps in genomic data")
3211 "This package provides tools for finding bumps in genomic data in order
3212 to identify differentially methylated regions in epigenetic epidemiology
3214 (license license:artistic2.0)))
3216 (define-public r-minfi
3223 (uri (bioconductor-uri "minfi" version))
3226 "0bl1sk9syy770d5wqa0k1y0wrs5x8sbj13px1v03v3693pdj081w"))))
3227 (build-system r-build-system)
3229 `(("r-beanplot" ,r-beanplot)
3230 ("r-biobase" ,r-biobase)
3231 ("r-biocgenerics" ,r-biocgenerics)
3232 ("r-biocparallel" ,r-biocparallel)
3233 ("r-biostrings" ,r-biostrings)
3234 ("r-bumphunter" ,r-bumphunter)
3235 ("r-data-table" ,r-data-table)
3236 ("r-delayedarray" ,r-delayedarray)
3237 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3238 ("r-genefilter" ,r-genefilter)
3239 ("r-genomeinfodb" ,r-genomeinfodb)
3240 ("r-genomicranges" ,r-genomicranges)
3241 ("r-geoquery" ,r-geoquery)
3242 ("r-hdf5array" ,r-hdf5array)
3243 ("r-illuminaio" ,r-illuminaio)
3244 ("r-iranges" ,r-iranges)
3245 ("r-lattice" ,r-lattice)
3246 ("r-limma" ,r-limma)
3248 ("r-mclust" ,r-mclust)
3250 ("r-nor1mix" ,r-nor1mix)
3251 ("r-preprocesscore" ,r-preprocesscore)
3252 ("r-quadprog" ,r-quadprog)
3253 ("r-rcolorbrewer" ,r-rcolorbrewer)
3254 ("r-reshape" ,r-reshape)
3255 ("r-s4vectors" ,r-s4vectors)
3256 ("r-siggenes" ,r-siggenes)
3257 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3259 `(("r-knitr" ,r-knitr)))
3260 (home-page "https://github.com/hansenlab/minfi")
3261 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
3263 "This package provides tools to analyze and visualize Illumina Infinium
3264 methylation arrays.")
3265 (license license:artistic2.0)))
3267 (define-public r-methylumi
3269 (name "r-methylumi")
3274 (uri (bioconductor-uri "methylumi" version))
3277 "0phb2dyndnk9rv79nx246cn1sc9wbzdqqbgl6402knc7dgh799wr"))))
3278 (build-system r-build-system)
3280 `(("r-annotate" ,r-annotate)
3281 ("r-annotationdbi" ,r-annotationdbi)
3282 ("r-biobase" ,r-biobase)
3283 ("r-biocgenerics" ,r-biocgenerics)
3284 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
3285 ("r-genefilter" ,r-genefilter)
3286 ("r-genomeinfodb" ,r-genomeinfodb)
3287 ("r-genomicranges" ,r-genomicranges)
3288 ("r-ggplot2" ,r-ggplot2)
3289 ("r-illuminaio" ,r-illuminaio)
3290 ("r-iranges" ,r-iranges)
3291 ("r-lattice" ,r-lattice)
3292 ("r-matrixstats" ,r-matrixstats)
3293 ("r-minfi" ,r-minfi)
3294 ("r-reshape2" ,r-reshape2)
3295 ("r-s4vectors" ,r-s4vectors)
3296 ("r-scales" ,r-scales)
3297 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3299 `(("r-knitr" ,r-knitr)))
3300 (home-page "https://bioconductor.org/packages/methylumi")
3301 (synopsis "Handle Illumina methylation data")
3303 "This package provides classes for holding and manipulating Illumina
3304 methylation data. Based on eSet, it can contain MIAME information, sample
3305 information, feature information, and multiple matrices of data. An
3306 \"intelligent\" import function, methylumiR can read the Illumina text files
3307 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
3308 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
3309 background correction, and quality control features for GoldenGate, Infinium,
3310 and Infinium HD arrays are also included.")
3311 (license license:gpl2)))
3313 (define-public r-lumi
3320 (uri (bioconductor-uri "lumi" version))
3323 "196izc4mdh8j4f04fsf8cqm99w1inzpwy34kwvhz6zvxj2ywn1i9"))))
3324 (build-system r-build-system)
3326 `(("r-affy" ,r-affy)
3327 ("r-annotate" ,r-annotate)
3328 ("r-annotationdbi" ,r-annotationdbi)
3329 ("r-biobase" ,r-biobase)
3331 ("r-genomicfeatures" ,r-genomicfeatures)
3332 ("r-genomicranges" ,r-genomicranges)
3333 ("r-kernsmooth" ,r-kernsmooth)
3334 ("r-lattice" ,r-lattice)
3336 ("r-methylumi" ,r-methylumi)
3338 ("r-nleqslv" ,r-nleqslv)
3339 ("r-preprocesscore" ,r-preprocesscore)
3340 ("r-rsqlite" ,r-rsqlite)))
3341 (home-page "https://bioconductor.org/packages/lumi")
3342 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
3344 "The lumi package provides an integrated solution for the Illumina
3345 microarray data analysis. It includes functions of Illumina
3346 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
3347 variance stabilization, normalization and gene annotation at the probe level.
3348 It also includes the functions of processing Illumina methylation microarrays,
3349 especially Illumina Infinium methylation microarrays.")
3350 (license license:lgpl2.0+)))
3352 (define-public r-linnorm
3359 (uri (bioconductor-uri "Linnorm" version))
3362 "143hdfswp5sda5al1igrm5gyn7a6mp1j7hjm5jsc300335lm3kgp"))))
3363 (properties `((upstream-name . "Linnorm")))
3364 (build-system r-build-system)
3366 `(("r-amap" ,r-amap)
3367 ("r-apcluster" ,r-apcluster)
3368 ("r-ellipse" ,r-ellipse)
3369 ("r-fastcluster" ,r-fastcluster)
3371 ("r-ggdendro" ,r-ggdendro)
3372 ("r-ggplot2" ,r-ggplot2)
3373 ("r-gmodels" ,r-gmodels)
3374 ("r-igraph" ,r-igraph)
3375 ("r-limma" ,r-limma)
3377 ("r-mclust" ,r-mclust)
3379 ("r-rcpparmadillo" ,r-rcpparmadillo)
3380 ("r-rtsne" ,r-rtsne)
3381 ("r-statmod" ,r-statmod)
3382 ("r-vegan" ,r-vegan)
3385 `(("r-knitr" ,r-knitr)))
3386 (home-page "http://www.jjwanglab.org/Linnorm/")
3387 (synopsis "Linear model and normality based transformation method")
3389 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
3390 count data or any large scale count data. It transforms such datasets for
3391 parametric tests. In addition to the transformtion function (@code{Linnorm}),
3392 the following pipelines are implemented:
3395 @item Library size/batch effect normalization (@code{Linnorm.Norm})
3396 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
3397 clustering or hierarchical clustering (@code{Linnorm.tSNE},
3398 @code{Linnorm.PCA}, @code{Linnorm.HClust})
3399 @item Differential expression analysis or differential peak detection using
3400 limma (@code{Linnorm.limma})
3401 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
3402 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
3403 @item Stable gene selection for scRNA-seq data; for users without or who do
3404 not want to rely on spike-in genes (@code{Linnorm.SGenes})
3405 @item Data imputation (@code{Linnorm.DataImput}).
3408 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
3409 @code{RnaXSim} function is included for simulating RNA-seq data for the
3410 evaluation of DEG analysis methods.")
3411 (license license:expat)))
3413 (define-public r-ioniser
3420 (uri (bioconductor-uri "IONiseR" version))
3423 "05fndlblczabva60gn6h0dijqxyn0wknrv8a925fgc4bn415g31w"))))
3424 (properties `((upstream-name . "IONiseR")))
3425 (build-system r-build-system)
3427 `(("r-biocgenerics" ,r-biocgenerics)
3428 ("r-biocparallel" ,r-biocparallel)
3429 ("r-biostrings" ,r-biostrings)
3430 ("r-bit64" ,r-bit64)
3431 ("r-dplyr" ,r-dplyr)
3432 ("r-ggplot2" ,r-ggplot2)
3433 ("r-magrittr" ,r-magrittr)
3434 ("r-rhdf5" ,r-rhdf5)
3435 ("r-shortread" ,r-shortread)
3436 ("r-stringr" ,r-stringr)
3437 ("r-tibble" ,r-tibble)
3438 ("r-tidyr" ,r-tidyr)
3439 ("r-xvector" ,r-xvector)))
3441 `(("r-knitr" ,r-knitr)))
3442 (home-page "https://bioconductor.org/packages/IONiseR/")
3443 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
3445 "IONiseR provides tools for the quality assessment of Oxford Nanopore
3446 MinION data. It extracts summary statistics from a set of fast5 files and can
3447 be used either before or after base calling. In addition to standard
3448 summaries of the read-types produced, it provides a number of plots for
3449 visualising metrics relative to experiment run time or spatially over the
3450 surface of a flowcell.")
3451 (license license:expat)))
3453 ;; This is a CRAN package, but it depends on packages from Bioconductor.
3454 (define-public r-gkmsvm
3461 (uri (cran-uri "gkmSVM" version))
3464 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
3465 (properties `((upstream-name . "gkmSVM")))
3466 (build-system r-build-system)
3468 `(("r-kernlab" ,r-kernlab)
3471 ("r-seqinr" ,r-seqinr)))
3472 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
3473 (synopsis "Gapped-kmer support vector machine")
3475 "This R package provides tools for training gapped-kmer SVM classifiers
3476 for DNA and protein sequences. This package supports several sequence
3477 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
3478 (license license:gpl2+)))
3480 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
3481 (define-public r-mutoss
3488 (uri (cran-uri "mutoss" version))
3491 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
3492 (properties `((upstream-name . "mutoss")))
3493 (build-system r-build-system)
3495 `(("r-multcomp" ,r-multcomp)
3496 ("r-multtest" ,r-multtest)
3497 ("r-mvtnorm" ,r-mvtnorm)
3498 ("r-plotrix" ,r-plotrix)))
3499 (home-page "https://github.com/kornl/mutoss/")
3500 (synopsis "Unified multiple testing procedures")
3502 "This package is designed to ease the application and comparison of
3503 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
3504 are standardized and usable by the accompanying mutossGUI package.")
3505 ;; Any version of the GPL.
3506 (license (list license:gpl2+ license:gpl3+))))
3508 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
3509 ;; from Bioconductor, so we put it here.
3510 (define-public r-metap
3517 (uri (cran-uri "metap" version))
3520 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
3521 (build-system r-build-system)
3523 `(("r-lattice" ,r-lattice)
3524 ("r-mutoss" ,r-mutoss)
3525 ("r-rdpack" ,r-rdpack)
3526 ("r-tfisher" ,r-tfisher)))
3527 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3528 (synopsis "Meta-analysis of significance values")
3530 "The canonical way to perform meta-analysis involves using effect sizes.
3531 When they are not available this package provides a number of methods for
3532 meta-analysis of significance values including the methods of Edgington,
3533 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3534 published results; and a routine for graphical display.")
3535 (license license:gpl2)))
3537 (define-public r-triform
3544 (uri (bioconductor-uri "triform" version))
3547 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
3548 (build-system r-build-system)
3550 `(("r-biocgenerics" ,r-biocgenerics)
3551 ("r-iranges" ,r-iranges)
3552 ("r-yaml" ,r-yaml)))
3553 (home-page "https://bioconductor.org/packages/triform/")
3554 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
3556 "The Triform algorithm uses model-free statistics to identify peak-like
3557 distributions of TF ChIP sequencing reads, taking advantage of an improved
3558 peak definition in combination with known profile characteristics.")
3559 (license license:gpl2)))
3561 (define-public r-varianttools
3563 (name "r-varianttools")
3568 (uri (bioconductor-uri "VariantTools" version))
3571 "0g93rljlmhk1d53z0bgi84i2cn5c3r1dpm8id2pv0nk9ncdh3yxx"))))
3572 (properties `((upstream-name . "VariantTools")))
3573 (build-system r-build-system)
3575 `(("r-biobase" ,r-biobase)
3576 ("r-biocgenerics" ,r-biocgenerics)
3577 ("r-biocparallel" ,r-biocparallel)
3578 ("r-biostrings" ,r-biostrings)
3579 ("r-bsgenome" ,r-bsgenome)
3580 ("r-genomeinfodb" ,r-genomeinfodb)
3581 ("r-genomicfeatures" ,r-genomicfeatures)
3582 ("r-genomicranges" ,r-genomicranges)
3583 ("r-iranges" ,r-iranges)
3584 ("r-matrix" ,r-matrix)
3585 ("r-rsamtools" ,r-rsamtools)
3586 ("r-rtracklayer" ,r-rtracklayer)
3587 ("r-s4vectors" ,r-s4vectors)
3588 ("r-variantannotation" ,r-variantannotation)))
3589 (home-page "https://bioconductor.org/packages/VariantTools/")
3590 (synopsis "Tools for exploratory analysis of variant calls")
3592 "Explore, diagnose, and compare variant calls using filters. The
3593 VariantTools package supports a workflow for loading data, calling single
3594 sample variants and tumor-specific somatic mutations or other sample-specific
3595 variant types (e.g., RNA editing). Most of the functions operate on
3596 alignments (BAM files) or datasets of called variants. The user is expected
3597 to have already aligned the reads with a separate tool, e.g., GSNAP via
3599 (license license:artistic2.0)))
3601 (define-public r-heatplus
3608 (uri (bioconductor-uri "Heatplus" version))
3611 "12nd0h8svx7qydv1shk0gdpvnbixf7qi6zh06881wsmxf5s970rw"))))
3612 (properties `((upstream-name . "Heatplus")))
3613 (build-system r-build-system)
3615 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
3616 (home-page "https://github.com/alexploner/Heatplus")
3617 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
3619 "This package provides tools to display a rectangular heatmap (intensity
3620 plot) of a data matrix. By default, both samples (columns) and features (row)
3621 of the matrix are sorted according to a hierarchical clustering, and the
3622 corresponding dendrogram is plotted. Optionally, panels with additional
3623 information about samples and features can be added to the plot.")
3624 (license license:gpl2+)))
3626 (define-public r-gosemsim
3633 (uri (bioconductor-uri "GOSemSim" version))
3636 "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
3637 (properties `((upstream-name . "GOSemSim")))
3638 (build-system r-build-system)
3640 `(("r-annotationdbi" ,r-annotationdbi)
3641 ("r-go-db" ,r-go-db)
3642 ("r-rcpp" ,r-rcpp)))
3644 `(("r-knitr" ,r-knitr)))
3645 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
3646 (synopsis "GO-terms semantic similarity measures")
3648 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
3649 quantitative ways to compute similarities between genes and gene groups, and
3650 have became important basis for many bioinformatics analysis approaches.
3651 GOSemSim is an R package for semantic similarity computation among GO terms,
3652 sets of GO terms, gene products and gene clusters.")
3653 (license license:artistic2.0)))
3655 (define-public r-anota
3662 (uri (bioconductor-uri "anota" version))
3665 "1ind5cyq85l63xpqmg2n9rg805s5amh48iiw05zqr8kih6hlilpm"))))
3666 (build-system r-build-system)
3668 `(("r-multtest" ,r-multtest)
3669 ("r-qvalue" ,r-qvalue)))
3670 (home-page "https://bioconductor.org/packages/anota/")
3671 (synopsis "Analysis of translational activity")
3673 "Genome wide studies of translational control is emerging as a tool to
3674 study various biological conditions. The output from such analysis is both
3675 the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively
3676 involved in translation (the actively translating mRNA level) for each mRNA.
3677 The standard analysis of such data strives towards identifying differential
3678 translational between two or more sample classes - i.e. differences in
3679 actively translated mRNA levels that are independent of underlying differences
3680 in cytosolic mRNA levels. This package allows for such analysis using partial
3681 variances and the random variance model. As 10s of thousands of mRNAs are
3682 analyzed in parallel the library performs a number of tests to assure that
3683 the data set is suitable for such analysis.")
3684 (license license:gpl3)))
3686 (define-public r-sigpathway
3688 (name "r-sigpathway")
3693 (uri (bioconductor-uri "sigPathway" version))
3696 "0a79sdvag80p7xcdz8mp8wiby36yxmappzycfd2rp36v9drjk0h5"))))
3697 (properties `((upstream-name . "sigPathway")))
3698 (build-system r-build-system)
3699 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
3700 (synopsis "Pathway analysis")
3702 "This package is used to conduct pathway analysis by calculating the NT_k
3703 and NE_k statistics in a statistical framework for determining whether a
3704 specified group of genes for a pathway has a coordinated association with a
3705 phenotype of interest.")
3706 (license license:gpl2)))
3708 (define-public r-fgsea
3715 (uri (bioconductor-uri "fgsea" version))
3718 "0zbjj8al1ps7immxixsn5g8lvbmpmxvqwqbpdgsicxp00gb9bybc"))))
3719 (build-system r-build-system)
3722 ("r-biocparallel" ,r-biocparallel)
3723 ("r-data-table" ,r-data-table)
3724 ("r-fastmatch" ,r-fastmatch)
3725 ("r-ggplot2" ,r-ggplot2)
3726 ("r-gridextra" ,r-gridextra)
3727 ("r-matrix" ,r-matrix)
3728 ("r-rcpp" ,r-rcpp)))
3730 `(("r-knitr" ,r-knitr)))
3731 (home-page "https://github.com/ctlab/fgsea/")
3732 (synopsis "Fast gene set enrichment analysis")
3734 "The package implements an algorithm for fast gene set enrichment
3735 analysis. Using the fast algorithm makes more permutations and gets
3736 more fine grained p-values, which allows using accurate standard approaches
3737 to multiple hypothesis correction.")
3738 (license license:expat)))
3740 (define-public r-dose
3747 (uri (bioconductor-uri "DOSE" version))
3750 "1j0wcg7w2ns3ag9d272cqlg3j62ag2xnc5gfsjl6g2ij5xkvylb8"))))
3751 (properties `((upstream-name . "DOSE")))
3752 (build-system r-build-system)
3754 `(("r-annotationdbi" ,r-annotationdbi)
3755 ("r-biocparallel" ,r-biocparallel)
3756 ("r-do-db" ,r-do-db)
3757 ("r-fgsea" ,r-fgsea)
3758 ("r-ggplot2" ,r-ggplot2)
3759 ("r-gosemsim" ,r-gosemsim)
3760 ("r-qvalue" ,r-qvalue)
3761 ("r-reshape2" ,r-reshape2)))
3763 `(("r-knitr" ,r-knitr)))
3764 (home-page "https://guangchuangyu.github.io/software/DOSE/")
3765 (synopsis "Disease ontology semantic and enrichment analysis")
3767 "This package implements five methods proposed by Resnik, Schlicker,
3768 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
3769 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
3770 including hypergeometric model and gene set enrichment analysis are also
3771 implemented for discovering disease associations of high-throughput biological
3773 (license license:artistic2.0)))
3775 (define-public r-enrichplot
3777 (name "r-enrichplot")
3782 (uri (bioconductor-uri "enrichplot" version))
3785 "01m3cp717ldfbz5w3yfywvjg6sfjzz7s3vlk7w268lmmcg6g6bz7"))))
3786 (build-system r-build-system)
3788 `(("r-annotationdbi" ,r-annotationdbi)
3789 ("r-cowplot" ,r-cowplot)
3791 ("r-europepmc" ,r-europepmc)
3792 ("r-ggplot2" ,r-ggplot2)
3793 ("r-ggplotify" ,r-ggplotify)
3794 ("r-ggraph" ,r-ggraph)
3795 ("r-ggridges" ,r-ggridges)
3796 ("r-gosemsim" ,r-gosemsim)
3797 ("r-gridextra" ,r-gridextra)
3798 ("r-igraph" ,r-igraph)
3800 ("r-purrr" ,r-purrr)
3801 ("r-rcolorbrewer" ,r-rcolorbrewer)
3802 ("r-reshape2" ,r-reshape2)
3803 ("r-scatterpie" ,r-scatterpie)))
3805 `(("r-knitr" ,r-knitr)))
3806 (home-page "https://github.com/GuangchuangYu/enrichplot")
3807 (synopsis "Visualization of functional enrichment result")
3809 "The enrichplot package implements several visualization methods for
3810 interpreting functional enrichment results obtained from ORA or GSEA analyses.
3811 All the visualization methods are developed based on ggplot2 graphics.")
3812 (license license:artistic2.0)))
3814 (define-public r-clusterprofiler
3816 (name "r-clusterprofiler")
3821 (uri (bioconductor-uri "clusterProfiler" version))
3824 "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
3826 `((upstream-name . "clusterProfiler")))
3827 (build-system r-build-system)
3829 `(("r-annotationdbi" ,r-annotationdbi)
3831 ("r-downloader" ,r-downloader)
3832 ("r-dplyr" ,r-dplyr)
3833 ("r-enrichplot" ,r-enrichplot)
3834 ("r-go-db" ,r-go-db)
3835 ("r-gosemsim" ,r-gosemsim)
3836 ("r-magrittr" ,r-magrittr)
3838 ("r-qvalue" ,r-qvalue)
3839 ("r-rlang" ,r-rlang)
3840 ("r-rvcheck" ,r-rvcheck)
3841 ("r-tidyr" ,r-tidyr)))
3843 `(("r-knitr" ,r-knitr)))
3844 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
3845 (synopsis "Analysis and visualization of functional profiles for gene clusters")
3847 "This package implements methods to analyze and visualize functional
3848 profiles (GO and KEGG) of gene and gene clusters.")
3849 (license license:artistic2.0)))
3851 (define-public r-mlinterfaces
3853 (name "r-mlinterfaces")
3858 (uri (bioconductor-uri "MLInterfaces" version))
3861 "0x3mnvb5a6kri4q5w0wfmx02v79my08zhmkaik9pqlprd7y5wynq"))))
3862 (properties `((upstream-name . "MLInterfaces")))
3863 (build-system r-build-system)
3865 `(("r-annotate" ,r-annotate)
3866 ("r-biobase" ,r-biobase)
3867 ("r-biocgenerics" ,r-biocgenerics)
3868 ("r-cluster" ,r-cluster)
3871 ("r-gdata" ,r-gdata)
3872 ("r-genefilter" ,r-genefilter)
3873 ("r-ggvis" ,r-ggvis)
3874 ("r-hwriter" ,r-hwriter)
3876 ("r-mlbench" ,r-mlbench)
3878 ("r-rcolorbrewer" ,r-rcolorbrewer)
3880 ("r-rpart" ,r-rpart)
3881 ("r-sfsmisc" ,r-sfsmisc)
3882 ("r-shiny" ,r-shiny)
3883 ("r-threejs" ,r-threejs)))
3884 (home-page "https://bioconductor.org/packages/MLInterfaces/")
3885 (synopsis "Interfaces to R machine learning procedures")
3887 "This package provides uniform interfaces to machine learning code for
3888 data in R and Bioconductor containers.")
3889 ;; Any version of the LGPL.
3890 (license license:lgpl2.1+)))
3892 (define-public r-annaffy
3899 (uri (bioconductor-uri "annaffy" version))
3902 "1rc9fb83by9jfgwfj2zhhbj93v296blwd8jl2rh7jj200mrpznn4"))))
3903 (build-system r-build-system)
3906 (modify-phases %standard-phases
3907 (add-after 'unpack 'remove-reference-to-non-free-data
3909 (substitute* "DESCRIPTION"
3913 `(("r-annotationdbi" ,r-annotationdbi)
3914 ("r-biobase" ,r-biobase)
3916 ("r-go-db" ,r-go-db)))
3917 (home-page "https://bioconductor.org/packages/annaffy/")
3918 (synopsis "Annotation tools for Affymetrix biological metadata")
3920 "This package provides functions for handling data from Bioconductor
3921 Affymetrix annotation data packages. It produces compact HTML and text
3922 reports including experimental data and URL links to many online databases.
3923 It allows searching of biological metadata using various criteria.")
3924 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
3925 ;; the LGPL 2.1 is included.
3926 (license license:lgpl2.1+)))
3928 (define-public r-a4core
3935 (uri (bioconductor-uri "a4Core" version))
3938 "1hn9lkaib1bx5n52as882f8zwsln8w40sx8hxbrnimjvgfxrbvnp"))))
3939 (properties `((upstream-name . "a4Core")))
3940 (build-system r-build-system)
3942 `(("r-biobase" ,r-biobase)
3943 ("r-glmnet" ,r-glmnet)))
3944 (home-page "https://bioconductor.org/packages/a4Core")
3945 (synopsis "Automated Affymetrix array analysis core package")
3947 "This is the core package for the automated analysis of Affymetrix
3949 (license license:gpl3)))
3951 (define-public r-a4classif
3953 (name "r-a4classif")
3958 (uri (bioconductor-uri "a4Classif" version))
3961 "0bj8m4nprw3maahd1qx9jjdxfip9ihbbpydbzwjxn6dlgw2i8mcr"))))
3962 (properties `((upstream-name . "a4Classif")))
3963 (build-system r-build-system)
3965 `(("r-a4core" ,r-a4core)
3966 ("r-a4preproc" ,r-a4preproc)
3967 ("r-glmnet" ,r-glmnet)
3968 ("r-mlinterfaces" ,r-mlinterfaces)
3971 ("r-varselrf" ,r-varselrf)))
3972 (home-page "https://bioconductor.org/packages/a4Classif/")
3973 (synopsis "Automated Affymetrix array analysis classification package")
3975 "This is the classification package for the automated analysis of
3976 Affymetrix arrays.")
3977 (license license:gpl3)))
3979 (define-public r-a4preproc
3981 (name "r-a4preproc")
3986 (uri (bioconductor-uri "a4Preproc" version))
3989 "1hy3jvhdjyjzzmw5wkil3cs26hvqnb056r09x0p2bjg5sc9hh8b8"))))
3990 (properties `((upstream-name . "a4Preproc")))
3991 (build-system r-build-system)
3993 `(("r-annotationdbi" ,r-annotationdbi)))
3994 (home-page "https://bioconductor.org/packages/a4Preproc/")
3995 (synopsis "Automated Affymetrix array analysis preprocessing package")
3997 "This is a package for the automated analysis of Affymetrix arrays. It
3998 is used for preprocessing the arrays.")
3999 (license license:gpl3)))
4001 (define-public r-a4reporting
4003 (name "r-a4reporting")
4008 (uri (bioconductor-uri "a4Reporting" version))
4011 "1jhlxqwfbgflcyzy9gyxznzcadj9zxchl3lfdlc4ffm0hwz5jl2f"))))
4012 (properties `((upstream-name . "a4Reporting")))
4013 (build-system r-build-system)
4015 `(("r-annaffy" ,r-annaffy)
4016 ("r-xtable" ,r-xtable)))
4017 (home-page "https://bioconductor.org/packages/a4Reporting/")
4018 (synopsis "Automated Affymetrix array analysis reporting package")
4020 "This is a package for the automated analysis of Affymetrix arrays. It
4021 provides reporting features.")
4022 (license license:gpl3)))
4024 (define-public r-a4base
4031 (uri (bioconductor-uri "a4Base" version))
4034 "0b7fy1wcydb9z43wb1663skswvhivn7ji15g00gqcshwkkiq4x02"))))
4035 (properties `((upstream-name . "a4Base")))
4036 (build-system r-build-system)
4038 `(("r-a4core" ,r-a4core)
4039 ("r-a4preproc" ,r-a4preproc)
4040 ("r-annaffy" ,r-annaffy)
4041 ("r-annotationdbi" ,r-annotationdbi)
4042 ("r-biobase" ,r-biobase)
4043 ("r-genefilter" ,r-genefilter)
4044 ("r-glmnet" ,r-glmnet)
4045 ("r-gplots" ,r-gplots)
4046 ("r-limma" ,r-limma)
4048 ("r-multtest" ,r-multtest)))
4049 (home-page "https://bioconductor.org/packages/a4Base/")
4050 (synopsis "Automated Affymetrix array analysis base package")
4052 "This package provides basic features for the automated analysis of
4053 Affymetrix arrays.")
4054 (license license:gpl3)))
4063 (uri (bioconductor-uri "a4" version))
4066 "1rzxg1h48jnlwqfjyyqzz6i3zlkfzc0i714rfplry7dyni6asgr7"))))
4067 (build-system r-build-system)
4069 `(("r-a4base" ,r-a4base)
4070 ("r-a4classif" ,r-a4classif)
4071 ("r-a4core" ,r-a4core)
4072 ("r-a4preproc" ,r-a4preproc)
4073 ("r-a4reporting" ,r-a4reporting)))
4074 (home-page "https://bioconductor.org/packages/a4/")
4075 (synopsis "Automated Affymetrix array analysis umbrella package")
4077 "This package provides a software suite for the automated analysis of
4078 Affymetrix arrays.")
4079 (license license:gpl3)))
4081 (define-public r-abseqr
4088 (uri (bioconductor-uri "abseqR" version))
4091 "0pzyfn0jv41rja6l4jbgwgsqy0q1d3kz23m9m6pc67p2a231i9c5"))))
4092 (properties `((upstream-name . "abseqR")))
4093 (build-system r-build-system)
4095 `(("pandoc" ,pandoc)
4096 ("pandoc-citeproc" ,pandoc-citeproc)))
4098 `(("r-biocparallel" ,r-biocparallel)
4099 ("r-biocstyle" ,r-biocstyle)
4100 ("r-circlize" ,r-circlize)
4101 ("r-flexdashboard" ,r-flexdashboard)
4102 ("r-ggcorrplot" ,r-ggcorrplot)
4103 ("r-ggdendro" ,r-ggdendro)
4104 ("r-ggplot2" ,r-ggplot2)
4105 ("r-gridextra" ,r-gridextra)
4106 ("r-knitr" ,r-knitr)
4107 ("r-plotly" ,r-plotly)
4110 ("r-rcolorbrewer" ,r-rcolorbrewer)
4111 ("r-reshape2" ,r-reshape2)
4112 ("r-rmarkdown" ,r-rmarkdown)
4113 ("r-stringr" ,r-stringr)
4114 ("r-vegan" ,r-vegan)
4115 ("r-venndiagram" ,r-venndiagram)))
4117 `(("r-knitr" ,r-knitr)))
4118 (home-page "https://github.com/malhamdoosh/abseqR")
4119 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4121 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4122 sequencing datasets generated from antibody libraries and abseqR is one of its
4123 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4124 capabilities and allows them to generate interactive HTML reports for the
4125 convenience of viewing and sharing with other researchers. Additionally,
4126 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4127 further downstream analysis on its output.")
4128 (license license:gpl3)))
4130 (define-public r-bacon
4137 (uri (bioconductor-uri "bacon" version))
4140 "066b9vyp8ivnzm9741mb5z763a7z40ar9m8w31yw84fjiv01v3dl"))))
4141 (build-system r-build-system)
4143 `(("r-biocparallel" ,r-biocparallel)
4144 ("r-ellipse" ,r-ellipse)
4145 ("r-ggplot2" ,r-ggplot2)))
4147 `(("r-knitr" ,r-knitr)))
4148 (home-page "https://bioconductor.org/packages/bacon/")
4149 (synopsis "Controlling bias and inflation in association studies")
4151 "Bacon can be used to remove inflation and bias often observed in
4152 epigenome- and transcriptome-wide association studies. To this end bacon
4153 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4154 fitting a three-component normal mixture on z-scores.")
4155 (license license:gpl2+)))
4157 (define-public r-rgadem
4164 (uri (bioconductor-uri "rGADEM" version))
4167 "14mflbwhhj9f3b05zdlsdjwxmpb120r23fy306qkvxjprdqn4sz8"))))
4168 (properties `((upstream-name . "rGADEM")))
4169 (build-system r-build-system)
4171 `(("r-biostrings" ,r-biostrings)
4172 ("r-bsgenome" ,r-bsgenome)
4173 ("r-genomicranges" ,r-genomicranges)
4174 ("r-iranges" ,r-iranges)
4175 ("r-seqlogo" ,r-seqlogo)))
4176 (home-page "https://bioconductor.org/packages/rGADEM/")
4177 (synopsis "De novo sequence motif discovery")
4179 "rGADEM is an efficient de novo motif discovery tool for large-scale
4180 genomic sequence data.")
4181 (license license:artistic2.0)))
4183 (define-public r-motiv
4190 (uri (bioconductor-uri "MotIV" version))
4193 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4194 (properties `((upstream-name . "MotIV")))
4195 (build-system r-build-system)
4199 `(("r-biocgenerics" ,r-biocgenerics)
4200 ("r-biostrings" ,r-biostrings)
4201 ("r-genomicranges" ,r-genomicranges)
4202 ("r-iranges" ,r-iranges)
4203 ("r-lattice" ,r-lattice)
4204 ("r-rgadem" ,r-rgadem)
4205 ("r-s4vectors" ,r-s4vectors)))
4206 (home-page "https://bioconductor.org/packages/MotIV/")
4207 (synopsis "Motif identification and validation")
4209 "This package is used for the identification and validation of sequence
4210 motifs. It makes use of STAMP for comparing a set of motifs to a given
4211 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4212 distributions, modules and filter motifs.")
4213 (license license:gpl2)))
4215 (define-public r-motifdb
4221 (uri (bioconductor-uri "MotifDb" version))
4223 (base32 "0ixmdqp0s0xv9ar85n2wirbbssrzlk8a892wam55jdsf9y8aabkm"))))
4224 (properties `((upstream-name . "MotifDb")))
4225 (build-system r-build-system)
4227 `(("r-biocgenerics" ,r-biocgenerics)
4228 ("r-biostrings" ,r-biostrings)
4229 ("r-genomicranges" ,r-genomicranges)
4230 ("r-iranges" ,r-iranges)
4231 ("r-rtracklayer" ,r-rtracklayer)
4232 ("r-s4vectors" ,r-s4vectors)
4233 ("r-splitstackshape" ,r-splitstackshape)))
4235 `(("r-knitr" ,r-knitr)))
4236 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4237 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4238 (description "This package provides more than 2000 annotated position
4239 frequency matrices from nine public sources, for multiple organisms.")
4240 (license license:artistic2.0)))
4242 (define-public r-motifbreakr
4244 (name "r-motifbreakr")
4248 (uri (bioconductor-uri "motifbreakR" version))
4250 (base32 "09czgmyjcycsvyvadpjddwwvqvxzd0ba3zhczh4mqc09gwa6vhlm"))))
4251 (properties `((upstream-name . "motifbreakR")))
4252 (build-system r-build-system)
4254 `(("r-biocgenerics" ,r-biocgenerics)
4255 ("r-biocparallel" ,r-biocparallel)
4256 ("r-biostrings" ,r-biostrings)
4257 ("r-bsgenome" ,r-bsgenome)
4258 ("r-genomeinfodb" ,r-genomeinfodb)
4259 ("r-genomicranges" ,r-genomicranges)
4260 ("r-grimport" ,r-grimport)
4262 ("r-iranges" ,r-iranges)
4263 ("r-matrixstats" ,r-matrixstats)
4264 ("r-motifdb" ,r-motifdb)
4265 ("r-motifstack" ,r-motifstack)
4266 ("r-rtracklayer" ,r-rtracklayer)
4267 ("r-s4vectors" ,r-s4vectors)
4268 ("r-stringr" ,r-stringr)
4269 ("r-summarizedexperiment" ,r-summarizedexperiment)
4270 ("r-tfmpvalue" ,r-tfmpvalue)
4271 ("r-variantannotation" ,r-variantannotation)))
4273 `(("r-knitr" ,r-knitr)))
4274 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4275 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4276 (description "This package allows biologists to judge in the first place
4277 whether the sequence surrounding the polymorphism is a good match, and in
4278 the second place how much information is gained or lost in one allele of
4279 the polymorphism relative to another. This package gives a choice of
4280 algorithms for interrogation of genomes with motifs from public sources:
4282 @item a weighted-sum probability matrix;
4283 @item log-probabilities;
4284 @item weighted by relative entropy.
4287 This package can predict effects for novel or previously described variants in
4288 public databases, making it suitable for tasks beyond the scope of its original
4289 design. Lastly, it can be used to interrogate any genome curated within
4291 (license license:gpl2+)))
4293 (define-public r-motifstack
4295 (name "r-motifstack")
4300 (uri (bioconductor-uri "motifStack" version))
4303 "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
4304 (properties `((upstream-name . "motifStack")))
4305 (build-system r-build-system)
4307 `(("r-ade4" ,r-ade4)
4308 ("r-biostrings" ,r-biostrings)
4309 ("r-ggplot2" ,r-ggplot2)
4310 ("r-grimport2" ,r-grimport2)
4311 ("r-htmlwidgets" ,r-htmlwidgets)
4312 ("r-motiv" ,r-motiv)
4313 ("r-scales" ,r-scales)
4316 `(("r-knitr" ,r-knitr)))
4317 (home-page "https://bioconductor.org/packages/motifStack/")
4318 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
4320 "The motifStack package is designed for graphic representation of
4321 multiple motifs with different similarity scores. It works with both DNA/RNA
4322 sequence motifs and amino acid sequence motifs. In addition, it provides the
4323 flexibility for users to customize the graphic parameters such as the font
4324 type and symbol colors.")
4325 (license license:gpl2+)))
4327 (define-public r-genomicscores
4329 (name "r-genomicscores")
4334 (uri (bioconductor-uri "GenomicScores" version))
4337 "0si2lgc37mkah4w990q1q2bf8xmshxj7cbx92bcrp0zaipjr96bb"))))
4338 (properties `((upstream-name . "GenomicScores")))
4339 (build-system r-build-system)
4341 `(("r-annotationhub" ,r-annotationhub)
4342 ("r-biobase" ,r-biobase)
4343 ("r-biocgenerics" ,r-biocgenerics)
4344 ("r-biostrings" ,r-biostrings)
4345 ("r-delayedarray" ,r-delayedarray)
4346 ("r-genomeinfodb" ,r-genomeinfodb)
4347 ("r-genomicranges" ,r-genomicranges)
4348 ("r-hdf5array" ,r-hdf5array)
4349 ("r-iranges" ,r-iranges)
4350 ("r-rhdf5" ,r-rhdf5)
4351 ("r-s4vectors" ,r-s4vectors)
4354 `(("r-knitr" ,r-knitr)))
4355 (home-page "https://github.com/rcastelo/GenomicScores/")
4356 (synopsis "Work with genome-wide position-specific scores")
4358 "This package provides infrastructure to store and access genome-wide
4359 position-specific scores within R and Bioconductor.")
4360 (license license:artistic2.0)))
4362 (define-public r-atacseqqc
4364 (name "r-atacseqqc")
4369 (uri (bioconductor-uri "ATACseqQC" version))
4372 "1gs9862hhh4gr1akij6ykhcj29s9dzg1vnj87hqrm19dfgl43qbh"))))
4373 (properties `((upstream-name . "ATACseqQC")))
4374 (build-system r-build-system)
4376 `(("r-biocgenerics" ,r-biocgenerics)
4377 ("r-biostrings" ,r-biostrings)
4378 ("r-bsgenome" ,r-bsgenome)
4379 ("r-chippeakanno" ,r-chippeakanno)
4380 ("r-edger" ,r-edger)
4381 ("r-genomeinfodb" ,r-genomeinfodb)
4382 ("r-genomicalignments" ,r-genomicalignments)
4383 ("r-genomicranges" ,r-genomicranges)
4384 ("r-genomicscores" ,r-genomicscores)
4385 ("r-iranges" ,r-iranges)
4386 ("r-kernsmooth" ,r-kernsmooth)
4387 ("r-limma" ,r-limma)
4388 ("r-motifstack" ,r-motifstack)
4389 ("r-preseqr" ,r-preseqr)
4390 ("r-randomforest" ,r-randomforest)
4391 ("r-rsamtools" ,r-rsamtools)
4392 ("r-rtracklayer" ,r-rtracklayer)
4393 ("r-s4vectors" ,r-s4vectors)))
4395 `(("r-knitr" ,r-knitr)))
4396 (home-page "https://bioconductor.org/packages/ATACseqQC/")
4397 (synopsis "ATAC-seq quality control")
4399 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
4400 sequencing, is a rapid and sensitive method for chromatin accessibility
4401 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
4402 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
4403 assess whether their ATAC-seq experiment is successful. It includes
4404 diagnostic plots of fragment size distribution, proportion of mitochondria
4405 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
4407 (license license:gpl2+)))
4409 (define-public r-gofuncr
4416 (uri (bioconductor-uri "GOfuncR" version))
4419 "1ixjkqb9wpwqfzxsg0h96c6fa63wrk72sfh6x4pq0kpyrcc0ind1"))))
4420 (properties `((upstream-name . "GOfuncR")))
4421 (build-system r-build-system)
4423 `(("r-annotationdbi" ,r-annotationdbi)
4424 ("r-genomicranges" ,r-genomicranges)
4425 ("r-gtools" ,r-gtools)
4426 ("r-iranges" ,r-iranges)
4427 ("r-mapplots" ,r-mapplots)
4429 ("r-vioplot" ,r-vioplot)))
4431 `(("r-knitr" ,r-knitr)))
4432 (home-page "https://bioconductor.org/packages/GOfuncR/")
4433 (synopsis "Gene ontology enrichment using FUNC")
4435 "GOfuncR performs a gene ontology enrichment analysis based on the
4436 ontology enrichment software FUNC. GO-annotations are obtained from
4437 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
4438 included in the package and updated regularly. GOfuncR provides the standard
4439 candidate vs background enrichment analysis using the hypergeometric test, as
4440 well as three additional tests:
4443 @item the Wilcoxon rank-sum test that is used when genes are ranked,
4444 @item a binomial test that is used when genes are associated with two counts,
4446 @item a Chi-square or Fisher's exact test that is used in cases when genes are
4447 associated with four counts.
4450 To correct for multiple testing and interdependency of the tests, family-wise
4451 error rates are computed based on random permutations of the gene-associated
4452 variables. GOfuncR also provides tools for exploring the ontology graph and
4453 the annotations, and options to take gene-length or spatial clustering of
4454 genes into account. It is also possible to provide custom gene coordinates,
4455 annotations and ontologies.")
4456 (license license:gpl2+)))
4458 (define-public r-abaenrichment
4460 (name "r-abaenrichment")
4465 (uri (bioconductor-uri "ABAEnrichment" version))
4468 "09ihbgxrhpcz2q7svldhm710a0yrhiqk9p0q0myv11c2w50ymwkw"))))
4469 (properties `((upstream-name . "ABAEnrichment")))
4470 (build-system r-build-system)
4472 `(("r-abadata" ,r-abadata)
4473 ("r-data-table" ,r-data-table)
4474 ("r-gofuncr" ,r-gofuncr)
4475 ("r-gplots" ,r-gplots)
4476 ("r-gtools" ,r-gtools)
4477 ("r-rcpp" ,r-rcpp)))
4479 `(("r-knitr" ,r-knitr)))
4480 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
4481 (synopsis "Gene expression enrichment in human brain regions")
4483 "The package ABAEnrichment is designed to test for enrichment of user
4484 defined candidate genes in the set of expressed genes in different human brain
4485 regions. The core function @code{aba_enrich} integrates the expression of the
4486 candidate gene set (averaged across donors) and the structural information of
4487 the brain using an ontology, both provided by the Allen Brain Atlas project.")
4488 (license license:gpl2+)))
4490 (define-public r-annotationfuncs
4492 (name "r-annotationfuncs")
4497 (uri (bioconductor-uri "AnnotationFuncs" version))
4500 "1yfsxzn7s1nlc3xz2yj39j6hmdfapc9qj9h0cd71gkaxj53ial7d"))))
4502 `((upstream-name . "AnnotationFuncs")))
4503 (build-system r-build-system)
4505 `(("r-annotationdbi" ,r-annotationdbi)
4507 (home-page "https://www.iysik.com/r/annotationfuncs")
4508 (synopsis "Annotation translation functions")
4510 "This package provides functions for handling translating between
4511 different identifieres using the Biocore Data Team data-packages (e.g.
4512 @code{org.Bt.eg.db}).")
4513 (license license:gpl2)))
4515 (define-public r-annotationtools
4517 (name "r-annotationtools")
4522 (uri (bioconductor-uri "annotationTools" version))
4525 "1b1yfnknr9vbn4y2mxdfyx57i5jbabhp9pwx8axlg2a7lawkfmdk"))))
4527 `((upstream-name . "annotationTools")))
4528 (build-system r-build-system)
4529 (propagated-inputs `(("r-biobase" ,r-biobase)))
4530 (home-page "https://bioconductor.org/packages/annotationTools/")
4531 (synopsis "Annotate microarrays and perform gene expression analyses")
4533 "This package provides functions to annotate microarrays, find orthologs,
4534 and integrate heterogeneous gene expression profiles using annotation and
4535 other molecular biology information available as flat file database (plain
4537 ;; Any version of the GPL.
4538 (license (list license:gpl2+))))
4540 (define-public r-allelicimbalance
4542 (name "r-allelicimbalance")
4547 (uri (bioconductor-uri "AllelicImbalance" version))
4550 "0irn4xdlvazdkv0055f45693y6zvqaz7j3vml5xscnh45ls6vmqr"))))
4552 `((upstream-name . "AllelicImbalance")))
4553 (build-system r-build-system)
4555 `(("r-annotationdbi" ,r-annotationdbi)
4556 ("r-biocgenerics" ,r-biocgenerics)
4557 ("r-biostrings" ,r-biostrings)
4558 ("r-bsgenome" ,r-bsgenome)
4559 ("r-genomeinfodb" ,r-genomeinfodb)
4560 ("r-genomicalignments" ,r-genomicalignments)
4561 ("r-genomicfeatures" ,r-genomicfeatures)
4562 ("r-genomicranges" ,r-genomicranges)
4563 ("r-gridextra" ,r-gridextra)
4565 ("r-iranges" ,r-iranges)
4566 ("r-lattice" ,r-lattice)
4567 ("r-latticeextra" ,r-latticeextra)
4569 ("r-rsamtools" ,r-rsamtools)
4570 ("r-s4vectors" ,r-s4vectors)
4571 ("r-seqinr" ,r-seqinr)
4572 ("r-summarizedexperiment" ,r-summarizedexperiment)
4573 ("r-variantannotation" ,r-variantannotation)))
4575 `(("r-knitr" ,r-knitr)))
4576 (home-page "https://github.com/pappewaio/AllelicImbalance")
4577 (synopsis "Investigate allele-specific expression")
4579 "This package provides a framework for allele-specific expression
4580 investigation using RNA-seq data.")
4581 (license license:gpl3)))
4583 (define-public r-aucell
4590 (uri (bioconductor-uri "AUCell" version))
4593 "0fgqkgjhf92vkljkwn44lm8cjvzq1lvk80nk6xhsp5q6s5isbmns"))))
4594 (properties `((upstream-name . "AUCell")))
4595 (build-system r-build-system)
4597 `(("r-biocgenerics" ,r-biocgenerics)
4598 ("r-data-table" ,r-data-table)
4599 ("r-gseabase" ,r-gseabase)
4600 ("r-mixtools" ,r-mixtools)
4601 ("r-r-utils" ,r-r-utils)
4602 ("r-s4vectors" ,r-s4vectors)
4603 ("r-shiny" ,r-shiny)
4604 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4606 `(("r-knitr" ,r-knitr)))
4607 (home-page "https://bioconductor.org/packages/AUCell/")
4608 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
4610 "AUCell identifies cells with active gene sets (e.g. signatures,
4611 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
4612 Under the Curve} (AUC) to calculate whether a critical subset of the input
4613 gene set is enriched within the expressed genes for each cell. The
4614 distribution of AUC scores across all the cells allows exploring the relative
4615 expression of the signature. Since the scoring method is ranking-based,
4616 AUCell is independent of the gene expression units and the normalization
4617 procedure. In addition, since the cells are evaluated individually, it can
4618 easily be applied to bigger datasets, subsetting the expression matrix if
4620 (license license:gpl3)))
4622 (define-public r-ebimage
4629 (uri (bioconductor-uri "EBImage" version))
4632 "13amrbh545hwk7sygndzyv7wpa0m2y0lzlwj89jm1xm62x577w9v"))))
4633 (properties `((upstream-name . "EBImage")))
4634 (build-system r-build-system)
4636 `(("r-abind" ,r-abind)
4637 ("r-biocgenerics" ,r-biocgenerics)
4638 ("r-fftwtools" ,r-fftwtools)
4639 ("r-htmltools" ,r-htmltools)
4640 ("r-htmlwidgets" ,r-htmlwidgets)
4642 ("r-locfit" ,r-locfit)
4644 ("r-rcurl" ,r-rcurl)
4645 ("r-tiff" ,r-tiff)))
4647 `(("r-knitr" ,r-knitr))) ; for vignettes
4648 (home-page "https://github.com/aoles/EBImage")
4649 (synopsis "Image processing and analysis toolbox for R")
4651 "EBImage provides general purpose functionality for image processing and
4652 analysis. In the context of (high-throughput) microscopy-based cellular
4653 assays, EBImage offers tools to segment cells and extract quantitative
4654 cellular descriptors. This allows the automation of such tasks using the R
4655 programming language and facilitates the use of other tools in the R
4656 environment for signal processing, statistical modeling, machine learning and
4657 visualization with image data.")
4658 ;; Any version of the LGPL.
4659 (license license:lgpl2.1+)))
4661 (define-public r-yamss
4668 (uri (bioconductor-uri "yamss" version))
4671 "00x2lnssgzbmhy5bb2m0f8rq2nsz3lb5xlp2vhkcagza39h3xb0c"))))
4672 (build-system r-build-system)
4674 `(("r-biocgenerics" ,r-biocgenerics)
4675 ("r-data-table" ,r-data-table)
4676 ("r-ebimage" ,r-ebimage)
4677 ("r-iranges" ,r-iranges)
4678 ("r-limma" ,r-limma)
4679 ("r-matrix" ,r-matrix)
4681 ("r-s4vectors" ,r-s4vectors)
4682 ("r-summarizedexperiment"
4683 ,r-summarizedexperiment)))
4685 `(("r-knitr" ,r-knitr)))
4686 (home-page "https://github.com/hansenlab/yamss")
4687 (synopsis "Tools for high-throughput metabolomics")
4689 "This package provides tools to analyze and visualize high-throughput
4690 metabolomics data acquired using chromatography-mass spectrometry. These tools
4691 preprocess data in a way that enables reliable and powerful differential
4693 (license license:artistic2.0)))
4695 (define-public r-gtrellis
4702 (uri (bioconductor-uri "gtrellis" version))
4705 "1v2l7r945xx4cf9s8m19csj7716n2ayxy05adkl8zqgxk0gxzqm1"))))
4706 (build-system r-build-system)
4708 `(("r-circlize" ,r-circlize)
4709 ("r-genomicranges" ,r-genomicranges)
4710 ("r-getoptlong" ,r-getoptlong)
4711 ("r-iranges" ,r-iranges)))
4713 `(("r-knitr" ,r-knitr)))
4714 (home-page "https://github.com/jokergoo/gtrellis")
4715 (synopsis "Genome level Trellis layout")
4717 "Genome level Trellis graph visualizes genomic data conditioned by
4718 genomic categories (e.g. chromosomes). For each genomic category, multiple
4719 dimensional data which are represented as tracks describe different features
4720 from different aspects. This package provides high flexibility to arrange
4721 genomic categories and to add self-defined graphics in the plot.")
4722 (license license:expat)))
4724 (define-public r-somaticsignatures
4726 (name "r-somaticsignatures")
4731 (uri (bioconductor-uri "SomaticSignatures" version))
4734 "0d34mss73w1jdnmilk060a1fywlfmqbnlir089q9m3q1p3x0j4c1"))))
4736 `((upstream-name . "SomaticSignatures")))
4737 (build-system r-build-system)
4739 `(("r-biobase" ,r-biobase)
4740 ("r-biostrings" ,r-biostrings)
4741 ("r-genomeinfodb" ,r-genomeinfodb)
4742 ("r-genomicranges" ,r-genomicranges)
4743 ("r-ggbio" ,r-ggbio)
4744 ("r-ggplot2" ,r-ggplot2)
4745 ("r-iranges" ,r-iranges)
4747 ("r-pcamethods" ,r-pcamethods)
4748 ("r-proxy" ,r-proxy)
4749 ("r-reshape2" ,r-reshape2)
4750 ("r-s4vectors" ,r-s4vectors)
4751 ("r-variantannotation" ,r-variantannotation)))
4753 `(("r-knitr" ,r-knitr)))
4754 (home-page "https://github.com/juliangehring/SomaticSignatures")
4755 (synopsis "Somatic signatures")
4757 "This package identifies mutational signatures of @dfn{single nucleotide
4758 variants} (SNVs). It provides a infrastructure related to the methodology
4759 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
4760 decomposition algorithms.")
4761 (license license:expat)))
4763 (define-public r-yapsa
4770 (uri (bioconductor-uri "YAPSA" version))
4773 "06lkf01vl4fyhj82srx8k870fhw76a1han0kp4jglh43b1c19c1k"))))
4774 (properties `((upstream-name . "YAPSA")))
4775 (build-system r-build-system)
4777 `(("r-biostrings" ,r-biostrings)
4778 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
4779 ("r-circlize" ,r-circlize)
4780 ("r-complexheatmap" ,r-complexheatmap)
4781 ("r-corrplot" ,r-corrplot)
4782 ("r-dendextend" ,r-dendextend)
4783 ("r-doparallel" ,r-doparallel)
4784 ("r-dplyr" ,r-dplyr)
4785 ("r-genomeinfodb" ,r-genomeinfodb)
4786 ("r-genomicranges" ,r-genomicranges)
4787 ("r-getoptlong" ,r-getoptlong)
4788 ("r-ggbeeswarm" ,r-ggbeeswarm)
4789 ("r-ggplot2" ,r-ggplot2)
4790 ("r-gridextra" ,r-gridextra)
4791 ("r-gtrellis" ,r-gtrellis)
4792 ("r-keggrest" ,r-keggrest)
4794 ("r-magrittr" ,r-magrittr)
4795 ("r-pmcmr" ,r-pmcmr)
4796 ("r-pracma" ,r-pracma)
4797 ("r-reshape2" ,r-reshape2)
4798 ("r-somaticsignatures" ,r-somaticsignatures)
4799 ("r-variantannotation" ,r-variantannotation)))
4801 `(("r-knitr" ,r-knitr)))
4802 (home-page "https://bioconductor.org/packages/YAPSA/")
4803 (synopsis "Yet another package for signature analysis")
4805 "This package provides functions and routines useful in the analysis of
4806 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
4807 functions to perform a signature analysis with known signatures and a
4808 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
4810 (license license:gpl3)))
4812 (define-public r-gcrma
4819 (uri (bioconductor-uri "gcrma" version))
4822 "1klbnygc1i5ac1x00bsk0rjw5h5dn6pn65fa3y9r09q47gpy1c5g"))))
4823 (build-system r-build-system)
4825 `(("r-affy" ,r-affy)
4826 ("r-affyio" ,r-affyio)
4827 ("r-biobase" ,r-biobase)
4828 ("r-biocmanager" ,r-biocmanager)
4829 ("r-biostrings" ,r-biostrings)
4830 ("r-xvector" ,r-xvector)))
4831 (home-page "https://bioconductor.org/packages/gcrma/")
4832 (synopsis "Background adjustment using sequence information")
4834 "Gcrma adjusts for background intensities in Affymetrix array data which
4835 include optical noise and @dfn{non-specific binding} (NSB). The main function
4836 @code{gcrma} converts background adjusted probe intensities to expression
4837 measures using the same normalization and summarization methods as a
4838 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
4839 to estimate probe affinity to NSB. The sequence information is summarized in
4840 a more complex way than the simple GC content. Instead, the base types (A, T,
4841 G or C) at each position along the probe determine the affinity of each probe.
4842 The parameters of the position-specific base contributions to the probe
4843 affinity is estimated in an NSB experiment in which only NSB but no
4844 gene-specific bidning is expected.")
4845 ;; Any version of the LGPL
4846 (license license:lgpl2.1+)))
4848 (define-public r-simpleaffy
4850 (name "r-simpleaffy")
4855 (uri (bioconductor-uri "simpleaffy" version))
4858 "040043spblr8v67lkn3nnxhgfmfh2iwaizph4fnms1ik6qz662x7"))))
4859 (build-system r-build-system)
4861 `(("r-affy" ,r-affy)
4862 ("r-biobase" ,r-biobase)
4863 ("r-biocgenerics" ,r-biocgenerics)
4864 ("r-gcrma" ,r-gcrma)
4865 ("r-genefilter" ,r-genefilter)))
4866 (home-page "https://bioconductor.org/packages/simpleaffy/")
4867 (synopsis "Very simple high level analysis of Affymetrix data")
4869 "This package provides high level functions for reading Affy @file{.CEL}
4870 files, phenotypic data, and then computing simple things with it, such as
4871 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
4872 library. It also has some basic scatter plot functions and mechanisms for
4873 generating high resolution journal figures.")
4874 (license license:gpl2+)))
4876 (define-public r-yaqcaffy
4883 (uri (bioconductor-uri "yaqcaffy" version))
4886 "1l0cblh9sfrsil15bjya7d8kkas8bj6klj2w3c4384njdsjsjcf0"))))
4887 (build-system r-build-system)
4889 `(("r-simpleaffy" ,r-simpleaffy)))
4890 (home-page "https://bioconductor.org/packages/yaqcaffy/")
4891 (synopsis "Affymetrix quality control and reproducibility analysis")
4893 "This is a package that can be used for quality control of Affymetrix
4894 GeneChip expression data and reproducibility analysis of human whole genome
4895 chips with the MAQC reference datasets.")
4896 (license license:artistic2.0)))
4898 (define-public r-quantro
4905 (uri (bioconductor-uri "quantro" version))
4908 "0ap9cl5z79wg44mnagjsk8py3kngb4f0ddnx85cbnwqkvb769zbz"))))
4909 (build-system r-build-system)
4911 `(("r-biobase" ,r-biobase)
4912 ("r-doparallel" ,r-doparallel)
4913 ("r-foreach" ,r-foreach)
4914 ("r-ggplot2" ,r-ggplot2)
4915 ("r-iterators" ,r-iterators)
4916 ("r-minfi" ,r-minfi)
4917 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4919 `(("r-knitr" ,r-knitr)))
4920 (home-page "https://bioconductor.org/packages/quantro/")
4921 (synopsis "Test for when to use quantile normalization")
4923 "This package provides a data-driven test for the assumptions of quantile
4924 normalization using raw data such as objects that inherit eSets (e.g.
4925 ExpressionSet, MethylSet). Group level information about each sample (such as
4926 Tumor / Normal status) must also be provided because the test assesses if
4927 there are global differences in the distributions between the user-defined
4929 (license license:gpl3+)))
4931 (define-public r-yarn
4938 (uri (bioconductor-uri "yarn" version))
4941 "1xdjwy1gkfg8lhgq4iwwmbi01903qljjs7yd96cvacmvgn8z6qvx"))))
4942 (build-system r-build-system)
4944 `(("r-biobase" ,r-biobase)
4945 ("r-biomart" ,r-biomart)
4946 ("r-downloader" ,r-downloader)
4947 ("r-edger" ,r-edger)
4948 ("r-gplots" ,r-gplots)
4949 ("r-limma" ,r-limma)
4950 ("r-matrixstats" ,r-matrixstats)
4951 ("r-preprocesscore" ,r-preprocesscore)
4952 ("r-quantro" ,r-quantro)
4953 ("r-rcolorbrewer" ,r-rcolorbrewer)
4954 ("r-readr" ,r-readr)))
4956 `(("r-knitr" ,r-knitr)))
4957 (home-page "https://bioconductor.org/packages/yarn/")
4958 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
4960 "Expedite large RNA-Seq analyses using a combination of previously
4961 developed tools. YARN is meant to make it easier for the user in performing
4962 basic mis-annotation quality control, filtering, and condition-aware
4963 normalization. YARN leverages many Bioconductor tools and statistical
4964 techniques to account for the large heterogeneity and sparsity found in very
4965 large RNA-seq experiments.")
4966 (license license:artistic2.0)))
4968 (define-public r-roar
4975 (uri (bioconductor-uri "roar" version))
4978 "069g887migvk70n0377dqr0fk7wjbz3w0asgk42bwhp8xpjfym6f"))))
4979 (build-system r-build-system)
4981 `(("r-biocgenerics" ,r-biocgenerics)
4982 ("r-genomeinfodb" ,r-genomeinfodb)
4983 ("r-genomicalignments" ,r-genomicalignments)
4984 ("r-genomicranges" ,r-genomicranges)
4985 ("r-iranges" ,r-iranges)
4986 ("r-rtracklayer" ,r-rtracklayer)
4987 ("r-s4vectors" ,r-s4vectors)
4988 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4989 (home-page "https://github.com/vodkatad/roar/")
4990 (synopsis "Identify differential APA usage from RNA-seq alignments")
4992 "This package provides tools for identifying preferential usage of APA
4993 sites, comparing two biological conditions, starting from known alternative
4994 sites and alignments obtained from standard RNA-seq experiments.")
4995 (license license:gpl3)))
4997 (define-public r-xbseq
5004 (uri (bioconductor-uri "XBSeq" version))
5007 "13br7x1q6dg8daxahskwq24f09wbxr8kyszl1z7dhc26bid2pvy0"))))
5008 (properties `((upstream-name . "XBSeq")))
5009 (build-system r-build-system)
5011 `(("r-biobase" ,r-biobase)
5012 ("r-deseq2" ,r-deseq2)
5013 ("r-dplyr" ,r-dplyr)
5014 ("r-ggplot2" ,r-ggplot2)
5015 ("r-locfit" ,r-locfit)
5016 ("r-magrittr" ,r-magrittr)
5017 ("r-matrixstats" ,r-matrixstats)
5018 ("r-pracma" ,r-pracma)
5019 ("r-roar" ,r-roar)))
5021 `(("r-knitr" ,r-knitr)))
5022 (home-page "https://github.com/Liuy12/XBSeq")
5023 (synopsis "Test for differential expression for RNA-seq data")
5025 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5026 expression} (DE), where a statistical model was established based on the
5027 assumption that observed signals are the convolution of true expression
5028 signals and sequencing noises. The mapped reads in non-exonic regions are
5029 considered as sequencing noises, which follows a Poisson distribution. Given
5030 measurable observed signal and background noise from RNA-seq data, true
5031 expression signals, assuming governed by the negative binomial distribution,
5032 can be delineated and thus the accurate detection of differential expressed
5034 (license license:gpl3+)))
5036 (define-public r-massspecwavelet
5038 (name "r-massspecwavelet")
5043 (uri (bioconductor-uri "MassSpecWavelet" version))
5046 "0nv1r68g7f1rps6sqaccd4n4x0i19wklvyabhp4b03cdk22gl3nq"))))
5048 `((upstream-name . "MassSpecWavelet")))
5049 (build-system r-build-system)
5051 `(("r-waveslim" ,r-waveslim)))
5052 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5053 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5055 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5056 data mainly through the use of wavelet transforms. It supports peak detection
5057 based on @dfn{Continuous Wavelet Transform} (CWT).")
5058 (license license:lgpl2.0+)))
5060 (define-public r-xcms
5067 (uri (bioconductor-uri "xcms" version))
5070 "1aa11gy1v7kkamv3hsnvdx715q8f1saw9p664j6wifyjj0hx13kn"))))
5071 (build-system r-build-system)
5073 `(("r-biobase" ,r-biobase)
5074 ("r-biocgenerics" ,r-biocgenerics)
5075 ("r-biocparallel" ,r-biocparallel)
5076 ("r-iranges" ,r-iranges)
5077 ("r-lattice" ,r-lattice)
5078 ("r-massspecwavelet" ,r-massspecwavelet)
5079 ("r-msnbase" ,r-msnbase)
5082 ("r-protgenerics" ,r-protgenerics)
5084 ("r-rcolorbrewer" ,r-rcolorbrewer)
5085 ("r-robustbase" ,r-robustbase)
5086 ("r-s4vectors" ,r-s4vectors)
5087 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5089 `(("r-knitr" ,r-knitr)))
5090 (home-page "https://bioconductor.org/packages/xcms/")
5091 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5093 "This package provides a framework for processing and visualization of
5094 chromatographically separated and single-spectra mass spectral data. It
5095 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5096 data for high-throughput, untargeted analyte profiling.")
5097 (license license:gpl2+)))
5099 (define-public r-wrench
5106 (uri (bioconductor-uri "Wrench" version))
5109 "05dyk3yvbqrzvinv3ig8ad9wffwr14z715cicsbxwxpv5lq84wx6"))))
5110 (properties `((upstream-name . "Wrench")))
5111 (build-system r-build-system)
5113 `(("r-limma" ,r-limma)
5114 ("r-locfit" ,r-locfit)
5115 ("r-matrixstats" ,r-matrixstats)))
5117 `(("r-knitr" ,r-knitr)))
5118 (home-page "https://github.com/HCBravoLab/Wrench")
5119 (synopsis "Wrench normalization for sparse count data")
5121 "Wrench is a package for normalization sparse genomic count data, like
5122 that arising from 16s metagenomic surveys.")
5123 (license license:artistic2.0)))
5125 (define-public r-wiggleplotr
5127 (name "r-wiggleplotr")
5132 (uri (bioconductor-uri "wiggleplotr" version))
5135 "1wknigh1md3w4h68caqlpq945maipdkpmw10hc2rlx4nbbpcnawp"))))
5136 (build-system r-build-system)
5138 `(("r-assertthat" ,r-assertthat)
5139 ("r-cowplot" ,r-cowplot)
5140 ("r-dplyr" ,r-dplyr)
5141 ("r-genomeinfodb" ,r-genomeinfodb)
5142 ("r-genomicranges" ,r-genomicranges)
5143 ("r-ggplot2" ,r-ggplot2)
5144 ("r-iranges" ,r-iranges)
5145 ("r-purrr" ,r-purrr)
5146 ("r-rtracklayer" ,r-rtracklayer)
5147 ("r-s4vectors" ,r-s4vectors)))
5149 `(("r-knitr" ,r-knitr)))
5150 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5151 (synopsis "Make read coverage plots from BigWig files")
5153 "This package provides tools to visualize read coverage from sequencing
5154 experiments together with genomic annotations (genes, transcripts, peaks).
5155 Introns of long transcripts can be rescaled to a fixed length for better
5156 visualization of exonic read coverage.")
5157 (license license:asl2.0)))
5159 (define-public r-widgettools
5161 (name "r-widgettools")
5166 (uri (bioconductor-uri "widgetTools" version))
5169 "0lrdpsgm9r7yfyyj5crvb7px4hrghxhmiic4iissz40slbfyvilx"))))
5170 (properties `((upstream-name . "widgetTools")))
5171 (build-system r-build-system)
5172 (home-page "https://bioconductor.org/packages/widgetTools/")
5173 (synopsis "Tools for creating interactive tcltk widgets")
5175 "This package contains tools to support the construction of tcltk
5177 ;; Any version of the LGPL.
5178 (license license:lgpl3+)))
5180 (define-public r-webbioc
5187 (uri (bioconductor-uri "webbioc" version))
5190 "16376ya5a5x2hwkl1v9y4r7np1drdwm912knnqg2dn90zmrdwr5f"))))
5191 (build-system r-build-system)
5193 `(("netpbm" ,netpbm)
5196 `(("r-affy" ,r-affy)
5197 ("r-annaffy" ,r-annaffy)
5198 ("r-biobase" ,r-biobase)
5199 ("r-biocmanager" ,r-biocmanager)
5200 ("r-gcrma" ,r-gcrma)
5201 ("r-multtest" ,r-multtest)
5202 ("r-qvalue" ,r-qvalue)
5204 (home-page "https://www.bioconductor.org/")
5205 (synopsis "Bioconductor web interface")
5207 "This package provides an integrated web interface for doing microarray
5208 analysis using several of the Bioconductor packages. It is intended to be
5209 deployed as a centralized bioinformatics resource for use by many users.
5210 Currently only Affymetrix oligonucleotide analysis is supported.")
5211 (license license:gpl2+)))
5213 (define-public r-zfpkm
5220 (uri (bioconductor-uri "zFPKM" version))
5223 "0scszhfqrgzhglz1a6kxfydq9dx8fqx28j3dypp91y5ah2w6mdys"))))
5224 (properties `((upstream-name . "zFPKM")))
5225 (build-system r-build-system)
5227 `(("r-checkmate" ,r-checkmate)
5228 ("r-dplyr" ,r-dplyr)
5229 ("r-ggplot2" ,r-ggplot2)
5230 ("r-summarizedexperiment" ,r-summarizedexperiment)
5231 ("r-tidyr" ,r-tidyr)))
5233 `(("r-knitr" ,r-knitr)))
5234 (home-page "https://github.com/ronammar/zFPKM/")
5235 (synopsis "Functions to facilitate zFPKM transformations")
5237 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5238 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5240 (license license:gpl3)))
5242 (define-public r-rbowtie2
5249 (uri (bioconductor-uri "Rbowtie2" version))
5252 "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
5253 (properties `((upstream-name . "Rbowtie2")))
5254 (build-system r-build-system)
5258 `(("r-knitr" ,r-knitr)))
5259 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5260 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5262 "This package provides an R wrapper of the popular @code{bowtie2}
5263 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5264 rapid adapter trimming, identification, and read merging.")
5265 (license license:gpl3+)))
5267 (define-public r-progeny
5274 (uri (bioconductor-uri "progeny" version))
5277 "09rq3nf9zm7w9djmx8xc8j3win3597p2v36zqgkhgkjwq5rkjgsh"))))
5278 (build-system r-build-system)
5280 `(("r-biobase" ,r-biobase)
5281 ("r-dplyr" ,r-dplyr)
5282 ("r-ggplot2" ,r-ggplot2)
5283 ("r-ggrepel" ,r-ggrepel)
5284 ("r-gridextra" ,r-gridextra)
5285 ("r-tidyr" ,r-tidyr)))
5287 `(("r-knitr" ,r-knitr)))
5288 (home-page "https://github.com/saezlab/progeny")
5289 (synopsis "Pathway responsive gene activity inference")
5291 "This package provides a function to infer pathway activity from gene
5292 expression. It contains the linear model inferred in the publication
5293 \"Perturbation-response genes reveal signaling footprints in cancer gene
5295 (license license:asl2.0)))
5297 (define-public r-arrmnormalization
5299 (name "r-arrmnormalization")
5304 (uri (bioconductor-uri "ARRmNormalization" version))
5307 "0zhhvr051fmh6g0bqrl525mkf094j1jnc57j201jlzmvdpkydlpv"))))
5309 `((upstream-name . "ARRmNormalization")))
5310 (build-system r-build-system)
5311 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
5312 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
5313 (synopsis "Adaptive robust regression normalization for methylation data")
5315 "This is a package to perform the @dfn{Adaptive Robust Regression
5316 method} (ARRm) for the normalization of methylation data from the Illumina
5317 Infinium HumanMethylation 450k assay.")
5318 (license license:artistic2.0)))
5320 (define-public r-biocfilecache
5322 (name "r-biocfilecache")
5327 (uri (bioconductor-uri "BiocFileCache" version))
5330 "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
5331 (properties `((upstream-name . "BiocFileCache")))
5332 (build-system r-build-system)
5334 `(("r-curl" ,r-curl)
5336 ("r-dbplyr" ,r-dbplyr)
5337 ("r-dplyr" ,r-dplyr)
5339 ("r-rappdirs" ,r-rappdirs)
5340 ("r-rsqlite" ,r-rsqlite)))
5342 `(("r-knitr" ,r-knitr)))
5343 (home-page "https://bioconductor.org/packages/BiocFileCache/")
5344 (synopsis "Manage files across sessions")
5346 "This package creates a persistent on-disk cache of files that the user
5347 can add, update, and retrieve. It is useful for managing resources (such as
5348 custom Txdb objects) that are costly or difficult to create, web resources,
5349 and data files used across sessions.")
5350 (license license:artistic2.0)))
5352 (define-public r-iclusterplus
5354 (name "r-iclusterplus")
5359 (uri (bioconductor-uri "iClusterPlus" version))
5362 "0j987xvxixdz0wnhgp4kgfcgz5jffrcdhmldrgpgv582qmf4r94w"))))
5363 (properties `((upstream-name . "iClusterPlus")))
5364 (build-system r-build-system)
5365 (native-inputs `(("gfortran" ,gfortran)))
5366 (home-page "https://bioconductor.org/packages/iClusterPlus/")
5367 (synopsis "Integrative clustering of multi-type genomic data")
5369 "iClusterPlus is developed for integrative clustering analysis of
5370 multi-type genomic data and is an enhanced version of iCluster proposed and
5371 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
5372 from the experiments where biological samples (e.g. tumor samples) are
5373 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
5374 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
5375 on. In the iClusterPlus model, binary observations such as somatic mutation
5376 are modeled as Binomial processes; categorical observations such as copy
5377 number states are realizations of Multinomial random variables; counts are
5378 modeled as Poisson random processes; and continuous measures are modeled by
5379 Gaussian distributions.")
5380 (license license:gpl2+)))
5382 (define-public r-rbowtie
5389 (uri (bioconductor-uri "Rbowtie" version))
5392 "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
5393 (properties `((upstream-name . "Rbowtie")))
5394 (build-system r-build-system)
5398 `(("r-knitr" ,r-knitr)))
5399 (home-page "https://bioconductor.org/packages/Rbowtie/")
5400 (synopsis "R bowtie wrapper")
5402 "This package provides an R wrapper around the popular bowtie short read
5403 aligner and around SpliceMap, a de novo splice junction discovery and
5405 (license license:artistic2.0)))
5407 (define-public r-sgseq
5414 (uri (bioconductor-uri "SGSeq" version))
5417 "11rxx7abjyga2sdcp4x4z3n8xjx6973sckyzmh9ax6r46kwhxq8c"))))
5418 (properties `((upstream-name . "SGSeq")))
5419 (build-system r-build-system)
5421 `(("r-annotationdbi" ,r-annotationdbi)
5422 ("r-biocgenerics" ,r-biocgenerics)
5423 ("r-biostrings" ,r-biostrings)
5424 ("r-genomeinfodb" ,r-genomeinfodb)
5425 ("r-genomicalignments" ,r-genomicalignments)
5426 ("r-genomicfeatures" ,r-genomicfeatures)
5427 ("r-genomicranges" ,r-genomicranges)
5428 ("r-igraph" ,r-igraph)
5429 ("r-iranges" ,r-iranges)
5430 ("r-rsamtools" ,r-rsamtools)
5431 ("r-rtracklayer" ,r-rtracklayer)
5432 ("r-runit" ,r-runit)
5433 ("r-s4vectors" ,r-s4vectors)
5434 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5436 `(("r-knitr" ,r-knitr)))
5437 (home-page "https://bioconductor.org/packages/SGSeq/")
5438 (synopsis "Splice event prediction and quantification from RNA-seq data")
5440 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
5441 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
5442 represented as a splice graph, which can be obtained from existing annotation
5443 or predicted from the mapped sequence reads. Splice events are identified
5444 from the graph and are quantified locally using structurally compatible reads
5445 at the start or end of each splice variant. The software includes functions
5446 for splice event prediction, quantification, visualization and
5448 (license license:artistic2.0)))
5450 (define-public r-rhisat2
5457 (uri (bioconductor-uri "Rhisat2" version))
5460 "0hhmcdnixkaqx9x9cl2vjaba3ri8m6wkbnbhxjmy51jwqzy2223a"))))
5461 (properties `((upstream-name . "Rhisat2")))
5462 (build-system r-build-system)
5465 (modify-phases %standard-phases
5466 (add-after 'unpack 'make-reproducible
5468 (substitute* "src/Makefile"
5469 (("`hostname`") "guix")
5471 ;; Avoid shelling out to "which".
5472 (("^CC =.*") (which "gcc"))
5473 (("^CPP =.*") (which "g++")))
5476 `(("r-genomicfeatures" ,r-genomicfeatures)
5477 ("r-genomicranges" ,r-genomicranges)
5478 ("r-sgseq" ,r-sgseq)))
5480 `(("r-knitr" ,r-knitr)))
5481 (home-page "https://github.com/fmicompbio/Rhisat2")
5482 (synopsis "R Wrapper for HISAT2 sequence aligner")
5484 "This package provides an R interface to the HISAT2 spliced short-read
5485 aligner by Kim et al. (2015). The package contains wrapper functions to
5486 create a genome index and to perform the read alignment to the generated
5488 (license license:gpl3)))
5490 (define-public r-quasr
5497 (uri (bioconductor-uri "QuasR" version))
5500 "0d87ajaaq8a7xgzl820qx5bvxw86ppab8clqk77sj02rfijnvjn8"))))
5501 (properties `((upstream-name . "QuasR")))
5502 (build-system r-build-system)
5506 `(("r-annotationdbi" ,r-annotationdbi)
5507 ("r-biobase" ,r-biobase)
5508 ("r-biocgenerics" ,r-biocgenerics)
5509 ("r-biocmanager" ,r-biocmanager)
5510 ("r-biocparallel" ,r-biocparallel)
5511 ("r-biostrings" ,r-biostrings)
5512 ("r-bsgenome" ,r-bsgenome)
5513 ("r-genomeinfodb" ,r-genomeinfodb)
5514 ("r-genomicalignments" ,r-genomicalignments)
5515 ("r-genomicfeatures" ,r-genomicfeatures)
5516 ("r-genomicfiles" ,r-genomicfiles)
5517 ("r-genomicranges" ,r-genomicranges)
5518 ("r-iranges" ,r-iranges)
5519 ("r-rbowtie" ,r-rbowtie)
5520 ("r-rhisat2" ,r-rhisat2)
5521 ("r-rhtslib" ,r-rhtslib)
5522 ("r-rsamtools" ,r-rsamtools)
5523 ("r-rtracklayer" ,r-rtracklayer)
5524 ("r-s4vectors" ,r-s4vectors)
5525 ("r-shortread" ,r-shortread)))
5527 `(("r-knitr" ,r-knitr)))
5528 (home-page "https://bioconductor.org/packages/QuasR/")
5529 (synopsis "Quantify and annotate short reads in R")
5531 "This package provides a framework for the quantification and analysis of
5532 short genomic reads. It covers a complete workflow starting from raw sequence
5533 reads, over creation of alignments and quality control plots, to the
5534 quantification of genomic regions of interest.")
5535 (license license:gpl2)))
5537 (define-public r-rqc
5544 (uri (bioconductor-uri "Rqc" version))
5547 "1qsm9r6xfsplk8zpf7p0k7fi86l8a74nx963sna8gzig5qgrvnm3"))))
5548 (properties `((upstream-name . "Rqc")))
5549 (build-system r-build-system)
5551 `(("r-biocgenerics" ,r-biocgenerics)
5552 ("r-biocparallel" ,r-biocparallel)
5553 ("r-biocstyle" ,r-biocstyle)
5554 ("r-biostrings" ,r-biostrings)
5555 ("r-biovizbase" ,r-biovizbase)
5556 ("r-genomicalignments" ,r-genomicalignments)
5557 ("r-genomicfiles" ,r-genomicfiles)
5558 ("r-ggplot2" ,r-ggplot2)
5559 ("r-iranges" ,r-iranges)
5560 ("r-knitr" ,r-knitr)
5561 ("r-markdown" ,r-markdown)
5564 ("r-reshape2" ,r-reshape2)
5565 ("r-rsamtools" ,r-rsamtools)
5566 ("r-s4vectors" ,r-s4vectors)
5567 ("r-shiny" ,r-shiny)
5568 ("r-shortread" ,r-shortread)))
5570 `(("r-knitr" ,r-knitr)))
5571 (home-page "https://github.com/labbcb/Rqc")
5572 (synopsis "Quality control tool for high-throughput sequencing data")
5574 "Rqc is an optimized tool designed for quality control and assessment of
5575 high-throughput sequencing data. It performs parallel processing of entire
5576 files and produces a report which contains a set of high-resolution
5578 (license license:gpl2+)))
5580 (define-public r-birewire
5587 (uri (bioconductor-uri "BiRewire" version))
5590 "0y7jb1abnik2y4ivpyqrgfl77rml6fhz88isd54l646ghslwxj0g"))))
5591 (properties `((upstream-name . "BiRewire")))
5592 (build-system r-build-system)
5594 `(("r-igraph" ,r-igraph)
5595 ("r-matrix" ,r-matrix)
5597 ("r-tsne" ,r-tsne)))
5598 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
5599 (synopsis "Tools for randomization of bipartite graphs")
5601 "This package provides functions for bipartite network rewiring through N
5602 consecutive switching steps and for the computation of the minimal number of
5603 switching steps to be performed in order to maximise the dissimilarity with
5604 respect to the original network. It includes functions for the analysis of
5605 the introduced randomness across the switching steps and several other
5606 routines to analyse the resulting networks and their natural projections.")
5607 (license license:gpl3)))
5609 (define-public r-birta
5616 (uri (bioconductor-uri "birta" version))
5619 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
5620 (build-system r-build-system)
5622 `(("r-biobase" ,r-biobase)
5623 ("r-limma" ,r-limma)
5624 ("r-mass" ,r-mass)))
5625 (home-page "https://bioconductor.org/packages/birta")
5626 (synopsis "Bayesian inference of regulation of transcriptional activity")
5628 "Expression levels of mRNA molecules are regulated by different
5629 processes, comprising inhibition or activation by transcription factors and
5630 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
5631 Inference of Regulation of Transcriptional Activity) uses the regulatory
5632 networks of transcription factors and miRNAs together with mRNA and miRNA
5633 expression data to predict switches in regulatory activity between two
5634 conditions. A Bayesian network is used to model the regulatory structure and
5635 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
5636 (license license:gpl2+)))
5638 (define-public r-multidataset
5640 (name "r-multidataset")
5645 (uri (bioconductor-uri "MultiDataSet" version))
5648 "0hjnj32m9wwlh2krdpdyl5jk1cakvlgki80z51mabhc62pajzf39"))))
5649 (properties `((upstream-name . "MultiDataSet")))
5650 (build-system r-build-system)
5652 `(("r-biobase" ,r-biobase)
5653 ("r-biocgenerics" ,r-biocgenerics)
5654 ("r-genomicranges" ,r-genomicranges)
5655 ("r-ggplot2" ,r-ggplot2)
5656 ("r-ggrepel" ,r-ggrepel)
5657 ("r-iranges" ,r-iranges)
5658 ("r-limma" ,r-limma)
5659 ("r-qqman" ,r-qqman)
5660 ("r-s4vectors" ,r-s4vectors)
5661 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5663 `(("r-knitr" ,r-knitr)))
5664 (home-page "https://bioconductor.org/packages/MultiDataSet/")
5665 (synopsis "Implementation of MultiDataSet and ResultSet")
5667 "This package provides an implementation of the BRGE's (Bioinformatic
5668 Research Group in Epidemiology from Center for Research in Environmental
5669 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
5670 integrating multi omics data sets and ResultSet is a container for omics
5671 results. This package contains base classes for MEAL and rexposome
5673 (license license:expat)))
5675 (define-public r-ropls
5682 (uri (bioconductor-uri "ropls" version))
5685 "1drww1mr0nira3qplyga6s3mljpjxshjgbn524kzxi0nrfbcvmnx"))))
5686 (build-system r-build-system)
5688 `(("r-biobase" ,r-biobase)
5689 ("r-multidataset" ,r-multidataset)))
5691 `(("r-knitr" ,r-knitr))) ; for vignettes
5692 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
5693 (synopsis "Multivariate analysis and feature selection of omics data")
5695 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
5696 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
5697 regression, classification, and feature selection of omics data where the
5698 number of variables exceeds the number of samples and with multicollinearity
5699 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
5700 separately model the variation correlated (predictive) to the factor of
5701 interest and the uncorrelated (orthogonal) variation. While performing
5702 similarly to PLS, OPLS facilitates interpretation.
5704 This package provides imlementations of PCA, PLS, and OPLS for multivariate
5705 analysis and feature selection of omics data. In addition to scores, loadings
5706 and weights plots, the package provides metrics and graphics to determine the
5707 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
5708 validity of the model by permutation testing, detect outliers, and perform
5709 feature selection (e.g. with Variable Importance in Projection or regression
5711 (license license:cecill)))
5713 (define-public r-biosigner
5715 (name "r-biosigner")
5720 (uri (bioconductor-uri "biosigner" version))
5723 "1v760q7hzaybkf2q9230rmr4phi8hglm59qwsjzvncxrhs3dpj06"))))
5724 (build-system r-build-system)
5726 `(("r-biobase" ,r-biobase)
5727 ("r-e1071" ,r-e1071)
5728 ("r-multidataset" ,r-multidataset)
5729 ("r-randomforest" ,r-randomforest)
5730 ("r-ropls" ,r-ropls)))
5732 `(("r-knitr" ,r-knitr)))
5733 (home-page "https://bioconductor.org/packages/biosigner/")
5734 (synopsis "Signature discovery from omics data")
5736 "Feature selection is critical in omics data analysis to extract
5737 restricted and meaningful molecular signatures from complex and high-dimension
5738 data, and to build robust classifiers. This package implements a method to
5739 assess the relevance of the variables for the prediction performances of the
5740 classifier. The approach can be run in parallel with the PLS-DA, Random
5741 Forest, and SVM binary classifiers. The signatures and the corresponding
5742 'restricted' models are returned, enabling future predictions on new
5744 (license license:cecill)))
5746 (define-public r-annotatr
5753 (uri (bioconductor-uri "annotatr" version))
5756 "0z3ydcybd81w543fw8fiblghndx5m28w8qsphh5vqj726i0nj8cl"))))
5757 (build-system r-build-system)
5759 `(("r-annotationdbi" ,r-annotationdbi)
5760 ("r-annotationhub" ,r-annotationhub)
5761 ("r-dplyr" ,r-dplyr)
5762 ("r-genomeinfodb" ,r-genomeinfodb)
5763 ("r-genomicfeatures" ,r-genomicfeatures)
5764 ("r-genomicranges" ,r-genomicranges)
5765 ("r-ggplot2" ,r-ggplot2)
5766 ("r-iranges" ,r-iranges)
5767 ("r-readr" ,r-readr)
5768 ("r-regioner" ,r-regioner)
5769 ("r-reshape2" ,r-reshape2)
5770 ("r-rtracklayer" ,r-rtracklayer)
5771 ("r-s4vectors" ,r-s4vectors)))
5773 `(("r-knitr" ,r-knitr)))
5774 (home-page "https://bioconductor.org/packages/annotatr/")
5775 (synopsis "Annotation of genomic regions to genomic annotations")
5777 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
5778 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
5779 to investigate the intersecting genomic annotations. Such annotations include
5780 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
5781 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
5782 enhancers. The annotatr package provides an easy way to summarize and
5783 visualize the intersection of genomic sites/regions with genomic
5785 (license license:gpl3)))
5787 (define-public r-rsubread
5794 (uri (bioconductor-uri "Rsubread" version))
5797 "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
5798 (properties `((upstream-name . "Rsubread")))
5799 (build-system r-build-system)
5800 (inputs `(("zlib" ,zlib)))
5802 `(("r-matrix" ,r-matrix)))
5803 (home-page "https://bioconductor.org/packages/Rsubread/")
5804 (synopsis "Subread sequence alignment and counting for R")
5806 "This package provides tools for alignment, quantification and analysis
5807 of second and third generation sequencing data. It includes functionality for
5808 read mapping, read counting, SNP calling, structural variant detection and
5809 gene fusion discovery. It can be applied to all major sequencing techologies
5810 and to both short and long sequence reads.")
5811 (license license:gpl3)))
5813 (define-public r-flowutils
5815 (name "r-flowutils")
5820 (uri (bioconductor-uri "flowUtils" version))
5823 "03jj4zyffm9kwzrg4vbsk6clc2v2m95wgalgqwzi31n9a2zyaza4"))))
5824 (properties `((upstream-name . "flowUtils")))
5825 (build-system r-build-system)
5827 `(("r-biobase" ,r-biobase)
5828 ("r-corpcor" ,r-corpcor)
5829 ("r-flowcore" ,r-flowcore)
5830 ("r-graph" ,r-graph)
5831 ("r-runit" ,r-runit)
5833 (home-page "https://github.com/jspidlen/flowUtils")
5834 (synopsis "Utilities for flow cytometry")
5836 "This package provides utilities for flow cytometry data.")
5837 (license license:artistic2.0)))
5839 (define-public r-consensusclusterplus
5841 (name "r-consensusclusterplus")
5846 (uri (bioconductor-uri "ConsensusClusterPlus" version))
5849 "06gq3a95h0km1hzbx1za8q0l7kla3jdzvn6cnfz43ijx4n3dzzcq"))))
5851 `((upstream-name . "ConsensusClusterPlus")))
5852 (build-system r-build-system)
5855 ("r-biobase" ,r-biobase)
5856 ("r-cluster" ,r-cluster)))
5857 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
5858 (synopsis "Clustering algorithm")
5860 "This package provides an implementation of an algorithm for determining
5861 cluster count and membership by stability evidence in unsupervised analysis.")
5862 (license license:gpl2)))
5864 (define-public r-cytolib
5871 (uri (bioconductor-uri "cytolib" version))
5874 "123d1wlymq8r8d83as380h1dgw6v4s317acyvp1lsg2cpfp3gslj"))))
5875 (properties `((upstream-name . "cytolib")))
5876 (build-system r-build-system)
5880 `(("r-knitr" ,r-knitr)))
5884 ("r-rcpparmadillo" ,r-rcpparmadillo)
5885 ("r-rcppparallel" ,r-rcppparallel)
5886 ("r-rhdf5lib" ,r-rhdf5lib)
5887 ("r-rprotobuflib" ,r-rprotobuflib)))
5888 (home-page "https://bioconductor.org/packages/cytolib/")
5889 (synopsis "C++ infrastructure for working with gated cytometry")
5891 "This package provides the core data structure and API to represent and
5892 interact with gated cytometry data.")
5893 (license license:artistic2.0)))
5895 (define-public r-flowcore
5902 (uri (bioconductor-uri "flowCore" version))
5905 "1xalndmfidfzqwlppdanx7cnm4ysznq21ingmykhxni86s42kd8p"))))
5906 (properties `((upstream-name . "flowCore")))
5907 (build-system r-build-system)
5910 ("r-biobase" ,r-biobase)
5911 ("r-biocgenerics" ,r-biocgenerics)
5912 ("r-cytolib" ,r-cytolib)
5913 ("r-matrixstats" ,r-matrixstats)
5915 ("r-rcpparmadillo" ,r-rcpparmadillo)
5916 ("r-rprotobuflib" ,r-rprotobuflib)))
5918 `(("r-knitr" ,r-knitr)))
5919 (home-page "https://bioconductor.org/packages/flowCore")
5920 (synopsis "Basic structures for flow cytometry data")
5922 "This package provides S4 data structures and basic functions to deal
5923 with flow cytometry data.")
5924 (license license:artistic2.0)))
5926 (define-public r-flowmeans
5928 (name "r-flowmeans")
5933 (uri (bioconductor-uri "flowMeans" version))
5936 "1sv5vpwm3qdhkn1gdrk3n674harjcni91g63sqzfmybiwq8dlym7"))))
5937 (properties `((upstream-name . "flowMeans")))
5938 (build-system r-build-system)
5940 `(("r-biobase" ,r-biobase)
5941 ("r-feature" ,r-feature)
5942 ("r-flowcore" ,r-flowcore)
5943 ("r-rrcov" ,r-rrcov)))
5944 (home-page "https://bioconductor.org/packages/flowMeans")
5945 (synopsis "Non-parametric flow cytometry data gating")
5947 "This package provides tools to identify cell populations in Flow
5948 Cytometry data using non-parametric clustering and segmented-regression-based
5949 change point detection.")
5950 (license license:artistic2.0)))
5952 (define-public r-ncdfflow
5959 (uri (bioconductor-uri "ncdfFlow" version))
5962 "0avxn2abh4fk1gkncrxz7jwzgvd90m3m0ly318q0z38cjhsw3j9f"))))
5963 (properties `((upstream-name . "ncdfFlow")))
5964 (build-system r-build-system)
5969 ("r-biobase" ,r-biobase)
5970 ("r-biocgenerics" ,r-biocgenerics)
5971 ("r-flowcore" ,r-flowcore)
5973 ("r-rcpparmadillo" ,r-rcpparmadillo)
5974 ("r-rhdf5lib" ,r-rhdf5lib)
5975 ("r-zlibbioc" ,r-zlibbioc)))
5977 `(("r-knitr" ,r-knitr)))
5978 (home-page "https://bioconductor.org/packages/ncdfFlow/")
5979 (synopsis "HDF5 based storage for flow cytometry data")
5981 "This package provides HDF5 storage based methods and functions for
5982 manipulation of flow cytometry data.")
5983 (license license:artistic2.0)))
5985 (define-public r-ggcyto
5992 (uri (bioconductor-uri "ggcyto" version))
5995 "1ih6ggay7jjxnx8blc2sk95g8d40gkim145jllkk8sqwl02g44p0"))))
5996 (properties `((upstream-name . "ggcyto")))
5997 (build-system r-build-system)
5999 `(("r-data-table" ,r-data-table)
6000 ("r-flowcore" ,r-flowcore)
6001 ("r-flowworkspace" ,r-flowworkspace)
6002 ("r-ggplot2" ,r-ggplot2)
6003 ("r-gridextra" ,r-gridextra)
6004 ("r-hexbin" ,r-hexbin)
6005 ("r-ncdfflow" ,r-ncdfflow)
6007 ("r-rcolorbrewer" ,r-rcolorbrewer)
6008 ("r-rlang" ,r-rlang)
6009 ("r-scales" ,r-scales)))
6011 `(("r-knitr" ,r-knitr)))
6012 (home-page "https://github.com/RGLab/ggcyto/issues")
6013 (synopsis "Visualize Cytometry data with ggplot")
6015 "With the dedicated fortify method implemented for @code{flowSet},
6016 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6017 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6018 and some custom layers also make it easy to add gates and population
6019 statistics to the plot.")
6020 (license license:artistic2.0)))
6022 (define-public r-flowviz
6029 (uri (bioconductor-uri "flowViz" version))
6032 "0f3jfwdmaq9wrgl737blk5gmpc29l9kb6nadqhxpvbjwqsnzx0yq"))))
6033 (properties `((upstream-name . "flowViz")))
6034 (build-system r-build-system)
6036 `(("r-biobase" ,r-biobase)
6037 ("r-flowcore" ,r-flowcore)
6038 ("r-hexbin" ,r-hexbin)
6039 ("r-idpmisc" ,r-idpmisc)
6040 ("r-kernsmooth" ,r-kernsmooth)
6041 ("r-lattice" ,r-lattice)
6042 ("r-latticeextra" ,r-latticeextra)
6044 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6046 `(("r-knitr" ,r-knitr)))
6047 (home-page "https://bioconductor.org/packages/flowViz/")
6048 (synopsis "Visualization for flow cytometry")
6050 "This package provides visualization tools for flow cytometry data.")
6051 (license license:artistic2.0)))
6053 (define-public r-flowclust
6055 (name "r-flowclust")
6060 (uri (bioconductor-uri "flowClust" version))
6063 "06mkq9y41jax07x4knhvhzgrkgqdvpvcw604bxdk6bv9wx3ipq5b"))))
6064 (properties `((upstream-name . "flowClust")))
6065 (build-system r-build-system)
6068 (list "--configure-args=--enable-bundled-gsl=no")))
6070 `(("r-biobase" ,r-biobase)
6071 ("r-biocgenerics" ,r-biocgenerics)
6073 ("r-corpcor" ,r-corpcor)
6074 ("r-ellipse" ,r-ellipse)
6075 ("r-flowcore" ,r-flowcore)
6076 ("r-flowviz" ,r-flowviz)
6077 ("r-graph" ,r-graph)
6078 ("r-mnormt" ,r-mnormt)))
6082 `(("pkg-config" ,pkg-config)
6083 ("r-knitr" ,r-knitr)))
6084 (home-page "https://bioconductor.org/packages/flowClust")
6085 (synopsis "Clustering for flow cytometry")
6087 "This package provides robust model-based clustering using a t-mixture
6088 model with Box-Cox transformation.")
6089 (license license:artistic2.0)))
6091 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6092 ;; make it use our protobuf package instead.
6093 (define-public r-rprotobuflib
6095 (name "r-rprotobuflib")
6100 (uri (bioconductor-uri "RProtoBufLib" version))
6103 "0kfinf9vzc1i5qxmaw832id557gr1vqdi1m8yiaxz83g37wh8vps"))))
6104 (properties `((upstream-name . "RProtoBufLib")))
6105 (build-system r-build-system)
6108 (modify-phases %standard-phases
6109 (add-after 'unpack 'unpack-bundled-sources
6111 (with-directory-excursion "src"
6112 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6115 `(("r-knitr" ,r-knitr)))
6116 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6117 (synopsis "C++ headers and static libraries of Protocol buffers")
6119 "This package provides the headers and static library of Protocol buffers
6120 for other R packages to compile and link against.")
6121 (license license:bsd-3)))
6123 (define-public r-flowworkspace
6125 (name "r-flowworkspace")
6130 (uri (bioconductor-uri "flowWorkspace" version))
6133 "123ny8n3jjgmsnpghk1dafxkwmcyr513gxi8y4h4qszq4s6ai15v"))))
6134 (properties `((upstream-name . "flowWorkspace")))
6135 (build-system r-build-system)
6138 ("r-biobase" ,r-biobase)
6139 ("r-biocgenerics" ,r-biocgenerics)
6140 ("r-cytolib" ,r-cytolib)
6141 ("r-data-table" ,r-data-table)
6142 ("r-digest" ,r-digest)
6143 ("r-dplyr" ,r-dplyr)
6144 ("r-flowcore" ,r-flowcore)
6145 ("r-ggplot2" ,r-ggplot2)
6146 ("r-graph" ,r-graph)
6147 ("r-lattice" ,r-lattice)
6148 ("r-latticeextra" ,r-latticeextra)
6149 ("r-matrixstats" ,r-matrixstats)
6150 ("r-ncdfflow" ,r-ncdfflow)
6153 ("r-rcpparmadillo" ,r-rcpparmadillo)
6154 ("r-rcppparallel" ,r-rcppparallel)
6155 ("r-rgraphviz" ,r-rgraphviz)
6156 ("r-rhdf5lib" ,r-rhdf5lib)
6157 ("r-rprotobuflib" ,r-rprotobuflib)
6158 ("r-scales" ,r-scales)
6159 ("r-stringr" ,r-stringr)
6162 `(("r-knitr" ,r-knitr)))
6163 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6164 (synopsis "Infrastructure for working with cytometry data")
6166 "This package is designed to facilitate comparison of automated gating
6167 methods against manual gating done in flowJo. This package allows you to
6168 import basic flowJo workspaces into BioConductor and replicate the gating from
6169 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6170 samples, compensation, and transformation are performed so that the output
6171 matches the flowJo analysis.")
6172 (license license:artistic2.0)))
6174 (define-public r-flowstats
6176 (name "r-flowstats")
6181 (uri (bioconductor-uri "flowStats" version))
6184 "1ygvxvd7y6jp907y0h3hycdwvw1fch16w84g06nk4f4g4kvrzdir"))))
6185 (properties `((upstream-name . "flowStats")))
6186 (build-system r-build-system)
6188 `(("r-biobase" ,r-biobase)
6189 ("r-biocgenerics" ,r-biocgenerics)
6190 ("r-cluster" ,r-cluster)
6192 ("r-flowcore" ,r-flowcore)
6193 ("r-flowviz" ,r-flowviz)
6194 ("r-flowworkspace" ,r-flowworkspace)
6195 ("r-kernsmooth" ,r-kernsmooth)
6197 ("r-lattice" ,r-lattice)
6199 ("r-ncdfflow" ,r-ncdfflow)
6200 ("r-rcolorbrewer" ,r-rcolorbrewer)
6201 ("r-rrcov" ,r-rrcov)))
6202 (home-page "http://www.github.com/RGLab/flowStats")
6203 (synopsis "Statistical methods for the analysis of flow cytometry data")
6205 "This package provides methods and functionality to analyze flow data
6206 that is beyond the basic infrastructure provided by the @code{flowCore}
6208 (license license:artistic2.0)))
6210 (define-public r-opencyto
6217 (uri (bioconductor-uri "openCyto" version))
6220 "10dyd6dddskv70vhpwfbsqdb8pb9i3ka0fgvl1h51wqlckbsj89m"))))
6221 (properties `((upstream-name . "openCyto")))
6222 (build-system r-build-system)
6224 `(("r-biobase" ,r-biobase)
6225 ("r-biocgenerics" ,r-biocgenerics)
6227 ("r-data-table" ,r-data-table)
6228 ("r-flowclust" ,r-flowclust)
6229 ("r-flowcore" ,r-flowcore)
6230 ("r-flowstats" ,r-flowstats)
6231 ("r-flowviz" ,r-flowviz)
6232 ("r-flowworkspace" ,r-flowworkspace)
6233 ("r-graph" ,r-graph)
6234 ("r-gtools" ,r-gtools)
6236 ("r-lattice" ,r-lattice)
6238 ("r-ncdfflow" ,r-ncdfflow)
6240 ("r-r-utils" ,r-r-utils)
6242 ("r-rcolorbrewer" ,r-rcolorbrewer)
6244 ("r-rrcov" ,r-rrcov)))
6246 `(("r-knitr" ,r-knitr)))
6247 (home-page "https://bioconductor.org/packages/openCyto")
6248 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6250 "This package is designed to facilitate the automated gating methods in a
6251 sequential way to mimic the manual gating strategy.")
6252 (license license:artistic2.0)))
6254 (define-public r-cytoml
6261 (uri (bioconductor-uri "CytoML" version))
6264 "174brv027mm90lydfg6hnhazwh8jy4vf6ial4hpsfalwa5jrz55n"))))
6265 (properties `((upstream-name . "CytoML")))
6266 (build-system r-build-system)
6268 `(("libxml2" ,libxml2)))
6270 `(("r-base64enc" ,r-base64enc)
6272 ("r-biobase" ,r-biobase)
6273 ("r-corpcor" ,r-corpcor)
6274 ("r-cytolib" ,r-cytolib)
6275 ("r-data-table" ,r-data-table)
6276 ("r-dplyr" ,r-dplyr)
6277 ("r-flowcore" ,r-flowcore)
6278 ("r-flowworkspace" ,r-flowworkspace)
6279 ("r-ggcyto" ,r-ggcyto)
6280 ("r-graph" ,r-graph)
6281 ("r-jsonlite" ,r-jsonlite)
6282 ("r-lattice" ,r-lattice)
6283 ("r-opencyto" ,r-opencyto)
6287 ("r-rcpparmadillo" ,r-rcpparmadillo)
6288 ("r-rcppparallel" ,r-rcppparallel)
6289 ("r-rgraphviz" ,r-rgraphviz)
6290 ("r-rhdf5lib" ,r-rhdf5lib)
6291 ("r-rprotobuflib" ,r-rprotobuflib)
6292 ("r-runit" ,r-runit)
6293 ("r-tibble" ,r-tibble)
6296 ("r-yaml" ,r-yaml)))
6298 `(("r-knitr" ,r-knitr)))
6299 (home-page "https://github.com/RGLab/CytoML")
6300 (synopsis "GatingML interface for cross platform cytometry data sharing")
6302 "This package provides an interface to implementations of the GatingML2.0
6303 standard to exchange gated cytometry data with other software platforms.")
6304 (license license:artistic2.0)))
6306 (define-public r-flowsom
6313 (uri (bioconductor-uri "FlowSOM" version))
6316 "1p17jv4q1dbcc47jpjy9hbcvzpwrx8waq7qpcj778jsyz6z6jh78"))))
6317 (properties `((upstream-name . "FlowSOM")))
6318 (build-system r-build-system)
6320 `(("r-biocgenerics" ,r-biocgenerics)
6321 ("r-consensusclusterplus" ,r-consensusclusterplus)
6322 ("r-cytoml" ,r-cytoml)
6323 ("r-flowcore" ,r-flowcore)
6324 ("r-flowworkspace" ,r-flowworkspace)
6325 ("r-igraph" ,r-igraph)
6326 ("r-rcolorbrewer" ,r-rcolorbrewer)
6329 (home-page "https://bioconductor.org/packages/FlowSOM/")
6330 (synopsis "Visualize and interpret cytometry data")
6332 "FlowSOM offers visualization options for cytometry data, by using
6333 self-organizing map clustering and minimal spanning trees.")
6334 (license license:gpl2+)))
6336 (define-public r-mixomics
6343 (uri (bioconductor-uri "mixOmics" version))
6346 "1nkqlvm9j1f4vfj3f3kyxqgan38rpa9imimvl9pwivvsfl647vvc"))))
6347 (properties `((upstream-name . "mixOmics")))
6348 (build-system r-build-system)
6350 `(("r-corpcor" ,r-corpcor)
6351 ("r-dplyr" ,r-dplyr)
6352 ("r-ellipse" ,r-ellipse)
6353 ("r-ggplot2" ,r-ggplot2)
6354 ("r-gridextra" ,r-gridextra)
6355 ("r-igraph" ,r-igraph)
6356 ("r-lattice" ,r-lattice)
6358 ("r-matrixstats" ,r-matrixstats)
6359 ("r-rarpack" ,r-rarpack)
6360 ("r-rcolorbrewer" ,r-rcolorbrewer)
6361 ("r-reshape2" ,r-reshape2)
6362 ("r-tidyr" ,r-tidyr)))
6364 `(("r-knitr" ,r-knitr)))
6365 (home-page "http://www.mixOmics.org")
6366 (synopsis "Multivariate methods for exploration of biological datasets")
6368 "mixOmics offers a wide range of multivariate methods for the exploration
6369 and integration of biological datasets with a particular focus on variable
6370 selection. The package proposes several sparse multivariate models we have
6371 developed to identify the key variables that are highly correlated, and/or
6372 explain the biological outcome of interest. The data that can be analysed
6373 with mixOmics may come from high throughput sequencing technologies, such as
6374 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
6375 also beyond the realm of omics (e.g. spectral imaging). The methods
6376 implemented in mixOmics can also handle missing values without having to
6377 delete entire rows with missing data.")
6378 (license license:gpl2+)))
6380 (define-public r-depecher
6387 (uri (bioconductor-uri "DepecheR" version))
6390 "0dscfl6wxpl5538jzkrwisdwbr873d38rzd19vl6z5br71jvpv3v"))))
6391 (properties `((upstream-name . "DepecheR")))
6392 (build-system r-build-system)
6394 `(("r-beanplot" ,r-beanplot)
6395 ("r-dosnow" ,r-dosnow)
6396 ("r-dplyr" ,r-dplyr)
6398 ("r-foreach" ,r-foreach)
6399 ("r-ggplot2" ,r-ggplot2)
6400 ("r-gplots" ,r-gplots)
6402 ("r-matrixstats" ,r-matrixstats)
6403 ("r-mixomics" ,r-mixomics)
6404 ("r-moments" ,r-moments)
6406 ("r-rcppeigen" ,r-rcppeigen)
6407 ("r-reshape2" ,r-reshape2)
6408 ("r-robustbase" ,r-robustbase)
6409 ("r-viridis" ,r-viridis)))
6411 `(("r-knitr" ,r-knitr)))
6412 (home-page "https://bioconductor.org/packages/DepecheR/")
6413 (synopsis "Identify traits of clusters in high-dimensional entities")
6415 "The purpose of this package is to identify traits in a dataset that can
6416 separate groups. This is done on two levels. First, clustering is performed,
6417 using an implementation of sparse K-means. Secondly, the generated clusters
6418 are used to predict outcomes of groups of individuals based on their
6419 distribution of observations in the different clusters. As certain clusters
6420 with separating information will be identified, and these clusters are defined
6421 by a sparse number of variables, this method can reduce the complexity of
6422 data, to only emphasize the data that actually matters.")
6423 (license license:expat)))
6425 (define-public r-rcistarget
6427 (name "r-rcistarget")
6432 (uri (bioconductor-uri "RcisTarget" version))
6435 "1lvi873dv0vhw53s1pmcilw8qwlywm9p2ybphcl168nzh6w31r4i"))))
6436 (properties `((upstream-name . "RcisTarget")))
6437 (build-system r-build-system)
6439 `(("r-aucell" ,r-aucell)
6440 ("r-biocgenerics" ,r-biocgenerics)
6441 ("r-data-table" ,r-data-table)
6442 ("r-feather" ,r-feather)
6443 ("r-gseabase" ,r-gseabase)
6444 ("r-r-utils" ,r-r-utils)
6445 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6447 `(("r-knitr" ,r-knitr)))
6448 (home-page "https://aertslab.org/#scenic")
6449 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
6451 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
6452 over-represented on a gene list. In a first step, RcisTarget selects DNA
6453 motifs that are significantly over-represented in the surroundings of the
6454 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
6455 achieved by using a database that contains genome-wide cross-species rankings
6456 for each motif. The motifs that are then annotated to TFs and those that have
6457 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
6458 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
6459 genes in the gene-set that are ranked above the leading edge).")
6460 (license license:gpl3)))
6462 (define-public r-cicero
6469 (uri (bioconductor-uri "cicero" version))
6472 "042ba6yfa7fksij2v7cwnp2sca3vmz7izn6fsxx9xswnncrkgcqh"))))
6473 (build-system r-build-system)
6475 `(("r-assertthat" ,r-assertthat)
6476 ("r-biobase" ,r-biobase)
6477 ("r-biocgenerics" ,r-biocgenerics)
6478 ("r-data-table" ,r-data-table)
6479 ("r-dplyr" ,r-dplyr)
6481 ("r-genomicranges" ,r-genomicranges)
6482 ("r-ggplot2" ,r-ggplot2)
6483 ("r-glasso" ,r-glasso)
6485 ("r-igraph" ,r-igraph)
6486 ("r-iranges" ,r-iranges)
6487 ("r-matrix" ,r-matrix)
6488 ("r-monocle" ,r-monocle)
6490 ("r-reshape2" ,r-reshape2)
6491 ("r-s4vectors" ,r-s4vectors)
6492 ("r-stringi" ,r-stringi)
6493 ("r-stringr" ,r-stringr)
6494 ("r-tibble" ,r-tibble)
6495 ("r-tidyr" ,r-tidyr)
6496 ("r-vgam" ,r-vgam)))
6498 `(("r-knitr" ,r-knitr)))
6499 (home-page "https://bioconductor.org/packages/cicero/")
6500 (synopsis "Predict cis-co-accessibility from single-cell data")
6502 "Cicero computes putative cis-regulatory maps from single-cell chromatin
6503 accessibility data. It also extends the monocle package for use in chromatin
6504 accessibility data.")
6505 (license license:expat)))
6507 ;; This is the latest commit on the "monocle3" branch.
6508 (define-public r-cicero-monocle3
6509 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
6511 (package (inherit r-cicero)
6512 (name "r-cicero-monocle3")
6513 (version (git-version "1.3.2" revision commit))
6518 (url "https://github.com/cole-trapnell-lab/cicero-release")
6520 (file-name (git-file-name name version))
6523 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
6525 `(("r-monocle3" ,r-monocle3)
6526 ,@(alist-delete "r-monocle"
6527 (package-propagated-inputs r-cicero)))))))
6529 (define-public r-cistopic
6530 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
6534 (version (git-version "0.2.1" revision commit))
6539 (url "https://github.com/aertslab/cisTopic")
6541 (file-name (git-file-name name version))
6544 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
6545 (build-system r-build-system)
6547 `(("r-aucell" ,r-aucell)
6548 ("r-data-table" ,r-data-table)
6549 ("r-dplyr" ,r-dplyr)
6550 ("r-dosnow" ,r-dosnow)
6552 ("r-feather" ,r-feather)
6553 ("r-fitdistrplus" ,r-fitdistrplus)
6554 ("r-genomicranges" ,r-genomicranges)
6555 ("r-ggplot2" ,r-ggplot2)
6557 ("r-matrix" ,r-matrix)
6559 ("r-rcistarget" ,r-rcistarget)
6560 ("r-rtracklayer" ,r-rtracklayer)
6561 ("r-s4vectors" ,r-s4vectors)))
6562 (home-page "https://github.com/aertslab/cisTopic")
6563 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
6565 "The sparse nature of single cell epigenomics data can be overruled using
6566 probabilistic modelling methods such as @dfn{Latent Dirichlet
6567 Allocation} (LDA). This package allows the probabilistic modelling of
6568 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
6569 includes functionalities to identify cell states based on the contribution of
6570 cisTopics and explore the nature and regulatory proteins driving them.")
6571 (license license:gpl3))))
6573 (define-public r-genie3
6580 (uri (bioconductor-uri "GENIE3" version))
6583 "1bsm0gxracsyg1wnaw3whvskghfpbgbm9navr8wdmxj2hjp3dqs7"))))
6584 (properties `((upstream-name . "GENIE3")))
6585 (build-system r-build-system)
6586 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
6588 `(("r-knitr" ,r-knitr)))
6589 (home-page "https://bioconductor.org/packages/GENIE3")
6590 (synopsis "Gene network inference with ensemble of trees")
6592 "This package implements the GENIE3 algorithm for inferring gene
6593 regulatory networks from expression data.")
6594 (license license:gpl2+)))
6596 (define-public r-roc
6603 (uri (bioconductor-uri "ROC" version))
6606 "0gmx3r77yl5fqrj5j2hamwynbis75qd62q28964kx16z33xfgx89"))))
6607 (properties `((upstream-name . "ROC")))
6608 (build-system r-build-system)
6610 `(("r-knitr" ,r-knitr)))
6611 (home-page "https://www.bioconductor.org/packages/ROC/")
6612 (synopsis "Utilities for ROC curves")
6614 "This package provides utilities for @dfn{Receiver Operating
6615 Characteristic} (ROC) curves, with a focus on micro arrays.")
6616 (license license:artistic2.0)))
6618 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
6620 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
6625 (uri (bioconductor-uri
6626 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
6627 version 'annotation))
6630 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
6633 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
6634 (build-system r-build-system)
6635 (propagated-inputs `(("r-minfi" ,r-minfi)))
6637 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
6638 (synopsis "Annotation for Illumina's 450k methylation arrays")
6640 "This package provides manifests and annotation for Illumina's 450k array
6642 (license license:artistic2.0)))
6644 (define-public r-watermelon
6646 (name "r-watermelon")
6651 (uri (bioconductor-uri "wateRmelon" version))
6654 "1c3a6bq3ggmv8kmdfrgiar6nwgircgzjrbgd9z9dqiin7j13gxwn"))))
6655 (properties `((upstream-name . "wateRmelon")))
6656 (build-system r-build-system)
6658 `(("r-biobase" ,r-biobase)
6659 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
6660 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
6661 ("r-illuminaio" ,r-illuminaio)
6662 ("r-limma" ,r-limma)
6664 ("r-matrixstats" ,r-matrixstats)
6665 ("r-methylumi" ,r-methylumi)
6667 (home-page "https://bioconductor.org/packages/wateRmelon/")
6668 (synopsis "Illumina 450 methylation array normalization and metrics")
6670 "The standard index of DNA methylation (beta) is computed from methylated
6671 and unmethylated signal intensities. Betas calculated from raw signal
6672 intensities perform well, but using 11 methylomic datasets we demonstrate that
6673 quantile normalization methods produce marked improvement. The commonly used
6674 procedure of normalizing betas is inferior to the separate normalization of M
6675 and U, and it is also advantageous to normalize Type I and Type II assays
6676 separately. This package provides 15 flavours of betas and three performance
6677 metrics, with methods for objects produced by the @code{methylumi} and
6678 @code{minfi} packages.")
6679 (license license:gpl3)))
6681 (define-public r-gdsfmt
6688 (uri (bioconductor-uri "gdsfmt" version))
6691 "0ipf60wylbhvwk9q3mbnak0f1n6k7spfh90s1c1c0b47ryxsri67"))
6692 (modules '((guix build utils)))
6693 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
6694 ;; them and link with system libraries instead.
6697 (for-each delete-file-recursively
6701 (substitute* "src/Makevars"
6702 (("all: \\$\\(SHLIB\\)") "all:")
6703 (("\\$\\(SHLIB\\): liblzma.a") "")
6704 (("(ZLIB|LZ4)/.*") "")
6705 (("CoreArray/dVLIntGDS.cpp.*")
6706 "CoreArray/dVLIntGDS.cpp")
6707 (("CoreArray/dVLIntGDS.o.*")
6708 "CoreArray/dVLIntGDS.o")
6709 (("PKG_LIBS = ./liblzma.a")
6710 "PKG_LIBS = -llz4"))
6711 (substitute* "src/CoreArray/dStream.h"
6712 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
6713 (string-append "include <" header ">")))
6715 (properties `((upstream-name . "gdsfmt")))
6716 (build-system r-build-system)
6722 `(("r-knitr" ,r-knitr)))
6723 (home-page "http://corearray.sourceforge.net/")
6725 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
6727 "This package provides a high-level R interface to CoreArray @dfn{Genomic
6728 Data Structure} (GDS) data files, which are portable across platforms with
6729 hierarchical structure to store multiple scalable array-oriented data sets
6730 with metadata information. It is suited for large-scale datasets, especially
6731 for data which are much larger than the available random-access memory. The
6732 @code{gdsfmt} package offers efficient operations specifically designed for
6733 integers of less than 8 bits, since a diploid genotype, like
6734 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
6735 byte. Data compression and decompression are available with relatively
6736 efficient random access. It is also allowed to read a GDS file in parallel
6737 with multiple R processes supported by the package @code{parallel}.")
6738 (license license:lgpl3)))
6740 (define-public r-bigmelon
6747 (uri (bioconductor-uri "bigmelon" version))
6750 "1cryjhbiacm45g097rpqgbva49hs5vdx4y4h5h2v1gw4k78hwb4y"))))
6751 (properties `((upstream-name . "bigmelon")))
6752 (build-system r-build-system)
6754 `(("r-biobase" ,r-biobase)
6755 ("r-biocgenerics" ,r-biocgenerics)
6756 ("r-gdsfmt" ,r-gdsfmt)
6757 ("r-geoquery" ,r-geoquery)
6758 ("r-methylumi" ,r-methylumi)
6759 ("r-minfi" ,r-minfi)
6760 ("r-watermelon" ,r-watermelon)))
6761 (home-page "https://bioconductor.org/packages/bigmelon/")
6762 (synopsis "Illumina methylation array analysis for large experiments")
6764 "This package provides methods for working with Illumina arrays using the
6765 @code{gdsfmt} package.")
6766 (license license:gpl3)))
6768 (define-public r-seqbias
6775 (uri (bioconductor-uri "seqbias" version))
6778 "0sy2fv98x4qfz9llns28jh1n4bi991jj856y8a5fbzpx7y990lai"))))
6779 (properties `((upstream-name . "seqbias")))
6780 (build-system r-build-system)
6782 `(("r-biostrings" ,r-biostrings)
6783 ("r-genomicranges" ,r-genomicranges)
6784 ("r-rhtslib" ,r-rhtslib)))
6786 `(("zlib" ,zlib))) ; This comes from rhtslib.
6787 (home-page "https://bioconductor.org/packages/seqbias/")
6788 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
6790 "This package implements a model of per-position sequencing bias in
6791 high-throughput sequencing data using a simple Bayesian network, the structure
6792 and parameters of which are trained on a set of aligned reads and a reference
6794 (license license:lgpl3)))
6796 (define-public r-snplocs-hsapiens-dbsnp144-grch37
6798 (name "r-snplocs-hsapiens-dbsnp144-grch37")
6802 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
6803 version 'annotation))
6806 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
6807 (build-system r-build-system)
6808 ;; As this package provides little more than a very large data file it
6809 ;; doesn't make sense to build substitutes.
6810 (arguments `(#:substitutable? #f))
6812 `(("r-biocgenerics" ,r-biocgenerics)
6813 ("r-s4vectors" ,r-s4vectors)
6814 ("r-iranges" ,r-iranges)
6815 ("r-genomeinfodb" ,r-genomeinfodb)
6816 ("r-genomicranges" ,r-genomicranges)
6817 ("r-bsgenome" ,r-bsgenome)
6818 ("r-biostrings" ,r-biostrings)))
6820 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
6821 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
6822 (description "This package provides SNP locations and alleles for Homo
6823 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
6824 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
6825 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
6826 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
6827 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
6828 the mitochondrion chromosome. Therefore, the SNPs in this package can be
6829 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
6830 correct position but this injection will exclude chrM (i.e. nothing will be
6831 injected in that sequence).")
6832 (license license:artistic2.0)))
6834 (define-public r-reqon
6841 (uri (bioconductor-uri "ReQON" version))
6844 "06m0hd4aqsxjyzhs8b1zys7lz8289qgwn7jp2dpln1j7cf02q4bz"))))
6845 (properties `((upstream-name . "ReQON")))
6846 (build-system r-build-system)
6848 `(("r-rjava" ,r-rjava)
6849 ("r-rsamtools" ,r-rsamtools)
6850 ("r-seqbias" ,r-seqbias)))
6851 (home-page "https://bioconductor.org/packages/ReQON/")
6852 (synopsis "Recalibrating quality of nucleotides")
6854 "This package provides an implementation of an algorithm for
6855 recalibrating the base quality scores for aligned sequencing data in BAM
6857 (license license:gpl2)))
6859 (define-public r-wavcluster
6861 (name "r-wavcluster")
6866 (uri (bioconductor-uri "wavClusteR" version))
6869 "0204czqjmkwhd6gznwxzb0vj3dg3aif628g8c30085aa2jljn9bk"))))
6870 (properties `((upstream-name . "wavClusteR")))
6871 (build-system r-build-system)
6873 `(("r-biocgenerics" ,r-biocgenerics)
6874 ("r-biostrings" ,r-biostrings)
6875 ("r-foreach" ,r-foreach)
6876 ("r-genomicfeatures" ,r-genomicfeatures)
6877 ("r-genomicranges" ,r-genomicranges)
6878 ("r-ggplot2" ,r-ggplot2)
6879 ("r-hmisc" ,r-hmisc)
6880 ("r-iranges" ,r-iranges)
6881 ("r-mclust" ,r-mclust)
6882 ("r-rsamtools" ,r-rsamtools)
6883 ("r-rtracklayer" ,r-rtracklayer)
6884 ("r-s4vectors" ,r-s4vectors)
6885 ("r-seqinr" ,r-seqinr)
6886 ("r-stringr" ,r-stringr)
6887 ("r-wmtsa" ,r-wmtsa)))
6889 `(("r-knitr" ,r-knitr)))
6890 (home-page "https://bioconductor.org/packages/wavClusteR/")
6891 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
6893 "This package provides an integrated pipeline for the analysis of
6894 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
6895 sequencing errors, SNPs and additional non-experimental sources by a non-
6896 parametric mixture model. The protein binding sites (clusters) are then
6897 resolved at high resolution and cluster statistics are estimated using a
6898 rigorous Bayesian framework. Post-processing of the results, data export for
6899 UCSC genome browser visualization and motif search analysis are provided. In
6900 addition, the package integrates RNA-Seq data to estimate the False
6901 Discovery Rate of cluster detection. Key functions support parallel multicore
6902 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
6903 be applied to the analysis of other NGS data obtained from experimental
6904 procedures that induce nucleotide substitutions (e.g. BisSeq).")
6905 (license license:gpl2)))
6907 (define-public r-timeseriesexperiment
6909 (name "r-timeseriesexperiment")
6914 (uri (bioconductor-uri "TimeSeriesExperiment" version))
6917 "1k0djvcsyjj1ayncvmi8nlqi3jdn5qp41y3fwsqg1cp0qsvx7zv3"))))
6919 `((upstream-name . "TimeSeriesExperiment")))
6920 (build-system r-build-system)
6922 `(("r-deseq2" ,r-deseq2)
6923 ("r-dplyr" ,r-dplyr)
6924 ("r-dynamictreecut" ,r-dynamictreecut)
6925 ("r-edger" ,r-edger)
6926 ("r-ggplot2" ,r-ggplot2)
6927 ("r-hmisc" ,r-hmisc)
6928 ("r-limma" ,r-limma)
6929 ("r-magrittr" ,r-magrittr)
6930 ("r-proxy" ,r-proxy)
6931 ("r-s4vectors" ,r-s4vectors)
6932 ("r-summarizedexperiment" ,r-summarizedexperiment)
6933 ("r-tibble" ,r-tibble)
6934 ("r-tidyr" ,r-tidyr)
6935 ("r-vegan" ,r-vegan)
6936 ("r-viridis" ,r-viridis)))
6938 `(("r-knitr" ,r-knitr)))
6939 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
6940 (synopsis "Analysis for short time-series data")
6942 "This package is a visualization and analysis toolbox for short time
6943 course data which includes dimensionality reduction, clustering, two-sample
6944 differential expression testing and gene ranking techniques. The package also
6945 provides methods for retrieving enriched pathways.")
6946 (license license:lgpl3+)))
6948 (define-public r-variantfiltering
6950 (name "r-variantfiltering")
6955 (uri (bioconductor-uri "VariantFiltering" version))
6958 "0lsrnybsbm9siyjv4nal6bmprj8ynwgk4n1145f4h52g78wq3br4"))))
6960 `((upstream-name . "VariantFiltering")))
6961 (build-system r-build-system)
6963 `(("r-annotationdbi" ,r-annotationdbi)
6964 ("r-biobase" ,r-biobase)
6965 ("r-biocgenerics" ,r-biocgenerics)
6966 ("r-biocparallel" ,r-biocparallel)
6967 ("r-biostrings" ,r-biostrings)
6968 ("r-bsgenome" ,r-bsgenome)
6970 ("r-genomeinfodb" ,r-genomeinfodb)
6971 ("r-genomicfeatures" ,r-genomicfeatures)
6972 ("r-genomicranges" ,r-genomicranges)
6973 ("r-genomicscores" ,r-genomicscores)
6974 ("r-graph" ,r-graph)
6976 ("r-iranges" ,r-iranges)
6978 ("r-rsamtools" ,r-rsamtools)
6979 ("r-s4vectors" ,r-s4vectors)
6980 ("r-shiny" ,r-shiny)
6981 ("r-shinyjs" ,r-shinyjs)
6982 ("r-shinythemes" ,r-shinythemes)
6983 ("r-shinytree" ,r-shinytree)
6984 ("r-summarizedexperiment" ,r-summarizedexperiment)
6985 ("r-variantannotation" ,r-variantannotation)
6986 ("r-xvector" ,r-xvector)))
6987 (home-page "https://github.com/rcastelo/VariantFiltering")
6988 (synopsis "Filtering of coding and non-coding genetic variants")
6990 "Filter genetic variants using different criteria such as inheritance
6991 model, amino acid change consequence, minor allele frequencies across human
6992 populations, splice site strength, conservation, etc.")
6993 (license license:artistic2.0)))
6995 (define-public r-genomegraphs
6997 (name "r-genomegraphs")
7002 (uri (bioconductor-uri "GenomeGraphs" version))
7005 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7006 (properties `((upstream-name . "GenomeGraphs")))
7007 (build-system r-build-system)
7009 `(("r-biomart" ,r-biomart)))
7010 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7011 (synopsis "Plotting genomic information from Ensembl")
7013 "Genomic data analyses requires integrated visualization of known genomic
7014 information and new experimental data. GenomeGraphs uses the biomaRt package
7015 to perform live annotation queries to Ensembl and translates this to e.g.
7016 gene/transcript structures in viewports of the grid graphics package. This
7017 results in genomic information plotted together with your data. Another
7018 strength of GenomeGraphs is to plot different data types such as array CGH,
7019 gene expression, sequencing and other data, together in one plot using the
7020 same genome coordinate system.")
7021 (license license:artistic2.0)))
7023 (define-public r-wavetiling
7025 (name "r-wavetiling")
7030 (uri (bioconductor-uri "waveTiling" version))
7033 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7034 (properties `((upstream-name . "waveTiling")))
7035 (build-system r-build-system)
7037 `(("r-affy" ,r-affy)
7038 ("r-biobase" ,r-biobase)
7039 ("r-biostrings" ,r-biostrings)
7040 ("r-genomegraphs" ,r-genomegraphs)
7041 ("r-genomicranges" ,r-genomicranges)
7042 ("r-iranges" ,r-iranges)
7043 ("r-oligo" ,r-oligo)
7044 ("r-oligoclasses" ,r-oligoclasses)
7045 ("r-preprocesscore" ,r-preprocesscore)
7046 ("r-waveslim" ,r-waveslim)))
7047 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7048 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7050 "This package is designed to conduct transcriptome analysis for tiling
7051 arrays based on fast wavelet-based functional models.")
7052 (license license:gpl2+)))
7054 (define-public r-variancepartition
7056 (name "r-variancepartition")
7061 (uri (bioconductor-uri "variancePartition" version))
7064 "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
7066 `((upstream-name . "variancePartition")))
7067 (build-system r-build-system)
7069 `(("r-biobase" ,r-biobase)
7070 ("r-biocparallel" ,r-biocparallel)
7071 ("r-colorramps" ,r-colorramps)
7072 ("r-doparallel" ,r-doparallel)
7073 ("r-foreach" ,r-foreach)
7074 ("r-ggplot2" ,r-ggplot2)
7075 ("r-gplots" ,r-gplots)
7076 ("r-iterators" ,r-iterators)
7077 ("r-limma" ,r-limma)
7079 ("r-lmertest" ,r-lmertest)
7081 ("r-pbkrtest" ,r-pbkrtest)
7082 ("r-progress" ,r-progress)
7083 ("r-reshape2" ,r-reshape2)
7084 ("r-scales" ,r-scales)))
7086 `(("r-knitr" ,r-knitr)))
7087 (home-page "https://bioconductor.org/packages/variancePartition/")
7088 (synopsis "Analyze variation in gene expression experiments")
7090 "This is a package providing tools to quantify and interpret multiple
7091 sources of biological and technical variation in gene expression experiments.
7092 It uses a linear mixed model to quantify variation in gene expression
7093 attributable to individual, tissue, time point, or technical variables. The
7094 package includes dream differential expression analysis for repeated
7096 (license license:gpl2+)))
7098 (define-public r-htqpcr
7105 (uri (bioconductor-uri "HTqPCR" version))
7108 "08bd5zkjdnz726s03bvvzv03va0xbrr818ipp6737z9g3nk9m81j"))))
7109 (properties `((upstream-name . "HTqPCR")))
7110 (build-system r-build-system)
7112 `(("r-affy" ,r-affy)
7113 ("r-biobase" ,r-biobase)
7114 ("r-gplots" ,r-gplots)
7115 ("r-limma" ,r-limma)
7116 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7117 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7118 "groups/bertone/software/HTqPCR.pdf"))
7119 (synopsis "Automated analysis of high-throughput qPCR data")
7121 "Analysis of Ct values from high throughput quantitative real-time
7122 PCR (qPCR) assays across multiple conditions or replicates. The input data
7123 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7124 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7125 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7126 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7127 loading, quality assessment, normalization, visualization and parametric or
7128 non-parametric testing for statistical significance in Ct values between
7129 features (e.g. genes, microRNAs).")
7130 (license license:artistic2.0)))
7132 (define-public r-unifiedwmwqpcr
7134 (name "r-unifiedwmwqpcr")
7139 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7142 "1l9gxq3askr3cz2a4bqsw7vjr1agivzvx651cblkygv57x08zf81"))))
7144 `((upstream-name . "unifiedWMWqPCR")))
7145 (build-system r-build-system)
7147 `(("r-biocgenerics" ,r-biocgenerics)
7148 ("r-htqpcr" ,r-htqpcr)))
7149 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7150 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7152 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7153 data. This modified test allows for testing differential expression in qPCR
7155 (license license:gpl2+)))
7157 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7159 (define-public r-activedriverwgs
7161 (name "r-activedriverwgs")
7166 (uri (cran-uri "ActiveDriverWGS" version))
7169 "0l6h0f54zjvcx19ngq3kp01dypsjqf28vssjm8yzccmpyacfypag"))))
7171 `((upstream-name . "ActiveDriverWGS")))
7172 (build-system r-build-system)
7174 `(("r-biostrings" ,r-biostrings)
7175 ("r-bsgenome" ,r-bsgenome)
7176 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7177 ("r-genomeinfodb" ,r-genomeinfodb)
7178 ("r-genomicranges" ,r-genomicranges)
7179 ("r-iranges" ,r-iranges)
7180 ("r-s4vectors" ,r-s4vectors)))
7182 `(("r-knitr" ,r-knitr)))
7183 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
7184 (synopsis "Driver discovery tool for cancer whole genomes")
7186 "This package provides a method for finding an enrichment of cancer
7187 simple somatic mutations (SNVs and Indels) in functional elements across the
7188 human genome. ActiveDriverWGS detects coding and noncoding driver elements
7189 using whole genome sequencing data.")
7190 (license license:gpl3)))
7192 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
7194 (define-public r-activepathways
7196 (name "r-activepathways")
7201 (uri (cran-uri "ActivePathways" version))
7204 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
7206 `((upstream-name . "ActivePathways")))
7207 (build-system r-build-system)
7209 `(("r-data-table" ,r-data-table)
7210 ("r-ggplot2" ,r-ggplot2)))
7212 `(("r-knitr" ,r-knitr)))
7213 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
7214 (synopsis "Multivariate pathway enrichment analysis")
7216 "This package represents an integrative method of analyzing multi omics
7217 data that conducts enrichment analysis of annotated gene sets. ActivePathways
7218 uses a statistical data fusion approach, rationalizes contributing evidence
7219 and highlights associated genes, improving systems-level understanding of
7220 cellular organization in health and disease.")
7221 (license license:gpl3)))
7223 (define-public r-bgmix
7230 (uri (bioconductor-uri "BGmix" version))
7233 "1pfi3hinjn6ymikadgj8dqm59h7mapf01wj86dbbvf8y1xqp8y8n"))))
7234 (properties `((upstream-name . "BGmix")))
7235 (build-system r-build-system)
7237 `(("r-kernsmooth" ,r-kernsmooth)))
7238 (home-page "https://bioconductor.org/packages/BGmix/")
7239 (synopsis "Bayesian models for differential gene expression")
7241 "This package provides fully Bayesian mixture models for differential
7243 (license license:gpl2)))
7245 (define-public r-bgx
7252 (uri (bioconductor-uri "bgx" version))
7255 "0r67a6m5hrnsxgk0f57hl5yaagi2wai2kpfyjjlhrck4rlm1sjcx"))))
7256 (properties `((upstream-name . "bgx")))
7257 (build-system r-build-system)
7259 `(("r-affy" ,r-affy)
7260 ("r-biobase" ,r-biobase)
7261 ("r-gcrma" ,r-gcrma)
7262 ("r-rcpp" ,r-rcpp)))
7263 (home-page "https://bioconductor.org/packages/bgx/")
7264 (synopsis "Bayesian gene expression")
7266 "This package provides tools for Bayesian integrated analysis of
7267 Affymetrix GeneChips.")
7268 (license license:gpl2)))
7270 (define-public r-bhc
7277 (uri (bioconductor-uri "BHC" version))
7280 "06milqjg2nl3ra47sxi7a2p2d3mbrx3wk168pqgimvs8snldd2xr"))))
7281 (properties `((upstream-name . "BHC")))
7282 (build-system r-build-system)
7283 (home-page "https://bioconductor.org/packages/BHC/")
7284 (synopsis "Bayesian hierarchical clustering")
7286 "The method implemented in this package performs bottom-up hierarchical
7287 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
7288 in the data and Bayesian model selection to decide at each step which clusters
7289 to merge. This avoids several limitations of traditional methods, for example
7290 how many clusters there should be and how to choose a principled distance
7291 metric. This implementation accepts multinomial (i.e. discrete, with 2+
7292 categories) or time-series data. This version also includes a randomised
7293 algorithm which is more efficient for larger data sets.")
7294 (license license:gpl3)))
7296 (define-public r-bicare
7303 (uri (bioconductor-uri "BicARE" version))
7306 "0llckbl3l26lf6wgjg7rxs8k1yrk043vvdhnkc6ncg33sydj383y"))))
7307 (properties `((upstream-name . "BicARE")))
7308 (build-system r-build-system)
7310 `(("r-biobase" ,r-biobase)
7311 ("r-gseabase" ,r-gseabase)
7312 ("r-multtest" ,r-multtest)))
7313 (home-page "http://bioinfo.curie.fr")
7314 (synopsis "Biclustering analysis and results exploration")
7316 "This is a package for biclustering analysis and exploration of
7318 (license license:gpl2)))
7320 (define-public r-bifet
7327 (uri (bioconductor-uri "BiFET" version))
7330 "1v2dshs09iy2glzq0vwxmr83x867j844i1ixsfcamvfq33fwbbr5"))))
7331 (properties `((upstream-name . "BiFET")))
7332 (build-system r-build-system)
7334 `(("r-genomicranges" ,r-genomicranges)
7335 ("r-poibin" ,r-poibin)))
7337 `(("r-knitr" ,r-knitr)))
7338 (home-page "https://bioconductor.org/packages/BiFET")
7339 (synopsis "Bias-free footprint enrichment test")
7341 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
7342 over-represented in target regions compared to background regions after
7343 correcting for the bias arising from the imbalance in read counts and GC
7344 contents between the target and background regions. For a given TF k, BiFET
7345 tests the null hypothesis that the target regions have the same probability of
7346 having footprints for the TF k as the background regions while correcting for
7347 the read count and GC content bias.")
7348 (license license:gpl3)))
7350 (define-public r-rsbml
7357 (uri (bioconductor-uri "rsbml" version))
7360 "1i1izznnwzrc6m7s3hblfff466icfvxl2gjdqaln8qfg9v87rslx"))))
7361 (properties `((upstream-name . "rsbml")))
7362 (build-system r-build-system)
7364 `(("libsbml" ,libsbml)
7367 `(("r-biocgenerics" ,r-biocgenerics)
7368 ("r-graph" ,r-graph)))
7370 `(("pkg-config" ,pkg-config)))
7371 (home-page "http://www.sbml.org")
7372 (synopsis "R support for SBML")
7374 "This package provides an R interface to libsbml for SBML parsing,
7375 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
7376 (license license:artistic2.0)))
7378 (define-public r-hypergraph
7380 (name "r-hypergraph")
7385 (uri (bioconductor-uri "hypergraph" version))
7388 "1iq9b9rzy3ikx8xszsjiv3p8l702n2h2s9w33797wcmkg4apslb7"))))
7389 (properties `((upstream-name . "hypergraph")))
7390 (build-system r-build-system)
7392 `(("r-graph" ,r-graph)))
7393 (home-page "https://bioconductor.org/packages/hypergraph")
7394 (synopsis "Hypergraph data structures")
7396 "This package implements some simple capabilities for representing and
7397 manipulating hypergraphs.")
7398 (license license:artistic2.0)))
7400 (define-public r-hyperdraw
7402 (name "r-hyperdraw")
7407 (uri (bioconductor-uri "hyperdraw" version))
7410 "1qzx5sqp7rpspk8g1j34p03ds1vmw0h7hpzb2ijpbvmsja5drzvf"))))
7411 (properties `((upstream-name . "hyperdraw")))
7412 (build-system r-build-system)
7413 (inputs `(("graphviz" ,graphviz)))
7415 `(("r-graph" ,r-graph)
7416 ("r-hypergraph" ,r-hypergraph)
7417 ("r-rgraphviz" ,r-rgraphviz)))
7418 (home-page "https://bioconductor.org/packages/hyperdraw")
7419 (synopsis "Visualizing hypergraphs")
7421 "This package provides functions for visualizing hypergraphs.")
7422 (license license:gpl2+)))
7424 (define-public r-biggr
7431 (uri (bioconductor-uri "BiGGR" version))
7434 "05afi6hsh1dv6lc6l0dfhvvi8k34wyzf1k1jimam7a6pbrhyy5dk"))))
7435 (properties `((upstream-name . "BiGGR")))
7436 (build-system r-build-system)
7438 `(("r-hyperdraw" ,r-hyperdraw)
7439 ("r-hypergraph" ,r-hypergraph)
7441 ("r-limsolve" ,r-limsolve)
7442 ("r-rsbml" ,r-rsbml)
7443 ("r-stringr" ,r-stringr)))
7444 (home-page "https://bioconductor.org/packages/BiGGR/")
7445 (synopsis "Constraint based modeling using metabolic reconstruction databases")
7447 "This package provides an interface to simulate metabolic reconstruction
7448 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
7449 reconstruction databases. The package facilitates @dfn{flux balance
7450 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
7451 networks and estimated fluxes can be visualized with hypergraphs.")
7452 (license license:gpl3+)))
7454 (define-public r-bigmemoryextras
7456 (name "r-bigmemoryextras")
7461 (uri (bioconductor-uri "bigmemoryExtras" version))
7464 "053bqcd3p4i7agj43ccjxfz40a1sxrymd49vdpfq8ypslkwk7g0g"))))
7466 `((upstream-name . "bigmemoryExtras")))
7467 (build-system r-build-system)
7469 `(("r-bigmemory" ,r-bigmemory)))
7471 `(("r-knitr" ,r-knitr)))
7472 (home-page "https://github.com/phaverty/bigmemoryExtras")
7473 (synopsis "Extension of the bigmemory package")
7475 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
7476 safety and convenience features to the @code{filebacked.big.matrix} class from
7477 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
7478 monitoring and gracefully restoring the connection to on-disk data and it also
7479 protects against accidental data modification with a filesystem-based
7480 permissions system. Utilities are provided for using @code{BigMatrix}-derived
7481 classes as @code{assayData} matrices within the @code{Biobase} package's
7482 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
7483 related to attaching to, and indexing into, file-backed matrices with
7484 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
7485 a file-backed matrix with factor properties.")
7486 (license license:artistic2.0)))
7488 (define-public r-bigpint
7495 (uri (bioconductor-uri "bigPint" version))
7498 "1m92ngkzimcc37byf0ziphrby8wmjd5hfa53gvfphgaakyj9bjg8"))))
7499 (properties `((upstream-name . "bigPint")))
7500 (build-system r-build-system)
7502 `(("r-delayedarray" ,r-delayedarray)
7503 ("r-dplyr" ,r-dplyr)
7504 ("r-ggally" ,r-ggally)
7505 ("r-ggplot2" ,r-ggplot2)
7506 ("r-gridextra" ,r-gridextra)
7507 ("r-hexbin" ,r-hexbin)
7508 ("r-hmisc" ,r-hmisc)
7509 ("r-htmlwidgets" ,r-htmlwidgets)
7510 ("r-plotly" ,r-plotly)
7512 ("r-rcolorbrewer" ,r-rcolorbrewer)
7513 ("r-reshape" ,r-reshape)
7514 ("r-shiny" ,r-shiny)
7515 ("r-shinycssloaders" ,r-shinycssloaders)
7516 ("r-shinydashboard" ,r-shinydashboard)
7517 ("r-stringr" ,r-stringr)
7518 ("r-summarizedexperiment" ,r-summarizedexperiment)
7519 ("r-tidyr" ,r-tidyr)))
7521 `(("r-knitr" ,r-knitr)))
7522 (home-page "https://github.com/lindsayrutter/bigPint")
7523 (synopsis "Big multivariate data plotted interactively")
7525 "This package provides methods for visualizing large multivariate
7526 datasets using static and interactive scatterplot matrices, parallel
7527 coordinate plots, volcano plots, and litre plots. It includes examples for
7528 visualizing RNA-sequencing datasets and differentially expressed genes.")
7529 (license license:gpl3)))
7531 (define-public r-chemminer
7533 (name "r-chemminer")
7538 (uri (bioconductor-uri "ChemmineR" version))
7541 "0cna5xsqflvhlp2k47asxyv3w4ympmz2wy2cwjyzlal6936fjikf"))))
7542 (properties `((upstream-name . "ChemmineR")))
7543 (build-system r-build-system)
7545 `(("r-base64enc" ,r-base64enc)
7547 ("r-biocgenerics" ,r-biocgenerics)
7549 ("r-digest" ,r-digest)
7551 ("r-ggplot2" ,r-ggplot2)
7552 ("r-gridextra" ,r-gridextra)
7555 ("r-rcurl" ,r-rcurl)
7556 ("r-rjson" ,r-rjson)
7557 ("r-rsvg" ,r-rsvg)))
7559 `(("r-knitr" ,r-knitr)))
7560 (home-page "https://github.com/girke-lab/ChemmineR")
7561 (synopsis "Cheminformatics toolkit for R")
7563 "ChemmineR is a cheminformatics package for analyzing drug-like small
7564 molecule data in R. It contains functions for efficient processing of large
7565 numbers of molecules, physicochemical/structural property predictions,
7566 structural similarity searching, classification and clustering of compound
7567 libraries with a wide spectrum of algorithms. In addition, it offers
7568 visualization functions for compound clustering results and chemical
7570 (license license:artistic2.0)))
7572 (define-public r-bioassayr
7574 (name "r-bioassayr")
7579 (uri (bioconductor-uri "bioassayR" version))
7582 "1n0gsnxcl0lplqk8rs5ygxrxpx389ddl6wv3ciyz9g2xry5biyfy"))))
7583 (properties `((upstream-name . "bioassayR")))
7584 (build-system r-build-system)
7586 `(("r-biocgenerics" ,r-biocgenerics)
7587 ("r-chemminer" ,r-chemminer)
7589 ("r-matrix" ,r-matrix)
7590 ("r-rjson" ,r-rjson)
7591 ("r-rsqlite" ,r-rsqlite)
7594 `(("r-knitr" ,r-knitr)))
7595 (home-page "https://github.com/TylerBackman/bioassayR")
7596 (synopsis "Cross-target analysis of small molecule bioactivity")
7598 "bioassayR is a computational tool that enables simultaneous analysis of
7599 thousands of bioassay experiments performed over a diverse set of compounds
7600 and biological targets. Unique features include support for large-scale
7601 cross-target analyses of both public and custom bioassays, generation of
7602 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
7603 preloaded database that provides access to a substantial portion of publicly
7604 available bioactivity data.")
7605 (license license:artistic2.0)))
7607 (define-public r-biobroom
7614 (uri (bioconductor-uri "biobroom" version))
7617 "06qcrprn58kbrr5kyw1jl6z88b9w9g8xs6rkhrbnz8k7rv373fhf"))))
7618 (properties `((upstream-name . "biobroom")))
7619 (build-system r-build-system)
7621 `(("r-biobase" ,r-biobase)
7622 ("r-broom" ,r-broom)
7623 ("r-dplyr" ,r-dplyr)
7624 ("r-tidyr" ,r-tidyr)))
7626 `(("r-knitr" ,r-knitr)))
7627 (home-page "https://github.com/StoreyLab/biobroom")
7628 (synopsis "Turn Bioconductor objects into tidy data frames")
7630 "This package contains methods for converting standard objects
7631 constructed by bioinformatics packages, especially those in Bioconductor, and
7632 converting them to @code{tidy} data. It thus serves as a complement to the
7633 @code{broom} package, and follows the same tidy, augment, glance division of
7634 tidying methods. Tidying data makes it easy to recombine, reshape and
7635 visualize bioinformatics analyses.")
7636 ;; Any version of the LGPL.
7637 (license license:lgpl3+)))
7639 (define-public r-graphite
7646 (uri (bioconductor-uri "graphite" version))
7649 "0rc9cw3picz1y0lwhbzpk03ciij8kij74m15qgzh2ykla7zprb2p"))))
7650 (properties `((upstream-name . "graphite")))
7651 (build-system r-build-system)
7653 `(("r-annotationdbi" ,r-annotationdbi)
7654 ("r-checkmate" ,r-checkmate)
7655 ("r-graph" ,r-graph)
7657 ("r-rappdirs" ,r-rappdirs)))
7658 (home-page "https://bioconductor.org/packages/graphite/")
7659 (synopsis "Networks from pathway databases")
7661 "Graphite provides networks derived from eight public pathway databases,
7662 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
7664 (license license:agpl3+)))
7666 (define-public r-reactomepa
7668 (name "r-reactomepa")
7673 (uri (bioconductor-uri "ReactomePA" version))
7676 "1ngilyn1mihwxs4sh5gk9y829xghdmh277cfw3vfgflz9sgwy21x"))))
7677 (properties `((upstream-name . "ReactomePA")))
7678 (build-system r-build-system)
7680 `(("r-annotationdbi" ,r-annotationdbi)
7682 ("r-enrichplot" ,r-enrichplot)
7683 ("r-ggplot2" ,r-ggplot2)
7684 ("r-ggraph" ,r-ggraph)
7685 ("r-graphite" ,r-graphite)
7686 ("r-igraph" ,r-igraph)
7687 ("r-reactome-db" ,r-reactome-db)))
7689 `(("r-knitr" ,r-knitr)))
7690 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
7691 (synopsis "Reactome pathway analysis")
7693 "This package provides functions for pathway analysis based on the
7694 REACTOME pathway database. It implements enrichment analysis, gene set
7695 enrichment analysis and several functions for visualization.")
7696 (license license:gpl2)))
7698 (define-public r-ebarrays
7705 (uri (bioconductor-uri "EBarrays" version))
7708 "00ld26bld8xgin9zqwxybahvhmqbrvr09jfphg0yr4j4zck6sqgf"))))
7709 (properties `((upstream-name . "EBarrays")))
7710 (build-system r-build-system)
7712 `(("r-biobase" ,r-biobase)
7713 ("r-cluster" ,r-cluster)
7714 ("r-lattice" ,r-lattice)))
7715 (home-page "https://bioconductor.org/packages/EBarrays/")
7716 (synopsis "Gene clustering and differential expression identification")
7718 "EBarrays provides tools for the analysis of replicated/unreplicated
7720 (license license:gpl2+)))
7722 (define-public r-bioccasestudies
7724 (name "r-bioccasestudies")
7729 (uri (bioconductor-uri "BiocCaseStudies" version))
7732 "0fadck1dk1zavpn9yrcwx6zgfi18fw5xfs8svgzipns6bq41j8ix"))))
7734 `((upstream-name . "BiocCaseStudies")))
7735 (build-system r-build-system)
7736 (propagated-inputs `(("r-biobase" ,r-biobase)))
7737 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
7738 (synopsis "Support for the case studies monograph")
7740 "This package provides software and data to support the case studies
7742 (license license:artistic2.0)))
7744 (define-public r-biocgraph
7746 (name "r-biocgraph")
7751 (uri (bioconductor-uri "biocGraph" version))
7754 "1372bm4y3czqhpki10pnprxfkfncfcsy59zzvf8wj6q03acaavrj"))))
7755 (properties `((upstream-name . "biocGraph")))
7756 (build-system r-build-system)
7758 `(("r-biocgenerics" ,r-biocgenerics)
7759 ("r-geneplotter" ,r-geneplotter)
7760 ("r-graph" ,r-graph)
7761 ("r-rgraphviz" ,r-rgraphviz)))
7762 (home-page "https://bioconductor.org/packages/biocGraph/")
7763 (synopsis "Graph examples and use cases in Bioinformatics")
7765 "This package provides examples and code that make use of the
7766 different graph related packages produced by Bioconductor.")
7767 (license license:artistic2.0)))
7769 (define-public r-experimenthub
7771 (name "r-experimenthub")
7776 (uri (bioconductor-uri "ExperimentHub" version))
7779 "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
7780 (properties `((upstream-name . "ExperimentHub")))
7781 (build-system r-build-system)
7783 `(("r-annotationhub" ,r-annotationhub)
7784 ("r-biocfilecache" ,r-biocfilecache)
7785 ("r-biocgenerics" ,r-biocgenerics)
7786 ("r-biocmanager" ,r-biocmanager)
7788 ("r-rappdirs" ,r-rappdirs)
7789 ("r-s4vectors" ,r-s4vectors)))
7791 `(("r-knitr" ,r-knitr)))
7792 (home-page "https://bioconductor.org/packages/ExperimentHub/")
7793 (synopsis "Client to access ExperimentHub resources")
7795 "This package provides a client for the Bioconductor ExperimentHub web
7796 resource. ExperimentHub provides a central location where curated data from
7797 experiments, publications or training courses can be accessed. Each resource
7798 has associated metadata, tags and date of modification. The client creates
7799 and manages a local cache of files retrieved enabling quick and reproducible
7801 (license license:artistic2.0)))
7803 (define-public r-multiassayexperiment
7805 (name "r-multiassayexperiment")
7810 (uri (bioconductor-uri "MultiAssayExperiment" version))
7813 "0qlfnd86999jqv2nd0ikixi2sfd449dyg3ml4nbs8ycs57c2irgh"))))
7815 `((upstream-name . "MultiAssayExperiment")))
7816 (build-system r-build-system)
7818 `(("r-biobase" ,r-biobase)
7819 ("r-biocgenerics" ,r-biocgenerics)
7820 ("r-genomicranges" ,r-genomicranges)
7821 ("r-iranges" ,r-iranges)
7822 ("r-s4vectors" ,r-s4vectors)
7823 ("r-summarizedexperiment" ,r-summarizedexperiment)
7824 ("r-tidyr" ,r-tidyr)))
7826 `(("r-knitr" ,r-knitr)))
7827 (home-page "https://waldronlab.io/MultiAssayExperiment/")
7828 (synopsis "Integration of multi-omics experiments in Bioconductor")
7830 "MultiAssayExperiment harmonizes data management of multiple assays
7831 performed on an overlapping set of specimens. It provides a familiar
7832 Bioconductor user experience by extending concepts from
7833 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
7834 classes for individual assays, and allowing subsetting by genomic ranges or
7836 (license license:artistic2.0)))
7838 (define-public r-bioconcotk
7840 (name "r-bioconcotk")
7845 (uri (bioconductor-uri "BiocOncoTK" version))
7848 "021qzygfwdnd3naz1iqq01zr3zxv3k7wm1lklik24vc7axshxbmk"))))
7849 (properties `((upstream-name . "BiocOncoTK")))
7850 (build-system r-build-system)
7852 `(("r-bigrquery" ,r-bigrquery)
7854 ("r-complexheatmap" ,r-complexheatmap)
7855 ("r-curatedtcgadata" ,r-curatedtcgadata)
7857 ("r-dplyr" ,r-dplyr)
7859 ("r-genomicfeatures" ,r-genomicfeatures)
7860 ("r-genomicranges" ,r-genomicranges)
7861 ("r-ggplot2" ,r-ggplot2)
7862 ("r-ggpubr" ,r-ggpubr)
7863 ("r-graph" ,r-graph)
7865 ("r-iranges" ,r-iranges)
7866 ("r-magrittr" ,r-magrittr)
7868 ("r-rgraphviz" ,r-rgraphviz)
7869 ("r-rjson" ,r-rjson)
7870 ("r-s4vectors" ,r-s4vectors)
7871 ("r-scales" ,r-scales)
7872 ("r-shiny" ,r-shiny)
7873 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7875 `(("r-knitr" ,r-knitr)))
7876 (home-page "https://bioconductor.org/packages/BiocOncoTK")
7877 (synopsis "Bioconductor components for general cancer genomics")
7879 "The purpose of this package is to provide a central interface to various
7880 tools for genome-scale analysis of cancer studies.")
7881 (license license:artistic2.0)))
7883 (define-public r-biocor
7890 (uri (bioconductor-uri "BioCor" version))
7893 "1xghclfqv8d23g72g8914br5zjx4sz9zihzczwwmpl15lghpnqwy"))))
7894 (properties `((upstream-name . "BioCor")))
7895 (build-system r-build-system)
7897 `(("r-biocparallel" ,r-biocparallel)
7898 ("r-gseabase" ,r-gseabase)
7899 ("r-matrix" ,r-matrix)))
7901 `(("r-knitr" ,r-knitr)))
7902 (home-page "https://llrs.github.io/BioCor/")
7903 (synopsis "Functional similarities")
7905 "This package provides tools to calculate functional similarities based
7906 on the pathways described on KEGG and REACTOME or in gene sets. These
7907 similarities can be calculated for pathways or gene sets, genes, or clusters
7908 and combined with other similarities. They can be used to improve networks,
7909 gene selection, testing relationships, and so on.")
7910 (license license:expat)))
7912 (define-public r-biocpkgtools
7914 (name "r-biocpkgtools")
7919 (uri (bioconductor-uri "BiocPkgTools" version))
7922 "0l5fvi1m4834n4h0iswbap135s9mpaiabw9czzn1r72ssz86vrcr"))))
7923 (properties `((upstream-name . "BiocPkgTools")))
7924 (build-system r-build-system)
7926 `(("r-biocfilecache" ,r-biocfilecache)
7927 ("r-biocmanager" ,r-biocmanager)
7928 ("r-biocviews" ,r-biocviews)
7929 ("r-dplyr" ,r-dplyr)
7932 ("r-graph" ,r-graph)
7933 ("r-htmltools" ,r-htmltools)
7934 ("r-htmlwidgets" ,r-htmlwidgets)
7936 ("r-igraph" ,r-igraph)
7937 ("r-jsonlite" ,r-jsonlite)
7938 ("r-magrittr" ,r-magrittr)
7939 ("r-rappdirs" ,r-rappdirs)
7941 ("r-readr" ,r-readr)
7943 ("r-rlang" ,r-rlang)
7944 ("r-rvest" ,r-rvest)
7945 ("r-stringr" ,r-stringr)
7946 ("r-tibble" ,r-tibble)
7947 ("r-tidyr" ,r-tidyr)
7948 ("r-tidyselect" ,r-tidyselect)
7949 ("r-xml2" ,r-xml2)))
7951 `(("r-knitr" ,r-knitr)))
7952 (home-page "https://github.com/seandavi/BiocPkgTools")
7953 (synopsis "Collection of tools for learning about Bioconductor packages")
7955 "Bioconductor has a rich ecosystem of metadata around packages, usage,
7956 and build status. This package is a simple collection of functions to access
7957 that metadata from R. The goal is to expose metadata for data mining and
7958 value-added functionality such as package searching, text mining, and
7959 analytics on packages.")
7960 (license license:expat)))
7962 (define-public r-biocset
7969 (uri (bioconductor-uri "BiocSet" version))
7972 "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
7973 (properties `((upstream-name . "BiocSet")))
7974 (build-system r-build-system)
7976 `(("r-annotationdbi" ,r-annotationdbi)
7977 ("r-dplyr" ,r-dplyr)
7978 ("r-keggrest" ,r-keggrest)
7980 ("r-rlang" ,r-rlang)
7981 ("r-rtracklayer" ,r-rtracklayer)
7982 ("r-tibble" ,r-tibble)))
7984 `(("r-knitr" ,r-knitr)))
7986 "https://bioconductor.org/packages/BiocSet")
7988 "Representing Different Biological Sets")
7990 "BiocSet displays different biological sets in a triple tibble format.
7991 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
7992 The user has the ability to activate one of these three tibbles to perform
7993 common functions from the @code{dplyr} package. Mapping functionality and
7994 accessing web references for elements/sets are also available in BiocSet.")
7995 (license license:artistic2.0)))
7997 (define-public r-biocworkflowtools
7999 (name "r-biocworkflowtools")
8004 (uri (bioconductor-uri "BiocWorkflowTools" version))
8007 "0p9r71ql67sdlgd5pv118lhz8b85pr5y4ijfwzcy8wrr8jwlbddy"))))
8009 `((upstream-name . "BiocWorkflowTools")))
8010 (build-system r-build-system)
8012 `(("r-biocstyle" ,r-biocstyle)
8013 ("r-bookdown" ,r-bookdown)
8014 ("r-git2r" ,r-git2r)
8016 ("r-knitr" ,r-knitr)
8017 ("r-rmarkdown" ,r-rmarkdown)
8018 ("r-rstudioapi" ,r-rstudioapi)
8019 ("r-stringr" ,r-stringr)
8020 ("r-usethis" ,r-usethis)))
8022 `(("r-knitr" ,r-knitr)))
8023 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
8024 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
8026 "This package provides functions to ease the transition between
8027 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
8028 (license license:expat)))
8030 (define-public r-biodist
8037 (uri (bioconductor-uri "bioDist" version))
8040 "17bvxk0anvsp29j5nbblvaymf8qgbj3sz4ir2l7wj8kb8jfi19cp"))))
8041 (properties `((upstream-name . "bioDist")))
8042 (build-system r-build-system)
8044 `(("r-biobase" ,r-biobase)
8045 ("r-kernsmooth" ,r-kernsmooth)))
8046 (home-page "https://bioconductor.org/packages/bioDist/")
8047 (synopsis "Different distance measures")
8049 "This package provides a collection of software tools for calculating
8050 distance measures.")
8051 (license license:artistic2.0)))
8053 (define-public r-pcatools
8060 (uri (bioconductor-uri "PCAtools" version))
8063 "0mnwqrhm1hmhzwrpidf6z207w1ycpm572snvpp5swlg6hnxq6bnc"))))
8064 (properties `((upstream-name . "PCAtools")))
8065 (build-system r-build-system)
8067 `(("r-beachmat" ,r-beachmat)
8069 ("r-biocparallel" ,r-biocparallel)
8070 ("r-biocsingular" ,r-biocsingular)
8071 ("r-cowplot" ,r-cowplot)
8072 ("r-delayedarray" ,r-delayedarray)
8073 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
8074 ("r-dqrng" ,r-dqrng)
8075 ("r-ggplot2" ,r-ggplot2)
8076 ("r-ggrepel" ,r-ggrepel)
8077 ("r-lattice" ,r-lattice)
8078 ("r-matrix" ,r-matrix)
8080 ("r-reshape2" ,r-reshape2)))
8081 (native-inputs `(("r-knitr" ,r-knitr)))
8082 (home-page "https://github.com/kevinblighe/PCAtools")
8083 (synopsis "PCAtools: everything Principal Components Analysis")
8085 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
8086 structure of the data without the need to build any model to represent it.
8087 This \"summary\" of the data is arrived at through a process of reduction that
8088 can transform the large number of variables into a lesser number that are
8089 uncorrelated (i.e. the 'principal components'), while at the same time being
8090 capable of easy interpretation on the original data. PCAtools provides
8091 functions for data exploration via PCA, and allows the user to generate
8092 publication-ready figures. PCA is performed via @code{BiocSingular}; users
8093 can also identify an optimal number of principal components via different
8094 metrics, such as the elbow method and Horn's parallel analysis, which has
8095 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
8096 dimensional mass cytometry data.")
8097 (license license:gpl3)))
8099 (define-public r-rgreat
8106 (uri (bioconductor-uri "rGREAT" version))
8109 "0n8dw9ibb2klsczcxvvinpi9l53w8cs436i0c8w2jmramayl593v"))))
8110 (properties `((upstream-name . "rGREAT")))
8111 (build-system r-build-system)
8113 `(("r-genomicranges" ,r-genomicranges)
8114 ("r-getoptlong" ,r-getoptlong)
8115 ("r-iranges" ,r-iranges)
8116 ("r-rcurl" ,r-rcurl)
8117 ("r-rjson" ,r-rjson)))
8118 (native-inputs `(("r-knitr" ,r-knitr)))
8119 (home-page "https://github.com/jokergoo/rGREAT")
8120 (synopsis "Client for GREAT analysis")
8122 "This package makes GREAT (Genomic Regions Enrichment of Annotations
8123 Tool) analysis automatic by constructing a HTTP POST request according to
8124 user's input and automatically retrieving results from GREAT web server.")
8125 (license license:expat)))
8127 (define-public r-m3c
8134 (uri (bioconductor-uri "M3C" version))
8137 "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
8138 (properties `((upstream-name . "M3C")))
8139 (build-system r-build-system)
8141 `(("r-cluster" ,r-cluster)
8142 ("r-corpcor" ,r-corpcor)
8143 ("r-doparallel" ,r-doparallel)
8144 ("r-dosnow" ,r-dosnow)
8145 ("r-foreach" ,r-foreach)
8146 ("r-ggplot2" ,r-ggplot2)
8147 ("r-matrix" ,r-matrix)
8148 ("r-matrixcalc" ,r-matrixcalc)
8149 ("r-rtsne" ,r-rtsne)
8150 ("r-umap" ,r-umap)))
8151 (native-inputs `(("r-knitr" ,r-knitr)))
8152 (home-page "https://bioconductor.org/packages/M3C")
8153 (synopsis "Monte Carlo reference-based consensus clustering")
8155 "M3C is a consensus clustering algorithm that uses a Monte Carlo
8156 simulation to eliminate overestimation of @code{K} and can reject the null
8157 hypothesis @code{K=1}.")
8158 (license license:agpl3+)))
8160 (define-public r-icens
8167 (uri (bioconductor-uri "Icens" version))
8170 "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))
8171 (properties `((upstream-name . "Icens")))
8172 (build-system r-build-system)
8174 `(("r-survival" ,r-survival)))
8175 (home-page "https://bioconductor.org/packages/Icens")
8176 (synopsis "NPMLE for censored and truncated data")
8178 "This package provides many functions for computing the
8179 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
8181 (license license:artistic2.0)))
8183 ;; This is a CRAN package but it depends on r-icens, which is published on
8185 (define-public r-interval
8192 (uri (cran-uri "interval" version))
8195 "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))
8196 (properties `((upstream-name . "interval")))
8197 (build-system r-build-system)
8199 `(("r-icens" ,r-icens)
8200 ("r-mlecens" ,r-mlecens)
8202 ("r-survival" ,r-survival)))
8203 (home-page "https://cran.r-project.org/web/packages/interval/")
8204 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
8206 "This package provides functions to fit nonparametric survival curves,
8207 plot them, and perform logrank or Wilcoxon type tests.")
8208 (license license:gpl2+)))
8210 ;; This is a CRAN package, but it depends on r-interval, which depends on a
8211 ;; Bioconductor package.
8212 (define-public r-fhtest
8219 (uri (cran-uri "FHtest" version))
8222 "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))
8223 (properties `((upstream-name . "FHtest")))
8224 (build-system r-build-system)
8226 `(("r-interval" ,r-interval)
8227 ("r-kmsurv" ,r-kmsurv)
8230 ("r-survival" ,r-survival)))
8231 (home-page "https://cran.r-project.org/web/packages/FHtest/")
8232 (synopsis "Tests for survival data based on the Fleming-Harrington class")
8234 "This package provides functions to compare two or more survival curves
8238 @item The Fleming-Harrington test for right-censored data based on
8239 permutations and on counting processes.
8240 @item An extension of the Fleming-Harrington test for interval-censored data
8241 based on a permutation distribution and on a score vector distribution.
8244 (license license:gpl2+)))