1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 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, 2022 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021, 2022 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>
14 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
16 ;;; This file is part of GNU Guix.
18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
19 ;;; under the terms of the GNU General Public License as published by
20 ;;; the Free Software Foundation; either version 3 of the License, or (at
21 ;;; your option) any later version.
23 ;;; GNU Guix is distributed in the hope that it will be useful, but
24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 ;;; GNU General Public License for more details.
28 ;;; You should have received a copy of the GNU General Public License
29 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
31 (define-module (gnu packages bioconductor)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix download)
35 #:use-module (guix git-download)
36 #:use-module (guix build-system r)
37 #:use-module (gnu packages)
38 #:use-module (gnu packages autotools)
39 #:use-module (gnu packages base)
40 #:use-module (gnu packages bioinformatics)
41 #:use-module (gnu packages boost)
42 #:use-module (gnu packages cran)
43 #:use-module (gnu packages compression)
44 #:use-module (gnu packages curl)
45 #:use-module (gnu packages docker)
46 #:use-module (gnu packages gcc)
47 #:use-module (gnu packages graph)
48 #:use-module (gnu packages graphviz)
49 #:use-module (gnu packages haskell-xyz)
50 #:use-module (gnu packages image)
51 #:use-module (gnu packages maths)
52 #:use-module (gnu packages netpbm)
53 #:use-module (gnu packages python)
54 #:use-module (gnu packages perl)
55 #:use-module (gnu packages pkg-config)
56 #:use-module (gnu packages statistics)
57 #:use-module (gnu packages web)
58 #:use-module (gnu packages xml)
59 #:use-module (srfi srfi-1))
64 (define-public r-org-eck12-eg-db
66 (name "r-org-eck12-eg-db")
71 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
73 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
75 `((upstream-name . "org.EcK12.eg.db")))
76 (build-system r-build-system)
78 (list r-annotationdbi))
79 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
80 (synopsis "Genome wide annotation for E coli strain K12")
82 "This package provides genome wide annotation for E coli strain K12,
83 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
84 National Center for Biotechnology Information (NCBI)’s database for
85 gene-specific information. Entrez Gene maintains records from genomes which
86 have been completely sequenced, which have an active research community to
87 submit gene-specific information, or which are scheduled for intense sequence
89 (license license:artistic2.0)))
91 (define-public r-org-bt-eg-db
93 (name "r-org-bt-eg-db")
98 (uri (bioconductor-uri
104 "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi"))))
105 (properties `((upstream-name . "org.Bt.eg.db")))
106 (build-system r-build-system)
108 (list r-annotationdbi))
109 (home-page "https://bioconductor.org/packages/org.Bt.eg.db")
110 (synopsis "Genome wide annotation for Bovine")
112 "This package provides genome wide annotations for Bovine, primarily
113 based on mapping using Entrez Gene identifiers.")
114 (license license:artistic2.0)))
116 (define-public r-reactome-db
118 (name "r-reactome-db")
123 (uri (bioconductor-uri "reactome.db" version 'annotation))
126 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
127 (properties `((upstream-name . "reactome.db")))
128 (build-system r-build-system)
130 (list r-annotationdbi))
131 (home-page "https://bioconductor.org/packages/reactome.db/")
132 (synopsis "Annotation maps for reactome")
134 "This package provides a set of annotation maps for the REACTOME
135 database, assembled using data from REACTOME.")
136 (license license:cc-by4.0)))
138 (define-public r-bsgenome-btaurus-ucsc-bostau8
140 (name "r-bsgenome-btaurus-ucsc-bostau8")
144 (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
145 version 'annotation))
148 "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
150 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
151 (build-system r-build-system)
155 "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
156 (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
157 (description "This package provides the full genome sequences for Bos
158 taurus (UCSC version bosTau8).")
159 (license license:artistic2.0)))
161 (define-public r-bsgenome-celegans-ucsc-ce6
163 (name "r-bsgenome-celegans-ucsc-ce6")
167 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
168 version 'annotation))
171 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
173 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
174 (build-system r-build-system)
178 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
179 (synopsis "Full genome sequences for Worm")
181 "This package provides full genome sequences for Caenorhabditis
182 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
184 (license license:artistic2.0)))
186 (define-public r-bsgenome-celegans-ucsc-ce10
188 (name "r-bsgenome-celegans-ucsc-ce10")
192 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
193 version 'annotation))
196 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
198 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
199 (build-system r-build-system)
203 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
204 (synopsis "Full genome sequences for Worm")
206 "This package provides full genome sequences for Caenorhabditis
207 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
209 (license license:artistic2.0)))
211 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
213 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
217 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
218 version 'annotation))
221 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
223 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
224 (build-system r-build-system)
228 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
229 (synopsis "Full genome sequences for Fly")
231 "This package provides full genome sequences for Drosophila
232 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
234 (license license:artistic2.0)))
236 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
238 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
242 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
243 version 'annotation))
246 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
248 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
249 (build-system r-build-system)
253 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
254 (synopsis "Full genome sequences for Fly")
256 "This package provides full genome sequences for Drosophila
257 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
258 Biostrings objects.")
259 (license license:artistic2.0)))
261 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
263 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
267 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
268 version 'annotation))
271 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
273 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
274 (build-system r-build-system)
276 (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
277 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
278 (synopsis "Full masked genome sequences for Fly")
280 "This package provides full masked genome sequences for Drosophila
281 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
282 Biostrings objects. The sequences are the same as in
283 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
284 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
285 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
286 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
287 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
288 (license license:artistic2.0)))
290 (define-public r-bsgenome-drerio-ucsc-danrer11
292 (name "r-bsgenome-drerio-ucsc-danrer11")
297 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
298 version 'annotation))
300 (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
301 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
302 (build-system r-build-system)
305 (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
306 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
308 "This package provides full genome sequences for Danio rerio (Zebrafish)
309 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
310 (license license:artistic2.0)))
312 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
314 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
318 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
319 version 'annotation))
322 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
324 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
325 (build-system r-build-system)
329 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
330 (synopsis "Full genome sequences for Homo sapiens")
332 "This package provides full genome sequences for Homo sapiens from
333 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
334 (license license:artistic2.0)))
336 (define-public r-bsgenome-hsapiens-ncbi-grch38
338 (name "r-bsgenome-hsapiens-ncbi-grch38")
343 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
344 version 'annotation))
347 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
348 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
349 (build-system r-build-system)
350 (propagated-inputs (list r-bsgenome))
352 "https://bioconductor.org/packages/release/data/annotation/html/\
353 BSgenome.Hsapiens.NCBI.GRCh38.html")
354 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
356 "This package provides full genome sequences for Homo sapiens (Human) as
357 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
358 (license license:artistic2.0)))
360 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
362 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
367 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
368 version 'annotation))
370 (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
372 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
373 (build-system r-build-system)
375 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
376 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
377 (synopsis "Full masked genome sequences for Homo sapiens")
379 "This package provides full genome sequences for Homo sapiens (Human) as
380 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
381 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
382 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
383 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
384 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
385 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
387 (license license:artistic2.0)))
389 (define-public r-bsgenome-mmusculus-ucsc-mm9
391 (name "r-bsgenome-mmusculus-ucsc-mm9")
395 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
396 version 'annotation))
399 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
401 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
402 (build-system r-build-system)
406 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
407 (synopsis "Full genome sequences for Mouse")
409 "This package provides full genome sequences for Mus musculus (Mouse) as
410 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
411 (license license:artistic2.0)))
413 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
415 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
419 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
420 version 'annotation))
423 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
425 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
426 (build-system r-build-system)
428 (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
429 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
430 (synopsis "Full masked genome sequences for Mouse")
432 "This package provides full genome sequences for Mus musculus (Mouse) as
433 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
434 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
435 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
436 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
437 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
438 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
440 (license license:artistic2.0)))
442 (define-public r-bsgenome-mmusculus-ucsc-mm10
444 (name "r-bsgenome-mmusculus-ucsc-mm10")
448 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
449 version 'annotation))
452 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
454 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
455 (build-system r-build-system)
459 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
460 (synopsis "Full genome sequences for Mouse")
462 "This package provides full genome sequences for Mus
463 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
464 in Biostrings objects.")
465 (license license:artistic2.0)))
467 (define-public r-genomeinfodbdata
469 (name "r-genomeinfodbdata")
473 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
476 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
478 `((upstream-name . "GenomeInfoDbData")))
479 (build-system r-build-system)
480 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
481 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
482 (description "This package contains data for mapping between NCBI taxonomy
483 ID and species. It is used by functions in the GenomeInfoDb package.")
484 (license license:artistic2.0)))
486 (define-public r-go-db
492 (uri (bioconductor-uri "GO.db" version 'annotation))
495 "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
497 `((upstream-name . "GO.db")))
498 (build-system r-build-system)
500 (list r-annotationdbi))
501 (home-page "https://bioconductor.org/packages/GO.db")
502 (synopsis "Annotation maps describing the entire Gene Ontology")
504 "The purpose of this GO.db annotation package is to provide detailed
505 information about the latest version of the Gene Ontologies.")
506 (license license:artistic2.0)))
508 (define-public r-homo-sapiens
510 (name "r-homo-sapiens")
514 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
517 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
519 `((upstream-name . "Homo.sapiens")))
520 (build-system r-build-system)
522 (list r-genomicfeatures
525 r-txdb-hsapiens-ucsc-hg19-knowngene
528 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
529 (synopsis "Annotation package for the Homo.sapiens object")
531 "This package contains the Homo.sapiens object to access data from
532 several related annotation packages.")
533 (license license:artistic2.0)))
535 (define-public r-mus-musculus
537 (name "r-mus-musculus")
542 (uri (bioconductor-uri "Mus.musculus" version 'annotation))
545 "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"))))
546 (properties `((upstream-name . "Mus.musculus")))
547 (build-system r-build-system)
549 (list r-annotationdbi
554 r-txdb-mmusculus-ucsc-mm10-knowngene))
555 (home-page "https://bioconductor.org/packages/Mus.musculus")
556 (synopsis "Annotation package for the Mus.musculus object")
558 "This package contains the @code{Mus.musculus} object to access data
559 from several related annotation packages.")
560 (license license:artistic2.0)))
562 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
564 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
569 (uri (bioconductor-uri
570 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
571 version 'annotation))
574 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
577 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
578 (build-system r-build-system)
579 (propagated-inputs (list r-minfi))
581 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
582 (synopsis "Annotation for Illumina's 450k methylation arrays")
584 "This package provides manifests and annotation for Illumina's 450k array
586 (license license:artistic2.0)))
588 (define-public r-org-ce-eg-db
590 (name "r-org-ce-eg-db")
594 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
597 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
599 `((upstream-name . "org.Ce.eg.db")))
600 (build-system r-build-system)
602 (list r-annotationdbi))
603 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
604 (synopsis "Genome wide annotation for Worm")
606 "This package provides mappings from Entrez gene identifiers to various
607 annotations for the genome of the model worm Caenorhabditis elegans.")
608 (license license:artistic2.0)))
610 (define-public r-org-dm-eg-db
612 (name "r-org-dm-eg-db")
616 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
619 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
621 `((upstream-name . "org.Dm.eg.db")))
622 (build-system r-build-system)
624 (list r-annotationdbi))
625 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
626 (synopsis "Genome wide annotation for Fly")
628 "This package provides mappings from Entrez gene identifiers to various
629 annotations for the genome of the model fruit fly Drosophila melanogaster.")
630 (license license:artistic2.0)))
632 (define-public r-org-dr-eg-db
634 (name "r-org-dr-eg-db")
638 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
641 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
643 `((upstream-name . "org.Dr.eg.db")))
644 (build-system r-build-system)
646 (list r-annotationdbi))
647 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
648 (synopsis "Annotation for Zebrafish")
650 "This package provides genome wide annotations for Zebrafish, primarily
651 based on mapping using Entrez Gene identifiers.")
652 (license license:artistic2.0)))
654 (define-public r-org-hs-eg-db
656 (name "r-org-hs-eg-db")
660 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
663 "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
665 `((upstream-name . "org.Hs.eg.db")))
666 (build-system r-build-system)
668 (list r-annotationdbi))
669 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
670 (synopsis "Genome wide annotation for Human")
672 "This package contains genome-wide annotations for Human, primarily based
673 on mapping using Entrez Gene identifiers.")
674 (license license:artistic2.0)))
676 (define-public r-org-mm-eg-db
678 (name "r-org-mm-eg-db")
682 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
685 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
687 `((upstream-name . "org.Mm.eg.db")))
688 (build-system r-build-system)
690 (list r-annotationdbi))
691 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
692 (synopsis "Genome wide annotation for Mouse")
694 "This package provides mappings from Entrez gene identifiers to various
695 annotations for the genome of the model mouse Mus musculus.")
696 (license license:artistic2.0)))
698 (define-public r-bsgenome-hsapiens-ucsc-hg19
700 (name "r-bsgenome-hsapiens-ucsc-hg19")
704 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
705 version 'annotation))
708 "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
710 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
711 (build-system r-build-system)
715 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
716 (synopsis "Full genome sequences for Homo sapiens")
718 "This package provides full genome sequences for Homo sapiens as provided
719 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
720 (license license:artistic2.0)))
722 (define-public r-bsgenome-hsapiens-ucsc-hg38
724 (name "r-bsgenome-hsapiens-ucsc-hg38")
728 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
729 version 'annotation))
731 (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"))))
733 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
734 (build-system r-build-system)
738 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
739 (synopsis "Full genome sequences for Homo sapiens")
741 "This package provides full genome sequences for Homo sapiens (Human)
742 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
743 (license license:artistic2.0)))
745 (define-public r-ensdb-hsapiens-v75
747 (name "r-ensdb-hsapiens-v75")
752 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
755 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
757 `((upstream-name . "EnsDb.Hsapiens.v75")))
758 (build-system r-build-system)
761 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
762 (synopsis "Ensembl based annotation package")
764 "This package exposes an annotation database generated from Ensembl.")
765 (license license:artistic2.0)))
767 (define-public r-ensdb-hsapiens-v86
769 (name "r-ensdb-hsapiens-v86")
774 (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation))
776 (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"))))
777 (properties `((upstream-name . "EnsDb.Hsapiens.v86")))
778 (build-system r-build-system)
779 (propagated-inputs (list r-ensembldb))
780 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86")
781 (synopsis "Ensembl based annotation package")
782 (description "This package exposes an annotation database generated from
784 (license license:artistic2.0)))
786 (define-public r-ensdb-mmusculus-v79
788 (name "r-ensdb-mmusculus-v79")
793 (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation))
795 (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7"))))
796 (properties `((upstream-name . "EnsDb.Mmusculus.v79")))
797 (build-system r-build-system)
798 (propagated-inputs (list r-ensembldb))
799 (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79")
800 (synopsis "Ensembl based annotation package")
801 (description "This package exposes an annotation database generated from
803 (license license:artistic2.0)))
805 (define-public r-snplocs-hsapiens-dbsnp144-grch37
807 (name "r-snplocs-hsapiens-dbsnp144-grch37")
811 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
812 version 'annotation))
815 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
816 (build-system r-build-system)
817 ;; As this package provides little more than a very large data file it
818 ;; doesn't make sense to build substitutes.
819 (arguments `(#:substitutable? #f))
829 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
830 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
831 (description "This package provides SNP locations and alleles for Homo
832 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
833 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
834 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
835 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
836 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
837 the mitochondrion chromosome. Therefore, the SNPs in this package can be
838 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
839 correct position but this injection will exclude chrM (i.e. nothing will be
840 injected in that sequence).")
841 (license license:artistic2.0)))
843 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
845 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
850 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
851 version 'annotation))
854 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
856 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
857 (build-system r-build-system)
859 (list r-annotationdbi r-genomicfeatures))
861 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
862 (synopsis "Annotation package for TxDb object(s)")
864 "This package exposes an annotation databases generated from UCSC by
865 exposing these as TxDb objects.")
866 (license license:artistic2.0)))
868 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
870 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
874 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
875 version 'annotation))
878 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
880 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
881 (build-system r-build-system)
883 (list r-genomicfeatures))
885 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
886 (synopsis "Annotation package for human genome in TxDb format")
888 "This package provides an annotation database of Homo sapiens genome
889 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
890 track. The database is exposed as a @code{TxDb} object.")
891 (license license:artistic2.0)))
893 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
895 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
899 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
900 version 'annotation))
902 (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879"))))
904 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
905 (build-system r-build-system)
907 (list r-annotationdbi r-genomicfeatures))
909 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
910 (synopsis "Annotation package for human genome in TxDb format")
912 "This package provides an annotation database of Homo sapiens genome
913 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
914 track. The database is exposed as a @code{TxDb} object.")
915 (license license:artistic2.0)))
917 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
919 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
923 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
924 version 'annotation))
927 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
929 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
930 (build-system r-build-system)
932 (list r-genomicfeatures r-annotationdbi))
934 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
935 (synopsis "Annotation package for mouse genome in TxDb format")
937 "This package provides an annotation database of Mouse genome data. It
938 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
939 database is exposed as a @code{TxDb} object.")
940 (license license:artistic2.0)))
942 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
944 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
948 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
949 version 'annotation))
952 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
954 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
955 (build-system r-build-system)
957 (list r-bsgenome r-genomicfeatures r-annotationdbi))
959 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
960 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
962 "This package loads a TxDb object, which is an R interface to
963 prefabricated databases contained in this package. This package provides
964 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
965 based on the knownGene track.")
966 (license license:artistic2.0)))
968 (define-public r-txdb-celegans-ucsc-ce6-ensgene
970 (name "r-txdb-celegans-ucsc-ce6-ensgene")
975 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
976 version 'annotation))
979 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
981 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
982 (build-system r-build-system)
984 (list r-annotationdbi r-genomicfeatures))
985 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
986 (synopsis "Annotation package for C elegans TxDb objects")
988 "This package exposes a C elegans annotation database generated from UCSC
989 by exposing these as TxDb objects.")
990 (license license:artistic2.0)))
992 (define-public r-fdb-infiniummethylation-hg19
994 (name "r-fdb-infiniummethylation-hg19")
998 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
999 version 'annotation))
1002 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
1004 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
1005 (build-system r-build-system)
1007 (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db
1008 r-txdb-hsapiens-ucsc-hg19-knowngene))
1009 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
1010 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
1012 "This is an annotation package for Illumina Infinium DNA methylation
1013 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
1015 (license license:artistic2.0)))
1017 (define-public r-illuminahumanmethylationepicmanifest
1019 (name "r-illuminahumanmethylationepicmanifest")
1023 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
1024 version 'annotation))
1027 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
1029 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
1030 (build-system r-build-system)
1033 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
1034 (synopsis "Manifest for Illumina's EPIC methylation arrays")
1036 "This is a manifest package for Illumina's EPIC methylation arrays.")
1037 (license license:artistic2.0)))
1039 (define-public r-do-db
1045 (uri (bioconductor-uri "DO.db" version 'annotation))
1048 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
1050 `((upstream-name . "DO.db")))
1051 (build-system r-build-system)
1053 (list r-annotationdbi))
1054 (home-page "https://www.bioconductor.org/packages/DO.db/")
1055 (synopsis "Annotation maps describing the entire Disease Ontology")
1057 "This package provides a set of annotation maps describing the entire
1059 (license license:artistic2.0)))
1061 (define-public r-hgu133plus2-db
1063 (name "r-hgu133plus2-db")
1068 (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
1070 (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
1071 (properties `((upstream-name . "hgu133plus2.db")))
1072 (build-system r-build-system)
1073 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
1074 (home-page "https://bioconductor.org/packages/hgu133plus2.db")
1075 (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
1077 "This package provides Affymetrix HG-U133_Plus_2 array annotation
1078 data (chip hgu133plus2) assembled using data from public repositories.")
1079 (license license:artistic2.0)))
1081 (define-public r-pfam-db
1088 (uri (bioconductor-uri "PFAM.db" version 'annotation))
1090 (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7"))))
1091 (properties `((upstream-name . "PFAM.db")))
1092 (build-system r-build-system)
1094 (list r-annotationdbi))
1095 (home-page "https://bioconductor.org/packages/PFAM.db")
1096 (synopsis "Set of protein ID mappings for PFAM")
1098 "This package provides a set of protein ID mappings for PFAM, assembled
1099 using data from public repositories.")
1100 (license license:artistic2.0)))
1102 (define-public r-phastcons100way-ucsc-hg19
1104 (name "r-phastcons100way-ucsc-hg19")
1109 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
1110 version 'annotation))
1113 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
1115 `((upstream-name . "phastCons100way.UCSC.hg19")))
1116 (build-system r-build-system)
1124 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
1125 (synopsis "UCSC phastCons conservation scores for hg19")
1127 "This package provides UCSC phastCons conservation scores for the human
1128 genome (hg19) calculated from multiple alignments with other 99 vertebrate
1130 (license license:artistic2.0)))
1135 (define-public r-abadata
1141 (uri (bioconductor-uri "ABAData" version 'experiment))
1144 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
1146 `((upstream-name . "ABAData")))
1147 (build-system r-build-system)
1149 (list r-annotationdbi))
1150 (home-page "https://www.bioconductor.org/packages/ABAData/")
1151 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
1153 "This package provides the data for the gene expression enrichment
1154 analysis conducted in the package ABAEnrichment. The package includes three
1155 datasets which are derived from the Allen Brain Atlas:
1158 @item Gene expression data from Human Brain (adults) averaged across donors,
1159 @item Gene expression data from the Developing Human Brain pooled into five
1160 age categories and averaged across donors, and
1161 @item a developmental effect score based on the Developing Human Brain
1165 All datasets are restricted to protein coding genes.")
1166 (license license:gpl2+)))
1168 (define-public r-adductdata
1170 (name "r-adductdata")
1174 (uri (bioconductor-uri "adductData" version 'experiment))
1176 (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48"))))
1177 (properties `((upstream-name . "adductData")))
1178 (build-system r-build-system)
1179 (propagated-inputs (list r-annotationhub r-experimenthub))
1180 (native-inputs (list r-knitr))
1181 (home-page "https://bioconductor.org/packages/adductData")
1182 (synopsis "Data from untargeted mass spectrometry of modifications to Cys34")
1184 "This package contains data from untargeted @dfn{mass spectrometry} (MS)
1185 of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
1187 (license license:artistic2.0)))
1189 (define-public r-aneufinderdata
1191 (name "r-aneufinderdata")
1195 (uri (bioconductor-uri "AneuFinderData" version 'experiment))
1197 (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7"))))
1198 (build-system r-build-system)
1199 (home-page "https://bioconductor.org/packages/AneuFinderData/")
1200 (synopsis "Data package for @code{AneuFinder}")
1201 (description "This package contains whole-genome single cell sequencing data for
1202 demonstration purposes in the @code{AneuFinder} package.")
1203 (license license:artistic2.0)))
1205 (define-public r-arrmdata
1211 (uri (bioconductor-uri "ARRmData" version 'experiment))
1213 (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p"))))
1215 `((upstream-name . "ARRmData")))
1216 (build-system r-build-system)
1217 (home-page "https://www.bioconductor.org/packages/ARRmData/")
1218 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
1220 "This package provides raw beta values from 36 samples across 3 groups
1221 from Illumina 450k methylation arrays.")
1222 (license license:artistic2.0)))
1224 (define-public r-bladderbatch
1226 (name "r-bladderbatch")
1230 (uri (bioconductor-uri "bladderbatch" version
1234 "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k"))))
1235 (properties `((upstream-name . "bladderbatch")))
1236 (build-system r-build-system)
1237 (propagated-inputs (list r-biobase))
1238 (home-page "https://bioconductor.org/packages/bladderbatch")
1239 (synopsis "Bladder gene expression data illustrating batch effects")
1241 "This package contains microarray gene expression data on 57 bladder samples from
1242 5 batches. The data are used as an illustrative example for the sva package.")
1243 (license license:artistic2.0)))
1245 (define-public r-biscuiteerdata
1247 (name "r-biscuiteerdata")
1252 (uri (bioconductor-uri "biscuiteerData" version 'experiment))
1254 (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
1256 `((upstream-name . "biscuiteerData")))
1257 (build-system r-build-system)
1259 (list r-annotationhub r-curl r-experimenthub))
1260 (native-inputs (list r-knitr))
1261 (home-page "https://bioconductor.org/packages/biscuiteerData")
1262 (synopsis "Data package for Biscuiteer")
1264 "This package contains default datasets used by the Bioconductor package
1266 (license license:gpl3)))
1268 (define-public r-celldex
1275 (uri (bioconductor-uri "celldex" version 'experiment))
1277 (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
1278 (properties `((upstream-name . "celldex")))
1279 (build-system r-build-system)
1281 (list r-annotationdbi
1284 r-delayedmatrixstats
1287 r-summarizedexperiment))
1288 (native-inputs (list r-knitr))
1289 (home-page "https://github.com/LTLA/celldex")
1290 (synopsis "Reference index for cell types")
1292 "This package provides a collection of reference expression datasets with
1293 curated cell type labels, for use in procedures like automated annotation of
1294 single-cell data or deconvolution of bulk RNA-seq.")
1295 (license license:gpl3)))
1297 (define-public r-chromstardata
1299 (name "r-chromstardata")
1304 (uri (bioconductor-uri "chromstaRData" version 'experiment))
1306 (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
1307 (properties `((upstream-name . "chromstaRData")))
1308 (build-system r-build-system)
1309 (home-page "https://bioconductor.org/packages/chromstaRData/")
1310 (synopsis "ChIP-seq data for demonstration purposes")
1312 "This package provides ChIP-seq data for demonstration purposes in the
1313 chromstaR package.")
1314 (license license:gpl3)))
1316 (define-public r-copyhelper
1318 (name "r-copyhelper")
1323 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
1325 (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
1326 (properties `((upstream-name . "CopyhelpeR")))
1327 (build-system r-build-system)
1328 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
1329 (synopsis "Helper files for CopywriteR")
1331 "This package contains the helper files that are required to run the
1332 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
1333 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
1334 mm10. In addition, it contains a blacklist filter to remove regions that
1335 display copy number variation. Files are stored as GRanges objects from the
1336 GenomicRanges Bioconductor package.")
1337 (license license:gpl2)))
1339 (define-public r-genelendatabase
1341 (name "r-genelendatabase")
1346 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
1348 (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
1350 `((upstream-name . "geneLenDataBase")))
1351 (build-system r-build-system)
1353 (list r-rtracklayer r-genomicfeatures))
1354 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
1355 (synopsis "Lengths of mRNA transcripts for a number of genomes")
1357 "This package provides the lengths of mRNA transcripts for a number of
1358 genomes and gene ID formats, largely based on the UCSC table browser.")
1359 (license license:lgpl2.0+)))
1361 (define-public r-genomationdata
1363 (name "r-genomationdata")
1368 (uri (bioconductor-uri "genomationData" version 'experiment))
1370 (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
1372 `((upstream-name . "genomationData")))
1373 (build-system r-build-system)
1374 ;; As this package provides little more than large data files, it doesn't
1375 ;; make sense to build substitutes.
1376 (arguments `(#:substitutable? #f))
1379 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
1380 (synopsis "Experimental data for use with the genomation package")
1382 "This package contains experimental genetic data for use with the
1383 genomation package. Included are Chip Seq, Methylation and Cage data,
1384 downloaded from Encode.")
1385 (license license:gpl3+)))
1387 (define-public r-macrophage
1389 (name "r-macrophage")
1393 (uri (bioconductor-uri "macrophage" version
1397 "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms"))))
1398 (properties `((upstream-name . "macrophage")))
1399 (build-system r-build-system)
1400 (native-inputs (list r-knitr))
1401 (home-page "https://bioconductor.org/packages/macrophage")
1402 (synopsis "Human macrophage immune response data")
1404 "This package provides the output of running @code{Salmon} on a set of 24
1405 RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and
1406 gene expression indicate a role for enhancer priming in immune response\", published
1407 in Nature Genetics, January 2018.")
1408 (license license:gpl2+)))
1410 (define-public r-msdata
1417 (uri (bioconductor-uri "msdata" version 'experiment))
1419 (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
1420 (properties `((upstream-name . "msdata")))
1421 (build-system r-build-system)
1422 (home-page "https://bioconductor.org/packages/msdata")
1423 (synopsis "Various Mass Spectrometry raw data example files")
1425 "This package provides Ion Trap positive ionization mode data in mzML file
1426 format. It includes a subset from 500-850 m/z and 1190-1310 seconds,
1427 including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
1428 III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
1429 LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
1430 files for various search engines.")
1431 (license license:gpl2+)))
1433 (define-public r-pasilla
1440 (uri (bioconductor-uri "pasilla" version 'experiment))
1442 (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
1443 (build-system r-build-system)
1444 (propagated-inputs (list r-dexseq))
1445 (native-inputs (list r-knitr))
1446 (home-page "https://www.bioconductor.org/packages/pasilla/")
1447 (synopsis "Data package with per-exon and per-gene read counts")
1448 (description "This package provides per-exon and per-gene read counts
1449 computed for selected genes from RNA-seq data that were presented in the
1450 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1451 by Brooks et al., Genome Research 2011.")
1452 (license license:lgpl2.1+)))
1454 (define-public r-hsmmsinglecell
1456 (name "r-hsmmsinglecell")
1461 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1463 (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
1465 `((upstream-name . "HSMMSingleCell")))
1466 (build-system r-build-system)
1467 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1468 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1470 "Skeletal myoblasts undergo a well-characterized sequence of
1471 morphological and transcriptional changes during differentiation. In this
1472 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1473 under high mitogen conditions (GM) and then differentiated by switching to
1474 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1475 hundred cells taken over a time-course of serum-induced differentiation.
1476 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1477 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1478 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1479 which were then sequenced to a depth of ~4 million reads per library,
1480 resulting in a complete gene expression profile for each cell.")
1481 (license license:artistic2.0)))
1483 (define-public r-all
1490 (uri (bioconductor-uri "ALL" version 'experiment))
1492 (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
1493 (properties `((upstream-name . "ALL")))
1494 (build-system r-build-system)
1497 (home-page "https://bioconductor.org/packages/ALL")
1498 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1500 "The data consist of microarrays from 128 different individuals with
1501 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1502 are available. The data have been normalized (using rma) and it is the
1503 jointly normalized data that are available here. The data are presented in
1504 the form of an @code{exprSet} object.")
1505 (license license:artistic2.0)))
1507 (define-public r-affydata
1514 (uri (bioconductor-uri "affydata" version 'experiment))
1516 (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
1517 (properties `((upstream-name . "affydata")))
1518 (build-system r-build-system)
1521 (home-page "https://bioconductor.org/packages/affydata/")
1522 (synopsis "Affymetrix data for demonstration purposes")
1524 "This package provides example datasets that represent 'real world
1525 examples' of Affymetrix data, unlike the artificial examples included in the
1526 package @code{affy}.")
1527 (license license:gpl2+)))
1529 (define-public r-gagedata
1536 (uri (bioconductor-uri "gageData" version 'experiment))
1538 (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
1539 (properties `((upstream-name . "gageData")))
1540 (build-system r-build-system)
1541 (home-page "https://bioconductor.org/packages/gageData")
1542 (synopsis "Auxiliary data for the gage package")
1544 "This is a supportive data package for the software package @code{gage}.
1545 However, the data supplied here are also useful for gene set or pathway
1546 analysis or microarray data analysis in general. In this package, we provide
1547 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1548 BMP6 (originally published as an demo dataset for GAGE, also registered as
1549 GSE13604 in GEO). This package also includes commonly used gene set data based
1550 on KEGG pathways and GO terms for major research species, including human,
1551 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1552 yeast are also included.")
1553 (license license:gpl2+)))
1555 (define-public r-curatedtcgadata
1557 (name "r-curatedtcgadata")
1562 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1564 (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
1566 `((upstream-name . "curatedTCGAData")))
1567 (build-system r-build-system)
1569 (list r-annotationhub
1572 r-multiassayexperiment
1574 r-summarizedexperiment))
1575 (native-inputs (list r-knitr))
1576 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1577 (synopsis "Curated data from The Cancer Genome Atlas")
1579 "This package provides publicly available data from The Cancer Genome
1580 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1581 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1582 number, mutation, microRNA, protein, and others) with clinical / pathological
1583 data. It also links assay barcodes with patient identifiers, enabling
1584 harmonized subsetting of rows (features) and columns (patients / samples)
1585 across the entire multi-'omics experiment.")
1586 (license license:artistic2.0)))
1588 (define-public r-parathyroidse
1590 (name "r-parathyroidse")
1594 (uri (bioconductor-uri "parathyroidSE" version
1598 "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16"))))
1599 (properties `((upstream-name . "parathyroidSE")))
1600 (build-system r-build-system)
1601 (propagated-inputs (list r-summarizedexperiment))
1602 (home-page "https://bioconductor.org/packages/parathyroidSE")
1603 (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors")
1605 "This package provides @code{RangedSummarizedExperiment} objects of read
1606 counts in genes and exonic parts for paired-end RNA-Seq data from experiments on
1607 primary cultures of parathyroid tumors. The sequencing was performed on tumor
1608 cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).")
1609 ;; The author(s) mentions only LGPL without any specific version.
1610 (license license:lgpl2.1+)))
1612 (define-public r-tcgabiolinksgui-data
1614 (name "r-tcgabiolinksgui-data")
1619 (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
1621 (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
1622 (properties `((upstream-name . "TCGAbiolinksGUI.data")))
1623 (build-system r-build-system)
1624 (native-inputs (list r-knitr))
1625 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
1626 (synopsis "Data for the TCGAbiolinksGUI package")
1627 (description "This package provides supporting data for the
1628 TCGAbiolinksGUI package.")
1629 (license license:gpl3)))
1631 (define-public r-tximportdata
1633 (name "r-tximportdata")
1637 (uri (bioconductor-uri "tximportData" version
1641 "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy"))))
1642 (properties `((upstream-name . "tximportData")))
1643 (build-system r-build-system)
1644 (native-inputs (list r-knitr))
1645 (home-page "https://bioconductor.org/packages/tximportData")
1646 (synopsis "Data for the tximport package")
1648 "This package provides the output of running various transcript abundance
1649 quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The
1650 quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon}
1651 and @code{Sailfish}. Alevin example output is also included.")
1652 (license license:gpl2+)))
1658 (define-public r-abarray
1664 (uri (bioconductor-uri "ABarray" version))
1667 "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
1668 (properties `((upstream-name . "ABarray")))
1669 (build-system r-build-system)
1670 (propagated-inputs (list r-biobase r-multtest))
1671 (home-page "https://bioconductor.org/packages/ABarray")
1673 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
1675 "The package @code{ABarray} is designed to work with Applied Biosystems
1676 whole genome microarray platform, as well as any other platform whose data can
1677 be transformed into expression data matrix. Functions include data
1678 preprocessing, filtering, control probe analysis, statistical analysis in one
1679 single function. A @dfn{graphical user interface} (GUI) is also provided. The
1680 raw data, processed data, graphics output and statistical results are organized
1681 into folders according to the analysis settings used.")
1682 (license license:gpl2+)))
1684 (define-public r-absseq
1690 (uri (bioconductor-uri "ABSSeq" version))
1693 "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
1694 (properties `((upstream-name . "ABSSeq")))
1695 (build-system r-build-system)
1696 (propagated-inputs (list r-limma r-locfit))
1697 (home-page "https://bioconductor.org/packages/ABSSeq")
1699 "RNA-Seq analysis based on modelling absolute expression differences")
1701 "This package implements a new RNA-Seq analysis method and integrates two
1702 modules: a basic model for pairwise comparison and a linear model for complex
1703 design. RNA-Seq quantifies gene expression with reads count, which usually
1704 consists of conditions (or treatments) and several replicates for each
1705 condition. This software infers differential expression directly by the
1706 counts difference between conditions. It assumes that the sum counts
1707 difference between conditions follow a negative binomial distribution. In
1708 addition, @code{ABSSeq} moderates the fold-changes by two steps: the
1709 expression level and gene-specific dispersion, that might facilitate the gene
1710 ranking by fold-change and visualization.")
1711 (license license:gpl3+)))
1713 (define-public r-adam
1719 (uri (bioconductor-uri "ADAM" version))
1722 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
1723 (properties `((upstream-name . "ADAM")))
1724 (build-system r-build-system)
1725 (propagated-inputs (list r-dplyr
1733 r-summarizedexperiment))
1734 (native-inputs (list r-knitr))
1735 (home-page "https://bioconductor.org/packages/ADAM")
1736 (synopsis "Gene activity and diversity analysis module")
1738 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
1739 package created to group a set of genes from comparative samples (control
1740 versus experiment) belonging to different species according to their respective
1741 functions. The corresponding roles are extracted from the default collections
1742 like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
1743 @code{ADAM} show their significance by calculating the p-values referring to
1744 gene diversity and activity. Each group of genes is called @dfn{Group of
1745 functionally associated genes} (GFAG).")
1746 (license license:gpl2+)))
1748 (define-public r-adamgui
1754 (uri (bioconductor-uri "ADAMgui" version))
1757 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
1758 (properties `((upstream-name . "ADAMgui")))
1759 (build-system r-build-system)
1781 (native-inputs (list r-knitr))
1782 (home-page "https://bioconductor.org/packages/ADAMgui/")
1783 (synopsis "GUI for gene activity and diversity analysis")
1785 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
1786 for the @code{ADAM} package. The @code{ADAMgui} package provides two
1787 shiny-based applications that allows the user to study the output of the
1788 @code{ADAM} package files through different plots. It's possible, for
1789 example, to choose a specific @dfn{group of functionally associated
1790 genes} (GFAG) and observe the gene expression behavior with the plots created
1791 with the @code{GFAGtargetUi} function. Features such as differential
1792 expression and fold change can be easily seen with aid of the plots made with
1793 the @code{GFAGpathUi} function.")
1794 (license license:gpl2+)))
1796 (define-public r-adimpute
1802 (uri (bioconductor-uri "ADImpute" version))
1805 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
1806 (properties `((upstream-name . "ADImpute")))
1807 (build-system r-build-system)
1809 (list r-biocparallel
1819 r-singlecellexperiment
1820 r-summarizedexperiment))
1821 (native-inputs (list r-knitr))
1822 (home-page "https://bioconductor.org/packages/ADImpute")
1823 (synopsis "Adaptive computational prediction for dropout imputations")
1825 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
1826 unable to quantify the expression levels of all genes in a cell, creating a
1827 need for the computational prediction of missing values (dropout imputation).
1828 Most existing dropout imputation methods are limited in the sense that they
1829 exclusively use the scRNA-seq dataset at hand and do not exploit external
1830 gene-gene relationship information. The @code{ADImpute} package proposes two
1831 methods to address this issue:
1834 @item a gene regulatory network-based approach using gene-gene relationships
1835 learnt from external data;
1836 @item a baseline approach corresponding to a sample-wide average.
1839 @code{ADImpute} implements these novel methods and also combines them with
1840 existing imputation methods like @code{DrImpute} and @code{SAVER}.
1841 @code{ADImpute} can learn the best performing method per gene and combine the
1842 results from different methods into an ensemble.")
1843 (license license:gpl3+)))
1845 (define-public r-adsplit
1851 (uri (bioconductor-uri "adSplit" version))
1854 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
1855 (properties `((upstream-name . "adSplit")))
1856 (build-system r-build-system)
1858 (list r-annotationdbi
1864 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
1865 (synopsis "Annotation-driven splits in microarray data")
1867 "This package implements clustering of microarray gene expression
1868 profiles according to functional annotations. For each term genes are
1869 annotated to, splits into two subclasses are computed and a significance of
1870 the supporting gene set is determined.")
1871 (license license:gpl2+)))
1873 (define-public r-affixcan
1879 (uri (bioconductor-uri "AffiXcan" version))
1882 "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
1883 (properties `((upstream-name . "AffiXcan")))
1884 (build-system r-build-system)
1886 (list r-biocparallel
1888 r-multiassayexperiment
1889 r-summarizedexperiment))
1890 (native-inputs (list r-knitr))
1891 (home-page "https://bioconductor.org/packages/AffiXcan")
1892 (synopsis "Functional approach to impute genetically regulated expression")
1894 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
1895 expression} (GReX) for a set of genes in a sample of individuals, using a
1896 method based on the @dfn{total binding affinity} (TBA). Statistical models to
1897 impute GReX can be trained with a training dataset where the real total
1898 expression values are known.")
1899 (license license:gpl3)))
1901 (define-public r-affyrnadegradation
1903 (name "r-affyrnadegradation")
1907 (uri (bioconductor-uri "AffyRNADegradation" version))
1910 "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
1911 (properties `((upstream-name . "AffyRNADegradation")))
1912 (build-system r-build-system)
1913 (propagated-inputs (list r-affy))
1914 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
1916 "Analyze and correct probe positional bias in data due to RNA degradation")
1918 "The @code{AffyRNADegradation} package helps with the assessment and
1919 correction of RNA degradation effects in Affymetrix 3 expression arrays. The
1920 parameter @code{d} gives a robust and accurate measure of RNA integrity. The
1921 correction removes the probe positional bias, and thus improves comparability
1922 of samples that are affected by RNA degradation.")
1923 ;; the R file header specifies GPL2 or later
1924 (license license:gpl2+)))
1926 (define-public r-agdex
1932 (uri (bioconductor-uri "AGDEX" version))
1935 "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
1936 (properties `((upstream-name . "AGDEX")))
1937 (build-system r-build-system)
1938 (propagated-inputs (list r-biobase r-gseabase))
1939 (home-page "https://bioconductor.org/packages/AGDEX")
1941 "Evaluate agreement of differential expression for cross-species genomics")
1943 "The objective of @code{AGDEX} is to evaluate whether the results of a
1944 pair of two-group differential expression analysis comparisons show a level of
1945 agreement that is greater than expected if the group labels for each two-group
1946 comparison are randomly assigned. The agreement is evaluated for the entire
1947 transcriptome and (optionally) for a collection of pre-defined gene-sets.
1948 Additionally, the procedure performs permutation-based differential expression
1949 and meta analysis at both gene and gene-set levels of the data from each
1951 (license license:gpl2+)))
1953 (define-public r-aggregatebiovar
1955 (name "r-aggregatebiovar")
1959 (uri (bioconductor-uri "aggregateBioVar" version))
1962 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
1963 (properties `((upstream-name . "aggregateBioVar")))
1964 (build-system r-build-system)
1969 r-singlecellexperiment
1970 r-summarizedexperiment
1972 (native-inputs (list r-knitr))
1973 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
1974 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
1976 "This package @code{aggregateBioVar} contains tools to summarize single
1977 cell gene expression profiles at the level of subject for single cell RNA-seq
1978 data collected from more than one subject (e.g. biological sample or technical
1979 replicates). A @code{SingleCellExperiment} object is taken as input and
1980 converted to a list of @code{SummarizedExperiment} objects, where each list
1981 element corresponds to an assigned cell type. The @code{SummarizedExperiment}
1982 objects contain aggregate gene-by-subject count matrices and inter-subject
1983 column metadata for individual subjects that can be processed using downstream
1984 bulk RNA-seq tools.")
1985 (license license:gpl3)))
1987 (define-public r-agilp
1993 (uri (bioconductor-uri "agilp" version))
1996 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
1997 (properties `((upstream-name . "agilp")))
1998 (build-system r-build-system)
1999 (home-page "https://bioconductor.org/packages/agilp")
2000 (synopsis "Processing of Agilent expression array")
2002 "This package aims to provide a pipeline for the low-level analysis of
2003 gene expression microarray data, primarily focused on the Agilent platform,
2004 but which also provides utilities which may be useful for other platforms.")
2005 ;; Some files are under GPLv2+ but the combined work is released under the
2007 (license license:gpl3)))
2009 (define-public r-adductomicsr
2011 (name "r-adductomicsr")
2015 (uri (bioconductor-uri "adductomicsR" version))
2018 "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
2019 (properties `((upstream-name . "adductomicsR")))
2020 (build-system r-build-system)
2043 (native-inputs (list r-knitr))
2044 (home-page "https://bioconductor.org/packages/adductomicsR")
2045 (synopsis "Processing of adductomic mass spectral datasets")
2047 "This package @code{adductomicsR} processes data generated by the
2048 @dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
2049 peptides from spectra that has been corrected for mass drift and retention
2050 time drift and quantifies level mass spectral peaks from @dfn{first stage of
2051 mass spectrometry} (MS1) data.")
2052 (license license:artistic2.0)))
2054 (define-public r-agimicrorna
2056 (name "r-agimicrorna")
2060 (uri (bioconductor-uri "AgiMicroRna" version))
2063 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
2064 (properties `((upstream-name . "AgiMicroRna")))
2065 (build-system r-build-system)
2072 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
2074 "Processing and differential expression analysis of Agilent microRNA chips")
2076 "@code{AgiMicroRna} provides useful functionality for the processing,
2077 quality assessment and differential expression analysis of Agilent microRNA
2078 array data. The package uses a limma-like structure to generate the processed
2079 data in order to make statistical inferences about differential expression
2080 using the linear model features implemented in limma. Standard Bioconductor
2081 objects are used so that other packages could be used as well.")
2082 (license license:gpl3)))
2084 (define-public r-amountain
2086 (name "r-amountain")
2090 (uri (bioconductor-uri "AMOUNTAIN" version))
2093 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
2094 (properties `((upstream-name . "AMOUNTAIN")))
2095 (build-system r-build-system)
2097 (native-inputs (list r-knitr))
2098 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
2099 (synopsis "Modules for multilayer weighted gene co-expression networks")
2101 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
2102 gene co-expression network) could be constructed only from expression profile.
2103 Different layers in such networks may represent different time points, multiple
2104 conditions or various species. @code{AMOUNTAIN} aims to search active modules
2105 in multi-layer WGCN using a continuous optimization approach.")
2106 (license license:gpl2+)))
2108 (define-public r-amaretto
2114 (uri (bioconductor-uri "AMARETTO" version))
2117 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
2118 (properties `((upstream-name . "AMARETTO")))
2119 (build-system r-build-system)
2121 (list r-biocfilecache
2139 r-multiassayexperiment
2145 (native-inputs (list r-knitr))
2146 (home-page "https://bioconductor.org/packages/AMARETTO")
2147 (synopsis "Regulatory network inference and driver gene evaluation")
2149 "This package @code{AMARETTO} represents an algorithm that integrates copy
2150 number, DNA methylation and gene expression data to identify a set of driver
2151 genes by analyzing cancer samples and connects them to clusters of co-expressed
2152 genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
2153 setting to identify cancer driver genes and their modules on multiple cancer
2154 sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
2155 and EMT, and modules that accurately predict survival and molecular subtypes.
2156 This allows @code{AMARETTO} to identify novel cancer driver genes directing
2157 canonical cancer pathways.")
2158 (license license:asl2.0)))
2160 (define-public r-anaquin
2166 (uri (bioconductor-uri "Anaquin" version))
2169 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
2170 (properties `((upstream-name . "Anaquin")))
2171 (build-system r-build-system)
2180 (native-inputs (list r-knitr))
2181 (home-page "https://www.sequinstandards.com/")
2182 (synopsis "Statistical analysis of sequins")
2184 "The project is intended to support the use of @dfn{sequins}(synthetic
2185 sequencing spike-in controls) owned and made available by the Garvan Institute
2186 of Medical Research. The goal is to provide a standard library for quantitative
2187 analysis, modelling, and visualization of spike-in controls.")
2188 (license license:bsd-3)))
2190 (define-public r-aneufinder
2192 (name "r-aneufinder")
2196 (uri (bioconductor-uri "AneuFinder" version))
2199 "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
2200 (build-system r-build-system)
2204 (list r-genomicranges
2225 (home-page "https://bioconductor.org/packages/AneuFinder/")
2226 (synopsis "Copy number variation analysis in single-cell-sequencing data")
2227 (description "This package implements functions for copy number variant
2228 calling, plotting, export and analysis from whole-genome single cell
2230 (license license:artistic2.0)))
2232 (define-public r-anf
2238 (uri (bioconductor-uri "ANF" version))
2241 "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
2242 (properties `((upstream-name . "ANF")))
2243 (build-system r-build-system)
2250 (native-inputs (list r-knitr))
2251 (home-page "https://bioconductor.org/packages/ANF")
2252 (synopsis "Affinity network fusion for complex patient clustering")
2254 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
2255 matrix construction and fusion as well as spectral clustering. This package is
2256 used for complex patient clustering by integrating multi-omic data through affinity
2258 (license license:gpl3)))
2260 (define-public r-annmap
2266 (uri (bioconductor-uri "annmap" version))
2269 "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
2270 (properties `((upstream-name . "annmap")))
2271 (build-system r-build-system)
2283 (home-page "https://github.com/cruk-mi/annmap")
2285 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
2287 "This package @code{annmap} provides annotation mappings for Affymetrix exon
2288 arrays and coordinate based queries to support deep sequencing data analysis.
2289 Database access is hidden behind the API which provides a set of functions such
2290 as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
2291 Functions to plot gene architecture and BAM file data are also provided.")
2292 (license license:gpl2)))
2294 (define-public r-antiprofiles
2296 (name "r-antiprofiles")
2300 (uri (bioconductor-uri "antiProfiles" version))
2303 "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
2304 (properties `((upstream-name . "antiProfiles")))
2305 (build-system r-build-system)
2309 (home-page "https://github.com/HCBravoLab/antiProfiles")
2310 (synopsis "Implementation of gene expression anti-profiles")
2312 "This package implements the gene expression anti-profiles method.
2313 Anti-profiles are a new approach for developing cancer genomic signatures that
2314 specifically take advantage of gene expression heterogeneity. They explicitly
2315 model increased gene expression variability in cancer to define robust and
2316 reproducible gene expression signatures capable of accurately distinguishing
2317 tumor samples from healthy controls.")
2318 (license license:artistic2.0)))
2320 (define-public r-baalchip
2326 (uri (bioconductor-uri "BaalChIP" version))
2329 "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
2330 (properties `((upstream-name . "BaalChIP")))
2331 (build-system r-build-system)
2332 (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
2346 (native-inputs (list r-knitr))
2347 (home-page "https://bioconductor.org/packages/BaalChIP")
2349 "Analysis of allele-specific transcription factor binding in cancer genomes")
2351 "This package offers functions to process multiple @code{ChIP-seq BAM}
2352 files and detect allele-specific events. It computes allele counts at
2353 individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
2354 control) steps to remove problematic variants, and utilizes a Bayesian
2355 framework to identify statistically significant allele-specific events.
2356 BaalChIP is able to account for copy number differences between the two
2357 alleles, a known phenotypical feature of cancer samples.")
2358 (license license:artistic2.0)))
2360 (define-public r-basespacer
2362 (name "r-basespacer")
2366 (uri (bioconductor-uri "BaseSpaceR" version))
2369 "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj"))))
2370 (properties `((upstream-name . "BaseSpaceR")))
2371 (build-system r-build-system)
2372 (propagated-inputs (list r-rcurl r-rjsonio))
2373 (home-page "https://bioconductor.org/packages/BaseSpaceR")
2374 (synopsis "R SDK for BaseSpace RESTful API")
2376 "This package provides an R interface to Illumina's BaseSpace cloud
2377 computing environment, enabling the fast development of data analysis and
2378 visualization tools. Besides providing an easy to use set of tools for
2379 manipulating the data from BaseSpace, it also facilitates the access to R's
2380 rich environment of statistical and data analysis tools.")
2381 (license license:asl2.0)))
2383 (define-public r-bac
2389 (uri (bioconductor-uri "BAC" version))
2392 "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2"))))
2393 (properties `((upstream-name . "BAC")))
2394 (build-system r-build-system)
2395 (home-page "https://bioconductor.org/packages/BAC")
2396 (synopsis "Bayesian analysis of Chip-chip experiment")
2398 "This package uses a Bayesian hierarchical model to detect enriched
2399 regions from ChIP-chip experiments. The common goal in analyzing this
2400 ChIP-chip data is to detect DNA-protein interactions from ChIP-chip
2401 experiments. The BAC package has mainly been tested with Affymetrix tiling
2402 array data. However, we expect it to work with other platforms (e.g. Agilent,
2403 Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so
2404 you will have to normalize your data beforehand.")
2405 (license license:artistic2.0)))
2407 (define-public r-biocversion
2409 (name "r-biocversion")
2414 (uri (bioconductor-uri "BiocVersion" version))
2417 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
2418 (properties `((upstream-name . "BiocVersion")))
2419 (build-system r-build-system)
2420 (home-page "https://bioconductor.org/packages/BiocVersion/")
2421 (synopsis "Set the appropriate version of Bioconductor packages")
2423 "This package provides repository information for the appropriate version
2425 (license license:artistic2.0)))
2427 (define-public r-biocgenerics
2429 (name "r-biocgenerics")
2433 (uri (bioconductor-uri "BiocGenerics" version))
2436 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
2438 `((upstream-name . "BiocGenerics")))
2439 (build-system r-build-system)
2440 (home-page "https://bioconductor.org/packages/BiocGenerics")
2441 (synopsis "S4 generic functions for Bioconductor")
2443 "This package provides S4 generic functions needed by many Bioconductor
2445 (license license:artistic2.0)))
2447 (define-public r-coverageview
2449 (name "r-coverageview")
2453 (uri (bioconductor-uri "CoverageView" version))
2456 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
2457 (build-system r-build-system)
2465 (home-page "https://bioconductor.org/packages/CoverageView/")
2466 (synopsis "Coverage visualization package for R")
2467 (description "This package provides a framework for the visualization of
2468 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
2469 be also used for genome-wide nucleosome positioning experiments or other
2470 experiment types where it is important to have a framework in order to inspect
2471 how the coverage distributed across the genome.")
2472 (license license:artistic2.0)))
2474 (define-public r-cummerbund
2476 (name "r-cummerbund")
2480 (uri (bioconductor-uri "cummeRbund" version))
2483 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
2484 (build-system r-build-system)
2496 (home-page "https://bioconductor.org/packages/cummeRbund/")
2497 (synopsis "Analyze Cufflinks high-throughput sequencing data")
2498 (description "This package allows for persistent storage, access,
2499 exploration, and manipulation of Cufflinks high-throughput sequencing
2500 data. In addition, provides numerous plotting functions for commonly
2501 used visualizations.")
2502 (license license:artistic2.0)))
2504 (define-public r-dearseq
2511 (uri (bioconductor-uri "dearseq" version))
2514 "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl"))))
2515 (build-system r-build-system)
2517 (list r-compquadform
2533 (home-page "https://github.com/borishejblum/dearseq")
2534 (synopsis "DEA for RNA-seq data through a robust variance component test")
2536 "This is a package for Differential Expression Analysis of RNA-seq data.
2537 It features a variance component score test accounting for data
2538 heteroscedasticity through precision weights. Perform both gene-wise and gene
2539 set analyses, and can deal with repeated or longitudinal data.")
2540 (license license:gpl2)))
2542 (define-public r-decipher
2548 (uri (bioconductor-uri "DECIPHER" version))
2551 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
2552 (build-system r-build-system)
2560 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
2561 (synopsis "Tools for deciphering and managing biological sequences")
2562 (description "This package provides a toolset for deciphering and managing
2563 biological sequences.")
2564 (license license:gpl3)))
2566 (define-public r-deconvr
2572 (uri (bioconductor-uri "deconvR" version))
2575 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
2576 (properties `((upstream-name . "deconvR")))
2577 (build-system r-build-system)
2596 (native-inputs (list r-knitr))
2597 (home-page "https://github.com/BIMSBbioinfo/deconvR")
2598 (synopsis "Simulation and deconvolution of omic profiles")
2600 "This package provides a collection of functions designed for analyzing
2601 deconvolution of the bulk sample(s) using an atlas of reference omic signature
2602 profiles and a user-selected model. Users are given the option to create or
2603 extend a reference atlas and,also simulate the desired size of the bulk
2604 signature profile of the reference cell types. The package includes the
2605 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
2606 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
2607 make mapping WGBS data to their probe IDs easier.")
2608 (license license:artistic2.0)))
2610 (define-public r-decoupler
2612 (name "r-decoupler")
2617 (uri (bioconductor-uri "decoupleR" version))
2619 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
2620 (properties `((upstream-name . "decoupleR")))
2621 (build-system r-build-system)
2634 (native-inputs (list r-knitr))
2635 (home-page "https://saezlab.github.io/decoupleR/")
2636 (synopsis "Computational methods to infer biological activities from omics data")
2638 "Many methods allow us to extract biological activities from omics data using
2639 information from prior knowledge resources, reducing the dimensionality for
2640 increased statistical power and better interpretability. decoupleR is a
2641 Bioconductor package containing different statistical methods to extract these
2642 signatures within a unified framework. decoupleR allows the user to flexibly
2643 test any method with any resource. It incorporates methods that take into
2644 account the sign and weight of network interactions. decoupleR can be used
2645 with any omic, as long as its features can be linked to a biological process
2646 based on prior knowledge. For example, in transcriptomics gene sets regulated
2647 by a transcription factor, or in phospho-proteomics phosphosites that are
2648 targeted by a kinase.")
2649 (license license:gpl3)))
2651 (define-public r-deepsnv
2657 (uri (bioconductor-uri "deepSNV" version))
2660 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
2661 (properties `((upstream-name . "deepSNV")))
2662 (build-system r-build-system)
2668 r-summarizedexperiment
2673 (home-page "https://github.com/gerstung-lab/deepSNV/")
2674 (synopsis "Detection of subclonal SNVs in deep sequencing data")
2676 "This package provides quantitative variant callers for detecting
2677 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
2678 The deepSNV algorithm is used for a comparative setup with a control experiment
2679 of the same loci and uses a beta-binomial model and a likelihood ratio test to
2680 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
2681 computes a Bayes classifier based on a beta-binomial model for variant calling
2682 with multiple samples for precisely estimating model parameters - such as local
2683 error rates and dispersion - and prior knowledge, e.g. from variation data
2684 bases such as COSMIC.")
2685 (license license:gpl3)))
2687 (define-public r-delayedarray
2689 (name "r-delayedarray")
2693 (uri (bioconductor-uri "DelayedArray" version))
2696 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
2698 `((upstream-name . "DelayedArray")))
2699 (build-system r-build-system)
2701 (list r-biocgenerics r-s4vectors r-iranges r-matrix
2705 (home-page "https://bioconductor.org/packages/DelayedArray")
2706 (synopsis "Delayed operations on array-like objects")
2708 "Wrapping an array-like object (typically an on-disk object) in a
2709 @code{DelayedArray} object allows one to perform common array operations on it
2710 without loading the object in memory. In order to reduce memory usage and
2711 optimize performance, operations on the object are either delayed or executed
2712 using a block processing mechanism. Note that this also works on in-memory
2713 array-like objects like @code{DataFrame} objects (typically with Rle columns),
2714 @code{Matrix} objects, and ordinary arrays and data frames.")
2715 (license license:artistic2.0)))
2717 (define-public r-derfinderhelper
2719 (name "r-derfinderhelper")
2724 (uri (bioconductor-uri "derfinderHelper" version))
2726 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
2727 (properties `((upstream-name . "derfinderHelper")))
2728 (build-system r-build-system)
2730 (list r-iranges r-matrix r-s4vectors))
2733 (home-page "https://github.com/leekgroup/derfinderHelper")
2734 (synopsis "Helper for derfinder")
2736 "This package speeds up the derfinder package when using multiple cores.
2737 It is particularly useful when using BiocParallel and it helps reduce the time
2738 spent loading the full derfinder package when running the F-statistics
2739 calculation in parallel.")
2740 (license license:artistic2.0)))
2742 (define-public r-drimseq
2749 (uri (bioconductor-uri "DRIMSeq" version))
2751 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
2752 (properties `((upstream-name . "DRIMSeq")))
2753 (build-system r-build-system)
2755 (list r-biocgenerics
2765 (native-inputs (list r-knitr))
2766 (home-page "https://bioconductor.org/packages/DRIMSeq")
2767 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
2769 "The package provides two frameworks. One for the differential
2770 transcript usage analysis between different conditions and one for the tuQTL
2771 analysis. Both are based on modeling the counts of genomic features (i.e.,
2772 transcripts) with the Dirichlet-multinomial distribution. The package also
2773 makes available functions for visualization and exploration of the data and
2775 (license license:gpl3+)))
2777 (define-public r-bluster
2783 (uri (bioconductor-uri "bluster" version))
2786 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
2787 (properties `((upstream-name . "bluster")))
2788 (build-system r-build-system)
2790 (list r-biocneighbors
2799 (home-page "https://bioconductor.org/packages/bluster")
2800 (synopsis "Clustering algorithms for Bioconductor")
2801 (description"This package wraps common clustering algorithms in an easily
2802 extended S4 framework. Backends are implemented for hierarchical, k-means
2803 and graph-based clustering. Several utilities are also provided to compare
2804 and evaluate clustering results.")
2805 (license license:gpl3)))
2807 (define-public r-ideoviz
2813 (uri (bioconductor-uri "IdeoViz" version))
2816 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
2817 (build-system r-build-system)
2825 (home-page "https://bioconductor.org/packages/IdeoViz/")
2826 (synopsis "Plots data along a chromosomal ideogram")
2827 (description "This package provides functions to plot data associated with
2828 arbitrary genomic intervals along chromosomal ideogram.")
2829 (license license:gpl2)))
2831 (define-public r-infercnv
2838 (uri (bioconductor-uri "infercnv" version))
2841 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
2842 (properties `((upstream-name . "infercnv")))
2843 (build-system r-build-system)
2844 (inputs (list python))
2873 r-singlecellexperiment
2874 r-summarizedexperiment
2876 (native-inputs (list r-knitr))
2877 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
2878 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
2880 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
2881 evidence for somatic large-scale chromosomal copy number alterations, such as gains
2882 or deletions of entire chromosomes or large segments of chromosomes. This is done
2883 by exploring expression intensity of genes across positions of a tumor genome in
2884 comparison to a set of reference \"normal\" cells. A heatmap is generated
2885 illustrating the relative expression intensities across each chromosome, and it
2886 often becomes readily apparent as to which regions of the tumor genome are
2887 over-abundant or less-abundant as compared to that of normal cells.")
2888 (license license:bsd-3)))
2890 (define-public r-iranges
2896 (uri (bioconductor-uri "IRanges" version))
2899 "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
2901 `((upstream-name . "IRanges")))
2902 (build-system r-build-system)
2904 (list r-biocgenerics r-s4vectors))
2905 (home-page "https://bioconductor.org/packages/IRanges")
2906 (synopsis "Infrastructure for manipulating intervals on sequences")
2908 "This package provides efficient low-level and highly reusable S4 classes
2909 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
2910 generally, data that can be organized sequentially (formally defined as
2911 @code{Vector} objects), as well as views on these @code{Vector} objects.
2912 Efficient list-like classes are also provided for storing big collections of
2913 instances of the basic classes. All classes in the package use consistent
2914 naming and share the same rich and consistent \"Vector API\" as much as
2916 (license license:artistic2.0)))
2918 (define-public r-isoformswitchanalyzer
2920 (name "r-isoformswitchanalyzer")
2925 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
2927 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
2928 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
2929 (build-system r-build-system)
2962 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
2963 (synopsis "Analyze alternative splicing in RNA-seq data")
2965 "This is a package for the analysis of alternative splicing and isoform
2966 switches with predicted functional consequences (e.g. gain/loss of protein
2967 domains etc.) from quantification of all types of RNASeq by tools such as
2968 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
2969 (license license:gpl2+)))
2971 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
2972 (define-public r-absfiltergsea
2974 (name "r-absfiltergsea")
2979 (uri (cran-uri "AbsFilterGSEA" version))
2981 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
2982 (properties `((upstream-name . "AbsFilterGSEA")))
2983 (build-system r-build-system)
2985 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
2986 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
2987 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
2989 "This package provides a function that performs gene-permuting of a gene-set
2990 enrichment analysis (GSEA) calculation with or without the absolute filtering.
2991 Without filtering, users can perform (original) two-tailed or one-tailed
2993 (license license:gpl2)))
2995 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
2996 (define-public r-bisquerna
2998 (name "r-bisquerna")
3002 (uri (cran-uri "BisqueRNA" version))
3005 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
3006 (properties `((upstream-name . "BisqueRNA")))
3007 (build-system r-build-system)
3009 (list r-biobase r-limsolve))
3012 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
3013 (synopsis "Decomposition of bulk expression with single-cell sequencing")
3014 (description "This package provides tools to accurately estimate cell type
3015 abundances from heterogeneous bulk expression. A reference-based method
3016 utilizes single-cell information to generate a signature matrix and
3017 transformation of bulk expression for accurate regression based estimates.
3018 A marker-based method utilizes known cell-specific marker genes to measure
3019 relative abundances across samples.")
3020 (license license:gpl3)))
3022 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
3023 ;; from Bioconductor.
3024 (define-public r-deconstructsigs
3026 (name "r-deconstructsigs")
3030 (uri (cran-uri "deconstructSigs" version))
3033 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
3035 `((upstream-name . "deconstructSigs")))
3036 (build-system r-build-system)
3038 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
3040 (home-page "https://github.com/raerose01/deconstructSigs")
3041 (synopsis "Identifies signatures present in a tumor sample")
3042 (description "This package takes sample information in the form of the
3043 fraction of mutations in each of 96 trinucleotide contexts and identifies
3044 the weighted combination of published signatures that, when summed, most
3045 closely reconstructs the mutational profile.")
3046 (license license:gpl2+)))
3048 ;; This is a CRAN package, but it depends on Bioconductor packages.
3049 (define-public r-jetset
3056 (uri (cran-uri "jetset" version))
3058 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
3059 (properties `((upstream-name . "jetset")))
3060 (build-system r-build-system)
3061 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
3062 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
3063 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
3065 "This package provides a one-to-one mapping from gene to \"best\" probe
3066 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
3067 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
3068 gene may be measured by multiple probe sets. This can present a mild
3069 conundrum when attempting to evaluate a gene \"signature\" that is defined by
3070 gene names rather than by specific probe sets. This package also includes the
3071 pre-calculated probe set quality scores that were used to define the
3073 (license license:artistic2.0)))
3075 ;; This is a CRAN package, but it depends on Bioconductor packages.
3076 (define-public r-nmf
3083 (uri (cran-uri "NMF" version))
3086 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
3087 (properties `((upstream-name . "NMF")))
3088 (build-system r-build-system)
3093 r-bigmemory ; suggested
3094 r-synchronicity ; suggested
3109 (home-page "http://renozao.github.io/NMF")
3110 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3112 "This package provides a framework to perform Non-negative Matrix
3113 Factorization (NMF). The package implements a set of already published
3114 algorithms and seeding methods, and provides a framework to test, develop and
3115 plug new or custom algorithms. Most of the built-in algorithms have been
3116 optimized in C++, and the main interface function provides an easy way of
3117 performing parallel computations on multicore machines.")
3118 (license license:gpl2+)))
3120 (define-public r-affy
3127 (uri (bioconductor-uri "affy" version))
3130 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
3131 (build-system r-build-system)
3141 (home-page "https://bioconductor.org/packages/affy")
3142 (synopsis "Methods for affymetrix oligonucleotide arrays")
3144 "This package contains functions for exploratory oligonucleotide array
3146 (license license:lgpl2.0+)))
3148 (define-public r-affycomp
3155 (uri (bioconductor-uri "affycomp" version))
3158 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
3159 (properties `((upstream-name . "affycomp")))
3160 (build-system r-build-system)
3161 (propagated-inputs (list r-biobase))
3162 (home-page "https://bioconductor.org/packages/affycomp/")
3163 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
3165 "The package contains functions that can be used to compare expression
3166 measures for Affymetrix Oligonucleotide Arrays.")
3167 (license license:gpl2+)))
3169 (define-public r-affycompatible
3171 (name "r-affycompatible")
3176 (uri (bioconductor-uri "AffyCompatible" version))
3179 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
3181 `((upstream-name . "AffyCompatible")))
3182 (build-system r-build-system)
3186 `(modify-phases %standard-phases
3187 (add-after 'unpack 'make-reproducible
3189 ;; Order DTD elements before generating R code from them.
3190 (substitute* "R/methods-AffyCompatible.R"
3193 elements <- dtd$elements
3194 ordered <- elements[order(names(elements))]\n"))
3195 (("elt in dtd\\$elements")
3197 ;; Use a predictable directory name for code generation.
3198 (mkdir-p "/tmp/NetAffxResourcePrototype")
3199 (substitute* "R/DataClasses.R"
3200 (("directory=tempdir\\(\\)")
3201 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
3203 (list r-biostrings r-rcurl r-xml))
3204 (home-page "https://bioconductor.org/packages/AffyCompatible/")
3205 (synopsis "Work with Affymetrix GeneChip files")
3207 "This package provides an interface to Affymetrix chip annotation and
3208 sample attribute files. The package allows an easy way for users to download
3209 and manage local data bases of Affynmetrix NetAffx annotation files. It also
3210 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
3211 Command Console} (AGCC)-compatible sample annotation files.")
3212 (license license:artistic2.0)))
3214 (define-public r-affycontam
3216 (name "r-affycontam")
3221 (uri (bioconductor-uri "affyContam" version))
3224 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
3225 (properties `((upstream-name . "affyContam")))
3226 (build-system r-build-system)
3228 (list r-affy r-affydata r-biobase))
3229 (home-page "https://bioconductor.org/packages/affyContam/")
3230 (synopsis "Structured corruption of Affymetrix CEL file data")
3232 "Microarray quality assessment is a major concern of microarray analysts.
3233 This package provides some simple approaches to in silico creation of quality
3234 problems in CEL-level data to help evaluate performance of quality metrics.")
3235 (license license:artistic2.0)))
3237 (define-public r-affycoretools
3239 (name "r-affycoretools")
3244 (uri (bioconductor-uri "affycoretools" version))
3247 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
3248 (properties `((upstream-name . "affycoretools")))
3249 (build-system r-build-system)
3272 (home-page "https://bioconductor.org/packages/affycoretools/")
3273 (synopsis "Functions for analyses with Affymetrix GeneChips")
3275 "This package provides various wrapper functions that have been written
3276 to streamline the more common analyses that a Biostatistician might see.")
3277 (license license:artistic2.0)))
3279 (define-public r-affyio
3286 (uri (bioconductor-uri "affyio" version))
3289 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
3290 (build-system r-build-system)
3295 (home-page "https://github.com/bmbolstad/affyio")
3296 (synopsis "Tools for parsing Affymetrix data files")
3298 "This package provides routines for parsing Affymetrix data files based
3299 upon file format information. The primary focus is on accessing the CEL and
3301 (license license:lgpl2.0+)))
3303 (define-public r-affxparser
3305 (name "r-affxparser")
3310 (uri (bioconductor-uri "affxparser" version))
3313 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
3314 (properties `((upstream-name . "affxparser")))
3315 (build-system r-build-system)
3316 (home-page "https://github.com/HenrikBengtsson/affxparser")
3317 (synopsis "Affymetrix File Parsing SDK")
3319 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
3320 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
3321 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
3322 are supported. Currently, there are methods for reading @dfn{chip definition
3323 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
3324 either in full or in part. For example, probe signals from a few probesets
3325 can be extracted very quickly from a set of CEL files into a convenient list
3327 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
3329 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
3331 (define-public r-annotate
3338 (uri (bioconductor-uri "annotate" version))
3341 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
3342 (build-system r-build-system)
3344 (list r-annotationdbi
3352 "https://bioconductor.org/packages/annotate")
3353 (synopsis "Annotation for microarrays")
3354 (description "This package provides R environments for the annotation of
3356 (license license:artistic2.0)))
3358 (define-public r-annotationdbi
3360 (name "r-annotationdbi")
3364 (uri (bioconductor-uri "AnnotationDbi" version))
3367 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
3369 `((upstream-name . "AnnotationDbi")))
3370 (build-system r-build-system)
3381 (home-page "https://bioconductor.org/packages/AnnotationDbi")
3382 (synopsis "Annotation database interface")
3384 "This package provides user interface and database connection code for
3385 annotation data packages using SQLite data storage.")
3386 (license license:artistic2.0)))
3388 (define-public r-annotationfilter
3390 (name "r-annotationfilter")
3394 (uri (bioconductor-uri "AnnotationFilter" version))
3397 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
3399 `((upstream-name . "AnnotationFilter")))
3400 (build-system r-build-system)
3402 (list r-genomicranges r-lazyeval))
3405 (home-page "https://github.com/Bioconductor/AnnotationFilter")
3406 (synopsis "Facilities for filtering Bioconductor annotation resources")
3408 "This package provides classes and other infrastructure to implement
3409 filters for manipulating Bioconductor annotation resources. The filters are
3410 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
3411 (license license:artistic2.0)))
3413 (define-public r-annotationforge
3415 (name "r-annotationforge")
3420 (uri (bioconductor-uri "AnnotationForge" version))
3423 "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v"))))
3425 `((upstream-name . "AnnotationForge")))
3426 (build-system r-build-system)
3428 (list r-annotationdbi
3438 (home-page "https://bioconductor.org/packages/AnnotationForge")
3439 (synopsis "Code for building annotation database packages")
3441 "This package provides code for generating Annotation packages and their
3442 databases. Packages produced are intended to be used with AnnotationDbi.")
3443 (license license:artistic2.0)))
3445 (define-public r-annotationhub
3447 (name "r-annotationhub")
3452 (uri (bioconductor-uri "AnnotationHub" version))
3455 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
3456 (properties `((upstream-name . "AnnotationHub")))
3457 (build-system r-build-system)
3459 (list r-annotationdbi
3467 r-interactivedisplaybase
3474 (home-page "https://bioconductor.org/packages/AnnotationHub")
3475 (synopsis "Client to access AnnotationHub resources")
3477 "This package provides a client for the Bioconductor AnnotationHub web
3478 resource. The AnnotationHub web resource provides a central location where
3479 genomic files (e.g. VCF, bed, wig) and other resources from standard
3480 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
3481 metadata about each resource, e.g., a textual description, tags, and date of
3482 modification. The client creates and manages a local cache of files retrieved
3483 by the user, helping with quick and reproducible access.")
3484 (license license:artistic2.0)))
3486 (define-public r-aroma-light
3488 (name "r-aroma-light")
3493 (uri (bioconductor-uri "aroma.light" version))
3496 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
3497 (properties `((upstream-name . "aroma.light")))
3498 (build-system r-build-system)
3500 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
3501 (home-page "https://github.com/HenrikBengtsson/aroma.light")
3502 (synopsis "Methods for normalization and visualization of microarray data")
3504 "This package provides methods for microarray analysis that take basic
3505 data types such as matrices and lists of vectors. These methods can be used
3506 standalone, be utilized in other packages, or be wrapped up in higher-level
3508 (license license:gpl2+)))
3510 (define-public r-bamsignals
3512 (name "r-bamsignals")
3517 (uri (bioconductor-uri "bamsignals" version))
3520 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
3521 (build-system r-build-system)
3523 (list r-biocgenerics
3531 (home-page "https://bioconductor.org/packages/bamsignals")
3532 (synopsis "Extract read count signals from bam files")
3534 "This package efficiently obtains count vectors from indexed bam
3535 files. It counts the number of nucleotide sequence reads in given genomic
3536 ranges and it computes reads profiles and coverage profiles. It also handles
3538 (license license:gpl2+)))
3540 (define-public r-biobase
3546 (uri (bioconductor-uri "Biobase" version))
3549 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
3551 `((upstream-name . "Biobase")))
3552 (build-system r-build-system)
3554 (list r-biocgenerics))
3555 (home-page "https://bioconductor.org/packages/Biobase")
3556 (synopsis "Base functions for Bioconductor")
3558 "This package provides functions that are needed by many other packages
3559 on Bioconductor or which replace R functions.")
3560 (license license:artistic2.0)))
3562 (define-public r-biomart
3568 (uri (bioconductor-uri "biomaRt" version))
3571 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
3573 `((upstream-name . "biomaRt")))
3574 (build-system r-build-system)
3576 (list r-annotationdbi
3587 (home-page "https://bioconductor.org/packages/biomaRt")
3588 (synopsis "Interface to BioMart databases")
3590 "biomaRt provides an interface to a growing collection of databases
3591 implementing the @url{BioMart software suite, http://www.biomart.org}. The
3592 package enables retrieval of large amounts of data in a uniform way without
3593 the need to know the underlying database schemas or write complex SQL queries.
3594 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
3595 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
3596 users direct access to a diverse set of data and enable a wide range of
3597 powerful online queries from gene annotation to database mining.")
3598 (license license:artistic2.0)))
3600 ;; This is a CRAN package, but it depends on a Bioconductor package:
3602 (define-public r-biomartr
3608 (uri (cran-uri "biomartr" version))
3611 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
3612 (properties `((upstream-name . "biomartr")))
3613 (build-system r-build-system)
3633 (native-inputs (list r-knitr))
3634 (home-page "https://docs.ropensci.org/biomartr/")
3635 (synopsis "Genomic data retrieval")
3637 "Perform large scale genomic data retrieval and functional annotation
3638 retrieval. This package aims to provide users with a standardized way to
3639 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
3640 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
3641 Furthermore, an interface to the BioMart database allows users to retrieve
3642 functional annotation for genomic loci. In addition, users can download
3643 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
3645 (license license:gpl2)))
3647 (define-public r-biocparallel
3649 (name "r-biocparallel")
3653 (uri (bioconductor-uri "BiocParallel" version))
3656 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
3658 `((upstream-name . "BiocParallel")))
3659 (build-system r-build-system)
3662 (modify-phases %standard-phases
3663 (add-after 'unpack 'make-reproducible
3665 ;; Remove generated documentation.
3666 (for-each delete-file
3667 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
3668 "inst/doc/Introduction_To_BiocParallel.pdf"
3669 "inst/doc/Errors_Logs_And_Debugging.pdf"
3670 "inst/doc/BiocParallel_BatchtoolsParam.R"
3671 "inst/doc/Introduction_To_BiocParallel.R"
3672 "inst/doc/Errors_Logs_And_Debugging.R"))
3674 ;; Remove time-dependent macro
3675 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
3676 "inst/doc/Introduction_To_BiocParallel.Rnw"
3677 "inst/doc/Errors_Logs_And_Debugging.Rnw"
3678 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
3679 "vignettes/Introduction_To_BiocParallel.Rnw"
3680 "vignettes/Errors_Logs_And_Debugging.Rnw")
3681 (("\\today") "later"))
3683 ;; Initialize the random number generator seed when building.
3684 (substitute* "R/rng.R"
3685 (("\"L'Ecuyer-CMRG\"\\)" m)
3687 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
3689 (list r-bh r-codetools r-futile-logger r-snow))
3692 (home-page "https://bioconductor.org/packages/BiocParallel")
3693 (synopsis "Bioconductor facilities for parallel evaluation")
3695 "This package provides modified versions and novel implementation of
3696 functions for parallel evaluation, tailored to use with Bioconductor
3698 (license (list license:gpl2+ license:gpl3+))))
3700 (define-public r-biostrings
3702 (name "r-biostrings")
3706 (uri (bioconductor-uri "Biostrings" version))
3709 "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"))))
3711 `((upstream-name . "Biostrings")))
3712 (build-system r-build-system)
3714 (list r-biocgenerics
3720 (home-page "https://bioconductor.org/packages/Biostrings")
3721 (synopsis "String objects and algorithms for biological sequences")
3723 "This package provides memory efficient string containers, string
3724 matching algorithms, and other utilities, for fast manipulation of large
3725 biological sequences or sets of sequences.")
3726 (license license:artistic2.0)))
3728 (define-public r-biovizbase
3730 (name "r-biovizbase")
3735 (uri (bioconductor-uri "biovizBase" version))
3738 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
3739 (properties `((upstream-name . "biovizBase")))
3740 (build-system r-build-system)
3742 (list r-annotationdbi
3759 r-summarizedexperiment
3760 r-variantannotation))
3761 (home-page "https://bioconductor.org/packages/biovizBase")
3762 (synopsis "Basic graphic utilities for visualization of genomic data")
3764 "The biovizBase package is designed to provide a set of utilities, color
3765 schemes and conventions for genomic data. It serves as the base for various
3766 high-level packages for biological data visualization. This saves development
3767 effort and encourages consistency.")
3768 (license license:artistic2.0)))
3770 (define-public r-bsgenome
3776 (uri (bioconductor-uri "BSgenome" version))
3779 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
3781 `((upstream-name . "BSgenome")))
3782 (build-system r-build-system)
3784 (list r-biocgenerics
3794 (home-page "https://bioconductor.org/packages/BSgenome")
3795 (synopsis "Infrastructure for Biostrings-based genome data packages")
3797 "This package provides infrastructure shared by all Biostrings-based
3798 genome data packages and support for efficient SNP representation.")
3799 (license license:artistic2.0)))
3801 (define-public r-category
3808 (uri (bioconductor-uri "Category" version))
3811 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
3812 (properties `((upstream-name . "Category")))
3813 (build-system r-build-system)
3825 (home-page "https://bioconductor.org/packages/Category")
3826 (synopsis "Category analysis")
3828 "This package provides a collection of tools for performing category
3830 (license license:artistic2.0)))
3832 (define-public r-chipseeker
3834 (name "r-chipseeker")
3838 (uri (bioconductor-uri "ChIPseeker" version))
3841 "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"))))
3842 (build-system r-build-system)
3846 (list r-annotationdbi
3865 r-txdb-hsapiens-ucsc-hg19-knowngene))
3866 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
3867 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
3868 (description "This package implements functions to retrieve the nearest
3869 genes around the peak, annotate genomic region of the peak, statstical methods
3870 for estimate the significance of overlap among ChIP peak data sets, and
3871 incorporate GEO database for user to compare the own dataset with those
3872 deposited in database. The comparison can be used to infer cooperative
3873 regulation and thus can be used to generate hypotheses. Several visualization
3874 functions are implemented to summarize the coverage of the peak experiment,
3875 average profile and heatmap of peaks binding to TSS regions, genomic
3876 annotation, distance to TSS, and overlap of peaks or genes.")
3877 (license license:artistic2.0)))
3879 (define-public r-chipseq
3886 (uri (bioconductor-uri "chipseq" version))
3889 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
3890 (build-system r-build-system)
3892 (list r-biocgenerics
3898 (home-page "https://bioconductor.org/packages/chipseq")
3899 (synopsis "Package for analyzing ChIPseq data")
3901 "This package provides tools for processing short read data from ChIPseq
3903 (license license:artistic2.0)))
3905 (define-public r-complexheatmap
3907 (name "r-complexheatmap")
3912 (uri (bioconductor-uri "ComplexHeatmap" version))
3915 "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"))))
3917 `((upstream-name . "ComplexHeatmap")))
3918 (build-system r-build-system)
3936 "https://github.com/jokergoo/ComplexHeatmap")
3937 (synopsis "Making Complex Heatmaps")
3939 "Complex heatmaps are efficient to visualize associations between
3940 different sources of data sets and reveal potential structures. This package
3941 provides a highly flexible way to arrange multiple heatmaps and supports
3942 self-defined annotation graphics.")
3943 (license license:gpl2+)))
3945 (define-public r-copywriter
3947 (name "r-copywriter")
3952 (uri (bioconductor-uri "CopywriteR" version))
3955 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
3956 (properties `((upstream-name . "CopywriteR")))
3957 (build-system r-build-system)
3959 (list r-biocparallel
3973 (home-page "https://github.com/PeeperLab/CopywriteR")
3974 (synopsis "Copy number information from targeted sequencing")
3976 "CopywriteR extracts DNA copy number information from targeted sequencing
3977 by utilizing off-target reads. It allows for extracting uniformly distributed
3978 copy number information, can be used without reference, and can be applied to
3979 sequencing data obtained from various techniques including chromatin
3980 immunoprecipitation and target enrichment on small gene panels. Thereby,
3981 CopywriteR constitutes a widely applicable alternative to available copy
3982 number detection tools.")
3983 (license license:gpl2)))
3985 (define-public r-deseq
3992 (uri (bioconductor-uri "DESeq" version))
3995 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
3996 (properties `((upstream-name . "DESeq")))
3997 (build-system r-build-system)
4007 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
4008 (synopsis "Differential gene expression analysis")
4010 "This package provides tools for estimating variance-mean dependence in
4011 count data from high-throughput genetic sequencing assays and for testing for
4012 differential expression based on a model using the negative binomial
4014 (license license:gpl3+)))
4016 (define-public r-deseq2
4023 (uri (bioconductor-uri "DESeq2" version))
4026 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
4027 (properties `((upstream-name . "DESeq2")))
4028 (build-system r-build-system)
4042 r-summarizedexperiment))
4045 (home-page "https://bioconductor.org/packages/DESeq2")
4046 (synopsis "Differential gene expression analysis")
4048 "This package provides functions to estimate variance-mean dependence in
4049 count data from high-throughput nucleotide sequencing assays and test for
4050 differential expression based on a model using the negative binomial
4052 (license license:lgpl3+)))
4054 (define-public r-dexseq
4061 (uri (bioconductor-uri "DEXSeq" version))
4064 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
4065 (properties `((upstream-name . "DEXSeq")))
4066 (build-system r-build-system)
4068 (list r-annotationdbi
4084 r-summarizedexperiment))
4087 (home-page "https://bioconductor.org/packages/DEXSeq")
4088 (synopsis "Inference of differential exon usage in RNA-Seq")
4090 "This package is focused on finding differential exon usage using RNA-seq
4091 exon counts between samples with different experimental designs. It provides
4092 functions that allows the user to make the necessary statistical tests based
4093 on a model that uses the negative binomial distribution to estimate the
4094 variance between biological replicates and generalized linear models for
4095 testing. The package also provides functions for the visualization and
4096 exploration of the results.")
4097 (license license:gpl3+)))
4099 (define-public r-diffcyt
4106 (uri (bioconductor-uri "diffcyt" version))
4108 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
4109 (properties `((upstream-name . "diffcyt")))
4110 (build-system r-build-system)
4124 r-summarizedexperiment
4126 (native-inputs (list r-knitr))
4127 (home-page "https://github.com/lmweber/diffcyt")
4128 (synopsis "Differential discovery in high-dimensional cytometry")
4130 "This package provides statistical methods for differential discovery
4131 analyses in high-dimensional cytometry data (including flow cytometry, mass
4132 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
4133 combination of high-resolution clustering and empirical Bayes moderated tests
4134 adapted from transcriptomics.")
4135 (license license:expat)))
4137 (define-public r-dirichletmultinomial
4139 (name "r-dirichletmultinomial")
4144 (uri (bioconductor-uri "DirichletMultinomial" version))
4147 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
4149 `((upstream-name . "DirichletMultinomial")))
4150 (build-system r-build-system)
4154 (list r-biocgenerics r-iranges r-s4vectors))
4155 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
4156 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
4158 "Dirichlet-multinomial mixture models can be used to describe variability
4159 in microbial metagenomic data. This package is an interface to code
4160 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
4162 (license license:lgpl3)))
4164 (define-public r-dittoseq
4170 (uri (bioconductor-uri "dittoSeq" version))
4173 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
4174 (properties `((upstream-name . "dittoSeq")))
4175 (build-system r-build-system)
4186 r-singlecellexperiment
4187 r-summarizedexperiment))
4188 (native-inputs (list r-knitr))
4189 (home-page "https://bioconductor.org/packages/dittoSeq")
4190 (synopsis "Single-cell and bulk RNA sequencing visualization")
4192 "This package provides a universal, user friendly, single-cell and bulk RNA
4193 sequencing visualization toolkit that allows highly customizable creation of
4194 color blindness friendly, publication-quality figures. dittoSeq accepts both
4195 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
4196 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
4197 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
4198 percent composition or expression across groups, and more. Customizations
4199 range from size and title adjustments to automatic generation of annotations
4200 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
4201 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
4202 many more. All with simple, discrete inputs. Color blindness friendliness is
4203 powered by legend adjustments (enlarged keys), and by allowing the use of
4204 shapes or letter-overlay in addition to the carefully selected
4205 code{dittoColors()}.")
4206 (license license:expat)))
4208 (define-public r-edaseq
4215 (uri (bioconductor-uri "EDASeq" version))
4218 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
4219 (properties `((upstream-name . "EDASeq")))
4220 (build-system r-build-system)
4222 (list r-annotationdbi
4236 (home-page "https://github.com/drisso/EDASeq")
4237 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
4239 "This package provides support for numerical and graphical summaries of
4240 RNA-Seq genomic read data. Provided within-lane normalization procedures to
4241 adjust for GC-content effect (or other gene-level effects) on read counts:
4242 loess robust local regression, global-scaling, and full-quantile
4243 normalization. Between-lane normalization procedures to adjust for
4244 distributional differences between lanes (e.g., sequencing depth):
4245 global-scaling and full-quantile normalization.")
4246 (license license:artistic2.0)))
4248 (define-public r-edger
4254 (uri (bioconductor-uri "edgeR" version))
4257 "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
4258 (properties `((upstream-name . "edgeR")))
4259 (build-system r-build-system)
4261 (list r-limma r-locfit r-rcpp))
4262 (home-page "http://bioinf.wehi.edu.au/edgeR")
4263 (synopsis "EdgeR does empirical analysis of digital gene expression data")
4264 (description "This package can do differential expression analysis of
4265 RNA-seq expression profiles with biological replication. It implements a range
4266 of statistical methodology based on the negative binomial distributions,
4267 including empirical Bayes estimation, exact tests, generalized linear models
4268 and quasi-likelihood tests. It be applied to differential signal analysis of
4269 other types of genomic data that produce counts, including ChIP-seq, SAGE and
4271 (license license:gpl2+)))
4273 (define-public r-ensembldb
4275 (name "r-ensembldb")
4280 (uri (bioconductor-uri "ensembldb" version))
4283 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
4284 (build-system r-build-system)
4286 (list r-annotationdbi
4304 (home-page "https://github.com/jotsetung/ensembldb")
4305 (synopsis "Utilities to create and use Ensembl-based annotation databases")
4307 "The package provides functions to create and use transcript-centric
4308 annotation databases/packages. The annotation for the databases are directly
4309 fetched from Ensembl using their Perl API. The functionality and data is
4310 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
4311 but, in addition to retrieve all gene/transcript models and annotations from
4312 the database, the @code{ensembldb} package also provides a filter framework
4313 allowing to retrieve annotations for specific entries like genes encoded on a
4314 chromosome region or transcript models of lincRNA genes.")
4315 ;; No version specified
4316 (license license:lgpl3+)))
4318 (define-public r-fastseg
4325 (uri (bioconductor-uri "fastseg" version))
4328 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
4329 (build-system r-build-system)
4331 (list r-biobase r-biocgenerics r-genomicranges r-iranges
4333 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
4334 (synopsis "Fast segmentation algorithm for genetic sequencing data")
4336 "Fastseg implements a very fast and efficient segmentation algorithm.
4337 It can segment data from DNA microarrays and data from next generation
4338 sequencing for example to detect copy number segments. Further it can segment
4339 data from RNA microarrays like tiling arrays to identify transcripts. Most
4340 generally, it can segment data given as a matrix or as a vector. Various data
4341 formats can be used as input to fastseg like expression set objects for
4342 microarrays or GRanges for sequencing data.")
4343 (license license:lgpl2.0+)))
4345 (define-public r-gage
4352 (uri (bioconductor-uri "gage" version))
4355 "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"))))
4356 (build-system r-build-system)
4358 (list r-annotationdbi r-go-db r-graph r-keggrest))
4359 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
4360 "articles/10.1186/1471-2105-10-161"))
4361 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
4363 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
4364 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
4365 data attributes including sample sizes, experimental designs, assay platforms,
4366 and other types of heterogeneity. The gage package provides functions for
4367 basic GAGE analysis, result processing and presentation. In addition, it
4368 provides demo microarray data and commonly used gene set data based on KEGG
4369 pathways and GO terms. These functions and data are also useful for gene set
4370 analysis using other methods.")
4371 (license license:gpl2+)))
4373 (define-public r-genefilter
4375 (name "r-genefilter")
4380 (uri (bioconductor-uri "genefilter" version))
4383 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
4384 (build-system r-build-system)
4386 (list gfortran r-knitr))
4388 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
4390 (home-page "https://bioconductor.org/packages/genefilter")
4391 (synopsis "Filter genes from high-throughput experiments")
4393 "This package provides basic functions for filtering genes from
4394 high-throughput sequencing experiments.")
4395 (license license:artistic2.0)))
4397 (define-public r-geneoverlap
4399 (name "r-geneoverlap")
4403 (uri (bioconductor-uri "GeneOverlap" version))
4406 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
4407 (build-system r-build-system)
4409 (list r-rcolorbrewer r-gplots))
4410 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
4411 (synopsis "Test and visualize gene overlaps")
4412 (description "This package can be used to test two sets of gene lists
4413 and visualize the results.")
4414 (license license:gpl3)))
4416 (define-public r-genomation
4418 (name "r-genomation")
4422 (uri (bioconductor-uri "genomation" version))
4425 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
4426 (build-system r-build-system)
4450 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
4451 (synopsis "Summary, annotation and visualization of genomic data")
4453 "This package provides a package for summary and annotation of genomic
4454 intervals. Users can visualize and quantify genomic intervals over
4455 pre-defined functional regions, such as promoters, exons, introns, etc. The
4456 genomic intervals represent regions with a defined chromosome position, which
4457 may be associated with a score, such as aligned reads from HT-seq experiments,
4458 TF binding sites, methylation scores, etc. The package can use any tabular
4459 genomic feature data as long as it has minimal information on the locations of
4460 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4461 (license license:artistic2.0)))
4463 (define-public r-genomeinfodb
4465 (name "r-genomeinfodb")
4469 (uri (bioconductor-uri "GenomeInfoDb" version))
4472 "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"))))
4474 `((upstream-name . "GenomeInfoDb")))
4475 (build-system r-build-system)
4477 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
4481 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
4482 (synopsis "Utilities for manipulating chromosome identifiers")
4484 "This package contains data and functions that define and allow
4485 translation between different chromosome sequence naming conventions (e.g.,
4486 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4487 names in their natural, rather than lexicographic, order.")
4488 (license license:artistic2.0)))
4490 (define-public r-genomicalignments
4492 (name "r-genomicalignments")
4496 (uri (bioconductor-uri "GenomicAlignments" version))
4499 "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
4501 `((upstream-name . "GenomicAlignments")))
4502 (build-system r-build-system)
4504 (list r-biocgenerics
4512 r-summarizedexperiment))
4513 (home-page "https://bioconductor.org/packages/GenomicAlignments")
4514 (synopsis "Representation and manipulation of short genomic alignments")
4516 "This package provides efficient containers for storing and manipulating
4517 short genomic alignments (typically obtained by aligning short reads to a
4518 reference genome). This includes read counting, computing the coverage,
4519 junction detection, and working with the nucleotide content of the
4521 (license license:artistic2.0)))
4523 (define-public r-genomicfeatures
4525 (name "r-genomicfeatures")
4529 (uri (bioconductor-uri "GenomicFeatures" version))
4532 "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"))))
4534 `((upstream-name . "GenomicFeatures")))
4535 (build-system r-build-system)
4537 (list r-annotationdbi
4554 (home-page "https://bioconductor.org/packages/GenomicFeatures")
4555 (synopsis "Tools for working with transcript centric annotations")
4557 "This package provides a set of tools and methods for making and
4558 manipulating transcript centric annotations. With these tools the user can
4559 easily download the genomic locations of the transcripts, exons and cds of a
4560 given organism, from either the UCSC Genome Browser or a BioMart
4561 database (more sources will be supported in the future). This information is
4562 then stored in a local database that keeps track of the relationship between
4563 transcripts, exons, cds and genes. Flexible methods are provided for
4564 extracting the desired features in a convenient format.")
4565 (license license:artistic2.0)))
4567 (define-public r-genomicfiles
4569 (name "r-genomicfiles")
4574 (uri (bioconductor-uri "GenomicFiles" version))
4577 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
4578 (properties `((upstream-name . "GenomicFiles")))
4579 (build-system r-build-system)
4581 (list r-biocgenerics
4591 r-summarizedexperiment
4592 r-variantannotation))
4593 (home-page "https://bioconductor.org/packages/GenomicFiles")
4594 (synopsis "Distributed computing by file or by range")
4596 "This package provides infrastructure for parallel computations
4597 distributed by file or by range. User defined mapper and reducer functions
4598 provide added flexibility for data combination and manipulation.")
4599 (license license:artistic2.0)))
4601 (define-public r-genomicranges
4603 (name "r-genomicranges")
4607 (uri (bioconductor-uri "GenomicRanges" version))
4610 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
4612 `((upstream-name . "GenomicRanges")))
4613 (build-system r-build-system)
4615 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
4618 (home-page "https://bioconductor.org/packages/GenomicRanges")
4619 (synopsis "Representation and manipulation of genomic intervals")
4621 "This package provides tools to efficiently represent and manipulate
4622 genomic annotations and alignments is playing a central role when it comes to
4623 analyzing high-throughput sequencing data (a.k.a. NGS data). The
4624 GenomicRanges package defines general purpose containers for storing and
4625 manipulating genomic intervals and variables defined along a genome.")
4626 (license license:artistic2.0)))
4628 (define-public r-gostats
4635 (uri (bioconductor-uri "GOstats" version))
4638 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
4639 (properties `((upstream-name . "GOstats")))
4640 (build-system r-build-system)
4651 (home-page "https://bioconductor.org/packages/GOstats")
4652 (synopsis "Tools for manipulating GO and microarrays")
4654 "This package provides a set of tools for interacting with GO and
4655 microarray data. A variety of basic manipulation tools for graphs, hypothesis
4656 testing and other simple calculations.")
4657 (license license:artistic2.0)))
4659 (define-public r-gseabase
4666 (uri (bioconductor-uri "GSEABase" version))
4669 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
4670 (properties `((upstream-name . "GSEABase")))
4671 (build-system r-build-system)
4681 (home-page "https://bioconductor.org/packages/GSEABase")
4682 (synopsis "Gene set enrichment data structures and methods")
4684 "This package provides classes and methods to support @dfn{Gene Set
4685 Enrichment Analysis} (GSEA).")
4686 (license license:artistic2.0)))
4688 (define-public r-hpar
4695 (uri (bioconductor-uri "hpar" version))
4698 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
4699 (build-system r-build-system)
4702 (home-page "https://bioconductor.org/packages/hpar/")
4703 (synopsis "Human Protein Atlas in R")
4704 (description "This package provides a simple interface to and data from
4705 the Human Protein Atlas project.")
4706 (license license:artistic2.0)))
4708 (define-public r-rhtslib
4715 (uri (bioconductor-uri "Rhtslib" version))
4718 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
4719 (properties `((upstream-name . "Rhtslib")))
4720 (build-system r-build-system)
4721 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
4722 ;; which makes R abort the build.
4723 (arguments '(#:configure-flags '("--no-staged-install")))
4725 (list curl zlib ; packages using rhtslib need to link with zlib
4728 (list pkg-config r-knitr))
4729 (home-page "https://github.com/nhayden/Rhtslib")
4730 (synopsis "High-throughput sequencing library as an R package")
4732 "This package provides the HTSlib C library for high-throughput
4733 nucleotide sequence analysis. The package is primarily useful to developers
4734 of other R packages who wish to make use of HTSlib.")
4735 (license license:lgpl2.0+)))
4737 (define-public r-impute
4743 (uri (bioconductor-uri "impute" version))
4746 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
4749 (build-system r-build-system)
4750 (home-page "https://bioconductor.org/packages/impute")
4751 (synopsis "Imputation for microarray data")
4753 "This package provides a function to impute missing gene expression
4754 microarray data, using nearest neighbor averaging.")
4755 (license license:gpl2+)))
4757 (define-public r-interactivedisplaybase
4759 (name "r-interactivedisplaybase")
4764 (uri (bioconductor-uri "interactiveDisplayBase" version))
4767 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
4769 `((upstream-name . "interactiveDisplayBase")))
4770 (build-system r-build-system)
4772 (list r-biocgenerics r-dt r-shiny))
4775 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
4776 (synopsis "Base package for web displays of Bioconductor objects")
4778 "This package contains the basic methods needed to generate interactive
4779 Shiny-based display methods for Bioconductor objects.")
4780 (license license:artistic2.0)))
4782 (define-public r-keggrest
4789 (uri (bioconductor-uri "KEGGREST" version))
4792 "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
4793 (properties `((upstream-name . "KEGGREST")))
4794 (build-system r-build-system)
4796 (list r-biostrings r-httr r-png))
4799 (home-page "https://bioconductor.org/packages/KEGGREST")
4800 (synopsis "Client-side REST access to KEGG")
4802 "This package provides a package that provides a client interface to the
4803 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
4804 (license license:artistic2.0)))
4806 (define-public r-lfa
4813 (uri (bioconductor-uri "lfa" version))
4815 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
4816 (properties `((upstream-name . "lfa")))
4817 (build-system r-build-system)
4818 (propagated-inputs (list r-corpcor))
4819 (native-inputs (list r-knitr))
4820 (home-page "https://github.com/StoreyLab/lfa")
4821 (synopsis "Logistic Factor Analysis for categorical data")
4823 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
4824 Binomial data via estimation of latent structure in the natural parameter.")
4825 (license license:gpl3)))
4827 (define-public r-limma
4833 (uri (bioconductor-uri "limma" version))
4836 "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"))))
4837 (build-system r-build-system)
4838 (home-page "http://bioinf.wehi.edu.au/limma")
4839 (synopsis "Package for linear models for microarray and RNA-seq data")
4840 (description "This package can be used for the analysis of gene expression
4841 studies, especially the use of linear models for analysing designed experiments
4842 and the assessment of differential expression. The analysis methods apply to
4843 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
4844 (license license:gpl2+)))
4846 (define-public r-made4
4852 (uri (bioconductor-uri "made4" version))
4855 "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
4856 (properties `((upstream-name . "made4")))
4857 (build-system r-build-system)
4864 r-summarizedexperiment))
4865 (native-inputs (list r-knitr))
4866 (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
4867 (synopsis "Multivariate analysis of microarray data using ADE4")
4869 "This is a package for multivariate data analysis and graphical display
4870 of microarray data. Functions are included for supervised dimension
4871 reduction (between group analysis) and joint dimension reduction of two
4872 datasets (coinertia analysis).")
4873 (license license:artistic2.0)))
4875 (define-public r-methylkit
4877 (name "r-methylkit")
4881 (uri (bioconductor-uri "methylKit" version))
4884 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
4885 (properties `((upstream-name . "methylKit")))
4886 (build-system r-build-system)
4908 (list r-knitr)) ; for vignettes
4909 (home-page "https://github.com/al2na/methylKit")
4911 "DNA methylation analysis from high-throughput bisulfite sequencing results")
4913 "MethylKit is an R package for DNA methylation analysis and annotation
4914 from high-throughput bisulfite sequencing. The package is designed to deal
4915 with sequencing data from @dfn{Reduced representation bisulfite
4916 sequencing} (RRBS) and its variants, but also target-capture methods and whole
4917 genome bisulfite sequencing. It also has functions to analyze base-pair
4918 resolution 5hmC data from experimental protocols such as oxBS-Seq and
4920 (license license:artistic2.0)))
4922 (define-public r-motifrg
4929 (uri (bioconductor-uri "motifRG" version))
4932 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
4933 (properties `((upstream-name . "motifRG")))
4934 (build-system r-build-system)
4938 r-bsgenome-hsapiens-ucsc-hg19
4942 (home-page "https://bioconductor.org/packages/motifRG")
4943 (synopsis "Discover motifs in high throughput sequencing data")
4945 "This package provides tools for discriminative motif discovery in high
4946 throughput genetic sequencing data sets using regression methods.")
4947 (license license:artistic2.0)))
4949 (define-public r-muscat
4956 (uri (bioconductor-uri "muscat" version))
4959 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
4960 (properties `((upstream-name . "muscat")))
4961 (build-system r-build-system)
4963 (list r-biocparallel
4984 r-singlecellexperiment
4985 r-summarizedexperiment
4988 (native-inputs (list r-knitr))
4989 (home-page "https://github.com/HelenaLC/muscat")
4990 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
4992 "This package @code{muscat} provides various methods and visualization tools
4993 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
4994 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
4995 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
4996 platform that mimics both single and multi-sample scRNA-seq data.")
4997 (license license:gpl3)))
4999 (define-public r-mutationalpatterns
5001 (name "r-mutationalpatterns")
5006 (uri (bioconductor-uri "MutationalPatterns" version))
5009 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
5010 (build-system r-build-system)
5014 (list r-biocgenerics
5017 ;; These two packages are suggested packages
5018 r-bsgenome-hsapiens-1000genomes-hs37d5
5019 r-bsgenome-hsapiens-ucsc-hg19
5037 r-variantannotation))
5038 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
5039 (synopsis "Extract and visualize mutational patterns in genomic data")
5040 (description "This package provides an extensive toolset for the
5041 characterization and visualization of a wide range of mutational patterns
5042 in SNV base substitution data.")
5043 (license license:expat)))
5045 (define-public r-msnbase
5052 (uri (bioconductor-uri "MSnbase" version))
5055 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
5056 (properties `((upstream-name . "MSnbase")))
5057 (build-system r-build-system)
5083 (home-page "https://github.com/lgatto/MSnbase")
5084 (synopsis "Base functions and classes for MS-based proteomics")
5086 "This package provides basic plotting, data manipulation and processing
5087 of mass spectrometry based proteomics data.")
5088 (license license:artistic2.0)))
5090 (define-public r-msnid
5097 (uri (bioconductor-uri "MSnID" version))
5100 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
5101 (properties `((upstream-name . "MSnID")))
5102 (build-system r-build-system)
5105 (modify-phases %standard-phases
5106 (add-after 'unpack 'set-HOME
5107 (lambda _ (setenv "HOME" "/tmp"))))))
5109 (list r-annotationdbi
5135 (home-page "https://bioconductor.org/packages/MSnID")
5136 (synopsis "Utilities for LC-MSn proteomics identifications")
5138 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
5139 from mzIdentML (leveraging the mzID package) or text files. After collating
5140 the search results from multiple datasets it assesses their identification
5141 quality and optimize filtering criteria to achieve the maximum number of
5142 identifications while not exceeding a specified false discovery rate. It also
5143 contains a number of utilities to explore the MS/MS results and assess missed
5144 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
5145 (license license:artistic2.0)))
5147 (define-public r-mzid
5154 (uri (bioconductor-uri "mzID" version))
5157 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
5158 (properties `((upstream-name . "mzID")))
5159 (build-system r-build-system)
5169 (home-page "https://bioconductor.org/packages/mzID")
5170 (synopsis "Parser for mzIdentML files")
5172 "This package provides a parser for mzIdentML files implemented using the
5173 XML package. The parser tries to be general and able to handle all types of
5174 mzIdentML files with the drawback of having less pretty output than a vendor
5176 (license license:gpl2+)))
5178 (define-public r-mzr
5185 (uri (bioconductor-uri "mzR" version))
5188 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
5189 (modules '((guix build utils)))
5191 '(delete-file-recursively "src/boost"))))
5192 (properties `((upstream-name . "mzR")))
5193 (build-system r-build-system)
5196 (modify-phases %standard-phases
5197 (add-after 'unpack 'use-system-boost
5199 (substitute* "src/Makevars"
5200 (("\\./boost/libs.*") "")
5201 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
5202 (("\\ARCH_OBJS=" line)
5204 "\nBOOST_LIBS=-lboost_system -lboost_regex \
5205 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
5207 (list boost ; use this instead of the bundled boost sources
5218 (home-page "https://github.com/sneumann/mzR/")
5219 (synopsis "Parser for mass spectrometry data files")
5221 "The mzR package provides a unified API to the common file formats and
5222 parsers available for mass spectrometry data. It comes with a wrapper for the
5223 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
5224 The package contains the original code written by the ISB, and a subset of the
5225 proteowizard library for mzML and mzIdentML. The netCDF reading code has
5226 previously been used in XCMS.")
5227 (license license:artistic2.0)))
5229 (define-public r-organism-dplyr
5231 (name "r-organism-dplyr")
5236 (uri (bioconductor-uri "Organism.dplyr" version))
5239 "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
5240 (properties `((upstream-name . "Organism.dplyr")))
5241 (build-system r-build-system)
5243 (list r-annotationdbi
5257 (native-inputs (list r-knitr))
5258 (home-page "https://bioconductor.org/packages/Organism.dplyr")
5259 (synopsis "Dplyr-based access to Bioconductor annotation resources")
5261 "This package provides an alternative interface to Bioconductor @code{
5262 annotation} resources, in particular the gene identifier mapping functionality
5263 of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
5264 functionality of the @code{TxDb} packages (e.g.,
5265 @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
5266 (license license:artistic2.0)))
5268 (define-public r-organismdbi
5270 (name "r-organismdbi")
5275 (uri (bioconductor-uri "OrganismDbi" version))
5278 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
5279 (properties `((upstream-name . "OrganismDbi")))
5280 (build-system r-build-system)
5282 (list r-annotationdbi
5293 (home-page "https://bioconductor.org/packages/OrganismDbi")
5294 (synopsis "Software to enable the smooth interfacing of database packages")
5295 (description "The package enables a simple unified interface to several
5296 annotation packages each of which has its own schema by taking advantage of
5297 the fact that each of these packages implements a select methods.")
5298 (license license:artistic2.0)))
5300 (define-public r-pcaexplorer
5302 (name "r-pcaexplorer")
5307 (uri (bioconductor-uri "pcaExplorer" version))
5310 "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
5311 (properties `((upstream-name . "pcaExplorer")))
5312 (build-system r-build-system)
5314 (list r-annotationdbi
5340 r-summarizedexperiment
5344 (native-inputs (list r-knitr))
5345 (home-page "https://github.com/federicomarini/pcaExplorer")
5347 "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
5349 "This package provides functionality for interactive visualization of RNA-seq
5350 datasets based on Principal Components Analysis. The methods provided allow for
5351 quick information extraction and effective data exploration. A Shiny
5352 application encapsulates the whole analysis.")
5353 (license license:expat)))
5355 (define-public r-pcamethods
5357 (name "r-pcamethods")
5362 (uri (bioconductor-uri "pcaMethods" version))
5365 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
5366 (properties `((upstream-name . "pcaMethods")))
5367 (build-system r-build-system)
5369 (list r-biobase r-biocgenerics r-mass r-rcpp))
5370 (home-page "https://github.com/hredestig/pcamethods")
5371 (synopsis "Collection of PCA methods")
5373 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
5374 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
5375 for missing value estimation is included for comparison. BPCA, PPCA and
5376 NipalsPCA may be used to perform PCA on incomplete data as well as for
5377 accurate missing value estimation. A set of methods for printing and plotting
5378 the results is also provided. All PCA methods make use of the same data
5379 structure (pcaRes) to provide a common interface to the PCA results.")
5380 (license license:gpl3+)))
5382 ;; This is a CRAN package, but it depends on a Bioconductor package:
5383 ;; r-aroma-light, r-dnacopy..
5384 (define-public r-pscbs
5391 (uri (cran-uri "PSCBS" version))
5393 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
5394 (properties `((upstream-name . "PSCBS")))
5395 (build-system r-build-system)
5398 (modify-phases %standard-phases
5399 (add-before 'install 'change-home-dir
5401 ;; Change from /homeless-shelter to /tmp for write permission.
5402 (setenv "HOME" "/tmp"))))))
5414 (list r-r-rsp ;used to build vignettes
5416 (home-page "https://github.com/HenrikBengtsson/PSCBS")
5417 (synopsis "Analysis of parent-specific DNA copy numbers")
5419 "This is a package for segmentation of allele-specific DNA copy number
5420 data and detection of regions with abnormal copy number within each parental
5421 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
5422 (license license:gpl2+)))
5424 (define-public r-protgenerics
5426 (name "r-protgenerics")
5431 (uri (bioconductor-uri "ProtGenerics" version))
5434 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
5435 (properties `((upstream-name . "ProtGenerics")))
5436 (build-system r-build-system)
5437 (home-page "https://github.com/lgatto/ProtGenerics")
5438 (synopsis "S4 generic functions for proteomics infrastructure")
5440 "This package provides S4 generic functions needed by Bioconductor
5441 proteomics packages.")
5442 (license license:artistic2.0)))
5444 (define-public r-rbgl
5451 (uri (bioconductor-uri "RBGL" version))
5454 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
5455 (properties `((upstream-name . "RBGL")))
5456 (build-system r-build-system)
5458 (list r-bh r-graph))
5459 (home-page "https://www.bioconductor.org/packages/RBGL")
5460 (synopsis "Interface to the Boost graph library")
5462 "This package provides a fairly extensive and comprehensive interface to
5463 the graph algorithms contained in the Boost library.")
5464 (license license:artistic2.0)))
5466 (define-public r-rcas
5472 (uri (bioconductor-uri "RCAS" version))
5475 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
5476 (properties `((upstream-name . "RCAS")))
5477 (build-system r-build-system)
5479 (list r-biocgenerics
5482 r-bsgenome-hsapiens-ucsc-hg19
5508 (synopsis "RNA-centric annotation system")
5510 "RCAS aims to be a standalone RNA-centric annotation system that provides
5511 intuitive reports and publication-ready graphics. This package provides the R
5512 library implementing most of the pipeline's features.")
5513 (home-page "https://github.com/BIMSBbioinfo/RCAS")
5514 (license license:artistic2.0)))
5516 (define-public r-regioner
5523 (uri (bioconductor-uri "regioneR" version))
5526 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
5527 (properties `((upstream-name . "regioneR")))
5528 (build-system r-build-system)
5540 (home-page "https://bioconductor.org/packages/regioneR/")
5541 (synopsis "Association analysis of genomic regions")
5542 (description "This package offers a statistical framework based on
5543 customizable permutation tests to assess the association between genomic
5544 region sets and other genomic features.")
5545 (license license:artistic2.0)))
5547 (define-public r-reportingtools
5549 (name "r-reportingtools")
5554 (uri (bioconductor-uri "ReportingTools" version))
5557 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
5559 `((upstream-name . "ReportingTools")))
5560 (build-system r-build-system)
5583 (home-page "https://bioconductor.org/packages/ReportingTools/")
5584 (synopsis "Tools for making reports in various formats")
5586 "The ReportingTools package enables users to easily display reports of
5587 analysis results generated from sources such as microarray and sequencing
5588 data. The package allows users to create HTML pages that may be viewed on a
5589 web browser, or in other formats. Users can generate tables with sortable and
5590 filterable columns, make and display plots, and link table entries to other
5591 data sources such as NCBI or larger plots within the HTML page. Using the
5592 package, users can also produce a table of contents page to link various
5593 reports together for a particular project that can be viewed in a web
5595 (license license:artistic2.0)))
5597 (define-public r-rhdf5
5603 (uri (bioconductor-uri "rhdf5" version))
5606 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
5607 (build-system r-build-system)
5609 (list r-rhdf5filters r-rhdf5lib))
5612 (home-page "https://bioconductor.org/packages/rhdf5")
5613 (synopsis "HDF5 interface to R")
5615 "This R/Bioconductor package provides an interface between HDF5 and R.
5616 HDF5's main features are the ability to store and access very large and/or
5617 complex datasets and a wide variety of metadata on mass storage (disk) through
5618 a completely portable file format. The rhdf5 package is thus suited for the
5619 exchange of large and/or complex datasets between R and other software
5620 package, and for letting R applications work on datasets that are larger than
5621 the available RAM.")
5622 (license license:artistic2.0)))
5624 (define-public r-rhdf5filters
5626 (name "r-rhdf5filters")
5631 (uri (bioconductor-uri "rhdf5filters" version))
5634 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
5635 (properties `((upstream-name . "rhdf5filters")))
5636 (build-system r-build-system)
5643 (home-page "https://github.com/grimbough/rhdf5filters")
5644 (synopsis "HDF5 compression filters")
5646 "This package provides a collection of compression filters for use with
5648 (license license:bsd-2)))
5650 (define-public r-rsamtools
5652 (name "r-rsamtools")
5656 (uri (bioconductor-uri "Rsamtools" version))
5659 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
5661 `((upstream-name . "Rsamtools")))
5662 (build-system r-build-system)
5665 (modify-phases %standard-phases
5666 (add-after 'unpack 'use-system-zlib
5668 (substitute* "DESCRIPTION"
5669 (("zlibbioc, ") ""))
5670 (substitute* "NAMESPACE"
5671 (("import\\(zlibbioc\\)") "")))))))
5673 (list r-biocgenerics
5683 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
5684 (synopsis "Interface to samtools, bcftools, and tabix")
5686 "This package provides an interface to the @code{samtools},
5687 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
5688 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
5689 tab-delimited (tabix) files.")
5690 (license license:expat)))
5692 ;; This is a CRAN package, but it depends on a Bioconductor package:
5694 (define-public r-restfulr
5701 (uri (cran-uri "restfulr" version))
5704 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
5705 (properties `((upstream-name . "restfulr")))
5706 (build-system r-build-system)
5708 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
5709 (home-page "https://cran.r-project.org/package=restfulr")
5710 (synopsis "R interface to RESTful web services")
5712 "This package models a RESTful service as if it were a nested R list.")
5713 (license license:artistic2.0)))
5715 (define-public r-rtracklayer
5717 (name "r-rtracklayer")
5721 (uri (bioconductor-uri "rtracklayer" version))
5724 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
5725 (build-system r-build-system)
5728 (modify-phases %standard-phases
5729 (add-after 'unpack 'use-system-zlib
5731 (substitute* "DESCRIPTION"
5732 ((" zlibbioc,") ""))
5733 (substitute* "NAMESPACE"
5734 (("import\\(zlibbioc\\)") "")))))))
5740 (list r-biocgenerics
5754 (home-page "https://bioconductor.org/packages/rtracklayer")
5755 (synopsis "R interface to genome browsers and their annotation tracks")
5757 "rtracklayer is an extensible framework for interacting with multiple
5758 genome browsers (currently UCSC built-in) and manipulating annotation tracks
5759 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
5760 built-in). The user may export/import tracks to/from the supported browsers,
5761 as well as query and modify the browser state, such as the current viewport.")
5762 (license license:artistic2.0)))
5764 ;; This is a CRAN package, but it depends on a Bioconductor package.
5765 (define-public r-samr
5772 (uri (cran-uri "samr" version))
5775 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
5776 (properties `((upstream-name . "samr")))
5777 (build-system r-build-system)
5785 (native-inputs (list gfortran))
5786 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
5787 (synopsis "Significance analysis of Microarrays")
5789 "This is a package for significance analysis of Microarrays for
5790 differential expression analysis, RNAseq data and related problems.")
5791 ;; Any version of the LGPL
5792 (license license:lgpl3+)))
5794 (define-public r-scannotatr
5796 (name "r-scannotatr")
5801 (uri (bioconductor-uri "scAnnotatR" version))
5803 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
5804 (properties `((upstream-name . "scAnnotatR")))
5805 (build-system r-build-system)
5807 (list r-annotationhub
5818 r-singlecellexperiment
5819 r-summarizedexperiment))
5820 (native-inputs (list r-knitr))
5821 (home-page "https://github.com/grisslab/scAnnotatR")
5822 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
5824 "This package comprises a set of pretrained machine learning models to
5825 predict basic immune cell types. This enables to quickly get a first
5826 annotation of the cell types present in the dataset without requiring prior
5827 knowledge. The package also lets you train using own models to predict new
5828 cell types based on specific research needs.")
5829 (license license:expat)))
5831 (define-public r-scdblfinder
5833 (name "r-scdblfinder")
5838 (uri (bioconductor-uri "scDblFinder" version))
5840 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
5841 (properties `((upstream-name . "scDblFinder")))
5842 (build-system r-build-system)
5844 (list r-biocgenerics
5862 r-singlecellexperiment
5863 r-summarizedexperiment
5865 (native-inputs (list r-knitr))
5866 (home-page "https://github.com/plger/scDblFinder")
5867 (synopsis "Detect multiplets in single-cell RNA sequencing data")
5869 "The scDblFinder package gathers various methods for the detection and
5870 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
5871 multiple cells captured within the same droplet or reaction volume). It
5872 includes methods formerly found in the scran package, and the new fast and
5873 comprehensive scDblFinder method.")
5874 (license license:gpl3)))
5876 (define-public r-scmap
5883 (uri (bioconductor-uri "scmap" version))
5885 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
5886 (properties `((upstream-name . "scmap")))
5887 (build-system r-build-system)
5902 r-singlecellexperiment
5903 r-summarizedexperiment))
5904 (native-inputs (list r-knitr))
5905 (home-page "https://github.com/hemberg-lab/scmap")
5906 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
5908 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
5909 composition of complex tissues since the technology allows researchers to
5910 define cell-types using unsupervised clustering of the transcriptome.
5911 However, due to differences in experimental methods and computational
5912 analyses, it is often challenging to directly compare the cells identified in
5913 two different experiments. @code{scmap} is a method for projecting cells from
5914 a scRNA-seq experiment onto the cell-types or individual cells identified in a
5915 different experiment.")
5916 (license license:gpl3)))
5918 (define-public r-scry
5924 (uri (bioconductor-uri "scry" version))
5927 "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
5928 (properties `((upstream-name . "scry")))
5929 (build-system r-build-system)
5931 (list r-biocsingular
5936 r-singlecellexperiment
5937 r-summarizedexperiment))
5938 (native-inputs (list r-knitr))
5939 (home-page "https://bioconductor.org/packages/scry.html")
5940 (synopsis "Small-count analysis methods for high-dimensional data")
5942 "Many modern biological datasets consist of small counts that are not
5943 well fit by standard linear-Gaussian methods such as principal component
5944 analysis. This package provides implementations of count-based feature
5945 selection and dimension reduction algorithms. These methods can be used to
5946 facilitate unsupervised analysis of any high-dimensional data such as
5947 single-cell RNA-seq.")
5948 (license license:artistic2.0)))
5950 (define-public r-seqlogo
5957 (uri (bioconductor-uri "seqLogo" version))
5960 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
5961 (properties `((upstream-name . "seqLogo")))
5962 (build-system r-build-system)
5965 (home-page "https://bioconductor.org/packages/seqLogo")
5966 (synopsis "Sequence logos for DNA sequence alignments")
5968 "seqLogo takes the position weight matrix of a DNA sequence motif and
5969 plots the corresponding sequence logo as introduced by Schneider and
5971 (license license:lgpl2.0+)))
5973 (define-public r-seqpattern
5975 (name "r-seqpattern")
5979 (uri (bioconductor-uri "seqPattern" version))
5982 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
5984 `((upstream-name . "seqPattern")))
5985 (build-system r-build-system)
5987 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
5988 (home-page "https://bioconductor.org/packages/seqPattern")
5989 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
5991 "This package provides tools to visualize oligonucleotide patterns and
5992 sequence motif occurrences across a large set of sequences centred at a common
5993 reference point and sorted by a user defined feature.")
5994 (license license:gpl3+)))
5996 (define-public r-shortread
5998 (name "r-shortread")
6003 (uri (bioconductor-uri "ShortRead" version))
6006 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
6007 (properties `((upstream-name . "ShortRead")))
6008 (build-system r-build-system)
6028 (home-page "https://bioconductor.org/packages/ShortRead")
6029 (synopsis "FASTQ input and manipulation tools")
6031 "This package implements sampling, iteration, and input of FASTQ files.
6032 It includes functions for filtering and trimming reads, and for generating a
6033 quality assessment report. Data are represented as
6034 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6035 purposes. The package also contains legacy support for early single-end,
6036 ungapped alignment formats.")
6037 (license license:artistic2.0)))
6039 (define-public r-simplifyenrichment
6041 (name "r-simplifyenrichment")
6046 (uri (bioconductor-uri "simplifyEnrichment" version))
6049 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
6051 `((upstream-name . "simplifyEnrichment")))
6052 (build-system r-build-system)
6054 (list r-annotationdbi
6071 (native-inputs (list r-knitr))
6072 (home-page "https://github.com/jokergoo/simplifyEnrichment")
6073 (synopsis "Simplify functional enrichment results")
6074 (description "This package provides a new clustering algorithm, binary
6075 cut, for clustering similarity matrices of functional terms is implemented in
6076 this package. It also provides functionalities for visualizing, summarizing
6077 and comparing the clusterings.")
6078 (license license:expat)))
6080 (define-public r-transcriptr
6082 (name "r-transcriptr")
6087 (uri (bioconductor-uri "transcriptR" version))
6089 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
6090 (properties `((upstream-name . "transcriptR")))
6091 (build-system r-build-system)
6093 (list r-biocgenerics
6108 (native-inputs (list r-knitr))
6109 (home-page "https://bioconductor.org/packages/transcriptR")
6110 (synopsis "Primary transcripts detection and quantification")
6112 "The differences in the RNA types being sequenced have an impact on the
6113 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
6114 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
6115 broader coverage of both exonic and intronic regions. The presence of
6116 intronic reads in GRO-seq type of data makes it possible to use it to
6117 computationally identify and quantify all de novo continuous regions of
6118 transcription distributed across the genome. This type of data, however, is
6119 more challenging to interpret and less common practice compared to mRNA-seq.
6120 One of the challenges for primary transcript detection concerns the
6121 simultaneous transcription of closely spaced genes, which needs to be properly
6122 divided into individually transcribed units. The R package transcriptR
6123 combines RNA-seq data with ChIP-seq data of histone modifications that mark
6124 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
6125 overcome this challenge. The advantage of this approach over the use of, for
6126 example, gene annotations is that this approach is data driven and therefore
6127 able to deal also with novel and case specific events.")
6128 (license license:gpl3)))
6130 (define-public r-trajectoryutils
6132 (name "r-trajectoryutils")
6137 (uri (bioconductor-uri "TrajectoryUtils" version))
6140 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
6142 `((upstream-name . "TrajectoryUtils")))
6143 (build-system r-build-system)
6145 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
6146 r-summarizedexperiment))
6147 (native-inputs (list r-knitr))
6148 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
6149 (synopsis "Single-cell trajectory analysis utilities")
6151 "This package implements low-level utilities for single-cell trajectory
6152 analysis, primarily intended for re-use inside higher-level packages. It
6153 includes a function to create a cluster-level minimum spanning tree and data
6154 structures to hold pseudotime inference results.")
6155 (license license:gpl3)))
6157 (define-public r-slingshot
6159 (name "r-slingshot")
6163 (uri (bioconductor-uri "slingshot" version))
6166 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
6167 (build-system r-build-system)
6173 r-singlecellexperiment
6174 r-summarizedexperiment
6178 (home-page "https://bioconductor.org/packages/slingshot")
6179 (synopsis "Tools for ordering single-cell sequencing")
6180 (description "This package provides functions for inferring continuous,
6181 branching lineage structures in low-dimensional data. Slingshot was designed
6182 to model developmental trajectories in single-cell RNA sequencing data and
6183 serve as a component in an analysis pipeline after dimensionality reduction
6184 and clustering. It is flexible enough to handle arbitrarily many branching
6185 events and allows for the incorporation of prior knowledge through supervised
6186 graph construction.")
6187 (license license:artistic2.0)))
6189 (define-public r-stager
6196 (uri (bioconductor-uri "stageR" version))
6198 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
6199 (properties `((upstream-name . "stageR")))
6200 (build-system r-build-system)
6201 (propagated-inputs (list r-summarizedexperiment))
6202 (native-inputs (list r-knitr))
6203 (home-page "https://bioconductor.org/packages/stageR")
6204 (synopsis "Stage-wise analysis of high throughput gene expression data")
6206 "The stageR package allows automated stage-wise analysis of
6207 high-throughput gene expression data. The method is published in Genome
6209 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
6210 (license license:gpl3)))
6212 (define-public r-stringdb
6219 (uri (bioconductor-uri "STRINGdb" version))
6221 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
6222 (properties `((upstream-name . "STRINGdb")))
6223 (build-system r-build-system)
6234 (home-page "https://git.bioconductor.org/packages/STRINGdb")
6235 (synopsis "Search tool for the retrieval of interacting proteins database")
6237 "The @code{STRINGdb} package provides an R interface to the STRING
6238 protein-protein interactions database. @url{https://www.string-db.org,
6239 STRING} is a database of known and predicted protein-protein interactions.
6240 The interactions include direct (physical) and indirect (functional)
6241 associations. Each interaction is associated with a combined confidence score
6242 that integrates the various evidences.")
6243 (license license:gpl2)))
6245 (define-public r-structuralvariantannotation
6247 (name "r-structuralvariantannotation")
6252 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
6254 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
6255 (build-system r-build-system)
6269 r-summarizedexperiment
6270 r-variantannotation))
6273 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
6274 (synopsis "R package designed to simplify structural variant analysis")
6276 "This package contains useful helper functions for dealing with structural
6277 variants in VCF format. The packages contains functions for parsing VCFs from
6278 a number of popular callers as well as functions for dealing with breakpoints
6279 involving two separate genomic loci encoded as GRanges objects.")
6280 (license license:gpl3)))
6282 (define-public r-summarizedexperiment
6284 (name "r-summarizedexperiment")
6288 (uri (bioconductor-uri "SummarizedExperiment" version))
6291 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
6293 `((upstream-name . "SummarizedExperiment")))
6294 (build-system r-build-system)
6307 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
6308 (synopsis "Container for representing genomic ranges by sample")
6310 "The SummarizedExperiment container contains one or more assays, each
6311 represented by a matrix-like object of numeric or other mode. The rows
6312 typically represent genomic ranges of interest and the columns represent
6314 (license license:artistic2.0)))
6316 (define-public r-sva
6323 (uri (bioconductor-uri "sva" version))
6326 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
6327 (build-system r-build-system)
6335 (home-page "https://bioconductor.org/packages/sva")
6336 (synopsis "Surrogate variable analysis")
6338 "This package contains functions for removing batch effects and other
6339 unwanted variation in high-throughput experiment. It also contains functions
6340 for identifying and building surrogate variables for high-dimensional data
6341 sets. Surrogate variables are covariates constructed directly from
6342 high-dimensional data like gene expression/RNA sequencing/methylation/brain
6343 imaging data that can be used in subsequent analyses to adjust for unknown,
6344 unmodeled, or latent sources of noise.")
6345 (license license:artistic2.0)))
6347 (define-public r-systempiper
6349 (name "r-systempiper")
6354 (uri (bioconductor-uri "systemPipeR" version))
6357 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
6358 (properties `((upstream-name . "systemPipeR")))
6359 (build-system r-build-system)
6361 (list r-biocgenerics
6372 r-summarizedexperiment
6376 (home-page "https://github.com/tgirke/systemPipeR")
6377 (synopsis "Next generation sequencing workflow and reporting environment")
6379 "This R package provides tools for building and running automated
6380 end-to-end analysis workflows for a wide range of @dfn{next generation
6381 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6382 Important features include a uniform workflow interface across different NGS
6383 applications, automated report generation, and support for running both R and
6384 command-line software, such as NGS aligners or peak/variant callers, on local
6385 computers or compute clusters. Efficient handling of complex sample sets and
6386 experimental designs is facilitated by a consistently implemented sample
6387 annotation infrastructure.")
6388 (license license:artistic2.0)))
6390 (define-public r-topgo
6396 (uri (bioconductor-uri "topGO" version))
6399 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
6401 `((upstream-name . "topGO")))
6402 (build-system r-build-system)
6404 (list r-annotationdbi
6413 (home-page "https://bioconductor.org/packages/topGO")
6414 (synopsis "Enrichment analysis for gene ontology")
6416 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6417 terms while accounting for the topology of the GO graph. Different test
6418 statistics and different methods for eliminating local similarities and
6419 dependencies between GO terms can be implemented and applied.")
6420 ;; Any version of the LGPL applies.
6421 (license license:lgpl2.1+)))
6423 (define-public r-tximport
6429 (uri (bioconductor-uri "tximport" version))
6432 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
6433 (build-system r-build-system)
6436 (home-page "https://bioconductor.org/packages/tximport")
6437 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
6439 "This package provides tools to import transcript-level abundance,
6440 estimated counts and transcript lengths, and to summarize them into matrices
6441 for use with downstream gene-level analysis packages. Average transcript
6442 length, weighted by sample-specific transcript abundance estimates, is
6443 provided as a matrix which can be used as an offset for different expression
6444 of gene-level counts.")
6445 (license license:gpl2+)))
6447 ;; This is a CRAN package, but it depends on a Bioconductor package.
6448 (define-public r-valr
6455 (uri (cran-uri "valr" version))
6458 "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
6459 (build-system r-build-system)
6467 r-rtracklayer ;bioconductor package
6472 (home-page "https://github.com/rnabioco/valr")
6473 (synopsis "Genome interval arithmetic in R")
6475 "This package enables you to read and manipulate genome intervals and
6476 signals. It provides functionality similar to command-line tool suites within
6477 R, enabling interactive analysis and visualization of genome-scale data.")
6478 (license license:expat)))
6480 (define-public r-variantannotation
6482 (name "r-variantannotation")
6486 (uri (bioconductor-uri "VariantAnnotation" version))
6489 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
6491 `((upstream-name . "VariantAnnotation")))
6493 (list r-annotationdbi
6504 r-summarizedexperiment
6511 (build-system r-build-system)
6512 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6513 (synopsis "Package for annotation of genetic variants")
6514 (description "This R package can annotate variants, compute amino acid
6515 coding changes and predict coding outcomes.")
6516 (license license:artistic2.0)))
6518 (define-public r-vsn
6525 (uri (bioconductor-uri "vsn" version))
6528 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
6529 (build-system r-build-system)
6531 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
6533 (list r-knitr)) ; for vignettes
6534 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
6535 (synopsis "Variance stabilization and calibration for microarray data")
6537 "The package implements a method for normalising microarray intensities,
6538 and works for single- and multiple-color arrays. It can also be used for data
6539 from other technologies, as long as they have similar format. The method uses
6540 a robust variant of the maximum-likelihood estimator for an
6541 additive-multiplicative error model and affine calibration. The model
6542 incorporates data calibration step (a.k.a. normalization), a model for the
6543 dependence of the variance on the mean intensity and a variance stabilizing
6544 data transformation. Differences between transformed intensities are
6545 analogous to \"normalized log-ratios\". However, in contrast to the latter,
6546 their variance is independent of the mean, and they are usually more sensitive
6547 and specific in detecting differential transcription.")
6548 (license license:artistic2.0)))
6550 ;; There is no source tarball, so we fetch the code from the Bioconductor git
6552 (define-public r-xcir
6553 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
6557 (version (git-version "1.8.0" revision commit))
6561 (url "https://git.bioconductor.org/packages/XCIR")
6563 (file-name (git-file-name name version))
6566 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
6567 (properties `((upstream-name . "XCIR")))
6568 (build-system r-build-system)
6569 (propagated-inputs (list r-biomart
6577 r-variantannotation))
6578 (native-inputs (list r-knitr))
6579 (home-page "https://github.com/SRenan/XCIR")
6580 (synopsis "Analysis of X chromosome inactivation")
6582 "This package is an R package that offers models and tools for subject
6583 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
6585 (license license:gpl2))))
6587 (define-public r-xina
6594 (uri (bioconductor-uri "XINA" version))
6596 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
6597 (properties `((upstream-name . "XINA")))
6598 (build-system r-build-system)
6607 (native-inputs (list r-knitr))
6608 (home-page "https://git.bioconductor.org/packages/XINA")
6609 (synopsis "Identifying proteins that exhibit similar patterns")
6611 "The aim of @code{XINA} is to determine which proteins exhibit similar
6612 patterns within and across experimental conditions, since proteins with
6613 co-abundance patterns may have common molecular functions. @code{XINA} imports
6614 multiple datasets, tags dataset in silico, and combines the data for subsequent
6615 subgrouping into multiple clusters. The result is a single output depicting
6616 the variation across all conditions. @code{XINA} not only extracts
6617 coabundance profiles within and across experiments, but also incorporates
6618 protein-protein interaction databases and integrative resources such as
6619 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
6620 molecular functions, respectively, and produces intuitive graphical outputs.")
6621 (license license:gpl3)))
6623 (define-public r-xmapbridge
6625 (name "r-xmapbridge")
6630 (uri (bioconductor-uri "xmapbridge" version))
6632 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
6633 (properties `((upstream-name . "xmapbridge")))
6634 (build-system r-build-system)
6635 (home-page "https://git.bioconductor.org/packages/xmapbridge")
6636 (synopsis "Display numeric data in the web based genome browser X:MAP")
6638 "The package @code{xmapbridge} can plot graphs in the X:Map genome
6639 browser. X:Map uses the Google Maps API to provide a scrollable view of the
6640 genome. It supports a number of species, and can be accessed at
6641 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
6642 suitable format. Graph plotting in R is done using calls to the functions
6643 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
6644 similar to those used by the standard plot methods in R. These result in data
6645 being written to a set of files (in a specific directory structure) that
6646 contain the data to be displayed, as well as some additional meta-data
6647 describing each of the graphs.")
6648 (license license:lgpl3)))
6650 (define-public r-xvector
6656 (uri (bioconductor-uri "XVector" version))
6659 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
6661 `((upstream-name . "XVector")))
6662 (build-system r-build-system)
6665 (modify-phases %standard-phases
6666 (add-after 'unpack 'use-system-zlib
6668 (substitute* "DESCRIPTION"
6669 (("zlibbioc, ") ""))
6670 (substitute* "NAMESPACE"
6671 (("import\\(zlibbioc\\)") ""))
6676 (list r-biocgenerics r-iranges r-s4vectors))
6677 (home-page "https://bioconductor.org/packages/XVector")
6678 (synopsis "Representation and manpulation of external sequences")
6680 "This package provides memory efficient S4 classes for storing sequences
6681 \"externally\" (behind an R external pointer, or on disk).")
6682 (license license:artistic2.0)))
6684 (define-public r-zlibbioc
6690 (uri (bioconductor-uri "zlibbioc" version))
6693 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
6695 `((upstream-name . "zlibbioc")))
6696 (build-system r-build-system)
6697 (home-page "https://bioconductor.org/packages/zlibbioc")
6698 (synopsis "Provider for zlib-1.2.5 to R packages")
6699 (description "This package uses the source code of zlib-1.2.5 to create
6700 libraries for systems that do not have these available via other means.")
6701 (license license:artistic2.0)))
6703 (define-public r-zellkonverter
6705 (name "r-zellkonverter")
6710 (uri (bioconductor-uri "zellkonverter" version))
6712 (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"))))
6713 (properties `((upstream-name . "zellkonverter")))
6714 (build-system r-build-system)
6722 r-singlecellexperiment
6723 r-summarizedexperiment))
6724 (native-inputs (list r-knitr))
6725 (home-page "https://github.com/theislab/zellkonverter")
6726 (synopsis "Conversion between AnnData and single-cell experiments objects")
6728 "This package provides methods to convert between Python AnnData objects
6729 and SingleCellExperiment objects. These are primarily intended for use by
6730 downstream Bioconductor packages that wrap Python methods for single-cell data
6731 analysis. It also includes functions to read and write H5AD files used for
6732 saving AnnData objects to disk.")
6733 (license license:expat)))
6735 (define-public r-geneplotter
6737 (name "r-geneplotter")
6742 (uri (bioconductor-uri "geneplotter" version))
6745 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
6746 (build-system r-build-system)
6754 (home-page "https://bioconductor.org/packages/geneplotter")
6755 (synopsis "Graphics functions for genomic data")
6757 "This package provides functions for plotting genomic data.")
6758 (license license:artistic2.0)))
6760 (define-public r-oligoclasses
6762 (name "r-oligoclasses")
6767 (uri (bioconductor-uri "oligoClasses" version))
6770 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
6771 (properties `((upstream-name . "oligoClasses")))
6772 (build-system r-build-system)
6786 r-summarizedexperiment))
6787 (home-page "https://bioconductor.org/packages/oligoClasses/")
6788 (synopsis "Classes for high-throughput arrays")
6790 "This package contains class definitions, validity checks, and
6791 initialization methods for classes used by the @code{oligo} and @code{crlmm}
6793 (license license:gpl2+)))
6795 (define-public r-oligo
6802 (uri (bioconductor-uri "oligo" version))
6805 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
6806 (properties `((upstream-name . "oligo")))
6807 (build-system r-build-system)
6808 (inputs (list zlib))
6823 (home-page "https://bioconductor.org/packages/oligo/")
6824 (synopsis "Preprocessing tools for oligonucleotide arrays")
6826 "This package provides a package to analyze oligonucleotide
6827 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
6828 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
6829 (license license:lgpl2.0+)))
6831 (define-public r-qvalue
6838 (uri (bioconductor-uri "qvalue" version))
6841 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
6842 (build-system r-build-system)
6844 (list r-ggplot2 r-reshape2))
6847 (home-page "https://github.com/StoreyLab/qvalue")
6848 (synopsis "Q-value estimation for false discovery rate control")
6850 "This package takes a list of p-values resulting from the simultaneous
6851 testing of many hypotheses and estimates their q-values and local @dfn{false
6852 discovery rate} (FDR) values. The q-value of a test measures the proportion
6853 of false positives incurred when that particular test is called significant.
6854 The local FDR measures the posterior probability the null hypothesis is true
6855 given the test's p-value. Various plots are automatically generated, allowing
6856 one to make sensible significance cut-offs. The software can be applied to
6857 problems in genomics, brain imaging, astrophysics, and data mining.")
6858 ;; Any version of the LGPL.
6859 (license license:lgpl3+)))
6861 (define r-rcppnumerical
6863 (name "r-rcppnumerical")
6867 (uri (cran-uri "RcppNumerical" version))
6870 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
6871 (properties `((upstream-name . "RcppNumerical")))
6872 (build-system r-build-system)
6874 `(("r-rcpp" ,r-rcpp)
6875 ("r-rcppeigen" ,r-rcppeigen)))
6877 `(("r-knitr" ,r-knitr)))
6878 (home-page "https://github.com/yixuan/RcppNumerical")
6879 (synopsis "Rcpp integration for numerical computing libraries")
6881 "This package provides a collection of libraries for numerical computing
6882 (numerical integration, optimization, etc.) and their integration with
6884 (license license:gpl2+)))
6886 (define-public r-apeglm
6892 (uri (bioconductor-uri "apeglm" version))
6895 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
6896 (properties `((upstream-name . "apeglm")))
6897 (build-system r-build-system)
6904 r-summarizedexperiment))
6905 (native-inputs (list r-knitr))
6906 (home-page "https://bioconductor.org/packages/apeglm")
6907 (synopsis "Approximate posterior estimation for GLM coefficients")
6908 (description "This package provides Bayesian shrinkage estimators for
6909 effect sizes for a variety of GLM models, using approximation of the
6910 posterior for individual coefficients.")
6911 (license license:gpl2)))
6913 (define-public r-greylistchip
6915 (name "r-greylistchip")
6919 (uri (bioconductor-uri "GreyListChIP" version))
6922 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
6923 (properties `((upstream-name . "GreyListChIP")))
6924 (build-system r-build-system)
6933 r-summarizedexperiment))
6934 (home-page "https://bioconductor.org/packages/GreyListChIP")
6935 (synopsis "Greylist artefact regions based on ChIP inputs")
6936 (description "This package identifies regions of ChIP experiments with high
6937 signal in the input, that lead to spurious peaks during peak calling.")
6938 (license license:artistic2.0)))
6940 (define-public r-diffbind
6947 (uri (bioconductor-uri "DiffBind" version))
6950 "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr"))))
6951 (properties `((upstream-name . "DiffBind")))
6952 (build-system r-build-system)
6975 r-summarizedexperiment
6977 (home-page "https://bioconductor.org/packages/DiffBind")
6978 (synopsis "Differential binding analysis of ChIP-Seq peak data")
6980 "This package computes differentially bound sites from multiple
6981 ChIP-seq experiments using affinity (quantitative) data. Also enables
6982 occupancy (overlap) analysis and plotting functions.")
6983 (license license:artistic2.0)))
6985 (define-public r-ripseeker
6987 (name "r-ripseeker")
6992 (uri (bioconductor-uri "RIPSeeker" version))
6995 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
6996 (properties `((upstream-name . "RIPSeeker")))
6997 (build-system r-build-system)
7002 r-summarizedexperiment
7006 (home-page "https://bioconductor.org/packages/RIPSeeker")
7008 "Identifying protein-associated transcripts from RIP-seq experiments")
7010 "This package infers and discriminates RIP peaks from RIP-seq alignments
7011 using two-state HMM with negative binomial emission probability. While
7012 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
7013 a suite of bioinformatics tools integrated within this self-contained software
7014 package comprehensively addressing issues ranging from post-alignments
7015 processing to visualization and annotation.")
7016 (license license:gpl2)))
7018 (define-public r-mbkmeans
7024 (uri (bioconductor-uri "mbkmeans" version))
7027 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
7028 (build-system r-build-system)
7042 r-singlecellexperiment
7043 r-summarizedexperiment))
7044 (home-page "https://bioconductor.org/packages/mbkmeans")
7045 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
7046 (description "This package implements the mini-batch k-means algorithm for
7047 large datasets, including support for on-disk data representation.")
7048 (license license:expat)))
7050 (define-public r-multtest
7057 (uri (bioconductor-uri "multtest" version))
7060 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
7061 (build-system r-build-system)
7063 (list r-survival r-biocgenerics r-biobase r-mass))
7064 (home-page "https://bioconductor.org/packages/multtest")
7065 (synopsis "Resampling-based multiple hypothesis testing")
7067 "This package can do non-parametric bootstrap and permutation
7068 resampling-based multiple testing procedures (including empirical Bayes
7069 methods) for controlling the family-wise error rate (FWER), generalized
7070 family-wise error rate (gFWER), tail probability of the proportion of
7071 false positives (TPPFP), and false discovery rate (FDR). Several choices
7072 of bootstrap-based null distribution are implemented (centered, centered
7073 and scaled, quantile-transformed). Single-step and step-wise methods are
7074 available. Tests based on a variety of T- and F-statistics (including
7075 T-statistics based on regression parameters from linear and survival models
7076 as well as those based on correlation parameters) are included. When probing
7077 hypotheses with T-statistics, users may also select a potentially faster null
7078 distribution which is multivariate normal with mean zero and variance
7079 covariance matrix derived from the vector influence function. Results are
7080 reported in terms of adjusted P-values, confidence regions and test statistic
7081 cutoffs. The procedures are directly applicable to identifying differentially
7082 expressed genes in DNA microarray experiments.")
7083 (license license:lgpl3)))
7085 (define-public r-graph
7091 (uri (bioconductor-uri "graph" version))
7094 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
7095 (build-system r-build-system)
7097 (list r-biocgenerics))
7098 (home-page "https://bioconductor.org/packages/graph")
7099 (synopsis "Handle graph data structures in R")
7101 "This package implements some simple graph handling capabilities for R.")
7102 (license license:artistic2.0)))
7104 ;; This is a CRAN package, but it depends on a Bioconductor package.
7105 (define-public r-ggm
7112 (uri (cran-uri "ggm" version))
7115 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
7116 (properties `((upstream-name . "ggm")))
7117 (build-system r-build-system)
7119 (list r-graph r-igraph))
7120 (home-page "https://cran.r-project.org/package=ggm")
7121 (synopsis "Functions for graphical Markov models")
7123 "This package provides functions and datasets for maximum likelihood
7124 fitting of some classes of graphical Markov models.")
7125 (license license:gpl2+)))
7127 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
7128 (define-public r-perfmeas
7135 (uri (cran-uri "PerfMeas" version))
7138 "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
7139 (properties `((upstream-name . "PerfMeas")))
7140 (build-system r-build-system)
7142 (list r-graph r-limma r-rbgl))
7143 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
7144 (synopsis "Performance measures for ranking and classification tasks")
7146 "This package implements different performance measures for
7147 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
7148 a given recall, F-score for single and multiple classes are available.")
7149 (license license:gpl2+)))
7151 ;; This is a CRAN package, but it depends on a Bioconductor package.
7152 (define-public r-codedepends
7154 (name "r-codedepends")
7159 (uri (cran-uri "CodeDepends" version))
7162 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
7163 (properties `((upstream-name . "CodeDepends")))
7164 (build-system r-build-system)
7166 (list r-codetools r-graph r-xml))
7167 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
7168 (synopsis "Analysis of R code for reproducible research and code comprehension")
7170 "This package provides tools for analyzing R expressions or blocks of
7171 code and determining the dependencies between them. It focuses on R scripts,
7172 but can be used on the bodies of functions. There are many facilities
7173 including the ability to summarize or get a high-level view of code,
7174 determining dependencies between variables, code improvement suggestions.")
7175 ;; Any version of the GPL
7176 (license (list license:gpl2+ license:gpl3+))))
7178 (define-public r-chippeakanno
7180 (name "r-chippeakanno")
7185 (uri (bioconductor-uri "ChIPpeakAnno" version))
7188 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
7189 (properties `((upstream-name . "ChIPpeakAnno")))
7190 (build-system r-build-system)
7192 (list r-annotationdbi
7215 r-summarizedexperiment
7219 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
7220 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
7222 "The package includes functions to retrieve the sequences around the peak,
7223 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
7224 custom features such as most conserved elements and other transcription factor
7225 binding sites supplied by users. Starting 2.0.5, new functions have been added
7226 for finding the peaks with bi-directional promoters with summary statistics
7227 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
7228 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
7229 enrichedGO (addGeneIDs).")
7230 (license license:gpl2+)))
7232 (define-public r-matrixgenerics
7234 (name "r-matrixgenerics")
7238 (uri (bioconductor-uri "MatrixGenerics" version))
7241 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
7243 `((upstream-name . "MatrixGenerics")))
7244 (build-system r-build-system)
7246 (list r-matrixstats))
7247 (home-page "https://bioconductor.org/packages/MatrixGenerics")
7248 (synopsis "S4 generic summary statistic functions for matrix-like objects")
7250 "This package provides S4 generic functions modeled after the
7251 @code{matrixStats} API for alternative matrix implementations. Packages with
7252 alternative matrix implementation can depend on this package and implement the
7253 generic functions that are defined here for a useful set of row and column
7254 summary statistics. Other package developers can import this package and
7255 handle a different matrix implementations without worrying about
7256 incompatibilities.")
7257 (license license:artistic2.0)))
7259 (define-public r-marray
7265 (uri (bioconductor-uri "marray" version))
7267 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
7268 (build-system r-build-system)
7271 (home-page "https://bioconductor.org/packages/marray")
7272 (synopsis "Exploratory analysis for two-color spotted microarray data")
7273 (description "This package contains class definitions for two-color spotted
7274 microarray data. It also includes functions for data input, diagnostic plots,
7275 normalization and quality checking.")
7276 (license license:lgpl2.0+)))
7278 (define-public r-cghbase
7284 (uri (bioconductor-uri "CGHbase" version))
7286 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
7287 (properties `((upstream-name . "CGHbase")))
7288 (build-system r-build-system)
7290 (list r-biobase r-marray))
7291 (home-page "https://bioconductor.org/packages/CGHbase")
7292 (synopsis "Base functions and classes for arrayCGH data analysis")
7293 (description "This package contains functions and classes that are needed by
7294 the @code{arrayCGH} packages.")
7295 (license license:gpl2+)))
7297 (define-public r-cghcall
7303 (uri (bioconductor-uri "CGHcall" version))
7305 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
7306 (properties `((upstream-name . "CGHcall")))
7307 (build-system r-build-system)
7309 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
7310 (home-page "https://bioconductor.org/packages/CGHcall")
7311 (synopsis "Base functions and classes for arrayCGH data analysis")
7312 (description "This package contains functions and classes that are needed by
7313 @code{arrayCGH} packages.")
7314 (license license:gpl2+)))
7316 (define-public r-qdnaseq
7322 (uri (bioconductor-uri "QDNAseq" version))
7324 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
7325 (properties `((upstream-name . "QDNAseq")))
7326 (build-system r-build-system)
7338 (home-page "https://bioconductor.org/packages/QDNAseq")
7339 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
7340 (description "The genome is divided into non-overlapping fixed-sized bins,
7341 number of sequence reads in each counted, adjusted with a simultaneous
7342 two-dimensional loess correction for sequence mappability and GC content, and
7343 filtered to remove spurious regions in the genome. Downstream steps of
7344 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
7346 (license license:gpl2+)))
7348 (define-public r-bayseq
7355 (uri (bioconductor-uri "baySeq" version))
7358 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
7359 (properties `((upstream-name . "baySeq")))
7360 (build-system r-build-system)
7362 (list r-abind r-edger r-genomicranges))
7363 (home-page "https://bioconductor.org/packages/baySeq/")
7364 (synopsis "Bayesian analysis of differential expression patterns in count data")
7366 "This package identifies differential expression in high-throughput count
7367 data, such as that derived from next-generation sequencing machines,
7368 calculating estimated posterior likelihoods of differential expression (or
7369 more complex hypotheses) via empirical Bayesian methods.")
7370 (license license:gpl3)))
7372 (define-public r-chipcomp
7379 (uri (bioconductor-uri "ChIPComp" version))
7382 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
7383 (properties `((upstream-name . "ChIPComp")))
7384 (build-system r-build-system)
7386 (list r-biocgenerics
7387 r-bsgenome-hsapiens-ucsc-hg19
7388 r-bsgenome-mmusculus-ucsc-mm9
7396 (home-page "https://bioconductor.org/packages/ChIPComp")
7397 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
7399 "ChIPComp implements a statistical method for quantitative comparison of
7400 multiple ChIP-seq datasets. It detects differentially bound sharp binding
7401 sites across multiple conditions considering matching control in ChIP-seq
7403 ;; Any version of the GPL.
7404 (license license:gpl3+)))
7406 (define-public r-riboprofiling
7408 (name "r-riboprofiling")
7413 (uri (bioconductor-uri "RiboProfiling" version))
7416 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
7417 (properties `((upstream-name . "RiboProfiling")))
7418 (build-system r-build-system)
7420 (list r-biocgenerics
7438 (home-page "https://bioconductor.org/packages/RiboProfiling/")
7439 (synopsis "Ribosome profiling data analysis")
7440 (description "Starting with a BAM file, this package provides the
7441 necessary functions for quality assessment, read start position recalibration,
7442 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
7443 of count data: pairs, log fold-change, codon frequency and coverage
7444 assessment, principal component analysis on codon coverage.")
7445 (license license:gpl3)))
7447 (define-public r-riboseqr
7454 (uri (bioconductor-uri "riboSeqR" version))
7457 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
7458 (properties `((upstream-name . "riboSeqR")))
7459 (build-system r-build-system)
7468 (home-page "https://bioconductor.org/packages/riboSeqR/")
7469 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
7471 "This package provides plotting functions, frameshift detection and
7472 parsing of genetic sequencing data from ribosome profiling experiments.")
7473 (license license:gpl3)))
7475 (define-public r-interactionset
7477 (name "r-interactionset")
7482 (uri (bioconductor-uri "InteractionSet" version))
7485 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
7487 `((upstream-name . "InteractionSet")))
7488 (build-system r-build-system)
7490 (list r-biocgenerics
7497 r-summarizedexperiment))
7500 (home-page "https://bioconductor.org/packages/InteractionSet")
7501 (synopsis "Base classes for storing genomic interaction data")
7503 "This package provides the @code{GInteractions},
7504 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
7505 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
7507 (license license:gpl3)))
7509 (define-public r-genomicinteractions
7511 (name "r-genomicinteractions")
7516 (uri (bioconductor-uri "GenomicInteractions" version))
7519 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
7521 `((upstream-name . "GenomicInteractions")))
7522 (build-system r-build-system)
7542 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
7543 (synopsis "R package for handling genomic interaction data")
7545 "This R package provides tools for handling genomic interaction data,
7546 such as ChIA-PET/Hi-C, annotating genomic features with interaction
7547 information and producing various plots and statistics.")
7548 (license license:gpl3)))
7550 (define-public r-ctc
7557 (uri (bioconductor-uri "ctc" version))
7560 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
7561 (build-system r-build-system)
7562 (propagated-inputs (list r-amap))
7563 (home-page "https://bioconductor.org/packages/ctc/")
7564 (synopsis "Cluster and tree conversion")
7566 "This package provides tools for exporting and importing classification
7567 trees and clusters to other programs.")
7568 (license license:gpl2)))
7570 (define-public r-goseq
7577 (uri (bioconductor-uri "goseq" version))
7580 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
7581 (build-system r-build-system)
7583 (list r-annotationdbi
7589 (home-page "https://bioconductor.org/packages/goseq/")
7590 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
7592 "This package provides tools to detect Gene Ontology and/or other user
7593 defined categories which are over/under represented in RNA-seq data.")
7594 (license license:lgpl2.0+)))
7596 (define-public r-glimma
7603 (uri (bioconductor-uri "Glimma" version))
7606 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
7607 (properties `((upstream-name . "Glimma")))
7608 (build-system r-build-system)
7616 r-summarizedexperiment))
7619 (home-page "https://github.com/Shians/Glimma")
7620 (synopsis "Interactive HTML graphics")
7622 "This package generates interactive visualisations for analysis of
7623 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
7624 HTML page. The interactions are built on top of the popular static
7625 representations of analysis results in order to provide additional
7627 (license license:lgpl3)))
7629 (define-public r-rots
7636 (uri (bioconductor-uri "ROTS" version))
7639 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
7640 (properties `((upstream-name . "ROTS")))
7641 (build-system r-build-system)
7643 (list r-biobase r-rcpp))
7644 (home-page "https://bioconductor.org/packages/ROTS/")
7645 (synopsis "Reproducibility-Optimized Test Statistic")
7647 "This package provides tools for calculating the
7648 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
7650 (license license:gpl2+)))
7652 (define-public r-plgem
7659 (uri (bioconductor-uri "plgem" version))
7662 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
7663 (build-system r-build-system)
7665 (list r-biobase r-mass))
7666 (home-page "http://www.genopolis.it")
7667 (synopsis "Detect differential expression in microarray and proteomics datasets")
7669 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
7670 model the variance-versus-mean dependence that exists in a variety of
7671 genome-wide datasets, including microarray and proteomics data. The use of
7672 PLGEM has been shown to improve the detection of differentially expressed
7673 genes or proteins in these datasets.")
7674 (license license:gpl2)))
7676 (define-public r-inspect
7683 (uri (bioconductor-uri "INSPEcT" version))
7686 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
7687 (properties `((upstream-name . "INSPEcT")))
7688 (build-system r-build-system)
7709 r-summarizedexperiment
7710 r-txdb-mmusculus-ucsc-mm9-knowngene))
7713 (home-page "https://bioconductor.org/packages/INSPEcT")
7714 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
7716 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
7717 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
7718 order to evaluate synthesis, processing and degradation rates and assess via
7719 modeling the rates that determines changes in mature mRNA levels.")
7720 (license license:gpl2)))
7722 (define-public r-dnabarcodes
7724 (name "r-dnabarcodes")
7729 (uri (bioconductor-uri "DNABarcodes" version))
7732 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
7733 (properties `((upstream-name . "DNABarcodes")))
7734 (build-system r-build-system)
7736 (list r-bh r-matrix r-rcpp))
7739 (home-page "https://bioconductor.org/packages/DNABarcodes")
7740 (synopsis "Create and analyze DNA barcodes")
7742 "This package offers tools to create DNA barcode sets capable of
7743 correcting insertion, deletion, and substitution errors. Existing barcodes
7744 can be analyzed regarding their minimal, maximal and average distances between
7745 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
7746 demultiplexed, i.e. assigned to their original reference barcode.")
7747 (license license:gpl2)))
7749 (define-public r-ruvseq
7756 (uri (bioconductor-uri "RUVSeq" version))
7759 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
7760 (properties `((upstream-name . "RUVSeq")))
7761 (build-system r-build-system)
7763 (list r-biobase r-edaseq r-edger r-mass))
7766 (home-page "https://github.com/drisso/RUVSeq")
7767 (synopsis "Remove unwanted variation from RNA-Seq data")
7769 "This package implements methods to @dfn{remove unwanted variation} (RUV)
7770 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
7772 (license license:artistic2.0)))
7774 (define-public r-biocneighbors
7776 (name "r-biocneighbors")
7781 (uri (bioconductor-uri "BiocNeighbors" version))
7784 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
7785 (properties `((upstream-name . "BiocNeighbors")))
7786 (build-system r-build-system)
7788 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
7791 (home-page "https://bioconductor.org/packages/BiocNeighbors")
7792 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
7794 "This package implements exact and approximate methods for nearest
7795 neighbor detection, in a framework that allows them to be easily switched
7796 within Bioconductor packages or workflows. The exact algorithm is implemented
7797 using pre-clustering with the k-means algorithm. Functions are also provided
7798 to search for all neighbors within a given distance. Parallelization is
7799 achieved for all methods using the BiocParallel framework.")
7800 (license license:gpl3)))
7802 (define-public r-scaledmatrix
7804 (name "r-scaledmatrix")
7809 (uri (bioconductor-uri "ScaledMatrix" version))
7812 "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"))))
7813 (properties `((upstream-name . "ScaledMatrix")))
7814 (build-system r-build-system)
7816 (list r-delayedarray r-matrix r-s4vectors))
7817 (native-inputs (list r-knitr))
7818 (home-page "https://github.com/LTLA/ScaledMatrix")
7819 (synopsis "Create a DelayedMatrix of scaled and centered values")
7821 "This package provides delayed computation of a matrix of scaled and
7822 centered values. The result is equivalent to using the @code{scale} function
7823 but avoids explicit realization of a dense matrix during block processing.
7824 This permits greater efficiency in common operations, most notably matrix
7826 (license license:gpl3)))
7828 (define-public r-treeio
7835 (uri (bioconductor-uri "treeio" version))
7838 "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"))))
7839 (properties `((upstream-name . "treeio")))
7840 (build-system r-build-system)
7849 (native-inputs (list r-knitr))
7850 (home-page "https://github.com/YuLab-SMU/treeio")
7851 (synopsis "Base classes and functions for Phylogenetic tree input and output")
7853 "This is an R package to make it easier to import and store phylogenetic
7854 trees with associated data; and to link external data from different sources
7855 to phylogeny. It also supports exporting phylogenetic trees with
7856 heterogeneous associated data to a single tree file and can be served as a
7857 platform for merging tree with associated data and converting file formats.")
7858 (license license:artistic2.0)))
7860 (define-public r-ggtree
7867 (uri (bioconductor-uri "ggtree" version))
7870 "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"))))
7871 (properties `((upstream-name . "ggtree")))
7872 (build-system r-build-system)
7887 (native-inputs (list r-knitr))
7888 (home-page "https://yulab-smu.top/treedata-book/")
7889 (synopsis "R package for visualization of trees and annotation data")
7891 "This package extends the ggplot2 plotting system which implements a
7892 grammar of graphics. ggtree is designed for visualization and annotation of
7893 phylogenetic trees and other tree-like structures with their annotation
7895 (license license:artistic2.0)))
7897 (define-public r-metapod
7904 (uri (bioconductor-uri "metapod" version))
7907 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
7908 (properties `((upstream-name . "metapod")))
7909 (build-system r-build-system)
7914 (home-page "https://bioconductor.org/packages/metapod")
7915 (synopsis "Meta-analyses on p-values of differential analyses")
7917 "This package implements a variety of methods for combining p-values in
7918 differential analyses of genome-scale datasets. Functions can combine
7919 p-values across different tests in the same analysis (e.g., genomic windows in
7920 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
7921 analyses (e.g., replicated comparisons, effect of different treatment
7922 conditions). Support is provided for handling log-transformed input p-values,
7923 missing values and weighting where appropriate.")
7924 (license license:gpl3)))
7926 (define-public r-biocsingular
7928 (name "r-biocsingular")
7933 (uri (bioconductor-uri "BiocSingular" version))
7936 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
7937 (properties `((upstream-name . "BiocSingular")))
7938 (build-system r-build-system)
7952 (home-page "https://github.com/LTLA/BiocSingular")
7953 (synopsis "Singular value decomposition for Bioconductor packages")
7955 "This package implements exact and approximate methods for singular value
7956 decomposition and principal components analysis, in a framework that allows
7957 them to be easily switched within Bioconductor packages or workflows. Where
7958 possible, parallelization is achieved using the BiocParallel framework.")
7959 (license license:gpl3)))
7961 (define-public r-destiny
7968 (uri (bioconductor-uri "destiny" version))
7971 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
7972 (build-system r-build-system)
7990 r-singlecellexperiment
7992 r-summarizedexperiment
7997 (list r-knitr r-nbconvertr)) ; for vignettes
7998 (home-page "https://bioconductor.org/packages/destiny/")
7999 (synopsis "Create and plot diffusion maps")
8000 (description "This package provides tools to create and plot diffusion
8002 ;; Any version of the GPL
8003 (license license:gpl3+)))
8005 (define-public r-savr
8012 (uri (bioconductor-uri "savR" version))
8015 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
8016 (properties `((upstream-name . "savR")))
8017 (build-system r-build-system)
8019 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
8020 (home-page "https://github.com/bcalder/savR")
8021 (synopsis "Parse and analyze Illumina SAV files")
8023 "This package provides tools to parse Illumina Sequence Analysis
8024 Viewer (SAV) files, access data, and generate QC plots.")
8025 (license license:agpl3+)))
8027 (define-public r-chipexoqual
8029 (name "r-chipexoqual")
8034 (uri (bioconductor-uri "ChIPexoQual" version))
8037 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
8038 (properties `((upstream-name . "ChIPexoQual")))
8039 (build-system r-build-system)
8041 (list r-biocparallel
8060 (home-page "https://github.com/keleslab/ChIPexoQual")
8061 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
8063 "This package provides a quality control pipeline for ChIP-exo/nexus
8065 (license license:gpl2+)))
8067 (define-public r-copynumber
8069 (name "r-copynumber")
8073 (uri (bioconductor-uri "copynumber" version))
8076 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
8077 (build-system r-build-system)
8079 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
8080 (home-page "https://bioconductor.org/packages/copynumber")
8081 (synopsis "Segmentation of single- and multi-track copy number data")
8083 "This package segments single- and multi-track copy number data by a
8084 penalized least squares regression method.")
8085 (license license:artistic2.0)))
8087 (define-public r-dnacopy
8094 (uri (bioconductor-uri "DNAcopy" version))
8097 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
8098 (properties `((upstream-name . "DNAcopy")))
8099 (build-system r-build-system)
8100 (native-inputs (list gfortran))
8101 (home-page "https://bioconductor.org/packages/DNAcopy")
8102 (synopsis "DNA copy number data analysis")
8104 "This package implements the @dfn{circular binary segmentation} (CBS)
8105 algorithm to segment DNA copy number data and identify genomic regions with
8106 abnormal copy number.")
8107 (license license:gpl2+)))
8109 ;; This is a CRAN package, but it uncharacteristically depends on a
8110 ;; Bioconductor package.
8111 (define-public r-htscluster
8113 (name "r-htscluster")
8118 (uri (cran-uri "HTSCluster" version))
8121 "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
8122 (properties `((upstream-name . "HTSCluster")))
8123 (build-system r-build-system)
8125 (list r-capushe r-edger r-plotrix))
8126 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
8127 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
8129 "This package provides a Poisson mixture model is implemented to cluster
8130 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
8131 estimation is performed using either the EM or CEM algorithm, and the slope
8132 heuristics are used for model selection (i.e., to choose the number of
8134 (license license:gpl3+)))
8136 (define-public r-deds
8143 (uri (bioconductor-uri "DEDS" version))
8146 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
8147 (properties `((upstream-name . "DEDS")))
8148 (build-system r-build-system)
8149 (home-page "https://bioconductor.org/packages/DEDS/")
8150 (synopsis "Differential expression via distance summary for microarray data")
8152 "This library contains functions that calculate various statistics of
8153 differential expression for microarray data, including t statistics, fold
8154 change, F statistics, SAM, moderated t and F statistics and B statistics. It
8155 also implements a new methodology called DEDS (Differential Expression via
8156 Distance Summary), which selects differentially expressed genes by integrating
8157 and summarizing a set of statistics using a weighted distance approach.")
8158 ;; Any version of the LGPL.
8159 (license license:lgpl3+)))
8161 ;; This is a CRAN package, but since it depends on a Bioconductor package we
8163 (define-public r-nbpseq
8170 (uri (cran-uri "NBPSeq" version))
8173 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
8174 (properties `((upstream-name . "NBPSeq")))
8175 (build-system r-build-system)
8178 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
8179 (synopsis "Negative binomial models for RNA-Seq data")
8181 "This package provides negative binomial models for two-group comparisons
8182 and regression inferences from RNA-sequencing data.")
8183 (license license:gpl2)))
8185 (define-public r-ebseq
8192 (uri (bioconductor-uri "EBSeq" version))
8195 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
8196 (properties `((upstream-name . "EBSeq")))
8197 (build-system r-build-system)
8199 (list r-blockmodeling r-gplots r-testthat))
8200 (home-page "https://bioconductor.org/packages/EBSeq")
8201 (synopsis "Differential expression analysis of RNA-seq data")
8203 "This package provides tools for differential expression analysis at both
8204 gene and isoform level using RNA-seq data")
8205 (license license:artistic2.0)))
8207 (define-public r-karyoploter
8209 (name "r-karyoploter")
8213 (uri (bioconductor-uri "karyoploteR" version))
8216 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
8217 (build-system r-build-system)
8219 (list r-annotationdbi
8233 r-variantannotation))
8236 (home-page "https://bioconductor.org/packages/karyoploteR/")
8237 (synopsis "Plot customizable linear genomes displaying arbitrary data")
8238 (description "This package creates karyotype plots of arbitrary genomes and
8239 offers a complete set of functions to plot arbitrary data on them. It mimics
8240 many R base graphics functions coupling them with a coordinate change function
8241 automatically mapping the chromosome and data coordinates into the plot
8243 (license license:artistic2.0)))
8245 (define-public r-lpsymphony
8247 (name "r-lpsymphony")
8252 (uri (bioconductor-uri "lpsymphony" version))
8255 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
8256 (build-system r-build-system)
8260 '(modify-phases %standard-phases
8261 (add-after 'unpack 'make-build-order-reproducible
8263 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
8264 "src/SYMPHONY/Cgl/configure")
8265 (("for file in `ls \\*/Makefile.in`")
8266 "for file in `ls */Makefile.in | sort`")))))))
8270 (list pkg-config r-knitr))
8271 (home-page "https://r-forge.r-project.org/projects/rsymphony")
8272 (synopsis "Symphony integer linear programming solver in R")
8274 "This package was derived from Rsymphony. The package provides an R
8275 interface to SYMPHONY, a linear programming solver written in C++. The main
8276 difference between this package and Rsymphony is that it includes the solver
8277 source code, while Rsymphony expects to find header and library files on the
8278 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
8279 to install interface to SYMPHONY.")
8280 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
8281 ;; lpsimphony is released under the same terms.
8282 (license license:epl1.0)))
8284 (define-public r-ihw
8291 (uri (bioconductor-uri "IHW" version))
8294 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
8295 (properties `((upstream-name . "IHW")))
8296 (build-system r-build-system)
8298 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
8301 (home-page "https://bioconductor.org/packages/IHW")
8302 (synopsis "Independent hypothesis weighting")
8304 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
8305 procedure that increases power compared to the method of Benjamini and
8306 Hochberg by assigning data-driven weights to each hypothesis. The input to
8307 IHW is a two-column table of p-values and covariates. The covariate can be
8308 any continuous-valued or categorical variable that is thought to be
8309 informative on the statistical properties of each hypothesis test, while it is
8310 independent of the p-value under the null hypothesis.")
8311 (license license:artistic2.0)))
8313 (define-public r-icobra
8320 (uri (bioconductor-uri "iCOBRA" version))
8323 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
8324 (properties `((upstream-name . "iCOBRA")))
8325 (build-system r-build-system)
8341 (home-page "https://bioconductor.org/packages/iCOBRA")
8342 (synopsis "Comparison and visualization of ranking and assignment methods")
8344 "This package provides functions for calculation and visualization of
8345 performance metrics for evaluation of ranking and binary
8346 classification (assignment) methods. It also contains a Shiny application for
8347 interactive exploration of results.")
8348 (license license:gpl2+)))
8350 (define-public r-residualmatrix
8352 (name "r-residualmatrix")
8357 (uri (bioconductor-uri "ResidualMatrix" version))
8360 "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"))))
8362 `((upstream-name . "ResidualMatrix")))
8363 (build-system r-build-system)
8365 (list r-delayedarray r-matrix r-s4vectors))
8368 (home-page "https://github.com/LTLA/ResidualMatrix")
8369 (synopsis "Create a DelayedMatrix of regression residuals")
8371 "This package implements tools for delayed computation of a matrix of
8372 residuals after fitting a linear model to each column of an input matrix. It
8373 also supports partial computation of residuals where selected factors are to
8374 be preserved in the output matrix. It implements a number of efficient
8375 methods for operating on the delayed matrix of residuals, most notably matrix
8376 multiplication and calculation of row/column sums or means.")
8377 (license license:gpl3)))
8379 (define-public r-batchelor
8381 (name "r-batchelor")
8386 (uri (bioconductor-uri "batchelor" version))
8389 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
8390 (properties `((upstream-name . "batchelor")))
8391 (build-system r-build-system)
8399 r-delayedmatrixstats
8407 r-singlecellexperiment
8408 r-summarizedexperiment))
8409 (native-inputs (list r-knitr))
8410 (home-page "https://bioconductor.org/packages/batchelor")
8411 (synopsis "Single-Cell Batch Correction Methods")
8413 "This package implements a variety of methods for batch correction of
8414 single-cell (RNA sequencing) data. This includes methods based on detecting
8415 mutually nearest neighbors, as well as several efficient variants of linear
8416 regression of the log-expression values. Functions are also provided to
8417 perform global rescaling to remove differences in depth between batches, and
8418 to perform a principal components analysis that is robust to differences in
8419 the numbers of cells across batches.")
8420 (license license:gpl3)))
8422 (define-public r-mast
8429 (uri (bioconductor-uri "MAST" version))
8432 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
8433 (properties `((upstream-name . "MAST")))
8434 (build-system r-build-system)
8445 r-singlecellexperiment
8447 r-summarizedexperiment))
8450 (home-page "https://github.com/RGLab/MAST/")
8451 (synopsis "Model-based analysis of single cell transcriptomics")
8453 "This package provides methods and models for handling zero-inflated
8454 single cell assay data.")
8455 (license license:gpl2+)))
8457 (define-public r-monocle
8464 (uri (bioconductor-uri "monocle" version))
8467 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
8468 (build-system r-build-system)
8502 (home-page "https://bioconductor.org/packages/monocle")
8503 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
8505 "Monocle performs differential expression and time-series analysis for
8506 single-cell expression experiments. It orders individual cells according to
8507 progress through a biological process, without knowing ahead of time which
8508 genes define progress through that process. Monocle also performs
8509 differential expression analysis, clustering, visualization, and other useful
8510 tasks on single cell expression data. It is designed to work with RNA-Seq and
8511 qPCR data, but could be used with other types as well.")
8512 (license license:artistic2.0)))
8514 (define-public r-leidenbase
8515 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
8518 (name "r-leidenbase")
8519 (version (git-version "0.1.9" revision commit))
8524 (url "https://github.com/cole-trapnell-lab/leidenbase")
8526 (file-name (git-file-name name version))
8529 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
8530 (properties `((upstream-name . "leidenbase")))
8531 (build-system r-build-system)
8538 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
8539 (synopsis "R and C wrappers to run the Leiden find_partition function")
8541 "This package provides an R to C interface that runs the Leiden
8542 community detection algorithm to find a basic partition. It runs the
8543 equivalent of the @code{find_partition} function. This package includes the
8544 required source code files from the official Leidenalg distribution and
8545 several functions from the R igraph package.")
8546 (license license:gpl3+))))
8548 (define-public r-sanssouci
8549 ;; sansscouci doesn't have a (versioned) release yet.
8550 ;; This is the latest commit as of packaging for Guix.
8551 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
8554 (name "r-sanssouci")
8555 (version (git-version "0" revision commit))
8559 (url "https://github.com/pneuvial/sanssouci.git")
8561 (file-name (git-file-name name version))
8564 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
8565 (build-system r-build-system)
8567 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
8568 (home-page "https://pneuvial.github.io/sanssouci")
8569 (synopsis "Post Hoc multiple testing inference")
8571 "The goal of sansSouci is to perform post hoc inference: in a multiple
8572 testing context, sansSouci provides statistical guarantees on possibly
8573 user-defined and/or data-driven sets of hypotheses.")
8574 (license license:gpl3))))
8576 (define-public r-monocle3
8584 (url "https://github.com/cole-trapnell-lab/monocle3")
8586 (file-name (git-file-name name version))
8589 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
8590 (build-system r-build-system)
8596 r-delayedmatrixstats
8631 r-singlecellexperiment
8636 (home-page "https://github.com/cole-trapnell-lab/monocle3")
8637 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
8639 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
8640 (license license:expat)))
8642 (define-public r-noiseq
8649 (uri (bioconductor-uri "NOISeq" version))
8652 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
8653 (properties `((upstream-name . "NOISeq")))
8654 (build-system r-build-system)
8656 (list r-biobase r-matrix))
8657 (home-page "https://bioconductor.org/packages/NOISeq")
8658 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
8660 "This package provides tools to support the analysis of RNA-seq
8661 expression data or other similar kind of data. It provides exploratory plots
8662 to evaluate saturation, count distribution, expression per chromosome, type of
8663 detected features, features length, etc. It also supports the analysis of
8664 differential expression between two experimental conditions with no parametric
8666 (license license:artistic2.0)))
8668 (define-public r-scdd
8675 (uri (bioconductor-uri "scDD" version))
8678 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
8679 (properties `((upstream-name . "scDD")))
8680 (build-system r-build-system)
8691 r-singlecellexperiment
8692 r-summarizedexperiment))
8695 (home-page "https://github.com/kdkorthauer/scDD")
8696 (synopsis "Mixture modeling of single-cell RNA-seq data")
8698 "This package implements a method to analyze single-cell RNA-seq data
8699 utilizing flexible Dirichlet Process mixture models. Genes with differential
8700 distributions of expression are classified into several interesting patterns
8701 of differences between two conditions. The package also includes functions
8702 for simulating data with these patterns from negative binomial
8704 (license license:gpl2)))
8706 (define-public r-scone
8713 (uri (bioconductor-uri "scone" version))
8716 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
8717 (build-system r-build-system)
8738 r-singlecellexperiment
8739 r-summarizedexperiment))
8742 (home-page "https://bioconductor.org/packages/scone")
8743 (synopsis "Single cell overview of normalized expression data")
8745 "SCONE is an R package for comparing and ranking the performance of
8746 different normalization schemes for single-cell RNA-seq and other
8747 high-throughput analyses.")
8748 (license license:artistic2.0)))
8750 (define-public r-geoquery
8757 (uri (bioconductor-uri "GEOquery" version))
8760 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
8761 (properties `((upstream-name . "GEOquery")))
8762 (build-system r-build-system)
8776 (home-page "https://github.com/seandavi/GEOquery/")
8777 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
8779 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
8780 microarray data. Given the rich and varied nature of this resource, it is
8781 only natural to want to apply BioConductor tools to these data. GEOquery is
8782 the bridge between GEO and BioConductor.")
8783 (license license:gpl2)))
8785 (define-public r-illuminaio
8787 (name "r-illuminaio")
8792 (uri (bioconductor-uri "illuminaio" version))
8795 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
8796 (build-system r-build-system)
8799 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
8800 (synopsis "Parse Illumina microarray output files")
8802 "This package provides tools for parsing Illumina's microarray output
8803 files, including IDAT.")
8804 (license license:gpl2)))
8806 (define-public r-siggenes
8813 (uri (bioconductor-uri "siggenes" version))
8816 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
8817 (build-system r-build-system)
8819 (list r-biobase r-multtest r-scrime))
8820 (home-page "https://bioconductor.org/packages/siggenes/")
8822 "Multiple testing using SAM and Efron's empirical Bayes approaches")
8824 "This package provides tools for the identification of differentially
8825 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
8826 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
8827 Bayes Analyses of Microarrays} (EBAM).")
8828 (license license:lgpl2.0+)))
8830 (define-public r-bumphunter
8832 (name "r-bumphunter")
8837 (uri (bioconductor-uri "bumphunter" version))
8840 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
8841 (build-system r-build-system)
8843 (list r-annotationdbi
8856 (home-page "https://github.com/ririzarr/bumphunter")
8857 (synopsis "Find bumps in genomic data")
8859 "This package provides tools for finding bumps in genomic data in order
8860 to identify differentially methylated regions in epigenetic epidemiology
8862 (license license:artistic2.0)))
8864 (define-public r-milor
8870 (uri (bioconductor-uri "miloR" version))
8873 "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
8874 (properties `((upstream-name . "miloR")))
8875 (build-system r-build-system)
8877 (list r-biocgenerics
8897 r-singlecellexperiment
8899 r-summarizedexperiment
8902 (native-inputs (list r-knitr))
8903 (home-page "https://marionilab.github.io/miloR")
8904 (synopsis "Differential neighbourhood abundance testing on a graph")
8906 "Milo performs single-cell differential abundance testing. Cell states
8907 are modelled as representative neighbourhoods on a nearest neighbour graph.
8908 Hypothesis testing is performed using a negative bionomial generalized linear
8910 (license license:gpl3)))
8912 (define-public r-minfi
8919 (uri (bioconductor-uri "minfi" version))
8922 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
8923 (build-system r-build-system)
8933 r-delayedmatrixstats
8953 r-summarizedexperiment))
8956 (home-page "https://github.com/hansenlab/minfi")
8957 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
8959 "This package provides tools to analyze and visualize Illumina Infinium
8960 methylation arrays.")
8961 (license license:artistic2.0)))
8963 (define-public r-methylumi
8965 (name "r-methylumi")
8970 (uri (bioconductor-uri "methylumi" version))
8973 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
8974 (build-system r-build-system)
8980 r-fdb-infiniummethylation-hg19
8994 r-summarizedexperiment))
8997 (home-page "https://bioconductor.org/packages/methylumi")
8998 (synopsis "Handle Illumina methylation data")
9000 "This package provides classes for holding and manipulating Illumina
9001 methylation data. Based on eSet, it can contain MIAME information, sample
9002 information, feature information, and multiple matrices of data. An
9003 \"intelligent\" import function, methylumiR can read the Illumina text files
9004 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
9005 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
9006 background correction, and quality control features for GoldenGate, Infinium,
9007 and Infinium HD arrays are also included.")
9008 (license license:gpl2)))
9010 (define-public r-lumi
9017 (uri (bioconductor-uri "lumi" version))
9020 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
9021 (build-system r-build-system)
9038 (home-page "https://bioconductor.org/packages/lumi")
9039 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
9041 "The lumi package provides an integrated solution for the Illumina
9042 microarray data analysis. It includes functions of Illumina
9043 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
9044 variance stabilization, normalization and gene annotation at the probe level.
9045 It also includes the functions of processing Illumina methylation microarrays,
9046 especially Illumina Infinium methylation microarrays.")
9047 (license license:lgpl2.0+)))
9049 (define-public r-linnorm
9056 (uri (bioconductor-uri "Linnorm" version))
9059 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
9060 (properties `((upstream-name . "Linnorm")))
9061 (build-system r-build-system)
9083 (home-page "http://www.jjwanglab.org/Linnorm/")
9084 (synopsis "Linear model and normality based transformation method")
9086 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
9087 count data or any large scale count data. It transforms such datasets for
9088 parametric tests. In addition to the transformtion function (@code{Linnorm}),
9089 the following pipelines are implemented:
9092 @item Library size/batch effect normalization (@code{Linnorm.Norm})
9093 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
9094 clustering or hierarchical clustering (@code{Linnorm.tSNE},
9095 @code{Linnorm.PCA}, @code{Linnorm.HClust})
9096 @item Differential expression analysis or differential peak detection using
9097 limma (@code{Linnorm.limma})
9098 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
9099 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
9100 @item Stable gene selection for scRNA-seq data; for users without or who do
9101 not want to rely on spike-in genes (@code{Linnorm.SGenes})
9102 @item Data imputation (@code{Linnorm.DataImput}).
9105 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
9106 @code{RnaXSim} function is included for simulating RNA-seq data for the
9107 evaluation of DEG analysis methods.")
9108 (license license:expat)))
9110 (define-public r-ioniser
9117 (uri (bioconductor-uri "IONiseR" version))
9120 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
9121 (properties `((upstream-name . "IONiseR")))
9122 (build-system r-build-system)
9124 (list r-biocgenerics
9139 (home-page "https://bioconductor.org/packages/IONiseR/")
9140 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
9142 "IONiseR provides tools for the quality assessment of Oxford Nanopore
9143 MinION data. It extracts summary statistics from a set of fast5 files and can
9144 be used either before or after base calling. In addition to standard
9145 summaries of the read-types produced, it provides a number of plots for
9146 visualising metrics relative to experiment run time or spatially over the
9147 surface of a flowcell.")
9148 (license license:expat)))
9150 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
9151 (define-public r-mutoss
9158 (uri (cran-uri "mutoss" version))
9161 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
9162 (properties `((upstream-name . "mutoss")))
9163 (build-system r-build-system)
9165 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
9166 (home-page "https://github.com/kornl/mutoss/")
9167 (synopsis "Unified multiple testing procedures")
9169 "This package is designed to ease the application and comparison of
9170 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
9171 are standardized and usable by the accompanying mutossGUI package.")
9172 ;; Any version of the GPL.
9173 (license (list license:gpl2+ license:gpl3+))))
9175 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
9176 ;; from Bioconductor, so we put it here.
9177 (define-public r-metap
9184 (uri (cran-uri "metap" version))
9187 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
9188 (build-system r-build-system)
9196 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
9197 (synopsis "Meta-analysis of significance values")
9199 "The canonical way to perform meta-analysis involves using effect sizes.
9200 When they are not available this package provides a number of methods for
9201 meta-analysis of significance values including the methods of Edgington,
9202 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
9203 published results; and a routine for graphical display.")
9204 (license license:gpl2)))
9206 (define-public r-tradeseq
9212 (uri (bioconductor-uri "tradeSeq" version))
9215 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
9216 (build-system r-build-system)
9232 r-singlecellexperiment
9234 r-summarizedexperiment
9240 (home-page "https://statomics.github.io/tradeSeq/index.html")
9241 (synopsis "Trajectory-based differential expression analysis")
9243 "This package provides a flexible method for fitting regression models that
9244 can be used to find genes that are differentially expressed along one or
9245 multiple lineages in a trajectory. Based on the fitted models, it uses a
9246 variety of tests suited to answer different questions of interest, e.g. the
9247 discovery of genes for which expression is associated with pseudotime, or which
9248 are differentially expressed (in a specific region) along the trajectory. It
9249 fits a negative binomial generalized additive model (GAM) for each gene, and
9250 performs inference on the parameters of the GAM.")
9251 (license license:expat)))
9253 (define-public r-triform
9260 (uri (bioconductor-uri "triform" version))
9263 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
9264 (build-system r-build-system)
9266 (list r-biocgenerics r-iranges r-yaml))
9267 (home-page "https://bioconductor.org/packages/triform/")
9268 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
9270 "The Triform algorithm uses model-free statistics to identify peak-like
9271 distributions of TF ChIP sequencing reads, taking advantage of an improved
9272 peak definition in combination with known profile characteristics.")
9273 (license license:gpl2)))
9275 (define-public r-varianttools
9277 (name "r-varianttools")
9282 (uri (bioconductor-uri "VariantTools" version))
9285 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
9286 (properties `((upstream-name . "VariantTools")))
9287 (build-system r-build-system)
9302 r-variantannotation))
9303 (home-page "https://bioconductor.org/packages/VariantTools/")
9304 (synopsis "Tools for exploratory analysis of variant calls")
9306 "Explore, diagnose, and compare variant calls using filters. The
9307 VariantTools package supports a workflow for loading data, calling single
9308 sample variants and tumor-specific somatic mutations or other sample-specific
9309 variant types (e.g., RNA editing). Most of the functions operate on
9310 alignments (BAM files) or datasets of called variants. The user is expected
9311 to have already aligned the reads with a separate tool, e.g., GSNAP via
9313 (license license:artistic2.0)))
9315 (define-public r-heatplus
9322 (uri (bioconductor-uri "Heatplus" version))
9325 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
9326 (properties `((upstream-name . "Heatplus")))
9327 (build-system r-build-system)
9329 (list r-rcolorbrewer))
9330 (home-page "https://github.com/alexploner/Heatplus")
9331 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
9333 "This package provides tools to display a rectangular heatmap (intensity
9334 plot) of a data matrix. By default, both samples (columns) and features (row)
9335 of the matrix are sorted according to a hierarchical clustering, and the
9336 corresponding dendrogram is plotted. Optionally, panels with additional
9337 information about samples and features can be added to the plot.")
9338 (license license:gpl2+)))
9340 (define-public r-gosemsim
9347 (uri (bioconductor-uri "GOSemSim" version))
9350 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
9351 (properties `((upstream-name . "GOSemSim")))
9352 (build-system r-build-system)
9354 (list r-annotationdbi r-go-db r-rcpp))
9357 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
9358 (synopsis "GO-terms semantic similarity measures")
9360 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
9361 quantitative ways to compute similarities between genes and gene groups, and
9362 have became important basis for many bioinformatics analysis approaches.
9363 GOSemSim is an R package for semantic similarity computation among GO terms,
9364 sets of GO terms, gene products and gene clusters.")
9365 (license license:artistic2.0)))
9367 (define-public r-anota
9374 (uri (bioconductor-uri "anota" version))
9377 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
9378 (build-system r-build-system)
9380 (list r-multtest r-qvalue))
9381 (home-page "https://bioconductor.org/packages/anota/")
9382 (synopsis "Analysis of translational activity")
9384 "Genome wide studies of translational control is emerging as a tool to
9385 study various biological conditions. The output from such analysis is both
9386 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
9387 involved in translation (the actively translating mRNA level) for each mRNA.
9388 The standard analysis of such data strives towards identifying differential
9389 translational between two or more sample classes - i.e., differences in
9390 actively translated mRNA levels that are independent of underlying differences
9391 in cytosolic mRNA levels. This package allows for such analysis using partial
9392 variances and the random variance model. As 10s of thousands of mRNAs are
9393 analyzed in parallel the library performs a number of tests to assure that
9394 the data set is suitable for such analysis.")
9395 (license license:gpl3)))
9397 (define-public r-sigpathway
9399 (name "r-sigpathway")
9404 (uri (bioconductor-uri "sigPathway" version))
9407 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
9408 (properties `((upstream-name . "sigPathway")))
9409 (build-system r-build-system)
9410 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
9411 (synopsis "Pathway analysis")
9413 "This package is used to conduct pathway analysis by calculating the NT_k
9414 and NE_k statistics in a statistical framework for determining whether a
9415 specified group of genes for a pathway has a coordinated association with a
9416 phenotype of interest.")
9417 (license license:gpl2)))
9419 (define-public r-fcscan
9426 (uri (bioconductor-uri "fcScan" version))
9428 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
9429 (properties `((upstream-name . "fcScan")))
9430 (build-system r-build-system)
9438 r-summarizedexperiment
9439 r-variantannotation))
9440 (native-inputs (list r-knitr))
9441 (home-page "https://bioconductor.org/packages/fcScan")
9442 (synopsis "Detect clusters of coordinates with user defined options")
9444 "This package is used to detect combination of genomic coordinates
9445 falling within a user defined window size along with user defined overlap
9446 between identified neighboring clusters. It can be used for genomic data
9447 where the clusters are built on a specific chromosome or specific strand.
9448 Clustering can be performed with a \"greedy\" option allowing thus the
9449 presence of additional sites within the allowed window size.")
9450 (license license:artistic2.0)))
9452 (define-public r-fgsea
9459 (uri (bioconductor-uri "fgsea" version))
9462 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
9463 (build-system r-build-system)
9475 (home-page "https://github.com/ctlab/fgsea/")
9476 (synopsis "Fast gene set enrichment analysis")
9478 "The package implements an algorithm for fast gene set enrichment
9479 analysis. Using the fast algorithm makes more permutations and gets
9480 more fine grained p-values, which allows using accurate standard approaches
9481 to multiple hypothesis correction.")
9482 (license license:expat)))
9484 (define-public r-dose
9491 (uri (bioconductor-uri "DOSE" version))
9494 "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"))))
9495 (properties `((upstream-name . "DOSE")))
9496 (build-system r-build-system)
9498 (list r-annotationdbi
9508 (home-page "https://guangchuangyu.github.io/software/DOSE/")
9509 (synopsis "Disease ontology semantic and enrichment analysis")
9511 "This package implements five methods proposed by Resnik, Schlicker,
9512 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
9513 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
9514 including hypergeometric model and gene set enrichment analysis are also
9515 implemented for discovering disease associations of high-throughput biological
9517 (license license:artistic2.0)))
9519 (define-public r-enrichplot
9521 (name "r-enrichplot")
9526 (uri (bioconductor-uri "enrichplot" version))
9529 "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"))))
9530 (build-system r-build-system)
9549 (home-page "https://github.com/GuangchuangYu/enrichplot")
9550 (synopsis "Visualization of functional enrichment result")
9552 "The enrichplot package implements several visualization methods for
9553 interpreting functional enrichment results obtained from ORA or GSEA analyses.
9554 All the visualization methods are developed based on ggplot2 graphics.")
9555 (license license:artistic2.0)))
9557 (define-public r-clusterprofiler
9559 (name "r-clusterprofiler")
9564 (uri (bioconductor-uri "clusterProfiler" version))
9567 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
9569 `((upstream-name . "clusterProfiler")))
9570 (build-system r-build-system)
9572 (list r-annotationdbi
9587 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
9588 (synopsis "Analysis and visualization of functional profiles for gene clusters")
9590 "This package implements methods to analyze and visualize functional
9591 profiles (GO and KEGG) of gene and gene clusters.")
9592 (license license:artistic2.0)))
9594 (define-public r-clusterexperiment
9596 (name "r-clusterexperiment")
9600 (uri (bioconductor-uri "clusterExperiment" version))
9603 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
9604 (build-system r-build-system)
9629 r-singlecellexperiment
9631 r-summarizedexperiment
9633 (home-page "https://bioconductor.org/packages/clusterExperiment/")
9634 (synopsis "Compare clusterings for single-cell sequencing")
9635 (description "This package provides functionality for running and comparing
9636 many different clusterings of single-cell sequencing data or other large mRNA
9637 expression data sets.")
9638 (license license:artistic2.0)))
9640 (define-public r-mlinterfaces
9642 (name "r-mlinterfaces")
9647 (uri (bioconductor-uri "MLInterfaces" version))
9650 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
9651 (properties `((upstream-name . "MLInterfaces")))
9652 (build-system r-build-system)
9674 (home-page "https://bioconductor.org/packages/MLInterfaces/")
9675 (synopsis "Interfaces to R machine learning procedures")
9677 "This package provides uniform interfaces to machine learning code for
9678 data in R and Bioconductor containers.")
9679 ;; Any version of the LGPL.
9680 (license license:lgpl2.1+)))
9682 (define-public r-annaffy
9689 (uri (bioconductor-uri "annaffy" version))
9692 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
9693 (build-system r-build-system)
9696 (modify-phases %standard-phases
9697 (add-after 'unpack 'remove-reference-to-non-free-data
9699 (substitute* "DESCRIPTION"
9700 ((", KEGG.db") "")))))))
9702 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
9703 (home-page "https://bioconductor.org/packages/annaffy/")
9704 (synopsis "Annotation tools for Affymetrix biological metadata")
9706 "This package provides functions for handling data from Bioconductor
9707 Affymetrix annotation data packages. It produces compact HTML and text
9708 reports including experimental data and URL links to many online databases.
9709 It allows searching of biological metadata using various criteria.")
9710 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
9711 ;; the LGPL 2.1 is included.
9712 (license license:lgpl2.1+)))
9714 (define-public r-a4core
9721 (uri (bioconductor-uri "a4Core" version))
9724 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
9725 (properties `((upstream-name . "a4Core")))
9726 (build-system r-build-system)
9728 (list r-biobase r-glmnet))
9731 (home-page "https://bioconductor.org/packages/a4Core")
9732 (synopsis "Automated Affymetrix array analysis core package")
9734 "This is the core package for the automated analysis of Affymetrix
9736 (license license:gpl3)))
9738 (define-public r-a4classif
9740 (name "r-a4classif")
9745 (uri (bioconductor-uri "a4Classif" version))
9748 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
9749 (properties `((upstream-name . "a4Classif")))
9750 (build-system r-build-system)
9761 (home-page "https://bioconductor.org/packages/a4Classif/")
9762 (synopsis "Automated Affymetrix array analysis classification package")
9764 "This is the classification package for the automated analysis of
9765 Affymetrix arrays.")
9766 (license license:gpl3)))
9768 (define-public r-a4preproc
9770 (name "r-a4preproc")
9775 (uri (bioconductor-uri "a4Preproc" version))
9778 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
9779 (properties `((upstream-name . "a4Preproc")))
9780 (build-system r-build-system)
9782 (list r-biobase r-biocgenerics))
9785 (home-page "https://bioconductor.org/packages/a4Preproc/")
9786 (synopsis "Automated Affymetrix array analysis preprocessing package")
9788 "This is a package for the automated analysis of Affymetrix arrays. It
9789 is used for preprocessing the arrays.")
9790 (license license:gpl3)))
9792 (define-public r-a4reporting
9794 (name "r-a4reporting")
9799 (uri (bioconductor-uri "a4Reporting" version))
9802 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
9803 (properties `((upstream-name . "a4Reporting")))
9804 (build-system r-build-system)
9809 (home-page "https://bioconductor.org/packages/a4Reporting/")
9810 (synopsis "Automated Affymetrix array analysis reporting package")
9812 "This is a package for the automated analysis of Affymetrix arrays. It
9813 provides reporting features.")
9814 (license license:gpl3)))
9816 (define-public r-a4base
9823 (uri (bioconductor-uri "a4Base" version))
9826 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
9827 (properties `((upstream-name . "a4Base")))
9828 (build-system r-build-system)
9840 (home-page "https://bioconductor.org/packages/a4Base/")
9841 (synopsis "Automated Affymetrix array analysis base package")
9843 "This package provides basic features for the automated analysis of
9844 Affymetrix arrays.")
9845 (license license:gpl3)))
9854 (uri (bioconductor-uri "a4" version))
9857 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
9858 (build-system r-build-system)
9860 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
9861 (home-page "https://bioconductor.org/packages/a4/")
9862 (synopsis "Automated Affymetrix array analysis umbrella package")
9864 "This package provides a software suite for the automated analysis of
9865 Affymetrix arrays.")
9866 (license license:gpl3)))
9868 (define-public r-abseqr
9875 (uri (bioconductor-uri "abseqR" version))
9878 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
9879 (properties `((upstream-name . "abseqR")))
9880 (build-system r-build-system)
9884 (list r-biocparallel
9904 (home-page "https://github.com/malhamdoosh/abseqR")
9905 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
9907 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
9908 sequencing datasets generated from antibody libraries and abseqR is one of its
9909 packages. AbseqR empowers the users of abseqPy with plotting and reporting
9910 capabilities and allows them to generate interactive HTML reports for the
9911 convenience of viewing and sharing with other researchers. Additionally,
9912 abseqR extends abseqPy to compare multiple repertoire analyses and perform
9913 further downstream analysis on its output.")
9914 (license license:gpl3)))
9916 (define-public r-bacon
9923 (uri (bioconductor-uri "bacon" version))
9926 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
9927 (build-system r-build-system)
9929 (list r-biocparallel r-ellipse r-ggplot2))
9932 (home-page "https://bioconductor.org/packages/bacon/")
9933 (synopsis "Controlling bias and inflation in association studies")
9935 "Bacon can be used to remove inflation and bias often observed in
9936 epigenome- and transcriptome-wide association studies. To this end bacon
9937 constructs an empirical null distribution using a Gibbs Sampling algorithm by
9938 fitting a three-component normal mixture on z-scores.")
9939 (license license:gpl2+)))
9941 (define-public r-rgadem
9948 (uri (bioconductor-uri "rGADEM" version))
9951 "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"))))
9952 (properties `((upstream-name . "rGADEM")))
9953 (build-system r-build-system)
9955 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
9956 (home-page "https://bioconductor.org/packages/rGADEM/")
9957 (synopsis "De novo sequence motif discovery")
9959 "rGADEM is an efficient de novo motif discovery tool for large-scale
9960 genomic sequence data.")
9961 (license license:artistic2.0)))
9963 (define-public r-motiv
9970 (uri (bioconductor-uri "MotIV" version))
9973 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
9974 (properties `((upstream-name . "MotIV")))
9975 (build-system r-build-system)
9979 (list r-biocgenerics
9986 (home-page "https://bioconductor.org/packages/MotIV/")
9987 (synopsis "Motif identification and validation")
9989 "This package is used for the identification and validation of sequence
9990 motifs. It makes use of STAMP for comparing a set of motifs to a given
9991 database (e.g. JASPAR). It can also be used to visualize motifs, motif
9992 distributions, modules and filter motifs.")
9993 (license license:gpl2)))
9995 (define-public r-motifdb
10001 (uri (bioconductor-uri "MotifDb" version))
10003 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
10004 (properties `((upstream-name . "MotifDb")))
10005 (build-system r-build-system)
10007 (list r-biocgenerics
10013 r-splitstackshape))
10016 (home-page "https://www.bioconductor.org/packages/MotifDb/")
10017 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
10018 (description "This package provides more than 2000 annotated position
10019 frequency matrices from nine public sources, for multiple organisms.")
10020 (license license:artistic2.0)))
10022 (define-public r-motifbreakr
10024 (name "r-motifbreakr")
10028 (uri (bioconductor-uri "motifbreakR" version))
10030 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
10031 (properties `((upstream-name . "motifbreakR")))
10032 (build-system r-build-system)
10034 (list r-biocgenerics
10048 r-summarizedexperiment
10050 r-variantannotation))
10053 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
10054 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
10055 (description "This package allows biologists to judge in the first place
10056 whether the sequence surrounding the polymorphism is a good match, and in
10057 the second place how much information is gained or lost in one allele of
10058 the polymorphism relative to another. This package gives a choice of
10059 algorithms for interrogation of genomes with motifs from public sources:
10061 @item a weighted-sum probability matrix;
10062 @item log-probabilities;
10063 @item weighted by relative entropy.
10066 This package can predict effects for novel or previously described variants in
10067 public databases, making it suitable for tasks beyond the scope of its original
10068 design. Lastly, it can be used to interrogate any genome curated within
10070 (license license:gpl2+)))
10072 (define-public r-motifstack
10074 (name "r-motifstack")
10079 (uri (bioconductor-uri "motifStack" version))
10082 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
10083 (properties `((upstream-name . "motifStack")))
10084 (build-system r-build-system)
10094 (home-page "https://bioconductor.org/packages/motifStack/")
10095 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
10097 "The motifStack package is designed for graphic representation of
10098 multiple motifs with different similarity scores. It works with both DNA/RNA
10099 sequence motifs and amino acid sequence motifs. In addition, it provides the
10100 flexibility for users to customize the graphic parameters such as the font
10101 type and symbol colors.")
10102 (license license:gpl2+)))
10104 (define-public r-genomicscores
10106 (name "r-genomicscores")
10111 (uri (bioconductor-uri "GenomicScores" version))
10114 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
10115 (properties `((upstream-name . "GenomicScores")))
10116 (build-system r-build-system)
10118 (list r-annotationhub
10135 (home-page "https://github.com/rcastelo/GenomicScores/")
10136 (synopsis "Work with genome-wide position-specific scores")
10138 "This package provides infrastructure to store and access genome-wide
10139 position-specific scores within R and Bioconductor.")
10140 (license license:artistic2.0)))
10142 (define-public r-atacseqqc
10144 (name "r-atacseqqc")
10149 (uri (bioconductor-uri "ATACseqQC" version))
10152 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
10153 (properties `((upstream-name . "ATACseqQC")))
10154 (build-system r-build-system)
10156 (list r-biocgenerics
10162 r-genomicalignments
10176 (home-page "https://bioconductor.org/packages/ATACseqQC/")
10177 (synopsis "ATAC-seq quality control")
10179 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
10180 sequencing, is a rapid and sensitive method for chromatin accessibility
10181 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
10182 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
10183 assess whether their ATAC-seq experiment is successful. It includes
10184 diagnostic plots of fragment size distribution, proportion of mitochondria
10185 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
10187 (license license:gpl2+)))
10189 (define-public r-gofuncr
10196 (uri (bioconductor-uri "GOfuncR" version))
10199 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
10200 (properties `((upstream-name . "GOfuncR")))
10201 (build-system r-build-system)
10203 (list r-annotationdbi
10212 (home-page "https://bioconductor.org/packages/GOfuncR/")
10213 (synopsis "Gene ontology enrichment using FUNC")
10215 "GOfuncR performs a gene ontology enrichment analysis based on the
10216 ontology enrichment software FUNC. GO-annotations are obtained from
10217 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
10218 included in the package and updated regularly. GOfuncR provides the standard
10219 candidate vs background enrichment analysis using the hypergeometric test, as
10220 well as three additional tests:
10223 @item the Wilcoxon rank-sum test that is used when genes are ranked,
10224 @item a binomial test that is used when genes are associated with two counts,
10226 @item a Chi-square or Fisher's exact test that is used in cases when genes are
10227 associated with four counts.
10230 To correct for multiple testing and interdependency of the tests, family-wise
10231 error rates are computed based on random permutations of the gene-associated
10232 variables. GOfuncR also provides tools for exploring the ontology graph and
10233 the annotations, and options to take gene-length or spatial clustering of
10234 genes into account. It is also possible to provide custom gene coordinates,
10235 annotations and ontologies.")
10236 (license license:gpl2+)))
10238 (define-public r-abaenrichment
10240 (name "r-abaenrichment")
10245 (uri (bioconductor-uri "ABAEnrichment" version))
10248 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
10249 (properties `((upstream-name . "ABAEnrichment")))
10250 (build-system r-build-system)
10260 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
10261 (synopsis "Gene expression enrichment in human brain regions")
10263 "The package ABAEnrichment is designed to test for enrichment of user
10264 defined candidate genes in the set of expressed genes in different human brain
10265 regions. The core function @code{aba_enrich} integrates the expression of the
10266 candidate gene set (averaged across donors) and the structural information of
10267 the brain using an ontology, both provided by the Allen Brain Atlas project.")
10268 (license license:gpl2+)))
10270 (define-public r-annotationfuncs
10272 (name "r-annotationfuncs")
10277 (uri (bioconductor-uri "AnnotationFuncs" version))
10280 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
10282 `((upstream-name . "AnnotationFuncs")))
10283 (build-system r-build-system)
10285 (list r-annotationdbi r-dbi))
10286 (home-page "https://www.iysik.com/r/annotationfuncs")
10287 (synopsis "Annotation translation functions")
10289 "This package provides functions for handling translating between
10290 different identifieres using the Biocore Data Team data-packages (e.g.
10291 @code{org.Bt.eg.db}).")
10292 (license license:gpl2)))
10294 (define-public r-annotationtools
10296 (name "r-annotationtools")
10301 (uri (bioconductor-uri "annotationTools" version))
10304 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
10306 `((upstream-name . "annotationTools")))
10307 (build-system r-build-system)
10308 (propagated-inputs (list r-biobase))
10309 (home-page "https://bioconductor.org/packages/annotationTools/")
10310 (synopsis "Annotate microarrays and perform gene expression analyses")
10312 "This package provides functions to annotate microarrays, find orthologs,
10313 and integrate heterogeneous gene expression profiles using annotation and
10314 other molecular biology information available as flat file database (plain
10316 ;; Any version of the GPL.
10317 (license (list license:gpl2+))))
10319 (define-public r-allelicimbalance
10321 (name "r-allelicimbalance")
10326 (uri (bioconductor-uri "AllelicImbalance" version))
10329 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
10331 `((upstream-name . "AllelicImbalance")))
10332 (build-system r-build-system)
10334 (list r-annotationdbi
10339 r-genomicalignments
10351 r-summarizedexperiment
10352 r-variantannotation))
10355 (home-page "https://github.com/pappewaio/AllelicImbalance")
10356 (synopsis "Investigate allele-specific expression")
10358 "This package provides a framework for allele-specific expression
10359 investigation using RNA-seq data.")
10360 (license license:gpl3)))
10362 (define-public r-aucell
10369 (uri (bioconductor-uri "AUCell" version))
10372 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
10373 (properties `((upstream-name . "AUCell")))
10374 (build-system r-build-system)
10376 (list r-biocgenerics
10379 r-delayedmatrixstats
10384 r-summarizedexperiment))
10387 (home-page "https://bioconductor.org/packages/AUCell/")
10388 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
10390 "AUCell identifies cells with active gene sets (e.g. signatures,
10391 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
10392 Under the Curve} (AUC) to calculate whether a critical subset of the input
10393 gene set is enriched within the expressed genes for each cell. The
10394 distribution of AUC scores across all the cells allows exploring the relative
10395 expression of the signature. Since the scoring method is ranking-based,
10396 AUCell is independent of the gene expression units and the normalization
10397 procedure. In addition, since the cells are evaluated individually, it can
10398 easily be applied to bigger datasets, subsetting the expression matrix if
10400 (license license:gpl3)))
10402 (define-public r-ebimage
10409 (uri (bioconductor-uri "EBImage" version))
10412 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
10413 (properties `((upstream-name . "EBImage")))
10414 (build-system r-build-system)
10427 (list r-knitr)) ; for vignettes
10428 (home-page "https://github.com/aoles/EBImage")
10429 (synopsis "Image processing and analysis toolbox for R")
10431 "EBImage provides general purpose functionality for image processing and
10432 analysis. In the context of (high-throughput) microscopy-based cellular
10433 assays, EBImage offers tools to segment cells and extract quantitative
10434 cellular descriptors. This allows the automation of such tasks using the R
10435 programming language and facilitates the use of other tools in the R
10436 environment for signal processing, statistical modeling, machine learning and
10437 visualization with image data.")
10438 ;; Any version of the LGPL.
10439 (license license:lgpl2.1+)))
10441 (define-public r-yamss
10448 (uri (bioconductor-uri "yamss" version))
10451 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
10452 (build-system r-build-system)
10454 (list r-biocgenerics
10462 r-summarizedexperiment))
10465 (home-page "https://github.com/hansenlab/yamss")
10466 (synopsis "Tools for high-throughput metabolomics")
10468 "This package provides tools to analyze and visualize high-throughput
10469 metabolomics data acquired using chromatography-mass spectrometry. These tools
10470 preprocess data in a way that enables reliable and powerful differential
10472 (license license:artistic2.0)))
10474 (define-public r-gtrellis
10476 (name "r-gtrellis")
10481 (uri (bioconductor-uri "gtrellis" version))
10484 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
10485 (build-system r-build-system)
10487 (list r-circlize r-genomicranges r-getoptlong r-iranges))
10490 (home-page "https://github.com/jokergoo/gtrellis")
10491 (synopsis "Genome level Trellis layout")
10493 "Genome level Trellis graph visualizes genomic data conditioned by
10494 genomic categories (e.g. chromosomes). For each genomic category, multiple
10495 dimensional data which are represented as tracks describe different features
10496 from different aspects. This package provides high flexibility to arrange
10497 genomic categories and to add self-defined graphics in the plot.")
10498 (license license:expat)))
10500 (define-public r-somaticsignatures
10502 (name "r-somaticsignatures")
10507 (uri (bioconductor-uri "SomaticSignatures" version))
10510 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
10512 `((upstream-name . "SomaticSignatures")))
10513 (build-system r-build-system)
10527 r-variantannotation))
10530 (home-page "https://github.com/juliangehring/SomaticSignatures")
10531 (synopsis "Somatic signatures")
10533 "This package identifies mutational signatures of @dfn{single nucleotide
10534 variants} (SNVs). It provides a infrastructure related to the methodology
10535 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
10536 decomposition algorithms.")
10537 (license license:expat)))
10539 (define-public r-yapsa
10546 (uri (bioconductor-uri "YAPSA" version))
10549 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
10550 (properties `((upstream-name . "YAPSA")))
10551 (build-system r-build-system)
10554 r-bsgenome-hsapiens-ucsc-hg19
10574 r-somaticsignatures
10575 r-variantannotation))
10578 (home-page "https://bioconductor.org/packages/YAPSA/")
10579 (synopsis "Yet another package for signature analysis")
10581 "This package provides functions and routines useful in the analysis of
10582 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
10583 functions to perform a signature analysis with known signatures and a
10584 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
10586 (license license:gpl3)))
10588 (define-public r-gcrma
10595 (uri (bioconductor-uri "gcrma" version))
10598 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
10599 (build-system r-build-system)
10607 (home-page "https://bioconductor.org/packages/gcrma/")
10608 (synopsis "Background adjustment using sequence information")
10610 "Gcrma adjusts for background intensities in Affymetrix array data which
10611 include optical noise and @dfn{non-specific binding} (NSB). The main function
10612 @code{gcrma} converts background adjusted probe intensities to expression
10613 measures using the same normalization and summarization methods as a
10614 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
10615 to estimate probe affinity to NSB. The sequence information is summarized in
10616 a more complex way than the simple GC content. Instead, the base types (A, T,
10617 G or C) at each position along the probe determine the affinity of each probe.
10618 The parameters of the position-specific base contributions to the probe
10619 affinity is estimated in an NSB experiment in which only NSB but no
10620 gene-specific binding is expected.")
10621 ;; Any version of the LGPL
10622 (license license:lgpl2.1+)))
10624 (define-public r-simpleaffy
10626 (name "r-simpleaffy")
10631 (uri (bioconductor-uri "simpleaffy" version))
10634 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
10635 (build-system r-build-system)
10637 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
10638 (home-page "https://bioconductor.org/packages/simpleaffy/")
10639 (synopsis "Very simple high level analysis of Affymetrix data")
10641 "This package provides high level functions for reading Affy @file{.CEL}
10642 files, phenotypic data, and then computing simple things with it, such as
10643 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
10644 library. It also has some basic scatter plot functions and mechanisms for
10645 generating high resolution journal figures.")
10646 (license license:gpl2+)))
10648 (define-public r-yaqcaffy
10650 (name "r-yaqcaffy")
10655 (uri (bioconductor-uri "yaqcaffy" version))
10658 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
10659 (build-system r-build-system)
10661 (list r-simpleaffy))
10662 (home-page "https://bioconductor.org/packages/yaqcaffy/")
10663 (synopsis "Affymetrix quality control and reproducibility analysis")
10665 "This is a package that can be used for quality control of Affymetrix
10666 GeneChip expression data and reproducibility analysis of human whole genome
10667 chips with the MAQC reference datasets.")
10668 (license license:artistic2.0)))
10670 (define-public r-quantro
10677 (uri (bioconductor-uri "quantro" version))
10680 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
10681 (build-system r-build-system)
10692 (home-page "https://bioconductor.org/packages/quantro/")
10693 (synopsis "Test for when to use quantile normalization")
10695 "This package provides a data-driven test for the assumptions of quantile
10696 normalization using raw data such as objects that inherit eSets (e.g.
10697 ExpressionSet, MethylSet). Group level information about each sample (such as
10698 Tumor / Normal status) must also be provided because the test assesses if
10699 there are global differences in the distributions between the user-defined
10701 (license license:gpl3+)))
10703 (define-public r-yarn
10710 (uri (bioconductor-uri "yarn" version))
10713 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
10714 (build-system r-build-system)
10729 (home-page "https://bioconductor.org/packages/yarn/")
10730 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
10732 "Expedite large RNA-Seq analyses using a combination of previously
10733 developed tools. YARN is meant to make it easier for the user in performing
10734 basic mis-annotation quality control, filtering, and condition-aware
10735 normalization. YARN leverages many Bioconductor tools and statistical
10736 techniques to account for the large heterogeneity and sparsity found in very
10737 large RNA-seq experiments.")
10738 (license license:artistic2.0)))
10740 (define-public r-roar
10747 (uri (bioconductor-uri "roar" version))
10750 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
10751 (build-system r-build-system)
10753 (list r-biocgenerics
10755 r-genomicalignments
10760 r-summarizedexperiment))
10761 (home-page "https://github.com/vodkatad/roar/")
10762 (synopsis "Identify differential APA usage from RNA-seq alignments")
10764 "This package provides tools for identifying preferential usage of APA
10765 sites, comparing two biological conditions, starting from known alternative
10766 sites and alignments obtained from standard RNA-seq experiments.")
10767 (license license:gpl3)))
10769 (define-public r-xbseq
10776 (uri (bioconductor-uri "XBSeq" version))
10779 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
10780 (properties `((upstream-name . "XBSeq")))
10781 (build-system r-build-system)
10794 (home-page "https://github.com/Liuy12/XBSeq")
10795 (synopsis "Test for differential expression for RNA-seq data")
10797 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
10798 expression} (DE), where a statistical model was established based on the
10799 assumption that observed signals are the convolution of true expression
10800 signals and sequencing noises. The mapped reads in non-exonic regions are
10801 considered as sequencing noises, which follows a Poisson distribution. Given
10802 measurable observed signal and background noise from RNA-seq data, true
10803 expression signals, assuming governed by the negative binomial distribution,
10804 can be delineated and thus the accurate detection of differential expressed
10806 (license license:gpl3+)))
10808 (define-public r-massspecwavelet
10810 (name "r-massspecwavelet")
10815 (uri (bioconductor-uri "MassSpecWavelet" version))
10818 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
10820 `((upstream-name . "MassSpecWavelet")))
10821 (build-system r-build-system)
10824 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
10825 (synopsis "Mass spectrum processing by wavelet-based algorithms")
10827 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
10828 data mainly through the use of wavelet transforms. It supports peak detection
10829 based on @dfn{Continuous Wavelet Transform} (CWT).")
10830 (license license:lgpl2.0+)))
10832 (define-public r-xcms
10839 (uri (bioconductor-uri "xcms" version))
10842 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
10843 (build-system r-build-system)
10861 r-summarizedexperiment))
10864 (home-page "https://bioconductor.org/packages/xcms/")
10865 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
10867 "This package provides a framework for processing and visualization of
10868 chromatographically separated and single-spectra mass spectral data. It
10869 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
10870 data for high-throughput, untargeted analyte profiling.")
10871 (license license:gpl2+)))
10873 (define-public r-wppi
10879 (uri (bioconductor-uri "wppi" version))
10882 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
10883 (properties `((upstream-name . "wppi")))
10884 (build-system r-build-system)
10885 ;; This is necessary because omnipathr attempts to write a configuration
10889 (modify-phases %standard-phases
10890 (add-after 'unpack 'set-HOME
10891 (lambda _ (setenv "HOME" "/tmp"))))))
10892 (propagated-inputs (list r-dplyr
10904 (native-inputs (list r-knitr))
10905 (home-page "https://github.com/AnaGalhoz37/wppi")
10906 (synopsis "Weighting protein-protein interactions")
10908 "This package predicts functional relevance of protein-protein
10909 interactions based on functional annotations such as Human Protein Ontology
10910 and Gene Ontology, and prioritizes genes based on network topology, functional
10911 scores and a path search algorithm.")
10912 (license license:expat)))
10914 (define-public r-wrench
10921 (uri (bioconductor-uri "Wrench" version))
10924 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
10925 (properties `((upstream-name . "Wrench")))
10926 (build-system r-build-system)
10928 (list r-limma r-locfit r-matrixstats))
10931 (home-page "https://github.com/HCBravoLab/Wrench")
10932 (synopsis "Wrench normalization for sparse count data")
10934 "Wrench is a package for normalization sparse genomic count data, like
10935 that arising from 16s metagenomic surveys.")
10936 (license license:artistic2.0)))
10938 (define-public r-wiggleplotr
10940 (name "r-wiggleplotr")
10945 (uri (bioconductor-uri "wiggleplotr" version))
10948 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
10949 (build-system r-build-system)
10963 (home-page "https://bioconductor.org/packages/wiggleplotr/")
10964 (synopsis "Make read coverage plots from BigWig files")
10966 "This package provides tools to visualize read coverage from sequencing
10967 experiments together with genomic annotations (genes, transcripts, peaks).
10968 Introns of long transcripts can be rescaled to a fixed length for better
10969 visualization of exonic read coverage.")
10970 (license license:asl2.0)))
10972 (define-public r-widgettools
10974 (name "r-widgettools")
10979 (uri (bioconductor-uri "widgetTools" version))
10982 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
10983 (properties `((upstream-name . "widgetTools")))
10984 (build-system r-build-system)
10985 (home-page "https://bioconductor.org/packages/widgetTools/")
10986 (synopsis "Tools for creating interactive tcltk widgets")
10988 "This package contains tools to support the construction of tcltk
10990 ;; Any version of the LGPL.
10991 (license license:lgpl3+)))
10993 (define-public r-webbioc
11000 (uri (bioconductor-uri "webbioc" version))
11003 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
11004 (build-system r-build-system)
11006 (list netpbm perl))
11016 (home-page "https://www.bioconductor.org/")
11017 (synopsis "Bioconductor web interface")
11019 "This package provides an integrated web interface for doing microarray
11020 analysis using several of the Bioconductor packages. It is intended to be
11021 deployed as a centralized bioinformatics resource for use by many users.
11022 Currently only Affymetrix oligonucleotide analysis is supported.")
11023 (license license:gpl2+)))
11025 (define-public r-zinbwave
11027 (name "r-zinbwave")
11032 (uri (bioconductor-uri "zinbwave" version))
11035 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
11036 (build-system r-build-system)
11038 (list r-biocparallel
11042 r-singlecellexperiment
11044 r-summarizedexperiment))
11047 (home-page "https://bioconductor.org/packages/zinbwave")
11048 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
11049 (description "This package implements a general and flexible zero-inflated
11050 negative binomial model that can be used to provide a low-dimensional
11051 representations of single-cell RNA-seq data. The model accounts for zero
11052 inflation (dropouts), over-dispersion, and the count nature of the data.
11053 The model also accounts for the difference in library sizes and optionally
11054 for batch effects and/or other covariates, avoiding the need for pre-normalize
11056 (license license:artistic2.0)))
11058 (define-public r-zfpkm
11065 (uri (bioconductor-uri "zFPKM" version))
11068 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
11069 (properties `((upstream-name . "zFPKM")))
11070 (build-system r-build-system)
11072 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
11075 (home-page "https://github.com/ronammar/zFPKM/")
11076 (synopsis "Functions to facilitate zFPKM transformations")
11078 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
11079 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
11081 (license license:gpl3)))
11083 (define-public r-rbowtie2
11085 (name "r-rbowtie2")
11090 (uri (bioconductor-uri "Rbowtie2" version))
11093 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
11094 (properties `((upstream-name . "Rbowtie2")))
11095 (build-system r-build-system)
11097 (list r-magrittr r-rsamtools))
11099 (list samtools zlib))
11102 (home-page "https://bioconductor.org/packages/Rbowtie2/")
11103 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
11105 "This package provides an R wrapper of the popular @code{bowtie2}
11106 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
11107 rapid adapter trimming, identification, and read merging.")
11108 (license license:gpl3+)))
11110 (define-public r-progeny
11117 (uri (bioconductor-uri "progeny" version))
11120 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
11121 (build-system r-build-system)
11133 (home-page "https://github.com/saezlab/progeny")
11134 (synopsis "Pathway responsive gene activity inference")
11136 "This package provides a function to infer pathway activity from gene
11137 expression. It contains the linear model inferred in the publication
11138 \"Perturbation-response genes reveal signaling footprints in cancer gene
11140 (license license:asl2.0)))
11142 (define-public r-arrmnormalization
11144 (name "r-arrmnormalization")
11149 (uri (bioconductor-uri "ARRmNormalization" version))
11152 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
11154 `((upstream-name . "ARRmNormalization")))
11155 (build-system r-build-system)
11156 (propagated-inputs (list r-arrmdata))
11157 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
11158 (synopsis "Adaptive robust regression normalization for methylation data")
11160 "This is a package to perform the @dfn{Adaptive Robust Regression
11161 method} (ARRm) for the normalization of methylation data from the Illumina
11162 Infinium HumanMethylation 450k assay.")
11163 (license license:artistic2.0)))
11165 (define-public r-biocfilecache
11167 (name "r-biocfilecache")
11172 (uri (bioconductor-uri "BiocFileCache" version))
11175 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
11176 (properties `((upstream-name . "BiocFileCache")))
11177 (build-system r-build-system)
11189 (home-page "https://bioconductor.org/packages/BiocFileCache/")
11190 (synopsis "Manage files across sessions")
11192 "This package creates a persistent on-disk cache of files that the user
11193 can add, update, and retrieve. It is useful for managing resources (such as
11194 custom Txdb objects) that are costly or difficult to create, web resources,
11195 and data files used across sessions.")
11196 (license license:artistic2.0)))
11198 (define-public r-iclusterplus
11200 (name "r-iclusterplus")
11205 (uri (bioconductor-uri "iClusterPlus" version))
11208 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
11209 (properties `((upstream-name . "iClusterPlus")))
11210 (build-system r-build-system)
11211 (native-inputs (list gfortran))
11212 (home-page "https://bioconductor.org/packages/iClusterPlus/")
11213 (synopsis "Integrative clustering of multi-type genomic data")
11215 "iClusterPlus is developed for integrative clustering analysis of
11216 multi-type genomic data and is an enhanced version of iCluster proposed and
11217 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
11218 from the experiments where biological samples (e.g. tumor samples) are
11219 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
11220 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
11221 on. In the iClusterPlus model, binary observations such as somatic mutation
11222 are modeled as Binomial processes; categorical observations such as copy
11223 number states are realizations of Multinomial random variables; counts are
11224 modeled as Poisson random processes; and continuous measures are modeled by
11225 Gaussian distributions.")
11226 (license license:gpl2+)))
11228 (define-public r-rbowtie
11235 (uri (bioconductor-uri "Rbowtie" version))
11238 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
11239 (properties `((upstream-name . "Rbowtie")))
11240 (build-system r-build-system)
11243 ;; Disable unsupported `popcnt' instructions on
11244 ;; architectures other than x86_64
11245 ,(if (string-prefix? "x86_64"
11246 (or (%current-target-system)
11247 (%current-system)))
11249 '(modify-phases %standard-phases
11250 (add-after 'unpack 'patch-sources
11252 (setenv "POPCNT_CAPABILITY" "0")))))))
11253 (inputs (list zlib))
11256 (home-page "https://bioconductor.org/packages/Rbowtie/")
11257 (synopsis "R bowtie wrapper")
11259 "This package provides an R wrapper around the popular bowtie short read
11260 aligner and around SpliceMap, a de novo splice junction discovery and
11262 (license license:artistic2.0)))
11264 (define-public r-sgseq
11271 (uri (bioconductor-uri "SGSeq" version))
11274 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
11275 (properties `((upstream-name . "SGSeq")))
11276 (build-system r-build-system)
11278 (list r-annotationdbi
11282 r-genomicalignments
11291 r-summarizedexperiment))
11294 (home-page "https://bioconductor.org/packages/SGSeq/")
11295 (synopsis "Splice event prediction and quantification from RNA-seq data")
11297 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
11298 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
11299 represented as a splice graph, which can be obtained from existing annotation
11300 or predicted from the mapped sequence reads. Splice events are identified
11301 from the graph and are quantified locally using structurally compatible reads
11302 at the start or end of each splice variant. The software includes functions
11303 for splice event prediction, quantification, visualization and
11305 (license license:artistic2.0)))
11307 (define-public r-rhisat2
11314 (uri (bioconductor-uri "Rhisat2" version))
11317 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
11318 (properties `((upstream-name . "Rhisat2")))
11319 (build-system r-build-system)
11322 (modify-phases %standard-phases
11323 (add-after 'unpack 'make-reproducible
11325 (substitute* "src/Makefile"
11326 (("`hostname`") "guix")
11328 ;; Avoid shelling out to "which".
11329 (("^CC =.*") (which "gcc"))
11330 (("^CPP =.*") (which "g++")))
11333 (list r-genomicfeatures r-genomicranges r-sgseq))
11336 (home-page "https://github.com/fmicompbio/Rhisat2")
11337 (synopsis "R Wrapper for HISAT2 sequence aligner")
11339 "This package provides an R interface to the HISAT2 spliced short-read
11340 aligner by Kim et al. (2015). The package contains wrapper functions to
11341 create a genome index and to perform the read alignment to the generated
11343 (license license:gpl3)))
11345 (define-public r-quasr
11352 (uri (bioconductor-uri "QuasR" version))
11355 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
11356 (properties `((upstream-name . "QuasR")))
11357 (build-system r-build-system)
11359 (list r-annotationdbi
11378 (home-page "https://bioconductor.org/packages/QuasR/")
11379 (synopsis "Quantify and annotate short reads in R")
11381 "This package provides a framework for the quantification and analysis of
11382 short genomic reads. It covers a complete workflow starting from raw sequence
11383 reads, over creation of alignments and quality control plots, to the
11384 quantification of genomic regions of interest.")
11385 (license license:gpl2)))
11387 (define-public r-rqc
11394 (uri (bioconductor-uri "Rqc" version))
11397 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
11398 (properties `((upstream-name . "Rqc")))
11399 (build-system r-build-system)
11401 (list r-biocgenerics
11406 r-genomicalignments
11421 (home-page "https://github.com/labbcb/Rqc")
11422 (synopsis "Quality control tool for high-throughput sequencing data")
11424 "Rqc is an optimized tool designed for quality control and assessment of
11425 high-throughput sequencing data. It performs parallel processing of entire
11426 files and produces a report which contains a set of high-resolution
11428 (license license:gpl2+)))
11430 (define-public r-birewire
11432 (name "r-birewire")
11437 (uri (bioconductor-uri "BiRewire" version))
11440 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
11441 (properties `((upstream-name . "BiRewire")))
11442 (build-system r-build-system)
11444 (list r-igraph r-matrix r-rtsne r-slam))
11445 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
11446 (synopsis "Tools for randomization of bipartite graphs")
11448 "This package provides functions for bipartite network rewiring through N
11449 consecutive switching steps and for the computation of the minimal number of
11450 switching steps to be performed in order to maximise the dissimilarity with
11451 respect to the original network. It includes functions for the analysis of
11452 the introduced randomness across the switching steps and several other
11453 routines to analyse the resulting networks and their natural projections.")
11454 (license license:gpl3)))
11456 (define-public r-birta
11463 (uri (bioconductor-uri "birta" version))
11466 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
11467 (build-system r-build-system)
11469 (list r-biobase r-limma r-mass))
11470 (home-page "https://bioconductor.org/packages/birta")
11471 (synopsis "Bayesian inference of regulation of transcriptional activity")
11473 "Expression levels of mRNA molecules are regulated by different
11474 processes, comprising inhibition or activation by transcription factors and
11475 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
11476 Inference of Regulation of Transcriptional Activity) uses the regulatory
11477 networks of transcription factors and miRNAs together with mRNA and miRNA
11478 expression data to predict switches in regulatory activity between two
11479 conditions. A Bayesian network is used to model the regulatory structure and
11480 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
11481 (license license:gpl2+)))
11483 (define-public r-multidataset
11485 (name "r-multidataset")
11490 (uri (bioconductor-uri "MultiDataSet" version))
11493 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
11494 (properties `((upstream-name . "MultiDataSet")))
11495 (build-system r-build-system)
11506 r-summarizedexperiment))
11509 (home-page "https://bioconductor.org/packages/MultiDataSet/")
11510 (synopsis "Implementation of MultiDataSet and ResultSet")
11512 "This package provides an implementation of the BRGE's (Bioinformatic
11513 Research Group in Epidemiology from Center for Research in Environmental
11514 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
11515 integrating multi omics data sets and ResultSet is a container for omics
11516 results. This package contains base classes for MEAL and rexposome
11518 (license license:expat)))
11520 (define-public r-ropls
11527 (uri (bioconductor-uri "ropls" version))
11530 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
11531 (build-system r-build-system)
11534 r-multiassayexperiment
11536 r-summarizedexperiment))
11538 (list r-knitr)) ; for vignettes
11539 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
11540 (synopsis "Multivariate analysis and feature selection of omics data")
11542 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
11543 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
11544 regression, classification, and feature selection of omics data where the
11545 number of variables exceeds the number of samples and with multicollinearity
11546 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
11547 separately model the variation correlated (predictive) to the factor of
11548 interest and the uncorrelated (orthogonal) variation. While performing
11549 similarly to PLS, OPLS facilitates interpretation.
11551 This package provides imlementations of PCA, PLS, and OPLS for multivariate
11552 analysis and feature selection of omics data. In addition to scores, loadings
11553 and weights plots, the package provides metrics and graphics to determine the
11554 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
11555 validity of the model by permutation testing, detect outliers, and perform
11556 feature selection (e.g. with Variable Importance in Projection or regression
11558 (license license:cecill)))
11560 (define-public r-biosigner
11562 (name "r-biosigner")
11567 (uri (bioconductor-uri "biosigner" version))
11570 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
11571 (build-system r-build-system)
11575 r-multiassayexperiment
11579 r-summarizedexperiment))
11582 (home-page "https://bioconductor.org/packages/biosigner/")
11583 (synopsis "Signature discovery from omics data")
11585 "Feature selection is critical in omics data analysis to extract
11586 restricted and meaningful molecular signatures from complex and high-dimension
11587 data, and to build robust classifiers. This package implements a method to
11588 assess the relevance of the variables for the prediction performances of the
11589 classifier. The approach can be run in parallel with the PLS-DA, Random
11590 Forest, and SVM binary classifiers. The signatures and the corresponding
11591 'restricted' models are returned, enabling future predictions on new
11593 (license license:cecill)))
11595 (define-public r-annotatr
11597 (name "r-annotatr")
11602 (uri (bioconductor-uri "annotatr" version))
11605 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
11606 (build-system r-build-system)
11608 (list r-annotationdbi
11623 (home-page "https://bioconductor.org/packages/annotatr/")
11624 (synopsis "Annotation of genomic regions to genomic annotations")
11626 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
11627 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
11628 to investigate the intersecting genomic annotations. Such annotations include
11629 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
11630 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
11631 enhancers. The annotatr package provides an easy way to summarize and
11632 visualize the intersection of genomic sites/regions with genomic
11634 (license license:gpl3)))
11636 (define-public r-rsubread
11638 (name "r-rsubread")
11643 (uri (bioconductor-uri "Rsubread" version))
11646 "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2"))))
11647 (properties `((upstream-name . "Rsubread")))
11648 (build-system r-build-system)
11649 (inputs (list zlib))
11652 (home-page "https://bioconductor.org/packages/Rsubread/")
11653 (synopsis "Subread sequence alignment and counting for R")
11655 "This package provides tools for alignment, quantification and analysis
11656 of second and third generation sequencing data. It includes functionality for
11657 read mapping, read counting, SNP calling, structural variant detection and
11658 gene fusion discovery. It can be applied to all major sequencing techologies
11659 and to both short and long sequence reads.")
11660 (license license:gpl3)))
11662 (define-public r-flowutils
11664 (name "r-flowutils")
11669 (uri (bioconductor-uri "flowUtils" version))
11672 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
11673 (properties `((upstream-name . "flowUtils")))
11674 (build-system r-build-system)
11682 (home-page "https://github.com/jspidlen/flowUtils")
11683 (synopsis "Utilities for flow cytometry")
11685 "This package provides utilities for flow cytometry data.")
11686 (license license:artistic2.0)))
11688 (define-public r-consensusclusterplus
11690 (name "r-consensusclusterplus")
11695 (uri (bioconductor-uri "ConsensusClusterPlus" version))
11698 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
11700 `((upstream-name . "ConsensusClusterPlus")))
11701 (build-system r-build-system)
11703 (list r-all r-biobase r-cluster))
11704 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
11705 (synopsis "Clustering algorithm")
11707 "This package provides an implementation of an algorithm for determining
11708 cluster count and membership by stability evidence in unsupervised analysis.")
11709 (license license:gpl2)))
11711 ;; This is the latest commit and it solves a bug from the latest release.
11712 (define-public r-cycombine
11713 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
11715 (name "r-cycombine")
11716 (version (git-version "0.2.6" revision commit))
11719 (uri (git-reference
11720 (url "https://github.com/biosurf/cyCombine")
11722 (file-name (git-file-name name version))
11725 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
11726 (properties `((upstream-name . "cyCombine")))
11727 (build-system r-build-system)
11745 (native-inputs (list r-knitr))
11746 (home-page "https://github.com/biosurf/cyCombine")
11747 (synopsis "Integration of single-cell cytometry datasets")
11749 "This package provides a method for combining single-cell cytometry
11750 datasets, which increases the analytical flexibility and the statistical power
11751 of the analyses while minimizing technical noise.")
11752 (license license:expat))))
11754 (define-public r-cytolib
11761 (uri (bioconductor-uri "cytolib" version))
11764 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
11765 (properties `((upstream-name . "cytolib")))
11766 (build-system r-build-system)
11776 (home-page "https://bioconductor.org/packages/cytolib/")
11777 (synopsis "C++ infrastructure for working with gated cytometry")
11779 "This package provides the core data structure and API to represent and
11780 interact with gated cytometry data.")
11781 (license license:artistic2.0)))
11783 (define-public r-flowcore
11785 (name "r-flowcore")
11790 (uri (bioconductor-uri "flowCore" version))
11793 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
11794 (properties `((upstream-name . "flowCore")))
11795 (build-system r-build-system)
11808 (home-page "https://bioconductor.org/packages/flowCore")
11809 (synopsis "Basic structures for flow cytometry data")
11811 "This package provides S4 data structures and basic functions to deal
11812 with flow cytometry data.")
11813 (license license:artistic2.0)))
11815 (define-public r-flowmeans
11817 (name "r-flowmeans")
11822 (uri (bioconductor-uri "flowMeans" version))
11825 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
11826 (properties `((upstream-name . "flowMeans")))
11827 (build-system r-build-system)
11829 (list r-biobase r-feature r-flowcore r-rrcov))
11830 (home-page "https://bioconductor.org/packages/flowMeans")
11831 (synopsis "Non-parametric flow cytometry data gating")
11833 "This package provides tools to identify cell populations in Flow
11834 Cytometry data using non-parametric clustering and segmented-regression-based
11835 change point detection.")
11836 (license license:artistic2.0)))
11838 (define-public r-ncdfflow
11840 (name "r-ncdfflow")
11845 (uri (bioconductor-uri "ncdfFlow" version))
11848 "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7"))))
11849 (properties `((upstream-name . "ncdfFlow")))
11850 (build-system r-build-system)
11862 (home-page "https://bioconductor.org/packages/ncdfFlow/")
11863 (synopsis "HDF5 based storage for flow cytometry data")
11865 "This package provides HDF5 storage based methods and functions for
11866 manipulation of flow cytometry data.")
11867 (license license:artistic2.0)))
11869 (define-public r-ggcyto
11876 (uri (bioconductor-uri "ggcyto" version))
11879 "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325"))))
11880 (properties `((upstream-name . "ggcyto")))
11881 (build-system r-build-system)
11896 (home-page "https://github.com/RGLab/ggcyto/issues")
11897 (synopsis "Visualize Cytometry data with ggplot")
11899 "With the dedicated fortify method implemented for @code{flowSet},
11900 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
11901 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
11902 and some custom layers also make it easy to add gates and population
11903 statistics to the plot.")
11904 (license license:artistic2.0)))
11906 (define-public r-flowviz
11913 (uri (bioconductor-uri "flowViz" version))
11916 "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95"))))
11917 (properties `((upstream-name . "flowViz")))
11918 (build-system r-build-system)
11931 (home-page "https://bioconductor.org/packages/flowViz/")
11932 (synopsis "Visualization for flow cytometry")
11934 "This package provides visualization tools for flow cytometry data.")
11935 (license license:artistic2.0)))
11937 (define-public r-flowclust
11939 (name "r-flowclust")
11944 (uri (bioconductor-uri "flowClust" version))
11947 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
11948 (properties `((upstream-name . "flowClust")))
11949 (build-system r-build-system)
11951 `(#:configure-flags
11952 (list "--configure-args=--enable-bundled-gsl=no")))
11961 (list pkg-config r-knitr))
11962 (home-page "https://bioconductor.org/packages/flowClust")
11963 (synopsis "Clustering for flow cytometry")
11965 "This package provides robust model-based clustering using a t-mixture
11966 model with Box-Cox transformation.")
11967 (license license:artistic2.0)))
11969 ;; TODO: this package bundles an old version of protobuf. It's not easy to
11970 ;; make it use our protobuf package instead.
11971 (define-public r-rprotobuflib
11973 (name "r-rprotobuflib")
11978 (uri (bioconductor-uri "RProtoBufLib" version))
11981 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
11982 (properties `((upstream-name . "RProtoBufLib")))
11983 (build-system r-build-system)
11986 (modify-phases %standard-phases
11987 (add-after 'unpack 'unpack-bundled-sources
11989 (with-directory-excursion "src"
11990 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
11993 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
11994 (synopsis "C++ headers and static libraries of Protocol buffers")
11996 "This package provides the headers and static library of Protocol buffers
11997 for other R packages to compile and link against.")
11998 (license license:bsd-3)))
12000 (define-public r-flowworkspace
12002 (name "r-flowworkspace")
12007 (uri (bioconductor-uri "flowWorkspace" version))
12010 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
12011 (properties `((upstream-name . "flowWorkspace")))
12012 (build-system r-build-system)
12043 (home-page "https://bioconductor.org/packages/flowWorkspace/")
12044 (synopsis "Infrastructure for working with cytometry data")
12046 "This package is designed to facilitate comparison of automated gating
12047 methods against manual gating done in flowJo. This package allows you to
12048 import basic flowJo workspaces into BioConductor and replicate the gating from
12049 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
12050 samples, compensation, and transformation are performed so that the output
12051 matches the flowJo analysis.")
12052 (license license:artistic2.0)))
12054 (define-public r-flowstats
12056 (name "r-flowstats")
12061 (uri (bioconductor-uri "flowStats" version))
12064 "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc"))))
12065 (properties `((upstream-name . "flowStats")))
12066 (build-system r-build-system)
12084 (home-page "http://www.github.com/RGLab/flowStats")
12085 (synopsis "Statistical methods for the analysis of flow cytometry data")
12087 "This package provides methods and functionality to analyze flow data
12088 that is beyond the basic infrastructure provided by the @code{flowCore}
12090 (license license:artistic2.0)))
12092 (define-public r-opencyto
12094 (name "r-opencyto")
12099 (uri (bioconductor-uri "openCyto" version))
12102 "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0"))))
12103 (properties `((upstream-name . "openCyto")))
12104 (build-system r-build-system)
12129 (home-page "https://bioconductor.org/packages/openCyto")
12130 (synopsis "Hierarchical gating pipeline for flow cytometry data")
12132 "This package is designed to facilitate the automated gating methods in a
12133 sequential way to mimic the manual gating strategy.")
12134 (license license:artistic2.0)))
12136 (define-public r-cytoml
12143 (uri (bioconductor-uri "CytoML" version))
12146 "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw"))))
12147 (properties `((upstream-name . "CytoML")))
12148 (build-system r-build-system)
12150 (list libxml2 zlib))
12181 (home-page "https://github.com/RGLab/CytoML")
12182 (synopsis "GatingML interface for cross platform cytometry data sharing")
12184 "This package provides an interface to implementations of the GatingML2.0
12185 standard to exchange gated cytometry data with other software platforms.")
12186 (license license:artistic2.0)))
12188 (define-public r-flowsom
12195 (uri (bioconductor-uri "FlowSOM" version))
12198 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
12199 (properties `((upstream-name . "FlowSOM")))
12200 (build-system r-build-system)
12202 (list r-biocgenerics
12204 r-consensusclusterplus
12224 (home-page "https://bioconductor.org/packages/FlowSOM/")
12225 (synopsis "Visualize and interpret cytometry data")
12227 "FlowSOM offers visualization options for cytometry data, by using
12228 self-organizing map clustering and minimal spanning trees.")
12229 (license license:gpl2+)))
12231 (define-public r-mixomics
12233 (name "r-mixomics")
12238 (uri (bioconductor-uri "mixOmics" version))
12241 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
12242 (properties `((upstream-name . "mixOmics")))
12243 (build-system r-build-system)
12245 (list r-biocparallel
12262 (home-page "http://www.mixOmics.org")
12263 (synopsis "Multivariate methods for exploration of biological datasets")
12265 "mixOmics offers a wide range of multivariate methods for the exploration
12266 and integration of biological datasets with a particular focus on variable
12267 selection. The package proposes several sparse multivariate models we have
12268 developed to identify the key variables that are highly correlated, and/or
12269 explain the biological outcome of interest. The data that can be analysed
12270 with mixOmics may come from high throughput sequencing technologies, such as
12271 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
12272 also beyond the realm of omics (e.g. spectral imaging). The methods
12273 implemented in mixOmics can also handle missing values without having to
12274 delete entire rows with missing data.")
12275 (license license:gpl2+)))
12277 (define-public r-depecher
12278 (package ;Source/Weave error
12279 (name "r-depecher")
12284 (uri (bioconductor-uri "DepecheR" version))
12287 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
12288 (properties `((upstream-name . "DepecheR")))
12289 (build-system r-build-system)
12310 (home-page "https://bioconductor.org/packages/DepecheR/")
12311 (synopsis "Identify traits of clusters in high-dimensional entities")
12313 "The purpose of this package is to identify traits in a dataset that can
12314 separate groups. This is done on two levels. First, clustering is performed,
12315 using an implementation of sparse K-means. Secondly, the generated clusters
12316 are used to predict outcomes of groups of individuals based on their
12317 distribution of observations in the different clusters. As certain clusters
12318 with separating information will be identified, and these clusters are defined
12319 by a sparse number of variables, this method can reduce the complexity of
12320 data, to only emphasize the data that actually matters.")
12321 (license license:expat)))
12323 (define-public r-rcistarget
12325 (name "r-rcistarget")
12330 (uri (bioconductor-uri "RcisTarget" version))
12333 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
12334 (properties `((upstream-name . "RcisTarget")))
12335 (build-system r-build-system)
12347 r-summarizedexperiment
12351 (home-page "https://aertslab.org/#scenic")
12352 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
12354 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
12355 over-represented on a gene list. In a first step, RcisTarget selects DNA
12356 motifs that are significantly over-represented in the surroundings of the
12357 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
12358 achieved by using a database that contains genome-wide cross-species rankings
12359 for each motif. The motifs that are then annotated to TFs and those that have
12360 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
12361 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
12362 genes in the gene-set that are ranked above the leading edge).")
12363 (license license:gpl3)))
12365 (define-public r-chicago
12372 (uri (bioconductor-uri "Chicago" version))
12375 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
12376 (properties `((upstream-name . "Chicago")))
12377 (build-system r-build-system)
12379 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
12380 (native-inputs (list r-knitr))
12381 (home-page "https://bioconductor.org/packages/Chicago")
12382 (synopsis "Capture Hi-C analysis of genomic organization")
12384 "This package provides a pipeline for analysing Capture Hi-C data.")
12385 (license license:artistic2.0)))
12387 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12389 (define-public r-ciara
12395 (uri (cran-uri "CIARA" version))
12398 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
12399 (properties `((upstream-name . "CIARA")))
12400 (build-system r-build-system)
12401 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
12402 (native-inputs (list r-knitr))
12403 (home-page "https://cran.r-project.org/package=CIARA")
12404 (synopsis "Cluster-independent algorithm for rare cell types identification")
12406 "This is a package to support identification of markers of rare cell
12407 types by looking at genes whose expression is confined in small regions of the
12408 expression space.")
12409 (license license:artistic2.0)))
12411 (define-public r-cicero
12418 (uri (bioconductor-uri "cicero" version))
12421 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
12422 (build-system r-build-system)
12448 (home-page "https://bioconductor.org/packages/cicero/")
12449 (synopsis "Predict cis-co-accessibility from single-cell data")
12451 "Cicero computes putative cis-regulatory maps from single-cell chromatin
12452 accessibility data. It also extends the monocle package for use in chromatin
12453 accessibility data.")
12454 (license license:expat)))
12456 ;; This is the latest commit on the "monocle3" branch.
12457 (define-public r-cicero-monocle3
12458 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
12460 (package (inherit r-cicero)
12461 (name "r-cicero-monocle3")
12462 (version (git-version "1.3.2" revision commit))
12466 (uri (git-reference
12467 (url "https://github.com/cole-trapnell-lab/cicero-release")
12469 (file-name (git-file-name name version))
12472 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
12474 (modify-inputs (package-propagated-inputs r-cicero)
12475 (delete "r-monocle")
12476 (prepend r-monocle3))))))
12478 (define-public r-circrnaprofiler
12480 (name "r-circrnaprofiler")
12485 (uri (bioconductor-uri "circRNAprofiler" version))
12488 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
12490 `((upstream-name . "circRNAprofiler")))
12491 (build-system r-build-system)
12493 (list r-annotationhub
12496 r-bsgenome-hsapiens-ucsc-hg19
12519 "https://github.com/Aufiero/circRNAprofiler")
12521 "Computational framework for the downstream analysis of circular RNA's")
12523 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
12524 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
12525 framework allows combining and analyzing circRNAs previously detected by
12526 multiple publicly available annotation-based circRNA detection tools. It
12527 covers different aspects of circRNAs analysis from differential expression
12528 analysis, evolutionary conservation, biogenesis to functional analysis.")
12529 (license license:gpl3)))
12531 (define-public r-cistopic
12533 (name "r-cistopic")
12538 (uri (git-reference
12539 (url "https://github.com/aertslab/cisTopic")
12540 (commit (string-append "v" version))))
12541 (file-name (git-file-name name version))
12544 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
12545 (build-system r-build-system)
12562 (home-page "https://github.com/aertslab/cisTopic")
12563 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
12565 "The sparse nature of single cell epigenomics data can be overruled using
12566 probabilistic modelling methods such as @dfn{Latent Dirichlet
12567 Allocation} (LDA). This package allows the probabilistic modelling of
12568 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
12569 includes functionalities to identify cell states based on the contribution of
12570 cisTopics and explore the nature and regulatory proteins driving them.")
12571 (license license:gpl3)))
12573 (define-public r-cistopic-next
12574 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
12577 (inherit r-cistopic)
12578 (name "r-cistopic-next")
12579 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
12580 ;; since the previous release is 2.1.0. Oh well.
12581 (version (git-version "0.3.0" revision commit))
12585 (uri (git-reference
12586 (url "https://github.com/aertslab/cisTopic")
12588 (file-name (git-file-name name version))
12591 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
12592 (properties `((upstream-name . "cisTopic")))
12613 (define-public r-genie3
12620 (uri (bioconductor-uri "GENIE3" version))
12623 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
12624 (properties `((upstream-name . "GENIE3")))
12625 (build-system r-build-system)
12627 (list r-dplyr r-reshape2))
12630 (home-page "https://bioconductor.org/packages/GENIE3")
12631 (synopsis "Gene network inference with ensemble of trees")
12633 "This package implements the GENIE3 algorithm for inferring gene
12634 regulatory networks from expression data.")
12635 (license license:gpl2+)))
12637 (define-public r-roc
12644 (uri (bioconductor-uri "ROC" version))
12647 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
12648 (properties `((upstream-name . "ROC")))
12649 (build-system r-build-system)
12652 (home-page "https://www.bioconductor.org/packages/ROC/")
12653 (synopsis "Utilities for ROC curves")
12655 "This package provides utilities for @dfn{Receiver Operating
12656 Characteristic} (ROC) curves, with a focus on micro arrays.")
12657 (license license:artistic2.0)))
12659 (define-public r-watermelon
12661 (name "r-watermelon")
12666 (uri (bioconductor-uri "wateRmelon" version))
12669 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
12670 (properties `((upstream-name . "wateRmelon")))
12671 (build-system r-build-system)
12674 r-illuminahumanmethylation450kanno-ilmn12-hg19
12683 (home-page "https://bioconductor.org/packages/wateRmelon/")
12684 (synopsis "Illumina 450 methylation array normalization and metrics")
12686 "The standard index of DNA methylation (beta) is computed from methylated
12687 and unmethylated signal intensities. Betas calculated from raw signal
12688 intensities perform well, but using 11 methylomic datasets we demonstrate that
12689 quantile normalization methods produce marked improvement. The commonly used
12690 procedure of normalizing betas is inferior to the separate normalization of M
12691 and U, and it is also advantageous to normalize Type I and Type II assays
12692 separately. This package provides 15 flavours of betas and three performance
12693 metrics, with methods for objects produced by the @code{methylumi} and
12694 @code{minfi} packages.")
12695 (license license:gpl3)))
12697 (define-public r-gdsfmt
12704 (uri (bioconductor-uri "gdsfmt" version))
12707 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
12708 (modules '((guix build utils)))
12709 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
12710 ;; them and link with system libraries instead.
12713 (for-each delete-file-recursively
12717 (substitute* "src/Makevars"
12718 (("all: \\$\\(SHLIB\\)") "all:")
12719 (("\\$\\(SHLIB\\): liblzma.a") "")
12720 (("^ (ZLIB|LZ4)/.*") "")
12721 (("CoreArray/dVLIntGDS.cpp.*")
12722 "CoreArray/dVLIntGDS.cpp")
12723 (("CoreArray/dVLIntGDS.o.*")
12724 "CoreArray/dVLIntGDS.o")
12725 (("PKG_LIBS = ./liblzma.a")
12726 "PKG_LIBS = -llz4"))
12727 (substitute* "src/CoreArray/dStream.h"
12728 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
12729 (string-append "include <" header ">")))))))
12730 (properties `((upstream-name . "gdsfmt")))
12731 (build-system r-build-system)
12733 (list lz4 xz zlib))
12736 (home-page "http://corearray.sourceforge.net/")
12738 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
12740 "This package provides a high-level R interface to CoreArray @dfn{Genomic
12741 Data Structure} (GDS) data files, which are portable across platforms with
12742 hierarchical structure to store multiple scalable array-oriented data sets
12743 with metadata information. It is suited for large-scale datasets, especially
12744 for data which are much larger than the available random-access memory. The
12745 @code{gdsfmt} package offers efficient operations specifically designed for
12746 integers of less than 8 bits, since a diploid genotype, like
12747 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
12748 byte. Data compression and decompression are available with relatively
12749 efficient random access. It is also allowed to read a GDS file in parallel
12750 with multiple R processes supported by the package @code{parallel}.")
12751 (license license:lgpl3)))
12753 (define-public r-bigmelon
12755 (name "r-bigmelon")
12760 (uri (bioconductor-uri "bigmelon" version))
12763 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
12764 (properties `((upstream-name . "bigmelon")))
12765 (build-system r-build-system)
12777 (home-page "https://bioconductor.org/packages/bigmelon/")
12778 (synopsis "Illumina methylation array analysis for large experiments")
12780 "This package provides methods for working with Illumina arrays using the
12781 @code{gdsfmt} package.")
12782 (license license:gpl3)))
12784 (define-public r-seqbias
12791 (uri (bioconductor-uri "seqbias" version))
12794 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
12795 (properties `((upstream-name . "seqbias")))
12796 (build-system r-build-system)
12798 (list r-biostrings r-genomicranges r-rhtslib))
12799 (home-page "https://bioconductor.org/packages/seqbias/")
12800 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
12802 "This package implements a model of per-position sequencing bias in
12803 high-throughput sequencing data using a simple Bayesian network, the structure
12804 and parameters of which are trained on a set of aligned reads and a reference
12806 (license license:lgpl3)))
12808 (define-public r-reqon
12815 (uri (bioconductor-uri "ReQON" version))
12818 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
12819 (properties `((upstream-name . "ReQON")))
12820 (build-system r-build-system)
12822 (list r-rjava r-rsamtools r-seqbias))
12823 (home-page "https://bioconductor.org/packages/ReQON/")
12824 (synopsis "Recalibrating quality of nucleotides")
12826 "This package provides an implementation of an algorithm for
12827 recalibrating the base quality scores for aligned sequencing data in BAM
12829 (license license:gpl2)))
12831 (define-public r-wavcluster
12833 (name "r-wavcluster")
12838 (uri (bioconductor-uri "wavClusteR" version))
12841 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
12842 (properties `((upstream-name . "wavClusteR")))
12843 (build-system r-build-system)
12845 (list r-biocgenerics
12861 (home-page "https://bioconductor.org/packages/wavClusteR/")
12862 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
12864 "This package provides an integrated pipeline for the analysis of
12865 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
12866 sequencing errors, SNPs and additional non-experimental sources by a non-
12867 parametric mixture model. The protein binding sites (clusters) are then
12868 resolved at high resolution and cluster statistics are estimated using a
12869 rigorous Bayesian framework. Post-processing of the results, data export for
12870 UCSC genome browser visualization and motif search analysis are provided. In
12871 addition, the package integrates RNA-Seq data to estimate the False
12872 Discovery Rate of cluster detection. Key functions support parallel multicore
12873 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
12874 be applied to the analysis of other NGS data obtained from experimental
12875 procedures that induce nucleotide substitutions (e.g. BisSeq).")
12876 (license license:gpl2)))
12878 (define-public r-timeseriesexperiment
12880 (name "r-timeseriesexperiment")
12885 (uri (bioconductor-uri "TimeSeriesExperiment" version))
12888 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
12890 `((upstream-name . "TimeSeriesExperiment")))
12891 (build-system r-build-system)
12903 r-summarizedexperiment
12910 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
12911 (synopsis "Analysis for short time-series data")
12913 "This package is a visualization and analysis toolbox for short time
12914 course data which includes dimensionality reduction, clustering, two-sample
12915 differential expression testing and gene ranking techniques. The package also
12916 provides methods for retrieving enriched pathways.")
12917 (license license:lgpl3+)))
12919 (define-public r-variantfiltering
12921 (name "r-variantfiltering")
12926 (uri (bioconductor-uri "VariantFiltering" version))
12929 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
12931 `((upstream-name . "VariantFiltering")))
12932 (build-system r-build-system)
12934 (list r-annotationdbi
12955 r-summarizedexperiment
12956 r-variantannotation
12958 (home-page "https://github.com/rcastelo/VariantFiltering")
12959 (synopsis "Filtering of coding and non-coding genetic variants")
12961 "Filter genetic variants using different criteria such as inheritance
12962 model, amino acid change consequence, minor allele frequencies across human
12963 populations, splice site strength, conservation, etc.")
12964 (license license:artistic2.0)))
12966 (define-public r-genomegraphs
12968 (name "r-genomegraphs")
12973 (uri (bioconductor-uri "GenomeGraphs" version))
12976 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
12977 (properties `((upstream-name . "GenomeGraphs")))
12978 (build-system r-build-system)
12981 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
12982 (synopsis "Plotting genomic information from Ensembl")
12984 "Genomic data analyses requires integrated visualization of known genomic
12985 information and new experimental data. GenomeGraphs uses the biomaRt package
12986 to perform live annotation queries to Ensembl and translates this to e.g.
12987 gene/transcript structures in viewports of the grid graphics package. This
12988 results in genomic information plotted together with your data. Another
12989 strength of GenomeGraphs is to plot different data types such as array CGH,
12990 gene expression, sequencing and other data, together in one plot using the
12991 same genome coordinate system.")
12992 (license license:artistic2.0)))
12994 (define-public r-wavetiling
12996 (name "r-wavetiling")
13001 (uri (bioconductor-uri "waveTiling" version))
13004 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
13005 (properties `((upstream-name . "waveTiling")))
13006 (build-system r-build-system)
13018 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
13019 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
13021 "This package is designed to conduct transcriptome analysis for tiling
13022 arrays based on fast wavelet-based functional models.")
13023 (license license:gpl2+)))
13025 (define-public r-variancepartition
13027 (name "r-variancepartition")
13032 (uri (bioconductor-uri "variancePartition" version))
13035 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
13037 `((upstream-name . "variancePartition")))
13038 (build-system r-build-system)
13062 (home-page "https://bioconductor.org/packages/variancePartition/")
13063 (synopsis "Analyze variation in gene expression experiments")
13065 "This is a package providing tools to quantify and interpret multiple
13066 sources of biological and technical variation in gene expression experiments.
13067 It uses a linear mixed model to quantify variation in gene expression
13068 attributable to individual, tissue, time point, or technical variables. The
13069 package includes dream differential expression analysis for repeated
13071 (license license:gpl2+)))
13073 (define-public r-htqpcr
13080 (uri (bioconductor-uri "HTqPCR" version))
13083 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
13084 (properties `((upstream-name . "HTqPCR")))
13085 (build-system r-build-system)
13087 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
13088 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
13089 "groups/bertone/software/HTqPCR.pdf"))
13090 (synopsis "Automated analysis of high-throughput qPCR data")
13092 "Analysis of Ct values from high throughput quantitative real-time
13093 PCR (qPCR) assays across multiple conditions or replicates. The input data
13094 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
13095 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
13096 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
13097 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
13098 loading, quality assessment, normalization, visualization and parametric or
13099 non-parametric testing for statistical significance in Ct values between
13100 features (e.g. genes, microRNAs).")
13101 (license license:artistic2.0)))
13103 (define-public r-unifiedwmwqpcr
13105 (name "r-unifiedwmwqpcr")
13110 (uri (bioconductor-uri "unifiedWMWqPCR" version))
13113 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
13115 `((upstream-name . "unifiedWMWqPCR")))
13116 (build-system r-build-system)
13118 (list r-biocgenerics r-htqpcr))
13119 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
13120 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
13122 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
13123 data. This modified test allows for testing differential expression in qPCR
13125 (license license:gpl2+)))
13127 (define-public r-universalmotif
13129 (name "r-universalmotif")
13134 (uri (bioconductor-uri "universalmotif" version))
13137 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
13139 `((upstream-name . "universalmotif")))
13140 (build-system r-build-system)
13143 (modify-phases %standard-phases
13144 (add-after 'unpack 'fix-reference-to-strip
13146 (substitute* "src/Makevars"
13147 (("/usr/bin/strip") (which "strip"))))))))
13149 (list r-biocgenerics
13162 "https://bioconductor.org/packages/universalmotif/")
13164 "Specific structures importer, modifier, and exporter for R")
13166 "This package allows importing most common @dfn{specific structure}
13167 (motif) types into R for use by functions provided by other Bioconductor
13168 motif-related packages. Motifs can be exported into most major motif formats
13169 from various classes as defined by other Bioconductor packages. A suite of
13170 motif and sequence manipulation and analysis functions are included, including
13171 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
13172 motifs, and others.")
13173 (license license:gpl3)))
13175 (define-public r-ace
13181 (uri (bioconductor-uri "ACE" version))
13184 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
13185 (properties `((upstream-name . "ACE")))
13186 (build-system r-build-system)
13187 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
13188 (native-inputs (list r-knitr))
13189 (home-page "https://github.com/tgac-vumc/ACE")
13191 "Absolute copy number estimation from low-coverage whole genome sequencing")
13193 "This package uses segmented copy number data to estimate tumor cell
13194 percentage and produce copy number plots displaying absolute copy numbers. For
13195 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
13196 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
13197 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
13198 subsequently run through all samples in the object(s), for which it will create
13199 individual subdirectories. For each sample, it will calculate how well the
13200 segments fit (the relative error) to integer copy numbers for each percentage
13201 of @dfn{tumor cells} (cells with divergent segments).")
13202 (license license:gpl2)))
13204 (define-public r-acgh
13210 (uri (bioconductor-uri "aCGH" version))
13213 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
13214 (properties `((upstream-name . "aCGH")))
13215 (build-system r-build-system)
13216 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
13217 (home-page "https://bioconductor.org/packages/aCGH")
13219 "Classes and functions for array comparative genomic hybridization data")
13221 "This package provides functions for reading
13222 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
13223 output files and clone information files, creation of @code{aCGH} objects for
13224 storing these data. Basic methods are accessing/replacing, subsetting,
13225 printing and plotting @code{aCGH} objects.")
13226 (license license:gpl2)))
13228 (define-public r-acme
13234 (uri (bioconductor-uri "ACME" version))
13237 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
13238 (properties `((upstream-name . "ACME")))
13239 (build-system r-build-system)
13240 (propagated-inputs (list r-biobase r-biocgenerics))
13241 (home-page "https://bioconductor.org/packages/aCGH/")
13242 (synopsis "Calculating microarray enrichment")
13244 "This package implements @dfn{algorithms for calculating microarray
13245 enrichment} (ACME), and it is a set of tools for analysing tiling array of
13246 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
13247 DNAse hypersensitivity, or other experiments that result in regions of the
13248 genome showing enrichment. It does not rely on a specific array technology
13249 (although the array should be a tiling array), is very general (can be applied
13250 in experiments resulting in regions of enrichment), and is very insensitive to
13251 array noise or normalization methods. It is also very fast and can be applied
13252 on whole-genome tiling array experiments quite easily with enough memory.")
13253 (license license:gpl2+)))
13255 (define-public r-acde
13261 (uri (bioconductor-uri "acde" version))
13264 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
13265 (properties `((upstream-name . "acde")))
13266 (build-system r-build-system)
13267 (propagated-inputs (list r-boot))
13268 (home-page "https://bioconductor.org/packages/acde")
13270 "Identification of differentially expressed genes with artificial components")
13272 "This package provides a multivariate inferential analysis method for
13273 detecting differentially expressed genes in gene expression data. It uses
13274 artificial components, close to the data's principal components but with an
13275 exact interpretation in terms of differential genetic expression, to identify
13276 differentially expressed genes while controlling the @dfn{false discovery
13278 (license license:gpl3)))
13280 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13282 (define-public r-activedriverwgs
13284 (name "r-activedriverwgs")
13289 (uri (cran-uri "ActiveDriverWGS" version))
13292 "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
13294 `((upstream-name . "ActiveDriverWGS")))
13295 (build-system r-build-system)
13299 r-bsgenome-hsapiens-ucsc-hg19
13300 r-bsgenome-hsapiens-ucsc-hg38
13301 r-bsgenome-mmusculus-ucsc-mm9
13302 r-bsgenome-mmusculus-ucsc-mm10
13309 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
13310 (synopsis "Driver discovery tool for cancer whole genomes")
13312 "This package provides a method for finding an enrichment of cancer
13313 simple somatic mutations (SNVs and Indels) in functional elements across the
13314 human genome. ActiveDriverWGS detects coding and noncoding driver elements
13315 using whole genome sequencing data.")
13316 (license license:gpl3)))
13318 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13320 (define-public r-activepathways
13322 (name "r-activepathways")
13327 (uri (cran-uri "ActivePathways" version))
13330 "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
13332 `((upstream-name . "ActivePathways")))
13333 (build-system r-build-system)
13335 (list r-data-table r-ggplot2))
13338 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
13339 (synopsis "Multivariate pathway enrichment analysis")
13341 "This package represents an integrative method of analyzing multi omics
13342 data that conducts enrichment analysis of annotated gene sets. ActivePathways
13343 uses a statistical data fusion approach, rationalizes contributing evidence
13344 and highlights associated genes, improving systems-level understanding of
13345 cellular organization in health and disease.")
13346 (license license:gpl3)))
13348 (define-public r-bgmix
13355 (uri (bioconductor-uri "BGmix" version))
13358 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
13359 (properties `((upstream-name . "BGmix")))
13360 (build-system r-build-system)
13362 (list r-kernsmooth))
13363 (home-page "https://bioconductor.org/packages/BGmix/")
13364 (synopsis "Bayesian models for differential gene expression")
13366 "This package provides fully Bayesian mixture models for differential
13368 (license license:gpl2)))
13370 (define-public r-bgx
13377 (uri (bioconductor-uri "bgx" version))
13380 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
13381 (properties `((upstream-name . "bgx")))
13382 (build-system r-build-system)
13386 '(modify-phases %standard-phases
13387 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
13389 (substitute* "configure.ac"
13390 (("AX_GCC_ARCHFLAG.*") ""))
13391 (delete-file "configure")
13392 (invoke "autoreconf" "-vif"))))))
13396 (list r-affy r-biobase r-gcrma r-rcpp))
13398 (list autoconf automake))
13399 (home-page "https://bioconductor.org/packages/bgx/")
13400 (synopsis "Bayesian gene expression")
13402 "This package provides tools for Bayesian integrated analysis of
13403 Affymetrix GeneChips.")
13404 (license license:gpl2)))
13406 (define-public r-bhc
13413 (uri (bioconductor-uri "BHC" version))
13416 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
13417 (properties `((upstream-name . "BHC")))
13418 (build-system r-build-system)
13419 (home-page "https://bioconductor.org/packages/BHC/")
13420 (synopsis "Bayesian hierarchical clustering")
13422 "The method implemented in this package performs bottom-up hierarchical
13423 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
13424 in the data and Bayesian model selection to decide at each step which clusters
13425 to merge. This avoids several limitations of traditional methods, for example
13426 how many clusters there should be and how to choose a principled distance
13427 metric. This implementation accepts multinomial (i.e. discrete, with 2+
13428 categories) or time-series data. This version also includes a randomised
13429 algorithm which is more efficient for larger data sets.")
13430 (license license:gpl3)))
13432 (define-public r-bicare
13439 (uri (bioconductor-uri "BicARE" version))
13442 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
13443 (properties `((upstream-name . "BicARE")))
13444 (build-system r-build-system)
13446 (list r-biobase r-gseabase r-multtest))
13447 (home-page "http://bioinfo.curie.fr")
13448 (synopsis "Biclustering analysis and results exploration")
13450 "This is a package for biclustering analysis and exploration of
13452 (license license:gpl2)))
13454 (define-public r-bifet
13461 (uri (bioconductor-uri "BiFET" version))
13464 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
13465 (properties `((upstream-name . "BiFET")))
13466 (build-system r-build-system)
13468 (list r-genomicranges r-poibin))
13471 (home-page "https://bioconductor.org/packages/BiFET")
13472 (synopsis "Bias-free footprint enrichment test")
13474 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
13475 over-represented in target regions compared to background regions after
13476 correcting for the bias arising from the imbalance in read counts and GC
13477 contents between the target and background regions. For a given TF k, BiFET
13478 tests the null hypothesis that the target regions have the same probability of
13479 having footprints for the TF k as the background regions while correcting for
13480 the read count and GC content bias.")
13481 (license license:gpl3)))
13483 (define-public r-rsbml
13490 (uri (bioconductor-uri "rsbml" version))
13493 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
13494 (properties `((upstream-name . "rsbml")))
13495 (build-system r-build-system)
13499 (list r-biocgenerics r-graph))
13502 (home-page "http://www.sbml.org")
13503 (synopsis "R support for SBML")
13505 "This package provides an R interface to libsbml for SBML parsing,
13506 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
13507 (license license:artistic2.0)))
13509 (define-public r-hypergraph
13511 (name "r-hypergraph")
13516 (uri (bioconductor-uri "hypergraph" version))
13519 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
13520 (properties `((upstream-name . "hypergraph")))
13521 (build-system r-build-system)
13524 (home-page "https://bioconductor.org/packages/hypergraph")
13525 (synopsis "Hypergraph data structures")
13527 "This package implements some simple capabilities for representing and
13528 manipulating hypergraphs.")
13529 (license license:artistic2.0)))
13531 (define-public r-hyperdraw
13533 (name "r-hyperdraw")
13538 (uri (bioconductor-uri "hyperdraw" version))
13541 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
13542 (properties `((upstream-name . "hyperdraw")))
13543 (build-system r-build-system)
13544 (inputs (list graphviz))
13546 (list r-graph r-hypergraph r-rgraphviz))
13547 (home-page "https://bioconductor.org/packages/hyperdraw")
13548 (synopsis "Visualizing hypergraphs")
13550 "This package provides functions for visualizing hypergraphs.")
13551 (license license:gpl2+)))
13553 (define-public r-biggr
13560 (uri (bioconductor-uri "BiGGR" version))
13563 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
13564 (properties `((upstream-name . "BiGGR")))
13565 (build-system r-build-system)
13573 (home-page "https://bioconductor.org/packages/BiGGR/")
13574 (synopsis "Constraint based modeling using metabolic reconstruction databases")
13576 "This package provides an interface to simulate metabolic reconstruction
13577 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
13578 reconstruction databases. The package facilitates @dfn{flux balance
13579 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
13580 networks and estimated fluxes can be visualized with hypergraphs.")
13581 (license license:gpl3+)))
13583 (define-public r-bigmemoryextras
13585 (name "r-bigmemoryextras")
13590 (uri (bioconductor-uri "bigmemoryExtras" version))
13593 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
13595 `((upstream-name . "bigmemoryExtras")))
13596 (build-system r-build-system)
13598 (list r-bigmemory))
13601 (home-page "https://github.com/phaverty/bigmemoryExtras")
13602 (synopsis "Extension of the bigmemory package")
13604 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
13605 safety and convenience features to the @code{filebacked.big.matrix} class from
13606 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
13607 monitoring and gracefully restoring the connection to on-disk data and it also
13608 protects against accidental data modification with a file-system-based
13609 permissions system. Utilities are provided for using @code{BigMatrix}-derived
13610 classes as @code{assayData} matrices within the @code{Biobase} package's
13611 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
13612 related to attaching to, and indexing into, file-backed matrices with
13613 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
13614 a file-backed matrix with factor properties.")
13615 (license license:artistic2.0)))
13617 (define-public r-bigpint
13624 (uri (bioconductor-uri "bigPint" version))
13627 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
13628 (properties `((upstream-name . "bigPint")))
13629 (build-system r-build-system)
13631 (list r-delayedarray
13647 r-summarizedexperiment
13651 (home-page "https://github.com/lindsayrutter/bigPint")
13652 (synopsis "Big multivariate data plotted interactively")
13654 "This package provides methods for visualizing large multivariate
13655 datasets using static and interactive scatterplot matrices, parallel
13656 coordinate plots, volcano plots, and litre plots. It includes examples for
13657 visualizing RNA-sequencing datasets and differentially expressed genes.")
13658 (license license:gpl3)))
13660 (define-public r-chemminer
13662 (name "r-chemminer")
13667 (uri (bioconductor-uri "ChemmineR" version))
13670 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
13671 (properties `((upstream-name . "ChemmineR")))
13672 (build-system r-build-system)
13691 (home-page "https://github.com/girke-lab/ChemmineR")
13692 (synopsis "Cheminformatics toolkit for R")
13694 "ChemmineR is a cheminformatics package for analyzing drug-like small
13695 molecule data in R. It contains functions for efficient processing of large
13696 numbers of molecules, physicochemical/structural property predictions,
13697 structural similarity searching, classification and clustering of compound
13698 libraries with a wide spectrum of algorithms. In addition, it offers
13699 visualization functions for compound clustering results and chemical
13701 (license license:artistic2.0)))
13703 (define-public r-fmcsr
13710 (uri (bioconductor-uri "fmcsR" version))
13712 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
13713 (properties `((upstream-name . "fmcsR")))
13714 (build-system r-build-system)
13716 (list r-biocgenerics r-chemminer r-runit))
13717 (native-inputs (list r-knitr))
13718 (home-page "https://github.com/girke-lab/fmcsR")
13719 (synopsis "Mismatch tolerant maximum common substructure searching")
13721 "The fmcsR package introduces an efficient @dfn{maximum common
13722 substructure} (MCS) algorithms combined with a novel matching strategy that
13723 allows for atom and/or bond mismatches in the substructures shared among two
13724 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
13725 strict MCSs, resulting in the identification of more common features in their
13726 source structures, as well as a higher sensitivity in finding compounds with
13727 weak structural similarities. The fmcsR package provides several utilities to
13728 use the FMCS algorithm for pairwise compound comparisons, structure similarity
13729 searching and clustering.")
13730 (license license:artistic2.0)))
13732 (define-public r-bioassayr
13734 (name "r-bioassayr")
13739 (uri (bioconductor-uri "bioassayR" version))
13742 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
13743 (properties `((upstream-name . "bioassayR")))
13744 (build-system r-build-system)
13746 (list r-biocgenerics
13755 (home-page "https://github.com/girke-lab/bioassayR")
13756 (synopsis "Cross-target analysis of small molecule bioactivity")
13758 "bioassayR is a computational tool that enables simultaneous analysis of
13759 thousands of bioassay experiments performed over a diverse set of compounds
13760 and biological targets. Unique features include support for large-scale
13761 cross-target analyses of both public and custom bioassays, generation of
13762 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
13763 preloaded database that provides access to a substantial portion of publicly
13764 available bioactivity data.")
13765 (license license:artistic2.0)))
13767 (define-public r-biobroom
13769 (name "r-biobroom")
13774 (uri (bioconductor-uri "biobroom" version))
13777 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
13778 (properties `((upstream-name . "biobroom")))
13779 (build-system r-build-system)
13781 (list r-biobase r-broom r-dplyr r-tidyr))
13784 (home-page "https://github.com/StoreyLab/biobroom")
13785 (synopsis "Turn Bioconductor objects into tidy data frames")
13787 "This package contains methods for converting standard objects
13788 constructed by bioinformatics packages, especially those in Bioconductor, and
13789 converting them to @code{tidy} data. It thus serves as a complement to the
13790 @code{broom} package, and follows the same tidy, augment, glance division of
13791 tidying methods. Tidying data makes it easy to recombine, reshape and
13792 visualize bioinformatics analyses.")
13793 ;; Any version of the LGPL.
13794 (license license:lgpl3+)))
13796 (define-public r-graphite
13798 (name "r-graphite")
13803 (uri (bioconductor-uri "graphite" version))
13806 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
13807 (properties `((upstream-name . "graphite")))
13808 (build-system r-build-system)
13810 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
13811 (home-page "https://bioconductor.org/packages/graphite/")
13812 (synopsis "Networks from pathway databases")
13814 "Graphite provides networks derived from eight public pathway databases,
13815 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
13817 (license license:agpl3+)))
13819 (define-public r-reactomepa
13821 (name "r-reactomepa")
13826 (uri (bioconductor-uri "ReactomePA" version))
13829 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
13830 (properties `((upstream-name . "ReactomePA")))
13831 (build-system r-build-system)
13833 (list r-annotationdbi
13843 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
13844 (synopsis "Reactome pathway analysis")
13846 "This package provides functions for pathway analysis based on the
13847 REACTOME pathway database. It implements enrichment analysis, gene set
13848 enrichment analysis and several functions for visualization.")
13849 (license license:gpl2)))
13851 (define-public r-ebarrays
13853 (name "r-ebarrays")
13858 (uri (bioconductor-uri "EBarrays" version))
13861 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
13862 (properties `((upstream-name . "EBarrays")))
13863 (build-system r-build-system)
13865 (list r-biobase r-cluster r-lattice))
13866 (home-page "https://bioconductor.org/packages/EBarrays/")
13867 (synopsis "Gene clustering and differential expression identification")
13869 "EBarrays provides tools for the analysis of replicated/unreplicated
13871 (license license:gpl2+)))
13873 (define-public r-bioccasestudies
13875 (name "r-bioccasestudies")
13880 (uri (bioconductor-uri "BiocCaseStudies" version))
13883 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
13885 `((upstream-name . "BiocCaseStudies")))
13886 (build-system r-build-system)
13887 (propagated-inputs (list r-biobase))
13888 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
13889 (synopsis "Support for the case studies monograph")
13891 "This package provides software and data to support the case studies
13893 (license license:artistic2.0)))
13895 (define-public r-bioccheck
13897 (name "r-bioccheck")
13901 (uri (bioconductor-uri "BiocCheck" version))
13904 "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw"))))
13906 `((upstream-name . "BiocCheck")))
13907 (build-system r-build-system)
13918 (home-page "https://bioconductor.org/packages/BiocCheck")
13919 (synopsis "Executes Bioconductor-specific package checks")
13920 (description "This package contains tools to perform additional quality
13921 checks on R packages that are to be submitted to the Bioconductor repository.")
13922 (license license:artistic2.0)))
13924 (define-public r-biocgraph
13926 (name "r-biocgraph")
13931 (uri (bioconductor-uri "biocGraph" version))
13934 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
13935 (properties `((upstream-name . "biocGraph")))
13936 (build-system r-build-system)
13938 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
13939 (home-page "https://bioconductor.org/packages/biocGraph/")
13940 (synopsis "Graph examples and use cases in Bioinformatics")
13942 "This package provides examples and code that make use of the
13943 different graph related packages produced by Bioconductor.")
13944 (license license:artistic2.0)))
13946 (define-public r-biocstyle
13948 (name "r-biocstyle")
13952 (uri (bioconductor-uri "BiocStyle" version))
13955 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
13957 `((upstream-name . "BiocStyle")))
13958 (build-system r-build-system)
13960 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
13963 (home-page "https://bioconductor.org/packages/BiocStyle")
13964 (synopsis "Bioconductor formatting styles")
13965 (description "This package provides standard formatting styles for
13966 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
13968 (license license:artistic2.0)))
13970 (define-public r-biocviews
13972 (name "r-biocviews")
13976 (uri (bioconductor-uri "biocViews" version))
13979 "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38"))))
13981 `((upstream-name . "biocViews")))
13982 (build-system r-build-system)
13991 (home-page "https://bioconductor.org/packages/biocViews")
13992 (synopsis "Bioconductor package categorization helper")
13993 (description "The purpose of biocViews is to create HTML pages that
13994 categorize packages in a Bioconductor package repository according to keywords,
13995 also known as views, in a controlled vocabulary.")
13996 (license license:artistic2.0)))
13998 (define-public r-experimenthub
14000 (name "r-experimenthub")
14005 (uri (bioconductor-uri "ExperimentHub" version))
14008 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
14009 (properties `((upstream-name . "ExperimentHub")))
14010 (build-system r-build-system)
14012 (list r-annotationhub
14021 (home-page "https://bioconductor.org/packages/ExperimentHub/")
14022 (synopsis "Client to access ExperimentHub resources")
14024 "This package provides a client for the Bioconductor ExperimentHub web
14025 resource. ExperimentHub provides a central location where curated data from
14026 experiments, publications or training courses can be accessed. Each resource
14027 has associated metadata, tags and date of modification. The client creates
14028 and manages a local cache of files retrieved enabling quick and reproducible
14030 (license license:artistic2.0)))
14032 (define-public r-grohmm
14039 (uri (bioconductor-uri "groHMM" version))
14042 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
14043 (properties `((upstream-name . "groHMM")))
14044 (build-system r-build-system)
14046 (list r-genomeinfodb
14047 r-genomicalignments
14053 (home-page "https://github.com/Kraus-Lab/groHMM")
14054 (synopsis "GRO-seq analysis pipeline")
14056 "This package provides a pipeline for the analysis of GRO-seq data.")
14057 (license license:gpl3+)))
14059 (define-public r-multiassayexperiment
14061 (name "r-multiassayexperiment")
14066 (uri (bioconductor-uri "MultiAssayExperiment" version))
14069 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
14071 `((upstream-name . "MultiAssayExperiment")))
14072 (build-system r-build-system)
14079 r-summarizedexperiment
14083 (home-page "https://waldronlab.io/MultiAssayExperiment/")
14084 (synopsis "Integration of multi-omics experiments in Bioconductor")
14086 "MultiAssayExperiment harmonizes data management of multiple assays
14087 performed on an overlapping set of specimens. It provides a familiar
14088 Bioconductor user experience by extending concepts from
14089 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
14090 classes for individual assays, and allowing subsetting by genomic ranges or
14092 (license license:artistic2.0)))
14094 (define-public r-bioconcotk
14096 (name "r-bioconcotk")
14101 (uri (bioconductor-uri "BiocOncoTK" version))
14104 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
14105 (properties `((upstream-name . "BiocOncoTK")))
14106 (build-system r-build-system)
14129 r-summarizedexperiment))
14132 (home-page "https://bioconductor.org/packages/BiocOncoTK")
14133 (synopsis "Bioconductor components for general cancer genomics")
14135 "The purpose of this package is to provide a central interface to various
14136 tools for genome-scale analysis of cancer studies.")
14137 (license license:artistic2.0)))
14139 (define-public r-biocor
14146 (uri (bioconductor-uri "BioCor" version))
14149 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
14150 (properties `((upstream-name . "BioCor")))
14151 (build-system r-build-system)
14153 (list r-biocparallel r-gseabase r-matrix))
14156 (home-page "https://llrs.github.io/BioCor/")
14157 (synopsis "Functional similarities")
14159 "This package provides tools to calculate functional similarities based
14160 on the pathways described on KEGG and REACTOME or in gene sets. These
14161 similarities can be calculated for pathways or gene sets, genes, or clusters
14162 and combined with other similarities. They can be used to improve networks,
14163 gene selection, testing relationships, and so on.")
14164 (license license:expat)))
14166 (define-public r-biocpkgtools
14168 (name "r-biocpkgtools")
14173 (uri (bioconductor-uri "BiocPkgTools" version))
14176 "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd"))))
14177 (properties `((upstream-name . "BiocPkgTools")))
14178 (build-system r-build-system)
14180 (list r-biocfilecache
14204 (home-page "https://github.com/seandavi/BiocPkgTools")
14205 (synopsis "Collection of tools for learning about Bioconductor packages")
14207 "Bioconductor has a rich ecosystem of metadata around packages, usage,
14208 and build status. This package is a simple collection of functions to access
14209 that metadata from R. The goal is to expose metadata for data mining and
14210 value-added functionality such as package searching, text mining, and
14211 analytics on packages.")
14212 (license license:expat)))
14214 (define-public r-biocset
14221 (uri (bioconductor-uri "BiocSet" version))
14224 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
14225 (properties `((upstream-name . "BiocSet")))
14226 (build-system r-build-system)
14228 (list r-annotationdbi
14241 "https://bioconductor.org/packages/BiocSet")
14243 "Representing Different Biological Sets")
14245 "BiocSet displays different biological sets in a triple tibble format.
14246 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
14247 The user has the ability to activate one of these three tibbles to perform
14248 common functions from the @code{dplyr} package. Mapping functionality and
14249 accessing web references for elements/sets are also available in BiocSet.")
14250 (license license:artistic2.0)))
14252 (define-public r-biocworkflowtools
14254 (name "r-biocworkflowtools")
14259 (uri (bioconductor-uri "BiocWorkflowTools" version))
14262 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
14264 `((upstream-name . "BiocWorkflowTools")))
14265 (build-system r-build-system)
14278 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
14279 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
14281 "This package provides functions to ease the transition between
14282 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
14283 (license license:expat)))
14285 (define-public r-biodist
14292 (uri (bioconductor-uri "bioDist" version))
14295 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
14296 (properties `((upstream-name . "bioDist")))
14297 (build-system r-build-system)
14299 (list r-biobase r-kernsmooth))
14300 (home-page "https://bioconductor.org/packages/bioDist/")
14301 (synopsis "Different distance measures")
14303 "This package provides a collection of software tools for calculating
14304 distance measures.")
14305 (license license:artistic2.0)))
14307 (define-public r-pcatools
14309 (name "r-pcatools")
14314 (uri (bioconductor-uri "PCAtools" version))
14317 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
14318 (properties `((upstream-name . "PCAtools")))
14319 (build-system r-build-system)
14327 r-delayedmatrixstats
14335 (native-inputs (list r-knitr))
14336 (home-page "https://github.com/kevinblighe/PCAtools")
14337 (synopsis "PCAtools: everything Principal Components Analysis")
14339 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
14340 structure of the data without the need to build any model to represent it.
14341 This \"summary\" of the data is arrived at through a process of reduction that
14342 can transform the large number of variables into a lesser number that are
14343 uncorrelated (i.e. the 'principal components'), while at the same time being
14344 capable of easy interpretation on the original data. PCAtools provides
14345 functions for data exploration via PCA, and allows the user to generate
14346 publication-ready figures. PCA is performed via @code{BiocSingular}; users
14347 can also identify an optimal number of principal components via different
14348 metrics, such as the elbow method and Horn's parallel analysis, which has
14349 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
14350 dimensional mass cytometry data.")
14351 (license license:gpl3)))
14353 (define-public r-rgreat
14360 (uri (bioconductor-uri "rGREAT" version))
14363 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
14364 (properties `((upstream-name . "rGREAT")))
14365 (build-system r-build-system)
14367 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
14368 (native-inputs (list r-knitr))
14369 (home-page "https://github.com/jokergoo/rGREAT")
14370 (synopsis "Client for GREAT analysis")
14372 "This package makes GREAT (Genomic Regions Enrichment of Annotations
14373 Tool) analysis automatic by constructing a HTTP POST request according to
14374 user's input and automatically retrieving results from GREAT web server.")
14375 (license license:expat)))
14377 (define-public r-m3c
14384 (uri (bioconductor-uri "M3C" version))
14387 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
14388 (properties `((upstream-name . "M3C")))
14389 (build-system r-build-system)
14401 (native-inputs (list r-knitr))
14402 (home-page "https://bioconductor.org/packages/M3C")
14403 (synopsis "Monte Carlo reference-based consensus clustering")
14405 "M3C is a consensus clustering algorithm that uses a Monte Carlo
14406 simulation to eliminate overestimation of @code{K} and can reject the null
14407 hypothesis @code{K=1}.")
14408 (license license:agpl3+)))
14410 (define-public r-icens
14417 (uri (bioconductor-uri "Icens" version))
14420 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
14421 (properties `((upstream-name . "Icens")))
14422 (build-system r-build-system)
14425 (home-page "https://bioconductor.org/packages/Icens")
14426 (synopsis "NPMLE for censored and truncated data")
14428 "This package provides many functions for computing the
14429 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
14431 (license license:artistic2.0)))
14433 ;; This is a CRAN package but it depends on r-icens, which is published on
14435 (define-public r-interval
14437 (name "r-interval")
14438 (version "1.1-0.8")
14442 (uri (cran-uri "interval" version))
14445 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
14446 (properties `((upstream-name . "interval")))
14447 (build-system r-build-system)
14449 (list r-icens r-mlecens r-perm r-survival))
14450 (home-page "https://cran.r-project.org/web/packages/interval/")
14451 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
14453 "This package provides functions to fit nonparametric survival curves,
14454 plot them, and perform logrank or Wilcoxon type tests.")
14455 (license license:gpl2+)))
14457 ;; This is a CRAN package, but it depends on r-interval, which depends on a
14458 ;; Bioconductor package.
14459 (define-public r-fhtest
14466 (uri (cran-uri "FHtest" version))
14469 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
14470 (properties `((upstream-name . "FHtest")))
14471 (build-system r-build-system)
14473 (list r-interval r-kmsurv r-mass r-perm r-survival))
14474 (home-page "https://cran.r-project.org/web/packages/FHtest/")
14475 (synopsis "Tests for survival data based on the Fleming-Harrington class")
14477 "This package provides functions to compare two or more survival curves
14481 @item The Fleming-Harrington test for right-censored data based on
14482 permutations and on counting processes.
14483 @item An extension of the Fleming-Harrington test for interval-censored data
14484 based on a permutation distribution and on a score vector distribution.
14487 (license license:gpl2+)))
14489 (define-public r-fourcseq
14491 (name "r-fourcseq")
14496 (uri (bioconductor-uri "FourCSeq" version))
14498 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
14499 (properties `((upstream-name . "FourCSeq")))
14500 (build-system r-build-system)
14506 r-genomicalignments
14516 r-summarizedexperiment))
14520 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
14521 (synopsis "Analysis of multiplexed 4C sequencing data")
14523 "This package is an R package dedicated to the analysis of (multiplexed)
14524 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
14525 interactions between DNA elements and identify differential interactions
14526 between conditions. The statistical analysis in R starts with individual bam
14527 files for each sample as inputs. To obtain these files, the package contains
14528 a Python script to demultiplex libraries and trim off primer sequences. With
14529 a standard alignment software the required bam files can be then be
14531 (license license:gpl3+)))
14533 (define-public r-preprocesscore
14535 (name "r-preprocesscore")
14540 (uri (bioconductor-uri "preprocessCore" version))
14543 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
14545 `((upstream-name . "preprocessCore")))
14546 (build-system r-build-system)
14547 (home-page "https://github.com/bmbolstad/preprocessCore")
14548 (synopsis "Collection of pre-processing functions")
14550 "This package provides a library of core pre-processing and normalization
14552 (license license:lgpl2.0+)))
14554 (define-public r-s4vectors
14556 (name "r-s4vectors")
14560 (uri (bioconductor-uri "S4Vectors" version))
14563 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
14565 `((upstream-name . "S4Vectors")))
14566 (build-system r-build-system)
14568 (list r-biocgenerics))
14569 (home-page "https://bioconductor.org/packages/S4Vectors")
14570 (synopsis "S4 implementation of vectors and lists")
14572 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
14573 classes and a set of generic functions that extend the semantic of ordinary
14574 vectors and lists in R. Package developers can easily implement vector-like
14575 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
14576 In addition, a few low-level concrete subclasses of general interest (e.g.
14577 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
14578 S4Vectors package itself.")
14579 (license license:artistic2.0)))
14581 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
14582 ;; Bioconductor package.
14583 (define-public r-wgcna
14590 (uri (cran-uri "WGCNA" version))
14593 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
14594 (properties `((upstream-name . "WGCNA")))
14595 (build-system r-build-system)
14597 (list r-annotationdbi
14610 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14611 (synopsis "Weighted correlation network analysis")
14613 "This package provides functions necessary to perform Weighted
14614 Correlation Network Analysis on high-dimensional data. It includes functions
14615 for rudimentary data cleaning, construction and summarization of correlation
14616 networks, module identification and functions for relating both variables and
14617 modules to sample traits. It also includes a number of utility functions for
14618 data manipulation and visualization.")
14619 (license license:gpl2+)))
14621 (define-public r-rgraphviz
14623 (name "r-rgraphviz")
14628 (uri (bioconductor-uri "Rgraphviz" version))
14631 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
14632 (properties `((upstream-name . "Rgraphviz")))
14633 (build-system r-build-system)
14636 (modify-phases %standard-phases
14637 (add-after 'unpack 'make-reproducible
14639 ;; The replacement value is taken from src/graphviz/builddate.h
14640 (substitute* "src/graphviz/configure"
14641 (("VERSION_DATE=.*")
14642 "VERSION_DATE=20200427.2341\n"))
14644 ;; FIXME: Rgraphviz bundles the sources of an older variant of
14645 ;; graphviz. It does not build with the latest version of graphviz, so
14646 ;; we do not add graphviz to the inputs.
14647 (inputs (list zlib))
14652 (home-page "https://bioconductor.org/packages/Rgraphviz")
14653 (synopsis "Plotting capabilities for R graph objects")
14655 "This package interfaces R with the graphviz library for plotting R graph
14656 objects from the @code{graph} package.")
14657 (license license:epl1.0)))
14659 (define-public r-fishpond
14661 (name "r-fishpond")
14665 (uri (bioconductor-uri "fishpond" version))
14668 "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym"))))
14669 (properties `((upstream-name . "fishpond")))
14670 (build-system r-build-system)
14671 (inputs (list zlib))
14683 r-singlecellexperiment
14684 r-summarizedexperiment
14686 (native-inputs (list r-knitr))
14687 (home-page "https://github.com/mikelove/fishpond")
14688 (synopsis "Downstream methods and tools for expression data")
14690 "The @code{fishpond} package contains methods for differential transcript
14691 and gene expression analysis of RNA-seq data using inferential replicates for
14692 uncertainty of abundance quantification, as generated by Gibbs sampling or
14693 bootstrap sampling. Also the package contains a number of utilities for
14694 working with Salmon and Alevin quantification files.")
14695 (license license:gpl2)))
14697 (define-public r-fithic
14703 (uri (bioconductor-uri "FitHiC" version))
14706 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
14707 (properties `((upstream-name . "FitHiC")))
14708 (build-system r-build-system)
14710 (list r-data-table r-fdrtool r-rcpp))
14713 (home-page "https://bioconductor.org/packages/FitHiC")
14714 (synopsis "Confidence estimation for intra-chromosomal contact maps")
14716 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
14717 intra-chromosomal contact maps produced by genome-wide genome architecture
14718 assays such as Hi-C.")
14719 (license license:gpl2+)))
14721 (define-public r-hitc
14727 (uri (bioconductor-uri "HiTC" version))
14730 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
14731 (properties `((upstream-name . "HiTC")))
14732 (build-system r-build-system)
14741 (home-page "https://bioconductor.org/packages/HiTC")
14742 (synopsis "High throughput chromosome conformation capture analysis")
14744 "The HiTC package was developed to explore high-throughput \"C\" data
14745 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
14746 quality controls, normalization, visualization, and further analysis are also
14748 (license license:artistic2.0)))
14750 (define-public r-hdf5array
14752 (name "r-hdf5array")
14757 (uri (bioconductor-uri "HDF5Array" version))
14760 "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9"))))
14761 (properties `((upstream-name . "HDF5Array")))
14762 (build-system r-build-system)
14766 (list r-biocgenerics
14774 (home-page "https://bioconductor.org/packages/HDF5Array")
14775 (synopsis "HDF5 back end for DelayedArray objects")
14776 (description "This package provides an array-like container for convenient
14777 access and manipulation of HDF5 datasets. It supports delayed operations and
14778 block processing.")
14779 (license license:artistic2.0)))
14781 (define-public r-rhdf5lib
14783 (name "r-rhdf5lib")
14788 (uri (bioconductor-uri "Rhdf5lib" version))
14791 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
14792 (modules '((guix build utils)))
14795 ;; Delete bundled binaries
14796 (delete-file-recursively "src/wininclude/")
14797 (delete-file-recursively "src/winlib/")
14798 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
14799 (properties `((upstream-name . "Rhdf5lib")))
14800 (build-system r-build-system)
14803 (modify-phases %standard-phases
14804 (add-after 'unpack 'do-not-use-bundled-hdf5
14805 (lambda* (#:key inputs #:allow-other-keys)
14806 (for-each delete-file '("configure" "configure.ac"))
14807 (substitute* "R/zzz.R"
14808 (("return\\(links\\)") "return(\" -lz\")"))
14809 (with-directory-excursion "src"
14810 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
14811 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
14813 ;; Remove timestamp and host system information to make
14814 ;; the build reproducible.
14815 (substitute* "hdf5/src/libhdf5.settings.in"
14816 (("Configured on: @CONFIG_DATE@")
14817 "Configured on: Guix")
14818 (("Uname information:.*")
14819 "Uname information: Linux\n")
14820 ;; Remove unnecessary store reference.
14822 "C Compiler: GCC\n"))
14823 (rename-file "hdf5/src/libhdf5.settings.in"
14824 "hdf5/src/libhdf5.settings")
14825 (rename-file "Makevars.in" "Makevars")
14826 (substitute* "Makevars"
14827 (("@BUILD_HDF5@") "")
14828 (("@COPY_SZIP@") "")
14829 (("@ZLIB_LIB@") "-lz")
14830 (("@ZLIB_INCLUDE@") "")
14831 (("HDF5_CXX_LIB=.*")
14832 (string-append "HDF5_CXX_LIB="
14833 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
14835 (string-append "HDF5_LIB="
14836 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
14837 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
14838 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
14839 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
14840 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
14841 (("HDF5_HL_LIB=.*")
14842 (string-append "HDF5_HL_LIB="
14843 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
14844 (("HDF5_HL_CXX_LIB=.*")
14845 (string-append "HDF5_HL_CXX_LIB="
14846 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
14847 ;; szip is non-free software
14848 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
14849 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
14851 (list hdf5-1.10 zlib))
14853 `(("hdf5-source" ,(package-source hdf5-1.10))
14854 ("r-knitr" ,r-knitr)))
14855 (home-page "https://bioconductor.org/packages/Rhdf5lib")
14856 (synopsis "HDF5 library as an R package")
14857 (description "This package provides C and C++ HDF5 libraries for use in R
14859 (license license:artistic2.0)))
14861 (define-public r-beachmat
14863 (name "r-beachmat")
14868 (uri (bioconductor-uri "beachmat" version))
14871 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
14872 (build-system r-build-system)
14874 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
14877 (home-page "https://bioconductor.org/packages/beachmat")
14878 (synopsis "Compiling Bioconductor to handle each matrix type")
14879 (description "This package provides a consistent C++ class interface for a
14880 variety of commonly used matrix types, including sparse and HDF5-backed
14882 (license license:gpl3)))
14884 ;; This package includes files that have been taken from kentutils. Some
14885 ;; parts of kentutils are not released under a free license, but this package
14886 ;; only uses files that are also found in the free parts of kentutils.
14887 (define-public r-cner
14894 (uri (bioconductor-uri "CNEr" version))
14896 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
14897 (properties `((upstream-name . "CNEr")))
14898 (build-system r-build-system)
14899 (inputs (list zlib))
14906 r-genomicalignments
14922 (home-page "https://github.com/ge11232002/CNEr")
14923 (synopsis "CNE Detection and Visualization")
14925 "This package provides tools for large-scale identification and
14926 advanced visualization of sets of conserved noncoding elements.")
14927 ;; For all files in src/ucsc "license is hereby granted for all use -
14928 ;; public, private or commercial"; this includes those files that don't
14929 ;; have a license header, because they are included in the free parts of
14930 ;; the kentutils package.
14931 (license (list license:gpl2
14932 (license:non-copyleft
14933 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
14935 (define-public r-tfbstools
14937 (name "r-tfbstools")
14942 (uri (bioconductor-uri "TFBSTools" version))
14945 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
14946 (properties `((upstream-name . "TFBSTools")))
14947 (build-system r-build-system)
14957 r-dirichletmultinomial
14969 (native-inputs (list r-knitr))
14970 (home-page "https://github.com/ge11232002/TFBSTools")
14971 (synopsis "Transcription factor binding site (TFBS) analysis")
14973 "TFBSTools is a package for the analysis and manipulation of
14974 transcription factor binding sites. It includes matrices conversion
14975 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
14976 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
14977 scan putative TFBS from sequence/alignment, query JASPAR database and
14978 provides a wrapper of de novo motif discovery software.")
14979 (license license:gpl2)))
14981 (define-public r-maftools
14983 (name "r-maftools")
14988 (uri (bioconductor-uri "maftools" version))
14990 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
14991 (properties `((upstream-name . "maftools")))
14992 (build-system r-build-system)
15000 (native-inputs (list r-knitr))
15001 (home-page "https://github.com/PoisonAlien/maftools")
15002 (synopsis "Summarize, analyze and visualize MAF files")
15004 "Analyze and visualize Mutation Annotation Format (MAF) files from large
15005 scale sequencing studies. This package provides various functions to perform
15006 most commonly used analyses in cancer genomics and to create feature rich
15007 customizable visualzations with minimal effort.")
15008 (license license:expat)))
15010 (define-public r-motifmatchr
15012 (name "r-motifmatchr")
15017 (uri (bioconductor-uri "motifmatchr" version))
15020 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
15021 (properties `((upstream-name . "motifmatchr")))
15022 (build-system r-build-system)
15034 r-summarizedexperiment
15036 (native-inputs (list r-knitr))
15037 (home-page "https://bioconductor.org/packages/motifmatchr")
15038 (synopsis "Fast motif matching in R")
15040 "Quickly find motif matches for many motifs and many sequences.
15041 This package wraps C++ code from the MOODS motif calling library.")
15042 (license license:gpl3)))
15044 (define-public r-chromvar
15046 (name "r-chromvar")
15051 (uri (bioconductor-uri "chromVAR" version))
15053 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
15054 (properties `((upstream-name . "chromVAR")))
15055 (build-system r-build-system)
15057 (list r-biocgenerics
15077 r-summarizedexperiment
15079 (native-inputs (list r-knitr))
15080 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
15081 (synopsis "Determine chromatin variation across regions")
15083 "This package @code{r-chromvar} determines variation in chromatin
15084 accessibility across sets of annotations or peaks. @code{r-chromvar} is
15085 designed primarily for single-cell or sparse chromatin accessibility data like
15086 single cell assay for transposase-accessible chromatin using
15087 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
15088 sequence (@code{DNAse-seq}) experiments.")
15089 (license license:expat)))
15091 (define-public r-singlecellexperiment
15093 (name "r-singlecellexperiment")
15098 (uri (bioconductor-uri "SingleCellExperiment" version))
15101 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
15103 `((upstream-name . "SingleCellExperiment")))
15104 (build-system r-build-system)
15106 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
15107 r-summarizedexperiment))
15110 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
15111 (synopsis "S4 classes for single cell data")
15112 (description "This package defines an S4 class for storing data from
15113 single-cell experiments. This includes specialized methods to store and
15114 retrieve spike-in information, dimensionality reduction coordinates and size
15115 factors for each cell, along with the usual metadata for genes and
15117 (license license:gpl3)))
15119 (define-public r-singler
15126 (uri (bioconductor-uri "SingleR" version))
15128 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
15129 (properties `((upstream-name . "SingleR")))
15130 (build-system r-build-system)
15137 r-delayedmatrixstats
15141 r-summarizedexperiment))
15142 (native-inputs (list r-knitr))
15143 (home-page "https://github.com/LTLA/SingleR")
15144 (synopsis "Reference-based single-cell RNA-seq annotation")
15146 "This package performs unbiased cell type recognition from single-cell
15147 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
15148 cell types to infer the cell of origin of each single cell independently.")
15149 (license license:gpl3)))
15151 (define-public r-scuttle
15158 (uri (bioconductor-uri "scuttle" version))
15161 "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671"))))
15162 (properties `((upstream-name . "scuttle")))
15163 (build-system r-build-system)
15169 r-delayedmatrixstats
15174 r-singlecellexperiment
15175 r-summarizedexperiment))
15176 (native-inputs (list r-knitr))
15177 (home-page "https://bioconductor.org/packages/scuttle")
15178 (synopsis "Single-cell RNA-Seq analysis utilities")
15180 "This package provides basic utility functions for performing single-cell
15181 analyses, focusing on simple normalization, quality control and data
15182 transformations. It also provides some helper functions to assist development
15183 of other packages.")
15184 (license license:gpl3)))
15186 (define-public r-scater
15192 (uri (bioconductor-uri "scater" version))
15195 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
15196 (build-system r-build-system)
15204 r-delayedmatrixstats
15216 r-singlecellexperiment
15217 r-summarizedexperiment
15221 (home-page "https://github.com/davismcc/scater")
15222 (synopsis "Single-cell analysis toolkit for gene expression data in R")
15223 (description "This package provides a collection of tools for doing
15224 various analyses of single-cell RNA-seq gene expression data, with a focus on
15226 (license license:gpl2+)))
15228 (define-public r-scran
15235 (uri (bioconductor-uri "scran" version))
15238 "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni"))))
15239 (build-system r-build-system)
15248 r-delayedmatrixstats
15258 r-singlecellexperiment
15260 r-summarizedexperiment))
15263 (home-page "https://bioconductor.org/packages/scran")
15264 (synopsis "Methods for single-cell RNA-Seq data analysis")
15265 (description "This package implements a variety of low-level analyses of
15266 single-cell RNA-seq data. Methods are provided for normalization of
15267 cell-specific biases, assignment of cell cycle phase, and detection of highly
15268 variable and significantly correlated genes.")
15269 (license license:gpl3)))
15271 (define-public r-sparsematrixstats
15273 (name "r-sparsematrixstats")
15278 (uri (bioconductor-uri "sparseMatrixStats" version))
15281 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
15283 `((upstream-name . "sparseMatrixStats")))
15284 (build-system r-build-system)
15286 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
15287 (native-inputs (list r-knitr))
15288 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
15289 (synopsis "Summary statistics for rows and columns of sparse matrices")
15291 "This package provides high performance functions for row and column
15292 operations on sparse matrices. Currently, the optimizations are limited to
15293 data in the column sparse format.")
15294 (license license:expat)))
15296 (define-public r-delayedmatrixstats
15298 (name "r-delayedmatrixstats")
15303 (uri (bioconductor-uri "DelayedMatrixStats" version))
15306 "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv"))))
15308 `((upstream-name . "DelayedMatrixStats")))
15309 (build-system r-build-system)
15311 (list r-delayedarray
15317 r-sparsematrixstats))
15320 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
15321 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
15323 "This package provides a port of the @code{matrixStats} API for use with
15324 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
15325 contains high-performing functions operating on rows and columns of
15326 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
15327 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
15328 are optimized per data type and for subsetted calculations such that both
15329 memory usage and processing time is minimized.")
15330 (license license:expat)))
15332 (define-public r-mscoreutils
15334 (name "r-mscoreutils")
15339 (uri (bioconductor-uri "MsCoreUtils" version))
15342 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
15343 (properties `((upstream-name . "MsCoreUtils")))
15344 (build-system r-build-system)
15346 (list r-clue r-mass r-rcpp r-s4vectors))
15349 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
15350 (synopsis "Core utils for mass spectrometry data")
15352 "This package defines low-level functions for mass spectrometry data and
15353 is independent of any high-level data structures. These functions include
15354 mass spectra processing functions (noise estimation, smoothing, binning),
15355 quantitative aggregation functions (median polish, robust summarisation,
15356 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
15357 well as misc helper functions, that are used across high-level data structure
15358 within the R for Mass Spectrometry packages.")
15359 (license license:artistic2.0)))
15361 (define-public r-msfeatures
15363 (name "r-msfeatures")
15368 (uri (bioconductor-uri "MsFeatures" version))
15370 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
15371 (properties `((upstream-name . "MsFeatures")))
15372 (build-system r-build-system)
15374 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
15377 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
15378 (synopsis "Functionality for mass spectrometry features")
15380 "The MsFeature package defines functionality for Mass Spectrometry
15381 features. This includes functions to group (LC-MS) features based on some of
15382 their properties, such as retention time (coeluting features), or correlation
15383 of signals across samples. This package hence can be used to group features, and
15384 its results can be used as an input for the @code{QFeatures} package which
15385 allows aggregating abundance levels of features within each group. This
15386 package defines concepts and functions for base and common data types,
15387 implementations for more specific data types are expected to be implemented in
15388 the respective packages (such as e.g. @code{xcms}).")
15389 (license license:artistic2.0)))
15391 (define-public r-biocio
15398 (uri (bioconductor-uri "BiocIO" version))
15401 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
15402 (properties `((upstream-name . "BiocIO")))
15403 (build-system r-build-system)
15405 (list r-biocgenerics r-s4vectors))
15408 (home-page "https://bioconductor.org/packages/BiocIO")
15409 (synopsis "Standard input and output for Bioconductor packages")
15411 "This package implements `import()` and `export()` standard generics for
15412 importing and exporting biological data formats. `import()` supports
15413 whole-file as well as chunk-wise iterative import. The `import()` interface
15414 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
15415 row or element-like components of the file resource), `select()` (on
15416 column-like components of the file resource) and `collect()`. The `import()`
15417 interface optionally provides transparent access to remote (e.g. via https)
15418 as well as local access. Developers can register a file extension, e.g.,
15419 `.loom` for dispatch from character-based URIs to specific `import()` /
15420 `export()` methods based on classes representing file types, e.g.,
15422 (license license:artistic2.0)))
15424 (define-public r-msmseda
15431 (uri (bioconductor-uri "msmsEDA" version))
15434 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
15435 (properties `((upstream-name . "msmsEDA")))
15436 (build-system r-build-system)
15438 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
15440 "https://bioconductor.org/packages/msmsEDA")
15441 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
15443 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
15444 experiments, and visualize de influence of the involved factors.")
15445 (license license:gpl2)))
15447 (define-public r-msmstests
15449 (name "r-msmstests")
15454 (uri (bioconductor-uri "msmsTests" version))
15457 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
15458 (properties `((upstream-name . "msmsTests")))
15459 (build-system r-build-system)
15461 (list r-edger r-msmseda r-msnbase r-qvalue))
15463 "https://bioconductor.org/packages/msmsTests")
15464 (synopsis "Differential LC-MS/MS expression tests")
15466 "This package provides statistical tests for label-free LC-MS/MS data
15467 by spectral counts, to discover differentially expressed proteins between two
15468 biological conditions. Three tests are available: Poisson GLM regression,
15469 quasi-likelihood GLM regression, and the negative binomial of the edgeR
15470 package. The three models admit blocking factors to control for nuisance
15471 variables. To assure a good level of reproducibility a post-test filter is
15472 available, where we may set the minimum effect size considered biologicaly
15473 relevant, and the minimum expression of the most abundant condition.")
15474 (license license:gpl2)))
15476 (define-public r-catalyst
15478 (name "r-catalyst")
15483 (uri (bioconductor-uri "CATALYST" version))
15486 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
15487 (properties `((upstream-name . "CATALYST")))
15488 (build-system r-build-system)
15492 r-consensusclusterplus
15514 r-singlecellexperiment
15515 r-summarizedexperiment))
15518 (home-page "https://github.com/HelenaLC/CATALYST")
15519 (synopsis "Cytometry data analysis tools")
15521 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
15522 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
15523 isotopes rather than fluorescent tags as reporters to label antibodies,
15524 thereby substantially decreasing spectral overlap and allowing for examination
15525 of over 50 parameters at the single cell level. While spectral overlap is
15526 significantly less pronounced in CyTOF than flow cytometry, spillover due to
15527 detection sensitivity, isotopic impurities, and oxide formation can impede
15528 data interpretability. @code{CATALYST} was designed to provide a pipeline for
15529 preprocessing of cytometry data, including:
15532 @item normalization using bead standards;
15533 @item single-cell deconvolution;
15534 @item bead-based compensation.
15537 (license license:gpl2+)))
15539 (define-public r-erma
15546 (uri (bioconductor-uri "erma" version))
15549 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
15550 (build-system r-build-system)
15552 (list r-annotationdbi
15565 r-summarizedexperiment))
15568 (home-page "https://bioconductor.org/packages/erma")
15569 (synopsis "Epigenomic road map adventures")
15571 "The epigenomics road map describes locations of epigenetic marks in DNA
15572 from a variety of cell types. Of interest are locations of histone
15573 modifications, sites of DNA methylation, and regions of accessible chromatin.
15574 This package presents a selection of elements of the road map including
15575 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
15576 by Ernst and Kellis.")
15577 (license license:artistic2.0)))
15579 (define-public r-ggbio
15586 (uri (bioconductor-uri "ggbio" version))
15589 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
15590 (build-system r-build-system)
15593 (modify-phases %standard-phases
15594 ;; See https://github.com/tengfei/ggbio/issues/117
15595 ;; This fix will be included in the next release.
15596 (add-after 'unpack 'fix-typo
15598 (substitute* "R/GGbio-class.R"
15599 (("fechable") "fetchable"))
15602 (list r-annotationdbi
15611 r-genomicalignments
15627 r-summarizedexperiment
15628 r-variantannotation))
15631 (home-page "http://www.tengfei.name/ggbio/")
15632 (synopsis "Visualization tools for genomic data")
15634 "The ggbio package extends and specializes the grammar of graphics for
15635 biological data. The graphics are designed to answer common scientific
15636 questions, in particular those often asked of high throughput genomics data.
15637 All core Bioconductor data structures are supported, where appropriate. The
15638 package supports detailed views of particular genomic regions, as well as
15639 genome-wide overviews. Supported overviews include ideograms and grand linear
15640 views. High-level plots include sequence fragment length, edge-linked
15641 interval to data view, mismatch pileup, and several splicing summaries.")
15642 (license license:artistic2.0)))
15644 (define-public r-gqtlbase
15646 (name "r-gqtlbase")
15651 (uri (bioconductor-uri "gQTLBase" version))
15654 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
15655 (properties `((upstream-name . "gQTLBase")))
15656 (build-system r-build-system)
15659 (modify-phases %standard-phases
15660 ;; This is an upstream bug.
15661 (add-after 'unpack 'fix-imports
15663 (substitute* "NAMESPACE"
15664 ((".*maxffmode.*") "")
15665 (("importFrom\\(ff,.*") "import(ff)\n"))
15680 r-summarizedexperiment))
15683 (home-page "https://bioconductor.org/packages/gQTLBase")
15684 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
15686 "The purpose of this package is to simplify the storage and interrogation
15687 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
15689 (license license:artistic2.0)))
15691 (define-public r-gqtlstats
15693 (name "r-gqtlstats")
15698 (uri (bioconductor-uri "gQTLstats" version))
15701 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
15702 (properties `((upstream-name . "gQTLstats")))
15703 (build-system r-build-system)
15705 (list r-annotationdbi
15733 r-summarizedexperiment
15734 r-variantannotation))
15737 (home-page "https://bioconductor.org/packages/gQTLstats")
15738 (synopsis "Computationally efficient analysis for eQTL and allied studies")
15740 "This package provides tools for the computationally efficient analysis
15741 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
15742 The software in this package aims to support refinements and functional
15743 interpretation of members of a collection of association statistics on a
15744 family of feature/genome hypotheses.")
15745 (license license:artistic2.0)))
15747 (define-public r-gviz
15754 (uri (bioconductor-uri "Gviz" version))
15757 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
15758 (properties `((upstream-name . "Gviz")))
15759 (build-system r-build-system)
15761 (list r-annotationdbi
15771 r-genomicalignments
15785 (home-page "https://bioconductor.org/packages/Gviz")
15786 (synopsis "Plotting data and annotation information along genomic coordinates")
15788 "Genomic data analyses requires integrated visualization of known genomic
15789 information and new experimental data. Gviz uses the biomaRt and the
15790 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
15791 and translates this to e.g. gene/transcript structures in viewports of the
15792 grid graphics package. This results in genomic information plotted together
15794 (license license:artistic2.0)))
15796 (define-public r-gwascat
15803 (uri (bioconductor-uri "gwascat" version))
15806 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
15807 (build-system r-build-system)
15809 (list r-annotationdbi
15820 r-variantannotation))
15823 (home-page "https://bioconductor.org/packages/gwascat")
15824 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
15826 "This package provides tools for representing and modeling data in the
15827 EMBL-EBI GWAS catalog.")
15828 (license license:artistic2.0)))
15830 (define-public r-kegggraph
15832 (name "r-kegggraph")
15837 (uri (bioconductor-uri "KEGGgraph" version))
15839 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
15840 (properties `((upstream-name . "KEGGgraph")))
15841 (build-system r-build-system)
15843 (list r-graph r-rcurl r-rgraphviz r-xml))
15844 (home-page "https://bioconductor.org/packages/KEGGgraph")
15845 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
15847 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
15848 object as well as a collection of tools to analyze, dissect and visualize these
15849 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
15850 maintaining all essential pathway attributes. The package offers
15851 functionalities including parsing, graph operation, visualization and etc.")
15852 (license license:gpl2+)))
15854 (define-public r-ldblock
15861 (uri (bioconductor-uri "ldblock" version))
15864 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
15865 (build-system r-build-system)
15867 (list r-biocgenerics
15868 r-ensdb-hsapiens-v75
15876 r-variantannotation))
15879 (home-page "https://bioconductor.org/packages/ldblock")
15880 (synopsis "Data structures for linkage disequilibrium measures in populations")
15882 "This package defines data structures for @dfn{linkage
15883 disequilibrium} (LD) measures in populations. Its purpose is to simplify
15884 handling of existing population-level data for the purpose of flexibly
15885 defining LD blocks.")
15886 (license license:artistic2.0)))
15888 ;; This is a CRAN package, but it depends on r-snpstats, which is a
15889 ;; Bioconductor package.
15890 (define-public r-ldheatmap
15892 (name "r-ldheatmap")
15897 (uri (cran-uri "LDheatmap" version))
15900 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
15901 (properties `((upstream-name . "LDheatmap")))
15902 (build-system r-build-system)
15904 (list r-genetics r-rcpp r-snpstats))
15905 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
15906 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
15908 "This package provides tools to produce a graphical display, as a heat
15909 map, of measures of pairwise linkage disequilibria between SNPs. Users may
15910 optionally include the physical locations or genetic map distances of each SNP
15912 (license license:gpl3)))
15914 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
15915 ;; Bioconductor package.
15916 (define-public r-abn
15923 (uri (cran-uri "abn" version))
15926 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
15927 (build-system r-build-system)
15940 (home-page "https://r-bayesian-networks.org/")
15941 (synopsis "Modelling multivariate data with additive bayesian networks")
15943 "Bayesian network analysis is a form of probabilistic graphical models
15944 which derives from empirical data a directed acyclic graph, DAG, describing
15945 the dependency structure between random variables. An additive Bayesian
15946 network model consists of a form of a DAG where each node comprises a
15947 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
15948 equivalent to Bayesian multivariate regression using graphical modelling, they
15949 generalises the usual multivariable regression, GLM, to multiple dependent
15950 variables. This package provides routines to help determine optimal Bayesian
15951 network models for a given data set, where these models are used to identify
15952 statistical dependencies in messy, complex data.")
15953 (license license:gpl2+)))
15955 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
15956 ;; Bioconductor package.
15957 (define-public r-spp
15963 (uri (cran-uri "spp" version))
15966 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
15967 (build-system r-build-system)
15971 (list r-bh r-catools r-rcpp r-rsamtools))
15972 (home-page "https://cran.r-project.org/web/packages/spp/")
15973 (synopsis "ChIP-Seq processing pipeline")
15974 (description "This package provides tools for analysis of ChIP-seq and
15975 other functional sequencing data.")
15976 (license license:gpl2)))
15978 (define-public r-pathview
15980 (name "r-pathview")
15985 (uri (bioconductor-uri "pathview" version))
15987 (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71"))))
15988 (properties `((upstream-name . "pathview")))
15989 (build-system r-build-system)
15991 (list r-annotationdbi
15999 (home-page "https://pathview.uncc.edu/")
16000 (synopsis "Tool set for pathway based data integration and visualization")
16002 "@code{r-pathview} is a tool set for pathway based data integration and
16003 visualization. It maps and renders a wide variety of biological data on
16004 relevant pathway graphs. All users need is to supply their data and specify
16005 the target pathway. This package automatically downloads the pathway graph
16006 data, parses the data file, maps user data to the pathway, and render pathway
16007 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
16008 integrates with pathway and gene set (enrichment) analysis tools for
16009 large-scale and fully automated analysis.")
16010 (license license:gpl3+)))
16012 (define-public r-snpstats
16014 (name "r-snpstats")
16019 (uri (bioconductor-uri "snpStats" version))
16022 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
16023 (properties `((upstream-name . "snpStats")))
16024 (build-system r-build-system)
16025 (inputs (list zlib))
16027 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
16028 (home-page "https://bioconductor.org/packages/snpStats")
16029 (synopsis "Methods for SNP association studies")
16031 "This package provides classes and statistical methods for large
16032 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
16033 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
16034 (license license:gpl3)))
16036 (define-public r-chromstar
16038 (name "r-chromstar")
16043 (uri (bioconductor-uri "chromstaR" version))
16046 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
16047 (properties `((upstream-name . "chromstaR")))
16048 (build-system r-build-system)
16056 r-genomicalignments
16064 (native-inputs (list r-knitr))
16065 (home-page "https://github.com/ataudt/chromstaR")
16066 (synopsis "Chromatin state analysis for ChIP-Seq data")
16068 "This package implements functions for combinatorial and differential
16069 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
16070 export to genome browser viewable files, and functions for enrichment
16072 (license license:artistic2.0)))
16074 (define-public r-guitar
16081 (uri (bioconductor-uri "Guitar" version))
16084 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
16085 (properties `((upstream-name . "Guitar")))
16086 (build-system r-build-system)
16088 (list r-annotationdbi
16098 (home-page "https://bioconductor.org/packages/Guitar")
16099 (synopsis "Visualize genomic features")
16101 "This package is designed for visualization of RNA-related genomic
16102 features with respect to the landmarks of RNA transcripts, i.e., transcription
16103 starting site, start codon, stop codon and transcription ending site.")
16104 (license license:gpl2)))
16106 (define-public r-sushi
16112 (uri (bioconductor-uri "Sushi" version))
16115 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
16116 (properties `((upstream-name . "Sushi")))
16117 (build-system r-build-system)
16119 (list r-biomart r-zoo))
16120 (home-page "https://bioconductor.org/packages/Sushi")
16121 (synopsis "Tools for visualizing genomics data")
16123 "This package provides flexible, quantitative, and integrative genomic
16124 visualizations for publication-quality multi-panel figures.")
16125 (license license:gpl2+)))
16127 (define-public r-ballgown
16129 (name "r-ballgown")
16134 (uri (bioconductor-uri "ballgown" version))
16137 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
16138 (properties `((upstream-name . "ballgown")))
16139 (build-system r-build-system)
16152 (home-page "https://bioconductor.org/packages/ballgown")
16153 (synopsis "Flexible, isoform-level differential expression analysis")
16155 "This package provides tools for statistical analysis of assembled
16156 transcriptomes, including flexible differential expression analysis,
16157 visualization of transcript structures, and matching of assembled transcripts
16159 (license license:artistic2.0)))
16161 (define-public r-megadepth
16163 (name "r-megadepth")
16168 (uri (bioconductor-uri "megadepth" version))
16171 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
16172 (properties `((upstream-name . "megadepth")))
16173 (build-system r-build-system)
16174 (inputs (list megadepth))
16185 (home-page "https://github.com/LieberInstitute/megadepth")
16186 (synopsis "BigWig and BAM related utilities")
16188 "This package provides an R interface to Megadepth. It is particularly
16189 useful for computing the coverage of a set of genomic regions across bigWig or
16190 BAM files. With this package, you can build base-pair coverage matrices for
16191 regions or annotations of your choice from BigWig files.")
16192 (license license:artistic2.0)))
16194 (define-public r-beclear
16201 (uri (bioconductor-uri "BEclear" version))
16204 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
16205 (properties `((upstream-name . "BEclear")))
16206 (build-system r-build-system)
16218 (home-page "https://github.com/uds-helms/BEclear")
16219 (synopsis "Correction of batch effects in DNA methylation data")
16221 "This package provides functions to detect and correct for batch effects
16222 in DNA methylation data. The core function is based on latent factor models
16223 and can also be used to predict missing values in any other matrix containing
16225 (license license:gpl3)))
16227 (define-public r-bgeecall
16229 (name "r-bgeecall")
16234 (uri (bioconductor-uri "BgeeCall" version))
16237 "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil"))))
16238 (properties `((upstream-name . "BgeeCall")))
16239 (build-system r-build-system)
16253 (native-inputs (list r-knitr))
16254 (home-page "https://github.com/BgeeDB/BgeeCall")
16255 (synopsis "RNA-Seq present/absent gene expression calls generation")
16257 "BgeeCall allows generating present/absent gene expression calls without
16258 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
16259 intergenic sequences. These sequences are generated based on expression of
16260 all RNA-Seq libraries of each species integrated in Bgee.")
16261 (license license:gpl3)))
16263 (define-public r-bgeedb
16270 (uri (bioconductor-uri "BgeeDB" version))
16273 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
16274 (properties `((upstream-name . "BgeeDB")))
16275 (build-system r-build-system)
16288 (native-inputs (list r-knitr))
16289 (home-page "https://github.com/BgeeDB/BgeeDB_R")
16290 (synopsis "Annotation and gene expression data retrieval from Bgee database")
16292 "This package provides a package for the annotation and gene expression
16293 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
16294 anatomical terms, mapped to genes by expression patterns.")
16295 (license license:gpl3)))
16297 (define-public r-biobtreer
16299 (name "r-biobtreer")
16304 (uri (bioconductor-uri "biobtreeR" version))
16307 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
16308 (properties `((upstream-name . "biobtreeR")))
16309 (build-system r-build-system)
16311 (list r-httpuv r-httr r-jsonlite r-stringi))
16312 (native-inputs (list r-knitr))
16313 (home-page "https://github.com/tamerh/biobtreeR")
16314 (synopsis "Use biobtree tool from R")
16316 "The biobtreeR package provides an interface to biobtree, a tool which
16317 covers large sets of bioinformatics datasets and allows search and chain
16318 mappings functionalities.")
16319 (license license:expat)))
16321 (define-public r-minet
16328 (uri (bioconductor-uri "minet" version))
16331 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
16332 (properties `((upstream-name . "minet")))
16333 (build-system r-build-system)
16336 (home-page "http://minet.meyerp.com")
16337 (synopsis "Mutual information networks")
16339 "This package implements various algorithms for inferring mutual
16340 information networks from data.")
16341 (license license:artistic2.0)))
16343 (define-public r-genetclassifier
16345 (name "r-genetclassifier")
16350 (uri (bioconductor-uri "geNetClassifier" version))
16353 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
16355 `((upstream-name . "geNetClassifier")))
16356 (build-system r-build-system)
16358 (list r-biobase r-e1071 r-ebarrays r-minet))
16359 (home-page "https://www.cicancer.org")
16360 (synopsis "Classify diseases and build gene networks using expression profiles")
16362 "This is a comprehensive package to automatically train and validate a
16363 multi-class SVM classifier based on gene expression data. It provides
16364 transparent selection of gene markers, their coexpression networks, and an
16365 interface to query the classifier.")
16366 (license license:gpl2+)))
16368 (define-public r-dir-expiry
16370 (name "r-dir-expiry")
16375 (uri (bioconductor-uri "dir.expiry" version))
16378 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
16379 (properties `((upstream-name . "dir.expiry")))
16380 (build-system r-build-system)
16381 (propagated-inputs (list r-filelock))
16382 (native-inputs (list r-knitr))
16383 (home-page "https://bioconductor.org/packages/dir.expiry")
16384 (synopsis "Managing expiration for cache directories")
16386 "This package implements an expiration system for access to versioned
16387 directories. Directories that have not been accessed by a registered function
16388 within a certain time frame are deleted. This aims to reduce disk usage by
16389 eliminating obsolete caches generated by old versions of packages.")
16390 (license license:gpl3)))
16392 (define-public r-basilisk-utils
16394 (name "r-basilisk-utils")
16399 (uri (bioconductor-uri "basilisk.utils" version))
16402 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
16404 `((upstream-name . "basilisk.utils")))
16405 (build-system r-build-system)
16407 (list r-dir-expiry))
16408 (native-inputs (list r-knitr))
16409 (home-page "https://bioconductor.org/packages/basilisk.utils")
16410 (synopsis "Basilisk installation utilities")
16412 "This package implements utilities for installation of the basilisk
16413 package, primarily for creation of the underlying Conda instance.")
16414 (license license:gpl3)))
16416 (define-public r-basilisk
16418 (name "r-basilisk")
16423 (uri (bioconductor-uri "basilisk" version))
16426 "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk"))))
16427 (properties `((upstream-name . "basilisk")))
16428 (build-system r-build-system)
16430 (list r-basilisk-utils r-dir-expiry r-reticulate))
16431 (native-inputs (list r-knitr))
16432 (home-page "https://bioconductor.org/packages/basilisk")
16433 (synopsis "Freeze Python dependencies inside Bioconductor packages")
16435 "This package installs a self-contained Conda instance that is managed by
16436 the R/Bioconductor installation machinery. This aims to provide a consistent
16437 Python environment that can be used reliably by Bioconductor packages.
16438 Functions are also provided to enable smooth interoperability of multiple
16439 Python environments in a single R session.")
16440 (license license:gpl3)))
16442 (define-public r-biocthis
16444 (name "r-biocthis")
16449 (uri (bioconductor-uri "biocthis" version))
16452 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
16453 (properties `((upstream-name . "biocthis")))
16454 (build-system r-build-system)
16457 (modify-phases %standard-phases
16458 (add-after 'unpack 'set-HOME
16459 (lambda _ (setenv "HOME" "/tmp"))))))
16461 (list r-biocmanager
16467 (native-inputs (list r-knitr))
16468 (home-page "https://github.com/lcolladotor/biocthis")
16469 (synopsis "Automate package and project setup for Bioconductor packages")
16471 "This package expands the @code{usethis} package with the goal of helping
16472 automate the process of creating R packages for Bioconductor or making them
16473 Bioconductor-friendly.")
16474 (license license:artistic2.0)))
16476 (define-public r-biocdockermanager
16478 (name "r-biocdockermanager")
16483 (uri (bioconductor-uri "BiocDockerManager" version))
16486 "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d"))))
16488 `((upstream-name . "BiocDockerManager")))
16489 (build-system r-build-system)
16497 (native-inputs (list r-knitr))
16498 (home-page "https://bioconductor.org/packages/BiocDockerManager")
16499 (synopsis "Access and manage Bioconductor Docker images")
16501 "This package works analogous to BiocManager but for Docker images. Use
16502 the BiocDockerManager package to install and manage Docker images provided by
16503 the Bioconductor project.")
16504 (license license:artistic2.0)))
16506 (define-public r-biodb
16513 (uri (bioconductor-uri "biodb" version))
16516 "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1"))))
16517 (properties `((upstream-name . "biodb")))
16518 (build-system r-build-system)
16520 (list r-biocfilecache
16538 (native-inputs (list r-knitr))
16539 (home-page "https://bioconductor.org/packages/biodb")
16540 (synopsis "Library for connecting to chemical and biological databases")
16542 "The biodb package provides access to standard remote chemical and
16543 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
16544 database files (CSV, SQLite), with easy retrieval of entries, access to web
16545 services, search of compounds by mass and/or name, and mass spectra matching
16546 for LCMS and MSMS. Its architecture as a development framework facilitates
16547 the development of new database connectors for local projects or inside
16548 separate published packages.")
16549 (license license:agpl3+)))
16551 (define-public r-biomformat
16553 (name "r-biomformat")
16558 (uri (bioconductor-uri "biomformat" version))
16561 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
16562 (properties `((upstream-name . "biomformat")))
16563 (build-system r-build-system)
16565 (list r-jsonlite r-matrix r-plyr r-rhdf5))
16566 (native-inputs (list r-knitr))
16567 (home-page "https://github.com/joey711/biomformat/")
16568 (synopsis "Interface package for the BIOM file format")
16570 "This is an R package for interfacing with the BIOM format. This package
16571 includes basic tools for reading biom-format files, accessing and subsetting
16572 data tables from a biom object (which is more complex than a single table), as
16573 well as limited support for writing a biom-object back to a biom-format file.
16574 The design of this API is intended to match the Python API and other tools
16575 included with the biom-format project, but with a decidedly \"R flavor\" that
16576 should be familiar to R users. This includes S4 classes and methods, as well
16577 as extensions of common core functions/methods.")
16578 (license license:gpl2)))
16580 (define-public r-mvcclass
16582 (name "r-mvcclass")
16587 (uri (bioconductor-uri "MVCClass" version))
16590 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
16591 (properties `((upstream-name . "MVCClass")))
16592 (build-system r-build-system)
16593 (home-page "https://bioconductor.org/packages/MVCClass")
16594 (synopsis "Model-View-Controller (MVC) classes")
16596 "This package contains classes used in model-view-controller (MVC)
16598 (license license:lgpl2.1+)))
16600 (define-public r-biomvcclass
16602 (name "r-biomvcclass")
16607 (uri (bioconductor-uri "BioMVCClass" version))
16610 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
16611 (properties `((upstream-name . "BioMVCClass")))
16612 (build-system r-build-system)
16614 (list r-biobase r-graph r-mvcclass r-rgraphviz))
16615 (home-page "https://bioconductor.org/packages/BioMVCClass")
16616 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
16618 "This package contains classes used in model-view-controller (MVC)
16620 (license license:lgpl2.1+)))
16622 (define-public r-biomvrcns
16624 (name "r-biomvrcns")
16629 (uri (bioconductor-uri "biomvRCNS" version))
16632 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
16633 (properties `((upstream-name . "biomvRCNS")))
16634 (build-system r-build-system)
16636 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
16637 (home-page "https://bioconductor.org/packages/biomvRCNS")
16638 (synopsis "Copy number study and segmentation for multivariate biological data")
16640 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
16641 homogeneous segmentation model are designed and implemented for segmentation
16642 genomic data, with the aim of assisting in transcripts detection using high
16643 throughput technology like RNA-seq or tiling array, and copy number analysis
16644 using aCGH or sequencing.")
16645 (license license:gpl2+)))
16647 (define-public r-bionero
16654 (uri (bioconductor-uri "BioNERO" version))
16657 "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp"))))
16658 (properties `((upstream-name . "BioNERO")))
16659 (build-system r-build-system)
16661 (list r-biocparallel
16678 r-summarizedexperiment
16683 (home-page "https://github.com/almeidasilvaf/BioNERO")
16684 (synopsis "Biological network reconstruction omnibus")
16686 "BioNERO aims to integrate all aspects of biological network inference in
16687 a single package, including data preprocessing, exploratory analyses, network
16688 inference, and analyses for biological interpretations. BioNERO can be used
16689 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
16690 from gene expression data. Additionally, it can be used to explore
16691 topological properties of protein-protein interaction (PPI) networks. GCN
16692 inference relies on the popular WGCNA algorithm. GRN inference is based on
16693 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
16694 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
16695 rank for each interaction pair. As all steps of network analyses are included
16696 in this package, BioNERO makes users avoid having to learn the syntaxes of
16697 several packages and how to communicate between them. Finally, users can also
16698 identify consensus modules across independent expression sets and calculate
16699 intra and interspecies module preservation statistics between different
16701 (license license:gpl3)))
16703 (define-public r-bionet
16710 (uri (bioconductor-uri "BioNet" version))
16713 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
16714 (properties `((upstream-name . "BioNet")))
16715 (build-system r-build-system)
16717 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
16718 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
16719 (synopsis "Functional analysis of biological networks")
16721 "This package provides functions for the integrated analysis of
16722 protein-protein interaction networks and the detection of functional modules.
16723 Different datasets can be integrated into the network by assigning p-values of
16724 statistical tests to the nodes of the network. E.g. p-values obtained from
16725 the differential expression of the genes from an Affymetrix array are assigned
16726 to the nodes of the network. By fitting a beta-uniform mixture model and
16727 calculating scores from the p-values, overall scores of network regions can be
16728 calculated and an integer linear programming algorithm identifies the maximum
16729 scoring subnetwork.")
16730 (license license:gpl2+)))
16732 (define-public r-bionetstat
16734 (name "r-bionetstat")
16739 (uri (bioconductor-uri "BioNetStat" version))
16742 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
16743 (properties `((upstream-name . "BioNetStat")))
16744 (build-system r-build-system)
16746 (list r-biocparallel
16766 (home-page "https://github.com/jardimViniciusC/BioNetStat")
16767 (synopsis "Biological network analysis")
16769 "This package provides a package to perform differential network
16770 analysis, differential node analysis (differential coexpression analysis),
16771 network and metabolic pathways view.")
16772 (license license:gpl3+)))
16774 (define-public r-bioqc
16781 (uri (bioconductor-uri "BioQC" version))
16784 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
16785 (properties `((upstream-name . "BioQC")))
16786 (build-system r-build-system)
16788 (list r-biobase r-edger r-rcpp))
16791 (home-page "https://accio.github.io/BioQC/")
16792 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
16794 "BioQC performs quality control of high-throughput expression data based
16795 on tissue gene signatures. It can detect tissue heterogeneity in gene
16796 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
16797 optimised for high performance.")
16798 (license license:gpl3+)))
16800 (define-public r-biotip
16807 (uri (bioconductor-uri "BioTIP" version))
16810 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
16811 (properties `((upstream-name . "BioTIP")))
16812 (build-system r-build-system)
16823 (home-page "https://github.com/xyang2uchicago/BioTIP")
16824 (synopsis "R package for characterization of biological tipping-point")
16826 "This package adopts tipping-point theory to transcriptome profiles to
16827 help unravel disease regulatory trajectory.")
16828 (license license:gpl2)))
16830 (define-public r-biotmle
16837 (uri (bioconductor-uri "biotmle" version))
16840 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
16841 (properties `((upstream-name . "biotmle")))
16842 (build-system r-build-system)
16853 r-summarizedexperiment
16858 (home-page "https://code.nimahejazi.org/biotmle/")
16859 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
16861 "This package provides tools for differential expression biomarker
16862 discovery based on microarray and next-generation sequencing data that
16863 leverage efficient semiparametric estimators of the average treatment effect
16864 for variable importance analysis. Estimation and inference of the (marginal)
16865 average treatment effects of potential biomarkers are computed by targeted
16866 minimum loss-based estimation, with joint, stable inference constructed across
16867 all biomarkers using a generalization of moderated statistics for use with the
16868 estimated efficient influence function. The procedure accommodates the use of
16869 ensemble machine learning for the estimation of nuisance functions.")
16870 (license license:expat)))
16872 (define-public r-bsseq
16879 (uri (bioconductor-uri "bsseq" version))
16882 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
16883 (properties `((upstream-name . "bsseq")))
16884 (build-system r-build-system)
16894 r-delayedmatrixstats
16908 r-summarizedexperiment))
16911 (home-page "https://github.com/hansenlab/bsseq")
16912 (synopsis "Analyze, manage and store bisulfite sequencing data")
16914 "This package provides a collection of tools for analyzing and
16915 visualizing bisulfite sequencing data.")
16916 (license license:artistic2.0)))
16918 (define-public r-dada2
16924 (uri (bioconductor-uri "dada2" version))
16927 "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x"))))
16928 (properties `((upstream-name . "dada2")))
16929 (build-system r-build-system)
16931 (list r-biocgenerics
16940 (native-inputs (list r-knitr))
16941 (home-page "https://benjjneb.github.io/dada2/")
16943 "Accurate, high-resolution sample inference from amplicon sequencing data")
16945 "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
16946 from high-throughput amplicon sequencing data, replacing the coarser and less
16947 accurate OTU clustering approach. The dada2 pipeline takes as input
16948 demultiplexed fastq files, and outputs the sequence variants and their
16949 sample-wise abundances after removing substitution and chimera errors.
16950 Taxonomic classification is available via a native implementation of the RDP
16951 naive Bayesian classifier, and species-level assignment to 16S rRNA gene
16952 fragments by exact matching.")
16953 (license license:lgpl2.0)))
16955 (define-public r-dmrseq
16962 (uri (bioconductor-uri "dmrseq" version))
16965 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
16966 (properties `((upstream-name . "dmrseq")))
16967 (build-system r-build-system)
16969 (list r-annotationhub
16974 r-delayedmatrixstats
16988 (home-page "https://bioconductor.org/packages/dmrseq")
16989 (synopsis "Detection and inference of differentially methylated regions")
16991 "This package implements an approach for scanning the genome to detect
16992 and perform accurate inference on differentially methylated regions from Whole
16993 Genome Bisulfite Sequencing data. The method is based on comparing detected
16994 regions to a pooled null distribution, that can be implemented even when as
16995 few as two samples per population are available. Region-level statistics are
16996 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
16997 with a nested autoregressive correlated error structure for the effect of
16998 interest on transformed methylation proportions.")
16999 (license license:expat)))
17001 (define-public r-omicade4
17003 (name "r-omicade4")
17007 (uri (bioconductor-uri "omicade4" version))
17010 "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
17011 (properties `((upstream-name . "omicade4")))
17012 (build-system r-build-system)
17013 (propagated-inputs (list r-ade4 r-biobase r-made4))
17014 (home-page "https://bioconductor.org/packages/omicade4")
17015 (synopsis "Multiple co-inertia analysis of omics datasets")
17017 "This package performes multiple co-inertia analysis of omics datasets.")
17018 (license license:gpl2)))
17020 (define-public r-omnipathr
17022 (name "r-omnipathr")
17027 (uri (bioconductor-uri "OmnipathR" version))
17029 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
17030 (properties `((upstream-name . "OmnipathR")))
17031 (build-system r-build-system)
17034 (modify-phases %standard-phases
17035 (add-after 'unpack 'set-HOME
17036 (lambda _ (setenv "HOME" "/tmp"))))))
17062 (native-inputs (list r-knitr))
17063 (home-page "https://saezlab.github.io/OmnipathR/")
17064 (synopsis "OmniPath web service client and more")
17066 "This package provides a client for the OmniPath web service and many
17067 other resources. It also includes functions to transform and pretty print
17068 some of the downloaded data, functions to access a number of other resources.
17069 Furthermore, OmnipathR features a close integration with the NicheNet method
17070 for ligand activity prediction from transcriptomics data.")
17071 (license license:expat)))
17073 (define-public r-biscuiteer
17075 (name "r-biscuiteer")
17080 (uri (bioconductor-uri "biscuiteer" version))
17083 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
17084 (properties `((upstream-name . "biscuiteer")))
17085 (build-system r-build-system)
17093 r-delayedmatrixstats
17112 r-summarizedexperiment
17113 r-variantannotation))
17116 (home-page "https://github.com/trichelab/biscuiteer")
17117 (synopsis "Convenience functions for the Biscuit package")
17119 "This package provides a test harness for bsseq loading of Biscuit
17120 output, summarization of WGBS data over defined regions and in mappable
17121 samples, with or without imputation, dropping of mostly-NA rows, age
17123 (license license:gpl3)))
17125 (define-public r-tcgabiolinks
17127 (name "r-tcgabiolinks")
17132 (uri (bioconductor-uri "TCGAbiolinks" version))
17134 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
17135 (properties `((upstream-name . "TCGAbiolinks")))
17136 (build-system r-build-system)
17155 r-summarizedexperiment
17156 r-tcgabiolinksgui-data
17161 (native-inputs (list r-knitr))
17162 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
17163 (synopsis "Integrative analysis with GDC data")
17165 "The aim of TCGAbiolinks is:
17168 @item facilitate GDC open-access data retrieval;
17169 @item prepare the data using the appropriate pre-processing strategies;
17170 @item provide the means to carry out different standard analyses, and;
17171 @item to easily reproduce earlier research results.
17174 In more detail, the package provides multiple methods for analysis (e.g.,
17175 differential expression analysis, identifying differentially methylated
17176 regions) and methods for visualization (e.g., survival plots, volcano plots,
17177 starburst plots) in order to easily develop complete analysis pipelines.")
17178 (license license:gpl3+)))
17180 (define-public r-tricycle
17182 (name "r-tricycle")
17186 (uri (bioconductor-uri "tricycle" version))
17189 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
17190 (properties `((upstream-name . "tricycle")))
17191 (build-system r-build-system)
17193 (list r-annotationdbi
17204 r-singlecellexperiment
17205 r-summarizedexperiment))
17206 (native-inputs (list r-knitr))
17207 (home-page "https://github.com/hansenlab/tricycle")
17208 (synopsis "Transferable representation and inference of cell cycle")
17210 "The package contains functions to infer and visualize cell cycle process
17211 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
17212 projecting new data to the previous learned biologically interpretable space.
17213 The @code{tricycle} provides a pre-learned cell cycle space, which could be
17214 used to infer cell cycle time of human and mouse single cell samples. In
17215 addition, it also offer functions to visualize cell cycle time on different
17216 embeddings and functions to build new reference.")
17217 (license license:gpl3)))
17219 (define-public r-tximeta
17226 (uri (bioconductor-uri "tximeta" version))
17229 "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8"))))
17230 (properties `((upstream-name . "tximeta")))
17231 (build-system r-build-system)
17233 (list r-annotationdbi
17245 r-summarizedexperiment
17250 (home-page "https://github.com/mikelove/tximeta")
17251 (synopsis "Transcript quantification import with automatic metadata")
17253 "This package implements transcript quantification import from Salmon and
17254 alevin with automatic attachment of transcript ranges and release information,
17255 and other associated metadata. De novo transcriptomes can be linked to the
17256 appropriate sources with linkedTxomes and shared for computational
17258 (license license:gpl2)))
17260 (define-public r-phyloseq
17262 (name "r-phyloseq")
17267 (uri (bioconductor-uri "phyloseq" version))
17269 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
17270 (properties `((upstream-name . "phyloseq")))
17271 (build-system r-build-system)
17291 (home-page "https://github.com/joey711/phyloseq")
17292 (synopsis "Handling and analysis of high-throughput microbiome census data")
17294 "Phyloseq provides a set of classes and tools to facilitate the import,
17295 storage, analysis, and graphical display of microbiome census data.")
17296 (license license:agpl3)))
17299 ;;; Avoid adding new packages to the end of this file. To reduce the chances
17300 ;;; of a merge conflict, place them above by existing packages with similar
17301 ;;; functionality or similar names.