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 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-biscuiteerdata
1226 (name "r-biscuiteerdata")
1231 (uri (bioconductor-uri "biscuiteerData" version 'experiment))
1233 (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
1235 `((upstream-name . "biscuiteerData")))
1236 (build-system r-build-system)
1238 (list r-annotationhub r-curl r-experimenthub))
1239 (native-inputs (list r-knitr))
1240 (home-page "https://bioconductor.org/packages/biscuiteerData")
1241 (synopsis "Data package for Biscuiteer")
1243 "This package contains default datasets used by the Bioconductor package
1245 (license license:gpl3)))
1247 (define-public r-celldex
1254 (uri (bioconductor-uri "celldex" version 'experiment))
1256 (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
1257 (properties `((upstream-name . "celldex")))
1258 (build-system r-build-system)
1260 (list r-annotationdbi
1263 r-delayedmatrixstats
1266 r-summarizedexperiment))
1267 (native-inputs (list r-knitr))
1268 (home-page "https://github.com/LTLA/celldex")
1269 (synopsis "Reference index for cell types")
1271 "This package provides a collection of reference expression datasets with
1272 curated cell type labels, for use in procedures like automated annotation of
1273 single-cell data or deconvolution of bulk RNA-seq.")
1274 (license license:gpl3)))
1276 (define-public r-chromstardata
1278 (name "r-chromstardata")
1283 (uri (bioconductor-uri "chromstaRData" version 'experiment))
1285 (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
1286 (properties `((upstream-name . "chromstaRData")))
1287 (build-system r-build-system)
1288 (home-page "https://bioconductor.org/packages/chromstaRData/")
1289 (synopsis "ChIP-seq data for demonstration purposes")
1291 "This package provides ChIP-seq data for demonstration purposes in the
1292 chromstaR package.")
1293 (license license:gpl3)))
1295 (define-public r-copyhelper
1297 (name "r-copyhelper")
1302 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
1304 (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
1305 (properties `((upstream-name . "CopyhelpeR")))
1306 (build-system r-build-system)
1307 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
1308 (synopsis "Helper files for CopywriteR")
1310 "This package contains the helper files that are required to run the
1311 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
1312 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
1313 mm10. In addition, it contains a blacklist filter to remove regions that
1314 display copy number variation. Files are stored as GRanges objects from the
1315 GenomicRanges Bioconductor package.")
1316 (license license:gpl2)))
1318 (define-public r-genelendatabase
1320 (name "r-genelendatabase")
1325 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
1327 (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
1329 `((upstream-name . "geneLenDataBase")))
1330 (build-system r-build-system)
1332 (list r-rtracklayer r-genomicfeatures))
1333 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
1334 (synopsis "Lengths of mRNA transcripts for a number of genomes")
1336 "This package provides the lengths of mRNA transcripts for a number of
1337 genomes and gene ID formats, largely based on the UCSC table browser.")
1338 (license license:lgpl2.0+)))
1340 (define-public r-genomationdata
1342 (name "r-genomationdata")
1347 (uri (bioconductor-uri "genomationData" version 'experiment))
1349 (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
1351 `((upstream-name . "genomationData")))
1352 (build-system r-build-system)
1353 ;; As this package provides little more than large data files, it doesn't
1354 ;; make sense to build substitutes.
1355 (arguments `(#:substitutable? #f))
1358 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
1359 (synopsis "Experimental data for use with the genomation package")
1361 "This package contains experimental genetic data for use with the
1362 genomation package. Included are Chip Seq, Methylation and Cage data,
1363 downloaded from Encode.")
1364 (license license:gpl3+)))
1366 (define-public r-msdata
1373 (uri (bioconductor-uri "msdata" version 'experiment))
1375 (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
1376 (properties `((upstream-name . "msdata")))
1377 (build-system r-build-system)
1378 (home-page "https://bioconductor.org/packages/msdata")
1379 (synopsis "Various Mass Spectrometry raw data example files")
1381 "This package provides Ion Trap positive ionization mode data in mzML file
1382 format. It includes a subset from 500-850 m/z and 1190-1310 seconds,
1383 including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
1384 III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
1385 LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
1386 files for various search engines.")
1387 (license license:gpl2+)))
1389 (define-public r-pasilla
1396 (uri (bioconductor-uri "pasilla" version 'experiment))
1398 (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
1399 (build-system r-build-system)
1400 (propagated-inputs (list r-dexseq))
1401 (native-inputs (list r-knitr))
1402 (home-page "https://www.bioconductor.org/packages/pasilla/")
1403 (synopsis "Data package with per-exon and per-gene read counts")
1404 (description "This package provides per-exon and per-gene read counts
1405 computed for selected genes from RNA-seq data that were presented in the
1406 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1407 by Brooks et al., Genome Research 2011.")
1408 (license license:lgpl2.1+)))
1410 (define-public r-hsmmsinglecell
1412 (name "r-hsmmsinglecell")
1417 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1419 (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
1421 `((upstream-name . "HSMMSingleCell")))
1422 (build-system r-build-system)
1423 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1424 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1426 "Skeletal myoblasts undergo a well-characterized sequence of
1427 morphological and transcriptional changes during differentiation. In this
1428 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1429 under high mitogen conditions (GM) and then differentiated by switching to
1430 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1431 hundred cells taken over a time-course of serum-induced differentiation.
1432 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1433 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1434 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1435 which were then sequenced to a depth of ~4 million reads per library,
1436 resulting in a complete gene expression profile for each cell.")
1437 (license license:artistic2.0)))
1439 (define-public r-all
1446 (uri (bioconductor-uri "ALL" version 'experiment))
1448 (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
1449 (properties `((upstream-name . "ALL")))
1450 (build-system r-build-system)
1453 (home-page "https://bioconductor.org/packages/ALL")
1454 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1456 "The data consist of microarrays from 128 different individuals with
1457 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1458 are available. The data have been normalized (using rma) and it is the
1459 jointly normalized data that are available here. The data are presented in
1460 the form of an @code{exprSet} object.")
1461 (license license:artistic2.0)))
1463 (define-public r-affydata
1470 (uri (bioconductor-uri "affydata" version 'experiment))
1472 (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
1473 (properties `((upstream-name . "affydata")))
1474 (build-system r-build-system)
1477 (home-page "https://bioconductor.org/packages/affydata/")
1478 (synopsis "Affymetrix data for demonstration purposes")
1480 "This package provides example datasets that represent 'real world
1481 examples' of Affymetrix data, unlike the artificial examples included in the
1482 package @code{affy}.")
1483 (license license:gpl2+)))
1485 (define-public r-gagedata
1492 (uri (bioconductor-uri "gageData" version 'experiment))
1494 (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
1495 (properties `((upstream-name . "gageData")))
1496 (build-system r-build-system)
1497 (home-page "https://bioconductor.org/packages/gageData")
1498 (synopsis "Auxiliary data for the gage package")
1500 "This is a supportive data package for the software package @code{gage}.
1501 However, the data supplied here are also useful for gene set or pathway
1502 analysis or microarray data analysis in general. In this package, we provide
1503 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1504 BMP6 (originally published as an demo dataset for GAGE, also registered as
1505 GSE13604 in GEO). This package also includes commonly used gene set data based
1506 on KEGG pathways and GO terms for major research species, including human,
1507 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1508 yeast are also included.")
1509 (license license:gpl2+)))
1511 (define-public r-curatedtcgadata
1513 (name "r-curatedtcgadata")
1518 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1520 (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
1522 `((upstream-name . "curatedTCGAData")))
1523 (build-system r-build-system)
1525 (list r-annotationhub
1528 r-multiassayexperiment
1530 r-summarizedexperiment))
1531 (native-inputs (list r-knitr))
1532 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1533 (synopsis "Curated data from The Cancer Genome Atlas")
1535 "This package provides publicly available data from The Cancer Genome
1536 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1537 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1538 number, mutation, microRNA, protein, and others) with clinical / pathological
1539 data. It also links assay barcodes with patient identifiers, enabling
1540 harmonized subsetting of rows (features) and columns (patients / samples)
1541 across the entire multi-'omics experiment.")
1542 (license license:artistic2.0)))
1544 (define-public r-tcgabiolinksgui-data
1546 (name "r-tcgabiolinksgui-data")
1551 (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
1553 (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
1554 (properties `((upstream-name . "TCGAbiolinksGUI.data")))
1555 (build-system r-build-system)
1556 (native-inputs (list r-knitr))
1557 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
1558 (synopsis "Data for the TCGAbiolinksGUI package")
1559 (description "This package provides supporting data for the
1560 TCGAbiolinksGUI package.")
1561 (license license:gpl3)))
1566 (define-public r-abarray
1572 (uri (bioconductor-uri "ABarray" version))
1575 "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
1576 (properties `((upstream-name . "ABarray")))
1577 (build-system r-build-system)
1578 (propagated-inputs (list r-biobase r-multtest))
1579 (home-page "https://bioconductor.org/packages/ABarray")
1581 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
1583 "The package @code{ABarray} is designed to work with Applied Biosystems
1584 whole genome microarray platform, as well as any other platform whose data can
1585 be transformed into expression data matrix. Functions include data
1586 preprocessing, filtering, control probe analysis, statistical analysis in one
1587 single function. A @dfn{graphical user interface} (GUI) is also provided. The
1588 raw data, processed data, graphics output and statistical results are organized
1589 into folders according to the analysis settings used.")
1590 (license license:gpl2+)))
1592 (define-public r-absseq
1598 (uri (bioconductor-uri "ABSSeq" version))
1601 "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
1602 (properties `((upstream-name . "ABSSeq")))
1603 (build-system r-build-system)
1604 (propagated-inputs (list r-limma r-locfit))
1605 (home-page "https://bioconductor.org/packages/ABSSeq")
1607 "RNA-Seq analysis based on modelling absolute expression differences")
1609 "This package implements a new RNA-Seq analysis method and integrates two
1610 modules: a basic model for pairwise comparison and a linear model for complex
1611 design. RNA-Seq quantifies gene expression with reads count, which usually
1612 consists of conditions (or treatments) and several replicates for each
1613 condition. This software infers differential expression directly by the
1614 counts difference between conditions. It assumes that the sum counts
1615 difference between conditions follow a negative binomial distribution. In
1616 addition, @code{ABSSeq} moderates the fold-changes by two steps: the
1617 expression level and gene-specific dispersion, that might facilitate the gene
1618 ranking by fold-change and visualization.")
1619 (license license:gpl3+)))
1621 (define-public r-adam
1627 (uri (bioconductor-uri "ADAM" version))
1630 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
1631 (properties `((upstream-name . "ADAM")))
1632 (build-system r-build-system)
1633 (propagated-inputs (list r-dplyr
1641 r-summarizedexperiment))
1642 (native-inputs (list r-knitr))
1643 (home-page "https://bioconductor.org/packages/ADAM")
1644 (synopsis "Gene activity and diversity analysis module")
1646 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
1647 package created to group a set of genes from comparative samples (control
1648 versus experiment) belonging to different species according to their respective
1649 functions. The corresponding roles are extracted from the default collections
1650 like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
1651 @code{ADAM} show their significance by calculating the p-values referring to
1652 gene diversity and activity. Each group of genes is called @dfn{Group of
1653 functionally associated genes} (GFAG).")
1654 (license license:gpl2+)))
1656 (define-public r-adamgui
1662 (uri (bioconductor-uri "ADAMgui" version))
1665 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
1666 (properties `((upstream-name . "ADAMgui")))
1667 (build-system r-build-system)
1689 (native-inputs (list r-knitr))
1690 (home-page "https://bioconductor.org/packages/ADAMgui/")
1691 (synopsis "GUI for gene activity and diversity analysis")
1693 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
1694 for the @code{ADAM} package. The @code{ADAMgui} package provides two
1695 shiny-based applications that allows the user to study the output of the
1696 @code{ADAM} package files through different plots. It's possible, for
1697 example, to choose a specific @dfn{group of functionally associated
1698 genes} (GFAG) and observe the gene expression behavior with the plots created
1699 with the @code{GFAGtargetUi} function. Features such as differential
1700 expression and fold change can be easily seen with aid of the plots made with
1701 the @code{GFAGpathUi} function.")
1702 (license license:gpl2+)))
1704 (define-public r-adimpute
1710 (uri (bioconductor-uri "ADImpute" version))
1713 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
1714 (properties `((upstream-name . "ADImpute")))
1715 (build-system r-build-system)
1717 (list r-biocparallel
1727 r-singlecellexperiment
1728 r-summarizedexperiment))
1729 (native-inputs (list r-knitr))
1730 (home-page "https://bioconductor.org/packages/ADImpute")
1731 (synopsis "Adaptive computational prediction for dropout imputations")
1733 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
1734 unable to quantify the expression levels of all genes in a cell, creating a
1735 need for the computational prediction of missing values (dropout imputation).
1736 Most existing dropout imputation methods are limited in the sense that they
1737 exclusively use the scRNA-seq dataset at hand and do not exploit external
1738 gene-gene relationship information. The @code{ADImpute} package proposes two
1739 methods to address this issue:
1742 @item a gene regulatory network-based approach using gene-gene relationships
1743 learnt from external data;
1744 @item a baseline approach corresponding to a sample-wide average.
1747 @code{ADImpute} implements these novel methods and also combines them with
1748 existing imputation methods like @code{DrImpute} and @code{SAVER}.
1749 @code{ADImpute} can learn the best performing method per gene and combine the
1750 results from different methods into an ensemble.")
1751 (license license:gpl3+)))
1753 (define-public r-adsplit
1759 (uri (bioconductor-uri "adSplit" version))
1762 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
1763 (properties `((upstream-name . "adSplit")))
1764 (build-system r-build-system)
1766 (list r-annotationdbi
1772 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
1773 (synopsis "Annotation-driven splits in microarray data")
1775 "This package implements clustering of microarray gene expression
1776 profiles according to functional annotations. For each term genes are
1777 annotated to, splits into two subclasses are computed and a significance of
1778 the supporting gene set is determined.")
1779 (license license:gpl2+)))
1781 (define-public r-affixcan
1787 (uri (bioconductor-uri "AffiXcan" version))
1790 "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
1791 (properties `((upstream-name . "AffiXcan")))
1792 (build-system r-build-system)
1794 (list r-biocparallel
1796 r-multiassayexperiment
1797 r-summarizedexperiment))
1798 (native-inputs (list r-knitr))
1799 (home-page "https://bioconductor.org/packages/AffiXcan")
1800 (synopsis "Functional approach to impute genetically regulated expression")
1802 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
1803 expression} (GReX) for a set of genes in a sample of individuals, using a
1804 method based on the @dfn{total binding affinity} (TBA). Statistical models to
1805 impute GReX can be trained with a training dataset where the real total
1806 expression values are known.")
1807 (license license:gpl3)))
1809 (define-public r-affyrnadegradation
1811 (name "r-affyrnadegradation")
1815 (uri (bioconductor-uri "AffyRNADegradation" version))
1818 "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
1819 (properties `((upstream-name . "AffyRNADegradation")))
1820 (build-system r-build-system)
1821 (propagated-inputs (list r-affy))
1822 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
1824 "Analyze and correct probe positional bias in data due to RNA degradation")
1826 "The @code{AffyRNADegradation} package helps with the assessment and
1827 correction of RNA degradation effects in Affymetrix 3 expression arrays. The
1828 parameter @code{d} gives a robust and accurate measure of RNA integrity. The
1829 correction removes the probe positional bias, and thus improves comparability
1830 of samples that are affected by RNA degradation.")
1831 ;; the R file header specifies GPL2 or later
1832 (license license:gpl2+)))
1834 (define-public r-agdex
1840 (uri (bioconductor-uri "AGDEX" version))
1843 "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
1844 (properties `((upstream-name . "AGDEX")))
1845 (build-system r-build-system)
1846 (propagated-inputs (list r-biobase r-gseabase))
1847 (home-page "https://bioconductor.org/packages/AGDEX")
1849 "Evaluate agreement of differential expression for cross-species genomics")
1851 "The objective of @code{AGDEX} is to evaluate whether the results of a
1852 pair of two-group differential expression analysis comparisons show a level of
1853 agreement that is greater than expected if the group labels for each two-group
1854 comparison are randomly assigned. The agreement is evaluated for the entire
1855 transcriptome and (optionally) for a collection of pre-defined gene-sets.
1856 Additionally, the procedure performs permutation-based differential expression
1857 and meta analysis at both gene and gene-set levels of the data from each
1859 (license license:gpl2+)))
1861 (define-public r-aggregatebiovar
1863 (name "r-aggregatebiovar")
1867 (uri (bioconductor-uri "aggregateBioVar" version))
1870 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
1871 (properties `((upstream-name . "aggregateBioVar")))
1872 (build-system r-build-system)
1877 r-singlecellexperiment
1878 r-summarizedexperiment
1880 (native-inputs (list r-knitr))
1881 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
1882 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
1884 "This package @code{aggregateBioVar} contains tools to summarize single
1885 cell gene expression profiles at the level of subject for single cell RNA-seq
1886 data collected from more than one subject (e.g. biological sample or technical
1887 replicates). A @code{SingleCellExperiment} object is taken as input and
1888 converted to a list of @code{SummarizedExperiment} objects, where each list
1889 element corresponds to an assigned cell type. The @code{SummarizedExperiment}
1890 objects contain aggregate gene-by-subject count matrices and inter-subject
1891 column metadata for individual subjects that can be processed using downstream
1892 bulk RNA-seq tools.")
1893 (license license:gpl3)))
1895 (define-public r-agilp
1901 (uri (bioconductor-uri "agilp" version))
1904 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
1905 (properties `((upstream-name . "agilp")))
1906 (build-system r-build-system)
1907 (home-page "https://bioconductor.org/packages/agilp")
1908 (synopsis "Processing of Agilent expression array")
1910 "This package aims to provide a pipeline for the low-level analysis of
1911 gene expression microarray data, primarily focused on the Agilent platform,
1912 but which also provides utilities which may be useful for other platforms.")
1913 ;; Some files are under GPLv2+ but the combined work is released under the
1915 (license license:gpl3)))
1917 (define-public r-adductomicsr
1919 (name "r-adductomicsr")
1923 (uri (bioconductor-uri "adductomicsR" version))
1926 "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
1927 (properties `((upstream-name . "adductomicsR")))
1928 (build-system r-build-system)
1951 (native-inputs (list r-knitr))
1952 (home-page "https://bioconductor.org/packages/adductomicsR")
1953 (synopsis "Processing of adductomic mass spectral datasets")
1955 "This package @code{adductomicsR} processes data generated by the
1956 @dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
1957 peptides from spectra that has been corrected for mass drift and retention
1958 time drift and quantifies level mass spectral peaks from @dfn{first stage of
1959 mass spectrometry} (MS1) data.")
1960 (license license:artistic2.0)))
1962 (define-public r-agimicrorna
1964 (name "r-agimicrorna")
1968 (uri (bioconductor-uri "AgiMicroRna" version))
1971 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
1972 (properties `((upstream-name . "AgiMicroRna")))
1973 (build-system r-build-system)
1980 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
1982 "Processing and differential expression analysis of Agilent microRNA chips")
1984 "@code{AgiMicroRna} provides useful functionality for the processing,
1985 quality assessment and differential expression analysis of Agilent microRNA
1986 array data. The package uses a limma-like structure to generate the processed
1987 data in order to make statistical inferences about differential expression
1988 using the linear model features implemented in limma. Standard Bioconductor
1989 objects are used so that other packages could be used as well.")
1990 (license license:gpl3)))
1992 (define-public r-amountain
1994 (name "r-amountain")
1998 (uri (bioconductor-uri "AMOUNTAIN" version))
2001 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
2002 (properties `((upstream-name . "AMOUNTAIN")))
2003 (build-system r-build-system)
2005 (native-inputs (list r-knitr))
2006 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
2007 (synopsis "Modules for multilayer weighted gene co-expression networks")
2009 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
2010 gene co-expression network) could be constructed only from expression profile.
2011 Different layers in such networks may represent different time points, multiple
2012 conditions or various species. @code{AMOUNTAIN} aims to search active modules
2013 in multi-layer WGCN using a continuous optimization approach.")
2014 (license license:gpl2+)))
2016 (define-public r-amaretto
2022 (uri (bioconductor-uri "AMARETTO" version))
2025 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
2026 (properties `((upstream-name . "AMARETTO")))
2027 (build-system r-build-system)
2029 (list r-biocfilecache
2047 r-multiassayexperiment
2053 (native-inputs (list r-knitr))
2054 (home-page "https://bioconductor.org/packages/AMARETTO")
2055 (synopsis "Regulatory network inference and driver gene evaluation")
2057 "This package @code{AMARETTO} represents an algorithm that integrates copy
2058 number, DNA methylation and gene expression data to identify a set of driver
2059 genes by analyzing cancer samples and connects them to clusters of co-expressed
2060 genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
2061 setting to identify cancer driver genes and their modules on multiple cancer
2062 sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
2063 and EMT, and modules that accurately predict survival and molecular subtypes.
2064 This allows @code{AMARETTO} to identify novel cancer driver genes directing
2065 canonical cancer pathways.")
2066 (license license:asl2.0)))
2068 (define-public r-anaquin
2074 (uri (bioconductor-uri "Anaquin" version))
2077 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
2078 (properties `((upstream-name . "Anaquin")))
2079 (build-system r-build-system)
2088 (native-inputs (list r-knitr))
2089 (home-page "https://www.sequinstandards.com/")
2090 (synopsis "Statistical analysis of sequins")
2092 "The project is intended to support the use of @dfn{sequins}(synthetic
2093 sequencing spike-in controls) owned and made available by the Garvan Institute
2094 of Medical Research. The goal is to provide a standard open source library for
2095 quantitative analysis, modelling and visualization of spike-in controls.")
2096 (license license:bsd-3)))
2098 (define-public r-aneufinder
2100 (name "r-aneufinder")
2104 (uri (bioconductor-uri "AneuFinder" version))
2107 "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
2108 (build-system r-build-system)
2112 (list r-genomicranges
2133 (home-page "https://bioconductor.org/packages/AneuFinder/")
2134 (synopsis "Copy number variation analysis in single-cell-sequencing data")
2135 (description "This package implements functions for copy number variant
2136 calling, plotting, export and analysis from whole-genome single cell
2138 (license license:artistic2.0)))
2140 (define-public r-anf
2146 (uri (bioconductor-uri "ANF" version))
2149 "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
2150 (properties `((upstream-name . "ANF")))
2151 (build-system r-build-system)
2158 (native-inputs (list r-knitr))
2159 (home-page "https://bioconductor.org/packages/ANF")
2160 (synopsis "Affinity network fusion for complex patient clustering")
2162 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
2163 matrix construction and fusion as well as spectral clustering. This package is
2164 used for complex patient clustering by integrating multi-omic data through affinity
2166 (license license:gpl3)))
2168 (define-public r-annmap
2174 (uri (bioconductor-uri "annmap" version))
2177 "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
2178 (properties `((upstream-name . "annmap")))
2179 (build-system r-build-system)
2191 (home-page "https://github.com/cruk-mi/annmap")
2193 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
2195 "This package @code{annmap} provides annotation mappings for Affymetrix exon
2196 arrays and coordinate based queries to support deep sequencing data analysis.
2197 Database access is hidden behind the API which provides a set of functions such
2198 as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
2199 Functions to plot gene architecture and BAM file data are also provided.")
2200 (license license:gpl2)))
2202 (define-public r-antiprofiles
2204 (name "r-antiprofiles")
2208 (uri (bioconductor-uri "antiProfiles" version))
2211 "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
2212 (properties `((upstream-name . "antiProfiles")))
2213 (build-system r-build-system)
2217 (home-page "https://github.com/HCBravoLab/antiProfiles")
2218 (synopsis "Implementation of gene expression anti-profiles")
2220 "This package implements the gene expression anti-profiles method.
2221 Anti-profiles are a new approach for developing cancer genomic signatures that
2222 specifically take advantage of gene expression heterogeneity. They explicitly
2223 model increased gene expression variability in cancer to define robust and
2224 reproducible gene expression signatures capable of accurately distinguishing
2225 tumor samples from healthy controls.")
2226 (license license:artistic2.0)))
2228 (define-public r-biocversion
2230 (name "r-biocversion")
2235 (uri (bioconductor-uri "BiocVersion" version))
2238 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
2239 (properties `((upstream-name . "BiocVersion")))
2240 (build-system r-build-system)
2241 (home-page "https://bioconductor.org/packages/BiocVersion/")
2242 (synopsis "Set the appropriate version of Bioconductor packages")
2244 "This package provides repository information for the appropriate version
2246 (license license:artistic2.0)))
2248 (define-public r-biocgenerics
2250 (name "r-biocgenerics")
2254 (uri (bioconductor-uri "BiocGenerics" version))
2257 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
2259 `((upstream-name . "BiocGenerics")))
2260 (build-system r-build-system)
2261 (home-page "https://bioconductor.org/packages/BiocGenerics")
2262 (synopsis "S4 generic functions for Bioconductor")
2264 "This package provides S4 generic functions needed by many Bioconductor
2266 (license license:artistic2.0)))
2268 (define-public r-coverageview
2270 (name "r-coverageview")
2274 (uri (bioconductor-uri "CoverageView" version))
2277 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
2278 (build-system r-build-system)
2286 (home-page "https://bioconductor.org/packages/CoverageView/")
2287 (synopsis "Coverage visualization package for R")
2288 (description "This package provides a framework for the visualization of
2289 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
2290 be also used for genome-wide nucleosome positioning experiments or other
2291 experiment types where it is important to have a framework in order to inspect
2292 how the coverage distributed across the genome.")
2293 (license license:artistic2.0)))
2295 (define-public r-cummerbund
2297 (name "r-cummerbund")
2301 (uri (bioconductor-uri "cummeRbund" version))
2304 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
2305 (build-system r-build-system)
2317 (home-page "https://bioconductor.org/packages/cummeRbund/")
2318 (synopsis "Analyze Cufflinks high-throughput sequencing data")
2319 (description "This package allows for persistent storage, access,
2320 exploration, and manipulation of Cufflinks high-throughput sequencing
2321 data. In addition, provides numerous plotting functions for commonly
2322 used visualizations.")
2323 (license license:artistic2.0)))
2325 (define-public r-dearseq
2332 (uri (bioconductor-uri "dearseq" version))
2335 "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1"))))
2336 (build-system r-build-system)
2338 (list r-compquadform
2354 (home-page "https://github.com/borishejblum/dearseq")
2355 (synopsis "DEA for RNA-seq data through a robust variance component test")
2357 "This is a package for Differential Expression Analysis of RNA-seq data.
2358 It features a variance component score test accounting for data
2359 heteroscedasticity through precision weights. Perform both gene-wise and gene
2360 set analyses, and can deal with repeated or longitudinal data.")
2361 (license license:gpl2)))
2363 (define-public r-decipher
2369 (uri (bioconductor-uri "DECIPHER" version))
2372 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
2373 (build-system r-build-system)
2381 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
2382 (synopsis "Tools for deciphering and managing biological sequences")
2383 (description "This package provides a toolset for deciphering and managing
2384 biological sequences.")
2385 (license license:gpl3)))
2387 (define-public r-deconvr
2393 (uri (bioconductor-uri "deconvR" version))
2396 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
2397 (properties `((upstream-name . "deconvR")))
2398 (build-system r-build-system)
2417 (native-inputs (list r-knitr))
2418 (home-page "https://github.com/BIMSBbioinfo/deconvR")
2419 (synopsis "Simulation and deconvolution of omic profiles")
2421 "This package provides a collection of functions designed for analyzing
2422 deconvolution of the bulk sample(s) using an atlas of reference omic signature
2423 profiles and a user-selected model. Users are given the option to create or
2424 extend a reference atlas and,also simulate the desired size of the bulk
2425 signature profile of the reference cell types. The package includes the
2426 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
2427 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
2428 make mapping WGBS data to their probe IDs easier.")
2429 (license license:artistic2.0)))
2431 (define-public r-decoupler
2433 (name "r-decoupler")
2438 (uri (bioconductor-uri "decoupleR" version))
2440 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
2441 (properties `((upstream-name . "decoupleR")))
2442 (build-system r-build-system)
2455 (native-inputs (list r-knitr))
2456 (home-page "https://saezlab.github.io/decoupleR/")
2457 (synopsis "Computational methods to infer biological activities from omics data")
2459 "Many methods allow us to extract biological activities from omics data using
2460 information from prior knowledge resources, reducing the dimensionality for
2461 increased statistical power and better interpretability. decoupleR is a
2462 Bioconductor package containing different statistical methods to extract these
2463 signatures within a unified framework. decoupleR allows the user to flexibly
2464 test any method with any resource. It incorporates methods that take into
2465 account the sign and weight of network interactions. decoupleR can be used
2466 with any omic, as long as its features can be linked to a biological process
2467 based on prior knowledge. For example, in transcriptomics gene sets regulated
2468 by a transcription factor, or in phospho-proteomics phosphosites that are
2469 targeted by a kinase.")
2470 (license license:gpl3)))
2472 (define-public r-deepsnv
2478 (uri (bioconductor-uri "deepSNV" version))
2481 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
2482 (properties `((upstream-name . "deepSNV")))
2483 (build-system r-build-system)
2489 r-summarizedexperiment
2494 (home-page "https://github.com/gerstung-lab/deepSNV/")
2495 (synopsis "Detection of subclonal SNVs in deep sequencing data")
2497 "This package provides quantitative variant callers for detecting
2498 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
2499 The deepSNV algorithm is used for a comparative setup with a control experiment
2500 of the same loci and uses a beta-binomial model and a likelihood ratio test to
2501 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
2502 computes a Bayes classifier based on a beta-binomial model for variant calling
2503 with multiple samples for precisely estimating model parameters - such as local
2504 error rates and dispersion - and prior knowledge, e.g. from variation data
2505 bases such as COSMIC.")
2506 (license license:gpl3)))
2508 (define-public r-delayedarray
2510 (name "r-delayedarray")
2514 (uri (bioconductor-uri "DelayedArray" version))
2517 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
2519 `((upstream-name . "DelayedArray")))
2520 (build-system r-build-system)
2522 (list r-biocgenerics r-s4vectors r-iranges r-matrix
2526 (home-page "https://bioconductor.org/packages/DelayedArray")
2527 (synopsis "Delayed operations on array-like objects")
2529 "Wrapping an array-like object (typically an on-disk object) in a
2530 @code{DelayedArray} object allows one to perform common array operations on it
2531 without loading the object in memory. In order to reduce memory usage and
2532 optimize performance, operations on the object are either delayed or executed
2533 using a block processing mechanism. Note that this also works on in-memory
2534 array-like objects like @code{DataFrame} objects (typically with Rle columns),
2535 @code{Matrix} objects, and ordinary arrays and data frames.")
2536 (license license:artistic2.0)))
2538 (define-public r-derfinderhelper
2540 (name "r-derfinderhelper")
2545 (uri (bioconductor-uri "derfinderHelper" version))
2547 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
2548 (properties `((upstream-name . "derfinderHelper")))
2549 (build-system r-build-system)
2551 (list r-iranges r-matrix r-s4vectors))
2554 (home-page "https://github.com/leekgroup/derfinderHelper")
2555 (synopsis "Helper for derfinder")
2557 "This package speeds up the derfinder package when using multiple cores.
2558 It is particularly useful when using BiocParallel and it helps reduce the time
2559 spent loading the full derfinder package when running the F-statistics
2560 calculation in parallel.")
2561 (license license:artistic2.0)))
2563 (define-public r-drimseq
2570 (uri (bioconductor-uri "DRIMSeq" version))
2572 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
2573 (properties `((upstream-name . "DRIMSeq")))
2574 (build-system r-build-system)
2576 (list r-biocgenerics
2586 (native-inputs (list r-knitr))
2587 (home-page "https://bioconductor.org/packages/DRIMSeq")
2588 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
2590 "The package provides two frameworks. One for the differential
2591 transcript usage analysis between different conditions and one for the tuQTL
2592 analysis. Both are based on modeling the counts of genomic features (i.e.,
2593 transcripts) with the Dirichlet-multinomial distribution. The package also
2594 makes available functions for visualization and exploration of the data and
2596 (license license:gpl3+)))
2598 (define-public r-bluster
2604 (uri (bioconductor-uri "bluster" version))
2607 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
2608 (properties `((upstream-name . "bluster")))
2609 (build-system r-build-system)
2611 (list r-biocneighbors
2620 (home-page "https://bioconductor.org/packages/bluster")
2621 (synopsis "Clustering algorithms for Bioconductor")
2622 (description"This package wraps common clustering algorithms in an easily
2623 extended S4 framework. Backends are implemented for hierarchical, k-means
2624 and graph-based clustering. Several utilities are also provided to compare
2625 and evaluate clustering results.")
2626 (license license:gpl3)))
2628 (define-public r-ideoviz
2634 (uri (bioconductor-uri "IdeoViz" version))
2637 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
2638 (build-system r-build-system)
2646 (home-page "https://bioconductor.org/packages/IdeoViz/")
2647 (synopsis "Plots data along a chromosomal ideogram")
2648 (description "This package provides functions to plot data associated with
2649 arbitrary genomic intervals along chromosomal ideogram.")
2650 (license license:gpl2)))
2652 (define-public r-infercnv
2659 (uri (bioconductor-uri "infercnv" version))
2662 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
2663 (properties `((upstream-name . "infercnv")))
2664 (build-system r-build-system)
2665 (inputs (list python))
2694 r-singlecellexperiment
2695 r-summarizedexperiment
2697 (native-inputs (list r-knitr))
2698 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
2699 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
2701 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
2702 evidence for somatic large-scale chromosomal copy number alterations, such as gains
2703 or deletions of entire chromosomes or large segments of chromosomes. This is done
2704 by exploring expression intensity of genes across positions of a tumor genome in
2705 comparison to a set of reference \"normal\" cells. A heatmap is generated
2706 illustrating the relative expression intensities across each chromosome, and it
2707 often becomes readily apparent as to which regions of the tumor genome are
2708 over-abundant or less-abundant as compared to that of normal cells.")
2709 (license license:bsd-3)))
2711 (define-public r-iranges
2717 (uri (bioconductor-uri "IRanges" version))
2720 "0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k"))))
2722 `((upstream-name . "IRanges")))
2723 (build-system r-build-system)
2725 (list r-biocgenerics r-s4vectors))
2726 (home-page "https://bioconductor.org/packages/IRanges")
2727 (synopsis "Infrastructure for manipulating intervals on sequences")
2729 "This package provides efficient low-level and highly reusable S4 classes
2730 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
2731 generally, data that can be organized sequentially (formally defined as
2732 @code{Vector} objects), as well as views on these @code{Vector} objects.
2733 Efficient list-like classes are also provided for storing big collections of
2734 instances of the basic classes. All classes in the package use consistent
2735 naming and share the same rich and consistent \"Vector API\" as much as
2737 (license license:artistic2.0)))
2739 (define-public r-isoformswitchanalyzer
2741 (name "r-isoformswitchanalyzer")
2746 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
2748 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
2749 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
2750 (build-system r-build-system)
2783 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
2784 (synopsis "Analyze alternative splicing in RNA-seq data")
2786 "This is a package for the analysis of alternative splicing and isoform
2787 switches with predicted functional consequences (e.g. gain/loss of protein
2788 domains etc.) from quantification of all types of RNASeq by tools such as
2789 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
2790 (license license:gpl2+)))
2792 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
2793 (define-public r-absfiltergsea
2795 (name "r-absfiltergsea")
2800 (uri (cran-uri "AbsFilterGSEA" version))
2802 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
2803 (properties `((upstream-name . "AbsFilterGSEA")))
2804 (build-system r-build-system)
2806 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
2807 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
2808 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
2810 "This package provides a function that performs gene-permuting of a gene-set
2811 enrichment analysis (GSEA) calculation with or without the absolute filtering.
2812 Without filtering, users can perform (original) two-tailed or one-tailed
2814 (license license:gpl2)))
2816 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
2817 (define-public r-bisquerna
2819 (name "r-bisquerna")
2823 (uri (cran-uri "BisqueRNA" version))
2826 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
2827 (properties `((upstream-name . "BisqueRNA")))
2828 (build-system r-build-system)
2830 (list r-biobase r-limsolve))
2833 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2834 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2835 (description "This package provides tools to accurately estimate cell type
2836 abundances from heterogeneous bulk expression. A reference-based method
2837 utilizes single-cell information to generate a signature matrix and
2838 transformation of bulk expression for accurate regression based estimates.
2839 A marker-based method utilizes known cell-specific marker genes to measure
2840 relative abundances across samples.")
2841 (license license:gpl3)))
2843 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
2844 ;; from Bioconductor.
2845 (define-public r-deconstructsigs
2847 (name "r-deconstructsigs")
2851 (uri (cran-uri "deconstructSigs" version))
2854 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
2856 `((upstream-name . "deconstructSigs")))
2857 (build-system r-build-system)
2859 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
2861 (home-page "https://github.com/raerose01/deconstructSigs")
2862 (synopsis "Identifies signatures present in a tumor sample")
2863 (description "This package takes sample information in the form of the
2864 fraction of mutations in each of 96 trinucleotide contexts and identifies
2865 the weighted combination of published signatures that, when summed, most
2866 closely reconstructs the mutational profile.")
2867 (license license:gpl2+)))
2869 ;; This is a CRAN package, but it depends on Bioconductor packages.
2870 (define-public r-jetset
2877 (uri (cran-uri "jetset" version))
2879 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
2880 (properties `((upstream-name . "jetset")))
2881 (build-system r-build-system)
2882 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
2883 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
2884 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
2886 "This package provides a one-to-one mapping from gene to \"best\" probe
2887 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
2888 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
2889 gene may be measured by multiple probe sets. This can present a mild
2890 conundrum when attempting to evaluate a gene \"signature\" that is defined by
2891 gene names rather than by specific probe sets. This package also includes the
2892 pre-calculated probe set quality scores that were used to define the
2894 (license license:artistic2.0)))
2896 ;; This is a CRAN package, but it depends on Bioconductor packages.
2897 (define-public r-nmf
2904 (uri (cran-uri "NMF" version))
2907 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
2908 (properties `((upstream-name . "NMF")))
2909 (build-system r-build-system)
2914 r-bigmemory ; suggested
2915 r-synchronicity ; suggested
2930 (home-page "http://renozao.github.io/NMF")
2931 (synopsis "Algorithms and framework for nonnegative matrix factorization")
2933 "This package provides a framework to perform Non-negative Matrix
2934 Factorization (NMF). The package implements a set of already published
2935 algorithms and seeding methods, and provides a framework to test, develop and
2936 plug new or custom algorithms. Most of the built-in algorithms have been
2937 optimized in C++, and the main interface function provides an easy way of
2938 performing parallel computations on multicore machines.")
2939 (license license:gpl2+)))
2941 (define-public r-affy
2948 (uri (bioconductor-uri "affy" version))
2951 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
2952 (build-system r-build-system)
2962 (home-page "https://bioconductor.org/packages/affy")
2963 (synopsis "Methods for affymetrix oligonucleotide arrays")
2965 "This package contains functions for exploratory oligonucleotide array
2967 (license license:lgpl2.0+)))
2969 (define-public r-affycomp
2976 (uri (bioconductor-uri "affycomp" version))
2979 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
2980 (properties `((upstream-name . "affycomp")))
2981 (build-system r-build-system)
2982 (propagated-inputs (list r-biobase))
2983 (home-page "https://bioconductor.org/packages/affycomp/")
2984 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
2986 "The package contains functions that can be used to compare expression
2987 measures for Affymetrix Oligonucleotide Arrays.")
2988 (license license:gpl2+)))
2990 (define-public r-affycompatible
2992 (name "r-affycompatible")
2997 (uri (bioconductor-uri "AffyCompatible" version))
3000 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
3002 `((upstream-name . "AffyCompatible")))
3003 (build-system r-build-system)
3007 `(modify-phases %standard-phases
3008 (add-after 'unpack 'make-reproducible
3010 ;; Order DTD elements before generating R code from them.
3011 (substitute* "R/methods-AffyCompatible.R"
3014 elements <- dtd$elements
3015 ordered <- elements[order(names(elements))]\n"))
3016 (("elt in dtd\\$elements")
3018 ;; Use a predictable directory name for code generation.
3019 (mkdir-p "/tmp/NetAffxResourcePrototype")
3020 (substitute* "R/DataClasses.R"
3021 (("directory=tempdir\\(\\)")
3022 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
3024 (list r-biostrings r-rcurl r-xml))
3025 (home-page "https://bioconductor.org/packages/AffyCompatible/")
3026 (synopsis "Work with Affymetrix GeneChip files")
3028 "This package provides an interface to Affymetrix chip annotation and
3029 sample attribute files. The package allows an easy way for users to download
3030 and manage local data bases of Affynmetrix NetAffx annotation files. It also
3031 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
3032 Command Console} (AGCC)-compatible sample annotation files.")
3033 (license license:artistic2.0)))
3035 (define-public r-affycontam
3037 (name "r-affycontam")
3042 (uri (bioconductor-uri "affyContam" version))
3045 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
3046 (properties `((upstream-name . "affyContam")))
3047 (build-system r-build-system)
3049 (list r-affy r-affydata r-biobase))
3050 (home-page "https://bioconductor.org/packages/affyContam/")
3051 (synopsis "Structured corruption of Affymetrix CEL file data")
3053 "Microarray quality assessment is a major concern of microarray analysts.
3054 This package provides some simple approaches to in silico creation of quality
3055 problems in CEL-level data to help evaluate performance of quality metrics.")
3056 (license license:artistic2.0)))
3058 (define-public r-affycoretools
3060 (name "r-affycoretools")
3065 (uri (bioconductor-uri "affycoretools" version))
3068 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
3069 (properties `((upstream-name . "affycoretools")))
3070 (build-system r-build-system)
3093 (home-page "https://bioconductor.org/packages/affycoretools/")
3094 (synopsis "Functions for analyses with Affymetrix GeneChips")
3096 "This package provides various wrapper functions that have been written
3097 to streamline the more common analyses that a Biostatistician might see.")
3098 (license license:artistic2.0)))
3100 (define-public r-affyio
3107 (uri (bioconductor-uri "affyio" version))
3110 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
3111 (build-system r-build-system)
3116 (home-page "https://github.com/bmbolstad/affyio")
3117 (synopsis "Tools for parsing Affymetrix data files")
3119 "This package provides routines for parsing Affymetrix data files based
3120 upon file format information. The primary focus is on accessing the CEL and
3122 (license license:lgpl2.0+)))
3124 (define-public r-affxparser
3126 (name "r-affxparser")
3131 (uri (bioconductor-uri "affxparser" version))
3134 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
3135 (properties `((upstream-name . "affxparser")))
3136 (build-system r-build-system)
3137 (home-page "https://github.com/HenrikBengtsson/affxparser")
3138 (synopsis "Affymetrix File Parsing SDK")
3140 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
3141 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
3142 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
3143 are supported. Currently, there are methods for reading @dfn{chip definition
3144 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
3145 either in full or in part. For example, probe signals from a few probesets
3146 can be extracted very quickly from a set of CEL files into a convenient list
3148 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
3150 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
3152 (define-public r-annotate
3159 (uri (bioconductor-uri "annotate" version))
3162 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
3163 (build-system r-build-system)
3165 (list r-annotationdbi
3173 "https://bioconductor.org/packages/annotate")
3174 (synopsis "Annotation for microarrays")
3175 (description "This package provides R environments for the annotation of
3177 (license license:artistic2.0)))
3179 (define-public r-annotationdbi
3181 (name "r-annotationdbi")
3185 (uri (bioconductor-uri "AnnotationDbi" version))
3188 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
3190 `((upstream-name . "AnnotationDbi")))
3191 (build-system r-build-system)
3202 (home-page "https://bioconductor.org/packages/AnnotationDbi")
3203 (synopsis "Annotation database interface")
3205 "This package provides user interface and database connection code for
3206 annotation data packages using SQLite data storage.")
3207 (license license:artistic2.0)))
3209 (define-public r-annotationfilter
3211 (name "r-annotationfilter")
3215 (uri (bioconductor-uri "AnnotationFilter" version))
3218 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
3220 `((upstream-name . "AnnotationFilter")))
3221 (build-system r-build-system)
3223 (list r-genomicranges r-lazyeval))
3226 (home-page "https://github.com/Bioconductor/AnnotationFilter")
3227 (synopsis "Facilities for filtering Bioconductor annotation resources")
3229 "This package provides classes and other infrastructure to implement
3230 filters for manipulating Bioconductor annotation resources. The filters are
3231 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
3232 (license license:artistic2.0)))
3234 (define-public r-annotationforge
3236 (name "r-annotationforge")
3241 (uri (bioconductor-uri "AnnotationForge" version))
3244 "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8"))))
3246 `((upstream-name . "AnnotationForge")))
3247 (build-system r-build-system)
3249 (list r-annotationdbi
3259 (home-page "https://bioconductor.org/packages/AnnotationForge")
3260 (synopsis "Code for building annotation database packages")
3262 "This package provides code for generating Annotation packages and their
3263 databases. Packages produced are intended to be used with AnnotationDbi.")
3264 (license license:artistic2.0)))
3266 (define-public r-annotationhub
3268 (name "r-annotationhub")
3273 (uri (bioconductor-uri "AnnotationHub" version))
3276 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
3277 (properties `((upstream-name . "AnnotationHub")))
3278 (build-system r-build-system)
3280 (list r-annotationdbi
3288 r-interactivedisplaybase
3295 (home-page "https://bioconductor.org/packages/AnnotationHub")
3296 (synopsis "Client to access AnnotationHub resources")
3298 "This package provides a client for the Bioconductor AnnotationHub web
3299 resource. The AnnotationHub web resource provides a central location where
3300 genomic files (e.g. VCF, bed, wig) and other resources from standard
3301 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
3302 metadata about each resource, e.g., a textual description, tags, and date of
3303 modification. The client creates and manages a local cache of files retrieved
3304 by the user, helping with quick and reproducible access.")
3305 (license license:artistic2.0)))
3307 (define-public r-aroma-light
3309 (name "r-aroma-light")
3314 (uri (bioconductor-uri "aroma.light" version))
3317 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
3318 (properties `((upstream-name . "aroma.light")))
3319 (build-system r-build-system)
3321 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
3322 (home-page "https://github.com/HenrikBengtsson/aroma.light")
3323 (synopsis "Methods for normalization and visualization of microarray data")
3325 "This package provides methods for microarray analysis that take basic
3326 data types such as matrices and lists of vectors. These methods can be used
3327 standalone, be utilized in other packages, or be wrapped up in higher-level
3329 (license license:gpl2+)))
3331 (define-public r-bamsignals
3333 (name "r-bamsignals")
3338 (uri (bioconductor-uri "bamsignals" version))
3341 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
3342 (build-system r-build-system)
3344 (list r-biocgenerics
3352 (home-page "https://bioconductor.org/packages/bamsignals")
3353 (synopsis "Extract read count signals from bam files")
3355 "This package efficiently obtains count vectors from indexed bam
3356 files. It counts the number of nucleotide sequence reads in given genomic
3357 ranges and it computes reads profiles and coverage profiles. It also handles
3359 (license license:gpl2+)))
3361 (define-public r-biobase
3367 (uri (bioconductor-uri "Biobase" version))
3370 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
3372 `((upstream-name . "Biobase")))
3373 (build-system r-build-system)
3375 (list r-biocgenerics))
3376 (home-page "https://bioconductor.org/packages/Biobase")
3377 (synopsis "Base functions for Bioconductor")
3379 "This package provides functions that are needed by many other packages
3380 on Bioconductor or which replace R functions.")
3381 (license license:artistic2.0)))
3383 (define-public r-biomart
3389 (uri (bioconductor-uri "biomaRt" version))
3392 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
3394 `((upstream-name . "biomaRt")))
3395 (build-system r-build-system)
3397 (list r-annotationdbi
3408 (home-page "https://bioconductor.org/packages/biomaRt")
3409 (synopsis "Interface to BioMart databases")
3411 "biomaRt provides an interface to a growing collection of databases
3412 implementing the @url{BioMart software suite, http://www.biomart.org}. The
3413 package enables retrieval of large amounts of data in a uniform way without
3414 the need to know the underlying database schemas or write complex SQL queries.
3415 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
3416 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
3417 users direct access to a diverse set of data and enable a wide range of
3418 powerful online queries from gene annotation to database mining.")
3419 (license license:artistic2.0)))
3421 ;; This is a CRAN package, but it depends on a Bioconductor package:
3423 (define-public r-biomartr
3429 (uri (cran-uri "biomartr" version))
3432 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
3433 (properties `((upstream-name . "biomartr")))
3434 (build-system r-build-system)
3454 (native-inputs (list r-knitr))
3455 (home-page "https://docs.ropensci.org/biomartr/")
3456 (synopsis "Genomic data retrieval")
3458 "Perform large scale genomic data retrieval and functional annotation
3459 retrieval. This package aims to provide users with a standardized way to
3460 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
3461 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
3462 Furthermore, an interface to the BioMart database allows users to retrieve
3463 functional annotation for genomic loci. In addition, users can download
3464 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
3466 (license license:gpl2)))
3468 (define-public r-biocparallel
3470 (name "r-biocparallel")
3474 (uri (bioconductor-uri "BiocParallel" version))
3477 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
3479 `((upstream-name . "BiocParallel")))
3480 (build-system r-build-system)
3483 (modify-phases %standard-phases
3484 (add-after 'unpack 'make-reproducible
3486 ;; Remove generated documentation.
3487 (for-each delete-file
3488 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
3489 "inst/doc/Introduction_To_BiocParallel.pdf"
3490 "inst/doc/Errors_Logs_And_Debugging.pdf"
3491 "inst/doc/BiocParallel_BatchtoolsParam.R"
3492 "inst/doc/Introduction_To_BiocParallel.R"
3493 "inst/doc/Errors_Logs_And_Debugging.R"))
3495 ;; Remove time-dependent macro
3496 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
3497 "inst/doc/Introduction_To_BiocParallel.Rnw"
3498 "inst/doc/Errors_Logs_And_Debugging.Rnw"
3499 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
3500 "vignettes/Introduction_To_BiocParallel.Rnw"
3501 "vignettes/Errors_Logs_And_Debugging.Rnw")
3502 (("\\today") "later"))
3504 ;; Initialize the random number generator seed when building.
3505 (substitute* "R/rng.R"
3506 (("\"L'Ecuyer-CMRG\"\\)" m)
3508 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
3510 (list r-bh r-codetools r-futile-logger r-snow))
3513 (home-page "https://bioconductor.org/packages/BiocParallel")
3514 (synopsis "Bioconductor facilities for parallel evaluation")
3516 "This package provides modified versions and novel implementation of
3517 functions for parallel evaluation, tailored to use with Bioconductor
3519 (license (list license:gpl2+ license:gpl3+))))
3521 (define-public r-biostrings
3523 (name "r-biostrings")
3527 (uri (bioconductor-uri "Biostrings" version))
3530 "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8"))))
3532 `((upstream-name . "Biostrings")))
3533 (build-system r-build-system)
3535 (list r-biocgenerics
3541 (home-page "https://bioconductor.org/packages/Biostrings")
3542 (synopsis "String objects and algorithms for biological sequences")
3544 "This package provides memory efficient string containers, string
3545 matching algorithms, and other utilities, for fast manipulation of large
3546 biological sequences or sets of sequences.")
3547 (license license:artistic2.0)))
3549 (define-public r-biovizbase
3551 (name "r-biovizbase")
3556 (uri (bioconductor-uri "biovizBase" version))
3559 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
3560 (properties `((upstream-name . "biovizBase")))
3561 (build-system r-build-system)
3563 (list r-annotationdbi
3580 r-summarizedexperiment
3581 r-variantannotation))
3582 (home-page "https://bioconductor.org/packages/biovizBase")
3583 (synopsis "Basic graphic utilities for visualization of genomic data")
3585 "The biovizBase package is designed to provide a set of utilities, color
3586 schemes and conventions for genomic data. It serves as the base for various
3587 high-level packages for biological data visualization. This saves development
3588 effort and encourages consistency.")
3589 (license license:artistic2.0)))
3591 (define-public r-bsgenome
3597 (uri (bioconductor-uri "BSgenome" version))
3600 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
3602 `((upstream-name . "BSgenome")))
3603 (build-system r-build-system)
3605 (list r-biocgenerics
3615 (home-page "https://bioconductor.org/packages/BSgenome")
3616 (synopsis "Infrastructure for Biostrings-based genome data packages")
3618 "This package provides infrastructure shared by all Biostrings-based
3619 genome data packages and support for efficient SNP representation.")
3620 (license license:artistic2.0)))
3622 (define-public r-category
3629 (uri (bioconductor-uri "Category" version))
3632 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
3633 (properties `((upstream-name . "Category")))
3634 (build-system r-build-system)
3646 (home-page "https://bioconductor.org/packages/Category")
3647 (synopsis "Category analysis")
3649 "This package provides a collection of tools for performing category
3651 (license license:artistic2.0)))
3653 (define-public r-chipseeker
3655 (name "r-chipseeker")
3659 (uri (bioconductor-uri "ChIPseeker" version))
3662 "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"))))
3663 (build-system r-build-system)
3667 (list r-annotationdbi
3685 r-txdb-hsapiens-ucsc-hg19-knowngene))
3686 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
3687 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
3688 (description "This package implements functions to retrieve the nearest
3689 genes around the peak, annotate genomic region of the peak, statstical methods
3690 for estimate the significance of overlap among ChIP peak data sets, and
3691 incorporate GEO database for user to compare the own dataset with those
3692 deposited in database. The comparison can be used to infer cooperative
3693 regulation and thus can be used to generate hypotheses. Several visualization
3694 functions are implemented to summarize the coverage of the peak experiment,
3695 average profile and heatmap of peaks binding to TSS regions, genomic
3696 annotation, distance to TSS, and overlap of peaks or genes.")
3697 (license license:artistic2.0)))
3699 (define-public r-chipseq
3706 (uri (bioconductor-uri "chipseq" version))
3709 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
3710 (build-system r-build-system)
3712 (list r-biocgenerics
3718 (home-page "https://bioconductor.org/packages/chipseq")
3719 (synopsis "Package for analyzing ChIPseq data")
3721 "This package provides tools for processing short read data from ChIPseq
3723 (license license:artistic2.0)))
3725 (define-public r-complexheatmap
3727 (name "r-complexheatmap")
3732 (uri (bioconductor-uri "ComplexHeatmap" version))
3735 "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65"))))
3737 `((upstream-name . "ComplexHeatmap")))
3738 (build-system r-build-system)
3756 "https://github.com/jokergoo/ComplexHeatmap")
3757 (synopsis "Making Complex Heatmaps")
3759 "Complex heatmaps are efficient to visualize associations between
3760 different sources of data sets and reveal potential structures. This package
3761 provides a highly flexible way to arrange multiple heatmaps and supports
3762 self-defined annotation graphics.")
3763 (license license:gpl2+)))
3765 (define-public r-copywriter
3767 (name "r-copywriter")
3772 (uri (bioconductor-uri "CopywriteR" version))
3775 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
3776 (properties `((upstream-name . "CopywriteR")))
3777 (build-system r-build-system)
3779 (list r-biocparallel
3793 (home-page "https://github.com/PeeperLab/CopywriteR")
3794 (synopsis "Copy number information from targeted sequencing")
3796 "CopywriteR extracts DNA copy number information from targeted sequencing
3797 by utilizing off-target reads. It allows for extracting uniformly distributed
3798 copy number information, can be used without reference, and can be applied to
3799 sequencing data obtained from various techniques including chromatin
3800 immunoprecipitation and target enrichment on small gene panels. Thereby,
3801 CopywriteR constitutes a widely applicable alternative to available copy
3802 number detection tools.")
3803 (license license:gpl2)))
3805 (define-public r-deseq
3812 (uri (bioconductor-uri "DESeq" version))
3815 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
3816 (properties `((upstream-name . "DESeq")))
3817 (build-system r-build-system)
3827 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
3828 (synopsis "Differential gene expression analysis")
3830 "This package provides tools for estimating variance-mean dependence in
3831 count data from high-throughput genetic sequencing assays and for testing for
3832 differential expression based on a model using the negative binomial
3834 (license license:gpl3+)))
3836 (define-public r-deseq2
3843 (uri (bioconductor-uri "DESeq2" version))
3846 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
3847 (properties `((upstream-name . "DESeq2")))
3848 (build-system r-build-system)
3862 r-summarizedexperiment))
3865 (home-page "https://bioconductor.org/packages/DESeq2")
3866 (synopsis "Differential gene expression analysis")
3868 "This package provides functions to estimate variance-mean dependence in
3869 count data from high-throughput nucleotide sequencing assays and test for
3870 differential expression based on a model using the negative binomial
3872 (license license:lgpl3+)))
3874 (define-public r-dexseq
3881 (uri (bioconductor-uri "DEXSeq" version))
3884 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
3885 (properties `((upstream-name . "DEXSeq")))
3886 (build-system r-build-system)
3888 (list r-annotationdbi
3904 r-summarizedexperiment))
3907 (home-page "https://bioconductor.org/packages/DEXSeq")
3908 (synopsis "Inference of differential exon usage in RNA-Seq")
3910 "This package is focused on finding differential exon usage using RNA-seq
3911 exon counts between samples with different experimental designs. It provides
3912 functions that allows the user to make the necessary statistical tests based
3913 on a model that uses the negative binomial distribution to estimate the
3914 variance between biological replicates and generalized linear models for
3915 testing. The package also provides functions for the visualization and
3916 exploration of the results.")
3917 (license license:gpl3+)))
3919 (define-public r-diffcyt
3926 (uri (bioconductor-uri "diffcyt" version))
3928 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
3929 (properties `((upstream-name . "diffcyt")))
3930 (build-system r-build-system)
3944 r-summarizedexperiment
3946 (native-inputs (list r-knitr))
3947 (home-page "https://github.com/lmweber/diffcyt")
3948 (synopsis "Differential discovery in high-dimensional cytometry")
3950 "This package provides statistical methods for differential discovery
3951 analyses in high-dimensional cytometry data (including flow cytometry, mass
3952 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
3953 combination of high-resolution clustering and empirical Bayes moderated tests
3954 adapted from transcriptomics.")
3955 (license license:expat)))
3957 (define-public r-dirichletmultinomial
3959 (name "r-dirichletmultinomial")
3964 (uri (bioconductor-uri "DirichletMultinomial" version))
3967 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
3969 `((upstream-name . "DirichletMultinomial")))
3970 (build-system r-build-system)
3974 (list r-biocgenerics r-iranges r-s4vectors))
3975 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
3976 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
3978 "Dirichlet-multinomial mixture models can be used to describe variability
3979 in microbial metagenomic data. This package is an interface to code
3980 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
3982 (license license:lgpl3)))
3984 (define-public r-dittoseq
3990 (uri (bioconductor-uri "dittoSeq" version))
3993 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
3994 (properties `((upstream-name . "dittoSeq")))
3995 (build-system r-build-system)
4006 r-singlecellexperiment
4007 r-summarizedexperiment))
4008 (native-inputs (list r-knitr))
4009 (home-page "https://bioconductor.org/packages/dittoSeq")
4010 (synopsis "Single-cell and bulk RNA sequencing visualization")
4012 "This package provides a universal, user friendly, single-cell and bulk RNA
4013 sequencing visualization toolkit that allows highly customizable creation of
4014 color blindness friendly, publication-quality figures. dittoSeq accepts both
4015 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
4016 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
4017 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
4018 percent composition or expression across groups, and more. Customizations
4019 range from size and title adjustments to automatic generation of annotations
4020 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
4021 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
4022 many more. All with simple, discrete inputs. Color blindness friendliness is
4023 powered by legend adjustments (enlarged keys), and by allowing the use of
4024 shapes or letter-overlay in addition to the carefully selected
4025 code{dittoColors()}.")
4026 (license license:expat)))
4028 (define-public r-edaseq
4035 (uri (bioconductor-uri "EDASeq" version))
4038 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
4039 (properties `((upstream-name . "EDASeq")))
4040 (build-system r-build-system)
4042 (list r-annotationdbi
4056 (home-page "https://github.com/drisso/EDASeq")
4057 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
4059 "This package provides support for numerical and graphical summaries of
4060 RNA-Seq genomic read data. Provided within-lane normalization procedures to
4061 adjust for GC-content effect (or other gene-level effects) on read counts:
4062 loess robust local regression, global-scaling, and full-quantile
4063 normalization. Between-lane normalization procedures to adjust for
4064 distributional differences between lanes (e.g., sequencing depth):
4065 global-scaling and full-quantile normalization.")
4066 (license license:artistic2.0)))
4068 (define-public r-edger
4074 (uri (bioconductor-uri "edgeR" version))
4077 "1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik"))))
4078 (properties `((upstream-name . "edgeR")))
4079 (build-system r-build-system)
4081 (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp
4082 (home-page "http://bioinf.wehi.edu.au/edgeR")
4083 (synopsis "EdgeR does empirical analysis of digital gene expression data")
4084 (description "This package can do differential expression analysis of
4085 RNA-seq expression profiles with biological replication. It implements a range
4086 of statistical methodology based on the negative binomial distributions,
4087 including empirical Bayes estimation, exact tests, generalized linear models
4088 and quasi-likelihood tests. It be applied to differential signal analysis of
4089 other types of genomic data that produce counts, including ChIP-seq, SAGE and
4091 (license license:gpl2+)))
4093 (define-public r-ensembldb
4095 (name "r-ensembldb")
4100 (uri (bioconductor-uri "ensembldb" version))
4103 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
4104 (build-system r-build-system)
4106 (list r-annotationdbi
4124 (home-page "https://github.com/jotsetung/ensembldb")
4125 (synopsis "Utilities to create and use Ensembl-based annotation databases")
4127 "The package provides functions to create and use transcript-centric
4128 annotation databases/packages. The annotation for the databases are directly
4129 fetched from Ensembl using their Perl API. The functionality and data is
4130 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
4131 but, in addition to retrieve all gene/transcript models and annotations from
4132 the database, the @code{ensembldb} package also provides a filter framework
4133 allowing to retrieve annotations for specific entries like genes encoded on a
4134 chromosome region or transcript models of lincRNA genes.")
4135 ;; No version specified
4136 (license license:lgpl3+)))
4138 (define-public r-fastseg
4145 (uri (bioconductor-uri "fastseg" version))
4148 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
4149 (build-system r-build-system)
4151 (list r-biobase r-biocgenerics r-genomicranges r-iranges
4153 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
4154 (synopsis "Fast segmentation algorithm for genetic sequencing data")
4156 "Fastseg implements a very fast and efficient segmentation algorithm.
4157 It can segment data from DNA microarrays and data from next generation
4158 sequencing for example to detect copy number segments. Further it can segment
4159 data from RNA microarrays like tiling arrays to identify transcripts. Most
4160 generally, it can segment data given as a matrix or as a vector. Various data
4161 formats can be used as input to fastseg like expression set objects for
4162 microarrays or GRanges for sequencing data.")
4163 (license license:lgpl2.0+)))
4165 (define-public r-gage
4172 (uri (bioconductor-uri "gage" version))
4175 "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"))))
4176 (build-system r-build-system)
4178 (list r-annotationdbi r-go-db r-graph r-keggrest))
4179 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
4180 "articles/10.1186/1471-2105-10-161"))
4181 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
4183 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
4184 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
4185 data attributes including sample sizes, experimental designs, assay platforms,
4186 and other types of heterogeneity. The gage package provides functions for
4187 basic GAGE analysis, result processing and presentation. In addition, it
4188 provides demo microarray data and commonly used gene set data based on KEGG
4189 pathways and GO terms. These functions and data are also useful for gene set
4190 analysis using other methods.")
4191 (license license:gpl2+)))
4193 (define-public r-genefilter
4195 (name "r-genefilter")
4200 (uri (bioconductor-uri "genefilter" version))
4203 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
4204 (build-system r-build-system)
4206 (list gfortran r-knitr))
4208 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
4210 (home-page "https://bioconductor.org/packages/genefilter")
4211 (synopsis "Filter genes from high-throughput experiments")
4213 "This package provides basic functions for filtering genes from
4214 high-throughput sequencing experiments.")
4215 (license license:artistic2.0)))
4217 (define-public r-geneoverlap
4219 (name "r-geneoverlap")
4223 (uri (bioconductor-uri "GeneOverlap" version))
4226 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
4227 (build-system r-build-system)
4229 (list r-rcolorbrewer r-gplots))
4230 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
4231 (synopsis "Test and visualize gene overlaps")
4232 (description "This package can be used to test two sets of gene lists
4233 and visualize the results.")
4234 (license license:gpl3)))
4236 (define-public r-genomation
4238 (name "r-genomation")
4242 (uri (bioconductor-uri "genomation" version))
4245 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
4246 (build-system r-build-system)
4270 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
4271 (synopsis "Summary, annotation and visualization of genomic data")
4273 "This package provides a package for summary and annotation of genomic
4274 intervals. Users can visualize and quantify genomic intervals over
4275 pre-defined functional regions, such as promoters, exons, introns, etc. The
4276 genomic intervals represent regions with a defined chromosome position, which
4277 may be associated with a score, such as aligned reads from HT-seq experiments,
4278 TF binding sites, methylation scores, etc. The package can use any tabular
4279 genomic feature data as long as it has minimal information on the locations of
4280 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4281 (license license:artistic2.0)))
4283 (define-public r-genomeinfodb
4285 (name "r-genomeinfodb")
4289 (uri (bioconductor-uri "GenomeInfoDb" version))
4292 "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh"))))
4294 `((upstream-name . "GenomeInfoDb")))
4295 (build-system r-build-system)
4297 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
4301 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
4302 (synopsis "Utilities for manipulating chromosome identifiers")
4304 "This package contains data and functions that define and allow
4305 translation between different chromosome sequence naming conventions (e.g.,
4306 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4307 names in their natural, rather than lexicographic, order.")
4308 (license license:artistic2.0)))
4310 (define-public r-genomicalignments
4312 (name "r-genomicalignments")
4316 (uri (bioconductor-uri "GenomicAlignments" version))
4319 "1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi"))))
4321 `((upstream-name . "GenomicAlignments")))
4322 (build-system r-build-system)
4324 (list r-biocgenerics
4332 r-summarizedexperiment))
4333 (home-page "https://bioconductor.org/packages/GenomicAlignments")
4334 (synopsis "Representation and manipulation of short genomic alignments")
4336 "This package provides efficient containers for storing and manipulating
4337 short genomic alignments (typically obtained by aligning short reads to a
4338 reference genome). This includes read counting, computing the coverage,
4339 junction detection, and working with the nucleotide content of the
4341 (license license:artistic2.0)))
4343 (define-public r-genomicfeatures
4345 (name "r-genomicfeatures")
4349 (uri (bioconductor-uri "GenomicFeatures" version))
4352 "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1"))))
4354 `((upstream-name . "GenomicFeatures")))
4355 (build-system r-build-system)
4357 (list r-annotationdbi
4374 (home-page "https://bioconductor.org/packages/GenomicFeatures")
4375 (synopsis "Tools for working with transcript centric annotations")
4377 "This package provides a set of tools and methods for making and
4378 manipulating transcript centric annotations. With these tools the user can
4379 easily download the genomic locations of the transcripts, exons and cds of a
4380 given organism, from either the UCSC Genome Browser or a BioMart
4381 database (more sources will be supported in the future). This information is
4382 then stored in a local database that keeps track of the relationship between
4383 transcripts, exons, cds and genes. Flexible methods are provided for
4384 extracting the desired features in a convenient format.")
4385 (license license:artistic2.0)))
4387 (define-public r-genomicfiles
4389 (name "r-genomicfiles")
4394 (uri (bioconductor-uri "GenomicFiles" version))
4397 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
4398 (properties `((upstream-name . "GenomicFiles")))
4399 (build-system r-build-system)
4401 (list r-biocgenerics
4411 r-summarizedexperiment
4412 r-variantannotation))
4413 (home-page "https://bioconductor.org/packages/GenomicFiles")
4414 (synopsis "Distributed computing by file or by range")
4416 "This package provides infrastructure for parallel computations
4417 distributed by file or by range. User defined mapper and reducer functions
4418 provide added flexibility for data combination and manipulation.")
4419 (license license:artistic2.0)))
4421 (define-public r-genomicranges
4423 (name "r-genomicranges")
4427 (uri (bioconductor-uri "GenomicRanges" version))
4430 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
4432 `((upstream-name . "GenomicRanges")))
4433 (build-system r-build-system)
4435 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
4438 (home-page "https://bioconductor.org/packages/GenomicRanges")
4439 (synopsis "Representation and manipulation of genomic intervals")
4441 "This package provides tools to efficiently represent and manipulate
4442 genomic annotations and alignments is playing a central role when it comes to
4443 analyzing high-throughput sequencing data (a.k.a. NGS data). The
4444 GenomicRanges package defines general purpose containers for storing and
4445 manipulating genomic intervals and variables defined along a genome.")
4446 (license license:artistic2.0)))
4448 (define-public r-gostats
4455 (uri (bioconductor-uri "GOstats" version))
4458 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
4459 (properties `((upstream-name . "GOstats")))
4460 (build-system r-build-system)
4471 (home-page "https://bioconductor.org/packages/GOstats")
4472 (synopsis "Tools for manipulating GO and microarrays")
4474 "This package provides a set of tools for interacting with GO and
4475 microarray data. A variety of basic manipulation tools for graphs, hypothesis
4476 testing and other simple calculations.")
4477 (license license:artistic2.0)))
4479 (define-public r-gseabase
4486 (uri (bioconductor-uri "GSEABase" version))
4489 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
4490 (properties `((upstream-name . "GSEABase")))
4491 (build-system r-build-system)
4501 (home-page "https://bioconductor.org/packages/GSEABase")
4502 (synopsis "Gene set enrichment data structures and methods")
4504 "This package provides classes and methods to support @dfn{Gene Set
4505 Enrichment Analysis} (GSEA).")
4506 (license license:artistic2.0)))
4508 (define-public r-hpar
4515 (uri (bioconductor-uri "hpar" version))
4518 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
4519 (build-system r-build-system)
4522 (home-page "https://bioconductor.org/packages/hpar/")
4523 (synopsis "Human Protein Atlas in R")
4524 (description "This package provides a simple interface to and data from
4525 the Human Protein Atlas project.")
4526 (license license:artistic2.0)))
4528 (define-public r-rhtslib
4535 (uri (bioconductor-uri "Rhtslib" version))
4538 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
4539 (properties `((upstream-name . "Rhtslib")))
4540 (build-system r-build-system)
4541 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
4542 ;; which makes R abort the build.
4543 (arguments '(#:configure-flags '("--no-staged-install")))
4545 (list curl zlib ; packages using rhtslib need to link with zlib
4548 (list pkg-config r-knitr))
4549 (home-page "https://github.com/nhayden/Rhtslib")
4550 (synopsis "High-throughput sequencing library as an R package")
4552 "This package provides the HTSlib C library for high-throughput
4553 nucleotide sequence analysis. The package is primarily useful to developers
4554 of other R packages who wish to make use of HTSlib.")
4555 (license license:lgpl2.0+)))
4557 (define-public r-impute
4563 (uri (bioconductor-uri "impute" version))
4566 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
4569 (build-system r-build-system)
4570 (home-page "https://bioconductor.org/packages/impute")
4571 (synopsis "Imputation for microarray data")
4573 "This package provides a function to impute missing gene expression
4574 microarray data, using nearest neighbor averaging.")
4575 (license license:gpl2+)))
4577 (define-public r-interactivedisplaybase
4579 (name "r-interactivedisplaybase")
4584 (uri (bioconductor-uri "interactiveDisplayBase" version))
4587 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
4589 `((upstream-name . "interactiveDisplayBase")))
4590 (build-system r-build-system)
4592 (list r-biocgenerics r-dt r-shiny))
4595 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
4596 (synopsis "Base package for web displays of Bioconductor objects")
4598 "This package contains the basic methods needed to generate interactive
4599 Shiny-based display methods for Bioconductor objects.")
4600 (license license:artistic2.0)))
4602 (define-public r-keggrest
4609 (uri (bioconductor-uri "KEGGREST" version))
4612 "1rn03w8y80prbvzahkvf8275haiymnjj1ijcgn55p3d0sb54yzgw"))))
4613 (properties `((upstream-name . "KEGGREST")))
4614 (build-system r-build-system)
4616 (list r-biostrings r-httr r-png))
4619 (home-page "https://bioconductor.org/packages/KEGGREST")
4620 (synopsis "Client-side REST access to KEGG")
4622 "This package provides a package that provides a client interface to the
4623 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
4624 (license license:artistic2.0)))
4626 (define-public r-lfa
4633 (uri (bioconductor-uri "lfa" version))
4635 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
4636 (properties `((upstream-name . "lfa")))
4637 (build-system r-build-system)
4638 (propagated-inputs (list r-corpcor))
4639 (native-inputs (list r-knitr))
4640 (home-page "https://github.com/StoreyLab/lfa")
4641 (synopsis "Logistic Factor Analysis for categorical data")
4643 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
4644 Binomial data via estimation of latent structure in the natural parameter.")
4645 (license license:gpl3)))
4647 (define-public r-limma
4653 (uri (bioconductor-uri "limma" version))
4656 "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65"))))
4657 (build-system r-build-system)
4658 (home-page "http://bioinf.wehi.edu.au/limma")
4659 (synopsis "Package for linear models for microarray and RNA-seq data")
4660 (description "This package can be used for the analysis of gene expression
4661 studies, especially the use of linear models for analysing designed experiments
4662 and the assessment of differential expression. The analysis methods apply to
4663 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
4664 (license license:gpl2+)))
4666 (define-public r-methylkit
4668 (name "r-methylkit")
4672 (uri (bioconductor-uri "methylKit" version))
4675 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
4676 (properties `((upstream-name . "methylKit")))
4677 (build-system r-build-system)
4699 (list r-knitr)) ; for vignettes
4700 (home-page "https://github.com/al2na/methylKit")
4702 "DNA methylation analysis from high-throughput bisulfite sequencing results")
4704 "MethylKit is an R package for DNA methylation analysis and annotation
4705 from high-throughput bisulfite sequencing. The package is designed to deal
4706 with sequencing data from @dfn{Reduced representation bisulfite
4707 sequencing} (RRBS) and its variants, but also target-capture methods and whole
4708 genome bisulfite sequencing. It also has functions to analyze base-pair
4709 resolution 5hmC data from experimental protocols such as oxBS-Seq and
4711 (license license:artistic2.0)))
4713 (define-public r-motifrg
4720 (uri (bioconductor-uri "motifRG" version))
4723 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
4724 (properties `((upstream-name . "motifRG")))
4725 (build-system r-build-system)
4729 r-bsgenome-hsapiens-ucsc-hg19
4733 (home-page "https://bioconductor.org/packages/motifRG")
4734 (synopsis "Discover motifs in high throughput sequencing data")
4736 "This package provides tools for discriminative motif discovery in high
4737 throughput genetic sequencing data sets using regression methods.")
4738 (license license:artistic2.0)))
4740 (define-public r-muscat
4747 (uri (bioconductor-uri "muscat" version))
4750 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
4751 (properties `((upstream-name . "muscat")))
4752 (build-system r-build-system)
4754 (list r-biocparallel
4775 r-singlecellexperiment
4776 r-summarizedexperiment
4779 (native-inputs (list r-knitr))
4780 (home-page "https://github.com/HelenaLC/muscat")
4781 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
4783 "This package @code{muscat} provides various methods and visualization tools
4784 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
4785 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
4786 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
4787 platform that mimics both single and multi-sample scRNA-seq data.")
4788 (license license:gpl3)))
4790 (define-public r-mutationalpatterns
4792 (name "r-mutationalpatterns")
4797 (uri (bioconductor-uri "MutationalPatterns" version))
4800 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
4801 (build-system r-build-system)
4805 (list r-biocgenerics
4808 ;; These two packages are suggested packages
4809 r-bsgenome-hsapiens-1000genomes-hs37d5
4810 r-bsgenome-hsapiens-ucsc-hg19
4828 r-variantannotation))
4829 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
4830 (synopsis "Extract and visualize mutational patterns in genomic data")
4831 (description "This package provides an extensive toolset for the
4832 characterization and visualization of a wide range of mutational patterns
4833 in SNV base substitution data.")
4834 (license license:expat)))
4836 (define-public r-msnbase
4843 (uri (bioconductor-uri "MSnbase" version))
4846 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
4847 (properties `((upstream-name . "MSnbase")))
4848 (build-system r-build-system)
4874 (home-page "https://github.com/lgatto/MSnbase")
4875 (synopsis "Base functions and classes for MS-based proteomics")
4877 "This package provides basic plotting, data manipulation and processing
4878 of mass spectrometry based proteomics data.")
4879 (license license:artistic2.0)))
4881 (define-public r-msnid
4888 (uri (bioconductor-uri "MSnID" version))
4891 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
4892 (properties `((upstream-name . "MSnID")))
4893 (build-system r-build-system)
4896 (modify-phases %standard-phases
4897 (add-after 'unpack 'set-HOME
4898 (lambda _ (setenv "HOME" "/tmp"))))))
4900 (list r-annotationdbi
4926 (home-page "https://bioconductor.org/packages/MSnID")
4927 (synopsis "Utilities for LC-MSn proteomics identifications")
4929 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
4930 from mzIdentML (leveraging the mzID package) or text files. After collating
4931 the search results from multiple datasets it assesses their identification
4932 quality and optimize filtering criteria to achieve the maximum number of
4933 identifications while not exceeding a specified false discovery rate. It also
4934 contains a number of utilities to explore the MS/MS results and assess missed
4935 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
4936 (license license:artistic2.0)))
4938 (define-public r-mzid
4945 (uri (bioconductor-uri "mzID" version))
4948 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
4949 (properties `((upstream-name . "mzID")))
4950 (build-system r-build-system)
4960 (home-page "https://bioconductor.org/packages/mzID")
4961 (synopsis "Parser for mzIdentML files")
4963 "This package provides a parser for mzIdentML files implemented using the
4964 XML package. The parser tries to be general and able to handle all types of
4965 mzIdentML files with the drawback of having less pretty output than a vendor
4967 (license license:gpl2+)))
4969 (define-public r-mzr
4976 (uri (bioconductor-uri "mzR" version))
4979 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
4980 (modules '((guix build utils)))
4982 '(delete-file-recursively "src/boost"))))
4983 (properties `((upstream-name . "mzR")))
4984 (build-system r-build-system)
4987 (modify-phases %standard-phases
4988 (add-after 'unpack 'use-system-boost
4990 (substitute* "src/Makevars"
4991 (("\\./boost/libs.*") "")
4992 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
4993 (("\\ARCH_OBJS=" line)
4995 "\nBOOST_LIBS=-lboost_system -lboost_regex \
4996 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
4998 (list boost ; use this instead of the bundled boost sources
5009 (home-page "https://github.com/sneumann/mzR/")
5010 (synopsis "Parser for mass spectrometry data files")
5012 "The mzR package provides a unified API to the common file formats and
5013 parsers available for mass spectrometry data. It comes with a wrapper for the
5014 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
5015 The package contains the original code written by the ISB, and a subset of the
5016 proteowizard library for mzML and mzIdentML. The netCDF reading code has
5017 previously been used in XCMS.")
5018 (license license:artistic2.0)))
5020 (define-public r-organismdbi
5022 (name "r-organismdbi")
5027 (uri (bioconductor-uri "OrganismDbi" version))
5030 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
5031 (properties `((upstream-name . "OrganismDbi")))
5032 (build-system r-build-system)
5034 (list r-annotationdbi
5045 (home-page "https://bioconductor.org/packages/OrganismDbi")
5046 (synopsis "Software to enable the smooth interfacing of database packages")
5047 (description "The package enables a simple unified interface to several
5048 annotation packages each of which has its own schema by taking advantage of
5049 the fact that each of these packages implements a select methods.")
5050 (license license:artistic2.0)))
5052 (define-public r-pcamethods
5054 (name "r-pcamethods")
5059 (uri (bioconductor-uri "pcaMethods" version))
5062 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
5063 (properties `((upstream-name . "pcaMethods")))
5064 (build-system r-build-system)
5066 (list r-biobase r-biocgenerics r-mass r-rcpp))
5067 (home-page "https://github.com/hredestig/pcamethods")
5068 (synopsis "Collection of PCA methods")
5070 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
5071 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
5072 for missing value estimation is included for comparison. BPCA, PPCA and
5073 NipalsPCA may be used to perform PCA on incomplete data as well as for
5074 accurate missing value estimation. A set of methods for printing and plotting
5075 the results is also provided. All PCA methods make use of the same data
5076 structure (pcaRes) to provide a common interface to the PCA results.")
5077 (license license:gpl3+)))
5079 ;; This is a CRAN package, but it depends on a Bioconductor package:
5080 ;; r-aroma-light, r-dnacopy..
5081 (define-public r-pscbs
5088 (uri (cran-uri "PSCBS" version))
5090 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
5091 (properties `((upstream-name . "PSCBS")))
5092 (build-system r-build-system)
5095 (modify-phases %standard-phases
5096 (add-before 'install 'change-home-dir
5098 ;; Change from /homeless-shelter to /tmp for write permission.
5099 (setenv "HOME" "/tmp"))))))
5111 (list r-r-rsp ;used to build vignettes
5113 (home-page "https://github.com/HenrikBengtsson/PSCBS")
5114 (synopsis "Analysis of parent-specific DNA copy numbers")
5116 "This is a package for segmentation of allele-specific DNA copy number
5117 data and detection of regions with abnormal copy number within each parental
5118 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
5119 (license license:gpl2+)))
5121 (define-public r-protgenerics
5123 (name "r-protgenerics")
5128 (uri (bioconductor-uri "ProtGenerics" version))
5131 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
5132 (properties `((upstream-name . "ProtGenerics")))
5133 (build-system r-build-system)
5134 (home-page "https://github.com/lgatto/ProtGenerics")
5135 (synopsis "S4 generic functions for proteomics infrastructure")
5137 "This package provides S4 generic functions needed by Bioconductor
5138 proteomics packages.")
5139 (license license:artistic2.0)))
5141 (define-public r-rbgl
5148 (uri (bioconductor-uri "RBGL" version))
5151 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
5152 (properties `((upstream-name . "RBGL")))
5153 (build-system r-build-system)
5155 (list r-bh r-graph))
5156 (home-page "https://www.bioconductor.org/packages/RBGL")
5157 (synopsis "Interface to the Boost graph library")
5159 "This package provides a fairly extensive and comprehensive interface to
5160 the graph algorithms contained in the Boost library.")
5161 (license license:artistic2.0)))
5163 (define-public r-rcas
5169 (uri (bioconductor-uri "RCAS" version))
5172 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
5173 (properties `((upstream-name . "RCAS")))
5174 (build-system r-build-system)
5176 (list r-biocgenerics
5179 r-bsgenome-hsapiens-ucsc-hg19
5205 (synopsis "RNA-centric annotation system")
5207 "RCAS aims to be a standalone RNA-centric annotation system that provides
5208 intuitive reports and publication-ready graphics. This package provides the R
5209 library implementing most of the pipeline's features.")
5210 (home-page "https://github.com/BIMSBbioinfo/RCAS")
5211 (license license:artistic2.0)))
5213 (define-public r-regioner
5220 (uri (bioconductor-uri "regioneR" version))
5223 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
5224 (properties `((upstream-name . "regioneR")))
5225 (build-system r-build-system)
5237 (home-page "https://bioconductor.org/packages/regioneR/")
5238 (synopsis "Association analysis of genomic regions")
5239 (description "This package offers a statistical framework based on
5240 customizable permutation tests to assess the association between genomic
5241 region sets and other genomic features.")
5242 (license license:artistic2.0)))
5244 (define-public r-reportingtools
5246 (name "r-reportingtools")
5251 (uri (bioconductor-uri "ReportingTools" version))
5254 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
5256 `((upstream-name . "ReportingTools")))
5257 (build-system r-build-system)
5280 (home-page "https://bioconductor.org/packages/ReportingTools/")
5281 (synopsis "Tools for making reports in various formats")
5283 "The ReportingTools package enables users to easily display reports of
5284 analysis results generated from sources such as microarray and sequencing
5285 data. The package allows users to create HTML pages that may be viewed on a
5286 web browser, or in other formats. Users can generate tables with sortable and
5287 filterable columns, make and display plots, and link table entries to other
5288 data sources such as NCBI or larger plots within the HTML page. Using the
5289 package, users can also produce a table of contents page to link various
5290 reports together for a particular project that can be viewed in a web
5292 (license license:artistic2.0)))
5294 (define-public r-rhdf5
5300 (uri (bioconductor-uri "rhdf5" version))
5303 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
5304 (build-system r-build-system)
5306 (list r-rhdf5filters r-rhdf5lib))
5309 (home-page "https://bioconductor.org/packages/rhdf5")
5310 (synopsis "HDF5 interface to R")
5312 "This R/Bioconductor package provides an interface between HDF5 and R.
5313 HDF5's main features are the ability to store and access very large and/or
5314 complex datasets and a wide variety of metadata on mass storage (disk) through
5315 a completely portable file format. The rhdf5 package is thus suited for the
5316 exchange of large and/or complex datasets between R and other software
5317 package, and for letting R applications work on datasets that are larger than
5318 the available RAM.")
5319 (license license:artistic2.0)))
5321 (define-public r-rhdf5filters
5323 (name "r-rhdf5filters")
5328 (uri (bioconductor-uri "rhdf5filters" version))
5331 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
5332 (properties `((upstream-name . "rhdf5filters")))
5333 (build-system r-build-system)
5340 (home-page "https://github.com/grimbough/rhdf5filters")
5341 (synopsis "HDF5 compression filters")
5343 "This package provides a collection of compression filters for use with
5345 (license license:bsd-2)))
5347 (define-public r-rsamtools
5349 (name "r-rsamtools")
5353 (uri (bioconductor-uri "Rsamtools" version))
5356 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
5358 `((upstream-name . "Rsamtools")))
5359 (build-system r-build-system)
5362 (modify-phases %standard-phases
5363 (add-after 'unpack 'use-system-zlib
5365 (substitute* "DESCRIPTION"
5366 (("zlibbioc, ") ""))
5367 (substitute* "NAMESPACE"
5368 (("import\\(zlibbioc\\)") "")))))))
5370 (list r-biocgenerics
5380 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
5381 (synopsis "Interface to samtools, bcftools, and tabix")
5383 "This package provides an interface to the @code{samtools},
5384 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
5385 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
5386 tab-delimited (tabix) files.")
5387 (license license:expat)))
5389 ;; This is a CRAN package, but it depends on a Bioconductor package:
5391 (define-public r-restfulr
5398 (uri (cran-uri "restfulr" version))
5401 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
5402 (properties `((upstream-name . "restfulr")))
5403 (build-system r-build-system)
5405 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
5406 (home-page "https://cran.r-project.org/package=restfulr")
5407 (synopsis "R interface to RESTful web services")
5409 "This package models a RESTful service as if it were a nested R list.")
5410 (license license:artistic2.0)))
5412 (define-public r-rtracklayer
5414 (name "r-rtracklayer")
5418 (uri (bioconductor-uri "rtracklayer" version))
5421 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
5422 (build-system r-build-system)
5425 (modify-phases %standard-phases
5426 (add-after 'unpack 'use-system-zlib
5428 (substitute* "DESCRIPTION"
5429 ((" zlibbioc,") ""))
5430 (substitute* "NAMESPACE"
5431 (("import\\(zlibbioc\\)") "")))))))
5437 (list r-biocgenerics
5451 (home-page "https://bioconductor.org/packages/rtracklayer")
5452 (synopsis "R interface to genome browsers and their annotation tracks")
5454 "rtracklayer is an extensible framework for interacting with multiple
5455 genome browsers (currently UCSC built-in) and manipulating annotation tracks
5456 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
5457 built-in). The user may export/import tracks to/from the supported browsers,
5458 as well as query and modify the browser state, such as the current viewport.")
5459 (license license:artistic2.0)))
5461 ;; This is a CRAN package, but it depends on a Bioconductor package.
5462 (define-public r-samr
5469 (uri (cran-uri "samr" version))
5472 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
5473 (properties `((upstream-name . "samr")))
5474 (build-system r-build-system)
5482 (native-inputs (list gfortran))
5483 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
5484 (synopsis "Significance analysis of Microarrays")
5486 "This is a package for significance analysis of Microarrays for
5487 differential expression analysis, RNAseq data and related problems.")
5488 ;; Any version of the LGPL
5489 (license license:lgpl3+)))
5491 (define-public r-scannotatr
5493 (name "r-scannotatr")
5498 (uri (bioconductor-uri "scAnnotatR" version))
5500 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
5501 (properties `((upstream-name . "scAnnotatR")))
5502 (build-system r-build-system)
5504 (list r-annotationhub
5515 r-singlecellexperiment
5516 r-summarizedexperiment))
5517 (native-inputs (list r-knitr))
5518 (home-page "https://github.com/grisslab/scAnnotatR")
5519 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
5521 "This package comprises a set of pretrained machine learning models to
5522 predict basic immune cell types. This enables to quickly get a first
5523 annotation of the cell types present in the dataset without requiring prior
5524 knowledge. The package also lets you train using own models to predict new
5525 cell types based on specific research needs.")
5526 (license license:expat)))
5528 (define-public r-scdblfinder
5530 (name "r-scdblfinder")
5535 (uri (bioconductor-uri "scDblFinder" version))
5537 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
5538 (properties `((upstream-name . "scDblFinder")))
5539 (build-system r-build-system)
5541 (list r-biocgenerics
5559 r-singlecellexperiment
5560 r-summarizedexperiment
5562 (native-inputs (list r-knitr))
5563 (home-page "https://github.com/plger/scDblFinder")
5564 (synopsis "Detect multiplets in single-cell RNA sequencing data")
5566 "The scDblFinder package gathers various methods for the detection and
5567 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
5568 multiple cells captured within the same droplet or reaction volume). It
5569 includes methods formerly found in the scran package, and the new fast and
5570 comprehensive scDblFinder method.")
5571 (license license:gpl3)))
5573 (define-public r-scmap
5580 (uri (bioconductor-uri "scmap" version))
5582 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
5583 (properties `((upstream-name . "scmap")))
5584 (build-system r-build-system)
5599 r-singlecellexperiment
5600 r-summarizedexperiment))
5601 (native-inputs (list r-knitr))
5602 (home-page "https://github.com/hemberg-lab/scmap")
5603 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
5605 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
5606 composition of complex tissues since the technology allows researchers to
5607 define cell-types using unsupervised clustering of the transcriptome.
5608 However, due to differences in experimental methods and computational
5609 analyses, it is often challenging to directly compare the cells identified in
5610 two different experiments. @code{scmap} is a method for projecting cells from
5611 a scRNA-seq experiment onto the cell-types or individual cells identified in a
5612 different experiment.")
5613 (license license:gpl3)))
5615 (define-public r-seqlogo
5622 (uri (bioconductor-uri "seqLogo" version))
5625 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
5626 (properties `((upstream-name . "seqLogo")))
5627 (build-system r-build-system)
5630 (home-page "https://bioconductor.org/packages/seqLogo")
5631 (synopsis "Sequence logos for DNA sequence alignments")
5633 "seqLogo takes the position weight matrix of a DNA sequence motif and
5634 plots the corresponding sequence logo as introduced by Schneider and
5636 (license license:lgpl2.0+)))
5638 (define-public r-seqpattern
5640 (name "r-seqpattern")
5644 (uri (bioconductor-uri "seqPattern" version))
5647 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
5649 `((upstream-name . "seqPattern")))
5650 (build-system r-build-system)
5652 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
5653 (home-page "https://bioconductor.org/packages/seqPattern")
5654 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
5656 "This package provides tools to visualize oligonucleotide patterns and
5657 sequence motif occurrences across a large set of sequences centred at a common
5658 reference point and sorted by a user defined feature.")
5659 (license license:gpl3+)))
5661 (define-public r-shortread
5663 (name "r-shortread")
5668 (uri (bioconductor-uri "ShortRead" version))
5671 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
5672 (properties `((upstream-name . "ShortRead")))
5673 (build-system r-build-system)
5693 (home-page "https://bioconductor.org/packages/ShortRead")
5694 (synopsis "FASTQ input and manipulation tools")
5696 "This package implements sampling, iteration, and input of FASTQ files.
5697 It includes functions for filtering and trimming reads, and for generating a
5698 quality assessment report. Data are represented as
5699 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
5700 purposes. The package also contains legacy support for early single-end,
5701 ungapped alignment formats.")
5702 (license license:artistic2.0)))
5704 (define-public r-simplifyenrichment
5706 (name "r-simplifyenrichment")
5711 (uri (bioconductor-uri "simplifyEnrichment" version))
5714 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
5716 `((upstream-name . "simplifyEnrichment")))
5717 (build-system r-build-system)
5719 (list r-annotationdbi
5736 (native-inputs (list r-knitr))
5737 (home-page "https://github.com/jokergoo/simplifyEnrichment")
5738 (synopsis "Simplify functional enrichment results")
5739 (description "This package provides a new clustering algorithm, binary
5740 cut, for clustering similarity matrices of functional terms is implemented in
5741 this package. It also provides functionalities for visualizing, summarizing
5742 and comparing the clusterings.")
5743 (license license:expat)))
5745 (define-public r-transcriptr
5747 (name "r-transcriptr")
5752 (uri (bioconductor-uri "transcriptR" version))
5754 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
5755 (properties `((upstream-name . "transcriptR")))
5756 (build-system r-build-system)
5758 (list r-biocgenerics
5773 (native-inputs (list r-knitr))
5774 (home-page "https://bioconductor.org/packages/transcriptR")
5775 (synopsis "Primary transcripts detection and quantification")
5777 "The differences in the RNA types being sequenced have an impact on the
5778 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
5779 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
5780 broader coverage of both exonic and intronic regions. The presence of
5781 intronic reads in GRO-seq type of data makes it possible to use it to
5782 computationally identify and quantify all de novo continuous regions of
5783 transcription distributed across the genome. This type of data, however, is
5784 more challenging to interpret and less common practice compared to mRNA-seq.
5785 One of the challenges for primary transcript detection concerns the
5786 simultaneous transcription of closely spaced genes, which needs to be properly
5787 divided into individually transcribed units. The R package transcriptR
5788 combines RNA-seq data with ChIP-seq data of histone modifications that mark
5789 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
5790 overcome this challenge. The advantage of this approach over the use of, for
5791 example, gene annotations is that this approach is data driven and therefore
5792 able to deal also with novel and case specific events.")
5793 (license license:gpl3)))
5795 (define-public r-trajectoryutils
5797 (name "r-trajectoryutils")
5802 (uri (bioconductor-uri "TrajectoryUtils" version))
5805 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
5807 `((upstream-name . "TrajectoryUtils")))
5808 (build-system r-build-system)
5810 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
5811 r-summarizedexperiment))
5812 (native-inputs (list r-knitr))
5813 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
5814 (synopsis "Single-cell trajectory analysis utilities")
5816 "This package implements low-level utilities for single-cell trajectory
5817 analysis, primarily intended for re-use inside higher-level packages. It
5818 includes a function to create a cluster-level minimum spanning tree and data
5819 structures to hold pseudotime inference results.")
5820 (license license:gpl3)))
5822 (define-public r-slingshot
5824 (name "r-slingshot")
5828 (uri (bioconductor-uri "slingshot" version))
5831 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
5832 (build-system r-build-system)
5838 r-singlecellexperiment
5839 r-summarizedexperiment
5843 (home-page "https://bioconductor.org/packages/slingshot")
5844 (synopsis "Tools for ordering single-cell sequencing")
5845 (description "This package provides functions for inferring continuous,
5846 branching lineage structures in low-dimensional data. Slingshot was designed
5847 to model developmental trajectories in single-cell RNA sequencing data and
5848 serve as a component in an analysis pipeline after dimensionality reduction
5849 and clustering. It is flexible enough to handle arbitrarily many branching
5850 events and allows for the incorporation of prior knowledge through supervised
5851 graph construction.")
5852 (license license:artistic2.0)))
5854 (define-public r-stager
5861 (uri (bioconductor-uri "stageR" version))
5863 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
5864 (properties `((upstream-name . "stageR")))
5865 (build-system r-build-system)
5866 (propagated-inputs (list r-summarizedexperiment))
5867 (native-inputs (list r-knitr))
5868 (home-page "https://bioconductor.org/packages/stageR")
5869 (synopsis "Stage-wise analysis of high throughput gene expression data")
5871 "The stageR package allows automated stage-wise analysis of
5872 high-throughput gene expression data. The method is published in Genome
5874 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
5875 (license license:gpl3)))
5877 (define-public r-stringdb
5884 (uri (bioconductor-uri "STRINGdb" version))
5886 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
5887 (properties `((upstream-name . "STRINGdb")))
5888 (build-system r-build-system)
5899 (home-page "https://git.bioconductor.org/packages/STRINGdb")
5900 (synopsis "Search tool for the retrieval of interacting proteins database")
5902 "The @code{STRINGdb} package provides an R interface to the STRING
5903 protein-protein interactions database. @url{https://www.string-db.org,
5904 STRING} is a database of known and predicted protein-protein interactions.
5905 The interactions include direct (physical) and indirect (functional)
5906 associations. Each interaction is associated with a combined confidence score
5907 that integrates the various evidences.")
5908 (license license:gpl2)))
5910 (define-public r-structuralvariantannotation
5912 (name "r-structuralvariantannotation")
5917 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
5919 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
5920 (build-system r-build-system)
5934 r-summarizedexperiment
5935 r-variantannotation))
5938 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
5939 (synopsis "R package designed to simplify structural variant analysis")
5941 "This package contains useful helper functions for dealing with structural
5942 variants in VCF format. The packages contains functions for parsing VCFs from
5943 a number of popular callers as well as functions for dealing with breakpoints
5944 involving two separate genomic loci encoded as GRanges objects.")
5945 (license license:gpl3)))
5947 (define-public r-summarizedexperiment
5949 (name "r-summarizedexperiment")
5953 (uri (bioconductor-uri "SummarizedExperiment" version))
5956 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
5958 `((upstream-name . "SummarizedExperiment")))
5959 (build-system r-build-system)
5972 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
5973 (synopsis "Container for representing genomic ranges by sample")
5975 "The SummarizedExperiment container contains one or more assays, each
5976 represented by a matrix-like object of numeric or other mode. The rows
5977 typically represent genomic ranges of interest and the columns represent
5979 (license license:artistic2.0)))
5981 (define-public r-sva
5988 (uri (bioconductor-uri "sva" version))
5991 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
5992 (build-system r-build-system)
6000 (home-page "https://bioconductor.org/packages/sva")
6001 (synopsis "Surrogate variable analysis")
6003 "This package contains functions for removing batch effects and other
6004 unwanted variation in high-throughput experiment. It also contains functions
6005 for identifying and building surrogate variables for high-dimensional data
6006 sets. Surrogate variables are covariates constructed directly from
6007 high-dimensional data like gene expression/RNA sequencing/methylation/brain
6008 imaging data that can be used in subsequent analyses to adjust for unknown,
6009 unmodeled, or latent sources of noise.")
6010 (license license:artistic2.0)))
6012 (define-public r-systempiper
6014 (name "r-systempiper")
6019 (uri (bioconductor-uri "systemPipeR" version))
6022 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
6023 (properties `((upstream-name . "systemPipeR")))
6024 (build-system r-build-system)
6026 (list r-biocgenerics
6037 r-summarizedexperiment
6041 (home-page "https://github.com/tgirke/systemPipeR")
6042 (synopsis "Next generation sequencing workflow and reporting environment")
6044 "This R package provides tools for building and running automated
6045 end-to-end analysis workflows for a wide range of @dfn{next generation
6046 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6047 Important features include a uniform workflow interface across different NGS
6048 applications, automated report generation, and support for running both R and
6049 command-line software, such as NGS aligners or peak/variant callers, on local
6050 computers or compute clusters. Efficient handling of complex sample sets and
6051 experimental designs is facilitated by a consistently implemented sample
6052 annotation infrastructure.")
6053 (license license:artistic2.0)))
6055 (define-public r-topgo
6061 (uri (bioconductor-uri "topGO" version))
6064 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
6066 `((upstream-name . "topGO")))
6067 (build-system r-build-system)
6069 (list r-annotationdbi
6078 (home-page "https://bioconductor.org/packages/topGO")
6079 (synopsis "Enrichment analysis for gene ontology")
6081 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6082 terms while accounting for the topology of the GO graph. Different test
6083 statistics and different methods for eliminating local similarities and
6084 dependencies between GO terms can be implemented and applied.")
6085 ;; Any version of the LGPL applies.
6086 (license license:lgpl2.1+)))
6088 (define-public r-tximport
6094 (uri (bioconductor-uri "tximport" version))
6097 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
6098 (build-system r-build-system)
6101 (home-page "https://bioconductor.org/packages/tximport")
6102 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
6104 "This package provides tools to import transcript-level abundance,
6105 estimated counts and transcript lengths, and to summarize them into matrices
6106 for use with downstream gene-level analysis packages. Average transcript
6107 length, weighted by sample-specific transcript abundance estimates, is
6108 provided as a matrix which can be used as an offset for different expression
6109 of gene-level counts.")
6110 (license license:gpl2+)))
6112 ;; This is a CRAN package, but it depends on a Bioconductor package.
6113 (define-public r-valr
6120 (uri (cran-uri "valr" version))
6123 "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k"))))
6124 (build-system r-build-system)
6132 r-rtracklayer ;bioconductor package
6137 (home-page "https://github.com/rnabioco/valr")
6138 (synopsis "Genome interval arithmetic in R")
6140 "This package enables you to read and manipulate genome intervals and
6141 signals. It provides functionality similar to command-line tool suites within
6142 R, enabling interactive analysis and visualization of genome-scale data.")
6143 (license license:expat)))
6145 (define-public r-variantannotation
6147 (name "r-variantannotation")
6151 (uri (bioconductor-uri "VariantAnnotation" version))
6154 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
6156 `((upstream-name . "VariantAnnotation")))
6158 (list r-annotationdbi
6169 r-summarizedexperiment
6176 (build-system r-build-system)
6177 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6178 (synopsis "Package for annotation of genetic variants")
6179 (description "This R package can annotate variants, compute amino acid
6180 coding changes and predict coding outcomes.")
6181 (license license:artistic2.0)))
6183 (define-public r-vsn
6190 (uri (bioconductor-uri "vsn" version))
6193 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
6194 (build-system r-build-system)
6196 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
6198 (list r-knitr)) ; for vignettes
6199 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
6200 (synopsis "Variance stabilization and calibration for microarray data")
6202 "The package implements a method for normalising microarray intensities,
6203 and works for single- and multiple-color arrays. It can also be used for data
6204 from other technologies, as long as they have similar format. The method uses
6205 a robust variant of the maximum-likelihood estimator for an
6206 additive-multiplicative error model and affine calibration. The model
6207 incorporates data calibration step (a.k.a. normalization), a model for the
6208 dependence of the variance on the mean intensity and a variance stabilizing
6209 data transformation. Differences between transformed intensities are
6210 analogous to \"normalized log-ratios\". However, in contrast to the latter,
6211 their variance is independent of the mean, and they are usually more sensitive
6212 and specific in detecting differential transcription.")
6213 (license license:artistic2.0)))
6215 ;; There is no source tarball, so we fetch the code from the Bioconductor git
6217 (define-public r-xcir
6218 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
6222 (version (git-version "1.8.0" revision commit))
6226 (url "https://git.bioconductor.org/packages/XCIR")
6228 (file-name (git-file-name name version))
6231 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
6232 (properties `((upstream-name . "XCIR")))
6233 (build-system r-build-system)
6234 (propagated-inputs (list r-biomart
6242 r-variantannotation))
6243 (native-inputs (list r-knitr))
6244 (home-page "https://github.com/SRenan/XCIR")
6245 (synopsis "Analysis of X chromosome inactivation")
6247 "This package is an R package that offers models and tools for subject
6248 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
6250 (license license:gpl2))))
6252 (define-public r-xina
6259 (uri (bioconductor-uri "XINA" version))
6261 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
6262 (properties `((upstream-name . "XINA")))
6263 (build-system r-build-system)
6272 (native-inputs (list r-knitr))
6273 (home-page "https://git.bioconductor.org/packages/XINA")
6274 (synopsis "Identifying proteins that exhibit similar patterns")
6276 "The aim of @code{XINA} is to determine which proteins exhibit similar
6277 patterns within and across experimental conditions, since proteins with
6278 co-abundance patterns may have common molecular functions. @code{XINA} imports
6279 multiple datasets, tags dataset in silico, and combines the data for subsequent
6280 subgrouping into multiple clusters. The result is a single output depicting
6281 the variation across all conditions. @code{XINA} not only extracts
6282 coabundance profiles within and across experiments, but also incorporates
6283 protein-protein interaction databases and integrative resources such as
6284 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
6285 molecular functions, respectively, and produces intuitive graphical outputs.")
6286 (license license:gpl3)))
6288 (define-public r-xmapbridge
6290 (name "r-xmapbridge")
6295 (uri (bioconductor-uri "xmapbridge" version))
6297 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
6298 (properties `((upstream-name . "xmapbridge")))
6299 (build-system r-build-system)
6300 (home-page "https://git.bioconductor.org/packages/xmapbridge")
6301 (synopsis "Display numeric data in the web based genome browser X:MAP")
6303 "The package @code{xmapbridge} can plot graphs in the X:Map genome
6304 browser. X:Map uses the Google Maps API to provide a scrollable view of the
6305 genome. It supports a number of species, and can be accessed at
6306 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
6307 suitable format. Graph plotting in R is done using calls to the functions
6308 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
6309 similar to those used by the standard plot methods in R. These result in data
6310 being written to a set of files (in a specific directory structure) that
6311 contain the data to be displayed, as well as some additional meta-data
6312 describing each of the graphs.")
6313 (license license:lgpl3)))
6315 (define-public r-xvector
6321 (uri (bioconductor-uri "XVector" version))
6324 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
6326 `((upstream-name . "XVector")))
6327 (build-system r-build-system)
6330 (modify-phases %standard-phases
6331 (add-after 'unpack 'use-system-zlib
6333 (substitute* "DESCRIPTION"
6334 (("zlibbioc, ") ""))
6335 (substitute* "NAMESPACE"
6336 (("import\\(zlibbioc\\)") ""))
6341 (list r-biocgenerics r-iranges r-s4vectors))
6342 (home-page "https://bioconductor.org/packages/XVector")
6343 (synopsis "Representation and manpulation of external sequences")
6345 "This package provides memory efficient S4 classes for storing sequences
6346 \"externally\" (behind an R external pointer, or on disk).")
6347 (license license:artistic2.0)))
6349 (define-public r-zlibbioc
6355 (uri (bioconductor-uri "zlibbioc" version))
6358 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
6360 `((upstream-name . "zlibbioc")))
6361 (build-system r-build-system)
6362 (home-page "https://bioconductor.org/packages/zlibbioc")
6363 (synopsis "Provider for zlib-1.2.5 to R packages")
6364 (description "This package uses the source code of zlib-1.2.5 to create
6365 libraries for systems that do not have these available via other means.")
6366 (license license:artistic2.0)))
6368 (define-public r-zellkonverter
6370 (name "r-zellkonverter")
6375 (uri (bioconductor-uri "zellkonverter" version))
6377 (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz"))))
6378 (properties `((upstream-name . "zellkonverter")))
6379 (build-system r-build-system)
6387 r-singlecellexperiment
6388 r-summarizedexperiment))
6389 (native-inputs (list r-knitr))
6390 (home-page "https://github.com/theislab/zellkonverter")
6391 (synopsis "Conversion between AnnData and single-cell experiments objects")
6393 "This package provides methods to convert between Python AnnData objects
6394 and SingleCellExperiment objects. These are primarily intended for use by
6395 downstream Bioconductor packages that wrap Python methods for single-cell data
6396 analysis. It also includes functions to read and write H5AD files used for
6397 saving AnnData objects to disk.")
6398 (license license:expat)))
6400 (define-public r-geneplotter
6402 (name "r-geneplotter")
6407 (uri (bioconductor-uri "geneplotter" version))
6410 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
6411 (build-system r-build-system)
6419 (home-page "https://bioconductor.org/packages/geneplotter")
6420 (synopsis "Graphics functions for genomic data")
6422 "This package provides functions for plotting genomic data.")
6423 (license license:artistic2.0)))
6425 (define-public r-oligoclasses
6427 (name "r-oligoclasses")
6432 (uri (bioconductor-uri "oligoClasses" version))
6435 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
6436 (properties `((upstream-name . "oligoClasses")))
6437 (build-system r-build-system)
6451 r-summarizedexperiment))
6452 (home-page "https://bioconductor.org/packages/oligoClasses/")
6453 (synopsis "Classes for high-throughput arrays")
6455 "This package contains class definitions, validity checks, and
6456 initialization methods for classes used by the @code{oligo} and @code{crlmm}
6458 (license license:gpl2+)))
6460 (define-public r-oligo
6467 (uri (bioconductor-uri "oligo" version))
6470 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
6471 (properties `((upstream-name . "oligo")))
6472 (build-system r-build-system)
6473 (inputs (list zlib))
6488 (home-page "https://bioconductor.org/packages/oligo/")
6489 (synopsis "Preprocessing tools for oligonucleotide arrays")
6491 "This package provides a package to analyze oligonucleotide
6492 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
6493 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
6494 (license license:lgpl2.0+)))
6496 (define-public r-qvalue
6503 (uri (bioconductor-uri "qvalue" version))
6506 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
6507 (build-system r-build-system)
6509 (list r-ggplot2 r-reshape2))
6512 (home-page "https://github.com/StoreyLab/qvalue")
6513 (synopsis "Q-value estimation for false discovery rate control")
6515 "This package takes a list of p-values resulting from the simultaneous
6516 testing of many hypotheses and estimates their q-values and local @dfn{false
6517 discovery rate} (FDR) values. The q-value of a test measures the proportion
6518 of false positives incurred when that particular test is called significant.
6519 The local FDR measures the posterior probability the null hypothesis is true
6520 given the test's p-value. Various plots are automatically generated, allowing
6521 one to make sensible significance cut-offs. The software can be applied to
6522 problems in genomics, brain imaging, astrophysics, and data mining.")
6523 ;; Any version of the LGPL.
6524 (license license:lgpl3+)))
6526 (define r-rcppnumerical
6528 (name "r-rcppnumerical")
6532 (uri (cran-uri "RcppNumerical" version))
6535 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
6536 (properties `((upstream-name . "RcppNumerical")))
6537 (build-system r-build-system)
6539 `(("r-rcpp" ,r-rcpp)
6540 ("r-rcppeigen" ,r-rcppeigen)))
6542 `(("r-knitr" ,r-knitr)))
6543 (home-page "https://github.com/yixuan/RcppNumerical")
6544 (synopsis "Rcpp integration for numerical computing libraries")
6545 (description "This package provides a collection of open source libraries
6546 for numerical computing (numerical integration, optimization, etc.) and their
6547 integration with @code{Rcpp}.")
6548 (license license:gpl2+)))
6550 (define-public r-apeglm
6556 (uri (bioconductor-uri "apeglm" version))
6559 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
6560 (properties `((upstream-name . "apeglm")))
6561 (build-system r-build-system)
6568 r-summarizedexperiment))
6569 (native-inputs (list r-knitr))
6570 (home-page "https://bioconductor.org/packages/apeglm")
6571 (synopsis "Approximate posterior estimation for GLM coefficients")
6572 (description "This package provides Bayesian shrinkage estimators for
6573 effect sizes for a variety of GLM models, using approximation of the
6574 posterior for individual coefficients.")
6575 (license license:gpl2)))
6577 (define-public r-greylistchip
6579 (name "r-greylistchip")
6583 (uri (bioconductor-uri "GreyListChIP" version))
6586 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
6587 (properties `((upstream-name . "GreyListChIP")))
6588 (build-system r-build-system)
6597 r-summarizedexperiment))
6598 (home-page "https://bioconductor.org/packages/GreyListChIP")
6599 (synopsis "Greylist artefact regions based on ChIP inputs")
6600 (description "This package identifies regions of ChIP experiments with high
6601 signal in the input, that lead to spurious peaks during peak calling.")
6602 (license license:artistic2.0)))
6604 (define-public r-diffbind
6611 (uri (bioconductor-uri "DiffBind" version))
6614 "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr"))))
6615 (properties `((upstream-name . "DiffBind")))
6616 (build-system r-build-system)
6639 r-summarizedexperiment
6641 (home-page "https://bioconductor.org/packages/DiffBind")
6642 (synopsis "Differential binding analysis of ChIP-Seq peak data")
6644 "This package computes differentially bound sites from multiple
6645 ChIP-seq experiments using affinity (quantitative) data. Also enables
6646 occupancy (overlap) analysis and plotting functions.")
6647 (license license:artistic2.0)))
6649 (define-public r-ripseeker
6651 (name "r-ripseeker")
6656 (uri (bioconductor-uri "RIPSeeker" version))
6659 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
6660 (properties `((upstream-name . "RIPSeeker")))
6661 (build-system r-build-system)
6666 r-summarizedexperiment
6670 (home-page "https://bioconductor.org/packages/RIPSeeker")
6672 "Identifying protein-associated transcripts from RIP-seq experiments")
6674 "This package infers and discriminates RIP peaks from RIP-seq alignments
6675 using two-state HMM with negative binomial emission probability. While
6676 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
6677 a suite of bioinformatics tools integrated within this self-contained software
6678 package comprehensively addressing issues ranging from post-alignments
6679 processing to visualization and annotation.")
6680 (license license:gpl2)))
6682 (define-public r-mbkmeans
6688 (uri (bioconductor-uri "mbkmeans" version))
6691 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
6692 (build-system r-build-system)
6706 r-singlecellexperiment
6707 r-summarizedexperiment))
6708 (home-page "https://bioconductor.org/packages/mbkmeans")
6709 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
6710 (description "This package implements the mini-batch k-means algorithm for
6711 large datasets, including support for on-disk data representation.")
6712 (license license:expat)))
6714 (define-public r-multtest
6721 (uri (bioconductor-uri "multtest" version))
6724 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
6725 (build-system r-build-system)
6727 (list r-survival r-biocgenerics r-biobase r-mass))
6728 (home-page "https://bioconductor.org/packages/multtest")
6729 (synopsis "Resampling-based multiple hypothesis testing")
6731 "This package can do non-parametric bootstrap and permutation
6732 resampling-based multiple testing procedures (including empirical Bayes
6733 methods) for controlling the family-wise error rate (FWER), generalized
6734 family-wise error rate (gFWER), tail probability of the proportion of
6735 false positives (TPPFP), and false discovery rate (FDR). Several choices
6736 of bootstrap-based null distribution are implemented (centered, centered
6737 and scaled, quantile-transformed). Single-step and step-wise methods are
6738 available. Tests based on a variety of T- and F-statistics (including
6739 T-statistics based on regression parameters from linear and survival models
6740 as well as those based on correlation parameters) are included. When probing
6741 hypotheses with T-statistics, users may also select a potentially faster null
6742 distribution which is multivariate normal with mean zero and variance
6743 covariance matrix derived from the vector influence function. Results are
6744 reported in terms of adjusted P-values, confidence regions and test statistic
6745 cutoffs. The procedures are directly applicable to identifying differentially
6746 expressed genes in DNA microarray experiments.")
6747 (license license:lgpl3)))
6749 (define-public r-graph
6755 (uri (bioconductor-uri "graph" version))
6758 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
6759 (build-system r-build-system)
6761 (list r-biocgenerics))
6762 (home-page "https://bioconductor.org/packages/graph")
6763 (synopsis "Handle graph data structures in R")
6765 "This package implements some simple graph handling capabilities for R.")
6766 (license license:artistic2.0)))
6768 ;; This is a CRAN package, but it depends on a Bioconductor package.
6769 (define-public r-ggm
6776 (uri (cran-uri "ggm" version))
6779 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
6780 (properties `((upstream-name . "ggm")))
6781 (build-system r-build-system)
6783 (list r-graph r-igraph))
6784 (home-page "https://cran.r-project.org/package=ggm")
6785 (synopsis "Functions for graphical Markov models")
6787 "This package provides functions and datasets for maximum likelihood
6788 fitting of some classes of graphical Markov models.")
6789 (license license:gpl2+)))
6791 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
6792 (define-public r-perfmeas
6799 (uri (cran-uri "PerfMeas" version))
6802 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
6803 (properties `((upstream-name . "PerfMeas")))
6804 (build-system r-build-system)
6806 (list r-graph r-limma r-rbgl))
6807 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
6808 (synopsis "Performance measures for ranking and classification tasks")
6810 "This package implements different performance measures for
6811 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
6812 a given recall, F-score for single and multiple classes are available.")
6813 (license license:gpl2+)))
6815 ;; This is a CRAN package, but it depends on a Bioconductor package.
6816 (define-public r-codedepends
6818 (name "r-codedepends")
6823 (uri (cran-uri "CodeDepends" version))
6826 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
6827 (properties `((upstream-name . "CodeDepends")))
6828 (build-system r-build-system)
6830 (list r-codetools r-graph r-xml))
6831 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
6832 (synopsis "Analysis of R code for reproducible research and code comprehension")
6834 "This package provides tools for analyzing R expressions or blocks of
6835 code and determining the dependencies between them. It focuses on R scripts,
6836 but can be used on the bodies of functions. There are many facilities
6837 including the ability to summarize or get a high-level view of code,
6838 determining dependencies between variables, code improvement suggestions.")
6839 ;; Any version of the GPL
6840 (license (list license:gpl2+ license:gpl3+))))
6842 (define-public r-chippeakanno
6844 (name "r-chippeakanno")
6849 (uri (bioconductor-uri "ChIPpeakAnno" version))
6852 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
6853 (properties `((upstream-name . "ChIPpeakAnno")))
6854 (build-system r-build-system)
6856 (list r-annotationdbi
6879 r-summarizedexperiment
6883 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
6884 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
6886 "The package includes functions to retrieve the sequences around the peak,
6887 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
6888 custom features such as most conserved elements and other transcription factor
6889 binding sites supplied by users. Starting 2.0.5, new functions have been added
6890 for finding the peaks with bi-directional promoters with summary statistics
6891 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
6892 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
6893 enrichedGO (addGeneIDs).")
6894 (license license:gpl2+)))
6896 (define-public r-matrixgenerics
6898 (name "r-matrixgenerics")
6902 (uri (bioconductor-uri "MatrixGenerics" version))
6905 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
6907 `((upstream-name . "MatrixGenerics")))
6908 (build-system r-build-system)
6910 (list r-matrixstats))
6911 (home-page "https://bioconductor.org/packages/MatrixGenerics")
6912 (synopsis "S4 generic summary statistic functions for matrix-like objects")
6914 "This package provides S4 generic functions modeled after the
6915 @code{matrixStats} API for alternative matrix implementations. Packages with
6916 alternative matrix implementation can depend on this package and implement the
6917 generic functions that are defined here for a useful set of row and column
6918 summary statistics. Other package developers can import this package and
6919 handle a different matrix implementations without worrying about
6920 incompatibilities.")
6921 (license license:artistic2.0)))
6923 (define-public r-marray
6929 (uri (bioconductor-uri "marray" version))
6931 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
6932 (build-system r-build-system)
6935 (home-page "https://bioconductor.org/packages/marray")
6936 (synopsis "Exploratory analysis for two-color spotted microarray data")
6937 (description "This package contains class definitions for two-color spotted
6938 microarray data. It also includes functions for data input, diagnostic plots,
6939 normalization and quality checking.")
6940 (license license:lgpl2.0+)))
6942 (define-public r-cghbase
6948 (uri (bioconductor-uri "CGHbase" version))
6950 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
6951 (properties `((upstream-name . "CGHbase")))
6952 (build-system r-build-system)
6954 (list r-biobase r-marray))
6955 (home-page "https://bioconductor.org/packages/CGHbase")
6956 (synopsis "Base functions and classes for arrayCGH data analysis")
6957 (description "This package contains functions and classes that are needed by
6958 the @code{arrayCGH} packages.")
6959 (license license:gpl2+)))
6961 (define-public r-cghcall
6967 (uri (bioconductor-uri "CGHcall" version))
6969 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
6970 (properties `((upstream-name . "CGHcall")))
6971 (build-system r-build-system)
6973 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
6974 (home-page "https://bioconductor.org/packages/CGHcall")
6975 (synopsis "Base functions and classes for arrayCGH data analysis")
6976 (description "This package contains functions and classes that are needed by
6977 @code{arrayCGH} packages.")
6978 (license license:gpl2+)))
6980 (define-public r-qdnaseq
6986 (uri (bioconductor-uri "QDNAseq" version))
6988 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
6989 (properties `((upstream-name . "QDNAseq")))
6990 (build-system r-build-system)
7002 (home-page "https://bioconductor.org/packages/QDNAseq")
7003 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
7004 (description "The genome is divided into non-overlapping fixed-sized bins,
7005 number of sequence reads in each counted, adjusted with a simultaneous
7006 two-dimensional loess correction for sequence mappability and GC content, and
7007 filtered to remove spurious regions in the genome. Downstream steps of
7008 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
7010 (license license:gpl2+)))
7012 (define-public r-bayseq
7019 (uri (bioconductor-uri "baySeq" version))
7022 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
7023 (properties `((upstream-name . "baySeq")))
7024 (build-system r-build-system)
7026 (list r-abind r-edger r-genomicranges))
7027 (home-page "https://bioconductor.org/packages/baySeq/")
7028 (synopsis "Bayesian analysis of differential expression patterns in count data")
7030 "This package identifies differential expression in high-throughput count
7031 data, such as that derived from next-generation sequencing machines,
7032 calculating estimated posterior likelihoods of differential expression (or
7033 more complex hypotheses) via empirical Bayesian methods.")
7034 (license license:gpl3)))
7036 (define-public r-chipcomp
7043 (uri (bioconductor-uri "ChIPComp" version))
7046 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
7047 (properties `((upstream-name . "ChIPComp")))
7048 (build-system r-build-system)
7050 (list r-biocgenerics
7051 r-bsgenome-hsapiens-ucsc-hg19
7052 r-bsgenome-mmusculus-ucsc-mm9
7060 (home-page "https://bioconductor.org/packages/ChIPComp")
7061 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
7063 "ChIPComp implements a statistical method for quantitative comparison of
7064 multiple ChIP-seq datasets. It detects differentially bound sharp binding
7065 sites across multiple conditions considering matching control in ChIP-seq
7067 ;; Any version of the GPL.
7068 (license license:gpl3+)))
7070 (define-public r-riboprofiling
7072 (name "r-riboprofiling")
7077 (uri (bioconductor-uri "RiboProfiling" version))
7080 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
7081 (properties `((upstream-name . "RiboProfiling")))
7082 (build-system r-build-system)
7084 (list r-biocgenerics
7102 (home-page "https://bioconductor.org/packages/RiboProfiling/")
7103 (synopsis "Ribosome profiling data analysis")
7104 (description "Starting with a BAM file, this package provides the
7105 necessary functions for quality assessment, read start position recalibration,
7106 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
7107 of count data: pairs, log fold-change, codon frequency and coverage
7108 assessment, principal component analysis on codon coverage.")
7109 (license license:gpl3)))
7111 (define-public r-riboseqr
7118 (uri (bioconductor-uri "riboSeqR" version))
7121 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
7122 (properties `((upstream-name . "riboSeqR")))
7123 (build-system r-build-system)
7132 (home-page "https://bioconductor.org/packages/riboSeqR/")
7133 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
7135 "This package provides plotting functions, frameshift detection and
7136 parsing of genetic sequencing data from ribosome profiling experiments.")
7137 (license license:gpl3)))
7139 (define-public r-interactionset
7141 (name "r-interactionset")
7146 (uri (bioconductor-uri "InteractionSet" version))
7149 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
7151 `((upstream-name . "InteractionSet")))
7152 (build-system r-build-system)
7154 (list r-biocgenerics
7161 r-summarizedexperiment))
7164 (home-page "https://bioconductor.org/packages/InteractionSet")
7165 (synopsis "Base classes for storing genomic interaction data")
7167 "This package provides the @code{GInteractions},
7168 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
7169 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
7171 (license license:gpl3)))
7173 (define-public r-genomicinteractions
7175 (name "r-genomicinteractions")
7180 (uri (bioconductor-uri "GenomicInteractions" version))
7183 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
7185 `((upstream-name . "GenomicInteractions")))
7186 (build-system r-build-system)
7206 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
7207 (synopsis "R package for handling genomic interaction data")
7209 "This R package provides tools for handling genomic interaction data,
7210 such as ChIA-PET/Hi-C, annotating genomic features with interaction
7211 information and producing various plots and statistics.")
7212 (license license:gpl3)))
7214 (define-public r-ctc
7221 (uri (bioconductor-uri "ctc" version))
7224 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
7225 (build-system r-build-system)
7226 (propagated-inputs (list r-amap))
7227 (home-page "https://bioconductor.org/packages/ctc/")
7228 (synopsis "Cluster and tree conversion")
7230 "This package provides tools for exporting and importing classification
7231 trees and clusters to other programs.")
7232 (license license:gpl2)))
7234 (define-public r-goseq
7241 (uri (bioconductor-uri "goseq" version))
7244 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
7245 (build-system r-build-system)
7247 (list r-annotationdbi
7253 (home-page "https://bioconductor.org/packages/goseq/")
7254 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
7256 "This package provides tools to detect Gene Ontology and/or other user
7257 defined categories which are over/under represented in RNA-seq data.")
7258 (license license:lgpl2.0+)))
7260 (define-public r-glimma
7267 (uri (bioconductor-uri "Glimma" version))
7270 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
7271 (properties `((upstream-name . "Glimma")))
7272 (build-system r-build-system)
7280 r-summarizedexperiment))
7283 (home-page "https://github.com/Shians/Glimma")
7284 (synopsis "Interactive HTML graphics")
7286 "This package generates interactive visualisations for analysis of
7287 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
7288 HTML page. The interactions are built on top of the popular static
7289 representations of analysis results in order to provide additional
7291 (license license:lgpl3)))
7293 (define-public r-rots
7300 (uri (bioconductor-uri "ROTS" version))
7303 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
7304 (properties `((upstream-name . "ROTS")))
7305 (build-system r-build-system)
7307 (list r-biobase r-rcpp))
7308 (home-page "https://bioconductor.org/packages/ROTS/")
7309 (synopsis "Reproducibility-Optimized Test Statistic")
7311 "This package provides tools for calculating the
7312 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
7314 (license license:gpl2+)))
7316 (define-public r-plgem
7323 (uri (bioconductor-uri "plgem" version))
7326 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
7327 (build-system r-build-system)
7329 (list r-biobase r-mass))
7330 (home-page "http://www.genopolis.it")
7331 (synopsis "Detect differential expression in microarray and proteomics datasets")
7333 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
7334 model the variance-versus-mean dependence that exists in a variety of
7335 genome-wide datasets, including microarray and proteomics data. The use of
7336 PLGEM has been shown to improve the detection of differentially expressed
7337 genes or proteins in these datasets.")
7338 (license license:gpl2)))
7340 (define-public r-inspect
7347 (uri (bioconductor-uri "INSPEcT" version))
7350 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
7351 (properties `((upstream-name . "INSPEcT")))
7352 (build-system r-build-system)
7373 r-summarizedexperiment
7374 r-txdb-mmusculus-ucsc-mm9-knowngene))
7377 (home-page "https://bioconductor.org/packages/INSPEcT")
7378 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
7380 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
7381 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
7382 order to evaluate synthesis, processing and degradation rates and assess via
7383 modeling the rates that determines changes in mature mRNA levels.")
7384 (license license:gpl2)))
7386 (define-public r-dnabarcodes
7388 (name "r-dnabarcodes")
7393 (uri (bioconductor-uri "DNABarcodes" version))
7396 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
7397 (properties `((upstream-name . "DNABarcodes")))
7398 (build-system r-build-system)
7400 (list r-bh r-matrix r-rcpp))
7403 (home-page "https://bioconductor.org/packages/DNABarcodes")
7404 (synopsis "Create and analyze DNA barcodes")
7406 "This package offers tools to create DNA barcode sets capable of
7407 correcting insertion, deletion, and substitution errors. Existing barcodes
7408 can be analyzed regarding their minimal, maximal and average distances between
7409 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
7410 demultiplexed, i.e. assigned to their original reference barcode.")
7411 (license license:gpl2)))
7413 (define-public r-ruvseq
7420 (uri (bioconductor-uri "RUVSeq" version))
7423 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
7424 (properties `((upstream-name . "RUVSeq")))
7425 (build-system r-build-system)
7427 (list r-biobase r-edaseq r-edger r-mass))
7430 (home-page "https://github.com/drisso/RUVSeq")
7431 (synopsis "Remove unwanted variation from RNA-Seq data")
7433 "This package implements methods to @dfn{remove unwanted variation} (RUV)
7434 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
7436 (license license:artistic2.0)))
7438 (define-public r-biocneighbors
7440 (name "r-biocneighbors")
7445 (uri (bioconductor-uri "BiocNeighbors" version))
7448 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
7449 (properties `((upstream-name . "BiocNeighbors")))
7450 (build-system r-build-system)
7452 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
7455 (home-page "https://bioconductor.org/packages/BiocNeighbors")
7456 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
7458 "This package implements exact and approximate methods for nearest
7459 neighbor detection, in a framework that allows them to be easily switched
7460 within Bioconductor packages or workflows. The exact algorithm is implemented
7461 using pre-clustering with the k-means algorithm. Functions are also provided
7462 to search for all neighbors within a given distance. Parallelization is
7463 achieved for all methods using the BiocParallel framework.")
7464 (license license:gpl3)))
7466 (define-public r-scaledmatrix
7468 (name "r-scaledmatrix")
7473 (uri (bioconductor-uri "ScaledMatrix" version))
7476 "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl"))))
7477 (properties `((upstream-name . "ScaledMatrix")))
7478 (build-system r-build-system)
7480 (list r-delayedarray r-matrix r-s4vectors))
7481 (native-inputs (list r-knitr))
7482 (home-page "https://github.com/LTLA/ScaledMatrix")
7483 (synopsis "Create a DelayedMatrix of scaled and centered values")
7485 "This package provides delayed computation of a matrix of scaled and
7486 centered values. The result is equivalent to using the @code{scale} function
7487 but avoids explicit realization of a dense matrix during block processing.
7488 This permits greater efficiency in common operations, most notably matrix
7490 (license license:gpl3)))
7492 (define-public r-treeio
7499 (uri (bioconductor-uri "treeio" version))
7502 "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla"))))
7503 (properties `((upstream-name . "treeio")))
7504 (build-system r-build-system)
7513 (native-inputs (list r-knitr))
7514 (home-page "https://github.com/YuLab-SMU/treeio")
7515 (synopsis "Base classes and functions for Phylogenetic tree input and output")
7517 "This is an R package to make it easier to import and store phylogenetic
7518 trees with associated data; and to link external data from different sources
7519 to phylogeny. It also supports exporting phylogenetic trees with
7520 heterogeneous associated data to a single tree file and can be served as a
7521 platform for merging tree with associated data and converting file formats.")
7522 (license license:artistic2.0)))
7524 (define-public r-ggtree
7531 (uri (bioconductor-uri "ggtree" version))
7534 "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4"))))
7535 (properties `((upstream-name . "ggtree")))
7536 (build-system r-build-system)
7551 (native-inputs (list r-knitr))
7552 (home-page "https://yulab-smu.top/treedata-book/")
7553 (synopsis "R package for visualization of trees and annotation data")
7555 "This package extends the ggplot2 plotting system which implements a
7556 grammar of graphics. ggtree is designed for visualization and annotation of
7557 phylogenetic trees and other tree-like structures with their annotation
7559 (license license:artistic2.0)))
7561 (define-public r-metapod
7568 (uri (bioconductor-uri "metapod" version))
7571 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
7572 (properties `((upstream-name . "metapod")))
7573 (build-system r-build-system)
7578 (home-page "https://bioconductor.org/packages/metapod")
7579 (synopsis "Meta-analyses on p-values of differential analyses")
7581 "This package implements a variety of methods for combining p-values in
7582 differential analyses of genome-scale datasets. Functions can combine
7583 p-values across different tests in the same analysis (e.g., genomic windows in
7584 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
7585 analyses (e.g., replicated comparisons, effect of different treatment
7586 conditions). Support is provided for handling log-transformed input p-values,
7587 missing values and weighting where appropriate.")
7588 (license license:gpl3)))
7590 (define-public r-biocsingular
7592 (name "r-biocsingular")
7597 (uri (bioconductor-uri "BiocSingular" version))
7600 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
7601 (properties `((upstream-name . "BiocSingular")))
7602 (build-system r-build-system)
7616 (home-page "https://github.com/LTLA/BiocSingular")
7617 (synopsis "Singular value decomposition for Bioconductor packages")
7619 "This package implements exact and approximate methods for singular value
7620 decomposition and principal components analysis, in a framework that allows
7621 them to be easily switched within Bioconductor packages or workflows. Where
7622 possible, parallelization is achieved using the BiocParallel framework.")
7623 (license license:gpl3)))
7625 (define-public r-destiny
7632 (uri (bioconductor-uri "destiny" version))
7635 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
7636 (build-system r-build-system)
7654 r-singlecellexperiment
7656 r-summarizedexperiment
7661 (list r-knitr r-nbconvertr)) ; for vignettes
7662 (home-page "https://bioconductor.org/packages/destiny/")
7663 (synopsis "Create and plot diffusion maps")
7664 (description "This package provides tools to create and plot diffusion
7666 ;; Any version of the GPL
7667 (license license:gpl3+)))
7669 (define-public r-savr
7676 (uri (bioconductor-uri "savR" version))
7679 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
7680 (properties `((upstream-name . "savR")))
7681 (build-system r-build-system)
7683 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
7684 (home-page "https://github.com/bcalder/savR")
7685 (synopsis "Parse and analyze Illumina SAV files")
7687 "This package provides tools to parse Illumina Sequence Analysis
7688 Viewer (SAV) files, access data, and generate QC plots.")
7689 (license license:agpl3+)))
7691 (define-public r-chipexoqual
7693 (name "r-chipexoqual")
7698 (uri (bioconductor-uri "ChIPexoQual" version))
7701 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
7702 (properties `((upstream-name . "ChIPexoQual")))
7703 (build-system r-build-system)
7705 (list r-biocparallel
7724 (home-page "https://github.com/keleslab/ChIPexoQual")
7725 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
7727 "This package provides a quality control pipeline for ChIP-exo/nexus
7729 (license license:gpl2+)))
7731 (define-public r-copynumber
7733 (name "r-copynumber")
7737 (uri (bioconductor-uri "copynumber" version))
7740 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
7741 (build-system r-build-system)
7743 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
7744 (home-page "https://bioconductor.org/packages/copynumber")
7745 (synopsis "Segmentation of single- and multi-track copy number data")
7747 "This package segments single- and multi-track copy number data by a
7748 penalized least squares regression method.")
7749 (license license:artistic2.0)))
7751 (define-public r-dnacopy
7758 (uri (bioconductor-uri "DNAcopy" version))
7761 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
7762 (properties `((upstream-name . "DNAcopy")))
7763 (build-system r-build-system)
7764 (native-inputs (list gfortran))
7765 (home-page "https://bioconductor.org/packages/DNAcopy")
7766 (synopsis "DNA copy number data analysis")
7768 "This package implements the @dfn{circular binary segmentation} (CBS)
7769 algorithm to segment DNA copy number data and identify genomic regions with
7770 abnormal copy number.")
7771 (license license:gpl2+)))
7773 ;; This is a CRAN package, but it uncharacteristically depends on a
7774 ;; Bioconductor package.
7775 (define-public r-htscluster
7777 (name "r-htscluster")
7782 (uri (cran-uri "HTSCluster" version))
7785 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
7786 (properties `((upstream-name . "HTSCluster")))
7787 (build-system r-build-system)
7789 (list r-capushe r-edger r-plotrix))
7790 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
7791 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
7793 "This package provides a Poisson mixture model is implemented to cluster
7794 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
7795 estimation is performed using either the EM or CEM algorithm, and the slope
7796 heuristics are used for model selection (i.e., to choose the number of
7798 (license license:gpl3+)))
7800 (define-public r-deds
7807 (uri (bioconductor-uri "DEDS" version))
7810 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
7811 (properties `((upstream-name . "DEDS")))
7812 (build-system r-build-system)
7813 (home-page "https://bioconductor.org/packages/DEDS/")
7814 (synopsis "Differential expression via distance summary for microarray data")
7816 "This library contains functions that calculate various statistics of
7817 differential expression for microarray data, including t statistics, fold
7818 change, F statistics, SAM, moderated t and F statistics and B statistics. It
7819 also implements a new methodology called DEDS (Differential Expression via
7820 Distance Summary), which selects differentially expressed genes by integrating
7821 and summarizing a set of statistics using a weighted distance approach.")
7822 ;; Any version of the LGPL.
7823 (license license:lgpl3+)))
7825 ;; This is a CRAN package, but since it depends on a Bioconductor package we
7827 (define-public r-nbpseq
7834 (uri (cran-uri "NBPSeq" version))
7837 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
7838 (properties `((upstream-name . "NBPSeq")))
7839 (build-system r-build-system)
7842 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
7843 (synopsis "Negative binomial models for RNA-Seq data")
7845 "This package provides negative binomial models for two-group comparisons
7846 and regression inferences from RNA-sequencing data.")
7847 (license license:gpl2)))
7849 (define-public r-ebseq
7856 (uri (bioconductor-uri "EBSeq" version))
7859 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
7860 (properties `((upstream-name . "EBSeq")))
7861 (build-system r-build-system)
7863 (list r-blockmodeling r-gplots r-testthat))
7864 (home-page "https://bioconductor.org/packages/EBSeq")
7865 (synopsis "Differential expression analysis of RNA-seq data")
7867 "This package provides tools for differential expression analysis at both
7868 gene and isoform level using RNA-seq data")
7869 (license license:artistic2.0)))
7871 (define-public r-karyoploter
7873 (name "r-karyoploter")
7877 (uri (bioconductor-uri "karyoploteR" version))
7880 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
7881 (build-system r-build-system)
7883 (list r-annotationdbi
7897 r-variantannotation))
7900 (home-page "https://bioconductor.org/packages/karyoploteR/")
7901 (synopsis "Plot customizable linear genomes displaying arbitrary data")
7902 (description "This package creates karyotype plots of arbitrary genomes and
7903 offers a complete set of functions to plot arbitrary data on them. It mimics
7904 many R base graphics functions coupling them with a coordinate change function
7905 automatically mapping the chromosome and data coordinates into the plot
7907 (license license:artistic2.0)))
7909 (define-public r-lpsymphony
7911 (name "r-lpsymphony")
7916 (uri (bioconductor-uri "lpsymphony" version))
7919 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
7920 (build-system r-build-system)
7924 '(modify-phases %standard-phases
7925 (add-after 'unpack 'make-build-order-reproducible
7927 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
7928 "src/SYMPHONY/Cgl/configure")
7929 (("for file in `ls \\*/Makefile.in`")
7930 "for file in `ls */Makefile.in | sort`")))))))
7934 (list pkg-config r-knitr))
7935 (home-page "https://r-forge.r-project.org/projects/rsymphony")
7936 (synopsis "Symphony integer linear programming solver in R")
7938 "This package was derived from Rsymphony. The package provides an R
7939 interface to SYMPHONY, a linear programming solver written in C++. The main
7940 difference between this package and Rsymphony is that it includes the solver
7941 source code, while Rsymphony expects to find header and library files on the
7942 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
7943 to install interface to SYMPHONY.")
7944 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
7945 ;; lpsimphony is released under the same terms.
7946 (license license:epl1.0)))
7948 (define-public r-ihw
7955 (uri (bioconductor-uri "IHW" version))
7958 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
7959 (properties `((upstream-name . "IHW")))
7960 (build-system r-build-system)
7962 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
7965 (home-page "https://bioconductor.org/packages/IHW")
7966 (synopsis "Independent hypothesis weighting")
7968 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
7969 procedure that increases power compared to the method of Benjamini and
7970 Hochberg by assigning data-driven weights to each hypothesis. The input to
7971 IHW is a two-column table of p-values and covariates. The covariate can be
7972 any continuous-valued or categorical variable that is thought to be
7973 informative on the statistical properties of each hypothesis test, while it is
7974 independent of the p-value under the null hypothesis.")
7975 (license license:artistic2.0)))
7977 (define-public r-icobra
7984 (uri (bioconductor-uri "iCOBRA" version))
7987 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
7988 (properties `((upstream-name . "iCOBRA")))
7989 (build-system r-build-system)
8005 (home-page "https://bioconductor.org/packages/iCOBRA")
8006 (synopsis "Comparison and visualization of ranking and assignment methods")
8008 "This package provides functions for calculation and visualization of
8009 performance metrics for evaluation of ranking and binary
8010 classification (assignment) methods. It also contains a Shiny application for
8011 interactive exploration of results.")
8012 (license license:gpl2+)))
8014 (define-public r-residualmatrix
8016 (name "r-residualmatrix")
8021 (uri (bioconductor-uri "ResidualMatrix" version))
8024 "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4"))))
8026 `((upstream-name . "ResidualMatrix")))
8027 (build-system r-build-system)
8029 (list r-delayedarray r-matrix r-s4vectors))
8032 (home-page "https://github.com/LTLA/ResidualMatrix")
8033 (synopsis "Create a DelayedMatrix of regression residuals")
8035 "This package implements tools for delayed computation of a matrix of
8036 residuals after fitting a linear model to each column of an input matrix. It
8037 also supports partial computation of residuals where selected factors are to
8038 be preserved in the output matrix. It implements a number of efficient
8039 methods for operating on the delayed matrix of residuals, most notably matrix
8040 multiplication and calculation of row/column sums or means.")
8041 (license license:gpl3)))
8043 (define-public r-batchelor
8045 (name "r-batchelor")
8050 (uri (bioconductor-uri "batchelor" version))
8053 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
8054 (properties `((upstream-name . "batchelor")))
8055 (build-system r-build-system)
8063 r-delayedmatrixstats
8071 r-singlecellexperiment
8072 r-summarizedexperiment))
8073 (native-inputs (list r-knitr))
8074 (home-page "https://bioconductor.org/packages/batchelor")
8075 (synopsis "Single-Cell Batch Correction Methods")
8077 "This package implements a variety of methods for batch correction of
8078 single-cell (RNA sequencing) data. This includes methods based on detecting
8079 mutually nearest neighbors, as well as several efficient variants of linear
8080 regression of the log-expression values. Functions are also provided to
8081 perform global rescaling to remove differences in depth between batches, and
8082 to perform a principal components analysis that is robust to differences in
8083 the numbers of cells across batches.")
8084 (license license:gpl3)))
8086 (define-public r-mast
8093 (uri (bioconductor-uri "MAST" version))
8096 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
8097 (properties `((upstream-name . "MAST")))
8098 (build-system r-build-system)
8109 r-singlecellexperiment
8111 r-summarizedexperiment))
8114 (home-page "https://github.com/RGLab/MAST/")
8115 (synopsis "Model-based analysis of single cell transcriptomics")
8117 "This package provides methods and models for handling zero-inflated
8118 single cell assay data.")
8119 (license license:gpl2+)))
8121 (define-public r-monocle
8128 (uri (bioconductor-uri "monocle" version))
8131 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
8132 (build-system r-build-system)
8166 (home-page "https://bioconductor.org/packages/monocle")
8167 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
8169 "Monocle performs differential expression and time-series analysis for
8170 single-cell expression experiments. It orders individual cells according to
8171 progress through a biological process, without knowing ahead of time which
8172 genes define progress through that process. Monocle also performs
8173 differential expression analysis, clustering, visualization, and other useful
8174 tasks on single cell expression data. It is designed to work with RNA-Seq and
8175 qPCR data, but could be used with other types as well.")
8176 (license license:artistic2.0)))
8178 (define-public r-leidenbase
8179 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
8182 (name "r-leidenbase")
8183 (version (git-version "0.1.9" revision commit))
8188 (url "https://github.com/cole-trapnell-lab/leidenbase")
8190 (file-name (git-file-name name version))
8193 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
8194 (properties `((upstream-name . "leidenbase")))
8195 (build-system r-build-system)
8202 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
8203 (synopsis "R and C wrappers to run the Leiden find_partition function")
8205 "This package provides an R to C interface that runs the Leiden
8206 community detection algorithm to find a basic partition. It runs the
8207 equivalent of the @code{find_partition} function. This package includes the
8208 required source code files from the official Leidenalg distribution and
8209 several functions from the R igraph package.")
8210 (license license:gpl3+))))
8212 (define-public r-sanssouci
8213 ;; sansscouci doesn't have a (versioned) release yet.
8214 ;; This is the latest commit as of packaging for Guix.
8215 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
8218 (name "r-sanssouci")
8219 (version (git-version "0" revision commit))
8223 (url "https://github.com/pneuvial/sanssouci.git")
8225 (file-name (git-file-name name version))
8228 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
8229 (build-system r-build-system)
8231 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
8232 (home-page "https://pneuvial.github.io/sanssouci")
8233 (synopsis "Post Hoc multiple testing inference")
8235 "The goal of sansSouci is to perform post hoc inference: in a multiple
8236 testing context, sansSouci provides statistical guarantees on possibly
8237 user-defined and/or data-driven sets of hypotheses.")
8238 (license license:gpl3))))
8240 (define-public r-monocle3
8248 (url "https://github.com/cole-trapnell-lab/monocle3")
8250 (file-name (git-file-name name version))
8253 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
8254 (build-system r-build-system)
8260 r-delayedmatrixstats
8295 r-singlecellexperiment
8300 (home-page "https://github.com/cole-trapnell-lab/monocle3")
8301 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
8303 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
8304 (license license:expat)))
8306 (define-public r-noiseq
8313 (uri (bioconductor-uri "NOISeq" version))
8316 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
8317 (properties `((upstream-name . "NOISeq")))
8318 (build-system r-build-system)
8320 (list r-biobase r-matrix))
8321 (home-page "https://bioconductor.org/packages/NOISeq")
8322 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
8324 "This package provides tools to support the analysis of RNA-seq
8325 expression data or other similar kind of data. It provides exploratory plots
8326 to evaluate saturation, count distribution, expression per chromosome, type of
8327 detected features, features length, etc. It also supports the analysis of
8328 differential expression between two experimental conditions with no parametric
8330 (license license:artistic2.0)))
8332 (define-public r-scdd
8339 (uri (bioconductor-uri "scDD" version))
8342 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
8343 (properties `((upstream-name . "scDD")))
8344 (build-system r-build-system)
8355 r-singlecellexperiment
8356 r-summarizedexperiment))
8359 (home-page "https://github.com/kdkorthauer/scDD")
8360 (synopsis "Mixture modeling of single-cell RNA-seq data")
8362 "This package implements a method to analyze single-cell RNA-seq data
8363 utilizing flexible Dirichlet Process mixture models. Genes with differential
8364 distributions of expression are classified into several interesting patterns
8365 of differences between two conditions. The package also includes functions
8366 for simulating data with these patterns from negative binomial
8368 (license license:gpl2)))
8370 (define-public r-scone
8377 (uri (bioconductor-uri "scone" version))
8380 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
8381 (build-system r-build-system)
8402 r-singlecellexperiment
8403 r-summarizedexperiment))
8406 (home-page "https://bioconductor.org/packages/scone")
8407 (synopsis "Single cell overview of normalized expression data")
8409 "SCONE is an R package for comparing and ranking the performance of
8410 different normalization schemes for single-cell RNA-seq and other
8411 high-throughput analyses.")
8412 (license license:artistic2.0)))
8414 (define-public r-geoquery
8421 (uri (bioconductor-uri "GEOquery" version))
8424 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
8425 (properties `((upstream-name . "GEOquery")))
8426 (build-system r-build-system)
8440 (home-page "https://github.com/seandavi/GEOquery/")
8441 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
8443 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
8444 microarray data. Given the rich and varied nature of this resource, it is
8445 only natural to want to apply BioConductor tools to these data. GEOquery is
8446 the bridge between GEO and BioConductor.")
8447 (license license:gpl2)))
8449 (define-public r-illuminaio
8451 (name "r-illuminaio")
8456 (uri (bioconductor-uri "illuminaio" version))
8459 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
8460 (build-system r-build-system)
8463 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
8464 (synopsis "Parse Illumina microarray output files")
8466 "This package provides tools for parsing Illumina's microarray output
8467 files, including IDAT.")
8468 (license license:gpl2)))
8470 (define-public r-siggenes
8477 (uri (bioconductor-uri "siggenes" version))
8480 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
8481 (build-system r-build-system)
8483 (list r-biobase r-multtest r-scrime))
8484 (home-page "https://bioconductor.org/packages/siggenes/")
8486 "Multiple testing using SAM and Efron's empirical Bayes approaches")
8488 "This package provides tools for the identification of differentially
8489 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
8490 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
8491 Bayes Analyses of Microarrays} (EBAM).")
8492 (license license:lgpl2.0+)))
8494 (define-public r-bumphunter
8496 (name "r-bumphunter")
8501 (uri (bioconductor-uri "bumphunter" version))
8504 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
8505 (build-system r-build-system)
8507 (list r-annotationdbi
8520 (home-page "https://github.com/ririzarr/bumphunter")
8521 (synopsis "Find bumps in genomic data")
8523 "This package provides tools for finding bumps in genomic data in order
8524 to identify differentially methylated regions in epigenetic epidemiology
8526 (license license:artistic2.0)))
8528 (define-public r-minfi
8535 (uri (bioconductor-uri "minfi" version))
8538 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
8539 (build-system r-build-system)
8549 r-delayedmatrixstats
8569 r-summarizedexperiment))
8572 (home-page "https://github.com/hansenlab/minfi")
8573 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
8575 "This package provides tools to analyze and visualize Illumina Infinium
8576 methylation arrays.")
8577 (license license:artistic2.0)))
8579 (define-public r-methylumi
8581 (name "r-methylumi")
8586 (uri (bioconductor-uri "methylumi" version))
8589 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
8590 (build-system r-build-system)
8596 r-fdb-infiniummethylation-hg19
8610 r-summarizedexperiment))
8613 (home-page "https://bioconductor.org/packages/methylumi")
8614 (synopsis "Handle Illumina methylation data")
8616 "This package provides classes for holding and manipulating Illumina
8617 methylation data. Based on eSet, it can contain MIAME information, sample
8618 information, feature information, and multiple matrices of data. An
8619 \"intelligent\" import function, methylumiR can read the Illumina text files
8620 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
8621 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
8622 background correction, and quality control features for GoldenGate, Infinium,
8623 and Infinium HD arrays are also included.")
8624 (license license:gpl2)))
8626 (define-public r-lumi
8633 (uri (bioconductor-uri "lumi" version))
8636 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
8637 (build-system r-build-system)
8654 (home-page "https://bioconductor.org/packages/lumi")
8655 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
8657 "The lumi package provides an integrated solution for the Illumina
8658 microarray data analysis. It includes functions of Illumina
8659 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
8660 variance stabilization, normalization and gene annotation at the probe level.
8661 It also includes the functions of processing Illumina methylation microarrays,
8662 especially Illumina Infinium methylation microarrays.")
8663 (license license:lgpl2.0+)))
8665 (define-public r-linnorm
8672 (uri (bioconductor-uri "Linnorm" version))
8675 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
8676 (properties `((upstream-name . "Linnorm")))
8677 (build-system r-build-system)
8699 (home-page "http://www.jjwanglab.org/Linnorm/")
8700 (synopsis "Linear model and normality based transformation method")
8702 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
8703 count data or any large scale count data. It transforms such datasets for
8704 parametric tests. In addition to the transformtion function (@code{Linnorm}),
8705 the following pipelines are implemented:
8708 @item Library size/batch effect normalization (@code{Linnorm.Norm})
8709 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
8710 clustering or hierarchical clustering (@code{Linnorm.tSNE},
8711 @code{Linnorm.PCA}, @code{Linnorm.HClust})
8712 @item Differential expression analysis or differential peak detection using
8713 limma (@code{Linnorm.limma})
8714 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
8715 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
8716 @item Stable gene selection for scRNA-seq data; for users without or who do
8717 not want to rely on spike-in genes (@code{Linnorm.SGenes})
8718 @item Data imputation (@code{Linnorm.DataImput}).
8721 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
8722 @code{RnaXSim} function is included for simulating RNA-seq data for the
8723 evaluation of DEG analysis methods.")
8724 (license license:expat)))
8726 (define-public r-ioniser
8733 (uri (bioconductor-uri "IONiseR" version))
8736 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
8737 (properties `((upstream-name . "IONiseR")))
8738 (build-system r-build-system)
8740 (list r-biocgenerics
8755 (home-page "https://bioconductor.org/packages/IONiseR/")
8756 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
8758 "IONiseR provides tools for the quality assessment of Oxford Nanopore
8759 MinION data. It extracts summary statistics from a set of fast5 files and can
8760 be used either before or after base calling. In addition to standard
8761 summaries of the read-types produced, it provides a number of plots for
8762 visualising metrics relative to experiment run time or spatially over the
8763 surface of a flowcell.")
8764 (license license:expat)))
8766 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
8767 (define-public r-mutoss
8774 (uri (cran-uri "mutoss" version))
8777 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
8778 (properties `((upstream-name . "mutoss")))
8779 (build-system r-build-system)
8781 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
8782 (home-page "https://github.com/kornl/mutoss/")
8783 (synopsis "Unified multiple testing procedures")
8785 "This package is designed to ease the application and comparison of
8786 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
8787 are standardized and usable by the accompanying mutossGUI package.")
8788 ;; Any version of the GPL.
8789 (license (list license:gpl2+ license:gpl3+))))
8791 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
8792 ;; from Bioconductor, so we put it here.
8793 (define-public r-metap
8800 (uri (cran-uri "metap" version))
8803 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
8804 (build-system r-build-system)
8812 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
8813 (synopsis "Meta-analysis of significance values")
8815 "The canonical way to perform meta-analysis involves using effect sizes.
8816 When they are not available this package provides a number of methods for
8817 meta-analysis of significance values including the methods of Edgington,
8818 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
8819 published results; and a routine for graphical display.")
8820 (license license:gpl2)))
8822 (define-public r-tradeseq
8828 (uri (bioconductor-uri "tradeSeq" version))
8831 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
8832 (build-system r-build-system)
8848 r-singlecellexperiment
8850 r-summarizedexperiment
8856 (home-page "https://statomics.github.io/tradeSeq/index.html")
8857 (synopsis "Trajectory-based differential expression analysis")
8859 "This package provides a flexible method for fitting regression models that
8860 can be used to find genes that are differentially expressed along one or
8861 multiple lineages in a trajectory. Based on the fitted models, it uses a
8862 variety of tests suited to answer different questions of interest, e.g. the
8863 discovery of genes for which expression is associated with pseudotime, or which
8864 are differentially expressed (in a specific region) along the trajectory. It
8865 fits a negative binomial generalized additive model (GAM) for each gene, and
8866 performs inference on the parameters of the GAM.")
8867 (license license:expat)))
8869 (define-public r-triform
8876 (uri (bioconductor-uri "triform" version))
8879 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
8880 (build-system r-build-system)
8882 (list r-biocgenerics r-iranges r-yaml))
8883 (home-page "https://bioconductor.org/packages/triform/")
8884 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
8886 "The Triform algorithm uses model-free statistics to identify peak-like
8887 distributions of TF ChIP sequencing reads, taking advantage of an improved
8888 peak definition in combination with known profile characteristics.")
8889 (license license:gpl2)))
8891 (define-public r-varianttools
8893 (name "r-varianttools")
8898 (uri (bioconductor-uri "VariantTools" version))
8901 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
8902 (properties `((upstream-name . "VariantTools")))
8903 (build-system r-build-system)
8918 r-variantannotation))
8919 (home-page "https://bioconductor.org/packages/VariantTools/")
8920 (synopsis "Tools for exploratory analysis of variant calls")
8922 "Explore, diagnose, and compare variant calls using filters. The
8923 VariantTools package supports a workflow for loading data, calling single
8924 sample variants and tumor-specific somatic mutations or other sample-specific
8925 variant types (e.g., RNA editing). Most of the functions operate on
8926 alignments (BAM files) or datasets of called variants. The user is expected
8927 to have already aligned the reads with a separate tool, e.g., GSNAP via
8929 (license license:artistic2.0)))
8931 (define-public r-heatplus
8938 (uri (bioconductor-uri "Heatplus" version))
8941 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
8942 (properties `((upstream-name . "Heatplus")))
8943 (build-system r-build-system)
8945 (list r-rcolorbrewer))
8946 (home-page "https://github.com/alexploner/Heatplus")
8947 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
8949 "This package provides tools to display a rectangular heatmap (intensity
8950 plot) of a data matrix. By default, both samples (columns) and features (row)
8951 of the matrix are sorted according to a hierarchical clustering, and the
8952 corresponding dendrogram is plotted. Optionally, panels with additional
8953 information about samples and features can be added to the plot.")
8954 (license license:gpl2+)))
8956 (define-public r-gosemsim
8963 (uri (bioconductor-uri "GOSemSim" version))
8966 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
8967 (properties `((upstream-name . "GOSemSim")))
8968 (build-system r-build-system)
8970 (list r-annotationdbi r-go-db r-rcpp))
8973 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
8974 (synopsis "GO-terms semantic similarity measures")
8976 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
8977 quantitative ways to compute similarities between genes and gene groups, and
8978 have became important basis for many bioinformatics analysis approaches.
8979 GOSemSim is an R package for semantic similarity computation among GO terms,
8980 sets of GO terms, gene products and gene clusters.")
8981 (license license:artistic2.0)))
8983 (define-public r-anota
8990 (uri (bioconductor-uri "anota" version))
8993 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
8994 (build-system r-build-system)
8996 (list r-multtest r-qvalue))
8997 (home-page "https://bioconductor.org/packages/anota/")
8998 (synopsis "Analysis of translational activity")
9000 "Genome wide studies of translational control is emerging as a tool to
9001 study various biological conditions. The output from such analysis is both
9002 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
9003 involved in translation (the actively translating mRNA level) for each mRNA.
9004 The standard analysis of such data strives towards identifying differential
9005 translational between two or more sample classes - i.e., differences in
9006 actively translated mRNA levels that are independent of underlying differences
9007 in cytosolic mRNA levels. This package allows for such analysis using partial
9008 variances and the random variance model. As 10s of thousands of mRNAs are
9009 analyzed in parallel the library performs a number of tests to assure that
9010 the data set is suitable for such analysis.")
9011 (license license:gpl3)))
9013 (define-public r-sigpathway
9015 (name "r-sigpathway")
9020 (uri (bioconductor-uri "sigPathway" version))
9023 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
9024 (properties `((upstream-name . "sigPathway")))
9025 (build-system r-build-system)
9026 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
9027 (synopsis "Pathway analysis")
9029 "This package is used to conduct pathway analysis by calculating the NT_k
9030 and NE_k statistics in a statistical framework for determining whether a
9031 specified group of genes for a pathway has a coordinated association with a
9032 phenotype of interest.")
9033 (license license:gpl2)))
9035 (define-public r-fcscan
9042 (uri (bioconductor-uri "fcScan" version))
9044 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
9045 (properties `((upstream-name . "fcScan")))
9046 (build-system r-build-system)
9054 r-summarizedexperiment
9055 r-variantannotation))
9056 (native-inputs (list r-knitr))
9057 (home-page "https://bioconductor.org/packages/fcScan")
9058 (synopsis "Detect clusters of coordinates with user defined options")
9060 "This package is used to detect combination of genomic coordinates
9061 falling within a user defined window size along with user defined overlap
9062 between identified neighboring clusters. It can be used for genomic data
9063 where the clusters are built on a specific chromosome or specific strand.
9064 Clustering can be performed with a \"greedy\" option allowing thus the
9065 presence of additional sites within the allowed window size.")
9066 (license license:artistic2.0)))
9068 (define-public r-fgsea
9075 (uri (bioconductor-uri "fgsea" version))
9078 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
9079 (build-system r-build-system)
9091 (home-page "https://github.com/ctlab/fgsea/")
9092 (synopsis "Fast gene set enrichment analysis")
9094 "The package implements an algorithm for fast gene set enrichment
9095 analysis. Using the fast algorithm makes more permutations and gets
9096 more fine grained p-values, which allows using accurate standard approaches
9097 to multiple hypothesis correction.")
9098 (license license:expat)))
9100 (define-public r-dose
9107 (uri (bioconductor-uri "DOSE" version))
9110 "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp"))))
9111 (properties `((upstream-name . "DOSE")))
9112 (build-system r-build-system)
9114 (list r-annotationdbi
9124 (home-page "https://guangchuangyu.github.io/software/DOSE/")
9125 (synopsis "Disease ontology semantic and enrichment analysis")
9127 "This package implements five methods proposed by Resnik, Schlicker,
9128 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
9129 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
9130 including hypergeometric model and gene set enrichment analysis are also
9131 implemented for discovering disease associations of high-throughput biological
9133 (license license:artistic2.0)))
9135 (define-public r-enrichplot
9137 (name "r-enrichplot")
9142 (uri (bioconductor-uri "enrichplot" version))
9145 "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"))))
9146 (build-system r-build-system)
9165 (home-page "https://github.com/GuangchuangYu/enrichplot")
9166 (synopsis "Visualization of functional enrichment result")
9168 "The enrichplot package implements several visualization methods for
9169 interpreting functional enrichment results obtained from ORA or GSEA analyses.
9170 All the visualization methods are developed based on ggplot2 graphics.")
9171 (license license:artistic2.0)))
9173 (define-public r-clusterprofiler
9175 (name "r-clusterprofiler")
9180 (uri (bioconductor-uri "clusterProfiler" version))
9183 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
9185 `((upstream-name . "clusterProfiler")))
9186 (build-system r-build-system)
9188 (list r-annotationdbi
9203 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
9204 (synopsis "Analysis and visualization of functional profiles for gene clusters")
9206 "This package implements methods to analyze and visualize functional
9207 profiles (GO and KEGG) of gene and gene clusters.")
9208 (license license:artistic2.0)))
9210 (define-public r-clusterexperiment
9212 (name "r-clusterexperiment")
9216 (uri (bioconductor-uri "clusterExperiment" version))
9219 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
9220 (build-system r-build-system)
9245 r-singlecellexperiment
9247 r-summarizedexperiment
9249 (home-page "https://bioconductor.org/packages/clusterExperiment/")
9250 (synopsis "Compare clusterings for single-cell sequencing")
9251 (description "This package provides functionality for running and comparing
9252 many different clusterings of single-cell sequencing data or other large mRNA
9253 expression data sets.")
9254 (license license:artistic2.0)))
9256 (define-public r-mlinterfaces
9258 (name "r-mlinterfaces")
9263 (uri (bioconductor-uri "MLInterfaces" version))
9266 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
9267 (properties `((upstream-name . "MLInterfaces")))
9268 (build-system r-build-system)
9290 (home-page "https://bioconductor.org/packages/MLInterfaces/")
9291 (synopsis "Interfaces to R machine learning procedures")
9293 "This package provides uniform interfaces to machine learning code for
9294 data in R and Bioconductor containers.")
9295 ;; Any version of the LGPL.
9296 (license license:lgpl2.1+)))
9298 (define-public r-annaffy
9305 (uri (bioconductor-uri "annaffy" version))
9308 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
9309 (build-system r-build-system)
9312 (modify-phases %standard-phases
9313 (add-after 'unpack 'remove-reference-to-non-free-data
9315 (substitute* "DESCRIPTION"
9316 ((", KEGG.db") "")))))))
9318 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
9319 (home-page "https://bioconductor.org/packages/annaffy/")
9320 (synopsis "Annotation tools for Affymetrix biological metadata")
9322 "This package provides functions for handling data from Bioconductor
9323 Affymetrix annotation data packages. It produces compact HTML and text
9324 reports including experimental data and URL links to many online databases.
9325 It allows searching of biological metadata using various criteria.")
9326 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
9327 ;; the LGPL 2.1 is included.
9328 (license license:lgpl2.1+)))
9330 (define-public r-a4core
9337 (uri (bioconductor-uri "a4Core" version))
9340 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
9341 (properties `((upstream-name . "a4Core")))
9342 (build-system r-build-system)
9344 (list r-biobase r-glmnet))
9347 (home-page "https://bioconductor.org/packages/a4Core")
9348 (synopsis "Automated Affymetrix array analysis core package")
9350 "This is the core package for the automated analysis of Affymetrix
9352 (license license:gpl3)))
9354 (define-public r-a4classif
9356 (name "r-a4classif")
9361 (uri (bioconductor-uri "a4Classif" version))
9364 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
9365 (properties `((upstream-name . "a4Classif")))
9366 (build-system r-build-system)
9377 (home-page "https://bioconductor.org/packages/a4Classif/")
9378 (synopsis "Automated Affymetrix array analysis classification package")
9380 "This is the classification package for the automated analysis of
9381 Affymetrix arrays.")
9382 (license license:gpl3)))
9384 (define-public r-a4preproc
9386 (name "r-a4preproc")
9391 (uri (bioconductor-uri "a4Preproc" version))
9394 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
9395 (properties `((upstream-name . "a4Preproc")))
9396 (build-system r-build-system)
9398 (list r-biobase r-biocgenerics))
9401 (home-page "https://bioconductor.org/packages/a4Preproc/")
9402 (synopsis "Automated Affymetrix array analysis preprocessing package")
9404 "This is a package for the automated analysis of Affymetrix arrays. It
9405 is used for preprocessing the arrays.")
9406 (license license:gpl3)))
9408 (define-public r-a4reporting
9410 (name "r-a4reporting")
9415 (uri (bioconductor-uri "a4Reporting" version))
9418 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
9419 (properties `((upstream-name . "a4Reporting")))
9420 (build-system r-build-system)
9425 (home-page "https://bioconductor.org/packages/a4Reporting/")
9426 (synopsis "Automated Affymetrix array analysis reporting package")
9428 "This is a package for the automated analysis of Affymetrix arrays. It
9429 provides reporting features.")
9430 (license license:gpl3)))
9432 (define-public r-a4base
9439 (uri (bioconductor-uri "a4Base" version))
9442 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
9443 (properties `((upstream-name . "a4Base")))
9444 (build-system r-build-system)
9456 (home-page "https://bioconductor.org/packages/a4Base/")
9457 (synopsis "Automated Affymetrix array analysis base package")
9459 "This package provides basic features for the automated analysis of
9460 Affymetrix arrays.")
9461 (license license:gpl3)))
9470 (uri (bioconductor-uri "a4" version))
9473 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
9474 (build-system r-build-system)
9476 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
9477 (home-page "https://bioconductor.org/packages/a4/")
9478 (synopsis "Automated Affymetrix array analysis umbrella package")
9480 "This package provides a software suite for the automated analysis of
9481 Affymetrix arrays.")
9482 (license license:gpl3)))
9484 (define-public r-abseqr
9491 (uri (bioconductor-uri "abseqR" version))
9494 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
9495 (properties `((upstream-name . "abseqR")))
9496 (build-system r-build-system)
9500 (list r-biocparallel
9520 (home-page "https://github.com/malhamdoosh/abseqR")
9521 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
9523 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
9524 sequencing datasets generated from antibody libraries and abseqR is one of its
9525 packages. AbseqR empowers the users of abseqPy with plotting and reporting
9526 capabilities and allows them to generate interactive HTML reports for the
9527 convenience of viewing and sharing with other researchers. Additionally,
9528 abseqR extends abseqPy to compare multiple repertoire analyses and perform
9529 further downstream analysis on its output.")
9530 (license license:gpl3)))
9532 (define-public r-bacon
9539 (uri (bioconductor-uri "bacon" version))
9542 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
9543 (build-system r-build-system)
9545 (list r-biocparallel r-ellipse r-ggplot2))
9548 (home-page "https://bioconductor.org/packages/bacon/")
9549 (synopsis "Controlling bias and inflation in association studies")
9551 "Bacon can be used to remove inflation and bias often observed in
9552 epigenome- and transcriptome-wide association studies. To this end bacon
9553 constructs an empirical null distribution using a Gibbs Sampling algorithm by
9554 fitting a three-component normal mixture on z-scores.")
9555 (license license:gpl2+)))
9557 (define-public r-rgadem
9564 (uri (bioconductor-uri "rGADEM" version))
9567 "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4"))))
9568 (properties `((upstream-name . "rGADEM")))
9569 (build-system r-build-system)
9571 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
9572 (home-page "https://bioconductor.org/packages/rGADEM/")
9573 (synopsis "De novo sequence motif discovery")
9575 "rGADEM is an efficient de novo motif discovery tool for large-scale
9576 genomic sequence data.")
9577 (license license:artistic2.0)))
9579 (define-public r-motiv
9586 (uri (bioconductor-uri "MotIV" version))
9589 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
9590 (properties `((upstream-name . "MotIV")))
9591 (build-system r-build-system)
9595 (list r-biocgenerics
9602 (home-page "https://bioconductor.org/packages/MotIV/")
9603 (synopsis "Motif identification and validation")
9605 "This package is used for the identification and validation of sequence
9606 motifs. It makes use of STAMP for comparing a set of motifs to a given
9607 database (e.g. JASPAR). It can also be used to visualize motifs, motif
9608 distributions, modules and filter motifs.")
9609 (license license:gpl2)))
9611 (define-public r-motifdb
9617 (uri (bioconductor-uri "MotifDb" version))
9619 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
9620 (properties `((upstream-name . "MotifDb")))
9621 (build-system r-build-system)
9623 (list r-biocgenerics
9632 (home-page "https://www.bioconductor.org/packages/MotifDb/")
9633 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
9634 (description "This package provides more than 2000 annotated position
9635 frequency matrices from nine public sources, for multiple organisms.")
9636 (license license:artistic2.0)))
9638 (define-public r-motifbreakr
9640 (name "r-motifbreakr")
9644 (uri (bioconductor-uri "motifbreakR" version))
9646 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
9647 (properties `((upstream-name . "motifbreakR")))
9648 (build-system r-build-system)
9650 (list r-biocgenerics
9664 r-summarizedexperiment
9666 r-variantannotation))
9669 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
9670 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
9671 (description "This package allows biologists to judge in the first place
9672 whether the sequence surrounding the polymorphism is a good match, and in
9673 the second place how much information is gained or lost in one allele of
9674 the polymorphism relative to another. This package gives a choice of
9675 algorithms for interrogation of genomes with motifs from public sources:
9677 @item a weighted-sum probability matrix;
9678 @item log-probabilities;
9679 @item weighted by relative entropy.
9682 This package can predict effects for novel or previously described variants in
9683 public databases, making it suitable for tasks beyond the scope of its original
9684 design. Lastly, it can be used to interrogate any genome curated within
9686 (license license:gpl2+)))
9688 (define-public r-motifstack
9690 (name "r-motifstack")
9695 (uri (bioconductor-uri "motifStack" version))
9698 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
9699 (properties `((upstream-name . "motifStack")))
9700 (build-system r-build-system)
9710 (home-page "https://bioconductor.org/packages/motifStack/")
9711 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
9713 "The motifStack package is designed for graphic representation of
9714 multiple motifs with different similarity scores. It works with both DNA/RNA
9715 sequence motifs and amino acid sequence motifs. In addition, it provides the
9716 flexibility for users to customize the graphic parameters such as the font
9717 type and symbol colors.")
9718 (license license:gpl2+)))
9720 (define-public r-genomicscores
9722 (name "r-genomicscores")
9727 (uri (bioconductor-uri "GenomicScores" version))
9730 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
9731 (properties `((upstream-name . "GenomicScores")))
9732 (build-system r-build-system)
9734 (list r-annotationhub
9751 (home-page "https://github.com/rcastelo/GenomicScores/")
9752 (synopsis "Work with genome-wide position-specific scores")
9754 "This package provides infrastructure to store and access genome-wide
9755 position-specific scores within R and Bioconductor.")
9756 (license license:artistic2.0)))
9758 (define-public r-atacseqqc
9760 (name "r-atacseqqc")
9765 (uri (bioconductor-uri "ATACseqQC" version))
9768 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
9769 (properties `((upstream-name . "ATACseqQC")))
9770 (build-system r-build-system)
9772 (list r-biocgenerics
9792 (home-page "https://bioconductor.org/packages/ATACseqQC/")
9793 (synopsis "ATAC-seq quality control")
9795 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
9796 sequencing, is a rapid and sensitive method for chromatin accessibility
9797 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
9798 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
9799 assess whether their ATAC-seq experiment is successful. It includes
9800 diagnostic plots of fragment size distribution, proportion of mitochondria
9801 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
9803 (license license:gpl2+)))
9805 (define-public r-gofuncr
9812 (uri (bioconductor-uri "GOfuncR" version))
9815 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
9816 (properties `((upstream-name . "GOfuncR")))
9817 (build-system r-build-system)
9819 (list r-annotationdbi
9828 (home-page "https://bioconductor.org/packages/GOfuncR/")
9829 (synopsis "Gene ontology enrichment using FUNC")
9831 "GOfuncR performs a gene ontology enrichment analysis based on the
9832 ontology enrichment software FUNC. GO-annotations are obtained from
9833 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
9834 included in the package and updated regularly. GOfuncR provides the standard
9835 candidate vs background enrichment analysis using the hypergeometric test, as
9836 well as three additional tests:
9839 @item the Wilcoxon rank-sum test that is used when genes are ranked,
9840 @item a binomial test that is used when genes are associated with two counts,
9842 @item a Chi-square or Fisher's exact test that is used in cases when genes are
9843 associated with four counts.
9846 To correct for multiple testing and interdependency of the tests, family-wise
9847 error rates are computed based on random permutations of the gene-associated
9848 variables. GOfuncR also provides tools for exploring the ontology graph and
9849 the annotations, and options to take gene-length or spatial clustering of
9850 genes into account. It is also possible to provide custom gene coordinates,
9851 annotations and ontologies.")
9852 (license license:gpl2+)))
9854 (define-public r-abaenrichment
9856 (name "r-abaenrichment")
9861 (uri (bioconductor-uri "ABAEnrichment" version))
9864 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
9865 (properties `((upstream-name . "ABAEnrichment")))
9866 (build-system r-build-system)
9876 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
9877 (synopsis "Gene expression enrichment in human brain regions")
9879 "The package ABAEnrichment is designed to test for enrichment of user
9880 defined candidate genes in the set of expressed genes in different human brain
9881 regions. The core function @code{aba_enrich} integrates the expression of the
9882 candidate gene set (averaged across donors) and the structural information of
9883 the brain using an ontology, both provided by the Allen Brain Atlas project.")
9884 (license license:gpl2+)))
9886 (define-public r-annotationfuncs
9888 (name "r-annotationfuncs")
9893 (uri (bioconductor-uri "AnnotationFuncs" version))
9896 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
9898 `((upstream-name . "AnnotationFuncs")))
9899 (build-system r-build-system)
9901 (list r-annotationdbi r-dbi))
9902 (home-page "https://www.iysik.com/r/annotationfuncs")
9903 (synopsis "Annotation translation functions")
9905 "This package provides functions for handling translating between
9906 different identifieres using the Biocore Data Team data-packages (e.g.
9907 @code{org.Bt.eg.db}).")
9908 (license license:gpl2)))
9910 (define-public r-annotationtools
9912 (name "r-annotationtools")
9917 (uri (bioconductor-uri "annotationTools" version))
9920 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
9922 `((upstream-name . "annotationTools")))
9923 (build-system r-build-system)
9924 (propagated-inputs (list r-biobase))
9925 (home-page "https://bioconductor.org/packages/annotationTools/")
9926 (synopsis "Annotate microarrays and perform gene expression analyses")
9928 "This package provides functions to annotate microarrays, find orthologs,
9929 and integrate heterogeneous gene expression profiles using annotation and
9930 other molecular biology information available as flat file database (plain
9932 ;; Any version of the GPL.
9933 (license (list license:gpl2+))))
9935 (define-public r-allelicimbalance
9937 (name "r-allelicimbalance")
9942 (uri (bioconductor-uri "AllelicImbalance" version))
9945 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
9947 `((upstream-name . "AllelicImbalance")))
9948 (build-system r-build-system)
9950 (list r-annotationdbi
9967 r-summarizedexperiment
9968 r-variantannotation))
9971 (home-page "https://github.com/pappewaio/AllelicImbalance")
9972 (synopsis "Investigate allele-specific expression")
9974 "This package provides a framework for allele-specific expression
9975 investigation using RNA-seq data.")
9976 (license license:gpl3)))
9978 (define-public r-aucell
9985 (uri (bioconductor-uri "AUCell" version))
9988 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
9989 (properties `((upstream-name . "AUCell")))
9990 (build-system r-build-system)
9992 (list r-biocgenerics
9995 r-delayedmatrixstats
10000 r-summarizedexperiment))
10003 (home-page "https://bioconductor.org/packages/AUCell/")
10004 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
10006 "AUCell identifies cells with active gene sets (e.g. signatures,
10007 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
10008 Under the Curve} (AUC) to calculate whether a critical subset of the input
10009 gene set is enriched within the expressed genes for each cell. The
10010 distribution of AUC scores across all the cells allows exploring the relative
10011 expression of the signature. Since the scoring method is ranking-based,
10012 AUCell is independent of the gene expression units and the normalization
10013 procedure. In addition, since the cells are evaluated individually, it can
10014 easily be applied to bigger datasets, subsetting the expression matrix if
10016 (license license:gpl3)))
10018 (define-public r-ebimage
10025 (uri (bioconductor-uri "EBImage" version))
10028 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
10029 (properties `((upstream-name . "EBImage")))
10030 (build-system r-build-system)
10043 (list r-knitr)) ; for vignettes
10044 (home-page "https://github.com/aoles/EBImage")
10045 (synopsis "Image processing and analysis toolbox for R")
10047 "EBImage provides general purpose functionality for image processing and
10048 analysis. In the context of (high-throughput) microscopy-based cellular
10049 assays, EBImage offers tools to segment cells and extract quantitative
10050 cellular descriptors. This allows the automation of such tasks using the R
10051 programming language and facilitates the use of other tools in the R
10052 environment for signal processing, statistical modeling, machine learning and
10053 visualization with image data.")
10054 ;; Any version of the LGPL.
10055 (license license:lgpl2.1+)))
10057 (define-public r-yamss
10064 (uri (bioconductor-uri "yamss" version))
10067 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
10068 (build-system r-build-system)
10070 (list r-biocgenerics
10078 r-summarizedexperiment))
10081 (home-page "https://github.com/hansenlab/yamss")
10082 (synopsis "Tools for high-throughput metabolomics")
10084 "This package provides tools to analyze and visualize high-throughput
10085 metabolomics data acquired using chromatography-mass spectrometry. These tools
10086 preprocess data in a way that enables reliable and powerful differential
10088 (license license:artistic2.0)))
10090 (define-public r-gtrellis
10092 (name "r-gtrellis")
10097 (uri (bioconductor-uri "gtrellis" version))
10100 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
10101 (build-system r-build-system)
10103 (list r-circlize r-genomicranges r-getoptlong r-iranges))
10106 (home-page "https://github.com/jokergoo/gtrellis")
10107 (synopsis "Genome level Trellis layout")
10109 "Genome level Trellis graph visualizes genomic data conditioned by
10110 genomic categories (e.g. chromosomes). For each genomic category, multiple
10111 dimensional data which are represented as tracks describe different features
10112 from different aspects. This package provides high flexibility to arrange
10113 genomic categories and to add self-defined graphics in the plot.")
10114 (license license:expat)))
10116 (define-public r-somaticsignatures
10118 (name "r-somaticsignatures")
10123 (uri (bioconductor-uri "SomaticSignatures" version))
10126 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
10128 `((upstream-name . "SomaticSignatures")))
10129 (build-system r-build-system)
10143 r-variantannotation))
10146 (home-page "https://github.com/juliangehring/SomaticSignatures")
10147 (synopsis "Somatic signatures")
10149 "This package identifies mutational signatures of @dfn{single nucleotide
10150 variants} (SNVs). It provides a infrastructure related to the methodology
10151 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
10152 decomposition algorithms.")
10153 (license license:expat)))
10155 (define-public r-yapsa
10162 (uri (bioconductor-uri "YAPSA" version))
10165 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
10166 (properties `((upstream-name . "YAPSA")))
10167 (build-system r-build-system)
10170 r-bsgenome-hsapiens-ucsc-hg19
10190 r-somaticsignatures
10191 r-variantannotation))
10194 (home-page "https://bioconductor.org/packages/YAPSA/")
10195 (synopsis "Yet another package for signature analysis")
10197 "This package provides functions and routines useful in the analysis of
10198 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
10199 functions to perform a signature analysis with known signatures and a
10200 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
10202 (license license:gpl3)))
10204 (define-public r-gcrma
10211 (uri (bioconductor-uri "gcrma" version))
10214 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
10215 (build-system r-build-system)
10223 (home-page "https://bioconductor.org/packages/gcrma/")
10224 (synopsis "Background adjustment using sequence information")
10226 "Gcrma adjusts for background intensities in Affymetrix array data which
10227 include optical noise and @dfn{non-specific binding} (NSB). The main function
10228 @code{gcrma} converts background adjusted probe intensities to expression
10229 measures using the same normalization and summarization methods as a
10230 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
10231 to estimate probe affinity to NSB. The sequence information is summarized in
10232 a more complex way than the simple GC content. Instead, the base types (A, T,
10233 G or C) at each position along the probe determine the affinity of each probe.
10234 The parameters of the position-specific base contributions to the probe
10235 affinity is estimated in an NSB experiment in which only NSB but no
10236 gene-specific binding is expected.")
10237 ;; Any version of the LGPL
10238 (license license:lgpl2.1+)))
10240 (define-public r-simpleaffy
10242 (name "r-simpleaffy")
10247 (uri (bioconductor-uri "simpleaffy" version))
10250 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
10251 (build-system r-build-system)
10253 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
10254 (home-page "https://bioconductor.org/packages/simpleaffy/")
10255 (synopsis "Very simple high level analysis of Affymetrix data")
10257 "This package provides high level functions for reading Affy @file{.CEL}
10258 files, phenotypic data, and then computing simple things with it, such as
10259 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
10260 library. It also has some basic scatter plot functions and mechanisms for
10261 generating high resolution journal figures.")
10262 (license license:gpl2+)))
10264 (define-public r-yaqcaffy
10266 (name "r-yaqcaffy")
10271 (uri (bioconductor-uri "yaqcaffy" version))
10274 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
10275 (build-system r-build-system)
10277 (list r-simpleaffy))
10278 (home-page "https://bioconductor.org/packages/yaqcaffy/")
10279 (synopsis "Affymetrix quality control and reproducibility analysis")
10281 "This is a package that can be used for quality control of Affymetrix
10282 GeneChip expression data and reproducibility analysis of human whole genome
10283 chips with the MAQC reference datasets.")
10284 (license license:artistic2.0)))
10286 (define-public r-quantro
10293 (uri (bioconductor-uri "quantro" version))
10296 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
10297 (build-system r-build-system)
10308 (home-page "https://bioconductor.org/packages/quantro/")
10309 (synopsis "Test for when to use quantile normalization")
10311 "This package provides a data-driven test for the assumptions of quantile
10312 normalization using raw data such as objects that inherit eSets (e.g.
10313 ExpressionSet, MethylSet). Group level information about each sample (such as
10314 Tumor / Normal status) must also be provided because the test assesses if
10315 there are global differences in the distributions between the user-defined
10317 (license license:gpl3+)))
10319 (define-public r-yarn
10326 (uri (bioconductor-uri "yarn" version))
10329 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
10330 (build-system r-build-system)
10345 (home-page "https://bioconductor.org/packages/yarn/")
10346 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
10348 "Expedite large RNA-Seq analyses using a combination of previously
10349 developed tools. YARN is meant to make it easier for the user in performing
10350 basic mis-annotation quality control, filtering, and condition-aware
10351 normalization. YARN leverages many Bioconductor tools and statistical
10352 techniques to account for the large heterogeneity and sparsity found in very
10353 large RNA-seq experiments.")
10354 (license license:artistic2.0)))
10356 (define-public r-roar
10363 (uri (bioconductor-uri "roar" version))
10366 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
10367 (build-system r-build-system)
10369 (list r-biocgenerics
10371 r-genomicalignments
10376 r-summarizedexperiment))
10377 (home-page "https://github.com/vodkatad/roar/")
10378 (synopsis "Identify differential APA usage from RNA-seq alignments")
10380 "This package provides tools for identifying preferential usage of APA
10381 sites, comparing two biological conditions, starting from known alternative
10382 sites and alignments obtained from standard RNA-seq experiments.")
10383 (license license:gpl3)))
10385 (define-public r-xbseq
10392 (uri (bioconductor-uri "XBSeq" version))
10395 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
10396 (properties `((upstream-name . "XBSeq")))
10397 (build-system r-build-system)
10410 (home-page "https://github.com/Liuy12/XBSeq")
10411 (synopsis "Test for differential expression for RNA-seq data")
10413 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
10414 expression} (DE), where a statistical model was established based on the
10415 assumption that observed signals are the convolution of true expression
10416 signals and sequencing noises. The mapped reads in non-exonic regions are
10417 considered as sequencing noises, which follows a Poisson distribution. Given
10418 measurable observed signal and background noise from RNA-seq data, true
10419 expression signals, assuming governed by the negative binomial distribution,
10420 can be delineated and thus the accurate detection of differential expressed
10422 (license license:gpl3+)))
10424 (define-public r-massspecwavelet
10426 (name "r-massspecwavelet")
10431 (uri (bioconductor-uri "MassSpecWavelet" version))
10434 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
10436 `((upstream-name . "MassSpecWavelet")))
10437 (build-system r-build-system)
10440 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
10441 (synopsis "Mass spectrum processing by wavelet-based algorithms")
10443 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
10444 data mainly through the use of wavelet transforms. It supports peak detection
10445 based on @dfn{Continuous Wavelet Transform} (CWT).")
10446 (license license:lgpl2.0+)))
10448 (define-public r-xcms
10455 (uri (bioconductor-uri "xcms" version))
10458 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
10459 (build-system r-build-system)
10477 r-summarizedexperiment))
10480 (home-page "https://bioconductor.org/packages/xcms/")
10481 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
10483 "This package provides a framework for processing and visualization of
10484 chromatographically separated and single-spectra mass spectral data. It
10485 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
10486 data for high-throughput, untargeted analyte profiling.")
10487 (license license:gpl2+)))
10489 (define-public r-wppi
10495 (uri (bioconductor-uri "wppi" version))
10498 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
10499 (properties `((upstream-name . "wppi")))
10500 (build-system r-build-system)
10501 ;; This is necessary because omnipathr attempts to write a configuration
10505 (modify-phases %standard-phases
10506 (add-after 'unpack 'set-HOME
10507 (lambda _ (setenv "HOME" "/tmp"))))))
10508 (propagated-inputs (list r-dplyr
10520 (native-inputs (list r-knitr))
10521 (home-page "https://github.com/AnaGalhoz37/wppi")
10522 (synopsis "Weighting protein-protein interactions")
10524 "This package predicts functional relevance of protein-protein
10525 interactions based on functional annotations such as Human Protein Ontology
10526 and Gene Ontology, and prioritizes genes based on network topology, functional
10527 scores and a path search algorithm.")
10528 (license license:expat)))
10530 (define-public r-wrench
10537 (uri (bioconductor-uri "Wrench" version))
10540 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
10541 (properties `((upstream-name . "Wrench")))
10542 (build-system r-build-system)
10544 (list r-limma r-locfit r-matrixstats))
10547 (home-page "https://github.com/HCBravoLab/Wrench")
10548 (synopsis "Wrench normalization for sparse count data")
10550 "Wrench is a package for normalization sparse genomic count data, like
10551 that arising from 16s metagenomic surveys.")
10552 (license license:artistic2.0)))
10554 (define-public r-wiggleplotr
10556 (name "r-wiggleplotr")
10561 (uri (bioconductor-uri "wiggleplotr" version))
10564 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
10565 (build-system r-build-system)
10579 (home-page "https://bioconductor.org/packages/wiggleplotr/")
10580 (synopsis "Make read coverage plots from BigWig files")
10582 "This package provides tools to visualize read coverage from sequencing
10583 experiments together with genomic annotations (genes, transcripts, peaks).
10584 Introns of long transcripts can be rescaled to a fixed length for better
10585 visualization of exonic read coverage.")
10586 (license license:asl2.0)))
10588 (define-public r-widgettools
10590 (name "r-widgettools")
10595 (uri (bioconductor-uri "widgetTools" version))
10598 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
10599 (properties `((upstream-name . "widgetTools")))
10600 (build-system r-build-system)
10601 (home-page "https://bioconductor.org/packages/widgetTools/")
10602 (synopsis "Tools for creating interactive tcltk widgets")
10604 "This package contains tools to support the construction of tcltk
10606 ;; Any version of the LGPL.
10607 (license license:lgpl3+)))
10609 (define-public r-webbioc
10616 (uri (bioconductor-uri "webbioc" version))
10619 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
10620 (build-system r-build-system)
10622 (list netpbm perl))
10632 (home-page "https://www.bioconductor.org/")
10633 (synopsis "Bioconductor web interface")
10635 "This package provides an integrated web interface for doing microarray
10636 analysis using several of the Bioconductor packages. It is intended to be
10637 deployed as a centralized bioinformatics resource for use by many users.
10638 Currently only Affymetrix oligonucleotide analysis is supported.")
10639 (license license:gpl2+)))
10641 (define-public r-zinbwave
10643 (name "r-zinbwave")
10648 (uri (bioconductor-uri "zinbwave" version))
10651 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
10652 (build-system r-build-system)
10654 (list r-biocparallel
10658 r-singlecellexperiment
10660 r-summarizedexperiment))
10663 (home-page "https://bioconductor.org/packages/zinbwave")
10664 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
10665 (description "This package implements a general and flexible zero-inflated
10666 negative binomial model that can be used to provide a low-dimensional
10667 representations of single-cell RNA-seq data. The model accounts for zero
10668 inflation (dropouts), over-dispersion, and the count nature of the data.
10669 The model also accounts for the difference in library sizes and optionally
10670 for batch effects and/or other covariates, avoiding the need for pre-normalize
10672 (license license:artistic2.0)))
10674 (define-public r-zfpkm
10681 (uri (bioconductor-uri "zFPKM" version))
10684 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
10685 (properties `((upstream-name . "zFPKM")))
10686 (build-system r-build-system)
10688 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
10691 (home-page "https://github.com/ronammar/zFPKM/")
10692 (synopsis "Functions to facilitate zFPKM transformations")
10694 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
10695 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
10697 (license license:gpl3)))
10699 (define-public r-rbowtie2
10701 (name "r-rbowtie2")
10706 (uri (bioconductor-uri "Rbowtie2" version))
10709 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
10710 (properties `((upstream-name . "Rbowtie2")))
10711 (build-system r-build-system)
10713 (list r-magrittr r-rsamtools))
10715 (list samtools zlib))
10718 (home-page "https://bioconductor.org/packages/Rbowtie2/")
10719 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
10721 "This package provides an R wrapper of the popular @code{bowtie2}
10722 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
10723 rapid adapter trimming, identification, and read merging.")
10724 (license license:gpl3+)))
10726 (define-public r-progeny
10733 (uri (bioconductor-uri "progeny" version))
10736 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
10737 (build-system r-build-system)
10749 (home-page "https://github.com/saezlab/progeny")
10750 (synopsis "Pathway responsive gene activity inference")
10752 "This package provides a function to infer pathway activity from gene
10753 expression. It contains the linear model inferred in the publication
10754 \"Perturbation-response genes reveal signaling footprints in cancer gene
10756 (license license:asl2.0)))
10758 (define-public r-arrmnormalization
10760 (name "r-arrmnormalization")
10765 (uri (bioconductor-uri "ARRmNormalization" version))
10768 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
10770 `((upstream-name . "ARRmNormalization")))
10771 (build-system r-build-system)
10772 (propagated-inputs (list r-arrmdata))
10773 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
10774 (synopsis "Adaptive robust regression normalization for methylation data")
10776 "This is a package to perform the @dfn{Adaptive Robust Regression
10777 method} (ARRm) for the normalization of methylation data from the Illumina
10778 Infinium HumanMethylation 450k assay.")
10779 (license license:artistic2.0)))
10781 (define-public r-biocfilecache
10783 (name "r-biocfilecache")
10788 (uri (bioconductor-uri "BiocFileCache" version))
10791 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
10792 (properties `((upstream-name . "BiocFileCache")))
10793 (build-system r-build-system)
10805 (home-page "https://bioconductor.org/packages/BiocFileCache/")
10806 (synopsis "Manage files across sessions")
10808 "This package creates a persistent on-disk cache of files that the user
10809 can add, update, and retrieve. It is useful for managing resources (such as
10810 custom Txdb objects) that are costly or difficult to create, web resources,
10811 and data files used across sessions.")
10812 (license license:artistic2.0)))
10814 (define-public r-iclusterplus
10816 (name "r-iclusterplus")
10821 (uri (bioconductor-uri "iClusterPlus" version))
10824 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
10825 (properties `((upstream-name . "iClusterPlus")))
10826 (build-system r-build-system)
10827 (native-inputs (list gfortran))
10828 (home-page "https://bioconductor.org/packages/iClusterPlus/")
10829 (synopsis "Integrative clustering of multi-type genomic data")
10831 "iClusterPlus is developed for integrative clustering analysis of
10832 multi-type genomic data and is an enhanced version of iCluster proposed and
10833 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
10834 from the experiments where biological samples (e.g. tumor samples) are
10835 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
10836 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
10837 on. In the iClusterPlus model, binary observations such as somatic mutation
10838 are modeled as Binomial processes; categorical observations such as copy
10839 number states are realizations of Multinomial random variables; counts are
10840 modeled as Poisson random processes; and continuous measures are modeled by
10841 Gaussian distributions.")
10842 (license license:gpl2+)))
10844 (define-public r-rbowtie
10851 (uri (bioconductor-uri "Rbowtie" version))
10854 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
10855 (properties `((upstream-name . "Rbowtie")))
10856 (build-system r-build-system)
10859 ;; Disable unsupported `popcnt' instructions on
10860 ;; architectures other than x86_64
10861 ,(if (string-prefix? "x86_64"
10862 (or (%current-target-system)
10863 (%current-system)))
10865 '(modify-phases %standard-phases
10866 (add-after 'unpack 'patch-sources
10868 (setenv "POPCNT_CAPABILITY" "0")))))))
10869 (inputs (list zlib))
10872 (home-page "https://bioconductor.org/packages/Rbowtie/")
10873 (synopsis "R bowtie wrapper")
10875 "This package provides an R wrapper around the popular bowtie short read
10876 aligner and around SpliceMap, a de novo splice junction discovery and
10878 (license license:artistic2.0)))
10880 (define-public r-sgseq
10887 (uri (bioconductor-uri "SGSeq" version))
10890 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
10891 (properties `((upstream-name . "SGSeq")))
10892 (build-system r-build-system)
10894 (list r-annotationdbi
10898 r-genomicalignments
10907 r-summarizedexperiment))
10910 (home-page "https://bioconductor.org/packages/SGSeq/")
10911 (synopsis "Splice event prediction and quantification from RNA-seq data")
10913 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
10914 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
10915 represented as a splice graph, which can be obtained from existing annotation
10916 or predicted from the mapped sequence reads. Splice events are identified
10917 from the graph and are quantified locally using structurally compatible reads
10918 at the start or end of each splice variant. The software includes functions
10919 for splice event prediction, quantification, visualization and
10921 (license license:artistic2.0)))
10923 (define-public r-rhisat2
10930 (uri (bioconductor-uri "Rhisat2" version))
10933 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
10934 (properties `((upstream-name . "Rhisat2")))
10935 (build-system r-build-system)
10938 (modify-phases %standard-phases
10939 (add-after 'unpack 'make-reproducible
10941 (substitute* "src/Makefile"
10942 (("`hostname`") "guix")
10944 ;; Avoid shelling out to "which".
10945 (("^CC =.*") (which "gcc"))
10946 (("^CPP =.*") (which "g++")))
10949 (list r-genomicfeatures r-genomicranges r-sgseq))
10952 (home-page "https://github.com/fmicompbio/Rhisat2")
10953 (synopsis "R Wrapper for HISAT2 sequence aligner")
10955 "This package provides an R interface to the HISAT2 spliced short-read
10956 aligner by Kim et al. (2015). The package contains wrapper functions to
10957 create a genome index and to perform the read alignment to the generated
10959 (license license:gpl3)))
10961 (define-public r-quasr
10968 (uri (bioconductor-uri "QuasR" version))
10971 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
10972 (properties `((upstream-name . "QuasR")))
10973 (build-system r-build-system)
10975 (list r-annotationdbi
10994 (home-page "https://bioconductor.org/packages/QuasR/")
10995 (synopsis "Quantify and annotate short reads in R")
10997 "This package provides a framework for the quantification and analysis of
10998 short genomic reads. It covers a complete workflow starting from raw sequence
10999 reads, over creation of alignments and quality control plots, to the
11000 quantification of genomic regions of interest.")
11001 (license license:gpl2)))
11003 (define-public r-rqc
11010 (uri (bioconductor-uri "Rqc" version))
11013 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
11014 (properties `((upstream-name . "Rqc")))
11015 (build-system r-build-system)
11017 (list r-biocgenerics
11022 r-genomicalignments
11037 (home-page "https://github.com/labbcb/Rqc")
11038 (synopsis "Quality control tool for high-throughput sequencing data")
11040 "Rqc is an optimized tool designed for quality control and assessment of
11041 high-throughput sequencing data. It performs parallel processing of entire
11042 files and produces a report which contains a set of high-resolution
11044 (license license:gpl2+)))
11046 (define-public r-birewire
11048 (name "r-birewire")
11053 (uri (bioconductor-uri "BiRewire" version))
11056 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
11057 (properties `((upstream-name . "BiRewire")))
11058 (build-system r-build-system)
11060 (list r-igraph r-matrix r-rtsne r-slam))
11061 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
11062 (synopsis "Tools for randomization of bipartite graphs")
11064 "This package provides functions for bipartite network rewiring through N
11065 consecutive switching steps and for the computation of the minimal number of
11066 switching steps to be performed in order to maximise the dissimilarity with
11067 respect to the original network. It includes functions for the analysis of
11068 the introduced randomness across the switching steps and several other
11069 routines to analyse the resulting networks and their natural projections.")
11070 (license license:gpl3)))
11072 (define-public r-birta
11079 (uri (bioconductor-uri "birta" version))
11082 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
11083 (build-system r-build-system)
11085 (list r-biobase r-limma r-mass))
11086 (home-page "https://bioconductor.org/packages/birta")
11087 (synopsis "Bayesian inference of regulation of transcriptional activity")
11089 "Expression levels of mRNA molecules are regulated by different
11090 processes, comprising inhibition or activation by transcription factors and
11091 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
11092 Inference of Regulation of Transcriptional Activity) uses the regulatory
11093 networks of transcription factors and miRNAs together with mRNA and miRNA
11094 expression data to predict switches in regulatory activity between two
11095 conditions. A Bayesian network is used to model the regulatory structure and
11096 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
11097 (license license:gpl2+)))
11099 (define-public r-multidataset
11101 (name "r-multidataset")
11106 (uri (bioconductor-uri "MultiDataSet" version))
11109 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
11110 (properties `((upstream-name . "MultiDataSet")))
11111 (build-system r-build-system)
11122 r-summarizedexperiment))
11125 (home-page "https://bioconductor.org/packages/MultiDataSet/")
11126 (synopsis "Implementation of MultiDataSet and ResultSet")
11128 "This package provides an implementation of the BRGE's (Bioinformatic
11129 Research Group in Epidemiology from Center for Research in Environmental
11130 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
11131 integrating multi omics data sets and ResultSet is a container for omics
11132 results. This package contains base classes for MEAL and rexposome
11134 (license license:expat)))
11136 (define-public r-ropls
11143 (uri (bioconductor-uri "ropls" version))
11146 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
11147 (build-system r-build-system)
11150 r-multiassayexperiment
11152 r-summarizedexperiment))
11154 (list r-knitr)) ; for vignettes
11155 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
11156 (synopsis "Multivariate analysis and feature selection of omics data")
11158 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
11159 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
11160 regression, classification, and feature selection of omics data where the
11161 number of variables exceeds the number of samples and with multicollinearity
11162 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
11163 separately model the variation correlated (predictive) to the factor of
11164 interest and the uncorrelated (orthogonal) variation. While performing
11165 similarly to PLS, OPLS facilitates interpretation.
11167 This package provides imlementations of PCA, PLS, and OPLS for multivariate
11168 analysis and feature selection of omics data. In addition to scores, loadings
11169 and weights plots, the package provides metrics and graphics to determine the
11170 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
11171 validity of the model by permutation testing, detect outliers, and perform
11172 feature selection (e.g. with Variable Importance in Projection or regression
11174 (license license:cecill)))
11176 (define-public r-biosigner
11178 (name "r-biosigner")
11183 (uri (bioconductor-uri "biosigner" version))
11186 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
11187 (build-system r-build-system)
11191 r-multiassayexperiment
11195 r-summarizedexperiment))
11198 (home-page "https://bioconductor.org/packages/biosigner/")
11199 (synopsis "Signature discovery from omics data")
11201 "Feature selection is critical in omics data analysis to extract
11202 restricted and meaningful molecular signatures from complex and high-dimension
11203 data, and to build robust classifiers. This package implements a method to
11204 assess the relevance of the variables for the prediction performances of the
11205 classifier. The approach can be run in parallel with the PLS-DA, Random
11206 Forest, and SVM binary classifiers. The signatures and the corresponding
11207 'restricted' models are returned, enabling future predictions on new
11209 (license license:cecill)))
11211 (define-public r-annotatr
11213 (name "r-annotatr")
11218 (uri (bioconductor-uri "annotatr" version))
11221 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
11222 (build-system r-build-system)
11224 (list r-annotationdbi
11239 (home-page "https://bioconductor.org/packages/annotatr/")
11240 (synopsis "Annotation of genomic regions to genomic annotations")
11242 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
11243 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
11244 to investigate the intersecting genomic annotations. Such annotations include
11245 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
11246 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
11247 enhancers. The annotatr package provides an easy way to summarize and
11248 visualize the intersection of genomic sites/regions with genomic
11250 (license license:gpl3)))
11252 (define-public r-rsubread
11254 (name "r-rsubread")
11259 (uri (bioconductor-uri "Rsubread" version))
11262 "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl"))))
11263 (properties `((upstream-name . "Rsubread")))
11264 (build-system r-build-system)
11265 (inputs (list zlib))
11268 (home-page "https://bioconductor.org/packages/Rsubread/")
11269 (synopsis "Subread sequence alignment and counting for R")
11271 "This package provides tools for alignment, quantification and analysis
11272 of second and third generation sequencing data. It includes functionality for
11273 read mapping, read counting, SNP calling, structural variant detection and
11274 gene fusion discovery. It can be applied to all major sequencing techologies
11275 and to both short and long sequence reads.")
11276 (license license:gpl3)))
11278 (define-public r-flowutils
11280 (name "r-flowutils")
11285 (uri (bioconductor-uri "flowUtils" version))
11288 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
11289 (properties `((upstream-name . "flowUtils")))
11290 (build-system r-build-system)
11298 (home-page "https://github.com/jspidlen/flowUtils")
11299 (synopsis "Utilities for flow cytometry")
11301 "This package provides utilities for flow cytometry data.")
11302 (license license:artistic2.0)))
11304 (define-public r-consensusclusterplus
11306 (name "r-consensusclusterplus")
11311 (uri (bioconductor-uri "ConsensusClusterPlus" version))
11314 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
11316 `((upstream-name . "ConsensusClusterPlus")))
11317 (build-system r-build-system)
11319 (list r-all r-biobase r-cluster))
11320 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
11321 (synopsis "Clustering algorithm")
11323 "This package provides an implementation of an algorithm for determining
11324 cluster count and membership by stability evidence in unsupervised analysis.")
11325 (license license:gpl2)))
11327 ;; This is the latest commit and it solves a bug from the latest release.
11328 (define-public r-cycombine
11329 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
11331 (name "r-cycombine")
11332 (version (git-version "0.2.6" revision commit))
11335 (uri (git-reference
11336 (url "https://github.com/biosurf/cyCombine")
11338 (file-name (git-file-name name version))
11341 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
11342 (properties `((upstream-name . "cyCombine")))
11343 (build-system r-build-system)
11361 (native-inputs (list r-knitr))
11362 (home-page "https://github.com/biosurf/cyCombine")
11363 (synopsis "Integration of single-cell cytometry datasets")
11365 "This package provides a method for combining single-cell cytometry
11366 datasets, which increases the analytical flexibility and the statistical power
11367 of the analyses while minimizing technical noise.")
11368 (license license:expat))))
11370 (define-public r-cytolib
11377 (uri (bioconductor-uri "cytolib" version))
11380 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
11381 (properties `((upstream-name . "cytolib")))
11382 (build-system r-build-system)
11392 (home-page "https://bioconductor.org/packages/cytolib/")
11393 (synopsis "C++ infrastructure for working with gated cytometry")
11395 "This package provides the core data structure and API to represent and
11396 interact with gated cytometry data.")
11397 (license license:artistic2.0)))
11399 (define-public r-flowcore
11401 (name "r-flowcore")
11406 (uri (bioconductor-uri "flowCore" version))
11409 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
11410 (properties `((upstream-name . "flowCore")))
11411 (build-system r-build-system)
11424 (home-page "https://bioconductor.org/packages/flowCore")
11425 (synopsis "Basic structures for flow cytometry data")
11427 "This package provides S4 data structures and basic functions to deal
11428 with flow cytometry data.")
11429 (license license:artistic2.0)))
11431 (define-public r-flowmeans
11433 (name "r-flowmeans")
11438 (uri (bioconductor-uri "flowMeans" version))
11441 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
11442 (properties `((upstream-name . "flowMeans")))
11443 (build-system r-build-system)
11445 (list r-biobase r-feature r-flowcore r-rrcov))
11446 (home-page "https://bioconductor.org/packages/flowMeans")
11447 (synopsis "Non-parametric flow cytometry data gating")
11449 "This package provides tools to identify cell populations in Flow
11450 Cytometry data using non-parametric clustering and segmented-regression-based
11451 change point detection.")
11452 (license license:artistic2.0)))
11454 (define-public r-ncdfflow
11456 (name "r-ncdfflow")
11461 (uri (bioconductor-uri "ncdfFlow" version))
11464 "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m"))))
11465 (properties `((upstream-name . "ncdfFlow")))
11466 (build-system r-build-system)
11478 (home-page "https://bioconductor.org/packages/ncdfFlow/")
11479 (synopsis "HDF5 based storage for flow cytometry data")
11481 "This package provides HDF5 storage based methods and functions for
11482 manipulation of flow cytometry data.")
11483 (license license:artistic2.0)))
11485 (define-public r-ggcyto
11492 (uri (bioconductor-uri "ggcyto" version))
11495 "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"))))
11496 (properties `((upstream-name . "ggcyto")))
11497 (build-system r-build-system)
11512 (home-page "https://github.com/RGLab/ggcyto/issues")
11513 (synopsis "Visualize Cytometry data with ggplot")
11515 "With the dedicated fortify method implemented for @code{flowSet},
11516 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
11517 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
11518 and some custom layers also make it easy to add gates and population
11519 statistics to the plot.")
11520 (license license:artistic2.0)))
11522 (define-public r-flowviz
11529 (uri (bioconductor-uri "flowViz" version))
11532 "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f"))))
11533 (properties `((upstream-name . "flowViz")))
11534 (build-system r-build-system)
11547 (home-page "https://bioconductor.org/packages/flowViz/")
11548 (synopsis "Visualization for flow cytometry")
11550 "This package provides visualization tools for flow cytometry data.")
11551 (license license:artistic2.0)))
11553 (define-public r-flowclust
11555 (name "r-flowclust")
11560 (uri (bioconductor-uri "flowClust" version))
11563 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
11564 (properties `((upstream-name . "flowClust")))
11565 (build-system r-build-system)
11567 `(#:configure-flags
11568 (list "--configure-args=--enable-bundled-gsl=no")))
11577 (list pkg-config r-knitr))
11578 (home-page "https://bioconductor.org/packages/flowClust")
11579 (synopsis "Clustering for flow cytometry")
11581 "This package provides robust model-based clustering using a t-mixture
11582 model with Box-Cox transformation.")
11583 (license license:artistic2.0)))
11585 ;; TODO: this package bundles an old version of protobuf. It's not easy to
11586 ;; make it use our protobuf package instead.
11587 (define-public r-rprotobuflib
11589 (name "r-rprotobuflib")
11594 (uri (bioconductor-uri "RProtoBufLib" version))
11597 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
11598 (properties `((upstream-name . "RProtoBufLib")))
11599 (build-system r-build-system)
11602 (modify-phases %standard-phases
11603 (add-after 'unpack 'unpack-bundled-sources
11605 (with-directory-excursion "src"
11606 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
11609 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
11610 (synopsis "C++ headers and static libraries of Protocol buffers")
11612 "This package provides the headers and static library of Protocol buffers
11613 for other R packages to compile and link against.")
11614 (license license:bsd-3)))
11616 (define-public r-flowworkspace
11618 (name "r-flowworkspace")
11623 (uri (bioconductor-uri "flowWorkspace" version))
11626 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
11627 (properties `((upstream-name . "flowWorkspace")))
11628 (build-system r-build-system)
11659 (home-page "https://bioconductor.org/packages/flowWorkspace/")
11660 (synopsis "Infrastructure for working with cytometry data")
11662 "This package is designed to facilitate comparison of automated gating
11663 methods against manual gating done in flowJo. This package allows you to
11664 import basic flowJo workspaces into BioConductor and replicate the gating from
11665 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
11666 samples, compensation, and transformation are performed so that the output
11667 matches the flowJo analysis.")
11668 (license license:artistic2.0)))
11670 (define-public r-flowstats
11672 (name "r-flowstats")
11677 (uri (bioconductor-uri "flowStats" version))
11680 "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj"))))
11681 (properties `((upstream-name . "flowStats")))
11682 (build-system r-build-system)
11700 (home-page "http://www.github.com/RGLab/flowStats")
11701 (synopsis "Statistical methods for the analysis of flow cytometry data")
11703 "This package provides methods and functionality to analyze flow data
11704 that is beyond the basic infrastructure provided by the @code{flowCore}
11706 (license license:artistic2.0)))
11708 (define-public r-opencyto
11710 (name "r-opencyto")
11715 (uri (bioconductor-uri "openCyto" version))
11718 "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y"))))
11719 (properties `((upstream-name . "openCyto")))
11720 (build-system r-build-system)
11745 (home-page "https://bioconductor.org/packages/openCyto")
11746 (synopsis "Hierarchical gating pipeline for flow cytometry data")
11748 "This package is designed to facilitate the automated gating methods in a
11749 sequential way to mimic the manual gating strategy.")
11750 (license license:artistic2.0)))
11752 (define-public r-cytoml
11759 (uri (bioconductor-uri "CytoML" version))
11762 "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"))))
11763 (properties `((upstream-name . "CytoML")))
11764 (build-system r-build-system)
11766 (list libxml2 zlib))
11797 (home-page "https://github.com/RGLab/CytoML")
11798 (synopsis "GatingML interface for cross platform cytometry data sharing")
11800 "This package provides an interface to implementations of the GatingML2.0
11801 standard to exchange gated cytometry data with other software platforms.")
11802 (license license:artistic2.0)))
11804 (define-public r-flowsom
11811 (uri (bioconductor-uri "FlowSOM" version))
11814 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
11815 (properties `((upstream-name . "FlowSOM")))
11816 (build-system r-build-system)
11818 (list r-biocgenerics
11820 r-consensusclusterplus
11840 (home-page "https://bioconductor.org/packages/FlowSOM/")
11841 (synopsis "Visualize and interpret cytometry data")
11843 "FlowSOM offers visualization options for cytometry data, by using
11844 self-organizing map clustering and minimal spanning trees.")
11845 (license license:gpl2+)))
11847 (define-public r-mixomics
11849 (name "r-mixomics")
11854 (uri (bioconductor-uri "mixOmics" version))
11857 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
11858 (properties `((upstream-name . "mixOmics")))
11859 (build-system r-build-system)
11861 (list r-biocparallel
11878 (home-page "http://www.mixOmics.org")
11879 (synopsis "Multivariate methods for exploration of biological datasets")
11881 "mixOmics offers a wide range of multivariate methods for the exploration
11882 and integration of biological datasets with a particular focus on variable
11883 selection. The package proposes several sparse multivariate models we have
11884 developed to identify the key variables that are highly correlated, and/or
11885 explain the biological outcome of interest. The data that can be analysed
11886 with mixOmics may come from high throughput sequencing technologies, such as
11887 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
11888 also beyond the realm of omics (e.g. spectral imaging). The methods
11889 implemented in mixOmics can also handle missing values without having to
11890 delete entire rows with missing data.")
11891 (license license:gpl2+)))
11893 (define-public r-depecher
11894 (package ;Source/Weave error
11895 (name "r-depecher")
11900 (uri (bioconductor-uri "DepecheR" version))
11903 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
11904 (properties `((upstream-name . "DepecheR")))
11905 (build-system r-build-system)
11926 (home-page "https://bioconductor.org/packages/DepecheR/")
11927 (synopsis "Identify traits of clusters in high-dimensional entities")
11929 "The purpose of this package is to identify traits in a dataset that can
11930 separate groups. This is done on two levels. First, clustering is performed,
11931 using an implementation of sparse K-means. Secondly, the generated clusters
11932 are used to predict outcomes of groups of individuals based on their
11933 distribution of observations in the different clusters. As certain clusters
11934 with separating information will be identified, and these clusters are defined
11935 by a sparse number of variables, this method can reduce the complexity of
11936 data, to only emphasize the data that actually matters.")
11937 (license license:expat)))
11939 (define-public r-rcistarget
11941 (name "r-rcistarget")
11946 (uri (bioconductor-uri "RcisTarget" version))
11949 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
11950 (properties `((upstream-name . "RcisTarget")))
11951 (build-system r-build-system)
11963 r-summarizedexperiment
11967 (home-page "https://aertslab.org/#scenic")
11968 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
11970 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
11971 over-represented on a gene list. In a first step, RcisTarget selects DNA
11972 motifs that are significantly over-represented in the surroundings of the
11973 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
11974 achieved by using a database that contains genome-wide cross-species rankings
11975 for each motif. The motifs that are then annotated to TFs and those that have
11976 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
11977 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
11978 genes in the gene-set that are ranked above the leading edge).")
11979 (license license:gpl3)))
11981 (define-public r-chicago
11988 (uri (bioconductor-uri "Chicago" version))
11991 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
11992 (properties `((upstream-name . "Chicago")))
11993 (build-system r-build-system)
11995 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
11996 (native-inputs (list r-knitr))
11997 (home-page "https://bioconductor.org/packages/Chicago")
11998 (synopsis "Capture Hi-C analysis of genomic organization")
12000 "This package provides a pipeline for analysing Capture Hi-C data.")
12001 (license license:artistic2.0)))
12003 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12005 (define-public r-ciara
12011 (uri (cran-uri "CIARA" version))
12014 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
12015 (properties `((upstream-name . "CIARA")))
12016 (build-system r-build-system)
12017 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
12018 (native-inputs (list r-knitr))
12019 (home-page "https://cran.r-project.org/package=CIARA")
12020 (synopsis "Cluster-independent algorithm for rare cell types identification")
12022 "This is a package to support identification of markers of rare cell
12023 types by looking at genes whose expression is confined in small regions of the
12024 expression space.")
12025 (license license:artistic2.0)))
12027 (define-public r-cicero
12034 (uri (bioconductor-uri "cicero" version))
12037 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
12038 (build-system r-build-system)
12064 (home-page "https://bioconductor.org/packages/cicero/")
12065 (synopsis "Predict cis-co-accessibility from single-cell data")
12067 "Cicero computes putative cis-regulatory maps from single-cell chromatin
12068 accessibility data. It also extends the monocle package for use in chromatin
12069 accessibility data.")
12070 (license license:expat)))
12072 ;; This is the latest commit on the "monocle3" branch.
12073 (define-public r-cicero-monocle3
12074 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
12076 (package (inherit r-cicero)
12077 (name "r-cicero-monocle3")
12078 (version (git-version "1.3.2" revision commit))
12082 (uri (git-reference
12083 (url "https://github.com/cole-trapnell-lab/cicero-release")
12085 (file-name (git-file-name name version))
12088 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
12090 (modify-inputs (package-propagated-inputs r-cicero)
12091 (delete "r-monocle")
12092 (prepend r-monocle3))))))
12094 (define-public r-circrnaprofiler
12096 (name "r-circrnaprofiler")
12101 (uri (bioconductor-uri "circRNAprofiler" version))
12104 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
12106 `((upstream-name . "circRNAprofiler")))
12107 (build-system r-build-system)
12109 (list r-annotationhub
12112 r-bsgenome-hsapiens-ucsc-hg19
12135 "https://github.com/Aufiero/circRNAprofiler")
12137 "Computational framework for the downstream analysis of circular RNA's")
12139 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
12140 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
12141 framework allows combining and analyzing circRNAs previously detected by
12142 multiple publicly available annotation-based circRNA detection tools. It
12143 covers different aspects of circRNAs analysis from differential expression
12144 analysis, evolutionary conservation, biogenesis to functional analysis.")
12145 (license license:gpl3)))
12147 (define-public r-cistopic
12149 (name "r-cistopic")
12154 (uri (git-reference
12155 (url "https://github.com/aertslab/cisTopic")
12156 (commit (string-append "v" version))))
12157 (file-name (git-file-name name version))
12160 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
12161 (build-system r-build-system)
12178 (home-page "https://github.com/aertslab/cisTopic")
12179 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
12181 "The sparse nature of single cell epigenomics data can be overruled using
12182 probabilistic modelling methods such as @dfn{Latent Dirichlet
12183 Allocation} (LDA). This package allows the probabilistic modelling of
12184 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
12185 includes functionalities to identify cell states based on the contribution of
12186 cisTopics and explore the nature and regulatory proteins driving them.")
12187 (license license:gpl3)))
12189 (define-public r-cistopic-next
12190 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
12193 (inherit r-cistopic)
12194 (name "r-cistopic-next")
12195 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
12196 ;; since the previous release is 2.1.0. Oh well.
12197 (version (git-version "0.3.0" revision commit))
12201 (uri (git-reference
12202 (url "https://github.com/aertslab/cisTopic")
12204 (file-name (git-file-name name version))
12207 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
12208 (properties `((upstream-name . "cisTopic")))
12229 (define-public r-genie3
12236 (uri (bioconductor-uri "GENIE3" version))
12239 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
12240 (properties `((upstream-name . "GENIE3")))
12241 (build-system r-build-system)
12243 (list r-dplyr r-reshape2))
12246 (home-page "https://bioconductor.org/packages/GENIE3")
12247 (synopsis "Gene network inference with ensemble of trees")
12249 "This package implements the GENIE3 algorithm for inferring gene
12250 regulatory networks from expression data.")
12251 (license license:gpl2+)))
12253 (define-public r-roc
12260 (uri (bioconductor-uri "ROC" version))
12263 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
12264 (properties `((upstream-name . "ROC")))
12265 (build-system r-build-system)
12268 (home-page "https://www.bioconductor.org/packages/ROC/")
12269 (synopsis "Utilities for ROC curves")
12271 "This package provides utilities for @dfn{Receiver Operating
12272 Characteristic} (ROC) curves, with a focus on micro arrays.")
12273 (license license:artistic2.0)))
12275 (define-public r-watermelon
12277 (name "r-watermelon")
12282 (uri (bioconductor-uri "wateRmelon" version))
12285 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
12286 (properties `((upstream-name . "wateRmelon")))
12287 (build-system r-build-system)
12290 r-illuminahumanmethylation450kanno-ilmn12-hg19
12299 (home-page "https://bioconductor.org/packages/wateRmelon/")
12300 (synopsis "Illumina 450 methylation array normalization and metrics")
12302 "The standard index of DNA methylation (beta) is computed from methylated
12303 and unmethylated signal intensities. Betas calculated from raw signal
12304 intensities perform well, but using 11 methylomic datasets we demonstrate that
12305 quantile normalization methods produce marked improvement. The commonly used
12306 procedure of normalizing betas is inferior to the separate normalization of M
12307 and U, and it is also advantageous to normalize Type I and Type II assays
12308 separately. This package provides 15 flavours of betas and three performance
12309 metrics, with methods for objects produced by the @code{methylumi} and
12310 @code{minfi} packages.")
12311 (license license:gpl3)))
12313 (define-public r-gdsfmt
12320 (uri (bioconductor-uri "gdsfmt" version))
12323 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
12324 (modules '((guix build utils)))
12325 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
12326 ;; them and link with system libraries instead.
12329 (for-each delete-file-recursively
12333 (substitute* "src/Makevars"
12334 (("all: \\$\\(SHLIB\\)") "all:")
12335 (("\\$\\(SHLIB\\): liblzma.a") "")
12336 (("^ (ZLIB|LZ4)/.*") "")
12337 (("CoreArray/dVLIntGDS.cpp.*")
12338 "CoreArray/dVLIntGDS.cpp")
12339 (("CoreArray/dVLIntGDS.o.*")
12340 "CoreArray/dVLIntGDS.o")
12341 (("PKG_LIBS = ./liblzma.a")
12342 "PKG_LIBS = -llz4"))
12343 (substitute* "src/CoreArray/dStream.h"
12344 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
12345 (string-append "include <" header ">")))))))
12346 (properties `((upstream-name . "gdsfmt")))
12347 (build-system r-build-system)
12349 (list lz4 xz zlib))
12352 (home-page "http://corearray.sourceforge.net/")
12354 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
12356 "This package provides a high-level R interface to CoreArray @dfn{Genomic
12357 Data Structure} (GDS) data files, which are portable across platforms with
12358 hierarchical structure to store multiple scalable array-oriented data sets
12359 with metadata information. It is suited for large-scale datasets, especially
12360 for data which are much larger than the available random-access memory. The
12361 @code{gdsfmt} package offers efficient operations specifically designed for
12362 integers of less than 8 bits, since a diploid genotype, like
12363 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
12364 byte. Data compression and decompression are available with relatively
12365 efficient random access. It is also allowed to read a GDS file in parallel
12366 with multiple R processes supported by the package @code{parallel}.")
12367 (license license:lgpl3)))
12369 (define-public r-bigmelon
12371 (name "r-bigmelon")
12376 (uri (bioconductor-uri "bigmelon" version))
12379 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
12380 (properties `((upstream-name . "bigmelon")))
12381 (build-system r-build-system)
12393 (home-page "https://bioconductor.org/packages/bigmelon/")
12394 (synopsis "Illumina methylation array analysis for large experiments")
12396 "This package provides methods for working with Illumina arrays using the
12397 @code{gdsfmt} package.")
12398 (license license:gpl3)))
12400 (define-public r-seqbias
12407 (uri (bioconductor-uri "seqbias" version))
12410 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
12411 (properties `((upstream-name . "seqbias")))
12412 (build-system r-build-system)
12414 (list r-biostrings r-genomicranges r-rhtslib))
12415 (home-page "https://bioconductor.org/packages/seqbias/")
12416 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
12418 "This package implements a model of per-position sequencing bias in
12419 high-throughput sequencing data using a simple Bayesian network, the structure
12420 and parameters of which are trained on a set of aligned reads and a reference
12422 (license license:lgpl3)))
12424 (define-public r-reqon
12431 (uri (bioconductor-uri "ReQON" version))
12434 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
12435 (properties `((upstream-name . "ReQON")))
12436 (build-system r-build-system)
12438 (list r-rjava r-rsamtools r-seqbias))
12439 (home-page "https://bioconductor.org/packages/ReQON/")
12440 (synopsis "Recalibrating quality of nucleotides")
12442 "This package provides an implementation of an algorithm for
12443 recalibrating the base quality scores for aligned sequencing data in BAM
12445 (license license:gpl2)))
12447 (define-public r-wavcluster
12449 (name "r-wavcluster")
12454 (uri (bioconductor-uri "wavClusteR" version))
12457 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
12458 (properties `((upstream-name . "wavClusteR")))
12459 (build-system r-build-system)
12461 (list r-biocgenerics
12477 (home-page "https://bioconductor.org/packages/wavClusteR/")
12478 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
12480 "This package provides an integrated pipeline for the analysis of
12481 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
12482 sequencing errors, SNPs and additional non-experimental sources by a non-
12483 parametric mixture model. The protein binding sites (clusters) are then
12484 resolved at high resolution and cluster statistics are estimated using a
12485 rigorous Bayesian framework. Post-processing of the results, data export for
12486 UCSC genome browser visualization and motif search analysis are provided. In
12487 addition, the package integrates RNA-Seq data to estimate the False
12488 Discovery Rate of cluster detection. Key functions support parallel multicore
12489 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
12490 be applied to the analysis of other NGS data obtained from experimental
12491 procedures that induce nucleotide substitutions (e.g. BisSeq).")
12492 (license license:gpl2)))
12494 (define-public r-timeseriesexperiment
12496 (name "r-timeseriesexperiment")
12501 (uri (bioconductor-uri "TimeSeriesExperiment" version))
12504 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
12506 `((upstream-name . "TimeSeriesExperiment")))
12507 (build-system r-build-system)
12519 r-summarizedexperiment
12526 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
12527 (synopsis "Analysis for short time-series data")
12529 "This package is a visualization and analysis toolbox for short time
12530 course data which includes dimensionality reduction, clustering, two-sample
12531 differential expression testing and gene ranking techniques. The package also
12532 provides methods for retrieving enriched pathways.")
12533 (license license:lgpl3+)))
12535 (define-public r-variantfiltering
12537 (name "r-variantfiltering")
12542 (uri (bioconductor-uri "VariantFiltering" version))
12545 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
12547 `((upstream-name . "VariantFiltering")))
12548 (build-system r-build-system)
12550 (list r-annotationdbi
12571 r-summarizedexperiment
12572 r-variantannotation
12574 (home-page "https://github.com/rcastelo/VariantFiltering")
12575 (synopsis "Filtering of coding and non-coding genetic variants")
12577 "Filter genetic variants using different criteria such as inheritance
12578 model, amino acid change consequence, minor allele frequencies across human
12579 populations, splice site strength, conservation, etc.")
12580 (license license:artistic2.0)))
12582 (define-public r-genomegraphs
12584 (name "r-genomegraphs")
12589 (uri (bioconductor-uri "GenomeGraphs" version))
12592 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
12593 (properties `((upstream-name . "GenomeGraphs")))
12594 (build-system r-build-system)
12597 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
12598 (synopsis "Plotting genomic information from Ensembl")
12600 "Genomic data analyses requires integrated visualization of known genomic
12601 information and new experimental data. GenomeGraphs uses the biomaRt package
12602 to perform live annotation queries to Ensembl and translates this to e.g.
12603 gene/transcript structures in viewports of the grid graphics package. This
12604 results in genomic information plotted together with your data. Another
12605 strength of GenomeGraphs is to plot different data types such as array CGH,
12606 gene expression, sequencing and other data, together in one plot using the
12607 same genome coordinate system.")
12608 (license license:artistic2.0)))
12610 (define-public r-wavetiling
12612 (name "r-wavetiling")
12617 (uri (bioconductor-uri "waveTiling" version))
12620 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
12621 (properties `((upstream-name . "waveTiling")))
12622 (build-system r-build-system)
12634 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
12635 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
12637 "This package is designed to conduct transcriptome analysis for tiling
12638 arrays based on fast wavelet-based functional models.")
12639 (license license:gpl2+)))
12641 (define-public r-variancepartition
12643 (name "r-variancepartition")
12648 (uri (bioconductor-uri "variancePartition" version))
12651 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
12653 `((upstream-name . "variancePartition")))
12654 (build-system r-build-system)
12678 (home-page "https://bioconductor.org/packages/variancePartition/")
12679 (synopsis "Analyze variation in gene expression experiments")
12681 "This is a package providing tools to quantify and interpret multiple
12682 sources of biological and technical variation in gene expression experiments.
12683 It uses a linear mixed model to quantify variation in gene expression
12684 attributable to individual, tissue, time point, or technical variables. The
12685 package includes dream differential expression analysis for repeated
12687 (license license:gpl2+)))
12689 (define-public r-htqpcr
12696 (uri (bioconductor-uri "HTqPCR" version))
12699 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
12700 (properties `((upstream-name . "HTqPCR")))
12701 (build-system r-build-system)
12703 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
12704 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
12705 "groups/bertone/software/HTqPCR.pdf"))
12706 (synopsis "Automated analysis of high-throughput qPCR data")
12708 "Analysis of Ct values from high throughput quantitative real-time
12709 PCR (qPCR) assays across multiple conditions or replicates. The input data
12710 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
12711 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
12712 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
12713 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
12714 loading, quality assessment, normalization, visualization and parametric or
12715 non-parametric testing for statistical significance in Ct values between
12716 features (e.g. genes, microRNAs).")
12717 (license license:artistic2.0)))
12719 (define-public r-unifiedwmwqpcr
12721 (name "r-unifiedwmwqpcr")
12726 (uri (bioconductor-uri "unifiedWMWqPCR" version))
12729 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
12731 `((upstream-name . "unifiedWMWqPCR")))
12732 (build-system r-build-system)
12734 (list r-biocgenerics r-htqpcr))
12735 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
12736 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
12738 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
12739 data. This modified test allows for testing differential expression in qPCR
12741 (license license:gpl2+)))
12743 (define-public r-universalmotif
12745 (name "r-universalmotif")
12750 (uri (bioconductor-uri "universalmotif" version))
12753 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
12755 `((upstream-name . "universalmotif")))
12756 (build-system r-build-system)
12759 (modify-phases %standard-phases
12760 (add-after 'unpack 'fix-reference-to-strip
12762 (substitute* "src/Makevars"
12763 (("/usr/bin/strip") (which "strip"))))))))
12765 (list r-biocgenerics
12778 "https://bioconductor.org/packages/universalmotif/")
12780 "Specific structures importer, modifier, and exporter for R")
12782 "This package allows importing most common @dfn{specific structure}
12783 (motif) types into R for use by functions provided by other Bioconductor
12784 motif-related packages. Motifs can be exported into most major motif formats
12785 from various classes as defined by other Bioconductor packages. A suite of
12786 motif and sequence manipulation and analysis functions are included, including
12787 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
12788 motifs, and others.")
12789 (license license:gpl3)))
12791 (define-public r-ace
12797 (uri (bioconductor-uri "ACE" version))
12800 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
12801 (properties `((upstream-name . "ACE")))
12802 (build-system r-build-system)
12803 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
12804 (native-inputs (list r-knitr))
12805 (home-page "https://github.com/tgac-vumc/ACE")
12807 "Absolute copy number estimation from low-coverage whole genome sequencing")
12809 "This package uses segmented copy number data to estimate tumor cell
12810 percentage and produce copy number plots displaying absolute copy numbers. For
12811 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
12812 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
12813 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
12814 subsequently run through all samples in the object(s), for which it will create
12815 individual subdirectories. For each sample, it will calculate how well the
12816 segments fit (the relative error) to integer copy numbers for each percentage
12817 of @dfn{tumor cells} (cells with divergent segments).")
12818 (license license:gpl2)))
12820 (define-public r-acgh
12826 (uri (bioconductor-uri "aCGH" version))
12829 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
12830 (properties `((upstream-name . "aCGH")))
12831 (build-system r-build-system)
12832 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
12833 (home-page "https://bioconductor.org/packages/aCGH")
12835 "Classes and functions for array comparative genomic hybridization data")
12837 "This package provides functions for reading
12838 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
12839 output files and clone information files, creation of @code{aCGH} objects for
12840 storing these data. Basic methods are accessing/replacing, subsetting,
12841 printing and plotting @code{aCGH} objects.")
12842 (license license:gpl2)))
12844 (define-public r-acme
12850 (uri (bioconductor-uri "ACME" version))
12853 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
12854 (properties `((upstream-name . "ACME")))
12855 (build-system r-build-system)
12856 (propagated-inputs (list r-biobase r-biocgenerics))
12857 (home-page "https://bioconductor.org/packages/aCGH/")
12858 (synopsis "Calculating microarray enrichment")
12860 "This package implements @dfn{algorithms for calculating microarray
12861 enrichment} (ACME), and it is a set of tools for analysing tiling array of
12862 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
12863 DNAse hypersensitivity, or other experiments that result in regions of the
12864 genome showing enrichment. It does not rely on a specific array technology
12865 (although the array should be a tiling array), is very general (can be applied
12866 in experiments resulting in regions of enrichment), and is very insensitive to
12867 array noise or normalization methods. It is also very fast and can be applied
12868 on whole-genome tiling array experiments quite easily with enough memory.")
12869 (license license:gpl2+)))
12871 (define-public r-acde
12877 (uri (bioconductor-uri "acde" version))
12880 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
12881 (properties `((upstream-name . "acde")))
12882 (build-system r-build-system)
12883 (propagated-inputs (list r-boot))
12884 (home-page "https://bioconductor.org/packages/acde")
12886 "Identification of differentially expressed genes with artificial components")
12888 "This package provides a multivariate inferential analysis method for
12889 detecting differentially expressed genes in gene expression data. It uses
12890 artificial components, close to the data's principal components but with an
12891 exact interpretation in terms of differential genetic expression, to identify
12892 differentially expressed genes while controlling the @dfn{false discovery
12894 (license license:gpl3)))
12896 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12898 (define-public r-activedriverwgs
12900 (name "r-activedriverwgs")
12905 (uri (cran-uri "ActiveDriverWGS" version))
12908 "13b5yazgv9kckcp6gck183mh1m0q8lc5ixagmcy9s8kv2wz7wq45"))))
12910 `((upstream-name . "ActiveDriverWGS")))
12911 (build-system r-build-system)
12915 r-bsgenome-hsapiens-ucsc-hg19
12916 r-bsgenome-hsapiens-ucsc-hg38
12917 r-bsgenome-mmusculus-ucsc-mm9
12918 r-bsgenome-mmusculus-ucsc-mm10
12925 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
12926 (synopsis "Driver discovery tool for cancer whole genomes")
12928 "This package provides a method for finding an enrichment of cancer
12929 simple somatic mutations (SNVs and Indels) in functional elements across the
12930 human genome. ActiveDriverWGS detects coding and noncoding driver elements
12931 using whole genome sequencing data.")
12932 (license license:gpl3)))
12934 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12936 (define-public r-activepathways
12938 (name "r-activepathways")
12943 (uri (cran-uri "ActivePathways" version))
12946 "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
12948 `((upstream-name . "ActivePathways")))
12949 (build-system r-build-system)
12951 (list r-data-table r-ggplot2))
12954 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
12955 (synopsis "Multivariate pathway enrichment analysis")
12957 "This package represents an integrative method of analyzing multi omics
12958 data that conducts enrichment analysis of annotated gene sets. ActivePathways
12959 uses a statistical data fusion approach, rationalizes contributing evidence
12960 and highlights associated genes, improving systems-level understanding of
12961 cellular organization in health and disease.")
12962 (license license:gpl3)))
12964 (define-public r-bgmix
12971 (uri (bioconductor-uri "BGmix" version))
12974 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
12975 (properties `((upstream-name . "BGmix")))
12976 (build-system r-build-system)
12978 (list r-kernsmooth))
12979 (home-page "https://bioconductor.org/packages/BGmix/")
12980 (synopsis "Bayesian models for differential gene expression")
12982 "This package provides fully Bayesian mixture models for differential
12984 (license license:gpl2)))
12986 (define-public r-bgx
12993 (uri (bioconductor-uri "bgx" version))
12996 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
12997 (properties `((upstream-name . "bgx")))
12998 (build-system r-build-system)
13002 '(modify-phases %standard-phases
13003 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
13005 (substitute* "configure.ac"
13006 (("AX_GCC_ARCHFLAG.*") ""))
13007 (delete-file "configure")
13008 (invoke "autoreconf" "-vif"))))))
13012 (list r-affy r-biobase r-gcrma r-rcpp))
13014 (list autoconf automake))
13015 (home-page "https://bioconductor.org/packages/bgx/")
13016 (synopsis "Bayesian gene expression")
13018 "This package provides tools for Bayesian integrated analysis of
13019 Affymetrix GeneChips.")
13020 (license license:gpl2)))
13022 (define-public r-bhc
13029 (uri (bioconductor-uri "BHC" version))
13032 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
13033 (properties `((upstream-name . "BHC")))
13034 (build-system r-build-system)
13035 (home-page "https://bioconductor.org/packages/BHC/")
13036 (synopsis "Bayesian hierarchical clustering")
13038 "The method implemented in this package performs bottom-up hierarchical
13039 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
13040 in the data and Bayesian model selection to decide at each step which clusters
13041 to merge. This avoids several limitations of traditional methods, for example
13042 how many clusters there should be and how to choose a principled distance
13043 metric. This implementation accepts multinomial (i.e. discrete, with 2+
13044 categories) or time-series data. This version also includes a randomised
13045 algorithm which is more efficient for larger data sets.")
13046 (license license:gpl3)))
13048 (define-public r-bicare
13055 (uri (bioconductor-uri "BicARE" version))
13058 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
13059 (properties `((upstream-name . "BicARE")))
13060 (build-system r-build-system)
13062 (list r-biobase r-gseabase r-multtest))
13063 (home-page "http://bioinfo.curie.fr")
13064 (synopsis "Biclustering analysis and results exploration")
13066 "This is a package for biclustering analysis and exploration of
13068 (license license:gpl2)))
13070 (define-public r-bifet
13077 (uri (bioconductor-uri "BiFET" version))
13080 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
13081 (properties `((upstream-name . "BiFET")))
13082 (build-system r-build-system)
13084 (list r-genomicranges r-poibin))
13087 (home-page "https://bioconductor.org/packages/BiFET")
13088 (synopsis "Bias-free footprint enrichment test")
13090 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
13091 over-represented in target regions compared to background regions after
13092 correcting for the bias arising from the imbalance in read counts and GC
13093 contents between the target and background regions. For a given TF k, BiFET
13094 tests the null hypothesis that the target regions have the same probability of
13095 having footprints for the TF k as the background regions while correcting for
13096 the read count and GC content bias.")
13097 (license license:gpl3)))
13099 (define-public r-rsbml
13106 (uri (bioconductor-uri "rsbml" version))
13109 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
13110 (properties `((upstream-name . "rsbml")))
13111 (build-system r-build-system)
13115 (list r-biocgenerics r-graph))
13118 (home-page "http://www.sbml.org")
13119 (synopsis "R support for SBML")
13121 "This package provides an R interface to libsbml for SBML parsing,
13122 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
13123 (license license:artistic2.0)))
13125 (define-public r-hypergraph
13127 (name "r-hypergraph")
13132 (uri (bioconductor-uri "hypergraph" version))
13135 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
13136 (properties `((upstream-name . "hypergraph")))
13137 (build-system r-build-system)
13140 (home-page "https://bioconductor.org/packages/hypergraph")
13141 (synopsis "Hypergraph data structures")
13143 "This package implements some simple capabilities for representing and
13144 manipulating hypergraphs.")
13145 (license license:artistic2.0)))
13147 (define-public r-hyperdraw
13149 (name "r-hyperdraw")
13154 (uri (bioconductor-uri "hyperdraw" version))
13157 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
13158 (properties `((upstream-name . "hyperdraw")))
13159 (build-system r-build-system)
13160 (inputs (list graphviz))
13162 (list r-graph r-hypergraph r-rgraphviz))
13163 (home-page "https://bioconductor.org/packages/hyperdraw")
13164 (synopsis "Visualizing hypergraphs")
13166 "This package provides functions for visualizing hypergraphs.")
13167 (license license:gpl2+)))
13169 (define-public r-biggr
13176 (uri (bioconductor-uri "BiGGR" version))
13179 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
13180 (properties `((upstream-name . "BiGGR")))
13181 (build-system r-build-system)
13189 (home-page "https://bioconductor.org/packages/BiGGR/")
13190 (synopsis "Constraint based modeling using metabolic reconstruction databases")
13192 "This package provides an interface to simulate metabolic reconstruction
13193 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
13194 reconstruction databases. The package facilitates @dfn{flux balance
13195 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
13196 networks and estimated fluxes can be visualized with hypergraphs.")
13197 (license license:gpl3+)))
13199 (define-public r-bigmemoryextras
13201 (name "r-bigmemoryextras")
13206 (uri (bioconductor-uri "bigmemoryExtras" version))
13209 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
13211 `((upstream-name . "bigmemoryExtras")))
13212 (build-system r-build-system)
13214 (list r-bigmemory))
13217 (home-page "https://github.com/phaverty/bigmemoryExtras")
13218 (synopsis "Extension of the bigmemory package")
13220 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
13221 safety and convenience features to the @code{filebacked.big.matrix} class from
13222 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
13223 monitoring and gracefully restoring the connection to on-disk data and it also
13224 protects against accidental data modification with a file-system-based
13225 permissions system. Utilities are provided for using @code{BigMatrix}-derived
13226 classes as @code{assayData} matrices within the @code{Biobase} package's
13227 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
13228 related to attaching to, and indexing into, file-backed matrices with
13229 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
13230 a file-backed matrix with factor properties.")
13231 (license license:artistic2.0)))
13233 (define-public r-bigpint
13240 (uri (bioconductor-uri "bigPint" version))
13243 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
13244 (properties `((upstream-name . "bigPint")))
13245 (build-system r-build-system)
13247 (list r-delayedarray
13263 r-summarizedexperiment
13267 (home-page "https://github.com/lindsayrutter/bigPint")
13268 (synopsis "Big multivariate data plotted interactively")
13270 "This package provides methods for visualizing large multivariate
13271 datasets using static and interactive scatterplot matrices, parallel
13272 coordinate plots, volcano plots, and litre plots. It includes examples for
13273 visualizing RNA-sequencing datasets and differentially expressed genes.")
13274 (license license:gpl3)))
13276 (define-public r-chemminer
13278 (name "r-chemminer")
13283 (uri (bioconductor-uri "ChemmineR" version))
13286 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
13287 (properties `((upstream-name . "ChemmineR")))
13288 (build-system r-build-system)
13307 (home-page "https://github.com/girke-lab/ChemmineR")
13308 (synopsis "Cheminformatics toolkit for R")
13310 "ChemmineR is a cheminformatics package for analyzing drug-like small
13311 molecule data in R. It contains functions for efficient processing of large
13312 numbers of molecules, physicochemical/structural property predictions,
13313 structural similarity searching, classification and clustering of compound
13314 libraries with a wide spectrum of algorithms. In addition, it offers
13315 visualization functions for compound clustering results and chemical
13317 (license license:artistic2.0)))
13319 (define-public r-fmcsr
13326 (uri (bioconductor-uri "fmcsR" version))
13328 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
13329 (properties `((upstream-name . "fmcsR")))
13330 (build-system r-build-system)
13332 (list r-biocgenerics r-chemminer r-runit))
13333 (native-inputs (list r-knitr))
13334 (home-page "https://github.com/girke-lab/fmcsR")
13335 (synopsis "Mismatch tolerant maximum common substructure searching")
13337 "The fmcsR package introduces an efficient @dfn{maximum common
13338 substructure} (MCS) algorithms combined with a novel matching strategy that
13339 allows for atom and/or bond mismatches in the substructures shared among two
13340 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
13341 strict MCSs, resulting in the identification of more common features in their
13342 source structures, as well as a higher sensitivity in finding compounds with
13343 weak structural similarities. The fmcsR package provides several utilities to
13344 use the FMCS algorithm for pairwise compound comparisons, structure similarity
13345 searching and clustering.")
13346 (license license:artistic2.0)))
13348 (define-public r-bioassayr
13350 (name "r-bioassayr")
13355 (uri (bioconductor-uri "bioassayR" version))
13358 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
13359 (properties `((upstream-name . "bioassayR")))
13360 (build-system r-build-system)
13362 (list r-biocgenerics
13371 (home-page "https://github.com/girke-lab/bioassayR")
13372 (synopsis "Cross-target analysis of small molecule bioactivity")
13374 "bioassayR is a computational tool that enables simultaneous analysis of
13375 thousands of bioassay experiments performed over a diverse set of compounds
13376 and biological targets. Unique features include support for large-scale
13377 cross-target analyses of both public and custom bioassays, generation of
13378 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
13379 preloaded database that provides access to a substantial portion of publicly
13380 available bioactivity data.")
13381 (license license:artistic2.0)))
13383 (define-public r-biobroom
13385 (name "r-biobroom")
13390 (uri (bioconductor-uri "biobroom" version))
13393 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
13394 (properties `((upstream-name . "biobroom")))
13395 (build-system r-build-system)
13397 (list r-biobase r-broom r-dplyr r-tidyr))
13400 (home-page "https://github.com/StoreyLab/biobroom")
13401 (synopsis "Turn Bioconductor objects into tidy data frames")
13403 "This package contains methods for converting standard objects
13404 constructed by bioinformatics packages, especially those in Bioconductor, and
13405 converting them to @code{tidy} data. It thus serves as a complement to the
13406 @code{broom} package, and follows the same tidy, augment, glance division of
13407 tidying methods. Tidying data makes it easy to recombine, reshape and
13408 visualize bioinformatics analyses.")
13409 ;; Any version of the LGPL.
13410 (license license:lgpl3+)))
13412 (define-public r-graphite
13414 (name "r-graphite")
13419 (uri (bioconductor-uri "graphite" version))
13422 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
13423 (properties `((upstream-name . "graphite")))
13424 (build-system r-build-system)
13426 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
13427 (home-page "https://bioconductor.org/packages/graphite/")
13428 (synopsis "Networks from pathway databases")
13430 "Graphite provides networks derived from eight public pathway databases,
13431 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
13433 (license license:agpl3+)))
13435 (define-public r-reactomepa
13437 (name "r-reactomepa")
13442 (uri (bioconductor-uri "ReactomePA" version))
13445 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
13446 (properties `((upstream-name . "ReactomePA")))
13447 (build-system r-build-system)
13449 (list r-annotationdbi
13459 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
13460 (synopsis "Reactome pathway analysis")
13462 "This package provides functions for pathway analysis based on the
13463 REACTOME pathway database. It implements enrichment analysis, gene set
13464 enrichment analysis and several functions for visualization.")
13465 (license license:gpl2)))
13467 (define-public r-ebarrays
13469 (name "r-ebarrays")
13474 (uri (bioconductor-uri "EBarrays" version))
13477 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
13478 (properties `((upstream-name . "EBarrays")))
13479 (build-system r-build-system)
13481 (list r-biobase r-cluster r-lattice))
13482 (home-page "https://bioconductor.org/packages/EBarrays/")
13483 (synopsis "Gene clustering and differential expression identification")
13485 "EBarrays provides tools for the analysis of replicated/unreplicated
13487 (license license:gpl2+)))
13489 (define-public r-bioccasestudies
13491 (name "r-bioccasestudies")
13496 (uri (bioconductor-uri "BiocCaseStudies" version))
13499 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
13501 `((upstream-name . "BiocCaseStudies")))
13502 (build-system r-build-system)
13503 (propagated-inputs (list r-biobase))
13504 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
13505 (synopsis "Support for the case studies monograph")
13507 "This package provides software and data to support the case studies
13509 (license license:artistic2.0)))
13511 (define-public r-bioccheck
13513 (name "r-bioccheck")
13517 (uri (bioconductor-uri "BiocCheck" version))
13520 "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"))))
13522 `((upstream-name . "BiocCheck")))
13523 (build-system r-build-system)
13534 (home-page "https://bioconductor.org/packages/BiocCheck")
13535 (synopsis "Executes Bioconductor-specific package checks")
13536 (description "This package contains tools to perform additional quality
13537 checks on R packages that are to be submitted to the Bioconductor repository.")
13538 (license license:artistic2.0)))
13540 (define-public r-biocgraph
13542 (name "r-biocgraph")
13547 (uri (bioconductor-uri "biocGraph" version))
13550 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
13551 (properties `((upstream-name . "biocGraph")))
13552 (build-system r-build-system)
13554 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
13555 (home-page "https://bioconductor.org/packages/biocGraph/")
13556 (synopsis "Graph examples and use cases in Bioinformatics")
13558 "This package provides examples and code that make use of the
13559 different graph related packages produced by Bioconductor.")
13560 (license license:artistic2.0)))
13562 (define-public r-biocstyle
13564 (name "r-biocstyle")
13568 (uri (bioconductor-uri "BiocStyle" version))
13571 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
13573 `((upstream-name . "BiocStyle")))
13574 (build-system r-build-system)
13576 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
13579 (home-page "https://bioconductor.org/packages/BiocStyle")
13580 (synopsis "Bioconductor formatting styles")
13581 (description "This package provides standard formatting styles for
13582 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
13584 (license license:artistic2.0)))
13586 (define-public r-biocviews
13588 (name "r-biocviews")
13592 (uri (bioconductor-uri "biocViews" version))
13595 "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126"))))
13597 `((upstream-name . "biocViews")))
13598 (build-system r-build-system)
13607 (home-page "https://bioconductor.org/packages/biocViews")
13608 (synopsis "Bioconductor package categorization helper")
13609 (description "The purpose of biocViews is to create HTML pages that
13610 categorize packages in a Bioconductor package repository according to keywords,
13611 also known as views, in a controlled vocabulary.")
13612 (license license:artistic2.0)))
13614 (define-public r-experimenthub
13616 (name "r-experimenthub")
13621 (uri (bioconductor-uri "ExperimentHub" version))
13624 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
13625 (properties `((upstream-name . "ExperimentHub")))
13626 (build-system r-build-system)
13628 (list r-annotationhub
13637 (home-page "https://bioconductor.org/packages/ExperimentHub/")
13638 (synopsis "Client to access ExperimentHub resources")
13640 "This package provides a client for the Bioconductor ExperimentHub web
13641 resource. ExperimentHub provides a central location where curated data from
13642 experiments, publications or training courses can be accessed. Each resource
13643 has associated metadata, tags and date of modification. The client creates
13644 and manages a local cache of files retrieved enabling quick and reproducible
13646 (license license:artistic2.0)))
13648 (define-public r-grohmm
13655 (uri (bioconductor-uri "groHMM" version))
13658 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
13659 (properties `((upstream-name . "groHMM")))
13660 (build-system r-build-system)
13662 (list r-genomeinfodb
13663 r-genomicalignments
13669 (home-page "https://github.com/Kraus-Lab/groHMM")
13670 (synopsis "GRO-seq analysis pipeline")
13672 "This package provides a pipeline for the analysis of GRO-seq data.")
13673 (license license:gpl3+)))
13675 (define-public r-multiassayexperiment
13677 (name "r-multiassayexperiment")
13682 (uri (bioconductor-uri "MultiAssayExperiment" version))
13685 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
13687 `((upstream-name . "MultiAssayExperiment")))
13688 (build-system r-build-system)
13695 r-summarizedexperiment
13699 (home-page "https://waldronlab.io/MultiAssayExperiment/")
13700 (synopsis "Integration of multi-omics experiments in Bioconductor")
13702 "MultiAssayExperiment harmonizes data management of multiple assays
13703 performed on an overlapping set of specimens. It provides a familiar
13704 Bioconductor user experience by extending concepts from
13705 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
13706 classes for individual assays, and allowing subsetting by genomic ranges or
13708 (license license:artistic2.0)))
13710 (define-public r-bioconcotk
13712 (name "r-bioconcotk")
13717 (uri (bioconductor-uri "BiocOncoTK" version))
13720 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
13721 (properties `((upstream-name . "BiocOncoTK")))
13722 (build-system r-build-system)
13745 r-summarizedexperiment))
13748 (home-page "https://bioconductor.org/packages/BiocOncoTK")
13749 (synopsis "Bioconductor components for general cancer genomics")
13751 "The purpose of this package is to provide a central interface to various
13752 tools for genome-scale analysis of cancer studies.")
13753 (license license:artistic2.0)))
13755 (define-public r-biocor
13762 (uri (bioconductor-uri "BioCor" version))
13765 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
13766 (properties `((upstream-name . "BioCor")))
13767 (build-system r-build-system)
13769 (list r-biocparallel r-gseabase r-matrix))
13772 (home-page "https://llrs.github.io/BioCor/")
13773 (synopsis "Functional similarities")
13775 "This package provides tools to calculate functional similarities based
13776 on the pathways described on KEGG and REACTOME or in gene sets. These
13777 similarities can be calculated for pathways or gene sets, genes, or clusters
13778 and combined with other similarities. They can be used to improve networks,
13779 gene selection, testing relationships, and so on.")
13780 (license license:expat)))
13782 (define-public r-biocpkgtools
13784 (name "r-biocpkgtools")
13789 (uri (bioconductor-uri "BiocPkgTools" version))
13792 "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"))))
13793 (properties `((upstream-name . "BiocPkgTools")))
13794 (build-system r-build-system)
13796 (list r-biocfilecache
13820 (home-page "https://github.com/seandavi/BiocPkgTools")
13821 (synopsis "Collection of tools for learning about Bioconductor packages")
13823 "Bioconductor has a rich ecosystem of metadata around packages, usage,
13824 and build status. This package is a simple collection of functions to access
13825 that metadata from R. The goal is to expose metadata for data mining and
13826 value-added functionality such as package searching, text mining, and
13827 analytics on packages.")
13828 (license license:expat)))
13830 (define-public r-biocset
13837 (uri (bioconductor-uri "BiocSet" version))
13840 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
13841 (properties `((upstream-name . "BiocSet")))
13842 (build-system r-build-system)
13844 (list r-annotationdbi
13857 "https://bioconductor.org/packages/BiocSet")
13859 "Representing Different Biological Sets")
13861 "BiocSet displays different biological sets in a triple tibble format.
13862 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
13863 The user has the ability to activate one of these three tibbles to perform
13864 common functions from the @code{dplyr} package. Mapping functionality and
13865 accessing web references for elements/sets are also available in BiocSet.")
13866 (license license:artistic2.0)))
13868 (define-public r-biocworkflowtools
13870 (name "r-biocworkflowtools")
13875 (uri (bioconductor-uri "BiocWorkflowTools" version))
13878 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
13880 `((upstream-name . "BiocWorkflowTools")))
13881 (build-system r-build-system)
13894 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
13895 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
13897 "This package provides functions to ease the transition between
13898 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
13899 (license license:expat)))
13901 (define-public r-biodist
13908 (uri (bioconductor-uri "bioDist" version))
13911 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
13912 (properties `((upstream-name . "bioDist")))
13913 (build-system r-build-system)
13915 (list r-biobase r-kernsmooth))
13916 (home-page "https://bioconductor.org/packages/bioDist/")
13917 (synopsis "Different distance measures")
13919 "This package provides a collection of software tools for calculating
13920 distance measures.")
13921 (license license:artistic2.0)))
13923 (define-public r-pcatools
13925 (name "r-pcatools")
13930 (uri (bioconductor-uri "PCAtools" version))
13933 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
13934 (properties `((upstream-name . "PCAtools")))
13935 (build-system r-build-system)
13943 r-delayedmatrixstats
13951 (native-inputs (list r-knitr))
13952 (home-page "https://github.com/kevinblighe/PCAtools")
13953 (synopsis "PCAtools: everything Principal Components Analysis")
13955 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
13956 structure of the data without the need to build any model to represent it.
13957 This \"summary\" of the data is arrived at through a process of reduction that
13958 can transform the large number of variables into a lesser number that are
13959 uncorrelated (i.e. the 'principal components'), while at the same time being
13960 capable of easy interpretation on the original data. PCAtools provides
13961 functions for data exploration via PCA, and allows the user to generate
13962 publication-ready figures. PCA is performed via @code{BiocSingular}; users
13963 can also identify an optimal number of principal components via different
13964 metrics, such as the elbow method and Horn's parallel analysis, which has
13965 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
13966 dimensional mass cytometry data.")
13967 (license license:gpl3)))
13969 (define-public r-rgreat
13976 (uri (bioconductor-uri "rGREAT" version))
13979 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
13980 (properties `((upstream-name . "rGREAT")))
13981 (build-system r-build-system)
13983 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
13984 (native-inputs (list r-knitr))
13985 (home-page "https://github.com/jokergoo/rGREAT")
13986 (synopsis "Client for GREAT analysis")
13988 "This package makes GREAT (Genomic Regions Enrichment of Annotations
13989 Tool) analysis automatic by constructing a HTTP POST request according to
13990 user's input and automatically retrieving results from GREAT web server.")
13991 (license license:expat)))
13993 (define-public r-m3c
14000 (uri (bioconductor-uri "M3C" version))
14003 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
14004 (properties `((upstream-name . "M3C")))
14005 (build-system r-build-system)
14017 (native-inputs (list r-knitr))
14018 (home-page "https://bioconductor.org/packages/M3C")
14019 (synopsis "Monte Carlo reference-based consensus clustering")
14021 "M3C is a consensus clustering algorithm that uses a Monte Carlo
14022 simulation to eliminate overestimation of @code{K} and can reject the null
14023 hypothesis @code{K=1}.")
14024 (license license:agpl3+)))
14026 (define-public r-icens
14033 (uri (bioconductor-uri "Icens" version))
14036 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
14037 (properties `((upstream-name . "Icens")))
14038 (build-system r-build-system)
14041 (home-page "https://bioconductor.org/packages/Icens")
14042 (synopsis "NPMLE for censored and truncated data")
14044 "This package provides many functions for computing the
14045 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
14047 (license license:artistic2.0)))
14049 ;; This is a CRAN package but it depends on r-icens, which is published on
14051 (define-public r-interval
14053 (name "r-interval")
14054 (version "1.1-0.8")
14058 (uri (cran-uri "interval" version))
14061 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
14062 (properties `((upstream-name . "interval")))
14063 (build-system r-build-system)
14065 (list r-icens r-mlecens r-perm r-survival))
14066 (home-page "https://cran.r-project.org/web/packages/interval/")
14067 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
14069 "This package provides functions to fit nonparametric survival curves,
14070 plot them, and perform logrank or Wilcoxon type tests.")
14071 (license license:gpl2+)))
14073 ;; This is a CRAN package, but it depends on r-interval, which depends on a
14074 ;; Bioconductor package.
14075 (define-public r-fhtest
14082 (uri (cran-uri "FHtest" version))
14085 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
14086 (properties `((upstream-name . "FHtest")))
14087 (build-system r-build-system)
14089 (list r-interval r-kmsurv r-mass r-perm r-survival))
14090 (home-page "https://cran.r-project.org/web/packages/FHtest/")
14091 (synopsis "Tests for survival data based on the Fleming-Harrington class")
14093 "This package provides functions to compare two or more survival curves
14097 @item The Fleming-Harrington test for right-censored data based on
14098 permutations and on counting processes.
14099 @item An extension of the Fleming-Harrington test for interval-censored data
14100 based on a permutation distribution and on a score vector distribution.
14103 (license license:gpl2+)))
14105 (define-public r-fourcseq
14107 (name "r-fourcseq")
14112 (uri (bioconductor-uri "FourCSeq" version))
14114 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
14115 (properties `((upstream-name . "FourCSeq")))
14116 (build-system r-build-system)
14122 r-genomicalignments
14132 r-summarizedexperiment))
14136 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
14137 (synopsis "Analysis of multiplexed 4C sequencing data")
14139 "This package is an R package dedicated to the analysis of (multiplexed)
14140 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
14141 interactions between DNA elements and identify differential interactions
14142 between conditions. The statistical analysis in R starts with individual bam
14143 files for each sample as inputs. To obtain these files, the package contains
14144 a Python script to demultiplex libraries and trim off primer sequences. With
14145 a standard alignment software the required bam files can be then be
14147 (license license:gpl3+)))
14149 (define-public r-preprocesscore
14151 (name "r-preprocesscore")
14156 (uri (bioconductor-uri "preprocessCore" version))
14159 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
14161 `((upstream-name . "preprocessCore")))
14162 (build-system r-build-system)
14163 (home-page "https://github.com/bmbolstad/preprocessCore")
14164 (synopsis "Collection of pre-processing functions")
14166 "This package provides a library of core pre-processing and normalization
14168 (license license:lgpl2.0+)))
14170 (define-public r-s4vectors
14172 (name "r-s4vectors")
14176 (uri (bioconductor-uri "S4Vectors" version))
14179 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
14181 `((upstream-name . "S4Vectors")))
14182 (build-system r-build-system)
14184 (list r-biocgenerics))
14185 (home-page "https://bioconductor.org/packages/S4Vectors")
14186 (synopsis "S4 implementation of vectors and lists")
14188 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
14189 classes and a set of generic functions that extend the semantic of ordinary
14190 vectors and lists in R. Package developers can easily implement vector-like
14191 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
14192 In addition, a few low-level concrete subclasses of general interest (e.g.
14193 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
14194 S4Vectors package itself.")
14195 (license license:artistic2.0)))
14197 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
14198 ;; Bioconductor package.
14199 (define-public r-wgcna
14206 (uri (cran-uri "WGCNA" version))
14209 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
14210 (properties `((upstream-name . "WGCNA")))
14211 (build-system r-build-system)
14213 (list r-annotationdbi
14226 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14227 (synopsis "Weighted correlation network analysis")
14229 "This package provides functions necessary to perform Weighted
14230 Correlation Network Analysis on high-dimensional data. It includes functions
14231 for rudimentary data cleaning, construction and summarization of correlation
14232 networks, module identification and functions for relating both variables and
14233 modules to sample traits. It also includes a number of utility functions for
14234 data manipulation and visualization.")
14235 (license license:gpl2+)))
14237 (define-public r-rgraphviz
14239 (name "r-rgraphviz")
14244 (uri (bioconductor-uri "Rgraphviz" version))
14247 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
14248 (properties `((upstream-name . "Rgraphviz")))
14249 (build-system r-build-system)
14252 (modify-phases %standard-phases
14253 (add-after 'unpack 'make-reproducible
14255 ;; The replacement value is taken from src/graphviz/builddate.h
14256 (substitute* "src/graphviz/configure"
14257 (("VERSION_DATE=.*")
14258 "VERSION_DATE=20200427.2341\n"))
14260 ;; FIXME: Rgraphviz bundles the sources of an older variant of
14261 ;; graphviz. It does not build with the latest version of graphviz, so
14262 ;; we do not add graphviz to the inputs.
14263 (inputs (list zlib))
14268 (home-page "https://bioconductor.org/packages/Rgraphviz")
14269 (synopsis "Plotting capabilities for R graph objects")
14271 "This package interfaces R with the graphviz library for plotting R graph
14272 objects from the @code{graph} package.")
14273 (license license:epl1.0)))
14275 (define-public r-fithic
14281 (uri (bioconductor-uri "FitHiC" version))
14284 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
14285 (properties `((upstream-name . "FitHiC")))
14286 (build-system r-build-system)
14288 (list r-data-table r-fdrtool r-rcpp))
14291 (home-page "https://bioconductor.org/packages/FitHiC")
14292 (synopsis "Confidence estimation for intra-chromosomal contact maps")
14294 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
14295 intra-chromosomal contact maps produced by genome-wide genome architecture
14296 assays such as Hi-C.")
14297 (license license:gpl2+)))
14299 (define-public r-hitc
14305 (uri (bioconductor-uri "HiTC" version))
14308 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
14309 (properties `((upstream-name . "HiTC")))
14310 (build-system r-build-system)
14319 (home-page "https://bioconductor.org/packages/HiTC")
14320 (synopsis "High throughput chromosome conformation capture analysis")
14322 "The HiTC package was developed to explore high-throughput \"C\" data
14323 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
14324 quality controls, normalization, visualization, and further analysis are also
14326 (license license:artistic2.0)))
14328 (define-public r-hdf5array
14330 (name "r-hdf5array")
14335 (uri (bioconductor-uri "HDF5Array" version))
14338 "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday"))))
14339 (properties `((upstream-name . "HDF5Array")))
14340 (build-system r-build-system)
14344 (list r-biocgenerics
14352 (home-page "https://bioconductor.org/packages/HDF5Array")
14353 (synopsis "HDF5 back end for DelayedArray objects")
14354 (description "This package provides an array-like container for convenient
14355 access and manipulation of HDF5 datasets. It supports delayed operations and
14356 block processing.")
14357 (license license:artistic2.0)))
14359 (define-public r-rhdf5lib
14361 (name "r-rhdf5lib")
14366 (uri (bioconductor-uri "Rhdf5lib" version))
14369 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
14370 (modules '((guix build utils)))
14373 ;; Delete bundled binaries
14374 (delete-file-recursively "src/wininclude/")
14375 (delete-file-recursively "src/winlib/")
14376 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
14377 (properties `((upstream-name . "Rhdf5lib")))
14378 (build-system r-build-system)
14381 (modify-phases %standard-phases
14382 (add-after 'unpack 'do-not-use-bundled-hdf5
14383 (lambda* (#:key inputs #:allow-other-keys)
14384 (for-each delete-file '("configure" "configure.ac"))
14385 (substitute* "R/zzz.R"
14386 (("return\\(links\\)") "return(\" -lz\")"))
14387 (with-directory-excursion "src"
14388 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
14389 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
14391 ;; Remove timestamp and host system information to make
14392 ;; the build reproducible.
14393 (substitute* "hdf5/src/libhdf5.settings.in"
14394 (("Configured on: @CONFIG_DATE@")
14395 "Configured on: Guix")
14396 (("Uname information:.*")
14397 "Uname information: Linux\n")
14398 ;; Remove unnecessary store reference.
14400 "C Compiler: GCC\n"))
14401 (rename-file "hdf5/src/libhdf5.settings.in"
14402 "hdf5/src/libhdf5.settings")
14403 (rename-file "Makevars.in" "Makevars")
14404 (substitute* "Makevars"
14405 (("@BUILD_HDF5@") "")
14406 (("@COPY_SZIP@") "")
14407 (("@ZLIB_LIB@") "-lz")
14408 (("@ZLIB_INCLUDE@") "")
14409 (("HDF5_CXX_LIB=.*")
14410 (string-append "HDF5_CXX_LIB="
14411 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
14413 (string-append "HDF5_LIB="
14414 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
14415 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
14416 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
14417 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
14418 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
14419 (("HDF5_HL_LIB=.*")
14420 (string-append "HDF5_HL_LIB="
14421 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
14422 (("HDF5_HL_CXX_LIB=.*")
14423 (string-append "HDF5_HL_CXX_LIB="
14424 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
14425 ;; szip is non-free software
14426 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
14427 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
14429 (list hdf5-1.10 zlib))
14431 `(("hdf5-source" ,(package-source hdf5-1.10))
14432 ("r-knitr" ,r-knitr)))
14433 (home-page "https://bioconductor.org/packages/Rhdf5lib")
14434 (synopsis "HDF5 library as an R package")
14435 (description "This package provides C and C++ HDF5 libraries for use in R
14437 (license license:artistic2.0)))
14439 (define-public r-beachmat
14441 (name "r-beachmat")
14446 (uri (bioconductor-uri "beachmat" version))
14449 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
14450 (build-system r-build-system)
14452 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
14455 (home-page "https://bioconductor.org/packages/beachmat")
14456 (synopsis "Compiling Bioconductor to handle each matrix type")
14457 (description "This package provides a consistent C++ class interface for a
14458 variety of commonly used matrix types, including sparse and HDF5-backed
14460 (license license:gpl3)))
14462 ;; This package includes files that have been taken from kentutils. Some
14463 ;; parts of kentutils are not released under a free license, but this package
14464 ;; only uses files that are also found in the free parts of kentutils.
14465 (define-public r-cner
14472 (uri (bioconductor-uri "CNEr" version))
14474 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
14475 (properties `((upstream-name . "CNEr")))
14476 (build-system r-build-system)
14477 (inputs (list zlib))
14484 r-genomicalignments
14500 (home-page "https://github.com/ge11232002/CNEr")
14501 (synopsis "CNE Detection and Visualization")
14503 "This package provides tools for large-scale identification and
14504 advanced visualization of sets of conserved noncoding elements.")
14505 ;; For all files in src/ucsc "license is hereby granted for all use -
14506 ;; public, private or commercial"; this includes those files that don't
14507 ;; have a license header, because they are included in the free parts of
14508 ;; the kentutils package.
14509 (license (list license:gpl2
14510 (license:non-copyleft
14511 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
14513 (define-public r-tfbstools
14515 (name "r-tfbstools")
14520 (uri (bioconductor-uri "TFBSTools" version))
14523 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
14524 (properties `((upstream-name . "TFBSTools")))
14525 (build-system r-build-system)
14535 r-dirichletmultinomial
14547 (native-inputs (list r-knitr))
14548 (home-page "https://github.com/ge11232002/TFBSTools")
14549 (synopsis "Transcription factor binding site (TFBS) analysis")
14551 "TFBSTools is a package for the analysis and manipulation of
14552 transcription factor binding sites. It includes matrices conversion
14553 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
14554 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
14555 scan putative TFBS from sequence/alignment, query JASPAR database and
14556 provides a wrapper of de novo motif discovery software.")
14557 (license license:gpl2)))
14559 (define-public r-maftools
14561 (name "r-maftools")
14566 (uri (bioconductor-uri "maftools" version))
14568 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
14569 (properties `((upstream-name . "maftools")))
14570 (build-system r-build-system)
14578 (native-inputs (list r-knitr))
14579 (home-page "https://github.com/PoisonAlien/maftools")
14580 (synopsis "Summarize, analyze and visualize MAF files")
14582 "Analyze and visualize Mutation Annotation Format (MAF) files from large
14583 scale sequencing studies. This package provides various functions to perform
14584 most commonly used analyses in cancer genomics and to create feature rich
14585 customizable visualzations with minimal effort.")
14586 (license license:expat)))
14588 (define-public r-motifmatchr
14590 (name "r-motifmatchr")
14595 (uri (bioconductor-uri "motifmatchr" version))
14598 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
14599 (properties `((upstream-name . "motifmatchr")))
14600 (build-system r-build-system)
14612 r-summarizedexperiment
14614 (native-inputs (list r-knitr))
14615 (home-page "https://bioconductor.org/packages/motifmatchr")
14616 (synopsis "Fast motif matching in R")
14618 "Quickly find motif matches for many motifs and many sequences.
14619 This package wraps C++ code from the MOODS motif calling library.")
14620 (license license:gpl3)))
14622 (define-public r-chromvar
14624 (name "r-chromvar")
14629 (uri (bioconductor-uri "chromVAR" version))
14631 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
14632 (properties `((upstream-name . "chromVAR")))
14633 (build-system r-build-system)
14635 (list r-biocgenerics
14655 r-summarizedexperiment
14657 (native-inputs (list r-knitr))
14658 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
14659 (synopsis "Determine chromatin variation across regions")
14661 "This package @code{r-chromvar} determines variation in chromatin
14662 accessibility across sets of annotations or peaks. @code{r-chromvar} is
14663 designed primarily for single-cell or sparse chromatin accessibility data like
14664 single cell assay for transposase-accessible chromatin using
14665 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
14666 sequence (@code{DNAse-seq}) experiments.")
14667 (license license:expat)))
14669 (define-public r-singlecellexperiment
14671 (name "r-singlecellexperiment")
14676 (uri (bioconductor-uri "SingleCellExperiment" version))
14679 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
14681 `((upstream-name . "SingleCellExperiment")))
14682 (build-system r-build-system)
14684 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
14685 r-summarizedexperiment))
14688 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
14689 (synopsis "S4 classes for single cell data")
14690 (description "This package defines an S4 class for storing data from
14691 single-cell experiments. This includes specialized methods to store and
14692 retrieve spike-in information, dimensionality reduction coordinates and size
14693 factors for each cell, along with the usual metadata for genes and
14695 (license license:gpl3)))
14697 (define-public r-singler
14704 (uri (bioconductor-uri "SingleR" version))
14706 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
14707 (properties `((upstream-name . "SingleR")))
14708 (build-system r-build-system)
14715 r-delayedmatrixstats
14719 r-summarizedexperiment))
14720 (native-inputs (list r-knitr))
14721 (home-page "https://github.com/LTLA/SingleR")
14722 (synopsis "Reference-based single-cell RNA-seq annotation")
14724 "This package performs unbiased cell type recognition from single-cell
14725 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
14726 cell types to infer the cell of origin of each single cell independently.")
14727 (license license:gpl3)))
14729 (define-public r-scuttle
14736 (uri (bioconductor-uri "scuttle" version))
14739 "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"))))
14740 (properties `((upstream-name . "scuttle")))
14741 (build-system r-build-system)
14747 r-delayedmatrixstats
14752 r-singlecellexperiment
14753 r-summarizedexperiment))
14754 (native-inputs (list r-knitr))
14755 (home-page "https://bioconductor.org/packages/scuttle")
14756 (synopsis "Single-cell RNA-Seq analysis utilities")
14758 "This package provides basic utility functions for performing single-cell
14759 analyses, focusing on simple normalization, quality control and data
14760 transformations. It also provides some helper functions to assist development
14761 of other packages.")
14762 (license license:gpl3)))
14764 (define-public r-scater
14770 (uri (bioconductor-uri "scater" version))
14773 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
14774 (build-system r-build-system)
14782 r-delayedmatrixstats
14794 r-singlecellexperiment
14795 r-summarizedexperiment
14799 (home-page "https://github.com/davismcc/scater")
14800 (synopsis "Single-cell analysis toolkit for gene expression data in R")
14801 (description "This package provides a collection of tools for doing
14802 various analyses of single-cell RNA-seq gene expression data, with a focus on
14804 (license license:gpl2+)))
14806 (define-public r-scran
14813 (uri (bioconductor-uri "scran" version))
14816 "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"))))
14817 (build-system r-build-system)
14826 r-delayedmatrixstats
14836 r-singlecellexperiment
14838 r-summarizedexperiment))
14841 (home-page "https://bioconductor.org/packages/scran")
14842 (synopsis "Methods for single-cell RNA-Seq data analysis")
14843 (description "This package implements a variety of low-level analyses of
14844 single-cell RNA-seq data. Methods are provided for normalization of
14845 cell-specific biases, assignment of cell cycle phase, and detection of highly
14846 variable and significantly correlated genes.")
14847 (license license:gpl3)))
14849 (define-public r-sparsematrixstats
14851 (name "r-sparsematrixstats")
14856 (uri (bioconductor-uri "sparseMatrixStats" version))
14859 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
14861 `((upstream-name . "sparseMatrixStats")))
14862 (build-system r-build-system)
14864 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
14865 (native-inputs (list r-knitr))
14866 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
14867 (synopsis "Summary statistics for rows and columns of sparse matrices")
14869 "This package provides high performance functions for row and column
14870 operations on sparse matrices. Currently, the optimizations are limited to
14871 data in the column sparse format.")
14872 (license license:expat)))
14874 (define-public r-delayedmatrixstats
14876 (name "r-delayedmatrixstats")
14881 (uri (bioconductor-uri "DelayedMatrixStats" version))
14884 "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"))))
14886 `((upstream-name . "DelayedMatrixStats")))
14887 (build-system r-build-system)
14889 (list r-delayedarray
14895 r-sparsematrixstats))
14898 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
14899 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
14901 "This package provides a port of the @code{matrixStats} API for use with
14902 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
14903 contains high-performing functions operating on rows and columns of
14904 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
14905 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
14906 are optimized per data type and for subsetted calculations such that both
14907 memory usage and processing time is minimized.")
14908 (license license:expat)))
14910 (define-public r-mscoreutils
14912 (name "r-mscoreutils")
14917 (uri (bioconductor-uri "MsCoreUtils" version))
14920 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
14921 (properties `((upstream-name . "MsCoreUtils")))
14922 (build-system r-build-system)
14924 (list r-clue r-mass r-rcpp r-s4vectors))
14927 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
14928 (synopsis "Core utils for mass spectrometry data")
14930 "This package defines low-level functions for mass spectrometry data and
14931 is independent of any high-level data structures. These functions include
14932 mass spectra processing functions (noise estimation, smoothing, binning),
14933 quantitative aggregation functions (median polish, robust summarisation,
14934 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
14935 well as misc helper functions, that are used across high-level data structure
14936 within the R for Mass Spectrometry packages.")
14937 (license license:artistic2.0)))
14939 (define-public r-msfeatures
14941 (name "r-msfeatures")
14946 (uri (bioconductor-uri "MsFeatures" version))
14948 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
14949 (properties `((upstream-name . "MsFeatures")))
14950 (build-system r-build-system)
14952 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
14955 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
14956 (synopsis "Functionality for mass spectrometry features")
14958 "The MsFeature package defines functionality for Mass Spectrometry
14959 features. This includes functions to group (LC-MS) features based on some of
14960 their properties, such as retention time (coeluting features), or correlation
14961 of signals across samples. This package hence can be used to group features, and
14962 its results can be used as an input for the @code{QFeatures} package which
14963 allows aggregating abundance levels of features within each group. This
14964 package defines concepts and functions for base and common data types,
14965 implementations for more specific data types are expected to be implemented in
14966 the respective packages (such as e.g. @code{xcms}).")
14967 (license license:artistic2.0)))
14969 (define-public r-biocio
14976 (uri (bioconductor-uri "BiocIO" version))
14979 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
14980 (properties `((upstream-name . "BiocIO")))
14981 (build-system r-build-system)
14983 (list r-biocgenerics r-s4vectors))
14986 (home-page "https://bioconductor.org/packages/BiocIO")
14987 (synopsis "Standard input and output for Bioconductor packages")
14989 "This package implements `import()` and `export()` standard generics for
14990 importing and exporting biological data formats. `import()` supports
14991 whole-file as well as chunk-wise iterative import. The `import()` interface
14992 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
14993 row or element-like components of the file resource), `select()` (on
14994 column-like components of the file resource) and `collect()`. The `import()`
14995 interface optionally provides transparent access to remote (e.g. via https)
14996 as well as local access. Developers can register a file extension, e.g.,
14997 `.loom` for dispatch from character-based URIs to specific `import()` /
14998 `export()` methods based on classes representing file types, e.g.,
15000 (license license:artistic2.0)))
15002 (define-public r-msmseda
15009 (uri (bioconductor-uri "msmsEDA" version))
15012 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
15013 (properties `((upstream-name . "msmsEDA")))
15014 (build-system r-build-system)
15016 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
15018 "https://bioconductor.org/packages/msmsEDA")
15019 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
15021 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
15022 experiments, and visualize de influence of the involved factors.")
15023 (license license:gpl2)))
15025 (define-public r-msmstests
15027 (name "r-msmstests")
15032 (uri (bioconductor-uri "msmsTests" version))
15035 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
15036 (properties `((upstream-name . "msmsTests")))
15037 (build-system r-build-system)
15039 (list r-edger r-msmseda r-msnbase r-qvalue))
15041 "https://bioconductor.org/packages/msmsTests")
15042 (synopsis "Differential LC-MS/MS expression tests")
15044 "This package provides statistical tests for label-free LC-MS/MS data
15045 by spectral counts, to discover differentially expressed proteins between two
15046 biological conditions. Three tests are available: Poisson GLM regression,
15047 quasi-likelihood GLM regression, and the negative binomial of the edgeR
15048 package. The three models admit blocking factors to control for nuisance
15049 variables. To assure a good level of reproducibility a post-test filter is
15050 available, where we may set the minimum effect size considered biologicaly
15051 relevant, and the minimum expression of the most abundant condition.")
15052 (license license:gpl2)))
15054 (define-public r-catalyst
15056 (name "r-catalyst")
15061 (uri (bioconductor-uri "CATALYST" version))
15064 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
15065 (properties `((upstream-name . "CATALYST")))
15066 (build-system r-build-system)
15070 r-consensusclusterplus
15092 r-singlecellexperiment
15093 r-summarizedexperiment))
15096 (home-page "https://github.com/HelenaLC/CATALYST")
15097 (synopsis "Cytometry data analysis tools")
15099 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
15100 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
15101 isotopes rather than fluorescent tags as reporters to label antibodies,
15102 thereby substantially decreasing spectral overlap and allowing for examination
15103 of over 50 parameters at the single cell level. While spectral overlap is
15104 significantly less pronounced in CyTOF than flow cytometry, spillover due to
15105 detection sensitivity, isotopic impurities, and oxide formation can impede
15106 data interpretability. @code{CATALYST} was designed to provide a pipeline for
15107 preprocessing of cytometry data, including:
15110 @item normalization using bead standards;
15111 @item single-cell deconvolution;
15112 @item bead-based compensation.
15115 (license license:gpl2+)))
15117 (define-public r-erma
15124 (uri (bioconductor-uri "erma" version))
15127 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
15128 (build-system r-build-system)
15130 (list r-annotationdbi
15143 r-summarizedexperiment))
15146 (home-page "https://bioconductor.org/packages/erma")
15147 (synopsis "Epigenomic road map adventures")
15149 "The epigenomics road map describes locations of epigenetic marks in DNA
15150 from a variety of cell types. Of interest are locations of histone
15151 modifications, sites of DNA methylation, and regions of accessible chromatin.
15152 This package presents a selection of elements of the road map including
15153 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
15154 by Ernst and Kellis.")
15155 (license license:artistic2.0)))
15157 (define-public r-ggbio
15164 (uri (bioconductor-uri "ggbio" version))
15167 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
15168 (build-system r-build-system)
15171 (modify-phases %standard-phases
15172 ;; See https://github.com/tengfei/ggbio/issues/117
15173 ;; This fix will be included in the next release.
15174 (add-after 'unpack 'fix-typo
15176 (substitute* "R/GGbio-class.R"
15177 (("fechable") "fetchable"))
15180 (list r-annotationdbi
15189 r-genomicalignments
15205 r-summarizedexperiment
15206 r-variantannotation))
15209 (home-page "http://www.tengfei.name/ggbio/")
15210 (synopsis "Visualization tools for genomic data")
15212 "The ggbio package extends and specializes the grammar of graphics for
15213 biological data. The graphics are designed to answer common scientific
15214 questions, in particular those often asked of high throughput genomics data.
15215 All core Bioconductor data structures are supported, where appropriate. The
15216 package supports detailed views of particular genomic regions, as well as
15217 genome-wide overviews. Supported overviews include ideograms and grand linear
15218 views. High-level plots include sequence fragment length, edge-linked
15219 interval to data view, mismatch pileup, and several splicing summaries.")
15220 (license license:artistic2.0)))
15222 (define-public r-gqtlbase
15224 (name "r-gqtlbase")
15229 (uri (bioconductor-uri "gQTLBase" version))
15232 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
15233 (properties `((upstream-name . "gQTLBase")))
15234 (build-system r-build-system)
15237 (modify-phases %standard-phases
15238 ;; This is an upstream bug.
15239 (add-after 'unpack 'fix-imports
15241 (substitute* "NAMESPACE"
15242 ((".*maxffmode.*") "")
15243 (("importFrom\\(ff,.*") "import(ff)\n"))
15258 r-summarizedexperiment))
15261 (home-page "https://bioconductor.org/packages/gQTLBase")
15262 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
15264 "The purpose of this package is to simplify the storage and interrogation
15265 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
15267 (license license:artistic2.0)))
15269 (define-public r-gqtlstats
15271 (name "r-gqtlstats")
15276 (uri (bioconductor-uri "gQTLstats" version))
15279 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
15280 (properties `((upstream-name . "gQTLstats")))
15281 (build-system r-build-system)
15283 (list r-annotationdbi
15311 r-summarizedexperiment
15312 r-variantannotation))
15315 (home-page "https://bioconductor.org/packages/gQTLstats")
15316 (synopsis "Computationally efficient analysis for eQTL and allied studies")
15318 "This package provides tools for the computationally efficient analysis
15319 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
15320 The software in this package aims to support refinements and functional
15321 interpretation of members of a collection of association statistics on a
15322 family of feature/genome hypotheses.")
15323 (license license:artistic2.0)))
15325 (define-public r-gviz
15332 (uri (bioconductor-uri "Gviz" version))
15335 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
15336 (properties `((upstream-name . "Gviz")))
15337 (build-system r-build-system)
15339 (list r-annotationdbi
15349 r-genomicalignments
15363 (home-page "https://bioconductor.org/packages/Gviz")
15364 (synopsis "Plotting data and annotation information along genomic coordinates")
15366 "Genomic data analyses requires integrated visualization of known genomic
15367 information and new experimental data. Gviz uses the biomaRt and the
15368 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
15369 and translates this to e.g. gene/transcript structures in viewports of the
15370 grid graphics package. This results in genomic information plotted together
15372 (license license:artistic2.0)))
15374 (define-public r-gwascat
15381 (uri (bioconductor-uri "gwascat" version))
15384 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
15385 (build-system r-build-system)
15387 (list r-annotationdbi
15398 r-variantannotation))
15401 (home-page "https://bioconductor.org/packages/gwascat")
15402 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
15404 "This package provides tools for representing and modeling data in the
15405 EMBL-EBI GWAS catalog.")
15406 (license license:artistic2.0)))
15408 (define-public r-kegggraph
15410 (name "r-kegggraph")
15415 (uri (bioconductor-uri "KEGGgraph" version))
15417 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
15418 (properties `((upstream-name . "KEGGgraph")))
15419 (build-system r-build-system)
15421 (list r-graph r-rcurl r-rgraphviz r-xml))
15422 (home-page "https://bioconductor.org/packages/KEGGgraph")
15423 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
15425 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
15426 object as well as a collection of tools to analyze, dissect and visualize these
15427 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
15428 maintaining all essential pathway attributes. The package offers
15429 functionalities including parsing, graph operation, visualization and etc.")
15430 (license license:gpl2+)))
15432 (define-public r-ldblock
15439 (uri (bioconductor-uri "ldblock" version))
15442 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
15443 (build-system r-build-system)
15445 (list r-biocgenerics
15446 r-ensdb-hsapiens-v75
15454 r-variantannotation))
15457 (home-page "https://bioconductor.org/packages/ldblock")
15458 (synopsis "Data structures for linkage disequilibrium measures in populations")
15460 "This package defines data structures for @dfn{linkage
15461 disequilibrium} (LD) measures in populations. Its purpose is to simplify
15462 handling of existing population-level data for the purpose of flexibly
15463 defining LD blocks.")
15464 (license license:artistic2.0)))
15466 ;; This is a CRAN package, but it depends on r-snpstats, which is a
15467 ;; Bioconductor package.
15468 (define-public r-ldheatmap
15470 (name "r-ldheatmap")
15475 (uri (cran-uri "LDheatmap" version))
15478 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
15479 (properties `((upstream-name . "LDheatmap")))
15480 (build-system r-build-system)
15482 (list r-genetics r-rcpp r-snpstats))
15483 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
15484 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
15486 "This package provides tools to produce a graphical display, as a heat
15487 map, of measures of pairwise linkage disequilibria between SNPs. Users may
15488 optionally include the physical locations or genetic map distances of each SNP
15490 (license license:gpl3)))
15492 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
15493 ;; Bioconductor package.
15494 (define-public r-abn
15501 (uri (cran-uri "abn" version))
15504 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
15505 (build-system r-build-system)
15518 (home-page "https://r-bayesian-networks.org/")
15519 (synopsis "Modelling multivariate data with additive bayesian networks")
15521 "Bayesian network analysis is a form of probabilistic graphical models
15522 which derives from empirical data a directed acyclic graph, DAG, describing
15523 the dependency structure between random variables. An additive Bayesian
15524 network model consists of a form of a DAG where each node comprises a
15525 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
15526 equivalent to Bayesian multivariate regression using graphical modelling, they
15527 generalises the usual multivariable regression, GLM, to multiple dependent
15528 variables. This package provides routines to help determine optimal Bayesian
15529 network models for a given data set, where these models are used to identify
15530 statistical dependencies in messy, complex data.")
15531 (license license:gpl2+)))
15533 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
15534 ;; Bioconductor package.
15535 (define-public r-spp
15541 (uri (cran-uri "spp" version))
15544 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
15545 (build-system r-build-system)
15549 (list r-bh r-catools r-rcpp r-rsamtools))
15550 (home-page "https://cran.r-project.org/web/packages/spp/")
15551 (synopsis "ChIP-Seq processing pipeline")
15552 (description "This package provides tools for analysis of ChIP-seq and
15553 other functional sequencing data.")
15554 (license license:gpl2)))
15556 (define-public r-pathview
15558 (name "r-pathview")
15563 (uri (bioconductor-uri "pathview" version))
15565 (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"))))
15566 (properties `((upstream-name . "pathview")))
15567 (build-system r-build-system)
15569 (list r-annotationdbi
15577 (home-page "https://pathview.uncc.edu/")
15578 (synopsis "Tool set for pathway based data integration and visualization")
15580 "@code{r-pathview} is a tool set for pathway based data integration and
15581 visualization. It maps and renders a wide variety of biological data on
15582 relevant pathway graphs. All users need is to supply their data and specify
15583 the target pathway. This package automatically downloads the pathway graph
15584 data, parses the data file, maps user data to the pathway, and render pathway
15585 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
15586 integrates with pathway and gene set (enrichment) analysis tools for
15587 large-scale and fully automated analysis.")
15588 (license license:gpl3+)))
15590 (define-public r-snpstats
15592 (name "r-snpstats")
15597 (uri (bioconductor-uri "snpStats" version))
15600 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
15601 (properties `((upstream-name . "snpStats")))
15602 (build-system r-build-system)
15603 (inputs (list zlib))
15605 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
15606 (home-page "https://bioconductor.org/packages/snpStats")
15607 (synopsis "Methods for SNP association studies")
15609 "This package provides classes and statistical methods for large
15610 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
15611 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
15612 (license license:gpl3)))
15614 (define-public r-chromstar
15616 (name "r-chromstar")
15621 (uri (bioconductor-uri "chromstaR" version))
15624 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
15625 (properties `((upstream-name . "chromstaR")))
15626 (build-system r-build-system)
15634 r-genomicalignments
15642 (native-inputs (list r-knitr))
15643 (home-page "https://github.com/ataudt/chromstaR")
15644 (synopsis "Chromatin state analysis for ChIP-Seq data")
15646 "This package implements functions for combinatorial and differential
15647 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
15648 export to genome browser viewable files, and functions for enrichment
15650 (license license:artistic2.0)))
15652 (define-public r-guitar
15659 (uri (bioconductor-uri "Guitar" version))
15662 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
15663 (properties `((upstream-name . "Guitar")))
15664 (build-system r-build-system)
15666 (list r-annotationdbi
15676 (home-page "https://bioconductor.org/packages/Guitar")
15677 (synopsis "Visualize genomic features")
15679 "This package is designed for visualization of RNA-related genomic
15680 features with respect to the landmarks of RNA transcripts, i.e., transcription
15681 starting site, start codon, stop codon and transcription ending site.")
15682 (license license:gpl2)))
15684 (define-public r-sushi
15690 (uri (bioconductor-uri "Sushi" version))
15693 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
15694 (properties `((upstream-name . "Sushi")))
15695 (build-system r-build-system)
15697 (list r-biomart r-zoo))
15698 (home-page "https://bioconductor.org/packages/Sushi")
15699 (synopsis "Tools for visualizing genomics data")
15701 "This package provides flexible, quantitative, and integrative genomic
15702 visualizations for publication-quality multi-panel figures.")
15703 (license license:gpl2+)))
15705 (define-public r-ballgown
15707 (name "r-ballgown")
15712 (uri (bioconductor-uri "ballgown" version))
15715 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
15716 (properties `((upstream-name . "ballgown")))
15717 (build-system r-build-system)
15730 (home-page "https://bioconductor.org/packages/ballgown")
15731 (synopsis "Flexible, isoform-level differential expression analysis")
15733 "This package provides tools for statistical analysis of assembled
15734 transcriptomes, including flexible differential expression analysis,
15735 visualization of transcript structures, and matching of assembled transcripts
15737 (license license:artistic2.0)))
15739 (define-public r-megadepth
15741 (name "r-megadepth")
15746 (uri (bioconductor-uri "megadepth" version))
15749 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
15750 (properties `((upstream-name . "megadepth")))
15751 (build-system r-build-system)
15752 (inputs (list megadepth))
15763 (home-page "https://github.com/LieberInstitute/megadepth")
15764 (synopsis "BigWig and BAM related utilities")
15766 "This package provides an R interface to Megadepth. It is particularly
15767 useful for computing the coverage of a set of genomic regions across bigWig or
15768 BAM files. With this package, you can build base-pair coverage matrices for
15769 regions or annotations of your choice from BigWig files.")
15770 (license license:artistic2.0)))
15772 (define-public r-beclear
15779 (uri (bioconductor-uri "BEclear" version))
15782 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
15783 (properties `((upstream-name . "BEclear")))
15784 (build-system r-build-system)
15796 (home-page "https://github.com/uds-helms/BEclear")
15797 (synopsis "Correction of batch effects in DNA methylation data")
15799 "This package provides functions to detect and correct for batch effects
15800 in DNA methylation data. The core function is based on latent factor models
15801 and can also be used to predict missing values in any other matrix containing
15803 (license license:gpl3)))
15805 (define-public r-bgeecall
15807 (name "r-bgeecall")
15812 (uri (bioconductor-uri "BgeeCall" version))
15815 "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"))))
15816 (properties `((upstream-name . "BgeeCall")))
15817 (build-system r-build-system)
15831 (native-inputs (list r-knitr))
15832 (home-page "https://github.com/BgeeDB/BgeeCall")
15833 (synopsis "RNA-Seq present/absent gene expression calls generation")
15835 "BgeeCall allows generating present/absent gene expression calls without
15836 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
15837 intergenic sequences. These sequences are generated based on expression of
15838 all RNA-Seq libraries of each species integrated in Bgee.")
15839 (license license:gpl3)))
15841 (define-public r-bgeedb
15848 (uri (bioconductor-uri "BgeeDB" version))
15851 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
15852 (properties `((upstream-name . "BgeeDB")))
15853 (build-system r-build-system)
15866 (native-inputs (list r-knitr))
15867 (home-page "https://github.com/BgeeDB/BgeeDB_R")
15868 (synopsis "Annotation and gene expression data retrieval from Bgee database")
15870 "This package provides a package for the annotation and gene expression
15871 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
15872 anatomical terms, mapped to genes by expression patterns.")
15873 (license license:gpl3)))
15875 (define-public r-biobtreer
15877 (name "r-biobtreer")
15882 (uri (bioconductor-uri "biobtreeR" version))
15885 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
15886 (properties `((upstream-name . "biobtreeR")))
15887 (build-system r-build-system)
15889 (list r-httpuv r-httr r-jsonlite r-stringi))
15890 (native-inputs (list r-knitr))
15891 (home-page "https://github.com/tamerh/biobtreeR")
15892 (synopsis "Use biobtree tool from R")
15894 "The biobtreeR package provides an interface to biobtree, a tool which
15895 covers large sets of bioinformatics datasets and allows search and chain
15896 mappings functionalities.")
15897 (license license:expat)))
15899 (define-public r-minet
15906 (uri (bioconductor-uri "minet" version))
15909 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
15910 (properties `((upstream-name . "minet")))
15911 (build-system r-build-system)
15914 (home-page "http://minet.meyerp.com")
15915 (synopsis "Mutual information networks")
15917 "This package implements various algorithms for inferring mutual
15918 information networks from data.")
15919 (license license:artistic2.0)))
15921 (define-public r-genetclassifier
15923 (name "r-genetclassifier")
15928 (uri (bioconductor-uri "geNetClassifier" version))
15931 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
15933 `((upstream-name . "geNetClassifier")))
15934 (build-system r-build-system)
15936 (list r-biobase r-e1071 r-ebarrays r-minet))
15937 (home-page "https://www.cicancer.org")
15938 (synopsis "Classify diseases and build gene networks using expression profiles")
15940 "This is a comprehensive package to automatically train and validate a
15941 multi-class SVM classifier based on gene expression data. It provides
15942 transparent selection of gene markers, their coexpression networks, and an
15943 interface to query the classifier.")
15944 (license license:gpl2+)))
15946 (define-public r-dir-expiry
15948 (name "r-dir-expiry")
15953 (uri (bioconductor-uri "dir.expiry" version))
15956 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
15957 (properties `((upstream-name . "dir.expiry")))
15958 (build-system r-build-system)
15959 (propagated-inputs (list r-filelock))
15960 (native-inputs (list r-knitr))
15961 (home-page "https://bioconductor.org/packages/dir.expiry")
15962 (synopsis "Managing expiration for cache directories")
15964 "This package implements an expiration system for access to versioned
15965 directories. Directories that have not been accessed by a registered function
15966 within a certain time frame are deleted. This aims to reduce disk usage by
15967 eliminating obsolete caches generated by old versions of packages.")
15968 (license license:gpl3)))
15970 (define-public r-basilisk-utils
15972 (name "r-basilisk-utils")
15977 (uri (bioconductor-uri "basilisk.utils" version))
15980 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
15982 `((upstream-name . "basilisk.utils")))
15983 (build-system r-build-system)
15985 (list r-dir-expiry))
15986 (native-inputs (list r-knitr))
15987 (home-page "https://bioconductor.org/packages/basilisk.utils")
15988 (synopsis "Basilisk installation utilities")
15990 "This package implements utilities for installation of the basilisk
15991 package, primarily for creation of the underlying Conda instance.")
15992 (license license:gpl3)))
15994 (define-public r-basilisk
15996 (name "r-basilisk")
16001 (uri (bioconductor-uri "basilisk" version))
16004 "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"))))
16005 (properties `((upstream-name . "basilisk")))
16006 (build-system r-build-system)
16008 (list r-basilisk-utils r-dir-expiry r-reticulate))
16009 (native-inputs (list r-knitr))
16010 (home-page "https://bioconductor.org/packages/basilisk")
16011 (synopsis "Freeze Python dependencies inside Bioconductor packages")
16013 "This package installs a self-contained Conda instance that is managed by
16014 the R/Bioconductor installation machinery. This aims to provide a consistent
16015 Python environment that can be used reliably by Bioconductor packages.
16016 Functions are also provided to enable smooth interoperability of multiple
16017 Python environments in a single R session.")
16018 (license license:gpl3)))
16020 (define-public r-biocthis
16022 (name "r-biocthis")
16027 (uri (bioconductor-uri "biocthis" version))
16030 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
16031 (properties `((upstream-name . "biocthis")))
16032 (build-system r-build-system)
16035 (modify-phases %standard-phases
16036 (add-after 'unpack 'set-HOME
16037 (lambda _ (setenv "HOME" "/tmp"))))))
16039 (list r-biocmanager
16045 (native-inputs (list r-knitr))
16046 (home-page "https://github.com/lcolladotor/biocthis")
16047 (synopsis "Automate package and project setup for Bioconductor packages")
16049 "This package expands the @code{usethis} package with the goal of helping
16050 automate the process of creating R packages for Bioconductor or making them
16051 Bioconductor-friendly.")
16052 (license license:artistic2.0)))
16054 (define-public r-biocdockermanager
16056 (name "r-biocdockermanager")
16061 (uri (bioconductor-uri "BiocDockerManager" version))
16064 "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"))))
16066 `((upstream-name . "BiocDockerManager")))
16067 (build-system r-build-system)
16075 (native-inputs (list r-knitr))
16076 (home-page "https://bioconductor.org/packages/BiocDockerManager")
16077 (synopsis "Access and manage Bioconductor Docker images")
16079 "This package works analogous to BiocManager but for Docker images. Use
16080 the BiocDockerManager package to install and manage Docker images provided by
16081 the Bioconductor project.")
16082 (license license:artistic2.0)))
16084 (define-public r-biodb
16091 (uri (bioconductor-uri "biodb" version))
16094 "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"))))
16095 (properties `((upstream-name . "biodb")))
16096 (build-system r-build-system)
16098 (list r-biocfilecache
16116 (native-inputs (list r-knitr))
16117 (home-page "https://bioconductor.org/packages/biodb")
16118 (synopsis "Library for connecting to chemical and biological databases")
16120 "The biodb package provides access to standard remote chemical and
16121 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
16122 database files (CSV, SQLite), with easy retrieval of entries, access to web
16123 services, search of compounds by mass and/or name, and mass spectra matching
16124 for LCMS and MSMS. Its architecture as a development framework facilitates
16125 the development of new database connectors for local projects or inside
16126 separate published packages.")
16127 (license license:agpl3+)))
16129 (define-public r-biomformat
16131 (name "r-biomformat")
16136 (uri (bioconductor-uri "biomformat" version))
16139 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
16140 (properties `((upstream-name . "biomformat")))
16141 (build-system r-build-system)
16143 (list r-jsonlite r-matrix r-plyr r-rhdf5))
16144 (native-inputs (list r-knitr))
16145 (home-page "https://github.com/joey711/biomformat/")
16146 (synopsis "Interface package for the BIOM file format")
16148 "This is an R package for interfacing with the BIOM format. This package
16149 includes basic tools for reading biom-format files, accessing and subsetting
16150 data tables from a biom object (which is more complex than a single table), as
16151 well as limited support for writing a biom-object back to a biom-format file.
16152 The design of this API is intended to match the Python API and other tools
16153 included with the biom-format project, but with a decidedly \"R flavor\" that
16154 should be familiar to R users. This includes S4 classes and methods, as well
16155 as extensions of common core functions/methods.")
16156 (license license:gpl2)))
16158 (define-public r-mvcclass
16160 (name "r-mvcclass")
16165 (uri (bioconductor-uri "MVCClass" version))
16168 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
16169 (properties `((upstream-name . "MVCClass")))
16170 (build-system r-build-system)
16171 (home-page "https://bioconductor.org/packages/MVCClass")
16172 (synopsis "Model-View-Controller (MVC) classes")
16174 "This package contains classes used in model-view-controller (MVC)
16176 (license license:lgpl2.1+)))
16178 (define-public r-biomvcclass
16180 (name "r-biomvcclass")
16185 (uri (bioconductor-uri "BioMVCClass" version))
16188 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
16189 (properties `((upstream-name . "BioMVCClass")))
16190 (build-system r-build-system)
16192 (list r-biobase r-graph r-mvcclass r-rgraphviz))
16193 (home-page "https://bioconductor.org/packages/BioMVCClass")
16194 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
16196 "This package contains classes used in model-view-controller (MVC)
16198 (license license:lgpl2.1+)))
16200 (define-public r-biomvrcns
16202 (name "r-biomvrcns")
16207 (uri (bioconductor-uri "biomvRCNS" version))
16210 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
16211 (properties `((upstream-name . "biomvRCNS")))
16212 (build-system r-build-system)
16214 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
16215 (home-page "https://bioconductor.org/packages/biomvRCNS")
16216 (synopsis "Copy number study and segmentation for multivariate biological data")
16218 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
16219 homogeneous segmentation model are designed and implemented for segmentation
16220 genomic data, with the aim of assisting in transcripts detection using high
16221 throughput technology like RNA-seq or tiling array, and copy number analysis
16222 using aCGH or sequencing.")
16223 (license license:gpl2+)))
16225 (define-public r-bionero
16232 (uri (bioconductor-uri "BioNERO" version))
16235 "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"))))
16236 (properties `((upstream-name . "BioNERO")))
16237 (build-system r-build-system)
16239 (list r-biocparallel
16256 r-summarizedexperiment
16261 (home-page "https://github.com/almeidasilvaf/BioNERO")
16262 (synopsis "Biological network reconstruction omnibus")
16264 "BioNERO aims to integrate all aspects of biological network inference in
16265 a single package, including data preprocessing, exploratory analyses, network
16266 inference, and analyses for biological interpretations. BioNERO can be used
16267 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
16268 from gene expression data. Additionally, it can be used to explore
16269 topological properties of protein-protein interaction (PPI) networks. GCN
16270 inference relies on the popular WGCNA algorithm. GRN inference is based on
16271 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
16272 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
16273 rank for each interaction pair. As all steps of network analyses are included
16274 in this package, BioNERO makes users avoid having to learn the syntaxes of
16275 several packages and how to communicate between them. Finally, users can also
16276 identify consensus modules across independent expression sets and calculate
16277 intra and interspecies module preservation statistics between different
16279 (license license:gpl3)))
16281 (define-public r-bionet
16288 (uri (bioconductor-uri "BioNet" version))
16291 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
16292 (properties `((upstream-name . "BioNet")))
16293 (build-system r-build-system)
16295 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
16296 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
16297 (synopsis "Functional analysis of biological networks")
16299 "This package provides functions for the integrated analysis of
16300 protein-protein interaction networks and the detection of functional modules.
16301 Different datasets can be integrated into the network by assigning p-values of
16302 statistical tests to the nodes of the network. E.g. p-values obtained from
16303 the differential expression of the genes from an Affymetrix array are assigned
16304 to the nodes of the network. By fitting a beta-uniform mixture model and
16305 calculating scores from the p-values, overall scores of network regions can be
16306 calculated and an integer linear programming algorithm identifies the maximum
16307 scoring subnetwork.")
16308 (license license:gpl2+)))
16310 (define-public r-bionetstat
16312 (name "r-bionetstat")
16317 (uri (bioconductor-uri "BioNetStat" version))
16320 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
16321 (properties `((upstream-name . "BioNetStat")))
16322 (build-system r-build-system)
16324 (list r-biocparallel
16344 (home-page "https://github.com/jardimViniciusC/BioNetStat")
16345 (synopsis "Biological network analysis")
16347 "This package provides a package to perform differential network
16348 analysis, differential node analysis (differential coexpression analysis),
16349 network and metabolic pathways view.")
16350 (license license:gpl3+)))
16352 (define-public r-bioqc
16359 (uri (bioconductor-uri "BioQC" version))
16362 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
16363 (properties `((upstream-name . "BioQC")))
16364 (build-system r-build-system)
16366 (list r-biobase r-edger r-rcpp))
16369 (home-page "https://accio.github.io/BioQC/")
16370 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
16372 "BioQC performs quality control of high-throughput expression data based
16373 on tissue gene signatures. It can detect tissue heterogeneity in gene
16374 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
16375 optimised for high performance.")
16376 (license license:gpl3+)))
16378 (define-public r-biotip
16385 (uri (bioconductor-uri "BioTIP" version))
16388 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
16389 (properties `((upstream-name . "BioTIP")))
16390 (build-system r-build-system)
16401 (home-page "https://github.com/xyang2uchicago/BioTIP")
16402 (synopsis "R package for characterization of biological tipping-point")
16404 "This package adopts tipping-point theory to transcriptome profiles to
16405 help unravel disease regulatory trajectory.")
16406 (license license:gpl2)))
16408 (define-public r-biotmle
16415 (uri (bioconductor-uri "biotmle" version))
16418 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
16419 (properties `((upstream-name . "biotmle")))
16420 (build-system r-build-system)
16431 r-summarizedexperiment
16436 (home-page "https://code.nimahejazi.org/biotmle/")
16437 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
16439 "This package provides tools for differential expression biomarker
16440 discovery based on microarray and next-generation sequencing data that
16441 leverage efficient semiparametric estimators of the average treatment effect
16442 for variable importance analysis. Estimation and inference of the (marginal)
16443 average treatment effects of potential biomarkers are computed by targeted
16444 minimum loss-based estimation, with joint, stable inference constructed across
16445 all biomarkers using a generalization of moderated statistics for use with the
16446 estimated efficient influence function. The procedure accommodates the use of
16447 ensemble machine learning for the estimation of nuisance functions.")
16448 (license license:expat)))
16450 (define-public r-bsseq
16457 (uri (bioconductor-uri "bsseq" version))
16460 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
16461 (properties `((upstream-name . "bsseq")))
16462 (build-system r-build-system)
16472 r-delayedmatrixstats
16486 r-summarizedexperiment))
16489 (home-page "https://github.com/hansenlab/bsseq")
16490 (synopsis "Analyze, manage and store bisulfite sequencing data")
16492 "This package provides a collection of tools for analyzing and
16493 visualizing bisulfite sequencing data.")
16494 (license license:artistic2.0)))
16496 (define-public r-dmrseq
16503 (uri (bioconductor-uri "dmrseq" version))
16506 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
16507 (properties `((upstream-name . "dmrseq")))
16508 (build-system r-build-system)
16510 (list r-annotationhub
16515 r-delayedmatrixstats
16529 (home-page "https://bioconductor.org/packages/dmrseq")
16530 (synopsis "Detection and inference of differentially methylated regions")
16532 "This package implements an approach for scanning the genome to detect
16533 and perform accurate inference on differentially methylated regions from Whole
16534 Genome Bisulfite Sequencing data. The method is based on comparing detected
16535 regions to a pooled null distribution, that can be implemented even when as
16536 few as two samples per population are available. Region-level statistics are
16537 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
16538 with a nested autoregressive correlated error structure for the effect of
16539 interest on transformed methylation proportions.")
16540 (license license:expat)))
16542 (define-public r-omnipathr
16544 (name "r-omnipathr")
16549 (uri (bioconductor-uri "OmnipathR" version))
16551 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
16552 (properties `((upstream-name . "OmnipathR")))
16553 (build-system r-build-system)
16556 (modify-phases %standard-phases
16557 (add-after 'unpack 'set-HOME
16558 (lambda _ (setenv "HOME" "/tmp"))))))
16584 (native-inputs (list r-knitr))
16585 (home-page "https://saezlab.github.io/OmnipathR/")
16586 (synopsis "OmniPath web service client and more")
16588 "This package provides a client for the OmniPath web service and many
16589 other resources. It also includes functions to transform and pretty print
16590 some of the downloaded data, functions to access a number of other resources.
16591 Furthermore, OmnipathR features a close integration with the NicheNet method
16592 for ligand activity prediction from transcriptomics data.")
16593 (license license:expat)))
16595 (define-public r-biscuiteer
16597 (name "r-biscuiteer")
16602 (uri (bioconductor-uri "biscuiteer" version))
16605 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
16606 (properties `((upstream-name . "biscuiteer")))
16607 (build-system r-build-system)
16615 r-delayedmatrixstats
16634 r-summarizedexperiment
16635 r-variantannotation))
16638 (home-page "https://github.com/trichelab/biscuiteer")
16639 (synopsis "Convenience functions for the Biscuit package")
16641 "This package provides a test harness for bsseq loading of Biscuit
16642 output, summarization of WGBS data over defined regions and in mappable
16643 samples, with or without imputation, dropping of mostly-NA rows, age
16645 (license license:gpl3)))
16647 (define-public r-tcgabiolinks
16649 (name "r-tcgabiolinks")
16654 (uri (bioconductor-uri "TCGAbiolinks" version))
16656 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
16657 (properties `((upstream-name . "TCGAbiolinks")))
16658 (build-system r-build-system)
16677 r-summarizedexperiment
16678 r-tcgabiolinksgui-data
16683 (native-inputs (list r-knitr))
16684 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
16685 (synopsis "Integrative analysis with GDC data")
16687 "The aim of TCGAbiolinks is:
16690 @item facilitate GDC open-access data retrieval;
16691 @item prepare the data using the appropriate pre-processing strategies;
16692 @item provide the means to carry out different standard analyses, and;
16693 @item to easily reproduce earlier research results.
16696 In more detail, the package provides multiple methods for analysis (e.g.,
16697 differential expression analysis, identifying differentially methylated
16698 regions) and methods for visualization (e.g., survival plots, volcano plots,
16699 starburst plots) in order to easily develop complete analysis pipelines.")
16700 (license license:gpl3+)))
16702 (define-public r-tricycle
16704 (name "r-tricycle")
16708 (uri (bioconductor-uri "tricycle" version))
16711 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
16712 (properties `((upstream-name . "tricycle")))
16713 (build-system r-build-system)
16715 (list r-annotationdbi
16726 r-singlecellexperiment
16727 r-summarizedexperiment))
16728 (native-inputs (list r-knitr))
16729 (home-page "https://github.com/hansenlab/tricycle")
16730 (synopsis "Transferable representation and inference of cell cycle")
16732 "The package contains functions to infer and visualize cell cycle process
16733 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
16734 projecting new data to the previous learned biologically interpretable space.
16735 The @code{tricycle} provides a pre-learned cell cycle space, which could be
16736 used to infer cell cycle time of human and mouse single cell samples. In
16737 addition, it also offer functions to visualize cell cycle time on different
16738 embeddings and functions to build new reference.")
16739 (license license:gpl3)))
16741 (define-public r-tximeta
16748 (uri (bioconductor-uri "tximeta" version))
16751 "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl"))))
16752 (properties `((upstream-name . "tximeta")))
16753 (build-system r-build-system)
16755 (list r-annotationdbi
16767 r-summarizedexperiment
16772 (home-page "https://github.com/mikelove/tximeta")
16773 (synopsis "Transcript quantification import with automatic metadata")
16775 "This package implements transcript quantification import from Salmon and
16776 alevin with automatic attachment of transcript ranges and release information,
16777 and other associated metadata. De novo transcriptomes can be linked to the
16778 appropriate sources with linkedTxomes and shared for computational
16780 (license license:gpl2)))
16782 (define-public r-phyloseq
16784 (name "r-phyloseq")
16789 (uri (bioconductor-uri "phyloseq" version))
16791 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
16792 (properties `((upstream-name . "phyloseq")))
16793 (build-system r-build-system)
16813 (home-page "https://github.com/joey711/phyloseq")
16814 (synopsis "Handling and analysis of high-throughput microbiome census data")
16816 "Phyloseq provides a set of classes and tools to facilitate the import,
16817 storage, analysis, and graphical display of microbiome census data.")
16818 (license license:agpl3)))
HCoop / jackhill / guix / guix.git / blob