1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 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, 2020, 2021 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>
12 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
13 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
15 ;;; This file is part of GNU Guix.
17 ;;; GNU Guix is free software; you can redistribute it and/or modify it
18 ;;; under the terms of the GNU General Public License as published by
19 ;;; the Free Software Foundation; either version 3 of the License, or (at
20 ;;; your option) any later version.
22 ;;; GNU Guix is distributed in the hope that it will be useful, but
23 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
24 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
25 ;;; GNU General Public License for more details.
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28 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
30 (define-module (gnu packages bioconductor)
31 #:use-module ((guix licenses) #:prefix license:)
32 #:use-module (guix packages)
33 #:use-module (guix download)
34 #:use-module (guix git-download)
35 #:use-module (guix build-system r)
36 #:use-module (gnu packages)
37 #:use-module (gnu packages base)
38 #:use-module (gnu packages bioinformatics)
39 #:use-module (gnu packages boost)
40 #:use-module (gnu packages cran)
41 #:use-module (gnu packages compression)
42 #:use-module (gnu packages curl)
43 #:use-module (gnu packages gcc)
44 #:use-module (gnu packages graph)
45 #:use-module (gnu packages graphviz)
46 #:use-module (gnu packages haskell-xyz)
47 #:use-module (gnu packages image)
48 #:use-module (gnu packages maths)
49 #:use-module (gnu packages netpbm)
50 #:use-module (gnu packages perl)
51 #:use-module (gnu packages pkg-config)
52 #:use-module (gnu packages statistics)
53 #:use-module (gnu packages web)
54 #:use-module (gnu packages xml)
55 #:use-module (srfi srfi-1))
60 (define-public r-org-eck12-eg-db
62 (name "r-org-eck12-eg-db")
67 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
69 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
71 `((upstream-name . "org.EcK12.eg.db")))
72 (build-system r-build-system)
74 `(("r-annotationdbi" ,r-annotationdbi)))
75 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
76 (synopsis "Genome wide annotation for E coli strain K12")
78 "This package provides genome wide annotation for E coli strain K12,
79 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
80 National Center for Biotechnology Information (NCBI)’s database for
81 gene-specific information. Entrez Gene maintains records from genomes which
82 have been completely sequenced, which have an active research community to
83 submit gene-specific information, or which are scheduled for intense sequence
85 (license license:artistic2.0)))
87 (define-public r-reactome-db
89 (name "r-reactome-db")
94 (uri (bioconductor-uri "reactome.db" version 'annotation))
97 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
98 (properties `((upstream-name . "reactome.db")))
99 (build-system r-build-system)
101 `(("r-annotationdbi" ,r-annotationdbi)))
102 (home-page "https://bioconductor.org/packages/reactome.db/")
103 (synopsis "Annotation maps for reactome")
105 "This package provides a set of annotation maps for the REACTOME
106 database, assembled using data from REACTOME.")
107 (license license:cc-by4.0)))
109 (define-public r-bsgenome-btaurus-ucsc-bostau8
111 (name "r-bsgenome-btaurus-ucsc-bostau8")
115 (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
116 version 'annotation))
119 "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
121 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
122 (build-system r-build-system)
124 `(("r-bsgenome" ,r-bsgenome)))
126 "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
127 (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
128 (description "This package provides the full genome sequences for Bos
129 taurus (UCSC version bosTau8).")
130 (license license:artistic2.0)))
132 (define-public r-bsgenome-celegans-ucsc-ce6
134 (name "r-bsgenome-celegans-ucsc-ce6")
138 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
139 version 'annotation))
142 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
144 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
145 (build-system r-build-system)
147 `(("r-bsgenome" ,r-bsgenome)))
149 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
150 (synopsis "Full genome sequences for Worm")
152 "This package provides full genome sequences for Caenorhabditis
153 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
155 (license license:artistic2.0)))
157 (define-public r-bsgenome-celegans-ucsc-ce10
159 (name "r-bsgenome-celegans-ucsc-ce10")
163 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
164 version 'annotation))
167 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
169 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
170 (build-system r-build-system)
172 `(("r-bsgenome" ,r-bsgenome)))
174 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
175 (synopsis "Full genome sequences for Worm")
177 "This package provides full genome sequences for Caenorhabditis
178 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
180 (license license:artistic2.0)))
182 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
184 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
188 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
189 version 'annotation))
192 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
194 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
195 (build-system r-build-system)
197 `(("r-bsgenome" ,r-bsgenome)))
199 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
200 (synopsis "Full genome sequences for Fly")
202 "This package provides full genome sequences for Drosophila
203 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
205 (license license:artistic2.0)))
207 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
209 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
213 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
214 version 'annotation))
217 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
219 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
220 (build-system r-build-system)
222 `(("r-bsgenome" ,r-bsgenome)))
224 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
225 (synopsis "Full genome sequences for Fly")
227 "This package provides full genome sequences for Drosophila
228 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
229 Biostrings objects.")
230 (license license:artistic2.0)))
232 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
234 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
238 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
239 version 'annotation))
242 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
244 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
245 (build-system r-build-system)
247 `(("r-bsgenome" ,r-bsgenome)
248 ("r-bsgenome-dmelanogaster-ucsc-dm3"
249 ,r-bsgenome-dmelanogaster-ucsc-dm3)))
250 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
251 (synopsis "Full masked genome sequences for Fly")
253 "This package provides full masked genome sequences for Drosophila
254 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
255 Biostrings objects. The sequences are the same as in
256 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
257 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
258 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
259 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
260 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
261 (license license:artistic2.0)))
263 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
265 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
269 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
270 version 'annotation))
273 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
275 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
276 (build-system r-build-system)
278 `(("r-bsgenome" ,r-bsgenome)))
280 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
281 (synopsis "Full genome sequences for Homo sapiens")
283 "This package provides full genome sequences for Homo sapiens from
284 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
285 (license license:artistic2.0)))
287 (define-public r-bsgenome-hsapiens-ncbi-grch38
289 (name "r-bsgenome-hsapiens-ncbi-grch38")
294 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
295 version 'annotation))
298 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
299 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
300 (build-system r-build-system)
301 (propagated-inputs `(("r-bsgenome" ,r-bsgenome)))
303 "https://bioconductor.org/packages/release/data/annotation/html/\
304 BSgenome.Hsapiens.NCBI.GRCh38.html")
305 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
307 "This package provides full genome sequences for Homo sapiens (Human) as
308 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
309 (license license:artistic2.0)))
311 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
313 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
317 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
318 version 'annotation))
321 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
323 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
324 (build-system r-build-system)
326 `(("r-bsgenome" ,r-bsgenome)
327 ("r-bsgenome-hsapiens-ucsc-hg19"
328 ,r-bsgenome-hsapiens-ucsc-hg19)))
329 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
330 (synopsis "Full masked genome sequences for Homo sapiens")
332 "This package provides full genome sequences for Homo sapiens (Human) as
333 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
334 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
335 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
336 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
337 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
338 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
340 (license license:artistic2.0)))
342 (define-public r-bsgenome-mmusculus-ucsc-mm9
344 (name "r-bsgenome-mmusculus-ucsc-mm9")
348 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
349 version 'annotation))
352 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
354 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
355 (build-system r-build-system)
357 `(("r-bsgenome" ,r-bsgenome)))
359 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
360 (synopsis "Full genome sequences for Mouse")
362 "This package provides full genome sequences for Mus musculus (Mouse) as
363 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
364 (license license:artistic2.0)))
366 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
368 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
372 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
373 version 'annotation))
376 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
378 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
379 (build-system r-build-system)
381 `(("r-bsgenome" ,r-bsgenome)
382 ("r-bsgenome-mmusculus-ucsc-mm9"
383 ,r-bsgenome-mmusculus-ucsc-mm9)))
384 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
385 (synopsis "Full masked genome sequences for Mouse")
387 "This package provides full genome sequences for Mus musculus (Mouse) as
388 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
389 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
390 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
391 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
392 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
393 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
395 (license license:artistic2.0)))
397 (define-public r-bsgenome-mmusculus-ucsc-mm10
399 (name "r-bsgenome-mmusculus-ucsc-mm10")
403 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
404 version 'annotation))
407 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
409 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
410 (build-system r-build-system)
412 `(("r-bsgenome" ,r-bsgenome)))
414 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
415 (synopsis "Full genome sequences for Mouse")
417 "This package provides full genome sequences for Mus
418 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
419 in Biostrings objects.")
420 (license license:artistic2.0)))
422 (define-public r-genomeinfodbdata
424 (name "r-genomeinfodbdata")
428 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
431 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
433 `((upstream-name . "GenomeInfoDbData")))
434 (build-system r-build-system)
435 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
436 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
437 (description "This package contains data for mapping between NCBI taxonomy
438 ID and species. It is used by functions in the GenomeInfoDb package.")
439 (license license:artistic2.0)))
441 (define-public r-go-db
447 (uri (bioconductor-uri "GO.db" version 'annotation))
450 "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
452 `((upstream-name . "GO.db")))
453 (build-system r-build-system)
455 `(("r-annotationdbi" ,r-annotationdbi)))
456 (home-page "https://bioconductor.org/packages/GO.db")
457 (synopsis "Annotation maps describing the entire Gene Ontology")
459 "The purpose of this GO.db annotation package is to provide detailed
460 information about the latest version of the Gene Ontologies.")
461 (license license:artistic2.0)))
463 (define-public r-homo-sapiens
465 (name "r-homo-sapiens")
469 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
472 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
474 `((upstream-name . "Homo.sapiens")))
475 (build-system r-build-system)
477 `(("r-genomicfeatures" ,r-genomicfeatures)
479 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
480 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)
481 ("r-organismdbi" ,r-organismdbi)
482 ("r-annotationdbi" ,r-annotationdbi)))
483 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
484 (synopsis "Annotation package for the Homo.sapiens object")
486 "This package contains the Homo.sapiens object to access data from
487 several related annotation packages.")
488 (license license:artistic2.0)))
490 (define-public r-org-ce-eg-db
492 (name "r-org-ce-eg-db")
496 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
499 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
501 `((upstream-name . "org.Ce.eg.db")))
502 (build-system r-build-system)
504 `(("r-annotationdbi" ,r-annotationdbi)))
505 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
506 (synopsis "Genome wide annotation for Worm")
508 "This package provides mappings from Entrez gene identifiers to various
509 annotations for the genome of the model worm Caenorhabditis elegans.")
510 (license license:artistic2.0)))
512 (define-public r-org-dm-eg-db
514 (name "r-org-dm-eg-db")
518 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
521 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
523 `((upstream-name . "org.Dm.eg.db")))
524 (build-system r-build-system)
526 `(("r-annotationdbi" ,r-annotationdbi)))
527 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
528 (synopsis "Genome wide annotation for Fly")
530 "This package provides mappings from Entrez gene identifiers to various
531 annotations for the genome of the model fruit fly Drosophila melanogaster.")
532 (license license:artistic2.0)))
534 (define-public r-org-dr-eg-db
536 (name "r-org-dr-eg-db")
540 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
543 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
545 `((upstream-name . "org.Dr.eg.db")))
546 (build-system r-build-system)
548 `(("r-annotationdbi" ,r-annotationdbi)))
549 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
550 (synopsis "Annotation for Zebrafish")
552 "This package provides genome wide annotations for Zebrafish, primarily
553 based on mapping using Entrez Gene identifiers.")
554 (license license:artistic2.0)))
556 (define-public r-org-hs-eg-db
558 (name "r-org-hs-eg-db")
562 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
565 "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
567 `((upstream-name . "org.Hs.eg.db")))
568 (build-system r-build-system)
570 `(("r-annotationdbi" ,r-annotationdbi)))
571 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
572 (synopsis "Genome wide annotation for Human")
574 "This package contains genome-wide annotations for Human, primarily based
575 on mapping using Entrez Gene identifiers.")
576 (license license:artistic2.0)))
578 (define-public r-org-mm-eg-db
580 (name "r-org-mm-eg-db")
584 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
587 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
589 `((upstream-name . "org.Mm.eg.db")))
590 (build-system r-build-system)
592 `(("r-annotationdbi" ,r-annotationdbi)))
593 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
594 (synopsis "Genome wide annotation for Mouse")
596 "This package provides mappings from Entrez gene identifiers to various
597 annotations for the genome of the model mouse Mus musculus.")
598 (license license:artistic2.0)))
600 (define-public r-bsgenome-hsapiens-ucsc-hg19
602 (name "r-bsgenome-hsapiens-ucsc-hg19")
606 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
607 version 'annotation))
610 "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8"))))
612 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
613 (build-system r-build-system)
615 `(("r-bsgenome" ,r-bsgenome)))
617 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
618 (synopsis "Full genome sequences for Homo sapiens")
620 "This package provides full genome sequences for Homo sapiens as provided
621 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
622 (license license:artistic2.0)))
624 (define-public r-bsgenome-hsapiens-ucsc-hg38
626 (name "r-bsgenome-hsapiens-ucsc-hg38")
630 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
631 version 'annotation))
634 "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi"))))
636 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
637 (build-system r-build-system)
639 `(("r-bsgenome" ,r-bsgenome)))
641 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
642 (synopsis "Full genome sequences for Homo sapiens")
644 "This package provides full genome sequences for Homo sapiens (Human)
645 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
646 (license license:artistic2.0)))
648 (define-public r-ensdb-hsapiens-v75
650 (name "r-ensdb-hsapiens-v75")
655 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
658 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
660 `((upstream-name . "EnsDb.Hsapiens.v75")))
661 (build-system r-build-system)
663 `(("r-ensembldb" ,r-ensembldb)))
664 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
665 (synopsis "Ensembl based annotation package")
667 "This package exposes an annotation database generated from Ensembl.")
668 (license license:artistic2.0)))
670 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
672 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
677 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
678 version 'annotation))
681 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
683 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
684 (build-system r-build-system)
686 `(("r-annotationdbi" ,r-annotationdbi)
687 ("r-genomicfeatures" ,r-genomicfeatures)))
689 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
690 (synopsis "Annotation package for TxDb object(s)")
692 "This package exposes an annotation databases generated from UCSC by
693 exposing these as TxDb objects.")
694 (license license:artistic2.0)))
696 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
698 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
702 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
703 version 'annotation))
706 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
708 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
709 (build-system r-build-system)
711 `(("r-genomicfeatures" ,r-genomicfeatures)))
713 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
714 (synopsis "Annotation package for human genome in TxDb format")
716 "This package provides an annotation database of Homo sapiens genome
717 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
718 track. The database is exposed as a @code{TxDb} object.")
719 (license license:artistic2.0)))
721 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
723 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
727 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
728 version 'annotation))
731 "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9"))))
733 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
734 (build-system r-build-system)
736 `(("r-genomicfeatures" ,r-genomicfeatures)))
738 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
739 (synopsis "Annotation package for human genome in TxDb format")
741 "This package provides an annotation database of Homo sapiens genome
742 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
743 track. The database is exposed as a @code{TxDb} object.")
744 (license license:artistic2.0)))
746 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
748 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
752 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
753 version 'annotation))
756 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
758 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
759 (build-system r-build-system)
761 `(("r-genomicfeatures" ,r-genomicfeatures)
762 ("r-annotationdbi" ,r-annotationdbi)))
764 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
765 (synopsis "Annotation package for mouse genome in TxDb format")
767 "This package provides an annotation database of Mouse genome data. It
768 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
769 database is exposed as a @code{TxDb} object.")
770 (license license:artistic2.0)))
772 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
774 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
778 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
779 version 'annotation))
782 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
784 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
785 (build-system r-build-system)
787 `(("r-bsgenome" ,r-bsgenome)
788 ("r-genomicfeatures" ,r-genomicfeatures)
789 ("r-annotationdbi" ,r-annotationdbi)))
791 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
792 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
794 "This package loads a TxDb object, which is an R interface to
795 prefabricated databases contained in this package. This package provides
796 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
797 based on the knownGene track.")
798 (license license:artistic2.0)))
800 (define-public r-txdb-celegans-ucsc-ce6-ensgene
802 (name "r-txdb-celegans-ucsc-ce6-ensgene")
807 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
808 version 'annotation))
811 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
813 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
814 (build-system r-build-system)
816 `(("r-annotationdbi" ,r-annotationdbi)
817 ("r-genomicfeatures" ,r-genomicfeatures)))
818 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
819 (synopsis "Annotation package for C elegans TxDb objects")
821 "This package exposes a C elegans annotation database generated from UCSC
822 by exposing these as TxDb objects.")
823 (license license:artistic2.0)))
825 (define-public r-fdb-infiniummethylation-hg19
827 (name "r-fdb-infiniummethylation-hg19")
831 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
832 version 'annotation))
835 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
837 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
838 (build-system r-build-system)
840 `(("r-biostrings" ,r-biostrings)
841 ("r-genomicfeatures" ,r-genomicfeatures)
842 ("r-annotationdbi" ,r-annotationdbi)
843 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
844 ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
845 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
846 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
848 "This is an annotation package for Illumina Infinium DNA methylation
849 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
851 (license license:artistic2.0)))
853 (define-public r-illuminahumanmethylationepicmanifest
855 (name "r-illuminahumanmethylationepicmanifest")
859 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
860 version 'annotation))
863 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
865 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
866 (build-system r-build-system)
868 `(("r-minfi" ,r-minfi)))
869 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
870 (synopsis "Manifest for Illumina's EPIC methylation arrays")
872 "This is a manifest package for Illumina's EPIC methylation arrays.")
873 (license license:artistic2.0)))
875 (define-public r-do-db
881 (uri (bioconductor-uri "DO.db" version 'annotation))
884 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
886 `((upstream-name . "DO.db")))
887 (build-system r-build-system)
889 `(("r-annotationdbi" ,r-annotationdbi)))
890 (home-page "https://www.bioconductor.org/packages/DO.db/")
891 (synopsis "Annotation maps describing the entire Disease Ontology")
893 "This package provides a set of annotation maps describing the entire
895 (license license:artistic2.0)))
897 (define-public r-pfam-db
904 (uri (bioconductor-uri "PFAM.db" version 'annotation))
907 "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s"))))
908 (properties `((upstream-name . "PFAM.db")))
909 (build-system r-build-system)
911 `(("r-annotationdbi" ,r-annotationdbi)))
912 (home-page "https://bioconductor.org/packages/PFAM.db")
913 (synopsis "Set of protein ID mappings for PFAM")
915 "This package provides a set of protein ID mappings for PFAM, assembled
916 using data from public repositories.")
917 (license license:artistic2.0)))
919 (define-public r-phastcons100way-ucsc-hg19
921 (name "r-phastcons100way-ucsc-hg19")
926 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
927 version 'annotation))
930 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
932 `((upstream-name . "phastCons100way.UCSC.hg19")))
933 (build-system r-build-system)
935 `(("r-bsgenome" ,r-bsgenome)
936 ("r-genomeinfodb" ,r-genomeinfodb)
937 ("r-genomicranges" ,r-genomicranges)
938 ("r-genomicscores" ,r-genomicscores)
939 ("r-iranges" ,r-iranges)
940 ("r-s4vectors" ,r-s4vectors)))
941 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
942 (synopsis "UCSC phastCons conservation scores for hg19")
944 "This package provides UCSC phastCons conservation scores for the human
945 genome (hg19) calculated from multiple alignments with other 99 vertebrate
947 (license license:artistic2.0)))
952 (define-public r-abadata
958 (uri (bioconductor-uri "ABAData" version 'experiment))
961 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
963 `((upstream-name . "ABAData")))
964 (build-system r-build-system)
966 `(("r-annotationdbi" ,r-annotationdbi)))
967 (home-page "https://www.bioconductor.org/packages/ABAData/")
968 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
970 "This package provides the data for the gene expression enrichment
971 analysis conducted in the package ABAEnrichment. The package includes three
972 datasets which are derived from the Allen Brain Atlas:
975 @item Gene expression data from Human Brain (adults) averaged across donors,
976 @item Gene expression data from the Developing Human Brain pooled into five
977 age categories and averaged across donors, and
978 @item a developmental effect score based on the Developing Human Brain
982 All datasets are restricted to protein coding genes.")
983 (license license:gpl2+)))
985 (define-public r-aneufinderdata
987 (name "r-aneufinderdata")
991 (uri (bioconductor-uri "AneuFinderData" version 'experiment))
994 "02vb3kmza5hv8bc424fdmfif608xvpdb759w8882kac8izpv29ks"))))
995 (build-system r-build-system)
996 (home-page "https://bioconductor.org/packages/AneuFinderData/")
997 (synopsis "Data package for @code{AneuFinder}")
998 (description "This package contains data used by @code{AneuFinder}.")
999 (license license:artistic2.0)))
1001 (define-public r-aneufinder
1003 (name "r-aneufinder")
1007 (uri (bioconductor-uri "AneuFinder" version))
1010 "0m6wphlriq7y21ih1p2kzml5jzcic79jc52kkk59dkjj8j88yllk"))))
1011 (build-system r-build-system)
1013 `(("r-knitr" ,r-knitr)))
1015 `(("r-genomicranges" ,r-genomicranges)
1016 ("r-aneufinderdata" ,r-aneufinderdata)
1018 ("r-foreach" ,r-foreach)
1019 ("r-doparallel" ,r-doparallel)
1020 ("r-biocgenerics" ,r-biocgenerics)
1021 ("r-s4vectors" ,r-s4vectors)
1022 ("r-genomeinfodb" ,r-genomeinfodb)
1023 ("r-iranges" ,r-iranges)
1024 ("r-rsamtools" ,r-rsamtools)
1025 ("r-bamsignals" ,r-bamsignals)
1026 ("r-dnacopy" ,r-dnacopy)
1027 ("r-biostrings" ,r-biostrings)
1028 ("r-genomicalignments" ,r-genomicalignments)
1029 ("r-ggplot2" ,r-ggplot2)
1030 ("r-reshape2" ,r-reshape2)
1031 ("r-ggdendro" ,r-ggdendro)
1032 ("r-ggrepel" ,r-ggrepel)
1033 ("r-reordercluster" ,r-reordercluster)
1034 ("r-mclust" ,r-mclust)
1035 ("r-cowplot" ,r-cowplot)))
1036 (home-page "https://bioconductor.org/packages/AneuFinder/")
1037 (synopsis "Copy number variation analysis in single-cell-sequencing data")
1038 (description "This package implements functions for copy number variant
1039 calling, plotting, export and analysis from whole-genome single cell
1041 (license license:artistic2.0)))
1043 (define-public r-arrmdata
1049 (uri (bioconductor-uri "ARRmData" version 'experiment))
1052 "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly"))))
1054 `((upstream-name . "ARRmData")))
1055 (build-system r-build-system)
1056 (home-page "https://www.bioconductor.org/packages/ARRmData/")
1057 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
1059 "This package provides raw beta values from 36 samples across 3 groups
1060 from Illumina 450k methylation arrays.")
1061 (license license:artistic2.0)))
1063 (define-public r-chromstardata
1065 (name "r-chromstardata")
1070 (uri (bioconductor-uri "chromstaRData" version 'experiment))
1073 "0ph80d53598635bb8g61acg5rqwnj8644a0gh297r4hgbvwlflab"))))
1074 (properties `((upstream-name . "chromstaRData")))
1075 (build-system r-build-system)
1076 (home-page "https://bioconductor.org/packages/chromstaRData/")
1077 (synopsis "ChIP-seq data for demonstration purposes")
1079 "This package provides ChIP-seq data for demonstration purposes in the
1080 chromstaR package.")
1081 (license license:gpl3)))
1083 (define-public r-copyhelper
1085 (name "r-copyhelper")
1090 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
1093 "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
1094 (properties `((upstream-name . "CopyhelpeR")))
1095 (build-system r-build-system)
1096 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
1097 (synopsis "Helper files for CopywriteR")
1099 "This package contains the helper files that are required to run the
1100 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
1101 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
1102 mm10. In addition, it contains a blacklist filter to remove regions that
1103 display copy number variation. Files are stored as GRanges objects from the
1104 GenomicRanges Bioconductor package.")
1105 (license license:gpl2)))
1107 (define-public r-genelendatabase
1109 (name "r-genelendatabase")
1114 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
1117 "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a"))))
1119 `((upstream-name . "geneLenDataBase")))
1120 (build-system r-build-system)
1122 `(("r-rtracklayer" ,r-rtracklayer)
1123 ("r-genomicfeatures" ,r-genomicfeatures)))
1124 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
1125 (synopsis "Lengths of mRNA transcripts for a number of genomes")
1127 "This package provides the lengths of mRNA transcripts for a number of
1128 genomes and gene ID formats, largely based on the UCSC table browser.")
1129 (license license:lgpl2.0+)))
1131 (define-public r-genomationdata
1133 (name "r-genomationdata")
1137 (uri (bioconductor-uri "genomationData" version 'experiment))
1140 "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
1142 `((upstream-name . "genomationData")))
1143 (build-system r-build-system)
1144 ;; As this package provides little more than large data files, it doesn't
1145 ;; make sense to build substitutes.
1146 (arguments `(#:substitutable? #f))
1148 `(("r-knitr" ,r-knitr)))
1149 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
1150 (synopsis "Experimental data for use with the genomation package")
1152 "This package contains experimental genetic data for use with the
1153 genomation package. Included are Chip Seq, Methylation and Cage data,
1154 downloaded from Encode.")
1155 (license license:gpl3+)))
1157 (define-public r-pasilla
1164 "http://bioconductor.org/packages/release/data/experiment"
1165 "/src/contrib/pasilla_" version ".tar.gz"))
1168 "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0"))))
1169 (build-system r-build-system)
1171 `(("r-biocstyle" ,r-biocstyle)
1172 ("r-dexseq" ,r-dexseq)
1173 ("r-knitr" ,r-knitr)
1174 ("r-rmarkdown" ,r-rmarkdown)))
1175 (home-page "https://www.bioconductor.org/packages/pasilla/")
1176 (synopsis "Data package with per-exon and per-gene read counts")
1177 (description "This package provides per-exon and per-gene read counts
1178 computed for selected genes from RNA-seq data that were presented in the
1179 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1180 by Brooks et al., Genome Research 2011.")
1181 (license license:lgpl2.1+)))
1183 (define-public r-hsmmsinglecell
1185 (name "r-hsmmsinglecell")
1189 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1192 "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9"))))
1194 `((upstream-name . "HSMMSingleCell")))
1195 (build-system r-build-system)
1196 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1197 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1199 "Skeletal myoblasts undergo a well-characterized sequence of
1200 morphological and transcriptional changes during differentiation. In this
1201 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1202 under high mitogen conditions (GM) and then differentiated by switching to
1203 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1204 hundred cells taken over a time-course of serum-induced differentiation.
1205 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1206 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1207 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1208 which were then sequenced to a depth of ~4 million reads per library,
1209 resulting in a complete gene expression profile for each cell.")
1210 (license license:artistic2.0)))
1212 (define-public r-all
1218 (uri (bioconductor-uri "ALL" version 'experiment))
1221 "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9"))))
1222 (properties `((upstream-name . "ALL")))
1223 (build-system r-build-system)
1225 `(("r-biobase" ,r-biobase)))
1226 (home-page "https://bioconductor.org/packages/ALL")
1227 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1229 "The data consist of microarrays from 128 different individuals with
1230 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1231 are available. The data have been normalized (using rma) and it is the
1232 jointly normalized data that are available here. The data are presented in
1233 the form of an @code{exprSet} object.")
1234 (license license:artistic2.0)))
1236 (define-public r-affydata
1243 (uri (bioconductor-uri "affydata" version 'experiment))
1246 "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5"))))
1247 (properties `((upstream-name . "affydata")))
1248 (build-system r-build-system)
1250 `(("r-affy" ,r-affy)))
1251 (home-page "https://bioconductor.org/packages/affydata/")
1252 (synopsis "Affymetrix data for demonstration purposes")
1254 "This package provides example datasets that represent 'real world
1255 examples' of Affymetrix data, unlike the artificial examples included in the
1256 package @code{affy}.")
1257 (license license:gpl2+)))
1259 (define-public r-gagedata
1266 (uri (bioconductor-uri "gageData" version 'experiment))
1268 (base32 "16lmnvmbykvbdgwyx7r2jc217gb9nidn81860v5kri99g97j4jdn"))))
1269 (properties `((upstream-name . "gageData")))
1270 (build-system r-build-system)
1271 (home-page "https://bioconductor.org/packages/gageData")
1272 (synopsis "Auxiliary data for the gage package")
1274 "This is a supportive data package for the software package @code{gage}.
1275 However, the data supplied here are also useful for gene set or pathway
1276 analysis or microarray data analysis in general. In this package, we provide
1277 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1278 BMP6 (originally published as an demo dataset for GAGE, also registered as
1279 GSE13604 in GEO). This package also includes commonly used gene set data based
1280 on KEGG pathways and GO terms for major research species, including human,
1281 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1282 yeast are also included.")
1283 (license license:gpl2+)))
1285 (define-public r-curatedtcgadata
1287 (name "r-curatedtcgadata")
1292 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1295 "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y"))))
1297 `((upstream-name . "curatedTCGAData")))
1298 (build-system r-build-system)
1300 `(("r-annotationhub" ,r-annotationhub)
1301 ("r-experimenthub" ,r-experimenthub)
1302 ("r-hdf5array" ,r-hdf5array)
1303 ("r-multiassayexperiment" ,r-multiassayexperiment)
1304 ("r-s4vectors" ,r-s4vectors)
1305 ("r-summarizedexperiment" ,r-summarizedexperiment)))
1306 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1307 (synopsis "Curated data from The Cancer Genome Atlas")
1309 "This package provides publicly available data from The Cancer Genome
1310 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1311 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1312 number, mutation, microRNA, protein, and others) with clinical / pathological
1313 data. It also links assay barcodes with patient identifiers, enabling
1314 harmonized subsetting of rows (features) and columns (patients / samples)
1315 across the entire multi-'omics experiment.")
1316 (license license:artistic2.0)))
1321 (define-public r-biocversion
1323 (name "r-biocversion")
1328 (uri (bioconductor-uri "BiocVersion" version))
1331 "0rsw8g4g1pcjw1zbx8x17yd3drhxqk4sx3cy3ddzy5731hl6mbfi"))))
1332 (properties `((upstream-name . "BiocVersion")))
1333 (build-system r-build-system)
1334 (home-page "https://bioconductor.org/packages/BiocVersion/")
1335 (synopsis "Set the appropriate version of Bioconductor packages")
1337 "This package provides repository information for the appropriate version
1339 (license license:artistic2.0)))
1341 (define-public r-biocgenerics
1343 (name "r-biocgenerics")
1347 (uri (bioconductor-uri "BiocGenerics" version))
1350 "1kv7lzmyki3hi771v01nml1v1hzz8pyhqqv0xcdzqy354mlgx4m6"))))
1352 `((upstream-name . "BiocGenerics")))
1353 (build-system r-build-system)
1354 (home-page "https://bioconductor.org/packages/BiocGenerics")
1355 (synopsis "S4 generic functions for Bioconductor")
1357 "This package provides S4 generic functions needed by many Bioconductor
1359 (license license:artistic2.0)))
1361 (define-public r-coverageview
1363 (name "r-coverageview")
1367 (uri (bioconductor-uri "CoverageView" version))
1370 "1xhirbjdw09cqm4xvysxqicvqjbahavwvs7shg4cb05gwyd2ha8g"))))
1371 (build-system r-build-system)
1373 `(("r-s4vectors" ,r-s4vectors)
1374 ("r-iranges" ,r-iranges)
1375 ("r-genomicranges" ,r-genomicranges)
1376 ("r-genomicalignments" ,r-genomicalignments)
1377 ("r-rtracklayer" ,r-rtracklayer)
1378 ("r-rsamtools" ,r-rsamtools)))
1379 (home-page "https://bioconductor.org/packages/CoverageView/")
1380 (synopsis "Coverage visualization package for R")
1381 (description "This package provides a framework for the visualization of
1382 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
1383 be also used for genome-wide nucleosome positioning experiments or other
1384 experiment types where it is important to have a framework in order to inspect
1385 how the coverage distributed across the genome.")
1386 (license license:artistic2.0)))
1388 (define-public r-cummerbund
1390 (name "r-cummerbund")
1394 (uri (bioconductor-uri "cummeRbund" version))
1397 "1avvmvrmldbscc7xd6a6k22xjykbzafvqf87wh5z9rx3qlzswsjx"))))
1398 (build-system r-build-system)
1400 `(("r-biobase" ,r-biobase)
1401 ("r-biocgenerics" ,r-biocgenerics)
1402 ("r-fastcluster" ,r-fastcluster)
1403 ("r-ggplot2" ,r-ggplot2)
1406 ("r-reshape2" ,r-reshape2)
1407 ("r-rsqlite" ,r-rsqlite)
1408 ("r-rtracklayer" ,r-rtracklayer)
1409 ("r-s4vectors" ,r-s4vectors)))
1410 (home-page "https://bioconductor.org/packages/cummeRbund/")
1411 (synopsis "Analyze Cufflinks high-throughput sequencing data")
1412 (description "This package allows for persistent storage, access,
1413 exploration, and manipulation of Cufflinks high-throughput sequencing
1414 data. In addition, provides numerous plotting functions for commonly
1415 used visualizations.")
1416 (license license:artistic2.0)))
1418 (define-public r-decipher
1424 (uri (bioconductor-uri "DECIPHER" version))
1427 "0mr7glkx2d37l9nszs52m0kycpm14vxl5gdp3z7i5j7yig1sw2nk"))))
1428 (build-system r-build-system)
1430 `(("r-biostrings" ,r-biostrings)
1432 ("r-iranges" ,r-iranges)
1433 ("r-rsqlite" ,r-rsqlite)
1434 ("r-s4vectors" ,r-s4vectors)
1435 ("r-xvector" ,r-xvector)))
1436 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
1437 (synopsis "Tools for deciphering and managing biological sequences")
1438 (description "This package provides a toolset for deciphering and managing
1439 biological sequences.")
1440 (license license:gpl3)))
1442 (define-public r-deepsnv
1448 (uri (bioconductor-uri "deepSNV" version))
1451 "0zz56hf417m7bgg2g2wpbaik30pi6h2nam1n5bviqgdn4mv8n0bs"))))
1452 (properties `((upstream-name . "deepSNV")))
1453 (build-system r-build-system)
1455 `(("r-biostrings" ,r-biostrings)
1456 ("r-genomicranges" ,r-genomicranges)
1457 ("r-iranges" ,r-iranges)
1458 ("r-rhtslib" ,r-rhtslib)
1459 ("r-summarizedexperiment" ,r-summarizedexperiment)
1460 ("r-variantannotation" ,r-variantannotation)
1461 ("r-vgam" ,r-vgam)))
1463 `(("r-knitr" ,r-knitr)))
1464 (home-page "https://github.com/gerstung-lab/deepSNV/")
1465 (synopsis "Detection of subclonal SNVs in deep sequencing data")
1467 "This package provides quantitative variant callers for detecting
1468 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
1469 The deepSNV algorithm is used for a comparative setup with a control experiment
1470 of the same loci and uses a beta-binomial model and a likelihood ratio test to
1471 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
1472 computes a Bayes classifier based on a beta-binomial model for variant calling
1473 with multiple samples for precisely estimating model parameters - such as local
1474 error rates and dispersion - and prior knowledge, e.g. from variation data
1475 bases such as COSMIC.")
1476 (license license:gpl3)))
1478 (define-public r-delayedarray
1480 (name "r-delayedarray")
1484 (uri (bioconductor-uri "DelayedArray" version))
1487 "0w632262dqzcnvq9s6jvc7naz93dayx51fsv05s0zb6cjwygbqjr"))))
1489 `((upstream-name . "DelayedArray")))
1490 (build-system r-build-system)
1492 `(("r-biocgenerics" ,r-biocgenerics)
1493 ("r-s4vectors" ,r-s4vectors)
1494 ("r-iranges" ,r-iranges)
1495 ("r-matrix" ,r-matrix)
1496 ("r-matrixgenerics" ,r-matrixgenerics)))
1498 `(("r-knitr" ,r-knitr)))
1499 (home-page "https://bioconductor.org/packages/DelayedArray")
1500 (synopsis "Delayed operations on array-like objects")
1502 "Wrapping an array-like object (typically an on-disk object) in a
1503 @code{DelayedArray} object allows one to perform common array operations on it
1504 without loading the object in memory. In order to reduce memory usage and
1505 optimize performance, operations on the object are either delayed or executed
1506 using a block processing mechanism. Note that this also works on in-memory
1507 array-like objects like @code{DataFrame} objects (typically with Rle columns),
1508 @code{Matrix} objects, and ordinary arrays and data frames.")
1509 (license license:artistic2.0)))
1511 (define-public r-bluster
1517 (uri (bioconductor-uri "bluster" version))
1520 "128zd5vwlhmrkq0bpp1dxnkrcqfz1mjmdjlla4wqbjv7v6yyn6lg"))))
1521 (properties `((upstream-name . "bluster")))
1522 (build-system r-build-system)
1524 `(("r-biocneighbors" ,r-biocneighbors)
1525 ("r-biocparallel" ,r-biocparallel)
1526 ("r-cluster" ,r-cluster)
1527 ("r-igraph" ,r-igraph)
1528 ("r-matrix" ,r-matrix)
1530 ("r-s4vectors" ,r-s4vectors)))
1532 `(("r-knitr" ,r-knitr)))
1533 (home-page "https://bioconductor.org/packages/bluster")
1534 (synopsis "Clustering algorithms for Bioconductor")
1535 (description"This package wraps common clustering algorithms in an easily
1536 extended S4 framework. Backends are implemented for hierarchical, k-means
1537 and graph-based clustering. Several utilities are also provided to compare
1538 and evaluate clustering results.")
1539 (license license:gpl3)))
1541 (define-public r-ideoviz
1547 (uri (bioconductor-uri "IdeoViz" version))
1550 "17sx0v5lq2zmg098ps4ksj1h0yla3vlh6s2w1ahqsq0nvm193scm"))))
1551 (build-system r-build-system)
1553 `(("r-biobase" ,r-biobase)
1554 ("r-iranges" ,r-iranges)
1555 ("r-genomicranges" ,r-genomicranges)
1556 ("r-rcolorbrewer" ,r-rcolorbrewer)
1557 ("r-rtracklayer" ,r-rtracklayer)
1558 ("r-genomeinfodb" ,r-genomeinfodb)))
1559 (home-page "https://bioconductor.org/packages/IdeoViz/")
1560 (synopsis "Plots data along a chromosomal ideogram")
1561 (description "This package provides functions to plot data associated with
1562 arbitrary genomic intervals along chromosomal ideogram.")
1563 (license license:gpl2)))
1565 (define-public r-iranges
1571 (uri (bioconductor-uri "IRanges" version))
1574 "0dzj8wqbjzilh2dsaj3ylx958xqrv0c688ayfq2r1z7rs75qy7kx"))))
1576 `((upstream-name . "IRanges")))
1577 (build-system r-build-system)
1579 `(("r-biocgenerics" ,r-biocgenerics)
1580 ("r-s4vectors" ,r-s4vectors)))
1581 (home-page "https://bioconductor.org/packages/IRanges")
1582 (synopsis "Infrastructure for manipulating intervals on sequences")
1584 "This package provides efficient low-level and highly reusable S4 classes
1585 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
1586 generally, data that can be organized sequentially (formally defined as
1587 @code{Vector} objects), as well as views on these @code{Vector} objects.
1588 Efficient list-like classes are also provided for storing big collections of
1589 instances of the basic classes. All classes in the package use consistent
1590 naming and share the same rich and consistent \"Vector API\" as much as
1592 (license license:artistic2.0)))
1594 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
1595 (define-public r-absfiltergsea
1597 (name "r-absfiltergsea")
1602 (uri (cran-uri "AbsFilterGSEA" version))
1604 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
1605 (properties `((upstream-name . "AbsFilterGSEA")))
1606 (build-system r-build-system)
1608 `(("r-biobase" ,r-biobase)
1609 ("r-deseq" ,r-deseq)
1610 ("r-limma" ,r-limma)
1612 ("r-rcpparmadillo" ,r-rcpparmadillo)))
1613 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
1614 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
1616 "This package provides a function that performs gene-permuting of a gene-set
1617 enrichment analysis (GSEA) calculation with or without the absolute filtering.
1618 Without filtering, users can perform (original) two-tailed or one-tailed
1620 (license license:gpl2)))
1622 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
1623 (define-public r-bisquerna
1625 (name "r-bisquerna")
1629 (uri (cran-uri "BisqueRNA" version))
1632 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
1633 (properties `((upstream-name . "BisqueRNA")))
1634 (build-system r-build-system)
1636 `(("r-biobase" ,r-biobase)
1637 ("r-limsolve" ,r-limsolve)))
1639 `(("r-knitr" ,r-knitr)))
1640 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
1641 (synopsis "Decomposition of bulk expression with single-cell sequencing")
1642 (description "This package provides tools to accurately estimate cell type
1643 abundances from heterogeneous bulk expression. A reference-based method
1644 utilizes single-cell information to generate a signature matrix and
1645 transformation of bulk expression for accurate regression based estimates.
1646 A marker-based method utilizes known cell-specific marker genes to measure
1647 relative abundances across samples.")
1648 (license license:gpl3)))
1650 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
1651 ;; from Bioconductor.
1652 (define-public r-deconstructsigs
1654 (name "r-deconstructsigs")
1658 (uri (cran-uri "deconstructSigs" version))
1661 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
1663 `((upstream-name . "deconstructSigs")))
1664 (build-system r-build-system)
1666 `(("r-bsgenome" ,r-bsgenome)
1667 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
1668 ("r-genomeinfodb" ,r-genomeinfodb)
1669 ("r-reshape2" ,r-reshape2)))
1670 (home-page "https://github.com/raerose01/deconstructSigs")
1671 (synopsis "Identifies signatures present in a tumor sample")
1672 (description "This package takes sample information in the form of the
1673 fraction of mutations in each of 96 trinucleotide contexts and identifies
1674 the weighted combination of published signatures that, when summed, most
1675 closely reconstructs the mutational profile.")
1676 (license license:gpl2+)))
1678 ;; This is a CRAN package, but it depends on Bioconductor packages.
1679 (define-public r-nmf
1686 (uri (cran-uri "NMF" version))
1689 "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
1690 (properties `((upstream-name . "NMF")))
1691 (build-system r-build-system)
1693 `(("r-cluster" ,r-cluster)
1694 ("r-biobase" ,r-biobase)
1695 ("r-biocmanager" ,r-biocmanager)
1696 ("r-bigmemory" ,r-bigmemory) ; suggested
1697 ("r-synchronicity" ,r-synchronicity) ; suggested
1698 ("r-colorspace" ,r-colorspace)
1699 ("r-digest" ,r-digest)
1700 ("r-doparallel" ,r-doparallel)
1701 ("r-foreach" ,r-foreach)
1702 ("r-ggplot2" ,r-ggplot2)
1703 ("r-gridbase" ,r-gridbase)
1704 ("r-pkgmaker" ,r-pkgmaker)
1705 ("r-rcolorbrewer" ,r-rcolorbrewer)
1706 ("r-registry" ,r-registry)
1707 ("r-reshape2" ,r-reshape2)
1708 ("r-rngtools" ,r-rngtools)
1709 ("r-stringr" ,r-stringr)))
1711 `(("r-knitr" ,r-knitr)))
1712 (home-page "http://renozao.github.io/NMF")
1713 (synopsis "Algorithms and framework for nonnegative matrix factorization")
1715 "This package provides a framework to perform Non-negative Matrix
1716 Factorization (NMF). The package implements a set of already published
1717 algorithms and seeding methods, and provides a framework to test, develop and
1718 plug new or custom algorithms. Most of the built-in algorithms have been
1719 optimized in C++, and the main interface function provides an easy way of
1720 performing parallel computations on multicore machines.")
1721 (license license:gpl2+)))
1723 (define-public r-affy
1730 (uri (bioconductor-uri "affy" version))
1733 "0vz5y92gqcm0qk57qlba85bk683lzdr7vkmxv109rq6i17vdkkrm"))))
1734 (build-system r-build-system)
1736 `(("r-affyio" ,r-affyio)
1737 ("r-biobase" ,r-biobase)
1738 ("r-biocgenerics" ,r-biocgenerics)
1739 ("r-biocmanager" ,r-biocmanager)
1740 ("r-preprocesscore" ,r-preprocesscore)
1741 ("r-zlibbioc" ,r-zlibbioc)))
1744 (home-page "https://bioconductor.org/packages/affy")
1745 (synopsis "Methods for affymetrix oligonucleotide arrays")
1747 "This package contains functions for exploratory oligonucleotide array
1749 (license license:lgpl2.0+)))
1751 (define-public r-affycomp
1758 (uri (bioconductor-uri "affycomp" version))
1761 "07my5scdh6h0y1bx1h9y5m4fa8bnmw389f83gkb7cf19w4vp36b2"))))
1762 (properties `((upstream-name . "affycomp")))
1763 (build-system r-build-system)
1764 (propagated-inputs `(("r-biobase" ,r-biobase)))
1765 (home-page "https://bioconductor.org/packages/affycomp/")
1766 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
1768 "The package contains functions that can be used to compare expression
1769 measures for Affymetrix Oligonucleotide Arrays.")
1770 (license license:gpl2+)))
1772 (define-public r-affycompatible
1774 (name "r-affycompatible")
1779 (uri (bioconductor-uri "AffyCompatible" version))
1782 "1xwz22wf2smsvmd0d5lfadbsgscnl3fl9msypy2mml38k048p6vj"))))
1784 `((upstream-name . "AffyCompatible")))
1785 (build-system r-build-system)
1787 `(("r-biostrings" ,r-biostrings)
1788 ("r-rcurl" ,r-rcurl)
1790 (home-page "https://bioconductor.org/packages/AffyCompatible/")
1791 (synopsis "Work with Affymetrix GeneChip files")
1793 "This package provides an interface to Affymetrix chip annotation and
1794 sample attribute files. The package allows an easy way for users to download
1795 and manage local data bases of Affynmetrix NetAffx annotation files. It also
1796 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
1797 Command Console} (AGCC)-compatible sample annotation files.")
1798 (license license:artistic2.0)))
1800 (define-public r-affycontam
1802 (name "r-affycontam")
1807 (uri (bioconductor-uri "affyContam" version))
1810 "0242ga68wrdk1kcmxfdbq73a0d3zhrzdlzkzphfg3q0zjbvg49jj"))))
1811 (properties `((upstream-name . "affyContam")))
1812 (build-system r-build-system)
1814 `(("r-affy" ,r-affy)
1815 ("r-affydata" ,r-affydata)
1816 ("r-biobase" ,r-biobase)))
1817 (home-page "https://bioconductor.org/packages/affyContam/")
1818 (synopsis "Structured corruption of Affymetrix CEL file data")
1820 "Microarray quality assessment is a major concern of microarray analysts.
1821 This package provides some simple approaches to in silico creation of quality
1822 problems in CEL-level data to help evaluate performance of quality metrics.")
1823 (license license:artistic2.0)))
1825 (define-public r-affycoretools
1827 (name "r-affycoretools")
1832 (uri (bioconductor-uri "affycoretools" version))
1835 "1dx861spr3kn1dxwhf43s5l1r7bmrq0h6538l3q64iiwzzc6krdh"))))
1836 (properties `((upstream-name . "affycoretools")))
1837 (build-system r-build-system)
1839 `(("r-affy" ,r-affy)
1840 ("r-annotationdbi" ,r-annotationdbi)
1841 ("r-biobase" ,r-biobase)
1842 ("r-biocgenerics" ,r-biocgenerics)
1844 ("r-edger" ,r-edger)
1845 ("r-gcrma" ,r-gcrma)
1846 ("r-glimma" ,r-glimma)
1847 ("r-ggplot2" ,r-ggplot2)
1848 ("r-gostats" ,r-gostats)
1849 ("r-gplots" ,r-gplots)
1850 ("r-hwriter" ,r-hwriter)
1851 ("r-lattice" ,r-lattice)
1852 ("r-limma" ,r-limma)
1853 ("r-oligoclasses" ,r-oligoclasses)
1854 ("r-reportingtools" ,r-reportingtools)
1855 ("r-rsqlite" ,r-rsqlite)
1856 ("r-s4vectors" ,r-s4vectors)
1857 ("r-xtable" ,r-xtable)))
1859 `(("r-knitr" ,r-knitr)))
1860 (home-page "https://bioconductor.org/packages/affycoretools/")
1861 (synopsis "Functions for analyses with Affymetrix GeneChips")
1863 "This package provides various wrapper functions that have been written
1864 to streamline the more common analyses that a Biostatistician might see.")
1865 (license license:artistic2.0)))
1867 (define-public r-affyio
1874 (uri (bioconductor-uri "affyio" version))
1877 "07kibqsm888g06qqqa4648ph877kriy74kprbri8nyx83y8aspjr"))))
1878 (build-system r-build-system)
1880 `(("r-zlibbioc" ,r-zlibbioc)))
1883 (home-page "https://github.com/bmbolstad/affyio")
1884 (synopsis "Tools for parsing Affymetrix data files")
1886 "This package provides routines for parsing Affymetrix data files based
1887 upon file format information. The primary focus is on accessing the CEL and
1889 (license license:lgpl2.0+)))
1891 (define-public r-affxparser
1893 (name "r-affxparser")
1898 (uri (bioconductor-uri "affxparser" version))
1901 "0n3yyrglzqzw0wqxl9igqvkj8qslw6yjkym3vcq0c93kkg7vk01l"))))
1902 (properties `((upstream-name . "affxparser")))
1903 (build-system r-build-system)
1904 (home-page "https://github.com/HenrikBengtsson/affxparser")
1905 (synopsis "Affymetrix File Parsing SDK")
1907 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
1908 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
1909 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
1910 are supported. Currently, there are methods for reading @dfn{chip definition
1911 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
1912 either in full or in part. For example, probe signals from a few probesets
1913 can be extracted very quickly from a set of CEL files into a convenient list
1915 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
1917 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
1919 (define-public r-annotate
1926 (uri (bioconductor-uri "annotate" version))
1929 "13ny596wh65sw7dbw0zd4h84d6k1w99g91c4sqy83mdzgpv73sz7"))))
1930 (build-system r-build-system)
1932 `(("r-annotationdbi" ,r-annotationdbi)
1933 ("r-biobase" ,r-biobase)
1934 ("r-biocgenerics" ,r-biocgenerics)
1938 ("r-xtable" ,r-xtable)))
1940 "https://bioconductor.org/packages/annotate")
1941 (synopsis "Annotation for microarrays")
1942 (description "This package provides R environments for the annotation of
1944 (license license:artistic2.0)))
1946 (define-public r-annotationdbi
1948 (name "r-annotationdbi")
1952 (uri (bioconductor-uri "AnnotationDbi" version))
1955 "117zh7iqa6phsrxrkv45kxraamm3vbfz5i1a8vkhyalhdbs5ssph"))))
1957 `((upstream-name . "AnnotationDbi")))
1958 (build-system r-build-system)
1960 `(("r-biobase" ,r-biobase)
1961 ("r-biocgenerics" ,r-biocgenerics)
1963 ("r-keggrest" ,r-keggrest)
1964 ("r-iranges" ,r-iranges)
1965 ("r-rsqlite" ,r-rsqlite)
1966 ("r-s4vectors" ,r-s4vectors)))
1968 `(("r-knitr" ,r-knitr)))
1969 (home-page "https://bioconductor.org/packages/AnnotationDbi")
1970 (synopsis "Annotation database interface")
1972 "This package provides user interface and database connection code for
1973 annotation data packages using SQLite data storage.")
1974 (license license:artistic2.0)))
1976 (define-public r-annotationfilter
1978 (name "r-annotationfilter")
1982 (uri (bioconductor-uri "AnnotationFilter" version))
1985 "0799jja6v7l3jsi26wbjalkr5lriaxid05xb5g36iq93myhaj0sa"))))
1987 `((upstream-name . "AnnotationFilter")))
1988 (build-system r-build-system)
1990 `(("r-genomicranges" ,r-genomicranges)
1991 ("r-lazyeval" ,r-lazyeval)))
1993 `(("r-knitr" ,r-knitr)))
1994 (home-page "https://github.com/Bioconductor/AnnotationFilter")
1995 (synopsis "Facilities for filtering Bioconductor annotation resources")
1997 "This package provides classes and other infrastructure to implement
1998 filters for manipulating Bioconductor annotation resources. The filters are
1999 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
2000 (license license:artistic2.0)))
2002 (define-public r-annotationforge
2004 (name "r-annotationforge")
2009 (uri (bioconductor-uri "AnnotationForge" version))
2012 "1by3diy0y4809k97cw97mp4j177gn1dzhqil8myij1r7b8sk7hax"))))
2014 `((upstream-name . "AnnotationForge")))
2015 (build-system r-build-system)
2017 `(("r-annotationdbi" ,r-annotationdbi)
2018 ("r-biobase" ,r-biobase)
2019 ("r-biocgenerics" ,r-biocgenerics)
2021 ("r-rcurl" ,r-rcurl)
2022 ("r-rsqlite" ,r-rsqlite)
2023 ("r-s4vectors" ,r-s4vectors)
2026 `(("r-knitr" ,r-knitr)))
2027 (home-page "https://bioconductor.org/packages/AnnotationForge")
2028 (synopsis "Code for building annotation database packages")
2030 "This package provides code for generating Annotation packages and their
2031 databases. Packages produced are intended to be used with AnnotationDbi.")
2032 (license license:artistic2.0)))
2034 (define-public r-annotationhub
2036 (name "r-annotationhub")
2041 (uri (bioconductor-uri "AnnotationHub" version))
2044 "1p9773fv7j7q4x1sjqqaw32qy9lqn2gf6gkynh1d8n1kd7v7sclp"))))
2045 (properties `((upstream-name . "AnnotationHub")))
2046 (build-system r-build-system)
2048 `(("r-annotationdbi" ,r-annotationdbi)
2049 ("r-biocfilecache" ,r-biocfilecache)
2050 ("r-biocgenerics" ,r-biocgenerics)
2051 ("r-biocmanager" ,r-biocmanager)
2052 ("r-biocversion" ,r-biocversion)
2054 ("r-dplyr" ,r-dplyr)
2056 ("r-interactivedisplaybase" ,r-interactivedisplaybase)
2057 ("r-rappdirs" ,r-rappdirs)
2058 ("r-rsqlite" ,r-rsqlite)
2059 ("r-s4vectors" ,r-s4vectors)
2060 ("r-yaml" ,r-yaml)))
2062 `(("r-knitr" ,r-knitr)))
2063 (home-page "https://bioconductor.org/packages/AnnotationHub")
2064 (synopsis "Client to access AnnotationHub resources")
2066 "This package provides a client for the Bioconductor AnnotationHub web
2067 resource. The AnnotationHub web resource provides a central location where
2068 genomic files (e.g. VCF, bed, wig) and other resources from standard
2069 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
2070 metadata about each resource, e.g., a textual description, tags, and date of
2071 modification. The client creates and manages a local cache of files retrieved
2072 by the user, helping with quick and reproducible access.")
2073 (license license:artistic2.0)))
2075 (define-public r-aroma-light
2077 (name "r-aroma-light")
2082 (uri (bioconductor-uri "aroma.light" version))
2085 "1yvq6l1p8cpijvlib4fn9y88ihn0gaalrmgx82jgrfmnszkqn3y5"))))
2086 (properties `((upstream-name . "aroma.light")))
2087 (build-system r-build-system)
2089 `(("r-matrixstats" ,r-matrixstats)
2090 ("r-r-methodss3" ,r-r-methodss3)
2092 ("r-r-utils" ,r-r-utils)))
2093 (home-page "https://github.com/HenrikBengtsson/aroma.light")
2094 (synopsis "Methods for normalization and visualization of microarray data")
2096 "This package provides methods for microarray analysis that take basic
2097 data types such as matrices and lists of vectors. These methods can be used
2098 standalone, be utilized in other packages, or be wrapped up in higher-level
2100 (license license:gpl2+)))
2102 (define-public r-bamsignals
2104 (name "r-bamsignals")
2109 (uri (bioconductor-uri "bamsignals" version))
2112 "1ljrip0jlxjcljqac7vzvwqbcqil5v4f4s4bhpq4akvdkshas6mn"))))
2113 (build-system r-build-system)
2115 `(("r-biocgenerics" ,r-biocgenerics)
2116 ("r-genomicranges" ,r-genomicranges)
2117 ("r-iranges" ,r-iranges)
2119 ("r-rhtslib" ,r-rhtslib)
2120 ("r-zlibbioc" ,r-zlibbioc)))
2122 `(("r-knitr" ,r-knitr)))
2123 (home-page "https://bioconductor.org/packages/bamsignals")
2124 (synopsis "Extract read count signals from bam files")
2126 "This package efficiently obtains count vectors from indexed bam
2127 files. It counts the number of nucleotide sequence reads in given genomic
2128 ranges and it computes reads profiles and coverage profiles. It also handles
2130 (license license:gpl2+)))
2132 (define-public r-biobase
2138 (uri (bioconductor-uri "Biobase" version))
2141 "1sg8w8860zhlz9s1pf75xa8asd2hyqsj13fh5xc37hf5yqdfkavr"))))
2143 `((upstream-name . "Biobase")))
2144 (build-system r-build-system)
2146 `(("r-biocgenerics" ,r-biocgenerics)))
2147 (home-page "https://bioconductor.org/packages/Biobase")
2148 (synopsis "Base functions for Bioconductor")
2150 "This package provides functions that are needed by many other packages
2151 on Bioconductor or which replace R functions.")
2152 (license license:artistic2.0)))
2154 (define-public r-biomart
2160 (uri (bioconductor-uri "biomaRt" version))
2163 "1h8lzd63qvy1y75nlnhazpkyhl6g1hz80baqg20gpxbv38wkyf55"))))
2165 `((upstream-name . "biomaRt")))
2166 (build-system r-build-system)
2168 `(("r-annotationdbi" ,r-annotationdbi)
2169 ("r-biocfilecache" ,r-biocfilecache)
2170 ("r-digest" ,r-digest)
2172 ("r-progress" ,r-progress)
2173 ("r-rappdirs" ,r-rappdirs)
2174 ("r-stringr" ,r-stringr)
2177 `(("r-knitr" ,r-knitr)))
2178 (home-page "https://bioconductor.org/packages/biomaRt")
2179 (synopsis "Interface to BioMart databases")
2181 "biomaRt provides an interface to a growing collection of databases
2182 implementing the @url{BioMart software suite, http://www.biomart.org}. The
2183 package enables retrieval of large amounts of data in a uniform way without
2184 the need to know the underlying database schemas or write complex SQL queries.
2185 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
2186 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
2187 users direct access to a diverse set of data and enable a wide range of
2188 powerful online queries from gene annotation to database mining.")
2189 (license license:artistic2.0)))
2191 (define-public r-biocparallel
2193 (name "r-biocparallel")
2197 (uri (bioconductor-uri "BiocParallel" version))
2200 "17w4gdajxxmsfgiwycp1d7rbxdqhc5jnngcb58ky0fv5xbv9f4j0"))))
2202 `((upstream-name . "BiocParallel")))
2203 (build-system r-build-system)
2206 (modify-phases %standard-phases
2207 (add-after 'unpack 'make-reproducible
2209 ;; Remove generated documentation.
2210 (for-each delete-file
2211 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
2212 "inst/doc/Introduction_To_BiocParallel.pdf"
2213 "inst/doc/Errors_Logs_And_Debugging.pdf"
2214 "inst/doc/BiocParallel_BatchtoolsParam.R"
2215 "inst/doc/Introduction_To_BiocParallel.R"
2216 "inst/doc/Errors_Logs_And_Debugging.R"))
2218 ;; Remove time-dependent macro
2219 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
2220 "inst/doc/Introduction_To_BiocParallel.Rnw"
2221 "inst/doc/Errors_Logs_And_Debugging.Rnw"
2222 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
2223 "vignettes/Introduction_To_BiocParallel.Rnw"
2224 "vignettes/Errors_Logs_And_Debugging.Rnw")
2225 (("\\today") "later"))
2227 ;; Initialize the random number generator seed when building.
2228 (substitute* "R/internal_rng_stream.R"
2229 (("\"L'Ecuyer-CMRG\"\\)" m)
2231 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
2233 `(("r-futile-logger" ,r-futile-logger)
2237 `(("r-knitr" ,r-knitr)))
2238 (home-page "https://bioconductor.org/packages/BiocParallel")
2239 (synopsis "Bioconductor facilities for parallel evaluation")
2241 "This package provides modified versions and novel implementation of
2242 functions for parallel evaluation, tailored to use with Bioconductor
2244 (license (list license:gpl2+ license:gpl3+))))
2246 (define-public r-biostrings
2248 (name "r-biostrings")
2252 (uri (bioconductor-uri "Biostrings" version))
2255 "0xidh6wp0l47g1j9x8d4fs91ky6pi5nzf85ry801gqd2gqajh2zy"))))
2257 `((upstream-name . "Biostrings")))
2258 (build-system r-build-system)
2260 `(("r-biocgenerics" ,r-biocgenerics)
2261 ("r-crayon" ,r-crayon)
2262 ("r-genomeinfodb" ,r-genomeinfodb)
2263 ("r-iranges" ,r-iranges)
2264 ("r-s4vectors" ,r-s4vectors)
2265 ("r-xvector" ,r-xvector)))
2266 (home-page "https://bioconductor.org/packages/Biostrings")
2267 (synopsis "String objects and algorithms for biological sequences")
2269 "This package provides memory efficient string containers, string
2270 matching algorithms, and other utilities, for fast manipulation of large
2271 biological sequences or sets of sequences.")
2272 (license license:artistic2.0)))
2274 (define-public r-biovizbase
2276 (name "r-biovizbase")
2281 (uri (bioconductor-uri "biovizBase" version))
2284 "14jyyg3ggdhaqhp0j4qf6dapykh76fygbaa4lr7czqbc5mr0iw23"))))
2285 (properties `((upstream-name . "biovizBase")))
2286 (build-system r-build-system)
2288 `(("r-annotationdbi" ,r-annotationdbi)
2289 ("r-annotationfilter" ,r-annotationfilter)
2290 ("r-biocgenerics" ,r-biocgenerics)
2291 ("r-biostrings" ,r-biostrings)
2292 ("r-dichromat" ,r-dichromat)
2293 ("r-ensembldb" ,r-ensembldb)
2294 ("r-genomeinfodb" ,r-genomeinfodb)
2295 ("r-genomicalignments" ,r-genomicalignments)
2296 ("r-genomicfeatures" ,r-genomicfeatures)
2297 ("r-genomicranges" ,r-genomicranges)
2298 ("r-hmisc" ,r-hmisc)
2299 ("r-iranges" ,r-iranges)
2300 ("r-rcolorbrewer" ,r-rcolorbrewer)
2301 ("r-rlang" ,r-rlang)
2302 ("r-rsamtools" ,r-rsamtools)
2303 ("r-s4vectors" ,r-s4vectors)
2304 ("r-scales" ,r-scales)
2305 ("r-summarizedexperiment" ,r-summarizedexperiment)
2306 ("r-variantannotation" ,r-variantannotation)))
2307 (home-page "https://bioconductor.org/packages/biovizBase")
2308 (synopsis "Basic graphic utilities for visualization of genomic data")
2310 "The biovizBase package is designed to provide a set of utilities, color
2311 schemes and conventions for genomic data. It serves as the base for various
2312 high-level packages for biological data visualization. This saves development
2313 effort and encourages consistency.")
2314 (license license:artistic2.0)))
2316 (define-public r-bsgenome
2322 (uri (bioconductor-uri "BSgenome" version))
2325 "1jhissp9ad1rn2p0bzr3yslbn84yqbaqgnn5p9hyacwr7mr091cn"))))
2327 `((upstream-name . "BSgenome")))
2328 (build-system r-build-system)
2330 `(("r-biocgenerics" ,r-biocgenerics)
2331 ("r-biostrings" ,r-biostrings)
2332 ("r-genomeinfodb" ,r-genomeinfodb)
2333 ("r-genomicranges" ,r-genomicranges)
2334 ("r-iranges" ,r-iranges)
2335 ("r-matrixstats" ,r-matrixstats)
2336 ("r-rsamtools" ,r-rsamtools)
2337 ("r-rtracklayer" ,r-rtracklayer)
2338 ("r-s4vectors" ,r-s4vectors)
2339 ("r-xvector" ,r-xvector)))
2340 (home-page "https://bioconductor.org/packages/BSgenome")
2341 (synopsis "Infrastructure for Biostrings-based genome data packages")
2343 "This package provides infrastructure shared by all Biostrings-based
2344 genome data packages and support for efficient SNP representation.")
2345 (license license:artistic2.0)))
2347 (define-public r-category
2354 (uri (bioconductor-uri "Category" version))
2357 "0f76pb7h8qc51mca5pq00m9p02sbkcj6ywfzli20qai2ykpfr71x"))))
2358 (properties `((upstream-name . "Category")))
2359 (build-system r-build-system)
2361 `(("r-annotate" ,r-annotate)
2362 ("r-annotationdbi" ,r-annotationdbi)
2363 ("r-biobase" ,r-biobase)
2364 ("r-biocgenerics" ,r-biocgenerics)
2365 ("r-genefilter" ,r-genefilter)
2366 ("r-graph" ,r-graph)
2367 ("r-gseabase" ,r-gseabase)
2368 ("r-matrix" ,r-matrix)
2371 (home-page "https://bioconductor.org/packages/Category")
2372 (synopsis "Category analysis")
2374 "This package provides a collection of tools for performing category
2376 (license license:artistic2.0)))
2378 (define-public r-chipseeker
2380 (name "r-chipseeker")
2384 (uri (bioconductor-uri "ChIPseeker" version))
2387 "18hdgml80770c0xgd06zrl8px1ql9fa65rirfkq07z7rzpnd23rw"))))
2388 (build-system r-build-system)
2390 `(("r-knitr" ,r-knitr)))
2392 `(("r-annotationdbi" ,r-annotationdbi)
2393 ("r-biocgenerics" ,r-biocgenerics)
2395 ("r-enrichplot" ,r-enrichplot)
2396 ("r-iranges" ,r-iranges)
2397 ("r-genomeinfodb" ,r-genomeinfodb)
2398 ("r-genomicranges" ,r-genomicranges)
2399 ("r-genomicfeatures" ,r-genomicfeatures)
2400 ("r-ggplot2" ,r-ggplot2)
2401 ("r-gplots" ,r-gplots)
2402 ("r-gtools" ,r-gtools)
2403 ("r-dplyr" ,r-dplyr)
2404 ("r-plotrix" ,r-plotrix)
2405 ("r-dplyr" ,r-dplyr)
2406 ("r-magrittr" ,r-magrittr)
2407 ("r-rcolorbrewer" ,r-rcolorbrewer)
2408 ("r-rtracklayer" ,r-rtracklayer)
2409 ("r-s4vectors" ,r-s4vectors)
2410 ("r-txdb-hsapiens-ucsc-hg19-knowngene"
2411 ,r-txdb-hsapiens-ucsc-hg19-knowngene)))
2412 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
2413 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
2414 (description "This package implements functions to retrieve the nearest
2415 genes around the peak, annotate genomic region of the peak, statstical methods
2416 for estimate the significance of overlap among ChIP peak data sets, and
2417 incorporate GEO database for user to compare the own dataset with those
2418 deposited in database. The comparison can be used to infer cooperative
2419 regulation and thus can be used to generate hypotheses. Several visualization
2420 functions are implemented to summarize the coverage of the peak experiment,
2421 average profile and heatmap of peaks binding to TSS regions, genomic
2422 annotation, distance to TSS, and overlap of peaks or genes.")
2423 (license license:artistic2.0)))
2425 (define-public r-chipseq
2432 (uri (bioconductor-uri "chipseq" version))
2435 "078p9h0zghlhpd6cr54nww1mk7q97imx8yqfayw5m2yq4097ivbi"))))
2436 (build-system r-build-system)
2438 `(("r-biocgenerics" ,r-biocgenerics)
2439 ("r-genomicranges" ,r-genomicranges)
2440 ("r-iranges" ,r-iranges)
2441 ("r-lattice" ,r-lattice)
2442 ("r-s4vectors" ,r-s4vectors)
2443 ("r-shortread" ,r-shortread)))
2444 (home-page "https://bioconductor.org/packages/chipseq")
2445 (synopsis "Package for analyzing ChIPseq data")
2447 "This package provides tools for processing short read data from ChIPseq
2449 (license license:artistic2.0)))
2451 (define-public r-complexheatmap
2453 (name "r-complexheatmap")
2458 (uri (bioconductor-uri "ComplexHeatmap" version))
2461 "0jl96msj1njdrvngg68s50vmphvhi2lfwlv34x07pcdzgkjjs41f"))))
2463 `((upstream-name . "ComplexHeatmap")))
2464 (build-system r-build-system)
2466 `(("r-cairo" ,r-cairo)
2467 ("r-circlize" ,r-circlize)
2469 ("r-colorspace" ,r-colorspace)
2470 ("r-digest" ,r-digest)
2471 ("r-doparallel" ,r-doparallel)
2472 ("r-foreach" ,r-foreach)
2473 ("r-getoptlong" ,r-getoptlong)
2474 ("r-globaloptions" ,r-globaloptions)
2475 ("r-iranges" ,r-iranges)
2476 ("r-matrixstats" ,r-matrixstats)
2478 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2480 `(("r-knitr" ,r-knitr)))
2482 "https://github.com/jokergoo/ComplexHeatmap")
2483 (synopsis "Making Complex Heatmaps")
2485 "Complex heatmaps are efficient to visualize associations between
2486 different sources of data sets and reveal potential structures. This package
2487 provides a highly flexible way to arrange multiple heatmaps and supports
2488 self-defined annotation graphics.")
2489 (license license:gpl2+)))
2491 (define-public r-copywriter
2493 (name "r-copywriter")
2498 (uri (bioconductor-uri "CopywriteR" version))
2501 "0pacs714d9b1fdz68pp9ca0x77d376s19lxb82np4l9fgx0rgkxp"))))
2502 (properties `((upstream-name . "CopywriteR")))
2503 (build-system r-build-system)
2505 `(("r-biocparallel" ,r-biocparallel)
2506 ("r-chipseq" ,r-chipseq)
2507 ("r-copyhelper" ,r-copyhelper)
2508 ("r-data-table" ,r-data-table)
2509 ("r-dnacopy" ,r-dnacopy)
2510 ("r-futile-logger" ,r-futile-logger)
2511 ("r-genomeinfodb" ,r-genomeinfodb)
2512 ("r-genomicalignments" ,r-genomicalignments)
2513 ("r-genomicranges" ,r-genomicranges)
2514 ("r-gtools" ,r-gtools)
2515 ("r-iranges" ,r-iranges)
2516 ("r-matrixstats" ,r-matrixstats)
2517 ("r-rsamtools" ,r-rsamtools)
2518 ("r-s4vectors" ,r-s4vectors)))
2519 (home-page "https://github.com/PeeperLab/CopywriteR")
2520 (synopsis "Copy number information from targeted sequencing")
2522 "CopywriteR extracts DNA copy number information from targeted sequencing
2523 by utilizing off-target reads. It allows for extracting uniformly distributed
2524 copy number information, can be used without reference, and can be applied to
2525 sequencing data obtained from various techniques including chromatin
2526 immunoprecipitation and target enrichment on small gene panels. Thereby,
2527 CopywriteR constitutes a widely applicable alternative to available copy
2528 number detection tools.")
2529 (license license:gpl2)))
2531 (define-public r-deseq
2538 (uri (bioconductor-uri "DESeq" version))
2541 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
2542 (properties `((upstream-name . "DESeq")))
2543 (build-system r-build-system)
2545 `(("r-biobase" ,r-biobase)
2546 ("r-biocgenerics" ,r-biocgenerics)
2547 ("r-genefilter" ,r-genefilter)
2548 ("r-geneplotter" ,r-geneplotter)
2549 ("r-lattice" ,r-lattice)
2550 ("r-locfit" ,r-locfit)
2552 ("r-rcolorbrewer" ,r-rcolorbrewer)))
2553 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
2554 (synopsis "Differential gene expression analysis")
2556 "This package provides tools for estimating variance-mean dependence in
2557 count data from high-throughput genetic sequencing assays and for testing for
2558 differential expression based on a model using the negative binomial
2560 (license license:gpl3+)))
2562 (define-public r-deseq2
2569 (uri (bioconductor-uri "DESeq2" version))
2572 "0r1brwmj7av0bj72jajn27vx3zs1bgg8qfbhf02fln6kf7im4kaz"))))
2573 (properties `((upstream-name . "DESeq2")))
2574 (build-system r-build-system)
2576 `(("r-biobase" ,r-biobase)
2577 ("r-biocgenerics" ,r-biocgenerics)
2578 ("r-biocparallel" ,r-biocparallel)
2579 ("r-genefilter" ,r-genefilter)
2580 ("r-geneplotter" ,r-geneplotter)
2581 ("r-genomicranges" ,r-genomicranges)
2582 ("r-ggplot2" ,r-ggplot2)
2583 ("r-iranges" ,r-iranges)
2584 ("r-locfit" ,r-locfit)
2586 ("r-rcpparmadillo" ,r-rcpparmadillo)
2587 ("r-s4vectors" ,r-s4vectors)
2588 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2590 `(("r-knitr" ,r-knitr)))
2591 (home-page "https://bioconductor.org/packages/DESeq2")
2592 (synopsis "Differential gene expression analysis")
2594 "This package provides functions to estimate variance-mean dependence in
2595 count data from high-throughput nucleotide sequencing assays and test for
2596 differential expression based on a model using the negative binomial
2598 (license license:lgpl3+)))
2600 (define-public r-dexseq
2607 (uri (bioconductor-uri "DEXSeq" version))
2610 "1zywh30f4j4rj0f9w6yk5xr9mvdbg8gicy3wsb8yxdnamadyr7x4"))))
2611 (properties `((upstream-name . "DEXSeq")))
2612 (build-system r-build-system)
2614 `(("r-annotationdbi" ,r-annotationdbi)
2615 ("r-biobase" ,r-biobase)
2616 ("r-biocgenerics" ,r-biocgenerics)
2617 ("r-biocparallel" ,r-biocparallel)
2618 ("r-biomart" ,r-biomart)
2619 ("r-deseq2" ,r-deseq2)
2620 ("r-genefilter" ,r-genefilter)
2621 ("r-geneplotter" ,r-geneplotter)
2622 ("r-genomicranges" ,r-genomicranges)
2623 ("r-hwriter" ,r-hwriter)
2624 ("r-iranges" ,r-iranges)
2625 ("r-rcolorbrewer" ,r-rcolorbrewer)
2626 ("r-rsamtools" ,r-rsamtools)
2627 ("r-s4vectors" ,r-s4vectors)
2628 ("r-statmod" ,r-statmod)
2629 ("r-stringr" ,r-stringr)
2630 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2632 `(("r-knitr" ,r-knitr)))
2633 (home-page "https://bioconductor.org/packages/DEXSeq")
2634 (synopsis "Inference of differential exon usage in RNA-Seq")
2636 "This package is focused on finding differential exon usage using RNA-seq
2637 exon counts between samples with different experimental designs. It provides
2638 functions that allows the user to make the necessary statistical tests based
2639 on a model that uses the negative binomial distribution to estimate the
2640 variance between biological replicates and generalized linear models for
2641 testing. The package also provides functions for the visualization and
2642 exploration of the results.")
2643 (license license:gpl3+)))
2645 (define-public r-dirichletmultinomial
2647 (name "r-dirichletmultinomial")
2652 (uri (bioconductor-uri "DirichletMultinomial" version))
2655 "0ikmj0300lfzj6q1vyahfyx5kwi5h59mds7ym4f2j1bbxqzy6ssl"))))
2657 `((upstream-name . "DirichletMultinomial")))
2658 (build-system r-build-system)
2662 `(("r-biocgenerics" ,r-biocgenerics)
2663 ("r-iranges" ,r-iranges)
2664 ("r-s4vectors" ,r-s4vectors)))
2665 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
2666 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
2668 "Dirichlet-multinomial mixture models can be used to describe variability
2669 in microbial metagenomic data. This package is an interface to code
2670 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
2672 (license license:lgpl3)))
2674 (define-public r-edaseq
2681 (uri (bioconductor-uri "EDASeq" version))
2684 "1mqpi2iz4azr31b3ajsqb4n9izjh85dx642844n059c8s2pfmivh"))))
2685 (properties `((upstream-name . "EDASeq")))
2686 (build-system r-build-system)
2688 `(("r-annotationdbi" ,r-annotationdbi)
2689 ("r-aroma-light" ,r-aroma-light)
2690 ("r-biobase" ,r-biobase)
2691 ("r-biocgenerics" ,r-biocgenerics)
2692 ("r-biocmanager" ,r-biocmanager)
2693 ("r-biomart" ,r-biomart)
2694 ("r-biostrings" ,r-biostrings)
2695 ("r-genomicfeatures" ,r-genomicfeatures)
2696 ("r-genomicranges" ,r-genomicranges)
2697 ("r-iranges" ,r-iranges)
2698 ("r-rsamtools" ,r-rsamtools)
2699 ("r-shortread" ,r-shortread)))
2701 `(("r-knitr" ,r-knitr)))
2702 (home-page "https://github.com/drisso/EDASeq")
2703 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
2705 "This package provides support for numerical and graphical summaries of
2706 RNA-Seq genomic read data. Provided within-lane normalization procedures to
2707 adjust for GC-content effect (or other gene-level effects) on read counts:
2708 loess robust local regression, global-scaling, and full-quantile
2709 normalization. Between-lane normalization procedures to adjust for
2710 distributional differences between lanes (e.g., sequencing depth):
2711 global-scaling and full-quantile normalization.")
2712 (license license:artistic2.0)))
2714 (define-public r-edger
2720 (uri (bioconductor-uri "edgeR" version))
2723 "1ikl9y6hj2p92nrb1ydxy2410b3wrax83rfy2imaj0vgfmhsgx6g"))))
2724 (properties `((upstream-name . "edgeR")))
2725 (build-system r-build-system)
2727 `(("r-limma" ,r-limma)
2728 ("r-locfit" ,r-locfit)
2730 ("r-statmod" ,r-statmod))) ;for estimateDisp
2731 (home-page "http://bioinf.wehi.edu.au/edgeR")
2732 (synopsis "EdgeR does empirical analysis of digital gene expression data")
2733 (description "This package can do differential expression analysis of
2734 RNA-seq expression profiles with biological replication. It implements a range
2735 of statistical methodology based on the negative binomial distributions,
2736 including empirical Bayes estimation, exact tests, generalized linear models
2737 and quasi-likelihood tests. It be applied to differential signal analysis of
2738 other types of genomic data that produce counts, including ChIP-seq, SAGE and
2740 (license license:gpl2+)))
2742 (define-public r-ensembldb
2744 (name "r-ensembldb")
2749 (uri (bioconductor-uri "ensembldb" version))
2752 "100m2mzxl4pmldqixzfdznnd4nqbykk2l7n4xazqjpnlpcldy2dj"))))
2753 (build-system r-build-system)
2755 `(("r-annotationdbi" ,r-annotationdbi)
2756 ("r-annotationfilter" ,r-annotationfilter)
2757 ("r-biobase" ,r-biobase)
2758 ("r-biocgenerics" ,r-biocgenerics)
2759 ("r-biostrings" ,r-biostrings)
2762 ("r-genomeinfodb" ,r-genomeinfodb)
2763 ("r-genomicfeatures" ,r-genomicfeatures)
2764 ("r-genomicranges" ,r-genomicranges)
2765 ("r-iranges" ,r-iranges)
2766 ("r-protgenerics" ,r-protgenerics)
2767 ("r-rsamtools" ,r-rsamtools)
2768 ("r-rsqlite" ,r-rsqlite)
2769 ("r-rtracklayer" ,r-rtracklayer)
2770 ("r-s4vectors" ,r-s4vectors)))
2772 `(("r-knitr" ,r-knitr)))
2773 (home-page "https://github.com/jotsetung/ensembldb")
2774 (synopsis "Utilities to create and use Ensembl-based annotation databases")
2776 "The package provides functions to create and use transcript-centric
2777 annotation databases/packages. The annotation for the databases are directly
2778 fetched from Ensembl using their Perl API. The functionality and data is
2779 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
2780 but, in addition to retrieve all gene/transcript models and annotations from
2781 the database, the @code{ensembldb} package also provides a filter framework
2782 allowing to retrieve annotations for specific entries like genes encoded on a
2783 chromosome region or transcript models of lincRNA genes.")
2784 ;; No version specified
2785 (license license:lgpl3+)))
2787 (define-public r-fastseg
2794 (uri (bioconductor-uri "fastseg" version))
2797 "006v7qs707xmnr35b7rw135pyvacrmhv55a3c53birkpsrjgkps0"))))
2798 (build-system r-build-system)
2800 `(("r-biobase" ,r-biobase)
2801 ("r-biocgenerics" ,r-biocgenerics)
2802 ("r-genomicranges" ,r-genomicranges)
2803 ("r-iranges" ,r-iranges)
2804 ("r-s4vectors" ,r-s4vectors)))
2805 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
2806 (synopsis "Fast segmentation algorithm for genetic sequencing data")
2808 "Fastseg implements a very fast and efficient segmentation algorithm.
2809 It can segment data from DNA microarrays and data from next generation
2810 sequencing for example to detect copy number segments. Further it can segment
2811 data from RNA microarrays like tiling arrays to identify transcripts. Most
2812 generally, it can segment data given as a matrix or as a vector. Various data
2813 formats can be used as input to fastseg like expression set objects for
2814 microarrays or GRanges for sequencing data.")
2815 (license license:lgpl2.0+)))
2817 (define-public r-gage
2824 (uri (bioconductor-uri "gage" version))
2827 "0z7hrwdm6my6p7z04bcpfhqk72pd0s1bdzvsiiym59qj79fbvb83"))))
2828 (build-system r-build-system)
2830 `(("r-annotationdbi" ,r-annotationdbi)
2831 ("r-go-db" ,r-go-db)
2832 ("r-graph" ,r-graph)
2833 ("r-keggrest" ,r-keggrest)))
2834 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
2835 "articles/10.1186/1471-2105-10-161"))
2836 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
2838 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
2839 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
2840 data attributes including sample sizes, experimental designs, assay platforms,
2841 and other types of heterogeneity. The gage package provides functions for
2842 basic GAGE analysis, result processing and presentation. In addition, it
2843 provides demo microarray data and commonly used gene set data based on KEGG
2844 pathways and GO terms. These functions and data are also useful for gene set
2845 analysis using other methods.")
2846 (license license:gpl2+)))
2848 (define-public r-genefilter
2850 (name "r-genefilter")
2855 (uri (bioconductor-uri "genefilter" version))
2858 "0dy9pmlb0pc9b4ks5fb9zgnmhc9f2mkqmsdlb7f5z88xmj68y4qk"))))
2859 (build-system r-build-system)
2861 `(("gfortran" ,gfortran)
2862 ("r-knitr" ,r-knitr)))
2864 `(("r-annotate" ,r-annotate)
2865 ("r-annotationdbi" ,r-annotationdbi)
2866 ("r-biobase" ,r-biobase)
2867 ("r-biocgenerics" ,r-biocgenerics)
2868 ("r-survival" ,r-survival)))
2869 (home-page "https://bioconductor.org/packages/genefilter")
2870 (synopsis "Filter genes from high-throughput experiments")
2872 "This package provides basic functions for filtering genes from
2873 high-throughput sequencing experiments.")
2874 (license license:artistic2.0)))
2876 (define-public r-geneoverlap
2878 (name "r-geneoverlap")
2882 (uri (bioconductor-uri "GeneOverlap" version))
2885 "1kfw3h68rvbafhklds6sfmviwv91nms8wk0ywzkjg5h3mmgxbsv9"))))
2886 (build-system r-build-system)
2888 `(("r-rcolorbrewer" ,r-rcolorbrewer)
2889 ("r-gplots" ,r-gplots)))
2890 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
2891 (synopsis "Test and visualize gene overlaps")
2892 (description "This package can be used to test two sets of gene lists
2893 and visualize the results.")
2894 (license license:gpl3)))
2896 (define-public r-genomation
2898 (name "r-genomation")
2902 (uri (bioconductor-uri "genomation" version))
2905 "0qa3b4mfd7l1sy4pw64zr2d90y5apah900krxjl4x39acygg0i2r"))))
2906 (build-system r-build-system)
2908 `(("r-biostrings" ,r-biostrings)
2909 ("r-bsgenome" ,r-bsgenome)
2910 ("r-data-table" ,r-data-table)
2911 ("r-genomeinfodb" ,r-genomeinfodb)
2912 ("r-genomicalignments" ,r-genomicalignments)
2913 ("r-genomicranges" ,r-genomicranges)
2914 ("r-ggplot2" ,r-ggplot2)
2915 ("r-gridbase" ,r-gridbase)
2916 ("r-impute" ,r-impute)
2917 ("r-iranges" ,r-iranges)
2918 ("r-matrixstats" ,r-matrixstats)
2919 ("r-plotrix" ,r-plotrix)
2922 ("r-readr" ,r-readr)
2923 ("r-reshape2" ,r-reshape2)
2924 ("r-rsamtools" ,r-rsamtools)
2925 ("r-rtracklayer" ,r-rtracklayer)
2926 ("r-s4vectors" ,r-s4vectors)
2927 ("r-seqpattern" ,r-seqpattern)))
2929 `(("r-knitr" ,r-knitr)))
2930 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
2931 (synopsis "Summary, annotation and visualization of genomic data")
2933 "This package provides a package for summary and annotation of genomic
2934 intervals. Users can visualize and quantify genomic intervals over
2935 pre-defined functional regions, such as promoters, exons, introns, etc. The
2936 genomic intervals represent regions with a defined chromosome position, which
2937 may be associated with a score, such as aligned reads from HT-seq experiments,
2938 TF binding sites, methylation scores, etc. The package can use any tabular
2939 genomic feature data as long as it has minimal information on the locations of
2940 genomic intervals. In addition, it can use BAM or BigWig files as input.")
2941 (license license:artistic2.0)))
2943 (define-public r-genomeinfodb
2945 (name "r-genomeinfodb")
2949 (uri (bioconductor-uri "GenomeInfoDb" version))
2952 "0wjd7sh7kr9lfcdbzm5jdynl84nfsl7nqvly92qqrdcxd2sjfr63"))))
2954 `((upstream-name . "GenomeInfoDb")))
2955 (build-system r-build-system)
2957 `(("r-biocgenerics" ,r-biocgenerics)
2958 ("r-genomeinfodbdata" ,r-genomeinfodbdata)
2959 ("r-iranges" ,r-iranges)
2960 ("r-rcurl" ,r-rcurl)
2961 ("r-s4vectors" ,r-s4vectors)))
2963 `(("r-knitr" ,r-knitr)))
2964 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
2965 (synopsis "Utilities for manipulating chromosome identifiers")
2967 "This package contains data and functions that define and allow
2968 translation between different chromosome sequence naming conventions (e.g.,
2969 \"chr1\" versus \"1\"), including a function that attempts to place sequence
2970 names in their natural, rather than lexicographic, order.")
2971 (license license:artistic2.0)))
2973 (define-public r-genomicalignments
2975 (name "r-genomicalignments")
2979 (uri (bioconductor-uri "GenomicAlignments" version))
2982 "00rq110jkh89nxgk05zh8kssxk8mb4dq0wjg3n7ivfmmm9wdwhp2"))))
2984 `((upstream-name . "GenomicAlignments")))
2985 (build-system r-build-system)
2987 `(("r-biocgenerics" ,r-biocgenerics)
2988 ("r-biocparallel" ,r-biocparallel)
2989 ("r-biostrings" ,r-biostrings)
2990 ("r-genomeinfodb" ,r-genomeinfodb)
2991 ("r-genomicranges" ,r-genomicranges)
2992 ("r-iranges" ,r-iranges)
2993 ("r-rsamtools" ,r-rsamtools)
2994 ("r-s4vectors" ,r-s4vectors)
2995 ("r-summarizedexperiment" ,r-summarizedexperiment)))
2996 (home-page "https://bioconductor.org/packages/GenomicAlignments")
2997 (synopsis "Representation and manipulation of short genomic alignments")
2999 "This package provides efficient containers for storing and manipulating
3000 short genomic alignments (typically obtained by aligning short reads to a
3001 reference genome). This includes read counting, computing the coverage,
3002 junction detection, and working with the nucleotide content of the
3004 (license license:artistic2.0)))
3006 (define-public r-genomicfeatures
3008 (name "r-genomicfeatures")
3012 (uri (bioconductor-uri "GenomicFeatures" version))
3015 "0y7lnvfcfrs72xbkn67xcqyz9csl5696mr2zl425fkhmnmimm4fg"))))
3017 `((upstream-name . "GenomicFeatures")))
3018 (build-system r-build-system)
3020 `(("r-annotationdbi" ,r-annotationdbi)
3021 ("r-biobase" ,r-biobase)
3022 ("r-biocgenerics" ,r-biocgenerics)
3023 ("r-biocio" ,r-biocio)
3024 ("r-biomart" ,r-biomart)
3025 ("r-biostrings" ,r-biostrings)
3027 ("r-genomeinfodb" ,r-genomeinfodb)
3028 ("r-genomicranges" ,r-genomicranges)
3029 ("r-iranges" ,r-iranges)
3030 ("r-rcurl" ,r-rcurl)
3031 ("r-rsqlite" ,r-rsqlite)
3032 ("r-rtracklayer" ,r-rtracklayer)
3033 ("r-s4vectors" ,r-s4vectors)
3034 ("r-xvector" ,r-xvector)))
3036 `(("r-knitr" ,r-knitr)))
3037 (home-page "https://bioconductor.org/packages/GenomicFeatures")
3038 (synopsis "Tools for working with transcript centric annotations")
3040 "This package provides a set of tools and methods for making and
3041 manipulating transcript centric annotations. With these tools the user can
3042 easily download the genomic locations of the transcripts, exons and cds of a
3043 given organism, from either the UCSC Genome Browser or a BioMart
3044 database (more sources will be supported in the future). This information is
3045 then stored in a local database that keeps track of the relationship between
3046 transcripts, exons, cds and genes. Flexible methods are provided for
3047 extracting the desired features in a convenient format.")
3048 (license license:artistic2.0)))
3050 (define-public r-genomicfiles
3052 (name "r-genomicfiles")
3057 (uri (bioconductor-uri "GenomicFiles" version))
3060 "1plh14m7w6calw5yxcxp7g4bg8q00ax85m517wap78bni975k13y"))))
3061 (properties `((upstream-name . "GenomicFiles")))
3062 (build-system r-build-system)
3064 `(("r-biocgenerics" ,r-biocgenerics)
3065 ("r-biocparallel" ,r-biocparallel)
3066 ("r-genomeinfodb" ,r-genomeinfodb)
3067 ("r-genomicalignments" ,r-genomicalignments)
3068 ("r-genomicranges" ,r-genomicranges)
3069 ("r-iranges" ,r-iranges)
3070 ("r-matrixgenerics" ,r-matrixgenerics)
3071 ("r-rsamtools" ,r-rsamtools)
3072 ("r-rtracklayer" ,r-rtracklayer)
3073 ("r-s4vectors" ,r-s4vectors)
3074 ("r-summarizedexperiment" ,r-summarizedexperiment)
3075 ("r-variantannotation" ,r-variantannotation)))
3076 (home-page "https://bioconductor.org/packages/GenomicFiles")
3077 (synopsis "Distributed computing by file or by range")
3079 "This package provides infrastructure for parallel computations
3080 distributed by file or by range. User defined mapper and reducer functions
3081 provide added flexibility for data combination and manipulation.")
3082 (license license:artistic2.0)))
3084 (define-public r-genomicranges
3086 (name "r-genomicranges")
3090 (uri (bioconductor-uri "GenomicRanges" version))
3093 "1qxc6dcwdlkan3hg0j9yfhz7gyi9qg671yj6zizsk6mzl7qqva0x"))))
3095 `((upstream-name . "GenomicRanges")))
3096 (build-system r-build-system)
3098 `(("r-biocgenerics" ,r-biocgenerics)
3099 ("r-genomeinfodb" ,r-genomeinfodb)
3100 ("r-iranges" ,r-iranges)
3101 ("r-s4vectors" ,r-s4vectors)
3102 ("r-xvector" ,r-xvector)))
3104 `(("r-knitr" ,r-knitr)))
3105 (home-page "https://bioconductor.org/packages/GenomicRanges")
3106 (synopsis "Representation and manipulation of genomic intervals")
3108 "This package provides tools to efficiently represent and manipulate
3109 genomic annotations and alignments is playing a central role when it comes to
3110 analyzing high-throughput sequencing data (a.k.a. NGS data). The
3111 GenomicRanges package defines general purpose containers for storing and
3112 manipulating genomic intervals and variables defined along a genome.")
3113 (license license:artistic2.0)))
3115 (define-public r-gostats
3122 (uri (bioconductor-uri "GOstats" version))
3125 "0jjswy6qmfgr2f6vk3y9pdvs9x91gn31h55qllgh0qb2cb26g9wa"))))
3126 (properties `((upstream-name . "GOstats")))
3127 (build-system r-build-system)
3129 `(("r-annotate" ,r-annotate)
3130 ("r-annotationdbi" ,r-annotationdbi)
3131 ("r-annotationforge" ,r-annotationforge)
3132 ("r-biobase" ,r-biobase)
3133 ("r-category" ,r-category)
3134 ("r-go-db" ,r-go-db)
3135 ("r-graph" ,r-graph)
3136 ("r-rgraphviz" ,r-rgraphviz)
3137 ("r-rbgl" ,r-rbgl)))
3138 (home-page "https://bioconductor.org/packages/GOstats")
3139 (synopsis "Tools for manipulating GO and microarrays")
3141 "This package provides a set of tools for interacting with GO and
3142 microarray data. A variety of basic manipulation tools for graphs, hypothesis
3143 testing and other simple calculations.")
3144 (license license:artistic2.0)))
3146 (define-public r-gseabase
3153 (uri (bioconductor-uri "GSEABase" version))
3156 "0946kkykms79mqnx262q20xzrrhv7cv723xh378335ff41qyf63n"))))
3157 (properties `((upstream-name . "GSEABase")))
3158 (build-system r-build-system)
3160 `(("r-annotate" ,r-annotate)
3161 ("r-annotationdbi" ,r-annotationdbi)
3162 ("r-biobase" ,r-biobase)
3163 ("r-biocgenerics" ,r-biocgenerics)
3164 ("r-graph" ,r-graph)
3167 `(("r-knitr" ,r-knitr)))
3168 (home-page "https://bioconductor.org/packages/GSEABase")
3169 (synopsis "Gene set enrichment data structures and methods")
3171 "This package provides classes and methods to support @dfn{Gene Set
3172 Enrichment Analysis} (GSEA).")
3173 (license license:artistic2.0)))
3175 (define-public r-hpar
3182 (uri (bioconductor-uri "hpar" version))
3185 "0q5pp04rq2gsh1kibvp8bvjkqc1kb46qpnj6agqp2vyqhrrfrm99"))))
3186 (build-system r-build-system)
3188 `(("r-knitr" ,r-knitr)))
3189 (home-page "https://bioconductor.org/packages/hpar/")
3190 (synopsis "Human Protein Atlas in R")
3191 (description "This package provides a simple interface to and data from
3192 the Human Protein Atlas project.")
3193 (license license:artistic2.0)))
3195 (define-public r-rhtslib
3202 (uri (bioconductor-uri "Rhtslib" version))
3205 "0acpgv98529ic2i2k03knz05akb6h51wbz7sr5zgi8gk4nmawrlf"))))
3206 (properties `((upstream-name . "Rhtslib")))
3207 (build-system r-build-system)
3208 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
3209 ;; which makes R abort the build.
3210 (arguments '(#:configure-flags '("--no-staged-install")))
3213 ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
3214 ("r-zlibbioc" ,r-zlibbioc)))
3216 `(("pkg-config" ,pkg-config)
3217 ("r-knitr" ,r-knitr)))
3218 (home-page "https://github.com/nhayden/Rhtslib")
3219 (synopsis "High-throughput sequencing library as an R package")
3221 "This package provides the HTSlib C library for high-throughput
3222 nucleotide sequence analysis. The package is primarily useful to developers
3223 of other R packages who wish to make use of HTSlib.")
3224 (license license:lgpl2.0+)))
3226 (define-public r-impute
3232 (uri (bioconductor-uri "impute" version))
3235 "0pprkv25avxhllddcssvqvy3nibmqkfwaq4xnlhka7858gyiyd1k"))))
3237 `(("gfortran" ,gfortran)))
3238 (build-system r-build-system)
3239 (home-page "https://bioconductor.org/packages/impute")
3240 (synopsis "Imputation for microarray data")
3242 "This package provides a function to impute missing gene expression
3243 microarray data, using nearest neighbor averaging.")
3244 (license license:gpl2+)))
3246 (define-public r-interactivedisplaybase
3248 (name "r-interactivedisplaybase")
3253 (uri (bioconductor-uri "interactiveDisplayBase" version))
3256 "00rgrrmglslgb6j7whp0m5dlyl4436r647br05rrpv8cxrmbs2iv"))))
3258 `((upstream-name . "interactiveDisplayBase")))
3259 (build-system r-build-system)
3261 `(("r-biocgenerics" ,r-biocgenerics)
3263 ("r-shiny" ,r-shiny)))
3265 `(("r-knitr" ,r-knitr)))
3266 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
3267 (synopsis "Base package for web displays of Bioconductor objects")
3269 "This package contains the basic methods needed to generate interactive
3270 Shiny-based display methods for Bioconductor objects.")
3271 (license license:artistic2.0)))
3273 (define-public r-keggrest
3280 (uri (bioconductor-uri "KEGGREST" version))
3283 "15313d20v3ziyn52fhc6fbzcy1kxjkdx18124bxhdfd14f4aypcd"))))
3284 (properties `((upstream-name . "KEGGREST")))
3285 (build-system r-build-system)
3287 `(("r-biostrings" ,r-biostrings)
3291 `(("r-knitr" ,r-knitr)))
3292 (home-page "https://bioconductor.org/packages/KEGGREST")
3293 (synopsis "Client-side REST access to KEGG")
3295 "This package provides a package that provides a client interface to the
3296 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
3297 (license license:artistic2.0)))
3299 (define-public r-limma
3305 (uri (bioconductor-uri "limma" version))
3308 "1mkpl2b1ksylc6dih4a6kgjjia8advikzmqmv762j4r7gya950pf"))))
3309 (build-system r-build-system)
3310 (home-page "http://bioinf.wehi.edu.au/limma")
3311 (synopsis "Package for linear models for microarray and RNA-seq data")
3312 (description "This package can be used for the analysis of gene expression
3313 studies, especially the use of linear models for analysing designed experiments
3314 and the assessment of differential expression. The analysis methods apply to
3315 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
3316 (license license:gpl2+)))
3318 (define-public r-methylkit
3320 (name "r-methylkit")
3324 (uri (bioconductor-uri "methylKit" version))
3327 "147nag4rz2xpjkkf8rmhja9k4ixjj1hsb0lq3lw7mw6q67zxsvf3"))))
3328 (properties `((upstream-name . "methylKit")))
3329 (build-system r-build-system)
3331 `(("r-data-table" ,r-data-table)
3332 ("r-emdbook" ,r-emdbook)
3333 ("r-fastseg" ,r-fastseg)
3334 ("r-genomeinfodb" ,r-genomeinfodb)
3335 ("r-genomicranges" ,r-genomicranges)
3336 ("r-gtools" ,r-gtools)
3337 ("r-iranges" ,r-iranges)
3338 ("r-kernsmooth" ,r-kernsmooth)
3339 ("r-limma" ,r-limma)
3340 ("r-mclust" ,r-mclust)
3342 ("r-qvalue" ,r-qvalue)
3343 ("r-r-utils" ,r-r-utils)
3345 ("r-rhtslib" ,r-rhtslib)
3346 ("r-rsamtools" ,r-rsamtools)
3347 ("r-rtracklayer" ,r-rtracklayer)
3348 ("r-s4vectors" ,r-s4vectors)
3349 ("r-zlibbioc" ,r-zlibbioc)))
3351 `(("r-knitr" ,r-knitr))) ; for vignettes
3352 (home-page "https://github.com/al2na/methylKit")
3354 "DNA methylation analysis from high-throughput bisulfite sequencing results")
3356 "MethylKit is an R package for DNA methylation analysis and annotation
3357 from high-throughput bisulfite sequencing. The package is designed to deal
3358 with sequencing data from @dfn{Reduced representation bisulfite
3359 sequencing} (RRBS) and its variants, but also target-capture methods and whole
3360 genome bisulfite sequencing. It also has functions to analyze base-pair
3361 resolution 5hmC data from experimental protocols such as oxBS-Seq and
3363 (license license:artistic2.0)))
3365 (define-public r-motifrg
3372 (uri (bioconductor-uri "motifRG" version))
3375 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
3376 (properties `((upstream-name . "motifRG")))
3377 (build-system r-build-system)
3379 `(("r-biostrings" ,r-biostrings)
3380 ("r-bsgenome" ,r-bsgenome)
3381 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
3382 ("r-iranges" ,r-iranges)
3383 ("r-seqlogo" ,r-seqlogo)
3384 ("r-xvector" ,r-xvector)))
3385 (home-page "https://bioconductor.org/packages/motifRG")
3386 (synopsis "Discover motifs in high throughput sequencing data")
3388 "This package provides tools for discriminative motif discovery in high
3389 throughput genetic sequencing data sets using regression methods.")
3390 (license license:artistic2.0)))
3392 (define-public r-mutationalpatterns
3394 (name "r-mutationalpatterns")
3399 (uri (bioconductor-uri "MutationalPatterns" version))
3402 "0433i4xbz8hrfaj8fxgzps3x8dqrl5vgwzg7qmp4cy5sb1lw5wvs"))))
3403 (build-system r-build-system)
3405 `(("r-knitr" ,r-knitr)))
3407 `(("r-biocgenerics" ,r-biocgenerics)
3408 ("r-biostrings" ,r-biostrings)
3409 ("r-bsgenome" ,r-bsgenome)
3410 ;; These two packages are suggested packages
3411 ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
3412 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
3413 ("r-cowplot" ,r-cowplot)
3414 ("r-dplyr" ,r-dplyr)
3415 ("r-genomeinfodb" ,r-genomeinfodb)
3416 ("r-genomicranges" ,r-genomicranges)
3417 ("r-ggalluvial" ,r-ggalluvial)
3418 ("r-ggdendro" ,r-ggdendro)
3419 ("r-ggplot2" ,r-ggplot2)
3420 ("r-iranges" ,r-iranges)
3421 ("r-magrittr" ,r-magrittr)
3423 ("r-pracma" ,r-pracma)
3424 ("r-purrr" ,r-purrr)
3425 ("r-s4vectors" ,r-s4vectors)
3426 ("r-stringr" ,r-stringr)
3427 ("r-tibble" ,r-tibble)
3428 ("r-tidyr" ,r-tidyr)
3429 ("r-variantannotation" ,r-variantannotation)))
3430 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
3431 (synopsis "Extract and visualize mutational patterns in genomic data")
3432 (description "This package provides an extensive toolset for the
3433 characterization and visualization of a wide range of mutational patterns
3434 in SNV base substitution data.")
3435 (license license:expat)))
3437 (define-public r-msnbase
3444 (uri (bioconductor-uri "MSnbase" version))
3447 "1z7s17j6zgb70m0khyf9icqlnbnzlivca7vw7j0vxyw417ld9lkr"))))
3448 (properties `((upstream-name . "MSnbase")))
3449 (build-system r-build-system)
3451 `(("r-affy" ,r-affy)
3452 ("r-biobase" ,r-biobase)
3453 ("r-biocgenerics" ,r-biocgenerics)
3454 ("r-biocparallel" ,r-biocparallel)
3455 ("r-digest" ,r-digest)
3456 ("r-ggplot2" ,r-ggplot2)
3457 ("r-impute" ,r-impute)
3458 ("r-iranges" ,r-iranges)
3459 ("r-lattice" ,r-lattice)
3460 ("r-maldiquant" ,r-maldiquant)
3462 ("r-mscoreutils" ,r-mscoreutils)
3465 ("r-pcamethods" ,r-pcamethods)
3467 ("r-protgenerics" ,r-protgenerics)
3469 ("r-s4vectors" ,r-s4vectors)
3470 ("r-scales" ,r-scales)
3474 `(("r-knitr" ,r-knitr)))
3475 (home-page "https://github.com/lgatto/MSnbase")
3476 (synopsis "Base functions and classes for MS-based proteomics")
3478 "This package provides basic plotting, data manipulation and processing
3479 of mass spectrometry based proteomics data.")
3480 (license license:artistic2.0)))
3482 (define-public r-msnid
3489 (uri (bioconductor-uri "MSnID" version))
3492 "0r3vgigf4fk0xzfg8gcvad01jdh0fysh6x22m9qy77x6glyrxcj2"))))
3493 (properties `((upstream-name . "MSnID")))
3494 (build-system r-build-system)
3497 (modify-phases %standard-phases
3498 (add-after 'unpack 'set-HOME
3499 (lambda _ (setenv "HOME" "/tmp"))))))
3501 `(("r-annotationdbi" ,r-annotationdbi)
3502 ("r-annotationhub" ,r-annotationhub)
3503 ("r-biobase" ,r-biobase)
3504 ("r-biocgenerics" ,r-biocgenerics)
3505 ("r-biocstyle" ,r-biocstyle)
3506 ("r-biostrings" ,r-biostrings)
3507 ("r-data-table" ,r-data-table)
3508 ("r-doparallel" ,r-doparallel)
3509 ("r-dplyr" ,r-dplyr)
3510 ("r-foreach" ,r-foreach)
3511 ("r-ggplot2" ,r-ggplot2)
3512 ("r-iterators" ,r-iterators)
3513 ("r-msnbase" ,r-msnbase)
3514 ("r-msmstests" ,r-msmstests)
3517 ("r-protgenerics" ,r-protgenerics)
3518 ("r-purrr" ,r-purrr)
3519 ("r-r-cache" ,r-r-cache)
3521 ("r-reshape2" ,r-reshape2)
3522 ("r-rlang" ,r-rlang)
3523 ("r-runit" ,r-runit)
3524 ("r-stringr" ,r-stringr)
3525 ("r-tibble" ,r-tibble)
3526 ("r-xtable" ,r-xtable)))
3527 (home-page "https://bioconductor.org/packages/MSnID")
3528 (synopsis "Utilities for LC-MSn proteomics identifications")
3530 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
3531 from mzIdentML (leveraging the mzID package) or text files. After collating
3532 the search results from multiple datasets it assesses their identification
3533 quality and optimize filtering criteria to achieve the maximum number of
3534 identifications while not exceeding a specified false discovery rate. It also
3535 contains a number of utilities to explore the MS/MS results and assess missed
3536 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
3537 (license license:artistic2.0)))
3539 (define-public r-mzid
3546 (uri (bioconductor-uri "mzID" version))
3549 "1wsy6frxa5602jqb1nlqv39mzgpid8wfyvb9m2jb6srv7p59rgys"))))
3550 (properties `((upstream-name . "mzID")))
3551 (build-system r-build-system)
3553 `(("r-doparallel" ,r-doparallel)
3554 ("r-foreach" ,r-foreach)
3555 ("r-iterators" ,r-iterators)
3557 ("r-protgenerics" ,r-protgenerics)
3560 `(("r-knitr" ,r-knitr)))
3561 (home-page "https://bioconductor.org/packages/mzID")
3562 (synopsis "Parser for mzIdentML files")
3564 "This package provides a parser for mzIdentML files implemented using the
3565 XML package. The parser tries to be general and able to handle all types of
3566 mzIdentML files with the drawback of having less pretty output than a vendor
3568 (license license:gpl2+)))
3570 (define-public r-mzr
3577 (uri (bioconductor-uri "mzR" version))
3580 "1m5xvnv0rxyrfri4jwyyryr13d55nyhqvfc5xxg5mpskw2v029kp"))
3581 (modules '((guix build utils)))
3584 (delete-file-recursively "src/boost")
3586 (properties `((upstream-name . "mzR")))
3587 (build-system r-build-system)
3590 (modify-phases %standard-phases
3591 (add-after 'unpack 'use-system-boost
3593 (substitute* "src/Makevars"
3594 (("\\./boost/libs.*") "")
3595 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
3596 (("\\ARCH_OBJS=" line)
3598 "\nBOOST_LIBS=-lboost_system -lboost_regex \
3599 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
3602 `(;; Our default boost package won't work here, unfortunately, even with
3603 ;; mzR version 2.26.0.
3604 ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
3607 `(("r-biobase" ,r-biobase)
3608 ("r-biocgenerics" ,r-biocgenerics)
3609 ("r-ncdf4" ,r-ncdf4)
3610 ("r-protgenerics" ,r-protgenerics)
3612 ("r-rhdf5lib" ,r-rhdf5lib)
3613 ("r-zlibbioc" ,r-zlibbioc)))
3615 `(("r-knitr" ,r-knitr)))
3616 (home-page "https://github.com/sneumann/mzR/")
3617 (synopsis "Parser for mass spectrometry data files")
3619 "The mzR package provides a unified API to the common file formats and
3620 parsers available for mass spectrometry data. It comes with a wrapper for the
3621 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
3622 The package contains the original code written by the ISB, and a subset of the
3623 proteowizard library for mzML and mzIdentML. The netCDF reading code has
3624 previously been used in XCMS.")
3625 (license license:artistic2.0)))
3627 (define-public r-organismdbi
3629 (name "r-organismdbi")
3634 (uri (bioconductor-uri "OrganismDbi" version))
3637 "0p8ccpdchdwci4kv9y07wdadzgms8nipvg6rm1rll35jcflnnkxi"))))
3638 (properties `((upstream-name . "OrganismDbi")))
3639 (build-system r-build-system)
3641 `(("r-annotationdbi" ,r-annotationdbi)
3642 ("r-biobase" ,r-biobase)
3643 ("r-biocgenerics" ,r-biocgenerics)
3644 ("r-biocmanager" ,r-biocmanager)
3646 ("r-genomicfeatures" ,r-genomicfeatures)
3647 ("r-genomicranges" ,r-genomicranges)
3648 ("r-graph" ,r-graph)
3649 ("r-iranges" ,r-iranges)
3651 ("r-s4vectors" ,r-s4vectors)))
3652 (home-page "https://bioconductor.org/packages/OrganismDbi")
3653 (synopsis "Software to enable the smooth interfacing of database packages")
3654 (description "The package enables a simple unified interface to several
3655 annotation packages each of which has its own schema by taking advantage of
3656 the fact that each of these packages implements a select methods.")
3657 (license license:artistic2.0)))
3659 (define-public r-pcamethods
3661 (name "r-pcamethods")
3666 (uri (bioconductor-uri "pcaMethods" version))
3669 "1ccqsxn487dy92c2d1iffh9917z4zq5ia92zv2h6pi00jjc6ymb5"))))
3670 (properties `((upstream-name . "pcaMethods")))
3671 (build-system r-build-system)
3673 `(("r-biobase" ,r-biobase)
3674 ("r-biocgenerics" ,r-biocgenerics)
3676 ("r-rcpp" ,r-rcpp)))
3677 (home-page "https://github.com/hredestig/pcamethods")
3678 (synopsis "Collection of PCA methods")
3680 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
3681 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
3682 for missing value estimation is included for comparison. BPCA, PPCA and
3683 NipalsPCA may be used to perform PCA on incomplete data as well as for
3684 accurate missing value estimation. A set of methods for printing and plotting
3685 the results is also provided. All PCA methods make use of the same data
3686 structure (pcaRes) to provide a common interface to the PCA results.")
3687 (license license:gpl3+)))
3689 (define-public r-protgenerics
3691 (name "r-protgenerics")
3696 (uri (bioconductor-uri "ProtGenerics" version))
3699 "1c79k8nc28782w5gxi7pkm8jmddq1hdw6khs9kgsp8dyk60ak6fq"))))
3700 (properties `((upstream-name . "ProtGenerics")))
3701 (build-system r-build-system)
3702 (home-page "https://github.com/lgatto/ProtGenerics")
3703 (synopsis "S4 generic functions for proteomics infrastructure")
3705 "This package provides S4 generic functions needed by Bioconductor
3706 proteomics packages.")
3707 (license license:artistic2.0)))
3709 (define-public r-rbgl
3716 (uri (bioconductor-uri "RBGL" version))
3719 "0l40ibf8g5s4ay83s92l198jjqc5l09hcmxqcjrpifvp5pjf9yy5"))))
3720 (properties `((upstream-name . "RBGL")))
3721 (build-system r-build-system)
3724 ("r-graph" ,r-graph)))
3725 (home-page "https://www.bioconductor.org/packages/RBGL")
3726 (synopsis "Interface to the Boost graph library")
3728 "This package provides a fairly extensive and comprehensive interface to
3729 the graph algorithms contained in the Boost library.")
3730 (license license:artistic2.0)))
3732 (define-public r-rcas
3738 (uri (bioconductor-uri "RCAS" version))
3741 "0l92v870ndna8zjqwzf22fb9vyhkh6942v4gaiqr1yc4qr521p5p"))))
3742 (properties `((upstream-name . "RCAS")))
3743 (build-system r-build-system)
3745 `(("r-biocgenerics" ,r-biocgenerics)
3746 ("r-biostrings" ,r-biostrings)
3747 ("r-bsgenome" ,r-bsgenome)
3748 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
3749 ("r-cowplot" ,r-cowplot)
3750 ("r-data-table" ,r-data-table)
3752 ("r-genomation" ,r-genomation)
3753 ("r-genomeinfodb" ,r-genomeinfodb)
3754 ("r-genomicfeatures" ,r-genomicfeatures)
3755 ("r-genomicranges" ,r-genomicranges)
3756 ("r-ggplot2" ,r-ggplot2)
3757 ("r-ggseqlogo" ,r-ggseqlogo)
3758 ("r-gprofiler2" ,r-gprofiler2)
3759 ("r-iranges" ,r-iranges)
3760 ("r-knitr" ,r-knitr)
3761 ("r-pbapply" ,r-pbapply)
3762 ("r-pheatmap" ,r-pheatmap)
3763 ("r-plotly" ,r-plotly)
3764 ("r-plotrix" ,r-plotrix)
3765 ("r-proxy" ,r-proxy)
3766 ("r-ranger" ,r-ranger)
3767 ("r-rsqlite" ,r-rsqlite)
3768 ("r-rtracklayer" ,r-rtracklayer)
3769 ("r-rmarkdown" ,r-rmarkdown)
3770 ("r-s4vectors" ,r-s4vectors)
3771 ("pandoc" ,pandoc)))
3773 `(("r-knitr" ,r-knitr)))
3774 (synopsis "RNA-centric annotation system")
3776 "RCAS aims to be a standalone RNA-centric annotation system that provides
3777 intuitive reports and publication-ready graphics. This package provides the R
3778 library implementing most of the pipeline's features.")
3779 (home-page "https://github.com/BIMSBbioinfo/RCAS")
3780 (license license:artistic2.0)))
3782 (define-public r-regioner
3789 (uri (bioconductor-uri "regioneR" version))
3792 "0xzzaz3cl6pyxfsg0d931v8k15wbd05s5mnsb7igxldc5qqg3nsl"))))
3793 (properties `((upstream-name . "regioneR")))
3794 (build-system r-build-system)
3796 `(("r-biostrings" ,r-biostrings)
3797 ("r-bsgenome" ,r-bsgenome)
3798 ("r-genomeinfodb" ,r-genomeinfodb)
3799 ("r-genomicranges" ,r-genomicranges)
3800 ("r-iranges" ,r-iranges)
3801 ("r-memoise" ,r-memoise)
3802 ("r-rtracklayer" ,r-rtracklayer)
3803 ("r-s4vectors" ,r-s4vectors)))
3805 `(("r-knitr" ,r-knitr)))
3806 (home-page "https://bioconductor.org/packages/regioneR/")
3807 (synopsis "Association analysis of genomic regions")
3808 (description "This package offers a statistical framework based on
3809 customizable permutation tests to assess the association between genomic
3810 region sets and other genomic features.")
3811 (license license:artistic2.0)))
3813 (define-public r-reportingtools
3815 (name "r-reportingtools")
3820 (uri (bioconductor-uri "ReportingTools" version))
3823 "0v6wzfswwcd1xdxgwa9gzlkmavr4p55jy11k84anh0rs0xx3dmmj"))))
3825 `((upstream-name . "ReportingTools")))
3826 (build-system r-build-system)
3828 `(("r-annotate" ,r-annotate)
3829 ("r-annotationdbi" ,r-annotationdbi)
3830 ("r-biobase" ,r-biobase)
3831 ("r-biocgenerics" ,r-biocgenerics)
3832 ("r-category" ,r-category)
3833 ("r-deseq2" ,r-deseq2)
3834 ("r-edger" ,r-edger)
3835 ("r-ggbio" ,r-ggbio)
3836 ("r-ggplot2" ,r-ggplot2)
3837 ("r-gostats" ,r-gostats)
3838 ("r-gseabase" ,r-gseabase)
3839 ("r-hwriter" ,r-hwriter)
3840 ("r-iranges" ,r-iranges)
3841 ("r-knitr" ,r-knitr)
3842 ("r-lattice" ,r-lattice)
3843 ("r-limma" ,r-limma)
3844 ("r-pfam-db" ,r-pfam-db)
3845 ("r-r-utils" ,r-r-utils)
3848 `(("r-knitr" ,r-knitr)))
3849 (home-page "https://bioconductor.org/packages/ReportingTools/")
3850 (synopsis "Tools for making reports in various formats")
3852 "The ReportingTools package enables users to easily display reports of
3853 analysis results generated from sources such as microarray and sequencing
3854 data. The package allows users to create HTML pages that may be viewed on a
3855 web browser, or in other formats. Users can generate tables with sortable and
3856 filterable columns, make and display plots, and link table entries to other
3857 data sources such as NCBI or larger plots within the HTML page. Using the
3858 package, users can also produce a table of contents page to link various
3859 reports together for a particular project that can be viewed in a web
3861 (license license:artistic2.0)))
3863 (define-public r-rhdf5
3869 (uri (bioconductor-uri "rhdf5" version))
3872 "1a5kw9ry9cr258al0x3q0ss5xn1ymscdypx51vzzgzamhy7dqakz"))))
3873 (build-system r-build-system)
3875 `(("r-rhdf5filters" ,r-rhdf5filters)
3876 ("r-rhdf5lib" ,r-rhdf5lib)))
3878 `(("r-knitr" ,r-knitr)))
3879 (home-page "https://bioconductor.org/packages/rhdf5")
3880 (synopsis "HDF5 interface to R")
3882 "This R/Bioconductor package provides an interface between HDF5 and R.
3883 HDF5's main features are the ability to store and access very large and/or
3884 complex datasets and a wide variety of metadata on mass storage (disk) through
3885 a completely portable file format. The rhdf5 package is thus suited for the
3886 exchange of large and/or complex datasets between R and other software
3887 package, and for letting R applications work on datasets that are larger than
3888 the available RAM.")
3889 (license license:artistic2.0)))
3891 (define-public r-rhdf5filters
3893 (name "r-rhdf5filters")
3898 (uri (bioconductor-uri "rhdf5filters" version))
3901 "133v0s452acspi4dbf6gsa2xrr0qza86jdjjbpwhdv6zfd1djbgc"))))
3902 (properties `((upstream-name . "rhdf5filters")))
3903 (build-system r-build-system)
3905 `(("r-rhdf5lib" ,r-rhdf5lib)))
3909 `(("r-knitr" ,r-knitr)))
3910 (home-page "https://github.com/grimbough/rhdf5filters")
3911 (synopsis "HDF5 compression filters")
3913 "This package provides a collection of compression filters for use with
3915 (license license:bsd-2)))
3917 (define-public r-rsamtools
3919 (name "r-rsamtools")
3923 (uri (bioconductor-uri "Rsamtools" version))
3926 "0arhh5bbx3pmxmkh5sjgczcswqy83d35r7cjhd2knpczdvrixaq5"))))
3928 `((upstream-name . "Rsamtools")))
3929 (build-system r-build-system)
3932 (modify-phases %standard-phases
3933 (add-after 'unpack 'use-system-zlib
3935 (substitute* "DESCRIPTION"
3936 (("zlibbioc, ") ""))
3937 (substitute* "NAMESPACE"
3938 (("import\\(zlibbioc\\)") "")))))))
3940 `(("r-biocgenerics" ,r-biocgenerics)
3941 ("r-biocparallel" ,r-biocparallel)
3942 ("r-biostrings" ,r-biostrings)
3943 ("r-bitops" ,r-bitops)
3944 ("r-genomeinfodb" ,r-genomeinfodb)
3945 ("r-genomicranges" ,r-genomicranges)
3946 ("r-iranges" ,r-iranges)
3947 ("r-rhtslib" ,r-rhtslib)
3948 ("r-s4vectors" ,r-s4vectors)
3949 ("r-xvector" ,r-xvector)))
3950 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
3951 (synopsis "Interface to samtools, bcftools, and tabix")
3953 "This package provides an interface to the @code{samtools},
3954 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
3955 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
3956 tab-delimited (tabix) files.")
3957 (license license:expat)))
3959 ;; This is a CRAN package, but it depends on a Bioconductor package:
3961 (define-public r-restfulr
3968 (uri (cran-uri "restfulr" version))
3971 "1dk45mzrr6ka92yjz7hfhkj12kpx1wg4szv1h1mg80mgga4ganbv"))))
3972 (properties `((upstream-name . "restfulr")))
3973 (build-system r-build-system)
3975 `(("r-rcurl" ,r-rcurl)
3976 ("r-rjson" ,r-rjson)
3977 ("r-s4vectors" ,r-s4vectors)
3979 ("r-yaml" ,r-yaml)))
3980 (home-page "https://cran.r-project.org/package=restfulr")
3981 (synopsis "R interface to RESTful web services")
3983 "This package models a RESTful service as if it were a nested R list.")
3984 (license license:artistic2.0)))
3986 (define-public r-rtracklayer
3988 (name "r-rtracklayer")
3992 (uri (bioconductor-uri "rtracklayer" version))
3995 "0iic0g0clsjd9ypdmfs6k52hrnmfszhxzg0xx89nszpasf69wghv"))))
3996 (build-system r-build-system)
3999 (modify-phases %standard-phases
4000 (add-after 'unpack 'use-system-zlib
4002 (substitute* "DESCRIPTION"
4003 ((" zlibbioc,") ""))
4004 (substitute* "NAMESPACE"
4005 (("import\\(zlibbioc\\)") "")))))))
4007 `(("pkg-config" ,pkg-config)))
4011 `(("r-biocgenerics" ,r-biocgenerics)
4012 ("r-biocio" ,r-biocio)
4013 ("r-biostrings" ,r-biostrings)
4014 ("r-genomeinfodb" ,r-genomeinfodb)
4015 ("r-genomicalignments" ,r-genomicalignments)
4016 ("r-genomicranges" ,r-genomicranges)
4017 ("r-iranges" ,r-iranges)
4018 ("r-rcurl" ,r-rcurl)
4019 ("r-restfulr" ,r-restfulr)
4020 ("r-rsamtools" ,r-rsamtools)
4021 ("r-s4vectors" ,r-s4vectors)
4023 ("r-xvector" ,r-xvector)
4024 ("r-zlibbioc" ,r-zlibbioc)))
4025 (home-page "https://bioconductor.org/packages/rtracklayer")
4026 (synopsis "R interface to genome browsers and their annotation tracks")
4028 "rtracklayer is an extensible framework for interacting with multiple
4029 genome browsers (currently UCSC built-in) and manipulating annotation tracks
4030 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
4031 built-in). The user may export/import tracks to/from the supported browsers,
4032 as well as query and modify the browser state, such as the current viewport.")
4033 (license license:artistic2.0)))
4035 ;; This is a CRAN package, but it depends on a Bioconductor package.
4036 (define-public r-samr
4043 (uri (cran-uri "samr" version))
4046 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
4047 (properties `((upstream-name . "samr")))
4048 (build-system r-build-system)
4051 ("r-impute" ,r-impute)
4052 ("r-matrixstats" ,r-matrixstats)
4053 ("r-openxlsx" ,r-openxlsx)
4054 ("r-shiny" ,r-shiny)
4055 ("r-shinyfiles" ,r-shinyfiles)))
4056 (native-inputs `(("gfortran" ,gfortran)))
4057 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
4058 (synopsis "Significance analysis of Microarrays")
4060 "This is a package for significance analysis of Microarrays for
4061 differential expression analysis, RNAseq data and related problems.")
4062 ;; Any version of the LGPL
4063 (license license:lgpl3+)))
4065 (define-public r-seqlogo
4072 (uri (bioconductor-uri "seqLogo" version))
4075 "1253sj1hc6bbrff0iv5xa3v9znqvisll0fy6fdjka9c778fn4mcp"))))
4076 (properties `((upstream-name . "seqLogo")))
4077 (build-system r-build-system)
4079 `(("r-knitr" ,r-knitr)))
4080 (home-page "https://bioconductor.org/packages/seqLogo")
4081 (synopsis "Sequence logos for DNA sequence alignments")
4083 "seqLogo takes the position weight matrix of a DNA sequence motif and
4084 plots the corresponding sequence logo as introduced by Schneider and
4086 (license license:lgpl2.0+)))
4088 (define-public r-seqpattern
4090 (name "r-seqpattern")
4094 (uri (bioconductor-uri "seqPattern" version))
4097 "0h74z84zyvfzclsm0g13b95hirn99185wc6lp53jkzah9yyi59ay"))))
4099 `((upstream-name . "seqPattern")))
4100 (build-system r-build-system)
4102 `(("r-biostrings" ,r-biostrings)
4103 ("r-genomicranges" ,r-genomicranges)
4104 ("r-iranges" ,r-iranges)
4105 ("r-kernsmooth" ,r-kernsmooth)
4106 ("r-plotrix" ,r-plotrix)))
4107 (home-page "https://bioconductor.org/packages/seqPattern")
4108 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
4110 "This package provides tools to visualize oligonucleotide patterns and
4111 sequence motif occurrences across a large set of sequences centred at a common
4112 reference point and sorted by a user defined feature.")
4113 (license license:gpl3+)))
4115 (define-public r-shortread
4117 (name "r-shortread")
4122 (uri (bioconductor-uri "ShortRead" version))
4125 "0zqinw3c6h5v1c5nhzkiziirws16nbviccgw8nj2d22r33dbqwp3"))))
4126 (properties `((upstream-name . "ShortRead")))
4127 (build-system r-build-system)
4131 `(("r-biobase" ,r-biobase)
4132 ("r-biocgenerics" ,r-biocgenerics)
4133 ("r-biocparallel" ,r-biocparallel)
4134 ("r-biostrings" ,r-biostrings)
4135 ("r-genomeinfodb" ,r-genomeinfodb)
4136 ("r-genomicalignments" ,r-genomicalignments)
4137 ("r-genomicranges" ,r-genomicranges)
4138 ("r-rhtslib" ,r-rhtslib)
4139 ("r-hwriter" ,r-hwriter)
4140 ("r-iranges" ,r-iranges)
4141 ("r-lattice" ,r-lattice)
4142 ("r-latticeextra" ,r-latticeextra)
4143 ("r-rsamtools" ,r-rsamtools)
4144 ("r-s4vectors" ,r-s4vectors)
4145 ("r-xvector" ,r-xvector)
4146 ("r-zlibbioc" ,r-zlibbioc)))
4147 (home-page "https://bioconductor.org/packages/ShortRead")
4148 (synopsis "FASTQ input and manipulation tools")
4150 "This package implements sampling, iteration, and input of FASTQ files.
4151 It includes functions for filtering and trimming reads, and for generating a
4152 quality assessment report. Data are represented as
4153 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
4154 purposes. The package also contains legacy support for early single-end,
4155 ungapped alignment formats.")
4156 (license license:artistic2.0)))
4158 (define-public r-trajectoryutils
4160 (name "r-trajectoryutils")
4165 (uri (bioconductor-uri "TrajectoryUtils" version))
4168 "1b7mg3ypp1ay98cav47h9vn692lx0n9b5b0hpansgnkr5prb823b"))))
4170 `((upstream-name . "TrajectoryUtils")))
4171 (build-system r-build-system)
4173 `(("r-igraph" ,r-igraph)
4174 ("r-matrix" ,r-matrix)
4175 ("r-s4vectors" ,r-s4vectors)
4176 ("r-singlecellexperiment" ,r-singlecellexperiment)
4177 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4178 (native-inputs `(("r-knitr" ,r-knitr)))
4179 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
4180 (synopsis "Single-cell trajectory analysis utilities")
4182 "This package implements low-level utilities for single-cell trajectory
4183 analysis, primarily intended for re-use inside higher-level packages. It
4184 includes a function to create a cluster-level minimum spanning tree and data
4185 structures to hold pseudotime inference results.")
4186 (license license:gpl3)))
4188 (define-public r-slingshot
4190 (name "r-slingshot")
4194 (uri (bioconductor-uri "slingshot" version))
4197 "1aqsz2kxwax8d8d5iv3zk5hlyk5aya1wbxs1wky2rgccw4d35whx"))))
4198 (build-system r-build-system)
4200 `(("r-igraph" ,r-igraph)
4201 ("r-matrixstats" ,r-matrixstats)
4202 ("r-princurve" ,r-princurve)
4203 ("r-s4vectors" ,r-s4vectors)
4204 ("r-singlecellexperiment" ,r-singlecellexperiment)
4205 ("r-summarizedexperiment" ,r-summarizedexperiment)
4206 ("r-trajectoryutils" ,r-trajectoryutils)))
4208 `(("r-knitr" ,r-knitr)))
4209 (home-page "https://bioconductor.org/packages/slingshot")
4210 (synopsis "Tools for ordering single-cell sequencing")
4211 (description "This package provides functions for inferring continuous,
4212 branching lineage structures in low-dimensional data. Slingshot was designed
4213 to model developmental trajectories in single-cell RNA sequencing data and
4214 serve as a component in an analysis pipeline after dimensionality reduction
4215 and clustering. It is flexible enough to handle arbitrarily many branching
4216 events and allows for the incorporation of prior knowledge through supervised
4217 graph construction.")
4218 (license license:artistic2.0)))
4220 (define-public r-structuralvariantannotation
4222 (name "r-structuralvariantannotation")
4227 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
4230 "10h63h1v87nvm3bfyr6dsjlbmzxf1vks30d0xz6q4hssqq9xlzgv"))))
4231 (build-system r-build-system)
4233 `(("r-assertthat" ,r-assertthat)
4234 ("r-biocgenerics" ,r-biocgenerics)
4235 ("r-biostrings" ,r-biostrings)
4236 ("r-dplyr" ,r-dplyr)
4237 ("r-genomicranges" ,r-genomicranges)
4238 ("r-rlang" ,r-rlang)
4239 ("r-rtracklayer" ,r-rtracklayer)
4240 ("r-stringr" ,r-stringr)
4241 ("r-variantannotation" ,r-variantannotation)))
4243 `(("r-knitr" ,r-knitr)))
4244 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
4245 (synopsis "R package designed to simplify structural variant analysis")
4247 "This package contains useful helper functions for dealing with structural
4248 variants in VCF format. The packages contains functions for parsing VCFs from
4249 a number of popular callers as well as functions for dealing with breakpoints
4250 involving two separate genomic loci encoded as GRanges objects.")
4251 (license license:gpl3)))
4253 (define-public r-summarizedexperiment
4255 (name "r-summarizedexperiment")
4259 (uri (bioconductor-uri "SummarizedExperiment" version))
4262 "16np5ik6jgbi68mhlib6yskywwbaa50mlr7m3sh1hqk889whfn1g"))))
4264 `((upstream-name . "SummarizedExperiment")))
4265 (build-system r-build-system)
4267 `(("r-biobase" ,r-biobase)
4268 ("r-biocgenerics" ,r-biocgenerics)
4269 ("r-delayedarray" ,r-delayedarray)
4270 ("r-genomeinfodb" ,r-genomeinfodb)
4271 ("r-genomicranges" ,r-genomicranges)
4272 ("r-iranges" ,r-iranges)
4273 ("r-matrix" ,r-matrix)
4274 ("r-matrixgenerics" ,r-matrixgenerics)
4275 ("r-s4vectors" ,r-s4vectors)))
4277 `(("r-knitr" ,r-knitr)))
4278 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
4279 (synopsis "Container for representing genomic ranges by sample")
4281 "The SummarizedExperiment container contains one or more assays, each
4282 represented by a matrix-like object of numeric or other mode. The rows
4283 typically represent genomic ranges of interest and the columns represent
4285 (license license:artistic2.0)))
4287 (define-public r-sva
4294 (uri (bioconductor-uri "sva" version))
4297 "12jkcybdfspabh7x124d44l9fj1hwwg3gvcqxvz5wpkiflc2vkji"))))
4298 (build-system r-build-system)
4300 `(("r-edger" ,r-edger)
4301 ("r-genefilter" ,r-genefilter)
4303 ("r-biocparallel" ,r-biocparallel)
4304 ("r-matrixstats" ,r-matrixstats)
4305 ("r-limma" ,r-limma)))
4306 (home-page "https://bioconductor.org/packages/sva")
4307 (synopsis "Surrogate variable analysis")
4309 "This package contains functions for removing batch effects and other
4310 unwanted variation in high-throughput experiment. It also contains functions
4311 for identifying and building surrogate variables for high-dimensional data
4312 sets. Surrogate variables are covariates constructed directly from
4313 high-dimensional data like gene expression/RNA sequencing/methylation/brain
4314 imaging data that can be used in subsequent analyses to adjust for unknown,
4315 unmodeled, or latent sources of noise.")
4316 (license license:artistic2.0)))
4318 (define-public r-systempiper
4320 (name "r-systempiper")
4325 (uri (bioconductor-uri "systemPipeR" version))
4328 "1apqi5ih06s37v7wpp13ybksiinrwj0ii6mx6vvvfkb6ix0wljws"))))
4329 (properties `((upstream-name . "systemPipeR")))
4330 (build-system r-build-system)
4332 `(("r-annotate" ,r-annotate)
4333 ("r-assertthat" ,r-assertthat)
4334 ("r-batchtools" ,r-batchtools)
4335 ("r-biostrings" ,r-biostrings)
4336 ("r-deseq2" ,r-deseq2)
4338 ("r-edger" ,r-edger)
4339 ("r-genomicfeatures" ,r-genomicfeatures)
4340 ("r-genomicranges" ,r-genomicranges)
4341 ("r-ggplot2" ,r-ggplot2)
4342 ("r-go-db" ,r-go-db)
4343 ("r-gostats" ,r-gostats)
4344 ("r-iranges" ,r-iranges)
4345 ("r-limma" ,r-limma)
4346 ("r-magrittr" ,r-magrittr)
4347 ("r-pheatmap" ,r-pheatmap)
4348 ("r-rjson" ,r-rjson)
4349 ("r-rsamtools" ,r-rsamtools)
4351 ("r-shortread" ,r-shortread)
4352 ("r-stringr" ,r-stringr)
4353 ("r-summarizedexperiment" ,r-summarizedexperiment)
4354 ("r-testthat" ,r-testthat)
4356 ("r-variantannotation" ,r-variantannotation)))
4358 `(("r-knitr" ,r-knitr)))
4359 (home-page "https://github.com/tgirke/systemPipeR")
4360 (synopsis "Next generation sequencing workflow and reporting environment")
4362 "This R package provides tools for building and running automated
4363 end-to-end analysis workflows for a wide range of @dfn{next generation
4364 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
4365 Important features include a uniform workflow interface across different NGS
4366 applications, automated report generation, and support for running both R and
4367 command-line software, such as NGS aligners or peak/variant callers, on local
4368 computers or compute clusters. Efficient handling of complex sample sets and
4369 experimental designs is facilitated by a consistently implemented sample
4370 annotation infrastructure.")
4371 (license license:artistic2.0)))
4373 (define-public r-topgo
4379 (uri (bioconductor-uri "topGO" version))
4382 "1ggi7yrhkyi85p3sfj3yd95n9mzq1xpff28ixa4dl9yzasks1v5a"))))
4384 `((upstream-name . "topGO")))
4385 (build-system r-build-system)
4387 `(("r-annotationdbi" ,r-annotationdbi)
4389 ("r-biobase" ,r-biobase)
4390 ("r-biocgenerics" ,r-biocgenerics)
4391 ("r-go-db" ,r-go-db)
4392 ("r-graph" ,r-graph)
4393 ("r-lattice" ,r-lattice)
4394 ("r-matrixstats" ,r-matrixstats)
4395 ("r-sparsem" ,r-sparsem)))
4396 (home-page "https://bioconductor.org/packages/topGO")
4397 (synopsis "Enrichment analysis for gene ontology")
4399 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
4400 terms while accounting for the topology of the GO graph. Different test
4401 statistics and different methods for eliminating local similarities and
4402 dependencies between GO terms can be implemented and applied.")
4403 ;; Any version of the LGPL applies.
4404 (license license:lgpl2.1+)))
4406 (define-public r-tximport
4412 (uri (bioconductor-uri "tximport" version))
4415 "0ip2yr0zspf2aagskxl4dwncr48dw5qb90an3sswnnh2dqdb82if"))))
4416 (build-system r-build-system)
4418 `(("r-knitr" ,r-knitr)))
4419 (home-page "https://bioconductor.org/packages/tximport")
4420 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
4422 "This package provides tools to import transcript-level abundance,
4423 estimated counts and transcript lengths, and to summarize them into matrices
4424 for use with downstream gene-level analysis packages. Average transcript
4425 length, weighted by sample-specific transcript abundance estimates, is
4426 provided as a matrix which can be used as an offset for different expression
4427 of gene-level counts.")
4428 (license license:gpl2+)))
4430 (define-public r-variantannotation
4432 (name "r-variantannotation")
4436 (uri (bioconductor-uri "VariantAnnotation" version))
4439 "0c9r00j8a3bs6n0dv4wi17jc1ljzvr3r2bi4h9axhcsf2ip906rh"))))
4441 `((upstream-name . "VariantAnnotation")))
4443 `(("r-annotationdbi" ,r-annotationdbi)
4444 ("r-biobase" ,r-biobase)
4445 ("r-biocgenerics" ,r-biocgenerics)
4446 ("r-biostrings" ,r-biostrings)
4447 ("r-bsgenome" ,r-bsgenome)
4449 ("r-genomeinfodb" ,r-genomeinfodb)
4450 ("r-genomicfeatures" ,r-genomicfeatures)
4451 ("r-genomicranges" ,r-genomicranges)
4452 ("r-iranges" ,r-iranges)
4453 ("r-matrixgenerics" ,r-matrixgenerics)
4454 ("r-summarizedexperiment" ,r-summarizedexperiment)
4455 ("r-rhtslib" ,r-rhtslib)
4456 ("r-rsamtools" ,r-rsamtools)
4457 ("r-rtracklayer" ,r-rtracklayer)
4458 ("r-s4vectors" ,r-s4vectors)
4459 ("r-xvector" ,r-xvector)
4460 ("r-zlibbioc" ,r-zlibbioc)))
4461 (build-system r-build-system)
4462 (home-page "https://bioconductor.org/packages/VariantAnnotation")
4463 (synopsis "Package for annotation of genetic variants")
4464 (description "This R package can annotate variants, compute amino acid
4465 coding changes and predict coding outcomes.")
4466 (license license:artistic2.0)))
4468 (define-public r-vsn
4475 (uri (bioconductor-uri "vsn" version))
4478 "0nppph3kv8z83368snb8s3n4vcqj829yyi1kh4q09qvq18rhvssv"))))
4479 (build-system r-build-system)
4481 `(("r-affy" ,r-affy)
4482 ("r-biobase" ,r-biobase)
4483 ("r-ggplot2" ,r-ggplot2)
4484 ("r-lattice" ,r-lattice)
4485 ("r-limma" ,r-limma)))
4487 `(("r-knitr" ,r-knitr))) ; for vignettes
4488 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
4489 (synopsis "Variance stabilization and calibration for microarray data")
4491 "The package implements a method for normalising microarray intensities,
4492 and works for single- and multiple-color arrays. It can also be used for data
4493 from other technologies, as long as they have similar format. The method uses
4494 a robust variant of the maximum-likelihood estimator for an
4495 additive-multiplicative error model and affine calibration. The model
4496 incorporates data calibration step (a.k.a. normalization), a model for the
4497 dependence of the variance on the mean intensity and a variance stabilizing
4498 data transformation. Differences between transformed intensities are
4499 analogous to \"normalized log-ratios\". However, in contrast to the latter,
4500 their variance is independent of the mean, and they are usually more sensitive
4501 and specific in detecting differential transcription.")
4502 (license license:artistic2.0)))
4504 (define-public r-xvector
4510 (uri (bioconductor-uri "XVector" version))
4513 "1cw34gd9iaspl0v737xl7rngq63zrj03a5ngai15ggrnv1sq2aqr"))))
4515 `((upstream-name . "XVector")))
4516 (build-system r-build-system)
4519 (modify-phases %standard-phases
4520 (add-after 'unpack 'use-system-zlib
4522 (substitute* "DESCRIPTION"
4523 (("zlibbioc, ") ""))
4524 (substitute* "NAMESPACE"
4525 (("import\\(zlibbioc\\)") ""))
4530 `(("r-biocgenerics" ,r-biocgenerics)
4531 ("r-iranges" ,r-iranges)
4532 ("r-s4vectors" ,r-s4vectors)))
4533 (home-page "https://bioconductor.org/packages/XVector")
4534 (synopsis "Representation and manpulation of external sequences")
4536 "This package provides memory efficient S4 classes for storing sequences
4537 \"externally\" (behind an R external pointer, or on disk).")
4538 (license license:artistic2.0)))
4540 (define-public r-zlibbioc
4546 (uri (bioconductor-uri "zlibbioc" version))
4549 "1dv5bf12kzk1yzyfs3g5syim16sbi44kalvzj2i2xcnxnl6x60ip"))))
4551 `((upstream-name . "zlibbioc")))
4552 (build-system r-build-system)
4553 (home-page "https://bioconductor.org/packages/zlibbioc")
4554 (synopsis "Provider for zlib-1.2.5 to R packages")
4555 (description "This package uses the source code of zlib-1.2.5 to create
4556 libraries for systems that do not have these available via other means.")
4557 (license license:artistic2.0)))
4559 (define-public r-geneplotter
4561 (name "r-geneplotter")
4566 (uri (bioconductor-uri "geneplotter" version))
4569 "1d085lfa3yif5wkys1fb0zzgg0cqwd1y18vasgqqdr6rva075d4z"))))
4570 (build-system r-build-system)
4572 `(("r-annotate" ,r-annotate)
4573 ("r-annotationdbi" ,r-annotationdbi)
4574 ("r-biobase" ,r-biobase)
4575 ("r-biocgenerics" ,r-biocgenerics)
4576 ("r-lattice" ,r-lattice)
4577 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4578 (home-page "https://bioconductor.org/packages/geneplotter")
4579 (synopsis "Graphics functions for genomic data")
4581 "This package provides functions for plotting genomic data.")
4582 (license license:artistic2.0)))
4584 (define-public r-oligoclasses
4586 (name "r-oligoclasses")
4591 (uri (bioconductor-uri "oligoClasses" version))
4594 "1nsfyfpj264h6y322pzz0i001b0m862j3skbq5rjwlrj1p8j2gi7"))))
4595 (properties `((upstream-name . "oligoClasses")))
4596 (build-system r-build-system)
4598 `(("r-affyio" ,r-affyio)
4599 ("r-biobase" ,r-biobase)
4600 ("r-biocgenerics" ,r-biocgenerics)
4601 ("r-biocmanager" ,r-biocmanager)
4602 ("r-biostrings" ,r-biostrings)
4605 ("r-foreach" ,r-foreach)
4606 ("r-genomicranges" ,r-genomicranges)
4607 ("r-iranges" ,r-iranges)
4608 ("r-rsqlite" ,r-rsqlite)
4609 ("r-s4vectors" ,r-s4vectors)
4610 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4611 (home-page "https://bioconductor.org/packages/oligoClasses/")
4612 (synopsis "Classes for high-throughput arrays")
4614 "This package contains class definitions, validity checks, and
4615 initialization methods for classes used by the @code{oligo} and @code{crlmm}
4617 (license license:gpl2+)))
4619 (define-public r-oligo
4626 (uri (bioconductor-uri "oligo" version))
4629 "0fyq77im6s79havjwbchhqhnllxs134jsi98g6msxz66h16lj3al"))))
4630 (properties `((upstream-name . "oligo")))
4631 (build-system r-build-system)
4632 (inputs `(("zlib" ,zlib)))
4634 `(("r-affxparser" ,r-affxparser)
4635 ("r-affyio" ,r-affyio)
4636 ("r-biobase" ,r-biobase)
4637 ("r-biocgenerics" ,r-biocgenerics)
4638 ("r-biostrings" ,r-biostrings)
4641 ("r-oligoclasses" ,r-oligoclasses)
4642 ("r-preprocesscore" ,r-preprocesscore)
4643 ("r-rsqlite" ,r-rsqlite)
4644 ("r-zlibbioc" ,r-zlibbioc)))
4646 `(("r-knitr" ,r-knitr)))
4647 (home-page "https://bioconductor.org/packages/oligo/")
4648 (synopsis "Preprocessing tools for oligonucleotide arrays")
4650 "This package provides a package to analyze oligonucleotide
4651 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
4652 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
4653 (license license:lgpl2.0+)))
4655 (define-public r-qvalue
4662 (uri (bioconductor-uri "qvalue" version))
4665 "0xssanffh1hr7f48mnazcpwi25rdp7mxlyb9nbf4q2mp7m40jnpm"))))
4666 (build-system r-build-system)
4668 `(("r-ggplot2" ,r-ggplot2)
4669 ("r-reshape2" ,r-reshape2)))
4671 `(("r-knitr" ,r-knitr)))
4672 (home-page "https://github.com/StoreyLab/qvalue")
4673 (synopsis "Q-value estimation for false discovery rate control")
4675 "This package takes a list of p-values resulting from the simultaneous
4676 testing of many hypotheses and estimates their q-values and local @dfn{false
4677 discovery rate} (FDR) values. The q-value of a test measures the proportion
4678 of false positives incurred when that particular test is called significant.
4679 The local FDR measures the posterior probability the null hypothesis is true
4680 given the test's p-value. Various plots are automatically generated, allowing
4681 one to make sensible significance cut-offs. The software can be applied to
4682 problems in genomics, brain imaging, astrophysics, and data mining.")
4683 ;; Any version of the LGPL.
4684 (license license:lgpl3+)))
4686 (define r-rcppnumerical
4688 (name "r-rcppnumerical")
4692 (uri (cran-uri "RcppNumerical" version))
4695 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
4696 (properties `((upstream-name . "RcppNumerical")))
4697 (build-system r-build-system)
4699 `(("r-rcpp" ,r-rcpp)
4700 ("r-rcppeigen" ,r-rcppeigen)))
4702 `(("r-knitr" ,r-knitr)))
4703 (home-page "https://github.com/yixuan/RcppNumerical")
4704 (synopsis "Rcpp integration for numerical computing libraries")
4705 (description "This package provides a collection of open source libraries
4706 for numerical computing (numerical integration, optimization, etc.) and their
4707 integration with @code{Rcpp}.")
4708 (license license:gpl2+)))
4710 (define-public r-apeglm
4716 (uri (bioconductor-uri "apeglm" version))
4719 "1xld6ar440achik4dbd7vhiw6jfj0sb96jm52n7hav5bv4gag3mh"))))
4720 (properties `((upstream-name . "apeglm")))
4721 (build-system r-build-system)
4723 `(("r-emdbook" ,r-emdbook)
4724 ("r-genomicranges" ,r-genomicranges)
4726 ("r-rcppeigen" ,r-rcppeigen)
4727 ("r-rcppnumerical" ,r-rcppnumerical)
4728 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4729 (native-inputs `(("r-knitr" ,r-knitr)))
4730 (home-page "https://bioconductor.org/packages/apeglm")
4731 (synopsis "Approximate posterior estimation for GLM coefficients")
4732 (description "This package provides Bayesian shrinkage estimators for
4733 effect sizes for a variety of GLM models, using approximation of the
4734 posterior for individual coefficients.")
4735 (license license:gpl2)))
4737 (define-public r-greylistchip
4739 (name "r-greylistchip")
4743 (uri (bioconductor-uri "GreyListChIP" version))
4746 "1g9ja8p90czx83ar0l9ran7m6aggvszdbqm714fq7z4rxq9b4hs3"))))
4747 (properties `((upstream-name . "GreyListChIP")))
4748 (build-system r-build-system)
4750 `(("r-bsgenome" ,r-bsgenome)
4751 ("r-genomeinfodb" ,r-genomeinfodb)
4752 ("r-genomicalignments" ,r-genomicalignments)
4753 ("r-genomicranges" ,r-genomicranges)
4755 ("r-rsamtools" ,r-rsamtools)
4756 ("r-rtracklayer" ,r-rtracklayer)
4757 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4758 (home-page "https://bioconductor.org/packages/GreyListChIP")
4759 (synopsis "Greylist artefact regions based on ChIP inputs")
4760 (description "This package identifies regions of ChIP experiments with high
4761 signal in the input, that lead to spurious peaks during peak calling.")
4762 (license license:artistic2.0)))
4764 (define-public r-diffbind
4771 (uri (bioconductor-uri "DiffBind" version))
4774 "12x80z1a8gihqrlaxmzk80nc5700la72lival58s4wjv4k2lhyf3"))))
4775 (properties `((upstream-name . "DiffBind")))
4776 (build-system r-build-system)
4778 `(("r-amap" ,r-amap)
4779 ("r-apeglm" ,r-apeglm)
4781 ("r-biocparallel" ,r-biocparallel)
4782 ("r-deseq2" ,r-deseq2)
4783 ("r-dplyr" ,r-dplyr)
4784 ("r-genomicalignments" ,r-genomicalignments)
4785 ("r-genomicranges" ,r-genomicranges)
4786 ("r-ggplot2" ,r-ggplot2)
4787 ("r-ggrepel" ,r-ggrepel)
4788 ("r-gplots" ,r-gplots)
4789 ("r-greylistchip" ,r-greylistchip)
4790 ("r-iranges" ,r-iranges)
4791 ("r-lattice" ,r-lattice)
4792 ("r-limma" ,r-limma)
4793 ("r-locfit" ,r-locfit)
4794 ("r-rcolorbrewer" , r-rcolorbrewer)
4796 ("r-rhtslib" ,r-rhtslib)
4797 ("r-rsamtools" ,r-rsamtools)
4798 ("r-s4vectors" ,r-s4vectors)
4799 ("r-summarizedexperiment" ,r-summarizedexperiment)
4800 ("r-systempiper" ,r-systempiper)))
4801 (home-page "https://bioconductor.org/packages/DiffBind")
4802 (synopsis "Differential binding analysis of ChIP-Seq peak data")
4804 "This package computes differentially bound sites from multiple
4805 ChIP-seq experiments using affinity (quantitative) data. Also enables
4806 occupancy (overlap) analysis and plotting functions.")
4807 (license license:artistic2.0)))
4809 (define-public r-ripseeker
4811 (name "r-ripseeker")
4816 (uri (bioconductor-uri "RIPSeeker" version))
4819 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
4820 (properties `((upstream-name . "RIPSeeker")))
4821 (build-system r-build-system)
4823 `(("r-s4vectors" ,r-s4vectors)
4824 ("r-iranges" ,r-iranges)
4825 ("r-genomicranges" ,r-genomicranges)
4826 ("r-summarizedexperiment" ,r-summarizedexperiment)
4827 ("r-rsamtools" ,r-rsamtools)
4828 ("r-genomicalignments" ,r-genomicalignments)
4829 ("r-rtracklayer" ,r-rtracklayer)))
4830 (home-page "https://bioconductor.org/packages/RIPSeeker")
4832 "Identifying protein-associated transcripts from RIP-seq experiments")
4834 "This package infers and discriminates RIP peaks from RIP-seq alignments
4835 using two-state HMM with negative binomial emission probability. While
4836 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
4837 a suite of bioinformatics tools integrated within this self-contained software
4838 package comprehensively addressing issues ranging from post-alignments
4839 processing to visualization and annotation.")
4840 (license license:gpl2)))
4842 (define-public r-mbkmeans
4848 (uri (bioconductor-uri "mbkmeans" version))
4851 "1k7ngpx4s50jplrsv19zzjr7izpdl9wwppb218ih5cp0ki1gcc2n"))))
4852 (build-system r-build-system)
4854 `(("r-knitr" ,r-knitr)))
4856 `(("r-beachmat" ,r-beachmat)
4857 ("r-benchmarkme" ,r-benchmarkme)
4858 ("r-biocparallel" ,r-biocparallel)
4859 ("r-clusterr" ,r-clusterr)
4860 ("r-delayedarray" ,r-delayedarray)
4861 ("r-matrix" ,r-matrix)
4863 ("r-rcpparmadillo" ,r-rcpparmadillo)
4864 ("r-rhdf5lib" ,r-rhdf5lib)
4865 ("r-s4vectors" ,r-s4vectors)
4866 ("r-singlecellexperiment" ,r-singlecellexperiment)
4867 ("r-summarizedexperiment" ,r-summarizedexperiment)))
4868 (home-page "https://bioconductor.org/packages/mbkmeans")
4869 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
4870 (description "This package implements the mini-batch k-means algorithm for
4871 large datasets, including support for on-disk data representation.")
4872 (license license:expat)))
4874 (define-public r-multtest
4881 (uri (bioconductor-uri "multtest" version))
4884 "1wi15v4llgv11hpb2j9h4a35nrnawnmvbz5d5dvgy8lhqrlq8w9a"))))
4885 (build-system r-build-system)
4887 `(("r-survival" ,r-survival)
4888 ("r-biocgenerics" ,r-biocgenerics)
4889 ("r-biobase" ,r-biobase)
4890 ("r-mass" ,r-mass)))
4891 (home-page "https://bioconductor.org/packages/multtest")
4892 (synopsis "Resampling-based multiple hypothesis testing")
4894 "This package can do non-parametric bootstrap and permutation
4895 resampling-based multiple testing procedures (including empirical Bayes
4896 methods) for controlling the family-wise error rate (FWER), generalized
4897 family-wise error rate (gFWER), tail probability of the proportion of
4898 false positives (TPPFP), and false discovery rate (FDR). Several choices
4899 of bootstrap-based null distribution are implemented (centered, centered
4900 and scaled, quantile-transformed). Single-step and step-wise methods are
4901 available. Tests based on a variety of T- and F-statistics (including
4902 T-statistics based on regression parameters from linear and survival models
4903 as well as those based on correlation parameters) are included. When probing
4904 hypotheses with T-statistics, users may also select a potentially faster null
4905 distribution which is multivariate normal with mean zero and variance
4906 covariance matrix derived from the vector influence function. Results are
4907 reported in terms of adjusted P-values, confidence regions and test statistic
4908 cutoffs. The procedures are directly applicable to identifying differentially
4909 expressed genes in DNA microarray experiments.")
4910 (license license:lgpl3)))
4912 (define-public r-graph
4918 (uri (bioconductor-uri "graph" version))
4921 "1i7s198d5kw4gk6nqqsd3vqaknj4493p822f2za8q95gv6x02rxa"))))
4922 (build-system r-build-system)
4924 `(("r-biocgenerics" ,r-biocgenerics)))
4925 (home-page "https://bioconductor.org/packages/graph")
4926 (synopsis "Handle graph data structures in R")
4928 "This package implements some simple graph handling capabilities for R.")
4929 (license license:artistic2.0)))
4931 ;; This is a CRAN package, but it depends on a Bioconductor package.
4932 (define-public r-ggm
4939 (uri (cran-uri "ggm" version))
4942 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
4943 (properties `((upstream-name . "ggm")))
4944 (build-system r-build-system)
4946 `(("r-graph" ,r-graph)
4947 ("r-igraph" ,r-igraph)))
4948 (home-page "https://cran.r-project.org/package=ggm")
4949 (synopsis "Functions for graphical Markov models")
4951 "This package provides functions and datasets for maximum likelihood
4952 fitting of some classes of graphical Markov models.")
4953 (license license:gpl2+)))
4955 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
4956 (define-public r-perfmeas
4963 (uri (cran-uri "PerfMeas" version))
4966 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
4967 (properties `((upstream-name . "PerfMeas")))
4968 (build-system r-build-system)
4970 `(("r-graph" ,r-graph)
4971 ("r-limma" ,r-limma)
4972 ("r-rbgl" ,r-rbgl)))
4973 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
4974 (synopsis "Performance measures for ranking and classification tasks")
4976 "This package implements different performance measures for
4977 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
4978 a given recall, F-score for single and multiple classes are available.")
4979 (license license:gpl2+)))
4981 ;; This is a CRAN package, but it depends on a Bioconductor package.
4982 (define-public r-codedepends
4984 (name "r-codedepends")
4989 (uri (cran-uri "CodeDepends" version))
4992 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
4993 (properties `((upstream-name . "CodeDepends")))
4994 (build-system r-build-system)
4996 `(("r-codetools" ,r-codetools)
4997 ("r-graph" ,r-graph)
4999 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
5000 (synopsis "Analysis of R code for reproducible research and code comprehension")
5002 "This package provides tools for analyzing R expressions or blocks of
5003 code and determining the dependencies between them. It focuses on R scripts,
5004 but can be used on the bodies of functions. There are many facilities
5005 including the ability to summarize or get a high-level view of code,
5006 determining dependencies between variables, code improvement suggestions.")
5007 ;; Any version of the GPL
5008 (license (list license:gpl2+ license:gpl3+))))
5010 (define-public r-chippeakanno
5012 (name "r-chippeakanno")
5017 (uri (bioconductor-uri "ChIPpeakAnno" version))
5020 "1wnmsdrb4wz2qprj5mnd3h0wx32y2mpy3xg7mjbgwlqn9bzpw3gk"))))
5021 (properties `((upstream-name . "ChIPpeakAnno")))
5022 (build-system r-build-system)
5024 `(("r-annotationdbi" ,r-annotationdbi)
5025 ("r-biocgenerics" ,r-biocgenerics)
5026 ("r-biomart" ,r-biomart)
5027 ("r-biostrings" ,r-biostrings)
5029 ("r-dplyr" ,r-dplyr)
5030 ("r-ensembldb" ,r-ensembldb)
5031 ("r-genomeinfodb" ,r-genomeinfodb)
5032 ("r-genomicalignments" ,r-genomicalignments)
5033 ("r-genomicfeatures" ,r-genomicfeatures)
5034 ("r-genomicranges" ,r-genomicranges)
5035 ("r-ggplot2" ,r-ggplot2)
5036 ("r-graph" ,r-graph)
5037 ("r-interactionset" ,r-interactionset)
5038 ("r-iranges" ,r-iranges)
5039 ("r-keggrest" ,r-keggrest)
5040 ("r-matrixstats" ,r-matrixstats)
5041 ("r-multtest" ,r-multtest)
5043 ("r-regioner" ,r-regioner)
5044 ("r-rsamtools" ,r-rsamtools)
5045 ("r-rtracklayer" ,r-rtracklayer)
5046 ("r-s4vectors" ,r-s4vectors)
5047 ("r-summarizedexperiment" ,r-summarizedexperiment)
5048 ("r-venndiagram" ,r-venndiagram)))
5050 `(("r-knitr" ,r-knitr)))
5051 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
5052 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
5054 "The package includes functions to retrieve the sequences around the peak,
5055 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
5056 custom features such as most conserved elements and other transcription factor
5057 binding sites supplied by users. Starting 2.0.5, new functions have been added
5058 for finding the peaks with bi-directional promoters with summary statistics
5059 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
5060 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
5061 enrichedGO (addGeneIDs).")
5062 (license license:gpl2+)))
5064 (define-public r-matrixgenerics
5066 (name "r-matrixgenerics")
5070 (uri (bioconductor-uri "MatrixGenerics" version))
5073 "1xq3a9ls125wfnhn13rdbsxzq3f6klsspx7h0znd6l67f5j5k25s"))))
5075 `((upstream-name . "MatrixGenerics")))
5076 (build-system r-build-system)
5078 `(("r-matrixstats" ,r-matrixstats)))
5079 (home-page "https://bioconductor.org/packages/MatrixGenerics")
5080 (synopsis "S4 generic summary statistic functions for matrix-like objects")
5082 "This package provides S4 generic functions modeled after the
5083 @code{matrixStats} API for alternative matrix implementations. Packages with
5084 alternative matrix implementation can depend on this package and implement the
5085 generic functions that are defined here for a useful set of row and column
5086 summary statistics. Other package developers can import this package and
5087 handle a different matrix implementations without worrying about
5088 incompatibilities.")
5089 (license license:artistic2.0)))
5091 (define-public r-marray
5097 (uri (bioconductor-uri "marray" version))
5099 (base32 "0wpmrhqpyv27h1hn31hzz21r74r7yqx79ljv8i8gn6ix8lf5ca56"))))
5100 (build-system r-build-system)
5102 `(("r-limma" ,r-limma)))
5103 (home-page "https://bioconductor.org/packages/marray")
5104 (synopsis "Exploratory analysis for two-color spotted microarray data")
5105 (description "This package contains class definitions for two-color spotted
5106 microarray data. It also includes functions for data input, diagnostic plots,
5107 normalization and quality checking.")
5108 (license license:lgpl2.0+)))
5110 (define-public r-cghbase
5116 (uri (bioconductor-uri "CGHbase" version))
5118 (base32 "1p87k4vw981k97d9bckmprrfg55jwd91658rgxzjj8hnschf28a4"))))
5119 (properties `((upstream-name . "CGHbase")))
5120 (build-system r-build-system)
5122 `(("r-biobase" ,r-biobase)
5123 ("r-marray" ,r-marray)))
5124 (home-page "https://bioconductor.org/packages/CGHbase")
5125 (synopsis "Base functions and classes for arrayCGH data analysis")
5126 (description "This package contains functions and classes that are needed by
5127 the @code{arrayCGH} packages.")
5128 (license license:gpl2+)))
5130 (define-public r-cghcall
5136 (uri (bioconductor-uri "CGHcall" version))
5138 (base32 "1zik04y2q0anzy85l0b4ryzkxpfx2fnmpwp5s7akyk1jfl2r8gw7"))))
5139 (properties `((upstream-name . "CGHcall")))
5140 (build-system r-build-system)
5142 `(("r-biobase" ,r-biobase)
5143 ("r-cghbase" ,r-cghbase)
5144 ("r-impute" ,r-impute)
5145 ("r-dnacopy" ,r-dnacopy)
5146 ("r-snowfall" ,r-snowfall)))
5147 (home-page "https://bioconductor.org/packages/CGHcall")
5148 (synopsis "Base functions and classes for arrayCGH data analysis")
5149 (description "This package contains functions and classes that are needed by
5150 @code{arrayCGH} packages.")
5151 (license license:gpl2+)))
5153 (define-public r-qdnaseq
5159 (uri (bioconductor-uri "QDNAseq" version))
5161 (base32 "1p4544xlarkbgs9kybrrawq3v7qr6ix62nrc6l7dcksh2ka69yzf"))))
5162 (properties `((upstream-name . "QDNAseq")))
5163 (build-system r-build-system)
5165 `(("r-biobase" ,r-biobase)
5166 ("r-cghbase" ,r-cghbase)
5167 ("r-cghcall" ,r-cghcall)
5168 ("r-dnacopy" ,r-dnacopy)
5169 ("r-future" ,r-future)
5170 ("r-future-apply" ,r-future-apply)
5171 ("r-genomicranges" ,r-genomicranges)
5172 ("r-iranges" ,r-iranges)
5173 ("r-matrixstats" ,r-matrixstats)
5174 ("r-r-utils" ,r-r-utils)
5175 ("r-rsamtools" ,r-rsamtools)))
5176 (home-page "https://bioconductor.org/packages/QDNAseq")
5177 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
5178 (description "The genome is divided into non-overlapping fixed-sized bins,
5179 number of sequence reads in each counted, adjusted with a simultaneous
5180 two-dimensional loess correction for sequence mappability and GC content, and
5181 filtered to remove spurious regions in the genome. Downstream steps of
5182 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
5184 (license license:gpl2+)))
5186 (define-public r-bayseq
5193 (uri (bioconductor-uri "baySeq" version))
5196 "0hyc0sl2nf18bz0jxbzim0v41zwh2rnnr7l3p6zkk9wnw5gn7bbc"))))
5197 (properties `((upstream-name . "baySeq")))
5198 (build-system r-build-system)
5200 `(("r-abind" ,r-abind)
5201 ("r-edger" ,r-edger)
5202 ("r-genomicranges" ,r-genomicranges)))
5203 (home-page "https://bioconductor.org/packages/baySeq/")
5204 (synopsis "Bayesian analysis of differential expression patterns in count data")
5206 "This package identifies differential expression in high-throughput count
5207 data, such as that derived from next-generation sequencing machines,
5208 calculating estimated posterior likelihoods of differential expression (or
5209 more complex hypotheses) via empirical Bayesian methods.")
5210 (license license:gpl3)))
5212 (define-public r-chipcomp
5219 (uri (bioconductor-uri "ChIPComp" version))
5222 "1kfxjh1mynrgqsy2q6byf03cbymqc8w7l7672iyd0wj5qzlif4h5"))))
5223 (properties `((upstream-name . "ChIPComp")))
5224 (build-system r-build-system)
5226 `(("r-biocgenerics" ,r-biocgenerics)
5227 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
5228 ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
5229 ("r-genomeinfodb" ,r-genomeinfodb)
5230 ("r-genomicranges" ,r-genomicranges)
5231 ("r-iranges" ,r-iranges)
5232 ("r-limma" ,r-limma)
5233 ("r-rsamtools" ,r-rsamtools)
5234 ("r-rtracklayer" ,r-rtracklayer)
5235 ("r-s4vectors" ,r-s4vectors)))
5236 (home-page "https://bioconductor.org/packages/ChIPComp")
5237 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
5239 "ChIPComp implements a statistical method for quantitative comparison of
5240 multiple ChIP-seq datasets. It detects differentially bound sharp binding
5241 sites across multiple conditions considering matching control in ChIP-seq
5243 ;; Any version of the GPL.
5244 (license license:gpl3+)))
5246 (define-public r-riboprofiling
5248 (name "r-riboprofiling")
5253 (uri (bioconductor-uri "RiboProfiling" version))
5256 "1jmd8yrv7p7hn4gdibg3svmhqxjyrnfp7cgsqg8zv862lgd75zsl"))))
5257 (properties `((upstream-name . "RiboProfiling")))
5258 (build-system r-build-system)
5260 `(("r-biocgenerics" ,r-biocgenerics)
5261 ("r-biostrings" ,r-biostrings)
5262 ("r-data-table" ,r-data-table)
5263 ("r-genomeinfodb" ,r-genomeinfodb)
5264 ("r-genomicalignments" ,r-genomicalignments)
5265 ("r-genomicfeatures" ,r-genomicfeatures)
5266 ("r-genomicranges" ,r-genomicranges)
5267 ("r-ggbio" ,r-ggbio)
5268 ("r-ggplot2" ,r-ggplot2)
5269 ("r-iranges" ,r-iranges)
5271 ("r-reshape2" ,r-reshape2)
5272 ("r-rsamtools" ,r-rsamtools)
5273 ("r-rtracklayer" ,r-rtracklayer)
5274 ("r-s4vectors" ,r-s4vectors)
5275 ("r-sqldf" ,r-sqldf)))
5277 `(("r-knitr" ,r-knitr)))
5278 (home-page "https://bioconductor.org/packages/RiboProfiling/")
5279 (synopsis "Ribosome profiling data analysis")
5280 (description "Starting with a BAM file, this package provides the
5281 necessary functions for quality assessment, read start position recalibration,
5282 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
5283 of count data: pairs, log fold-change, codon frequency and coverage
5284 assessment, principal component analysis on codon coverage.")
5285 (license license:gpl3)))
5287 (define-public r-riboseqr
5294 (uri (bioconductor-uri "riboSeqR" version))
5297 "1m5w2j35wr0lzwir4s58z757vrcsj5mglsqrkvs241k0hlmn06qa"))))
5298 (properties `((upstream-name . "riboSeqR")))
5299 (build-system r-build-system)
5301 `(("r-abind" ,r-abind)
5302 ("r-bayseq" ,r-bayseq)
5303 ("r-genomeinfodb" ,r-genomeinfodb)
5304 ("r-genomicranges" ,r-genomicranges)
5305 ("r-iranges" ,r-iranges)
5306 ("r-rsamtools" ,r-rsamtools)
5307 ("r-seqlogo" ,r-seqlogo)))
5308 (home-page "https://bioconductor.org/packages/riboSeqR/")
5309 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
5311 "This package provides plotting functions, frameshift detection and
5312 parsing of genetic sequencing data from ribosome profiling experiments.")
5313 (license license:gpl3)))
5315 (define-public r-interactionset
5317 (name "r-interactionset")
5322 (uri (bioconductor-uri "InteractionSet" version))
5325 "034xidjmn67n1471fnpdmz7gjm6p05cj8sp9nssc3gxdzn54a6xb"))))
5327 `((upstream-name . "InteractionSet")))
5328 (build-system r-build-system)
5330 `(("r-biocgenerics" ,r-biocgenerics)
5331 ("r-genomeinfodb" ,r-genomeinfodb)
5332 ("r-genomicranges" ,r-genomicranges)
5333 ("r-iranges" ,r-iranges)
5334 ("r-matrix" ,r-matrix)
5336 ("r-s4vectors" ,r-s4vectors)
5337 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5339 `(("r-knitr" ,r-knitr)))
5340 (home-page "https://bioconductor.org/packages/InteractionSet")
5341 (synopsis "Base classes for storing genomic interaction data")
5343 "This package provides the @code{GInteractions},
5344 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
5345 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
5347 (license license:gpl3)))
5349 (define-public r-genomicinteractions
5351 (name "r-genomicinteractions")
5356 (uri (bioconductor-uri "GenomicInteractions" version))
5359 "0zjl7rp5fk14kqsx0bkbpq6hqahbkiyvwa9aggp4kfb8hnmz9qal"))))
5361 `((upstream-name . "GenomicInteractions")))
5362 (build-system r-build-system)
5364 `(("r-biobase" ,r-biobase)
5365 ("r-biocgenerics" ,r-biocgenerics)
5366 ("r-data-table" ,r-data-table)
5367 ("r-dplyr" ,r-dplyr)
5368 ("r-genomeinfodb" ,r-genomeinfodb)
5369 ("r-genomicranges" ,r-genomicranges)
5370 ("r-ggplot2" ,r-ggplot2)
5371 ("r-gridextra" ,r-gridextra)
5373 ("r-igraph" ,r-igraph)
5374 ("r-interactionset" ,r-interactionset)
5375 ("r-iranges" ,r-iranges)
5376 ("r-rsamtools" ,r-rsamtools)
5377 ("r-rtracklayer" ,r-rtracklayer)
5378 ("r-s4vectors" ,r-s4vectors)
5379 ("r-stringr" ,r-stringr)))
5381 `(("r-knitr" ,r-knitr)))
5382 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
5383 (synopsis "R package for handling genomic interaction data")
5385 "This R package provides tools for handling genomic interaction data,
5386 such as ChIA-PET/Hi-C, annotating genomic features with interaction
5387 information and producing various plots and statistics.")
5388 (license license:gpl3)))
5390 (define-public r-ctc
5397 (uri (bioconductor-uri "ctc" version))
5400 "1v8aysvy6a3r1iafc3xvk885c128kb3pb9zpcdhdjcn0by96k8hh"))))
5401 (build-system r-build-system)
5402 (propagated-inputs `(("r-amap" ,r-amap)))
5403 (home-page "https://bioconductor.org/packages/ctc/")
5404 (synopsis "Cluster and tree conversion")
5406 "This package provides tools for exporting and importing classification
5407 trees and clusters to other programs.")
5408 (license license:gpl2)))
5410 (define-public r-goseq
5417 (uri (bioconductor-uri "goseq" version))
5420 "07qrxssx4rb8r958r1smx8xfpzdxpp55hci3201hcmz3mxz77i0s"))))
5421 (build-system r-build-system)
5423 `(("r-annotationdbi" ,r-annotationdbi)
5424 ("r-biasedurn" ,r-biasedurn)
5425 ("r-biocgenerics" ,r-biocgenerics)
5426 ("r-genelendatabase" ,r-genelendatabase)
5427 ("r-go-db" ,r-go-db)
5428 ("r-mgcv" ,r-mgcv)))
5429 (home-page "https://bioconductor.org/packages/goseq/")
5430 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
5432 "This package provides tools to detect Gene Ontology and/or other user
5433 defined categories which are over/under represented in RNA-seq data.")
5434 (license license:lgpl2.0+)))
5436 (define-public r-glimma
5443 (uri (bioconductor-uri "Glimma" version))
5446 "0dsk8qmwimzmd1x4k4jwg9q11jm1ahn8cw0gzd6s2gmigfls4hsa"))))
5447 (properties `((upstream-name . "Glimma")))
5448 (build-system r-build-system)
5450 `(("r-deseq2" ,r-deseq2)
5451 ("r-edger" ,r-edger)
5452 ("r-htmlwidgets" ,r-htmlwidgets)
5453 ("r-jsonlite" ,r-jsonlite)
5454 ("r-limma" ,r-limma)
5455 ("r-s4vectors" ,r-s4vectors)
5456 ("r-summarizedexperiment" ,r-summarizedexperiment)))
5458 `(("r-knitr" ,r-knitr)))
5459 (home-page "https://github.com/Shians/Glimma")
5460 (synopsis "Interactive HTML graphics")
5462 "This package generates interactive visualisations for analysis of
5463 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
5464 HTML page. The interactions are built on top of the popular static
5465 representations of analysis results in order to provide additional
5467 (license license:lgpl3)))
5469 (define-public r-rots
5476 (uri (bioconductor-uri "ROTS" version))
5479 "18wyi73l95df182vg3m014sxwdbpggr61vsbazhyw4vyx2fnzmpl"))))
5480 (properties `((upstream-name . "ROTS")))
5481 (build-system r-build-system)
5483 `(("r-biobase" ,r-biobase)
5484 ("r-rcpp" ,r-rcpp)))
5485 (home-page "https://bioconductor.org/packages/ROTS/")
5486 (synopsis "Reproducibility-Optimized Test Statistic")
5488 "This package provides tools for calculating the
5489 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
5491 (license license:gpl2+)))
5493 (define-public r-plgem
5500 (uri (bioconductor-uri "plgem" version))
5503 "1rz5jk5bgpk7gjknx79jyslahjg46q2f4bx6dgd0vwmarc29a45z"))))
5504 (build-system r-build-system)
5506 `(("r-biobase" ,r-biobase)
5507 ("r-mass" ,r-mass)))
5508 (home-page "http://www.genopolis.it")
5509 (synopsis "Detect differential expression in microarray and proteomics datasets")
5511 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
5512 model the variance-versus-mean dependence that exists in a variety of
5513 genome-wide datasets, including microarray and proteomics data. The use of
5514 PLGEM has been shown to improve the detection of differentially expressed
5515 genes or proteins in these datasets.")
5516 (license license:gpl2)))
5518 (define-public r-inspect
5525 (uri (bioconductor-uri "INSPEcT" version))
5528 "0jh5db9dv5pb6b50sg22x8q55m3h0h0nkmb9mivvvp22dhyrd82z"))))
5529 (properties `((upstream-name . "INSPEcT")))
5530 (build-system r-build-system)
5532 `(("r-biobase" ,r-biobase)
5533 ("r-biocgenerics" ,r-biocgenerics)
5534 ("r-biocparallel" ,r-biocparallel)
5535 ("r-deseq2" ,r-deseq2)
5536 ("r-desolve" ,r-desolve)
5537 ("r-gdata" ,r-gdata)
5538 ("r-genomeinfodb" ,r-genomeinfodb)
5539 ("r-genomicalignments" ,r-genomicalignments)
5540 ("r-genomicfeatures" ,r-genomicfeatures)
5541 ("r-genomicranges" ,r-genomicranges)
5542 ("r-iranges" ,r-iranges)
5543 ("r-kernsmooth" ,r-kernsmooth)
5544 ("r-plgem" ,r-plgem)
5546 ("r-rootsolve" ,r-rootsolve)
5547 ("r-rsamtools" ,r-rsamtools)
5548 ("r-rtracklayer" ,r-rtracklayer)
5549 ("r-s4vectors" ,r-s4vectors)
5550 ("r-shiny" ,r-shiny)
5551 ("r-summarizedexperiment" ,r-summarizedexperiment)
5552 ("r-txdb-mmusculus-ucsc-mm9-knowngene"
5553 ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
5555 `(("r-knitr" ,r-knitr)))
5556 (home-page "https://bioconductor.org/packages/INSPEcT")
5557 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
5559 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
5560 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
5561 order to evaluate synthesis, processing and degradation rates and assess via
5562 modeling the rates that determines changes in mature mRNA levels.")
5563 (license license:gpl2)))
5565 (define-public r-dnabarcodes
5567 (name "r-dnabarcodes")
5572 (uri (bioconductor-uri "DNABarcodes" version))
5575 "1wiqmzjcb7flp7ldcgbx91asxxrmm1rg9pcfljniab9xcsldhksp"))))
5576 (properties `((upstream-name . "DNABarcodes")))
5577 (build-system r-build-system)
5580 ("r-matrix" ,r-matrix)
5581 ("r-rcpp" ,r-rcpp)))
5583 `(("r-knitr" ,r-knitr)))
5584 (home-page "https://bioconductor.org/packages/DNABarcodes")
5585 (synopsis "Create and analyze DNA barcodes")
5587 "This package offers tools to create DNA barcode sets capable of
5588 correcting insertion, deletion, and substitution errors. Existing barcodes
5589 can be analyzed regarding their minimal, maximal and average distances between
5590 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
5591 demultiplexed, i.e. assigned to their original reference barcode.")
5592 (license license:gpl2)))
5594 (define-public r-ruvseq
5601 (uri (bioconductor-uri "RUVSeq" version))
5604 "1fy0k1p0m209lzjpd5jhfnifa22lrn63qq3a3kn5g0xhbbmijzac"))))
5605 (properties `((upstream-name . "RUVSeq")))
5606 (build-system r-build-system)
5608 `(("r-biobase" ,r-biobase)
5609 ("r-edaseq" ,r-edaseq)
5610 ("r-edger" ,r-edger)
5611 ("r-mass" ,r-mass)))
5613 `(("r-knitr" ,r-knitr)))
5614 (home-page "https://github.com/drisso/RUVSeq")
5615 (synopsis "Remove unwanted variation from RNA-Seq data")
5617 "This package implements methods to @dfn{remove unwanted variation} (RUV)
5618 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
5620 (license license:artistic2.0)))
5622 (define-public r-biocneighbors
5624 (name "r-biocneighbors")
5629 (uri (bioconductor-uri "BiocNeighbors" version))
5632 "0cjidi18wjip9xzx83890wjk40vvjq06prf1ag4m2kac47w01r7v"))))
5633 (properties `((upstream-name . "BiocNeighbors")))
5634 (build-system r-build-system)
5636 `(("r-biocparallel" ,r-biocparallel)
5637 ("r-matrix" ,r-matrix)
5639 ("r-rcpphnsw" ,r-rcpphnsw)
5640 ("r-s4vectors" ,r-s4vectors)))
5642 `(("r-knitr" ,r-knitr)))
5643 (home-page "https://bioconductor.org/packages/BiocNeighbors")
5644 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
5646 "This package implements exact and approximate methods for nearest
5647 neighbor detection, in a framework that allows them to be easily switched
5648 within Bioconductor packages or workflows. The exact algorithm is implemented
5649 using pre-clustering with the k-means algorithm. Functions are also provided
5650 to search for all neighbors within a given distance. Parallelization is
5651 achieved for all methods using the BiocParallel framework.")
5652 (license license:gpl3)))
5654 (define-public r-scaledmatrix
5656 (name "r-scaledmatrix")
5661 (uri (bioconductor-uri "ScaledMatrix" version))
5664 "1j96fvw1waqxbv5c8myfmhsidq370z03yz13yqmrs4nn1rpn1a06"))))
5665 (properties `((upstream-name . "ScaledMatrix")))
5666 (build-system r-build-system)
5668 `(("r-delayedarray" ,r-delayedarray)
5669 ("r-matrix" ,r-matrix)
5670 ("r-s4vectors" ,r-s4vectors)))
5671 (native-inputs `(("r-knitr" ,r-knitr)))
5672 (home-page "https://github.com/LTLA/ScaledMatrix")
5673 (synopsis "Create a DelayedMatrix of scaled and centered values")
5675 "This package provides delayed computation of a matrix of scaled and
5676 centered values. The result is equivalent to using the @code{scale} function
5677 but avoids explicit realization of a dense matrix during block processing.
5678 This permits greater efficiency in common operations, most notably matrix
5680 (license license:gpl3)))
5682 (define-public r-treeio
5689 (uri (bioconductor-uri "treeio" version))
5692 "0ypl4h80m08sf7r4zfvqgvpsz46x15wvcl1idq5pd813bp1w2sws"))))
5693 (properties `((upstream-name . "treeio")))
5694 (build-system r-build-system)
5697 ("r-dplyr" ,r-dplyr)
5698 ("r-jsonlite" ,r-jsonlite)
5699 ("r-magrittr" ,r-magrittr)
5700 ("r-rlang" ,r-rlang)
5701 ("r-tibble" ,r-tibble)
5702 ("r-tidytree" ,r-tidytree)))
5703 (native-inputs `(("r-knitr" ,r-knitr)))
5704 (home-page "https://github.com/YuLab-SMU/treeio")
5705 (synopsis "Base classes and functions for Phylogenetic tree input and output")
5707 "This is an R package to make it easier to import and store phylogenetic
5708 trees with associated data; and to link external data from different sources
5709 to phylogeny. It also supports exporting phylogenetic trees with
5710 heterogeneous associated data to a single tree file and can be served as a
5711 platform for merging tree with associated data and converting file formats.")
5712 (license license:artistic2.0)))
5714 (define-public r-ggtree
5721 (uri (bioconductor-uri "ggtree" version))
5724 "0i665b5jxgsv3ncxmczy7n0h911br44dw9f7m4jwv3pjmr5mm6vk"))))
5725 (properties `((upstream-name . "ggtree")))
5726 (build-system r-build-system)
5729 ("r-aplot" ,r-aplot)
5730 ("r-dplyr" ,r-dplyr)
5731 ("r-ggplot2" ,r-ggplot2)
5732 ("r-magrittr" ,r-magrittr)
5733 ("r-purrr" ,r-purrr)
5734 ("r-rlang" ,r-rlang)
5735 ("r-rvcheck" ,r-rvcheck)
5736 ("r-scales" ,r-scales)
5737 ("r-tidyr" ,r-tidyr)
5738 ("r-tidytree" ,r-tidytree)
5739 ("r-treeio" ,r-treeio)))
5740 (native-inputs `(("r-knitr" ,r-knitr)))
5741 (home-page "https://yulab-smu.top/treedata-book/")
5742 (synopsis "R package for visualization of trees and annotation data")
5744 "This package extends the ggplot2 plotting system which implements a
5745 grammar of graphics. ggtree is designed for visualization and annotation of
5746 phylogenetic trees and other tree-like structures with their annotation
5748 (license license:artistic2.0)))
5750 (define-public r-metapod
5757 (uri (bioconductor-uri "metapod" version))
5760 "1hbcwr6d8gyrf4azh0gi588xkrg6gz7gsb5hbvzqkhplbsp6shlv"))))
5761 (properties `((upstream-name . "metapod")))
5762 (build-system r-build-system)
5764 `(("r-rcpp" ,r-rcpp)))
5766 `(("r-knitr" ,r-knitr)))
5767 (home-page "https://bioconductor.org/packages/metapod")
5768 (synopsis "Meta-analyses on p-values of differential analyses")
5770 "This package implements a variety of methods for combining p-values in
5771 differential analyses of genome-scale datasets. Functions can combine
5772 p-values across different tests in the same analysis (e.g., genomic windows in
5773 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
5774 analyses (e.g., replicated comparisons, effect of different treatment
5775 conditions). Support is provided for handling log-transformed input p-values,
5776 missing values and weighting where appropriate.")
5777 (license license:gpl3)))
5779 (define-public r-biocsingular
5781 (name "r-biocsingular")
5786 (uri (bioconductor-uri "BiocSingular" version))
5789 "1l0xgc3z5ci5sid198nsgg0k5i40rh877jybzmy0ify7rzv8carp"))))
5790 (properties `((upstream-name . "BiocSingular")))
5791 (build-system r-build-system)
5793 `(("r-beachmat" ,r-beachmat)
5794 ("r-biocgenerics" ,r-biocgenerics)
5795 ("r-biocparallel" ,r-biocparallel)
5796 ("r-delayedarray" ,r-delayedarray)
5797 ("r-irlba" ,r-irlba)
5798 ("r-matrix" ,r-matrix)
5801 ("r-s4vectors" ,r-s4vectors)
5802 ("r-scaledmatrix" ,r-scaledmatrix)))
5804 `(("r-knitr" ,r-knitr)))
5805 (home-page "https://github.com/LTLA/BiocSingular")
5806 (synopsis "Singular value decomposition for Bioconductor packages")
5808 "This package implements exact and approximate methods for singular value
5809 decomposition and principal components analysis, in a framework that allows
5810 them to be easily switched within Bioconductor packages or workflows. Where
5811 possible, parallelization is achieved using the BiocParallel framework.")
5812 (license license:gpl3)))
5814 (define-public r-destiny
5821 (uri (bioconductor-uri "destiny" version))
5824 "1i7f5q02zvpfaxhd76fbw0h1wfgjphyn5hrmrjpvlnv4ardzsir2"))))
5825 (build-system r-build-system)
5827 `(("r-biobase" ,r-biobase)
5828 ("r-biocgenerics" ,r-biocgenerics)
5829 ("r-ggplot-multistats" ,r-ggplot-multistats)
5830 ("r-ggplot2" ,r-ggplot2)
5831 ("r-ggthemes" ,r-ggthemes)
5832 ("r-irlba" ,r-irlba)
5833 ("r-knn-covertree" ,r-knn-covertree)
5834 ("r-matrix" ,r-matrix)
5835 ("r-pcamethods" ,r-pcamethods)
5836 ("r-proxy" ,r-proxy)
5838 ("r-rcppeigen" ,r-rcppeigen)
5839 ("r-rcpphnsw" ,r-rcpphnsw)
5840 ("r-rspectra" ,r-rspectra)
5841 ("r-scales" ,r-scales)
5842 ("r-scatterplot3d" ,r-scatterplot3d)
5843 ("r-singlecellexperiment" ,r-singlecellexperiment)
5844 ("r-smoother" ,r-smoother)
5845 ("r-summarizedexperiment" ,r-summarizedexperiment)
5846 ("r-tidyr" ,r-tidyr)
5847 ("r-tidyselect" ,r-tidyselect)
5850 `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes
5851 (home-page "https://bioconductor.org/packages/destiny/")
5852 (synopsis "Create and plot diffusion maps")
5853 (description "This package provides tools to create and plot diffusion
5855 ;; Any version of the GPL
5856 (license license:gpl3+)))
5858 (define-public r-savr
5865 (uri (bioconductor-uri "savR" version))
5868 "1ynp334hm76zf05j4f6vha6r16s5f2ncxx9yviq4rxidk9r723jq"))))
5869 (properties `((upstream-name . "savR")))
5870 (build-system r-build-system)
5872 `(("r-ggplot2" ,r-ggplot2)
5873 ("r-gridextra" ,r-gridextra)
5874 ("r-reshape2" ,r-reshape2)
5875 ("r-scales" ,r-scales)
5877 (home-page "https://github.com/bcalder/savR")
5878 (synopsis "Parse and analyze Illumina SAV files")
5880 "This package provides tools to parse Illumina Sequence Analysis
5881 Viewer (SAV) files, access data, and generate QC plots.")
5882 (license license:agpl3+)))
5884 (define-public r-chipexoqual
5886 (name "r-chipexoqual")
5891 (uri (bioconductor-uri "ChIPexoQual" version))
5894 "0fbrf5s6pz115djm7xw95k1d0p7svi40aacbb3d52wmx5azwj424"))))
5895 (properties `((upstream-name . "ChIPexoQual")))
5896 (build-system r-build-system)
5898 `(("r-biocparallel" ,r-biocparallel)
5899 ("r-biovizbase" ,r-biovizbase)
5900 ("r-broom" ,r-broom)
5901 ("r-data-table" ,r-data-table)
5902 ("r-dplyr" ,r-dplyr)
5903 ("r-genomeinfodb" ,r-genomeinfodb)
5904 ("r-genomicalignments" ,r-genomicalignments)
5905 ("r-genomicranges" ,r-genomicranges)
5906 ("r-ggplot2" ,r-ggplot2)
5907 ("r-hexbin" ,r-hexbin)
5908 ("r-iranges" ,r-iranges)
5909 ("r-rcolorbrewer" ,r-rcolorbrewer)
5910 ("r-rmarkdown" ,r-rmarkdown)
5911 ("r-rsamtools" ,r-rsamtools)
5912 ("r-s4vectors" ,r-s4vectors)
5913 ("r-scales" ,r-scales)
5914 ("r-viridis" ,r-viridis)))
5916 `(("r-knitr" ,r-knitr)))
5917 (home-page "https://github.com/keleslab/ChIPexoQual")
5918 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
5920 "This package provides a quality control pipeline for ChIP-exo/nexus
5922 (license license:gpl2+)))
5924 (define-public r-copynumber
5926 (name "r-copynumber")
5930 (uri (bioconductor-uri "copynumber" version))
5933 "03pvjzjrcsbjfw3855s3whfzin45vaipy7cahnj6fywdysvh8hps"))))
5934 (build-system r-build-system)
5936 `(("r-s4vectors" ,r-s4vectors)
5937 ("r-iranges" ,r-iranges)
5938 ("r-genomicranges" ,r-genomicranges)
5939 ("r-biocgenerics" ,r-biocgenerics)))
5940 (home-page "https://bioconductor.org/packages/copynumber")
5941 (synopsis "Segmentation of single- and multi-track copy number data")
5943 "This package segments single- and multi-track copy number data by a
5944 penalized least squares regression method.")
5945 (license license:artistic2.0)))
5947 (define-public r-dnacopy
5954 (uri (bioconductor-uri "DNAcopy" version))
5957 "0mgq814f6c2271d2lxg763bsnv3ma4ari5xa4x1rbksv8yvcjc4d"))))
5958 (properties `((upstream-name . "DNAcopy")))
5959 (build-system r-build-system)
5960 (native-inputs `(("gfortran" ,gfortran)))
5961 (home-page "https://bioconductor.org/packages/DNAcopy")
5962 (synopsis "DNA copy number data analysis")
5964 "This package implements the @dfn{circular binary segmentation} (CBS)
5965 algorithm to segment DNA copy number data and identify genomic regions with
5966 abnormal copy number.")
5967 (license license:gpl2+)))
5969 ;; This is a CRAN package, but it uncharacteristically depends on a
5970 ;; Bioconductor package.
5971 (define-public r-htscluster
5973 (name "r-htscluster")
5978 (uri (cran-uri "HTSCluster" version))
5981 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
5982 (properties `((upstream-name . "HTSCluster")))
5983 (build-system r-build-system)
5985 `(("r-capushe" ,r-capushe)
5986 ("r-edger" ,r-edger)
5987 ("r-plotrix" ,r-plotrix)))
5988 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
5989 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
5991 "This package provides a Poisson mixture model is implemented to cluster
5992 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
5993 estimation is performed using either the EM or CEM algorithm, and the slope
5994 heuristics are used for model selection (i.e., to choose the number of
5996 (license license:gpl3+)))
5998 (define-public r-deds
6005 (uri (bioconductor-uri "DEDS" version))
6008 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
6009 (properties `((upstream-name . "DEDS")))
6010 (build-system r-build-system)
6011 (home-page "https://bioconductor.org/packages/DEDS/")
6012 (synopsis "Differential expression via distance summary for microarray data")
6014 "This library contains functions that calculate various statistics of
6015 differential expression for microarray data, including t statistics, fold
6016 change, F statistics, SAM, moderated t and F statistics and B statistics. It
6017 also implements a new methodology called DEDS (Differential Expression via
6018 Distance Summary), which selects differentially expressed genes by integrating
6019 and summarizing a set of statistics using a weighted distance approach.")
6020 ;; Any version of the LGPL.
6021 (license license:lgpl3+)))
6023 ;; This is a CRAN package, but since it depends on a Bioconductor package we
6025 (define-public r-nbpseq
6032 (uri (cran-uri "NBPSeq" version))
6035 "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by"))))
6036 (properties `((upstream-name . "NBPSeq")))
6037 (build-system r-build-system)
6039 `(("r-qvalue" ,r-qvalue)))
6040 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
6041 (synopsis "Negative binomial models for RNA-Seq data")
6043 "This package provides negative binomial models for two-group comparisons
6044 and regression inferences from RNA-sequencing data.")
6045 (license license:gpl2)))
6047 (define-public r-ebseq
6054 (uri (bioconductor-uri "EBSeq" version))
6057 "0h5v3vrb90zim80bdnr3aw58g3h7zjqa4l9i0jwx5j19ywf54fdz"))))
6058 (properties `((upstream-name . "EBSeq")))
6059 (build-system r-build-system)
6061 `(("r-blockmodeling" ,r-blockmodeling)
6062 ("r-gplots" ,r-gplots)
6063 ("r-testthat" ,r-testthat)))
6064 (home-page "https://bioconductor.org/packages/EBSeq")
6065 (synopsis "Differential expression analysis of RNA-seq data")
6067 "This package provides tools for differential expression analysis at both
6068 gene and isoform level using RNA-seq data")
6069 (license license:artistic2.0)))
6071 (define-public r-karyoploter
6073 (name "r-karyoploter")
6077 (uri (bioconductor-uri "karyoploteR" version))
6080 "11sgxz2xz685pgm8mf0hzm6aryx4fj5g3dlffjzpqxh3awfqa19p"))))
6081 (build-system r-build-system)
6083 `(("r-annotationdbi" ,r-annotationdbi)
6084 ("r-bamsignals" ,r-bamsignals)
6085 ("r-bezier" ,r-bezier)
6086 ("r-biovizbase" ,r-biovizbase)
6087 ("r-digest" ,r-digest)
6088 ("r-genomeinfodb" ,r-genomeinfodb)
6089 ("r-genomicfeatures" ,r-genomicfeatures)
6090 ("r-genomicranges" ,r-genomicranges)
6091 ("r-iranges" ,r-iranges)
6092 ("r-memoise" ,r-memoise)
6093 ("r-regioner" ,r-regioner)
6094 ("r-rsamtools" ,r-rsamtools)
6095 ("r-rtracklayer" ,r-rtracklayer)
6096 ("r-s4vectors" ,r-s4vectors)
6097 ("r-variantannotation" ,r-variantannotation)))
6099 `(("r-knitr" ,r-knitr)))
6100 (home-page "https://bioconductor.org/packages/karyoploteR/")
6101 (synopsis "Plot customizable linear genomes displaying arbitrary data")
6102 (description "This package creates karyotype plots of arbitrary genomes and
6103 offers a complete set of functions to plot arbitrary data on them. It mimics
6104 many R base graphics functions coupling them with a coordinate change function
6105 automatically mapping the chromosome and data coordinates into the plot
6107 (license license:artistic2.0)))
6109 (define-public r-lpsymphony
6111 (name "r-lpsymphony")
6116 (uri (bioconductor-uri "lpsymphony" version))
6119 "0aw4b3p5z8ys7zlwy8s3bsqk03xwx42311yxr7q14w3f7sn3shzn"))))
6120 (build-system r-build-system)
6124 `(("pkg-config" ,pkg-config)
6125 ("r-knitr" ,r-knitr)))
6126 (home-page "https://r-forge.r-project.org/projects/rsymphony")
6127 (synopsis "Symphony integer linear programming solver in R")
6129 "This package was derived from Rsymphony. The package provides an R
6130 interface to SYMPHONY, a linear programming solver written in C++. The main
6131 difference between this package and Rsymphony is that it includes the solver
6132 source code, while Rsymphony expects to find header and library files on the
6133 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
6134 to install interface to SYMPHONY.")
6135 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
6136 ;; lpsimphony is released under the same terms.
6137 (license license:epl1.0)))
6139 (define-public r-ihw
6146 (uri (bioconductor-uri "IHW" version))
6149 "0b393a8ayzbnrgkk562w1dj7avacpb3wc7yq7awiki24wi5g2lfw"))))
6150 (properties `((upstream-name . "IHW")))
6151 (build-system r-build-system)
6153 `(("r-biocgenerics" ,r-biocgenerics)
6154 ("r-fdrtool" ,r-fdrtool)
6155 ("r-lpsymphony" ,r-lpsymphony)
6156 ("r-slam" ,r-slam)))
6158 `(("r-knitr" ,r-knitr)))
6159 (home-page "https://bioconductor.org/packages/IHW")
6160 (synopsis "Independent hypothesis weighting")
6162 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
6163 procedure that increases power compared to the method of Benjamini and
6164 Hochberg by assigning data-driven weights to each hypothesis. The input to
6165 IHW is a two-column table of p-values and covariates. The covariate can be
6166 any continuous-valued or categorical variable that is thought to be
6167 informative on the statistical properties of each hypothesis test, while it is
6168 independent of the p-value under the null hypothesis.")
6169 (license license:artistic2.0)))
6171 (define-public r-icobra
6178 (uri (bioconductor-uri "iCOBRA" version))
6181 "190rkx3sivj68in36hhin5v535yd6fvlvm7l90w1bl38zpb7p6jn"))))
6182 (properties `((upstream-name . "iCOBRA")))
6183 (build-system r-build-system)
6185 `(("r-dplyr" ,r-dplyr)
6187 ("r-ggplot2" ,r-ggplot2)
6188 ("r-limma" ,r-limma)
6189 ("r-reshape2" ,r-reshape2)
6191 ("r-scales" ,r-scales)
6192 ("r-shiny" ,r-shiny)
6193 ("r-shinybs" ,r-shinybs)
6194 ("r-shinydashboard" ,r-shinydashboard)
6195 ("r-upsetr" ,r-upsetr)))
6197 `(("r-knitr" ,r-knitr)))
6198 (home-page "https://bioconductor.org/packages/iCOBRA")
6199 (synopsis "Comparison and visualization of ranking and assignment methods")
6201 "This package provides functions for calculation and visualization of
6202 performance metrics for evaluation of ranking and binary
6203 classification (assignment) methods. It also contains a Shiny application for
6204 interactive exploration of results.")
6205 (license license:gpl2+)))
6207 (define-public r-mast
6214 (uri (bioconductor-uri "MAST" version))
6217 "1gkpagam5rap36viyr3n4psa658x9vckrxap1h67jasiiyrcfz2d"))))
6218 (properties `((upstream-name . "MAST")))
6219 (build-system r-build-system)
6221 `(("r-abind" ,r-abind)
6222 ("r-biobase" ,r-biobase)
6223 ("r-biocgenerics" ,r-biocgenerics)
6224 ("r-data-table" ,r-data-table)
6225 ("r-ggplot2" ,r-ggplot2)
6227 ("r-progress" ,r-progress)
6228 ("r-reshape2" ,r-reshape2)
6229 ("r-s4vectors" ,r-s4vectors)
6230 ("r-singlecellexperiment" ,r-singlecellexperiment)
6231 ("r-stringr" ,r-stringr)
6232 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6234 `(("r-knitr" ,r-knitr)))
6235 (home-page "https://github.com/RGLab/MAST/")
6236 (synopsis "Model-based analysis of single cell transcriptomics")
6238 "This package provides methods and models for handling zero-inflated
6239 single cell assay data.")
6240 (license license:gpl2+)))
6242 (define-public r-monocle
6249 (uri (bioconductor-uri "monocle" version))
6252 "05j1vc51f39xalggdq27y7218gkr3zq7fh7jhzsb4jj7fpn837ry"))))
6253 (build-system r-build-system)
6255 `(("r-biobase" ,r-biobase)
6256 ("r-biocgenerics" ,r-biocgenerics)
6257 ("r-biocviews" ,r-biocviews)
6258 ("r-cluster" ,r-cluster)
6259 ("r-combinat" ,r-combinat)
6260 ("r-ddrtree" ,r-ddrtree)
6261 ("r-densityclust" ,r-densityclust)
6262 ("r-dplyr" ,r-dplyr)
6263 ("r-fastica" ,r-fastica)
6264 ("r-ggplot2" ,r-ggplot2)
6265 ("r-hsmmsinglecell" ,r-hsmmsinglecell)
6266 ("r-igraph" ,r-igraph)
6267 ("r-irlba" ,r-irlba)
6268 ("r-limma" ,r-limma)
6270 ("r-matrix" ,r-matrix)
6271 ("r-matrixstats" ,r-matrixstats)
6272 ("r-pheatmap" ,r-pheatmap)
6274 ("r-proxy" ,r-proxy)
6275 ("r-qlcmatrix" ,r-qlcmatrix)
6278 ("r-reshape2" ,r-reshape2)
6279 ("r-rtsne" ,r-rtsne)
6281 ("r-stringr" ,r-stringr)
6282 ("r-tibble" ,r-tibble)
6284 ("r-viridis" ,r-viridis)))
6286 `(("r-knitr" ,r-knitr)))
6287 (home-page "https://bioconductor.org/packages/monocle")
6288 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
6290 "Monocle performs differential expression and time-series analysis for
6291 single-cell expression experiments. It orders individual cells according to
6292 progress through a biological process, without knowing ahead of time which
6293 genes define progress through that process. Monocle also performs
6294 differential expression analysis, clustering, visualization, and other useful
6295 tasks on single cell expression data. It is designed to work with RNA-Seq and
6296 qPCR data, but could be used with other types as well.")
6297 (license license:artistic2.0)))
6299 (define-public r-monocle3
6307 (url "https://github.com/cole-trapnell-lab/monocle3")
6309 (file-name (git-file-name name version))
6312 "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls"))))
6313 (build-system r-build-system)
6315 `(("r-biobase" ,r-biobase)
6316 ("r-biocgenerics" ,r-biocgenerics)
6317 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
6318 ("r-dplyr" ,r-dplyr)
6319 ("r-ggplot2" ,r-ggplot2)
6320 ("r-ggrepel" ,r-ggrepel)
6322 ("r-htmlwidgets" ,r-htmlwidgets)
6323 ("r-igraph" ,r-igraph)
6324 ("r-irlba" ,r-irlba)
6325 ("r-limma" ,r-limma)
6326 ("r-lmtest" ,r-lmtest)
6328 ("r-matrix" ,r-matrix)
6329 ("r-matrix-utils" ,r-matrix-utils)
6330 ("r-pbapply" ,r-pbapply)
6331 ("r-pbmcapply" ,r-pbmcapply)
6332 ("r-pheatmap" ,r-pheatmap)
6333 ("r-plotly" ,r-plotly)
6335 ("r-proxy" ,r-proxy)
6337 ("r-purrr" ,r-purrr)
6340 ("r-rcppparallel" ,r-rcppparallel)
6341 ("r-reshape2" ,r-reshape2)
6342 ("r-reticulate" ,r-reticulate)
6343 ("r-rhpcblasctl" ,r-rhpcblasctl)
6344 ("r-rtsne" ,r-rtsne)
6345 ("r-shiny" ,r-shiny)
6347 ("r-spdep" ,r-spdep)
6348 ("r-speedglm" ,r-speedglm)
6349 ("r-stringr" ,r-stringr)
6350 ("r-singlecellexperiment" ,r-singlecellexperiment)
6351 ("r-tibble" ,r-tibble)
6352 ("r-tidyr" ,r-tidyr)
6354 ("r-viridis" ,r-viridis)))
6355 (home-page "https://github.com/cole-trapnell-lab/monocle3")
6356 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
6358 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
6359 (license license:expat)))
6361 (define-public r-noiseq
6368 (uri (bioconductor-uri "NOISeq" version))
6371 "18d51dv2ygsm7kkwal341f1wrwrazyns0045j00vld367kic8jiz"))))
6372 (properties `((upstream-name . "NOISeq")))
6373 (build-system r-build-system)
6375 `(("r-biobase" ,r-biobase)
6376 ("r-matrix" ,r-matrix)))
6377 (home-page "https://bioconductor.org/packages/NOISeq")
6378 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
6380 "This package provides tools to support the analysis of RNA-seq
6381 expression data or other similar kind of data. It provides exploratory plots
6382 to evaluate saturation, count distribution, expression per chromosome, type of
6383 detected features, features length, etc. It also supports the analysis of
6384 differential expression between two experimental conditions with no parametric
6386 (license license:artistic2.0)))
6388 (define-public r-scdd
6395 (uri (bioconductor-uri "scDD" version))
6398 "1dw9m3m99apmbs32461c6lnmy81n5hxbhz3p8jk419gajkh4v1ji"))))
6399 (properties `((upstream-name . "scDD")))
6400 (build-system r-build-system)
6403 ("r-biocparallel" ,r-biocparallel)
6404 ("r-ebseq" ,r-ebseq)
6405 ("r-fields" ,r-fields)
6406 ("r-ggplot2" ,r-ggplot2)
6407 ("r-mclust" ,r-mclust)
6408 ("r-outliers" ,r-outliers)
6409 ("r-s4vectors" ,r-s4vectors)
6410 ("r-scran" ,r-scran)
6411 ("r-singlecellexperiment" ,r-singlecellexperiment)
6412 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6414 `(("r-knitr" ,r-knitr)))
6415 (home-page "https://github.com/kdkorthauer/scDD")
6416 (synopsis "Mixture modeling of single-cell RNA-seq data")
6418 "This package implements a method to analyze single-cell RNA-seq data
6419 utilizing flexible Dirichlet Process mixture models. Genes with differential
6420 distributions of expression are classified into several interesting patterns
6421 of differences between two conditions. The package also includes functions
6422 for simulating data with these patterns from negative binomial
6424 (license license:gpl2)))
6426 (define-public r-scone
6433 (uri (bioconductor-uri "scone" version))
6436 "1wlky6nkdpz8fya81l6zaxlxc30wyp2gkyh94y5995jwddll38z5"))))
6437 (build-system r-build-system)
6439 `(("r-aroma-light" ,r-aroma-light)
6440 ("r-biocparallel" ,r-biocparallel)
6442 ("r-class" ,r-class)
6443 ("r-cluster" ,r-cluster)
6444 ("r-compositions" ,r-compositions)
6445 ("r-diptest" ,r-diptest)
6446 ("r-edger" ,r-edger)
6448 ("r-gplots" ,r-gplots)
6449 ("r-hexbin" ,r-hexbin)
6450 ("r-limma" ,r-limma)
6451 ("r-matrixgenerics" ,r-matrixgenerics)
6452 ("r-matrixstats" ,r-matrixstats)
6453 ("r-mixtools" ,r-mixtools)
6454 ("r-rarpack" ,r-rarpack)
6455 ("r-rcolorbrewer" ,r-rcolorbrewer)
6456 ("r-rhdf5" ,r-rhdf5)
6457 ("r-ruvseq" ,r-ruvseq)
6458 ("r-singlecellexperiment" ,r-singlecellexperiment)
6459 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6461 `(("r-knitr" ,r-knitr)))
6462 (home-page "https://bioconductor.org/packages/scone")
6463 (synopsis "Single cell overview of normalized expression data")
6465 "SCONE is an R package for comparing and ranking the performance of
6466 different normalization schemes for single-cell RNA-seq and other
6467 high-throughput analyses.")
6468 (license license:artistic2.0)))
6470 (define-public r-geoquery
6477 (uri (bioconductor-uri "GEOquery" version))
6480 "0jhkdbcd03d5n8vn3xkad6f21xjkawyxc9rdwcj8vwc8alx730am"))))
6481 (properties `((upstream-name . "GEOquery")))
6482 (build-system r-build-system)
6484 `(("r-biobase" ,r-biobase)
6485 ("r-dplyr" ,r-dplyr)
6487 ("r-limma" ,r-limma)
6488 ("r-magrittr" ,r-magrittr)
6489 ("r-readr" ,r-readr)
6490 ("r-tidyr" ,r-tidyr)
6491 ("r-xml2" ,r-xml2)))
6493 `(("r-knitr" ,r-knitr)))
6494 (home-page "https://github.com/seandavi/GEOquery/")
6495 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
6497 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
6498 microarray data. Given the rich and varied nature of this resource, it is
6499 only natural to want to apply BioConductor tools to these data. GEOquery is
6500 the bridge between GEO and BioConductor.")
6501 (license license:gpl2)))
6503 (define-public r-illuminaio
6505 (name "r-illuminaio")
6510 (uri (bioconductor-uri "illuminaio" version))
6513 "1sy0i3nbzsw4ymdxaiwpyx1vcg9yp3i8xfjcymqwhv95j3kyglv9"))))
6514 (build-system r-build-system)
6516 `(("r-base64" ,r-base64)))
6517 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
6518 (synopsis "Parse Illumina microarray output files")
6520 "This package provides tools for parsing Illumina's microarray output
6521 files, including IDAT.")
6522 (license license:gpl2)))
6524 (define-public r-siggenes
6531 (uri (bioconductor-uri "siggenes" version))
6534 "0lva0f255fcpy625frvij4n14q7nw4jcx8n2hlkxid4mgkfqwlhf"))))
6535 (build-system r-build-system)
6537 `(("r-biobase" ,r-biobase)
6538 ("r-multtest" ,r-multtest)
6539 ("r-scrime" ,r-scrime)))
6540 (home-page "https://bioconductor.org/packages/siggenes/")
6542 "Multiple testing using SAM and Efron's empirical Bayes approaches")
6544 "This package provides tools for the identification of differentially
6545 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
6546 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
6547 Bayes Analyses of Microarrays} (EBAM).")
6548 (license license:lgpl2.0+)))
6550 (define-public r-bumphunter
6552 (name "r-bumphunter")
6557 (uri (bioconductor-uri "bumphunter" version))
6560 "0wi38vwfi8qr10x4xifhylxx7vfc6fqvqs649iq7lf0y7islwq2v"))))
6561 (build-system r-build-system)
6563 `(("r-annotationdbi" ,r-annotationdbi)
6564 ("r-biocgenerics" ,r-biocgenerics)
6565 ("r-dorng" ,r-dorng)
6566 ("r-foreach" ,r-foreach)
6567 ("r-genomeinfodb" ,r-genomeinfodb)
6568 ("r-genomicfeatures" ,r-genomicfeatures)
6569 ("r-genomicranges" ,r-genomicranges)
6570 ("r-iranges" ,r-iranges)
6571 ("r-iterators" ,r-iterators)
6572 ("r-limma" ,r-limma)
6573 ("r-locfit" ,r-locfit)
6574 ("r-matrixstats" ,r-matrixstats)
6575 ("r-s4vectors" ,r-s4vectors)))
6576 (home-page "https://github.com/ririzarr/bumphunter")
6577 (synopsis "Find bumps in genomic data")
6579 "This package provides tools for finding bumps in genomic data in order
6580 to identify differentially methylated regions in epigenetic epidemiology
6582 (license license:artistic2.0)))
6584 (define-public r-minfi
6591 (uri (bioconductor-uri "minfi" version))
6594 "189lzppvrz6bw2kpppawgsfjyh2ahyy8bi9z8srpas67qf2r8jmj"))))
6595 (build-system r-build-system)
6597 `(("r-beanplot" ,r-beanplot)
6598 ("r-biobase" ,r-biobase)
6599 ("r-biocgenerics" ,r-biocgenerics)
6600 ("r-biocparallel" ,r-biocparallel)
6601 ("r-biostrings" ,r-biostrings)
6602 ("r-bumphunter" ,r-bumphunter)
6603 ("r-data-table" ,r-data-table)
6604 ("r-delayedarray" ,r-delayedarray)
6605 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
6606 ("r-genefilter" ,r-genefilter)
6607 ("r-genomeinfodb" ,r-genomeinfodb)
6608 ("r-genomicranges" ,r-genomicranges)
6609 ("r-geoquery" ,r-geoquery)
6610 ("r-hdf5array" ,r-hdf5array)
6611 ("r-illuminaio" ,r-illuminaio)
6612 ("r-iranges" ,r-iranges)
6613 ("r-lattice" ,r-lattice)
6614 ("r-limma" ,r-limma)
6616 ("r-mclust" ,r-mclust)
6618 ("r-nor1mix" ,r-nor1mix)
6619 ("r-preprocesscore" ,r-preprocesscore)
6620 ("r-quadprog" ,r-quadprog)
6621 ("r-rcolorbrewer" ,r-rcolorbrewer)
6622 ("r-reshape" ,r-reshape)
6623 ("r-s4vectors" ,r-s4vectors)
6624 ("r-siggenes" ,r-siggenes)
6625 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6627 `(("r-knitr" ,r-knitr)))
6628 (home-page "https://github.com/hansenlab/minfi")
6629 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
6631 "This package provides tools to analyze and visualize Illumina Infinium
6632 methylation arrays.")
6633 (license license:artistic2.0)))
6635 (define-public r-methylumi
6637 (name "r-methylumi")
6642 (uri (bioconductor-uri "methylumi" version))
6645 "1941rc524ssx8gwhmwk40mgfrhddfs6hgldvs7bi22r29gm4y7qj"))))
6646 (build-system r-build-system)
6648 `(("r-annotate" ,r-annotate)
6649 ("r-annotationdbi" ,r-annotationdbi)
6650 ("r-biobase" ,r-biobase)
6651 ("r-biocgenerics" ,r-biocgenerics)
6652 ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19)
6653 ("r-genefilter" ,r-genefilter)
6654 ("r-genomeinfodb" ,r-genomeinfodb)
6655 ("r-genomicranges" ,r-genomicranges)
6656 ("r-ggplot2" ,r-ggplot2)
6657 ("r-illuminaio" ,r-illuminaio)
6658 ("r-iranges" ,r-iranges)
6659 ("r-lattice" ,r-lattice)
6660 ("r-matrixstats" ,r-matrixstats)
6661 ("r-minfi" ,r-minfi)
6662 ("r-reshape2" ,r-reshape2)
6663 ("r-s4vectors" ,r-s4vectors)
6664 ("r-scales" ,r-scales)
6665 ("r-summarizedexperiment" ,r-summarizedexperiment)))
6667 `(("r-knitr" ,r-knitr)))
6668 (home-page "https://bioconductor.org/packages/methylumi")
6669 (synopsis "Handle Illumina methylation data")
6671 "This package provides classes for holding and manipulating Illumina
6672 methylation data. Based on eSet, it can contain MIAME information, sample
6673 information, feature information, and multiple matrices of data. An
6674 \"intelligent\" import function, methylumiR can read the Illumina text files
6675 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
6676 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
6677 background correction, and quality control features for GoldenGate, Infinium,
6678 and Infinium HD arrays are also included.")
6679 (license license:gpl2)))
6681 (define-public r-lumi
6688 (uri (bioconductor-uri "lumi" version))
6691 "0qjdxjdzfnnxcm07bf51v38388s5qf1i03l1sdb9jf3gxdh8yh02"))))
6692 (build-system r-build-system)
6694 `(("r-affy" ,r-affy)
6695 ("r-annotate" ,r-annotate)
6696 ("r-annotationdbi" ,r-annotationdbi)
6697 ("r-biobase" ,r-biobase)
6699 ("r-genomicfeatures" ,r-genomicfeatures)
6700 ("r-genomicranges" ,r-genomicranges)
6701 ("r-kernsmooth" ,r-kernsmooth)
6702 ("r-lattice" ,r-lattice)
6704 ("r-methylumi" ,r-methylumi)
6706 ("r-nleqslv" ,r-nleqslv)
6707 ("r-preprocesscore" ,r-preprocesscore)
6708 ("r-rsqlite" ,r-rsqlite)))
6709 (home-page "https://bioconductor.org/packages/lumi")
6710 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
6712 "The lumi package provides an integrated solution for the Illumina
6713 microarray data analysis. It includes functions of Illumina
6714 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
6715 variance stabilization, normalization and gene annotation at the probe level.
6716 It also includes the functions of processing Illumina methylation microarrays,
6717 especially Illumina Infinium methylation microarrays.")
6718 (license license:lgpl2.0+)))
6720 (define-public r-linnorm
6727 (uri (bioconductor-uri "Linnorm" version))
6730 "035hrniycqadmkwg8rmzw8szv0amhy31390izy91rfrld31v2yy7"))))
6731 (properties `((upstream-name . "Linnorm")))
6732 (build-system r-build-system)
6734 `(("r-amap" ,r-amap)
6735 ("r-apcluster" ,r-apcluster)
6736 ("r-ellipse" ,r-ellipse)
6737 ("r-fastcluster" ,r-fastcluster)
6739 ("r-ggdendro" ,r-ggdendro)
6740 ("r-ggplot2" ,r-ggplot2)
6741 ("r-gmodels" ,r-gmodels)
6742 ("r-igraph" ,r-igraph)
6743 ("r-limma" ,r-limma)
6745 ("r-mclust" ,r-mclust)
6747 ("r-rcpparmadillo" ,r-rcpparmadillo)
6748 ("r-rtsne" ,r-rtsne)
6749 ("r-statmod" ,r-statmod)
6750 ("r-vegan" ,r-vegan)
6753 `(("r-knitr" ,r-knitr)))
6754 (home-page "http://www.jjwanglab.org/Linnorm/")
6755 (synopsis "Linear model and normality based transformation method")
6757 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
6758 count data or any large scale count data. It transforms such datasets for
6759 parametric tests. In addition to the transformtion function (@code{Linnorm}),
6760 the following pipelines are implemented:
6763 @item Library size/batch effect normalization (@code{Linnorm.Norm})
6764 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
6765 clustering or hierarchical clustering (@code{Linnorm.tSNE},
6766 @code{Linnorm.PCA}, @code{Linnorm.HClust})
6767 @item Differential expression analysis or differential peak detection using
6768 limma (@code{Linnorm.limma})
6769 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
6770 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
6771 @item Stable gene selection for scRNA-seq data; for users without or who do
6772 not want to rely on spike-in genes (@code{Linnorm.SGenes})
6773 @item Data imputation (@code{Linnorm.DataImput}).
6776 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
6777 @code{RnaXSim} function is included for simulating RNA-seq data for the
6778 evaluation of DEG analysis methods.")
6779 (license license:expat)))
6781 (define-public r-ioniser
6788 (uri (bioconductor-uri "IONiseR" version))
6791 "0fknlwdfd49v09zspg0337b0zzc8hqza3563yrw51viw3g35d6q3"))))
6792 (properties `((upstream-name . "IONiseR")))
6793 (build-system r-build-system)
6795 `(("r-biocgenerics" ,r-biocgenerics)
6796 ("r-biocparallel" ,r-biocparallel)
6797 ("r-biostrings" ,r-biostrings)
6798 ("r-bit64" ,r-bit64)
6799 ("r-dplyr" ,r-dplyr)
6800 ("r-ggplot2" ,r-ggplot2)
6801 ("r-magrittr" ,r-magrittr)
6802 ("r-rhdf5" ,r-rhdf5)
6803 ("r-shortread" ,r-shortread)
6804 ("r-stringr" ,r-stringr)
6805 ("r-tibble" ,r-tibble)
6806 ("r-tidyr" ,r-tidyr)
6807 ("r-xvector" ,r-xvector)))
6809 `(("r-knitr" ,r-knitr)))
6810 (home-page "https://bioconductor.org/packages/IONiseR/")
6811 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
6813 "IONiseR provides tools for the quality assessment of Oxford Nanopore
6814 MinION data. It extracts summary statistics from a set of fast5 files and can
6815 be used either before or after base calling. In addition to standard
6816 summaries of the read-types produced, it provides a number of plots for
6817 visualising metrics relative to experiment run time or spatially over the
6818 surface of a flowcell.")
6819 (license license:expat)))
6821 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
6822 (define-public r-mutoss
6829 (uri (cran-uri "mutoss" version))
6832 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
6833 (properties `((upstream-name . "mutoss")))
6834 (build-system r-build-system)
6836 `(("r-multcomp" ,r-multcomp)
6837 ("r-multtest" ,r-multtest)
6838 ("r-mvtnorm" ,r-mvtnorm)
6839 ("r-plotrix" ,r-plotrix)))
6840 (home-page "https://github.com/kornl/mutoss/")
6841 (synopsis "Unified multiple testing procedures")
6843 "This package is designed to ease the application and comparison of
6844 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
6845 are standardized and usable by the accompanying mutossGUI package.")
6846 ;; Any version of the GPL.
6847 (license (list license:gpl2+ license:gpl3+))))
6849 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
6850 ;; from Bioconductor, so we put it here.
6851 (define-public r-metap
6858 (uri (cran-uri "metap" version))
6861 "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz"))))
6862 (build-system r-build-system)
6864 `(("r-lattice" ,r-lattice)
6865 ("r-mutoss" ,r-mutoss)
6866 ("r-rdpack" ,r-rdpack)
6867 ("r-tfisher" ,r-tfisher)))
6868 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
6869 (synopsis "Meta-analysis of significance values")
6871 "The canonical way to perform meta-analysis involves using effect sizes.
6872 When they are not available this package provides a number of methods for
6873 meta-analysis of significance values including the methods of Edgington,
6874 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
6875 published results; and a routine for graphical display.")
6876 (license license:gpl2)))
6878 (define-public r-tradeseq
6884 (uri (bioconductor-uri "tradeSeq" version))
6887 "0fgmb309pvqf3chdhqgbd4lzhahcj5g71sica33nzn98qhipldx7"))))
6888 (build-system r-build-system)
6890 `(("r-biobase" ,r-biobase)
6891 ("r-biocparallel" ,r-biocparallel)
6892 ("r-edger" ,r-edger)
6893 ("r-ggplot2" ,r-ggplot2)
6894 ("r-igraph" ,r-igraph)
6895 ("r-magrittr" ,r-magrittr)
6896 ("r-matrix" ,r-matrix)
6897 ("r-matrixstats" ,r-matrixstats)
6899 ("r-monocle" ,r-monocle)
6900 ("r-pbapply" ,r-pbapply)
6901 ("r-princurve" ,r-princurve)
6902 ("r-rcolorbrewer" ,r-rcolorbrewer)
6903 ("r-s4vectors" ,r-s4vectors)
6904 ("r-singlecellexperiment" ,r-singlecellexperiment)
6905 ("r-slingshot" ,r-slingshot)
6906 ("r-summarizedexperiment" ,r-summarizedexperiment)
6907 ("r-tibble" ,r-tibble)
6908 ("r-viridis" ,r-viridis)))
6910 `(("r-knitr" ,r-knitr)))
6911 (home-page "https://statomics.github.io/tradeSeq/index.html")
6912 (synopsis "Trajectory-based differential expression analysis")
6914 "This package provides a flexible method for fitting regression models that
6915 can be used to find genes that are differentially expressed along one or
6916 multiple lineages in a trajectory. Based on the fitted models, it uses a
6917 variety of tests suited to answer different questions of interest, e.g. the
6918 discovery of genes for which expression is associated with pseudotime, or which
6919 are differentially expressed (in a specific region) along the trajectory. It
6920 fits a negative binomial generalized additive model (GAM) for each gene, and
6921 performs inference on the parameters of the GAM.")
6922 (license license:expat)))
6924 (define-public r-triform
6931 (uri (bioconductor-uri "triform" version))
6934 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
6935 (build-system r-build-system)
6937 `(("r-biocgenerics" ,r-biocgenerics)
6938 ("r-iranges" ,r-iranges)
6939 ("r-yaml" ,r-yaml)))
6940 (home-page "https://bioconductor.org/packages/triform/")
6941 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
6943 "The Triform algorithm uses model-free statistics to identify peak-like
6944 distributions of TF ChIP sequencing reads, taking advantage of an improved
6945 peak definition in combination with known profile characteristics.")
6946 (license license:gpl2)))
6948 (define-public r-varianttools
6950 (name "r-varianttools")
6955 (uri (bioconductor-uri "VariantTools" version))
6958 "1gpzrln2clfrja8rzxhsis6bi1xqglh3h2lhvqlnrx4lqxhbkv9c"))))
6959 (properties `((upstream-name . "VariantTools")))
6960 (build-system r-build-system)
6962 `(("r-biobase" ,r-biobase)
6963 ("r-biocgenerics" ,r-biocgenerics)
6964 ("r-biocparallel" ,r-biocparallel)
6965 ("r-biostrings" ,r-biostrings)
6966 ("r-bsgenome" ,r-bsgenome)
6967 ("r-genomeinfodb" ,r-genomeinfodb)
6968 ("r-genomicfeatures" ,r-genomicfeatures)
6969 ("r-genomicranges" ,r-genomicranges)
6970 ("r-iranges" ,r-iranges)
6971 ("r-matrix" ,r-matrix)
6972 ("r-rsamtools" ,r-rsamtools)
6973 ("r-rtracklayer" ,r-rtracklayer)
6974 ("r-s4vectors" ,r-s4vectors)
6975 ("r-variantannotation" ,r-variantannotation)))
6976 (home-page "https://bioconductor.org/packages/VariantTools/")
6977 (synopsis "Tools for exploratory analysis of variant calls")
6979 "Explore, diagnose, and compare variant calls using filters. The
6980 VariantTools package supports a workflow for loading data, calling single
6981 sample variants and tumor-specific somatic mutations or other sample-specific
6982 variant types (e.g., RNA editing). Most of the functions operate on
6983 alignments (BAM files) or datasets of called variants. The user is expected
6984 to have already aligned the reads with a separate tool, e.g., GSNAP via
6986 (license license:artistic2.0)))
6988 (define-public r-heatplus
6995 (uri (bioconductor-uri "Heatplus" version))
6998 "0xwg3sxmihg3p6v3nxgrqy0nrqxi6razg3b3rjh2gcb2vv8gcqng"))))
6999 (properties `((upstream-name . "Heatplus")))
7000 (build-system r-build-system)
7002 `(("r-rcolorbrewer" ,r-rcolorbrewer)))
7003 (home-page "https://github.com/alexploner/Heatplus")
7004 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
7006 "This package provides tools to display a rectangular heatmap (intensity
7007 plot) of a data matrix. By default, both samples (columns) and features (row)
7008 of the matrix are sorted according to a hierarchical clustering, and the
7009 corresponding dendrogram is plotted. Optionally, panels with additional
7010 information about samples and features can be added to the plot.")
7011 (license license:gpl2+)))
7013 (define-public r-gosemsim
7020 (uri (bioconductor-uri "GOSemSim" version))
7023 "1fzmaxjzyvq6xj5ny1sjijdwi4krzjgyaz52fczpwrxijq5pnyn1"))))
7024 (properties `((upstream-name . "GOSemSim")))
7025 (build-system r-build-system)
7027 `(("r-annotationdbi" ,r-annotationdbi)
7028 ("r-go-db" ,r-go-db)
7029 ("r-rcpp" ,r-rcpp)))
7031 `(("r-knitr" ,r-knitr)))
7032 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
7033 (synopsis "GO-terms semantic similarity measures")
7035 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
7036 quantitative ways to compute similarities between genes and gene groups, and
7037 have became important basis for many bioinformatics analysis approaches.
7038 GOSemSim is an R package for semantic similarity computation among GO terms,
7039 sets of GO terms, gene products and gene clusters.")
7040 (license license:artistic2.0)))
7042 (define-public r-anota
7049 (uri (bioconductor-uri "anota" version))
7052 "039bmcv5l44gszb6xapbihp3mfqdaaa8mfc05y702p78i7x93g5y"))))
7053 (build-system r-build-system)
7055 `(("r-multtest" ,r-multtest)
7056 ("r-qvalue" ,r-qvalue)))
7057 (home-page "https://bioconductor.org/packages/anota/")
7058 (synopsis "Analysis of translational activity")
7060 "Genome wide studies of translational control is emerging as a tool to
7061 study various biological conditions. The output from such analysis is both
7062 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
7063 involved in translation (the actively translating mRNA level) for each mRNA.
7064 The standard analysis of such data strives towards identifying differential
7065 translational between two or more sample classes - i.e. differences in
7066 actively translated mRNA levels that are independent of underlying differences
7067 in cytosolic mRNA levels. This package allows for such analysis using partial
7068 variances and the random variance model. As 10s of thousands of mRNAs are
7069 analyzed in parallel the library performs a number of tests to assure that
7070 the data set is suitable for such analysis.")
7071 (license license:gpl3)))
7073 (define-public r-sigpathway
7075 (name "r-sigpathway")
7080 (uri (bioconductor-uri "sigPathway" version))
7083 "1xz5nbw5dzyah8az7mpwj8m27fsvpi2jjhfg3n27dsv8rvdncqi8"))))
7084 (properties `((upstream-name . "sigPathway")))
7085 (build-system r-build-system)
7086 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
7087 (synopsis "Pathway analysis")
7089 "This package is used to conduct pathway analysis by calculating the NT_k
7090 and NE_k statistics in a statistical framework for determining whether a
7091 specified group of genes for a pathway has a coordinated association with a
7092 phenotype of interest.")
7093 (license license:gpl2)))
7095 (define-public r-fgsea
7102 (uri (bioconductor-uri "fgsea" version))
7105 "1mhdgy46nxgv7v54bk9bqfy0vgjzl1law7zy718swdd762xn6g9d"))))
7106 (build-system r-build-system)
7109 ("r-biocparallel" ,r-biocparallel)
7110 ("r-data-table" ,r-data-table)
7111 ("r-fastmatch" ,r-fastmatch)
7112 ("r-ggplot2" ,r-ggplot2)
7113 ("r-gridextra" ,r-gridextra)
7114 ("r-matrix" ,r-matrix)
7115 ("r-rcpp" ,r-rcpp)))
7117 `(("r-knitr" ,r-knitr)))
7118 (home-page "https://github.com/ctlab/fgsea/")
7119 (synopsis "Fast gene set enrichment analysis")
7121 "The package implements an algorithm for fast gene set enrichment
7122 analysis. Using the fast algorithm makes more permutations and gets
7123 more fine grained p-values, which allows using accurate standard approaches
7124 to multiple hypothesis correction.")
7125 (license license:expat)))
7127 (define-public r-dose
7134 (uri (bioconductor-uri "DOSE" version))
7137 "1x9cg6qlvbcdb965jh01w07ibc4lj30ikq1v312rdih3sn6zsdck"))))
7138 (properties `((upstream-name . "DOSE")))
7139 (build-system r-build-system)
7141 `(("r-annotationdbi" ,r-annotationdbi)
7142 ("r-biocparallel" ,r-biocparallel)
7143 ("r-do-db" ,r-do-db)
7144 ("r-fgsea" ,r-fgsea)
7145 ("r-ggplot2" ,r-ggplot2)
7146 ("r-gosemsim" ,r-gosemsim)
7147 ("r-qvalue" ,r-qvalue)
7148 ("r-reshape2" ,r-reshape2)))
7150 `(("r-knitr" ,r-knitr)))
7151 (home-page "https://guangchuangyu.github.io/software/DOSE/")
7152 (synopsis "Disease ontology semantic and enrichment analysis")
7154 "This package implements five methods proposed by Resnik, Schlicker,
7155 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
7156 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
7157 including hypergeometric model and gene set enrichment analysis are also
7158 implemented for discovering disease associations of high-throughput biological
7160 (license license:artistic2.0)))
7162 (define-public r-enrichplot
7164 (name "r-enrichplot")
7169 (uri (bioconductor-uri "enrichplot" version))
7172 "0nvjwwzpmhsfkxqrn8v1a1wcrvr3xl1wn5dy89vsrdydyv31gdc6"))))
7173 (build-system r-build-system)
7175 `(("r-cowplot" ,r-cowplot)
7177 ("r-ggplot2" ,r-ggplot2)
7178 ("r-ggraph" ,r-ggraph)
7179 ("r-ggtree" ,r-ggtree)
7180 ("r-gosemsim" ,r-gosemsim)
7181 ("r-igraph" ,r-igraph)
7182 ("r-magrittr" ,r-magrittr)
7184 ("r-purrr" ,r-purrr)
7185 ("r-rcolorbrewer" ,r-rcolorbrewer)
7186 ("r-reshape2" ,r-reshape2)
7187 ("r-scatterpie" ,r-scatterpie)
7188 ("r-shadowtext" ,r-shadowtext)))
7190 `(("r-knitr" ,r-knitr)))
7191 (home-page "https://github.com/GuangchuangYu/enrichplot")
7192 (synopsis "Visualization of functional enrichment result")
7194 "The enrichplot package implements several visualization methods for
7195 interpreting functional enrichment results obtained from ORA or GSEA analyses.
7196 All the visualization methods are developed based on ggplot2 graphics.")
7197 (license license:artistic2.0)))
7199 (define-public r-clusterprofiler
7201 (name "r-clusterprofiler")
7206 (uri (bioconductor-uri "clusterProfiler" version))
7209 "1lmrb6ddpx1p3kdrwszhxq6nndmbiqipzrclk64mnp63y7g50q56"))))
7211 `((upstream-name . "clusterProfiler")))
7212 (build-system r-build-system)
7214 `(("r-annotationdbi" ,r-annotationdbi)
7216 ("r-downloader" ,r-downloader)
7217 ("r-dplyr" ,r-dplyr)
7218 ("r-enrichplot" ,r-enrichplot)
7219 ("r-go-db" ,r-go-db)
7220 ("r-gosemsim" ,r-gosemsim)
7221 ("r-magrittr" ,r-magrittr)
7223 ("r-qvalue" ,r-qvalue)
7224 ("r-rlang" ,r-rlang)
7225 ("r-rvcheck" ,r-rvcheck)
7226 ("r-tidyr" ,r-tidyr)))
7228 `(("r-knitr" ,r-knitr)))
7229 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
7230 (synopsis "Analysis and visualization of functional profiles for gene clusters")
7232 "This package implements methods to analyze and visualize functional
7233 profiles (GO and KEGG) of gene and gene clusters.")
7234 (license license:artistic2.0)))
7236 (define-public r-clusterexperiment
7238 (name "r-clusterexperiment")
7242 (uri (bioconductor-uri "clusterExperiment" version))
7245 "1fhmayciwn1m124b4dcs3gzbghgk9f7a7qmjnvvxc958cywcwkx5"))))
7246 (build-system r-build-system)
7248 `(("r-knitr" ,r-knitr)))
7251 ("r-biocgenerics" ,r-biocgenerics)
7252 ("r-biocsingular" ,r-biocsingular)
7253 ("r-cluster" ,r-cluster)
7254 ("r-delayedarray" ,r-delayedarray)
7255 ("r-edger" ,r-edger)
7256 ("r-hdf5array" ,r-hdf5array)
7257 ("r-howmany" ,r-howmany)
7258 ("r-kernlab" ,r-kernlab)
7259 ("r-limma" ,r-limma)
7260 ("r-locfdr" ,r-locfdr)
7261 ("r-matrix" ,r-matrix)
7262 ("r-matrixstats" ,r-matrixstats)
7263 ("r-mbkmeans" ,r-mbkmeans)
7265 ("r-phylobase" ,r-phylobase)
7266 ("r-pracma" ,r-pracma)
7267 ("r-rcolorbrewer" ,r-rcolorbrewer)
7269 ("r-s4vectors" ,r-s4vectors)
7270 ("r-scales" ,r-scales)
7271 ("r-singlecellexperiment" ,r-singlecellexperiment)
7272 ("r-stringr" ,r-stringr)
7273 ("r-summarizedexperiment" ,r-summarizedexperiment)
7274 ("r-zinbwave" ,r-zinbwave)))
7275 (home-page "https://bioconductor.org/packages/clusterExperiment/")
7276 (synopsis "Compare clusterings for single-cell sequencing")
7277 (description "This package provides functionality for running and comparing
7278 many different clusterings of single-cell sequencing data or other large mRNA
7279 expression data sets.")
7280 (license license:artistic2.0)))
7282 (define-public r-mlinterfaces
7284 (name "r-mlinterfaces")
7289 (uri (bioconductor-uri "MLInterfaces" version))
7292 "0ipzv7wdvfqhdyjiak956qq201igsdxm6dr6rh3dj6cssgsrnrpb"))))
7293 (properties `((upstream-name . "MLInterfaces")))
7294 (build-system r-build-system)
7296 `(("r-annotate" ,r-annotate)
7297 ("r-biobase" ,r-biobase)
7298 ("r-biocgenerics" ,r-biocgenerics)
7299 ("r-cluster" ,r-cluster)
7302 ("r-gdata" ,r-gdata)
7303 ("r-genefilter" ,r-genefilter)
7304 ("r-ggvis" ,r-ggvis)
7305 ("r-hwriter" ,r-hwriter)
7306 ("r-magrittr" ,r-magrittr)
7308 ("r-mlbench" ,r-mlbench)
7310 ("r-rcolorbrewer" ,r-rcolorbrewer)
7312 ("r-rpart" ,r-rpart)
7313 ("r-sfsmisc" ,r-sfsmisc)
7314 ("r-shiny" ,r-shiny)
7315 ("r-threejs" ,r-threejs)))
7316 (home-page "https://bioconductor.org/packages/MLInterfaces/")
7317 (synopsis "Interfaces to R machine learning procedures")
7319 "This package provides uniform interfaces to machine learning code for
7320 data in R and Bioconductor containers.")
7321 ;; Any version of the LGPL.
7322 (license license:lgpl2.1+)))
7324 (define-public r-annaffy
7331 (uri (bioconductor-uri "annaffy" version))
7334 "071qr68dn8k3mvwgpllbk2a4g6f6yyv2087q5rmpb22lkfvi4hwv"))))
7335 (build-system r-build-system)
7338 (modify-phases %standard-phases
7339 (add-after 'unpack 'remove-reference-to-non-free-data
7341 (substitute* "DESCRIPTION"
7342 ((", KEGG.db") "")))))))
7344 `(("r-annotationdbi" ,r-annotationdbi)
7345 ("r-biobase" ,r-biobase)
7346 ("r-biocmanager" ,r-biocmanager)
7348 ("r-go-db" ,r-go-db)))
7349 (home-page "https://bioconductor.org/packages/annaffy/")
7350 (synopsis "Annotation tools for Affymetrix biological metadata")
7352 "This package provides functions for handling data from Bioconductor
7353 Affymetrix annotation data packages. It produces compact HTML and text
7354 reports including experimental data and URL links to many online databases.
7355 It allows searching of biological metadata using various criteria.")
7356 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
7357 ;; the LGPL 2.1 is included.
7358 (license license:lgpl2.1+)))
7360 (define-public r-a4core
7367 (uri (bioconductor-uri "a4Core" version))
7370 "00fi753nsayv0xspavw8r9ni1sim8ng33hp3d3kj2b8ihygd1s10"))))
7371 (properties `((upstream-name . "a4Core")))
7372 (build-system r-build-system)
7374 `(("r-biobase" ,r-biobase)
7375 ("r-glmnet" ,r-glmnet)))
7377 `(("r-knitr" ,r-knitr)))
7378 (home-page "https://bioconductor.org/packages/a4Core")
7379 (synopsis "Automated Affymetrix array analysis core package")
7381 "This is the core package for the automated analysis of Affymetrix
7383 (license license:gpl3)))
7385 (define-public r-a4classif
7387 (name "r-a4classif")
7392 (uri (bioconductor-uri "a4Classif" version))
7395 "1lz85bys5dp5d1ir9c9c4wy85wkk62s14niyzzxaqrxpsji2p2iw"))))
7396 (properties `((upstream-name . "a4Classif")))
7397 (build-system r-build-system)
7399 `(("r-a4core" ,r-a4core)
7400 ("r-a4preproc" ,r-a4preproc)
7401 ("r-biobase" ,r-biobase)
7402 ("r-glmnet" ,r-glmnet)
7405 ("r-varselrf" ,r-varselrf)))
7407 `(("r-knitr" ,r-knitr)))
7408 (home-page "https://bioconductor.org/packages/a4Classif/")
7409 (synopsis "Automated Affymetrix array analysis classification package")
7411 "This is the classification package for the automated analysis of
7412 Affymetrix arrays.")
7413 (license license:gpl3)))
7415 (define-public r-a4preproc
7417 (name "r-a4preproc")
7422 (uri (bioconductor-uri "a4Preproc" version))
7425 "1jibm2f5glzsrvl64hxc5sf59d4w6ry0f663p619hfr44mi1mpri"))))
7426 (properties `((upstream-name . "a4Preproc")))
7427 (build-system r-build-system)
7429 `(("r-biobase" ,r-biobase)
7430 ("r-biocgenerics" ,r-biocgenerics)))
7432 `(("r-knitr" ,r-knitr)))
7433 (home-page "https://bioconductor.org/packages/a4Preproc/")
7434 (synopsis "Automated Affymetrix array analysis preprocessing package")
7436 "This is a package for the automated analysis of Affymetrix arrays. It
7437 is used for preprocessing the arrays.")
7438 (license license:gpl3)))
7440 (define-public r-a4reporting
7442 (name "r-a4reporting")
7447 (uri (bioconductor-uri "a4Reporting" version))
7450 "09jjfby5znmg2fdkhpbinx2v21zrfa44qq7cylcn9ipffqx3pk86"))))
7451 (properties `((upstream-name . "a4Reporting")))
7452 (build-system r-build-system)
7454 `(("r-xtable" ,r-xtable)))
7456 `(("r-knitr" ,r-knitr)))
7457 (home-page "https://bioconductor.org/packages/a4Reporting/")
7458 (synopsis "Automated Affymetrix array analysis reporting package")
7460 "This is a package for the automated analysis of Affymetrix arrays. It
7461 provides reporting features.")
7462 (license license:gpl3)))
7464 (define-public r-a4base
7471 (uri (bioconductor-uri "a4Base" version))
7474 "101w4i0w8n7qhki22qr8l8wk8w6zalzmcywqm2g4238qv7xbnr8p"))))
7475 (properties `((upstream-name . "a4Base")))
7476 (build-system r-build-system)
7478 `(("r-a4core" ,r-a4core)
7479 ("r-a4preproc" ,r-a4preproc)
7480 ("r-annaffy" ,r-annaffy)
7481 ("r-biobase" ,r-biobase)
7482 ("r-genefilter" ,r-genefilter)
7483 ("r-glmnet" ,r-glmnet)
7484 ("r-gplots" ,r-gplots)
7485 ("r-limma" ,r-limma)
7487 ("r-multtest" ,r-multtest)))
7488 (home-page "https://bioconductor.org/packages/a4Base/")
7489 (synopsis "Automated Affymetrix array analysis base package")
7491 "This package provides basic features for the automated analysis of
7492 Affymetrix arrays.")
7493 (license license:gpl3)))
7502 (uri (bioconductor-uri "a4" version))
7505 "0bwn185admy5k99fkd2dhhvy7x1f75r0mqn5k24dbbg0paw6nnr8"))))
7506 (build-system r-build-system)
7508 `(("r-a4base" ,r-a4base)
7509 ("r-a4classif" ,r-a4classif)
7510 ("r-a4core" ,r-a4core)
7511 ("r-a4preproc" ,r-a4preproc)
7512 ("r-a4reporting" ,r-a4reporting)))
7513 (home-page "https://bioconductor.org/packages/a4/")
7514 (synopsis "Automated Affymetrix array analysis umbrella package")
7516 "This package provides a software suite for the automated analysis of
7517 Affymetrix arrays.")
7518 (license license:gpl3)))
7520 (define-public r-abseqr
7527 (uri (bioconductor-uri "abseqR" version))
7530 "1xvk84gd1lfq1icrfwwd6y79zywrisfnc3knprigzzax31aks32c"))))
7531 (properties `((upstream-name . "abseqR")))
7532 (build-system r-build-system)
7534 `(("pandoc" ,pandoc)))
7536 `(("r-biocparallel" ,r-biocparallel)
7537 ("r-biocstyle" ,r-biocstyle)
7538 ("r-circlize" ,r-circlize)
7539 ("r-flexdashboard" ,r-flexdashboard)
7540 ("r-ggcorrplot" ,r-ggcorrplot)
7541 ("r-ggdendro" ,r-ggdendro)
7542 ("r-ggplot2" ,r-ggplot2)
7543 ("r-gridextra" ,r-gridextra)
7544 ("r-knitr" ,r-knitr)
7545 ("r-plotly" ,r-plotly)
7548 ("r-rcolorbrewer" ,r-rcolorbrewer)
7549 ("r-reshape2" ,r-reshape2)
7550 ("r-rmarkdown" ,r-rmarkdown)
7551 ("r-stringr" ,r-stringr)
7552 ("r-vegan" ,r-vegan)
7553 ("r-venndiagram" ,r-venndiagram)))
7555 `(("r-knitr" ,r-knitr)))
7556 (home-page "https://github.com/malhamdoosh/abseqR")
7557 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
7559 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
7560 sequencing datasets generated from antibody libraries and abseqR is one of its
7561 packages. AbseqR empowers the users of abseqPy with plotting and reporting
7562 capabilities and allows them to generate interactive HTML reports for the
7563 convenience of viewing and sharing with other researchers. Additionally,
7564 abseqR extends abseqPy to compare multiple repertoire analyses and perform
7565 further downstream analysis on its output.")
7566 (license license:gpl3)))
7568 (define-public r-bacon
7575 (uri (bioconductor-uri "bacon" version))
7578 "1yp0675n1g8rxdjdd7w8al5c9jq96h0kfm8218mc50z0p2fasgbj"))))
7579 (build-system r-build-system)
7581 `(("r-biocparallel" ,r-biocparallel)
7582 ("r-ellipse" ,r-ellipse)
7583 ("r-ggplot2" ,r-ggplot2)))
7585 `(("r-knitr" ,r-knitr)))
7586 (home-page "https://bioconductor.org/packages/bacon/")
7587 (synopsis "Controlling bias and inflation in association studies")
7589 "Bacon can be used to remove inflation and bias often observed in
7590 epigenome- and transcriptome-wide association studies. To this end bacon
7591 constructs an empirical null distribution using a Gibbs Sampling algorithm by
7592 fitting a three-component normal mixture on z-scores.")
7593 (license license:gpl2+)))
7595 (define-public r-rgadem
7602 (uri (bioconductor-uri "rGADEM" version))
7605 "05drbhjqn5kik6k4h03vr3d2b6pv5rm65lsnkyx4caxxcdii4jzm"))))
7606 (properties `((upstream-name . "rGADEM")))
7607 (build-system r-build-system)
7609 `(("r-biostrings" ,r-biostrings)
7610 ("r-bsgenome" ,r-bsgenome)
7611 ("r-genomicranges" ,r-genomicranges)
7612 ("r-iranges" ,r-iranges)
7613 ("r-seqlogo" ,r-seqlogo)))
7614 (home-page "https://bioconductor.org/packages/rGADEM/")
7615 (synopsis "De novo sequence motif discovery")
7617 "rGADEM is an efficient de novo motif discovery tool for large-scale
7618 genomic sequence data.")
7619 (license license:artistic2.0)))
7621 (define-public r-motiv
7628 (uri (bioconductor-uri "MotIV" version))
7631 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
7632 (properties `((upstream-name . "MotIV")))
7633 (build-system r-build-system)
7637 `(("r-biocgenerics" ,r-biocgenerics)
7638 ("r-biostrings" ,r-biostrings)
7639 ("r-genomicranges" ,r-genomicranges)
7640 ("r-iranges" ,r-iranges)
7641 ("r-lattice" ,r-lattice)
7642 ("r-rgadem" ,r-rgadem)
7643 ("r-s4vectors" ,r-s4vectors)))
7644 (home-page "https://bioconductor.org/packages/MotIV/")
7645 (synopsis "Motif identification and validation")
7647 "This package is used for the identification and validation of sequence
7648 motifs. It makes use of STAMP for comparing a set of motifs to a given
7649 database (e.g. JASPAR). It can also be used to visualize motifs, motif
7650 distributions, modules and filter motifs.")
7651 (license license:gpl2)))
7653 (define-public r-motifdb
7659 (uri (bioconductor-uri "MotifDb" version))
7661 (base32 "04cmgg5mw1cqbg95zyfc2imykmdxyff16w26rq97xghcxwiq2b3z"))))
7662 (properties `((upstream-name . "MotifDb")))
7663 (build-system r-build-system)
7665 `(("r-biocgenerics" ,r-biocgenerics)
7666 ("r-biostrings" ,r-biostrings)
7667 ("r-genomicranges" ,r-genomicranges)
7668 ("r-iranges" ,r-iranges)
7669 ("r-rtracklayer" ,r-rtracklayer)
7670 ("r-s4vectors" ,r-s4vectors)
7671 ("r-splitstackshape" ,r-splitstackshape)))
7673 `(("r-knitr" ,r-knitr)))
7674 (home-page "https://www.bioconductor.org/packages/MotifDb/")
7675 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
7676 (description "This package provides more than 2000 annotated position
7677 frequency matrices from nine public sources, for multiple organisms.")
7678 (license license:artistic2.0)))
7680 (define-public r-motifbreakr
7682 (name "r-motifbreakr")
7686 (uri (bioconductor-uri "motifbreakR" version))
7688 (base32 "0i18qriznad4lr6ynzmz01k5yavs5m3h7hd0adbyg8lppbzm6hh4"))))
7689 (properties `((upstream-name . "motifbreakR")))
7690 (build-system r-build-system)
7692 `(("r-biocgenerics" ,r-biocgenerics)
7693 ("r-biocparallel" ,r-biocparallel)
7694 ("r-biostrings" ,r-biostrings)
7695 ("r-bsgenome" ,r-bsgenome)
7696 ("r-genomeinfodb" ,r-genomeinfodb)
7697 ("r-genomicranges" ,r-genomicranges)
7698 ("r-grimport" ,r-grimport)
7700 ("r-iranges" ,r-iranges)
7701 ("r-matrixstats" ,r-matrixstats)
7702 ("r-motifdb" ,r-motifdb)
7703 ("r-motifstack" ,r-motifstack)
7704 ("r-rtracklayer" ,r-rtracklayer)
7705 ("r-s4vectors" ,r-s4vectors)
7706 ("r-stringr" ,r-stringr)
7707 ("r-summarizedexperiment" ,r-summarizedexperiment)
7708 ("r-tfmpvalue" ,r-tfmpvalue)
7709 ("r-variantannotation" ,r-variantannotation)))
7711 `(("r-knitr" ,r-knitr)))
7712 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
7713 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
7714 (description "This package allows biologists to judge in the first place
7715 whether the sequence surrounding the polymorphism is a good match, and in
7716 the second place how much information is gained or lost in one allele of
7717 the polymorphism relative to another. This package gives a choice of
7718 algorithms for interrogation of genomes with motifs from public sources:
7720 @item a weighted-sum probability matrix;
7721 @item log-probabilities;
7722 @item weighted by relative entropy.
7725 This package can predict effects for novel or previously described variants in
7726 public databases, making it suitable for tasks beyond the scope of its original
7727 design. Lastly, it can be used to interrogate any genome curated within
7729 (license license:gpl2+)))
7731 (define-public r-motifstack
7733 (name "r-motifstack")
7738 (uri (bioconductor-uri "motifStack" version))
7741 "0yn348kmw7v46iym913ncx4yh5nxzmba8bdys52s12ldgjja53gp"))))
7742 (properties `((upstream-name . "motifStack")))
7743 (build-system r-build-system)
7745 `(("r-ade4" ,r-ade4)
7746 ("r-biostrings" ,r-biostrings)
7747 ("r-ggplot2" ,r-ggplot2)
7748 ("r-htmlwidgets" ,r-htmlwidgets)
7751 `(("r-knitr" ,r-knitr)))
7752 (home-page "https://bioconductor.org/packages/motifStack/")
7753 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
7755 "The motifStack package is designed for graphic representation of
7756 multiple motifs with different similarity scores. It works with both DNA/RNA
7757 sequence motifs and amino acid sequence motifs. In addition, it provides the
7758 flexibility for users to customize the graphic parameters such as the font
7759 type and symbol colors.")
7760 (license license:gpl2+)))
7762 (define-public r-genomicscores
7764 (name "r-genomicscores")
7769 (uri (bioconductor-uri "GenomicScores" version))
7772 "1b8982fj0r7igj749wljsdfn3c985w8n3d5gbhr5rw73llfb8x6w"))))
7773 (properties `((upstream-name . "GenomicScores")))
7774 (build-system r-build-system)
7776 `(("r-annotationhub" ,r-annotationhub)
7777 ("r-biobase" ,r-biobase)
7778 ("r-biocfilecache" ,r-biocfilecache)
7779 ("r-biocgenerics" ,r-biocgenerics)
7780 ("r-biocmanager" ,r-biocmanager)
7781 ("r-biostrings" ,r-biostrings)
7782 ("r-delayedarray" ,r-delayedarray)
7783 ("r-genomeinfodb" ,r-genomeinfodb)
7784 ("r-genomicranges" ,r-genomicranges)
7785 ("r-hdf5array" ,r-hdf5array)
7786 ("r-iranges" ,r-iranges)
7787 ("r-rhdf5" ,r-rhdf5)
7788 ("r-s4vectors" ,r-s4vectors)
7791 `(("r-knitr" ,r-knitr)))
7792 (home-page "https://github.com/rcastelo/GenomicScores/")
7793 (synopsis "Work with genome-wide position-specific scores")
7795 "This package provides infrastructure to store and access genome-wide
7796 position-specific scores within R and Bioconductor.")
7797 (license license:artistic2.0)))
7799 (define-public r-atacseqqc
7801 (name "r-atacseqqc")
7806 (uri (bioconductor-uri "ATACseqQC" version))
7809 "168g3xkhjzrfjpa1ynifdyfhsxx3rpyrbybsarlzr9kslw1cdkxl"))))
7810 (properties `((upstream-name . "ATACseqQC")))
7811 (build-system r-build-system)
7813 `(("r-biocgenerics" ,r-biocgenerics)
7814 ("r-biostrings" ,r-biostrings)
7815 ("r-bsgenome" ,r-bsgenome)
7816 ("r-chippeakanno" ,r-chippeakanno)
7817 ("r-edger" ,r-edger)
7818 ("r-genomeinfodb" ,r-genomeinfodb)
7819 ("r-genomicalignments" ,r-genomicalignments)
7820 ("r-genomicranges" ,r-genomicranges)
7821 ("r-genomicscores" ,r-genomicscores)
7822 ("r-iranges" ,r-iranges)
7823 ("r-kernsmooth" ,r-kernsmooth)
7824 ("r-limma" ,r-limma)
7825 ("r-motifstack" ,r-motifstack)
7826 ("r-preseqr" ,r-preseqr)
7827 ("r-randomforest" ,r-randomforest)
7828 ("r-rsamtools" ,r-rsamtools)
7829 ("r-rtracklayer" ,r-rtracklayer)
7830 ("r-s4vectors" ,r-s4vectors)))
7832 `(("r-knitr" ,r-knitr)))
7833 (home-page "https://bioconductor.org/packages/ATACseqQC/")
7834 (synopsis "ATAC-seq quality control")
7836 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
7837 sequencing, is a rapid and sensitive method for chromatin accessibility
7838 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
7839 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
7840 assess whether their ATAC-seq experiment is successful. It includes
7841 diagnostic plots of fragment size distribution, proportion of mitochondria
7842 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
7844 (license license:gpl2+)))
7846 (define-public r-gofuncr
7853 (uri (bioconductor-uri "GOfuncR" version))
7856 "0lp2gmjlsk1yqxim5pi26i27iijw11lrcxmji7ynlag359yfnynd"))))
7857 (properties `((upstream-name . "GOfuncR")))
7858 (build-system r-build-system)
7860 `(("r-annotationdbi" ,r-annotationdbi)
7861 ("r-genomicranges" ,r-genomicranges)
7862 ("r-gtools" ,r-gtools)
7863 ("r-iranges" ,r-iranges)
7864 ("r-mapplots" ,r-mapplots)
7866 ("r-vioplot" ,r-vioplot)))
7868 `(("r-knitr" ,r-knitr)))
7869 (home-page "https://bioconductor.org/packages/GOfuncR/")
7870 (synopsis "Gene ontology enrichment using FUNC")
7872 "GOfuncR performs a gene ontology enrichment analysis based on the
7873 ontology enrichment software FUNC. GO-annotations are obtained from
7874 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
7875 included in the package and updated regularly. GOfuncR provides the standard
7876 candidate vs background enrichment analysis using the hypergeometric test, as
7877 well as three additional tests:
7880 @item the Wilcoxon rank-sum test that is used when genes are ranked,
7881 @item a binomial test that is used when genes are associated with two counts,
7883 @item a Chi-square or Fisher's exact test that is used in cases when genes are
7884 associated with four counts.
7887 To correct for multiple testing and interdependency of the tests, family-wise
7888 error rates are computed based on random permutations of the gene-associated
7889 variables. GOfuncR also provides tools for exploring the ontology graph and
7890 the annotations, and options to take gene-length or spatial clustering of
7891 genes into account. It is also possible to provide custom gene coordinates,
7892 annotations and ontologies.")
7893 (license license:gpl2+)))
7895 (define-public r-abaenrichment
7897 (name "r-abaenrichment")
7902 (uri (bioconductor-uri "ABAEnrichment" version))
7905 "15v5n6d3mnj9d86swkh9agfvrsd065dldaywm1adwmkhhk525wmd"))))
7906 (properties `((upstream-name . "ABAEnrichment")))
7907 (build-system r-build-system)
7909 `(("r-abadata" ,r-abadata)
7910 ("r-data-table" ,r-data-table)
7911 ("r-gofuncr" ,r-gofuncr)
7912 ("r-gplots" ,r-gplots)
7913 ("r-gtools" ,r-gtools)
7914 ("r-rcpp" ,r-rcpp)))
7916 `(("r-knitr" ,r-knitr)))
7917 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
7918 (synopsis "Gene expression enrichment in human brain regions")
7920 "The package ABAEnrichment is designed to test for enrichment of user
7921 defined candidate genes in the set of expressed genes in different human brain
7922 regions. The core function @code{aba_enrich} integrates the expression of the
7923 candidate gene set (averaged across donors) and the structural information of
7924 the brain using an ontology, both provided by the Allen Brain Atlas project.")
7925 (license license:gpl2+)))
7927 (define-public r-annotationfuncs
7929 (name "r-annotationfuncs")
7934 (uri (bioconductor-uri "AnnotationFuncs" version))
7937 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
7939 `((upstream-name . "AnnotationFuncs")))
7940 (build-system r-build-system)
7942 `(("r-annotationdbi" ,r-annotationdbi)
7944 (home-page "https://www.iysik.com/r/annotationfuncs")
7945 (synopsis "Annotation translation functions")
7947 "This package provides functions for handling translating between
7948 different identifieres using the Biocore Data Team data-packages (e.g.
7949 @code{org.Bt.eg.db}).")
7950 (license license:gpl2)))
7952 (define-public r-annotationtools
7954 (name "r-annotationtools")
7959 (uri (bioconductor-uri "annotationTools" version))
7962 "18dd8saqx17fplvv5sbfz4p9fy7ksy3n9348rd3qlczihcrh9i3w"))))
7964 `((upstream-name . "annotationTools")))
7965 (build-system r-build-system)
7966 (propagated-inputs `(("r-biobase" ,r-biobase)))
7967 (home-page "https://bioconductor.org/packages/annotationTools/")
7968 (synopsis "Annotate microarrays and perform gene expression analyses")
7970 "This package provides functions to annotate microarrays, find orthologs,
7971 and integrate heterogeneous gene expression profiles using annotation and
7972 other molecular biology information available as flat file database (plain
7974 ;; Any version of the GPL.
7975 (license (list license:gpl2+))))
7977 (define-public r-allelicimbalance
7979 (name "r-allelicimbalance")
7984 (uri (bioconductor-uri "AllelicImbalance" version))
7987 "1mn6975npncmfjlpjs3s2pgsrm32xgvnyl2vh1922l6vra97dkrc"))))
7989 `((upstream-name . "AllelicImbalance")))
7990 (build-system r-build-system)
7992 `(("r-annotationdbi" ,r-annotationdbi)
7993 ("r-biocgenerics" ,r-biocgenerics)
7994 ("r-biostrings" ,r-biostrings)
7995 ("r-bsgenome" ,r-bsgenome)
7996 ("r-genomeinfodb" ,r-genomeinfodb)
7997 ("r-genomicalignments" ,r-genomicalignments)
7998 ("r-genomicfeatures" ,r-genomicfeatures)
7999 ("r-genomicranges" ,r-genomicranges)
8000 ("r-gridextra" ,r-gridextra)
8002 ("r-iranges" ,r-iranges)
8003 ("r-lattice" ,r-lattice)
8004 ("r-latticeextra" ,r-latticeextra)
8006 ("r-rsamtools" ,r-rsamtools)
8007 ("r-s4vectors" ,r-s4vectors)
8008 ("r-seqinr" ,r-seqinr)
8009 ("r-summarizedexperiment" ,r-summarizedexperiment)
8010 ("r-variantannotation" ,r-variantannotation)))
8012 `(("r-knitr" ,r-knitr)))
8013 (home-page "https://github.com/pappewaio/AllelicImbalance")
8014 (synopsis "Investigate allele-specific expression")
8016 "This package provides a framework for allele-specific expression
8017 investigation using RNA-seq data.")
8018 (license license:gpl3)))
8020 (define-public r-aucell
8027 (uri (bioconductor-uri "AUCell" version))
8030 "0qdac3qalcki20r90k40cc8d0lfywzn9pffg9d719yvs7nrsfdjr"))))
8031 (properties `((upstream-name . "AUCell")))
8032 (build-system r-build-system)
8034 `(("r-biocgenerics" ,r-biocgenerics)
8035 ("r-data-table" ,r-data-table)
8036 ("r-gseabase" ,r-gseabase)
8037 ("r-mixtools" ,r-mixtools)
8038 ("r-r-utils" ,r-r-utils)
8039 ("r-s4vectors" ,r-s4vectors)
8040 ("r-shiny" ,r-shiny)
8041 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8043 `(("r-knitr" ,r-knitr)))
8044 (home-page "https://bioconductor.org/packages/AUCell/")
8045 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
8047 "AUCell identifies cells with active gene sets (e.g. signatures,
8048 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
8049 Under the Curve} (AUC) to calculate whether a critical subset of the input
8050 gene set is enriched within the expressed genes for each cell. The
8051 distribution of AUC scores across all the cells allows exploring the relative
8052 expression of the signature. Since the scoring method is ranking-based,
8053 AUCell is independent of the gene expression units and the normalization
8054 procedure. In addition, since the cells are evaluated individually, it can
8055 easily be applied to bigger datasets, subsetting the expression matrix if
8057 (license license:gpl3)))
8059 (define-public r-ebimage
8066 (uri (bioconductor-uri "EBImage" version))
8069 "1z3cxxg593d66nczz5hh2hdj1d87wc0lxrzc5sn6bp43n351q8h3"))))
8070 (properties `((upstream-name . "EBImage")))
8071 (build-system r-build-system)
8073 `(("r-abind" ,r-abind)
8074 ("r-biocgenerics" ,r-biocgenerics)
8075 ("r-fftwtools" ,r-fftwtools)
8076 ("r-htmltools" ,r-htmltools)
8077 ("r-htmlwidgets" ,r-htmlwidgets)
8079 ("r-locfit" ,r-locfit)
8081 ("r-rcurl" ,r-rcurl)
8082 ("r-tiff" ,r-tiff)))
8084 `(("r-knitr" ,r-knitr))) ; for vignettes
8085 (home-page "https://github.com/aoles/EBImage")
8086 (synopsis "Image processing and analysis toolbox for R")
8088 "EBImage provides general purpose functionality for image processing and
8089 analysis. In the context of (high-throughput) microscopy-based cellular
8090 assays, EBImage offers tools to segment cells and extract quantitative
8091 cellular descriptors. This allows the automation of such tasks using the R
8092 programming language and facilitates the use of other tools in the R
8093 environment for signal processing, statistical modeling, machine learning and
8094 visualization with image data.")
8095 ;; Any version of the LGPL.
8096 (license license:lgpl2.1+)))
8098 (define-public r-yamss
8105 (uri (bioconductor-uri "yamss" version))
8108 "1al615x778h17jqiyhiyf6djaq9iygs1hlbrna6y4xc0f2kvgxld"))))
8109 (build-system r-build-system)
8111 `(("r-biocgenerics" ,r-biocgenerics)
8112 ("r-data-table" ,r-data-table)
8113 ("r-ebimage" ,r-ebimage)
8114 ("r-iranges" ,r-iranges)
8115 ("r-limma" ,r-limma)
8116 ("r-matrix" ,r-matrix)
8118 ("r-s4vectors" ,r-s4vectors)
8119 ("r-summarizedexperiment"
8120 ,r-summarizedexperiment)))
8122 `(("r-knitr" ,r-knitr)))
8123 (home-page "https://github.com/hansenlab/yamss")
8124 (synopsis "Tools for high-throughput metabolomics")
8126 "This package provides tools to analyze and visualize high-throughput
8127 metabolomics data acquired using chromatography-mass spectrometry. These tools
8128 preprocess data in a way that enables reliable and powerful differential
8130 (license license:artistic2.0)))
8132 (define-public r-gtrellis
8139 (uri (bioconductor-uri "gtrellis" version))
8142 "0l5271cpzjlm4m0v6xcdg2vxlbhn53x1fd59ynb9jwll93av5h1f"))))
8143 (build-system r-build-system)
8145 `(("r-circlize" ,r-circlize)
8146 ("r-genomicranges" ,r-genomicranges)
8147 ("r-getoptlong" ,r-getoptlong)
8148 ("r-iranges" ,r-iranges)))
8150 `(("r-knitr" ,r-knitr)))
8151 (home-page "https://github.com/jokergoo/gtrellis")
8152 (synopsis "Genome level Trellis layout")
8154 "Genome level Trellis graph visualizes genomic data conditioned by
8155 genomic categories (e.g. chromosomes). For each genomic category, multiple
8156 dimensional data which are represented as tracks describe different features
8157 from different aspects. This package provides high flexibility to arrange
8158 genomic categories and to add self-defined graphics in the plot.")
8159 (license license:expat)))
8161 (define-public r-somaticsignatures
8163 (name "r-somaticsignatures")
8168 (uri (bioconductor-uri "SomaticSignatures" version))
8171 "0jr11c9hz7m49xc8pi6xrr5fhbv68vafvqpzhr0pmm51vvr1vfs9"))))
8173 `((upstream-name . "SomaticSignatures")))
8174 (build-system r-build-system)
8176 `(("r-biobase" ,r-biobase)
8177 ("r-biostrings" ,r-biostrings)
8178 ("r-genomeinfodb" ,r-genomeinfodb)
8179 ("r-genomicranges" ,r-genomicranges)
8180 ("r-ggbio" ,r-ggbio)
8181 ("r-ggplot2" ,r-ggplot2)
8182 ("r-iranges" ,r-iranges)
8184 ("r-pcamethods" ,r-pcamethods)
8185 ("r-proxy" ,r-proxy)
8186 ("r-reshape2" ,r-reshape2)
8187 ("r-s4vectors" ,r-s4vectors)
8188 ("r-variantannotation" ,r-variantannotation)))
8190 `(("r-knitr" ,r-knitr)))
8191 (home-page "https://github.com/juliangehring/SomaticSignatures")
8192 (synopsis "Somatic signatures")
8194 "This package identifies mutational signatures of @dfn{single nucleotide
8195 variants} (SNVs). It provides a infrastructure related to the methodology
8196 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
8197 decomposition algorithms.")
8198 (license license:expat)))
8200 (define-public r-yapsa
8207 (uri (bioconductor-uri "YAPSA" version))
8210 "1xfkgjlm0rxz82qcaqzx95cwirxifd9dsswjg3zcqmz03v7a0gz2"))))
8211 (properties `((upstream-name . "YAPSA")))
8212 (build-system r-build-system)
8214 `(("r-biostrings" ,r-biostrings)
8215 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
8216 ("r-circlize" ,r-circlize)
8217 ("r-complexheatmap" ,r-complexheatmap)
8218 ("r-corrplot" ,r-corrplot)
8219 ("r-dendextend" ,r-dendextend)
8220 ("r-doparallel" ,r-doparallel)
8221 ("r-dplyr" ,r-dplyr)
8222 ("r-genomeinfodb" ,r-genomeinfodb)
8223 ("r-genomicranges" ,r-genomicranges)
8224 ("r-getoptlong" ,r-getoptlong)
8225 ("r-ggbeeswarm" ,r-ggbeeswarm)
8226 ("r-ggplot2" ,r-ggplot2)
8227 ("r-gridextra" ,r-gridextra)
8228 ("r-gtrellis" ,r-gtrellis)
8229 ("r-keggrest" ,r-keggrest)
8230 ("r-limsolve" ,r-limsolve)
8231 ("r-magrittr" ,r-magrittr)
8232 ("r-pmcmr" ,r-pmcmr)
8233 ("r-pracma" ,r-pracma)
8234 ("r-reshape2" ,r-reshape2)
8235 ("r-somaticsignatures" ,r-somaticsignatures)
8236 ("r-variantannotation" ,r-variantannotation)))
8238 `(("r-knitr" ,r-knitr)))
8239 (home-page "https://bioconductor.org/packages/YAPSA/")
8240 (synopsis "Yet another package for signature analysis")
8242 "This package provides functions and routines useful in the analysis of
8243 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
8244 functions to perform a signature analysis with known signatures and a
8245 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
8247 (license license:gpl3)))
8249 (define-public r-gcrma
8256 (uri (bioconductor-uri "gcrma" version))
8259 "1z4abw9s2hs3csnx25nli7fpvb3rh3l0swzl0wfqp087fcs78pxi"))))
8260 (build-system r-build-system)
8262 `(("r-affy" ,r-affy)
8263 ("r-affyio" ,r-affyio)
8264 ("r-biobase" ,r-biobase)
8265 ("r-biocmanager" ,r-biocmanager)
8266 ("r-biostrings" ,r-biostrings)
8267 ("r-xvector" ,r-xvector)))
8268 (home-page "https://bioconductor.org/packages/gcrma/")
8269 (synopsis "Background adjustment using sequence information")
8271 "Gcrma adjusts for background intensities in Affymetrix array data which
8272 include optical noise and @dfn{non-specific binding} (NSB). The main function
8273 @code{gcrma} converts background adjusted probe intensities to expression
8274 measures using the same normalization and summarization methods as a
8275 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
8276 to estimate probe affinity to NSB. The sequence information is summarized in
8277 a more complex way than the simple GC content. Instead, the base types (A, T,
8278 G or C) at each position along the probe determine the affinity of each probe.
8279 The parameters of the position-specific base contributions to the probe
8280 affinity is estimated in an NSB experiment in which only NSB but no
8281 gene-specific binding is expected.")
8282 ;; Any version of the LGPL
8283 (license license:lgpl2.1+)))
8285 (define-public r-simpleaffy
8287 (name "r-simpleaffy")
8292 (uri (bioconductor-uri "simpleaffy" version))
8295 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
8296 (build-system r-build-system)
8298 `(("r-affy" ,r-affy)
8299 ("r-biobase" ,r-biobase)
8300 ("r-biocgenerics" ,r-biocgenerics)
8301 ("r-gcrma" ,r-gcrma)
8302 ("r-genefilter" ,r-genefilter)))
8303 (home-page "https://bioconductor.org/packages/simpleaffy/")
8304 (synopsis "Very simple high level analysis of Affymetrix data")
8306 "This package provides high level functions for reading Affy @file{.CEL}
8307 files, phenotypic data, and then computing simple things with it, such as
8308 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
8309 library. It also has some basic scatter plot functions and mechanisms for
8310 generating high resolution journal figures.")
8311 (license license:gpl2+)))
8313 (define-public r-yaqcaffy
8320 (uri (bioconductor-uri "yaqcaffy" version))
8323 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
8324 (build-system r-build-system)
8326 `(("r-simpleaffy" ,r-simpleaffy)))
8327 (home-page "https://bioconductor.org/packages/yaqcaffy/")
8328 (synopsis "Affymetrix quality control and reproducibility analysis")
8330 "This is a package that can be used for quality control of Affymetrix
8331 GeneChip expression data and reproducibility analysis of human whole genome
8332 chips with the MAQC reference datasets.")
8333 (license license:artistic2.0)))
8335 (define-public r-quantro
8342 (uri (bioconductor-uri "quantro" version))
8345 "1fkma2ic448h2lrlza8ipg65gpfsz4fhlxcnjpmzhhmzp2xi2p4a"))))
8346 (build-system r-build-system)
8348 `(("r-biobase" ,r-biobase)
8349 ("r-doparallel" ,r-doparallel)
8350 ("r-foreach" ,r-foreach)
8351 ("r-ggplot2" ,r-ggplot2)
8352 ("r-iterators" ,r-iterators)
8353 ("r-minfi" ,r-minfi)
8354 ("r-rcolorbrewer" ,r-rcolorbrewer)))
8356 `(("r-knitr" ,r-knitr)))
8357 (home-page "https://bioconductor.org/packages/quantro/")
8358 (synopsis "Test for when to use quantile normalization")
8360 "This package provides a data-driven test for the assumptions of quantile
8361 normalization using raw data such as objects that inherit eSets (e.g.
8362 ExpressionSet, MethylSet). Group level information about each sample (such as
8363 Tumor / Normal status) must also be provided because the test assesses if
8364 there are global differences in the distributions between the user-defined
8366 (license license:gpl3+)))
8368 (define-public r-yarn
8375 (uri (bioconductor-uri "yarn" version))
8378 "1x07l255x52z6cgdc2j8285shqszhr034xm5686rp6d35vah55ji"))))
8379 (build-system r-build-system)
8381 `(("r-biobase" ,r-biobase)
8382 ("r-biomart" ,r-biomart)
8383 ("r-downloader" ,r-downloader)
8384 ("r-edger" ,r-edger)
8385 ("r-gplots" ,r-gplots)
8386 ("r-limma" ,r-limma)
8387 ("r-matrixstats" ,r-matrixstats)
8388 ("r-preprocesscore" ,r-preprocesscore)
8389 ("r-quantro" ,r-quantro)
8390 ("r-rcolorbrewer" ,r-rcolorbrewer)
8391 ("r-readr" ,r-readr)))
8393 `(("r-knitr" ,r-knitr)))
8394 (home-page "https://bioconductor.org/packages/yarn/")
8395 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
8397 "Expedite large RNA-Seq analyses using a combination of previously
8398 developed tools. YARN is meant to make it easier for the user in performing
8399 basic mis-annotation quality control, filtering, and condition-aware
8400 normalization. YARN leverages many Bioconductor tools and statistical
8401 techniques to account for the large heterogeneity and sparsity found in very
8402 large RNA-seq experiments.")
8403 (license license:artistic2.0)))
8405 (define-public r-roar
8412 (uri (bioconductor-uri "roar" version))
8415 "0vp0n90rvjm8rzwkbrxa3fasb9val56bz2srz72xwsl3jzb5yk6w"))))
8416 (build-system r-build-system)
8418 `(("r-biocgenerics" ,r-biocgenerics)
8419 ("r-genomeinfodb" ,r-genomeinfodb)
8420 ("r-genomicalignments" ,r-genomicalignments)
8421 ("r-genomicranges" ,r-genomicranges)
8422 ("r-iranges" ,r-iranges)
8423 ("r-rtracklayer" ,r-rtracklayer)
8424 ("r-s4vectors" ,r-s4vectors)
8425 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8426 (home-page "https://github.com/vodkatad/roar/")
8427 (synopsis "Identify differential APA usage from RNA-seq alignments")
8429 "This package provides tools for identifying preferential usage of APA
8430 sites, comparing two biological conditions, starting from known alternative
8431 sites and alignments obtained from standard RNA-seq experiments.")
8432 (license license:gpl3)))
8434 (define-public r-xbseq
8441 (uri (bioconductor-uri "XBSeq" version))
8444 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
8445 (properties `((upstream-name . "XBSeq")))
8446 (build-system r-build-system)
8448 `(("r-biobase" ,r-biobase)
8449 ("r-deseq2" ,r-deseq2)
8450 ("r-dplyr" ,r-dplyr)
8451 ("r-ggplot2" ,r-ggplot2)
8452 ("r-locfit" ,r-locfit)
8453 ("r-magrittr" ,r-magrittr)
8454 ("r-matrixstats" ,r-matrixstats)
8455 ("r-pracma" ,r-pracma)
8456 ("r-roar" ,r-roar)))
8458 `(("r-knitr" ,r-knitr)))
8459 (home-page "https://github.com/Liuy12/XBSeq")
8460 (synopsis "Test for differential expression for RNA-seq data")
8462 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
8463 expression} (DE), where a statistical model was established based on the
8464 assumption that observed signals are the convolution of true expression
8465 signals and sequencing noises. The mapped reads in non-exonic regions are
8466 considered as sequencing noises, which follows a Poisson distribution. Given
8467 measurable observed signal and background noise from RNA-seq data, true
8468 expression signals, assuming governed by the negative binomial distribution,
8469 can be delineated and thus the accurate detection of differential expressed
8471 (license license:gpl3+)))
8473 (define-public r-massspecwavelet
8475 (name "r-massspecwavelet")
8480 (uri (bioconductor-uri "MassSpecWavelet" version))
8483 "1cs32sig1yvqn9xs0cvhfpmkh2lbllx7aab80sz58x03wnx8v60z"))))
8485 `((upstream-name . "MassSpecWavelet")))
8486 (build-system r-build-system)
8488 `(("r-waveslim" ,r-waveslim)))
8489 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
8490 (synopsis "Mass spectrum processing by wavelet-based algorithms")
8492 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
8493 data mainly through the use of wavelet transforms. It supports peak detection
8494 based on @dfn{Continuous Wavelet Transform} (CWT).")
8495 (license license:lgpl2.0+)))
8497 (define-public r-xcms
8504 (uri (bioconductor-uri "xcms" version))
8507 "1fs72lkgz1jik1smi6bb4f8jh6rrlpxdh3a5hydrnnndfxkz5kwx"))))
8508 (build-system r-build-system)
8510 `(("r-biobase" ,r-biobase)
8511 ("r-biocgenerics" ,r-biocgenerics)
8512 ("r-biocparallel" ,r-biocparallel)
8513 ("r-iranges" ,r-iranges)
8514 ("r-lattice" ,r-lattice)
8515 ("r-massspecwavelet" ,r-massspecwavelet)
8516 ("r-mscoreutils" ,r-mscoreutils)
8517 ("r-msnbase" ,r-msnbase)
8520 ("r-protgenerics" ,r-protgenerics)
8522 ("r-rcolorbrewer" ,r-rcolorbrewer)
8523 ("r-robustbase" ,r-robustbase)
8524 ("r-s4vectors" ,r-s4vectors)
8525 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8527 `(("r-knitr" ,r-knitr)))
8528 (home-page "https://bioconductor.org/packages/xcms/")
8529 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
8531 "This package provides a framework for processing and visualization of
8532 chromatographically separated and single-spectra mass spectral data. It
8533 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
8534 data for high-throughput, untargeted analyte profiling.")
8535 (license license:gpl2+)))
8537 (define-public r-wrench
8544 (uri (bioconductor-uri "Wrench" version))
8547 "0yssmqayaryrc0asjjqxdipqdfg309llrzldx38jrfgdsza6bvs0"))))
8548 (properties `((upstream-name . "Wrench")))
8549 (build-system r-build-system)
8551 `(("r-limma" ,r-limma)
8552 ("r-locfit" ,r-locfit)
8553 ("r-matrixstats" ,r-matrixstats)))
8555 `(("r-knitr" ,r-knitr)))
8556 (home-page "https://github.com/HCBravoLab/Wrench")
8557 (synopsis "Wrench normalization for sparse count data")
8559 "Wrench is a package for normalization sparse genomic count data, like
8560 that arising from 16s metagenomic surveys.")
8561 (license license:artistic2.0)))
8563 (define-public r-wiggleplotr
8565 (name "r-wiggleplotr")
8570 (uri (bioconductor-uri "wiggleplotr" version))
8573 "13f3g6fcc29k0g21mhnypm3nc6qqjw867vamvfkdzynspsfb32ga"))))
8574 (build-system r-build-system)
8576 `(("r-assertthat" ,r-assertthat)
8577 ("r-cowplot" ,r-cowplot)
8578 ("r-dplyr" ,r-dplyr)
8579 ("r-genomeinfodb" ,r-genomeinfodb)
8580 ("r-genomicranges" ,r-genomicranges)
8581 ("r-ggplot2" ,r-ggplot2)
8582 ("r-iranges" ,r-iranges)
8583 ("r-purrr" ,r-purrr)
8584 ("r-rtracklayer" ,r-rtracklayer)
8585 ("r-s4vectors" ,r-s4vectors)))
8587 `(("r-knitr" ,r-knitr)))
8588 (home-page "https://bioconductor.org/packages/wiggleplotr/")
8589 (synopsis "Make read coverage plots from BigWig files")
8591 "This package provides tools to visualize read coverage from sequencing
8592 experiments together with genomic annotations (genes, transcripts, peaks).
8593 Introns of long transcripts can be rescaled to a fixed length for better
8594 visualization of exonic read coverage.")
8595 (license license:asl2.0)))
8597 (define-public r-widgettools
8599 (name "r-widgettools")
8604 (uri (bioconductor-uri "widgetTools" version))
8607 "186xgpgyfyi4angxhz6558lfpzvvszzlpyfr8xnbccs3gshk3db2"))))
8608 (properties `((upstream-name . "widgetTools")))
8609 (build-system r-build-system)
8610 (home-page "https://bioconductor.org/packages/widgetTools/")
8611 (synopsis "Tools for creating interactive tcltk widgets")
8613 "This package contains tools to support the construction of tcltk
8615 ;; Any version of the LGPL.
8616 (license license:lgpl3+)))
8618 (define-public r-webbioc
8625 (uri (bioconductor-uri "webbioc" version))
8628 "1mpdw477j78s2nvlf2lzm6mdjcpamyyazjn060h9q3apawn6zajx"))))
8629 (build-system r-build-system)
8631 `(("netpbm" ,netpbm)
8634 `(("r-affy" ,r-affy)
8635 ("r-annaffy" ,r-annaffy)
8636 ("r-biobase" ,r-biobase)
8637 ("r-biocmanager" ,r-biocmanager)
8638 ("r-gcrma" ,r-gcrma)
8639 ("r-multtest" ,r-multtest)
8640 ("r-qvalue" ,r-qvalue)
8642 (home-page "https://www.bioconductor.org/")
8643 (synopsis "Bioconductor web interface")
8645 "This package provides an integrated web interface for doing microarray
8646 analysis using several of the Bioconductor packages. It is intended to be
8647 deployed as a centralized bioinformatics resource for use by many users.
8648 Currently only Affymetrix oligonucleotide analysis is supported.")
8649 (license license:gpl2+)))
8651 (define-public r-zinbwave
8658 (uri (bioconductor-uri "zinbwave" version))
8661 "0xgjbk35wl1vjqyq4y5c7hna8hkgmf56xjaxcph9bs2q7mbdnqwf"))))
8662 (build-system r-build-system)
8664 `(("r-biocparallel" ,r-biocparallel)
8665 ("r-edger" ,r-edger)
8666 ("r-genefilter" ,r-genefilter)
8667 ("r-matrix" ,r-matrix)
8668 ("r-singlecellexperiment" ,r-singlecellexperiment)
8669 ("r-softimpute" ,r-softimpute)
8670 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8672 `(("r-knitr" ,r-knitr)))
8673 (home-page "https://bioconductor.org/packages/zinbwave")
8674 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
8675 (description "This package implements a general and flexible zero-inflated
8676 negative binomial model that can be used to provide a low-dimensional
8677 representations of single-cell RNA-seq data. The model accounts for zero
8678 inflation (dropouts), over-dispersion, and the count nature of the data.
8679 The model also accounts for the difference in library sizes and optionally
8680 for batch effects and/or other covariates, avoiding the need for pre-normalize
8682 (license license:artistic2.0)))
8684 (define-public r-zfpkm
8691 (uri (bioconductor-uri "zFPKM" version))
8694 "1k7xaxr2gn26y8bps5l32g2axfhdn07nbk4q3qcx32d5jm75qkx2"))))
8695 (properties `((upstream-name . "zFPKM")))
8696 (build-system r-build-system)
8698 `(("r-checkmate" ,r-checkmate)
8699 ("r-dplyr" ,r-dplyr)
8700 ("r-ggplot2" ,r-ggplot2)
8701 ("r-summarizedexperiment" ,r-summarizedexperiment)
8702 ("r-tidyr" ,r-tidyr)))
8704 `(("r-knitr" ,r-knitr)))
8705 (home-page "https://github.com/ronammar/zFPKM/")
8706 (synopsis "Functions to facilitate zFPKM transformations")
8708 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
8709 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
8711 (license license:gpl3)))
8713 (define-public r-rbowtie2
8720 (uri (bioconductor-uri "Rbowtie2" version))
8723 "0r5yqjal48xlcv5cidi7p3zwygvsllmv2zzkwkc9kfq083l2i4ih"))))
8724 (properties `((upstream-name . "Rbowtie2")))
8725 (build-system r-build-system)
8729 `(("r-knitr" ,r-knitr)))
8730 (home-page "https://bioconductor.org/packages/Rbowtie2/")
8731 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
8733 "This package provides an R wrapper of the popular @code{bowtie2}
8734 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
8735 rapid adapter trimming, identification, and read merging.")
8736 (license license:gpl3+)))
8738 (define-public r-progeny
8745 (uri (bioconductor-uri "progeny" version))
8748 "10vpjvl4wps857xiy8rpzr82jzdfbc5rgwh3ir3my26lfws4hfz8"))))
8749 (build-system r-build-system)
8751 `(("r-biobase" ,r-biobase)
8752 ("r-dplyr" ,r-dplyr)
8753 ("r-ggplot2" ,r-ggplot2)
8754 ("r-ggrepel" ,r-ggrepel)
8755 ("r-gridextra" ,r-gridextra)
8756 ("r-tidyr" ,r-tidyr)))
8758 `(("r-knitr" ,r-knitr)))
8759 (home-page "https://github.com/saezlab/progeny")
8760 (synopsis "Pathway responsive gene activity inference")
8762 "This package provides a function to infer pathway activity from gene
8763 expression. It contains the linear model inferred in the publication
8764 \"Perturbation-response genes reveal signaling footprints in cancer gene
8766 (license license:asl2.0)))
8768 (define-public r-arrmnormalization
8770 (name "r-arrmnormalization")
8775 (uri (bioconductor-uri "ARRmNormalization" version))
8778 "0ni3vblcadhwxaq1pf1n9jn66cp3bqch68ww4c8zh19zagil2y7r"))))
8780 `((upstream-name . "ARRmNormalization")))
8781 (build-system r-build-system)
8782 (propagated-inputs `(("r-arrmdata" ,r-arrmdata)))
8783 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
8784 (synopsis "Adaptive robust regression normalization for methylation data")
8786 "This is a package to perform the @dfn{Adaptive Robust Regression
8787 method} (ARRm) for the normalization of methylation data from the Illumina
8788 Infinium HumanMethylation 450k assay.")
8789 (license license:artistic2.0)))
8791 (define-public r-biocfilecache
8793 (name "r-biocfilecache")
8798 (uri (bioconductor-uri "BiocFileCache" version))
8801 "0ymg4hmabk233qgassld62achjylm12rnidxbakfkx4dvvlbhxxv"))))
8802 (properties `((upstream-name . "BiocFileCache")))
8803 (build-system r-build-system)
8805 `(("r-curl" ,r-curl)
8807 ("r-dbplyr" ,r-dbplyr)
8808 ("r-dplyr" ,r-dplyr)
8809 ("r-filelock" ,r-filelock)
8811 ("r-rappdirs" ,r-rappdirs)
8812 ("r-rsqlite" ,r-rsqlite)))
8814 `(("r-knitr" ,r-knitr)))
8815 (home-page "https://bioconductor.org/packages/BiocFileCache/")
8816 (synopsis "Manage files across sessions")
8818 "This package creates a persistent on-disk cache of files that the user
8819 can add, update, and retrieve. It is useful for managing resources (such as
8820 custom Txdb objects) that are costly or difficult to create, web resources,
8821 and data files used across sessions.")
8822 (license license:artistic2.0)))
8824 (define-public r-iclusterplus
8826 (name "r-iclusterplus")
8831 (uri (bioconductor-uri "iClusterPlus" version))
8834 "1haj25c4cmmjjvh181b41a9pvkh92f7k2w4ljn17iqg31vm45za1"))))
8835 (properties `((upstream-name . "iClusterPlus")))
8836 (build-system r-build-system)
8837 (native-inputs `(("gfortran" ,gfortran)))
8838 (home-page "https://bioconductor.org/packages/iClusterPlus/")
8839 (synopsis "Integrative clustering of multi-type genomic data")
8841 "iClusterPlus is developed for integrative clustering analysis of
8842 multi-type genomic data and is an enhanced version of iCluster proposed and
8843 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
8844 from the experiments where biological samples (e.g. tumor samples) are
8845 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
8846 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
8847 on. In the iClusterPlus model, binary observations such as somatic mutation
8848 are modeled as Binomial processes; categorical observations such as copy
8849 number states are realizations of Multinomial random variables; counts are
8850 modeled as Poisson random processes; and continuous measures are modeled by
8851 Gaussian distributions.")
8852 (license license:gpl2+)))
8854 (define-public r-rbowtie
8861 (uri (bioconductor-uri "Rbowtie" version))
8864 "0mfikbrs28q7r3lnsq0jma5x6nkrnm3q46242jh35w9c969jk5yy"))))
8865 (properties `((upstream-name . "Rbowtie")))
8866 (build-system r-build-system)
8870 `(("r-knitr" ,r-knitr)))
8871 (home-page "https://bioconductor.org/packages/Rbowtie/")
8872 (synopsis "R bowtie wrapper")
8874 "This package provides an R wrapper around the popular bowtie short read
8875 aligner and around SpliceMap, a de novo splice junction discovery and
8877 (license license:artistic2.0)))
8879 (define-public r-sgseq
8886 (uri (bioconductor-uri "SGSeq" version))
8889 "0i1yaw8h8gibakvaf1xd6nnjx2bsb2s9c0q74rbq9lm7haihivp6"))))
8890 (properties `((upstream-name . "SGSeq")))
8891 (build-system r-build-system)
8893 `(("r-annotationdbi" ,r-annotationdbi)
8894 ("r-biocgenerics" ,r-biocgenerics)
8895 ("r-biostrings" ,r-biostrings)
8896 ("r-genomeinfodb" ,r-genomeinfodb)
8897 ("r-genomicalignments" ,r-genomicalignments)
8898 ("r-genomicfeatures" ,r-genomicfeatures)
8899 ("r-genomicranges" ,r-genomicranges)
8900 ("r-igraph" ,r-igraph)
8901 ("r-iranges" ,r-iranges)
8902 ("r-rsamtools" ,r-rsamtools)
8903 ("r-rtracklayer" ,r-rtracklayer)
8904 ("r-runit" ,r-runit)
8905 ("r-s4vectors" ,r-s4vectors)
8906 ("r-summarizedexperiment" ,r-summarizedexperiment)))
8908 `(("r-knitr" ,r-knitr)))
8909 (home-page "https://bioconductor.org/packages/SGSeq/")
8910 (synopsis "Splice event prediction and quantification from RNA-seq data")
8912 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
8913 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
8914 represented as a splice graph, which can be obtained from existing annotation
8915 or predicted from the mapped sequence reads. Splice events are identified
8916 from the graph and are quantified locally using structurally compatible reads
8917 at the start or end of each splice variant. The software includes functions
8918 for splice event prediction, quantification, visualization and
8920 (license license:artistic2.0)))
8922 (define-public r-rhisat2
8929 (uri (bioconductor-uri "Rhisat2" version))
8932 "1hqahh5h22mj2crqp6r9xnm111xmfgk39c100rcaziqrpdy5npk8"))))
8933 (properties `((upstream-name . "Rhisat2")))
8934 (build-system r-build-system)
8937 (modify-phases %standard-phases
8938 (add-after 'unpack 'make-reproducible
8940 (substitute* "src/Makefile"
8941 (("`hostname`") "guix")
8943 ;; Avoid shelling out to "which".
8944 (("^CC =.*") (which "gcc"))
8945 (("^CPP =.*") (which "g++")))
8948 `(("r-genomicfeatures" ,r-genomicfeatures)
8949 ("r-genomicranges" ,r-genomicranges)
8950 ("r-sgseq" ,r-sgseq)))
8952 `(("r-knitr" ,r-knitr)))
8953 (home-page "https://github.com/fmicompbio/Rhisat2")
8954 (synopsis "R Wrapper for HISAT2 sequence aligner")
8956 "This package provides an R interface to the HISAT2 spliced short-read
8957 aligner by Kim et al. (2015). The package contains wrapper functions to
8958 create a genome index and to perform the read alignment to the generated
8960 (license license:gpl3)))
8962 (define-public r-quasr
8969 (uri (bioconductor-uri "QuasR" version))
8972 "1635ff11ahzjrh3cdcxrq5bgd100n444k7mc0maz0jx21vj8qqb1"))))
8973 (properties `((upstream-name . "QuasR")))
8974 (build-system r-build-system)
8976 `(("r-annotationdbi" ,r-annotationdbi)
8977 ("r-biobase" ,r-biobase)
8978 ("r-biocgenerics" ,r-biocgenerics)
8979 ("r-biocmanager" ,r-biocmanager)
8980 ("r-biocparallel" ,r-biocparallel)
8981 ("r-biostrings" ,r-biostrings)
8982 ("r-bsgenome" ,r-bsgenome)
8983 ("r-genomeinfodb" ,r-genomeinfodb)
8984 ("r-genomicfeatures" ,r-genomicfeatures)
8985 ("r-genomicfiles" ,r-genomicfiles)
8986 ("r-genomicranges" ,r-genomicranges)
8987 ("r-iranges" ,r-iranges)
8988 ("r-rbowtie" ,r-rbowtie)
8989 ("r-rhtslib" ,r-rhtslib)
8990 ("r-rsamtools" ,r-rsamtools)
8991 ("r-rtracklayer" ,r-rtracklayer)
8992 ("r-s4vectors" ,r-s4vectors)
8993 ("r-shortread" ,r-shortread)))
8995 `(("r-knitr" ,r-knitr)))
8996 (home-page "https://bioconductor.org/packages/QuasR/")
8997 (synopsis "Quantify and annotate short reads in R")
8999 "This package provides a framework for the quantification and analysis of
9000 short genomic reads. It covers a complete workflow starting from raw sequence
9001 reads, over creation of alignments and quality control plots, to the
9002 quantification of genomic regions of interest.")
9003 (license license:gpl2)))
9005 (define-public r-rqc
9012 (uri (bioconductor-uri "Rqc" version))
9015 "02hwj2vd003x0zf273ndnwh7kxy6wc3sz14d3kryp2w2aqjj826f"))))
9016 (properties `((upstream-name . "Rqc")))
9017 (build-system r-build-system)
9019 `(("r-biocgenerics" ,r-biocgenerics)
9020 ("r-biocparallel" ,r-biocparallel)
9021 ("r-biocstyle" ,r-biocstyle)
9022 ("r-biostrings" ,r-biostrings)
9023 ("r-biovizbase" ,r-biovizbase)
9024 ("r-genomicalignments" ,r-genomicalignments)
9025 ("r-genomicfiles" ,r-genomicfiles)
9026 ("r-ggplot2" ,r-ggplot2)
9027 ("r-iranges" ,r-iranges)
9028 ("r-knitr" ,r-knitr)
9029 ("r-markdown" ,r-markdown)
9032 ("r-reshape2" ,r-reshape2)
9033 ("r-rsamtools" ,r-rsamtools)
9034 ("r-s4vectors" ,r-s4vectors)
9035 ("r-shiny" ,r-shiny)
9036 ("r-shortread" ,r-shortread)))
9038 `(("r-knitr" ,r-knitr)))
9039 (home-page "https://github.com/labbcb/Rqc")
9040 (synopsis "Quality control tool for high-throughput sequencing data")
9042 "Rqc is an optimized tool designed for quality control and assessment of
9043 high-throughput sequencing data. It performs parallel processing of entire
9044 files and produces a report which contains a set of high-resolution
9046 (license license:gpl2+)))
9048 (define-public r-birewire
9055 (uri (bioconductor-uri "BiRewire" version))
9058 "0p6mr67mkw54490sv4dvkyh8l0xkpjfbqy532vi8l41i40qg3gry"))))
9059 (properties `((upstream-name . "BiRewire")))
9060 (build-system r-build-system)
9062 `(("r-igraph" ,r-igraph)
9063 ("r-matrix" ,r-matrix)
9065 ("r-tsne" ,r-tsne)))
9066 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
9067 (synopsis "Tools for randomization of bipartite graphs")
9069 "This package provides functions for bipartite network rewiring through N
9070 consecutive switching steps and for the computation of the minimal number of
9071 switching steps to be performed in order to maximise the dissimilarity with
9072 respect to the original network. It includes functions for the analysis of
9073 the introduced randomness across the switching steps and several other
9074 routines to analyse the resulting networks and their natural projections.")
9075 (license license:gpl3)))
9077 (define-public r-birta
9084 (uri (bioconductor-uri "birta" version))
9087 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
9088 (build-system r-build-system)
9090 `(("r-biobase" ,r-biobase)
9091 ("r-limma" ,r-limma)
9092 ("r-mass" ,r-mass)))
9093 (home-page "https://bioconductor.org/packages/birta")
9094 (synopsis "Bayesian inference of regulation of transcriptional activity")
9096 "Expression levels of mRNA molecules are regulated by different
9097 processes, comprising inhibition or activation by transcription factors and
9098 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
9099 Inference of Regulation of Transcriptional Activity) uses the regulatory
9100 networks of transcription factors and miRNAs together with mRNA and miRNA
9101 expression data to predict switches in regulatory activity between two
9102 conditions. A Bayesian network is used to model the regulatory structure and
9103 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
9104 (license license:gpl2+)))
9106 (define-public r-multidataset
9108 (name "r-multidataset")
9113 (uri (bioconductor-uri "MultiDataSet" version))
9116 "1hyk40xgmy50rqxwdvc64d3pgz5vsg8vmlj5cp5m0n5m0adxcdfj"))))
9117 (properties `((upstream-name . "MultiDataSet")))
9118 (build-system r-build-system)
9120 `(("r-biobase" ,r-biobase)
9121 ("r-biocgenerics" ,r-biocgenerics)
9122 ("r-genomicranges" ,r-genomicranges)
9123 ("r-ggplot2" ,r-ggplot2)
9124 ("r-ggrepel" ,r-ggrepel)
9125 ("r-iranges" ,r-iranges)
9126 ("r-limma" ,r-limma)
9127 ("r-qqman" ,r-qqman)
9128 ("r-s4vectors" ,r-s4vectors)
9129 ("r-summarizedexperiment" ,r-summarizedexperiment)))
9131 `(("r-knitr" ,r-knitr)))
9132 (home-page "https://bioconductor.org/packages/MultiDataSet/")
9133 (synopsis "Implementation of MultiDataSet and ResultSet")
9135 "This package provides an implementation of the BRGE's (Bioinformatic
9136 Research Group in Epidemiology from Center for Research in Environmental
9137 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
9138 integrating multi omics data sets and ResultSet is a container for omics
9139 results. This package contains base classes for MEAL and rexposome
9141 (license license:expat)))
9143 (define-public r-ropls
9150 (uri (bioconductor-uri "ropls" version))
9153 "1j99kdywyljqzdcns5ysh590w4w8iiwzpddpfk5c8d4whax7vk5b"))))
9154 (build-system r-build-system)
9156 `(("r-biobase" ,r-biobase)
9157 ("r-multidataset" ,r-multidataset)))
9159 `(("r-knitr" ,r-knitr))) ; for vignettes
9160 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
9161 (synopsis "Multivariate analysis and feature selection of omics data")
9163 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
9164 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
9165 regression, classification, and feature selection of omics data where the
9166 number of variables exceeds the number of samples and with multicollinearity
9167 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
9168 separately model the variation correlated (predictive) to the factor of
9169 interest and the uncorrelated (orthogonal) variation. While performing
9170 similarly to PLS, OPLS facilitates interpretation.
9172 This package provides imlementations of PCA, PLS, and OPLS for multivariate
9173 analysis and feature selection of omics data. In addition to scores, loadings
9174 and weights plots, the package provides metrics and graphics to determine the
9175 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
9176 validity of the model by permutation testing, detect outliers, and perform
9177 feature selection (e.g. with Variable Importance in Projection or regression
9179 (license license:cecill)))
9181 (define-public r-biosigner
9183 (name "r-biosigner")
9188 (uri (bioconductor-uri "biosigner" version))
9191 "159fbkymn92li7dinsm56nsacjp8wnhsljv7airgs9m82p8wd5sl"))))
9192 (build-system r-build-system)
9194 `(("r-biobase" ,r-biobase)
9195 ("r-e1071" ,r-e1071)
9196 ("r-multidataset" ,r-multidataset)
9197 ("r-randomforest" ,r-randomforest)
9198 ("r-ropls" ,r-ropls)))
9200 `(("r-knitr" ,r-knitr)))
9201 (home-page "https://bioconductor.org/packages/biosigner/")
9202 (synopsis "Signature discovery from omics data")
9204 "Feature selection is critical in omics data analysis to extract
9205 restricted and meaningful molecular signatures from complex and high-dimension
9206 data, and to build robust classifiers. This package implements a method to
9207 assess the relevance of the variables for the prediction performances of the
9208 classifier. The approach can be run in parallel with the PLS-DA, Random
9209 Forest, and SVM binary classifiers. The signatures and the corresponding
9210 'restricted' models are returned, enabling future predictions on new
9212 (license license:cecill)))
9214 (define-public r-annotatr
9221 (uri (bioconductor-uri "annotatr" version))
9224 "0pcf4jrq05bmfxph41hmdx1x147k1ay5fl2h488y1s4h8qm3c67p"))))
9225 (build-system r-build-system)
9227 `(("r-annotationdbi" ,r-annotationdbi)
9228 ("r-annotationhub" ,r-annotationhub)
9229 ("r-dplyr" ,r-dplyr)
9230 ("r-genomeinfodb" ,r-genomeinfodb)
9231 ("r-genomicfeatures" ,r-genomicfeatures)
9232 ("r-genomicranges" ,r-genomicranges)
9233 ("r-ggplot2" ,r-ggplot2)
9234 ("r-iranges" ,r-iranges)
9235 ("r-readr" ,r-readr)
9236 ("r-regioner" ,r-regioner)
9237 ("r-reshape2" ,r-reshape2)
9238 ("r-rtracklayer" ,r-rtracklayer)
9239 ("r-s4vectors" ,r-s4vectors)))
9241 `(("r-knitr" ,r-knitr)))
9242 (home-page "https://bioconductor.org/packages/annotatr/")
9243 (synopsis "Annotation of genomic regions to genomic annotations")
9245 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
9246 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
9247 to investigate the intersecting genomic annotations. Such annotations include
9248 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
9249 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
9250 enhancers. The annotatr package provides an easy way to summarize and
9251 visualize the intersection of genomic sites/regions with genomic
9253 (license license:gpl3)))
9255 (define-public r-rsubread
9262 (uri (bioconductor-uri "Rsubread" version))
9265 "007pbvxkhh930zdkgjaihannjbpbfnbizp3ffc2vyxygw0r4vz68"))))
9266 (properties `((upstream-name . "Rsubread")))
9267 (build-system r-build-system)
9268 (inputs `(("zlib" ,zlib)))
9270 `(("r-matrix" ,r-matrix)))
9271 (home-page "https://bioconductor.org/packages/Rsubread/")
9272 (synopsis "Subread sequence alignment and counting for R")
9274 "This package provides tools for alignment, quantification and analysis
9275 of second and third generation sequencing data. It includes functionality for
9276 read mapping, read counting, SNP calling, structural variant detection and
9277 gene fusion discovery. It can be applied to all major sequencing techologies
9278 and to both short and long sequence reads.")
9279 (license license:gpl3)))
9281 (define-public r-flowutils
9283 (name "r-flowutils")
9288 (uri (bioconductor-uri "flowUtils" version))
9291 "1sdwgyvrsz0pp60zdfrcgb7bs8s87j7257p8ck813ydizc324x9w"))))
9292 (properties `((upstream-name . "flowUtils")))
9293 (build-system r-build-system)
9295 `(("r-biobase" ,r-biobase)
9296 ("r-corpcor" ,r-corpcor)
9297 ("r-flowcore" ,r-flowcore)
9298 ("r-graph" ,r-graph)
9299 ("r-runit" ,r-runit)
9301 (home-page "https://github.com/jspidlen/flowUtils")
9302 (synopsis "Utilities for flow cytometry")
9304 "This package provides utilities for flow cytometry data.")
9305 (license license:artistic2.0)))
9307 (define-public r-consensusclusterplus
9309 (name "r-consensusclusterplus")
9314 (uri (bioconductor-uri "ConsensusClusterPlus" version))
9317 "163nr50nyvwrsajmm0cgxp70pqk61mgw0k7ams694hcb42162j8b"))))
9319 `((upstream-name . "ConsensusClusterPlus")))
9320 (build-system r-build-system)
9323 ("r-biobase" ,r-biobase)
9324 ("r-cluster" ,r-cluster)))
9325 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
9326 (synopsis "Clustering algorithm")
9328 "This package provides an implementation of an algorithm for determining
9329 cluster count and membership by stability evidence in unsupervised analysis.")
9330 (license license:gpl2)))
9332 (define-public r-cytolib
9339 (uri (bioconductor-uri "cytolib" version))
9342 "0wl7zqwv0i38dfzqfsz40n3mcbxi38ffn1rbd5pm9s7hq16zr4nv"))))
9343 (properties `((upstream-name . "cytolib")))
9344 (build-system r-build-system)
9346 `(("r-knitr" ,r-knitr)))
9350 ("r-rcpparmadillo" ,r-rcpparmadillo)
9351 ("r-rcppparallel" ,r-rcppparallel)
9352 ("r-rhdf5lib" ,r-rhdf5lib)
9353 ("r-rprotobuflib" ,r-rprotobuflib)))
9354 (home-page "https://bioconductor.org/packages/cytolib/")
9355 (synopsis "C++ infrastructure for working with gated cytometry")
9357 "This package provides the core data structure and API to represent and
9358 interact with gated cytometry data.")
9359 (license license:artistic2.0)))
9361 (define-public r-flowcore
9368 (uri (bioconductor-uri "flowCore" version))
9371 "13xpbkxi53rxmhvpdiy6bydmhicmxd2gi96d9c1qx4lkss2f14nc"))))
9372 (properties `((upstream-name . "flowCore")))
9373 (build-system r-build-system)
9376 ("r-biobase" ,r-biobase)
9377 ("r-biocgenerics" ,r-biocgenerics)
9378 ("r-cytolib" ,r-cytolib)
9379 ("r-matrixstats" ,r-matrixstats)
9381 ("r-rcpparmadillo" ,r-rcpparmadillo)
9382 ("r-rprotobuflib" ,r-rprotobuflib)
9383 ("r-s4vectors" ,r-s4vectors)))
9385 `(("r-knitr" ,r-knitr)))
9386 (home-page "https://bioconductor.org/packages/flowCore")
9387 (synopsis "Basic structures for flow cytometry data")
9389 "This package provides S4 data structures and basic functions to deal
9390 with flow cytometry data.")
9391 (license license:artistic2.0)))
9393 (define-public r-flowmeans
9395 (name "r-flowmeans")
9400 (uri (bioconductor-uri "flowMeans" version))
9403 "1awskkq48qhv4v9glxgfqi0kgwqd62fbj641k4vvxfcwsf2c7bfg"))))
9404 (properties `((upstream-name . "flowMeans")))
9405 (build-system r-build-system)
9407 `(("r-biobase" ,r-biobase)
9408 ("r-feature" ,r-feature)
9409 ("r-flowcore" ,r-flowcore)
9410 ("r-rrcov" ,r-rrcov)))
9411 (home-page "https://bioconductor.org/packages/flowMeans")
9412 (synopsis "Non-parametric flow cytometry data gating")
9414 "This package provides tools to identify cell populations in Flow
9415 Cytometry data using non-parametric clustering and segmented-regression-based
9416 change point detection.")
9417 (license license:artistic2.0)))
9419 (define-public r-ncdfflow
9426 (uri (bioconductor-uri "ncdfFlow" version))
9429 "1lm88qnfv6rnnr7wmgbvwyj272imjjjn7h3agxqqzsbmn8vyrnf0"))))
9430 (properties `((upstream-name . "ncdfFlow")))
9431 (build-system r-build-system)
9434 ("r-biobase" ,r-biobase)
9435 ("r-biocgenerics" ,r-biocgenerics)
9436 ("r-flowcore" ,r-flowcore)
9438 ("r-rcpparmadillo" ,r-rcpparmadillo)
9439 ("r-rhdf5lib" ,r-rhdf5lib)
9440 ("r-zlibbioc" ,r-zlibbioc)))
9442 `(("r-knitr" ,r-knitr)))
9443 (home-page "https://bioconductor.org/packages/ncdfFlow/")
9444 (synopsis "HDF5 based storage for flow cytometry data")
9446 "This package provides HDF5 storage based methods and functions for
9447 manipulation of flow cytometry data.")
9448 (license license:artistic2.0)))
9450 (define-public r-ggcyto
9457 (uri (bioconductor-uri "ggcyto" version))
9460 "0jd6m84m4znnpix4bcgdby7mnflsn206f5x2vw9n8rxnwzx77wpg"))))
9461 (properties `((upstream-name . "ggcyto")))
9462 (build-system r-build-system)
9464 `(("r-data-table" ,r-data-table)
9465 ("r-flowcore" ,r-flowcore)
9466 ("r-flowworkspace" ,r-flowworkspace)
9467 ("r-ggplot2" ,r-ggplot2)
9468 ("r-gridextra" ,r-gridextra)
9469 ("r-hexbin" ,r-hexbin)
9470 ("r-ncdfflow" ,r-ncdfflow)
9472 ("r-rcolorbrewer" ,r-rcolorbrewer)
9473 ("r-rlang" ,r-rlang)
9474 ("r-scales" ,r-scales)))
9476 `(("r-knitr" ,r-knitr)))
9477 (home-page "https://github.com/RGLab/ggcyto/issues")
9478 (synopsis "Visualize Cytometry data with ggplot")
9480 "With the dedicated fortify method implemented for @code{flowSet},
9481 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
9482 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
9483 and some custom layers also make it easy to add gates and population
9484 statistics to the plot.")
9485 (license license:artistic2.0)))
9487 (define-public r-flowviz
9494 (uri (bioconductor-uri "flowViz" version))
9497 "17x04xwyw2pp5zkhgvrmxkb8cbrv9wql6xhjsfpq0n6yd9dxqc1v"))))
9498 (properties `((upstream-name . "flowViz")))
9499 (build-system r-build-system)
9501 `(("r-biobase" ,r-biobase)
9502 ("r-flowcore" ,r-flowcore)
9503 ("r-hexbin" ,r-hexbin)
9504 ("r-idpmisc" ,r-idpmisc)
9505 ("r-kernsmooth" ,r-kernsmooth)
9506 ("r-lattice" ,r-lattice)
9507 ("r-latticeextra" ,r-latticeextra)
9509 ("r-rcolorbrewer" ,r-rcolorbrewer)))
9511 `(("r-knitr" ,r-knitr)))
9512 (home-page "https://bioconductor.org/packages/flowViz/")
9513 (synopsis "Visualization for flow cytometry")
9515 "This package provides visualization tools for flow cytometry data.")
9516 (license license:artistic2.0)))
9518 (define-public r-flowclust
9520 (name "r-flowclust")
9525 (uri (bioconductor-uri "flowClust" version))
9528 "03xsmprrkxwkaksjlaxwp54mqfb3zlg6dbqhp87w78fwscisv76b"))))
9529 (properties `((upstream-name . "flowClust")))
9530 (build-system r-build-system)
9533 (list "--configure-args=--enable-bundled-gsl=no")))
9535 `(("r-biobase" ,r-biobase)
9536 ("r-biocgenerics" ,r-biocgenerics)
9538 ("r-corpcor" ,r-corpcor)
9539 ("r-ellipse" ,r-ellipse)
9540 ("r-flowcore" ,r-flowcore)
9541 ("r-flowviz" ,r-flowviz)
9542 ("r-graph" ,r-graph)
9543 ("r-mnormt" ,r-mnormt)))
9547 `(("pkg-config" ,pkg-config)
9548 ("r-knitr" ,r-knitr)))
9549 (home-page "https://bioconductor.org/packages/flowClust")
9550 (synopsis "Clustering for flow cytometry")
9552 "This package provides robust model-based clustering using a t-mixture
9553 model with Box-Cox transformation.")
9554 (license license:artistic2.0)))
9556 ;; TODO: this package bundles an old version of protobuf. It's not easy to
9557 ;; make it use our protobuf package instead.
9558 (define-public r-rprotobuflib
9560 (name "r-rprotobuflib")
9565 (uri (bioconductor-uri "RProtoBufLib" version))
9568 "1hyds97ay4mn7nl830yh9v8mlasgsljsx5wsrhz2zsmbbyx6wbnb"))))
9569 (properties `((upstream-name . "RProtoBufLib")))
9570 (build-system r-build-system)
9573 (modify-phases %standard-phases
9574 (add-after 'unpack 'unpack-bundled-sources
9576 (with-directory-excursion "src"
9577 (invoke "tar" "xf" "protobuf-3.13.0.tar.gz")))))))
9579 `(("r-knitr" ,r-knitr)))
9580 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
9581 (synopsis "C++ headers and static libraries of Protocol buffers")
9583 "This package provides the headers and static library of Protocol buffers
9584 for other R packages to compile and link against.")
9585 (license license:bsd-3)))
9587 (define-public r-flowworkspace
9589 (name "r-flowworkspace")
9594 (uri (bioconductor-uri "flowWorkspace" version))
9597 "1a9qb2dcvwgb3z0vdbbzn1rzy77d3da72kirs272344hdx9b2cx9"))))
9598 (properties `((upstream-name . "flowWorkspace")))
9599 (build-system r-build-system)
9601 `(("r-aws-s3" ,r-aws-s3)
9602 ("r-aws-signature" ,r-aws-signature)
9604 ("r-biobase" ,r-biobase)
9605 ("r-biocgenerics" ,r-biocgenerics)
9606 ("r-cytolib" ,r-cytolib)
9607 ("r-data-table" ,r-data-table)
9608 ("r-delayedarray" ,r-delayedarray)
9609 ("r-digest" ,r-digest)
9610 ("r-dplyr" ,r-dplyr)
9611 ("r-flowcore" ,r-flowcore)
9612 ("r-ggplot2" ,r-ggplot2)
9613 ("r-graph" ,r-graph)
9614 ("r-lattice" ,r-lattice)
9615 ("r-latticeextra" ,r-latticeextra)
9616 ("r-matrixstats" ,r-matrixstats)
9617 ("r-ncdfflow" ,r-ncdfflow)
9620 ("r-rcpparmadillo" ,r-rcpparmadillo)
9621 ("r-rcppparallel" ,r-rcppparallel)
9622 ("r-rgraphviz" ,r-rgraphviz)
9623 ("r-rhdf5lib" ,r-rhdf5lib)
9624 ("r-rprotobuflib" ,r-rprotobuflib)
9625 ("r-s4vectors" ,r-s4vectors)
9626 ("r-scales" ,r-scales)
9629 `(("r-knitr" ,r-knitr)))
9630 (home-page "https://bioconductor.org/packages/flowWorkspace/")
9631 (synopsis "Infrastructure for working with cytometry data")
9633 "This package is designed to facilitate comparison of automated gating
9634 methods against manual gating done in flowJo. This package allows you to
9635 import basic flowJo workspaces into BioConductor and replicate the gating from
9636 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
9637 samples, compensation, and transformation are performed so that the output
9638 matches the flowJo analysis.")
9639 (license license:artistic2.0)))
9641 (define-public r-flowstats
9643 (name "r-flowstats")
9648 (uri (bioconductor-uri "flowStats" version))
9651 "1yr5m7qmhmm52c70z3d0zy4zgf0hja7r2ig9yljv5w86bzm962x6"))))
9652 (properties `((upstream-name . "flowStats")))
9653 (build-system r-build-system)
9655 `(("r-biobase" ,r-biobase)
9656 ("r-biocgenerics" ,r-biocgenerics)
9657 ("r-cluster" ,r-cluster)
9659 ("r-flowcore" ,r-flowcore)
9660 ("r-flowviz" ,r-flowviz)
9661 ("r-flowworkspace" ,r-flowworkspace)
9662 ("r-kernsmooth" ,r-kernsmooth)
9664 ("r-lattice" ,r-lattice)
9666 ("r-ncdfflow" ,r-ncdfflow)
9667 ("r-rcolorbrewer" ,r-rcolorbrewer)
9668 ("r-rrcov" ,r-rrcov)))
9669 (home-page "http://www.github.com/RGLab/flowStats")
9670 (synopsis "Statistical methods for the analysis of flow cytometry data")
9672 "This package provides methods and functionality to analyze flow data
9673 that is beyond the basic infrastructure provided by the @code{flowCore}
9675 (license license:artistic2.0)))
9677 (define-public r-opencyto
9684 (uri (bioconductor-uri "openCyto" version))
9687 "1par1d5pk1rjg15q7i5z5wqma7xg6fycb826a823wk8wr52a885x"))))
9688 (properties `((upstream-name . "openCyto")))
9689 (build-system r-build-system)
9691 `(("r-biobase" ,r-biobase)
9692 ("r-biocgenerics" ,r-biocgenerics)
9694 ("r-data-table" ,r-data-table)
9695 ("r-flowclust" ,r-flowclust)
9696 ("r-flowcore" ,r-flowcore)
9697 ("r-flowstats" ,r-flowstats)
9698 ("r-flowviz" ,r-flowviz)
9699 ("r-flowworkspace" ,r-flowworkspace)
9700 ("r-graph" ,r-graph)
9701 ("r-gtools" ,r-gtools)
9703 ("r-lattice" ,r-lattice)
9705 ("r-ncdfflow" ,r-ncdfflow)
9707 ("r-r-utils" ,r-r-utils)
9709 ("r-rcolorbrewer" ,r-rcolorbrewer)
9711 ("r-rrcov" ,r-rrcov)))
9713 `(("r-knitr" ,r-knitr)))
9714 (home-page "https://bioconductor.org/packages/openCyto")
9715 (synopsis "Hierarchical gating pipeline for flow cytometry data")
9717 "This package is designed to facilitate the automated gating methods in a
9718 sequential way to mimic the manual gating strategy.")
9719 (license license:artistic2.0)))
9721 (define-public r-cytoml
9728 (uri (bioconductor-uri "CytoML" version))
9731 "0ixy7mmnipk8wy61wz6qy7jfbc5zhs6p5iqaii8hdprjnb841ri7"))))
9732 (properties `((upstream-name . "CytoML")))
9733 (build-system r-build-system)
9735 `(("libxml2" ,libxml2)
9738 `(("r-base64enc" ,r-base64enc)
9740 ("r-biobase" ,r-biobase)
9741 ("r-corpcor" ,r-corpcor)
9742 ("r-cytolib" ,r-cytolib)
9743 ("r-data-table" ,r-data-table)
9744 ("r-dplyr" ,r-dplyr)
9745 ("r-flowcore" ,r-flowcore)
9746 ("r-flowworkspace" ,r-flowworkspace)
9747 ("r-ggcyto" ,r-ggcyto)
9748 ("r-graph" ,r-graph)
9749 ("r-jsonlite" ,r-jsonlite)
9750 ("r-lattice" ,r-lattice)
9751 ("r-opencyto" ,r-opencyto)
9755 ("r-rcpparmadillo" ,r-rcpparmadillo)
9756 ("r-rcppparallel" ,r-rcppparallel)
9757 ("r-rgraphviz" ,r-rgraphviz)
9758 ("r-rhdf5lib" ,r-rhdf5lib)
9759 ("r-rprotobuflib" ,r-rprotobuflib)
9760 ("r-runit" ,r-runit)
9761 ("r-tibble" ,r-tibble)
9764 ("r-yaml" ,r-yaml)))
9766 `(("r-knitr" ,r-knitr)))
9767 (home-page "https://github.com/RGLab/CytoML")
9768 (synopsis "GatingML interface for cross platform cytometry data sharing")
9770 "This package provides an interface to implementations of the GatingML2.0
9771 standard to exchange gated cytometry data with other software platforms.")
9772 (license license:artistic2.0)))
9774 (define-public r-flowsom
9781 (uri (bioconductor-uri "FlowSOM" version))
9784 "18h7p7g3w9imyd1c93jllgp4kd74z96cs85wcqfhmd26nx18hl82"))))
9785 (properties `((upstream-name . "FlowSOM")))
9786 (build-system r-build-system)
9788 `(("r-biocgenerics" ,r-biocgenerics)
9789 ("r-colorramps" ,r-colorramps)
9790 ("r-consensusclusterplus" ,r-consensusclusterplus)
9791 ("r-cytoml" ,r-cytoml)
9792 ("r-dplyr" ,r-dplyr)
9793 ("r-flowcore" ,r-flowcore)
9794 ("r-flowworkspace" ,r-flowworkspace)
9795 ("r-ggforce" ,r-ggforce)
9796 ("r-ggnewscale" ,r-ggnewscale)
9797 ("r-ggplot2" ,r-ggplot2)
9798 ("r-ggpointdensity" ,r-ggpointdensity)
9799 ("r-ggpubr" ,r-ggpubr)
9800 ("r-ggrepel" ,r-ggrepel)
9801 ("r-igraph" ,r-igraph)
9802 ("r-magrittr" ,r-magrittr)
9803 ("r-pheatmap" ,r-pheatmap)
9804 ("r-rcolorbrewer" ,r-rcolorbrewer)
9805 ("r-rlang" ,r-rlang)
9806 ("r-rtsne" ,r-rtsne)
9807 ("r-scattermore" ,r-scattermore)
9808 ("r-tidyr" ,r-tidyr)
9810 (home-page "https://bioconductor.org/packages/FlowSOM/")
9811 (synopsis "Visualize and interpret cytometry data")
9813 "FlowSOM offers visualization options for cytometry data, by using
9814 self-organizing map clustering and minimal spanning trees.")
9815 (license license:gpl2+)))
9817 (define-public r-mixomics
9824 (uri (bioconductor-uri "mixOmics" version))
9827 "1hri5rrqf8vq3c6pivfamv60yz9mf9rrdpdd5bw2h24lghm2x8rw"))))
9828 (properties `((upstream-name . "mixOmics")))
9829 (build-system r-build-system)
9831 `(("r-biocparallel" ,r-biocparallel)
9832 ("r-corpcor" ,r-corpcor)
9833 ("r-dplyr" ,r-dplyr)
9834 ("r-ellipse" ,r-ellipse)
9835 ("r-ggrepel" ,r-ggrepel)
9836 ("r-ggplot2" ,r-ggplot2)
9837 ("r-gridextra" ,r-gridextra)
9838 ("r-igraph" ,r-igraph)
9839 ("r-lattice" ,r-lattice)
9841 ("r-matrixstats" ,r-matrixstats)
9842 ("r-rarpack" ,r-rarpack)
9843 ("r-rcolorbrewer" ,r-rcolorbrewer)
9844 ("r-reshape2" ,r-reshape2)
9845 ("r-tidyr" ,r-tidyr)))
9847 `(("r-knitr" ,r-knitr)))
9848 (home-page "http://www.mixOmics.org")
9849 (synopsis "Multivariate methods for exploration of biological datasets")
9851 "mixOmics offers a wide range of multivariate methods for the exploration
9852 and integration of biological datasets with a particular focus on variable
9853 selection. The package proposes several sparse multivariate models we have
9854 developed to identify the key variables that are highly correlated, and/or
9855 explain the biological outcome of interest. The data that can be analysed
9856 with mixOmics may come from high throughput sequencing technologies, such as
9857 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
9858 also beyond the realm of omics (e.g. spectral imaging). The methods
9859 implemented in mixOmics can also handle missing values without having to
9860 delete entire rows with missing data.")
9861 (license license:gpl2+)))
9863 (define-public r-depecher
9864 (package ;Source/Weave error
9870 (uri (bioconductor-uri "DepecheR" version))
9873 "04vxc43p3kpsx0vksk2nwmy9p56h35z2mc8j9p2wm29zaz1y8j3p"))))
9874 (properties `((upstream-name . "DepecheR")))
9875 (build-system r-build-system)
9877 `(("r-beanplot" ,r-beanplot)
9878 ("r-dosnow" ,r-dosnow)
9879 ("r-dplyr" ,r-dplyr)
9881 ("r-foreach" ,r-foreach)
9882 ("r-ggplot2" ,r-ggplot2)
9883 ("r-gmodels" ,r-gmodels)
9884 ("r-gplots" ,r-gplots)
9886 ("r-matrixstats" ,r-matrixstats)
9887 ("r-mixomics" ,r-mixomics)
9888 ("r-moments" ,r-moments)
9890 ("r-rcppeigen" ,r-rcppeigen)
9891 ("r-reshape2" ,r-reshape2)
9892 ("r-robustbase" ,r-robustbase)
9893 ("r-viridis" ,r-viridis)))
9895 `(("r-knitr" ,r-knitr)))
9896 (home-page "https://bioconductor.org/packages/DepecheR/")
9897 (synopsis "Identify traits of clusters in high-dimensional entities")
9899 "The purpose of this package is to identify traits in a dataset that can
9900 separate groups. This is done on two levels. First, clustering is performed,
9901 using an implementation of sparse K-means. Secondly, the generated clusters
9902 are used to predict outcomes of groups of individuals based on their
9903 distribution of observations in the different clusters. As certain clusters
9904 with separating information will be identified, and these clusters are defined
9905 by a sparse number of variables, this method can reduce the complexity of
9906 data, to only emphasize the data that actually matters.")
9907 (license license:expat)))
9909 (define-public r-rcistarget
9911 (name "r-rcistarget")
9916 (uri (bioconductor-uri "RcisTarget" version))
9919 "1yh0l11vnslgr6zsbpgc8mc4aa32zy34f5yrz98hkcdl53iw5y7f"))))
9920 (properties `((upstream-name . "RcisTarget")))
9921 (build-system r-build-system)
9923 `(("r-arrow" ,r-arrow)
9924 ("r-aucell" ,r-aucell)
9925 ("r-biocgenerics" ,r-biocgenerics)
9926 ("r-data-table" ,r-data-table)
9927 ("r-dplyr" ,r-dplyr)
9928 ("r-feather" ,r-feather)
9929 ("r-genomeinfodb" ,r-genomeinfodb)
9930 ("r-genomicranges" ,r-genomicranges)
9931 ("r-gseabase" ,r-gseabase)
9932 ("r-r-utils" ,r-r-utils)
9933 ("r-summarizedexperiment" ,r-summarizedexperiment)
9934 ("r-tibble" ,r-tibble)))
9936 `(("r-knitr" ,r-knitr)))
9937 (home-page "https://aertslab.org/#scenic")
9938 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
9940 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
9941 over-represented on a gene list. In a first step, RcisTarget selects DNA
9942 motifs that are significantly over-represented in the surroundings of the
9943 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
9944 achieved by using a database that contains genome-wide cross-species rankings
9945 for each motif. The motifs that are then annotated to TFs and those that have
9946 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
9947 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
9948 genes in the gene-set that are ranked above the leading edge).")
9949 (license license:gpl3)))
9951 (define-public r-cicero
9958 (uri (bioconductor-uri "cicero" version))
9961 "0kw16zf9004d1zlwsswhbcb7p77nabpd1fjagznff3zyan9fpdxf"))))
9962 (build-system r-build-system)
9964 `(("r-assertthat" ,r-assertthat)
9965 ("r-biobase" ,r-biobase)
9966 ("r-biocgenerics" ,r-biocgenerics)
9967 ("r-data-table" ,r-data-table)
9968 ("r-dplyr" ,r-dplyr)
9970 ("r-genomicranges" ,r-genomicranges)
9971 ("r-ggplot2" ,r-ggplot2)
9972 ("r-glasso" ,r-glasso)
9974 ("r-igraph" ,r-igraph)
9975 ("r-iranges" ,r-iranges)
9976 ("r-matrix" ,r-matrix)
9977 ("r-monocle" ,r-monocle)
9979 ("r-reshape2" ,r-reshape2)
9980 ("r-s4vectors" ,r-s4vectors)
9981 ("r-stringi" ,r-stringi)
9982 ("r-stringr" ,r-stringr)
9983 ("r-tibble" ,r-tibble)
9984 ("r-tidyr" ,r-tidyr)
9985 ("r-vgam" ,r-vgam)))
9987 `(("r-knitr" ,r-knitr)))
9988 (home-page "https://bioconductor.org/packages/cicero/")
9989 (synopsis "Predict cis-co-accessibility from single-cell data")
9991 "Cicero computes putative cis-regulatory maps from single-cell chromatin
9992 accessibility data. It also extends the monocle package for use in chromatin
9993 accessibility data.")
9994 (license license:expat)))
9996 ;; This is the latest commit on the "monocle3" branch.
9997 (define-public r-cicero-monocle3
9998 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
10000 (package (inherit r-cicero)
10001 (name "r-cicero-monocle3")
10002 (version (git-version "1.3.2" revision commit))
10006 (uri (git-reference
10007 (url "https://github.com/cole-trapnell-lab/cicero-release")
10009 (file-name (git-file-name name version))
10012 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
10014 `(("r-monocle3" ,r-monocle3)
10015 ,@(alist-delete "r-monocle"
10016 (package-propagated-inputs r-cicero)))))))
10018 (define-public r-circrnaprofiler
10020 (name "r-circrnaprofiler")
10025 (uri (bioconductor-uri "circRNAprofiler" version))
10028 "1hif40vfg2lkbyf6abbkxbdm3b1biw6gxnh6ca2sydvi3y5l2ys2"))))
10030 `((upstream-name . "circRNAprofiler")))
10031 (build-system r-build-system)
10033 `(("r-annotationhub" ,r-annotationhub)
10034 ("r-biostrings" ,r-biostrings)
10035 ("r-bsgenome" ,r-bsgenome)
10036 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
10037 ("r-deseq2" ,r-deseq2)
10038 ("r-dplyr" ,r-dplyr)
10039 ("r-edger" ,r-edger)
10040 ("r-genomeinfodb" ,r-genomeinfodb)
10041 ("r-genomicranges" ,r-genomicranges)
10042 ("r-ggplot2" ,r-ggplot2)
10043 ("r-gwascat" ,r-gwascat)
10044 ("r-iranges" ,r-iranges)
10045 ("r-magrittr" ,r-magrittr)
10046 ("r-r-utils" ,r-r-utils)
10047 ("r-readr" ,r-readr)
10048 ("r-reshape2" ,r-reshape2)
10049 ("r-rlang" ,r-rlang)
10050 ("r-rtracklayer" ,r-rtracklayer)
10051 ("r-s4vectors" ,r-s4vectors)
10052 ("r-seqinr" ,r-seqinr)
10053 ("r-stringi" ,r-stringi)
10054 ("r-stringr" ,r-stringr)
10055 ("r-universalmotif" ,r-universalmotif)))
10057 `(("r-knitr" ,r-knitr)))
10059 "https://github.com/Aufiero/circRNAprofiler")
10061 "Computational framework for the downstream analysis of circular RNA's")
10063 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
10064 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
10065 framework allows combining and analyzing circRNAs previously detected by
10066 multiple publicly available annotation-based circRNA detection tools. It
10067 covers different aspects of circRNAs analysis from differential expression
10068 analysis, evolutionary conservation, biogenesis to functional analysis.")
10069 (license license:gpl3)))
10071 (define-public r-cistopic
10072 (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
10075 (name "r-cistopic")
10076 (version (git-version "0.2.1" revision commit))
10080 (uri (git-reference
10081 (url "https://github.com/aertslab/cisTopic")
10083 (file-name (git-file-name name version))
10086 "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
10087 (build-system r-build-system)
10089 `(("r-aucell" ,r-aucell)
10090 ("r-data-table" ,r-data-table)
10091 ("r-dplyr" ,r-dplyr)
10092 ("r-dosnow" ,r-dosnow)
10094 ("r-feather" ,r-feather)
10095 ("r-fitdistrplus" ,r-fitdistrplus)
10096 ("r-genomicranges" ,r-genomicranges)
10097 ("r-ggplot2" ,r-ggplot2)
10099 ("r-matrix" ,r-matrix)
10101 ("r-rcistarget" ,r-rcistarget)
10102 ("r-rtracklayer" ,r-rtracklayer)
10103 ("r-s4vectors" ,r-s4vectors)))
10104 (home-page "https://github.com/aertslab/cisTopic")
10105 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
10107 "The sparse nature of single cell epigenomics data can be overruled using
10108 probabilistic modelling methods such as @dfn{Latent Dirichlet
10109 Allocation} (LDA). This package allows the probabilistic modelling of
10110 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
10111 includes functionalities to identify cell states based on the contribution of
10112 cisTopics and explore the nature and regulatory proteins driving them.")
10113 (license license:gpl3))))
10115 (define-public r-genie3
10122 (uri (bioconductor-uri "GENIE3" version))
10125 "1v54dzcz654wfm3npbp8gb55v49im0fm547cz3hvsidq4zhi3l1b"))))
10126 (properties `((upstream-name . "GENIE3")))
10127 (build-system r-build-system)
10129 `(("r-dplyr" ,r-dplyr)
10130 ("r-reshape2" ,r-reshape2)))
10132 `(("r-knitr" ,r-knitr)))
10133 (home-page "https://bioconductor.org/packages/GENIE3")
10134 (synopsis "Gene network inference with ensemble of trees")
10136 "This package implements the GENIE3 algorithm for inferring gene
10137 regulatory networks from expression data.")
10138 (license license:gpl2+)))
10140 (define-public r-roc
10147 (uri (bioconductor-uri "ROC" version))
10150 "0ff5rcpyybgjzsfbhaslim0m02n3bksv1r9v7bq0gg0iyzll0rjc"))))
10151 (properties `((upstream-name . "ROC")))
10152 (build-system r-build-system)
10154 `(("r-knitr" ,r-knitr)))
10155 (home-page "https://www.bioconductor.org/packages/ROC/")
10156 (synopsis "Utilities for ROC curves")
10158 "This package provides utilities for @dfn{Receiver Operating
10159 Characteristic} (ROC) curves, with a focus on micro arrays.")
10160 (license license:artistic2.0)))
10162 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
10164 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
10169 (uri (bioconductor-uri
10170 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
10171 version 'annotation))
10174 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
10177 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
10178 (build-system r-build-system)
10179 (propagated-inputs `(("r-minfi" ,r-minfi)))
10181 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
10182 (synopsis "Annotation for Illumina's 450k methylation arrays")
10184 "This package provides manifests and annotation for Illumina's 450k array
10186 (license license:artistic2.0)))
10188 (define-public r-watermelon
10190 (name "r-watermelon")
10195 (uri (bioconductor-uri "wateRmelon" version))
10198 "1qar8z0nf33bqr488swig0bfq8lnvcdjcxvw3q3b0hkkvybn27zw"))))
10199 (properties `((upstream-name . "wateRmelon")))
10200 (build-system r-build-system)
10202 `(("r-biobase" ,r-biobase)
10203 ("r-illuminahumanmethylation450kanno-ilmn12-hg19"
10204 ,r-illuminahumanmethylation450kanno-ilmn12-hg19)
10205 ("r-illuminaio" ,r-illuminaio)
10206 ("r-limma" ,r-limma)
10208 ("r-matrixstats" ,r-matrixstats)
10209 ("r-methylumi" ,r-methylumi)
10211 (home-page "https://bioconductor.org/packages/wateRmelon/")
10212 (synopsis "Illumina 450 methylation array normalization and metrics")
10214 "The standard index of DNA methylation (beta) is computed from methylated
10215 and unmethylated signal intensities. Betas calculated from raw signal
10216 intensities perform well, but using 11 methylomic datasets we demonstrate that
10217 quantile normalization methods produce marked improvement. The commonly used
10218 procedure of normalizing betas is inferior to the separate normalization of M
10219 and U, and it is also advantageous to normalize Type I and Type II assays
10220 separately. This package provides 15 flavours of betas and three performance
10221 metrics, with methods for objects produced by the @code{methylumi} and
10222 @code{minfi} packages.")
10223 (license license:gpl3)))
10225 (define-public r-gdsfmt
10232 (uri (bioconductor-uri "gdsfmt" version))
10235 "119qdivd7vaaqkjb0nrwidi6g26hh8znhif3g4prqn7x5pl2clvy"))
10236 (modules '((guix build utils)))
10237 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
10238 ;; them and link with system libraries instead.
10241 (for-each delete-file-recursively
10245 (substitute* "src/Makevars"
10246 (("all: \\$\\(SHLIB\\)") "all:")
10247 (("\\$\\(SHLIB\\): liblzma.a") "")
10248 (("(ZLIB|LZ4)/.*") "")
10249 (("CoreArray/dVLIntGDS.cpp.*")
10250 "CoreArray/dVLIntGDS.cpp")
10251 (("CoreArray/dVLIntGDS.o.*")
10252 "CoreArray/dVLIntGDS.o")
10253 (("PKG_LIBS = ./liblzma.a")
10254 "PKG_LIBS = -llz4"))
10255 (substitute* "src/CoreArray/dStream.h"
10256 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
10257 (string-append "include <" header ">")))
10259 (properties `((upstream-name . "gdsfmt")))
10260 (build-system r-build-system)
10266 `(("r-knitr" ,r-knitr)))
10267 (home-page "http://corearray.sourceforge.net/")
10269 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
10271 "This package provides a high-level R interface to CoreArray @dfn{Genomic
10272 Data Structure} (GDS) data files, which are portable across platforms with
10273 hierarchical structure to store multiple scalable array-oriented data sets
10274 with metadata information. It is suited for large-scale datasets, especially
10275 for data which are much larger than the available random-access memory. The
10276 @code{gdsfmt} package offers efficient operations specifically designed for
10277 integers of less than 8 bits, since a diploid genotype, like
10278 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
10279 byte. Data compression and decompression are available with relatively
10280 efficient random access. It is also allowed to read a GDS file in parallel
10281 with multiple R processes supported by the package @code{parallel}.")
10282 (license license:lgpl3)))
10284 (define-public r-bigmelon
10286 (name "r-bigmelon")
10291 (uri (bioconductor-uri "bigmelon" version))
10294 "061f0hc4m4nvdr6298pg3inpx1z2bpsm9nlxqs3v7n58q15xyzri"))))
10295 (properties `((upstream-name . "bigmelon")))
10296 (build-system r-build-system)
10298 `(("r-biobase" ,r-biobase)
10299 ("r-biocgenerics" ,r-biocgenerics)
10300 ("r-gdsfmt" ,r-gdsfmt)
10301 ("r-geoquery" ,r-geoquery)
10302 ("r-methylumi" ,r-methylumi)
10303 ("r-minfi" ,r-minfi)
10304 ("r-watermelon" ,r-watermelon)))
10305 (home-page "https://bioconductor.org/packages/bigmelon/")
10306 (synopsis "Illumina methylation array analysis for large experiments")
10308 "This package provides methods for working with Illumina arrays using the
10309 @code{gdsfmt} package.")
10310 (license license:gpl3)))
10312 (define-public r-seqbias
10319 (uri (bioconductor-uri "seqbias" version))
10322 "06w43plv4x1pafybq633n7adqp9yj3bvaaamq7vylmkfbcx3nl8k"))))
10323 (properties `((upstream-name . "seqbias")))
10324 (build-system r-build-system)
10326 `(("r-biostrings" ,r-biostrings)
10327 ("r-genomicranges" ,r-genomicranges)
10328 ("r-rhtslib" ,r-rhtslib)))
10329 (home-page "https://bioconductor.org/packages/seqbias/")
10330 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
10332 "This package implements a model of per-position sequencing bias in
10333 high-throughput sequencing data using a simple Bayesian network, the structure
10334 and parameters of which are trained on a set of aligned reads and a reference
10336 (license license:lgpl3)))
10338 (define-public r-snplocs-hsapiens-dbsnp144-grch37
10340 (name "r-snplocs-hsapiens-dbsnp144-grch37")
10341 (version "0.99.20")
10344 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
10345 version 'annotation))
10348 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
10349 (build-system r-build-system)
10350 ;; As this package provides little more than a very large data file it
10351 ;; doesn't make sense to build substitutes.
10352 (arguments `(#:substitutable? #f))
10354 `(("r-biocgenerics" ,r-biocgenerics)
10355 ("r-s4vectors" ,r-s4vectors)
10356 ("r-iranges" ,r-iranges)
10357 ("r-genomeinfodb" ,r-genomeinfodb)
10358 ("r-genomicranges" ,r-genomicranges)
10359 ("r-bsgenome" ,r-bsgenome)
10360 ("r-biostrings" ,r-biostrings)))
10362 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
10363 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
10364 (description "This package provides SNP locations and alleles for Homo
10365 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
10366 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
10367 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
10368 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
10369 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
10370 the mitochondrion chromosome. Therefore, the SNPs in this package can be
10371 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
10372 correct position but this injection will exclude chrM (i.e. nothing will be
10373 injected in that sequence).")
10374 (license license:artistic2.0)))
10376 (define-public r-reqon
10383 (uri (bioconductor-uri "ReQON" version))
10386 "1z13avbxwvvhh03arjfnaipznynifsi8k2hzw4kappz24f7lwmza"))))
10387 (properties `((upstream-name . "ReQON")))
10388 (build-system r-build-system)
10390 `(("r-rjava" ,r-rjava)
10391 ("r-rsamtools" ,r-rsamtools)
10392 ("r-seqbias" ,r-seqbias)))
10393 (home-page "https://bioconductor.org/packages/ReQON/")
10394 (synopsis "Recalibrating quality of nucleotides")
10396 "This package provides an implementation of an algorithm for
10397 recalibrating the base quality scores for aligned sequencing data in BAM
10399 (license license:gpl2)))
10401 (define-public r-wavcluster
10403 (name "r-wavcluster")
10408 (uri (bioconductor-uri "wavClusteR" version))
10411 "1sydzrqydfv1ik2h08xkxlx6xrv866bf0if6v5wch9l3krh0sych"))))
10412 (properties `((upstream-name . "wavClusteR")))
10413 (build-system r-build-system)
10415 `(("r-biocgenerics" ,r-biocgenerics)
10416 ("r-biostrings" ,r-biostrings)
10417 ("r-foreach" ,r-foreach)
10418 ("r-genomicfeatures" ,r-genomicfeatures)
10419 ("r-genomicranges" ,r-genomicranges)
10420 ("r-ggplot2" ,r-ggplot2)
10421 ("r-hmisc" ,r-hmisc)
10422 ("r-iranges" ,r-iranges)
10423 ("r-mclust" ,r-mclust)
10424 ("r-rsamtools" ,r-rsamtools)
10425 ("r-rtracklayer" ,r-rtracklayer)
10426 ("r-s4vectors" ,r-s4vectors)
10427 ("r-seqinr" ,r-seqinr)
10428 ("r-stringr" ,r-stringr)))
10430 `(("r-knitr" ,r-knitr)))
10431 (home-page "https://bioconductor.org/packages/wavClusteR/")
10432 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
10434 "This package provides an integrated pipeline for the analysis of
10435 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
10436 sequencing errors, SNPs and additional non-experimental sources by a non-
10437 parametric mixture model. The protein binding sites (clusters) are then
10438 resolved at high resolution and cluster statistics are estimated using a
10439 rigorous Bayesian framework. Post-processing of the results, data export for
10440 UCSC genome browser visualization and motif search analysis are provided. In
10441 addition, the package integrates RNA-Seq data to estimate the False
10442 Discovery Rate of cluster detection. Key functions support parallel multicore
10443 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
10444 be applied to the analysis of other NGS data obtained from experimental
10445 procedures that induce nucleotide substitutions (e.g. BisSeq).")
10446 (license license:gpl2)))
10448 (define-public r-timeseriesexperiment
10450 (name "r-timeseriesexperiment")
10455 (uri (bioconductor-uri "TimeSeriesExperiment" version))
10458 "10xgihjssnc6i03819p9gnzwfc7znanic514ar3yxzl3fhxy3yyy"))))
10460 `((upstream-name . "TimeSeriesExperiment")))
10461 (build-system r-build-system)
10463 `(("r-deseq2" ,r-deseq2)
10464 ("r-dplyr" ,r-dplyr)
10465 ("r-dynamictreecut" ,r-dynamictreecut)
10466 ("r-edger" ,r-edger)
10467 ("r-ggplot2" ,r-ggplot2)
10468 ("r-hmisc" ,r-hmisc)
10469 ("r-limma" ,r-limma)
10470 ("r-magrittr" ,r-magrittr)
10471 ("r-proxy" ,r-proxy)
10472 ("r-s4vectors" ,r-s4vectors)
10473 ("r-summarizedexperiment" ,r-summarizedexperiment)
10474 ("r-tibble" ,r-tibble)
10475 ("r-tidyr" ,r-tidyr)
10476 ("r-vegan" ,r-vegan)
10477 ("r-viridis" ,r-viridis)))
10479 `(("r-knitr" ,r-knitr)))
10480 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
10481 (synopsis "Analysis for short time-series data")
10483 "This package is a visualization and analysis toolbox for short time
10484 course data which includes dimensionality reduction, clustering, two-sample
10485 differential expression testing and gene ranking techniques. The package also
10486 provides methods for retrieving enriched pathways.")
10487 (license license:lgpl3+)))
10489 (define-public r-variantfiltering
10491 (name "r-variantfiltering")
10496 (uri (bioconductor-uri "VariantFiltering" version))
10499 "0abhrk53csd9jz9sv4q1qr74jax9mbj2icbz1iilf1123nvnjypd"))))
10501 `((upstream-name . "VariantFiltering")))
10502 (build-system r-build-system)
10504 `(("r-annotationdbi" ,r-annotationdbi)
10505 ("r-biobase" ,r-biobase)
10506 ("r-biocgenerics" ,r-biocgenerics)
10507 ("r-biocparallel" ,r-biocparallel)
10508 ("r-biostrings" ,r-biostrings)
10509 ("r-bsgenome" ,r-bsgenome)
10511 ("r-genomeinfodb" ,r-genomeinfodb)
10512 ("r-genomicfeatures" ,r-genomicfeatures)
10513 ("r-genomicranges" ,r-genomicranges)
10514 ("r-genomicscores" ,r-genomicscores)
10515 ("r-graph" ,r-graph)
10517 ("r-iranges" ,r-iranges)
10519 ("r-rsamtools" ,r-rsamtools)
10520 ("r-s4vectors" ,r-s4vectors)
10521 ("r-shiny" ,r-shiny)
10522 ("r-shinyjs" ,r-shinyjs)
10523 ("r-shinythemes" ,r-shinythemes)
10524 ("r-shinytree" ,r-shinytree)
10525 ("r-summarizedexperiment" ,r-summarizedexperiment)
10526 ("r-variantannotation" ,r-variantannotation)
10527 ("r-xvector" ,r-xvector)))
10528 (home-page "https://github.com/rcastelo/VariantFiltering")
10529 (synopsis "Filtering of coding and non-coding genetic variants")
10531 "Filter genetic variants using different criteria such as inheritance
10532 model, amino acid change consequence, minor allele frequencies across human
10533 populations, splice site strength, conservation, etc.")
10534 (license license:artistic2.0)))
10536 (define-public r-genomegraphs
10538 (name "r-genomegraphs")
10543 (uri (bioconductor-uri "GenomeGraphs" version))
10546 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
10547 (properties `((upstream-name . "GenomeGraphs")))
10548 (build-system r-build-system)
10550 `(("r-biomart" ,r-biomart)))
10551 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
10552 (synopsis "Plotting genomic information from Ensembl")
10554 "Genomic data analyses requires integrated visualization of known genomic
10555 information and new experimental data. GenomeGraphs uses the biomaRt package
10556 to perform live annotation queries to Ensembl and translates this to e.g.
10557 gene/transcript structures in viewports of the grid graphics package. This
10558 results in genomic information plotted together with your data. Another
10559 strength of GenomeGraphs is to plot different data types such as array CGH,
10560 gene expression, sequencing and other data, together in one plot using the
10561 same genome coordinate system.")
10562 (license license:artistic2.0)))
10564 (define-public r-wavetiling
10566 (name "r-wavetiling")
10571 (uri (bioconductor-uri "waveTiling" version))
10574 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
10575 (properties `((upstream-name . "waveTiling")))
10576 (build-system r-build-system)
10578 `(("r-affy" ,r-affy)
10579 ("r-biobase" ,r-biobase)
10580 ("r-biostrings" ,r-biostrings)
10581 ("r-genomegraphs" ,r-genomegraphs)
10582 ("r-genomicranges" ,r-genomicranges)
10583 ("r-iranges" ,r-iranges)
10584 ("r-oligo" ,r-oligo)
10585 ("r-oligoclasses" ,r-oligoclasses)
10586 ("r-preprocesscore" ,r-preprocesscore)
10587 ("r-waveslim" ,r-waveslim)))
10588 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
10589 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
10591 "This package is designed to conduct transcriptome analysis for tiling
10592 arrays based on fast wavelet-based functional models.")
10593 (license license:gpl2+)))
10595 (define-public r-variancepartition
10597 (name "r-variancepartition")
10602 (uri (bioconductor-uri "variancePartition" version))
10605 "1pqy2g9pg8pswmkrs2fzlkwwliw2r7f33h05bci5bz41b8ribpzj"))))
10607 `((upstream-name . "variancePartition")))
10608 (build-system r-build-system)
10610 `(("r-biobase" ,r-biobase)
10611 ("r-biocparallel" ,r-biocparallel)
10612 ("r-colorramps" ,r-colorramps)
10613 ("r-doparallel" ,r-doparallel)
10614 ("r-foreach" ,r-foreach)
10615 ("r-ggplot2" ,r-ggplot2)
10616 ("r-gplots" ,r-gplots)
10617 ("r-iterators" ,r-iterators)
10618 ("r-limma" ,r-limma)
10620 ("r-lmertest" ,r-lmertest)
10622 ("r-pbkrtest" ,r-pbkrtest)
10623 ("r-progress" ,r-progress)
10624 ("r-reshape2" ,r-reshape2)
10625 ("r-scales" ,r-scales)))
10627 `(("r-knitr" ,r-knitr)))
10628 (home-page "https://bioconductor.org/packages/variancePartition/")
10629 (synopsis "Analyze variation in gene expression experiments")
10631 "This is a package providing tools to quantify and interpret multiple
10632 sources of biological and technical variation in gene expression experiments.
10633 It uses a linear mixed model to quantify variation in gene expression
10634 attributable to individual, tissue, time point, or technical variables. The
10635 package includes dream differential expression analysis for repeated
10637 (license license:gpl2+)))
10639 (define-public r-htqpcr
10646 (uri (bioconductor-uri "HTqPCR" version))
10649 "1y3ik5a9w66jby6682jfm8mn2883s8yfv4xw8a8v1f6q2d1j938l"))))
10650 (properties `((upstream-name . "HTqPCR")))
10651 (build-system r-build-system)
10653 `(("r-affy" ,r-affy)
10654 ("r-biobase" ,r-biobase)
10655 ("r-gplots" ,r-gplots)
10656 ("r-limma" ,r-limma)
10657 ("r-rcolorbrewer" ,r-rcolorbrewer)))
10658 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
10659 "groups/bertone/software/HTqPCR.pdf"))
10660 (synopsis "Automated analysis of high-throughput qPCR data")
10662 "Analysis of Ct values from high throughput quantitative real-time
10663 PCR (qPCR) assays across multiple conditions or replicates. The input data
10664 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
10665 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
10666 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
10667 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
10668 loading, quality assessment, normalization, visualization and parametric or
10669 non-parametric testing for statistical significance in Ct values between
10670 features (e.g. genes, microRNAs).")
10671 (license license:artistic2.0)))
10673 (define-public r-unifiedwmwqpcr
10675 (name "r-unifiedwmwqpcr")
10680 (uri (bioconductor-uri "unifiedWMWqPCR" version))
10683 "1clcz610sl3s0mjf84j21xgrmjhkxcc4h292ljwq5yzbkk68g896"))))
10685 `((upstream-name . "unifiedWMWqPCR")))
10686 (build-system r-build-system)
10688 `(("r-biocgenerics" ,r-biocgenerics)
10689 ("r-htqpcr" ,r-htqpcr)))
10690 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
10691 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
10693 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
10694 data. This modified test allows for testing differential expression in qPCR
10696 (license license:gpl2+)))
10698 (define-public r-universalmotif
10700 (name "r-universalmotif")
10705 (uri (bioconductor-uri "universalmotif" version))
10708 "1hwp7802r4pr7yafzir9afqaim9l0vznglm35b0gxaca8k7a3jvy"))))
10710 `((upstream-name . "universalmotif")))
10711 (build-system r-build-system)
10714 (modify-phases %standard-phases
10715 (add-after 'unpack 'fix-reference-to-strip
10717 (substitute* "src/Makevars"
10718 (("/usr/bin/strip") (which "strip"))))))))
10720 `(("r-biocgenerics" ,r-biocgenerics)
10721 ("r-biostrings" ,r-biostrings)
10722 ("r-ggplot2" ,r-ggplot2)
10723 ("r-iranges" ,r-iranges)
10726 ("r-rcppthread" ,r-rcppthread)
10727 ("r-rlang" ,r-rlang)
10728 ("r-s4vectors" ,r-s4vectors)
10729 ("r-yaml" ,r-yaml)))
10731 `(("r-knitr" ,r-knitr)))
10733 "https://bioconductor.org/packages/universalmotif/")
10735 "Specific structures importer, modifier, and exporter for R")
10737 "This package allows importing most common @dfn{specific structure}
10738 (motif) types into R for use by functions provided by other Bioconductor
10739 motif-related packages. Motifs can be exported into most major motif formats
10740 from various classes as defined by other Bioconductor packages. A suite of
10741 motif and sequence manipulation and analysis functions are included, including
10742 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
10743 motifs, and others.")
10744 (license license:gpl3)))
10746 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
10748 (define-public r-activedriverwgs
10750 (name "r-activedriverwgs")
10755 (uri (cran-uri "ActiveDriverWGS" version))
10758 "06mvakdc8d2pn91p0sr4ixc561s4ia5h1cvd1p7pqd6s50dy4say"))))
10760 `((upstream-name . "ActiveDriverWGS")))
10761 (build-system r-build-system)
10763 `(("r-biostrings" ,r-biostrings)
10764 ("r-bsgenome" ,r-bsgenome)
10765 ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
10766 ("r-genomeinfodb" ,r-genomeinfodb)
10767 ("r-genomicranges" ,r-genomicranges)
10768 ("r-iranges" ,r-iranges)
10769 ("r-s4vectors" ,r-s4vectors)))
10771 `(("r-knitr" ,r-knitr)))
10772 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
10773 (synopsis "Driver discovery tool for cancer whole genomes")
10775 "This package provides a method for finding an enrichment of cancer
10776 simple somatic mutations (SNVs and Indels) in functional elements across the
10777 human genome. ActiveDriverWGS detects coding and noncoding driver elements
10778 using whole genome sequencing data.")
10779 (license license:gpl3)))
10781 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
10783 (define-public r-activepathways
10785 (name "r-activepathways")
10790 (uri (cran-uri "ActivePathways" version))
10793 "1hxy760x141ykrpqdbfldq4ggj1svj3lsrpwi4rb2x7r4lna937l"))))
10795 `((upstream-name . "ActivePathways")))
10796 (build-system r-build-system)
10798 `(("r-data-table" ,r-data-table)
10799 ("r-ggplot2" ,r-ggplot2)))
10801 `(("r-knitr" ,r-knitr)))
10802 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
10803 (synopsis "Multivariate pathway enrichment analysis")
10805 "This package represents an integrative method of analyzing multi omics
10806 data that conducts enrichment analysis of annotated gene sets. ActivePathways
10807 uses a statistical data fusion approach, rationalizes contributing evidence
10808 and highlights associated genes, improving systems-level understanding of
10809 cellular organization in health and disease.")
10810 (license license:gpl3)))
10812 (define-public r-bgmix
10819 (uri (bioconductor-uri "BGmix" version))
10822 "1gp40ddspblpszzm4k4r7ysgx883iwdfqc5ds23p2q1ml9idwgvv"))))
10823 (properties `((upstream-name . "BGmix")))
10824 (build-system r-build-system)
10826 `(("r-kernsmooth" ,r-kernsmooth)))
10827 (home-page "https://bioconductor.org/packages/BGmix/")
10828 (synopsis "Bayesian models for differential gene expression")
10830 "This package provides fully Bayesian mixture models for differential
10832 (license license:gpl2)))
10834 (define-public r-bgx
10841 (uri (bioconductor-uri "bgx" version))
10844 "18n6j2ihv85rhai5sf5k3mwf9nkc2nl2sinx3rrs6sbl529g4mw4"))))
10845 (properties `((upstream-name . "bgx")))
10846 (build-system r-build-system)
10848 `(("r-affy" ,r-affy)
10849 ("r-biobase" ,r-biobase)
10850 ("r-gcrma" ,r-gcrma)
10851 ("r-rcpp" ,r-rcpp)))
10852 (home-page "https://bioconductor.org/packages/bgx/")
10853 (synopsis "Bayesian gene expression")
10855 "This package provides tools for Bayesian integrated analysis of
10856 Affymetrix GeneChips.")
10857 (license license:gpl2)))
10859 (define-public r-bhc
10866 (uri (bioconductor-uri "BHC" version))
10869 "0aaawm7h3ppyyhd7hi14rpynagnxx4730f5vxizj5bpzwbclp6h9"))))
10870 (properties `((upstream-name . "BHC")))
10871 (build-system r-build-system)
10872 (home-page "https://bioconductor.org/packages/BHC/")
10873 (synopsis "Bayesian hierarchical clustering")
10875 "The method implemented in this package performs bottom-up hierarchical
10876 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
10877 in the data and Bayesian model selection to decide at each step which clusters
10878 to merge. This avoids several limitations of traditional methods, for example
10879 how many clusters there should be and how to choose a principled distance
10880 metric. This implementation accepts multinomial (i.e. discrete, with 2+
10881 categories) or time-series data. This version also includes a randomised
10882 algorithm which is more efficient for larger data sets.")
10883 (license license:gpl3)))
10885 (define-public r-bicare
10892 (uri (bioconductor-uri "BicARE" version))
10895 "0j3gs4xcdgaca2c62jf2h86skbbxm1c9g2khs5bsa8fmkskr6vl9"))))
10896 (properties `((upstream-name . "BicARE")))
10897 (build-system r-build-system)
10899 `(("r-biobase" ,r-biobase)
10900 ("r-gseabase" ,r-gseabase)
10901 ("r-multtest" ,r-multtest)))
10902 (home-page "http://bioinfo.curie.fr")
10903 (synopsis "Biclustering analysis and results exploration")
10905 "This is a package for biclustering analysis and exploration of
10907 (license license:gpl2)))
10909 (define-public r-bifet
10916 (uri (bioconductor-uri "BiFET" version))
10919 "1fwy7ws0bn67557s0kcw8pbln2jg834n6kfbs8297ps07nxr0lpj"))))
10920 (properties `((upstream-name . "BiFET")))
10921 (build-system r-build-system)
10923 `(("r-genomicranges" ,r-genomicranges)
10924 ("r-poibin" ,r-poibin)))
10926 `(("r-knitr" ,r-knitr)))
10927 (home-page "https://bioconductor.org/packages/BiFET")
10928 (synopsis "Bias-free footprint enrichment test")
10930 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
10931 over-represented in target regions compared to background regions after
10932 correcting for the bias arising from the imbalance in read counts and GC
10933 contents between the target and background regions. For a given TF k, BiFET
10934 tests the null hypothesis that the target regions have the same probability of
10935 having footprints for the TF k as the background regions while correcting for
10936 the read count and GC content bias.")
10937 (license license:gpl3)))
10939 (define-public r-rsbml
10946 (uri (bioconductor-uri "rsbml" version))
10949 "017xwra6ms7kx6sg3ksw1vr9zn23imc2qjgpmjikx7mgbak125xh"))))
10950 (properties `((upstream-name . "rsbml")))
10951 (build-system r-build-system)
10953 `(("libsbml" ,libsbml)))
10955 `(("r-biocgenerics" ,r-biocgenerics)
10956 ("r-graph" ,r-graph)))
10958 `(("pkg-config" ,pkg-config)))
10959 (home-page "http://www.sbml.org")
10960 (synopsis "R support for SBML")
10962 "This package provides an R interface to libsbml for SBML parsing,
10963 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
10964 (license license:artistic2.0)))
10966 (define-public r-hypergraph
10968 (name "r-hypergraph")
10973 (uri (bioconductor-uri "hypergraph" version))
10976 "01knpd964m2g9vwd7c72qnc8g2p2pzhvk7lin4mhvcmb3pvsdlh7"))))
10977 (properties `((upstream-name . "hypergraph")))
10978 (build-system r-build-system)
10980 `(("r-graph" ,r-graph)))
10981 (home-page "https://bioconductor.org/packages/hypergraph")
10982 (synopsis "Hypergraph data structures")
10984 "This package implements some simple capabilities for representing and
10985 manipulating hypergraphs.")
10986 (license license:artistic2.0)))
10988 (define-public r-hyperdraw
10990 (name "r-hyperdraw")
10995 (uri (bioconductor-uri "hyperdraw" version))
10998 "1qkxixkgvvfha0ii8rwwcbrbjmbbxsy8afv5ymcq01k3hbykx44r"))))
10999 (properties `((upstream-name . "hyperdraw")))
11000 (build-system r-build-system)
11001 (inputs `(("graphviz" ,graphviz)))
11003 `(("r-graph" ,r-graph)
11004 ("r-hypergraph" ,r-hypergraph)
11005 ("r-rgraphviz" ,r-rgraphviz)))
11006 (home-page "https://bioconductor.org/packages/hyperdraw")
11007 (synopsis "Visualizing hypergraphs")
11009 "This package provides functions for visualizing hypergraphs.")
11010 (license license:gpl2+)))
11012 (define-public r-biggr
11019 (uri (bioconductor-uri "BiGGR" version))
11022 "1y9659pxm65w51zvrz36girb3qvfc64zijjkxmg6xn4pbc8vv1wf"))))
11023 (properties `((upstream-name . "BiGGR")))
11024 (build-system r-build-system)
11026 `(("r-hyperdraw" ,r-hyperdraw)
11027 ("r-hypergraph" ,r-hypergraph)
11029 ("r-limsolve" ,r-limsolve)
11030 ("r-rsbml" ,r-rsbml)
11031 ("r-stringr" ,r-stringr)))
11032 (home-page "https://bioconductor.org/packages/BiGGR/")
11033 (synopsis "Constraint based modeling using metabolic reconstruction databases")
11035 "This package provides an interface to simulate metabolic reconstruction
11036 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
11037 reconstruction databases. The package facilitates @dfn{flux balance
11038 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
11039 networks and estimated fluxes can be visualized with hypergraphs.")
11040 (license license:gpl3+)))
11042 (define-public r-bigmemoryextras
11044 (name "r-bigmemoryextras")
11049 (uri (bioconductor-uri "bigmemoryExtras" version))
11052 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
11054 `((upstream-name . "bigmemoryExtras")))
11055 (build-system r-build-system)
11057 `(("r-bigmemory" ,r-bigmemory)))
11059 `(("r-knitr" ,r-knitr)))
11060 (home-page "https://github.com/phaverty/bigmemoryExtras")
11061 (synopsis "Extension of the bigmemory package")
11063 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
11064 safety and convenience features to the @code{filebacked.big.matrix} class from
11065 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
11066 monitoring and gracefully restoring the connection to on-disk data and it also
11067 protects against accidental data modification with a file-system-based
11068 permissions system. Utilities are provided for using @code{BigMatrix}-derived
11069 classes as @code{assayData} matrices within the @code{Biobase} package's
11070 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
11071 related to attaching to, and indexing into, file-backed matrices with
11072 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
11073 a file-backed matrix with factor properties.")
11074 (license license:artistic2.0)))
11076 (define-public r-bigpint
11083 (uri (bioconductor-uri "bigPint" version))
11086 "0yrg9x1a92zmz7j5hk77cph1jg82mkpr7k7qi9fdr6z5nqq6fgz6"))))
11087 (properties `((upstream-name . "bigPint")))
11088 (build-system r-build-system)
11090 `(("r-delayedarray" ,r-delayedarray)
11091 ("r-dplyr" ,r-dplyr)
11092 ("r-ggally" ,r-ggally)
11093 ("r-ggplot2" ,r-ggplot2)
11094 ("r-gridextra" ,r-gridextra)
11095 ("r-hexbin" ,r-hexbin)
11096 ("r-hmisc" ,r-hmisc)
11097 ("r-htmlwidgets" ,r-htmlwidgets)
11098 ("r-plotly" ,r-plotly)
11100 ("r-rcolorbrewer" ,r-rcolorbrewer)
11101 ("r-reshape" ,r-reshape)
11102 ("r-shiny" ,r-shiny)
11103 ("r-shinycssloaders" ,r-shinycssloaders)
11104 ("r-shinydashboard" ,r-shinydashboard)
11105 ("r-stringr" ,r-stringr)
11106 ("r-summarizedexperiment" ,r-summarizedexperiment)
11107 ("r-tidyr" ,r-tidyr)))
11109 `(("r-knitr" ,r-knitr)))
11110 (home-page "https://github.com/lindsayrutter/bigPint")
11111 (synopsis "Big multivariate data plotted interactively")
11113 "This package provides methods for visualizing large multivariate
11114 datasets using static and interactive scatterplot matrices, parallel
11115 coordinate plots, volcano plots, and litre plots. It includes examples for
11116 visualizing RNA-sequencing datasets and differentially expressed genes.")
11117 (license license:gpl3)))
11119 (define-public r-chemminer
11121 (name "r-chemminer")
11126 (uri (bioconductor-uri "ChemmineR" version))
11129 "1z59npqk7hnqzhjdnry6lfqlyxfzwqprp7bmbdzs4rp22pzcv1v8"))))
11130 (properties `((upstream-name . "ChemmineR")))
11131 (build-system r-build-system)
11133 `(("r-base64enc" ,r-base64enc)
11135 ("r-biocgenerics" ,r-biocgenerics)
11137 ("r-digest" ,r-digest)
11139 ("r-ggplot2" ,r-ggplot2)
11140 ("r-gridextra" ,r-gridextra)
11143 ("r-rcurl" ,r-rcurl)
11144 ("r-rjson" ,r-rjson)
11145 ("r-rsvg" ,r-rsvg)))
11147 `(("r-knitr" ,r-knitr)))
11148 (home-page "https://github.com/girke-lab/ChemmineR")
11149 (synopsis "Cheminformatics toolkit for R")
11151 "ChemmineR is a cheminformatics package for analyzing drug-like small
11152 molecule data in R. It contains functions for efficient processing of large
11153 numbers of molecules, physicochemical/structural property predictions,
11154 structural similarity searching, classification and clustering of compound
11155 libraries with a wide spectrum of algorithms. In addition, it offers
11156 visualization functions for compound clustering results and chemical
11158 (license license:artistic2.0)))
11160 (define-public r-bioassayr
11162 (name "r-bioassayr")
11167 (uri (bioconductor-uri "bioassayR" version))
11170 "1mlv80w8a7l8cii3dfqvanvh0qdqvcg8c1iiq4xlyvkjxfs64ka1"))))
11171 (properties `((upstream-name . "bioassayR")))
11172 (build-system r-build-system)
11174 `(("r-biocgenerics" ,r-biocgenerics)
11175 ("r-chemminer" ,r-chemminer)
11177 ("r-matrix" ,r-matrix)
11178 ("r-rjson" ,r-rjson)
11179 ("r-rsqlite" ,r-rsqlite)
11182 `(("r-knitr" ,r-knitr)))
11183 (home-page "https://github.com/girke-lab/bioassayR")
11184 (synopsis "Cross-target analysis of small molecule bioactivity")
11186 "bioassayR is a computational tool that enables simultaneous analysis of
11187 thousands of bioassay experiments performed over a diverse set of compounds
11188 and biological targets. Unique features include support for large-scale
11189 cross-target analyses of both public and custom bioassays, generation of
11190 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
11191 preloaded database that provides access to a substantial portion of publicly
11192 available bioactivity data.")
11193 (license license:artistic2.0)))
11195 (define-public r-biobroom
11197 (name "r-biobroom")
11202 (uri (bioconductor-uri "biobroom" version))
11205 "1ybyhmrcvj6k1laxw9bc8jbn533frkzh9k8kl1ibd5pi368rfqzn"))))
11206 (properties `((upstream-name . "biobroom")))
11207 (build-system r-build-system)
11209 `(("r-biobase" ,r-biobase)
11210 ("r-broom" ,r-broom)
11211 ("r-dplyr" ,r-dplyr)
11212 ("r-tidyr" ,r-tidyr)))
11214 `(("r-knitr" ,r-knitr)))
11215 (home-page "https://github.com/StoreyLab/biobroom")
11216 (synopsis "Turn Bioconductor objects into tidy data frames")
11218 "This package contains methods for converting standard objects
11219 constructed by bioinformatics packages, especially those in Bioconductor, and
11220 converting them to @code{tidy} data. It thus serves as a complement to the
11221 @code{broom} package, and follows the same tidy, augment, glance division of
11222 tidying methods. Tidying data makes it easy to recombine, reshape and
11223 visualize bioinformatics analyses.")
11224 ;; Any version of the LGPL.
11225 (license license:lgpl3+)))
11227 (define-public r-graphite
11229 (name "r-graphite")
11234 (uri (bioconductor-uri "graphite" version))
11237 "11bgz6951nfygxp3fm0190gf2bb5zplis1bc0am4757liw4qybhf"))))
11238 (properties `((upstream-name . "graphite")))
11239 (build-system r-build-system)
11241 `(("r-annotationdbi" ,r-annotationdbi)
11242 ("r-checkmate" ,r-checkmate)
11243 ("r-graph" ,r-graph)
11245 ("r-rappdirs" ,r-rappdirs)))
11247 `(("r-knitr" ,r-knitr)))
11248 (home-page "https://bioconductor.org/packages/graphite/")
11249 (synopsis "Networks from pathway databases")
11251 "Graphite provides networks derived from eight public pathway databases,
11252 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
11254 (license license:agpl3+)))
11256 (define-public r-reactomepa
11258 (name "r-reactomepa")
11263 (uri (bioconductor-uri "ReactomePA" version))
11266 "1293z89ai766c559axgr7mz5x4564gyl9xqzf6s8s0aj1xb35gqf"))))
11267 (properties `((upstream-name . "ReactomePA")))
11268 (build-system r-build-system)
11270 `(("r-annotationdbi" ,r-annotationdbi)
11272 ("r-enrichplot" ,r-enrichplot)
11273 ("r-ggplot2" ,r-ggplot2)
11274 ("r-ggraph" ,r-ggraph)
11275 ("r-graphite" ,r-graphite)
11276 ("r-igraph" ,r-igraph)
11277 ("r-reactome-db" ,r-reactome-db)))
11279 `(("r-knitr" ,r-knitr)))
11280 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
11281 (synopsis "Reactome pathway analysis")
11283 "This package provides functions for pathway analysis based on the
11284 REACTOME pathway database. It implements enrichment analysis, gene set
11285 enrichment analysis and several functions for visualization.")
11286 (license license:gpl2)))
11288 (define-public r-ebarrays
11290 (name "r-ebarrays")
11295 (uri (bioconductor-uri "EBarrays" version))
11298 "1k1kl0m7wzaqpv7i20pfav2a6jf93bhri4w7qdikmvkf011n9422"))))
11299 (properties `((upstream-name . "EBarrays")))
11300 (build-system r-build-system)
11302 `(("r-biobase" ,r-biobase)
11303 ("r-cluster" ,r-cluster)
11304 ("r-lattice" ,r-lattice)))
11305 (home-page "https://bioconductor.org/packages/EBarrays/")
11306 (synopsis "Gene clustering and differential expression identification")
11308 "EBarrays provides tools for the analysis of replicated/unreplicated
11310 (license license:gpl2+)))
11312 (define-public r-bioccasestudies
11314 (name "r-bioccasestudies")
11319 (uri (bioconductor-uri "BiocCaseStudies" version))
11322 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
11324 `((upstream-name . "BiocCaseStudies")))
11325 (build-system r-build-system)
11326 (propagated-inputs `(("r-biobase" ,r-biobase)))
11327 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
11328 (synopsis "Support for the case studies monograph")
11330 "This package provides software and data to support the case studies
11332 (license license:artistic2.0)))
11334 (define-public r-bioccheck
11336 (name "r-bioccheck")
11340 (uri (bioconductor-uri "BiocCheck" version))
11343 "1h0l5w33c9jpc20pynq634qmx8jbfa802d7jslmf4haljmrxm4a1"))))
11345 `((upstream-name . "BiocCheck")))
11346 (build-system r-build-system)
11348 `(("r-codetools" ,r-codetools)
11349 ("r-graph" ,r-graph)
11351 ("r-knitr" ,r-knitr)
11352 ("r-optparse" ,r-optparse)
11353 ("r-biocmanager" ,r-biocmanager)
11354 ("r-biocviews" ,r-biocviews)
11355 ("r-stringdist" ,r-stringdist)))
11357 `(("r-knitr" ,r-knitr)))
11358 (home-page "https://bioconductor.org/packages/BiocCheck")
11359 (synopsis "Executes Bioconductor-specific package checks")
11360 (description "This package contains tools to perform additional quality
11361 checks on R packages that are to be submitted to the Bioconductor repository.")
11362 (license license:artistic2.0)))
11364 (define-public r-biocgraph
11366 (name "r-biocgraph")
11371 (uri (bioconductor-uri "biocGraph" version))
11374 "12bmj9kdlylp02cfwviak7y323ndccl2694rvi4cdg4vsx7v3ya3"))))
11375 (properties `((upstream-name . "biocGraph")))
11376 (build-system r-build-system)
11378 `(("r-biocgenerics" ,r-biocgenerics)
11379 ("r-geneplotter" ,r-geneplotter)
11380 ("r-graph" ,r-graph)
11381 ("r-rgraphviz" ,r-rgraphviz)))
11382 (home-page "https://bioconductor.org/packages/biocGraph/")
11383 (synopsis "Graph examples and use cases in Bioinformatics")
11385 "This package provides examples and code that make use of the
11386 different graph related packages produced by Bioconductor.")
11387 (license license:artistic2.0)))
11389 (define-public r-biocstyle
11391 (name "r-biocstyle")
11395 (uri (bioconductor-uri "BiocStyle" version))
11398 "062zhy33a2c70ibqghnjxcys0wbqc998aza8nnygk4zmpd4iyy1z"))))
11400 `((upstream-name . "BiocStyle")))
11401 (build-system r-build-system)
11403 `(("r-biocmanager" ,r-biocmanager)
11404 ("r-bookdown" ,r-bookdown)
11405 ("r-knitr" ,r-knitr)
11406 ("r-rmarkdown" ,r-rmarkdown)
11407 ("r-yaml" ,r-yaml)))
11409 `(("r-knitr" ,r-knitr)))
11410 (home-page "https://bioconductor.org/packages/BiocStyle")
11411 (synopsis "Bioconductor formatting styles")
11412 (description "This package provides standard formatting styles for
11413 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
11415 (license license:artistic2.0)))
11417 (define-public r-biocviews
11419 (name "r-biocviews")
11423 (uri (bioconductor-uri "biocViews" version))
11426 "0pc5ll59vm8a9s1nrdc7p9wk11a52rrz669fsrrqd8qapa8p6wfd"))))
11428 `((upstream-name . "biocViews")))
11429 (build-system r-build-system)
11431 `(("r-biobase" ,r-biobase)
11432 ("r-biocmanager" ,r-biocmanager)
11433 ("r-graph" ,r-graph)
11435 ("r-rcurl" ,r-rcurl)
11437 ("r-runit" ,r-runit)))
11438 (home-page "https://bioconductor.org/packages/biocViews")
11439 (synopsis "Bioconductor package categorization helper")
11440 (description "The purpose of biocViews is to create HTML pages that
11441 categorize packages in a Bioconductor package repository according to keywords,
11442 also known as views, in a controlled vocabulary.")
11443 (license license:artistic2.0)))
11445 (define-public r-experimenthub
11447 (name "r-experimenthub")
11452 (uri (bioconductor-uri "ExperimentHub" version))
11455 "1mzmw3100lf33yhz27nbxncrjk5bprlackrjcwf8xdhcaidg40p4"))))
11456 (properties `((upstream-name . "ExperimentHub")))
11457 (build-system r-build-system)
11459 `(("r-annotationhub" ,r-annotationhub)
11460 ("r-biocfilecache" ,r-biocfilecache)
11461 ("r-biocgenerics" ,r-biocgenerics)
11462 ("r-biocmanager" ,r-biocmanager)
11464 ("r-rappdirs" ,r-rappdirs)
11465 ("r-s4vectors" ,r-s4vectors)))
11467 `(("r-knitr" ,r-knitr)))
11468 (home-page "https://bioconductor.org/packages/ExperimentHub/")
11469 (synopsis "Client to access ExperimentHub resources")
11471 "This package provides a client for the Bioconductor ExperimentHub web
11472 resource. ExperimentHub provides a central location where curated data from
11473 experiments, publications or training courses can be accessed. Each resource
11474 has associated metadata, tags and date of modification. The client creates
11475 and manages a local cache of files retrieved enabling quick and reproducible
11477 (license license:artistic2.0)))
11479 (define-public r-grohmm
11486 (uri (bioconductor-uri "groHMM" version))
11489 "1h63vg1iskw79ijg5h1b9097ams8pp3kvnlawlfci6xfli07xpkj"))))
11490 (properties `((upstream-name . "groHMM")))
11491 (build-system r-build-system)
11493 `(("r-genomeinfodb" ,r-genomeinfodb)
11494 ("r-genomicalignments" ,r-genomicalignments)
11495 ("r-genomicranges" ,r-genomicranges)
11496 ("r-iranges" ,r-iranges)
11498 ("r-rtracklayer" ,r-rtracklayer)
11499 ("r-s4vectors" ,r-s4vectors)))
11500 (home-page "https://github.com/Kraus-Lab/groHMM")
11501 (synopsis "GRO-seq analysis pipeline")
11503 "This package provides a pipeline for the analysis of GRO-seq data.")
11504 (license license:gpl3+)))
11506 (define-public r-multiassayexperiment
11508 (name "r-multiassayexperiment")
11513 (uri (bioconductor-uri "MultiAssayExperiment" version))
11516 "0l0arf3q1f6zy6pdgsy3h5n523sg1hlilv7lj7snr5814idgdj51"))))
11518 `((upstream-name . "MultiAssayExperiment")))
11519 (build-system r-build-system)
11521 `(("r-biobase" ,r-biobase)
11522 ("r-biocgenerics" ,r-biocgenerics)
11523 ("r-genomicranges" ,r-genomicranges)
11524 ("r-iranges" ,r-iranges)
11525 ("r-s4vectors" ,r-s4vectors)
11526 ("r-summarizedexperiment" ,r-summarizedexperiment)
11527 ("r-tidyr" ,r-tidyr)))
11529 `(("r-knitr" ,r-knitr)))
11530 (home-page "https://waldronlab.io/MultiAssayExperiment/")
11531 (synopsis "Integration of multi-omics experiments in Bioconductor")
11533 "MultiAssayExperiment harmonizes data management of multiple assays
11534 performed on an overlapping set of specimens. It provides a familiar
11535 Bioconductor user experience by extending concepts from
11536 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
11537 classes for individual assays, and allowing subsetting by genomic ranges or
11539 (license license:artistic2.0)))
11541 (define-public r-bioconcotk
11543 (name "r-bioconcotk")
11548 (uri (bioconductor-uri "BiocOncoTK" version))
11551 "0y396lx2mh9izb07lz83j35wydfj808ihc74jlgras03a3g335p2"))))
11552 (properties `((upstream-name . "BiocOncoTK")))
11553 (build-system r-build-system)
11555 `(("r-bigrquery" ,r-bigrquery)
11557 ("r-complexheatmap" ,r-complexheatmap)
11558 ("r-curatedtcgadata" ,r-curatedtcgadata)
11560 ("r-dplyr" ,r-dplyr)
11562 ("r-genomicfeatures" ,r-genomicfeatures)
11563 ("r-genomicranges" ,r-genomicranges)
11564 ("r-ggplot2" ,r-ggplot2)
11565 ("r-ggpubr" ,r-ggpubr)
11566 ("r-graph" ,r-graph)
11568 ("r-iranges" ,r-iranges)
11569 ("r-magrittr" ,r-magrittr)
11571 ("r-rgraphviz" ,r-rgraphviz)
11572 ("r-rjson" ,r-rjson)
11573 ("r-s4vectors" ,r-s4vectors)
11574 ("r-scales" ,r-scales)
11575 ("r-shiny" ,r-shiny)
11576 ("r-summarizedexperiment" ,r-summarizedexperiment)))
11578 `(("r-knitr" ,r-knitr)))
11579 (home-page "https://bioconductor.org/packages/BiocOncoTK")
11580 (synopsis "Bioconductor components for general cancer genomics")
11582 "The purpose of this package is to provide a central interface to various
11583 tools for genome-scale analysis of cancer studies.")
11584 (license license:artistic2.0)))
11586 (define-public r-biocor
11593 (uri (bioconductor-uri "BioCor" version))
11596 "135rga7mwpzy8ypvriqpbmlh9l5yf61s9s1sa9615qfab14jh06b"))))
11597 (properties `((upstream-name . "BioCor")))
11598 (build-system r-build-system)
11600 `(("r-biocparallel" ,r-biocparallel)
11601 ("r-gseabase" ,r-gseabase)
11602 ("r-matrix" ,r-matrix)))
11604 `(("r-knitr" ,r-knitr)))
11605 (home-page "https://llrs.github.io/BioCor/")
11606 (synopsis "Functional similarities")
11608 "This package provides tools to calculate functional similarities based
11609 on the pathways described on KEGG and REACTOME or in gene sets. These
11610 similarities can be calculated for pathways or gene sets, genes, or clusters
11611 and combined with other similarities. They can be used to improve networks,
11612 gene selection, testing relationships, and so on.")
11613 (license license:expat)))
11615 (define-public r-biocpkgtools
11617 (name "r-biocpkgtools")
11622 (uri (bioconductor-uri "BiocPkgTools" version))
11625 "18a9mbzfmkipnv1cc9h3rhn9jxdp7nzywp0bz7hvmsaffv4p4skc"))))
11626 (properties `((upstream-name . "BiocPkgTools")))
11627 (build-system r-build-system)
11629 `(("r-biocfilecache" ,r-biocfilecache)
11630 ("r-biocmanager" ,r-biocmanager)
11631 ("r-biocviews" ,r-biocviews)
11632 ("r-dplyr" ,r-dplyr)
11635 ("r-graph" ,r-graph)
11636 ("r-htmltools" ,r-htmltools)
11637 ("r-htmlwidgets" ,r-htmlwidgets)
11639 ("r-igraph" ,r-igraph)
11640 ("r-jsonlite" ,r-jsonlite)
11641 ("r-magrittr" ,r-magrittr)
11643 ("r-readr" ,r-readr)
11645 ("r-rlang" ,r-rlang)
11646 ("r-rvest" ,r-rvest)
11647 ("r-stringr" ,r-stringr)
11648 ("r-tibble" ,r-tibble)
11649 ("r-tidyr" ,r-tidyr)
11650 ("r-tidyselect" ,r-tidyselect)
11651 ("r-xml2" ,r-xml2)))
11653 `(("r-knitr" ,r-knitr)))
11654 (home-page "https://github.com/seandavi/BiocPkgTools")
11655 (synopsis "Collection of tools for learning about Bioconductor packages")
11657 "Bioconductor has a rich ecosystem of metadata around packages, usage,
11658 and build status. This package is a simple collection of functions to access
11659 that metadata from R. The goal is to expose metadata for data mining and
11660 value-added functionality such as package searching, text mining, and
11661 analytics on packages.")
11662 (license license:expat)))
11664 (define-public r-biocset
11671 (uri (bioconductor-uri "BiocSet" version))
11674 "18zr0r4b4rblfmsiilipqdfxn9fgymx75hlxzx1wk3bm71ryk078"))))
11675 (properties `((upstream-name . "BiocSet")))
11676 (build-system r-build-system)
11678 `(("r-annotationdbi" ,r-annotationdbi)
11679 ("r-biocio" ,r-biocio)
11680 ("r-dplyr" ,r-dplyr)
11681 ("r-keggrest" ,r-keggrest)
11682 ("r-ontologyindex" ,r-ontologyindex)
11684 ("r-rlang" ,r-rlang)
11685 ("r-s4vectors" ,r-s4vectors)
11686 ("r-tibble" ,r-tibble)
11687 ("r-tidyr" ,r-tidyr)))
11689 `(("r-knitr" ,r-knitr)))
11691 "https://bioconductor.org/packages/BiocSet")
11693 "Representing Different Biological Sets")
11695 "BiocSet displays different biological sets in a triple tibble format.
11696 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
11697 The user has the ability to activate one of these three tibbles to perform
11698 common functions from the @code{dplyr} package. Mapping functionality and
11699 accessing web references for elements/sets are also available in BiocSet.")
11700 (license license:artistic2.0)))
11702 (define-public r-biocworkflowtools
11704 (name "r-biocworkflowtools")
11709 (uri (bioconductor-uri "BiocWorkflowTools" version))
11712 "1a32bwgnxaw0gv2gij2p4rm0a6l06jjhidvfz2v4k900pz1w79av"))))
11714 `((upstream-name . "BiocWorkflowTools")))
11715 (build-system r-build-system)
11717 `(("r-biocstyle" ,r-biocstyle)
11718 ("r-bookdown" ,r-bookdown)
11719 ("r-git2r" ,r-git2r)
11721 ("r-knitr" ,r-knitr)
11722 ("r-rmarkdown" ,r-rmarkdown)
11723 ("r-rstudioapi" ,r-rstudioapi)
11724 ("r-stringr" ,r-stringr)
11725 ("r-usethis" ,r-usethis)))
11727 `(("r-knitr" ,r-knitr)))
11728 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
11729 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
11731 "This package provides functions to ease the transition between
11732 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
11733 (license license:expat)))
11735 (define-public r-biodist
11742 (uri (bioconductor-uri "bioDist" version))
11745 "1y1x9q9aa76gbhsyfn638rxp5icjvq30fv3a4205xh7g5jwlf6yw"))))
11746 (properties `((upstream-name . "bioDist")))
11747 (build-system r-build-system)
11749 `(("r-biobase" ,r-biobase)
11750 ("r-kernsmooth" ,r-kernsmooth)))
11751 (home-page "https://bioconductor.org/packages/bioDist/")
11752 (synopsis "Different distance measures")
11754 "This package provides a collection of software tools for calculating
11755 distance measures.")
11756 (license license:artistic2.0)))
11758 (define-public r-pcatools
11760 (name "r-pcatools")
11765 (uri (bioconductor-uri "PCAtools" version))
11768 "11idi9fwvyhkakbm63qxcdhkany8gbskis04z0p5a39lppq8ks31"))))
11769 (properties `((upstream-name . "PCAtools")))
11770 (build-system r-build-system)
11772 `(("r-beachmat" ,r-beachmat)
11774 ("r-biocparallel" ,r-biocparallel)
11775 ("r-biocsingular" ,r-biocsingular)
11776 ("r-cowplot" ,r-cowplot)
11777 ("r-delayedarray" ,r-delayedarray)
11778 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
11779 ("r-dqrng" ,r-dqrng)
11780 ("r-ggplot2" ,r-ggplot2)
11781 ("r-ggrepel" ,r-ggrepel)
11782 ("r-lattice" ,r-lattice)
11783 ("r-matrix" ,r-matrix)
11785 ("r-reshape2" ,r-reshape2)))
11786 (native-inputs `(("r-knitr" ,r-knitr)))
11787 (home-page "https://github.com/kevinblighe/PCAtools")
11788 (synopsis "PCAtools: everything Principal Components Analysis")
11790 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
11791 structure of the data without the need to build any model to represent it.
11792 This \"summary\" of the data is arrived at through a process of reduction that
11793 can transform the large number of variables into a lesser number that are
11794 uncorrelated (i.e. the 'principal components'), while at the same time being
11795 capable of easy interpretation on the original data. PCAtools provides
11796 functions for data exploration via PCA, and allows the user to generate
11797 publication-ready figures. PCA is performed via @code{BiocSingular}; users
11798 can also identify an optimal number of principal components via different
11799 metrics, such as the elbow method and Horn's parallel analysis, which has
11800 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
11801 dimensional mass cytometry data.")
11802 (license license:gpl3)))
11804 (define-public r-rgreat
11811 (uri (bioconductor-uri "rGREAT" version))
11814 "0ads9c9i8b39wvjih057zlyivj8zpsqjxf6r97yflz4sbi1jmcji"))))
11815 (properties `((upstream-name . "rGREAT")))
11816 (build-system r-build-system)
11818 `(("r-genomicranges" ,r-genomicranges)
11819 ("r-getoptlong" ,r-getoptlong)
11820 ("r-iranges" ,r-iranges)
11821 ("r-rcurl" ,r-rcurl)
11822 ("r-rjson" ,r-rjson)))
11823 (native-inputs `(("r-knitr" ,r-knitr)))
11824 (home-page "https://github.com/jokergoo/rGREAT")
11825 (synopsis "Client for GREAT analysis")
11827 "This package makes GREAT (Genomic Regions Enrichment of Annotations
11828 Tool) analysis automatic by constructing a HTTP POST request according to
11829 user's input and automatically retrieving results from GREAT web server.")
11830 (license license:expat)))
11832 (define-public r-m3c
11839 (uri (bioconductor-uri "M3C" version))
11842 "17gj4haa4ywc6bmppm342jzppl3inqa94235yspikij6c098vrmc"))))
11843 (properties `((upstream-name . "M3C")))
11844 (build-system r-build-system)
11846 `(("r-cluster" ,r-cluster)
11847 ("r-corpcor" ,r-corpcor)
11848 ("r-doparallel" ,r-doparallel)
11849 ("r-dosnow" ,r-dosnow)
11850 ("r-foreach" ,r-foreach)
11851 ("r-ggplot2" ,r-ggplot2)
11852 ("r-matrix" ,r-matrix)
11853 ("r-matrixcalc" ,r-matrixcalc)
11854 ("r-rtsne" ,r-rtsne)
11855 ("r-umap" ,r-umap)))
11856 (native-inputs `(("r-knitr" ,r-knitr)))
11857 (home-page "https://bioconductor.org/packages/M3C")
11858 (synopsis "Monte Carlo reference-based consensus clustering")
11860 "M3C is a consensus clustering algorithm that uses a Monte Carlo
11861 simulation to eliminate overestimation of @code{K} and can reject the null
11862 hypothesis @code{K=1}.")
11863 (license license:agpl3+)))
11865 (define-public r-icens
11872 (uri (bioconductor-uri "Icens" version))
11875 "1rzgwxx4w2bqsaz0xmkhi4w9zsxgms80xf59zg1xp1camyhaihlz"))))
11876 (properties `((upstream-name . "Icens")))
11877 (build-system r-build-system)
11879 `(("r-survival" ,r-survival)))
11880 (home-page "https://bioconductor.org/packages/Icens")
11881 (synopsis "NPMLE for censored and truncated data")
11883 "This package provides many functions for computing the
11884 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
11886 (license license:artistic2.0)))
11888 ;; This is a CRAN package but it depends on r-icens, which is published on
11890 (define-public r-interval
11892 (name "r-interval")
11893 (version "1.1-0.7")
11897 (uri (cran-uri "interval" version))
11900 "1b31lh0sv7lzy76230djipahxa10lblbr37kdiigr6hp3dd1xmz9"))))
11901 (properties `((upstream-name . "interval")))
11902 (build-system r-build-system)
11904 `(("r-icens" ,r-icens)
11905 ("r-mlecens" ,r-mlecens)
11907 ("r-survival" ,r-survival)))
11908 (home-page "https://cran.r-project.org/web/packages/interval/")
11909 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
11911 "This package provides functions to fit nonparametric survival curves,
11912 plot them, and perform logrank or Wilcoxon type tests.")
11913 (license license:gpl2+)))
11915 ;; This is a CRAN package, but it depends on r-interval, which depends on a
11916 ;; Bioconductor package.
11917 (define-public r-fhtest
11924 (uri (cran-uri "FHtest" version))
11927 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
11928 (properties `((upstream-name . "FHtest")))
11929 (build-system r-build-system)
11931 `(("r-interval" ,r-interval)
11932 ("r-kmsurv" ,r-kmsurv)
11935 ("r-survival" ,r-survival)))
11936 (home-page "https://cran.r-project.org/web/packages/FHtest/")
11937 (synopsis "Tests for survival data based on the Fleming-Harrington class")
11939 "This package provides functions to compare two or more survival curves
11943 @item The Fleming-Harrington test for right-censored data based on
11944 permutations and on counting processes.
11945 @item An extension of the Fleming-Harrington test for interval-censored data
11946 based on a permutation distribution and on a score vector distribution.
11949 (license license:gpl2+)))
11951 (define-public r-fourcseq
11953 (name "r-fourcseq")
11958 (uri (bioconductor-uri "FourCSeq" version))
11960 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
11961 (properties `((upstream-name . "FourCSeq")))
11962 (build-system r-build-system)
11964 `(("r-biobase" ,r-biobase)
11965 ("r-biostrings" ,r-biostrings)
11966 ("r-deseq2" ,r-deseq2)
11968 ("r-genomicalignments" ,r-genomicalignments)
11969 ("r-genomicranges" ,r-genomicranges)
11970 ("r-ggbio" ,r-ggbio)
11971 ("r-ggplot2" ,r-ggplot2)
11972 ("r-gtools" ,r-gtools)
11974 ("r-matrix" ,r-matrix)
11975 ("r-reshape2" ,r-reshape2)
11976 ("r-rsamtools" ,r-rsamtools)
11977 ("r-rtracklayer" ,r-rtracklayer)
11978 ("r-summarizedexperiment" ,r-summarizedexperiment)))
11980 `(("r-knitr" ,r-knitr)))
11982 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
11983 (synopsis "Analysis of multiplexed 4C sequencing data")
11985 "This package is an R package dedicated to the analysis of (multiplexed)
11986 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
11987 interactions between DNA elements and identify differential interactions
11988 between conditions. The statistical analysis in R starts with individual bam
11989 files for each sample as inputs. To obtain these files, the package contains
11990 a Python script to demultiplex libraries and trim off primer sequences. With
11991 a standard alignment software the required bam files can be then be
11993 (license license:gpl3+)))
11995 (define-public r-preprocesscore
11997 (name "r-preprocesscore")
12002 (uri (bioconductor-uri "preprocessCore" version))
12005 "17a00blz4kvhmsk92bp5alj9kdpy7h1id7nk4vqxakhkb2jabr20"))))
12007 `((upstream-name . "preprocessCore")))
12008 (build-system r-build-system)
12009 (home-page "https://github.com/bmbolstad/preprocessCore")
12010 (synopsis "Collection of pre-processing functions")
12012 "This package provides a library of core pre-processing and normalization
12014 (license license:lgpl2.0+)))
12016 (define-public r-s4vectors
12018 (name "r-s4vectors")
12022 (uri (bioconductor-uri "S4Vectors" version))
12025 "0v5vxmg0a27ivgymmzfl595rcb1m3dz27r2wzbk1j97rlpwy1p4q"))))
12027 `((upstream-name . "S4Vectors")))
12028 (build-system r-build-system)
12030 `(("r-biocgenerics" ,r-biocgenerics)))
12031 (home-page "https://bioconductor.org/packages/S4Vectors")
12032 (synopsis "S4 implementation of vectors and lists")
12034 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
12035 classes and a set of generic functions that extend the semantic of ordinary
12036 vectors and lists in R. Package developers can easily implement vector-like
12037 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
12038 In addition, a few low-level concrete subclasses of general interest (e.g.
12039 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
12040 S4Vectors package itself.")
12041 (license license:artistic2.0)))
12043 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
12044 ;; Bioconductor package.
12045 (define-public r-wgcna
12052 (uri (cran-uri "WGCNA" version))
12055 "1m6b4a2xpb02c1ajndhk8qlqnhwxa7lkkwj6nzv3l618jy1kp15r"))))
12056 (properties `((upstream-name . "WGCNA")))
12057 (build-system r-build-system)
12059 `(("r-annotationdbi" ,r-annotationdbi)
12060 ("r-doparallel" ,r-doparallel)
12061 ("r-dynamictreecut" ,r-dynamictreecut)
12062 ("r-fastcluster" ,r-fastcluster)
12063 ("r-foreach" ,r-foreach)
12064 ("r-go-db" ,r-go-db)
12065 ("r-hmisc" ,r-hmisc)
12066 ("r-impute" ,r-impute)
12068 ("r-survival" ,r-survival)
12069 ("r-matrixstats" ,r-matrixstats)
12070 ("r-preprocesscore" ,r-preprocesscore)))
12072 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
12073 (synopsis "Weighted correlation network analysis")
12075 "This package provides functions necessary to perform Weighted
12076 Correlation Network Analysis on high-dimensional data. It includes functions
12077 for rudimentary data cleaning, construction and summarization of correlation
12078 networks, module identification and functions for relating both variables and
12079 modules to sample traits. It also includes a number of utility functions for
12080 data manipulation and visualization.")
12081 (license license:gpl2+)))
12083 (define-public r-rgraphviz
12085 (name "r-rgraphviz")
12090 (uri (bioconductor-uri "Rgraphviz" version))
12093 "0d0xq1vgr4b165cn4wg7zmfjyc1d9ir4amgs196j4cgrhpmrnl8s"))))
12094 (properties `((upstream-name . "Rgraphviz")))
12095 (build-system r-build-system)
12098 (modify-phases %standard-phases
12099 (add-after 'unpack 'make-reproducible
12101 ;; The replacement value is taken from src/graphviz/builddate.h
12102 (substitute* "src/graphviz/configure"
12103 (("VERSION_DATE=.*")
12104 "VERSION_DATE=20200427.2341\n"))
12106 ;; FIXME: Rgraphviz bundles the sources of an older variant of
12107 ;; graphviz. It does not build with the latest version of graphviz, so
12108 ;; we do not add graphviz to the inputs.
12109 (inputs `(("zlib" ,zlib)))
12111 `(("r-graph" ,r-graph)))
12113 `(("pkg-config" ,pkg-config)))
12114 (home-page "https://bioconductor.org/packages/Rgraphviz")
12115 (synopsis "Plotting capabilities for R graph objects")
12117 "This package interfaces R with the graphviz library for plotting R graph
12118 objects from the @code{graph} package.")
12119 (license license:epl1.0)))
12121 (define-public r-fithic
12127 (uri (bioconductor-uri "FitHiC" version))
12130 "1p8a6lis5yswaj647bjw89harlarnsxmvjzz63fn1l6gxrwhh8bx"))))
12131 (properties `((upstream-name . "FitHiC")))
12132 (build-system r-build-system)
12134 `(("r-data-table" ,r-data-table)
12135 ("r-fdrtool" ,r-fdrtool)
12136 ("r-rcpp" ,r-rcpp)))
12138 `(("r-knitr" ,r-knitr)))
12139 (home-page "https://bioconductor.org/packages/FitHiC")
12140 (synopsis "Confidence estimation for intra-chromosomal contact maps")
12142 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
12143 intra-chromosomal contact maps produced by genome-wide genome architecture
12144 assays such as Hi-C.")
12145 (license license:gpl2+)))
12147 (define-public r-hitc
12153 (uri (bioconductor-uri "HiTC" version))
12156 "0s3kfqs3zlmq61hxdmxpmi9gfs9w3byckw7xzp1hrhdbsl46yvgq"))))
12157 (properties `((upstream-name . "HiTC")))
12158 (build-system r-build-system)
12160 `(("r-biostrings" ,r-biostrings)
12161 ("r-genomeinfodb" ,r-genomeinfodb)
12162 ("r-genomicranges" ,r-genomicranges)
12163 ("r-iranges" ,r-iranges)
12164 ("r-matrix" ,r-matrix)
12165 ("r-rcolorbrewer" ,r-rcolorbrewer)
12166 ("r-rtracklayer" ,r-rtracklayer)))
12167 (home-page "https://bioconductor.org/packages/HiTC")
12168 (synopsis "High throughput chromosome conformation capture analysis")
12170 "The HiTC package was developed to explore high-throughput \"C\" data
12171 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
12172 quality controls, normalization, visualization, and further analysis are also
12174 (license license:artistic2.0)))
12176 (define-public r-hdf5array
12178 (name "r-hdf5array")
12183 (uri (bioconductor-uri "HDF5Array" version))
12186 "1718hplz5qlbwxwb87509bl7lir9kilvn1s7p2haz551pg48zvrc"))))
12187 (properties `((upstream-name . "HDF5Array")))
12188 (build-system r-build-system)
12192 `(("r-biocgenerics" ,r-biocgenerics)
12193 ("r-delayedarray" ,r-delayedarray)
12194 ("r-iranges" ,r-iranges)
12195 ("r-matrix" ,r-matrix)
12196 ("r-rhdf5" ,r-rhdf5)
12197 ("r-rhdf5filters" ,r-rhdf5filters)
12198 ("r-rhdf5lib" ,r-rhdf5lib)
12199 ("r-s4vectors" ,r-s4vectors)))
12200 (home-page "https://bioconductor.org/packages/HDF5Array")
12201 (synopsis "HDF5 back end for DelayedArray objects")
12202 (description "This package provides an array-like container for convenient
12203 access and manipulation of HDF5 datasets. It supports delayed operations and
12204 block processing.")
12205 (license license:artistic2.0)))
12207 (define-public r-rhdf5lib
12209 (name "r-rhdf5lib")
12214 (uri (bioconductor-uri "Rhdf5lib" version))
12217 "1ypqmd4nz4hxlb2qsay7f5784dqdjhc3b19pckzkhb65bfycdn87"))
12218 (modules '((guix build utils)))
12221 ;; Delete bundled binaries
12222 (delete-file-recursively "src/wininclude/")
12223 (delete-file-recursively "src/winlib-8.3.0/")
12224 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")
12226 (properties `((upstream-name . "Rhdf5lib")))
12227 (build-system r-build-system)
12230 (modify-phases %standard-phases
12231 (add-after 'unpack 'do-not-use-bundled-hdf5
12232 (lambda* (#:key inputs #:allow-other-keys)
12233 (for-each delete-file '("configure" "configure.ac"))
12234 ;; Do not make other packages link with the proprietary libsz.
12235 (substitute* "R/zzz.R"
12236 ((" \"%s/libsz.a\"") "")
12237 (("patharch, .getDynamicLinks")
12238 ".getDynamicLinks"))
12239 (with-directory-excursion "src"
12240 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
12241 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
12243 ;; Remove timestamp and host system information to make
12244 ;; the build reproducible.
12245 (substitute* "hdf5/src/libhdf5.settings.in"
12246 (("Configured on: @CONFIG_DATE@")
12247 "Configured on: Guix")
12248 (("Uname information:.*")
12249 "Uname information: Linux\n")
12250 ;; Remove unnecessary store reference.
12252 "C Compiler: GCC\n"))
12253 (rename-file "hdf5/src/libhdf5.settings.in"
12254 "hdf5/src/libhdf5.settings")
12255 (rename-file "Makevars.in" "Makevars")
12256 (substitute* "Makevars"
12257 (("@ZLIB_LIB@") "-lz")
12258 (("@ZLIB_INCLUDE@") "")
12259 (("HDF5_CXX_LIB=.*")
12260 (string-append "HDF5_CXX_LIB="
12261 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
12263 (string-append "HDF5_LIB="
12264 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
12265 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
12266 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
12267 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
12268 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
12269 (("HDF5_HL_LIB=.*")
12270 (string-append "HDF5_HL_LIB="
12271 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
12272 (("HDF5_HL_CXX_LIB=.*")
12273 (string-append "HDF5_HL_CXX_LIB="
12274 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
12275 ;; szip is non-free software
12276 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
12277 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
12279 `(("hdf5" ,hdf5-1.10)
12282 `(("hdf5-source" ,(package-source hdf5-1.10))
12283 ("r-knitr" ,r-knitr)))
12284 (home-page "https://bioconductor.org/packages/Rhdf5lib")
12285 (synopsis "HDF5 library as an R package")
12286 (description "This package provides C and C++ HDF5 libraries for use in R
12288 (license license:artistic2.0)))
12290 (define-public r-beachmat
12292 (name "r-beachmat")
12297 (uri (bioconductor-uri "beachmat" version))
12300 "16p6shab4y8sy1adn4qr05ysvwmvs9idliccixafvx9icv5sla86"))))
12301 (build-system r-build-system)
12303 `(("r-biocgenerics" ,r-biocgenerics)
12304 ("r-delayedarray" ,r-delayedarray)
12305 ("r-matrix" ,r-matrix)
12306 ("r-rcpp" ,r-rcpp)))
12308 `(("r-knitr" ,r-knitr)))
12309 (home-page "https://bioconductor.org/packages/beachmat")
12310 (synopsis "Compiling Bioconductor to handle each matrix type")
12311 (description "This package provides a consistent C++ class interface for a
12312 variety of commonly used matrix types, including sparse and HDF5-backed
12314 (license license:gpl3)))
12316 ;; This package includes files that have been taken from kentutils. Some
12317 ;; parts of kentutils are not released under a free license, but this package
12318 ;; only uses files that are also found in the free parts of kentutils.
12319 (define-public r-cner
12326 (uri (bioconductor-uri "CNEr" version))
12328 (base32 "13w0gsfm7k29dp5nb0c9sb2ix506ph6dixsjis6xxcz6acq7lg2k"))))
12329 (properties `((upstream-name . "CNEr")))
12330 (build-system r-build-system)
12331 (inputs `(("zlib" ,zlib)))
12333 `(("r-annotate" ,r-annotate)
12334 ("r-biocgenerics" ,r-biocgenerics)
12335 ("r-biostrings" ,r-biostrings)
12337 ("r-genomeinfodb" ,r-genomeinfodb)
12338 ("r-genomicalignments" ,r-genomicalignments)
12339 ("r-genomicranges" ,r-genomicranges)
12340 ("r-ggplot2" ,r-ggplot2)
12341 ("r-go-db" ,r-go-db)
12342 ("r-iranges" ,r-iranges)
12343 ("r-keggrest" ,r-keggrest)
12344 ("r-powerlaw" ,r-powerlaw)
12345 ("r-r-utils" ,r-r-utils)
12346 ("r-readr" ,r-readr)
12347 ("r-reshape2" ,r-reshape2)
12348 ("r-rsqlite" ,r-rsqlite)
12349 ("r-rtracklayer" ,r-rtracklayer)
12350 ("r-s4vectors" ,r-s4vectors)
12351 ("r-xvector" ,r-xvector)))
12353 `(("r-knitr" ,r-knitr)))
12354 (home-page "https://github.com/ge11232002/CNEr")
12355 (synopsis "CNE Detection and Visualization")
12357 "This package provides tools for large-scale identification and
12358 advanced visualization of sets of conserved noncoding elements.")
12359 ;; For all files in src/ucsc "license is hereby granted for all use -
12360 ;; public, private or commercial"; this includes those files that don't
12361 ;; have a license header, because they are included in the free parts of
12362 ;; the kentutils package.
12363 (license (list license:gpl2
12364 (license:non-copyleft
12365 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
12367 (define-public r-tfbstools
12369 (name "r-tfbstools")
12374 (uri (bioconductor-uri "TFBSTools" version))
12377 "1avgjv2nyr28cla0z9dvh3v0hr1f561sz2as1k53a42irbjk0var"))))
12378 (properties `((upstream-name . "TFBSTools")))
12379 (build-system r-build-system)
12381 `(("r-biobase" ,r-biobase)
12382 ("r-biocgenerics" ,r-biocgenerics)
12383 ("r-biocparallel" ,r-biocparallel)
12384 ("r-biostrings" ,r-biostrings)
12385 ("r-bsgenome" ,r-bsgenome)
12386 ("r-catools" ,r-catools)
12389 ("r-dirichletmultinomial" ,r-dirichletmultinomial)
12390 ("r-genomeinfodb" ,r-genomeinfodb)
12391 ("r-genomicranges" ,r-genomicranges)
12392 ("r-gtools" ,r-gtools)
12393 ("r-iranges" ,r-iranges)
12394 ("r-rsqlite" ,r-rsqlite)
12395 ("r-rtracklayer" ,r-rtracklayer)
12396 ("r-s4vectors" ,r-s4vectors)
12397 ("r-seqlogo" ,r-seqlogo)
12398 ("r-tfmpvalue" ,r-tfmpvalue)
12400 ("r-xvector" ,r-xvector)))
12401 (native-inputs `(("r-knitr" ,r-knitr)))
12402 (home-page "https://github.com/ge11232002/TFBSTools")
12403 (synopsis "Transcription factor binding site (TFBS) analysis")
12405 "TFBSTools is a package for the analysis and manipulation of
12406 transcription factor binding sites. It includes matrices conversion
12407 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
12408 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
12409 scan putative TFBS from sequence/alignment, query JASPAR database and
12410 provides a wrapper of de novo motif discovery software.")
12411 (license license:gpl2)))
12413 (define-public r-motifmatchr
12415 (name "r-motifmatchr")
12420 (uri (bioconductor-uri "motifmatchr" version))
12423 "1vif3dp4lv4jz1pxsq0ig791ir8q65jmrlqmkyfxpfxfj5alqnbm"))))
12424 (properties `((upstream-name . "motifmatchr")))
12425 (build-system r-build-system)
12427 `(("r-biostrings" ,r-biostrings)
12428 ("r-bsgenome" ,r-bsgenome)
12429 ("r-genomeinfodb" ,r-genomeinfodb)
12430 ("r-genomicranges" ,r-genomicranges)
12431 ("r-iranges" ,r-iranges)
12432 ("r-matrix" ,r-matrix)
12434 ("r-rcpparmadillo" ,r-rcpparmadillo)
12435 ("r-rsamtools" ,r-rsamtools)
12436 ("r-s4vectors" ,r-s4vectors)
12437 ("r-summarizedexperiment" ,r-summarizedexperiment)
12438 ("r-tfbstools" ,r-tfbstools)))
12439 (native-inputs `(("r-knitr" ,r-knitr)))
12440 (home-page "https://bioconductor.org/packages/motifmatchr")
12441 (synopsis "Fast motif matching in R")
12443 "Quickly find motif matches for many motifs and many sequences.
12444 This package wraps C++ code from the MOODS motif calling library.")
12445 (license license:gpl3)))
12447 (define-public r-chromvar
12449 (name "r-chromvar")
12454 (uri (bioconductor-uri "chromVAR" version))
12456 (base32 "1birmwvcvl2hb5ygbsb3wvbdfayqqs53j1bks46cbkq7ybigfyar"))))
12457 (properties `((upstream-name . "chromVAR")))
12458 (build-system r-build-system)
12460 `(("r-biocgenerics" ,r-biocgenerics)
12461 ("r-biocparallel" ,r-biocparallel)
12462 ("r-biostrings" ,r-biostrings)
12463 ("r-bsgenome" ,r-bsgenome)
12465 ("r-genomeinfodb" ,r-genomeinfodb)
12466 ("r-genomicranges" ,r-genomicranges)
12467 ("r-ggplot2" ,r-ggplot2)
12468 ("r-iranges" ,r-iranges)
12469 ("r-matrix" ,r-matrix)
12470 ("r-miniui" ,r-miniui)
12471 ("r-nabor" ,r-nabor)
12472 ("r-plotly" ,r-plotly)
12473 ("r-rcolorbrewer" ,r-rcolorbrewer)
12475 ("r-rcpparmadillo" ,r-rcpparmadillo)
12476 ("r-rsamtools" ,r-rsamtools)
12477 ("r-rtsne" ,r-rtsne)
12478 ("r-s4vectors" ,r-s4vectors)
12479 ("r-shiny" ,r-shiny)
12480 ("r-summarizedexperiment" ,r-summarizedexperiment)
12481 ("r-tfbstools" ,r-tfbstools)))
12482 (native-inputs `(("r-knitr" ,r-knitr)))
12483 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
12484 (synopsis "Determine chromatin variation across regions")
12486 "This package @code{r-chromvar} determines variation in chromatin
12487 accessibility across sets of annotations or peaks. @code{r-chromvar} is
12488 designed primarily for single-cell or sparse chromatin accessibility data like
12489 single cell assay for transposase-accessible chromatin using
12490 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
12491 sequence (@code{DNAse-seq}) experiments.")
12492 (license license:expat)))
12494 (define-public r-singlecellexperiment
12496 (name "r-singlecellexperiment")
12501 (uri (bioconductor-uri "SingleCellExperiment" version))
12504 "1bwdhx0ss0s8f4xdgwd7x48apn849x4dyb5hbyglcz31r5vh1qgz"))))
12506 `((upstream-name . "SingleCellExperiment")))
12507 (build-system r-build-system)
12509 `(("r-biocgenerics" ,r-biocgenerics)
12510 ("r-delayedarray" ,r-delayedarray)
12511 ("r-genomicranges" ,r-genomicranges)
12512 ("r-s4vectors" ,r-s4vectors)
12513 ("r-summarizedexperiment" ,r-summarizedexperiment)))
12515 `(("r-knitr" ,r-knitr)))
12516 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
12517 (synopsis "S4 classes for single cell data")
12518 (description "This package defines an S4 class for storing data from
12519 single-cell experiments. This includes specialized methods to store and
12520 retrieve spike-in information, dimensionality reduction coordinates and size
12521 factors for each cell, along with the usual metadata for genes and
12523 (license license:gpl3)))
12525 (define-public r-scuttle
12532 (uri (bioconductor-uri "scuttle" version))
12535 "1vxmgm52n5z2m1a7d4c5ajp5d35rdq7j3hln9qn7188zk9ijjsz5"))))
12536 (properties `((upstream-name . "scuttle")))
12537 (build-system r-build-system)
12539 `(("r-beachmat" ,r-beachmat)
12540 ("r-biocgenerics" ,r-biocgenerics)
12541 ("r-biocparallel" ,r-biocparallel)
12542 ("r-delayedarray" ,r-delayedarray)
12543 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
12544 ("r-genomicranges" ,r-genomicranges)
12545 ("r-matrix" ,r-matrix)
12547 ("r-s4vectors" ,r-s4vectors)
12548 ("r-singlecellexperiment" ,r-singlecellexperiment)
12549 ("r-summarizedexperiment" ,r-summarizedexperiment)))
12550 (native-inputs `(("r-knitr" ,r-knitr)))
12551 (home-page "https://bioconductor.org/packages/scuttle")
12552 (synopsis "Single-cell RNA-Seq analysis utilities")
12554 "This package provides basic utility functions for performing single-cell
12555 analyses, focusing on simple normalization, quality control and data
12556 transformations. It also provides some helper functions to assist development
12557 of other packages.")
12558 (license license:gpl3)))
12560 (define-public r-scater
12566 (uri (bioconductor-uri "scater" version))
12569 "0rppbd0mfyi41wb56i499mk3nj2ljhgnv3bv0k2p31bngvmb03j5"))))
12570 (build-system r-build-system)
12572 `(("r-beachmat" ,r-beachmat)
12573 ("r-biocgenerics" ,r-biocgenerics)
12574 ("r-biocneighbors" ,r-biocneighbors)
12575 ("r-biocparallel" ,r-biocparallel)
12576 ("r-biocsingular" ,r-biocsingular)
12577 ("r-delayedarray" ,r-delayedarray)
12578 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
12579 ("r-ggbeeswarm" ,r-ggbeeswarm)
12580 ("r-ggplot2" ,r-ggplot2)
12581 ("r-gridextra" ,r-gridextra)
12582 ("r-matrix" ,r-matrix)
12583 ("r-rcolorbrewer" ,r-rcolorbrewer)
12584 ("r-rlang" ,r-rlang)
12585 ("r-rtsne" ,r-rtsne)
12586 ("r-s4vectors" ,r-s4vectors)
12587 ("r-scuttle" ,r-scuttle)
12588 ("r-singlecellexperiment" ,r-singlecellexperiment)
12589 ("r-summarizedexperiment" ,r-summarizedexperiment)
12590 ("r-viridis" ,r-viridis)))
12592 `(("r-knitr" ,r-knitr)))
12593 (home-page "https://github.com/davismcc/scater")
12594 (synopsis "Single-cell analysis toolkit for gene expression data in R")
12595 (description "This package provides a collection of tools for doing
12596 various analyses of single-cell RNA-seq gene expression data, with a focus on
12598 (license license:gpl2+)))
12600 (define-public r-scran
12607 (uri (bioconductor-uri "scran" version))
12610 "0ilzp6ngw9pq88gk79iic2zxfh5jaic6lnq3xfwc9a269bjylff0"))))
12611 (build-system r-build-system)
12613 `(("r-beachmat" ,r-beachmat)
12615 ("r-biocgenerics" ,r-biocgenerics)
12616 ("r-biocparallel" ,r-biocparallel)
12617 ("r-biocsingular" ,r-biocsingular)
12618 ("r-bluster" ,r-bluster)
12619 ("r-delayedarray" ,r-delayedarray)
12620 ("r-delayedmatrixstats" ,r-delayedmatrixstats)
12621 ("r-dqrng" ,r-dqrng)
12622 ("r-edger" ,r-edger)
12623 ("r-igraph" ,r-igraph)
12624 ("r-limma" ,r-limma)
12625 ("r-matrix" ,r-matrix)
12626 ("r-metapod" ,r-metapod)
12628 ("r-s4vectors" ,r-s4vectors)
12629 ("r-scuttle" ,r-scuttle)
12630 ("r-singlecellexperiment" ,r-singlecellexperiment)
12631 ("r-statmod" ,r-statmod)
12632 ("r-summarizedexperiment" ,r-summarizedexperiment)))
12634 `(("r-knitr" ,r-knitr)))
12635 (home-page "https://bioconductor.org/packages/scran")
12636 (synopsis "Methods for single-cell RNA-Seq data analysis")
12637 (description "This package implements a variety of low-level analyses of
12638 single-cell RNA-seq data. Methods are provided for normalization of
12639 cell-specific biases, assignment of cell cycle phase, and detection of highly
12640 variable and significantly correlated genes.")
12641 (license license:gpl3)))
12643 (define-public r-sparsematrixstats
12645 (name "r-sparsematrixstats")
12650 (uri (bioconductor-uri "sparseMatrixStats" version))
12653 "0ilspddfkqpnf2lng9jjs2ahv6vlc6sap69fzkcw314rha59kncr"))))
12655 `((upstream-name . "sparseMatrixStats")))
12656 (build-system r-build-system)
12658 `(("r-matrix" ,r-matrix)
12659 ("r-matrixgenerics" ,r-matrixgenerics)
12660 ("r-matrixstats" ,r-matrixstats)
12661 ("r-rcpp" ,r-rcpp)))
12662 (native-inputs `(("r-knitr" ,r-knitr)))
12663 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
12664 (synopsis "Summary statistics for rows and columns of sparse matrices")
12666 "This package provides high performance functions for row and column
12667 operations on sparse matrices. Currently, the optimizations are limited to
12668 data in the column sparse format.")
12669 (license license:expat)))
12671 (define-public r-delayedmatrixstats
12673 (name "r-delayedmatrixstats")
12678 (uri (bioconductor-uri "DelayedMatrixStats" version))
12681 "02r68rzmc54m353fpw5ampyv26i5622bc7iihfqlpy6p3033lpqk"))))
12683 `((upstream-name . "DelayedMatrixStats")))
12684 (build-system r-build-system)
12686 `(("r-delayedarray" ,r-delayedarray)
12687 ("r-iranges" ,r-iranges)
12688 ("r-matrix" ,r-matrix)
12689 ("r-matrixgenerics" ,r-matrixgenerics)
12690 ("r-matrixstats" ,r-matrixstats)
12691 ("r-s4vectors" ,r-s4vectors)
12692 ("r-sparsematrixstats" ,r-sparsematrixstats)))
12694 `(("r-knitr" ,r-knitr)))
12695 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
12696 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
12698 "This package provides a port of the @code{matrixStats} API for use with
12699 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
12700 contains high-performing functions operating on rows and columns of
12701 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
12702 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
12703 are optimized per data type and for subsetted calculations such that both
12704 memory usage and processing time is minimized.")
12705 (license license:expat)))
12707 (define-public r-mscoreutils
12709 (name "r-mscoreutils")
12714 (uri (bioconductor-uri "MsCoreUtils" version))
12717 "13g8a726vsyjs6m1kd42vf8avdnmhykxhl6z3j2njzkp2jg17pd8"))))
12718 (properties `((upstream-name . "MsCoreUtils")))
12719 (build-system r-build-system)
12721 `(("r-clue" ,r-clue)
12724 ("r-s4vectors" ,r-s4vectors)))
12726 `(("r-knitr" ,r-knitr)))
12727 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
12728 (synopsis "Core utils for mass spectrometry data")
12730 "This package defines low-level functions for mass spectrometry data and
12731 is independent of any high-level data structures. These functions include
12732 mass spectra processing functions (noise estimation, smoothing, binning),
12733 quantitative aggregation functions (median polish, robust summarisation,
12734 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
12735 well as misc helper functions, that are used across high-level data structure
12736 within the R for Mass Spectrometry packages.")
12737 (license license:artistic2.0)))
12739 (define-public r-biocio
12746 (uri (bioconductor-uri "BiocIO" version))
12749 "0skwnpxl6fkqihidpqrfzzh7b05x11j6jwkiinmhggmv0ggjb5ph"))))
12750 (properties `((upstream-name . "BiocIO")))
12751 (build-system r-build-system)
12753 `(("r-biocgenerics" ,r-biocgenerics)
12754 ("r-s4vectors" ,r-s4vectors)))
12756 `(("r-knitr" ,r-knitr)))
12757 (home-page "https://bioconductor.org/packages/BiocIO")
12758 (synopsis "Standard input and output for Bioconductor packages")
12760 "This package implements `import()` and `export()` standard generics for
12761 importing and exporting biological data formats. `import()` supports
12762 whole-file as well as chunk-wise iterative import. The `import()` interface
12763 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
12764 row or element-like components of the file resource), `select()` (on
12765 column-like components of the file resource) and `collect()`. The `import()`
12766 interface optionally provides transparent access to remote (e.g. via https)
12767 as well as local access. Developers can register a file extension, e.g.,
12768 `.loom` for dispatch from character-based URIs to specific `import()` /
12769 `export()` methods based on classes representing file types, e.g.,
12771 (license license:artistic2.0)))
12773 (define-public r-msmseda
12780 (uri (bioconductor-uri "msmsEDA" version))
12783 "1llmy8msxmrqik3s3439wffma1662vwvvcaz8q0a4g5ridkmdbrx"))))
12784 (properties `((upstream-name . "msmsEDA")))
12785 (build-system r-build-system)
12787 `(("r-gplots" ,r-gplots)
12789 ("r-msnbase" ,r-msnbase)
12790 ("r-rcolorbrewer" ,r-rcolorbrewer)))
12792 "https://bioconductor.org/packages/msmsEDA")
12793 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
12795 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
12796 experiments, and visualize de influence of the involved factors.")
12797 (license license:gpl2)))
12799 (define-public r-msmstests
12801 (name "r-msmstests")
12806 (uri (bioconductor-uri "msmsTests" version))
12809 "1zsnmzj1qvjdwz7mwg9wrsk5iskpqs0f6jccqn8mxy9dgkskmp0j"))))
12810 (properties `((upstream-name . "msmsTests")))
12811 (build-system r-build-system)
12813 `(("r-edger" ,r-edger)
12814 ("r-msmseda" ,r-msmseda)
12815 ("r-msnbase" ,r-msnbase)
12816 ("r-qvalue" ,r-qvalue)))
12818 "https://bioconductor.org/packages/msmsTests")
12819 (synopsis "Differential LC-MS/MS expression tests")
12821 "This package provides statistical tests for label-free LC-MS/MS data
12822 by spectral counts, to discover differentially expressed proteins between two
12823 biological conditions. Three tests are available: Poisson GLM regression,
12824 quasi-likelihood GLM regression, and the negative binomial of the edgeR
12825 package. The three models admit blocking factors to control for nuisance
12826 variables. To assure a good level of reproducibility a post-test filter is
12827 available, where we may set the minimum effect size considered biologicaly
12828 relevant, and the minimum expression of the most abundant condition.")
12829 (license license:gpl2)))
12831 (define-public r-catalyst
12833 (name "r-catalyst")
12838 (uri (bioconductor-uri "CATALYST" version))
12841 "04b5kcvkfiw4ina11x3qf5kwrb7056zihm7xp1919bqm8k7nl3mn"))))
12842 (properties `((upstream-name . "CATALYST")))
12843 (build-system r-build-system)
12845 `(("r-circlize" ,r-circlize)
12846 ("r-complexheatmap" ,r-complexheatmap)
12847 ("r-consensusclusterplus" ,r-consensusclusterplus)
12848 ("r-cowplot" ,r-cowplot)
12849 ("r-data-table" ,r-data-table)
12850 ("r-dplyr" ,r-dplyr)
12852 ("r-flowcore" ,r-flowcore)
12853 ("r-flowsom" ,r-flowsom)
12854 ("r-ggplot2" ,r-ggplot2)
12855 ("r-ggrepel" ,r-ggrepel)
12856 ("r-ggridges" ,r-ggridges)
12857 ("r-gridextra" ,r-gridextra)
12858 ("r-magrittr" ,r-magrittr)
12859 ("r-matrix" ,r-matrix)
12860 ("r-matrixstats" ,r-matrixstats)
12862 ("r-purrr" ,r-purrr)
12863 ("r-rcolorbrewer" ,r-rcolorbrewer)
12864 ("r-reshape2" ,r-reshape2)
12865 ("r-rtsne" ,r-rtsne)
12866 ("r-s4vectors" ,r-s4vectors)
12867 ("r-scales" ,r-scales)
12868 ("r-scater" ,r-scater)
12869 ("r-singlecellexperiment" ,r-singlecellexperiment)
12870 ("r-summarizedexperiment" ,r-summarizedexperiment)))
12872 `(("r-knitr" ,r-knitr)))
12874 "https://github.com/HelenaLC/CATALYST")
12875 (synopsis "Cytometry data analysis tools")
12877 "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
12878 cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
12879 reporters to label antibodies, thereby substantially decreasing spectral
12880 overlap and allowing for examination of over 50 parameters at the single cell
12881 level. While spectral overlap is significantly less pronounced in CyTOF than
12882 flow cytometry, spillover due to detection sensitivity, isotopic impurities,
12883 and oxide formation can impede data interpretability. We designed
12884 CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
12885 preprocessing of cytometry data, including i) normalization using bead
12886 standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
12887 (license license:gpl2+)))
12889 (define-public r-erma
12896 (uri (bioconductor-uri "erma" version))
12899 "1k2j1xhv0vwn45xmh8ds0gz812px5hnpgzvp37ngsdn4j5ai1l0k"))))
12900 (build-system r-build-system)
12902 `(("r-annotationdbi" ,r-annotationdbi)
12903 ("r-biobase" ,r-biobase)
12904 ("r-biocgenerics" ,r-biocgenerics)
12905 ("r-biocparallel" ,r-biocparallel)
12906 ("r-genomeinfodb" ,r-genomeinfodb)
12907 ("r-genomicfiles" ,r-genomicfiles)
12908 ("r-genomicranges" ,r-genomicranges)
12909 ("r-ggplot2" ,r-ggplot2)
12910 ("r-homo-sapiens" ,r-homo-sapiens)
12911 ("r-iranges" ,r-iranges)
12912 ("r-rtracklayer" ,r-rtracklayer)
12913 ("r-s4vectors" ,r-s4vectors)
12914 ("r-shiny" ,r-shiny)
12915 ("r-summarizedexperiment" ,r-summarizedexperiment)))
12917 `(("r-knitr" ,r-knitr)))
12918 (home-page "https://bioconductor.org/packages/erma")
12919 (synopsis "Epigenomic road map adventures")
12921 "The epigenomics road map describes locations of epigenetic marks in DNA
12922 from a variety of cell types. Of interest are locations of histone
12923 modifications, sites of DNA methylation, and regions of accessible chromatin.
12924 This package presents a selection of elements of the road map including
12925 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
12926 by Ernst and Kellis.")
12927 (license license:artistic2.0)))
12929 (define-public r-ggbio
12936 (uri (bioconductor-uri "ggbio" version))
12939 "0vabil4jzrlv01aibqjhdkvrv2bf2kkpsidrkjj06isqr5fz54lw"))))
12940 (build-system r-build-system)
12943 (modify-phases %standard-phases
12944 ;; See https://github.com/tengfei/ggbio/issues/117
12945 ;; This fix will be included in the next release.
12946 (add-after 'unpack 'fix-typo
12948 (substitute* "R/GGbio-class.R"
12949 (("fechable") "fetchable"))
12952 `(("r-annotationdbi" ,r-annotationdbi)
12953 ("r-annotationfilter" ,r-annotationfilter)
12954 ("r-biobase" ,r-biobase)
12955 ("r-biocgenerics" ,r-biocgenerics)
12956 ("r-biostrings" ,r-biostrings)
12957 ("r-biovizbase" ,r-biovizbase)
12958 ("r-bsgenome" ,r-bsgenome)
12959 ("r-ensembldb" ,r-ensembldb)
12960 ("r-genomeinfodb" ,r-genomeinfodb)
12961 ("r-genomicalignments" ,r-genomicalignments)
12962 ("r-genomicfeatures" ,r-genomicfeatures)
12963 ("r-genomicranges" ,r-genomicranges)
12964 ("r-ggally" ,r-ggally)
12965 ("r-ggplot2" ,r-ggplot2)
12966 ("r-gridextra" ,r-gridextra)
12967 ("r-gtable" ,r-gtable)
12968 ("r-hmisc" ,r-hmisc)
12969 ("r-iranges" ,r-iranges)
12970 ("r-organismdbi" ,r-organismdbi)
12971 ("r-reshape2" ,r-reshape2)
12972 ("r-rlang" ,r-rlang)
12973 ("r-rsamtools" ,r-rsamtools)
12974 ("r-rtracklayer" ,r-rtracklayer)
12975 ("r-s4vectors" ,r-s4vectors)
12976 ("r-scales" ,r-scales)
12977 ("r-summarizedexperiment" ,r-summarizedexperiment)
12978 ("r-variantannotation" ,r-variantannotation)))
12980 `(("r-knitr" ,r-knitr)))
12981 (home-page "http://www.tengfei.name/ggbio/")
12982 (synopsis "Visualization tools for genomic data")
12984 "The ggbio package extends and specializes the grammar of graphics for
12985 biological data. The graphics are designed to answer common scientific
12986 questions, in particular those often asked of high throughput genomics data.
12987 All core Bioconductor data structures are supported, where appropriate. The
12988 package supports detailed views of particular genomic regions, as well as
12989 genome-wide overviews. Supported overviews include ideograms and grand linear
12990 views. High-level plots include sequence fragment length, edge-linked
12991 interval to data view, mismatch pileup, and several splicing summaries.")
12992 (license license:artistic2.0)))
12994 (define-public r-gqtlbase
12996 (name "r-gqtlbase")
13001 (uri (bioconductor-uri "gQTLBase" version))
13004 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
13005 (properties `((upstream-name . "gQTLBase")))
13006 (build-system r-build-system)
13009 (modify-phases %standard-phases
13010 ;; This is an upstream bug.
13011 (add-after 'unpack 'fix-imports
13013 (substitute* "NAMESPACE"
13014 ((".*maxffmode.*") "")
13015 (("importFrom\\(ff,.*") "import(ff)\n"))
13018 `(("r-batchjobs" ,r-batchjobs)
13019 ("r-bbmisc" ,r-bbmisc)
13020 ("r-biocgenerics" ,r-biocgenerics)
13022 ("r-doparallel" ,r-doparallel)
13024 ("r-ffbase" ,r-ffbase)
13025 ("r-foreach" ,r-foreach)
13026 ("r-genomicfiles" ,r-genomicfiles)
13027 ("r-genomicranges" ,r-genomicranges)
13028 ("r-rtracklayer" ,r-rtracklayer)
13029 ("r-s4vectors" ,r-s4vectors)
13030 ("r-summarizedexperiment" ,r-summarizedexperiment)))
13032 `(("r-knitr" ,r-knitr)))
13033 (home-page "https://bioconductor.org/packages/gQTLBase")
13034 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
13036 "The purpose of this package is to simplify the storage and interrogation
13037 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
13039 (license license:artistic2.0)))
13041 (define-public r-gqtlstats
13043 (name "r-gqtlstats")
13048 (uri (bioconductor-uri "gQTLstats" version))
13051 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
13052 (properties `((upstream-name . "gQTLstats")))
13053 (build-system r-build-system)
13055 `(("r-annotationdbi" ,r-annotationdbi)
13056 ("r-batchjobs" ,r-batchjobs)
13057 ("r-bbmisc" ,r-bbmisc)
13058 ("r-beeswarm" ,r-beeswarm)
13059 ("r-biobase" ,r-biobase)
13060 ("r-biocgenerics" ,r-biocgenerics)
13061 ("r-doparallel" ,r-doparallel)
13062 ("r-dplyr" ,r-dplyr)
13064 ("r-ffbase" ,r-ffbase)
13065 ("r-foreach" ,r-foreach)
13066 ("r-genomeinfodb" ,r-genomeinfodb)
13067 ("r-genomicfeatures" ,r-genomicfeatures)
13068 ("r-genomicfiles" ,r-genomicfiles)
13069 ("r-genomicranges" ,r-genomicranges)
13070 ("r-ggbeeswarm" ,r-ggbeeswarm)
13071 ("r-ggplot2" ,r-ggplot2)
13072 ("r-gqtlbase" ,r-gqtlbase)
13073 ("r-hardyweinberg" ,r-hardyweinberg)
13074 ("r-homo-sapiens" ,r-homo-sapiens)
13075 ("r-iranges" ,r-iranges)
13076 ("r-limma" ,r-limma)
13078 ("r-plotly" ,r-plotly)
13079 ("r-reshape2" ,r-reshape2)
13080 ("r-s4vectors" ,r-s4vectors)
13081 ("r-shiny" ,r-shiny)
13082 ("r-snpstats" ,r-snpstats)
13083 ("r-summarizedexperiment" ,r-summarizedexperiment)
13084 ("r-variantannotation" ,r-variantannotation)))
13086 `(("r-knitr" ,r-knitr)))
13087 (home-page "https://bioconductor.org/packages/gQTLstats")
13088 (synopsis "Computationally efficient analysis for eQTL and allied studies")
13090 "This package provides tools for the computationally efficient analysis
13091 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
13092 The software in this package aims to support refinements and functional
13093 interpretation of members of a collection of association statistics on a
13094 family of feature/genome hypotheses.")
13095 (license license:artistic2.0)))
13097 (define-public r-gviz
13104 (uri (bioconductor-uri "Gviz" version))
13107 "0bmlfz9ri1gkwyl605a2hqi5b8jdpvynrxwghwmrsd657ip6c7n1"))))
13108 (properties `((upstream-name . "Gviz")))
13109 (build-system r-build-system)
13111 `(("r-annotationdbi" ,r-annotationdbi)
13112 ("r-biobase" ,r-biobase)
13113 ("r-biocgenerics" ,r-biocgenerics)
13114 ("r-biomart" ,r-biomart)
13115 ("r-biostrings" ,r-biostrings)
13116 ("r-biovizbase" ,r-biovizbase)
13117 ("r-bsgenome" ,r-bsgenome)
13118 ("r-digest" ,r-digest)
13119 ("r-ensembldb" ,r-ensembldb)
13120 ("r-genomeinfodb" ,r-genomeinfodb)
13121 ("r-genomicalignments" ,r-genomicalignments)
13122 ("r-genomicfeatures" ,r-genomicfeatures)
13123 ("r-genomicranges" ,r-genomicranges)
13124 ("r-iranges" ,r-iranges)
13125 ("r-lattice" ,r-lattice)
13126 ("r-latticeextra" ,r-latticeextra)
13127 ("r-matrixstats" ,r-matrixstats)
13128 ("r-rcolorbrewer" ,r-rcolorbrewer)
13129 ("r-rsamtools" ,r-rsamtools)
13130 ("r-rtracklayer" ,r-rtracklayer)
13131 ("r-s4vectors" ,r-s4vectors)
13132 ("r-xvector" ,r-xvector)))
13134 `(("r-knitr" ,r-knitr)))
13135 (home-page "https://bioconductor.org/packages/Gviz")
13136 (synopsis "Plotting data and annotation information along genomic coordinates")
13138 "Genomic data analyses requires integrated visualization of known genomic
13139 information and new experimental data. Gviz uses the biomaRt and the
13140 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
13141 and translates this to e.g. gene/transcript structures in viewports of the
13142 grid graphics package. This results in genomic information plotted together
13144 (license license:artistic2.0)))
13146 (define-public r-gwascat
13153 (uri (bioconductor-uri "gwascat" version))
13156 "1aqi1ny93virnzsxkh9ccx3mws70bgv0r8nwgla09vffb7f16nna"))))
13157 (build-system r-build-system)
13159 `(("r-annotationdbi" ,r-annotationdbi)
13160 ("r-biocfilecache" ,r-biocfilecache)
13161 ("r-biostrings" ,r-biostrings)
13162 ("r-genomeinfodb" ,r-genomeinfodb)
13163 ("r-genomicfeatures" ,r-genomicfeatures)
13164 ("r-genomicranges" ,r-genomicranges)
13165 ("r-iranges" ,r-iranges)
13166 ("r-readr" ,r-readr)
13167 ("r-s4vectors" ,r-s4vectors)
13168 ("r-snpstats" ,r-snpstats)
13169 ("r-variantannotation" ,r-variantannotation)))
13171 `(("r-knitr" ,r-knitr)))
13172 (home-page "https://bioconductor.org/packages/gwascat")
13173 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
13175 "This package provides tools for representing and modeling data in the
13176 EMBL-EBI GWAS catalog.")
13177 (license license:artistic2.0)))
13179 (define-public r-kegggraph
13181 (name "r-kegggraph")
13186 (uri (bioconductor-uri "KEGGgraph" version))
13188 (base32 "1h293hn02ysm923bh9gxk87xv663xiqchqcvpaxpla9c3yrgkx2v"))))
13189 (properties `((upstream-name . "KEGGgraph")))
13190 (build-system r-build-system)
13192 `(("r-graph" ,r-graph)
13193 ("r-rcurl" ,r-rcurl)
13195 (home-page "https://bioconductor.org/packages/KEGGgraph")
13196 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
13198 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
13199 object as well as a collection of tools to analyze, dissect and visualize these
13200 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
13201 maintaining all essential pathway attributes. The package offers
13202 functionalities including parsing, graph operation, visualization and etc.")
13203 (license license:gpl2+)))
13205 (define-public r-ldblock
13212 (uri (bioconductor-uri "ldblock" version))
13215 "09i3ikv0axks9g842z1pjsc8x0fba51zyyc218h0bylbi1n9cdkm"))))
13216 (build-system r-build-system)
13218 `(("r-biocgenerics" ,r-biocgenerics)
13219 ("r-ensdb-hsapiens-v75" ,r-ensdb-hsapiens-v75)
13220 ("r-ensembldb" ,r-ensembldb)
13221 ("r-genomeinfodb" ,r-genomeinfodb)
13222 ("r-genomicfiles" ,r-genomicfiles)
13224 ("r-matrix" ,r-matrix)
13225 ("r-rsamtools" ,r-rsamtools)
13226 ("r-snpstats" ,r-snpstats)
13227 ("r-variantannotation" ,r-variantannotation)))
13229 `(("r-knitr" ,r-knitr)))
13230 (home-page "https://bioconductor.org/packages/ldblock")
13231 (synopsis "Data structures for linkage disequilibrium measures in populations")
13233 "This package defines data structures for @dfn{linkage
13234 disequilibrium} (LD) measures in populations. Its purpose is to simplify
13235 handling of existing population-level data for the purpose of flexibly
13236 defining LD blocks.")
13237 (license license:artistic2.0)))
13239 ;; This is a CRAN package, but it depends on r-snpstats, which is a
13240 ;; Bioconductor package.
13241 (define-public r-ldheatmap
13243 (name "r-ldheatmap")
13248 (uri (cran-uri "LDheatmap" version))
13251 "1jp578cf29qcgx95w10lpymlwx2pgjsf0nypwkl9b8g635gkisq7"))))
13252 (properties `((upstream-name . "LDheatmap")))
13253 (build-system r-build-system)
13255 `(("r-genetics" ,r-genetics)
13257 ("r-snpstats" ,r-snpstats)))
13258 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
13259 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13261 "This package provides tools to produce a graphical display, as a heat
13262 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13263 optionally include the physical locations or genetic map distances of each SNP
13265 (license license:gpl3)))
13267 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
13268 ;; Bioconductor package.
13269 (define-public r-abn
13276 (uri (cran-uri "abn" version))
13279 "1fqmhw0mhdl6az1gpg0byvx5snhz1pl3fqikhyfjcjrc9xbsq8yw"))))
13280 (build-system r-build-system)
13284 `(("r-lme4" ,r-lme4)
13287 ("r-rcpparmadillo" ,r-rcpparmadillo)
13288 ("r-rgraphviz" ,r-rgraphviz)
13289 ("r-rjags" ,r-rjags)))
13290 (home-page "https://r-bayesian-networks.org/")
13291 (synopsis "Modelling multivariate data with additive bayesian networks")
13293 "Bayesian network analysis is a form of probabilistic graphical models
13294 which derives from empirical data a directed acyclic graph, DAG, describing
13295 the dependency structure between random variables. An additive Bayesian
13296 network model consists of a form of a DAG where each node comprises a
13297 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
13298 equivalent to Bayesian multivariate regression using graphical modelling, they
13299 generalises the usual multivariable regression, GLM, to multiple dependent
13300 variables. This package provides routines to help determine optimal Bayesian
13301 network models for a given data set, where these models are used to identify
13302 statistical dependencies in messy, complex data.")
13303 (license license:gpl2+)))
13305 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
13306 ;; Bioconductor package.
13307 (define-public r-spp
13313 (uri (cran-uri "spp" version))
13316 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
13317 (build-system r-build-system)
13322 ("r-catools" ,r-catools)
13324 ("r-rsamtools" ,r-rsamtools)))
13325 (home-page "https://cran.r-project.org/web/packages/spp/")
13326 (synopsis "ChIP-Seq processing pipeline")
13327 (description "This package provides tools for analysis of ChIP-seq and
13328 other functional sequencing data.")
13329 (license license:gpl2)))
13331 (define-public r-pathview
13333 (name "r-pathview")
13338 (uri (bioconductor-uri "pathview" version))
13340 (base32 "11fisiksw1y64ii9q8p2znyp9w8mlqzgiaacmycw59rngkjlmbs4"))))
13341 (properties `((upstream-name . "pathview")))
13342 (build-system r-build-system)
13344 `(("r-annotationdbi" ,r-annotationdbi)
13345 ("r-graph" ,r-graph)
13346 ("r-kegggraph" ,r-kegggraph)
13347 ("r-keggrest" ,r-keggrest)
13348 ("r-org-hs-eg-db" ,r-org-hs-eg-db)
13350 ("r-rgraphviz" ,r-rgraphviz)
13352 (home-page "https://pathview.uncc.edu/")
13353 (synopsis "Tool set for pathway based data integration and visualization")
13355 "@code{r-pathview} is a tool set for pathway based data integration and
13356 visualization. It maps and renders a wide variety of biological data on
13357 relevant pathway graphs. All users need is to supply their data and specify
13358 the target pathway. This package automatically downloads the pathway graph
13359 data, parses the data file, maps user data to the pathway, and render pathway
13360 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
13361 integrates with pathway and gene set (enrichment) analysis tools for
13362 large-scale and fully automated analysis.")
13363 (license license:gpl3+)))
13365 (define-public r-snpstats
13367 (name "r-snpstats")
13372 (uri (bioconductor-uri "snpStats" version))
13375 "1298a71swwav53yf9kfqkdpach3818plqcbw0lgb6sibs8y8ff24"))))
13376 (properties `((upstream-name . "snpStats")))
13377 (build-system r-build-system)
13378 (inputs `(("zlib" ,zlib)))
13380 `(("r-biocgenerics" ,r-biocgenerics)
13381 ("r-matrix" ,r-matrix)
13382 ("r-survival" ,r-survival)
13383 ("r-zlibbioc" ,r-zlibbioc)))
13384 (home-page "https://bioconductor.org/packages/snpStats")
13385 (synopsis "Methods for SNP association studies")
13387 "This package provides classes and statistical methods for large
13388 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
13389 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
13390 (license license:gpl3)))
13392 (define-public r-chromstar
13394 (name "r-chromstar")
13399 (uri (bioconductor-uri "chromstaR" version))
13402 "0vgpb7g2cncdn82hia2yzzachyns2zbd7906662g990qjnp2xlm1"))))
13403 (properties `((upstream-name . "chromstaR")))
13404 (build-system r-build-system)
13406 `(("r-bamsignals" ,r-bamsignals)
13407 ("r-biocgenerics" ,r-biocgenerics)
13408 ("r-chromstardata" ,r-chromstardata)
13409 ("r-doparallel" ,r-doparallel)
13410 ("r-foreach" ,r-foreach)
13411 ("r-genomeinfodb" ,r-genomeinfodb)
13412 ("r-genomicalignments" ,r-genomicalignments)
13413 ("r-genomicranges" ,r-genomicranges)
13414 ("r-ggplot2" ,r-ggplot2)
13415 ("r-iranges" ,r-iranges)
13416 ("r-mvtnorm" ,r-mvtnorm)
13417 ("r-reshape2" ,r-reshape2)
13418 ("r-rsamtools" ,r-rsamtools)
13419 ("r-s4vectors" ,r-s4vectors)))
13420 (native-inputs `(("r-knitr" ,r-knitr)))
13421 (home-page "https://github.com/ataudt/chromstaR")
13422 (synopsis "Chromatin state analysis for ChIP-Seq data")
13424 "This package implements functions for combinatorial and differential
13425 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
13426 export to genome browser viewable files, and functions for enrichment
13428 (license license:artistic2.0)))
13430 (define-public r-guitar
13437 (uri (bioconductor-uri "Guitar" version))
13440 "0lvfrpgrvmrz4f4qmsii70hw10h72zh1g1alv2sf6a6ixhndm0mz"))))
13441 (properties `((upstream-name . "Guitar")))
13442 (build-system r-build-system)
13444 `(("r-annotationdbi" ,r-annotationdbi)
13445 ("r-dplyr" ,r-dplyr)
13446 ("r-genomicfeatures" ,r-genomicfeatures)
13447 ("r-genomicranges" ,r-genomicranges)
13448 ("r-ggplot2" ,r-ggplot2)
13449 ("r-knitr" ,r-knitr)
13450 ("r-magrittr" ,r-magrittr)
13451 ("r-rtracklayer" ,r-rtracklayer)))
13453 `(("r-knitr" ,r-knitr)))
13454 (home-page "https://bioconductor.org/packages/Guitar")
13455 (synopsis "Visualize genomic features")
13457 "This package is designed for visualization of RNA-related genomic
13458 features with respect to the landmarks of RNA transcripts, i.e., transcription
13459 starting site, start codon, stop codon and transcription ending site.")
13460 (license license:gpl2)))
13462 (define-public r-sushi
13468 (uri (bioconductor-uri "Sushi" version))
13471 "0ksj4f9z14mjsv6ssg5dwhpldw4r7wpdsln2if5g486mm1c56r8p"))))
13472 (properties `((upstream-name . "Sushi")))
13473 (build-system r-build-system)
13475 `(("r-biomart" ,r-biomart)
13477 (home-page "https://bioconductor.org/packages/Sushi")
13478 (synopsis "Tools for visualizing genomics data")
13480 "This package provides flexible, quantitative, and integrative genomic
13481 visualizations for publication-quality multi-panel figures.")
13482 (license license:gpl2+)))