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 © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
11 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
13 ;;; This file is part of GNU Guix.
15 ;;; GNU Guix is free software; you can redistribute it and/or modify it
16 ;;; under the terms of the GNU General Public License as published by
17 ;;; the Free Software Foundation; either version 3 of the License, or (at
18 ;;; your option) any later version.
20 ;;; GNU Guix is distributed in the hope that it will be useful, but
21 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
22 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 ;;; GNU General Public License for more details.
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26 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
28 (define-module (gnu packages bioconductor)
29 #:use-module ((guix licenses) #:prefix license:)
30 #:use-module (guix packages)
31 #:use-module (guix download)
32 #:use-module (guix git-download)
33 #:use-module (guix build-system r)
34 #:use-module (gnu packages)
35 #:use-module (gnu packages base)
36 #:use-module (gnu packages bioinformatics)
37 #:use-module (gnu packages cran)
38 #:use-module (gnu packages compression)
39 #:use-module (gnu packages gcc)
40 #:use-module (gnu packages graph)
41 #:use-module (gnu packages graphviz)
42 #:use-module (gnu packages haskell-xyz)
43 #:use-module (gnu packages image)
44 #:use-module (gnu packages maths)
45 #:use-module (gnu packages netpbm)
46 #:use-module (gnu packages perl)
47 #:use-module (gnu packages pkg-config)
48 #:use-module (gnu packages statistics)
49 #:use-module (gnu packages web)
50 #:use-module (gnu packages xml)
51 #:use-module (srfi srfi-1))
56 (define-public r-org-eck12-eg-db
58 (name "r-org-eck12-eg-db")
63 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
65 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
67 `((upstream-name . "org.EcK12.eg.db")))
68 (build-system r-build-system)
70 `(("r-annotationdbi" ,r-annotationdbi)))
71 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
72 (synopsis "Genome wide annotation for E coli strain K12")
74 "This package provides genome wide annotation for E coli strain K12,
75 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
76 National Center for Biotechnology Information (NCBI)’s database for
77 gene-specific information. Entrez Gene maintains records from genomes which
78 have been completely sequenced, which have an active research community to
79 submit gene-specific information, or which are scheduled for intense sequence
81 (license license:artistic2.0)))
83 (define-public r-reactome-db
85 (name "r-reactome-db")
90 (uri (bioconductor-uri "reactome.db" version 'annotation))
93 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
94 (properties `((upstream-name . "reactome.db")))
95 (build-system r-build-system)
97 `(("r-annotationdbi" ,r-annotationdbi)))
98 (home-page "https://bioconductor.org/packages/reactome.db/")
99 (synopsis "Annotation maps for reactome")
101 "This package provides a set of annotation maps for the REACTOME
102 database, assembled using data from REACTOME.")
103 (license license:cc-by4.0)))
105 (define-public r-bsgenome-celegans-ucsc-ce6
107 (name "r-bsgenome-celegans-ucsc-ce6")
111 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
112 version 'annotation))
115 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
117 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
118 (build-system r-build-system)
120 `(("r-bsgenome" ,r-bsgenome)))
122 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
123 (synopsis "Full genome sequences for Worm")
125 "This package provides full genome sequences for Caenorhabditis
126 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
128 (license license:artistic2.0)))
130 (define-public r-bsgenome-celegans-ucsc-ce10
132 (name "r-bsgenome-celegans-ucsc-ce10")
136 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
137 version 'annotation))
140 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
142 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
143 (build-system r-build-system)
145 `(("r-bsgenome" ,r-bsgenome)))
147 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
148 (synopsis "Full genome sequences for Worm")
150 "This package provides full genome sequences for Caenorhabditis
151 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
153 (license license:artistic2.0)))
155 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
157 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
161 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
162 version 'annotation))
165 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
167 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
168 (build-system r-build-system)
170 `(("r-bsgenome" ,r-bsgenome)))
172 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
173 (synopsis "Full genome sequences for Fly")
175 "This package provides full genome sequences for Drosophila
176 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
178 (license license:artistic2.0)))
180 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
182 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
186 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
187 version 'annotation))
190 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
192 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
193 (build-system r-build-system)
195 `(("r-bsgenome" ,r-bsgenome)))
197 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
198 (synopsis "Full genome sequences for Fly")
200 "This package provides full genome sequences for Drosophila
201 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
202 Biostrings objects.")
203 (license license:artistic2.0)))
205 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
207 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
211 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
212 version 'annotation))
215 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
217 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
218 (build-system r-build-system)
220 `(("r-bsgenome" ,r-bsgenome)
221 ("r-bsgenome-dmelanogaster-ucsc-dm3"
222 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
223 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
224 (synopsis "Full masked genome sequences for Fly")
226 "This package provides full masked genome sequences for Drosophila
227 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
228 Biostrings objects. The sequences are the same as in
229 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
230 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
231 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
232 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
233 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
234 (license license:artistic2.0)))
236 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
238 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
242 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
243 version 'annotation))
246 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
248 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
249 (build-system r-build-system)
251 `(("r-bsgenome" ,r-bsgenome)))
253 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
254 (synopsis "Full genome sequences for Homo sapiens")
256 "This package provides full genome sequences for Homo sapiens from
257 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
258 (license license:artistic2.0)))
260 (define-public r-bsgenome-hsapiens-ncbi-grch38
262 (name "r-bsgenome-hsapiens-ncbi-grch38")
267 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
268 version 'annotation))
271 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
272 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
273 (build-system r-build-system)
274 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
276 "https://bioconductor.org/packages/release/data/annotation/html/\
277 BSgenome.Hsapiens.NCBI.GRCh38.html")
278 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
280 "This package provides full genome sequences for Homo sapiens (Human) as
281 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
282 (license license:artistic2.0)))
284 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
286 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
290 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
291 version 'annotation))
294 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
296 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
297 (build-system r-build-system)
299 `(("r-bsgenome" ,r-bsgenome)
300 ("r-bsgenome-hsapiens-ucsc-hg19"
301 ,r-bsgenome-hsapiens-ucsc-hg19)))
302 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
303 (synopsis "Full masked genome sequences for Homo sapiens")
305 "This package provides full genome sequences for Homo sapiens (Human) as
306 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
307 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
308 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
309 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
310 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
311 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
313 (license license:artistic2.0)))
315 (define-public r-bsgenome-mmusculus-ucsc-mm9
317 (name "r-bsgenome-mmusculus-ucsc-mm9")
321 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
322 version 'annotation))
325 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
327 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
328 (build-system r-build-system)
330 `(("r-bsgenome" ,r-bsgenome)))
332 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
333 (synopsis "Full genome sequences for Mouse")
335 "This package provides full genome sequences for Mus musculus (Mouse) as
336 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
337 (license license:artistic2.0)))
339 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
341 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
345 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
346 version 'annotation))
349 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
351 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
352 (build-system r-build-system)
354 `(("r-bsgenome" ,r-bsgenome)
355 ("r-bsgenome-mmusculus-ucsc-mm9"
356 ,r-bsgenome-mmusculus-ucsc-mm9)))
357 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
358 (synopsis "Full masked genome sequences for Mouse")
360 "This package provides full genome sequences for Mus musculus (Mouse) as
361 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
362 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
363 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
364 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
365 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
366 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
368 (license license:artistic2.0)))
370 (define-public r-bsgenome-mmusculus-ucsc-mm10
372 (name "r-bsgenome-mmusculus-ucsc-mm10")
376 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
377 version 'annotation))
380 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
382 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
383 (build-system r-build-system)
385 `(("r-bsgenome" ,r-bsgenome)))
387 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
388 (synopsis "Full genome sequences for Mouse")
390 "This package provides full genome sequences for Mus
391 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
392 in Biostrings objects.")
393 (license license:artistic2.0)))
395 (define-public r-genomeinfodbdata
397 (name "r-genomeinfodbdata")
401 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
404 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
406 `((upstream-name . "GenomeInfoDbData")))
407 (build-system r-build-system)
408 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
409 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
410 (description "This package contains data for mapping between NCBI taxonomy
411 ID and species. It is used by functions in the GenomeInfoDb package.")
412 (license license:artistic2.0)))
414 (define-public r-homo-sapiens
416 (name "r-homo-sapiens")
420 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
423 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
425 `((upstream-name . "Homo.sapiens")))
426 (build-system r-build-system)
428 `(("r-genomicfeatures" ,r-genomicfeatures)
430 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
431 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
432 ("r-organismdbi" ,r-organismdbi)
433 ("r-annotationdbi" ,r-annotationdbi)))
434 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
435 (synopsis "Annotation package for the Homo.sapiens object")
437 "This package contains the Homo.sapiens object to access data from
438 several related annotation packages.")
439 (license license:artistic2.0)))
441 (define-public r-org-ce-eg-db
443 (name "r-org-ce-eg-db")
447 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
450 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
452 `((upstream-name . "org.Ce.eg.db")))
453 (build-system r-build-system)
455 `(("r-annotationdbi" ,r-annotationdbi)))
456 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
457 (synopsis "Genome wide annotation for Worm")
459 "This package provides mappings from Entrez gene identifiers to various
460 annotations for the genome of the model worm Caenorhabditis elegans.")
461 (license license:artistic2.0)))
463 (define-public r-org-dm-eg-db
465 (name "r-org-dm-eg-db")
469 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
472 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
474 `((upstream-name . "org.Dm.eg.db")))
475 (build-system r-build-system)
477 `(("r-annotationdbi" ,r-annotationdbi)))
478 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
479 (synopsis "Genome wide annotation for Fly")
481 "This package provides mappings from Entrez gene identifiers to various
482 annotations for the genome of the model fruit fly Drosophila melanogaster.")
483 (license license:artistic2.0)))
485 (define-public r-org-dr-eg-db
487 (name "r-org-dr-eg-db")
491 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
494 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
496 `((upstream-name . "org.Dr.eg.db")))
497 (build-system r-build-system)
499 `(("r-annotationdbi" ,r-annotationdbi)))
500 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
501 (synopsis "Annotation for Zebrafish")
503 "This package provides genome wide annotations for Zebrafish, primarily
504 based on mapping using Entrez Gene identifiers.")
505 (license license:artistic2.0)))
507 (define-public r-org-hs-eg-db
509 (name "r-org-hs-eg-db")
513 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
516 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
518 `((upstream-name . "org.Hs.eg.db")))
519 (build-system r-build-system)
521 `(("r-annotationdbi" ,r-annotationdbi)))
522 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
523 (synopsis "Genome wide annotation for Human")
525 "This package contains genome-wide annotations for Human, primarily based
526 on mapping using Entrez Gene identifiers.")
527 (license license:artistic2.0)))
529 (define-public r-org-mm-eg-db
531 (name "r-org-mm-eg-db")
535 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
538 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
540 `((upstream-name . "org.Mm.eg.db")))
541 (build-system r-build-system)
543 `(("r-annotationdbi" ,r-annotationdbi)))
544 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
545 (synopsis "Genome wide annotation for Mouse")
547 "This package provides mappings from Entrez gene identifiers to various
548 annotations for the genome of the model mouse Mus musculus.")
549 (license license:artistic2.0)))
551 (define-public r-bsgenome-hsapiens-ucsc-hg19
553 (name "r-bsgenome-hsapiens-ucsc-hg19")
557 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
558 version 'annotation))
561 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
563 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
564 (build-system r-build-system)
566 `(("r-bsgenome" ,r-bsgenome)))
568 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
569 (synopsis "Full genome sequences for Homo sapiens")
571 "This package provides full genome sequences for Homo sapiens as provided
572 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
573 (license license:artistic2.0)))
575 (define-public r-bsgenome-hsapiens-ucsc-hg38
577 (name "r-bsgenome-hsapiens-ucsc-hg38")
581 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
582 version 'annotation))
585 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
587 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
588 (build-system r-build-system)
590 `(("r-bsgenome" ,r-bsgenome)))
592 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
593 (synopsis "Full genome sequences for Homo sapiens")
595 "This package provides full genome sequences for Homo sapiens (Human)
596 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
597 (license license:artistic2.0)))
599 (define-public r-ensdb-hsapiens-v75
601 (name "r-ensdb-hsapiens-v75")
606 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
609 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
611 `((upstream-name . "EnsDb.Hsapiens.v75")))
612 (build-system r-build-system)
614 `(("r-ensembldb" ,r-ensembldb)))
615 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
616 (synopsis "Ensembl based annotation package")
618 "This package exposes an annotation database generated from Ensembl.")
619 (license license:artistic2.0)))
621 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
623 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
627 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
628 version 'annotation))
631 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
633 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
634 (build-system r-build-system)
636 `(("r-genomicfeatures" ,r-genomicfeatures)))
638 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
639 (synopsis "Annotation package for human genome in TxDb format")
641 "This package provides an annotation database of Homo sapiens genome
642 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
643 track. The database is exposed as a @code{TxDb} object.")
644 (license license:artistic2.0)))
646 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
648 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
652 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
653 version 'annotation))
656 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
658 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
659 (build-system r-build-system)
661 `(("r-genomicfeatures" ,r-genomicfeatures)))
663 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
664 (synopsis "Annotation package for human genome in TxDb format")
666 "This package provides an annotation database of Homo sapiens genome
667 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
668 track. The database is exposed as a @code{TxDb} object.")
669 (license license:artistic2.0)))
671 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
673 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
677 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
678 version 'annotation))
681 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
683 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
684 (build-system r-build-system)
686 `(("r-genomicfeatures" ,r-genomicfeatures)
687 ("r-annotationdbi" ,r-annotationdbi)))
689 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
690 (synopsis "Annotation package for mouse genome in TxDb format")
692 "This package provides an annotation database of Mouse genome data. It
693 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
694 database is exposed as a @code{TxDb} object.")
695 (license license:artistic2.0)))
697 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
699 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
703 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
704 version 'annotation))
707 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
709 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
710 (build-system r-build-system)
712 `(("r-bsgenome" ,r-bsgenome)
713 ("r-genomicfeatures" ,r-genomicfeatures)
714 ("r-annotationdbi" ,r-annotationdbi)))
716 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
717 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
719 "This package loads a TxDb object, which is an R interface to
720 prefabricated databases contained in this package. This package provides
721 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
722 based on the knownGene track.")
723 (license license:artistic2.0)))
725 (define-public r-txdb-celegans-ucsc-ce6-ensgene
727 (name "r-txdb-celegans-ucsc-ce6-ensgene")
732 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
733 version 'annotation))
736 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
738 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
739 (build-system r-build-system)
741 `(("r-annotationdbi" ,r-annotationdbi)
742 ("r-genomicfeatures" ,r-genomicfeatures)))
743 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
744 (synopsis "Annotation package for C elegans TxDb objects")
746 "This package exposes a C elegans annotation database generated from UCSC
747 by exposing these as TxDb objects.")
748 (license license:artistic2.0)))
750 (define-public r-fdb-infiniummethylation-hg19
752 (name "r-fdb-infiniummethylation-hg19")
756 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
757 version 'annotation))
760 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
762 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
763 (build-system r-build-system)
765 `(("r-biostrings" ,r-biostrings)
766 ("r-genomicfeatures" ,r-genomicfeatures)
767 ("r-annotationdbi" ,r-annotationdbi)
768 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
769 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
770 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
771 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
773 "This is an annotation package for Illumina Infinium DNA methylation
774 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
776 (license license:artistic2.0)))
778 (define-public r-illuminahumanmethylationepicmanifest
780 (name "r-illuminahumanmethylationepicmanifest")
784 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
785 version 'annotation))
788 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
790 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
791 (build-system r-build-system)
793 `(("r-minfi" ,r-minfi)))
794 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
795 (synopsis "Manifest for Illumina's EPIC methylation arrays")
797 "This is a manifest package for Illumina's EPIC methylation arrays.")
798 (license license:artistic2.0)))
800 (define-public r-do-db
806 (uri (bioconductor-uri "DO.db" version 'annotation))
809 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
811 `((upstream-name . "DO.db")))
812 (build-system r-build-system)
814 `(("r-annotationdbi" ,r-annotationdbi)))
815 (home-page "https://www.bioconductor.org/packages/DO.db/")
816 (synopsis "Annotation maps describing the entire Disease Ontology")
818 "This package provides a set of annotation maps describing the entire
820 (license license:artistic2.0)))
822 (define-public r-pfam-db
829 (uri (bioconductor-uri "PFAM.db" version 'annotation))
832 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
833 (properties `((upstream-name . "PFAM.db")))
834 (build-system r-build-system)
836 `(("r-annotationdbi" ,r-annotationdbi)))
837 (home-page "https://bioconductor.org/packages/PFAM.db")
838 (synopsis "Set of protein ID mappings for PFAM")
840 "This package provides a set of protein ID mappings for PFAM, assembled
841 using data from public repositories.")
842 (license license:artistic2.0)))
844 (define-public r-phastcons100way-ucsc-hg19
846 (name "r-phastcons100way-ucsc-hg19")
851 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
852 version 'annotation))
855 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
857 `((upstream-name . "phastCons100way.UCSC.hg19")))
858 (build-system r-build-system)
860 `(("r-bsgenome" ,r-bsgenome)
861 ("r-genomeinfodb" ,r-genomeinfodb)
862 ("r-genomicranges" ,r-genomicranges)
863 ("r-genomicscores" ,r-genomicscores)
864 ("r-iranges" ,r-iranges)
865 ("r-s4vectors" ,r-s4vectors)))
866 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
867 (synopsis "UCSC phastCons conservation scores for hg19")
869 "This package provides UCSC phastCons conservation scores for the human
870 genome (hg19) calculated from multiple alignments with other 99 vertebrate
872 (license license:artistic2.0)))
877 (define-public r-abadata
883 (uri (bioconductor-uri "ABAData" version 'experiment))
886 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
888 `((upstream-name . "ABAData")))
889 (build-system r-build-system)
891 `(("r-annotationdbi" ,r-annotationdbi)))
892 (home-page "https://www.bioconductor.org/packages/ABAData/")
893 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
895 "This package provides the data for the gene expression enrichment
896 analysis conducted in the package ABAEnrichment. The package includes three
897 datasets which are derived from the Allen Brain Atlas:
900 @item Gene expression data from Human Brain (adults) averaged across donors,
901 @item Gene expression data from the Developing Human Brain pooled into five
902 age categories and averaged across donors, and
903 @item a developmental effect score based on the Developing Human Brain
907 All datasets are restricted to protein coding genes.")
908 (license license:gpl2+)))
910 (define-public r-arrmdata
916 (uri (bioconductor-uri "ARRmData" version 'experiment))
919 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
921 `((upstream-name . "ARRmData")))
922 (build-system r-build-system)
923 (home-page "https://www.bioconductor.org/packages/ARRmData/")
924 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
926 "This package provides raw beta values from 36 samples across 3 groups
927 from Illumina 450k methylation arrays.")
928 (license license:artistic2.0)))
930 (define-public r-genelendatabase
932 (name "r-genelendatabase")
937 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
940 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
942 `((upstream-name . "geneLenDataBase")))
943 (build-system r-build-system)
945 `(("r-rtracklayer" ,r-rtracklayer)
946 ("r-genomicfeatures" ,r-genomicfeatures)))
947 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
948 (synopsis "Lengths of mRNA transcripts for a number of genomes")
950 "This package provides the lengths of mRNA transcripts for a number of
951 genomes and gene ID formats, largely based on the UCSC table browser.")
952 (license license:lgpl2.0+)))
954 (define-public r-pasilla
961 "http://bioconductor.org/packages/release/data/experiment"
962 "/src/contrib/pasilla_" version ".tar.gz"))
965 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
966 (build-system r-build-system)
968 `(("r-biocstyle" ,r-biocstyle)
969 ("r-dexseq" ,r-dexseq)
971 ("r-rmarkdown" ,r-rmarkdown)))
972 (home-page "https://www.bioconductor.org/packages/pasilla/")
973 (synopsis "Data package with per-exon and per-gene read counts")
974 (description "This package provides per-exon and per-gene read counts
975 computed for selected genes from RNA-seq data that were presented in the
976 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
977 by Brooks et al., Genome Research 2011.")
978 (license license:lgpl2.1+)))
980 (define-public r-hsmmsinglecell
982 (name "r-hsmmsinglecell")
986 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
989 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
991 `((upstream-name . "HSMMSingleCell")))
992 (build-system r-build-system)
993 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
994 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
996 "Skeletal myoblasts undergo a well-characterized sequence of
997 morphological and transcriptional changes during differentiation. In this
998 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
999 under high mitogen conditions (GM) and then differentiated by switching to
1000 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1001 hundred cells taken over a time-course of serum-induced differentiation.
1002 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1003 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1004 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1005 which were then sequenced to a depth of ~4 million reads per library,
1006 resulting in a complete gene expression profile for each cell.")
1007 (license license:artistic2.0)))
1009 (define-public r-all
1015 (uri (bioconductor-uri "ALL" version 'experiment))
1018 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1019 (properties `((upstream-name . "ALL")))
1020 (build-system r-build-system)
1022 `(("r-biobase" ,r-biobase)))
1023 (home-page "https://bioconductor.org/packages/ALL")
1024 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1026 "The data consist of microarrays from 128 different individuals with
1027 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1028 are available. The data have been normalized (using rma) and it is the
1029 jointly normalized data that are available here. The data are presented in
1030 the form of an @code{exprSet} object.")
1031 (license license:artistic2.0)))
1033 (define-public r-affydata
1040 (uri (bioconductor-uri "affydata" version 'experiment))
1043 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1044 (properties `((upstream-name . "affydata")))
1045 (build-system r-build-system)
1047 `(("r-affy" ,r-affy)))
1048 (home-page "https://bioconductor.org/packages/affydata/")
1049 (synopsis "Affymetrix data for demonstration purposes")
1051 "This package provides example datasets that represent 'real world
1052 examples' of Affymetrix data, unlike the artificial examples included in the
1053 package @code{affy}.")
1054 (license license:gpl2+)))
1056 (define-public r-gagedata
1063 (uri (bioconductor-uri "gageData" version 'experiment))
1065 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
1066 (properties `((upstream-name . "gageData")))
1067 (build-system r-build-system)
1068 (home-page "https://bioconductor.org/packages/gageData")
1069 (synopsis "Auxillary data for gage package")
1071 "This is a supportive data package for the software package @code{gage}.
1072 However, the data supplied here are also useful for gene set or pathway
1073 analysis or microarray data analysis in general. In this package, we provide
1074 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1075 BMP6 (originally published as an demo dataset for GAGE, also registered as
1076 GSE13604 in GEO). This package also includes commonly used gene set data based
1077 on KEGG pathways and GO terms for major research species, including human,
1078 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1079 yeast are also included.")
1080 (license license:gpl2+)))
1082 (define-public r-curatedtcgadata
1084 (name "r-curatedtcgadata")
1089 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1092 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1094 `((upstream-name . "curatedTCGAData")))
1095 (build-system r-build-system)
1097 `(("r-annotationhub" ,r-annotationhub)
1098 ("r-experimenthub" ,r-experimenthub)
1099 ("r-hdf5array" ,r-hdf5array)
1100 ("r-multiassayexperiment" ,r-multiassayexperiment)
1101 ("r-s4vectors" ,r-s4vectors)
1102 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1103 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1104 (synopsis "Curated data from The Cancer Genome Atlas")
1106 "This package provides publicly available data from The Cancer Genome
1107 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1108 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1109 number, mutation, microRNA, protein, and others) with clinical / pathological
1110 data. It also links assay barcodes with patient identifiers, enabling
1111 harmonized subsetting of rows (features) and columns (patients / samples)
1112 across the entire multi-'omics experiment.")
1113 (license license:artistic2.0)))
1118 (define-public r-biocversion
1120 (name "r-biocversion")
1125 (uri (bioconductor-uri "BiocVersion" version))
1128 "1cj9swyf4zbkdq45bhw0kymh2aghkwimxjlfj5r2j7kdiyh6n3rk"))))
1129 (properties `((upstream-name . "BiocVersion")))
1130 (build-system r-build-system)
1131 (home-page "https://bioconductor.org/packages/BiocVersion/")
1132 (synopsis "Set the appropriate version of Bioconductor packages")
1134 "This package provides repository information for the appropriate version
1136 (license license:artistic2.0)))
1138 (define-public r-biocgenerics
1140 (name "r-biocgenerics")
1144 (uri (bioconductor-uri "BiocGenerics" version))
1147 "1y9pgangz2f0n9v3zj8brz8bv7a1yjsncdnd5h1l7zv0c0j9fh9q"))))
1149 `((upstream-name . "BiocGenerics")))
1150 (build-system r-build-system)
1151 (home-page "https://bioconductor.org/packages/BiocGenerics")
1152 (synopsis "S4 generic functions for Bioconductor")
1154 "This package provides S4 generic functions needed by many Bioconductor
1156 (license license:artistic2.0)))
1158 (define-public r-coverageview
1160 (name "r-coverageview")
1164 (uri (bioconductor-uri "CoverageView" version))
1167 "1k89gzqhd8ca8s9gk5bfzringnc5nayqbwzwwy35fls1cg96qmsj"))))
1168 (build-system r-build-system)
1170 `(("r-s4vectors" ,r-s4vectors)
1171 ("r-iranges" ,r-iranges)
1172 ("r-genomicranges" ,r-genomicranges)
1173 ("r-genomicalignments" ,r-genomicalignments)
1174 ("r-rtracklayer" ,r-rtracklayer)
1175 ("r-rsamtools" ,r-rsamtools)))
1176 (home-page "https://bioconductor.org/packages/CoverageView/")
1177 (synopsis "Coverage visualization package for R")
1178 (description "This package provides a framework for the visualization of
1179 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1180 be also used for genome-wide nucleosome positioning experiments or other
1181 experiment types where it is important to have a framework in order to inspect
1182 how the coverage distributed across the genome.")
1183 (license license:artistic2.0)))
1185 (define-public r-cummerbund
1187 (name "r-cummerbund")
1191 (uri (bioconductor-uri "cummeRbund" version))
1194 "1x7rby50api1c66al6a0i92q82ydjmh3h8l2k7hj0ffpn8c5pdgj"))))
1195 (build-system r-build-system)
1197 `(("r-biobase" ,r-biobase)
1198 ("r-biocgenerics" ,r-biocgenerics)
1199 ("r-fastcluster" ,r-fastcluster)
1200 ("r-ggplot2" ,r-ggplot2)
1203 ("r-reshape2" ,r-reshape2)
1204 ("r-rsqlite" ,r-rsqlite)
1205 ("r-rtracklayer" ,r-rtracklayer)
1206 ("r-s4vectors" ,r-s4vectors)))
1207 (home-page "https://bioconductor.org/packages/cummeRbund/")
1208 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1209 (description "This package allows for persistent storage, access,
1210 exploration, and manipulation of Cufflinks high-throughput sequencing
1211 data. In addition, provides numerous plotting functions for commonly
1212 used visualizations.")
1213 (license license:artistic2.0)))
1215 (define-public r-bluster
1221 (uri (bioconductor-uri "bluster" version))
1224 "0izrf82m5znyrgai5y5jss4k2brabh4ajxdvnlwwc92l5bw7jp61"))))
1225 (properties `((upstream-name . "bluster")))
1226 (build-system r-build-system)
1228 `(("r-biocneighbors" ,r-biocneighbors)
1229 ("r-biocparallel" ,r-biocparallel)
1230 ("r-igraph" ,r-igraph)
1231 ("r-matrix" ,r-matrix)
1233 ("r-s4vectors" ,r-s4vectors)))
1235 `(("r-knitr" ,r-knitr)))
1236 (home-page "https://bioconductor.org/packages/bluster")
1237 (synopsis "Clustering algorithms for Bioconductor")
1238 (description"This package wraps common clustering algorithms in an easily
1239 extended S4 framework. Backends are implemented for hierarchical, k-means
1240 and graph-based clustering. Several utilities are also provided to compare
1241 and evaluate clustering results.")
1242 (license license:gpl3)))
1244 (define-public r-ideoviz
1250 (uri (bioconductor-uri "IdeoViz" version))
1253 "1k5c0skr6pvpcvkak9f0a088w5wsx4fl3jb9a76gyyni4nkj7djq"))))
1254 (build-system r-build-system)
1256 `(("r-biobase" ,r-biobase)
1257 ("r-iranges" ,r-iranges)
1258 ("r-genomicranges" ,r-genomicranges)
1259 ("r-rcolorbrewer" ,r-rcolorbrewer)
1260 ("r-rtracklayer" ,r-rtracklayer)
1261 ("r-genomeinfodb" ,r-genomeinfodb)))
1262 (home-page "https://bioconductor.org/packages/IdeoViz/")
1263 (synopsis "Plots data along a chromosomal ideogram")
1264 (description "This package provides functions to plot data associated with
1265 arbitrary genomic intervals along chromosomal ideogram.")
1266 (license license:gpl2)))
1268 (define-public r-iranges
1274 (uri (bioconductor-uri "IRanges" version))
1277 "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52"))))
1279 `((upstream-name . "IRanges")))
1280 (build-system r-build-system)
1282 `(("r-biocgenerics" ,r-biocgenerics)
1283 ("r-s4vectors" ,r-s4vectors)))
1284 (home-page "https://bioconductor.org/packages/IRanges")
1285 (synopsis "Infrastructure for manipulating intervals on sequences")
1287 "This package provides efficient low-level and highly reusable S4 classes
1288 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
1289 generally, data that can be organized sequentially (formally defined as
1290 @code{Vector} objects), as well as views on these @code{Vector} objects.
1291 Efficient list-like classes are also provided for storing big collections of
1292 instances of the basic classes. All classes in the package use consistent
1293 naming and share the same rich and consistent \"Vector API\" as much as
1295 (license license:artistic2.0)))
1297 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
1298 ;; from Bioconductor.
1299 (define-public r-deconstructsigs
1301 (name "r-deconstructsigs")
1305 (uri (cran-uri "deconstructSigs" version))
1308 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
1310 `((upstream-name . "deconstructSigs")))
1311 (build-system r-build-system)
1313 `(("r-bsgenome" ,r-bsgenome)
1314 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1315 ("r-genomeinfodb" ,r-genomeinfodb)
1316 ("r-reshape2" ,r-reshape2)))
1317 (home-page "https://github.com/raerose01/deconstructSigs")
1318 (synopsis "Identifies signatures present in a tumor sample")
1319 (description "This package takes sample information in the form of the
1320 fraction of mutations in each of 96 trinucleotide contexts and identifies
1321 the weighted combination of published signatures that, when summed, most
1322 closely reconstructs the mutational profile.")
1323 (license license:gpl2+)))
1325 ;; This is a CRAN package, but it depends on Bioconductor packages.
1326 (define-public r-nmf
1333 (uri (cran-uri "NMF" version))
1336 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
1337 (properties `((upstream-name . "NMF")))
1338 (build-system r-build-system)
1340 `(("r-cluster" ,r-cluster)
1341 ("r-biobase" ,r-biobase)
1342 ("r-biocmanager" ,r-biocmanager)
1343 ("r-bigmemory" ,r-bigmemory) ; suggested
1344 ("r-synchronicity" ,r-synchronicity) ; suggested
1345 ("r-colorspace" ,r-colorspace)
1346 ("r-digest" ,r-digest)
1347 ("r-doparallel" ,r-doparallel)
1348 ("r-foreach" ,r-foreach)
1349 ("r-ggplot2" ,r-ggplot2)
1350 ("r-gridbase" ,r-gridbase)
1351 ("r-pkgmaker" ,r-pkgmaker)
1352 ("r-rcolorbrewer" ,r-rcolorbrewer)
1353 ("r-registry" ,r-registry)
1354 ("r-reshape2" ,r-reshape2)
1355 ("r-rngtools" ,r-rngtools)
1356 ("r-stringr" ,r-stringr)))
1358 `(("r-knitr" ,r-knitr)))
1359 (home-page "http://renozao.github.io/NMF")
1360 (synopsis "Algorithms and framework for nonnegative matrix factorization")
1362 "This package provides a framework to perform Non-negative Matrix
1363 Factorization (NMF). The package implements a set of already published
1364 algorithms and seeding methods, and provides a framework to test, develop and
1365 plug new or custom algorithms. Most of the built-in algorithms have been
1366 optimized in C++, and the main interface function provides an easy way of
1367 performing parallel computations on multicore machines.")
1368 (license license:gpl2+)))
1370 (define-public r-affycomp
1377 (uri (bioconductor-uri "affycomp" version))
1380 "106gz4rami04r0ffc7rxkrv92s3yrcnlqnyykd5s8lrkndbihrpk"))))
1381 (properties `((upstream-name . "affycomp")))
1382 (build-system r-build-system)
1383 (propagated-inputs `(("r-biobase" ,r-biobase)))
1384 (home-page "https://bioconductor.org/packages/affycomp/")
1385 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1387 "The package contains functions that can be used to compare expression
1388 measures for Affymetrix Oligonucleotide Arrays.")
1389 (license license:gpl2+)))
1391 (define-public r-affycompatible
1393 (name "r-affycompatible")
1398 (uri (bioconductor-uri "AffyCompatible" version))
1401 "0pcs51miy45bky26i1d4iarbjh569gssb5g4fr26bzgjmq19yl7x"))))
1403 `((upstream-name . "AffyCompatible")))
1404 (build-system r-build-system)
1406 `(("r-biostrings" ,r-biostrings)
1407 ("r-rcurl" ,r-rcurl)
1409 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1410 (synopsis "Work with Affymetrix GeneChip files")
1412 "This package provides an interface to Affymetrix chip annotation and
1413 sample attribute files. The package allows an easy way for users to download
1414 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1415 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1416 Command Console} (AGCC)-compatible sample annotation files.")
1417 (license license:artistic2.0)))
1419 (define-public r-affycontam
1421 (name "r-affycontam")
1426 (uri (bioconductor-uri "affyContam" version))
1429 "0pi5fll5868sb80vb9kbymz6gkjv58f0abk6zwn407cnyjhr342b"))))
1430 (properties `((upstream-name . "affyContam")))
1431 (build-system r-build-system)
1433 `(("r-affy" ,r-affy)
1434 ("r-affydata" ,r-affydata)
1435 ("r-biobase" ,r-biobase)))
1436 (home-page "https://bioconductor.org/packages/affyContam/")
1437 (synopsis "Structured corruption of Affymetrix CEL file data")
1439 "Microarray quality assessment is a major concern of microarray analysts.
1440 This package provides some simple approaches to in silico creation of quality
1441 problems in CEL-level data to help evaluate performance of quality metrics.")
1442 (license license:artistic2.0)))
1444 (define-public r-affycoretools
1446 (name "r-affycoretools")
1451 (uri (bioconductor-uri "affycoretools" version))
1454 "0jacgwylg7wjw3xk3ga2sb1wkdklm5glamhbmqgvzm5kdjnl0rv0"))))
1455 (properties `((upstream-name . "affycoretools")))
1456 (build-system r-build-system)
1458 `(("r-affy" ,r-affy)
1459 ("r-annotationdbi" ,r-annotationdbi)
1460 ("r-biobase" ,r-biobase)
1461 ("r-biocgenerics" ,r-biocgenerics)
1463 ("r-edger" ,r-edger)
1464 ("r-gcrma" ,r-gcrma)
1465 ("r-glimma" ,r-glimma)
1466 ("r-ggplot2" ,r-ggplot2)
1467 ("r-gostats" ,r-gostats)
1468 ("r-gplots" ,r-gplots)
1469 ("r-hwriter" ,r-hwriter)
1470 ("r-lattice" ,r-lattice)
1471 ("r-limma" ,r-limma)
1472 ("r-oligoclasses" ,r-oligoclasses)
1473 ("r-reportingtools" ,r-reportingtools)
1474 ("r-rsqlite" ,r-rsqlite)
1475 ("r-s4vectors" ,r-s4vectors)
1476 ("r-xtable" ,r-xtable)))
1478 `(("r-knitr" ,r-knitr)))
1479 (home-page "https://bioconductor.org/packages/affycoretools/")
1480 (synopsis "Functions for analyses with Affymetrix GeneChips")
1482 "This package provides various wrapper functions that have been written
1483 to streamline the more common analyses that a Biostatistician might see.")
1484 (license license:artistic2.0)))
1486 (define-public r-affxparser
1488 (name "r-affxparser")
1493 (uri (bioconductor-uri "affxparser" version))
1496 "13h4iwskvgwgxid9f60gzb1zndgbhdlbn9ixv5waihy1jkcbn24p"))))
1497 (properties `((upstream-name . "affxparser")))
1498 (build-system r-build-system)
1499 (home-page "https://github.com/HenrikBengtsson/affxparser")
1500 (synopsis "Affymetrix File Parsing SDK")
1502 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1503 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1504 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1505 are supported. Currently, there are methods for reading @dfn{chip definition
1506 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1507 either in full or in part. For example, probe signals from a few probesets
1508 can be extracted very quickly from a set of CEL files into a convenient list
1510 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1512 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1514 (define-public r-annotate
1521 (uri (bioconductor-uri "annotate" version))
1524 "1rql591x56532m8n4axdkfkhkbcsz5hfrf7271s0lmkvy84i7z6l"))))
1525 (build-system r-build-system)
1527 `(("r-annotationdbi" ,r-annotationdbi)
1528 ("r-biobase" ,r-biobase)
1529 ("r-biocgenerics" ,r-biocgenerics)
1533 ("r-xtable" ,r-xtable)))
1535 "https://bioconductor.org/packages/annotate")
1536 (synopsis "Annotation for microarrays")
1537 (description "This package provides R environments for the annotation of
1539 (license license:artistic2.0)))
1541 (define-public r-annotationforge
1543 (name "r-annotationforge")
1548 (uri (bioconductor-uri "AnnotationForge" version))
1551 "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7"))))
1553 `((upstream-name . "AnnotationForge")))
1554 (build-system r-build-system)
1556 `(("r-annotationdbi" ,r-annotationdbi)
1557 ("r-biobase" ,r-biobase)
1558 ("r-biocgenerics" ,r-biocgenerics)
1560 ("r-rcurl" ,r-rcurl)
1561 ("r-rsqlite" ,r-rsqlite)
1562 ("r-s4vectors" ,r-s4vectors)
1565 `(("r-knitr" ,r-knitr)))
1566 (home-page "https://bioconductor.org/packages/AnnotationForge")
1567 (synopsis "Code for building annotation database packages")
1569 "This package provides code for generating Annotation packages and their
1570 databases. Packages produced are intended to be used with AnnotationDbi.")
1571 (license license:artistic2.0)))
1573 (define-public r-category
1580 (uri (bioconductor-uri "Category" version))
1583 "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr"))))
1584 (properties `((upstream-name . "Category")))
1585 (build-system r-build-system)
1587 `(("r-annotate" ,r-annotate)
1588 ("r-annotationdbi" ,r-annotationdbi)
1589 ("r-biobase" ,r-biobase)
1590 ("r-biocgenerics" ,r-biocgenerics)
1591 ("r-genefilter" ,r-genefilter)
1592 ("r-graph" ,r-graph)
1593 ("r-gseabase" ,r-gseabase)
1594 ("r-matrix" ,r-matrix)
1597 (home-page "https://bioconductor.org/packages/Category")
1598 (synopsis "Category analysis")
1600 "This package provides a collection of tools for performing category
1602 (license license:artistic2.0)))
1604 (define-public r-deseq2
1611 (uri (bioconductor-uri "DESeq2" version))
1614 "1i0jpzsm1vl7q6qdmplj45w13lsaycxrx5pazlanjba2khn79k19"))))
1615 (properties `((upstream-name . "DESeq2")))
1616 (build-system r-build-system)
1618 `(("r-biobase" ,r-biobase)
1619 ("r-biocgenerics" ,r-biocgenerics)
1620 ("r-biocparallel" ,r-biocparallel)
1621 ("r-genefilter" ,r-genefilter)
1622 ("r-geneplotter" ,r-geneplotter)
1623 ("r-genomicranges" ,r-genomicranges)
1624 ("r-ggplot2" ,r-ggplot2)
1625 ("r-iranges" ,r-iranges)
1626 ("r-locfit" ,r-locfit)
1628 ("r-rcpparmadillo" ,r-rcpparmadillo)
1629 ("r-s4vectors" ,r-s4vectors)
1630 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1632 `(("r-knitr" ,r-knitr)))
1633 (home-page "https://bioconductor.org/packages/DESeq2")
1634 (synopsis "Differential gene expression analysis")
1636 "This package provides functions to estimate variance-mean dependence in
1637 count data from high-throughput nucleotide sequencing assays and test for
1638 differential expression based on a model using the negative binomial
1640 (license license:lgpl3+)))
1642 (define-public r-dexseq
1649 (uri (bioconductor-uri "DEXSeq" version))
1652 "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi"))))
1653 (properties `((upstream-name . "DEXSeq")))
1654 (build-system r-build-system)
1656 `(("r-annotationdbi" ,r-annotationdbi)
1657 ("r-biobase" ,r-biobase)
1658 ("r-biocgenerics" ,r-biocgenerics)
1659 ("r-biocparallel" ,r-biocparallel)
1660 ("r-biomart" ,r-biomart)
1661 ("r-deseq2" ,r-deseq2)
1662 ("r-genefilter" ,r-genefilter)
1663 ("r-geneplotter" ,r-geneplotter)
1664 ("r-genomicranges" ,r-genomicranges)
1665 ("r-hwriter" ,r-hwriter)
1666 ("r-iranges" ,r-iranges)
1667 ("r-rcolorbrewer" ,r-rcolorbrewer)
1668 ("r-rsamtools" ,r-rsamtools)
1669 ("r-s4vectors" ,r-s4vectors)
1670 ("r-statmod" ,r-statmod)
1671 ("r-stringr" ,r-stringr)
1672 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1674 `(("r-knitr" ,r-knitr)))
1675 (home-page "https://bioconductor.org/packages/DEXSeq")
1676 (synopsis "Inference of differential exon usage in RNA-Seq")
1678 "This package is focused on finding differential exon usage using RNA-seq
1679 exon counts between samples with different experimental designs. It provides
1680 functions that allows the user to make the necessary statistical tests based
1681 on a model that uses the negative binomial distribution to estimate the
1682 variance between biological replicates and generalized linear models for
1683 testing. The package also provides functions for the visualization and
1684 exploration of the results.")
1685 (license license:gpl3+)))
1687 (define-public r-edger
1693 (uri (bioconductor-uri "edgeR" version))
1696 "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp"))))
1697 (properties `((upstream-name . "edgeR")))
1698 (build-system r-build-system)
1700 `(("r-limma" ,r-limma)
1701 ("r-locfit" ,r-locfit)
1703 ("r-statmod" ,r-statmod))) ;for estimateDisp
1704 (home-page "http://bioinf.wehi.edu.au/edgeR")
1705 (synopsis "EdgeR does empirical analysis of digital gene expression data")
1706 (description "This package can do differential expression analysis of
1707 RNA-seq expression profiles with biological replication. It implements a range
1708 of statistical methodology based on the negative binomial distributions,
1709 including empirical Bayes estimation, exact tests, generalized linear models
1710 and quasi-likelihood tests. It be applied to differential signal analysis of
1711 other types of genomic data that produce counts, including ChIP-seq, SAGE and
1713 (license license:gpl2+)))
1715 (define-public r-genefilter
1717 (name "r-genefilter")
1722 (uri (bioconductor-uri "genefilter" version))
1725 "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn"))))
1726 (build-system r-build-system)
1728 `(("gfortran" ,gfortran)
1729 ("r-knitr" ,r-knitr)))
1731 `(("r-annotate" ,r-annotate)
1732 ("r-annotationdbi" ,r-annotationdbi)
1733 ("r-biobase" ,r-biobase)
1734 ("r-biocgenerics" ,r-biocgenerics)
1735 ("r-survival" ,r-survival)))
1736 (home-page "https://bioconductor.org/packages/genefilter")
1737 (synopsis "Filter genes from high-throughput experiments")
1739 "This package provides basic functions for filtering genes from
1740 high-throughput sequencing experiments.")
1741 (license license:artistic2.0)))
1743 (define-public r-genomeinfodb
1745 (name "r-genomeinfodb")
1749 (uri (bioconductor-uri "GenomeInfoDb" version))
1752 "1sbhdpgabqbi749ixih8nlmq5id7sg8y6kkfj46r00642rc293ys"))))
1754 `((upstream-name . "GenomeInfoDb")))
1755 (build-system r-build-system)
1757 `(("r-biocgenerics" ,r-biocgenerics)
1758 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
1759 ("r-iranges" ,r-iranges)
1760 ("r-rcurl" ,r-rcurl)
1761 ("r-s4vectors" ,r-s4vectors)))
1763 `(("r-knitr" ,r-knitr)))
1764 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
1765 (synopsis "Utilities for manipulating chromosome identifiers")
1767 "This package contains data and functions that define and allow
1768 translation between different chromosome sequence naming conventions (e.g.,
1769 \"chr1\" versus \"1\"), including a function that attempts to place sequence
1770 names in their natural, rather than lexicographic, order.")
1771 (license license:artistic2.0)))
1773 (define-public r-gostats
1780 (uri (bioconductor-uri "GOstats" version))
1783 "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j"))))
1784 (properties `((upstream-name . "GOstats")))
1785 (build-system r-build-system)
1787 `(("r-annotate" ,r-annotate)
1788 ("r-annotationdbi" ,r-annotationdbi)
1789 ("r-annotationforge" ,r-annotationforge)
1790 ("r-biobase" ,r-biobase)
1791 ("r-category" ,r-category)
1792 ("r-go-db" ,r-go-db)
1793 ("r-graph" ,r-graph)
1794 ("r-rgraphviz" ,r-rgraphviz)
1795 ("r-rbgl" ,r-rbgl)))
1796 (home-page "https://bioconductor.org/packages/GOstats")
1797 (synopsis "Tools for manipulating GO and microarrays")
1799 "This package provides a set of tools for interacting with GO and
1800 microarray data. A variety of basic manipulation tools for graphs, hypothesis
1801 testing and other simple calculations.")
1802 (license license:artistic2.0)))
1804 (define-public r-gseabase
1811 (uri (bioconductor-uri "GSEABase" version))
1814 "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i"))))
1815 (properties `((upstream-name . "GSEABase")))
1816 (build-system r-build-system)
1818 `(("r-annotate" ,r-annotate)
1819 ("r-annotationdbi" ,r-annotationdbi)
1820 ("r-biobase" ,r-biobase)
1821 ("r-biocgenerics" ,r-biocgenerics)
1822 ("r-graph" ,r-graph)
1825 `(("r-knitr" ,r-knitr)))
1826 (home-page "https://bioconductor.org/packages/GSEABase")
1827 (synopsis "Gene set enrichment data structures and methods")
1829 "This package provides classes and methods to support @dfn{Gene Set
1830 Enrichment Analysis} (GSEA).")
1831 (license license:artistic2.0)))
1833 (define-public r-hpar
1840 (uri (bioconductor-uri "hpar" version))
1843 "0h10b0fyblpsnxj60rpbk99z7snrkkb5jssmf0v27s6d445jq2zr"))))
1844 (build-system r-build-system)
1846 `(("r-knitr" ,r-knitr)))
1847 (home-page "https://bioconductor.org/packages/hpar/")
1848 (synopsis "Human Protein Atlas in R")
1849 (description "This package provides a simple interface to and data from
1850 the Human Protein Atlas project.")
1851 (license license:artistic2.0)))
1853 (define-public r-rbgl
1860 (uri (bioconductor-uri "RBGL" version))
1863 "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz"))))
1864 (properties `((upstream-name . "RBGL")))
1865 (build-system r-build-system)
1868 ("r-graph" ,r-graph)))
1869 (home-page "https://www.bioconductor.org/packages/RBGL")
1870 (synopsis "Interface to the Boost graph library")
1872 "This package provides a fairly extensive and comprehensive interface to
1873 the graph algorithms contained in the Boost library.")
1874 (license license:artistic2.0)))
1876 (define-public r-regioner
1883 (uri (bioconductor-uri "regioneR" version))
1886 "0c2khfyrgy3y68cj6b07s91hplabbj70xwdgwrf2bsd9h6gknjdi"))))
1887 (properties `((upstream-name . "regioneR")))
1888 (build-system r-build-system)
1890 `(("r-biostrings" ,r-biostrings)
1891 ("r-bsgenome" ,r-bsgenome)
1892 ("r-genomeinfodb" ,r-genomeinfodb)
1893 ("r-genomicranges" ,r-genomicranges)
1894 ("r-iranges" ,r-iranges)
1895 ("r-memoise" ,r-memoise)
1896 ("r-rtracklayer" ,r-rtracklayer)
1897 ("r-s4vectors" ,r-s4vectors)))
1899 `(("r-knitr" ,r-knitr)))
1900 (home-page "https://bioconductor.org/packages/regioneR/")
1901 (synopsis "Association analysis of genomic regions")
1902 (description "This package offers a statistical framework based on
1903 customizable permutation tests to assess the association between genomic
1904 region sets and other genomic features.")
1905 (license license:artistic2.0)))
1907 (define-public r-reportingtools
1909 (name "r-reportingtools")
1914 (uri (bioconductor-uri "ReportingTools" version))
1917 "1vvra7l29s7lnq996nwlpzbkrbdkr3ivkgmfp4kndfykxsl9q4vb"))))
1919 `((upstream-name . "ReportingTools")))
1920 (build-system r-build-system)
1922 `(("r-annotate" ,r-annotate)
1923 ("r-annotationdbi" ,r-annotationdbi)
1924 ("r-biobase" ,r-biobase)
1925 ("r-biocgenerics" ,r-biocgenerics)
1926 ("r-category" ,r-category)
1927 ("r-deseq2" ,r-deseq2)
1928 ("r-edger" ,r-edger)
1929 ("r-ggbio" ,r-ggbio)
1930 ("r-ggplot2" ,r-ggplot2)
1931 ("r-gostats" ,r-gostats)
1932 ("r-gseabase" ,r-gseabase)
1933 ("r-hwriter" ,r-hwriter)
1934 ("r-iranges" ,r-iranges)
1935 ("r-knitr" ,r-knitr)
1936 ("r-lattice" ,r-lattice)
1937 ("r-limma" ,r-limma)
1938 ("r-pfam-db" ,r-pfam-db)
1939 ("r-r-utils" ,r-r-utils)
1942 `(("r-knitr" ,r-knitr)))
1943 (home-page "https://bioconductor.org/packages/ReportingTools/")
1944 (synopsis "Tools for making reports in various formats")
1946 "The ReportingTools package enables users to easily display reports of
1947 analysis results generated from sources such as microarray and sequencing
1948 data. The package allows users to create HTML pages that may be viewed on a
1949 web browser, or in other formats. Users can generate tables with sortable and
1950 filterable columns, make and display plots, and link table entries to other
1951 data sources such as NCBI or larger plots within the HTML page. Using the
1952 package, users can also produce a table of contents page to link various
1953 reports together for a particular project that can be viewed in a web
1955 (license license:artistic2.0)))
1957 (define-public r-shortread
1959 (name "r-shortread")
1964 (uri (bioconductor-uri "ShortRead" version))
1967 "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9"))))
1968 (properties `((upstream-name . "ShortRead")))
1969 (build-system r-build-system)
1973 `(("r-biobase" ,r-biobase)
1974 ("r-biocgenerics" ,r-biocgenerics)
1975 ("r-biocparallel" ,r-biocparallel)
1976 ("r-biostrings" ,r-biostrings)
1977 ("r-genomeinfodb" ,r-genomeinfodb)
1978 ("r-genomicalignments" ,r-genomicalignments)
1979 ("r-genomicranges" ,r-genomicranges)
1980 ("r-rhtslib" ,r-rhtslib)
1981 ("r-hwriter" ,r-hwriter)
1982 ("r-iranges" ,r-iranges)
1983 ("r-lattice" ,r-lattice)
1984 ("r-latticeextra" ,r-latticeextra)
1985 ("r-rsamtools" ,r-rsamtools)
1986 ("r-s4vectors" ,r-s4vectors)
1987 ("r-xvector" ,r-xvector)
1988 ("r-zlibbioc" ,r-zlibbioc)))
1989 (home-page "https://bioconductor.org/packages/ShortRead")
1990 (synopsis "FASTQ input and manipulation tools")
1992 "This package implements sampling, iteration, and input of FASTQ files.
1993 It includes functions for filtering and trimming reads, and for generating a
1994 quality assessment report. Data are represented as
1995 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
1996 purposes. The package also contains legacy support for early single-end,
1997 ungapped alignment formats.")
1998 (license license:artistic2.0)))
2000 (define-public r-systempiper
2002 (name "r-systempiper")
2007 (uri (bioconductor-uri "systemPipeR" version))
2010 "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki"))))
2011 (properties `((upstream-name . "systemPipeR")))
2012 (build-system r-build-system)
2014 `(("r-annotate" ,r-annotate)
2015 ("r-assertthat" ,r-assertthat)
2016 ("r-batchtools" ,r-batchtools)
2017 ("r-biostrings" ,r-biostrings)
2018 ("r-deseq2" ,r-deseq2)
2020 ("r-edger" ,r-edger)
2021 ("r-genomicfeatures" ,r-genomicfeatures)
2022 ("r-genomicranges" ,r-genomicranges)
2023 ("r-ggplot2" ,r-ggplot2)
2024 ("r-go-db" ,r-go-db)
2025 ("r-gostats" ,r-gostats)
2026 ("r-iranges" ,r-iranges)
2027 ("r-limma" ,r-limma)
2028 ("r-magrittr" ,r-magrittr)
2029 ("r-pheatmap" ,r-pheatmap)
2030 ("r-rjson" ,r-rjson)
2031 ("r-rsamtools" ,r-rsamtools)
2033 ("r-shortread" ,r-shortread)
2034 ("r-stringr" ,r-stringr)
2035 ("r-summarizedexperiment" ,r-summarizedexperiment)
2037 ("r-variantannotation" ,r-variantannotation)))
2039 `(("r-knitr" ,r-knitr)))
2040 (home-page "https://github.com/tgirke/systemPipeR")
2041 (synopsis "Next generation sequencing workflow and reporting environment")
2043 "This R package provides tools for building and running automated
2044 end-to-end analysis workflows for a wide range of @dfn{next generation
2045 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
2046 Important features include a uniform workflow interface across different NGS
2047 applications, automated report generation, and support for running both R and
2048 command-line software, such as NGS aligners or peak/variant callers, on local
2049 computers or compute clusters. Efficient handling of complex sample sets and
2050 experimental designs is facilitated by a consistently implemented sample
2051 annotation infrastructure.")
2052 (license license:artistic2.0)))
2054 (define-public r-variantannotation
2056 (name "r-variantannotation")
2060 (uri (bioconductor-uri "VariantAnnotation" version))
2063 "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw"))))
2065 `((upstream-name . "VariantAnnotation")))
2067 `(("r-annotationdbi" ,r-annotationdbi)
2068 ("r-biobase" ,r-biobase)
2069 ("r-biocgenerics" ,r-biocgenerics)
2070 ("r-biostrings" ,r-biostrings)
2071 ("r-bsgenome" ,r-bsgenome)
2073 ("r-genomeinfodb" ,r-genomeinfodb)
2074 ("r-genomicfeatures" ,r-genomicfeatures)
2075 ("r-genomicranges" ,r-genomicranges)
2076 ("r-iranges" ,r-iranges)
2077 ("r-matrixgenerics" ,r-matrixgenerics)
2078 ("r-summarizedexperiment" ,r-summarizedexperiment)
2079 ("r-rhtslib" ,r-rhtslib)
2080 ("r-rsamtools" ,r-rsamtools)
2081 ("r-rtracklayer" ,r-rtracklayer)
2082 ("r-s4vectors" ,r-s4vectors)
2083 ("r-xvector" ,r-xvector)
2084 ("r-zlibbioc" ,r-zlibbioc)))
2085 (build-system r-build-system)
2086 (home-page "https://bioconductor.org/packages/VariantAnnotation")
2087 (synopsis "Package for annotation of genetic variants")
2088 (description "This R package can annotate variants, compute amino acid
2089 coding changes and predict coding outcomes.")
2090 (license license:artistic2.0)))
2092 (define-public r-geneplotter
2094 (name "r-geneplotter")
2099 (uri (bioconductor-uri "geneplotter" version))
2102 "1f8nr60n1nig1gdy85wqdhpzxvp9r4chygxm8xpy882mdvfv6rqx"))))
2103 (build-system r-build-system)
2105 `(("r-annotate" ,r-annotate)
2106 ("r-annotationdbi" ,r-annotationdbi)
2107 ("r-biobase" ,r-biobase)
2108 ("r-biocgenerics" ,r-biocgenerics)
2109 ("r-lattice" ,r-lattice)
2110 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2111 (home-page "https://bioconductor.org/packages/geneplotter")
2112 (synopsis "Graphics functions for genomic data")
2114 "This package provides functions for plotting genomic data.")
2115 (license license:artistic2.0)))
2117 (define-public r-oligoclasses
2119 (name "r-oligoclasses")
2124 (uri (bioconductor-uri "oligoClasses" version))
2127 "19p6h0cgnma5md5mm9bn6rxfhr0a9znljgdbvsqybms6asvh18gy"))))
2128 (properties `((upstream-name . "oligoClasses")))
2129 (build-system r-build-system)
2131 `(("r-affyio" ,r-affyio)
2132 ("r-biobase" ,r-biobase)
2133 ("r-biocgenerics" ,r-biocgenerics)
2134 ("r-biocmanager" ,r-biocmanager)
2135 ("r-biostrings" ,r-biostrings)
2138 ("r-foreach" ,r-foreach)
2139 ("r-genomicranges" ,r-genomicranges)
2140 ("r-iranges" ,r-iranges)
2141 ("r-rsqlite" ,r-rsqlite)
2142 ("r-s4vectors" ,r-s4vectors)
2143 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2144 (home-page "https://bioconductor.org/packages/oligoClasses/")
2145 (synopsis "Classes for high-throughput arrays")
2147 "This package contains class definitions, validity checks, and
2148 initialization methods for classes used by the @code{oligo} and @code{crlmm}
2150 (license license:gpl2+)))
2152 (define-public r-oligo
2159 (uri (bioconductor-uri "oligo" version))
2162 "0cpfkvxpni7an361li0k0qlfcraj7z9zv71r25dbly5kp3dql7k3"))))
2163 (properties `((upstream-name . "oligo")))
2164 (build-system r-build-system)
2165 (inputs `(("zlib" ,zlib)))
2167 `(("r-affxparser" ,r-affxparser)
2168 ("r-affyio" ,r-affyio)
2169 ("r-biobase" ,r-biobase)
2170 ("r-biocgenerics" ,r-biocgenerics)
2171 ("r-biostrings" ,r-biostrings)
2174 ("r-oligoclasses" ,r-oligoclasses)
2175 ("r-preprocesscore" ,r-preprocesscore)
2176 ("r-rsqlite" ,r-rsqlite)
2177 ("r-zlibbioc" ,r-zlibbioc)))
2179 `(("r-knitr" ,r-knitr)))
2180 (home-page "https://bioconductor.org/packages/oligo/")
2181 (synopsis "Preprocessing tools for oligonucleotide arrays")
2183 "This package provides a package to analyze oligonucleotide
2184 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
2185 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
2186 (license license:lgpl2.0+)))
2188 (define-public r-qvalue
2195 (uri (bioconductor-uri "qvalue" version))
2198 "0xbww16lz0k2p4mmq1aqd7iz7d8rvzgw1gm55jy6xbx19ymj64i5"))))
2199 (build-system r-build-system)
2201 `(("r-ggplot2" ,r-ggplot2)
2202 ("r-reshape2" ,r-reshape2)))
2204 `(("r-knitr" ,r-knitr)))
2205 (home-page "https://github.com/StoreyLab/qvalue")
2206 (synopsis "Q-value estimation for false discovery rate control")
2208 "This package takes a list of p-values resulting from the simultaneous
2209 testing of many hypotheses and estimates their q-values and local @dfn{false
2210 discovery rate} (FDR) values. The q-value of a test measures the proportion
2211 of false positives incurred when that particular test is called significant.
2212 The local FDR measures the posterior probability the null hypothesis is true
2213 given the test's p-value. Various plots are automatically generated, allowing
2214 one to make sensible significance cut-offs. The software can be applied to
2215 problems in genomics, brain imaging, astrophysics, and data mining.")
2216 ;; Any version of the LGPL.
2217 (license license:lgpl3+)))
2219 (define r-rcppnumerical
2221 (name "r-rcppnumerical")
2225 (uri (cran-uri "RcppNumerical" version))
2228 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
2229 (properties `((upstream-name . "RcppNumerical")))
2230 (build-system r-build-system)
2232 `(("r-rcpp" ,r-rcpp)
2233 ("r-rcppeigen" ,r-rcppeigen)))
2235 `(("r-knitr" ,r-knitr)))
2236 (home-page "https://github.com/yixuan/RcppNumerical")
2237 (synopsis "Rcpp integration for numerical computing libraries")
2238 (description "This package provides a collection of open source libraries
2239 for numerical computing (numerical integration, optimization, etc.) and their
2240 integration with @code{Rcpp}.")
2241 (license license:gpl2+)))
2243 (define-public r-apeglm
2249 (uri (bioconductor-uri "apeglm" version))
2252 "0pix1fhxk2q89p2745fgsmxwics9rf10l392qhw3rw6v6ynhims2"))))
2253 (properties `((upstream-name . "apeglm")))
2254 (build-system r-build-system)
2256 `(("r-emdbook" ,r-emdbook)
2257 ("r-genomicranges" ,r-genomicranges)
2259 ("r-rcppeigen" ,r-rcppeigen)
2260 ("r-rcppnumerical" ,r-rcppnumerical)
2261 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2262 (native-inputs `(("r-knitr" ,r-knitr)))
2263 (home-page "https://bioconductor.org/packages/apeglm")
2264 (synopsis "Approximate posterior estimation for GLM coefficients")
2265 (description "This package provides Bayesian shrinkage estimators for
2266 effect sizes for a variety of GLM models, using approximation of the
2267 posterior for individual coefficients.")
2268 (license license:gpl2)))
2270 (define-public r-greylistchip
2272 (name "r-greylistchip")
2276 (uri (bioconductor-uri "GreyListChIP" version))
2279 "1d1yvza1aw3vs3di6mrra5l52ig0p9bpzprrqvknjaz5i4yb8ma6"))))
2280 (properties `((upstream-name . "GreyListChIP")))
2281 (build-system r-build-system)
2283 `(("r-bsgenome" ,r-bsgenome)
2284 ("r-genomeinfodb" ,r-genomeinfodb)
2285 ("r-genomicalignments" ,r-genomicalignments)
2286 ("r-genomicranges" ,r-genomicranges)
2288 ("r-rsamtools" ,r-rsamtools)
2289 ("r-rtracklayer" ,r-rtracklayer)
2290 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2291 (home-page "https://bioconductor.org/packages/GreyListChIP")
2292 (synopsis "Greylist artefact regions based on ChIP inputs")
2293 (description "This package identifies regions of ChIP experiments with high
2294 signal in the input, that lead to spurious peaks during peak calling.")
2295 (license license:artistic2.0)))
2297 (define-public r-diffbind
2304 (uri (bioconductor-uri "DiffBind" version))
2307 "1siabhjd0w7bb6v2gfhsm9j7c7c86z8m6lfsyl8p84h0zhjs2vrw"))))
2308 (properties `((upstream-name . "DiffBind")))
2309 (build-system r-build-system)
2311 `(("r-amap" ,r-amap)
2312 ("r-apeglm" ,r-apeglm)
2314 ("r-biocparallel" ,r-biocparallel)
2315 ("r-deseq2" ,r-deseq2)
2316 ("r-dplyr" ,r-dplyr)
2317 ("r-genomicalignments" ,r-genomicalignments)
2318 ("r-genomicranges" ,r-genomicranges)
2319 ("r-ggplot2" ,r-ggplot2)
2320 ("r-ggrepel" ,r-ggrepel)
2321 ("r-gplots" ,r-gplots)
2322 ("r-greylistchip" ,r-greylistchip)
2323 ("r-iranges" ,r-iranges)
2324 ("r-lattice" ,r-lattice)
2325 ("r-limma" ,r-limma)
2326 ("r-locfit" ,r-locfit)
2327 ("r-rcolorbrewer" , r-rcolorbrewer)
2329 ("r-rhtslib" ,r-rhtslib)
2330 ("r-rsamtools" ,r-rsamtools)
2331 ("r-s4vectors" ,r-s4vectors)
2332 ("r-summarizedexperiment" ,r-summarizedexperiment)
2333 ("r-systempiper" ,r-systempiper)))
2334 (home-page "https://bioconductor.org/packages/DiffBind")
2335 (synopsis "Differential binding analysis of ChIP-Seq peak data")
2337 "This package computes differentially bound sites from multiple
2338 ChIP-seq experiments using affinity (quantitative) data. Also enables
2339 occupancy (overlap) analysis and plotting functions.")
2340 (license license:artistic2.0)))
2342 (define-public r-ripseeker
2344 (name "r-ripseeker")
2349 (uri (bioconductor-uri "RIPSeeker" version))
2352 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
2353 (properties `((upstream-name . "RIPSeeker")))
2354 (build-system r-build-system)
2356 `(("r-s4vectors" ,r-s4vectors)
2357 ("r-iranges" ,r-iranges)
2358 ("r-genomicranges" ,r-genomicranges)
2359 ("r-summarizedexperiment" ,r-summarizedexperiment)
2360 ("r-rsamtools" ,r-rsamtools)
2361 ("r-genomicalignments" ,r-genomicalignments)
2362 ("r-rtracklayer" ,r-rtracklayer)))
2363 (home-page "https://bioconductor.org/packages/RIPSeeker")
2365 "Identifying protein-associated transcripts from RIP-seq experiments")
2367 "This package infers and discriminates RIP peaks from RIP-seq alignments
2368 using two-state HMM with negative binomial emission probability. While
2369 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
2370 a suite of bioinformatics tools integrated within this self-contained software
2371 package comprehensively addressing issues ranging from post-alignments
2372 processing to visualization and annotation.")
2373 (license license:gpl2)))
2375 (define-public r-multtest
2382 (uri (bioconductor-uri "multtest" version))
2385 "06vixd81nh3nxrc6km73p7c4bwln1zm39fa9gp7gj272vsxkx53q"))))
2386 (build-system r-build-system)
2388 `(("r-survival" ,r-survival)
2389 ("r-biocgenerics" ,r-biocgenerics)
2390 ("r-biobase" ,r-biobase)
2391 ("r-mass" ,r-mass)))
2392 (home-page "https://bioconductor.org/packages/multtest")
2393 (synopsis "Resampling-based multiple hypothesis testing")
2395 "This package can do non-parametric bootstrap and permutation
2396 resampling-based multiple testing procedures (including empirical Bayes
2397 methods) for controlling the family-wise error rate (FWER), generalized
2398 family-wise error rate (gFWER), tail probability of the proportion of
2399 false positives (TPPFP), and false discovery rate (FDR). Several choices
2400 of bootstrap-based null distribution are implemented (centered, centered
2401 and scaled, quantile-transformed). Single-step and step-wise methods are
2402 available. Tests based on a variety of T- and F-statistics (including
2403 T-statistics based on regression parameters from linear and survival models
2404 as well as those based on correlation parameters) are included. When probing
2405 hypotheses with T-statistics, users may also select a potentially faster null
2406 distribution which is multivariate normal with mean zero and variance
2407 covariance matrix derived from the vector influence function. Results are
2408 reported in terms of adjusted P-values, confidence regions and test statistic
2409 cutoffs. The procedures are directly applicable to identifying differentially
2410 expressed genes in DNA microarray experiments.")
2411 (license license:lgpl3)))
2413 (define-public r-graph
2419 (uri (bioconductor-uri "graph" version))
2422 "0wr7j2pasvi3srvg9z3n034ljk8mldcixny6b3kmqbqm8dqy9py4"))))
2423 (build-system r-build-system)
2425 `(("r-biocgenerics" ,r-biocgenerics)))
2426 (home-page "https://bioconductor.org/packages/graph")
2427 (synopsis "Handle graph data structures in R")
2429 "This package implements some simple graph handling capabilities for R.")
2430 (license license:artistic2.0)))
2432 ;; This is a CRAN package, but it depends on a Bioconductor package.
2433 (define-public r-ggm
2440 (uri (cran-uri "ggm" version))
2443 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
2444 (properties `((upstream-name . "ggm")))
2445 (build-system r-build-system)
2447 `(("r-graph" ,r-graph)
2448 ("r-igraph" ,r-igraph)))
2449 (home-page "https://cran.r-project.org/package=ggm")
2450 (synopsis "Functions for graphical Markov models")
2452 "This package provides functions and datasets for maximum likelihood
2453 fitting of some classes of graphical Markov models.")
2454 (license license:gpl2+)))
2456 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
2457 (define-public r-perfmeas
2464 (uri (cran-uri "PerfMeas" version))
2467 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
2468 (properties `((upstream-name . "PerfMeas")))
2469 (build-system r-build-system)
2471 `(("r-graph" ,r-graph)
2472 ("r-limma" ,r-limma)
2473 ("r-rbgl" ,r-rbgl)))
2474 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
2475 (synopsis "Performance measures for ranking and classification tasks")
2477 "This package implements different performance measures for
2478 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
2479 a given recall, F-score for single and multiple classes are available.")
2480 (license license:gpl2+)))
2482 ;; This is a CRAN package, but it depends on a Bioconductor package.
2483 (define-public r-codedepends
2485 (name "r-codedepends")
2490 (uri (cran-uri "CodeDepends" version))
2493 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
2494 (properties `((upstream-name . "CodeDepends")))
2495 (build-system r-build-system)
2497 `(("r-codetools" ,r-codetools)
2498 ("r-graph" ,r-graph)
2500 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
2501 (synopsis "Analysis of R code for reproducible research and code comprehension")
2503 "This package provides tools for analyzing R expressions or blocks of
2504 code and determining the dependencies between them. It focuses on R scripts,
2505 but can be used on the bodies of functions. There are many facilities
2506 including the ability to summarize or get a high-level view of code,
2507 determining dependencies between variables, code improvement suggestions.")
2508 ;; Any version of the GPL
2509 (license (list license:gpl2+ license:gpl3+))))
2511 (define-public r-chippeakanno
2513 (name "r-chippeakanno")
2518 (uri (bioconductor-uri "ChIPpeakAnno" version))
2521 "0qdkwjv8s46d1kmgg2chijv7yzy9sv49kiks18w8x2z89prn15gj"))))
2522 (properties `((upstream-name . "ChIPpeakAnno")))
2523 (build-system r-build-system)
2525 `(("r-annotationdbi" ,r-annotationdbi)
2526 ("r-biocgenerics" ,r-biocgenerics)
2527 ("r-biomart" ,r-biomart)
2528 ("r-biostrings" ,r-biostrings)
2530 ("r-ensembldb" ,r-ensembldb)
2531 ("r-genomeinfodb" ,r-genomeinfodb)
2532 ("r-genomicalignments" ,r-genomicalignments)
2533 ("r-genomicfeatures" ,r-genomicfeatures)
2534 ("r-genomicranges" ,r-genomicranges)
2535 ("r-ggplot2" ,r-ggplot2)
2536 ("r-graph" ,r-graph)
2537 ("r-iranges" ,r-iranges)
2538 ("r-keggrest" ,r-keggrest)
2539 ("r-matrixstats" ,r-matrixstats)
2540 ("r-multtest" ,r-multtest)
2542 ("r-regioner" ,r-regioner)
2543 ("r-rsamtools" ,r-rsamtools)
2544 ("r-rtracklayer" ,r-rtracklayer)
2545 ("r-s4vectors" ,r-s4vectors)
2546 ("r-summarizedexperiment" ,r-summarizedexperiment)
2547 ("r-venndiagram" ,r-venndiagram)))
2549 `(("r-knitr" ,r-knitr)))
2550 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
2551 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
2553 "The package includes functions to retrieve the sequences around the peak,
2554 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
2555 custom features such as most conserved elements and other transcription factor
2556 binding sites supplied by users. Starting 2.0.5, new functions have been added
2557 for finding the peaks with bi-directional promoters with summary statistics
2558 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
2559 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
2560 enrichedGO (addGeneIDs).")
2561 (license license:gpl2+)))
2563 (define-public r-matrixgenerics
2565 (name "r-matrixgenerics")
2569 (uri (bioconductor-uri "MatrixGenerics" version))
2572 "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb"))))
2574 `((upstream-name . "MatrixGenerics")))
2575 (build-system r-build-system)
2577 `(("r-matrixstats" ,r-matrixstats)))
2578 (home-page "https://bioconductor.org/packages/MatrixGenerics")
2579 (synopsis "S4 generic summary statistic functions for matrix-like objects")
2581 "This package provides S4 generic functions modeled after the
2582 @code{matrixStats} API for alternative matrix implementations. Packages with
2583 alternative matrix implementation can depend on this package and implement the
2584 generic functions that are defined here for a useful set of row and column
2585 summary statistics. Other package developers can import this package and
2586 handle a different matrix implementations without worrying about
2587 incompatibilities.")
2588 (license license:artistic2.0)))
2590 (define-public r-marray
2596 (uri (bioconductor-uri "marray" version))
2598 (base32 "1kkgv166gzvlj8p58vzam3hcaz8mypi3hhpdsjhaszwg6nav4ray"))))
2599 (build-system r-build-system)
2601 `(("r-limma" ,r-limma)))
2602 (home-page "https://bioconductor.org/packages/marray")
2603 (synopsis "Exploratory analysis for two-color spotted microarray data")
2604 (description "This package contains class definitions for two-color spotted
2605 microarray data. It also includes functions for data input, diagnostic plots,
2606 normalization and quality checking.")
2607 (license license:lgpl2.0+)))
2609 (define-public r-cghbase
2615 (uri (bioconductor-uri "CGHbase" version))
2617 (base32 "10zhjmls3f63cj0bnywjb97zhrj7x3xsq6yjhvf5cclxc4kcrcx4"))))
2618 (properties `((upstream-name . "CGHbase")))
2619 (build-system r-build-system)
2621 `(("r-biobase" ,r-biobase)
2622 ("r-marray" ,r-marray)))
2623 (home-page "https://bioconductor.org/packages/CGHbase")
2624 (synopsis "Base functions and classes for arrayCGH data analysis")
2625 (description "This package contains functions and classes that are needed by
2626 the @code{arrayCGH} packages.")
2627 (license license:gpl2+)))
2629 (define-public r-cghcall
2635 (uri (bioconductor-uri "CGHcall" version))
2637 (base32 "1a6k87xfm79wnsc30k5aziakv51h4dd9zqw81q8bd72hc3fpz8ba"))))
2638 (properties `((upstream-name . "CGHcall")))
2639 (build-system r-build-system)
2641 `(("r-biobase" ,r-biobase)
2642 ("r-cghbase" ,r-cghbase)
2643 ("r-impute" ,r-impute)
2644 ("r-dnacopy" ,r-dnacopy)
2645 ("r-snowfall" ,r-snowfall)))
2646 (home-page "https://bioconductor.org/packages/CGHcall")
2647 (synopsis "Base functions and classes for arrayCGH data analysis")
2648 (description "This package contains functions and classes that are needed by
2649 @code{arrayCGH} packages.")
2650 (license license:gpl2+)))
2652 (define-public r-qdnaseq
2658 (uri (bioconductor-uri "QDNAseq" version))
2660 (base32 "1njka1ldaj12id3m2z8ghlrm2lg0n5pxsxyv5gpjnsiabnnaw6ph"))))
2661 (properties `((upstream-name . "QDNAseq")))
2662 (build-system r-build-system)
2664 `(("r-biobase" ,r-biobase)
2665 ("r-cghbase" ,r-cghbase)
2666 ("r-cghcall" ,r-cghcall)
2667 ("r-dnacopy" ,r-dnacopy)
2668 ("r-future" ,r-future)
2669 ("r-future-apply" ,r-future-apply)
2670 ("r-genomicranges" ,r-genomicranges)
2671 ("r-iranges" ,r-iranges)
2672 ("r-matrixstats" ,r-matrixstats)
2673 ("r-r-utils" ,r-r-utils)
2674 ("r-rsamtools" ,r-rsamtools)))
2675 (home-page "https://bioconductor.org/packages/QDNAseq")
2676 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
2677 (description "The genome is divided into non-overlapping fixed-sized bins,
2678 number of sequence reads in each counted, adjusted with a simultaneous
2679 two-dimensional loess correction for sequence mappability and GC content, and
2680 filtered to remove spurious regions in the genome. Downstream steps of
2681 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
2683 (license license:gpl2+)))
2685 (define-public r-bayseq
2692 (uri (bioconductor-uri "baySeq" version))
2695 "1496inlw0x4mfy3g2v7j9ips96sf7576ydnfn6hvn2m6rz2ls215"))))
2696 (properties `((upstream-name . "baySeq")))
2697 (build-system r-build-system)
2699 `(("r-abind" ,r-abind)
2700 ("r-edger" ,r-edger)
2701 ("r-genomicranges" ,r-genomicranges)))
2702 (home-page "https://bioconductor.org/packages/baySeq/")
2703 (synopsis "Bayesian analysis of differential expression patterns in count data")
2705 "This package identifies differential expression in high-throughput count
2706 data, such as that derived from next-generation sequencing machines,
2707 calculating estimated posterior likelihoods of differential expression (or
2708 more complex hypotheses) via empirical Bayesian methods.")
2709 (license license:gpl3)))
2711 (define-public r-chipcomp
2718 (uri (bioconductor-uri "ChIPComp" version))
2721 "0dbypfgys74snmyf982183ilzg6vamfw1d5y0lp5p8zxbffh2xl7"))))
2722 (properties `((upstream-name . "ChIPComp")))
2723 (build-system r-build-system)
2725 `(("r-biocgenerics" ,r-biocgenerics)
2726 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
2727 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
2728 ("r-genomeinfodb" ,r-genomeinfodb)
2729 ("r-genomicranges" ,r-genomicranges)
2730 ("r-iranges" ,r-iranges)
2731 ("r-limma" ,r-limma)
2732 ("r-rsamtools" ,r-rsamtools)
2733 ("r-rtracklayer" ,r-rtracklayer)
2734 ("r-s4vectors" ,r-s4vectors)))
2735 (home-page "https://bioconductor.org/packages/ChIPComp")
2736 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
2738 "ChIPComp implements a statistical method for quantitative comparison of
2739 multiple ChIP-seq datasets. It detects differentially bound sharp binding
2740 sites across multiple conditions considering matching control in ChIP-seq
2742 ;; Any version of the GPL.
2743 (license license:gpl3+)))
2745 (define-public r-riboprofiling
2747 (name "r-riboprofiling")
2752 (uri (bioconductor-uri "RiboProfiling" version))
2755 "112071w7aw7cwckipq0dll1lssl7pwafma4v9jj9sx12rjcj57xg"))))
2756 (properties `((upstream-name . "RiboProfiling")))
2757 (build-system r-build-system)
2759 `(("r-biocgenerics" ,r-biocgenerics)
2760 ("r-biostrings" ,r-biostrings)
2761 ("r-data-table" ,r-data-table)
2762 ("r-genomeinfodb" ,r-genomeinfodb)
2763 ("r-genomicalignments" ,r-genomicalignments)
2764 ("r-genomicfeatures" ,r-genomicfeatures)
2765 ("r-genomicranges" ,r-genomicranges)
2766 ("r-ggbio" ,r-ggbio)
2767 ("r-ggplot2" ,r-ggplot2)
2768 ("r-iranges" ,r-iranges)
2770 ("r-reshape2" ,r-reshape2)
2771 ("r-rsamtools" ,r-rsamtools)
2772 ("r-rtracklayer" ,r-rtracklayer)
2773 ("r-s4vectors" ,r-s4vectors)
2774 ("r-sqldf" ,r-sqldf)))
2776 `(("r-knitr" ,r-knitr)))
2777 (home-page "https://bioconductor.org/packages/RiboProfiling/")
2778 (synopsis "Ribosome profiling data analysis")
2779 (description "Starting with a BAM file, this package provides the
2780 necessary functions for quality assessment, read start position recalibration,
2781 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
2782 of count data: pairs, log fold-change, codon frequency and coverage
2783 assessment, principal component analysis on codon coverage.")
2784 (license license:gpl3)))
2786 (define-public r-riboseqr
2793 (uri (bioconductor-uri "riboSeqR" version))
2796 "07i64gch14rsbjlfv17s689wzlqbi7hcqhcw21pp6cw8bvhvd5xr"))))
2797 (properties `((upstream-name . "riboSeqR")))
2798 (build-system r-build-system)
2800 `(("r-abind" ,r-abind)
2801 ("r-bayseq" ,r-bayseq)
2802 ("r-genomeinfodb" ,r-genomeinfodb)
2803 ("r-genomicranges" ,r-genomicranges)
2804 ("r-iranges" ,r-iranges)
2805 ("r-rsamtools" ,r-rsamtools)
2806 ("r-seqlogo" ,r-seqlogo)))
2807 (home-page "https://bioconductor.org/packages/riboSeqR/")
2808 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
2810 "This package provides plotting functions, frameshift detection and
2811 parsing of genetic sequencing data from ribosome profiling experiments.")
2812 (license license:gpl3)))
2814 (define-public r-interactionset
2816 (name "r-interactionset")
2821 (uri (bioconductor-uri "InteractionSet" version))
2824 "14lp23b298wr3r7ggcfvas0xlf1866cpla0rv7dz589f50z6bj31"))))
2826 `((upstream-name . "InteractionSet")))
2827 (build-system r-build-system)
2829 `(("r-biocgenerics" ,r-biocgenerics)
2830 ("r-genomeinfodb" ,r-genomeinfodb)
2831 ("r-genomicranges" ,r-genomicranges)
2832 ("r-iranges" ,r-iranges)
2833 ("r-matrix" ,r-matrix)
2835 ("r-s4vectors" ,r-s4vectors)
2836 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2838 `(("r-knitr" ,r-knitr)))
2839 (home-page "https://bioconductor.org/packages/InteractionSet")
2840 (synopsis "Base classes for storing genomic interaction data")
2842 "This package provides the @code{GInteractions},
2843 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
2844 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
2846 (license license:gpl3)))
2848 (define-public r-genomicinteractions
2850 (name "r-genomicinteractions")
2855 (uri (bioconductor-uri "GenomicInteractions" version))
2858 "0ad0a5cadchx1rkqj4cc8k0y1zf34jgp1406hvik5zabr7xijkbd"))))
2860 `((upstream-name . "GenomicInteractions")))
2861 (build-system r-build-system)
2863 `(("r-biobase" ,r-biobase)
2864 ("r-biocgenerics" ,r-biocgenerics)
2865 ("r-data-table" ,r-data-table)
2866 ("r-dplyr" ,r-dplyr)
2867 ("r-genomeinfodb" ,r-genomeinfodb)
2868 ("r-genomicranges" ,r-genomicranges)
2869 ("r-ggplot2" ,r-ggplot2)
2870 ("r-gridextra" ,r-gridextra)
2872 ("r-igraph" ,r-igraph)
2873 ("r-interactionset" ,r-interactionset)
2874 ("r-iranges" ,r-iranges)
2875 ("r-rsamtools" ,r-rsamtools)
2876 ("r-rtracklayer" ,r-rtracklayer)
2877 ("r-s4vectors" ,r-s4vectors)
2878 ("r-stringr" ,r-stringr)))
2880 `(("r-knitr" ,r-knitr)))
2881 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
2882 (synopsis "R package for handling genomic interaction data")
2884 "This R package provides tools for handling genomic interaction data,
2885 such as ChIA-PET/Hi-C, annotating genomic features with interaction
2886 information and producing various plots and statistics.")
2887 (license license:gpl3)))
2889 (define-public r-ctc
2896 (uri (bioconductor-uri "ctc" version))
2899 "1nwlphbfba3w8ixck02k5c84qm4flnp9fd68li0jn5a08qi9gmyp"))))
2900 (build-system r-build-system)
2901 (propagated-inputs `(("r-amap" ,r-amap)))
2902 (home-page "https://bioconductor.org/packages/ctc/")
2903 (synopsis "Cluster and tree conversion")
2905 "This package provides tools for exporting and importing classification
2906 trees and clusters to other programs.")
2907 (license license:gpl2)))
2909 (define-public r-goseq
2916 (uri (bioconductor-uri "goseq" version))
2919 "18fs3m4kl3zahn42j20rjvxy83irscgqx0dvid7va4majvsib509"))))
2920 (build-system r-build-system)
2922 `(("r-annotationdbi" ,r-annotationdbi)
2923 ("r-biasedurn" ,r-biasedurn)
2924 ("r-biocgenerics" ,r-biocgenerics)
2925 ("r-genelendatabase" ,r-genelendatabase)
2926 ("r-go-db" ,r-go-db)
2927 ("r-mgcv" ,r-mgcv)))
2928 (home-page "https://bioconductor.org/packages/goseq/")
2929 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
2931 "This package provides tools to detect Gene Ontology and/or other user
2932 defined categories which are over/under represented in RNA-seq data.")
2933 (license license:lgpl2.0+)))
2935 (define-public r-glimma
2942 (uri (bioconductor-uri "Glimma" version))
2945 "0gy30v30lw27frhmw39pzacqzrv2vwj5rsp6gb3yifllrahdiffv"))))
2946 (properties `((upstream-name . "Glimma")))
2947 (build-system r-build-system)
2949 `(("r-deseq2" ,r-deseq2)
2950 ("r-edger" ,r-edger)
2951 ("r-htmlwidgets" ,r-htmlwidgets)
2952 ("r-jsonlite" ,r-jsonlite)
2953 ("r-limma" ,r-limma)
2954 ("r-s4vectors" ,r-s4vectors)
2955 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2957 `(("r-knitr" ,r-knitr)))
2958 (home-page "https://github.com/Shians/Glimma")
2959 (synopsis "Interactive HTML graphics")
2961 "This package generates interactive visualisations for analysis of
2962 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
2963 HTML page. The interactions are built on top of the popular static
2964 representations of analysis results in order to provide additional
2966 (license license:lgpl3)))
2968 (define-public r-rots
2975 (uri (bioconductor-uri "ROTS" version))
2978 "0qk0gfhgr14g13zlfyf5101b5s8cma7j3r8a92q93h0axy8ka23n"))))
2979 (properties `((upstream-name . "ROTS")))
2980 (build-system r-build-system)
2982 `(("r-biobase" ,r-biobase)
2983 ("r-rcpp" ,r-rcpp)))
2984 (home-page "https://bioconductor.org/packages/ROTS/")
2985 (synopsis "Reproducibility-Optimized Test Statistic")
2987 "This package provides tools for calculating the
2988 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
2990 (license license:gpl2+)))
2992 (define-public r-plgem
2999 (uri (bioconductor-uri "plgem" version))
3002 "039gqwsm1v6q8v8b248nm8g9gnsk379mfx65rbgdmh3chsd8pm8a"))))
3003 (build-system r-build-system)
3005 `(("r-biobase" ,r-biobase)
3006 ("r-mass" ,r-mass)))
3007 (home-page "http://www.genopolis.it")
3008 (synopsis "Detect differential expression in microarray and proteomics datasets")
3010 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
3011 model the variance-versus-mean dependence that exists in a variety of
3012 genome-wide datasets, including microarray and proteomics data. The use of
3013 PLGEM has been shown to improve the detection of differentially expressed
3014 genes or proteins in these datasets.")
3015 (license license:gpl2)))
3017 (define-public r-inspect
3024 (uri (bioconductor-uri "INSPEcT" version))
3027 "1jymvi5mf7vhs58zfh290pacfswgvkw09rmbirmr24kxcgl30483"))))
3028 (properties `((upstream-name . "INSPEcT")))
3029 (build-system r-build-system)
3031 `(("r-biobase" ,r-biobase)
3032 ("r-biocgenerics" ,r-biocgenerics)
3033 ("r-biocparallel" ,r-biocparallel)
3034 ("r-deseq2" ,r-deseq2)
3035 ("r-desolve" ,r-desolve)
3036 ("r-gdata" ,r-gdata)
3037 ("r-genomeinfodb" ,r-genomeinfodb)
3038 ("r-genomicalignments" ,r-genomicalignments)
3039 ("r-genomicfeatures" ,r-genomicfeatures)
3040 ("r-genomicranges" ,r-genomicranges)
3041 ("r-iranges" ,r-iranges)
3042 ("r-kernsmooth" ,r-kernsmooth)
3043 ("r-plgem" ,r-plgem)
3045 ("r-rootsolve" ,r-rootsolve)
3046 ("r-rsamtools" ,r-rsamtools)
3047 ("r-rtracklayer" ,r-rtracklayer)
3048 ("r-s4vectors" ,r-s4vectors)
3049 ("r-shiny" ,r-shiny)
3050 ("r-summarizedexperiment" ,r-summarizedexperiment)
3051 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
3052 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
3054 `(("r-knitr" ,r-knitr)))
3055 (home-page "https://bioconductor.org/packages/INSPEcT")
3056 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
3058 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
3059 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
3060 order to evaluate synthesis, processing and degradation rates and assess via
3061 modeling the rates that determines changes in mature mRNA levels.")
3062 (license license:gpl2)))
3064 (define-public r-dnabarcodes
3066 (name "r-dnabarcodes")
3071 (uri (bioconductor-uri "DNABarcodes" version))
3074 "0zzf6xgg6k1gdig8zvpawck2bgmamsc0k43j4pl4xsz9an6dmzbg"))))
3075 (properties `((upstream-name . "DNABarcodes")))
3076 (build-system r-build-system)
3079 ("r-matrix" ,r-matrix)
3080 ("r-rcpp" ,r-rcpp)))
3082 `(("r-knitr" ,r-knitr)))
3083 (home-page "https://bioconductor.org/packages/DNABarcodes")
3084 (synopsis "Create and analyze DNA barcodes")
3086 "This package offers tools to create DNA barcode sets capable of
3087 correcting insertion, deletion, and substitution errors. Existing barcodes
3088 can be analyzed regarding their minimal, maximal and average distances between
3089 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
3090 demultiplexed, i.e. assigned to their original reference barcode.")
3091 (license license:gpl2)))
3093 (define-public r-ruvseq
3100 (uri (bioconductor-uri "RUVSeq" version))
3103 "1anrybyrzpajr5434svyfbaypjai6x0ifsmqvjgimmxq3xqhv0jh"))))
3104 (properties `((upstream-name . "RUVSeq")))
3105 (build-system r-build-system)
3107 `(("r-biobase" ,r-biobase)
3108 ("r-edaseq" ,r-edaseq)
3109 ("r-edger" ,r-edger)
3110 ("r-mass" ,r-mass)))
3112 `(("r-knitr" ,r-knitr)))
3113 (home-page "https://github.com/drisso/RUVSeq")
3114 (synopsis "Remove unwanted variation from RNA-Seq data")
3116 "This package implements methods to @dfn{remove unwanted variation} (RUV)
3117 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
3119 (license license:artistic2.0)))
3121 (define-public r-biocneighbors
3123 (name "r-biocneighbors")
3128 (uri (bioconductor-uri "BiocNeighbors" version))
3131 "19gyl917lf5ydy5hgj0hnc388rw5sbj83awav9js2yr2zmbgn4d7"))))
3132 (properties `((upstream-name . "BiocNeighbors")))
3133 (build-system r-build-system)
3135 `(("r-biocparallel" ,r-biocparallel)
3136 ("r-matrix" ,r-matrix)
3138 ("r-rcpphnsw" ,r-rcpphnsw)
3139 ("r-s4vectors" ,r-s4vectors)))
3141 `(("r-knitr" ,r-knitr)))
3142 (home-page "https://bioconductor.org/packages/BiocNeighbors")
3143 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
3145 "This package implements exact and approximate methods for nearest
3146 neighbor detection, in a framework that allows them to be easily switched
3147 within Bioconductor packages or workflows. The exact algorithm is implemented
3148 using pre-clustering with the k-means algorithm. Functions are also provided
3149 to search for all neighbors within a given distance. Parallelization is
3150 achieved for all methods using the BiocParallel framework.")
3151 (license license:gpl3)))
3153 (define-public r-biocsingular
3155 (name "r-biocsingular")
3160 (uri (bioconductor-uri "BiocSingular" version))
3163 "1hczix1h14d19hzcsngqkqqnqkprs41phzlcird8haxnw9bs03ni"))))
3164 (properties `((upstream-name . "BiocSingular")))
3165 (build-system r-build-system)
3167 `(("r-beachmat" ,r-beachmat)
3168 ("r-biocgenerics" ,r-biocgenerics)
3169 ("r-biocparallel" ,r-biocparallel)
3170 ("r-delayedarray" ,r-delayedarray)
3171 ("r-irlba" ,r-irlba)
3172 ("r-matrix" ,r-matrix)
3175 ("r-s4vectors" ,r-s4vectors)))
3177 `(("r-knitr" ,r-knitr)))
3178 (home-page "https://github.com/LTLA/BiocSingular")
3179 (synopsis "Singular value decomposition for Bioconductor packages")
3181 "This package implements exact and approximate methods for singular value
3182 decomposition and principal components analysis, in a framework that allows
3183 them to be easily switched within Bioconductor packages or workflows. Where
3184 possible, parallelization is achieved using the BiocParallel framework.")
3185 (license license:gpl3)))
3187 (define-public r-destiny
3194 (uri (bioconductor-uri "destiny" version))
3197 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
3198 (build-system r-build-system)
3200 `(("r-biobase" ,r-biobase)
3201 ("r-biocgenerics" ,r-biocgenerics)
3202 ("r-ggplot-multistats" ,r-ggplot-multistats)
3203 ("r-ggplot2" ,r-ggplot2)
3204 ("r-ggthemes" ,r-ggthemes)
3205 ("r-irlba" ,r-irlba)
3206 ("r-knn-covertree" ,r-knn-covertree)
3207 ("r-matrix" ,r-matrix)
3208 ("r-pcamethods" ,r-pcamethods)
3209 ("r-proxy" ,r-proxy)
3211 ("r-rcppeigen" ,r-rcppeigen)
3212 ("r-rcpphnsw" ,r-rcpphnsw)
3213 ("r-rspectra" ,r-rspectra)
3214 ("r-scales" ,r-scales)
3215 ("r-scatterplot3d" ,r-scatterplot3d)
3216 ("r-singlecellexperiment" ,r-singlecellexperiment)
3217 ("r-smoother" ,r-smoother)
3218 ("r-summarizedexperiment" ,r-summarizedexperiment)
3219 ("r-tidyr" ,r-tidyr)
3220 ("r-tidyselect" ,r-tidyselect)
3223 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
3224 (home-page "https://bioconductor.org/packages/destiny/")
3225 (synopsis "Create and plot diffusion maps")
3226 (description "This package provides tools to create and plot diffusion
3228 ;; Any version of the GPL
3229 (license license:gpl3+)))
3231 (define-public r-savr
3238 (uri (bioconductor-uri "savR" version))
3241 "1vha9b7gndwjzvrzr1hdhv3wc6a1s2n9grxwfd78yb2lkysf4hic"))))
3242 (properties `((upstream-name . "savR")))
3243 (build-system r-build-system)
3245 `(("r-ggplot2" ,r-ggplot2)
3246 ("r-gridextra" ,r-gridextra)
3247 ("r-reshape2" ,r-reshape2)
3248 ("r-scales" ,r-scales)
3250 (home-page "https://github.com/bcalder/savR")
3251 (synopsis "Parse and analyze Illumina SAV files")
3253 "This package provides tools to parse Illumina Sequence Analysis
3254 Viewer (SAV) files, access data, and generate QC plots.")
3255 (license license:agpl3+)))
3257 (define-public r-chipexoqual
3259 (name "r-chipexoqual")
3264 (uri (bioconductor-uri "ChIPexoQual" version))
3267 "15r5jgkfwwfqpw4v4q2ddmglm3bfw002nnbnzn1s0v2b1w3bgiag"))))
3268 (properties `((upstream-name . "ChIPexoQual")))
3269 (build-system r-build-system)
3271 `(("r-biocparallel" ,r-biocparallel)
3272 ("r-biovizbase" ,r-biovizbase)
3273 ("r-broom" ,r-broom)
3274 ("r-data-table" ,r-data-table)
3275 ("r-dplyr" ,r-dplyr)
3276 ("r-genomeinfodb" ,r-genomeinfodb)
3277 ("r-genomicalignments" ,r-genomicalignments)
3278 ("r-genomicranges" ,r-genomicranges)
3279 ("r-ggplot2" ,r-ggplot2)
3280 ("r-hexbin" ,r-hexbin)
3281 ("r-iranges" ,r-iranges)
3282 ("r-rcolorbrewer" ,r-rcolorbrewer)
3283 ("r-rmarkdown" ,r-rmarkdown)
3284 ("r-rsamtools" ,r-rsamtools)
3285 ("r-s4vectors" ,r-s4vectors)
3286 ("r-scales" ,r-scales)
3287 ("r-viridis" ,r-viridis)))
3289 `(("r-knitr" ,r-knitr)))
3290 (home-page "https://github.com/keleslab/ChIPexoQual")
3291 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
3293 "This package provides a quality control pipeline for ChIP-exo/nexus
3295 (license license:gpl2+)))
3297 (define-public r-copynumber
3299 (name "r-copynumber")
3303 (uri (bioconductor-uri "copynumber" version))
3306 "00fyfy3kpz33v1hqisd5m5xdazwjmjrfj8ssbf6p9m3am2ar23gm"))))
3307 (build-system r-build-system)
3309 `(("r-s4vectors" ,r-s4vectors)
3310 ("r-iranges" ,r-iranges)
3311 ("r-genomicranges" ,r-genomicranges)
3312 ("r-biocgenerics" ,r-biocgenerics)))
3313 (home-page "https://bioconductor.org/packages/copynumber")
3314 (synopsis "Segmentation of single- and multi-track copy number data")
3316 "This package segments single- and multi-track copy number data by a
3317 penalized least squares regression method.")
3318 (license license:artistic2.0)))
3320 (define-public r-dnacopy
3327 (uri (bioconductor-uri "DNAcopy" version))
3330 "0km5af4iw8a0m6by933lgdi5246jafyfxk6fsqdiwg07v9wxw5hc"))))
3331 (properties `((upstream-name . "DNAcopy")))
3332 (build-system r-build-system)
3333 (native-inputs `(("gfortran" ,gfortran)))
3334 (home-page "https://bioconductor.org/packages/DNAcopy")
3335 (synopsis "DNA copy number data analysis")
3337 "This package implements the @dfn{circular binary segmentation} (CBS)
3338 algorithm to segment DNA copy number data and identify genomic regions with
3339 abnormal copy number.")
3340 (license license:gpl2+)))
3342 ;; This is a CRAN package, but it uncharacteristically depends on a
3343 ;; Bioconductor package.
3344 (define-public r-htscluster
3346 (name "r-htscluster")
3351 (uri (cran-uri "HTSCluster" version))
3354 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
3355 (properties `((upstream-name . "HTSCluster")))
3356 (build-system r-build-system)
3358 `(("r-capushe" ,r-capushe)
3359 ("r-edger" ,r-edger)
3360 ("r-plotrix" ,r-plotrix)))
3361 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
3362 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
3364 "This package provides a Poisson mixture model is implemented to cluster
3365 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
3366 estimation is performed using either the EM or CEM algorithm, and the slope
3367 heuristics are used for model selection (i.e., to choose the number of
3369 (license license:gpl3+)))
3371 (define-public r-deds
3378 (uri (bioconductor-uri "DEDS" version))
3381 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
3382 (properties `((upstream-name . "DEDS")))
3383 (build-system r-build-system)
3384 (home-page "https://bioconductor.org/packages/DEDS/")
3385 (synopsis "Differential expression via distance summary for microarray data")
3387 "This library contains functions that calculate various statistics of
3388 differential expression for microarray data, including t statistics, fold
3389 change, F statistics, SAM, moderated t and F statistics and B statistics. It
3390 also implements a new methodology called DEDS (Differential Expression via
3391 Distance Summary), which selects differentially expressed genes by integrating
3392 and summarizing a set of statistics using a weighted distance approach.")
3393 ;; Any version of the LGPL.
3394 (license license:lgpl3+)))
3396 ;; This is a CRAN package, but since it depends on a Bioconductor package we
3398 (define-public r-nbpseq
3405 (uri (cran-uri "NBPSeq" version))
3408 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
3409 (properties `((upstream-name . "NBPSeq")))
3410 (build-system r-build-system)
3412 `(("r-qvalue" ,r-qvalue)))
3413 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
3414 (synopsis "Negative binomial models for RNA-Seq data")
3416 "This package provides negative binomial models for two-group comparisons
3417 and regression inferences from RNA-sequencing data.")
3418 (license license:gpl2)))
3420 (define-public r-ebseq
3427 (uri (bioconductor-uri "EBSeq" version))
3430 "1x2489xaqg85v7n3yhqs0nh9ha6dn4m167dkc6akzig4xivwjjny"))))
3431 (properties `((upstream-name . "EBSeq")))
3432 (build-system r-build-system)
3434 `(("r-blockmodeling" ,r-blockmodeling)
3435 ("r-gplots" ,r-gplots)
3436 ("r-testthat" ,r-testthat)))
3437 (home-page "https://bioconductor.org/packages/EBSeq")
3438 (synopsis "Differential expression analysis of RNA-seq data")
3440 "This package provides tools for differential expression analysis at both
3441 gene and isoform level using RNA-seq data")
3442 (license license:artistic2.0)))
3444 (define-public r-karyoploter
3446 (name "r-karyoploter")
3450 (uri (bioconductor-uri "karyoploteR" version))
3453 "1agw49mckm3g33igqdp9lr8a4ky8nhivaxrs7d00dvzk0diqwdb2"))))
3454 (build-system r-build-system)
3456 `(("r-annotationdbi" ,r-annotationdbi)
3457 ("r-bamsignals" ,r-bamsignals)
3458 ("r-bezier" ,r-bezier)
3459 ("r-biovizbase" ,r-biovizbase)
3460 ("r-digest" ,r-digest)
3461 ("r-genomeinfodb" ,r-genomeinfodb)
3462 ("r-genomicfeatures" ,r-genomicfeatures)
3463 ("r-genomicranges" ,r-genomicranges)
3464 ("r-iranges" ,r-iranges)
3465 ("r-memoise" ,r-memoise)
3466 ("r-regioner" ,r-regioner)
3467 ("r-rsamtools" ,r-rsamtools)
3468 ("r-rtracklayer" ,r-rtracklayer)
3469 ("r-s4vectors" ,r-s4vectors)
3470 ("r-variantannotation" ,r-variantannotation)))
3472 `(("r-knitr" ,r-knitr)))
3473 (home-page "https://bioconductor.org/packages/karyoploteR/")
3474 (synopsis "Plot customizable linear genomes displaying arbitrary data")
3475 (description "This package creates karyotype plots of arbitrary genomes and
3476 offers a complete set of functions to plot arbitrary data on them. It mimics
3477 many R base graphics functions coupling them with a coordinate change function
3478 automatically mapping the chromosome and data coordinates into the plot
3480 (license license:artistic2.0)))
3482 (define-public r-lpsymphony
3484 (name "r-lpsymphony")
3489 (uri (bioconductor-uri "lpsymphony" version))
3492 "0f9qjfv7rp1y3mwscnjz3pph7m40zgz55xcdhyii6k1iw2vyaxx9"))))
3493 (build-system r-build-system)
3497 `(("pkg-config" ,pkg-config)
3498 ("r-knitr" ,r-knitr)))
3499 (home-page "https://r-forge.r-project.org/projects/rsymphony")
3500 (synopsis "Symphony integer linear programming solver in R")
3502 "This package was derived from Rsymphony. The package provides an R
3503 interface to SYMPHONY, a linear programming solver written in C++. The main
3504 difference between this package and Rsymphony is that it includes the solver
3505 source code, while Rsymphony expects to find header and library files on the
3506 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
3507 to install interface to SYMPHONY.")
3508 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
3509 ;; lpsimphony is released under the same terms.
3510 (license license:epl1.0)))
3512 (define-public r-ihw
3519 (uri (bioconductor-uri "IHW" version))
3522 "04szg3bj5cjixxcp8j3inmj0fzk2mg8gp2w2b33x0im8ik24qiw0"))))
3523 (properties `((upstream-name . "IHW")))
3524 (build-system r-build-system)
3526 `(("r-biocgenerics" ,r-biocgenerics)
3527 ("r-fdrtool" ,r-fdrtool)
3528 ("r-lpsymphony" ,r-lpsymphony)
3529 ("r-slam" ,r-slam)))
3531 `(("r-knitr" ,r-knitr)))
3532 (home-page "https://bioconductor.org/packages/IHW")
3533 (synopsis "Independent hypothesis weighting")
3535 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
3536 procedure that increases power compared to the method of Benjamini and
3537 Hochberg by assigning data-driven weights to each hypothesis. The input to
3538 IHW is a two-column table of p-values and covariates. The covariate can be
3539 any continuous-valued or categorical variable that is thought to be
3540 informative on the statistical properties of each hypothesis test, while it is
3541 independent of the p-value under the null hypothesis.")
3542 (license license:artistic2.0)))
3544 (define-public r-icobra
3551 (uri (bioconductor-uri "iCOBRA" version))
3554 "0knqvvfi5y53jk8s2g2bqgxnh2pbdf38676fk7pkdp1r2j6cbi3s"))))
3555 (properties `((upstream-name . "iCOBRA")))
3556 (build-system r-build-system)
3558 `(("r-dplyr" ,r-dplyr)
3560 ("r-ggplot2" ,r-ggplot2)
3561 ("r-limma" ,r-limma)
3562 ("r-reshape2" ,r-reshape2)
3564 ("r-scales" ,r-scales)
3565 ("r-shiny" ,r-shiny)
3566 ("r-shinybs" ,r-shinybs)
3567 ("r-shinydashboard" ,r-shinydashboard)
3568 ("r-upsetr" ,r-upsetr)))
3570 `(("r-knitr" ,r-knitr)))
3571 (home-page "https://bioconductor.org/packages/iCOBRA")
3572 (synopsis "Comparison and visualization of ranking and assignment methods")
3574 "This package provides functions for calculation and visualization of
3575 performance metrics for evaluation of ranking and binary
3576 classification (assignment) methods. It also contains a Shiny application for
3577 interactive exploration of results.")
3578 (license license:gpl2+)))
3580 (define-public r-mast
3587 (uri (bioconductor-uri "MAST" version))
3590 "11qr7n9i4masqz0yzikddchyn223m8dy6zv461dly07fd43qi9mn"))))
3591 (properties `((upstream-name . "MAST")))
3592 (build-system r-build-system)
3594 `(("r-abind" ,r-abind)
3595 ("r-biobase" ,r-biobase)
3596 ("r-biocgenerics" ,r-biocgenerics)
3597 ("r-data-table" ,r-data-table)
3598 ("r-ggplot2" ,r-ggplot2)
3600 ("r-progress" ,r-progress)
3601 ("r-reshape2" ,r-reshape2)
3602 ("r-s4vectors" ,r-s4vectors)
3603 ("r-singlecellexperiment" ,r-singlecellexperiment)
3604 ("r-stringr" ,r-stringr)
3605 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3607 `(("r-knitr" ,r-knitr)))
3608 (home-page "https://github.com/RGLab/MAST/")
3609 (synopsis "Model-based analysis of single cell transcriptomics")
3611 "This package provides methods and models for handling zero-inflated
3612 single cell assay data.")
3613 (license license:gpl2+)))
3615 (define-public r-monocle
3622 (uri (bioconductor-uri "monocle" version))
3625 "1k3hwi9aspjy75arigg7i1w7ygf112y12cndibf2bhpz2phzwslx"))))
3626 (build-system r-build-system)
3628 `(("r-biobase" ,r-biobase)
3629 ("r-biocgenerics" ,r-biocgenerics)
3630 ("r-biocviews" ,r-biocviews)
3631 ("r-cluster" ,r-cluster)
3632 ("r-combinat" ,r-combinat)
3633 ("r-ddrtree" ,r-ddrtree)
3634 ("r-densityclust" ,r-densityclust)
3635 ("r-dplyr" ,r-dplyr)
3636 ("r-fastica" ,r-fastica)
3637 ("r-ggplot2" ,r-ggplot2)
3638 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
3639 ("r-igraph" ,r-igraph)
3640 ("r-irlba" ,r-irlba)
3641 ("r-limma" ,r-limma)
3643 ("r-matrix" ,r-matrix)
3644 ("r-matrixstats" ,r-matrixstats)
3645 ("r-pheatmap" ,r-pheatmap)
3647 ("r-proxy" ,r-proxy)
3648 ("r-qlcmatrix" ,r-qlcmatrix)
3651 ("r-reshape2" ,r-reshape2)
3652 ("r-rtsne" ,r-rtsne)
3654 ("r-stringr" ,r-stringr)
3655 ("r-tibble" ,r-tibble)
3657 ("r-viridis" ,r-viridis)))
3659 `(("r-knitr" ,r-knitr)))
3660 (home-page "https://bioconductor.org/packages/monocle")
3661 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
3663 "Monocle performs differential expression and time-series analysis for
3664 single-cell expression experiments. It orders individual cells according to
3665 progress through a biological process, without knowing ahead of time which
3666 genes define progress through that process. Monocle also performs
3667 differential expression analysis, clustering, visualization, and other useful
3668 tasks on single cell expression data. It is designed to work with RNA-Seq and
3669 qPCR data, but could be used with other types as well.")
3670 (license license:artistic2.0)))
3672 (define-public r-monocle3
3680 (url "https://github.com/cole-trapnell-lab/monocle3")
3682 (file-name (git-file-name name version))
3685 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
3686 (build-system r-build-system)
3688 `(("r-biobase" ,r-biobase)
3689 ("r-biocgenerics" ,r-biocgenerics)
3690 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3691 ("r-dplyr" ,r-dplyr)
3692 ("r-ggplot2" ,r-ggplot2)
3693 ("r-ggrepel" ,r-ggrepel)
3695 ("r-htmlwidgets" ,r-htmlwidgets)
3696 ("r-igraph" ,r-igraph)
3697 ("r-irlba" ,r-irlba)
3698 ("r-limma" ,r-limma)
3699 ("r-lmtest" ,r-lmtest)
3701 ("r-matrix" ,r-matrix)
3702 ("r-matrix-utils" ,r-matrix-utils)
3703 ("r-pbapply" ,r-pbapply)
3704 ("r-pbmcapply" ,r-pbmcapply)
3705 ("r-pheatmap" ,r-pheatmap)
3706 ("r-plotly" ,r-plotly)
3708 ("r-proxy" ,r-proxy)
3710 ("r-purrr" ,r-purrr)
3713 ("r-rcppparallel" ,r-rcppparallel)
3714 ("r-reshape2" ,r-reshape2)
3715 ("r-reticulate" ,r-reticulate)
3716 ("r-rhpcblasctl" ,r-rhpcblasctl)
3717 ("r-rtsne" ,r-rtsne)
3718 ("r-shiny" ,r-shiny)
3720 ("r-spdep" ,r-spdep)
3721 ("r-speedglm" ,r-speedglm)
3722 ("r-stringr" ,r-stringr)
3723 ("r-singlecellexperiment" ,r-singlecellexperiment)
3724 ("r-tibble" ,r-tibble)
3725 ("r-tidyr" ,r-tidyr)
3727 ("r-viridis" ,r-viridis)))
3728 (home-page "https://github.com/cole-trapnell-lab/monocle3")
3729 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
3731 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
3732 (license license:expat)))
3734 (define-public r-noiseq
3741 (uri (bioconductor-uri "NOISeq" version))
3744 "08qlavakclgzk345bliam4cfjhsy39n4s6m1biqpq94n9qp00x8f"))))
3745 (properties `((upstream-name . "NOISeq")))
3746 (build-system r-build-system)
3748 `(("r-biobase" ,r-biobase)
3749 ("r-matrix" ,r-matrix)))
3750 (home-page "https://bioconductor.org/packages/NOISeq")
3751 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
3753 "This package provides tools to support the analysis of RNA-seq
3754 expression data or other similar kind of data. It provides exploratory plots
3755 to evaluate saturation, count distribution, expression per chromosome, type of
3756 detected features, features length, etc. It also supports the analysis of
3757 differential expression between two experimental conditions with no parametric
3759 (license license:artistic2.0)))
3761 (define-public r-scdd
3768 (uri (bioconductor-uri "scDD" version))
3771 "07l07fq5633ccq5d3l35dm34pwvaqfa3b3qwpn5v5xn99f5hfz0g"))))
3772 (properties `((upstream-name . "scDD")))
3773 (build-system r-build-system)
3776 ("r-biocparallel" ,r-biocparallel)
3777 ("r-ebseq" ,r-ebseq)
3778 ("r-fields" ,r-fields)
3779 ("r-ggplot2" ,r-ggplot2)
3780 ("r-mclust" ,r-mclust)
3781 ("r-outliers" ,r-outliers)
3782 ("r-s4vectors" ,r-s4vectors)
3783 ("r-scran" ,r-scran)
3784 ("r-singlecellexperiment" ,r-singlecellexperiment)
3785 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3787 `(("r-knitr" ,r-knitr)))
3788 (home-page "https://github.com/kdkorthauer/scDD")
3789 (synopsis "Mixture modeling of single-cell RNA-seq data")
3791 "This package implements a method to analyze single-cell RNA-seq data
3792 utilizing flexible Dirichlet Process mixture models. Genes with differential
3793 distributions of expression are classified into several interesting patterns
3794 of differences between two conditions. The package also includes functions
3795 for simulating data with these patterns from negative binomial
3797 (license license:gpl2)))
3799 (define-public r-scone
3806 (uri (bioconductor-uri "scone" version))
3809 "1lnyxcrw3kn5gi3n59dwdhkqps58cjxfknsjsj53qz5rv8iiqz73"))))
3810 (build-system r-build-system)
3812 `(("r-aroma-light" ,r-aroma-light)
3813 ("r-biocparallel" ,r-biocparallel)
3815 ("r-class" ,r-class)
3816 ("r-cluster" ,r-cluster)
3817 ("r-compositions" ,r-compositions)
3818 ("r-diptest" ,r-diptest)
3819 ("r-edger" ,r-edger)
3821 ("r-gplots" ,r-gplots)
3822 ("r-hexbin" ,r-hexbin)
3823 ("r-limma" ,r-limma)
3824 ("r-matrixstats" ,r-matrixstats)
3825 ("r-mixtools" ,r-mixtools)
3826 ("r-rarpack" ,r-rarpack)
3827 ("r-rcolorbrewer" ,r-rcolorbrewer)
3828 ("r-rhdf5" ,r-rhdf5)
3829 ("r-ruvseq" ,r-ruvseq)
3830 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3832 `(("r-knitr" ,r-knitr)))
3833 (home-page "https://bioconductor.org/packages/scone")
3834 (synopsis "Single cell overview of normalized expression data")
3836 "SCONE is an R package for comparing and ranking the performance of
3837 different normalization schemes for single-cell RNA-seq and other
3838 high-throughput analyses.")
3839 (license license:artistic2.0)))
3841 (define-public r-geoquery
3848 (uri (bioconductor-uri "GEOquery" version))
3851 "1jzhgnd404wkz978vbqzwbgixr7yk98c7s9q1fzlyax4f8l0cpi4"))))
3852 (properties `((upstream-name . "GEOquery")))
3853 (build-system r-build-system)
3855 `(("r-biobase" ,r-biobase)
3856 ("r-dplyr" ,r-dplyr)
3858 ("r-limma" ,r-limma)
3859 ("r-magrittr" ,r-magrittr)
3860 ("r-readr" ,r-readr)
3861 ("r-tidyr" ,r-tidyr)
3862 ("r-xml2" ,r-xml2)))
3864 `(("r-knitr" ,r-knitr)))
3865 (home-page "https://github.com/seandavi/GEOquery/")
3866 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
3868 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
3869 microarray data. Given the rich and varied nature of this resource, it is
3870 only natural to want to apply BioConductor tools to these data. GEOquery is
3871 the bridge between GEO and BioConductor.")
3872 (license license:gpl2)))
3874 (define-public r-illuminaio
3876 (name "r-illuminaio")
3881 (uri (bioconductor-uri "illuminaio" version))
3884 "1yqm2fqw5ka7qywbal3p7axlwm1r0wibsr33n5xjma1dl9pi8fay"))))
3885 (build-system r-build-system)
3887 `(("r-base64" ,r-base64)))
3888 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
3889 (synopsis "Parse Illumina microarray output files")
3891 "This package provides tools for parsing Illumina's microarray output
3892 files, including IDAT.")
3893 (license license:gpl2)))
3895 (define-public r-siggenes
3902 (uri (bioconductor-uri "siggenes" version))
3905 "08wi2i6pqx06v13533y3mpli5fb637h0xfwcwy67ya9j2ygypv7w"))))
3906 (build-system r-build-system)
3908 `(("r-biobase" ,r-biobase)
3909 ("r-multtest" ,r-multtest)
3910 ("r-scrime" ,r-scrime)))
3911 (home-page "https://bioconductor.org/packages/siggenes/")
3913 "Multiple testing using SAM and Efron's empirical Bayes approaches")
3915 "This package provides tools for the identification of differentially
3916 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
3917 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
3918 Bayes Analyses of Microarrays} (EBAM).")
3919 (license license:lgpl2.0+)))
3921 (define-public r-bumphunter
3923 (name "r-bumphunter")
3928 (uri (bioconductor-uri "bumphunter" version))
3931 "0hfl820kfxydv5kpgyly7sibv2sp6dqsmc78qm33n81w4z4j0mkk"))))
3932 (build-system r-build-system)
3934 `(("r-annotationdbi" ,r-annotationdbi)
3935 ("r-biocgenerics" ,r-biocgenerics)
3936 ("r-dorng" ,r-dorng)
3937 ("r-foreach" ,r-foreach)
3938 ("r-genomeinfodb" ,r-genomeinfodb)
3939 ("r-genomicfeatures" ,r-genomicfeatures)
3940 ("r-genomicranges" ,r-genomicranges)
3941 ("r-iranges" ,r-iranges)
3942 ("r-iterators" ,r-iterators)
3943 ("r-limma" ,r-limma)
3944 ("r-locfit" ,r-locfit)
3945 ("r-matrixstats" ,r-matrixstats)
3946 ("r-s4vectors" ,r-s4vectors)))
3947 (home-page "https://github.com/ririzarr/bumphunter")
3948 (synopsis "Find bumps in genomic data")
3950 "This package provides tools for finding bumps in genomic data in order
3951 to identify differentially methylated regions in epigenetic epidemiology
3953 (license license:artistic2.0)))
3955 (define-public r-minfi
3962 (uri (bioconductor-uri "minfi" version))
3965 "1x3ksp6syl54hds7wgm4p9yj4mznhhhhk20ijn3i2jc3k8xqcqfi"))))
3966 (build-system r-build-system)
3968 `(("r-beanplot" ,r-beanplot)
3969 ("r-biobase" ,r-biobase)
3970 ("r-biocgenerics" ,r-biocgenerics)
3971 ("r-biocparallel" ,r-biocparallel)
3972 ("r-biostrings" ,r-biostrings)
3973 ("r-bumphunter" ,r-bumphunter)
3974 ("r-data-table" ,r-data-table)
3975 ("r-delayedarray" ,r-delayedarray)
3976 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
3977 ("r-genefilter" ,r-genefilter)
3978 ("r-genomeinfodb" ,r-genomeinfodb)
3979 ("r-genomicranges" ,r-genomicranges)
3980 ("r-geoquery" ,r-geoquery)
3981 ("r-hdf5array" ,r-hdf5array)
3982 ("r-illuminaio" ,r-illuminaio)
3983 ("r-iranges" ,r-iranges)
3984 ("r-lattice" ,r-lattice)
3985 ("r-limma" ,r-limma)
3987 ("r-mclust" ,r-mclust)
3989 ("r-nor1mix" ,r-nor1mix)
3990 ("r-preprocesscore" ,r-preprocesscore)
3991 ("r-quadprog" ,r-quadprog)
3992 ("r-rcolorbrewer" ,r-rcolorbrewer)
3993 ("r-reshape" ,r-reshape)
3994 ("r-s4vectors" ,r-s4vectors)
3995 ("r-siggenes" ,r-siggenes)
3996 ("r-summarizedexperiment" ,r-summarizedexperiment)))
3998 `(("r-knitr" ,r-knitr)))
3999 (home-page "https://github.com/hansenlab/minfi")
4000 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
4002 "This package provides tools to analyze and visualize Illumina Infinium
4003 methylation arrays.")
4004 (license license:artistic2.0)))
4006 (define-public r-methylumi
4008 (name "r-methylumi")
4013 (uri (bioconductor-uri "methylumi" version))
4016 "00w5affxzirf6ffiznk33papwwvwsk2zgy6xvsx7iaf5kvnak2nh"))))
4017 (build-system r-build-system)
4019 `(("r-annotate" ,r-annotate)
4020 ("r-annotationdbi" ,r-annotationdbi)
4021 ("r-biobase" ,r-biobase)
4022 ("r-biocgenerics" ,r-biocgenerics)
4023 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
4024 ("r-genefilter" ,r-genefilter)
4025 ("r-genomeinfodb" ,r-genomeinfodb)
4026 ("r-genomicranges" ,r-genomicranges)
4027 ("r-ggplot2" ,r-ggplot2)
4028 ("r-illuminaio" ,r-illuminaio)
4029 ("r-iranges" ,r-iranges)
4030 ("r-lattice" ,r-lattice)
4031 ("r-matrixstats" ,r-matrixstats)
4032 ("r-minfi" ,r-minfi)
4033 ("r-reshape2" ,r-reshape2)
4034 ("r-s4vectors" ,r-s4vectors)
4035 ("r-scales" ,r-scales)
4036 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4038 `(("r-knitr" ,r-knitr)))
4039 (home-page "https://bioconductor.org/packages/methylumi")
4040 (synopsis "Handle Illumina methylation data")
4042 "This package provides classes for holding and manipulating Illumina
4043 methylation data. Based on eSet, it can contain MIAME information, sample
4044 information, feature information, and multiple matrices of data. An
4045 \"intelligent\" import function, methylumiR can read the Illumina text files
4046 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
4047 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
4048 background correction, and quality control features for GoldenGate, Infinium,
4049 and Infinium HD arrays are also included.")
4050 (license license:gpl2)))
4052 (define-public r-lumi
4059 (uri (bioconductor-uri "lumi" version))
4062 "19asap8vhm3g8hyvpr8l7mw071dsa1d95wx46lh8m6achffngqv3"))))
4063 (build-system r-build-system)
4065 `(("r-affy" ,r-affy)
4066 ("r-annotate" ,r-annotate)
4067 ("r-annotationdbi" ,r-annotationdbi)
4068 ("r-biobase" ,r-biobase)
4070 ("r-genomicfeatures" ,r-genomicfeatures)
4071 ("r-genomicranges" ,r-genomicranges)
4072 ("r-kernsmooth" ,r-kernsmooth)
4073 ("r-lattice" ,r-lattice)
4075 ("r-methylumi" ,r-methylumi)
4077 ("r-nleqslv" ,r-nleqslv)
4078 ("r-preprocesscore" ,r-preprocesscore)
4079 ("r-rsqlite" ,r-rsqlite)))
4080 (home-page "https://bioconductor.org/packages/lumi")
4081 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
4083 "The lumi package provides an integrated solution for the Illumina
4084 microarray data analysis. It includes functions of Illumina
4085 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
4086 variance stabilization, normalization and gene annotation at the probe level.
4087 It also includes the functions of processing Illumina methylation microarrays,
4088 especially Illumina Infinium methylation microarrays.")
4089 (license license:lgpl2.0+)))
4091 (define-public r-linnorm
4098 (uri (bioconductor-uri "Linnorm" version))
4101 "1is1kp5av01kqqph16xl7w1dqbyd0q85pgqfv9gqkk8m53635cz3"))))
4102 (properties `((upstream-name . "Linnorm")))
4103 (build-system r-build-system)
4105 `(("r-amap" ,r-amap)
4106 ("r-apcluster" ,r-apcluster)
4107 ("r-ellipse" ,r-ellipse)
4108 ("r-fastcluster" ,r-fastcluster)
4110 ("r-ggdendro" ,r-ggdendro)
4111 ("r-ggplot2" ,r-ggplot2)
4112 ("r-gmodels" ,r-gmodels)
4113 ("r-igraph" ,r-igraph)
4114 ("r-limma" ,r-limma)
4116 ("r-mclust" ,r-mclust)
4118 ("r-rcpparmadillo" ,r-rcpparmadillo)
4119 ("r-rtsne" ,r-rtsne)
4120 ("r-statmod" ,r-statmod)
4121 ("r-vegan" ,r-vegan)
4124 `(("r-knitr" ,r-knitr)))
4125 (home-page "http://www.jjwanglab.org/Linnorm/")
4126 (synopsis "Linear model and normality based transformation method")
4128 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
4129 count data or any large scale count data. It transforms such datasets for
4130 parametric tests. In addition to the transformtion function (@code{Linnorm}),
4131 the following pipelines are implemented:
4134 @item Library size/batch effect normalization (@code{Linnorm.Norm})
4135 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
4136 clustering or hierarchical clustering (@code{Linnorm.tSNE},
4137 @code{Linnorm.PCA}, @code{Linnorm.HClust})
4138 @item Differential expression analysis or differential peak detection using
4139 limma (@code{Linnorm.limma})
4140 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
4141 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
4142 @item Stable gene selection for scRNA-seq data; for users without or who do
4143 not want to rely on spike-in genes (@code{Linnorm.SGenes})
4144 @item Data imputation (@code{Linnorm.DataImput}).
4147 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
4148 @code{RnaXSim} function is included for simulating RNA-seq data for the
4149 evaluation of DEG analysis methods.")
4150 (license license:expat)))
4152 (define-public r-ioniser
4159 (uri (bioconductor-uri "IONiseR" version))
4162 "0cfa64d3qv881sa9d665rfki91jaz2spg0zfrb24m37948qzk1lx"))))
4163 (properties `((upstream-name . "IONiseR")))
4164 (build-system r-build-system)
4166 `(("r-biocgenerics" ,r-biocgenerics)
4167 ("r-biocparallel" ,r-biocparallel)
4168 ("r-biostrings" ,r-biostrings)
4169 ("r-bit64" ,r-bit64)
4170 ("r-dplyr" ,r-dplyr)
4171 ("r-ggplot2" ,r-ggplot2)
4172 ("r-magrittr" ,r-magrittr)
4173 ("r-rhdf5" ,r-rhdf5)
4174 ("r-shortread" ,r-shortread)
4175 ("r-stringr" ,r-stringr)
4176 ("r-tibble" ,r-tibble)
4177 ("r-tidyr" ,r-tidyr)
4178 ("r-xvector" ,r-xvector)))
4180 `(("r-knitr" ,r-knitr)))
4181 (home-page "https://bioconductor.org/packages/IONiseR/")
4182 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
4184 "IONiseR provides tools for the quality assessment of Oxford Nanopore
4185 MinION data. It extracts summary statistics from a set of fast5 files and can
4186 be used either before or after base calling. In addition to standard
4187 summaries of the read-types produced, it provides a number of plots for
4188 visualising metrics relative to experiment run time or spatially over the
4189 surface of a flowcell.")
4190 (license license:expat)))
4192 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
4193 (define-public r-mutoss
4200 (uri (cran-uri "mutoss" version))
4203 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
4204 (properties `((upstream-name . "mutoss")))
4205 (build-system r-build-system)
4207 `(("r-multcomp" ,r-multcomp)
4208 ("r-multtest" ,r-multtest)
4209 ("r-mvtnorm" ,r-mvtnorm)
4210 ("r-plotrix" ,r-plotrix)))
4211 (home-page "https://github.com/kornl/mutoss/")
4212 (synopsis "Unified multiple testing procedures")
4214 "This package is designed to ease the application and comparison of
4215 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
4216 are standardized and usable by the accompanying mutossGUI package.")
4217 ;; Any version of the GPL.
4218 (license (list license:gpl2+ license:gpl3+))))
4220 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
4221 ;; from Bioconductor, so we put it here.
4222 (define-public r-metap
4229 (uri (cran-uri "metap" version))
4232 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
4233 (build-system r-build-system)
4235 `(("r-lattice" ,r-lattice)
4236 ("r-mutoss" ,r-mutoss)
4237 ("r-rdpack" ,r-rdpack)
4238 ("r-tfisher" ,r-tfisher)))
4239 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4240 (synopsis "Meta-analysis of significance values")
4242 "The canonical way to perform meta-analysis involves using effect sizes.
4243 When they are not available this package provides a number of methods for
4244 meta-analysis of significance values including the methods of Edgington,
4245 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4246 published results; and a routine for graphical display.")
4247 (license license:gpl2)))
4249 (define-public r-triform
4256 (uri (bioconductor-uri "triform" version))
4259 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
4260 (build-system r-build-system)
4262 `(("r-biocgenerics" ,r-biocgenerics)
4263 ("r-iranges" ,r-iranges)
4264 ("r-yaml" ,r-yaml)))
4265 (home-page "https://bioconductor.org/packages/triform/")
4266 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
4268 "The Triform algorithm uses model-free statistics to identify peak-like
4269 distributions of TF ChIP sequencing reads, taking advantage of an improved
4270 peak definition in combination with known profile characteristics.")
4271 (license license:gpl2)))
4273 (define-public r-varianttools
4275 (name "r-varianttools")
4280 (uri (bioconductor-uri "VariantTools" version))
4283 "1im4g9p419mikkh4v585yf5f23d13chy67znk4g2mii2i1cd1c89"))))
4284 (properties `((upstream-name . "VariantTools")))
4285 (build-system r-build-system)
4287 `(("r-biobase" ,r-biobase)
4288 ("r-biocgenerics" ,r-biocgenerics)
4289 ("r-biocparallel" ,r-biocparallel)
4290 ("r-biostrings" ,r-biostrings)
4291 ("r-bsgenome" ,r-bsgenome)
4292 ("r-genomeinfodb" ,r-genomeinfodb)
4293 ("r-genomicfeatures" ,r-genomicfeatures)
4294 ("r-genomicranges" ,r-genomicranges)
4295 ("r-iranges" ,r-iranges)
4296 ("r-matrix" ,r-matrix)
4297 ("r-rsamtools" ,r-rsamtools)
4298 ("r-rtracklayer" ,r-rtracklayer)
4299 ("r-s4vectors" ,r-s4vectors)
4300 ("r-variantannotation" ,r-variantannotation)))
4301 (home-page "https://bioconductor.org/packages/VariantTools/")
4302 (synopsis "Tools for exploratory analysis of variant calls")
4304 "Explore, diagnose, and compare variant calls using filters. The
4305 VariantTools package supports a workflow for loading data, calling single
4306 sample variants and tumor-specific somatic mutations or other sample-specific
4307 variant types (e.g., RNA editing). Most of the functions operate on
4308 alignments (BAM files) or datasets of called variants. The user is expected
4309 to have already aligned the reads with a separate tool, e.g., GSNAP via
4311 (license license:artistic2.0)))
4313 (define-public r-heatplus
4320 (uri (bioconductor-uri "Heatplus" version))
4323 "0vp8y0242k6q07yjk4sg2w7mlk5pgzhjgqkxa79c5ypkyp095a8n"))))
4324 (properties `((upstream-name . "Heatplus")))
4325 (build-system r-build-system)
4327 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
4328 (home-page "https://github.com/alexploner/Heatplus")
4329 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
4331 "This package provides tools to display a rectangular heatmap (intensity
4332 plot) of a data matrix. By default, both samples (columns) and features (row)
4333 of the matrix are sorted according to a hierarchical clustering, and the
4334 corresponding dendrogram is plotted. Optionally, panels with additional
4335 information about samples and features can be added to the plot.")
4336 (license license:gpl2+)))
4338 (define-public r-gosemsim
4345 (uri (bioconductor-uri "GOSemSim" version))
4348 "1hk1626172scja2gr6axy98czblz0zljiqgqaknsv2xj6frhxcgs"))))
4349 (properties `((upstream-name . "GOSemSim")))
4350 (build-system r-build-system)
4352 `(("r-annotationdbi" ,r-annotationdbi)
4353 ("r-go-db" ,r-go-db)
4354 ("r-rcpp" ,r-rcpp)))
4356 `(("r-knitr" ,r-knitr)))
4357 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
4358 (synopsis "GO-terms semantic similarity measures")
4360 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
4361 quantitative ways to compute similarities between genes and gene groups, and
4362 have became important basis for many bioinformatics analysis approaches.
4363 GOSemSim is an R package for semantic similarity computation among GO terms,
4364 sets of GO terms, gene products and gene clusters.")
4365 (license license:artistic2.0)))
4367 (define-public r-anota
4374 (uri (bioconductor-uri "anota" version))
4377 "02s061q6dfw1czppqiklb0fz6q0mjyqgxg6926b2dpqpz8hv690x"))))
4378 (build-system r-build-system)
4380 `(("r-multtest" ,r-multtest)
4381 ("r-qvalue" ,r-qvalue)))
4382 (home-page "https://bioconductor.org/packages/anota/")
4383 (synopsis "Analysis of translational activity")
4385 "Genome wide studies of translational control is emerging as a tool to
4386 study various biological conditions. The output from such analysis is both
4387 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
4388 involved in translation (the actively translating mRNA level) for each mRNA.
4389 The standard analysis of such data strives towards identifying differential
4390 translational between two or more sample classes - i.e. differences in
4391 actively translated mRNA levels that are independent of underlying differences
4392 in cytosolic mRNA levels. This package allows for such analysis using partial
4393 variances and the random variance model. As 10s of thousands of mRNAs are
4394 analyzed in parallel the library performs a number of tests to assure that
4395 the data set is suitable for such analysis.")
4396 (license license:gpl3)))
4398 (define-public r-sigpathway
4400 (name "r-sigpathway")
4405 (uri (bioconductor-uri "sigPathway" version))
4408 "1fkw0ss471pllqxyjyif5lr35cr8sqpx31x0ccjp85lm3blws72l"))))
4409 (properties `((upstream-name . "sigPathway")))
4410 (build-system r-build-system)
4411 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
4412 (synopsis "Pathway analysis")
4414 "This package is used to conduct pathway analysis by calculating the NT_k
4415 and NE_k statistics in a statistical framework for determining whether a
4416 specified group of genes for a pathway has a coordinated association with a
4417 phenotype of interest.")
4418 (license license:gpl2)))
4420 (define-public r-fgsea
4427 (uri (bioconductor-uri "fgsea" version))
4430 "0jmkkayabx3m0lyyc2mxd4vdvv7gv7fbk1r884gplnf2zgsx068n"))))
4431 (build-system r-build-system)
4434 ("r-biocparallel" ,r-biocparallel)
4435 ("r-data-table" ,r-data-table)
4436 ("r-fastmatch" ,r-fastmatch)
4437 ("r-ggplot2" ,r-ggplot2)
4438 ("r-gridextra" ,r-gridextra)
4439 ("r-matrix" ,r-matrix)
4440 ("r-rcpp" ,r-rcpp)))
4442 `(("r-knitr" ,r-knitr)))
4443 (home-page "https://github.com/ctlab/fgsea/")
4444 (synopsis "Fast gene set enrichment analysis")
4446 "The package implements an algorithm for fast gene set enrichment
4447 analysis. Using the fast algorithm makes more permutations and gets
4448 more fine grained p-values, which allows using accurate standard approaches
4449 to multiple hypothesis correction.")
4450 (license license:expat)))
4452 (define-public r-dose
4459 (uri (bioconductor-uri "DOSE" version))
4462 "149hpf690jls5r5g84sh2hqs10qbqi94syhxfv8n2f800fk7lgy4"))))
4463 (properties `((upstream-name . "DOSE")))
4464 (build-system r-build-system)
4466 `(("r-annotationdbi" ,r-annotationdbi)
4467 ("r-biocparallel" ,r-biocparallel)
4468 ("r-do-db" ,r-do-db)
4469 ("r-fgsea" ,r-fgsea)
4470 ("r-ggplot2" ,r-ggplot2)
4471 ("r-gosemsim" ,r-gosemsim)
4472 ("r-qvalue" ,r-qvalue)
4473 ("r-reshape2" ,r-reshape2)))
4475 `(("r-knitr" ,r-knitr)))
4476 (home-page "https://guangchuangyu.github.io/software/DOSE/")
4477 (synopsis "Disease ontology semantic and enrichment analysis")
4479 "This package implements five methods proposed by Resnik, Schlicker,
4480 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
4481 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
4482 including hypergeometric model and gene set enrichment analysis are also
4483 implemented for discovering disease associations of high-throughput biological
4485 (license license:artistic2.0)))
4487 (define-public r-enrichplot
4489 (name "r-enrichplot")
4494 (uri (bioconductor-uri "enrichplot" version))
4497 "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv"))))
4498 (build-system r-build-system)
4500 `(("r-cowplot" ,r-cowplot)
4502 ("r-ggplot2" ,r-ggplot2)
4503 ("r-ggraph" ,r-ggraph)
4504 ("r-gosemsim" ,r-gosemsim)
4505 ("r-igraph" ,r-igraph)
4506 ("r-magrittr" ,r-magrittr)
4508 ("r-purrr" ,r-purrr)
4509 ("r-rcolorbrewer" ,r-rcolorbrewer)
4510 ("r-reshape2" ,r-reshape2)
4511 ("r-scatterpie" ,r-scatterpie)
4512 ("r-shadowtext" ,r-shadowtext)))
4514 `(("r-knitr" ,r-knitr)))
4515 (home-page "https://github.com/GuangchuangYu/enrichplot")
4516 (synopsis "Visualization of functional enrichment result")
4518 "The enrichplot package implements several visualization methods for
4519 interpreting functional enrichment results obtained from ORA or GSEA analyses.
4520 All the visualization methods are developed based on ggplot2 graphics.")
4521 (license license:artistic2.0)))
4523 (define-public r-clusterprofiler
4525 (name "r-clusterprofiler")
4530 (uri (bioconductor-uri "clusterProfiler" version))
4533 "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si"))))
4535 `((upstream-name . "clusterProfiler")))
4536 (build-system r-build-system)
4538 `(("r-annotationdbi" ,r-annotationdbi)
4540 ("r-downloader" ,r-downloader)
4541 ("r-dplyr" ,r-dplyr)
4542 ("r-enrichplot" ,r-enrichplot)
4543 ("r-go-db" ,r-go-db)
4544 ("r-gosemsim" ,r-gosemsim)
4545 ("r-magrittr" ,r-magrittr)
4547 ("r-qvalue" ,r-qvalue)
4548 ("r-rlang" ,r-rlang)
4549 ("r-rvcheck" ,r-rvcheck)
4550 ("r-tidyr" ,r-tidyr)))
4552 `(("r-knitr" ,r-knitr)))
4553 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
4554 (synopsis "Analysis and visualization of functional profiles for gene clusters")
4556 "This package implements methods to analyze and visualize functional
4557 profiles (GO and KEGG) of gene and gene clusters.")
4558 (license license:artistic2.0)))
4560 (define-public r-mlinterfaces
4562 (name "r-mlinterfaces")
4567 (uri (bioconductor-uri "MLInterfaces" version))
4570 "1j920h1657rc5agd1vrkzk126npfhw7pzr7p7gwg4i0h0wv25q3r"))))
4571 (properties `((upstream-name . "MLInterfaces")))
4572 (build-system r-build-system)
4574 `(("r-annotate" ,r-annotate)
4575 ("r-biobase" ,r-biobase)
4576 ("r-biocgenerics" ,r-biocgenerics)
4577 ("r-cluster" ,r-cluster)
4580 ("r-gdata" ,r-gdata)
4581 ("r-genefilter" ,r-genefilter)
4582 ("r-ggvis" ,r-ggvis)
4583 ("r-hwriter" ,r-hwriter)
4585 ("r-mlbench" ,r-mlbench)
4587 ("r-rcolorbrewer" ,r-rcolorbrewer)
4589 ("r-rpart" ,r-rpart)
4590 ("r-sfsmisc" ,r-sfsmisc)
4591 ("r-shiny" ,r-shiny)
4592 ("r-threejs" ,r-threejs)))
4593 (home-page "https://bioconductor.org/packages/MLInterfaces/")
4594 (synopsis "Interfaces to R machine learning procedures")
4596 "This package provides uniform interfaces to machine learning code for
4597 data in R and Bioconductor containers.")
4598 ;; Any version of the LGPL.
4599 (license license:lgpl2.1+)))
4601 (define-public r-annaffy
4608 (uri (bioconductor-uri "annaffy" version))
4611 "1szlr33lq98pd3kx6n9l07lhr93swbk6vjpvb2n9f7716k39mi4i"))))
4612 (build-system r-build-system)
4615 (modify-phases %standard-phases
4616 (add-after 'unpack 'remove-reference-to-non-free-data
4618 (substitute* "DESCRIPTION"
4622 `(("r-annotationdbi" ,r-annotationdbi)
4623 ("r-biobase" ,r-biobase)
4625 ("r-go-db" ,r-go-db)))
4626 (home-page "https://bioconductor.org/packages/annaffy/")
4627 (synopsis "Annotation tools for Affymetrix biological metadata")
4629 "This package provides functions for handling data from Bioconductor
4630 Affymetrix annotation data packages. It produces compact HTML and text
4631 reports including experimental data and URL links to many online databases.
4632 It allows searching of biological metadata using various criteria.")
4633 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
4634 ;; the LGPL 2.1 is included.
4635 (license license:lgpl2.1+)))
4637 (define-public r-a4core
4644 (uri (bioconductor-uri "a4Core" version))
4647 "13mzhn92kqpbn58zmh96f6frkm85sv9137mldfzaljf6snk0spg2"))))
4648 (properties `((upstream-name . "a4Core")))
4649 (build-system r-build-system)
4651 `(("r-biobase" ,r-biobase)
4652 ("r-glmnet" ,r-glmnet)))
4654 `(("r-knitr" ,r-knitr)))
4655 (home-page "https://bioconductor.org/packages/a4Core")
4656 (synopsis "Automated Affymetrix array analysis core package")
4658 "This is the core package for the automated analysis of Affymetrix
4660 (license license:gpl3)))
4662 (define-public r-a4classif
4664 (name "r-a4classif")
4669 (uri (bioconductor-uri "a4Classif" version))
4672 "03fln0x1am5fqhj4fpkx1yq58paqha086bhhr8az8j0vsq1r7wcz"))))
4673 (properties `((upstream-name . "a4Classif")))
4674 (build-system r-build-system)
4676 `(("r-a4core" ,r-a4core)
4677 ("r-a4preproc" ,r-a4preproc)
4678 ("r-biobase" ,r-biobase)
4679 ("r-glmnet" ,r-glmnet)
4682 ("r-varselrf" ,r-varselrf)))
4684 `(("r-knitr" ,r-knitr)))
4685 (home-page "https://bioconductor.org/packages/a4Classif/")
4686 (synopsis "Automated Affymetrix array analysis classification package")
4688 "This is the classification package for the automated analysis of
4689 Affymetrix arrays.")
4690 (license license:gpl3)))
4692 (define-public r-a4preproc
4694 (name "r-a4preproc")
4699 (uri (bioconductor-uri "a4Preproc" version))
4702 "1j8jhal83x1xpmsaw8iwv2r32i1ghzm6n0ipjk06yqa9f6zb7f7i"))))
4703 (properties `((upstream-name . "a4Preproc")))
4704 (build-system r-build-system)
4706 `(("r-biobase" ,r-biobase)
4707 ("r-biocgenerics" ,r-biocgenerics)))
4709 `(("r-knitr" ,r-knitr)))
4710 (home-page "https://bioconductor.org/packages/a4Preproc/")
4711 (synopsis "Automated Affymetrix array analysis preprocessing package")
4713 "This is a package for the automated analysis of Affymetrix arrays. It
4714 is used for preprocessing the arrays.")
4715 (license license:gpl3)))
4717 (define-public r-a4reporting
4719 (name "r-a4reporting")
4724 (uri (bioconductor-uri "a4Reporting" version))
4727 "1jx4ym3hyix8gwr8d2r38w1wj7siv6ynzhwanczcjf1naws3dqpy"))))
4728 (properties `((upstream-name . "a4Reporting")))
4729 (build-system r-build-system)
4731 `(("r-xtable" ,r-xtable)))
4733 `(("r-knitr" ,r-knitr)))
4734 (home-page "https://bioconductor.org/packages/a4Reporting/")
4735 (synopsis "Automated Affymetrix array analysis reporting package")
4737 "This is a package for the automated analysis of Affymetrix arrays. It
4738 provides reporting features.")
4739 (license license:gpl3)))
4741 (define-public r-a4base
4748 (uri (bioconductor-uri "a4Base" version))
4751 "0bqagjmg3yjmdzxv4j7685jjhgb261pq60b5qkfffr1lfnz27lsp"))))
4752 (properties `((upstream-name . "a4Base")))
4753 (build-system r-build-system)
4755 `(("r-a4core" ,r-a4core)
4756 ("r-a4preproc" ,r-a4preproc)
4757 ("r-annaffy" ,r-annaffy)
4758 ("r-biobase" ,r-biobase)
4759 ("r-genefilter" ,r-genefilter)
4760 ("r-glmnet" ,r-glmnet)
4761 ("r-gplots" ,r-gplots)
4762 ("r-limma" ,r-limma)
4764 ("r-multtest" ,r-multtest)))
4765 (home-page "https://bioconductor.org/packages/a4Base/")
4766 (synopsis "Automated Affymetrix array analysis base package")
4768 "This package provides basic features for the automated analysis of
4769 Affymetrix arrays.")
4770 (license license:gpl3)))
4779 (uri (bioconductor-uri "a4" version))
4782 "12q09dhxjl7yrd5m2y7a03kv5614dp144ajmskp5q9x2gvz30f79"))))
4783 (build-system r-build-system)
4785 `(("r-a4base" ,r-a4base)
4786 ("r-a4classif" ,r-a4classif)
4787 ("r-a4core" ,r-a4core)
4788 ("r-a4preproc" ,r-a4preproc)
4789 ("r-a4reporting" ,r-a4reporting)))
4790 (home-page "https://bioconductor.org/packages/a4/")
4791 (synopsis "Automated Affymetrix array analysis umbrella package")
4793 "This package provides a software suite for the automated analysis of
4794 Affymetrix arrays.")
4795 (license license:gpl3)))
4797 (define-public r-abseqr
4804 (uri (bioconductor-uri "abseqR" version))
4807 "0lh7kcsp3yb3s8s8j6w9k1by8i16q7r2a49z8y1xjmkcb2klsi3f"))))
4808 (properties `((upstream-name . "abseqR")))
4809 (build-system r-build-system)
4811 `(("pandoc" ,pandoc)))
4813 `(("r-biocparallel" ,r-biocparallel)
4814 ("r-biocstyle" ,r-biocstyle)
4815 ("r-circlize" ,r-circlize)
4816 ("r-flexdashboard" ,r-flexdashboard)
4817 ("r-ggcorrplot" ,r-ggcorrplot)
4818 ("r-ggdendro" ,r-ggdendro)
4819 ("r-ggplot2" ,r-ggplot2)
4820 ("r-gridextra" ,r-gridextra)
4821 ("r-knitr" ,r-knitr)
4822 ("r-plotly" ,r-plotly)
4825 ("r-rcolorbrewer" ,r-rcolorbrewer)
4826 ("r-reshape2" ,r-reshape2)
4827 ("r-rmarkdown" ,r-rmarkdown)
4828 ("r-stringr" ,r-stringr)
4829 ("r-vegan" ,r-vegan)
4830 ("r-venndiagram" ,r-venndiagram)))
4832 `(("r-knitr" ,r-knitr)))
4833 (home-page "https://github.com/malhamdoosh/abseqR")
4834 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
4836 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
4837 sequencing datasets generated from antibody libraries and abseqR is one of its
4838 packages. AbseqR empowers the users of abseqPy with plotting and reporting
4839 capabilities and allows them to generate interactive HTML reports for the
4840 convenience of viewing and sharing with other researchers. Additionally,
4841 abseqR extends abseqPy to compare multiple repertoire analyses and perform
4842 further downstream analysis on its output.")
4843 (license license:gpl3)))
4845 (define-public r-bacon
4852 (uri (bioconductor-uri "bacon" version))
4855 "0cv4zhs075mz8c5gdwhr45v14fb1lyi3rlwjfqyz15dmmnzlxw47"))))
4856 (build-system r-build-system)
4858 `(("r-biocparallel" ,r-biocparallel)
4859 ("r-ellipse" ,r-ellipse)
4860 ("r-ggplot2" ,r-ggplot2)))
4862 `(("r-knitr" ,r-knitr)))
4863 (home-page "https://bioconductor.org/packages/bacon/")
4864 (synopsis "Controlling bias and inflation in association studies")
4866 "Bacon can be used to remove inflation and bias often observed in
4867 epigenome- and transcriptome-wide association studies. To this end bacon
4868 constructs an empirical null distribution using a Gibbs Sampling algorithm by
4869 fitting a three-component normal mixture on z-scores.")
4870 (license license:gpl2+)))
4872 (define-public r-rgadem
4879 (uri (bioconductor-uri "rGADEM" version))
4882 "0x13glgkcnjg4qsn0v0qgzy6bgmghqpvgwfww2ha641p0c5i9qzw"))))
4883 (properties `((upstream-name . "rGADEM")))
4884 (build-system r-build-system)
4886 `(("r-biostrings" ,r-biostrings)
4887 ("r-bsgenome" ,r-bsgenome)
4888 ("r-genomicranges" ,r-genomicranges)
4889 ("r-iranges" ,r-iranges)
4890 ("r-seqlogo" ,r-seqlogo)))
4891 (home-page "https://bioconductor.org/packages/rGADEM/")
4892 (synopsis "De novo sequence motif discovery")
4894 "rGADEM is an efficient de novo motif discovery tool for large-scale
4895 genomic sequence data.")
4896 (license license:artistic2.0)))
4898 (define-public r-motiv
4905 (uri (bioconductor-uri "MotIV" version))
4908 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
4909 (properties `((upstream-name . "MotIV")))
4910 (build-system r-build-system)
4914 `(("r-biocgenerics" ,r-biocgenerics)
4915 ("r-biostrings" ,r-biostrings)
4916 ("r-genomicranges" ,r-genomicranges)
4917 ("r-iranges" ,r-iranges)
4918 ("r-lattice" ,r-lattice)
4919 ("r-rgadem" ,r-rgadem)
4920 ("r-s4vectors" ,r-s4vectors)))
4921 (home-page "https://bioconductor.org/packages/MotIV/")
4922 (synopsis "Motif identification and validation")
4924 "This package is used for the identification and validation of sequence
4925 motifs. It makes use of STAMP for comparing a set of motifs to a given
4926 database (e.g. JASPAR). It can also be used to visualize motifs, motif
4927 distributions, modules and filter motifs.")
4928 (license license:gpl2)))
4930 (define-public r-motifdb
4936 (uri (bioconductor-uri "MotifDb" version))
4938 (base32 "0gfk1dgw7gd2y4cnmfdzpzjqkvvikcwx20h0fp7aiq8f0zfwlav5"))))
4939 (properties `((upstream-name . "MotifDb")))
4940 (build-system r-build-system)
4942 `(("r-biocgenerics" ,r-biocgenerics)
4943 ("r-biostrings" ,r-biostrings)
4944 ("r-genomicranges" ,r-genomicranges)
4945 ("r-iranges" ,r-iranges)
4946 ("r-rtracklayer" ,r-rtracklayer)
4947 ("r-s4vectors" ,r-s4vectors)
4948 ("r-splitstackshape" ,r-splitstackshape)))
4950 `(("r-knitr" ,r-knitr)))
4951 (home-page "https://www.bioconductor.org/packages/MotifDb/")
4952 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
4953 (description "This package provides more than 2000 annotated position
4954 frequency matrices from nine public sources, for multiple organisms.")
4955 (license license:artistic2.0)))
4957 (define-public r-motifbreakr
4959 (name "r-motifbreakr")
4963 (uri (bioconductor-uri "motifbreakR" version))
4965 (base32 "0nni6i7h51kz0ch8ls9c9jzd7fjmc9wsavp11hx6w6bmhnh3k4n7"))))
4966 (properties `((upstream-name . "motifbreakR")))
4967 (build-system r-build-system)
4969 `(("r-biocgenerics" ,r-biocgenerics)
4970 ("r-biocparallel" ,r-biocparallel)
4971 ("r-biostrings" ,r-biostrings)
4972 ("r-bsgenome" ,r-bsgenome)
4973 ("r-genomeinfodb" ,r-genomeinfodb)
4974 ("r-genomicranges" ,r-genomicranges)
4975 ("r-grimport" ,r-grimport)
4977 ("r-iranges" ,r-iranges)
4978 ("r-matrixstats" ,r-matrixstats)
4979 ("r-motifdb" ,r-motifdb)
4980 ("r-motifstack" ,r-motifstack)
4981 ("r-rtracklayer" ,r-rtracklayer)
4982 ("r-s4vectors" ,r-s4vectors)
4983 ("r-stringr" ,r-stringr)
4984 ("r-summarizedexperiment" ,r-summarizedexperiment)
4985 ("r-tfmpvalue" ,r-tfmpvalue)
4986 ("r-variantannotation" ,r-variantannotation)))
4988 `(("r-knitr" ,r-knitr)))
4989 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
4990 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
4991 (description "This package allows biologists to judge in the first place
4992 whether the sequence surrounding the polymorphism is a good match, and in
4993 the second place how much information is gained or lost in one allele of
4994 the polymorphism relative to another. This package gives a choice of
4995 algorithms for interrogation of genomes with motifs from public sources:
4997 @item a weighted-sum probability matrix;
4998 @item log-probabilities;
4999 @item weighted by relative entropy.
5002 This package can predict effects for novel or previously described variants in
5003 public databases, making it suitable for tasks beyond the scope of its original
5004 design. Lastly, it can be used to interrogate any genome curated within
5006 (license license:gpl2+)))
5008 (define-public r-motifstack
5010 (name "r-motifstack")
5015 (uri (bioconductor-uri "motifStack" version))
5018 "1psqpdbgbad31bd8hg5bl62qi5s9rl75nzm85igfpxar3zwwxjlb"))))
5019 (properties `((upstream-name . "motifStack")))
5020 (build-system r-build-system)
5022 `(("r-ade4" ,r-ade4)
5023 ("r-biostrings" ,r-biostrings)
5024 ("r-ggplot2" ,r-ggplot2)
5025 ("r-htmlwidgets" ,r-htmlwidgets)
5028 `(("r-knitr" ,r-knitr)))
5029 (home-page "https://bioconductor.org/packages/motifStack/")
5030 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
5032 "The motifStack package is designed for graphic representation of
5033 multiple motifs with different similarity scores. It works with both DNA/RNA
5034 sequence motifs and amino acid sequence motifs. In addition, it provides the
5035 flexibility for users to customize the graphic parameters such as the font
5036 type and symbol colors.")
5037 (license license:gpl2+)))
5039 (define-public r-genomicscores
5041 (name "r-genomicscores")
5046 (uri (bioconductor-uri "GenomicScores" version))
5049 "1492xirsgag2dsr6ys9wm3a65sq826p9hcdg3b4dm1wbxgdfx6jr"))))
5050 (properties `((upstream-name . "GenomicScores")))
5051 (build-system r-build-system)
5053 `(("r-annotationhub" ,r-annotationhub)
5054 ("r-biobase" ,r-biobase)
5055 ("r-biocfilecache" ,r-biocfilecache)
5056 ("r-biocgenerics" ,r-biocgenerics)
5057 ("r-biocmanager" ,r-biocmanager)
5058 ("r-biostrings" ,r-biostrings)
5059 ("r-delayedarray" ,r-delayedarray)
5060 ("r-genomeinfodb" ,r-genomeinfodb)
5061 ("r-genomicranges" ,r-genomicranges)
5062 ("r-hdf5array" ,r-hdf5array)
5063 ("r-iranges" ,r-iranges)
5064 ("r-rhdf5" ,r-rhdf5)
5065 ("r-s4vectors" ,r-s4vectors)
5068 `(("r-knitr" ,r-knitr)))
5069 (home-page "https://github.com/rcastelo/GenomicScores/")
5070 (synopsis "Work with genome-wide position-specific scores")
5072 "This package provides infrastructure to store and access genome-wide
5073 position-specific scores within R and Bioconductor.")
5074 (license license:artistic2.0)))
5076 (define-public r-atacseqqc
5078 (name "r-atacseqqc")
5083 (uri (bioconductor-uri "ATACseqQC" version))
5086 "04sn0zl4m60i5jvqz5rmhc4qwcgrhk6rhznrygmm93k9v363mbn9"))))
5087 (properties `((upstream-name . "ATACseqQC")))
5088 (build-system r-build-system)
5090 `(("r-biocgenerics" ,r-biocgenerics)
5091 ("r-biostrings" ,r-biostrings)
5092 ("r-bsgenome" ,r-bsgenome)
5093 ("r-chippeakanno" ,r-chippeakanno)
5094 ("r-edger" ,r-edger)
5095 ("r-genomeinfodb" ,r-genomeinfodb)
5096 ("r-genomicalignments" ,r-genomicalignments)
5097 ("r-genomicranges" ,r-genomicranges)
5098 ("r-genomicscores" ,r-genomicscores)
5099 ("r-iranges" ,r-iranges)
5100 ("r-kernsmooth" ,r-kernsmooth)
5101 ("r-limma" ,r-limma)
5102 ("r-motifstack" ,r-motifstack)
5103 ("r-preseqr" ,r-preseqr)
5104 ("r-randomforest" ,r-randomforest)
5105 ("r-rsamtools" ,r-rsamtools)
5106 ("r-rtracklayer" ,r-rtracklayer)
5107 ("r-s4vectors" ,r-s4vectors)))
5109 `(("r-knitr" ,r-knitr)))
5110 (home-page "https://bioconductor.org/packages/ATACseqQC/")
5111 (synopsis "ATAC-seq quality control")
5113 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
5114 sequencing, is a rapid and sensitive method for chromatin accessibility
5115 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
5116 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
5117 assess whether their ATAC-seq experiment is successful. It includes
5118 diagnostic plots of fragment size distribution, proportion of mitochondria
5119 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
5121 (license license:gpl2+)))
5123 (define-public r-gofuncr
5130 (uri (bioconductor-uri "GOfuncR" version))
5133 "1ah4v2jj508wjsmrncw58wjq2cyris7bnzfw6kr7jp9n4dvn33mq"))))
5134 (properties `((upstream-name . "GOfuncR")))
5135 (build-system r-build-system)
5137 `(("r-annotationdbi" ,r-annotationdbi)
5138 ("r-genomicranges" ,r-genomicranges)
5139 ("r-gtools" ,r-gtools)
5140 ("r-iranges" ,r-iranges)
5141 ("r-mapplots" ,r-mapplots)
5143 ("r-vioplot" ,r-vioplot)))
5145 `(("r-knitr" ,r-knitr)))
5146 (home-page "https://bioconductor.org/packages/GOfuncR/")
5147 (synopsis "Gene ontology enrichment using FUNC")
5149 "GOfuncR performs a gene ontology enrichment analysis based on the
5150 ontology enrichment software FUNC. GO-annotations are obtained from
5151 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
5152 included in the package and updated regularly. GOfuncR provides the standard
5153 candidate vs background enrichment analysis using the hypergeometric test, as
5154 well as three additional tests:
5157 @item the Wilcoxon rank-sum test that is used when genes are ranked,
5158 @item a binomial test that is used when genes are associated with two counts,
5160 @item a Chi-square or Fisher's exact test that is used in cases when genes are
5161 associated with four counts.
5164 To correct for multiple testing and interdependency of the tests, family-wise
5165 error rates are computed based on random permutations of the gene-associated
5166 variables. GOfuncR also provides tools for exploring the ontology graph and
5167 the annotations, and options to take gene-length or spatial clustering of
5168 genes into account. It is also possible to provide custom gene coordinates,
5169 annotations and ontologies.")
5170 (license license:gpl2+)))
5172 (define-public r-abaenrichment
5174 (name "r-abaenrichment")
5179 (uri (bioconductor-uri "ABAEnrichment" version))
5182 "0i0214ap9f6lnyawdgcdsds6g3g9qqji3wbn6ln6rs698gjs9w9c"))))
5183 (properties `((upstream-name . "ABAEnrichment")))
5184 (build-system r-build-system)
5186 `(("r-abadata" ,r-abadata)
5187 ("r-data-table" ,r-data-table)
5188 ("r-gofuncr" ,r-gofuncr)
5189 ("r-gplots" ,r-gplots)
5190 ("r-gtools" ,r-gtools)
5191 ("r-rcpp" ,r-rcpp)))
5193 `(("r-knitr" ,r-knitr)))
5194 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
5195 (synopsis "Gene expression enrichment in human brain regions")
5197 "The package ABAEnrichment is designed to test for enrichment of user
5198 defined candidate genes in the set of expressed genes in different human brain
5199 regions. The core function @code{aba_enrich} integrates the expression of the
5200 candidate gene set (averaged across donors) and the structural information of
5201 the brain using an ontology, both provided by the Allen Brain Atlas project.")
5202 (license license:gpl2+)))
5204 (define-public r-annotationfuncs
5206 (name "r-annotationfuncs")
5211 (uri (bioconductor-uri "AnnotationFuncs" version))
5214 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
5216 `((upstream-name . "AnnotationFuncs")))
5217 (build-system r-build-system)
5219 `(("r-annotationdbi" ,r-annotationdbi)
5221 (home-page "https://www.iysik.com/r/annotationfuncs")
5222 (synopsis "Annotation translation functions")
5224 "This package provides functions for handling translating between
5225 different identifieres using the Biocore Data Team data-packages (e.g.
5226 @code{org.Bt.eg.db}).")
5227 (license license:gpl2)))
5229 (define-public r-annotationtools
5231 (name "r-annotationtools")
5236 (uri (bioconductor-uri "annotationTools" version))
5239 "1q3c30hqxjgar3gm8d7h4rw3m7cgc11cgv9q0fwv5abj075cj224"))))
5241 `((upstream-name . "annotationTools")))
5242 (build-system r-build-system)
5243 (propagated-inputs `(("r-biobase" ,r-biobase)))
5244 (home-page "https://bioconductor.org/packages/annotationTools/")
5245 (synopsis "Annotate microarrays and perform gene expression analyses")
5247 "This package provides functions to annotate microarrays, find orthologs,
5248 and integrate heterogeneous gene expression profiles using annotation and
5249 other molecular biology information available as flat file database (plain
5251 ;; Any version of the GPL.
5252 (license (list license:gpl2+))))
5254 (define-public r-allelicimbalance
5256 (name "r-allelicimbalance")
5261 (uri (bioconductor-uri "AllelicImbalance" version))
5264 "1hk08kwxjlg2jb59bwv9fbc446pyf6knkscfj757nl6yjf11akbl"))))
5266 `((upstream-name . "AllelicImbalance")))
5267 (build-system r-build-system)
5269 `(("r-annotationdbi" ,r-annotationdbi)
5270 ("r-biocgenerics" ,r-biocgenerics)
5271 ("r-biostrings" ,r-biostrings)
5272 ("r-bsgenome" ,r-bsgenome)
5273 ("r-genomeinfodb" ,r-genomeinfodb)
5274 ("r-genomicalignments" ,r-genomicalignments)
5275 ("r-genomicfeatures" ,r-genomicfeatures)
5276 ("r-genomicranges" ,r-genomicranges)
5277 ("r-gridextra" ,r-gridextra)
5279 ("r-iranges" ,r-iranges)
5280 ("r-lattice" ,r-lattice)
5281 ("r-latticeextra" ,r-latticeextra)
5283 ("r-rsamtools" ,r-rsamtools)
5284 ("r-s4vectors" ,r-s4vectors)
5285 ("r-seqinr" ,r-seqinr)
5286 ("r-summarizedexperiment" ,r-summarizedexperiment)
5287 ("r-variantannotation" ,r-variantannotation)))
5289 `(("r-knitr" ,r-knitr)))
5290 (home-page "https://github.com/pappewaio/AllelicImbalance")
5291 (synopsis "Investigate allele-specific expression")
5293 "This package provides a framework for allele-specific expression
5294 investigation using RNA-seq data.")
5295 (license license:gpl3)))
5297 (define-public r-aucell
5304 (uri (bioconductor-uri "AUCell" version))
5307 "0ibsf3nid27hipr03z7phh0yzwfj8bqza6n6g7wfghpls4l12ipx"))))
5308 (properties `((upstream-name . "AUCell")))
5309 (build-system r-build-system)
5311 `(("r-biocgenerics" ,r-biocgenerics)
5312 ("r-data-table" ,r-data-table)
5313 ("r-gseabase" ,r-gseabase)
5314 ("r-mixtools" ,r-mixtools)
5315 ("r-r-utils" ,r-r-utils)
5316 ("r-s4vectors" ,r-s4vectors)
5317 ("r-shiny" ,r-shiny)
5318 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5320 `(("r-knitr" ,r-knitr)))
5321 (home-page "https://bioconductor.org/packages/AUCell/")
5322 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
5324 "AUCell identifies cells with active gene sets (e.g. signatures,
5325 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
5326 Under the Curve} (AUC) to calculate whether a critical subset of the input
5327 gene set is enriched within the expressed genes for each cell. The
5328 distribution of AUC scores across all the cells allows exploring the relative
5329 expression of the signature. Since the scoring method is ranking-based,
5330 AUCell is independent of the gene expression units and the normalization
5331 procedure. In addition, since the cells are evaluated individually, it can
5332 easily be applied to bigger datasets, subsetting the expression matrix if
5334 (license license:gpl3)))
5336 (define-public r-ebimage
5343 (uri (bioconductor-uri "EBImage" version))
5346 "0qi8bbix5bjahs73ljhfvidlbj8hz5m5j0sb9cjxlngnnldbh4ww"))))
5347 (properties `((upstream-name . "EBImage")))
5348 (build-system r-build-system)
5350 `(("r-abind" ,r-abind)
5351 ("r-biocgenerics" ,r-biocgenerics)
5352 ("r-fftwtools" ,r-fftwtools)
5353 ("r-htmltools" ,r-htmltools)
5354 ("r-htmlwidgets" ,r-htmlwidgets)
5356 ("r-locfit" ,r-locfit)
5358 ("r-rcurl" ,r-rcurl)
5359 ("r-tiff" ,r-tiff)))
5361 `(("r-knitr" ,r-knitr))) ; for vignettes
5362 (home-page "https://github.com/aoles/EBImage")
5363 (synopsis "Image processing and analysis toolbox for R")
5365 "EBImage provides general purpose functionality for image processing and
5366 analysis. In the context of (high-throughput) microscopy-based cellular
5367 assays, EBImage offers tools to segment cells and extract quantitative
5368 cellular descriptors. This allows the automation of such tasks using the R
5369 programming language and facilitates the use of other tools in the R
5370 environment for signal processing, statistical modeling, machine learning and
5371 visualization with image data.")
5372 ;; Any version of the LGPL.
5373 (license license:lgpl2.1+)))
5375 (define-public r-yamss
5382 (uri (bioconductor-uri "yamss" version))
5385 "0cxzn7j9apjcabbvvii16kn4whwd9khcyz867w5ag3zdxwvg7l7w"))))
5386 (build-system r-build-system)
5388 `(("r-biocgenerics" ,r-biocgenerics)
5389 ("r-data-table" ,r-data-table)
5390 ("r-ebimage" ,r-ebimage)
5391 ("r-iranges" ,r-iranges)
5392 ("r-limma" ,r-limma)
5393 ("r-matrix" ,r-matrix)
5395 ("r-s4vectors" ,r-s4vectors)
5396 ("r-summarizedexperiment"
5397 ,r-summarizedexperiment)))
5399 `(("r-knitr" ,r-knitr)))
5400 (home-page "https://github.com/hansenlab/yamss")
5401 (synopsis "Tools for high-throughput metabolomics")
5403 "This package provides tools to analyze and visualize high-throughput
5404 metabolomics data acquired using chromatography-mass spectrometry. These tools
5405 preprocess data in a way that enables reliable and powerful differential
5407 (license license:artistic2.0)))
5409 (define-public r-gtrellis
5416 (uri (bioconductor-uri "gtrellis" version))
5419 "14mpavkxlp9d1kccwi4b9hi7x8md5j4s1g17ivqsj38lxqjvg5gw"))))
5420 (build-system r-build-system)
5422 `(("r-circlize" ,r-circlize)
5423 ("r-genomicranges" ,r-genomicranges)
5424 ("r-getoptlong" ,r-getoptlong)
5425 ("r-iranges" ,r-iranges)))
5427 `(("r-knitr" ,r-knitr)))
5428 (home-page "https://github.com/jokergoo/gtrellis")
5429 (synopsis "Genome level Trellis layout")
5431 "Genome level Trellis graph visualizes genomic data conditioned by
5432 genomic categories (e.g. chromosomes). For each genomic category, multiple
5433 dimensional data which are represented as tracks describe different features
5434 from different aspects. This package provides high flexibility to arrange
5435 genomic categories and to add self-defined graphics in the plot.")
5436 (license license:expat)))
5438 (define-public r-somaticsignatures
5440 (name "r-somaticsignatures")
5445 (uri (bioconductor-uri "SomaticSignatures" version))
5448 "1pwf9ws0klcij27w22p0nh924yp5h2jsidp54ppp7mnx08iv0801"))))
5450 `((upstream-name . "SomaticSignatures")))
5451 (build-system r-build-system)
5453 `(("r-biobase" ,r-biobase)
5454 ("r-biostrings" ,r-biostrings)
5455 ("r-genomeinfodb" ,r-genomeinfodb)
5456 ("r-genomicranges" ,r-genomicranges)
5457 ("r-ggbio" ,r-ggbio)
5458 ("r-ggplot2" ,r-ggplot2)
5459 ("r-iranges" ,r-iranges)
5461 ("r-pcamethods" ,r-pcamethods)
5462 ("r-proxy" ,r-proxy)
5463 ("r-reshape2" ,r-reshape2)
5464 ("r-s4vectors" ,r-s4vectors)
5465 ("r-variantannotation" ,r-variantannotation)))
5467 `(("r-knitr" ,r-knitr)))
5468 (home-page "https://github.com/juliangehring/SomaticSignatures")
5469 (synopsis "Somatic signatures")
5471 "This package identifies mutational signatures of @dfn{single nucleotide
5472 variants} (SNVs). It provides a infrastructure related to the methodology
5473 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
5474 decomposition algorithms.")
5475 (license license:expat)))
5477 (define-public r-yapsa
5484 (uri (bioconductor-uri "YAPSA" version))
5487 "1vwccrp01p8i42axbaz1bqq173la18ldrzmrjawr5nkjjkvddbpb"))))
5488 (properties `((upstream-name . "YAPSA")))
5489 (build-system r-build-system)
5491 `(("r-biostrings" ,r-biostrings)
5492 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5493 ("r-circlize" ,r-circlize)
5494 ("r-complexheatmap" ,r-complexheatmap)
5495 ("r-corrplot" ,r-corrplot)
5496 ("r-dendextend" ,r-dendextend)
5497 ("r-doparallel" ,r-doparallel)
5498 ("r-dplyr" ,r-dplyr)
5499 ("r-genomeinfodb" ,r-genomeinfodb)
5500 ("r-genomicranges" ,r-genomicranges)
5501 ("r-getoptlong" ,r-getoptlong)
5502 ("r-ggbeeswarm" ,r-ggbeeswarm)
5503 ("r-ggplot2" ,r-ggplot2)
5504 ("r-gridextra" ,r-gridextra)
5505 ("r-gtrellis" ,r-gtrellis)
5506 ("r-keggrest" ,r-keggrest)
5507 ("r-limsolve" ,r-limsolve)
5508 ("r-magrittr" ,r-magrittr)
5509 ("r-pmcmr" ,r-pmcmr)
5510 ("r-pracma" ,r-pracma)
5511 ("r-reshape2" ,r-reshape2)
5512 ("r-somaticsignatures" ,r-somaticsignatures)
5513 ("r-variantannotation" ,r-variantannotation)))
5515 `(("r-knitr" ,r-knitr)))
5516 (home-page "https://bioconductor.org/packages/YAPSA/")
5517 (synopsis "Yet another package for signature analysis")
5519 "This package provides functions and routines useful in the analysis of
5520 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
5521 functions to perform a signature analysis with known signatures and a
5522 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
5524 (license license:gpl3)))
5526 (define-public r-gcrma
5533 (uri (bioconductor-uri "gcrma" version))
5536 "1v1x13iwcv6c9x7r1iz2598rwlyzic67jbqcajg24ib6lcfn9f00"))))
5537 (build-system r-build-system)
5539 `(("r-affy" ,r-affy)
5540 ("r-affyio" ,r-affyio)
5541 ("r-biobase" ,r-biobase)
5542 ("r-biocmanager" ,r-biocmanager)
5543 ("r-biostrings" ,r-biostrings)
5544 ("r-xvector" ,r-xvector)))
5545 (home-page "https://bioconductor.org/packages/gcrma/")
5546 (synopsis "Background adjustment using sequence information")
5548 "Gcrma adjusts for background intensities in Affymetrix array data which
5549 include optical noise and @dfn{non-specific binding} (NSB). The main function
5550 @code{gcrma} converts background adjusted probe intensities to expression
5551 measures using the same normalization and summarization methods as a
5552 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
5553 to estimate probe affinity to NSB. The sequence information is summarized in
5554 a more complex way than the simple GC content. Instead, the base types (A, T,
5555 G or C) at each position along the probe determine the affinity of each probe.
5556 The parameters of the position-specific base contributions to the probe
5557 affinity is estimated in an NSB experiment in which only NSB but no
5558 gene-specific binding is expected.")
5559 ;; Any version of the LGPL
5560 (license license:lgpl2.1+)))
5562 (define-public r-simpleaffy
5564 (name "r-simpleaffy")
5569 (uri (bioconductor-uri "simpleaffy" version))
5572 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
5573 (build-system r-build-system)
5575 `(("r-affy" ,r-affy)
5576 ("r-biobase" ,r-biobase)
5577 ("r-biocgenerics" ,r-biocgenerics)
5578 ("r-gcrma" ,r-gcrma)
5579 ("r-genefilter" ,r-genefilter)))
5580 (home-page "https://bioconductor.org/packages/simpleaffy/")
5581 (synopsis "Very simple high level analysis of Affymetrix data")
5583 "This package provides high level functions for reading Affy @file{.CEL}
5584 files, phenotypic data, and then computing simple things with it, such as
5585 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
5586 library. It also has some basic scatter plot functions and mechanisms for
5587 generating high resolution journal figures.")
5588 (license license:gpl2+)))
5590 (define-public r-yaqcaffy
5597 (uri (bioconductor-uri "yaqcaffy" version))
5600 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
5601 (build-system r-build-system)
5603 `(("r-simpleaffy" ,r-simpleaffy)))
5604 (home-page "https://bioconductor.org/packages/yaqcaffy/")
5605 (synopsis "Affymetrix quality control and reproducibility analysis")
5607 "This is a package that can be used for quality control of Affymetrix
5608 GeneChip expression data and reproducibility analysis of human whole genome
5609 chips with the MAQC reference datasets.")
5610 (license license:artistic2.0)))
5612 (define-public r-quantro
5619 (uri (bioconductor-uri "quantro" version))
5622 "1mq4hda73idkq0lkfrhcmiz4kkalfn47dh3i75br5fi33mdgc0k2"))))
5623 (build-system r-build-system)
5625 `(("r-biobase" ,r-biobase)
5626 ("r-doparallel" ,r-doparallel)
5627 ("r-foreach" ,r-foreach)
5628 ("r-ggplot2" ,r-ggplot2)
5629 ("r-iterators" ,r-iterators)
5630 ("r-minfi" ,r-minfi)
5631 ("r-rcolorbrewer" ,r-rcolorbrewer)))
5633 `(("r-knitr" ,r-knitr)))
5634 (home-page "https://bioconductor.org/packages/quantro/")
5635 (synopsis "Test for when to use quantile normalization")
5637 "This package provides a data-driven test for the assumptions of quantile
5638 normalization using raw data such as objects that inherit eSets (e.g.
5639 ExpressionSet, MethylSet). Group level information about each sample (such as
5640 Tumor / Normal status) must also be provided because the test assesses if
5641 there are global differences in the distributions between the user-defined
5643 (license license:gpl3+)))
5645 (define-public r-yarn
5652 (uri (bioconductor-uri "yarn" version))
5655 "0p8wz5jn601vxbbxkm73ps3fx0j1y56nr2qf6y8k80vgrk7bv5gp"))))
5656 (build-system r-build-system)
5658 `(("r-biobase" ,r-biobase)
5659 ("r-biomart" ,r-biomart)
5660 ("r-downloader" ,r-downloader)
5661 ("r-edger" ,r-edger)
5662 ("r-gplots" ,r-gplots)
5663 ("r-limma" ,r-limma)
5664 ("r-matrixstats" ,r-matrixstats)
5665 ("r-preprocesscore" ,r-preprocesscore)
5666 ("r-quantro" ,r-quantro)
5667 ("r-rcolorbrewer" ,r-rcolorbrewer)
5668 ("r-readr" ,r-readr)))
5670 `(("r-knitr" ,r-knitr)))
5671 (home-page "https://bioconductor.org/packages/yarn/")
5672 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
5674 "Expedite large RNA-Seq analyses using a combination of previously
5675 developed tools. YARN is meant to make it easier for the user in performing
5676 basic mis-annotation quality control, filtering, and condition-aware
5677 normalization. YARN leverages many Bioconductor tools and statistical
5678 techniques to account for the large heterogeneity and sparsity found in very
5679 large RNA-seq experiments.")
5680 (license license:artistic2.0)))
5682 (define-public r-roar
5689 (uri (bioconductor-uri "roar" version))
5692 "0spidrcjnrcli0whkf6h8pa1i9dg9arjbm7b1skxbs6dn2k4yyqw"))))
5693 (build-system r-build-system)
5695 `(("r-biocgenerics" ,r-biocgenerics)
5696 ("r-genomeinfodb" ,r-genomeinfodb)
5697 ("r-genomicalignments" ,r-genomicalignments)
5698 ("r-genomicranges" ,r-genomicranges)
5699 ("r-iranges" ,r-iranges)
5700 ("r-rtracklayer" ,r-rtracklayer)
5701 ("r-s4vectors" ,r-s4vectors)
5702 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5703 (home-page "https://github.com/vodkatad/roar/")
5704 (synopsis "Identify differential APA usage from RNA-seq alignments")
5706 "This package provides tools for identifying preferential usage of APA
5707 sites, comparing two biological conditions, starting from known alternative
5708 sites and alignments obtained from standard RNA-seq experiments.")
5709 (license license:gpl3)))
5711 (define-public r-xbseq
5718 (uri (bioconductor-uri "XBSeq" version))
5721 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
5722 (properties `((upstream-name . "XBSeq")))
5723 (build-system r-build-system)
5725 `(("r-biobase" ,r-biobase)
5726 ("r-deseq2" ,r-deseq2)
5727 ("r-dplyr" ,r-dplyr)
5728 ("r-ggplot2" ,r-ggplot2)
5729 ("r-locfit" ,r-locfit)
5730 ("r-magrittr" ,r-magrittr)
5731 ("r-matrixstats" ,r-matrixstats)
5732 ("r-pracma" ,r-pracma)
5733 ("r-roar" ,r-roar)))
5735 `(("r-knitr" ,r-knitr)))
5736 (home-page "https://github.com/Liuy12/XBSeq")
5737 (synopsis "Test for differential expression for RNA-seq data")
5739 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
5740 expression} (DE), where a statistical model was established based on the
5741 assumption that observed signals are the convolution of true expression
5742 signals and sequencing noises. The mapped reads in non-exonic regions are
5743 considered as sequencing noises, which follows a Poisson distribution. Given
5744 measurable observed signal and background noise from RNA-seq data, true
5745 expression signals, assuming governed by the negative binomial distribution,
5746 can be delineated and thus the accurate detection of differential expressed
5748 (license license:gpl3+)))
5750 (define-public r-massspecwavelet
5752 (name "r-massspecwavelet")
5757 (uri (bioconductor-uri "MassSpecWavelet" version))
5760 "1vvxbxc538raqdsy0x9ln41vjhp2aw1nrh4k35y3s9mhb1jlzzv3"))))
5762 `((upstream-name . "MassSpecWavelet")))
5763 (build-system r-build-system)
5765 `(("r-waveslim" ,r-waveslim)))
5766 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
5767 (synopsis "Mass spectrum processing by wavelet-based algorithms")
5769 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
5770 data mainly through the use of wavelet transforms. It supports peak detection
5771 based on @dfn{Continuous Wavelet Transform} (CWT).")
5772 (license license:lgpl2.0+)))
5774 (define-public r-xcms
5781 (uri (bioconductor-uri "xcms" version))
5784 "17kyybj093mj0g2sbfmjp19mmkww4w025n6zc0hbznqb94vkc8fv"))))
5785 (build-system r-build-system)
5787 `(("r-biobase" ,r-biobase)
5788 ("r-biocgenerics" ,r-biocgenerics)
5789 ("r-biocparallel" ,r-biocparallel)
5790 ("r-iranges" ,r-iranges)
5791 ("r-lattice" ,r-lattice)
5792 ("r-massspecwavelet" ,r-massspecwavelet)
5793 ("r-mscoreutils" ,r-mscoreutils)
5794 ("r-msnbase" ,r-msnbase)
5797 ("r-protgenerics" ,r-protgenerics)
5799 ("r-rcolorbrewer" ,r-rcolorbrewer)
5800 ("r-robustbase" ,r-robustbase)
5801 ("r-s4vectors" ,r-s4vectors)
5802 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5804 `(("r-knitr" ,r-knitr)))
5805 (home-page "https://bioconductor.org/packages/xcms/")
5806 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
5808 "This package provides a framework for processing and visualization of
5809 chromatographically separated and single-spectra mass spectral data. It
5810 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
5811 data for high-throughput, untargeted analyte profiling.")
5812 (license license:gpl2+)))
5814 (define-public r-wrench
5821 (uri (bioconductor-uri "Wrench" version))
5824 "01z7rd9fn6cpab3dxgwfpfjlq6vsqb8jhbzvhcqn9v2vqc2pridx"))))
5825 (properties `((upstream-name . "Wrench")))
5826 (build-system r-build-system)
5828 `(("r-limma" ,r-limma)
5829 ("r-locfit" ,r-locfit)
5830 ("r-matrixstats" ,r-matrixstats)))
5832 `(("r-knitr" ,r-knitr)))
5833 (home-page "https://github.com/HCBravoLab/Wrench")
5834 (synopsis "Wrench normalization for sparse count data")
5836 "Wrench is a package for normalization sparse genomic count data, like
5837 that arising from 16s metagenomic surveys.")
5838 (license license:artistic2.0)))
5840 (define-public r-wiggleplotr
5842 (name "r-wiggleplotr")
5847 (uri (bioconductor-uri "wiggleplotr" version))
5850 "1k4wlh5ayb1w4dr6dydqfgm3415qhsfmshmi6zjyyhhkd2626vad"))))
5851 (build-system r-build-system)
5853 `(("r-assertthat" ,r-assertthat)
5854 ("r-cowplot" ,r-cowplot)
5855 ("r-dplyr" ,r-dplyr)
5856 ("r-genomeinfodb" ,r-genomeinfodb)
5857 ("r-genomicranges" ,r-genomicranges)
5858 ("r-ggplot2" ,r-ggplot2)
5859 ("r-iranges" ,r-iranges)
5860 ("r-purrr" ,r-purrr)
5861 ("r-rtracklayer" ,r-rtracklayer)
5862 ("r-s4vectors" ,r-s4vectors)))
5864 `(("r-knitr" ,r-knitr)))
5865 (home-page "https://bioconductor.org/packages/wiggleplotr/")
5866 (synopsis "Make read coverage plots from BigWig files")
5868 "This package provides tools to visualize read coverage from sequencing
5869 experiments together with genomic annotations (genes, transcripts, peaks).
5870 Introns of long transcripts can be rescaled to a fixed length for better
5871 visualization of exonic read coverage.")
5872 (license license:asl2.0)))
5874 (define-public r-widgettools
5876 (name "r-widgettools")
5881 (uri (bioconductor-uri "widgetTools" version))
5884 "172f0pmsspd9lss557cmxzjfsbansimjyhwdiahg8pqrayhwvf2w"))))
5885 (properties `((upstream-name . "widgetTools")))
5886 (build-system r-build-system)
5887 (home-page "https://bioconductor.org/packages/widgetTools/")
5888 (synopsis "Tools for creating interactive tcltk widgets")
5890 "This package contains tools to support the construction of tcltk
5892 ;; Any version of the LGPL.
5893 (license license:lgpl3+)))
5895 (define-public r-webbioc
5902 (uri (bioconductor-uri "webbioc" version))
5905 "1nnmr4ddi07x7sy89fgdn7iwz5k4l8n5ca3xjnlbpwxycza793vj"))))
5906 (build-system r-build-system)
5908 `(("netpbm" ,netpbm)
5911 `(("r-affy" ,r-affy)
5912 ("r-annaffy" ,r-annaffy)
5913 ("r-biobase" ,r-biobase)
5914 ("r-biocmanager" ,r-biocmanager)
5915 ("r-gcrma" ,r-gcrma)
5916 ("r-multtest" ,r-multtest)
5917 ("r-qvalue" ,r-qvalue)
5919 (home-page "https://www.bioconductor.org/")
5920 (synopsis "Bioconductor web interface")
5922 "This package provides an integrated web interface for doing microarray
5923 analysis using several of the Bioconductor packages. It is intended to be
5924 deployed as a centralized bioinformatics resource for use by many users.
5925 Currently only Affymetrix oligonucleotide analysis is supported.")
5926 (license license:gpl2+)))
5928 (define-public r-zfpkm
5935 (uri (bioconductor-uri "zFPKM" version))
5938 "1sa7m7mzzr92c9ickial5701414rab233lq1il1sm9yfdkf8s9fm"))))
5939 (properties `((upstream-name . "zFPKM")))
5940 (build-system r-build-system)
5942 `(("r-checkmate" ,r-checkmate)
5943 ("r-dplyr" ,r-dplyr)
5944 ("r-ggplot2" ,r-ggplot2)
5945 ("r-summarizedexperiment" ,r-summarizedexperiment)
5946 ("r-tidyr" ,r-tidyr)))
5948 `(("r-knitr" ,r-knitr)))
5949 (home-page "https://github.com/ronammar/zFPKM/")
5950 (synopsis "Functions to facilitate zFPKM transformations")
5952 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
5953 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
5955 (license license:gpl3)))
5957 (define-public r-rbowtie2
5964 (uri (bioconductor-uri "Rbowtie2" version))
5967 "1pcdcqn82ray73bajjnx5zgs98m56acviq3adbzga0cfqf6wiqx5"))))
5968 (properties `((upstream-name . "Rbowtie2")))
5969 (build-system r-build-system)
5973 `(("r-knitr" ,r-knitr)))
5974 (home-page "https://bioconductor.org/packages/Rbowtie2/")
5975 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
5977 "This package provides an R wrapper of the popular @code{bowtie2}
5978 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
5979 rapid adapter trimming, identification, and read merging.")
5980 (license license:gpl3+)))
5982 (define-public r-progeny
5989 (uri (bioconductor-uri "progeny" version))
5992 "00lhzz4plmx5128khs298n6zv9204mhqv548lxxdhaw18b16vwm7"))))
5993 (build-system r-build-system)
5995 `(("r-biobase" ,r-biobase)
5996 ("r-dplyr" ,r-dplyr)
5997 ("r-ggplot2" ,r-ggplot2)
5998 ("r-ggrepel" ,r-ggrepel)
5999 ("r-gridextra" ,r-gridextra)
6000 ("r-tidyr" ,r-tidyr)))
6002 `(("r-knitr" ,r-knitr)))
6003 (home-page "https://github.com/saezlab/progeny")
6004 (synopsis "Pathway responsive gene activity inference")
6006 "This package provides a function to infer pathway activity from gene
6007 expression. It contains the linear model inferred in the publication
6008 \"Perturbation-response genes reveal signaling footprints in cancer gene
6010 (license license:asl2.0)))
6012 (define-public r-arrmnormalization
6014 (name "r-arrmnormalization")
6019 (uri (bioconductor-uri "ARRmNormalization" version))
6022 "1ximvi0jbwmymx6iy70qfyr9j26x5arlarra9fzs5hq05jif6q95"))))
6024 `((upstream-name . "ARRmNormalization")))
6025 (build-system r-build-system)
6026 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
6027 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
6028 (synopsis "Adaptive robust regression normalization for methylation data")
6030 "This is a package to perform the @dfn{Adaptive Robust Regression
6031 method} (ARRm) for the normalization of methylation data from the Illumina
6032 Infinium HumanMethylation 450k assay.")
6033 (license license:artistic2.0)))
6035 (define-public r-biocfilecache
6037 (name "r-biocfilecache")
6042 (uri (bioconductor-uri "BiocFileCache" version))
6045 "0r032a033636bxap0vvb02jvjqiynzj9npqd8603qnwmhvvfi5z1"))))
6046 (properties `((upstream-name . "BiocFileCache")))
6047 (build-system r-build-system)
6049 `(("r-curl" ,r-curl)
6051 ("r-dbplyr" ,r-dbplyr)
6052 ("r-dplyr" ,r-dplyr)
6054 ("r-rappdirs" ,r-rappdirs)
6055 ("r-rsqlite" ,r-rsqlite)))
6057 `(("r-knitr" ,r-knitr)))
6058 (home-page "https://bioconductor.org/packages/BiocFileCache/")
6059 (synopsis "Manage files across sessions")
6061 "This package creates a persistent on-disk cache of files that the user
6062 can add, update, and retrieve. It is useful for managing resources (such as
6063 custom Txdb objects) that are costly or difficult to create, web resources,
6064 and data files used across sessions.")
6065 (license license:artistic2.0)))
6067 (define-public r-iclusterplus
6069 (name "r-iclusterplus")
6074 (uri (bioconductor-uri "iClusterPlus" version))
6077 "02ji84dsbn4wir8sim4qy8h57524mnrsq51wxc7n8ybp5x7n9k9q"))))
6078 (properties `((upstream-name . "iClusterPlus")))
6079 (build-system r-build-system)
6080 (native-inputs `(("gfortran" ,gfortran)))
6081 (home-page "https://bioconductor.org/packages/iClusterPlus/")
6082 (synopsis "Integrative clustering of multi-type genomic data")
6084 "iClusterPlus is developed for integrative clustering analysis of
6085 multi-type genomic data and is an enhanced version of iCluster proposed and
6086 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
6087 from the experiments where biological samples (e.g. tumor samples) are
6088 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
6089 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
6090 on. In the iClusterPlus model, binary observations such as somatic mutation
6091 are modeled as Binomial processes; categorical observations such as copy
6092 number states are realizations of Multinomial random variables; counts are
6093 modeled as Poisson random processes; and continuous measures are modeled by
6094 Gaussian distributions.")
6095 (license license:gpl2+)))
6097 (define-public r-rbowtie
6104 (uri (bioconductor-uri "Rbowtie" version))
6107 "0rgxqc3sbq7phnrn9a6z361725h4zi2mi985i43n7fi3csif7507"))))
6108 (properties `((upstream-name . "Rbowtie")))
6109 (build-system r-build-system)
6113 `(("r-knitr" ,r-knitr)))
6114 (home-page "https://bioconductor.org/packages/Rbowtie/")
6115 (synopsis "R bowtie wrapper")
6117 "This package provides an R wrapper around the popular bowtie short read
6118 aligner and around SpliceMap, a de novo splice junction discovery and
6120 (license license:artistic2.0)))
6122 (define-public r-sgseq
6129 (uri (bioconductor-uri "SGSeq" version))
6132 "1nfhy5kgyz56b6pyxcq8kflqwnhl9nlffszwpqb5fdh5ibz8xbjx"))))
6133 (properties `((upstream-name . "SGSeq")))
6134 (build-system r-build-system)
6136 `(("r-annotationdbi" ,r-annotationdbi)
6137 ("r-biocgenerics" ,r-biocgenerics)
6138 ("r-biostrings" ,r-biostrings)
6139 ("r-genomeinfodb" ,r-genomeinfodb)
6140 ("r-genomicalignments" ,r-genomicalignments)
6141 ("r-genomicfeatures" ,r-genomicfeatures)
6142 ("r-genomicranges" ,r-genomicranges)
6143 ("r-igraph" ,r-igraph)
6144 ("r-iranges" ,r-iranges)
6145 ("r-rsamtools" ,r-rsamtools)
6146 ("r-rtracklayer" ,r-rtracklayer)
6147 ("r-runit" ,r-runit)
6148 ("r-s4vectors" ,r-s4vectors)
6149 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6151 `(("r-knitr" ,r-knitr)))
6152 (home-page "https://bioconductor.org/packages/SGSeq/")
6153 (synopsis "Splice event prediction and quantification from RNA-seq data")
6155 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
6156 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
6157 represented as a splice graph, which can be obtained from existing annotation
6158 or predicted from the mapped sequence reads. Splice events are identified
6159 from the graph and are quantified locally using structurally compatible reads
6160 at the start or end of each splice variant. The software includes functions
6161 for splice event prediction, quantification, visualization and
6163 (license license:artistic2.0)))
6165 (define-public r-rhisat2
6172 (uri (bioconductor-uri "Rhisat2" version))
6175 "0f9x2qcazml0zjcgyy0kdphnww4d1m62rn0ijcqlhy1bng6ihwwb"))))
6176 (properties `((upstream-name . "Rhisat2")))
6177 (build-system r-build-system)
6180 (modify-phases %standard-phases
6181 (add-after 'unpack 'make-reproducible
6183 (substitute* "src/Makefile"
6184 (("`hostname`") "guix")
6186 ;; Avoid shelling out to "which".
6187 (("^CC =.*") (which "gcc"))
6188 (("^CPP =.*") (which "g++")))
6191 `(("r-genomicfeatures" ,r-genomicfeatures)
6192 ("r-genomicranges" ,r-genomicranges)
6193 ("r-sgseq" ,r-sgseq)))
6195 `(("r-knitr" ,r-knitr)))
6196 (home-page "https://github.com/fmicompbio/Rhisat2")
6197 (synopsis "R Wrapper for HISAT2 sequence aligner")
6199 "This package provides an R interface to the HISAT2 spliced short-read
6200 aligner by Kim et al. (2015). The package contains wrapper functions to
6201 create a genome index and to perform the read alignment to the generated
6203 (license license:gpl3)))
6205 (define-public r-quasr
6212 (uri (bioconductor-uri "QuasR" version))
6215 "032m01q34nnmvbhcb2g3pz2fqmgcw5464m74m1m0h7x9bl04a5k8"))))
6216 (properties `((upstream-name . "QuasR")))
6217 (build-system r-build-system)
6219 `(("r-annotationdbi" ,r-annotationdbi)
6220 ("r-biobase" ,r-biobase)
6221 ("r-biocgenerics" ,r-biocgenerics)
6222 ("r-biocmanager" ,r-biocmanager)
6223 ("r-biocparallel" ,r-biocparallel)
6224 ("r-biostrings" ,r-biostrings)
6225 ("r-bsgenome" ,r-bsgenome)
6226 ("r-genomeinfodb" ,r-genomeinfodb)
6227 ("r-genomicalignments" ,r-genomicalignments)
6228 ("r-genomicfeatures" ,r-genomicfeatures)
6229 ("r-genomicfiles" ,r-genomicfiles)
6230 ("r-genomicranges" ,r-genomicranges)
6231 ("r-iranges" ,r-iranges)
6232 ("r-rbowtie" ,r-rbowtie)
6233 ("r-rhisat2" ,r-rhisat2)
6234 ("r-rhtslib" ,r-rhtslib)
6235 ("r-rsamtools" ,r-rsamtools)
6236 ("r-rtracklayer" ,r-rtracklayer)
6237 ("r-s4vectors" ,r-s4vectors)
6238 ("r-shortread" ,r-shortread)))
6240 `(("r-knitr" ,r-knitr)))
6241 (home-page "https://bioconductor.org/packages/QuasR/")
6242 (synopsis "Quantify and annotate short reads in R")
6244 "This package provides a framework for the quantification and analysis of
6245 short genomic reads. It covers a complete workflow starting from raw sequence
6246 reads, over creation of alignments and quality control plots, to the
6247 quantification of genomic regions of interest.")
6248 (license license:gpl2)))
6250 (define-public r-rqc
6257 (uri (bioconductor-uri "Rqc" version))
6260 "083c3ql0gndb6y7m9d3rpbkimyw8cj8jyv77mwwjhq49lzwsg6n9"))))
6261 (properties `((upstream-name . "Rqc")))
6262 (build-system r-build-system)
6264 `(("r-biocgenerics" ,r-biocgenerics)
6265 ("r-biocparallel" ,r-biocparallel)
6266 ("r-biocstyle" ,r-biocstyle)
6267 ("r-biostrings" ,r-biostrings)
6268 ("r-biovizbase" ,r-biovizbase)
6269 ("r-genomicalignments" ,r-genomicalignments)
6270 ("r-genomicfiles" ,r-genomicfiles)
6271 ("r-ggplot2" ,r-ggplot2)
6272 ("r-iranges" ,r-iranges)
6273 ("r-knitr" ,r-knitr)
6274 ("r-markdown" ,r-markdown)
6277 ("r-reshape2" ,r-reshape2)
6278 ("r-rsamtools" ,r-rsamtools)
6279 ("r-s4vectors" ,r-s4vectors)
6280 ("r-shiny" ,r-shiny)
6281 ("r-shortread" ,r-shortread)))
6283 `(("r-knitr" ,r-knitr)))
6284 (home-page "https://github.com/labbcb/Rqc")
6285 (synopsis "Quality control tool for high-throughput sequencing data")
6287 "Rqc is an optimized tool designed for quality control and assessment of
6288 high-throughput sequencing data. It performs parallel processing of entire
6289 files and produces a report which contains a set of high-resolution
6291 (license license:gpl2+)))
6293 (define-public r-birewire
6300 (uri (bioconductor-uri "BiRewire" version))
6303 "1h9zjjd5krsjpbxlmsbzwx7kbishn0z6mpm8zmrcpmbfrprp38qw"))))
6304 (properties `((upstream-name . "BiRewire")))
6305 (build-system r-build-system)
6307 `(("r-igraph" ,r-igraph)
6308 ("r-matrix" ,r-matrix)
6310 ("r-tsne" ,r-tsne)))
6311 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
6312 (synopsis "Tools for randomization of bipartite graphs")
6314 "This package provides functions for bipartite network rewiring through N
6315 consecutive switching steps and for the computation of the minimal number of
6316 switching steps to be performed in order to maximise the dissimilarity with
6317 respect to the original network. It includes functions for the analysis of
6318 the introduced randomness across the switching steps and several other
6319 routines to analyse the resulting networks and their natural projections.")
6320 (license license:gpl3)))
6322 (define-public r-birta
6329 (uri (bioconductor-uri "birta" version))
6332 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
6333 (build-system r-build-system)
6335 `(("r-biobase" ,r-biobase)
6336 ("r-limma" ,r-limma)
6337 ("r-mass" ,r-mass)))
6338 (home-page "https://bioconductor.org/packages/birta")
6339 (synopsis "Bayesian inference of regulation of transcriptional activity")
6341 "Expression levels of mRNA molecules are regulated by different
6342 processes, comprising inhibition or activation by transcription factors and
6343 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
6344 Inference of Regulation of Transcriptional Activity) uses the regulatory
6345 networks of transcription factors and miRNAs together with mRNA and miRNA
6346 expression data to predict switches in regulatory activity between two
6347 conditions. A Bayesian network is used to model the regulatory structure and
6348 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
6349 (license license:gpl2+)))
6351 (define-public r-multidataset
6353 (name "r-multidataset")
6358 (uri (bioconductor-uri "MultiDataSet" version))
6361 "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4"))))
6362 (properties `((upstream-name . "MultiDataSet")))
6363 (build-system r-build-system)
6365 `(("r-biobase" ,r-biobase)
6366 ("r-biocgenerics" ,r-biocgenerics)
6367 ("r-genomicranges" ,r-genomicranges)
6368 ("r-ggplot2" ,r-ggplot2)
6369 ("r-ggrepel" ,r-ggrepel)
6370 ("r-iranges" ,r-iranges)
6371 ("r-limma" ,r-limma)
6372 ("r-qqman" ,r-qqman)
6373 ("r-s4vectors" ,r-s4vectors)
6374 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6376 `(("r-knitr" ,r-knitr)))
6377 (home-page "https://bioconductor.org/packages/MultiDataSet/")
6378 (synopsis "Implementation of MultiDataSet and ResultSet")
6380 "This package provides an implementation of the BRGE's (Bioinformatic
6381 Research Group in Epidemiology from Center for Research in Environmental
6382 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
6383 integrating multi omics data sets and ResultSet is a container for omics
6384 results. This package contains base classes for MEAL and rexposome
6386 (license license:expat)))
6388 (define-public r-ropls
6395 (uri (bioconductor-uri "ropls" version))
6398 "1h76s89hsafrkshpkx7vjinfni9lzfpnbfyg3fhkkrwpp1fnwyj5"))))
6399 (build-system r-build-system)
6401 `(("r-biobase" ,r-biobase)
6402 ("r-multidataset" ,r-multidataset)))
6404 `(("r-knitr" ,r-knitr))) ; for vignettes
6405 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
6406 (synopsis "Multivariate analysis and feature selection of omics data")
6408 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
6409 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
6410 regression, classification, and feature selection of omics data where the
6411 number of variables exceeds the number of samples and with multicollinearity
6412 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
6413 separately model the variation correlated (predictive) to the factor of
6414 interest and the uncorrelated (orthogonal) variation. While performing
6415 similarly to PLS, OPLS facilitates interpretation.
6417 This package provides imlementations of PCA, PLS, and OPLS for multivariate
6418 analysis and feature selection of omics data. In addition to scores, loadings
6419 and weights plots, the package provides metrics and graphics to determine the
6420 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
6421 validity of the model by permutation testing, detect outliers, and perform
6422 feature selection (e.g. with Variable Importance in Projection or regression
6424 (license license:cecill)))
6426 (define-public r-biosigner
6428 (name "r-biosigner")
6433 (uri (bioconductor-uri "biosigner" version))
6436 "0i18j4fk91x5017yk1l35c58k5aby22yh81zkp59irphpv9akvjn"))))
6437 (build-system r-build-system)
6439 `(("r-biobase" ,r-biobase)
6440 ("r-e1071" ,r-e1071)
6441 ("r-multidataset" ,r-multidataset)
6442 ("r-randomforest" ,r-randomforest)
6443 ("r-ropls" ,r-ropls)))
6445 `(("r-knitr" ,r-knitr)))
6446 (home-page "https://bioconductor.org/packages/biosigner/")
6447 (synopsis "Signature discovery from omics data")
6449 "Feature selection is critical in omics data analysis to extract
6450 restricted and meaningful molecular signatures from complex and high-dimension
6451 data, and to build robust classifiers. This package implements a method to
6452 assess the relevance of the variables for the prediction performances of the
6453 classifier. The approach can be run in parallel with the PLS-DA, Random
6454 Forest, and SVM binary classifiers. The signatures and the corresponding
6455 'restricted' models are returned, enabling future predictions on new
6457 (license license:cecill)))
6459 (define-public r-annotatr
6466 (uri (bioconductor-uri "annotatr" version))
6469 "0dq67snpqxl9mifljm6zlnkdb0ghjwday0fvcn3i7zmrfszgzyf9"))))
6470 (build-system r-build-system)
6472 `(("r-annotationdbi" ,r-annotationdbi)
6473 ("r-annotationhub" ,r-annotationhub)
6474 ("r-dplyr" ,r-dplyr)
6475 ("r-genomeinfodb" ,r-genomeinfodb)
6476 ("r-genomicfeatures" ,r-genomicfeatures)
6477 ("r-genomicranges" ,r-genomicranges)
6478 ("r-ggplot2" ,r-ggplot2)
6479 ("r-iranges" ,r-iranges)
6480 ("r-readr" ,r-readr)
6481 ("r-regioner" ,r-regioner)
6482 ("r-reshape2" ,r-reshape2)
6483 ("r-rtracklayer" ,r-rtracklayer)
6484 ("r-s4vectors" ,r-s4vectors)))
6486 `(("r-knitr" ,r-knitr)))
6487 (home-page "https://bioconductor.org/packages/annotatr/")
6488 (synopsis "Annotation of genomic regions to genomic annotations")
6490 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
6491 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
6492 to investigate the intersecting genomic annotations. Such annotations include
6493 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
6494 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
6495 enhancers. The annotatr package provides an easy way to summarize and
6496 visualize the intersection of genomic sites/regions with genomic
6498 (license license:gpl3)))
6500 (define-public r-rsubread
6507 (uri (bioconductor-uri "Rsubread" version))
6510 "1wczrw5jb69x45hd3rdqqs9vkysdqwlxn9h3kjzn57r4x5q7jrra"))))
6511 (properties `((upstream-name . "Rsubread")))
6512 (build-system r-build-system)
6513 (inputs `(("zlib" ,zlib)))
6515 `(("r-matrix" ,r-matrix)))
6516 (home-page "https://bioconductor.org/packages/Rsubread/")
6517 (synopsis "Subread sequence alignment and counting for R")
6519 "This package provides tools for alignment, quantification and analysis
6520 of second and third generation sequencing data. It includes functionality for
6521 read mapping, read counting, SNP calling, structural variant detection and
6522 gene fusion discovery. It can be applied to all major sequencing techologies
6523 and to both short and long sequence reads.")
6524 (license license:gpl3)))
6526 (define-public r-flowutils
6528 (name "r-flowutils")
6533 (uri (bioconductor-uri "flowUtils" version))
6536 "1q4g666nd51j24hcp2wxla1bdi77kbfd4i0pxgp7rs2jf7200k09"))))
6537 (properties `((upstream-name . "flowUtils")))
6538 (build-system r-build-system)
6540 `(("r-biobase" ,r-biobase)
6541 ("r-corpcor" ,r-corpcor)
6542 ("r-flowcore" ,r-flowcore)
6543 ("r-graph" ,r-graph)
6544 ("r-runit" ,r-runit)
6546 (home-page "https://github.com/jspidlen/flowUtils")
6547 (synopsis "Utilities for flow cytometry")
6549 "This package provides utilities for flow cytometry data.")
6550 (license license:artistic2.0)))
6552 (define-public r-consensusclusterplus
6554 (name "r-consensusclusterplus")
6559 (uri (bioconductor-uri "ConsensusClusterPlus" version))
6562 "06h85l1mg2kpjprylzz44nhxp64k211plhch5qhg39wp0fk34lfp"))))
6564 `((upstream-name . "ConsensusClusterPlus")))
6565 (build-system r-build-system)
6568 ("r-biobase" ,r-biobase)
6569 ("r-cluster" ,r-cluster)))
6570 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
6571 (synopsis "Clustering algorithm")
6573 "This package provides an implementation of an algorithm for determining
6574 cluster count and membership by stability evidence in unsupervised analysis.")
6575 (license license:gpl2)))
6577 (define-public r-cytolib
6584 (uri (bioconductor-uri "cytolib" version))
6587 "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r"))))
6588 (properties `((upstream-name . "cytolib")))
6589 (build-system r-build-system)
6592 (modify-phases %standard-phases
6593 (add-after 'unpack 'fix-linking
6595 (substitute* "src/Makevars.in"
6596 ;; This is to avoid having a plain directory on the list of
6597 ;; libraries to link.
6598 (("\\(RHDF5_LIBS\\)" match)
6599 (string-append match "/libhdf5.a")))
6602 `(("r-knitr" ,r-knitr)
6603 ("pkg-config" ,pkg-config)))
6607 ("r-rcpparmadillo" ,r-rcpparmadillo)
6608 ("r-rcppparallel" ,r-rcppparallel)
6609 ("r-rhdf5lib" ,r-rhdf5lib)
6610 ("r-rprotobuflib" ,r-rprotobuflib)))
6611 (home-page "https://bioconductor.org/packages/cytolib/")
6612 (synopsis "C++ infrastructure for working with gated cytometry")
6614 "This package provides the core data structure and API to represent and
6615 interact with gated cytometry data.")
6616 (license license:artistic2.0)))
6618 (define-public r-flowcore
6625 (uri (bioconductor-uri "flowCore" version))
6628 "001ickrl2asdl0zwpdjqkl1w7137nzxbryamxihgya394jw73xr8"))))
6629 (properties `((upstream-name . "flowCore")))
6630 (build-system r-build-system)
6633 ("r-biobase" ,r-biobase)
6634 ("r-biocgenerics" ,r-biocgenerics)
6635 ("r-cytolib" ,r-cytolib)
6636 ("r-matrixstats" ,r-matrixstats)
6638 ("r-rcpparmadillo" ,r-rcpparmadillo)
6639 ("r-rprotobuflib" ,r-rprotobuflib)
6640 ("r-s4vectors" ,r-s4vectors)))
6642 `(("r-knitr" ,r-knitr)))
6643 (home-page "https://bioconductor.org/packages/flowCore")
6644 (synopsis "Basic structures for flow cytometry data")
6646 "This package provides S4 data structures and basic functions to deal
6647 with flow cytometry data.")
6648 (license license:artistic2.0)))
6650 (define-public r-flowmeans
6652 (name "r-flowmeans")
6657 (uri (bioconductor-uri "flowMeans" version))
6660 "02y5b3iqjlqjlxrqq0l24dr68sjaniz26jqf14cnnwz1xg5hz734"))))
6661 (properties `((upstream-name . "flowMeans")))
6662 (build-system r-build-system)
6664 `(("r-biobase" ,r-biobase)
6665 ("r-feature" ,r-feature)
6666 ("r-flowcore" ,r-flowcore)
6667 ("r-rrcov" ,r-rrcov)))
6668 (home-page "https://bioconductor.org/packages/flowMeans")
6669 (synopsis "Non-parametric flow cytometry data gating")
6671 "This package provides tools to identify cell populations in Flow
6672 Cytometry data using non-parametric clustering and segmented-regression-based
6673 change point detection.")
6674 (license license:artistic2.0)))
6676 (define-public r-ncdfflow
6683 (uri (bioconductor-uri "ncdfFlow" version))
6686 "1knqc3ic2vpck7n7m7adxjz3ac70ra89d5gvlgp9r2q3kgaciwac"))))
6687 (properties `((upstream-name . "ncdfFlow")))
6688 (build-system r-build-system)
6691 (modify-phases %standard-phases
6692 (add-after 'unpack 'fix-linking
6694 (substitute* "src/Makevars"
6695 ;; This is to avoid having a plain directory on the list of
6696 ;; libraries to link.
6697 (("\\(RHDF5_LIBS\\)" match)
6698 (string-append match "/libhdf5.a")))
6702 ("r-biobase" ,r-biobase)
6703 ("r-biocgenerics" ,r-biocgenerics)
6704 ("r-flowcore" ,r-flowcore)
6706 ("r-rcpparmadillo" ,r-rcpparmadillo)
6707 ("r-rhdf5lib" ,r-rhdf5lib)
6708 ("r-zlibbioc" ,r-zlibbioc)))
6710 `(("r-knitr" ,r-knitr)))
6711 (home-page "https://bioconductor.org/packages/ncdfFlow/")
6712 (synopsis "HDF5 based storage for flow cytometry data")
6714 "This package provides HDF5 storage based methods and functions for
6715 manipulation of flow cytometry data.")
6716 (license license:artistic2.0)))
6718 (define-public r-ggcyto
6725 (uri (bioconductor-uri "ggcyto" version))
6728 "0myjvhm9jjb9cih5nlka3f9zg5ncy8gy3krpdpa0618jdglvgr1m"))))
6729 (properties `((upstream-name . "ggcyto")))
6730 (build-system r-build-system)
6732 `(("r-data-table" ,r-data-table)
6733 ("r-flowcore" ,r-flowcore)
6734 ("r-flowworkspace" ,r-flowworkspace)
6735 ("r-ggplot2" ,r-ggplot2)
6736 ("r-gridextra" ,r-gridextra)
6737 ("r-hexbin" ,r-hexbin)
6738 ("r-ncdfflow" ,r-ncdfflow)
6740 ("r-rcolorbrewer" ,r-rcolorbrewer)
6741 ("r-rlang" ,r-rlang)
6742 ("r-scales" ,r-scales)))
6744 `(("r-knitr" ,r-knitr)))
6745 (home-page "https://github.com/RGLab/ggcyto/issues")
6746 (synopsis "Visualize Cytometry data with ggplot")
6748 "With the dedicated fortify method implemented for @code{flowSet},
6749 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
6750 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
6751 and some custom layers also make it easy to add gates and population
6752 statistics to the plot.")
6753 (license license:artistic2.0)))
6755 (define-public r-flowviz
6762 (uri (bioconductor-uri "flowViz" version))
6765 "1s6jrn2a7hv984xvm6gyn8k3hnma8qidrw9kgj9z5128hv330z7k"))))
6766 (properties `((upstream-name . "flowViz")))
6767 (build-system r-build-system)
6769 `(("r-biobase" ,r-biobase)
6770 ("r-flowcore" ,r-flowcore)
6771 ("r-hexbin" ,r-hexbin)
6772 ("r-idpmisc" ,r-idpmisc)
6773 ("r-kernsmooth" ,r-kernsmooth)
6774 ("r-lattice" ,r-lattice)
6775 ("r-latticeextra" ,r-latticeextra)
6777 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6779 `(("r-knitr" ,r-knitr)))
6780 (home-page "https://bioconductor.org/packages/flowViz/")
6781 (synopsis "Visualization for flow cytometry")
6783 "This package provides visualization tools for flow cytometry data.")
6784 (license license:artistic2.0)))
6786 (define-public r-flowclust
6788 (name "r-flowclust")
6793 (uri (bioconductor-uri "flowClust" version))
6796 "1ml3y5wq68jbyr7l5j4zs79bj5bbwzmn5gx41yi88hq78iwkscrq"))))
6797 (properties `((upstream-name . "flowClust")))
6798 (build-system r-build-system)
6801 (list "--configure-args=--enable-bundled-gsl=no")))
6803 `(("r-biobase" ,r-biobase)
6804 ("r-biocgenerics" ,r-biocgenerics)
6806 ("r-corpcor" ,r-corpcor)
6807 ("r-ellipse" ,r-ellipse)
6808 ("r-flowcore" ,r-flowcore)
6809 ("r-flowviz" ,r-flowviz)
6810 ("r-graph" ,r-graph)
6811 ("r-mnormt" ,r-mnormt)))
6815 `(("pkg-config" ,pkg-config)
6816 ("r-knitr" ,r-knitr)))
6817 (home-page "https://bioconductor.org/packages/flowClust")
6818 (synopsis "Clustering for flow cytometry")
6820 "This package provides robust model-based clustering using a t-mixture
6821 model with Box-Cox transformation.")
6822 (license license:artistic2.0)))
6824 ;; TODO: this package bundles an old version of protobuf. It's not easy to
6825 ;; make it use our protobuf package instead.
6826 (define-public r-rprotobuflib
6828 (name "r-rprotobuflib")
6833 (uri (bioconductor-uri "RProtoBufLib" version))
6836 "09n4ny3ymfkja2br4rrr2n9dzw3hs7qijhcq4mj0avr86i27llqz"))))
6837 (properties `((upstream-name . "RProtoBufLib")))
6838 (build-system r-build-system)
6841 (modify-phases %standard-phases
6842 (add-after 'unpack 'unpack-bundled-sources
6844 (with-directory-excursion "src"
6845 (invoke "tar" "xf" "protobuf-3.10.0.tar.gz"))
6848 `(("r-knitr" ,r-knitr)))
6849 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
6850 (synopsis "C++ headers and static libraries of Protocol buffers")
6852 "This package provides the headers and static library of Protocol buffers
6853 for other R packages to compile and link against.")
6854 (license license:bsd-3)))
6856 (define-public r-flowworkspace
6858 (name "r-flowworkspace")
6863 (uri (bioconductor-uri "flowWorkspace" version))
6866 "19svh32jq1dpq3ayhpd5r8bw0iax8d9kdvpvc23gx2pf16g1j5ag"))))
6867 (properties `((upstream-name . "flowWorkspace")))
6868 (build-system r-build-system)
6871 (modify-phases %standard-phases
6872 (add-after 'unpack 'fix-linking
6874 (substitute* "src/Makevars"
6875 ;; This is to avoid having a plain directory on the list of
6876 ;; libraries to link.
6877 (("\\{h5lib\\}" match)
6878 (string-append match "/libhdf5.a")))
6881 `(("r-aws-s3" ,r-aws-s3)
6882 ("r-aws-signature" ,r-aws-signature)
6884 ("r-biobase" ,r-biobase)
6885 ("r-biocgenerics" ,r-biocgenerics)
6886 ("r-cytolib" ,r-cytolib)
6887 ("r-data-table" ,r-data-table)
6888 ("r-digest" ,r-digest)
6889 ("r-dplyr" ,r-dplyr)
6890 ("r-flowcore" ,r-flowcore)
6891 ("r-ggplot2" ,r-ggplot2)
6892 ("r-graph" ,r-graph)
6893 ("r-lattice" ,r-lattice)
6894 ("r-latticeextra" ,r-latticeextra)
6895 ("r-matrixstats" ,r-matrixstats)
6896 ("r-ncdfflow" ,r-ncdfflow)
6899 ("r-rcpparmadillo" ,r-rcpparmadillo)
6900 ("r-rcppparallel" ,r-rcppparallel)
6901 ("r-rgraphviz" ,r-rgraphviz)
6902 ("r-rhdf5lib" ,r-rhdf5lib)
6903 ("r-rprotobuflib" ,r-rprotobuflib)
6904 ("r-scales" ,r-scales)
6907 `(("r-knitr" ,r-knitr)))
6908 (home-page "https://bioconductor.org/packages/flowWorkspace/")
6909 (synopsis "Infrastructure for working with cytometry data")
6911 "This package is designed to facilitate comparison of automated gating
6912 methods against manual gating done in flowJo. This package allows you to
6913 import basic flowJo workspaces into BioConductor and replicate the gating from
6914 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
6915 samples, compensation, and transformation are performed so that the output
6916 matches the flowJo analysis.")
6917 (license license:artistic2.0)))
6919 (define-public r-flowstats
6921 (name "r-flowstats")
6926 (uri (bioconductor-uri "flowStats" version))
6929 "1i6nrwc55k4bn4qprgs6npy7wf8537m429yncqsygsv47z21ix6x"))))
6930 (properties `((upstream-name . "flowStats")))
6931 (build-system r-build-system)
6933 `(("r-biobase" ,r-biobase)
6934 ("r-biocgenerics" ,r-biocgenerics)
6935 ("r-cluster" ,r-cluster)
6937 ("r-flowcore" ,r-flowcore)
6938 ("r-flowviz" ,r-flowviz)
6939 ("r-flowworkspace" ,r-flowworkspace)
6940 ("r-kernsmooth" ,r-kernsmooth)
6942 ("r-lattice" ,r-lattice)
6944 ("r-ncdfflow" ,r-ncdfflow)
6945 ("r-rcolorbrewer" ,r-rcolorbrewer)
6946 ("r-rrcov" ,r-rrcov)))
6947 (home-page "http://www.github.com/RGLab/flowStats")
6948 (synopsis "Statistical methods for the analysis of flow cytometry data")
6950 "This package provides methods and functionality to analyze flow data
6951 that is beyond the basic infrastructure provided by the @code{flowCore}
6953 (license license:artistic2.0)))
6955 (define-public r-opencyto
6962 (uri (bioconductor-uri "openCyto" version))
6965 "02dymy5fa0wjd4pql3jdv1d65mak7ra4il96va7c0km8s87rn40v"))))
6966 (properties `((upstream-name . "openCyto")))
6967 (build-system r-build-system)
6969 `(("r-biobase" ,r-biobase)
6970 ("r-biocgenerics" ,r-biocgenerics)
6972 ("r-data-table" ,r-data-table)
6973 ("r-flowclust" ,r-flowclust)
6974 ("r-flowcore" ,r-flowcore)
6975 ("r-flowstats" ,r-flowstats)
6976 ("r-flowviz" ,r-flowviz)
6977 ("r-flowworkspace" ,r-flowworkspace)
6978 ("r-graph" ,r-graph)
6979 ("r-gtools" ,r-gtools)
6981 ("r-lattice" ,r-lattice)
6983 ("r-ncdfflow" ,r-ncdfflow)
6985 ("r-r-utils" ,r-r-utils)
6987 ("r-rcolorbrewer" ,r-rcolorbrewer)
6989 ("r-rrcov" ,r-rrcov)))
6991 `(("r-knitr" ,r-knitr)))
6992 (home-page "https://bioconductor.org/packages/openCyto")
6993 (synopsis "Hierarchical gating pipeline for flow cytometry data")
6995 "This package is designed to facilitate the automated gating methods in a
6996 sequential way to mimic the manual gating strategy.")
6997 (license license:artistic2.0)))
6999 (define-public r-cytoml
7006 (uri (bioconductor-uri "CytoML" version))
7009 "0ckjb7bkz0cy46scrv4vl9w37g54c0yihvzmbkzilip1ikpvhxd1"))))
7010 (properties `((upstream-name . "CytoML")))
7011 (build-system r-build-system)
7014 (modify-phases %standard-phases
7015 (add-after 'unpack 'fix-linking
7017 (substitute* "src/Makevars.in"
7018 ;; This is to avoid having a plain directory on the list of
7019 ;; libraries to link.
7020 (("\\{h5lib\\}" match)
7021 (string-append match "/libhdf5.a")))
7024 `(("libxml2" ,libxml2)
7027 `(("r-base64enc" ,r-base64enc)
7029 ("r-biobase" ,r-biobase)
7030 ("r-corpcor" ,r-corpcor)
7031 ("r-cytolib" ,r-cytolib)
7032 ("r-data-table" ,r-data-table)
7033 ("r-dplyr" ,r-dplyr)
7034 ("r-flowcore" ,r-flowcore)
7035 ("r-flowworkspace" ,r-flowworkspace)
7036 ("r-ggcyto" ,r-ggcyto)
7037 ("r-graph" ,r-graph)
7038 ("r-jsonlite" ,r-jsonlite)
7039 ("r-lattice" ,r-lattice)
7040 ("r-opencyto" ,r-opencyto)
7044 ("r-rcpparmadillo" ,r-rcpparmadillo)
7045 ("r-rcppparallel" ,r-rcppparallel)
7046 ("r-rgraphviz" ,r-rgraphviz)
7047 ("r-rhdf5lib" ,r-rhdf5lib)
7048 ("r-rprotobuflib" ,r-rprotobuflib)
7049 ("r-runit" ,r-runit)
7050 ("r-tibble" ,r-tibble)
7053 ("r-yaml" ,r-yaml)))
7055 `(("r-knitr" ,r-knitr)))
7056 (home-page "https://github.com/RGLab/CytoML")
7057 (synopsis "GatingML interface for cross platform cytometry data sharing")
7059 "This package provides an interface to implementations of the GatingML2.0
7060 standard to exchange gated cytometry data with other software platforms.")
7061 (license license:artistic2.0)))
7063 (define-public r-flowsom
7070 (uri (bioconductor-uri "FlowSOM" version))
7073 "0gydp6q6zqkadw356k9br646zfynz8gk9ckbx9d297x503j5sgwf"))))
7074 (properties `((upstream-name . "FlowSOM")))
7075 (build-system r-build-system)
7077 `(("r-biocgenerics" ,r-biocgenerics)
7078 ("r-consensusclusterplus" ,r-consensusclusterplus)
7079 ("r-cytoml" ,r-cytoml)
7080 ("r-flowcore" ,r-flowcore)
7081 ("r-flowworkspace" ,r-flowworkspace)
7082 ("r-igraph" ,r-igraph)
7083 ("r-rcolorbrewer" ,r-rcolorbrewer)
7086 (home-page "https://bioconductor.org/packages/FlowSOM/")
7087 (synopsis "Visualize and interpret cytometry data")
7089 "FlowSOM offers visualization options for cytometry data, by using
7090 self-organizing map clustering and minimal spanning trees.")
7091 (license license:gpl2+)))
7093 (define-public r-mixomics
7100 (uri (bioconductor-uri "mixOmics" version))
7103 "0q43ay5r0qsx0zjjnrq24fk6pq5cimviky5lm4w2mbjclqf0gv0q"))))
7104 (properties `((upstream-name . "mixOmics")))
7105 (build-system r-build-system)
7107 `(("r-corpcor" ,r-corpcor)
7108 ("r-dplyr" ,r-dplyr)
7109 ("r-ellipse" ,r-ellipse)
7110 ("r-ggrepel" ,r-ggrepel)
7111 ("r-ggplot2" ,r-ggplot2)
7112 ("r-gridextra" ,r-gridextra)
7113 ("r-igraph" ,r-igraph)
7114 ("r-lattice" ,r-lattice)
7116 ("r-matrixstats" ,r-matrixstats)
7117 ("r-rarpack" ,r-rarpack)
7118 ("r-rcolorbrewer" ,r-rcolorbrewer)
7119 ("r-reshape2" ,r-reshape2)
7120 ("r-tidyr" ,r-tidyr)))
7122 `(("r-knitr" ,r-knitr)))
7123 (home-page "http://www.mixOmics.org")
7124 (synopsis "Multivariate methods for exploration of biological datasets")
7126 "mixOmics offers a wide range of multivariate methods for the exploration
7127 and integration of biological datasets with a particular focus on variable
7128 selection. The package proposes several sparse multivariate models we have
7129 developed to identify the key variables that are highly correlated, and/or
7130 explain the biological outcome of interest. The data that can be analysed
7131 with mixOmics may come from high throughput sequencing technologies, such as
7132 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
7133 also beyond the realm of omics (e.g. spectral imaging). The methods
7134 implemented in mixOmics can also handle missing values without having to
7135 delete entire rows with missing data.")
7136 (license license:gpl2+)))
7138 (define-public r-depecher
7139 (package ;Source/Weave error
7145 (uri (bioconductor-uri "DepecheR" version))
7148 "0c7yv3a7k22nhhw3601n8jdl61cjmlny9b3nfrzsp78mkxi0h469"))))
7149 (properties `((upstream-name . "DepecheR")))
7150 (build-system r-build-system)
7152 `(("r-beanplot" ,r-beanplot)
7153 ("r-dosnow" ,r-dosnow)
7154 ("r-dplyr" ,r-dplyr)
7156 ("r-foreach" ,r-foreach)
7157 ("r-ggplot2" ,r-ggplot2)
7158 ("r-gmodels" ,r-gmodels)
7159 ("r-gplots" ,r-gplots)
7161 ("r-matrixstats" ,r-matrixstats)
7162 ("r-mixomics" ,r-mixomics)
7163 ("r-moments" ,r-moments)
7165 ("r-rcppeigen" ,r-rcppeigen)
7166 ("r-reshape2" ,r-reshape2)
7167 ("r-robustbase" ,r-robustbase)
7168 ("r-viridis" ,r-viridis)))
7170 `(("r-knitr" ,r-knitr)))
7171 (home-page "https://bioconductor.org/packages/DepecheR/")
7172 (synopsis "Identify traits of clusters in high-dimensional entities")
7174 "The purpose of this package is to identify traits in a dataset that can
7175 separate groups. This is done on two levels. First, clustering is performed,
7176 using an implementation of sparse K-means. Secondly, the generated clusters
7177 are used to predict outcomes of groups of individuals based on their
7178 distribution of observations in the different clusters. As certain clusters
7179 with separating information will be identified, and these clusters are defined
7180 by a sparse number of variables, this method can reduce the complexity of
7181 data, to only emphasize the data that actually matters.")
7182 (license license:expat)))
7184 (define-public r-rcistarget
7186 (name "r-rcistarget")
7191 (uri (bioconductor-uri "RcisTarget" version))
7194 "0a711jzxl1kggpk3ln68xzc5y30my4nbs1mxx8951pyi3jvzjfyf"))))
7195 (properties `((upstream-name . "RcisTarget")))
7196 (build-system r-build-system)
7198 `(("r-aucell" ,r-aucell)
7199 ("r-biocgenerics" ,r-biocgenerics)
7200 ("r-data-table" ,r-data-table)
7201 ("r-feather" ,r-feather)
7202 ("r-gseabase" ,r-gseabase)
7203 ("r-r-utils" ,r-r-utils)
7204 ("r-summarizedexperiment" ,r-summarizedexperiment)))
7206 `(("r-knitr" ,r-knitr)))
7207 (home-page "https://aertslab.org/#scenic")
7208 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
7210 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
7211 over-represented on a gene list. In a first step, RcisTarget selects DNA
7212 motifs that are significantly over-represented in the surroundings of the
7213 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
7214 achieved by using a database that contains genome-wide cross-species rankings
7215 for each motif. The motifs that are then annotated to TFs and those that have
7216 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
7217 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
7218 genes in the gene-set that are ranked above the leading edge).")
7219 (license license:gpl3)))
7221 (define-public r-cicero
7228 (uri (bioconductor-uri "cicero" version))
7231 "12y857p4p0m7k72bimli8wjn9cd0gxjwcs3n7ri9pn9l9d42krqr"))))
7232 (build-system r-build-system)
7234 `(("r-assertthat" ,r-assertthat)
7235 ("r-biobase" ,r-biobase)
7236 ("r-biocgenerics" ,r-biocgenerics)
7237 ("r-data-table" ,r-data-table)
7238 ("r-dplyr" ,r-dplyr)
7240 ("r-genomicranges" ,r-genomicranges)
7241 ("r-ggplot2" ,r-ggplot2)
7242 ("r-glasso" ,r-glasso)
7244 ("r-igraph" ,r-igraph)
7245 ("r-iranges" ,r-iranges)
7246 ("r-matrix" ,r-matrix)
7247 ("r-monocle" ,r-monocle)
7249 ("r-reshape2" ,r-reshape2)
7250 ("r-s4vectors" ,r-s4vectors)
7251 ("r-stringi" ,r-stringi)
7252 ("r-stringr" ,r-stringr)
7253 ("r-tibble" ,r-tibble)
7254 ("r-tidyr" ,r-tidyr)
7255 ("r-vgam" ,r-vgam)))
7257 `(("r-knitr" ,r-knitr)))
7258 (home-page "https://bioconductor.org/packages/cicero/")
7259 (synopsis "Predict cis-co-accessibility from single-cell data")
7261 "Cicero computes putative cis-regulatory maps from single-cell chromatin
7262 accessibility data. It also extends the monocle package for use in chromatin
7263 accessibility data.")
7264 (license license:expat)))
7266 ;; This is the latest commit on the "monocle3" branch.
7267 (define-public r-cicero-monocle3
7268 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
7270 (package (inherit r-cicero)
7271 (name "r-cicero-monocle3")
7272 (version (git-version "1.3.2" revision commit))
7277 (url "https://github.com/cole-trapnell-lab/cicero-release")
7279 (file-name (git-file-name name version))
7282 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
7284 `(("r-monocle3" ,r-monocle3)
7285 ,@(alist-delete "r-monocle"
7286 (package-propagated-inputs r-cicero)))))))
7288 (define-public r-circrnaprofiler
7290 (name "r-circrnaprofiler")
7295 (uri (bioconductor-uri "circRNAprofiler" version))
7298 "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
7300 `((upstream-name . "circRNAprofiler")))
7301 (build-system r-build-system)
7303 `(("r-annotationhub" ,r-annotationhub)
7304 ("r-biostrings" ,r-biostrings)
7305 ("r-bsgenome" ,r-bsgenome)
7306 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
7307 ("r-deseq2" ,r-deseq2)
7308 ("r-dplyr" ,r-dplyr)
7309 ("r-edger" ,r-edger)
7310 ("r-genomeinfodb" ,r-genomeinfodb)
7311 ("r-genomicranges" ,r-genomicranges)
7312 ("r-ggplot2" ,r-ggplot2)
7313 ("r-gwascat" ,r-gwascat)
7314 ("r-iranges" ,r-iranges)
7315 ("r-magrittr" ,r-magrittr)
7316 ("r-r-utils" ,r-r-utils)
7317 ("r-readr" ,r-readr)
7318 ("r-reshape2" ,r-reshape2)
7319 ("r-rlang" ,r-rlang)
7320 ("r-rtracklayer" ,r-rtracklayer)
7321 ("r-s4vectors" ,r-s4vectors)
7322 ("r-seqinr" ,r-seqinr)
7323 ("r-stringi" ,r-stringi)
7324 ("r-stringr" ,r-stringr)
7325 ("r-universalmotif" ,r-universalmotif)))
7327 `(("r-knitr" ,r-knitr)))
7329 "https://github.com/Aufiero/circRNAprofiler")
7331 "Computational framework for the downstream analysis of circular RNA's")
7333 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
7334 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
7335 framework allows to combine and analyze circRNAs previously detected by
7336 multiple publicly available annotation-based circRNA detection tools. It
7337 covers different aspects of circRNAs analysis from differential expression
7338 analysis, evolutionary conservation, biogenesis to functional analysis.")
7339 (license license:gpl3)))
7341 (define-public r-cistopic
7342 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
7346 (version (git-version "0.2.1" revision commit))
7351 (url "https://github.com/aertslab/cisTopic")
7353 (file-name (git-file-name name version))
7356 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
7357 (build-system r-build-system)
7359 `(("r-aucell" ,r-aucell)
7360 ("r-data-table" ,r-data-table)
7361 ("r-dplyr" ,r-dplyr)
7362 ("r-dosnow" ,r-dosnow)
7364 ("r-feather" ,r-feather)
7365 ("r-fitdistrplus" ,r-fitdistrplus)
7366 ("r-genomicranges" ,r-genomicranges)
7367 ("r-ggplot2" ,r-ggplot2)
7369 ("r-matrix" ,r-matrix)
7371 ("r-rcistarget" ,r-rcistarget)
7372 ("r-rtracklayer" ,r-rtracklayer)
7373 ("r-s4vectors" ,r-s4vectors)))
7374 (home-page "https://github.com/aertslab/cisTopic")
7375 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
7377 "The sparse nature of single cell epigenomics data can be overruled using
7378 probabilistic modelling methods such as @dfn{Latent Dirichlet
7379 Allocation} (LDA). This package allows the probabilistic modelling of
7380 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
7381 includes functionalities to identify cell states based on the contribution of
7382 cisTopics and explore the nature and regulatory proteins driving them.")
7383 (license license:gpl3))))
7385 (define-public r-genie3
7392 (uri (bioconductor-uri "GENIE3" version))
7395 "1z7qkv0cgdx2plhc7xdz6s7vwdjhzcdadi35wg3fl6xpids5njf5"))))
7396 (properties `((upstream-name . "GENIE3")))
7397 (build-system r-build-system)
7398 (propagated-inputs `(("r-reshape2" ,r-reshape2)))
7400 `(("r-knitr" ,r-knitr)))
7401 (home-page "https://bioconductor.org/packages/GENIE3")
7402 (synopsis "Gene network inference with ensemble of trees")
7404 "This package implements the GENIE3 algorithm for inferring gene
7405 regulatory networks from expression data.")
7406 (license license:gpl2+)))
7408 (define-public r-roc
7415 (uri (bioconductor-uri "ROC" version))
7418 "02b9n42z3kjrfxpdf3glqvimd79nhnycq00mb09fzhkpp5zl43c9"))))
7419 (properties `((upstream-name . "ROC")))
7420 (build-system r-build-system)
7422 `(("r-knitr" ,r-knitr)))
7423 (home-page "https://www.bioconductor.org/packages/ROC/")
7424 (synopsis "Utilities for ROC curves")
7426 "This package provides utilities for @dfn{Receiver Operating
7427 Characteristic} (ROC) curves, with a focus on micro arrays.")
7428 (license license:artistic2.0)))
7430 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
7432 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
7437 (uri (bioconductor-uri
7438 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
7439 version 'annotation))
7442 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
7445 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
7446 (build-system r-build-system)
7447 (propagated-inputs `(("r-minfi" ,r-minfi)))
7449 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
7450 (synopsis "Annotation for Illumina's 450k methylation arrays")
7452 "This package provides manifests and annotation for Illumina's 450k array
7454 (license license:artistic2.0)))
7456 (define-public r-watermelon
7458 (name "r-watermelon")
7463 (uri (bioconductor-uri "wateRmelon" version))
7466 "1sc2nxg9bafpvlwqhky2p5b6fkimkk9v3xcab9kvwnj6szrb6p3f"))))
7467 (properties `((upstream-name . "wateRmelon")))
7468 (build-system r-build-system)
7470 `(("r-biobase" ,r-biobase)
7471 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
7472 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
7473 ("r-illuminaio" ,r-illuminaio)
7474 ("r-limma" ,r-limma)
7476 ("r-matrixstats" ,r-matrixstats)
7477 ("r-methylumi" ,r-methylumi)
7479 (home-page "https://bioconductor.org/packages/wateRmelon/")
7480 (synopsis "Illumina 450 methylation array normalization and metrics")
7482 "The standard index of DNA methylation (beta) is computed from methylated
7483 and unmethylated signal intensities. Betas calculated from raw signal
7484 intensities perform well, but using 11 methylomic datasets we demonstrate that
7485 quantile normalization methods produce marked improvement. The commonly used
7486 procedure of normalizing betas is inferior to the separate normalization of M
7487 and U, and it is also advantageous to normalize Type I and Type II assays
7488 separately. This package provides 15 flavours of betas and three performance
7489 metrics, with methods for objects produced by the @code{methylumi} and
7490 @code{minfi} packages.")
7491 (license license:gpl3)))
7493 (define-public r-gdsfmt
7500 (uri (bioconductor-uri "gdsfmt" version))
7503 "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n"))
7504 (modules '((guix build utils)))
7505 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
7506 ;; them and link with system libraries instead.
7509 (for-each delete-file-recursively
7513 (substitute* "src/Makevars"
7514 (("all: \\$\\(SHLIB\\)") "all:")
7515 (("\\$\\(SHLIB\\): liblzma.a") "")
7516 (("(ZLIB|LZ4)/.*") "")
7517 (("CoreArray/dVLIntGDS.cpp.*")
7518 "CoreArray/dVLIntGDS.cpp")
7519 (("CoreArray/dVLIntGDS.o.*")
7520 "CoreArray/dVLIntGDS.o")
7521 (("PKG_LIBS = ./liblzma.a")
7522 "PKG_LIBS = -llz4"))
7523 (substitute* "src/CoreArray/dStream.h"
7524 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
7525 (string-append "include <" header ">")))
7527 (properties `((upstream-name . "gdsfmt")))
7528 (build-system r-build-system)
7534 `(("r-knitr" ,r-knitr)))
7535 (home-page "http://corearray.sourceforge.net/")
7537 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
7539 "This package provides a high-level R interface to CoreArray @dfn{Genomic
7540 Data Structure} (GDS) data files, which are portable across platforms with
7541 hierarchical structure to store multiple scalable array-oriented data sets
7542 with metadata information. It is suited for large-scale datasets, especially
7543 for data which are much larger than the available random-access memory. The
7544 @code{gdsfmt} package offers efficient operations specifically designed for
7545 integers of less than 8 bits, since a diploid genotype, like
7546 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
7547 byte. Data compression and decompression are available with relatively
7548 efficient random access. It is also allowed to read a GDS file in parallel
7549 with multiple R processes supported by the package @code{parallel}.")
7550 (license license:lgpl3)))
7552 (define-public r-bigmelon
7559 (uri (bioconductor-uri "bigmelon" version))
7562 "0hj5njwx7n681vigkq4560f9dm7mdjgvcwbgp5nbdn1fb2z24bk7"))))
7563 (properties `((upstream-name . "bigmelon")))
7564 (build-system r-build-system)
7566 `(("r-biobase" ,r-biobase)
7567 ("r-biocgenerics" ,r-biocgenerics)
7568 ("r-gdsfmt" ,r-gdsfmt)
7569 ("r-geoquery" ,r-geoquery)
7570 ("r-methylumi" ,r-methylumi)
7571 ("r-minfi" ,r-minfi)
7572 ("r-watermelon" ,r-watermelon)))
7573 (home-page "https://bioconductor.org/packages/bigmelon/")
7574 (synopsis "Illumina methylation array analysis for large experiments")
7576 "This package provides methods for working with Illumina arrays using the
7577 @code{gdsfmt} package.")
7578 (license license:gpl3)))
7580 (define-public r-seqbias
7587 (uri (bioconductor-uri "seqbias" version))
7590 "1m634sidmk6c603k2gflyiddkns9vr6ij591nmab523xk5r2f4b2"))))
7591 (properties `((upstream-name . "seqbias")))
7592 (build-system r-build-system)
7594 `(("r-biostrings" ,r-biostrings)
7595 ("r-genomicranges" ,r-genomicranges)
7596 ("r-rhtslib" ,r-rhtslib)))
7597 (home-page "https://bioconductor.org/packages/seqbias/")
7598 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
7600 "This package implements a model of per-position sequencing bias in
7601 high-throughput sequencing data using a simple Bayesian network, the structure
7602 and parameters of which are trained on a set of aligned reads and a reference
7604 (license license:lgpl3)))
7606 (define-public r-snplocs-hsapiens-dbsnp144-grch37
7608 (name "r-snplocs-hsapiens-dbsnp144-grch37")
7612 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
7613 version 'annotation))
7616 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
7617 (build-system r-build-system)
7618 ;; As this package provides little more than a very large data file it
7619 ;; doesn't make sense to build substitutes.
7620 (arguments `(#:substitutable? #f))
7622 `(("r-biocgenerics" ,r-biocgenerics)
7623 ("r-s4vectors" ,r-s4vectors)
7624 ("r-iranges" ,r-iranges)
7625 ("r-genomeinfodb" ,r-genomeinfodb)
7626 ("r-genomicranges" ,r-genomicranges)
7627 ("r-bsgenome" ,r-bsgenome)
7628 ("r-biostrings" ,r-biostrings)))
7630 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
7631 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
7632 (description "This package provides SNP locations and alleles for Homo
7633 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
7634 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
7635 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
7636 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
7637 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
7638 the mitochondrion chromosome. Therefore, the SNPs in this package can be
7639 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
7640 correct position but this injection will exclude chrM (i.e. nothing will be
7641 injected in that sequence).")
7642 (license license:artistic2.0)))
7644 (define-public r-reqon
7651 (uri (bioconductor-uri "ReQON" version))
7654 "1yz0r0rrk4n6dnqbdq41lvs5z8l6vkx729m0a7f29svw4dbc6mdq"))))
7655 (properties `((upstream-name . "ReQON")))
7656 (build-system r-build-system)
7658 `(("r-rjava" ,r-rjava)
7659 ("r-rsamtools" ,r-rsamtools)
7660 ("r-seqbias" ,r-seqbias)))
7661 (home-page "https://bioconductor.org/packages/ReQON/")
7662 (synopsis "Recalibrating quality of nucleotides")
7664 "This package provides an implementation of an algorithm for
7665 recalibrating the base quality scores for aligned sequencing data in BAM
7667 (license license:gpl2)))
7669 (define-public r-wavcluster
7671 (name "r-wavcluster")
7676 (uri (bioconductor-uri "wavClusteR" version))
7679 "18cg0jbr3rjyx31wwyag1n5gams55pbd2rvb99i3g80q9hvswawi"))))
7680 (properties `((upstream-name . "wavClusteR")))
7681 (build-system r-build-system)
7683 `(("r-biocgenerics" ,r-biocgenerics)
7684 ("r-biostrings" ,r-biostrings)
7685 ("r-foreach" ,r-foreach)
7686 ("r-genomicfeatures" ,r-genomicfeatures)
7687 ("r-genomicranges" ,r-genomicranges)
7688 ("r-ggplot2" ,r-ggplot2)
7689 ("r-hmisc" ,r-hmisc)
7690 ("r-iranges" ,r-iranges)
7691 ("r-mclust" ,r-mclust)
7692 ("r-rsamtools" ,r-rsamtools)
7693 ("r-rtracklayer" ,r-rtracklayer)
7694 ("r-s4vectors" ,r-s4vectors)
7695 ("r-seqinr" ,r-seqinr)
7696 ("r-stringr" ,r-stringr)))
7698 `(("r-knitr" ,r-knitr)))
7699 (home-page "https://bioconductor.org/packages/wavClusteR/")
7700 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
7702 "This package provides an integrated pipeline for the analysis of
7703 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
7704 sequencing errors, SNPs and additional non-experimental sources by a non-
7705 parametric mixture model. The protein binding sites (clusters) are then
7706 resolved at high resolution and cluster statistics are estimated using a
7707 rigorous Bayesian framework. Post-processing of the results, data export for
7708 UCSC genome browser visualization and motif search analysis are provided. In
7709 addition, the package integrates RNA-Seq data to estimate the False
7710 Discovery Rate of cluster detection. Key functions support parallel multicore
7711 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
7712 be applied to the analysis of other NGS data obtained from experimental
7713 procedures that induce nucleotide substitutions (e.g. BisSeq).")
7714 (license license:gpl2)))
7716 (define-public r-timeseriesexperiment
7718 (name "r-timeseriesexperiment")
7723 (uri (bioconductor-uri "TimeSeriesExperiment" version))
7726 "1jx0rk660mfzk7rfhamnp0disx3bv456cqi9hyaz2wcbcdrlvcjn"))))
7728 `((upstream-name . "TimeSeriesExperiment")))
7729 (build-system r-build-system)
7731 `(("r-deseq2" ,r-deseq2)
7732 ("r-dplyr" ,r-dplyr)
7733 ("r-dynamictreecut" ,r-dynamictreecut)
7734 ("r-edger" ,r-edger)
7735 ("r-ggplot2" ,r-ggplot2)
7736 ("r-hmisc" ,r-hmisc)
7737 ("r-limma" ,r-limma)
7738 ("r-magrittr" ,r-magrittr)
7739 ("r-proxy" ,r-proxy)
7740 ("r-s4vectors" ,r-s4vectors)
7741 ("r-summarizedexperiment" ,r-summarizedexperiment)
7742 ("r-tibble" ,r-tibble)
7743 ("r-tidyr" ,r-tidyr)
7744 ("r-vegan" ,r-vegan)
7745 ("r-viridis" ,r-viridis)))
7747 `(("r-knitr" ,r-knitr)))
7748 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
7749 (synopsis "Analysis for short time-series data")
7751 "This package is a visualization and analysis toolbox for short time
7752 course data which includes dimensionality reduction, clustering, two-sample
7753 differential expression testing and gene ranking techniques. The package also
7754 provides methods for retrieving enriched pathways.")
7755 (license license:lgpl3+)))
7757 (define-public r-variantfiltering
7759 (name "r-variantfiltering")
7764 (uri (bioconductor-uri "VariantFiltering" version))
7767 "0zy53knvyk8wy3hmnsxc0w9qkhvx6xhviskvx7rwmrsi7pz531l5"))))
7769 `((upstream-name . "VariantFiltering")))
7770 (build-system r-build-system)
7772 `(("r-annotationdbi" ,r-annotationdbi)
7773 ("r-biobase" ,r-biobase)
7774 ("r-biocgenerics" ,r-biocgenerics)
7775 ("r-biocparallel" ,r-biocparallel)
7776 ("r-biostrings" ,r-biostrings)
7777 ("r-bsgenome" ,r-bsgenome)
7779 ("r-genomeinfodb" ,r-genomeinfodb)
7780 ("r-genomicfeatures" ,r-genomicfeatures)
7781 ("r-genomicranges" ,r-genomicranges)
7782 ("r-genomicscores" ,r-genomicscores)
7783 ("r-graph" ,r-graph)
7785 ("r-iranges" ,r-iranges)
7787 ("r-rsamtools" ,r-rsamtools)
7788 ("r-s4vectors" ,r-s4vectors)
7789 ("r-shiny" ,r-shiny)
7790 ("r-shinyjs" ,r-shinyjs)
7791 ("r-shinythemes" ,r-shinythemes)
7792 ("r-shinytree" ,r-shinytree)
7793 ("r-summarizedexperiment" ,r-summarizedexperiment)
7794 ("r-variantannotation" ,r-variantannotation)
7795 ("r-xvector" ,r-xvector)))
7796 (home-page "https://github.com/rcastelo/VariantFiltering")
7797 (synopsis "Filtering of coding and non-coding genetic variants")
7799 "Filter genetic variants using different criteria such as inheritance
7800 model, amino acid change consequence, minor allele frequencies across human
7801 populations, splice site strength, conservation, etc.")
7802 (license license:artistic2.0)))
7804 (define-public r-genomegraphs
7806 (name "r-genomegraphs")
7811 (uri (bioconductor-uri "GenomeGraphs" version))
7814 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
7815 (properties `((upstream-name . "GenomeGraphs")))
7816 (build-system r-build-system)
7818 `(("r-biomart" ,r-biomart)))
7819 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
7820 (synopsis "Plotting genomic information from Ensembl")
7822 "Genomic data analyses requires integrated visualization of known genomic
7823 information and new experimental data. GenomeGraphs uses the biomaRt package
7824 to perform live annotation queries to Ensembl and translates this to e.g.
7825 gene/transcript structures in viewports of the grid graphics package. This
7826 results in genomic information plotted together with your data. Another
7827 strength of GenomeGraphs is to plot different data types such as array CGH,
7828 gene expression, sequencing and other data, together in one plot using the
7829 same genome coordinate system.")
7830 (license license:artistic2.0)))
7832 (define-public r-wavetiling
7834 (name "r-wavetiling")
7839 (uri (bioconductor-uri "waveTiling" version))
7842 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
7843 (properties `((upstream-name . "waveTiling")))
7844 (build-system r-build-system)
7846 `(("r-affy" ,r-affy)
7847 ("r-biobase" ,r-biobase)
7848 ("r-biostrings" ,r-biostrings)
7849 ("r-genomegraphs" ,r-genomegraphs)
7850 ("r-genomicranges" ,r-genomicranges)
7851 ("r-iranges" ,r-iranges)
7852 ("r-oligo" ,r-oligo)
7853 ("r-oligoclasses" ,r-oligoclasses)
7854 ("r-preprocesscore" ,r-preprocesscore)
7855 ("r-waveslim" ,r-waveslim)))
7856 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
7857 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
7859 "This package is designed to conduct transcriptome analysis for tiling
7860 arrays based on fast wavelet-based functional models.")
7861 (license license:gpl2+)))
7863 (define-public r-variancepartition
7865 (name "r-variancepartition")
7870 (uri (bioconductor-uri "variancePartition" version))
7873 "0fisaqd5v8xy9rz9l1zs62k1n2h4k1irzgwj46ci947l52x1qhah"))))
7875 `((upstream-name . "variancePartition")))
7876 (build-system r-build-system)
7878 `(("r-biobase" ,r-biobase)
7879 ("r-biocparallel" ,r-biocparallel)
7880 ("r-colorramps" ,r-colorramps)
7881 ("r-doparallel" ,r-doparallel)
7882 ("r-foreach" ,r-foreach)
7883 ("r-ggplot2" ,r-ggplot2)
7884 ("r-gplots" ,r-gplots)
7885 ("r-iterators" ,r-iterators)
7886 ("r-limma" ,r-limma)
7888 ("r-lmertest" ,r-lmertest)
7890 ("r-pbkrtest" ,r-pbkrtest)
7891 ("r-progress" ,r-progress)
7892 ("r-reshape2" ,r-reshape2)
7893 ("r-scales" ,r-scales)))
7895 `(("r-knitr" ,r-knitr)))
7896 (home-page "https://bioconductor.org/packages/variancePartition/")
7897 (synopsis "Analyze variation in gene expression experiments")
7899 "This is a package providing tools to quantify and interpret multiple
7900 sources of biological and technical variation in gene expression experiments.
7901 It uses a linear mixed model to quantify variation in gene expression
7902 attributable to individual, tissue, time point, or technical variables. The
7903 package includes dream differential expression analysis for repeated
7905 (license license:gpl2+)))
7907 (define-public r-htqpcr
7914 (uri (bioconductor-uri "HTqPCR" version))
7917 "1fzjx6psr41naq9ycpnv3lxlgkiyrpn7r2wl1i4gz45f3lax0yji"))))
7918 (properties `((upstream-name . "HTqPCR")))
7919 (build-system r-build-system)
7921 `(("r-affy" ,r-affy)
7922 ("r-biobase" ,r-biobase)
7923 ("r-gplots" ,r-gplots)
7924 ("r-limma" ,r-limma)
7925 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7926 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
7927 "groups/bertone/software/HTqPCR.pdf"))
7928 (synopsis "Automated analysis of high-throughput qPCR data")
7930 "Analysis of Ct values from high throughput quantitative real-time
7931 PCR (qPCR) assays across multiple conditions or replicates. The input data
7932 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
7933 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
7934 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
7935 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
7936 loading, quality assessment, normalization, visualization and parametric or
7937 non-parametric testing for statistical significance in Ct values between
7938 features (e.g. genes, microRNAs).")
7939 (license license:artistic2.0)))
7941 (define-public r-unifiedwmwqpcr
7943 (name "r-unifiedwmwqpcr")
7948 (uri (bioconductor-uri "unifiedWMWqPCR" version))
7951 "1ad5a7gy43l8x1rf5lgqiy2bv6fgah7cbnp4lrqwshphlnr30ndv"))))
7953 `((upstream-name . "unifiedWMWqPCR")))
7954 (build-system r-build-system)
7956 `(("r-biocgenerics" ,r-biocgenerics)
7957 ("r-htqpcr" ,r-htqpcr)))
7958 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
7959 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
7961 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
7962 data. This modified test allows for testing differential expression in qPCR
7964 (license license:gpl2+)))
7966 (define-public r-universalmotif
7968 (name "r-universalmotif")
7973 (uri (bioconductor-uri "universalmotif" version))
7976 "1ys2kbayc1rzv8nzi60208yfslm4kzynndfg7vw2n0c30dvzycrc"))))
7978 `((upstream-name . "universalmotif")))
7979 (build-system r-build-system)
7982 (modify-phases %standard-phases
7983 (add-after 'unpack 'fix-reference-to-strip
7985 (substitute* "src/Makevars"
7986 (("/usr/bin/strip") (which "strip"))))))))
7988 `(("r-biocgenerics" ,r-biocgenerics)
7989 ("r-biostrings" ,r-biostrings)
7990 ("r-ggplot2" ,r-ggplot2)
7991 ("r-ggseqlogo" ,r-ggseqlogo)
7992 ("r-iranges" ,r-iranges)
7995 ("r-rcppthread" ,r-rcppthread)
7996 ("r-rdpack" ,r-rdpack)
7997 ("r-rlang" ,r-rlang)
7998 ("r-s4vectors" ,r-s4vectors)
7999 ("r-yaml" ,r-yaml)))
8001 `(("r-knitr" ,r-knitr)))
8003 "https://bioconductor.org/packages/universalmotif/")
8005 "Specific structures importer, modifier, and exporter for R")
8007 "This package allows importing most common @dfn{specific structure}
8008 (motif) types into R for use by functions provided by other Bioconductor
8009 motif-related packages. Motifs can be exported into most major motif formats
8010 from various classes as defined by other Bioconductor packages. A suite of
8011 motif and sequence manipulation and analysis functions are included, including
8012 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
8013 motifs, and others.")
8014 (license license:gpl3)))
8016 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8018 (define-public r-activedriverwgs
8020 (name "r-activedriverwgs")
8025 (uri (cran-uri "ActiveDriverWGS" version))
8028 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
8030 `((upstream-name . "ActiveDriverWGS")))
8031 (build-system r-build-system)
8033 `(("r-biostrings" ,r-biostrings)
8034 ("r-bsgenome" ,r-bsgenome)
8035 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8036 ("r-genomeinfodb" ,r-genomeinfodb)
8037 ("r-genomicranges" ,r-genomicranges)
8038 ("r-iranges" ,r-iranges)
8039 ("r-s4vectors" ,r-s4vectors)))
8041 `(("r-knitr" ,r-knitr)))
8042 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
8043 (synopsis "Driver discovery tool for cancer whole genomes")
8045 "This package provides a method for finding an enrichment of cancer
8046 simple somatic mutations (SNVs and Indels) in functional elements across the
8047 human genome. ActiveDriverWGS detects coding and noncoding driver elements
8048 using whole genome sequencing data.")
8049 (license license:gpl3)))
8051 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
8053 (define-public r-activepathways
8055 (name "r-activepathways")
8060 (uri (cran-uri "ActivePathways" version))
8063 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
8065 `((upstream-name . "ActivePathways")))
8066 (build-system r-build-system)
8068 `(("r-data-table" ,r-data-table)
8069 ("r-ggplot2" ,r-ggplot2)))
8071 `(("r-knitr" ,r-knitr)))
8072 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
8073 (synopsis "Multivariate pathway enrichment analysis")
8075 "This package represents an integrative method of analyzing multi omics
8076 data that conducts enrichment analysis of annotated gene sets. ActivePathways
8077 uses a statistical data fusion approach, rationalizes contributing evidence
8078 and highlights associated genes, improving systems-level understanding of
8079 cellular organization in health and disease.")
8080 (license license:gpl3)))
8082 (define-public r-bgmix
8089 (uri (bioconductor-uri "BGmix" version))
8092 "0r9gjqajarg5mivxhqdzn8m8hmfarmzbplp3zqyyznccri03pv50"))))
8093 (properties `((upstream-name . "BGmix")))
8094 (build-system r-build-system)
8096 `(("r-kernsmooth" ,r-kernsmooth)))
8097 (home-page "https://bioconductor.org/packages/BGmix/")
8098 (synopsis "Bayesian models for differential gene expression")
8100 "This package provides fully Bayesian mixture models for differential
8102 (license license:gpl2)))
8104 (define-public r-bgx
8111 (uri (bioconductor-uri "bgx" version))
8114 "0gm4wv9drqvg9r4f0id1ivrfgv0nvh0hb6hp63b3jd14092777im"))))
8115 (properties `((upstream-name . "bgx")))
8116 (build-system r-build-system)
8118 `(("r-affy" ,r-affy)
8119 ("r-biobase" ,r-biobase)
8120 ("r-gcrma" ,r-gcrma)
8121 ("r-rcpp" ,r-rcpp)))
8122 (home-page "https://bioconductor.org/packages/bgx/")
8123 (synopsis "Bayesian gene expression")
8125 "This package provides tools for Bayesian integrated analysis of
8126 Affymetrix GeneChips.")
8127 (license license:gpl2)))
8129 (define-public r-bhc
8136 (uri (bioconductor-uri "BHC" version))
8139 "1n2rkbj8j10f38d40wvi6mwjxnrlfx71a48ab07bp2s0hwhxd7yn"))))
8140 (properties `((upstream-name . "BHC")))
8141 (build-system r-build-system)
8142 (home-page "https://bioconductor.org/packages/BHC/")
8143 (synopsis "Bayesian hierarchical clustering")
8145 "The method implemented in this package performs bottom-up hierarchical
8146 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
8147 in the data and Bayesian model selection to decide at each step which clusters
8148 to merge. This avoids several limitations of traditional methods, for example
8149 how many clusters there should be and how to choose a principled distance
8150 metric. This implementation accepts multinomial (i.e. discrete, with 2+
8151 categories) or time-series data. This version also includes a randomised
8152 algorithm which is more efficient for larger data sets.")
8153 (license license:gpl3)))
8155 (define-public r-bicare
8162 (uri (bioconductor-uri "BicARE" version))
8165 "1np3967rjx54hbjsynvya75lcsqa6zic6frw5fjwqybwv2pzzw2k"))))
8166 (properties `((upstream-name . "BicARE")))
8167 (build-system r-build-system)
8169 `(("r-biobase" ,r-biobase)
8170 ("r-gseabase" ,r-gseabase)
8171 ("r-multtest" ,r-multtest)))
8172 (home-page "http://bioinfo.curie.fr")
8173 (synopsis "Biclustering analysis and results exploration")
8175 "This is a package for biclustering analysis and exploration of
8177 (license license:gpl2)))
8179 (define-public r-bifet
8186 (uri (bioconductor-uri "BiFET" version))
8189 "191m1xhsj4l64rrh67hqiz1rdkfhw0gfd5aymf3x0xm710l3rh4a"))))
8190 (properties `((upstream-name . "BiFET")))
8191 (build-system r-build-system)
8193 `(("r-genomicranges" ,r-genomicranges)
8194 ("r-poibin" ,r-poibin)))
8196 `(("r-knitr" ,r-knitr)))
8197 (home-page "https://bioconductor.org/packages/BiFET")
8198 (synopsis "Bias-free footprint enrichment test")
8200 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
8201 over-represented in target regions compared to background regions after
8202 correcting for the bias arising from the imbalance in read counts and GC
8203 contents between the target and background regions. For a given TF k, BiFET
8204 tests the null hypothesis that the target regions have the same probability of
8205 having footprints for the TF k as the background regions while correcting for
8206 the read count and GC content bias.")
8207 (license license:gpl3)))
8209 (define-public r-rsbml
8216 (uri (bioconductor-uri "rsbml" version))
8219 "0vrjfhwcpc699sq78pkm022fam3ahar8h3lx3fr879dd21k02g61"))))
8220 (properties `((upstream-name . "rsbml")))
8221 (build-system r-build-system)
8223 `(("libsbml" ,libsbml)
8226 `(("r-biocgenerics" ,r-biocgenerics)
8227 ("r-graph" ,r-graph)))
8229 `(("pkg-config" ,pkg-config)))
8230 (home-page "http://www.sbml.org")
8231 (synopsis "R support for SBML")
8233 "This package provides an R interface to libsbml for SBML parsing,
8234 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
8235 (license license:artistic2.0)))
8237 (define-public r-hypergraph
8239 (name "r-hypergraph")
8244 (uri (bioconductor-uri "hypergraph" version))
8247 "1p5mzr2aiqqc1j2inh45abjvqhid9jqv6wiym1xxnz16mpaa7q97"))))
8248 (properties `((upstream-name . "hypergraph")))
8249 (build-system r-build-system)
8251 `(("r-graph" ,r-graph)))
8252 (home-page "https://bioconductor.org/packages/hypergraph")
8253 (synopsis "Hypergraph data structures")
8255 "This package implements some simple capabilities for representing and
8256 manipulating hypergraphs.")
8257 (license license:artistic2.0)))
8259 (define-public r-hyperdraw
8261 (name "r-hyperdraw")
8266 (uri (bioconductor-uri "hyperdraw" version))
8269 "0z3a3lpz7s0fw023fxldkgxvl2dl1wn8agnyj09sky11ainxdayz"))))
8270 (properties `((upstream-name . "hyperdraw")))
8271 (build-system r-build-system)
8272 (inputs `(("graphviz" ,graphviz)))
8274 `(("r-graph" ,r-graph)
8275 ("r-hypergraph" ,r-hypergraph)
8276 ("r-rgraphviz" ,r-rgraphviz)))
8277 (home-page "https://bioconductor.org/packages/hyperdraw")
8278 (synopsis "Visualizing hypergraphs")
8280 "This package provides functions for visualizing hypergraphs.")
8281 (license license:gpl2+)))
8283 (define-public r-biggr
8290 (uri (bioconductor-uri "BiGGR" version))
8293 "1hlsnss6071ck4ky1akxp1dnv3vmd8f85drdziqmm4nc2dfrr14y"))))
8294 (properties `((upstream-name . "BiGGR")))
8295 (build-system r-build-system)
8297 `(("r-hyperdraw" ,r-hyperdraw)
8298 ("r-hypergraph" ,r-hypergraph)
8300 ("r-limsolve" ,r-limsolve)
8301 ("r-rsbml" ,r-rsbml)
8302 ("r-stringr" ,r-stringr)))
8303 (home-page "https://bioconductor.org/packages/BiGGR/")
8304 (synopsis "Constraint based modeling using metabolic reconstruction databases")
8306 "This package provides an interface to simulate metabolic reconstruction
8307 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
8308 reconstruction databases. The package facilitates @dfn{flux balance
8309 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
8310 networks and estimated fluxes can be visualized with hypergraphs.")
8311 (license license:gpl3+)))
8313 (define-public r-bigmemoryextras
8315 (name "r-bigmemoryextras")
8320 (uri (bioconductor-uri "bigmemoryExtras" version))
8323 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
8325 `((upstream-name . "bigmemoryExtras")))
8326 (build-system r-build-system)
8328 `(("r-bigmemory" ,r-bigmemory)))
8330 `(("r-knitr" ,r-knitr)))
8331 (home-page "https://github.com/phaverty/bigmemoryExtras")
8332 (synopsis "Extension of the bigmemory package")
8334 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
8335 safety and convenience features to the @code{filebacked.big.matrix} class from
8336 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
8337 monitoring and gracefully restoring the connection to on-disk data and it also
8338 protects against accidental data modification with a file-system-based
8339 permissions system. Utilities are provided for using @code{BigMatrix}-derived
8340 classes as @code{assayData} matrices within the @code{Biobase} package's
8341 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
8342 related to attaching to, and indexing into, file-backed matrices with
8343 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
8344 a file-backed matrix with factor properties.")
8345 (license license:artistic2.0)))
8347 (define-public r-bigpint
8354 (uri (bioconductor-uri "bigPint" version))
8357 "1axgapy4iyx059777m9faczwwj03h3i5dyrs0rlc84axzhzd2kis"))))
8358 (properties `((upstream-name . "bigPint")))
8359 (build-system r-build-system)
8361 `(("r-delayedarray" ,r-delayedarray)
8362 ("r-dplyr" ,r-dplyr)
8363 ("r-ggally" ,r-ggally)
8364 ("r-ggplot2" ,r-ggplot2)
8365 ("r-gridextra" ,r-gridextra)
8366 ("r-hexbin" ,r-hexbin)
8367 ("r-hmisc" ,r-hmisc)
8368 ("r-htmlwidgets" ,r-htmlwidgets)
8369 ("r-plotly" ,r-plotly)
8371 ("r-rcolorbrewer" ,r-rcolorbrewer)
8372 ("r-reshape" ,r-reshape)
8373 ("r-shiny" ,r-shiny)
8374 ("r-shinycssloaders" ,r-shinycssloaders)
8375 ("r-shinydashboard" ,r-shinydashboard)
8376 ("r-stringr" ,r-stringr)
8377 ("r-summarizedexperiment" ,r-summarizedexperiment)
8378 ("r-tidyr" ,r-tidyr)))
8380 `(("r-knitr" ,r-knitr)))
8381 (home-page "https://github.com/lindsayrutter/bigPint")
8382 (synopsis "Big multivariate data plotted interactively")
8384 "This package provides methods for visualizing large multivariate
8385 datasets using static and interactive scatterplot matrices, parallel
8386 coordinate plots, volcano plots, and litre plots. It includes examples for
8387 visualizing RNA-sequencing datasets and differentially expressed genes.")
8388 (license license:gpl3)))
8390 (define-public r-chemminer
8392 (name "r-chemminer")
8397 (uri (bioconductor-uri "ChemmineR" version))
8400 "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
8401 (properties `((upstream-name . "ChemmineR")))
8402 (build-system r-build-system)
8404 `(("r-base64enc" ,r-base64enc)
8406 ("r-biocgenerics" ,r-biocgenerics)
8408 ("r-digest" ,r-digest)
8410 ("r-ggplot2" ,r-ggplot2)
8411 ("r-gridextra" ,r-gridextra)
8414 ("r-rcurl" ,r-rcurl)
8415 ("r-rjson" ,r-rjson)
8416 ("r-rsvg" ,r-rsvg)))
8418 `(("r-knitr" ,r-knitr)))
8419 (home-page "https://github.com/girke-lab/ChemmineR")
8420 (synopsis "Cheminformatics toolkit for R")
8422 "ChemmineR is a cheminformatics package for analyzing drug-like small
8423 molecule data in R. It contains functions for efficient processing of large
8424 numbers of molecules, physicochemical/structural property predictions,
8425 structural similarity searching, classification and clustering of compound
8426 libraries with a wide spectrum of algorithms. In addition, it offers
8427 visualization functions for compound clustering results and chemical
8429 (license license:artistic2.0)))
8431 (define-public r-bioassayr
8433 (name "r-bioassayr")
8438 (uri (bioconductor-uri "bioassayR" version))
8441 "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
8442 (properties `((upstream-name . "bioassayR")))
8443 (build-system r-build-system)
8445 `(("r-biocgenerics" ,r-biocgenerics)
8446 ("r-chemminer" ,r-chemminer)
8448 ("r-matrix" ,r-matrix)
8449 ("r-rjson" ,r-rjson)
8450 ("r-rsqlite" ,r-rsqlite)
8453 `(("r-knitr" ,r-knitr)))
8454 (home-page "https://github.com/girke-lab/bioassayR")
8455 (synopsis "Cross-target analysis of small molecule bioactivity")
8457 "bioassayR is a computational tool that enables simultaneous analysis of
8458 thousands of bioassay experiments performed over a diverse set of compounds
8459 and biological targets. Unique features include support for large-scale
8460 cross-target analyses of both public and custom bioassays, generation of
8461 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
8462 preloaded database that provides access to a substantial portion of publicly
8463 available bioactivity data.")
8464 (license license:artistic2.0)))
8466 (define-public r-biobroom
8473 (uri (bioconductor-uri "biobroom" version))
8476 "07wzamwl07p20s932aym2jkf6c1zz7d9h7kyby5ka4pw4abynlrv"))))
8477 (properties `((upstream-name . "biobroom")))
8478 (build-system r-build-system)
8480 `(("r-biobase" ,r-biobase)
8481 ("r-broom" ,r-broom)
8482 ("r-dplyr" ,r-dplyr)
8483 ("r-tidyr" ,r-tidyr)))
8485 `(("r-knitr" ,r-knitr)))
8486 (home-page "https://github.com/StoreyLab/biobroom")
8487 (synopsis "Turn Bioconductor objects into tidy data frames")
8489 "This package contains methods for converting standard objects
8490 constructed by bioinformatics packages, especially those in Bioconductor, and
8491 converting them to @code{tidy} data. It thus serves as a complement to the
8492 @code{broom} package, and follows the same tidy, augment, glance division of
8493 tidying methods. Tidying data makes it easy to recombine, reshape and
8494 visualize bioinformatics analyses.")
8495 ;; Any version of the LGPL.
8496 (license license:lgpl3+)))
8498 (define-public r-graphite
8505 (uri (bioconductor-uri "graphite" version))
8508 "1ihza8m397qfvr79fhghs2knmw862hwz2akysy39r8hndv6lc7wk"))))
8509 (properties `((upstream-name . "graphite")))
8510 (build-system r-build-system)
8512 `(("r-annotationdbi" ,r-annotationdbi)
8513 ("r-checkmate" ,r-checkmate)
8514 ("r-graph" ,r-graph)
8516 ("r-rappdirs" ,r-rappdirs)))
8517 (home-page "https://bioconductor.org/packages/graphite/")
8518 (synopsis "Networks from pathway databases")
8520 "Graphite provides networks derived from eight public pathway databases,
8521 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
8523 (license license:agpl3+)))
8525 (define-public r-reactomepa
8527 (name "r-reactomepa")
8532 (uri (bioconductor-uri "ReactomePA" version))
8535 "04b2ng9jp2bsfbg3wnbg6m6a5c3szcmbypk1lx34i63228g8z98m"))))
8536 (properties `((upstream-name . "ReactomePA")))
8537 (build-system r-build-system)
8539 `(("r-annotationdbi" ,r-annotationdbi)
8541 ("r-enrichplot" ,r-enrichplot)
8542 ("r-ggplot2" ,r-ggplot2)
8543 ("r-ggraph" ,r-ggraph)
8544 ("r-graphite" ,r-graphite)
8545 ("r-igraph" ,r-igraph)
8546 ("r-reactome-db" ,r-reactome-db)))
8548 `(("r-knitr" ,r-knitr)))
8549 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
8550 (synopsis "Reactome pathway analysis")
8552 "This package provides functions for pathway analysis based on the
8553 REACTOME pathway database. It implements enrichment analysis, gene set
8554 enrichment analysis and several functions for visualization.")
8555 (license license:gpl2)))
8557 (define-public r-ebarrays
8564 (uri (bioconductor-uri "EBarrays" version))
8567 "1r2dl19my1hqkq01fqk48pk3agb98vgrplj56kb4srhz2xm0w9pd"))))
8568 (properties `((upstream-name . "EBarrays")))
8569 (build-system r-build-system)
8571 `(("r-biobase" ,r-biobase)
8572 ("r-cluster" ,r-cluster)
8573 ("r-lattice" ,r-lattice)))
8574 (home-page "https://bioconductor.org/packages/EBarrays/")
8575 (synopsis "Gene clustering and differential expression identification")
8577 "EBarrays provides tools for the analysis of replicated/unreplicated
8579 (license license:gpl2+)))
8581 (define-public r-bioccasestudies
8583 (name "r-bioccasestudies")
8588 (uri (bioconductor-uri "BiocCaseStudies" version))
8591 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
8593 `((upstream-name . "BiocCaseStudies")))
8594 (build-system r-build-system)
8595 (propagated-inputs `(("r-biobase" ,r-biobase)))
8596 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
8597 (synopsis "Support for the case studies monograph")
8599 "This package provides software and data to support the case studies
8601 (license license:artistic2.0)))
8603 (define-public r-bioccheck
8605 (name "r-bioccheck")
8609 (uri (bioconductor-uri "BiocCheck" version))
8612 "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib"))))
8614 `((upstream-name . "BiocCheck")))
8615 (build-system r-build-system)
8618 (modify-phases %standard-phases
8619 ;; This package can be used by calling BiocCheck(<package>) from
8620 ;; within R, or by running R CMD BiocCheck <package>. This phase
8621 ;; makes sure the latter works. For this to work, the BiocCheck
8622 ;; script must be somewhere on the PATH (not the R bin directory).
8623 (add-after 'install 'install-bioccheck-subcommand
8624 (lambda* (#:key outputs #:allow-other-keys)
8625 (let* ((out (assoc-ref outputs "out"))
8626 (dest-dir (string-append out "/bin"))
8628 (string-append out "/site-library/BiocCheck/script/")))
8630 (symlink (string-append script-dir "/checkBadDeps.R")
8631 (string-append dest-dir "/checkBadDeps.R"))
8632 (symlink (string-append script-dir "/BiocCheck")
8633 (string-append dest-dir "/BiocCheck")))
8636 `(("r-codetools" ,r-codetools)
8637 ("r-graph" ,r-graph)
8639 ("r-knitr" ,r-knitr)
8640 ("r-optparse" ,r-optparse)
8641 ("r-biocmanager" ,r-biocmanager)
8642 ("r-biocviews" ,r-biocviews)
8643 ("r-stringdist" ,r-stringdist)))
8645 `(("r-knitr" ,r-knitr)))
8646 (home-page "https://bioconductor.org/packages/BiocCheck")
8647 (synopsis "Executes Bioconductor-specific package checks")
8648 (description "This package contains tools to perform additional quality
8649 checks on R packages that are to be submitted to the Bioconductor repository.")
8650 (license license:artistic2.0)))
8652 (define-public r-biocgraph
8654 (name "r-biocgraph")
8659 (uri (bioconductor-uri "biocGraph" version))
8662 "02y7vizc6jv8y9r8chsda4yysim0ch45i3rasqvv7m85zqsskf75"))))
8663 (properties `((upstream-name . "biocGraph")))
8664 (build-system r-build-system)
8666 `(("r-biocgenerics" ,r-biocgenerics)
8667 ("r-geneplotter" ,r-geneplotter)
8668 ("r-graph" ,r-graph)
8669 ("r-rgraphviz" ,r-rgraphviz)))
8670 (home-page "https://bioconductor.org/packages/biocGraph/")
8671 (synopsis "Graph examples and use cases in Bioinformatics")
8673 "This package provides examples and code that make use of the
8674 different graph related packages produced by Bioconductor.")
8675 (license license:artistic2.0)))
8677 (define-public r-biocstyle
8679 (name "r-biocstyle")
8683 (uri (bioconductor-uri "BiocStyle" version))
8686 "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp"))))
8688 `((upstream-name . "BiocStyle")))
8689 (build-system r-build-system)
8691 `(("r-biocmanager" ,r-biocmanager)
8692 ("r-bookdown" ,r-bookdown)
8693 ("r-knitr" ,r-knitr)
8694 ("r-rmarkdown" ,r-rmarkdown)
8695 ("r-yaml" ,r-yaml)))
8697 `(("r-knitr" ,r-knitr)))
8698 (home-page "https://bioconductor.org/packages/BiocStyle")
8699 (synopsis "Bioconductor formatting styles")
8700 (description "This package provides standard formatting styles for
8701 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
8703 (license license:artistic2.0)))
8705 (define-public r-biocviews
8707 (name "r-biocviews")
8711 (uri (bioconductor-uri "biocViews" version))
8714 "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4"))))
8716 `((upstream-name . "biocViews")))
8717 (build-system r-build-system)
8719 `(("r-biobase" ,r-biobase)
8720 ("r-biocmanager" ,r-biocmanager)
8721 ("r-graph" ,r-graph)
8723 ("r-rcurl" ,r-rcurl)
8725 ("r-runit" ,r-runit)))
8726 (home-page "https://bioconductor.org/packages/biocViews")
8727 (synopsis "Bioconductor package categorization helper")
8728 (description "The purpose of biocViews is to create HTML pages that
8729 categorize packages in a Bioconductor package repository according to keywords,
8730 also known as views, in a controlled vocabulary.")
8731 (license license:artistic2.0)))
8733 (define-public r-experimenthub
8735 (name "r-experimenthub")
8740 (uri (bioconductor-uri "ExperimentHub" version))
8743 "1zi7vsrhf1hj27rlzrxl4jd81fqh1yhn0svp2d9w71fizsi71akg"))))
8744 (properties `((upstream-name . "ExperimentHub")))
8745 (build-system r-build-system)
8747 `(("r-annotationhub" ,r-annotationhub)
8748 ("r-biocfilecache" ,r-biocfilecache)
8749 ("r-biocgenerics" ,r-biocgenerics)
8750 ("r-biocmanager" ,r-biocmanager)
8752 ("r-rappdirs" ,r-rappdirs)
8753 ("r-s4vectors" ,r-s4vectors)))
8755 `(("r-knitr" ,r-knitr)))
8756 (home-page "https://bioconductor.org/packages/ExperimentHub/")
8757 (synopsis "Client to access ExperimentHub resources")
8759 "This package provides a client for the Bioconductor ExperimentHub web
8760 resource. ExperimentHub provides a central location where curated data from
8761 experiments, publications or training courses can be accessed. Each resource
8762 has associated metadata, tags and date of modification. The client creates
8763 and manages a local cache of files retrieved enabling quick and reproducible
8765 (license license:artistic2.0)))
8767 (define-public r-grohmm
8774 (uri (bioconductor-uri "groHMM" version))
8777 "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx"))))
8778 (properties `((upstream-name . "groHMM")))
8779 (build-system r-build-system)
8781 `(("r-genomeinfodb" ,r-genomeinfodb)
8782 ("r-genomicalignments" ,r-genomicalignments)
8783 ("r-genomicranges" ,r-genomicranges)
8784 ("r-iranges" ,r-iranges)
8786 ("r-rtracklayer" ,r-rtracklayer)
8787 ("r-s4vectors" ,r-s4vectors)))
8788 (home-page "https://github.com/Kraus-Lab/groHMM")
8789 (synopsis "GRO-seq analysis pipeline")
8791 "This package provides a pipeline for the analysis of GRO-seq data.")
8792 (license license:gpl3+)))
8794 (define-public r-multiassayexperiment
8796 (name "r-multiassayexperiment")
8801 (uri (bioconductor-uri "MultiAssayExperiment" version))
8804 "1nx3gikl8vr54862h6wl0q30arnpynla085219lhh61ziswdffrs"))))
8806 `((upstream-name . "MultiAssayExperiment")))
8807 (build-system r-build-system)
8809 `(("r-biobase" ,r-biobase)
8810 ("r-biocgenerics" ,r-biocgenerics)
8811 ("r-genomicranges" ,r-genomicranges)
8812 ("r-iranges" ,r-iranges)
8813 ("r-s4vectors" ,r-s4vectors)
8814 ("r-summarizedexperiment" ,r-summarizedexperiment)
8815 ("r-tidyr" ,r-tidyr)))
8817 `(("r-knitr" ,r-knitr)))
8818 (home-page "https://waldronlab.io/MultiAssayExperiment/")
8819 (synopsis "Integration of multi-omics experiments in Bioconductor")
8821 "MultiAssayExperiment harmonizes data management of multiple assays
8822 performed on an overlapping set of specimens. It provides a familiar
8823 Bioconductor user experience by extending concepts from
8824 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
8825 classes for individual assays, and allowing subsetting by genomic ranges or
8827 (license license:artistic2.0)))
8829 (define-public r-bioconcotk
8831 (name "r-bioconcotk")
8836 (uri (bioconductor-uri "BiocOncoTK" version))
8839 "1jwp0gww2xyx8qfv5h4y0v3g66mmlyrd1v64xn91si4fsymk4108"))))
8840 (properties `((upstream-name . "BiocOncoTK")))
8841 (build-system r-build-system)
8843 `(("r-bigrquery" ,r-bigrquery)
8845 ("r-complexheatmap" ,r-complexheatmap)
8846 ("r-curatedtcgadata" ,r-curatedtcgadata)
8848 ("r-dplyr" ,r-dplyr)
8850 ("r-genomicfeatures" ,r-genomicfeatures)
8851 ("r-genomicranges" ,r-genomicranges)
8852 ("r-ggplot2" ,r-ggplot2)
8853 ("r-ggpubr" ,r-ggpubr)
8854 ("r-graph" ,r-graph)
8856 ("r-iranges" ,r-iranges)
8857 ("r-magrittr" ,r-magrittr)
8859 ("r-rgraphviz" ,r-rgraphviz)
8860 ("r-rjson" ,r-rjson)
8861 ("r-s4vectors" ,r-s4vectors)
8862 ("r-scales" ,r-scales)
8863 ("r-shiny" ,r-shiny)
8864 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8866 `(("r-knitr" ,r-knitr)))
8867 (home-page "https://bioconductor.org/packages/BiocOncoTK")
8868 (synopsis "Bioconductor components for general cancer genomics")
8870 "The purpose of this package is to provide a central interface to various
8871 tools for genome-scale analysis of cancer studies.")
8872 (license license:artistic2.0)))
8874 (define-public r-biocor
8881 (uri (bioconductor-uri "BioCor" version))
8884 "12slrdn98h43j3y7klk3chrwa2ycwm4krhz3l3kfzbxr834mhy19"))))
8885 (properties `((upstream-name . "BioCor")))
8886 (build-system r-build-system)
8888 `(("r-biocparallel" ,r-biocparallel)
8889 ("r-gseabase" ,r-gseabase)
8890 ("r-matrix" ,r-matrix)))
8892 `(("r-knitr" ,r-knitr)))
8893 (home-page "https://llrs.github.io/BioCor/")
8894 (synopsis "Functional similarities")
8896 "This package provides tools to calculate functional similarities based
8897 on the pathways described on KEGG and REACTOME or in gene sets. These
8898 similarities can be calculated for pathways or gene sets, genes, or clusters
8899 and combined with other similarities. They can be used to improve networks,
8900 gene selection, testing relationships, and so on.")
8901 (license license:expat)))
8903 (define-public r-biocpkgtools
8905 (name "r-biocpkgtools")
8910 (uri (bioconductor-uri "BiocPkgTools" version))
8913 "12j4vag40zdgrxfzaqvf3ly7776qyziryz04c3jqzgsqfvzvzz8m"))))
8914 (properties `((upstream-name . "BiocPkgTools")))
8915 (build-system r-build-system)
8917 `(("r-biocfilecache" ,r-biocfilecache)
8918 ("r-biocmanager" ,r-biocmanager)
8919 ("r-biocviews" ,r-biocviews)
8920 ("r-dplyr" ,r-dplyr)
8923 ("r-graph" ,r-graph)
8924 ("r-htmltools" ,r-htmltools)
8925 ("r-htmlwidgets" ,r-htmlwidgets)
8927 ("r-igraph" ,r-igraph)
8928 ("r-jsonlite" ,r-jsonlite)
8929 ("r-magrittr" ,r-magrittr)
8930 ("r-rappdirs" ,r-rappdirs)
8932 ("r-readr" ,r-readr)
8934 ("r-rlang" ,r-rlang)
8935 ("r-rvest" ,r-rvest)
8936 ("r-stringr" ,r-stringr)
8937 ("r-tibble" ,r-tibble)
8938 ("r-tidyr" ,r-tidyr)
8939 ("r-tidyselect" ,r-tidyselect)
8940 ("r-xml2" ,r-xml2)))
8942 `(("r-knitr" ,r-knitr)))
8943 (home-page "https://github.com/seandavi/BiocPkgTools")
8944 (synopsis "Collection of tools for learning about Bioconductor packages")
8946 "Bioconductor has a rich ecosystem of metadata around packages, usage,
8947 and build status. This package is a simple collection of functions to access
8948 that metadata from R. The goal is to expose metadata for data mining and
8949 value-added functionality such as package searching, text mining, and
8950 analytics on packages.")
8951 (license license:expat)))
8953 (define-public r-biocset
8960 (uri (bioconductor-uri "BiocSet" version))
8963 "16pjg09i0j5qk9s9qzm6fq5q0bgwb4wgqvp6scs06ajgrr07qjqg"))))
8964 (properties `((upstream-name . "BiocSet")))
8965 (build-system r-build-system)
8967 `(("r-annotationdbi" ,r-annotationdbi)
8968 ("r-biocio" ,r-biocio)
8969 ("r-dplyr" ,r-dplyr)
8970 ("r-keggrest" ,r-keggrest)
8971 ("r-ontologyindex" ,r-ontologyindex)
8973 ("r-rlang" ,r-rlang)
8974 ("r-s4vectors" ,r-s4vectors)
8975 ("r-tibble" ,r-tibble)
8976 ("r-tidyr" ,r-tidyr)))
8978 `(("r-knitr" ,r-knitr)))
8980 "https://bioconductor.org/packages/BiocSet")
8982 "Representing Different Biological Sets")
8984 "BiocSet displays different biological sets in a triple tibble format.
8985 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
8986 The user has the ability to activate one of these three tibbles to perform
8987 common functions from the @code{dplyr} package. Mapping functionality and
8988 accessing web references for elements/sets are also available in BiocSet.")
8989 (license license:artistic2.0)))
8991 (define-public r-biocworkflowtools
8993 (name "r-biocworkflowtools")
8998 (uri (bioconductor-uri "BiocWorkflowTools" version))
9001 "0lvckdy20bhgyhqbccp0rdfi2p6vvip694r27qwpyi5092nfmqh6"))))
9003 `((upstream-name . "BiocWorkflowTools")))
9004 (build-system r-build-system)
9006 `(("r-biocstyle" ,r-biocstyle)
9007 ("r-bookdown" ,r-bookdown)
9008 ("r-git2r" ,r-git2r)
9010 ("r-knitr" ,r-knitr)
9011 ("r-rmarkdown" ,r-rmarkdown)
9012 ("r-rstudioapi" ,r-rstudioapi)
9013 ("r-stringr" ,r-stringr)
9014 ("r-usethis" ,r-usethis)))
9016 `(("r-knitr" ,r-knitr)))
9017 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
9018 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
9020 "This package provides functions to ease the transition between
9021 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
9022 (license license:expat)))
9024 (define-public r-biodist
9031 (uri (bioconductor-uri "bioDist" version))
9034 "10p4iajpyqgqb35743jm1a33lwbsmax2g4vz9fbbhn2cpiq3chap"))))
9035 (properties `((upstream-name . "bioDist")))
9036 (build-system r-build-system)
9038 `(("r-biobase" ,r-biobase)
9039 ("r-kernsmooth" ,r-kernsmooth)))
9040 (home-page "https://bioconductor.org/packages/bioDist/")
9041 (synopsis "Different distance measures")
9043 "This package provides a collection of software tools for calculating
9044 distance measures.")
9045 (license license:artistic2.0)))
9047 (define-public r-pcatools
9054 (uri (bioconductor-uri "PCAtools" version))
9057 "1fz9h99yyn49b5rcnkg2kjdfmczfwnc44fpwbia0izj6gx192phb"))))
9058 (properties `((upstream-name . "PCAtools")))
9059 (build-system r-build-system)
9061 `(("r-beachmat" ,r-beachmat)
9063 ("r-biocparallel" ,r-biocparallel)
9064 ("r-biocsingular" ,r-biocsingular)
9065 ("r-cowplot" ,r-cowplot)
9066 ("r-delayedarray" ,r-delayedarray)
9067 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9068 ("r-dqrng" ,r-dqrng)
9069 ("r-ggplot2" ,r-ggplot2)
9070 ("r-ggrepel" ,r-ggrepel)
9071 ("r-lattice" ,r-lattice)
9072 ("r-matrix" ,r-matrix)
9074 ("r-reshape2" ,r-reshape2)))
9075 (native-inputs `(("r-knitr" ,r-knitr)))
9076 (home-page "https://github.com/kevinblighe/PCAtools")
9077 (synopsis "PCAtools: everything Principal Components Analysis")
9079 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
9080 structure of the data without the need to build any model to represent it.
9081 This \"summary\" of the data is arrived at through a process of reduction that
9082 can transform the large number of variables into a lesser number that are
9083 uncorrelated (i.e. the 'principal components'), while at the same time being
9084 capable of easy interpretation on the original data. PCAtools provides
9085 functions for data exploration via PCA, and allows the user to generate
9086 publication-ready figures. PCA is performed via @code{BiocSingular}; users
9087 can also identify an optimal number of principal components via different
9088 metrics, such as the elbow method and Horn's parallel analysis, which has
9089 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
9090 dimensional mass cytometry data.")
9091 (license license:gpl3)))
9093 (define-public r-rgreat
9100 (uri (bioconductor-uri "rGREAT" version))
9103 "0p2b8cqxibxxmsh687y7yvlvr2a5ipiz53jb4wsr8ddypynb1asj"))))
9104 (properties `((upstream-name . "rGREAT")))
9105 (build-system r-build-system)
9107 `(("r-genomicranges" ,r-genomicranges)
9108 ("r-getoptlong" ,r-getoptlong)
9109 ("r-iranges" ,r-iranges)
9110 ("r-rcurl" ,r-rcurl)
9111 ("r-rjson" ,r-rjson)))
9112 (native-inputs `(("r-knitr" ,r-knitr)))
9113 (home-page "https://github.com/jokergoo/rGREAT")
9114 (synopsis "Client for GREAT analysis")
9116 "This package makes GREAT (Genomic Regions Enrichment of Annotations
9117 Tool) analysis automatic by constructing a HTTP POST request according to
9118 user's input and automatically retrieving results from GREAT web server.")
9119 (license license:expat)))
9121 (define-public r-m3c
9128 (uri (bioconductor-uri "M3C" version))
9131 "05ygi4fd85hh17mlww5wcww8d5z5zvkn2r46s4n6g18mcbv8snv5"))))
9132 (properties `((upstream-name . "M3C")))
9133 (build-system r-build-system)
9135 `(("r-cluster" ,r-cluster)
9136 ("r-corpcor" ,r-corpcor)
9137 ("r-doparallel" ,r-doparallel)
9138 ("r-dosnow" ,r-dosnow)
9139 ("r-foreach" ,r-foreach)
9140 ("r-ggplot2" ,r-ggplot2)
9141 ("r-matrix" ,r-matrix)
9142 ("r-matrixcalc" ,r-matrixcalc)
9143 ("r-rtsne" ,r-rtsne)
9144 ("r-umap" ,r-umap)))
9145 (native-inputs `(("r-knitr" ,r-knitr)))
9146 (home-page "https://bioconductor.org/packages/M3C")
9147 (synopsis "Monte Carlo reference-based consensus clustering")
9149 "M3C is a consensus clustering algorithm that uses a Monte Carlo
9150 simulation to eliminate overestimation of @code{K} and can reject the null
9151 hypothesis @code{K=1}.")
9152 (license license:agpl3+)))
9154 (define-public r-icens
9161 (uri (bioconductor-uri "Icens" version))
9164 "1w94mvh8pai77h4fcaiyacmzs58n4kbiq6bm4z0hk24j1ywph3dr"))))
9165 (properties `((upstream-name . "Icens")))
9166 (build-system r-build-system)
9168 `(("r-survival" ,r-survival)))
9169 (home-page "https://bioconductor.org/packages/Icens")
9170 (synopsis "NPMLE for censored and truncated data")
9172 "This package provides many functions for computing the
9173 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
9175 (license license:artistic2.0)))
9177 ;; This is a CRAN package but it depends on r-icens, which is published on
9179 (define-public r-interval
9186 (uri (cran-uri "interval" version))
9189 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
9190 (properties `((upstream-name . "interval")))
9191 (build-system r-build-system)
9193 `(("r-icens" ,r-icens)
9194 ("r-mlecens" ,r-mlecens)
9196 ("r-survival" ,r-survival)))
9197 (home-page "https://cran.r-project.org/web/packages/interval/")
9198 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
9200 "This package provides functions to fit nonparametric survival curves,
9201 plot them, and perform logrank or Wilcoxon type tests.")
9202 (license license:gpl2+)))
9204 ;; This is a CRAN package, but it depends on r-interval, which depends on a
9205 ;; Bioconductor package.
9206 (define-public r-fhtest
9213 (uri (cran-uri "FHtest" version))
9216 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
9217 (properties `((upstream-name . "FHtest")))
9218 (build-system r-build-system)
9220 `(("r-interval" ,r-interval)
9221 ("r-kmsurv" ,r-kmsurv)
9224 ("r-survival" ,r-survival)))
9225 (home-page "https://cran.r-project.org/web/packages/FHtest/")
9226 (synopsis "Tests for survival data based on the Fleming-Harrington class")
9228 "This package provides functions to compare two or more survival curves
9232 @item The Fleming-Harrington test for right-censored data based on
9233 permutations and on counting processes.
9234 @item An extension of the Fleming-Harrington test for interval-censored data
9235 based on a permutation distribution and on a score vector distribution.
9238 (license license:gpl2+)))
9240 (define-public r-fourcseq
9247 (uri (bioconductor-uri "FourCSeq" version))
9249 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
9250 (properties `((upstream-name . "FourCSeq")))
9251 (build-system r-build-system)
9253 `(("r-biobase" ,r-biobase)
9254 ("r-biostrings" ,r-biostrings)
9255 ("r-deseq2" ,r-deseq2)
9257 ("r-genomicalignments" ,r-genomicalignments)
9258 ("r-genomicranges" ,r-genomicranges)
9259 ("r-ggbio" ,r-ggbio)
9260 ("r-ggplot2" ,r-ggplot2)
9261 ("r-gtools" ,r-gtools)
9263 ("r-matrix" ,r-matrix)
9264 ("r-reshape2" ,r-reshape2)
9265 ("r-rsamtools" ,r-rsamtools)
9266 ("r-rtracklayer" ,r-rtracklayer)
9267 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9269 `(("r-knitr" ,r-knitr)))
9271 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
9272 (synopsis "Analysis of multiplexed 4C sequencing data")
9274 "This package is an R package dedicated to the analysis of (multiplexed)
9275 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
9276 interactions between DNA elements and identify differential interactions
9277 between conditions. The statistical analysis in R starts with individual bam
9278 files for each sample as inputs. To obtain these files, the package contains
9279 a Python script to demultiplex libraries and trim off primer sequences. With
9280 a standard alignment software the required bam files can be then be
9282 (license license:gpl3+)))
9284 (define-public r-preprocesscore
9286 (name "r-preprocesscore")
9291 (uri (bioconductor-uri "preprocessCore" version))
9294 "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll"))))
9296 `((upstream-name . "preprocessCore")))
9297 (build-system r-build-system)
9298 (home-page "https://github.com/bmbolstad/preprocessCore")
9299 (synopsis "Collection of pre-processing functions")
9301 "This package provides a library of core pre-processing and normalization
9303 (license license:lgpl2.0+)))
9305 (define-public r-s4vectors
9307 (name "r-s4vectors")
9311 (uri (bioconductor-uri "S4Vectors" version))
9314 "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh"))))
9316 `((upstream-name . "S4Vectors")))
9317 (build-system r-build-system)
9319 `(("r-biocgenerics" ,r-biocgenerics)))
9320 (home-page "https://bioconductor.org/packages/S4Vectors")
9321 (synopsis "S4 implementation of vectors and lists")
9323 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
9324 classes and a set of generic functions that extend the semantic of ordinary
9325 vectors and lists in R. Package developers can easily implement vector-like
9326 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
9327 In addition, a few low-level concrete subclasses of general interest (e.g.
9328 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
9329 S4Vectors package itself.")
9330 (license license:artistic2.0)))
9332 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
9333 ;; Bioconductor package.
9334 (define-public r-wgcna
9341 (uri (cran-uri "WGCNA" version))
9344 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
9345 (properties `((upstream-name . "WGCNA")))
9346 (build-system r-build-system)
9348 `(("r-annotationdbi" ,r-annotationdbi)
9349 ("r-doparallel" ,r-doparallel)
9350 ("r-dynamictreecut" ,r-dynamictreecut)
9351 ("r-fastcluster" ,r-fastcluster)
9352 ("r-foreach" ,r-foreach)
9353 ("r-go-db" ,r-go-db)
9354 ("r-hmisc" ,r-hmisc)
9355 ("r-impute" ,r-impute)
9357 ("r-survival" ,r-survival)
9358 ("r-matrixstats" ,r-matrixstats)
9359 ("r-preprocesscore" ,r-preprocesscore)))
9361 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
9362 (synopsis "Weighted correlation network analysis")
9364 "This package provides functions necessary to perform Weighted
9365 Correlation Network Analysis on high-dimensional data. It includes functions
9366 for rudimentary data cleaning, construction and summarization of correlation
9367 networks, module identification and functions for relating both variables and
9368 modules to sample traits. It also includes a number of utility functions for
9369 data manipulation and visualization.")
9370 (license license:gpl2+)))
9372 (define-public r-rgraphviz
9374 (name "r-rgraphviz")
9379 (uri (bioconductor-uri "Rgraphviz" version))
9382 "1k0nrskak2v5xv7za226r3wypja3zxxmmc0cxz2imjhlgnkbha77"))))
9383 (properties `((upstream-name . "Rgraphviz")))
9384 (build-system r-build-system)
9387 (modify-phases %standard-phases
9388 (add-after 'unpack 'make-reproducible
9390 ;; The replacement value is taken from src/graphviz/builddate.h
9391 (substitute* "src/graphviz/configure"
9392 (("VERSION_DATE=.*")
9393 "VERSION_DATE=20200427.2341\n"))
9395 ;; FIXME: Rgraphviz bundles the sources of an older variant of
9396 ;; graphviz. It does not build with the latest version of graphviz, so
9397 ;; we do not add graphviz to the inputs.
9398 (inputs `(("zlib" ,zlib)))
9400 `(("r-graph" ,r-graph)))
9402 `(("pkg-config" ,pkg-config)))
9403 (home-page "https://bioconductor.org/packages/Rgraphviz")
9404 (synopsis "Plotting capabilities for R graph objects")
9406 "This package interfaces R with the graphviz library for plotting R graph
9407 objects from the @code{graph} package.")
9408 (license license:epl1.0)))
9410 (define-public r-fithic
9416 (uri (bioconductor-uri "FitHiC" version))
9419 "1sdfkqc6s7m9whkzr0mllzzfjzhj2g54ncjwxj8q0azjgszrfwd2"))))
9420 (properties `((upstream-name . "FitHiC")))
9421 (build-system r-build-system)
9423 `(("r-data-table" ,r-data-table)
9424 ("r-fdrtool" ,r-fdrtool)
9425 ("r-rcpp" ,r-rcpp)))
9427 `(("r-knitr" ,r-knitr)))
9428 (home-page "https://bioconductor.org/packages/FitHiC")
9429 (synopsis "Confidence estimation for intra-chromosomal contact maps")
9431 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
9432 intra-chromosomal contact maps produced by genome-wide genome architecture
9433 assays such as Hi-C.")
9434 (license license:gpl2+)))
9436 (define-public r-hitc
9442 (uri (bioconductor-uri "HiTC" version))
9445 "1xbh36qgmzl8b6xq0hnl41li2x18yma50fq0v4dglh2ddn7as9iy"))))
9446 (properties `((upstream-name . "HiTC")))
9447 (build-system r-build-system)
9449 `(("r-biostrings" ,r-biostrings)
9450 ("r-genomeinfodb" ,r-genomeinfodb)
9451 ("r-genomicranges" ,r-genomicranges)
9452 ("r-iranges" ,r-iranges)
9453 ("r-matrix" ,r-matrix)
9454 ("r-rcolorbrewer" ,r-rcolorbrewer)
9455 ("r-rtracklayer" ,r-rtracklayer)))
9456 (home-page "https://bioconductor.org/packages/HiTC")
9457 (synopsis "High throughput chromosome conformation capture analysis")
9459 "The HiTC package was developed to explore high-throughput \"C\" data
9460 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
9461 quality controls, normalization, visualization, and further analysis are also
9463 (license license:artistic2.0)))
9465 (define-public r-hdf5array
9467 (name "r-hdf5array")
9472 (uri (bioconductor-uri "HDF5Array" version))
9475 "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g"))))
9476 (properties `((upstream-name . "HDF5Array")))
9477 (build-system r-build-system)
9480 (modify-phases %standard-phases
9481 (add-after 'unpack 'fix-linking
9483 (substitute* "src/Makevars"
9484 ;; This is to avoid having a plain directory on the list of
9485 ;; libraries to link.
9486 (("\\(RHDF5LIB_LIBS\\)" match)
9487 (string-append match "/libhdf5.a")))
9492 `(("r-biocgenerics" ,r-biocgenerics)
9493 ("r-delayedarray" ,r-delayedarray)
9494 ("r-iranges" ,r-iranges)
9495 ("r-matrix" ,r-matrix)
9496 ("r-rhdf5" ,r-rhdf5)
9497 ("r-rhdf5lib" ,r-rhdf5lib)
9498 ("r-s4vectors" ,r-s4vectors)))
9499 (home-page "https://bioconductor.org/packages/HDF5Array")
9500 (synopsis "HDF5 back end for DelayedArray objects")
9501 (description "This package provides an array-like container for convenient
9502 access and manipulation of HDF5 datasets. It supports delayed operations and
9504 (license license:artistic2.0)))
9506 (define-public r-rhdf5lib
9513 (uri (bioconductor-uri "Rhdf5lib" version))
9516 "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28"))
9517 (modules '((guix build utils)))
9520 ;; Delete bundled binaries
9521 (delete-file-recursively "src/wininclude/")
9522 (delete-file-recursively "src/winlib-4.9.3/")
9523 (delete-file-recursively "src/winlib-8.3.0/")
9524 (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
9526 (properties `((upstream-name . "Rhdf5lib")))
9527 (build-system r-build-system)
9530 (modify-phases %standard-phases
9531 (add-after 'unpack 'do-not-use-bundled-hdf5
9532 (lambda* (#:key inputs #:allow-other-keys)
9533 (for-each delete-file '("configure" "configure.ac"))
9534 ;; Do not make other packages link with the proprietary libsz.
9535 (substitute* "R/zzz.R"
9536 ((" \"%s/libsz.a\"") ""))
9537 (with-directory-excursion "src"
9538 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
9539 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
9541 ;; Remove timestamp and host system information to make
9542 ;; the build reproducible.
9543 (substitute* "hdf5/src/libhdf5.settings.in"
9544 (("Configured on: @CONFIG_DATE@")
9545 "Configured on: Guix")
9546 (("Uname information:.*")
9547 "Uname information: Linux\n")
9548 ;; Remove unnecessary store reference.
9550 "C Compiler: GCC\n"))
9551 (rename-file "hdf5/src/libhdf5.settings.in"
9552 "hdf5/src/libhdf5.settings")
9553 (rename-file "Makevars.in" "Makevars")
9554 (substitute* "Makevars"
9555 (("@ZLIB_LIB@") "-lz")
9556 (("@ZLIB_INCLUDE@") "")
9557 (("HDF5_CXX_LIB=.*")
9558 (string-append "HDF5_CXX_LIB="
9559 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
9561 (string-append "HDF5_LIB="
9562 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
9563 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
9564 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
9565 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
9566 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
9568 (string-append "HDF5_HL_LIB="
9569 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
9570 (("HDF5_HL_CXX_LIB=.*")
9571 (string-append "HDF5_HL_CXX_LIB="
9572 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
9573 ;; szip is non-free software
9574 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
9575 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n")))
9580 `(("hdf5" ,hdf5-1.10)))
9582 `(("hdf5-source" ,(package-source hdf5-1.10))
9583 ("r-knitr" ,r-knitr)))
9584 (home-page "https://bioconductor.org/packages/Rhdf5lib")
9585 (synopsis "HDF5 library as an R package")
9586 (description "This package provides C and C++ HDF5 libraries for use in R
9588 (license license:artistic2.0)))
9590 (define-public r-beachmat
9597 (uri (bioconductor-uri "beachmat" version))
9600 "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji"))))
9601 (build-system r-build-system)
9603 `(("r-biocgenerics" ,r-biocgenerics)
9604 ("r-delayedarray" ,r-delayedarray)
9605 ("r-matrix" ,r-matrix)))
9607 `(("r-knitr" ,r-knitr)))
9608 (home-page "https://bioconductor.org/packages/beachmat")
9609 (synopsis "Compiling Bioconductor to handle each matrix type")
9610 (description "This package provides a consistent C++ class interface for a
9611 variety of commonly used matrix types, including sparse and HDF5-backed
9613 (license license:gpl3)))
9615 ;; This package includes files that have been taken from kentutils. Some
9616 ;; parts of kentutils are not released under a free license, but this package
9617 ;; only uses files that are also found in the free parts of kentutils.
9618 (define-public r-cner
9625 (uri (bioconductor-uri "CNEr" version))
9627 (base32 "0qy4pm23vyy23zwsjkf0mpf2c0p54nq26w9lq7j0ld4bx9l3jc6c"))))
9628 (properties `((upstream-name . "CNEr")))
9629 (build-system r-build-system)
9630 (inputs `(("zlib" ,zlib)))
9632 `(("r-annotate" ,r-annotate)
9633 ("r-biocgenerics" ,r-biocgenerics)
9634 ("r-biostrings" ,r-biostrings)
9636 ("r-genomeinfodb" ,r-genomeinfodb)
9637 ("r-genomicalignments" ,r-genomicalignments)
9638 ("r-genomicranges" ,r-genomicranges)
9639 ("r-ggplot2" ,r-ggplot2)
9640 ("r-go-db" ,r-go-db)
9641 ("r-iranges" ,r-iranges)
9642 ("r-keggrest" ,r-keggrest)
9643 ("r-powerlaw" ,r-powerlaw)
9644 ("r-r-utils" ,r-r-utils)
9645 ("r-readr" ,r-readr)
9646 ("r-reshape2" ,r-reshape2)
9647 ("r-rsqlite" ,r-rsqlite)
9648 ("r-rtracklayer" ,r-rtracklayer)
9649 ("r-s4vectors" ,r-s4vectors)
9650 ("r-xvector" ,r-xvector)))
9652 `(("r-knitr" ,r-knitr)))
9653 (home-page "https://github.com/ge11232002/CNEr")
9654 (synopsis "CNE Detection and Visualization")
9656 "This package provides tools for large-scale identification and
9657 advanced visualization of sets of conserved noncoding elements.")
9658 ;; For all files in src/ucsc "license is hereby granted for all use -
9659 ;; public, private or commercial"; this includes those files that don't
9660 ;; have a license header, because they are included in the free parts of
9661 ;; the kentutils package.
9662 (license (list license:gpl2
9663 (license:non-copyleft
9664 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
9666 (define-public r-tfbstools
9668 (name "r-tfbstools")
9673 (uri (bioconductor-uri "TFBSTools" version))
9676 "0p42hnwhipmcvrsqk3s8qfiian1fvh6izfd9m961bsx99r2clnha"))))
9677 (properties `((upstream-name . "TFBSTools")))
9678 (build-system r-build-system)
9680 `(("r-biobase" ,r-biobase)
9681 ("r-biocgenerics" ,r-biocgenerics)
9682 ("r-biocparallel" ,r-biocparallel)
9683 ("r-biostrings" ,r-biostrings)
9684 ("r-bsgenome" ,r-bsgenome)
9685 ("r-catools" ,r-catools)
9688 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
9689 ("r-genomeinfodb" ,r-genomeinfodb)
9690 ("r-genomicranges" ,r-genomicranges)
9691 ("r-gtools" ,r-gtools)
9692 ("r-iranges" ,r-iranges)
9693 ("r-rsqlite" ,r-rsqlite)
9694 ("r-rtracklayer" ,r-rtracklayer)
9695 ("r-s4vectors" ,r-s4vectors)
9696 ("r-seqlogo" ,r-seqlogo)
9697 ("r-tfmpvalue" ,r-tfmpvalue)
9699 ("r-xvector" ,r-xvector)))
9700 (native-inputs `(("r-knitr" ,r-knitr)))
9701 (home-page "https://github.com/ge11232002/TFBSTools")
9702 (synopsis "Transcription factor binding site (TFBS) analysis")
9704 "TFBSTools is a package for the analysis and manipulation of
9705 transcription factor binding sites. It includes matrices conversion
9706 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
9707 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
9708 scan putative TFBS from sequence/alignment, query JASPAR database and
9709 provides a wrapper of de novo motif discovery software.")
9710 (license license:gpl2)))
9712 (define-public r-motifmatchr
9714 (name "r-motifmatchr")
9719 (uri (bioconductor-uri "motifmatchr" version))
9722 "0zrpn0hqdg0hm80ydkfpiqncwyb8y0xp6mlin7g955p8zcpcm67z"))))
9723 (properties `((upstream-name . "motifmatchr")))
9724 (build-system r-build-system)
9726 `(("r-biostrings" ,r-biostrings)
9727 ("r-bsgenome" ,r-bsgenome)
9728 ("r-genomeinfodb" ,r-genomeinfodb)
9729 ("r-genomicranges" ,r-genomicranges)
9730 ("r-iranges" ,r-iranges)
9731 ("r-matrix" ,r-matrix)
9733 ("r-rcpparmadillo" ,r-rcpparmadillo)
9734 ("r-rsamtools" ,r-rsamtools)
9735 ("r-s4vectors" ,r-s4vectors)
9736 ("r-summarizedexperiment" ,r-summarizedexperiment)
9737 ("r-tfbstools" ,r-tfbstools)))
9738 (native-inputs `(("r-knitr" ,r-knitr)))
9739 (home-page "https://bioconductor.org/packages/motifmatchr")
9740 (synopsis "Fast motif matching in R")
9742 "Quickly find motif matches for many motifs and many sequences.
9743 This package wraps C++ code from the MOODS motif calling library.")
9744 (license license:gpl3)))
9746 (define-public r-chromvar
9753 (uri (bioconductor-uri "chromVAR" version))
9755 (base32 "0dn04ijgq8fncn2bkvnd0lnabjg2s4mpb91b3kwvv3nkgjgfx819"))))
9756 (properties `((upstream-name . "chromVAR")))
9757 (build-system r-build-system)
9759 `(("r-biocgenerics" ,r-biocgenerics)
9760 ("r-biocparallel" ,r-biocparallel)
9761 ("r-biostrings" ,r-biostrings)
9762 ("r-bsgenome" ,r-bsgenome)
9764 ("r-genomeinfodb" ,r-genomeinfodb)
9765 ("r-genomicranges" ,r-genomicranges)
9766 ("r-ggplot2" ,r-ggplot2)
9767 ("r-iranges" ,r-iranges)
9768 ("r-matrix" ,r-matrix)
9769 ("r-miniui" ,r-miniui)
9770 ("r-nabor" ,r-nabor)
9771 ("r-plotly" ,r-plotly)
9772 ("r-rcolorbrewer" ,r-rcolorbrewer)
9774 ("r-rcpparmadillo" ,r-rcpparmadillo)
9775 ("r-rsamtools" ,r-rsamtools)
9776 ("r-rtsne" ,r-rtsne)
9777 ("r-s4vectors" ,r-s4vectors)
9778 ("r-shiny" ,r-shiny)
9779 ("r-summarizedexperiment" ,r-summarizedexperiment)
9780 ("r-tfbstools" ,r-tfbstools)))
9781 (native-inputs `(("r-knitr" ,r-knitr)))
9782 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
9783 (synopsis "Determine chromatin variation across regions")
9785 "This package @code{r-chromvar} determines variation in chromatin
9786 accessibility across sets of annotations or peaks. @code{r-chromvar} is
9787 designed primarily for single-cell or sparse chromatin accessibility data like
9788 single cell assay for transposase-accessible chromatin using
9789 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
9790 sequence (@code{DNAse-seq}) experiments.")
9791 (license license:expat)))
9793 (define-public r-singlecellexperiment
9795 (name "r-singlecellexperiment")
9800 (uri (bioconductor-uri "SingleCellExperiment" version))
9803 "0wpgb2rhxxlclpmwl08iyfy204f7gpj8ijd0qdy4j41c58bl4qm2"))))
9805 `((upstream-name . "SingleCellExperiment")))
9806 (build-system r-build-system)
9808 `(("r-biocgenerics" ,r-biocgenerics)
9809 ("r-s4vectors" ,r-s4vectors)
9810 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9812 `(("r-knitr" ,r-knitr)))
9813 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
9814 (synopsis "S4 classes for single cell data")
9815 (description "This package defines an S4 class for storing data from
9816 single-cell experiments. This includes specialized methods to store and
9817 retrieve spike-in information, dimensionality reduction coordinates and size
9818 factors for each cell, along with the usual metadata for genes and
9820 (license license:gpl3)))
9822 (define-public r-scuttle
9829 (uri (bioconductor-uri "scuttle" version))
9832 "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8"))))
9833 (properties `((upstream-name . "scuttle")))
9834 (build-system r-build-system)
9836 `(("r-beachmat" ,r-beachmat)
9837 ("r-biocgenerics" ,r-biocgenerics)
9838 ("r-biocparallel" ,r-biocparallel)
9839 ("r-delayedarray" ,r-delayedarray)
9840 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9841 ("r-genomicranges" ,r-genomicranges)
9842 ("r-matrix" ,r-matrix)
9844 ("r-s4vectors" ,r-s4vectors)
9845 ("r-singlecellexperiment" ,r-singlecellexperiment)
9846 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9847 (native-inputs `(("r-knitr" ,r-knitr)))
9848 (home-page "https://bioconductor.org/packages/scuttle")
9849 (synopsis "Single-cell RNA-Seq analysis utilities")
9851 "This package provides basic utility functions for performing single-cell
9852 analyses, focusing on simple normalization, quality control and data
9853 transformations. It also provides some helper functions to assist development
9854 of other packages.")
9855 (license license:gpl3)))
9857 (define-public r-scater
9863 (uri (bioconductor-uri "scater" version))
9866 "0k1ls5gqv1zsn1w2kszhmbhwfccfjw8khk36s5zbf90rbbkw5609"))))
9867 (build-system r-build-system)
9869 `(("r-biocgenerics" ,r-biocgenerics)
9870 ("r-biocneighbors" ,r-biocneighbors)
9871 ("r-biocparallel" ,r-biocparallel)
9872 ("r-biocsingular" ,r-biocsingular)
9873 ("r-delayedarray" ,r-delayedarray)
9874 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9875 ("r-ggbeeswarm" ,r-ggbeeswarm)
9876 ("r-ggplot2" ,r-ggplot2)
9877 ("r-gridextra" ,r-gridextra)
9878 ("r-matrix" ,r-matrix)
9879 ("r-rlang" ,r-rlang)
9880 ("r-s4vectors" ,r-s4vectors)
9881 ("r-scuttle" ,r-scuttle)
9882 ("r-singlecellexperiment" ,r-singlecellexperiment)
9883 ("r-summarizedexperiment" ,r-summarizedexperiment)
9884 ("r-viridis" ,r-viridis)))
9886 `(("r-knitr" ,r-knitr)))
9887 (home-page "https://github.com/davismcc/scater")
9888 (synopsis "Single-cell analysis toolkit for gene expression data in R")
9889 (description "This package provides a collection of tools for doing
9890 various analyses of single-cell RNA-seq gene expression data, with a focus on
9892 (license license:gpl2+)))
9894 (define-public r-scran
9901 (uri (bioconductor-uri "scran" version))
9904 "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1"))))
9905 (build-system r-build-system)
9907 `(("r-beachmat" ,r-beachmat)
9909 ("r-biocgenerics" ,r-biocgenerics)
9910 ("r-biocneighbors" ,r-biocneighbors)
9911 ("r-biocparallel" ,r-biocparallel)
9912 ("r-biocsingular" ,r-biocsingular)
9913 ("r-bluster" ,r-bluster)
9914 ("r-delayedarray" ,r-delayedarray)
9915 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
9916 ("r-dqrng" ,r-dqrng)
9917 ("r-edger" ,r-edger)
9918 ("r-igraph" ,r-igraph)
9919 ("r-limma" ,r-limma)
9920 ("r-matrix" ,r-matrix)
9922 ("r-s4vectors" ,r-s4vectors)
9923 ("r-scuttle" ,r-scuttle)
9924 ("r-singlecellexperiment" ,r-singlecellexperiment)
9925 ("r-statmod" ,r-statmod)
9926 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9928 `(("r-knitr" ,r-knitr)))
9929 (home-page "https://bioconductor.org/packages/scran")
9930 (synopsis "Methods for single-cell RNA-Seq data analysis")
9931 (description "This package implements a variety of low-level analyses of
9932 single-cell RNA-seq data. Methods are provided for normalization of
9933 cell-specific biases, assignment of cell cycle phase, and detection of highly
9934 variable and significantly correlated genes.")
9935 (license license:gpl3)))
9937 (define-public r-sparsematrixstats
9939 (name "r-sparsematrixstats")
9944 (uri (bioconductor-uri "sparseMatrixStats" version))
9947 "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii"))))
9949 `((upstream-name . "sparseMatrixStats")))
9950 (build-system r-build-system)
9952 `(("r-matrix" ,r-matrix)
9953 ("r-matrixgenerics" ,r-matrixgenerics)
9954 ("r-matrixstats" ,r-matrixstats)
9955 ("r-rcpp" ,r-rcpp)))
9956 (native-inputs `(("r-knitr" ,r-knitr)))
9957 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
9958 (synopsis "Summary statistics for rows and columns of sparse matrices")
9960 "This package provides high performance functions for row and column
9961 operations on sparse matrices. Currently, the optimizations are limited to
9962 data in the column sparse format.")
9963 (license license:expat)))
9965 (define-public r-delayedmatrixstats
9967 (name "r-delayedmatrixstats")
9972 (uri (bioconductor-uri "DelayedMatrixStats" version))
9975 "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h"))))
9977 `((upstream-name . "DelayedMatrixStats")))
9978 (build-system r-build-system)
9980 `(("r-biocparallel" ,r-biocparallel)
9981 ("r-delayedarray" ,r-delayedarray)
9982 ("r-hdf5array" ,r-hdf5array)
9983 ("r-iranges" ,r-iranges)
9984 ("r-matrix" ,r-matrix)
9985 ("r-matrixgenerics" ,r-matrixgenerics)
9986 ("r-matrixstats" ,r-matrixstats)
9987 ("r-s4vectors" ,r-s4vectors)
9988 ("r-sparsematrixstats" ,r-sparsematrixstats)))
9990 `(("r-knitr" ,r-knitr)))
9991 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
9992 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
9994 "This package provides a port of the @code{matrixStats} API for use with
9995 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
9996 contains high-performing functions operating on rows and columns of
9997 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
9998 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
9999 are optimized per data type and for subsetted calculations such that both
10000 memory usage and processing time is minimized.")
10001 (license license:expat)))
10003 (define-public r-mscoreutils
10005 (name "r-mscoreutils")
10010 (uri (bioconductor-uri "MsCoreUtils" version))
10013 "0fa3bcf2cmzf5y8wjs7pnzs26qwgqnrrl4hj4sa4fp9kv8z80630"))))
10014 (properties `((upstream-name . "MsCoreUtils")))
10015 (build-system r-build-system)
10017 `(("r-mass" ,r-mass)
10019 ("r-s4vectors" ,r-s4vectors)))
10021 `(("r-knitr" ,r-knitr)))
10022 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
10023 (synopsis "Core utils for mass spectrometry data")
10025 "This package defines low-level functions for mass spectrometry data and
10026 is independent of any high-level data structures. These functions include
10027 mass spectra processing functions (noise estimation, smoothing, binning),
10028 quantitative aggregation functions (median polish, robust summarisation,
10029 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
10030 well as misc helper functions, that are used across high-level data structure
10031 within the R for Mass Spectrometry packages.")
10032 (license license:artistic2.0)))
10034 (define-public r-biocio
10041 (uri (bioconductor-uri "BiocIO" version))
10044 "06gg5ra3r7q4b6mz14c2s9d453cnh1lxh517ffl9f8dr8vwv5s18"))))
10045 (properties `((upstream-name . "BiocIO")))
10046 (build-system r-build-system)
10048 `(("r-biocgenerics" ,r-biocgenerics)
10049 ("r-genomicranges" ,r-genomicranges)
10050 ("r-rcurl" ,r-rcurl)
10051 ("r-s4vectors" ,r-s4vectors)))
10053 `(("r-knitr" ,r-knitr)))
10054 (home-page "https://bioconductor.org/packages/BiocIO")
10055 (synopsis "Standard input and output for Bioconductor packages")
10057 "This package implements `import()` and `export()` standard generics for
10058 importing and exporting biological data formats. `import()` supports
10059 whole-file as well as chunk-wise iterative import. The `import()` interface
10060 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
10061 row or element-like components of the file resource), `select()` (on
10062 column-like components of the file resource) and `collect()`. The `import()`
10063 interface optionally provides transparent access to remote (e.g. via https)
10064 as well as local access. Developers can register a file extension, e.g.,
10065 `.loom` for dispatch from character-based URIs to specific `import()` /
10066 `export()` methods based on classes representing file types, e.g.,
10068 (license license:artistic2.0)))
10070 (define-public r-msmseda
10077 (uri (bioconductor-uri "msmsEDA" version))
10080 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
10081 (properties `((upstream-name . "msmsEDA")))
10082 (build-system r-build-system)
10084 `(("r-gplots" ,r-gplots)
10086 ("r-msnbase" ,r-msnbase)
10087 ("r-rcolorbrewer" ,r-rcolorbrewer)))
10089 "https://bioconductor.org/packages/msmsEDA")
10090 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
10092 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
10093 experiments, and visualize de influence of the involved factors.")
10094 (license license:gpl2)))
10096 (define-public r-msmstests
10098 (name "r-msmstests")
10103 (uri (bioconductor-uri "msmsTests" version))
10106 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
10107 (properties `((upstream-name . "msmsTests")))
10108 (build-system r-build-system)
10110 `(("r-edger" ,r-edger)
10111 ("r-msmseda" ,r-msmseda)
10112 ("r-msnbase" ,r-msnbase)
10113 ("r-qvalue" ,r-qvalue)))
10115 "https://bioconductor.org/packages/msmsTests")
10116 (synopsis "Differential LC-MS/MS expression tests")
10118 "This packages provides statistical tests for label-free LC-MS/MS data
10119 by spectral counts, to discover differentially expressed proteins between two
10120 biological conditions. Three tests are available: Poisson GLM regression,
10121 quasi-likelihood GLM regression, and the negative binomial of the edgeR
10122 package.The three models admit blocking factors to control for nuissance
10123 variables.To assure a good level of reproducibility a post-test filter is
10124 available, where we may set the minimum effect size considered biologicaly
10125 relevant, and the minimum expression of the most abundant condition.")
10126 (license license:gpl2)))
10128 (define-public r-catalyst
10130 (name "r-catalyst")
10135 (uri (bioconductor-uri "CATALYST" version))
10138 "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
10139 (properties `((upstream-name . "CATALYST")))
10140 (build-system r-build-system)
10142 `(("r-circlize" ,r-circlize)
10143 ("r-complexheatmap" ,r-complexheatmap)
10144 ("r-consensusclusterplus" ,r-consensusclusterplus)
10145 ("r-cowplot" ,r-cowplot)
10146 ("r-data-table" ,r-data-table)
10147 ("r-dplyr" ,r-dplyr)
10149 ("r-flowcore" ,r-flowcore)
10150 ("r-flowsom" ,r-flowsom)
10151 ("r-ggplot2" ,r-ggplot2)
10152 ("r-ggrepel" ,r-ggrepel)
10153 ("r-ggridges" ,r-ggridges)
10154 ("r-gridextra" ,r-gridextra)
10155 ("r-magrittr" ,r-magrittr)
10156 ("r-matrix" ,r-matrix)
10157 ("r-matrixstats" ,r-matrixstats)
10159 ("r-purrr" ,r-purrr)
10160 ("r-rcolorbrewer" ,r-rcolorbrewer)
10161 ("r-reshape2" ,r-reshape2)
10162 ("r-rtsne" ,r-rtsne)
10163 ("r-s4vectors" ,r-s4vectors)
10164 ("r-scales" ,r-scales)
10165 ("r-scater" ,r-scater)
10166 ("r-singlecellexperiment" ,r-singlecellexperiment)
10167 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10169 `(("r-knitr" ,r-knitr)))
10171 "https://github.com/HelenaLC/CATALYST")
10172 (synopsis "Cytometry data analysis tools")
10174 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
10175 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
10176 reporters to label antibodies, thereby substantially decreasing spectral
10177 overlap and allowing for examination of over 50 parameters at the single cell
10178 level. While spectral overlap is significantly less pronounced in CyTOF than
10179 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
10180 and oxide formation can impede data interpretability. We designed
10181 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
10182 preprocessing of cytometry data, including i) normalization using bead
10183 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
10184 (license license:gpl2+)))
10186 (define-public r-erma
10193 (uri (bioconductor-uri "erma" version))
10196 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
10197 (build-system r-build-system)
10199 `(("r-annotationdbi" ,r-annotationdbi)
10200 ("r-biobase" ,r-biobase)
10201 ("r-biocgenerics" ,r-biocgenerics)
10202 ("r-biocparallel" ,r-biocparallel)
10203 ("r-genomeinfodb" ,r-genomeinfodb)
10204 ("r-genomicfiles" ,r-genomicfiles)
10205 ("r-genomicranges" ,r-genomicranges)
10206 ("r-ggplot2" ,r-ggplot2)
10207 ("r-homo-sapiens" ,r-homo-sapiens)
10208 ("r-iranges" ,r-iranges)
10209 ("r-rtracklayer" ,r-rtracklayer)
10210 ("r-s4vectors" ,r-s4vectors)
10211 ("r-shiny" ,r-shiny)
10212 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10214 `(("r-knitr" ,r-knitr)))
10215 (home-page "https://bioconductor.org/packages/erma")
10216 (synopsis "Epigenomic road map adventures")
10218 "The epigenomics road map describes locations of epigenetic marks in DNA
10219 from a variety of cell types. Of interest are locations of histone
10220 modifications, sites of DNA methylation, and regions of accessible chromatin.
10221 This package presents a selection of elements of the road map including
10222 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
10223 by Ernst and Kellis.")
10224 (license license:artistic2.0)))
10226 (define-public r-ggbio
10233 (uri (bioconductor-uri "ggbio" version))
10236 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
10237 (build-system r-build-system)
10240 (modify-phases %standard-phases
10241 ;; See https://github.com/tengfei/ggbio/issues/117
10242 ;; This fix will be included in the next release.
10243 (add-after 'unpack 'fix-typo
10245 (substitute* "R/GGbio-class.R"
10246 (("fechable") "fetchable"))
10249 `(("r-annotationdbi" ,r-annotationdbi)
10250 ("r-annotationfilter" ,r-annotationfilter)
10251 ("r-biobase" ,r-biobase)
10252 ("r-biocgenerics" ,r-biocgenerics)
10253 ("r-biostrings" ,r-biostrings)
10254 ("r-biovizbase" ,r-biovizbase)
10255 ("r-bsgenome" ,r-bsgenome)
10256 ("r-ensembldb" ,r-ensembldb)
10257 ("r-genomeinfodb" ,r-genomeinfodb)
10258 ("r-genomicalignments" ,r-genomicalignments)
10259 ("r-genomicfeatures" ,r-genomicfeatures)
10260 ("r-genomicranges" ,r-genomicranges)
10261 ("r-ggally" ,r-ggally)
10262 ("r-ggplot2" ,r-ggplot2)
10263 ("r-gridextra" ,r-gridextra)
10264 ("r-gtable" ,r-gtable)
10265 ("r-hmisc" ,r-hmisc)
10266 ("r-iranges" ,r-iranges)
10267 ("r-organismdbi" ,r-organismdbi)
10268 ("r-reshape2" ,r-reshape2)
10269 ("r-rlang" ,r-rlang)
10270 ("r-rsamtools" ,r-rsamtools)
10271 ("r-rtracklayer" ,r-rtracklayer)
10272 ("r-s4vectors" ,r-s4vectors)
10273 ("r-scales" ,r-scales)
10274 ("r-summarizedexperiment" ,r-summarizedexperiment)
10275 ("r-variantannotation" ,r-variantannotation)))
10277 `(("r-knitr" ,r-knitr)))
10278 (home-page "http://www.tengfei.name/ggbio/")
10279 (synopsis "Visualization tools for genomic data")
10281 "The ggbio package extends and specializes the grammar of graphics for
10282 biological data. The graphics are designed to answer common scientific
10283 questions, in particular those often asked of high throughput genomics data.
10284 All core Bioconductor data structures are supported, where appropriate. The
10285 package supports detailed views of particular genomic regions, as well as
10286 genome-wide overviews. Supported overviews include ideograms and grand linear
10287 views. High-level plots include sequence fragment length, edge-linked
10288 interval to data view, mismatch pileup, and several splicing summaries.")
10289 (license license:artistic2.0)))
10291 (define-public r-gqtlbase
10293 (name "r-gqtlbase")
10298 (uri (bioconductor-uri "gQTLBase" version))
10301 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
10302 (properties `((upstream-name . "gQTLBase")))
10303 (build-system r-build-system)
10306 (modify-phases %standard-phases
10307 ;; This is an upstream bug.
10308 (add-after 'unpack 'fix-imports
10310 (substitute* "NAMESPACE"
10311 ((".*maxffmode.*") "")
10312 (("importFrom\\(ff,.*") "import(ff)\n"))
10315 `(("r-batchjobs" ,r-batchjobs)
10316 ("r-bbmisc" ,r-bbmisc)
10317 ("r-biocgenerics" ,r-biocgenerics)
10319 ("r-doparallel" ,r-doparallel)
10321 ("r-ffbase" ,r-ffbase)
10322 ("r-foreach" ,r-foreach)
10323 ("r-genomicfiles" ,r-genomicfiles)
10324 ("r-genomicranges" ,r-genomicranges)
10325 ("r-rtracklayer" ,r-rtracklayer)
10326 ("r-s4vectors" ,r-s4vectors)
10327 ("r-summarizedexperiment" ,r-summarizedexperiment)))
10329 `(("r-knitr" ,r-knitr)))
10330 (home-page "https://bioconductor.org/packages/gQTLBase")
10331 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
10333 "The purpose of this package is to simplify the storage and interrogation
10334 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
10336 (license license:artistic2.0)))
10338 (define-public r-gqtlstats
10340 (name "r-gqtlstats")
10345 (uri (bioconductor-uri "gQTLstats" version))
10348 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
10349 (properties `((upstream-name . "gQTLstats")))
10350 (build-system r-build-system)
10352 `(("r-annotationdbi" ,r-annotationdbi)
10353 ("r-batchjobs" ,r-batchjobs)
10354 ("r-bbmisc" ,r-bbmisc)
10355 ("r-beeswarm" ,r-beeswarm)
10356 ("r-biobase" ,r-biobase)
10357 ("r-biocgenerics" ,r-biocgenerics)
10358 ("r-doparallel" ,r-doparallel)
10359 ("r-dplyr" ,r-dplyr)
10361 ("r-ffbase" ,r-ffbase)
10362 ("r-foreach" ,r-foreach)
10363 ("r-genomeinfodb" ,r-genomeinfodb)
10364 ("r-genomicfeatures" ,r-genomicfeatures)
10365 ("r-genomicfiles" ,r-genomicfiles)
10366 ("r-genomicranges" ,r-genomicranges)
10367 ("r-ggbeeswarm" ,r-ggbeeswarm)
10368 ("r-ggplot2" ,r-ggplot2)
10369 ("r-gqtlbase" ,r-gqtlbase)
10370 ("r-hardyweinberg" ,r-hardyweinberg)
10371 ("r-homo-sapiens" ,r-homo-sapiens)
10372 ("r-iranges" ,r-iranges)
10373 ("r-limma" ,r-limma)
10375 ("r-plotly" ,r-plotly)
10376 ("r-reshape2" ,r-reshape2)
10377 ("r-s4vectors" ,r-s4vectors)
10378 ("r-shiny" ,r-shiny)
10379 ("r-snpstats" ,r-snpstats)
10380 ("r-summarizedexperiment" ,r-summarizedexperiment)
10381 ("r-variantannotation" ,r-variantannotation)))
10383 `(("r-knitr" ,r-knitr)))
10384 (home-page "https://bioconductor.org/packages/gQTLstats")
10385 (synopsis "Computationally efficient analysis for eQTL and allied studies")
10387 "This package provides tools for the computationally efficient analysis
10388 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
10389 The software in this package aims to support refinements and functional
10390 interpretation of members of a collection of association statistics on a
10391 family of feature/genome hypotheses.")
10392 (license license:artistic2.0)))
10394 (define-public r-gviz
10401 (uri (bioconductor-uri "Gviz" version))
10404 "0v7bz46b91dnrr55ah42ljj1i2xs3090s4w0lw8098pag00p4vh2"))))
10405 (properties `((upstream-name . "Gviz")))
10406 (build-system r-build-system)
10408 `(("r-annotationdbi" ,r-annotationdbi)
10409 ("r-biobase" ,r-biobase)
10410 ("r-biocgenerics" ,r-biocgenerics)
10411 ("r-biomart" ,r-biomart)
10412 ("r-biostrings" ,r-biostrings)
10413 ("r-biovizbase" ,r-biovizbase)
10414 ("r-bsgenome" ,r-bsgenome)
10415 ("r-digest" ,r-digest)
10416 ("r-ensembldb" ,r-ensembldb)
10417 ("r-genomeinfodb" ,r-genomeinfodb)
10418 ("r-genomicalignments" ,r-genomicalignments)
10419 ("r-genomicfeatures" ,r-genomicfeatures)
10420 ("r-genomicranges" ,r-genomicranges)
10421 ("r-iranges" ,r-iranges)
10422 ("r-lattice" ,r-lattice)
10423 ("r-latticeextra" ,r-latticeextra)
10424 ("r-matrixstats" ,r-matrixstats)
10425 ("r-rcolorbrewer" ,r-rcolorbrewer)
10426 ("r-rsamtools" ,r-rsamtools)
10427 ("r-rtracklayer" ,r-rtracklayer)
10428 ("r-s4vectors" ,r-s4vectors)
10429 ("r-xvector" ,r-xvector)))
10431 `(("r-knitr" ,r-knitr)))
10432 (home-page "https://bioconductor.org/packages/Gviz")
10433 (synopsis "Plotting data and annotation information along genomic coordinates")
10435 "Genomic data analyses requires integrated visualization of known genomic
10436 information and new experimental data. Gviz uses the biomaRt and the
10437 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
10438 and translates this to e.g. gene/transcript structures in viewports of the
10439 grid graphics package. This results in genomic information plotted together
10441 (license license:artistic2.0)))
10443 (define-public r-gwascat
10450 (uri (bioconductor-uri "gwascat" version))
10453 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
10454 (build-system r-build-system)
10456 `(("r-annotationdbi" ,r-annotationdbi)
10457 ("r-biocfilecache" ,r-biocfilecache)
10458 ("r-biostrings" ,r-biostrings)
10459 ("r-genomeinfodb" ,r-genomeinfodb)
10460 ("r-genomicfeatures" ,r-genomicfeatures)
10461 ("r-genomicranges" ,r-genomicranges)
10462 ("r-iranges" ,r-iranges)
10463 ("r-readr" ,r-readr)
10464 ("r-s4vectors" ,r-s4vectors)
10465 ("r-snpstats" ,r-snpstats)
10466 ("r-variantannotation" ,r-variantannotation)))
10468 `(("r-knitr" ,r-knitr)))
10469 (home-page "https://bioconductor.org/packages/gwascat")
10470 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
10472 "This package provides tools for representing and modeling data in the
10473 EMBL-EBI GWAS catalog.")
10474 (license license:artistic2.0)))
10476 (define-public r-kegggraph
10478 (name "r-kegggraph")
10483 (uri (bioconductor-uri "KEGGgraph" version))
10485 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
10486 (properties `((upstream-name . "KEGGgraph")))
10487 (build-system r-build-system)
10489 `(("r-graph" ,r-graph)
10490 ("r-rcurl" ,r-rcurl)
10492 (home-page "https://bioconductor.org/packages/KEGGgraph")
10493 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
10495 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
10496 object as well as a collection of tools to analyze, dissect and visualize these
10497 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
10498 maintaining all essential pathway attributes. The package offers
10499 functionalities including parsing, graph operation, visualization and etc.")
10500 (license license:gpl2+)))
10502 (define-public r-ldblock
10509 (uri (bioconductor-uri "ldblock" version))
10512 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
10513 (build-system r-build-system)
10515 `(("r-biocgenerics" ,r-biocgenerics)
10516 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
10517 ("r-ensembldb" ,r-ensembldb)
10518 ("r-genomeinfodb" ,r-genomeinfodb)
10519 ("r-genomicfiles" ,r-genomicfiles)
10521 ("r-matrix" ,r-matrix)
10522 ("r-rsamtools" ,r-rsamtools)
10523 ("r-snpstats" ,r-snpstats)
10524 ("r-variantannotation" ,r-variantannotation)))
10526 `(("r-knitr" ,r-knitr)))
10527 (home-page "https://bioconductor.org/packages/ldblock")
10528 (synopsis "Data structures for linkage disequilibrium measures in populations")
10530 "This package defines data structures for @dfn{linkage
10531 disequilibrium} (LD) measures in populations. Its purpose is to simplify
10532 handling of existing population-level data for the purpose of flexibly
10533 defining LD blocks.")
10534 (license license:artistic2.0)))
10536 ;; This is a CRAN package, but it depends on r-snpstats, which is a
10537 ;; Bioconductor package.
10538 (define-public r-ldheatmap
10540 (name "r-ldheatmap")
10545 (uri (cran-uri "LDheatmap" version))
10548 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
10549 (properties `((upstream-name . "LDheatmap")))
10550 (build-system r-build-system)
10552 `(("r-genetics" ,r-genetics)
10554 ("r-snpstats" ,r-snpstats)))
10555 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
10556 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
10558 "This package provides tools to produce a graphical display, as a heat
10559 map, of measures of pairwise linkage disequilibria between SNPs. Users may
10560 optionally include the physical locations or genetic map distances of each SNP
10562 (license license:gpl3)))
10564 (define-public r-pathview
10566 (name "r-pathview")
10571 (uri (bioconductor-uri "pathview" version))
10573 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
10574 (properties `((upstream-name . "pathview")))
10575 (build-system r-build-system)
10577 `(("r-annotationdbi" ,r-annotationdbi)
10578 ("r-graph" ,r-graph)
10579 ("r-kegggraph" ,r-kegggraph)
10580 ("r-keggrest" ,r-keggrest)
10581 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
10583 ("r-rgraphviz" ,r-rgraphviz)
10585 (home-page "https://pathview.uncc.edu/")
10586 (synopsis "Tool set for pathway based data integration and visualization")
10588 "@code{r-pathview} is a tool set for pathway based data integration and
10589 visualization. It maps and renders a wide variety of biological data on
10590 relevant pathway graphs. All users need is to supply their data and specify
10591 the target pathway. This package automatically downloads the pathway graph
10592 data, parses the data file, maps user data to the pathway, and render pathway
10593 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
10594 integrates with pathway and gene set (enrichment) analysis tools for
10595 large-scale and fully automated analysis.")
10596 (license license:gpl3+)))
10598 (define-public r-snpstats
10600 (name "r-snpstats")
10605 (uri (bioconductor-uri "snpStats" version))
10608 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
10609 (properties `((upstream-name . "snpStats")))
10610 (build-system r-build-system)
10611 (inputs `(("zlib" ,zlib)))
10613 `(("r-biocgenerics" ,r-biocgenerics)
10614 ("r-matrix" ,r-matrix)
10615 ("r-survival" ,r-survival)
10616 ("r-zlibbioc" ,r-zlibbioc)))
10617 (home-page "https://bioconductor.org/packages/snpStats")
10618 (synopsis "Methods for SNP association studies")
10620 "This package provides classes and statistical methods for large
10621 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
10622 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
10623 (license license:gpl3)))
10625 (define-public r-sushi
10631 (uri (bioconductor-uri "Sushi" version))
10634 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
10635 (properties `((upstream-name . "Sushi")))
10636 (build-system r-build-system)
10638 `(("r-biomart" ,r-biomart)
10640 (home-page "https://bioconductor.org/packages/Sushi")
10641 (synopsis "Tools for visualizing genomics data")
10643 "This package provides flexible, quantitative, and integrative genomic
10644 visualizations for publication-quality multi-panel figures.")
10645 (license license:gpl2+)))