1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
11 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
12 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
13 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
14 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
16 ;;; This file is part of GNU Guix.
18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
19 ;;; under the terms of the GNU General Public License as published by
20 ;;; the Free Software Foundation; either version 3 of the License, or (at
21 ;;; your option) any later version.
23 ;;; GNU Guix is distributed in the hope that it will be useful, but
24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 ;;; GNU General Public License for more details.
28 ;;; You should have received a copy of the GNU General Public License
29 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
31 (define-module (gnu packages bioconductor)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix download)
35 #:use-module (guix git-download)
36 #:use-module (guix build-system r)
37 #:use-module (gnu packages)
38 #:use-module (gnu packages autotools)
39 #:use-module (gnu packages base)
40 #:use-module (gnu packages bioinformatics)
41 #:use-module (gnu packages boost)
42 #:use-module (gnu packages cran)
43 #:use-module (gnu packages compression)
44 #:use-module (gnu packages curl)
45 #:use-module (gnu packages docker)
46 #:use-module (gnu packages gcc)
47 #:use-module (gnu packages graph)
48 #:use-module (gnu packages graphviz)
49 #:use-module (gnu packages haskell-xyz)
50 #:use-module (gnu packages image)
51 #:use-module (gnu packages maths)
52 #:use-module (gnu packages netpbm)
53 #:use-module (gnu packages python)
54 #:use-module (gnu packages perl)
55 #:use-module (gnu packages pkg-config)
56 #:use-module (gnu packages statistics)
57 #:use-module (gnu packages web)
58 #:use-module (gnu packages xml)
59 #:use-module (srfi srfi-1))
64 (define-public r-org-eck12-eg-db
66 (name "r-org-eck12-eg-db")
71 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
73 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
75 `((upstream-name . "org.EcK12.eg.db")))
76 (build-system r-build-system)
78 (list r-annotationdbi))
79 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
80 (synopsis "Genome wide annotation for E coli strain K12")
82 "This package provides genome wide annotation for E coli strain K12,
83 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
84 National Center for Biotechnology Information (NCBI)’s database for
85 gene-specific information. Entrez Gene maintains records from genomes which
86 have been completely sequenced, which have an active research community to
87 submit gene-specific information, or which are scheduled for intense sequence
89 (license license:artistic2.0)))
91 (define-public r-org-bt-eg-db
93 (name "r-org-bt-eg-db")
98 (uri (bioconductor-uri
104 "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi"))))
105 (properties `((upstream-name . "org.Bt.eg.db")))
106 (build-system r-build-system)
108 (list r-annotationdbi))
109 (home-page "https://bioconductor.org/packages/org.Bt.eg.db")
110 (synopsis "Genome wide annotation for Bovine")
112 "This package provides genome wide annotations for Bovine, primarily
113 based on mapping using Entrez Gene identifiers.")
114 (license license:artistic2.0)))
116 (define-public r-reactome-db
118 (name "r-reactome-db")
123 (uri (bioconductor-uri "reactome.db" version 'annotation))
126 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
127 (properties `((upstream-name . "reactome.db")))
128 (build-system r-build-system)
130 (list r-annotationdbi))
131 (home-page "https://bioconductor.org/packages/reactome.db/")
132 (synopsis "Annotation maps for reactome")
134 "This package provides a set of annotation maps for the REACTOME
135 database, assembled using data from REACTOME.")
136 (license license:cc-by4.0)))
138 (define-public r-bsgenome-btaurus-ucsc-bostau8
140 (name "r-bsgenome-btaurus-ucsc-bostau8")
144 (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
145 version 'annotation))
148 "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
150 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
151 (build-system r-build-system)
155 "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
156 (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
157 (description "This package provides the full genome sequences for Bos
158 taurus (UCSC version bosTau8).")
159 (license license:artistic2.0)))
161 (define-public r-bsgenome-celegans-ucsc-ce6
163 (name "r-bsgenome-celegans-ucsc-ce6")
167 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
168 version 'annotation))
171 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
173 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
174 (build-system r-build-system)
178 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
179 (synopsis "Full genome sequences for Worm")
181 "This package provides full genome sequences for Caenorhabditis
182 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
184 (license license:artistic2.0)))
186 (define-public r-bsgenome-celegans-ucsc-ce10
188 (name "r-bsgenome-celegans-ucsc-ce10")
192 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
193 version 'annotation))
196 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
198 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
199 (build-system r-build-system)
203 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
204 (synopsis "Full genome sequences for Worm")
206 "This package provides full genome sequences for Caenorhabditis
207 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
209 (license license:artistic2.0)))
211 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
213 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
217 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
218 version 'annotation))
221 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
223 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
224 (build-system r-build-system)
228 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
229 (synopsis "Full genome sequences for Fly")
231 "This package provides full genome sequences for Drosophila
232 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
234 (license license:artistic2.0)))
236 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
238 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
242 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
243 version 'annotation))
246 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
248 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
249 (build-system r-build-system)
253 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
254 (synopsis "Full genome sequences for Fly")
256 "This package provides full genome sequences for Drosophila
257 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
258 Biostrings objects.")
259 (license license:artistic2.0)))
261 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
263 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
267 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
268 version 'annotation))
271 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
273 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
274 (build-system r-build-system)
276 (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
277 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
278 (synopsis "Full masked genome sequences for Fly")
280 "This package provides full masked genome sequences for Drosophila
281 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
282 Biostrings objects. The sequences are the same as in
283 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
284 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
285 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
286 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
287 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
288 (license license:artistic2.0)))
290 (define-public r-bsgenome-drerio-ucsc-danrer11
292 (name "r-bsgenome-drerio-ucsc-danrer11")
297 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
298 version 'annotation))
300 (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
301 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
302 (build-system r-build-system)
305 (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
306 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
308 "This package provides full genome sequences for Danio rerio (Zebrafish)
309 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
310 (license license:artistic2.0)))
312 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
314 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
318 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
319 version 'annotation))
322 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
324 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
325 (build-system r-build-system)
329 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
330 (synopsis "Full genome sequences for Homo sapiens")
332 "This package provides full genome sequences for Homo sapiens from
333 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
334 (license license:artistic2.0)))
336 (define-public r-bsgenome-hsapiens-ncbi-grch38
338 (name "r-bsgenome-hsapiens-ncbi-grch38")
343 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
344 version 'annotation))
347 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
348 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
349 (build-system r-build-system)
350 (propagated-inputs (list r-bsgenome))
352 "https://bioconductor.org/packages/release/data/annotation/html/\
353 BSgenome.Hsapiens.NCBI.GRCh38.html")
354 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
356 "This package provides full genome sequences for Homo sapiens (Human) as
357 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
358 (license license:artistic2.0)))
360 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
362 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
367 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
368 version 'annotation))
370 (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
372 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
373 (build-system r-build-system)
375 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
376 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
377 (synopsis "Full masked genome sequences for Homo sapiens")
379 "This package provides full genome sequences for Homo sapiens (Human) as
380 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
381 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
382 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
383 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
384 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
385 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
387 (license license:artistic2.0)))
389 (define-public r-bsgenome-mmusculus-ucsc-mm9
391 (name "r-bsgenome-mmusculus-ucsc-mm9")
395 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
396 version 'annotation))
399 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
401 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
402 (build-system r-build-system)
406 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
407 (synopsis "Full genome sequences for Mouse")
409 "This package provides full genome sequences for Mus musculus (Mouse) as
410 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
411 (license license:artistic2.0)))
413 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
415 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
419 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
420 version 'annotation))
423 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
425 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
426 (build-system r-build-system)
428 (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
429 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
430 (synopsis "Full masked genome sequences for Mouse")
432 "This package provides full genome sequences for Mus musculus (Mouse) as
433 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
434 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
435 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
436 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
437 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
438 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
440 (license license:artistic2.0)))
442 (define-public r-bsgenome-mmusculus-ucsc-mm10
444 (name "r-bsgenome-mmusculus-ucsc-mm10")
448 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
449 version 'annotation))
452 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
454 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
455 (build-system r-build-system)
459 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
460 (synopsis "Full genome sequences for Mouse")
462 "This package provides full genome sequences for Mus
463 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
464 in Biostrings objects.")
465 (license license:artistic2.0)))
467 (define-public r-genomeinfodbdata
469 (name "r-genomeinfodbdata")
473 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
476 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
478 `((upstream-name . "GenomeInfoDbData")))
479 (build-system r-build-system)
480 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
481 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
482 (description "This package contains data for mapping between NCBI taxonomy
483 ID and species. It is used by functions in the GenomeInfoDb package.")
484 (license license:artistic2.0)))
486 (define-public r-go-db
492 (uri (bioconductor-uri "GO.db" version 'annotation))
495 "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
497 `((upstream-name . "GO.db")))
498 (build-system r-build-system)
500 (list r-annotationdbi))
501 (home-page "https://bioconductor.org/packages/GO.db")
502 (synopsis "Annotation maps describing the entire Gene Ontology")
504 "The purpose of this GO.db annotation package is to provide detailed
505 information about the latest version of the Gene Ontologies.")
506 (license license:artistic2.0)))
508 (define-public r-homo-sapiens
510 (name "r-homo-sapiens")
514 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
517 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
519 `((upstream-name . "Homo.sapiens")))
520 (build-system r-build-system)
522 (list r-genomicfeatures
525 r-txdb-hsapiens-ucsc-hg19-knowngene
528 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
529 (synopsis "Annotation package for the Homo.sapiens object")
531 "This package contains the Homo.sapiens object to access data from
532 several related annotation packages.")
533 (license license:artistic2.0)))
535 (define-public r-mus-musculus
537 (name "r-mus-musculus")
542 (uri (bioconductor-uri "Mus.musculus" version 'annotation))
545 "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"))))
546 (properties `((upstream-name . "Mus.musculus")))
547 (build-system r-build-system)
549 (list r-annotationdbi
554 r-txdb-mmusculus-ucsc-mm10-knowngene))
555 (home-page "https://bioconductor.org/packages/Mus.musculus")
556 (synopsis "Annotation package for the Mus.musculus object")
558 "This package contains the @code{Mus.musculus} object to access data
559 from several related annotation packages.")
560 (license license:artistic2.0)))
562 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
564 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
569 (uri (bioconductor-uri
570 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
571 version 'annotation))
574 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
577 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
578 (build-system r-build-system)
579 (propagated-inputs (list r-minfi))
581 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
582 (synopsis "Annotation for Illumina's 450k methylation arrays")
584 "This package provides manifests and annotation for Illumina's 450k array
586 (license license:artistic2.0)))
588 (define-public r-org-ce-eg-db
590 (name "r-org-ce-eg-db")
594 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
597 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
599 `((upstream-name . "org.Ce.eg.db")))
600 (build-system r-build-system)
602 (list r-annotationdbi))
603 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
604 (synopsis "Genome wide annotation for Worm")
606 "This package provides mappings from Entrez gene identifiers to various
607 annotations for the genome of the model worm Caenorhabditis elegans.")
608 (license license:artistic2.0)))
610 (define-public r-org-dm-eg-db
612 (name "r-org-dm-eg-db")
616 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
619 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
621 `((upstream-name . "org.Dm.eg.db")))
622 (build-system r-build-system)
624 (list r-annotationdbi))
625 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
626 (synopsis "Genome wide annotation for Fly")
628 "This package provides mappings from Entrez gene identifiers to various
629 annotations for the genome of the model fruit fly Drosophila melanogaster.")
630 (license license:artistic2.0)))
632 (define-public r-org-dr-eg-db
634 (name "r-org-dr-eg-db")
638 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
641 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
643 `((upstream-name . "org.Dr.eg.db")))
644 (build-system r-build-system)
646 (list r-annotationdbi))
647 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
648 (synopsis "Annotation for Zebrafish")
650 "This package provides genome wide annotations for Zebrafish, primarily
651 based on mapping using Entrez Gene identifiers.")
652 (license license:artistic2.0)))
654 (define-public r-org-hs-eg-db
656 (name "r-org-hs-eg-db")
660 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
663 "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
665 `((upstream-name . "org.Hs.eg.db")))
666 (build-system r-build-system)
668 (list r-annotationdbi))
669 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
670 (synopsis "Genome wide annotation for Human")
672 "This package contains genome-wide annotations for Human, primarily based
673 on mapping using Entrez Gene identifiers.")
674 (license license:artistic2.0)))
676 (define-public r-org-mm-eg-db
678 (name "r-org-mm-eg-db")
682 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
685 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
687 `((upstream-name . "org.Mm.eg.db")))
688 (build-system r-build-system)
690 (list r-annotationdbi))
691 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
692 (synopsis "Genome wide annotation for Mouse")
694 "This package provides mappings from Entrez gene identifiers to various
695 annotations for the genome of the model mouse Mus musculus.")
696 (license license:artistic2.0)))
698 (define-public r-bsgenome-hsapiens-ucsc-hg19
700 (name "r-bsgenome-hsapiens-ucsc-hg19")
704 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
705 version 'annotation))
708 "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
710 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
711 (build-system r-build-system)
715 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
716 (synopsis "Full genome sequences for Homo sapiens")
718 "This package provides full genome sequences for Homo sapiens as provided
719 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
720 (license license:artistic2.0)))
722 (define-public r-bsgenome-hsapiens-ucsc-hg38
724 (name "r-bsgenome-hsapiens-ucsc-hg38")
728 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
729 version 'annotation))
731 (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"))))
733 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
734 (build-system r-build-system)
738 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
739 (synopsis "Full genome sequences for Homo sapiens")
741 "This package provides full genome sequences for Homo sapiens (Human)
742 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
743 (license license:artistic2.0)))
745 (define-public r-ensdb-hsapiens-v75
747 (name "r-ensdb-hsapiens-v75")
752 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
755 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
757 `((upstream-name . "EnsDb.Hsapiens.v75")))
758 (build-system r-build-system)
761 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
762 (synopsis "Ensembl based annotation package")
764 "This package exposes an annotation database generated from Ensembl.")
765 (license license:artistic2.0)))
767 (define-public r-ensdb-hsapiens-v86
769 (name "r-ensdb-hsapiens-v86")
774 (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation))
776 (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"))))
777 (properties `((upstream-name . "EnsDb.Hsapiens.v86")))
778 (build-system r-build-system)
779 (propagated-inputs (list r-ensembldb))
780 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86")
781 (synopsis "Ensembl based annotation package")
782 (description "This package exposes an annotation database generated from
784 (license license:artistic2.0)))
786 (define-public r-ensdb-mmusculus-v79
788 (name "r-ensdb-mmusculus-v79")
793 (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation))
795 (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7"))))
796 (properties `((upstream-name . "EnsDb.Mmusculus.v79")))
797 (build-system r-build-system)
798 (propagated-inputs (list r-ensembldb))
799 (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79")
800 (synopsis "Ensembl based annotation package")
801 (description "This package exposes an annotation database generated from
803 (license license:artistic2.0)))
805 (define-public r-snplocs-hsapiens-dbsnp144-grch37
807 (name "r-snplocs-hsapiens-dbsnp144-grch37")
811 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
812 version 'annotation))
815 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
816 (build-system r-build-system)
817 ;; As this package provides little more than a very large data file it
818 ;; doesn't make sense to build substitutes.
819 (arguments `(#:substitutable? #f))
829 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
830 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
831 (description "This package provides SNP locations and alleles for Homo
832 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
833 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
834 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
835 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
836 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
837 the mitochondrion chromosome. Therefore, the SNPs in this package can be
838 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
839 correct position but this injection will exclude chrM (i.e. nothing will be
840 injected in that sequence).")
841 (license license:artistic2.0)))
843 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
845 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
850 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
851 version 'annotation))
854 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
856 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
857 (build-system r-build-system)
859 (list r-annotationdbi r-genomicfeatures))
861 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
862 (synopsis "Annotation package for TxDb object(s)")
864 "This package exposes an annotation databases generated from UCSC by
865 exposing these as TxDb objects.")
866 (license license:artistic2.0)))
868 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
870 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
874 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
875 version 'annotation))
878 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
880 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
881 (build-system r-build-system)
883 (list r-genomicfeatures))
885 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
886 (synopsis "Annotation package for human genome in TxDb format")
888 "This package provides an annotation database of Homo sapiens genome
889 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
890 track. The database is exposed as a @code{TxDb} object.")
891 (license license:artistic2.0)))
893 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
895 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
899 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
900 version 'annotation))
902 (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879"))))
904 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
905 (build-system r-build-system)
907 (list r-annotationdbi r-genomicfeatures))
909 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
910 (synopsis "Annotation package for human genome in TxDb format")
912 "This package provides an annotation database of Homo sapiens genome
913 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
914 track. The database is exposed as a @code{TxDb} object.")
915 (license license:artistic2.0)))
917 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
919 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
923 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
924 version 'annotation))
927 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
929 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
930 (build-system r-build-system)
932 (list r-genomicfeatures r-annotationdbi))
934 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
935 (synopsis "Annotation package for mouse genome in TxDb format")
937 "This package provides an annotation database of Mouse genome data. It
938 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
939 database is exposed as a @code{TxDb} object.")
940 (license license:artistic2.0)))
942 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
944 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
948 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
949 version 'annotation))
952 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
954 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
955 (build-system r-build-system)
957 (list r-bsgenome r-genomicfeatures r-annotationdbi))
959 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
960 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
962 "This package loads a TxDb object, which is an R interface to
963 prefabricated databases contained in this package. This package provides
964 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
965 based on the knownGene track.")
966 (license license:artistic2.0)))
968 (define-public r-txdb-celegans-ucsc-ce6-ensgene
970 (name "r-txdb-celegans-ucsc-ce6-ensgene")
975 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
976 version 'annotation))
979 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
981 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
982 (build-system r-build-system)
984 (list r-annotationdbi r-genomicfeatures))
985 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
986 (synopsis "Annotation package for C elegans TxDb objects")
988 "This package exposes a C elegans annotation database generated from UCSC
989 by exposing these as TxDb objects.")
990 (license license:artistic2.0)))
992 (define-public r-fdb-infiniummethylation-hg19
994 (name "r-fdb-infiniummethylation-hg19")
998 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
999 version 'annotation))
1002 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
1004 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
1005 (build-system r-build-system)
1007 (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db
1008 r-txdb-hsapiens-ucsc-hg19-knowngene))
1009 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
1010 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
1012 "This is an annotation package for Illumina Infinium DNA methylation
1013 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
1015 (license license:artistic2.0)))
1017 (define-public r-illuminahumanmethylationepicmanifest
1019 (name "r-illuminahumanmethylationepicmanifest")
1023 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
1024 version 'annotation))
1027 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
1029 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
1030 (build-system r-build-system)
1033 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
1034 (synopsis "Manifest for Illumina's EPIC methylation arrays")
1036 "This is a manifest package for Illumina's EPIC methylation arrays.")
1037 (license license:artistic2.0)))
1039 (define-public r-do-db
1045 (uri (bioconductor-uri "DO.db" version 'annotation))
1048 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
1050 `((upstream-name . "DO.db")))
1051 (build-system r-build-system)
1053 (list r-annotationdbi))
1054 (home-page "https://www.bioconductor.org/packages/DO.db/")
1055 (synopsis "Annotation maps describing the entire Disease Ontology")
1057 "This package provides a set of annotation maps describing the entire
1059 (license license:artistic2.0)))
1061 (define-public r-hgu133plus2-db
1063 (name "r-hgu133plus2-db")
1068 (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
1070 (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
1071 (properties `((upstream-name . "hgu133plus2.db")))
1072 (build-system r-build-system)
1073 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
1074 (home-page "https://bioconductor.org/packages/hgu133plus2.db")
1075 (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
1077 "This package provides Affymetrix HG-U133_Plus_2 array annotation
1078 data (chip hgu133plus2) assembled using data from public repositories.")
1079 (license license:artistic2.0)))
1081 (define-public r-pfam-db
1088 (uri (bioconductor-uri "PFAM.db" version 'annotation))
1090 (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7"))))
1091 (properties `((upstream-name . "PFAM.db")))
1092 (build-system r-build-system)
1094 (list r-annotationdbi))
1095 (home-page "https://bioconductor.org/packages/PFAM.db")
1096 (synopsis "Set of protein ID mappings for PFAM")
1098 "This package provides a set of protein ID mappings for PFAM, assembled
1099 using data from public repositories.")
1100 (license license:artistic2.0)))
1102 (define-public r-phastcons100way-ucsc-hg19
1104 (name "r-phastcons100way-ucsc-hg19")
1109 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
1110 version 'annotation))
1113 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
1115 `((upstream-name . "phastCons100way.UCSC.hg19")))
1116 (build-system r-build-system)
1124 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
1125 (synopsis "UCSC phastCons conservation scores for hg19")
1127 "This package provides UCSC phastCons conservation scores for the human
1128 genome (hg19) calculated from multiple alignments with other 99 vertebrate
1130 (license license:artistic2.0)))
1135 (define-public r-abadata
1141 (uri (bioconductor-uri "ABAData" version 'experiment))
1144 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
1146 `((upstream-name . "ABAData")))
1147 (build-system r-build-system)
1149 (list r-annotationdbi))
1150 (home-page "https://www.bioconductor.org/packages/ABAData/")
1151 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
1153 "This package provides the data for the gene expression enrichment
1154 analysis conducted in the package ABAEnrichment. The package includes three
1155 datasets which are derived from the Allen Brain Atlas:
1158 @item Gene expression data from Human Brain (adults) averaged across donors,
1159 @item Gene expression data from the Developing Human Brain pooled into five
1160 age categories and averaged across donors, and
1161 @item a developmental effect score based on the Developing Human Brain
1165 All datasets are restricted to protein coding genes.")
1166 (license license:gpl2+)))
1168 (define-public r-adductdata
1170 (name "r-adductdata")
1174 (uri (bioconductor-uri "adductData" version 'experiment))
1176 (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48"))))
1177 (properties `((upstream-name . "adductData")))
1178 (build-system r-build-system)
1179 (propagated-inputs (list r-annotationhub r-experimenthub))
1180 (native-inputs (list r-knitr))
1181 (home-page "https://bioconductor.org/packages/adductData")
1182 (synopsis "Data from untargeted mass spectrometry of modifications to Cys34")
1184 "This package contains data from untargeted @dfn{mass spectrometry} (MS)
1185 of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
1187 (license license:artistic2.0)))
1189 (define-public r-aneufinderdata
1191 (name "r-aneufinderdata")
1195 (uri (bioconductor-uri "AneuFinderData" version 'experiment))
1197 (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7"))))
1198 (build-system r-build-system)
1199 (home-page "https://bioconductor.org/packages/AneuFinderData/")
1200 (synopsis "Data package for @code{AneuFinder}")
1201 (description "This package contains whole-genome single cell sequencing data for
1202 demonstration purposes in the @code{AneuFinder} package.")
1203 (license license:artistic2.0)))
1205 (define-public r-arrmdata
1211 (uri (bioconductor-uri "ARRmData" version 'experiment))
1213 (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p"))))
1215 `((upstream-name . "ARRmData")))
1216 (build-system r-build-system)
1217 (home-page "https://www.bioconductor.org/packages/ARRmData/")
1218 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
1220 "This package provides raw beta values from 36 samples across 3 groups
1221 from Illumina 450k methylation arrays.")
1222 (license license:artistic2.0)))
1224 (define-public r-bladderbatch
1226 (name "r-bladderbatch")
1230 (uri (bioconductor-uri "bladderbatch" version
1234 "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k"))))
1235 (properties `((upstream-name . "bladderbatch")))
1236 (build-system r-build-system)
1237 (propagated-inputs (list r-biobase))
1238 (home-page "https://bioconductor.org/packages/bladderbatch")
1239 (synopsis "Bladder gene expression data illustrating batch effects")
1241 "This package contains microarray gene expression data on 57 bladder samples from
1242 5 batches. The data are used as an illustrative example for the sva package.")
1243 (license license:artistic2.0)))
1245 (define-public r-biscuiteerdata
1247 (name "r-biscuiteerdata")
1252 (uri (bioconductor-uri "biscuiteerData" version 'experiment))
1254 (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
1256 `((upstream-name . "biscuiteerData")))
1257 (build-system r-build-system)
1259 (list r-annotationhub r-curl r-experimenthub))
1260 (native-inputs (list r-knitr))
1261 (home-page "https://bioconductor.org/packages/biscuiteerData")
1262 (synopsis "Data package for Biscuiteer")
1264 "This package contains default datasets used by the Bioconductor package
1266 (license license:gpl3)))
1268 (define-public r-celldex
1275 (uri (bioconductor-uri "celldex" version 'experiment))
1277 (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
1278 (properties `((upstream-name . "celldex")))
1279 (build-system r-build-system)
1281 (list r-annotationdbi
1284 r-delayedmatrixstats
1287 r-summarizedexperiment))
1288 (native-inputs (list r-knitr))
1289 (home-page "https://github.com/LTLA/celldex")
1290 (synopsis "Reference index for cell types")
1292 "This package provides a collection of reference expression datasets with
1293 curated cell type labels, for use in procedures like automated annotation of
1294 single-cell data or deconvolution of bulk RNA-seq.")
1295 (license license:gpl3)))
1297 (define-public r-chromstardata
1299 (name "r-chromstardata")
1304 (uri (bioconductor-uri "chromstaRData" version 'experiment))
1306 (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
1307 (properties `((upstream-name . "chromstaRData")))
1308 (build-system r-build-system)
1309 (home-page "https://bioconductor.org/packages/chromstaRData/")
1310 (synopsis "ChIP-seq data for demonstration purposes")
1312 "This package provides ChIP-seq data for demonstration purposes in the
1313 chromstaR package.")
1314 (license license:gpl3)))
1316 (define-public r-copyhelper
1318 (name "r-copyhelper")
1323 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
1325 (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
1326 (properties `((upstream-name . "CopyhelpeR")))
1327 (build-system r-build-system)
1328 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
1329 (synopsis "Helper files for CopywriteR")
1331 "This package contains the helper files that are required to run the
1332 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
1333 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
1334 mm10. In addition, it contains a blacklist filter to remove regions that
1335 display copy number variation. Files are stored as GRanges objects from the
1336 GenomicRanges Bioconductor package.")
1337 (license license:gpl2)))
1339 (define-public r-genelendatabase
1341 (name "r-genelendatabase")
1346 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
1348 (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
1350 `((upstream-name . "geneLenDataBase")))
1351 (build-system r-build-system)
1353 (list r-rtracklayer r-genomicfeatures))
1354 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
1355 (synopsis "Lengths of mRNA transcripts for a number of genomes")
1357 "This package provides the lengths of mRNA transcripts for a number of
1358 genomes and gene ID formats, largely based on the UCSC table browser.")
1359 (license license:lgpl2.0+)))
1361 (define-public r-genomationdata
1363 (name "r-genomationdata")
1368 (uri (bioconductor-uri "genomationData" version 'experiment))
1370 (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
1372 `((upstream-name . "genomationData")))
1373 (build-system r-build-system)
1374 ;; As this package provides little more than large data files, it doesn't
1375 ;; make sense to build substitutes.
1376 (arguments `(#:substitutable? #f))
1379 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
1380 (synopsis "Experimental data for use with the genomation package")
1382 "This package contains experimental genetic data for use with the
1383 genomation package. Included are Chip Seq, Methylation and Cage data,
1384 downloaded from Encode.")
1385 (license license:gpl3+)))
1387 (define-public r-msdata
1394 (uri (bioconductor-uri "msdata" version 'experiment))
1396 (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
1397 (properties `((upstream-name . "msdata")))
1398 (build-system r-build-system)
1399 (home-page "https://bioconductor.org/packages/msdata")
1400 (synopsis "Various Mass Spectrometry raw data example files")
1402 "This package provides Ion Trap positive ionization mode data in mzML file
1403 format. It includes a subset from 500-850 m/z and 1190-1310 seconds,
1404 including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
1405 III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
1406 LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
1407 files for various search engines.")
1408 (license license:gpl2+)))
1410 (define-public r-pasilla
1417 (uri (bioconductor-uri "pasilla" version 'experiment))
1419 (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
1420 (build-system r-build-system)
1421 (propagated-inputs (list r-dexseq))
1422 (native-inputs (list r-knitr))
1423 (home-page "https://www.bioconductor.org/packages/pasilla/")
1424 (synopsis "Data package with per-exon and per-gene read counts")
1425 (description "This package provides per-exon and per-gene read counts
1426 computed for selected genes from RNA-seq data that were presented in the
1427 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1428 by Brooks et al., Genome Research 2011.")
1429 (license license:lgpl2.1+)))
1431 (define-public r-hsmmsinglecell
1433 (name "r-hsmmsinglecell")
1438 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1440 (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
1442 `((upstream-name . "HSMMSingleCell")))
1443 (build-system r-build-system)
1444 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1445 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1447 "Skeletal myoblasts undergo a well-characterized sequence of
1448 morphological and transcriptional changes during differentiation. In this
1449 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1450 under high mitogen conditions (GM) and then differentiated by switching to
1451 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1452 hundred cells taken over a time-course of serum-induced differentiation.
1453 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1454 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1455 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1456 which were then sequenced to a depth of ~4 million reads per library,
1457 resulting in a complete gene expression profile for each cell.")
1458 (license license:artistic2.0)))
1460 (define-public r-all
1467 (uri (bioconductor-uri "ALL" version 'experiment))
1469 (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
1470 (properties `((upstream-name . "ALL")))
1471 (build-system r-build-system)
1474 (home-page "https://bioconductor.org/packages/ALL")
1475 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1477 "The data consist of microarrays from 128 different individuals with
1478 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1479 are available. The data have been normalized (using rma) and it is the
1480 jointly normalized data that are available here. The data are presented in
1481 the form of an @code{exprSet} object.")
1482 (license license:artistic2.0)))
1484 (define-public r-affydata
1491 (uri (bioconductor-uri "affydata" version 'experiment))
1493 (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
1494 (properties `((upstream-name . "affydata")))
1495 (build-system r-build-system)
1498 (home-page "https://bioconductor.org/packages/affydata/")
1499 (synopsis "Affymetrix data for demonstration purposes")
1501 "This package provides example datasets that represent 'real world
1502 examples' of Affymetrix data, unlike the artificial examples included in the
1503 package @code{affy}.")
1504 (license license:gpl2+)))
1506 (define-public r-gagedata
1513 (uri (bioconductor-uri "gageData" version 'experiment))
1515 (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
1516 (properties `((upstream-name . "gageData")))
1517 (build-system r-build-system)
1518 (home-page "https://bioconductor.org/packages/gageData")
1519 (synopsis "Auxiliary data for the gage package")
1521 "This is a supportive data package for the software package @code{gage}.
1522 However, the data supplied here are also useful for gene set or pathway
1523 analysis or microarray data analysis in general. In this package, we provide
1524 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1525 BMP6 (originally published as an demo dataset for GAGE, also registered as
1526 GSE13604 in GEO). This package also includes commonly used gene set data based
1527 on KEGG pathways and GO terms for major research species, including human,
1528 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1529 yeast are also included.")
1530 (license license:gpl2+)))
1532 (define-public r-curatedtcgadata
1534 (name "r-curatedtcgadata")
1539 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1541 (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
1543 `((upstream-name . "curatedTCGAData")))
1544 (build-system r-build-system)
1546 (list r-annotationhub
1549 r-multiassayexperiment
1551 r-summarizedexperiment))
1552 (native-inputs (list r-knitr))
1553 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1554 (synopsis "Curated data from The Cancer Genome Atlas")
1556 "This package provides publicly available data from The Cancer Genome
1557 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1558 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1559 number, mutation, microRNA, protein, and others) with clinical / pathological
1560 data. It also links assay barcodes with patient identifiers, enabling
1561 harmonized subsetting of rows (features) and columns (patients / samples)
1562 across the entire multi-'omics experiment.")
1563 (license license:artistic2.0)))
1565 (define-public r-parathyroidse
1567 (name "r-parathyroidse")
1571 (uri (bioconductor-uri "parathyroidSE" version
1575 "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16"))))
1576 (properties `((upstream-name . "parathyroidSE")))
1577 (build-system r-build-system)
1578 (propagated-inputs (list r-summarizedexperiment))
1579 (home-page "https://bioconductor.org/packages/parathyroidSE")
1580 (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors")
1582 "This package provides @code{RangedSummarizedExperiment} objects of read
1583 counts in genes and exonic parts for paired-end RNA-Seq data from experiments on
1584 primary cultures of parathyroid tumors. The sequencing was performed on tumor
1585 cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).")
1586 ;; The author(s) mentions only LGPL without any specific version.
1587 (license license:lgpl2.1+)))
1589 (define-public r-tcgabiolinksgui-data
1591 (name "r-tcgabiolinksgui-data")
1596 (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
1598 (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
1599 (properties `((upstream-name . "TCGAbiolinksGUI.data")))
1600 (build-system r-build-system)
1601 (native-inputs (list r-knitr))
1602 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
1603 (synopsis "Data for the TCGAbiolinksGUI package")
1604 (description "This package provides supporting data for the
1605 TCGAbiolinksGUI package.")
1606 (license license:gpl3)))
1611 (define-public r-abarray
1617 (uri (bioconductor-uri "ABarray" version))
1620 "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
1621 (properties `((upstream-name . "ABarray")))
1622 (build-system r-build-system)
1623 (propagated-inputs (list r-biobase r-multtest))
1624 (home-page "https://bioconductor.org/packages/ABarray")
1626 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
1628 "The package @code{ABarray} is designed to work with Applied Biosystems
1629 whole genome microarray platform, as well as any other platform whose data can
1630 be transformed into expression data matrix. Functions include data
1631 preprocessing, filtering, control probe analysis, statistical analysis in one
1632 single function. A @dfn{graphical user interface} (GUI) is also provided. The
1633 raw data, processed data, graphics output and statistical results are organized
1634 into folders according to the analysis settings used.")
1635 (license license:gpl2+)))
1637 (define-public r-absseq
1643 (uri (bioconductor-uri "ABSSeq" version))
1646 "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
1647 (properties `((upstream-name . "ABSSeq")))
1648 (build-system r-build-system)
1649 (propagated-inputs (list r-limma r-locfit))
1650 (home-page "https://bioconductor.org/packages/ABSSeq")
1652 "RNA-Seq analysis based on modelling absolute expression differences")
1654 "This package implements a new RNA-Seq analysis method and integrates two
1655 modules: a basic model for pairwise comparison and a linear model for complex
1656 design. RNA-Seq quantifies gene expression with reads count, which usually
1657 consists of conditions (or treatments) and several replicates for each
1658 condition. This software infers differential expression directly by the
1659 counts difference between conditions. It assumes that the sum counts
1660 difference between conditions follow a negative binomial distribution. In
1661 addition, @code{ABSSeq} moderates the fold-changes by two steps: the
1662 expression level and gene-specific dispersion, that might facilitate the gene
1663 ranking by fold-change and visualization.")
1664 (license license:gpl3+)))
1666 (define-public r-adam
1672 (uri (bioconductor-uri "ADAM" version))
1675 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
1676 (properties `((upstream-name . "ADAM")))
1677 (build-system r-build-system)
1678 (propagated-inputs (list r-dplyr
1686 r-summarizedexperiment))
1687 (native-inputs (list r-knitr))
1688 (home-page "https://bioconductor.org/packages/ADAM")
1689 (synopsis "Gene activity and diversity analysis module")
1691 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
1692 package created to group a set of genes from comparative samples (control
1693 versus experiment) belonging to different species according to their respective
1694 functions. The corresponding roles are extracted from the default collections
1695 like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
1696 @code{ADAM} show their significance by calculating the p-values referring to
1697 gene diversity and activity. Each group of genes is called @dfn{Group of
1698 functionally associated genes} (GFAG).")
1699 (license license:gpl2+)))
1701 (define-public r-adamgui
1707 (uri (bioconductor-uri "ADAMgui" version))
1710 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
1711 (properties `((upstream-name . "ADAMgui")))
1712 (build-system r-build-system)
1734 (native-inputs (list r-knitr))
1735 (home-page "https://bioconductor.org/packages/ADAMgui/")
1736 (synopsis "GUI for gene activity and diversity analysis")
1738 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
1739 for the @code{ADAM} package. The @code{ADAMgui} package provides two
1740 shiny-based applications that allows the user to study the output of the
1741 @code{ADAM} package files through different plots. It's possible, for
1742 example, to choose a specific @dfn{group of functionally associated
1743 genes} (GFAG) and observe the gene expression behavior with the plots created
1744 with the @code{GFAGtargetUi} function. Features such as differential
1745 expression and fold change can be easily seen with aid of the plots made with
1746 the @code{GFAGpathUi} function.")
1747 (license license:gpl2+)))
1749 (define-public r-adimpute
1755 (uri (bioconductor-uri "ADImpute" version))
1758 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
1759 (properties `((upstream-name . "ADImpute")))
1760 (build-system r-build-system)
1762 (list r-biocparallel
1772 r-singlecellexperiment
1773 r-summarizedexperiment))
1774 (native-inputs (list r-knitr))
1775 (home-page "https://bioconductor.org/packages/ADImpute")
1776 (synopsis "Adaptive computational prediction for dropout imputations")
1778 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
1779 unable to quantify the expression levels of all genes in a cell, creating a
1780 need for the computational prediction of missing values (dropout imputation).
1781 Most existing dropout imputation methods are limited in the sense that they
1782 exclusively use the scRNA-seq dataset at hand and do not exploit external
1783 gene-gene relationship information. The @code{ADImpute} package proposes two
1784 methods to address this issue:
1787 @item a gene regulatory network-based approach using gene-gene relationships
1788 learnt from external data;
1789 @item a baseline approach corresponding to a sample-wide average.
1792 @code{ADImpute} implements these novel methods and also combines them with
1793 existing imputation methods like @code{DrImpute} and @code{SAVER}.
1794 @code{ADImpute} can learn the best performing method per gene and combine the
1795 results from different methods into an ensemble.")
1796 (license license:gpl3+)))
1798 (define-public r-adsplit
1804 (uri (bioconductor-uri "adSplit" version))
1807 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
1808 (properties `((upstream-name . "adSplit")))
1809 (build-system r-build-system)
1811 (list r-annotationdbi
1817 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
1818 (synopsis "Annotation-driven splits in microarray data")
1820 "This package implements clustering of microarray gene expression
1821 profiles according to functional annotations. For each term genes are
1822 annotated to, splits into two subclasses are computed and a significance of
1823 the supporting gene set is determined.")
1824 (license license:gpl2+)))
1826 (define-public r-affixcan
1832 (uri (bioconductor-uri "AffiXcan" version))
1835 "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
1836 (properties `((upstream-name . "AffiXcan")))
1837 (build-system r-build-system)
1839 (list r-biocparallel
1841 r-multiassayexperiment
1842 r-summarizedexperiment))
1843 (native-inputs (list r-knitr))
1844 (home-page "https://bioconductor.org/packages/AffiXcan")
1845 (synopsis "Functional approach to impute genetically regulated expression")
1847 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
1848 expression} (GReX) for a set of genes in a sample of individuals, using a
1849 method based on the @dfn{total binding affinity} (TBA). Statistical models to
1850 impute GReX can be trained with a training dataset where the real total
1851 expression values are known.")
1852 (license license:gpl3)))
1854 (define-public r-affyrnadegradation
1856 (name "r-affyrnadegradation")
1860 (uri (bioconductor-uri "AffyRNADegradation" version))
1863 "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
1864 (properties `((upstream-name . "AffyRNADegradation")))
1865 (build-system r-build-system)
1866 (propagated-inputs (list r-affy))
1867 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
1869 "Analyze and correct probe positional bias in data due to RNA degradation")
1871 "The @code{AffyRNADegradation} package helps with the assessment and
1872 correction of RNA degradation effects in Affymetrix 3 expression arrays. The
1873 parameter @code{d} gives a robust and accurate measure of RNA integrity. The
1874 correction removes the probe positional bias, and thus improves comparability
1875 of samples that are affected by RNA degradation.")
1876 ;; the R file header specifies GPL2 or later
1877 (license license:gpl2+)))
1879 (define-public r-agdex
1885 (uri (bioconductor-uri "AGDEX" version))
1888 "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
1889 (properties `((upstream-name . "AGDEX")))
1890 (build-system r-build-system)
1891 (propagated-inputs (list r-biobase r-gseabase))
1892 (home-page "https://bioconductor.org/packages/AGDEX")
1894 "Evaluate agreement of differential expression for cross-species genomics")
1896 "The objective of @code{AGDEX} is to evaluate whether the results of a
1897 pair of two-group differential expression analysis comparisons show a level of
1898 agreement that is greater than expected if the group labels for each two-group
1899 comparison are randomly assigned. The agreement is evaluated for the entire
1900 transcriptome and (optionally) for a collection of pre-defined gene-sets.
1901 Additionally, the procedure performs permutation-based differential expression
1902 and meta analysis at both gene and gene-set levels of the data from each
1904 (license license:gpl2+)))
1906 (define-public r-aggregatebiovar
1908 (name "r-aggregatebiovar")
1912 (uri (bioconductor-uri "aggregateBioVar" version))
1915 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
1916 (properties `((upstream-name . "aggregateBioVar")))
1917 (build-system r-build-system)
1922 r-singlecellexperiment
1923 r-summarizedexperiment
1925 (native-inputs (list r-knitr))
1926 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
1927 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
1929 "This package @code{aggregateBioVar} contains tools to summarize single
1930 cell gene expression profiles at the level of subject for single cell RNA-seq
1931 data collected from more than one subject (e.g. biological sample or technical
1932 replicates). A @code{SingleCellExperiment} object is taken as input and
1933 converted to a list of @code{SummarizedExperiment} objects, where each list
1934 element corresponds to an assigned cell type. The @code{SummarizedExperiment}
1935 objects contain aggregate gene-by-subject count matrices and inter-subject
1936 column metadata for individual subjects that can be processed using downstream
1937 bulk RNA-seq tools.")
1938 (license license:gpl3)))
1940 (define-public r-agilp
1946 (uri (bioconductor-uri "agilp" version))
1949 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
1950 (properties `((upstream-name . "agilp")))
1951 (build-system r-build-system)
1952 (home-page "https://bioconductor.org/packages/agilp")
1953 (synopsis "Processing of Agilent expression array")
1955 "This package aims to provide a pipeline for the low-level analysis of
1956 gene expression microarray data, primarily focused on the Agilent platform,
1957 but which also provides utilities which may be useful for other platforms.")
1958 ;; Some files are under GPLv2+ but the combined work is released under the
1960 (license license:gpl3)))
1962 (define-public r-adductomicsr
1964 (name "r-adductomicsr")
1968 (uri (bioconductor-uri "adductomicsR" version))
1971 "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
1972 (properties `((upstream-name . "adductomicsR")))
1973 (build-system r-build-system)
1996 (native-inputs (list r-knitr))
1997 (home-page "https://bioconductor.org/packages/adductomicsR")
1998 (synopsis "Processing of adductomic mass spectral datasets")
2000 "This package @code{adductomicsR} processes data generated by the
2001 @dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
2002 peptides from spectra that has been corrected for mass drift and retention
2003 time drift and quantifies level mass spectral peaks from @dfn{first stage of
2004 mass spectrometry} (MS1) data.")
2005 (license license:artistic2.0)))
2007 (define-public r-agimicrorna
2009 (name "r-agimicrorna")
2013 (uri (bioconductor-uri "AgiMicroRna" version))
2016 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
2017 (properties `((upstream-name . "AgiMicroRna")))
2018 (build-system r-build-system)
2025 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
2027 "Processing and differential expression analysis of Agilent microRNA chips")
2029 "@code{AgiMicroRna} provides useful functionality for the processing,
2030 quality assessment and differential expression analysis of Agilent microRNA
2031 array data. The package uses a limma-like structure to generate the processed
2032 data in order to make statistical inferences about differential expression
2033 using the linear model features implemented in limma. Standard Bioconductor
2034 objects are used so that other packages could be used as well.")
2035 (license license:gpl3)))
2037 (define-public r-amountain
2039 (name "r-amountain")
2043 (uri (bioconductor-uri "AMOUNTAIN" version))
2046 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
2047 (properties `((upstream-name . "AMOUNTAIN")))
2048 (build-system r-build-system)
2050 (native-inputs (list r-knitr))
2051 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
2052 (synopsis "Modules for multilayer weighted gene co-expression networks")
2054 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
2055 gene co-expression network) could be constructed only from expression profile.
2056 Different layers in such networks may represent different time points, multiple
2057 conditions or various species. @code{AMOUNTAIN} aims to search active modules
2058 in multi-layer WGCN using a continuous optimization approach.")
2059 (license license:gpl2+)))
2061 (define-public r-amaretto
2067 (uri (bioconductor-uri "AMARETTO" version))
2070 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
2071 (properties `((upstream-name . "AMARETTO")))
2072 (build-system r-build-system)
2074 (list r-biocfilecache
2092 r-multiassayexperiment
2098 (native-inputs (list r-knitr))
2099 (home-page "https://bioconductor.org/packages/AMARETTO")
2100 (synopsis "Regulatory network inference and driver gene evaluation")
2102 "This package @code{AMARETTO} represents an algorithm that integrates copy
2103 number, DNA methylation and gene expression data to identify a set of driver
2104 genes by analyzing cancer samples and connects them to clusters of co-expressed
2105 genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
2106 setting to identify cancer driver genes and their modules on multiple cancer
2107 sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
2108 and EMT, and modules that accurately predict survival and molecular subtypes.
2109 This allows @code{AMARETTO} to identify novel cancer driver genes directing
2110 canonical cancer pathways.")
2111 (license license:asl2.0)))
2113 (define-public r-anaquin
2119 (uri (bioconductor-uri "Anaquin" version))
2122 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
2123 (properties `((upstream-name . "Anaquin")))
2124 (build-system r-build-system)
2133 (native-inputs (list r-knitr))
2134 (home-page "https://www.sequinstandards.com/")
2135 (synopsis "Statistical analysis of sequins")
2137 "The project is intended to support the use of @dfn{sequins}(synthetic
2138 sequencing spike-in controls) owned and made available by the Garvan Institute
2139 of Medical Research. The goal is to provide a standard library for quantitative
2140 analysis, modelling, and visualization of spike-in controls.")
2141 (license license:bsd-3)))
2143 (define-public r-aneufinder
2145 (name "r-aneufinder")
2149 (uri (bioconductor-uri "AneuFinder" version))
2152 "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
2153 (build-system r-build-system)
2157 (list r-genomicranges
2178 (home-page "https://bioconductor.org/packages/AneuFinder/")
2179 (synopsis "Copy number variation analysis in single-cell-sequencing data")
2180 (description "This package implements functions for copy number variant
2181 calling, plotting, export and analysis from whole-genome single cell
2183 (license license:artistic2.0)))
2185 (define-public r-anf
2191 (uri (bioconductor-uri "ANF" version))
2194 "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
2195 (properties `((upstream-name . "ANF")))
2196 (build-system r-build-system)
2203 (native-inputs (list r-knitr))
2204 (home-page "https://bioconductor.org/packages/ANF")
2205 (synopsis "Affinity network fusion for complex patient clustering")
2207 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
2208 matrix construction and fusion as well as spectral clustering. This package is
2209 used for complex patient clustering by integrating multi-omic data through affinity
2211 (license license:gpl3)))
2213 (define-public r-annmap
2219 (uri (bioconductor-uri "annmap" version))
2222 "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
2223 (properties `((upstream-name . "annmap")))
2224 (build-system r-build-system)
2236 (home-page "https://github.com/cruk-mi/annmap")
2238 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
2240 "This package @code{annmap} provides annotation mappings for Affymetrix exon
2241 arrays and coordinate based queries to support deep sequencing data analysis.
2242 Database access is hidden behind the API which provides a set of functions such
2243 as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
2244 Functions to plot gene architecture and BAM file data are also provided.")
2245 (license license:gpl2)))
2247 (define-public r-antiprofiles
2249 (name "r-antiprofiles")
2253 (uri (bioconductor-uri "antiProfiles" version))
2256 "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
2257 (properties `((upstream-name . "antiProfiles")))
2258 (build-system r-build-system)
2262 (home-page "https://github.com/HCBravoLab/antiProfiles")
2263 (synopsis "Implementation of gene expression anti-profiles")
2265 "This package implements the gene expression anti-profiles method.
2266 Anti-profiles are a new approach for developing cancer genomic signatures that
2267 specifically take advantage of gene expression heterogeneity. They explicitly
2268 model increased gene expression variability in cancer to define robust and
2269 reproducible gene expression signatures capable of accurately distinguishing
2270 tumor samples from healthy controls.")
2271 (license license:artistic2.0)))
2273 (define-public r-biocversion
2275 (name "r-biocversion")
2280 (uri (bioconductor-uri "BiocVersion" version))
2283 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
2284 (properties `((upstream-name . "BiocVersion")))
2285 (build-system r-build-system)
2286 (home-page "https://bioconductor.org/packages/BiocVersion/")
2287 (synopsis "Set the appropriate version of Bioconductor packages")
2289 "This package provides repository information for the appropriate version
2291 (license license:artistic2.0)))
2293 (define-public r-biocgenerics
2295 (name "r-biocgenerics")
2299 (uri (bioconductor-uri "BiocGenerics" version))
2302 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
2304 `((upstream-name . "BiocGenerics")))
2305 (build-system r-build-system)
2306 (home-page "https://bioconductor.org/packages/BiocGenerics")
2307 (synopsis "S4 generic functions for Bioconductor")
2309 "This package provides S4 generic functions needed by many Bioconductor
2311 (license license:artistic2.0)))
2313 (define-public r-coverageview
2315 (name "r-coverageview")
2319 (uri (bioconductor-uri "CoverageView" version))
2322 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
2323 (build-system r-build-system)
2331 (home-page "https://bioconductor.org/packages/CoverageView/")
2332 (synopsis "Coverage visualization package for R")
2333 (description "This package provides a framework for the visualization of
2334 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
2335 be also used for genome-wide nucleosome positioning experiments or other
2336 experiment types where it is important to have a framework in order to inspect
2337 how the coverage distributed across the genome.")
2338 (license license:artistic2.0)))
2340 (define-public r-cummerbund
2342 (name "r-cummerbund")
2346 (uri (bioconductor-uri "cummeRbund" version))
2349 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
2350 (build-system r-build-system)
2362 (home-page "https://bioconductor.org/packages/cummeRbund/")
2363 (synopsis "Analyze Cufflinks high-throughput sequencing data")
2364 (description "This package allows for persistent storage, access,
2365 exploration, and manipulation of Cufflinks high-throughput sequencing
2366 data. In addition, provides numerous plotting functions for commonly
2367 used visualizations.")
2368 (license license:artistic2.0)))
2370 (define-public r-dearseq
2377 (uri (bioconductor-uri "dearseq" version))
2380 "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl"))))
2381 (build-system r-build-system)
2383 (list r-compquadform
2399 (home-page "https://github.com/borishejblum/dearseq")
2400 (synopsis "DEA for RNA-seq data through a robust variance component test")
2402 "This is a package for Differential Expression Analysis of RNA-seq data.
2403 It features a variance component score test accounting for data
2404 heteroscedasticity through precision weights. Perform both gene-wise and gene
2405 set analyses, and can deal with repeated or longitudinal data.")
2406 (license license:gpl2)))
2408 (define-public r-decipher
2414 (uri (bioconductor-uri "DECIPHER" version))
2417 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
2418 (build-system r-build-system)
2426 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
2427 (synopsis "Tools for deciphering and managing biological sequences")
2428 (description "This package provides a toolset for deciphering and managing
2429 biological sequences.")
2430 (license license:gpl3)))
2432 (define-public r-deconvr
2438 (uri (bioconductor-uri "deconvR" version))
2441 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
2442 (properties `((upstream-name . "deconvR")))
2443 (build-system r-build-system)
2462 (native-inputs (list r-knitr))
2463 (home-page "https://github.com/BIMSBbioinfo/deconvR")
2464 (synopsis "Simulation and deconvolution of omic profiles")
2466 "This package provides a collection of functions designed for analyzing
2467 deconvolution of the bulk sample(s) using an atlas of reference omic signature
2468 profiles and a user-selected model. Users are given the option to create or
2469 extend a reference atlas and,also simulate the desired size of the bulk
2470 signature profile of the reference cell types. The package includes the
2471 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
2472 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
2473 make mapping WGBS data to their probe IDs easier.")
2474 (license license:artistic2.0)))
2476 (define-public r-decoupler
2478 (name "r-decoupler")
2483 (uri (bioconductor-uri "decoupleR" version))
2485 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
2486 (properties `((upstream-name . "decoupleR")))
2487 (build-system r-build-system)
2500 (native-inputs (list r-knitr))
2501 (home-page "https://saezlab.github.io/decoupleR/")
2502 (synopsis "Computational methods to infer biological activities from omics data")
2504 "Many methods allow us to extract biological activities from omics data using
2505 information from prior knowledge resources, reducing the dimensionality for
2506 increased statistical power and better interpretability. decoupleR is a
2507 Bioconductor package containing different statistical methods to extract these
2508 signatures within a unified framework. decoupleR allows the user to flexibly
2509 test any method with any resource. It incorporates methods that take into
2510 account the sign and weight of network interactions. decoupleR can be used
2511 with any omic, as long as its features can be linked to a biological process
2512 based on prior knowledge. For example, in transcriptomics gene sets regulated
2513 by a transcription factor, or in phospho-proteomics phosphosites that are
2514 targeted by a kinase.")
2515 (license license:gpl3)))
2517 (define-public r-deepsnv
2523 (uri (bioconductor-uri "deepSNV" version))
2526 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
2527 (properties `((upstream-name . "deepSNV")))
2528 (build-system r-build-system)
2534 r-summarizedexperiment
2539 (home-page "https://github.com/gerstung-lab/deepSNV/")
2540 (synopsis "Detection of subclonal SNVs in deep sequencing data")
2542 "This package provides quantitative variant callers for detecting
2543 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
2544 The deepSNV algorithm is used for a comparative setup with a control experiment
2545 of the same loci and uses a beta-binomial model and a likelihood ratio test to
2546 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
2547 computes a Bayes classifier based on a beta-binomial model for variant calling
2548 with multiple samples for precisely estimating model parameters - such as local
2549 error rates and dispersion - and prior knowledge, e.g. from variation data
2550 bases such as COSMIC.")
2551 (license license:gpl3)))
2553 (define-public r-delayedarray
2555 (name "r-delayedarray")
2559 (uri (bioconductor-uri "DelayedArray" version))
2562 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
2564 `((upstream-name . "DelayedArray")))
2565 (build-system r-build-system)
2567 (list r-biocgenerics r-s4vectors r-iranges r-matrix
2571 (home-page "https://bioconductor.org/packages/DelayedArray")
2572 (synopsis "Delayed operations on array-like objects")
2574 "Wrapping an array-like object (typically an on-disk object) in a
2575 @code{DelayedArray} object allows one to perform common array operations on it
2576 without loading the object in memory. In order to reduce memory usage and
2577 optimize performance, operations on the object are either delayed or executed
2578 using a block processing mechanism. Note that this also works on in-memory
2579 array-like objects like @code{DataFrame} objects (typically with Rle columns),
2580 @code{Matrix} objects, and ordinary arrays and data frames.")
2581 (license license:artistic2.0)))
2583 (define-public r-derfinderhelper
2585 (name "r-derfinderhelper")
2590 (uri (bioconductor-uri "derfinderHelper" version))
2592 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
2593 (properties `((upstream-name . "derfinderHelper")))
2594 (build-system r-build-system)
2596 (list r-iranges r-matrix r-s4vectors))
2599 (home-page "https://github.com/leekgroup/derfinderHelper")
2600 (synopsis "Helper for derfinder")
2602 "This package speeds up the derfinder package when using multiple cores.
2603 It is particularly useful when using BiocParallel and it helps reduce the time
2604 spent loading the full derfinder package when running the F-statistics
2605 calculation in parallel.")
2606 (license license:artistic2.0)))
2608 (define-public r-drimseq
2615 (uri (bioconductor-uri "DRIMSeq" version))
2617 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
2618 (properties `((upstream-name . "DRIMSeq")))
2619 (build-system r-build-system)
2621 (list r-biocgenerics
2631 (native-inputs (list r-knitr))
2632 (home-page "https://bioconductor.org/packages/DRIMSeq")
2633 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
2635 "The package provides two frameworks. One for the differential
2636 transcript usage analysis between different conditions and one for the tuQTL
2637 analysis. Both are based on modeling the counts of genomic features (i.e.,
2638 transcripts) with the Dirichlet-multinomial distribution. The package also
2639 makes available functions for visualization and exploration of the data and
2641 (license license:gpl3+)))
2643 (define-public r-bluster
2649 (uri (bioconductor-uri "bluster" version))
2652 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
2653 (properties `((upstream-name . "bluster")))
2654 (build-system r-build-system)
2656 (list r-biocneighbors
2665 (home-page "https://bioconductor.org/packages/bluster")
2666 (synopsis "Clustering algorithms for Bioconductor")
2667 (description"This package wraps common clustering algorithms in an easily
2668 extended S4 framework. Backends are implemented for hierarchical, k-means
2669 and graph-based clustering. Several utilities are also provided to compare
2670 and evaluate clustering results.")
2671 (license license:gpl3)))
2673 (define-public r-ideoviz
2679 (uri (bioconductor-uri "IdeoViz" version))
2682 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
2683 (build-system r-build-system)
2691 (home-page "https://bioconductor.org/packages/IdeoViz/")
2692 (synopsis "Plots data along a chromosomal ideogram")
2693 (description "This package provides functions to plot data associated with
2694 arbitrary genomic intervals along chromosomal ideogram.")
2695 (license license:gpl2)))
2697 (define-public r-infercnv
2704 (uri (bioconductor-uri "infercnv" version))
2707 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
2708 (properties `((upstream-name . "infercnv")))
2709 (build-system r-build-system)
2710 (inputs (list python))
2739 r-singlecellexperiment
2740 r-summarizedexperiment
2742 (native-inputs (list r-knitr))
2743 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
2744 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
2746 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
2747 evidence for somatic large-scale chromosomal copy number alterations, such as gains
2748 or deletions of entire chromosomes or large segments of chromosomes. This is done
2749 by exploring expression intensity of genes across positions of a tumor genome in
2750 comparison to a set of reference \"normal\" cells. A heatmap is generated
2751 illustrating the relative expression intensities across each chromosome, and it
2752 often becomes readily apparent as to which regions of the tumor genome are
2753 over-abundant or less-abundant as compared to that of normal cells.")
2754 (license license:bsd-3)))
2756 (define-public r-iranges
2762 (uri (bioconductor-uri "IRanges" version))
2765 "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
2767 `((upstream-name . "IRanges")))
2768 (build-system r-build-system)
2770 (list r-biocgenerics r-s4vectors))
2771 (home-page "https://bioconductor.org/packages/IRanges")
2772 (synopsis "Infrastructure for manipulating intervals on sequences")
2774 "This package provides efficient low-level and highly reusable S4 classes
2775 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
2776 generally, data that can be organized sequentially (formally defined as
2777 @code{Vector} objects), as well as views on these @code{Vector} objects.
2778 Efficient list-like classes are also provided for storing big collections of
2779 instances of the basic classes. All classes in the package use consistent
2780 naming and share the same rich and consistent \"Vector API\" as much as
2782 (license license:artistic2.0)))
2784 (define-public r-isoformswitchanalyzer
2786 (name "r-isoformswitchanalyzer")
2791 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
2793 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
2794 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
2795 (build-system r-build-system)
2828 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
2829 (synopsis "Analyze alternative splicing in RNA-seq data")
2831 "This is a package for the analysis of alternative splicing and isoform
2832 switches with predicted functional consequences (e.g. gain/loss of protein
2833 domains etc.) from quantification of all types of RNASeq by tools such as
2834 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
2835 (license license:gpl2+)))
2837 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
2838 (define-public r-absfiltergsea
2840 (name "r-absfiltergsea")
2845 (uri (cran-uri "AbsFilterGSEA" version))
2847 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
2848 (properties `((upstream-name . "AbsFilterGSEA")))
2849 (build-system r-build-system)
2851 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
2852 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
2853 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
2855 "This package provides a function that performs gene-permuting of a gene-set
2856 enrichment analysis (GSEA) calculation with or without the absolute filtering.
2857 Without filtering, users can perform (original) two-tailed or one-tailed
2859 (license license:gpl2)))
2861 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
2862 (define-public r-bisquerna
2864 (name "r-bisquerna")
2868 (uri (cran-uri "BisqueRNA" version))
2871 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
2872 (properties `((upstream-name . "BisqueRNA")))
2873 (build-system r-build-system)
2875 (list r-biobase r-limsolve))
2878 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2879 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2880 (description "This package provides tools to accurately estimate cell type
2881 abundances from heterogeneous bulk expression. A reference-based method
2882 utilizes single-cell information to generate a signature matrix and
2883 transformation of bulk expression for accurate regression based estimates.
2884 A marker-based method utilizes known cell-specific marker genes to measure
2885 relative abundances across samples.")
2886 (license license:gpl3)))
2888 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
2889 ;; from Bioconductor.
2890 (define-public r-deconstructsigs
2892 (name "r-deconstructsigs")
2896 (uri (cran-uri "deconstructSigs" version))
2899 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
2901 `((upstream-name . "deconstructSigs")))
2902 (build-system r-build-system)
2904 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
2906 (home-page "https://github.com/raerose01/deconstructSigs")
2907 (synopsis "Identifies signatures present in a tumor sample")
2908 (description "This package takes sample information in the form of the
2909 fraction of mutations in each of 96 trinucleotide contexts and identifies
2910 the weighted combination of published signatures that, when summed, most
2911 closely reconstructs the mutational profile.")
2912 (license license:gpl2+)))
2914 ;; This is a CRAN package, but it depends on Bioconductor packages.
2915 (define-public r-jetset
2922 (uri (cran-uri "jetset" version))
2924 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
2925 (properties `((upstream-name . "jetset")))
2926 (build-system r-build-system)
2927 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
2928 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
2929 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
2931 "This package provides a one-to-one mapping from gene to \"best\" probe
2932 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
2933 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
2934 gene may be measured by multiple probe sets. This can present a mild
2935 conundrum when attempting to evaluate a gene \"signature\" that is defined by
2936 gene names rather than by specific probe sets. This package also includes the
2937 pre-calculated probe set quality scores that were used to define the
2939 (license license:artistic2.0)))
2941 ;; This is a CRAN package, but it depends on Bioconductor packages.
2942 (define-public r-nmf
2949 (uri (cran-uri "NMF" version))
2952 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
2953 (properties `((upstream-name . "NMF")))
2954 (build-system r-build-system)
2959 r-bigmemory ; suggested
2960 r-synchronicity ; suggested
2975 (home-page "http://renozao.github.io/NMF")
2976 (synopsis "Algorithms and framework for nonnegative matrix factorization")
2978 "This package provides a framework to perform Non-negative Matrix
2979 Factorization (NMF). The package implements a set of already published
2980 algorithms and seeding methods, and provides a framework to test, develop and
2981 plug new or custom algorithms. Most of the built-in algorithms have been
2982 optimized in C++, and the main interface function provides an easy way of
2983 performing parallel computations on multicore machines.")
2984 (license license:gpl2+)))
2986 (define-public r-affy
2993 (uri (bioconductor-uri "affy" version))
2996 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
2997 (build-system r-build-system)
3007 (home-page "https://bioconductor.org/packages/affy")
3008 (synopsis "Methods for affymetrix oligonucleotide arrays")
3010 "This package contains functions for exploratory oligonucleotide array
3012 (license license:lgpl2.0+)))
3014 (define-public r-affycomp
3021 (uri (bioconductor-uri "affycomp" version))
3024 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
3025 (properties `((upstream-name . "affycomp")))
3026 (build-system r-build-system)
3027 (propagated-inputs (list r-biobase))
3028 (home-page "https://bioconductor.org/packages/affycomp/")
3029 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
3031 "The package contains functions that can be used to compare expression
3032 measures for Affymetrix Oligonucleotide Arrays.")
3033 (license license:gpl2+)))
3035 (define-public r-affycompatible
3037 (name "r-affycompatible")
3042 (uri (bioconductor-uri "AffyCompatible" version))
3045 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
3047 `((upstream-name . "AffyCompatible")))
3048 (build-system r-build-system)
3052 `(modify-phases %standard-phases
3053 (add-after 'unpack 'make-reproducible
3055 ;; Order DTD elements before generating R code from them.
3056 (substitute* "R/methods-AffyCompatible.R"
3059 elements <- dtd$elements
3060 ordered <- elements[order(names(elements))]\n"))
3061 (("elt in dtd\\$elements")
3063 ;; Use a predictable directory name for code generation.
3064 (mkdir-p "/tmp/NetAffxResourcePrototype")
3065 (substitute* "R/DataClasses.R"
3066 (("directory=tempdir\\(\\)")
3067 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
3069 (list r-biostrings r-rcurl r-xml))
3070 (home-page "https://bioconductor.org/packages/AffyCompatible/")
3071 (synopsis "Work with Affymetrix GeneChip files")
3073 "This package provides an interface to Affymetrix chip annotation and
3074 sample attribute files. The package allows an easy way for users to download
3075 and manage local data bases of Affynmetrix NetAffx annotation files. It also
3076 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
3077 Command Console} (AGCC)-compatible sample annotation files.")
3078 (license license:artistic2.0)))
3080 (define-public r-affycontam
3082 (name "r-affycontam")
3087 (uri (bioconductor-uri "affyContam" version))
3090 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
3091 (properties `((upstream-name . "affyContam")))
3092 (build-system r-build-system)
3094 (list r-affy r-affydata r-biobase))
3095 (home-page "https://bioconductor.org/packages/affyContam/")
3096 (synopsis "Structured corruption of Affymetrix CEL file data")
3098 "Microarray quality assessment is a major concern of microarray analysts.
3099 This package provides some simple approaches to in silico creation of quality
3100 problems in CEL-level data to help evaluate performance of quality metrics.")
3101 (license license:artistic2.0)))
3103 (define-public r-affycoretools
3105 (name "r-affycoretools")
3110 (uri (bioconductor-uri "affycoretools" version))
3113 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
3114 (properties `((upstream-name . "affycoretools")))
3115 (build-system r-build-system)
3138 (home-page "https://bioconductor.org/packages/affycoretools/")
3139 (synopsis "Functions for analyses with Affymetrix GeneChips")
3141 "This package provides various wrapper functions that have been written
3142 to streamline the more common analyses that a Biostatistician might see.")
3143 (license license:artistic2.0)))
3145 (define-public r-affyio
3152 (uri (bioconductor-uri "affyio" version))
3155 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
3156 (build-system r-build-system)
3161 (home-page "https://github.com/bmbolstad/affyio")
3162 (synopsis "Tools for parsing Affymetrix data files")
3164 "This package provides routines for parsing Affymetrix data files based
3165 upon file format information. The primary focus is on accessing the CEL and
3167 (license license:lgpl2.0+)))
3169 (define-public r-affxparser
3171 (name "r-affxparser")
3176 (uri (bioconductor-uri "affxparser" version))
3179 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
3180 (properties `((upstream-name . "affxparser")))
3181 (build-system r-build-system)
3182 (home-page "https://github.com/HenrikBengtsson/affxparser")
3183 (synopsis "Affymetrix File Parsing SDK")
3185 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
3186 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
3187 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
3188 are supported. Currently, there are methods for reading @dfn{chip definition
3189 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
3190 either in full or in part. For example, probe signals from a few probesets
3191 can be extracted very quickly from a set of CEL files into a convenient list
3193 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
3195 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
3197 (define-public r-annotate
3204 (uri (bioconductor-uri "annotate" version))
3207 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
3208 (build-system r-build-system)
3210 (list r-annotationdbi
3218 "https://bioconductor.org/packages/annotate")
3219 (synopsis "Annotation for microarrays")
3220 (description "This package provides R environments for the annotation of
3222 (license license:artistic2.0)))
3224 (define-public r-annotationdbi
3226 (name "r-annotationdbi")
3230 (uri (bioconductor-uri "AnnotationDbi" version))
3233 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
3235 `((upstream-name . "AnnotationDbi")))
3236 (build-system r-build-system)
3247 (home-page "https://bioconductor.org/packages/AnnotationDbi")
3248 (synopsis "Annotation database interface")
3250 "This package provides user interface and database connection code for
3251 annotation data packages using SQLite data storage.")
3252 (license license:artistic2.0)))
3254 (define-public r-annotationfilter
3256 (name "r-annotationfilter")
3260 (uri (bioconductor-uri "AnnotationFilter" version))
3263 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
3265 `((upstream-name . "AnnotationFilter")))
3266 (build-system r-build-system)
3268 (list r-genomicranges r-lazyeval))
3271 (home-page "https://github.com/Bioconductor/AnnotationFilter")
3272 (synopsis "Facilities for filtering Bioconductor annotation resources")
3274 "This package provides classes and other infrastructure to implement
3275 filters for manipulating Bioconductor annotation resources. The filters are
3276 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
3277 (license license:artistic2.0)))
3279 (define-public r-annotationforge
3281 (name "r-annotationforge")
3286 (uri (bioconductor-uri "AnnotationForge" version))
3289 "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v"))))
3291 `((upstream-name . "AnnotationForge")))
3292 (build-system r-build-system)
3294 (list r-annotationdbi
3304 (home-page "https://bioconductor.org/packages/AnnotationForge")
3305 (synopsis "Code for building annotation database packages")
3307 "This package provides code for generating Annotation packages and their
3308 databases. Packages produced are intended to be used with AnnotationDbi.")
3309 (license license:artistic2.0)))
3311 (define-public r-annotationhub
3313 (name "r-annotationhub")
3318 (uri (bioconductor-uri "AnnotationHub" version))
3321 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
3322 (properties `((upstream-name . "AnnotationHub")))
3323 (build-system r-build-system)
3325 (list r-annotationdbi
3333 r-interactivedisplaybase
3340 (home-page "https://bioconductor.org/packages/AnnotationHub")
3341 (synopsis "Client to access AnnotationHub resources")
3343 "This package provides a client for the Bioconductor AnnotationHub web
3344 resource. The AnnotationHub web resource provides a central location where
3345 genomic files (e.g. VCF, bed, wig) and other resources from standard
3346 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
3347 metadata about each resource, e.g., a textual description, tags, and date of
3348 modification. The client creates and manages a local cache of files retrieved
3349 by the user, helping with quick and reproducible access.")
3350 (license license:artistic2.0)))
3352 (define-public r-aroma-light
3354 (name "r-aroma-light")
3359 (uri (bioconductor-uri "aroma.light" version))
3362 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
3363 (properties `((upstream-name . "aroma.light")))
3364 (build-system r-build-system)
3366 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
3367 (home-page "https://github.com/HenrikBengtsson/aroma.light")
3368 (synopsis "Methods for normalization and visualization of microarray data")
3370 "This package provides methods for microarray analysis that take basic
3371 data types such as matrices and lists of vectors. These methods can be used
3372 standalone, be utilized in other packages, or be wrapped up in higher-level
3374 (license license:gpl2+)))
3376 (define-public r-bamsignals
3378 (name "r-bamsignals")
3383 (uri (bioconductor-uri "bamsignals" version))
3386 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
3387 (build-system r-build-system)
3389 (list r-biocgenerics
3397 (home-page "https://bioconductor.org/packages/bamsignals")
3398 (synopsis "Extract read count signals from bam files")
3400 "This package efficiently obtains count vectors from indexed bam
3401 files. It counts the number of nucleotide sequence reads in given genomic
3402 ranges and it computes reads profiles and coverage profiles. It also handles
3404 (license license:gpl2+)))
3406 (define-public r-biobase
3412 (uri (bioconductor-uri "Biobase" version))
3415 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
3417 `((upstream-name . "Biobase")))
3418 (build-system r-build-system)
3420 (list r-biocgenerics))
3421 (home-page "https://bioconductor.org/packages/Biobase")
3422 (synopsis "Base functions for Bioconductor")
3424 "This package provides functions that are needed by many other packages
3425 on Bioconductor or which replace R functions.")
3426 (license license:artistic2.0)))
3428 (define-public r-biomart
3434 (uri (bioconductor-uri "biomaRt" version))
3437 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
3439 `((upstream-name . "biomaRt")))
3440 (build-system r-build-system)
3442 (list r-annotationdbi
3453 (home-page "https://bioconductor.org/packages/biomaRt")
3454 (synopsis "Interface to BioMart databases")
3456 "biomaRt provides an interface to a growing collection of databases
3457 implementing the @url{BioMart software suite, http://www.biomart.org}. The
3458 package enables retrieval of large amounts of data in a uniform way without
3459 the need to know the underlying database schemas or write complex SQL queries.
3460 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
3461 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
3462 users direct access to a diverse set of data and enable a wide range of
3463 powerful online queries from gene annotation to database mining.")
3464 (license license:artistic2.0)))
3466 ;; This is a CRAN package, but it depends on a Bioconductor package:
3468 (define-public r-biomartr
3474 (uri (cran-uri "biomartr" version))
3477 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
3478 (properties `((upstream-name . "biomartr")))
3479 (build-system r-build-system)
3499 (native-inputs (list r-knitr))
3500 (home-page "https://docs.ropensci.org/biomartr/")
3501 (synopsis "Genomic data retrieval")
3503 "Perform large scale genomic data retrieval and functional annotation
3504 retrieval. This package aims to provide users with a standardized way to
3505 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
3506 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
3507 Furthermore, an interface to the BioMart database allows users to retrieve
3508 functional annotation for genomic loci. In addition, users can download
3509 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
3511 (license license:gpl2)))
3513 (define-public r-biocparallel
3515 (name "r-biocparallel")
3519 (uri (bioconductor-uri "BiocParallel" version))
3522 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
3524 `((upstream-name . "BiocParallel")))
3525 (build-system r-build-system)
3528 (modify-phases %standard-phases
3529 (add-after 'unpack 'make-reproducible
3531 ;; Remove generated documentation.
3532 (for-each delete-file
3533 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
3534 "inst/doc/Introduction_To_BiocParallel.pdf"
3535 "inst/doc/Errors_Logs_And_Debugging.pdf"
3536 "inst/doc/BiocParallel_BatchtoolsParam.R"
3537 "inst/doc/Introduction_To_BiocParallel.R"
3538 "inst/doc/Errors_Logs_And_Debugging.R"))
3540 ;; Remove time-dependent macro
3541 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
3542 "inst/doc/Introduction_To_BiocParallel.Rnw"
3543 "inst/doc/Errors_Logs_And_Debugging.Rnw"
3544 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
3545 "vignettes/Introduction_To_BiocParallel.Rnw"
3546 "vignettes/Errors_Logs_And_Debugging.Rnw")
3547 (("\\today") "later"))
3549 ;; Initialize the random number generator seed when building.
3550 (substitute* "R/rng.R"
3551 (("\"L'Ecuyer-CMRG\"\\)" m)
3553 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
3555 (list r-bh r-codetools r-futile-logger r-snow))
3558 (home-page "https://bioconductor.org/packages/BiocParallel")
3559 (synopsis "Bioconductor facilities for parallel evaluation")
3561 "This package provides modified versions and novel implementation of
3562 functions for parallel evaluation, tailored to use with Bioconductor
3564 (license (list license:gpl2+ license:gpl3+))))
3566 (define-public r-biostrings
3568 (name "r-biostrings")
3572 (uri (bioconductor-uri "Biostrings" version))
3575 "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"))))
3577 `((upstream-name . "Biostrings")))
3578 (build-system r-build-system)
3580 (list r-biocgenerics
3586 (home-page "https://bioconductor.org/packages/Biostrings")
3587 (synopsis "String objects and algorithms for biological sequences")
3589 "This package provides memory efficient string containers, string
3590 matching algorithms, and other utilities, for fast manipulation of large
3591 biological sequences or sets of sequences.")
3592 (license license:artistic2.0)))
3594 (define-public r-biovizbase
3596 (name "r-biovizbase")
3601 (uri (bioconductor-uri "biovizBase" version))
3604 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
3605 (properties `((upstream-name . "biovizBase")))
3606 (build-system r-build-system)
3608 (list r-annotationdbi
3625 r-summarizedexperiment
3626 r-variantannotation))
3627 (home-page "https://bioconductor.org/packages/biovizBase")
3628 (synopsis "Basic graphic utilities for visualization of genomic data")
3630 "The biovizBase package is designed to provide a set of utilities, color
3631 schemes and conventions for genomic data. It serves as the base for various
3632 high-level packages for biological data visualization. This saves development
3633 effort and encourages consistency.")
3634 (license license:artistic2.0)))
3636 (define-public r-bsgenome
3642 (uri (bioconductor-uri "BSgenome" version))
3645 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
3647 `((upstream-name . "BSgenome")))
3648 (build-system r-build-system)
3650 (list r-biocgenerics
3660 (home-page "https://bioconductor.org/packages/BSgenome")
3661 (synopsis "Infrastructure for Biostrings-based genome data packages")
3663 "This package provides infrastructure shared by all Biostrings-based
3664 genome data packages and support for efficient SNP representation.")
3665 (license license:artistic2.0)))
3667 (define-public r-category
3674 (uri (bioconductor-uri "Category" version))
3677 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
3678 (properties `((upstream-name . "Category")))
3679 (build-system r-build-system)
3691 (home-page "https://bioconductor.org/packages/Category")
3692 (synopsis "Category analysis")
3694 "This package provides a collection of tools for performing category
3696 (license license:artistic2.0)))
3698 (define-public r-chipseeker
3700 (name "r-chipseeker")
3704 (uri (bioconductor-uri "ChIPseeker" version))
3707 "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"))))
3708 (build-system r-build-system)
3712 (list r-annotationdbi
3731 r-txdb-hsapiens-ucsc-hg19-knowngene))
3732 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
3733 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
3734 (description "This package implements functions to retrieve the nearest
3735 genes around the peak, annotate genomic region of the peak, statstical methods
3736 for estimate the significance of overlap among ChIP peak data sets, and
3737 incorporate GEO database for user to compare the own dataset with those
3738 deposited in database. The comparison can be used to infer cooperative
3739 regulation and thus can be used to generate hypotheses. Several visualization
3740 functions are implemented to summarize the coverage of the peak experiment,
3741 average profile and heatmap of peaks binding to TSS regions, genomic
3742 annotation, distance to TSS, and overlap of peaks or genes.")
3743 (license license:artistic2.0)))
3745 (define-public r-chipseq
3752 (uri (bioconductor-uri "chipseq" version))
3755 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
3756 (build-system r-build-system)
3758 (list r-biocgenerics
3764 (home-page "https://bioconductor.org/packages/chipseq")
3765 (synopsis "Package for analyzing ChIPseq data")
3767 "This package provides tools for processing short read data from ChIPseq
3769 (license license:artistic2.0)))
3771 (define-public r-complexheatmap
3773 (name "r-complexheatmap")
3778 (uri (bioconductor-uri "ComplexHeatmap" version))
3781 "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"))))
3783 `((upstream-name . "ComplexHeatmap")))
3784 (build-system r-build-system)
3802 "https://github.com/jokergoo/ComplexHeatmap")
3803 (synopsis "Making Complex Heatmaps")
3805 "Complex heatmaps are efficient to visualize associations between
3806 different sources of data sets and reveal potential structures. This package
3807 provides a highly flexible way to arrange multiple heatmaps and supports
3808 self-defined annotation graphics.")
3809 (license license:gpl2+)))
3811 (define-public r-copywriter
3813 (name "r-copywriter")
3818 (uri (bioconductor-uri "CopywriteR" version))
3821 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
3822 (properties `((upstream-name . "CopywriteR")))
3823 (build-system r-build-system)
3825 (list r-biocparallel
3839 (home-page "https://github.com/PeeperLab/CopywriteR")
3840 (synopsis "Copy number information from targeted sequencing")
3842 "CopywriteR extracts DNA copy number information from targeted sequencing
3843 by utilizing off-target reads. It allows for extracting uniformly distributed
3844 copy number information, can be used without reference, and can be applied to
3845 sequencing data obtained from various techniques including chromatin
3846 immunoprecipitation and target enrichment on small gene panels. Thereby,
3847 CopywriteR constitutes a widely applicable alternative to available copy
3848 number detection tools.")
3849 (license license:gpl2)))
3851 (define-public r-deseq
3858 (uri (bioconductor-uri "DESeq" version))
3861 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
3862 (properties `((upstream-name . "DESeq")))
3863 (build-system r-build-system)
3873 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
3874 (synopsis "Differential gene expression analysis")
3876 "This package provides tools for estimating variance-mean dependence in
3877 count data from high-throughput genetic sequencing assays and for testing for
3878 differential expression based on a model using the negative binomial
3880 (license license:gpl3+)))
3882 (define-public r-deseq2
3889 (uri (bioconductor-uri "DESeq2" version))
3892 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
3893 (properties `((upstream-name . "DESeq2")))
3894 (build-system r-build-system)
3908 r-summarizedexperiment))
3911 (home-page "https://bioconductor.org/packages/DESeq2")
3912 (synopsis "Differential gene expression analysis")
3914 "This package provides functions to estimate variance-mean dependence in
3915 count data from high-throughput nucleotide sequencing assays and test for
3916 differential expression based on a model using the negative binomial
3918 (license license:lgpl3+)))
3920 (define-public r-dexseq
3927 (uri (bioconductor-uri "DEXSeq" version))
3930 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
3931 (properties `((upstream-name . "DEXSeq")))
3932 (build-system r-build-system)
3934 (list r-annotationdbi
3950 r-summarizedexperiment))
3953 (home-page "https://bioconductor.org/packages/DEXSeq")
3954 (synopsis "Inference of differential exon usage in RNA-Seq")
3956 "This package is focused on finding differential exon usage using RNA-seq
3957 exon counts between samples with different experimental designs. It provides
3958 functions that allows the user to make the necessary statistical tests based
3959 on a model that uses the negative binomial distribution to estimate the
3960 variance between biological replicates and generalized linear models for
3961 testing. The package also provides functions for the visualization and
3962 exploration of the results.")
3963 (license license:gpl3+)))
3965 (define-public r-diffcyt
3972 (uri (bioconductor-uri "diffcyt" version))
3974 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
3975 (properties `((upstream-name . "diffcyt")))
3976 (build-system r-build-system)
3990 r-summarizedexperiment
3992 (native-inputs (list r-knitr))
3993 (home-page "https://github.com/lmweber/diffcyt")
3994 (synopsis "Differential discovery in high-dimensional cytometry")
3996 "This package provides statistical methods for differential discovery
3997 analyses in high-dimensional cytometry data (including flow cytometry, mass
3998 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
3999 combination of high-resolution clustering and empirical Bayes moderated tests
4000 adapted from transcriptomics.")
4001 (license license:expat)))
4003 (define-public r-dirichletmultinomial
4005 (name "r-dirichletmultinomial")
4010 (uri (bioconductor-uri "DirichletMultinomial" version))
4013 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
4015 `((upstream-name . "DirichletMultinomial")))
4016 (build-system r-build-system)
4020 (list r-biocgenerics r-iranges r-s4vectors))
4021 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
4022 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
4024 "Dirichlet-multinomial mixture models can be used to describe variability
4025 in microbial metagenomic data. This package is an interface to code
4026 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
4028 (license license:lgpl3)))
4030 (define-public r-dittoseq
4036 (uri (bioconductor-uri "dittoSeq" version))
4039 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
4040 (properties `((upstream-name . "dittoSeq")))
4041 (build-system r-build-system)
4052 r-singlecellexperiment
4053 r-summarizedexperiment))
4054 (native-inputs (list r-knitr))
4055 (home-page "https://bioconductor.org/packages/dittoSeq")
4056 (synopsis "Single-cell and bulk RNA sequencing visualization")
4058 "This package provides a universal, user friendly, single-cell and bulk RNA
4059 sequencing visualization toolkit that allows highly customizable creation of
4060 color blindness friendly, publication-quality figures. dittoSeq accepts both
4061 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
4062 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
4063 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
4064 percent composition or expression across groups, and more. Customizations
4065 range from size and title adjustments to automatic generation of annotations
4066 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
4067 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
4068 many more. All with simple, discrete inputs. Color blindness friendliness is
4069 powered by legend adjustments (enlarged keys), and by allowing the use of
4070 shapes or letter-overlay in addition to the carefully selected
4071 code{dittoColors()}.")
4072 (license license:expat)))
4074 (define-public r-edaseq
4081 (uri (bioconductor-uri "EDASeq" version))
4084 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
4085 (properties `((upstream-name . "EDASeq")))
4086 (build-system r-build-system)
4088 (list r-annotationdbi
4102 (home-page "https://github.com/drisso/EDASeq")
4103 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
4105 "This package provides support for numerical and graphical summaries of
4106 RNA-Seq genomic read data. Provided within-lane normalization procedures to
4107 adjust for GC-content effect (or other gene-level effects) on read counts:
4108 loess robust local regression, global-scaling, and full-quantile
4109 normalization. Between-lane normalization procedures to adjust for
4110 distributional differences between lanes (e.g., sequencing depth):
4111 global-scaling and full-quantile normalization.")
4112 (license license:artistic2.0)))
4114 (define-public r-edger
4120 (uri (bioconductor-uri "edgeR" version))
4123 "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
4124 (properties `((upstream-name . "edgeR")))
4125 (build-system r-build-system)
4127 (list r-limma r-locfit r-rcpp))
4128 (home-page "http://bioinf.wehi.edu.au/edgeR")
4129 (synopsis "EdgeR does empirical analysis of digital gene expression data")
4130 (description "This package can do differential expression analysis of
4131 RNA-seq expression profiles with biological replication. It implements a range
4132 of statistical methodology based on the negative binomial distributions,
4133 including empirical Bayes estimation, exact tests, generalized linear models
4134 and quasi-likelihood tests. It be applied to differential signal analysis of
4135 other types of genomic data that produce counts, including ChIP-seq, SAGE and
4137 (license license:gpl2+)))
4139 (define-public r-ensembldb
4141 (name "r-ensembldb")
4146 (uri (bioconductor-uri "ensembldb" version))
4149 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
4150 (build-system r-build-system)
4152 (list r-annotationdbi
4170 (home-page "https://github.com/jotsetung/ensembldb")
4171 (synopsis "Utilities to create and use Ensembl-based annotation databases")
4173 "The package provides functions to create and use transcript-centric
4174 annotation databases/packages. The annotation for the databases are directly
4175 fetched from Ensembl using their Perl API. The functionality and data is
4176 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
4177 but, in addition to retrieve all gene/transcript models and annotations from
4178 the database, the @code{ensembldb} package also provides a filter framework
4179 allowing to retrieve annotations for specific entries like genes encoded on a
4180 chromosome region or transcript models of lincRNA genes.")
4181 ;; No version specified
4182 (license license:lgpl3+)))
4184 (define-public r-fastseg
4191 (uri (bioconductor-uri "fastseg" version))
4194 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
4195 (build-system r-build-system)
4197 (list r-biobase r-biocgenerics r-genomicranges r-iranges
4199 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
4200 (synopsis "Fast segmentation algorithm for genetic sequencing data")
4202 "Fastseg implements a very fast and efficient segmentation algorithm.
4203 It can segment data from DNA microarrays and data from next generation
4204 sequencing for example to detect copy number segments. Further it can segment
4205 data from RNA microarrays like tiling arrays to identify transcripts. Most
4206 generally, it can segment data given as a matrix or as a vector. Various data
4207 formats can be used as input to fastseg like expression set objects for
4208 microarrays or GRanges for sequencing data.")
4209 (license license:lgpl2.0+)))
4211 (define-public r-gage
4218 (uri (bioconductor-uri "gage" version))
4221 "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"))))
4222 (build-system r-build-system)
4224 (list r-annotationdbi r-go-db r-graph r-keggrest))
4225 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
4226 "articles/10.1186/1471-2105-10-161"))
4227 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
4229 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
4230 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
4231 data attributes including sample sizes, experimental designs, assay platforms,
4232 and other types of heterogeneity. The gage package provides functions for
4233 basic GAGE analysis, result processing and presentation. In addition, it
4234 provides demo microarray data and commonly used gene set data based on KEGG
4235 pathways and GO terms. These functions and data are also useful for gene set
4236 analysis using other methods.")
4237 (license license:gpl2+)))
4239 (define-public r-genefilter
4241 (name "r-genefilter")
4246 (uri (bioconductor-uri "genefilter" version))
4249 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
4250 (build-system r-build-system)
4252 (list gfortran r-knitr))
4254 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
4256 (home-page "https://bioconductor.org/packages/genefilter")
4257 (synopsis "Filter genes from high-throughput experiments")
4259 "This package provides basic functions for filtering genes from
4260 high-throughput sequencing experiments.")
4261 (license license:artistic2.0)))
4263 (define-public r-geneoverlap
4265 (name "r-geneoverlap")
4269 (uri (bioconductor-uri "GeneOverlap" version))
4272 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
4273 (build-system r-build-system)
4275 (list r-rcolorbrewer r-gplots))
4276 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
4277 (synopsis "Test and visualize gene overlaps")
4278 (description "This package can be used to test two sets of gene lists
4279 and visualize the results.")
4280 (license license:gpl3)))
4282 (define-public r-genomation
4284 (name "r-genomation")
4288 (uri (bioconductor-uri "genomation" version))
4291 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
4292 (build-system r-build-system)
4316 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
4317 (synopsis "Summary, annotation and visualization of genomic data")
4319 "This package provides a package for summary and annotation of genomic
4320 intervals. Users can visualize and quantify genomic intervals over
4321 pre-defined functional regions, such as promoters, exons, introns, etc. The
4322 genomic intervals represent regions with a defined chromosome position, which
4323 may be associated with a score, such as aligned reads from HT-seq experiments,
4324 TF binding sites, methylation scores, etc. The package can use any tabular
4325 genomic feature data as long as it has minimal information on the locations of
4326 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4327 (license license:artistic2.0)))
4329 (define-public r-genomeinfodb
4331 (name "r-genomeinfodb")
4335 (uri (bioconductor-uri "GenomeInfoDb" version))
4338 "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"))))
4340 `((upstream-name . "GenomeInfoDb")))
4341 (build-system r-build-system)
4343 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
4347 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
4348 (synopsis "Utilities for manipulating chromosome identifiers")
4350 "This package contains data and functions that define and allow
4351 translation between different chromosome sequence naming conventions (e.g.,
4352 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4353 names in their natural, rather than lexicographic, order.")
4354 (license license:artistic2.0)))
4356 (define-public r-genomicalignments
4358 (name "r-genomicalignments")
4362 (uri (bioconductor-uri "GenomicAlignments" version))
4365 "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
4367 `((upstream-name . "GenomicAlignments")))
4368 (build-system r-build-system)
4370 (list r-biocgenerics
4378 r-summarizedexperiment))
4379 (home-page "https://bioconductor.org/packages/GenomicAlignments")
4380 (synopsis "Representation and manipulation of short genomic alignments")
4382 "This package provides efficient containers for storing and manipulating
4383 short genomic alignments (typically obtained by aligning short reads to a
4384 reference genome). This includes read counting, computing the coverage,
4385 junction detection, and working with the nucleotide content of the
4387 (license license:artistic2.0)))
4389 (define-public r-genomicfeatures
4391 (name "r-genomicfeatures")
4395 (uri (bioconductor-uri "GenomicFeatures" version))
4398 "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"))))
4400 `((upstream-name . "GenomicFeatures")))
4401 (build-system r-build-system)
4403 (list r-annotationdbi
4420 (home-page "https://bioconductor.org/packages/GenomicFeatures")
4421 (synopsis "Tools for working with transcript centric annotations")
4423 "This package provides a set of tools and methods for making and
4424 manipulating transcript centric annotations. With these tools the user can
4425 easily download the genomic locations of the transcripts, exons and cds of a
4426 given organism, from either the UCSC Genome Browser or a BioMart
4427 database (more sources will be supported in the future). This information is
4428 then stored in a local database that keeps track of the relationship between
4429 transcripts, exons, cds and genes. Flexible methods are provided for
4430 extracting the desired features in a convenient format.")
4431 (license license:artistic2.0)))
4433 (define-public r-genomicfiles
4435 (name "r-genomicfiles")
4440 (uri (bioconductor-uri "GenomicFiles" version))
4443 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
4444 (properties `((upstream-name . "GenomicFiles")))
4445 (build-system r-build-system)
4447 (list r-biocgenerics
4457 r-summarizedexperiment
4458 r-variantannotation))
4459 (home-page "https://bioconductor.org/packages/GenomicFiles")
4460 (synopsis "Distributed computing by file or by range")
4462 "This package provides infrastructure for parallel computations
4463 distributed by file or by range. User defined mapper and reducer functions
4464 provide added flexibility for data combination and manipulation.")
4465 (license license:artistic2.0)))
4467 (define-public r-genomicranges
4469 (name "r-genomicranges")
4473 (uri (bioconductor-uri "GenomicRanges" version))
4476 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
4478 `((upstream-name . "GenomicRanges")))
4479 (build-system r-build-system)
4481 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
4484 (home-page "https://bioconductor.org/packages/GenomicRanges")
4485 (synopsis "Representation and manipulation of genomic intervals")
4487 "This package provides tools to efficiently represent and manipulate
4488 genomic annotations and alignments is playing a central role when it comes to
4489 analyzing high-throughput sequencing data (a.k.a. NGS data). The
4490 GenomicRanges package defines general purpose containers for storing and
4491 manipulating genomic intervals and variables defined along a genome.")
4492 (license license:artistic2.0)))
4494 (define-public r-gostats
4501 (uri (bioconductor-uri "GOstats" version))
4504 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
4505 (properties `((upstream-name . "GOstats")))
4506 (build-system r-build-system)
4517 (home-page "https://bioconductor.org/packages/GOstats")
4518 (synopsis "Tools for manipulating GO and microarrays")
4520 "This package provides a set of tools for interacting with GO and
4521 microarray data. A variety of basic manipulation tools for graphs, hypothesis
4522 testing and other simple calculations.")
4523 (license license:artistic2.0)))
4525 (define-public r-gseabase
4532 (uri (bioconductor-uri "GSEABase" version))
4535 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
4536 (properties `((upstream-name . "GSEABase")))
4537 (build-system r-build-system)
4547 (home-page "https://bioconductor.org/packages/GSEABase")
4548 (synopsis "Gene set enrichment data structures and methods")
4550 "This package provides classes and methods to support @dfn{Gene Set
4551 Enrichment Analysis} (GSEA).")
4552 (license license:artistic2.0)))
4554 (define-public r-hpar
4561 (uri (bioconductor-uri "hpar" version))
4564 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
4565 (build-system r-build-system)
4568 (home-page "https://bioconductor.org/packages/hpar/")
4569 (synopsis "Human Protein Atlas in R")
4570 (description "This package provides a simple interface to and data from
4571 the Human Protein Atlas project.")
4572 (license license:artistic2.0)))
4574 (define-public r-rhtslib
4581 (uri (bioconductor-uri "Rhtslib" version))
4584 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
4585 (properties `((upstream-name . "Rhtslib")))
4586 (build-system r-build-system)
4587 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
4588 ;; which makes R abort the build.
4589 (arguments '(#:configure-flags '("--no-staged-install")))
4591 (list curl zlib ; packages using rhtslib need to link with zlib
4594 (list pkg-config r-knitr))
4595 (home-page "https://github.com/nhayden/Rhtslib")
4596 (synopsis "High-throughput sequencing library as an R package")
4598 "This package provides the HTSlib C library for high-throughput
4599 nucleotide sequence analysis. The package is primarily useful to developers
4600 of other R packages who wish to make use of HTSlib.")
4601 (license license:lgpl2.0+)))
4603 (define-public r-impute
4609 (uri (bioconductor-uri "impute" version))
4612 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
4615 (build-system r-build-system)
4616 (home-page "https://bioconductor.org/packages/impute")
4617 (synopsis "Imputation for microarray data")
4619 "This package provides a function to impute missing gene expression
4620 microarray data, using nearest neighbor averaging.")
4621 (license license:gpl2+)))
4623 (define-public r-interactivedisplaybase
4625 (name "r-interactivedisplaybase")
4630 (uri (bioconductor-uri "interactiveDisplayBase" version))
4633 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
4635 `((upstream-name . "interactiveDisplayBase")))
4636 (build-system r-build-system)
4638 (list r-biocgenerics r-dt r-shiny))
4641 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
4642 (synopsis "Base package for web displays of Bioconductor objects")
4644 "This package contains the basic methods needed to generate interactive
4645 Shiny-based display methods for Bioconductor objects.")
4646 (license license:artistic2.0)))
4648 (define-public r-keggrest
4655 (uri (bioconductor-uri "KEGGREST" version))
4658 "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
4659 (properties `((upstream-name . "KEGGREST")))
4660 (build-system r-build-system)
4662 (list r-biostrings r-httr r-png))
4665 (home-page "https://bioconductor.org/packages/KEGGREST")
4666 (synopsis "Client-side REST access to KEGG")
4668 "This package provides a package that provides a client interface to the
4669 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
4670 (license license:artistic2.0)))
4672 (define-public r-lfa
4679 (uri (bioconductor-uri "lfa" version))
4681 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
4682 (properties `((upstream-name . "lfa")))
4683 (build-system r-build-system)
4684 (propagated-inputs (list r-corpcor))
4685 (native-inputs (list r-knitr))
4686 (home-page "https://github.com/StoreyLab/lfa")
4687 (synopsis "Logistic Factor Analysis for categorical data")
4689 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
4690 Binomial data via estimation of latent structure in the natural parameter.")
4691 (license license:gpl3)))
4693 (define-public r-limma
4699 (uri (bioconductor-uri "limma" version))
4702 "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"))))
4703 (build-system r-build-system)
4704 (home-page "http://bioinf.wehi.edu.au/limma")
4705 (synopsis "Package for linear models for microarray and RNA-seq data")
4706 (description "This package can be used for the analysis of gene expression
4707 studies, especially the use of linear models for analysing designed experiments
4708 and the assessment of differential expression. The analysis methods apply to
4709 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
4710 (license license:gpl2+)))
4712 (define-public r-made4
4718 (uri (bioconductor-uri "made4" version))
4721 "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
4722 (properties `((upstream-name . "made4")))
4723 (build-system r-build-system)
4730 r-summarizedexperiment))
4731 (native-inputs (list r-knitr))
4732 (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
4733 (synopsis "Multivariate analysis of microarray data using ADE4")
4735 "This is a package for multivariate data analysis and graphical display
4736 of microarray data. Functions are included for supervised dimension
4737 reduction (between group analysis) and joint dimension reduction of two
4738 datasets (coinertia analysis).")
4739 (license license:artistic2.0)))
4741 (define-public r-methylkit
4743 (name "r-methylkit")
4747 (uri (bioconductor-uri "methylKit" version))
4750 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
4751 (properties `((upstream-name . "methylKit")))
4752 (build-system r-build-system)
4774 (list r-knitr)) ; for vignettes
4775 (home-page "https://github.com/al2na/methylKit")
4777 "DNA methylation analysis from high-throughput bisulfite sequencing results")
4779 "MethylKit is an R package for DNA methylation analysis and annotation
4780 from high-throughput bisulfite sequencing. The package is designed to deal
4781 with sequencing data from @dfn{Reduced representation bisulfite
4782 sequencing} (RRBS) and its variants, but also target-capture methods and whole
4783 genome bisulfite sequencing. It also has functions to analyze base-pair
4784 resolution 5hmC data from experimental protocols such as oxBS-Seq and
4786 (license license:artistic2.0)))
4788 (define-public r-motifrg
4795 (uri (bioconductor-uri "motifRG" version))
4798 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
4799 (properties `((upstream-name . "motifRG")))
4800 (build-system r-build-system)
4804 r-bsgenome-hsapiens-ucsc-hg19
4808 (home-page "https://bioconductor.org/packages/motifRG")
4809 (synopsis "Discover motifs in high throughput sequencing data")
4811 "This package provides tools for discriminative motif discovery in high
4812 throughput genetic sequencing data sets using regression methods.")
4813 (license license:artistic2.0)))
4815 (define-public r-muscat
4822 (uri (bioconductor-uri "muscat" version))
4825 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
4826 (properties `((upstream-name . "muscat")))
4827 (build-system r-build-system)
4829 (list r-biocparallel
4850 r-singlecellexperiment
4851 r-summarizedexperiment
4854 (native-inputs (list r-knitr))
4855 (home-page "https://github.com/HelenaLC/muscat")
4856 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
4858 "This package @code{muscat} provides various methods and visualization tools
4859 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
4860 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
4861 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
4862 platform that mimics both single and multi-sample scRNA-seq data.")
4863 (license license:gpl3)))
4865 (define-public r-mutationalpatterns
4867 (name "r-mutationalpatterns")
4872 (uri (bioconductor-uri "MutationalPatterns" version))
4875 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
4876 (build-system r-build-system)
4880 (list r-biocgenerics
4883 ;; These two packages are suggested packages
4884 r-bsgenome-hsapiens-1000genomes-hs37d5
4885 r-bsgenome-hsapiens-ucsc-hg19
4903 r-variantannotation))
4904 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
4905 (synopsis "Extract and visualize mutational patterns in genomic data")
4906 (description "This package provides an extensive toolset for the
4907 characterization and visualization of a wide range of mutational patterns
4908 in SNV base substitution data.")
4909 (license license:expat)))
4911 (define-public r-msnbase
4918 (uri (bioconductor-uri "MSnbase" version))
4921 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
4922 (properties `((upstream-name . "MSnbase")))
4923 (build-system r-build-system)
4949 (home-page "https://github.com/lgatto/MSnbase")
4950 (synopsis "Base functions and classes for MS-based proteomics")
4952 "This package provides basic plotting, data manipulation and processing
4953 of mass spectrometry based proteomics data.")
4954 (license license:artistic2.0)))
4956 (define-public r-msnid
4963 (uri (bioconductor-uri "MSnID" version))
4966 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
4967 (properties `((upstream-name . "MSnID")))
4968 (build-system r-build-system)
4971 (modify-phases %standard-phases
4972 (add-after 'unpack 'set-HOME
4973 (lambda _ (setenv "HOME" "/tmp"))))))
4975 (list r-annotationdbi
5001 (home-page "https://bioconductor.org/packages/MSnID")
5002 (synopsis "Utilities for LC-MSn proteomics identifications")
5004 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
5005 from mzIdentML (leveraging the mzID package) or text files. After collating
5006 the search results from multiple datasets it assesses their identification
5007 quality and optimize filtering criteria to achieve the maximum number of
5008 identifications while not exceeding a specified false discovery rate. It also
5009 contains a number of utilities to explore the MS/MS results and assess missed
5010 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
5011 (license license:artistic2.0)))
5013 (define-public r-mzid
5020 (uri (bioconductor-uri "mzID" version))
5023 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
5024 (properties `((upstream-name . "mzID")))
5025 (build-system r-build-system)
5035 (home-page "https://bioconductor.org/packages/mzID")
5036 (synopsis "Parser for mzIdentML files")
5038 "This package provides a parser for mzIdentML files implemented using the
5039 XML package. The parser tries to be general and able to handle all types of
5040 mzIdentML files with the drawback of having less pretty output than a vendor
5042 (license license:gpl2+)))
5044 (define-public r-mzr
5051 (uri (bioconductor-uri "mzR" version))
5054 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
5055 (modules '((guix build utils)))
5057 '(delete-file-recursively "src/boost"))))
5058 (properties `((upstream-name . "mzR")))
5059 (build-system r-build-system)
5062 (modify-phases %standard-phases
5063 (add-after 'unpack 'use-system-boost
5065 (substitute* "src/Makevars"
5066 (("\\./boost/libs.*") "")
5067 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
5068 (("\\ARCH_OBJS=" line)
5070 "\nBOOST_LIBS=-lboost_system -lboost_regex \
5071 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
5073 (list boost ; use this instead of the bundled boost sources
5084 (home-page "https://github.com/sneumann/mzR/")
5085 (synopsis "Parser for mass spectrometry data files")
5087 "The mzR package provides a unified API to the common file formats and
5088 parsers available for mass spectrometry data. It comes with a wrapper for the
5089 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
5090 The package contains the original code written by the ISB, and a subset of the
5091 proteowizard library for mzML and mzIdentML. The netCDF reading code has
5092 previously been used in XCMS.")
5093 (license license:artistic2.0)))
5095 (define-public r-organism-dplyr
5097 (name "r-organism-dplyr")
5102 (uri (bioconductor-uri "Organism.dplyr" version))
5105 "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
5106 (properties `((upstream-name . "Organism.dplyr")))
5107 (build-system r-build-system)
5109 (list r-annotationdbi
5123 (native-inputs (list r-knitr))
5124 (home-page "https://bioconductor.org/packages/Organism.dplyr")
5125 (synopsis "Dplyr-based access to Bioconductor annotation resources")
5127 "This package provides an alternative interface to Bioconductor @code{
5128 annotation} resources, in particular the gene identifier mapping functionality
5129 of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
5130 functionality of the @code{TxDb} packages (e.g.,
5131 @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
5132 (license license:artistic2.0)))
5134 (define-public r-organismdbi
5136 (name "r-organismdbi")
5141 (uri (bioconductor-uri "OrganismDbi" version))
5144 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
5145 (properties `((upstream-name . "OrganismDbi")))
5146 (build-system r-build-system)
5148 (list r-annotationdbi
5159 (home-page "https://bioconductor.org/packages/OrganismDbi")
5160 (synopsis "Software to enable the smooth interfacing of database packages")
5161 (description "The package enables a simple unified interface to several
5162 annotation packages each of which has its own schema by taking advantage of
5163 the fact that each of these packages implements a select methods.")
5164 (license license:artistic2.0)))
5166 (define-public r-pcaexplorer
5168 (name "r-pcaexplorer")
5173 (uri (bioconductor-uri "pcaExplorer" version))
5176 "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
5177 (properties `((upstream-name . "pcaExplorer")))
5178 (build-system r-build-system)
5180 (list r-annotationdbi
5206 r-summarizedexperiment
5210 (native-inputs (list r-knitr))
5211 (home-page "https://github.com/federicomarini/pcaExplorer")
5213 "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
5215 "This package provides functionality for interactive visualization of RNA-seq
5216 datasets based on Principal Components Analysis. The methods provided allow for
5217 quick information extraction and effective data exploration. A Shiny
5218 application encapsulates the whole analysis.")
5219 (license license:expat)))
5221 (define-public r-pcamethods
5223 (name "r-pcamethods")
5228 (uri (bioconductor-uri "pcaMethods" version))
5231 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
5232 (properties `((upstream-name . "pcaMethods")))
5233 (build-system r-build-system)
5235 (list r-biobase r-biocgenerics r-mass r-rcpp))
5236 (home-page "https://github.com/hredestig/pcamethods")
5237 (synopsis "Collection of PCA methods")
5239 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
5240 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
5241 for missing value estimation is included for comparison. BPCA, PPCA and
5242 NipalsPCA may be used to perform PCA on incomplete data as well as for
5243 accurate missing value estimation. A set of methods for printing and plotting
5244 the results is also provided. All PCA methods make use of the same data
5245 structure (pcaRes) to provide a common interface to the PCA results.")
5246 (license license:gpl3+)))
5248 ;; This is a CRAN package, but it depends on a Bioconductor package:
5249 ;; r-aroma-light, r-dnacopy..
5250 (define-public r-pscbs
5257 (uri (cran-uri "PSCBS" version))
5259 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
5260 (properties `((upstream-name . "PSCBS")))
5261 (build-system r-build-system)
5264 (modify-phases %standard-phases
5265 (add-before 'install 'change-home-dir
5267 ;; Change from /homeless-shelter to /tmp for write permission.
5268 (setenv "HOME" "/tmp"))))))
5280 (list r-r-rsp ;used to build vignettes
5282 (home-page "https://github.com/HenrikBengtsson/PSCBS")
5283 (synopsis "Analysis of parent-specific DNA copy numbers")
5285 "This is a package for segmentation of allele-specific DNA copy number
5286 data and detection of regions with abnormal copy number within each parental
5287 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
5288 (license license:gpl2+)))
5290 (define-public r-protgenerics
5292 (name "r-protgenerics")
5297 (uri (bioconductor-uri "ProtGenerics" version))
5300 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
5301 (properties `((upstream-name . "ProtGenerics")))
5302 (build-system r-build-system)
5303 (home-page "https://github.com/lgatto/ProtGenerics")
5304 (synopsis "S4 generic functions for proteomics infrastructure")
5306 "This package provides S4 generic functions needed by Bioconductor
5307 proteomics packages.")
5308 (license license:artistic2.0)))
5310 (define-public r-rbgl
5317 (uri (bioconductor-uri "RBGL" version))
5320 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
5321 (properties `((upstream-name . "RBGL")))
5322 (build-system r-build-system)
5324 (list r-bh r-graph))
5325 (home-page "https://www.bioconductor.org/packages/RBGL")
5326 (synopsis "Interface to the Boost graph library")
5328 "This package provides a fairly extensive and comprehensive interface to
5329 the graph algorithms contained in the Boost library.")
5330 (license license:artistic2.0)))
5332 (define-public r-rcas
5338 (uri (bioconductor-uri "RCAS" version))
5341 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
5342 (properties `((upstream-name . "RCAS")))
5343 (build-system r-build-system)
5345 (list r-biocgenerics
5348 r-bsgenome-hsapiens-ucsc-hg19
5374 (synopsis "RNA-centric annotation system")
5376 "RCAS aims to be a standalone RNA-centric annotation system that provides
5377 intuitive reports and publication-ready graphics. This package provides the R
5378 library implementing most of the pipeline's features.")
5379 (home-page "https://github.com/BIMSBbioinfo/RCAS")
5380 (license license:artistic2.0)))
5382 (define-public r-regioner
5389 (uri (bioconductor-uri "regioneR" version))
5392 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
5393 (properties `((upstream-name . "regioneR")))
5394 (build-system r-build-system)
5406 (home-page "https://bioconductor.org/packages/regioneR/")
5407 (synopsis "Association analysis of genomic regions")
5408 (description "This package offers a statistical framework based on
5409 customizable permutation tests to assess the association between genomic
5410 region sets and other genomic features.")
5411 (license license:artistic2.0)))
5413 (define-public r-reportingtools
5415 (name "r-reportingtools")
5420 (uri (bioconductor-uri "ReportingTools" version))
5423 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
5425 `((upstream-name . "ReportingTools")))
5426 (build-system r-build-system)
5449 (home-page "https://bioconductor.org/packages/ReportingTools/")
5450 (synopsis "Tools for making reports in various formats")
5452 "The ReportingTools package enables users to easily display reports of
5453 analysis results generated from sources such as microarray and sequencing
5454 data. The package allows users to create HTML pages that may be viewed on a
5455 web browser, or in other formats. Users can generate tables with sortable and
5456 filterable columns, make and display plots, and link table entries to other
5457 data sources such as NCBI or larger plots within the HTML page. Using the
5458 package, users can also produce a table of contents page to link various
5459 reports together for a particular project that can be viewed in a web
5461 (license license:artistic2.0)))
5463 (define-public r-rhdf5
5469 (uri (bioconductor-uri "rhdf5" version))
5472 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
5473 (build-system r-build-system)
5475 (list r-rhdf5filters r-rhdf5lib))
5478 (home-page "https://bioconductor.org/packages/rhdf5")
5479 (synopsis "HDF5 interface to R")
5481 "This R/Bioconductor package provides an interface between HDF5 and R.
5482 HDF5's main features are the ability to store and access very large and/or
5483 complex datasets and a wide variety of metadata on mass storage (disk) through
5484 a completely portable file format. The rhdf5 package is thus suited for the
5485 exchange of large and/or complex datasets between R and other software
5486 package, and for letting R applications work on datasets that are larger than
5487 the available RAM.")
5488 (license license:artistic2.0)))
5490 (define-public r-rhdf5filters
5492 (name "r-rhdf5filters")
5497 (uri (bioconductor-uri "rhdf5filters" version))
5500 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
5501 (properties `((upstream-name . "rhdf5filters")))
5502 (build-system r-build-system)
5509 (home-page "https://github.com/grimbough/rhdf5filters")
5510 (synopsis "HDF5 compression filters")
5512 "This package provides a collection of compression filters for use with
5514 (license license:bsd-2)))
5516 (define-public r-rsamtools
5518 (name "r-rsamtools")
5522 (uri (bioconductor-uri "Rsamtools" version))
5525 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
5527 `((upstream-name . "Rsamtools")))
5528 (build-system r-build-system)
5531 (modify-phases %standard-phases
5532 (add-after 'unpack 'use-system-zlib
5534 (substitute* "DESCRIPTION"
5535 (("zlibbioc, ") ""))
5536 (substitute* "NAMESPACE"
5537 (("import\\(zlibbioc\\)") "")))))))
5539 (list r-biocgenerics
5549 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
5550 (synopsis "Interface to samtools, bcftools, and tabix")
5552 "This package provides an interface to the @code{samtools},
5553 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
5554 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
5555 tab-delimited (tabix) files.")
5556 (license license:expat)))
5558 ;; This is a CRAN package, but it depends on a Bioconductor package:
5560 (define-public r-restfulr
5567 (uri (cran-uri "restfulr" version))
5570 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
5571 (properties `((upstream-name . "restfulr")))
5572 (build-system r-build-system)
5574 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
5575 (home-page "https://cran.r-project.org/package=restfulr")
5576 (synopsis "R interface to RESTful web services")
5578 "This package models a RESTful service as if it were a nested R list.")
5579 (license license:artistic2.0)))
5581 (define-public r-rtracklayer
5583 (name "r-rtracklayer")
5587 (uri (bioconductor-uri "rtracklayer" version))
5590 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
5591 (build-system r-build-system)
5594 (modify-phases %standard-phases
5595 (add-after 'unpack 'use-system-zlib
5597 (substitute* "DESCRIPTION"
5598 ((" zlibbioc,") ""))
5599 (substitute* "NAMESPACE"
5600 (("import\\(zlibbioc\\)") "")))))))
5606 (list r-biocgenerics
5620 (home-page "https://bioconductor.org/packages/rtracklayer")
5621 (synopsis "R interface to genome browsers and their annotation tracks")
5623 "rtracklayer is an extensible framework for interacting with multiple
5624 genome browsers (currently UCSC built-in) and manipulating annotation tracks
5625 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
5626 built-in). The user may export/import tracks to/from the supported browsers,
5627 as well as query and modify the browser state, such as the current viewport.")
5628 (license license:artistic2.0)))
5630 ;; This is a CRAN package, but it depends on a Bioconductor package.
5631 (define-public r-samr
5638 (uri (cran-uri "samr" version))
5641 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
5642 (properties `((upstream-name . "samr")))
5643 (build-system r-build-system)
5651 (native-inputs (list gfortran))
5652 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
5653 (synopsis "Significance analysis of Microarrays")
5655 "This is a package for significance analysis of Microarrays for
5656 differential expression analysis, RNAseq data and related problems.")
5657 ;; Any version of the LGPL
5658 (license license:lgpl3+)))
5660 (define-public r-scannotatr
5662 (name "r-scannotatr")
5667 (uri (bioconductor-uri "scAnnotatR" version))
5669 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
5670 (properties `((upstream-name . "scAnnotatR")))
5671 (build-system r-build-system)
5673 (list r-annotationhub
5684 r-singlecellexperiment
5685 r-summarizedexperiment))
5686 (native-inputs (list r-knitr))
5687 (home-page "https://github.com/grisslab/scAnnotatR")
5688 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
5690 "This package comprises a set of pretrained machine learning models to
5691 predict basic immune cell types. This enables to quickly get a first
5692 annotation of the cell types present in the dataset without requiring prior
5693 knowledge. The package also lets you train using own models to predict new
5694 cell types based on specific research needs.")
5695 (license license:expat)))
5697 (define-public r-scdblfinder
5699 (name "r-scdblfinder")
5704 (uri (bioconductor-uri "scDblFinder" version))
5706 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
5707 (properties `((upstream-name . "scDblFinder")))
5708 (build-system r-build-system)
5710 (list r-biocgenerics
5728 r-singlecellexperiment
5729 r-summarizedexperiment
5731 (native-inputs (list r-knitr))
5732 (home-page "https://github.com/plger/scDblFinder")
5733 (synopsis "Detect multiplets in single-cell RNA sequencing data")
5735 "The scDblFinder package gathers various methods for the detection and
5736 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
5737 multiple cells captured within the same droplet or reaction volume). It
5738 includes methods formerly found in the scran package, and the new fast and
5739 comprehensive scDblFinder method.")
5740 (license license:gpl3)))
5742 (define-public r-scmap
5749 (uri (bioconductor-uri "scmap" version))
5751 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
5752 (properties `((upstream-name . "scmap")))
5753 (build-system r-build-system)
5768 r-singlecellexperiment
5769 r-summarizedexperiment))
5770 (native-inputs (list r-knitr))
5771 (home-page "https://github.com/hemberg-lab/scmap")
5772 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
5774 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
5775 composition of complex tissues since the technology allows researchers to
5776 define cell-types using unsupervised clustering of the transcriptome.
5777 However, due to differences in experimental methods and computational
5778 analyses, it is often challenging to directly compare the cells identified in
5779 two different experiments. @code{scmap} is a method for projecting cells from
5780 a scRNA-seq experiment onto the cell-types or individual cells identified in a
5781 different experiment.")
5782 (license license:gpl3)))
5784 (define-public r-scry
5790 (uri (bioconductor-uri "scry" version))
5793 "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
5794 (properties `((upstream-name . "scry")))
5795 (build-system r-build-system)
5797 (list r-biocsingular
5802 r-singlecellexperiment
5803 r-summarizedexperiment))
5804 (native-inputs (list r-knitr))
5805 (home-page "https://bioconductor.org/packages/scry.html")
5806 (synopsis "Small-count analysis methods for high-dimensional data")
5808 "Many modern biological datasets consist of small counts that are not
5809 well fit by standard linear-Gaussian methods such as principal component
5810 analysis. This package provides implementations of count-based feature
5811 selection and dimension reduction algorithms. These methods can be used to
5812 facilitate unsupervised analysis of any high-dimensional data such as
5813 single-cell RNA-seq.")
5814 (license license:artistic2.0)))
5816 (define-public r-seqlogo
5823 (uri (bioconductor-uri "seqLogo" version))
5826 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
5827 (properties `((upstream-name . "seqLogo")))
5828 (build-system r-build-system)
5831 (home-page "https://bioconductor.org/packages/seqLogo")
5832 (synopsis "Sequence logos for DNA sequence alignments")
5834 "seqLogo takes the position weight matrix of a DNA sequence motif and
5835 plots the corresponding sequence logo as introduced by Schneider and
5837 (license license:lgpl2.0+)))
5839 (define-public r-seqpattern
5841 (name "r-seqpattern")
5845 (uri (bioconductor-uri "seqPattern" version))
5848 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
5850 `((upstream-name . "seqPattern")))
5851 (build-system r-build-system)
5853 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
5854 (home-page "https://bioconductor.org/packages/seqPattern")
5855 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
5857 "This package provides tools to visualize oligonucleotide patterns and
5858 sequence motif occurrences across a large set of sequences centred at a common
5859 reference point and sorted by a user defined feature.")
5860 (license license:gpl3+)))
5862 (define-public r-shortread
5864 (name "r-shortread")
5869 (uri (bioconductor-uri "ShortRead" version))
5872 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
5873 (properties `((upstream-name . "ShortRead")))
5874 (build-system r-build-system)
5894 (home-page "https://bioconductor.org/packages/ShortRead")
5895 (synopsis "FASTQ input and manipulation tools")
5897 "This package implements sampling, iteration, and input of FASTQ files.
5898 It includes functions for filtering and trimming reads, and for generating a
5899 quality assessment report. Data are represented as
5900 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
5901 purposes. The package also contains legacy support for early single-end,
5902 ungapped alignment formats.")
5903 (license license:artistic2.0)))
5905 (define-public r-simplifyenrichment
5907 (name "r-simplifyenrichment")
5912 (uri (bioconductor-uri "simplifyEnrichment" version))
5915 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
5917 `((upstream-name . "simplifyEnrichment")))
5918 (build-system r-build-system)
5920 (list r-annotationdbi
5937 (native-inputs (list r-knitr))
5938 (home-page "https://github.com/jokergoo/simplifyEnrichment")
5939 (synopsis "Simplify functional enrichment results")
5940 (description "This package provides a new clustering algorithm, binary
5941 cut, for clustering similarity matrices of functional terms is implemented in
5942 this package. It also provides functionalities for visualizing, summarizing
5943 and comparing the clusterings.")
5944 (license license:expat)))
5946 (define-public r-transcriptr
5948 (name "r-transcriptr")
5953 (uri (bioconductor-uri "transcriptR" version))
5955 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
5956 (properties `((upstream-name . "transcriptR")))
5957 (build-system r-build-system)
5959 (list r-biocgenerics
5974 (native-inputs (list r-knitr))
5975 (home-page "https://bioconductor.org/packages/transcriptR")
5976 (synopsis "Primary transcripts detection and quantification")
5978 "The differences in the RNA types being sequenced have an impact on the
5979 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
5980 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
5981 broader coverage of both exonic and intronic regions. The presence of
5982 intronic reads in GRO-seq type of data makes it possible to use it to
5983 computationally identify and quantify all de novo continuous regions of
5984 transcription distributed across the genome. This type of data, however, is
5985 more challenging to interpret and less common practice compared to mRNA-seq.
5986 One of the challenges for primary transcript detection concerns the
5987 simultaneous transcription of closely spaced genes, which needs to be properly
5988 divided into individually transcribed units. The R package transcriptR
5989 combines RNA-seq data with ChIP-seq data of histone modifications that mark
5990 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
5991 overcome this challenge. The advantage of this approach over the use of, for
5992 example, gene annotations is that this approach is data driven and therefore
5993 able to deal also with novel and case specific events.")
5994 (license license:gpl3)))
5996 (define-public r-trajectoryutils
5998 (name "r-trajectoryutils")
6003 (uri (bioconductor-uri "TrajectoryUtils" version))
6006 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
6008 `((upstream-name . "TrajectoryUtils")))
6009 (build-system r-build-system)
6011 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
6012 r-summarizedexperiment))
6013 (native-inputs (list r-knitr))
6014 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
6015 (synopsis "Single-cell trajectory analysis utilities")
6017 "This package implements low-level utilities for single-cell trajectory
6018 analysis, primarily intended for re-use inside higher-level packages. It
6019 includes a function to create a cluster-level minimum spanning tree and data
6020 structures to hold pseudotime inference results.")
6021 (license license:gpl3)))
6023 (define-public r-slingshot
6025 (name "r-slingshot")
6029 (uri (bioconductor-uri "slingshot" version))
6032 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
6033 (build-system r-build-system)
6039 r-singlecellexperiment
6040 r-summarizedexperiment
6044 (home-page "https://bioconductor.org/packages/slingshot")
6045 (synopsis "Tools for ordering single-cell sequencing")
6046 (description "This package provides functions for inferring continuous,
6047 branching lineage structures in low-dimensional data. Slingshot was designed
6048 to model developmental trajectories in single-cell RNA sequencing data and
6049 serve as a component in an analysis pipeline after dimensionality reduction
6050 and clustering. It is flexible enough to handle arbitrarily many branching
6051 events and allows for the incorporation of prior knowledge through supervised
6052 graph construction.")
6053 (license license:artistic2.0)))
6055 (define-public r-stager
6062 (uri (bioconductor-uri "stageR" version))
6064 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
6065 (properties `((upstream-name . "stageR")))
6066 (build-system r-build-system)
6067 (propagated-inputs (list r-summarizedexperiment))
6068 (native-inputs (list r-knitr))
6069 (home-page "https://bioconductor.org/packages/stageR")
6070 (synopsis "Stage-wise analysis of high throughput gene expression data")
6072 "The stageR package allows automated stage-wise analysis of
6073 high-throughput gene expression data. The method is published in Genome
6075 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
6076 (license license:gpl3)))
6078 (define-public r-stringdb
6085 (uri (bioconductor-uri "STRINGdb" version))
6087 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
6088 (properties `((upstream-name . "STRINGdb")))
6089 (build-system r-build-system)
6100 (home-page "https://git.bioconductor.org/packages/STRINGdb")
6101 (synopsis "Search tool for the retrieval of interacting proteins database")
6103 "The @code{STRINGdb} package provides an R interface to the STRING
6104 protein-protein interactions database. @url{https://www.string-db.org,
6105 STRING} is a database of known and predicted protein-protein interactions.
6106 The interactions include direct (physical) and indirect (functional)
6107 associations. Each interaction is associated with a combined confidence score
6108 that integrates the various evidences.")
6109 (license license:gpl2)))
6111 (define-public r-structuralvariantannotation
6113 (name "r-structuralvariantannotation")
6118 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
6120 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
6121 (build-system r-build-system)
6135 r-summarizedexperiment
6136 r-variantannotation))
6139 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
6140 (synopsis "R package designed to simplify structural variant analysis")
6142 "This package contains useful helper functions for dealing with structural
6143 variants in VCF format. The packages contains functions for parsing VCFs from
6144 a number of popular callers as well as functions for dealing with breakpoints
6145 involving two separate genomic loci encoded as GRanges objects.")
6146 (license license:gpl3)))
6148 (define-public r-summarizedexperiment
6150 (name "r-summarizedexperiment")
6154 (uri (bioconductor-uri "SummarizedExperiment" version))
6157 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
6159 `((upstream-name . "SummarizedExperiment")))
6160 (build-system r-build-system)
6173 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
6174 (synopsis "Container for representing genomic ranges by sample")
6176 "The SummarizedExperiment container contains one or more assays, each
6177 represented by a matrix-like object of numeric or other mode. The rows
6178 typically represent genomic ranges of interest and the columns represent
6180 (license license:artistic2.0)))
6182 (define-public r-sva
6189 (uri (bioconductor-uri "sva" version))
6192 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
6193 (build-system r-build-system)
6201 (home-page "https://bioconductor.org/packages/sva")
6202 (synopsis "Surrogate variable analysis")
6204 "This package contains functions for removing batch effects and other
6205 unwanted variation in high-throughput experiment. It also contains functions
6206 for identifying and building surrogate variables for high-dimensional data
6207 sets. Surrogate variables are covariates constructed directly from
6208 high-dimensional data like gene expression/RNA sequencing/methylation/brain
6209 imaging data that can be used in subsequent analyses to adjust for unknown,
6210 unmodeled, or latent sources of noise.")
6211 (license license:artistic2.0)))
6213 (define-public r-systempiper
6215 (name "r-systempiper")
6220 (uri (bioconductor-uri "systemPipeR" version))
6223 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
6224 (properties `((upstream-name . "systemPipeR")))
6225 (build-system r-build-system)
6227 (list r-biocgenerics
6238 r-summarizedexperiment
6242 (home-page "https://github.com/tgirke/systemPipeR")
6243 (synopsis "Next generation sequencing workflow and reporting environment")
6245 "This R package provides tools for building and running automated
6246 end-to-end analysis workflows for a wide range of @dfn{next generation
6247 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6248 Important features include a uniform workflow interface across different NGS
6249 applications, automated report generation, and support for running both R and
6250 command-line software, such as NGS aligners or peak/variant callers, on local
6251 computers or compute clusters. Efficient handling of complex sample sets and
6252 experimental designs is facilitated by a consistently implemented sample
6253 annotation infrastructure.")
6254 (license license:artistic2.0)))
6256 (define-public r-topgo
6262 (uri (bioconductor-uri "topGO" version))
6265 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
6267 `((upstream-name . "topGO")))
6268 (build-system r-build-system)
6270 (list r-annotationdbi
6279 (home-page "https://bioconductor.org/packages/topGO")
6280 (synopsis "Enrichment analysis for gene ontology")
6282 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6283 terms while accounting for the topology of the GO graph. Different test
6284 statistics and different methods for eliminating local similarities and
6285 dependencies between GO terms can be implemented and applied.")
6286 ;; Any version of the LGPL applies.
6287 (license license:lgpl2.1+)))
6289 (define-public r-tximport
6295 (uri (bioconductor-uri "tximport" version))
6298 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
6299 (build-system r-build-system)
6302 (home-page "https://bioconductor.org/packages/tximport")
6303 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
6305 "This package provides tools to import transcript-level abundance,
6306 estimated counts and transcript lengths, and to summarize them into matrices
6307 for use with downstream gene-level analysis packages. Average transcript
6308 length, weighted by sample-specific transcript abundance estimates, is
6309 provided as a matrix which can be used as an offset for different expression
6310 of gene-level counts.")
6311 (license license:gpl2+)))
6313 ;; This is a CRAN package, but it depends on a Bioconductor package.
6314 (define-public r-valr
6321 (uri (cran-uri "valr" version))
6324 "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
6325 (build-system r-build-system)
6333 r-rtracklayer ;bioconductor package
6338 (home-page "https://github.com/rnabioco/valr")
6339 (synopsis "Genome interval arithmetic in R")
6341 "This package enables you to read and manipulate genome intervals and
6342 signals. It provides functionality similar to command-line tool suites within
6343 R, enabling interactive analysis and visualization of genome-scale data.")
6344 (license license:expat)))
6346 (define-public r-variantannotation
6348 (name "r-variantannotation")
6352 (uri (bioconductor-uri "VariantAnnotation" version))
6355 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
6357 `((upstream-name . "VariantAnnotation")))
6359 (list r-annotationdbi
6370 r-summarizedexperiment
6377 (build-system r-build-system)
6378 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6379 (synopsis "Package for annotation of genetic variants")
6380 (description "This R package can annotate variants, compute amino acid
6381 coding changes and predict coding outcomes.")
6382 (license license:artistic2.0)))
6384 (define-public r-vsn
6391 (uri (bioconductor-uri "vsn" version))
6394 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
6395 (build-system r-build-system)
6397 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
6399 (list r-knitr)) ; for vignettes
6400 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
6401 (synopsis "Variance stabilization and calibration for microarray data")
6403 "The package implements a method for normalising microarray intensities,
6404 and works for single- and multiple-color arrays. It can also be used for data
6405 from other technologies, as long as they have similar format. The method uses
6406 a robust variant of the maximum-likelihood estimator for an
6407 additive-multiplicative error model and affine calibration. The model
6408 incorporates data calibration step (a.k.a. normalization), a model for the
6409 dependence of the variance on the mean intensity and a variance stabilizing
6410 data transformation. Differences between transformed intensities are
6411 analogous to \"normalized log-ratios\". However, in contrast to the latter,
6412 their variance is independent of the mean, and they are usually more sensitive
6413 and specific in detecting differential transcription.")
6414 (license license:artistic2.0)))
6416 ;; There is no source tarball, so we fetch the code from the Bioconductor git
6418 (define-public r-xcir
6419 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
6423 (version (git-version "1.8.0" revision commit))
6427 (url "https://git.bioconductor.org/packages/XCIR")
6429 (file-name (git-file-name name version))
6432 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
6433 (properties `((upstream-name . "XCIR")))
6434 (build-system r-build-system)
6435 (propagated-inputs (list r-biomart
6443 r-variantannotation))
6444 (native-inputs (list r-knitr))
6445 (home-page "https://github.com/SRenan/XCIR")
6446 (synopsis "Analysis of X chromosome inactivation")
6448 "This package is an R package that offers models and tools for subject
6449 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
6451 (license license:gpl2))))
6453 (define-public r-xina
6460 (uri (bioconductor-uri "XINA" version))
6462 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
6463 (properties `((upstream-name . "XINA")))
6464 (build-system r-build-system)
6473 (native-inputs (list r-knitr))
6474 (home-page "https://git.bioconductor.org/packages/XINA")
6475 (synopsis "Identifying proteins that exhibit similar patterns")
6477 "The aim of @code{XINA} is to determine which proteins exhibit similar
6478 patterns within and across experimental conditions, since proteins with
6479 co-abundance patterns may have common molecular functions. @code{XINA} imports
6480 multiple datasets, tags dataset in silico, and combines the data for subsequent
6481 subgrouping into multiple clusters. The result is a single output depicting
6482 the variation across all conditions. @code{XINA} not only extracts
6483 coabundance profiles within and across experiments, but also incorporates
6484 protein-protein interaction databases and integrative resources such as
6485 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
6486 molecular functions, respectively, and produces intuitive graphical outputs.")
6487 (license license:gpl3)))
6489 (define-public r-xmapbridge
6491 (name "r-xmapbridge")
6496 (uri (bioconductor-uri "xmapbridge" version))
6498 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
6499 (properties `((upstream-name . "xmapbridge")))
6500 (build-system r-build-system)
6501 (home-page "https://git.bioconductor.org/packages/xmapbridge")
6502 (synopsis "Display numeric data in the web based genome browser X:MAP")
6504 "The package @code{xmapbridge} can plot graphs in the X:Map genome
6505 browser. X:Map uses the Google Maps API to provide a scrollable view of the
6506 genome. It supports a number of species, and can be accessed at
6507 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
6508 suitable format. Graph plotting in R is done using calls to the functions
6509 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
6510 similar to those used by the standard plot methods in R. These result in data
6511 being written to a set of files (in a specific directory structure) that
6512 contain the data to be displayed, as well as some additional meta-data
6513 describing each of the graphs.")
6514 (license license:lgpl3)))
6516 (define-public r-xvector
6522 (uri (bioconductor-uri "XVector" version))
6525 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
6527 `((upstream-name . "XVector")))
6528 (build-system r-build-system)
6531 (modify-phases %standard-phases
6532 (add-after 'unpack 'use-system-zlib
6534 (substitute* "DESCRIPTION"
6535 (("zlibbioc, ") ""))
6536 (substitute* "NAMESPACE"
6537 (("import\\(zlibbioc\\)") ""))
6542 (list r-biocgenerics r-iranges r-s4vectors))
6543 (home-page "https://bioconductor.org/packages/XVector")
6544 (synopsis "Representation and manpulation of external sequences")
6546 "This package provides memory efficient S4 classes for storing sequences
6547 \"externally\" (behind an R external pointer, or on disk).")
6548 (license license:artistic2.0)))
6550 (define-public r-zlibbioc
6556 (uri (bioconductor-uri "zlibbioc" version))
6559 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
6561 `((upstream-name . "zlibbioc")))
6562 (build-system r-build-system)
6563 (home-page "https://bioconductor.org/packages/zlibbioc")
6564 (synopsis "Provider for zlib-1.2.5 to R packages")
6565 (description "This package uses the source code of zlib-1.2.5 to create
6566 libraries for systems that do not have these available via other means.")
6567 (license license:artistic2.0)))
6569 (define-public r-zellkonverter
6571 (name "r-zellkonverter")
6576 (uri (bioconductor-uri "zellkonverter" version))
6578 (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"))))
6579 (properties `((upstream-name . "zellkonverter")))
6580 (build-system r-build-system)
6588 r-singlecellexperiment
6589 r-summarizedexperiment))
6590 (native-inputs (list r-knitr))
6591 (home-page "https://github.com/theislab/zellkonverter")
6592 (synopsis "Conversion between AnnData and single-cell experiments objects")
6594 "This package provides methods to convert between Python AnnData objects
6595 and SingleCellExperiment objects. These are primarily intended for use by
6596 downstream Bioconductor packages that wrap Python methods for single-cell data
6597 analysis. It also includes functions to read and write H5AD files used for
6598 saving AnnData objects to disk.")
6599 (license license:expat)))
6601 (define-public r-geneplotter
6603 (name "r-geneplotter")
6608 (uri (bioconductor-uri "geneplotter" version))
6611 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
6612 (build-system r-build-system)
6620 (home-page "https://bioconductor.org/packages/geneplotter")
6621 (synopsis "Graphics functions for genomic data")
6623 "This package provides functions for plotting genomic data.")
6624 (license license:artistic2.0)))
6626 (define-public r-oligoclasses
6628 (name "r-oligoclasses")
6633 (uri (bioconductor-uri "oligoClasses" version))
6636 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
6637 (properties `((upstream-name . "oligoClasses")))
6638 (build-system r-build-system)
6652 r-summarizedexperiment))
6653 (home-page "https://bioconductor.org/packages/oligoClasses/")
6654 (synopsis "Classes for high-throughput arrays")
6656 "This package contains class definitions, validity checks, and
6657 initialization methods for classes used by the @code{oligo} and @code{crlmm}
6659 (license license:gpl2+)))
6661 (define-public r-oligo
6668 (uri (bioconductor-uri "oligo" version))
6671 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
6672 (properties `((upstream-name . "oligo")))
6673 (build-system r-build-system)
6674 (inputs (list zlib))
6689 (home-page "https://bioconductor.org/packages/oligo/")
6690 (synopsis "Preprocessing tools for oligonucleotide arrays")
6692 "This package provides a package to analyze oligonucleotide
6693 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
6694 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
6695 (license license:lgpl2.0+)))
6697 (define-public r-qvalue
6704 (uri (bioconductor-uri "qvalue" version))
6707 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
6708 (build-system r-build-system)
6710 (list r-ggplot2 r-reshape2))
6713 (home-page "https://github.com/StoreyLab/qvalue")
6714 (synopsis "Q-value estimation for false discovery rate control")
6716 "This package takes a list of p-values resulting from the simultaneous
6717 testing of many hypotheses and estimates their q-values and local @dfn{false
6718 discovery rate} (FDR) values. The q-value of a test measures the proportion
6719 of false positives incurred when that particular test is called significant.
6720 The local FDR measures the posterior probability the null hypothesis is true
6721 given the test's p-value. Various plots are automatically generated, allowing
6722 one to make sensible significance cut-offs. The software can be applied to
6723 problems in genomics, brain imaging, astrophysics, and data mining.")
6724 ;; Any version of the LGPL.
6725 (license license:lgpl3+)))
6727 (define r-rcppnumerical
6729 (name "r-rcppnumerical")
6733 (uri (cran-uri "RcppNumerical" version))
6736 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
6737 (properties `((upstream-name . "RcppNumerical")))
6738 (build-system r-build-system)
6740 `(("r-rcpp" ,r-rcpp)
6741 ("r-rcppeigen" ,r-rcppeigen)))
6743 `(("r-knitr" ,r-knitr)))
6744 (home-page "https://github.com/yixuan/RcppNumerical")
6745 (synopsis "Rcpp integration for numerical computing libraries")
6747 "This package provides a collection of libraries for numerical computing
6748 (numerical integration, optimization, etc.) and their integration with
6750 (license license:gpl2+)))
6752 (define-public r-apeglm
6758 (uri (bioconductor-uri "apeglm" version))
6761 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
6762 (properties `((upstream-name . "apeglm")))
6763 (build-system r-build-system)
6770 r-summarizedexperiment))
6771 (native-inputs (list r-knitr))
6772 (home-page "https://bioconductor.org/packages/apeglm")
6773 (synopsis "Approximate posterior estimation for GLM coefficients")
6774 (description "This package provides Bayesian shrinkage estimators for
6775 effect sizes for a variety of GLM models, using approximation of the
6776 posterior for individual coefficients.")
6777 (license license:gpl2)))
6779 (define-public r-greylistchip
6781 (name "r-greylistchip")
6785 (uri (bioconductor-uri "GreyListChIP" version))
6788 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
6789 (properties `((upstream-name . "GreyListChIP")))
6790 (build-system r-build-system)
6799 r-summarizedexperiment))
6800 (home-page "https://bioconductor.org/packages/GreyListChIP")
6801 (synopsis "Greylist artefact regions based on ChIP inputs")
6802 (description "This package identifies regions of ChIP experiments with high
6803 signal in the input, that lead to spurious peaks during peak calling.")
6804 (license license:artistic2.0)))
6806 (define-public r-diffbind
6813 (uri (bioconductor-uri "DiffBind" version))
6816 "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr"))))
6817 (properties `((upstream-name . "DiffBind")))
6818 (build-system r-build-system)
6841 r-summarizedexperiment
6843 (home-page "https://bioconductor.org/packages/DiffBind")
6844 (synopsis "Differential binding analysis of ChIP-Seq peak data")
6846 "This package computes differentially bound sites from multiple
6847 ChIP-seq experiments using affinity (quantitative) data. Also enables
6848 occupancy (overlap) analysis and plotting functions.")
6849 (license license:artistic2.0)))
6851 (define-public r-ripseeker
6853 (name "r-ripseeker")
6858 (uri (bioconductor-uri "RIPSeeker" version))
6861 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
6862 (properties `((upstream-name . "RIPSeeker")))
6863 (build-system r-build-system)
6868 r-summarizedexperiment
6872 (home-page "https://bioconductor.org/packages/RIPSeeker")
6874 "Identifying protein-associated transcripts from RIP-seq experiments")
6876 "This package infers and discriminates RIP peaks from RIP-seq alignments
6877 using two-state HMM with negative binomial emission probability. While
6878 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
6879 a suite of bioinformatics tools integrated within this self-contained software
6880 package comprehensively addressing issues ranging from post-alignments
6881 processing to visualization and annotation.")
6882 (license license:gpl2)))
6884 (define-public r-mbkmeans
6890 (uri (bioconductor-uri "mbkmeans" version))
6893 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
6894 (build-system r-build-system)
6908 r-singlecellexperiment
6909 r-summarizedexperiment))
6910 (home-page "https://bioconductor.org/packages/mbkmeans")
6911 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
6912 (description "This package implements the mini-batch k-means algorithm for
6913 large datasets, including support for on-disk data representation.")
6914 (license license:expat)))
6916 (define-public r-multtest
6923 (uri (bioconductor-uri "multtest" version))
6926 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
6927 (build-system r-build-system)
6929 (list r-survival r-biocgenerics r-biobase r-mass))
6930 (home-page "https://bioconductor.org/packages/multtest")
6931 (synopsis "Resampling-based multiple hypothesis testing")
6933 "This package can do non-parametric bootstrap and permutation
6934 resampling-based multiple testing procedures (including empirical Bayes
6935 methods) for controlling the family-wise error rate (FWER), generalized
6936 family-wise error rate (gFWER), tail probability of the proportion of
6937 false positives (TPPFP), and false discovery rate (FDR). Several choices
6938 of bootstrap-based null distribution are implemented (centered, centered
6939 and scaled, quantile-transformed). Single-step and step-wise methods are
6940 available. Tests based on a variety of T- and F-statistics (including
6941 T-statistics based on regression parameters from linear and survival models
6942 as well as those based on correlation parameters) are included. When probing
6943 hypotheses with T-statistics, users may also select a potentially faster null
6944 distribution which is multivariate normal with mean zero and variance
6945 covariance matrix derived from the vector influence function. Results are
6946 reported in terms of adjusted P-values, confidence regions and test statistic
6947 cutoffs. The procedures are directly applicable to identifying differentially
6948 expressed genes in DNA microarray experiments.")
6949 (license license:lgpl3)))
6951 (define-public r-graph
6957 (uri (bioconductor-uri "graph" version))
6960 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
6961 (build-system r-build-system)
6963 (list r-biocgenerics))
6964 (home-page "https://bioconductor.org/packages/graph")
6965 (synopsis "Handle graph data structures in R")
6967 "This package implements some simple graph handling capabilities for R.")
6968 (license license:artistic2.0)))
6970 ;; This is a CRAN package, but it depends on a Bioconductor package.
6971 (define-public r-ggm
6978 (uri (cran-uri "ggm" version))
6981 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
6982 (properties `((upstream-name . "ggm")))
6983 (build-system r-build-system)
6985 (list r-graph r-igraph))
6986 (home-page "https://cran.r-project.org/package=ggm")
6987 (synopsis "Functions for graphical Markov models")
6989 "This package provides functions and datasets for maximum likelihood
6990 fitting of some classes of graphical Markov models.")
6991 (license license:gpl2+)))
6993 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
6994 (define-public r-perfmeas
7001 (uri (cran-uri "PerfMeas" version))
7004 "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
7005 (properties `((upstream-name . "PerfMeas")))
7006 (build-system r-build-system)
7008 (list r-graph r-limma r-rbgl))
7009 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
7010 (synopsis "Performance measures for ranking and classification tasks")
7012 "This package implements different performance measures for
7013 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
7014 a given recall, F-score for single and multiple classes are available.")
7015 (license license:gpl2+)))
7017 ;; This is a CRAN package, but it depends on a Bioconductor package.
7018 (define-public r-codedepends
7020 (name "r-codedepends")
7025 (uri (cran-uri "CodeDepends" version))
7028 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
7029 (properties `((upstream-name . "CodeDepends")))
7030 (build-system r-build-system)
7032 (list r-codetools r-graph r-xml))
7033 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
7034 (synopsis "Analysis of R code for reproducible research and code comprehension")
7036 "This package provides tools for analyzing R expressions or blocks of
7037 code and determining the dependencies between them. It focuses on R scripts,
7038 but can be used on the bodies of functions. There are many facilities
7039 including the ability to summarize or get a high-level view of code,
7040 determining dependencies between variables, code improvement suggestions.")
7041 ;; Any version of the GPL
7042 (license (list license:gpl2+ license:gpl3+))))
7044 (define-public r-chippeakanno
7046 (name "r-chippeakanno")
7051 (uri (bioconductor-uri "ChIPpeakAnno" version))
7054 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
7055 (properties `((upstream-name . "ChIPpeakAnno")))
7056 (build-system r-build-system)
7058 (list r-annotationdbi
7081 r-summarizedexperiment
7085 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
7086 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
7088 "The package includes functions to retrieve the sequences around the peak,
7089 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
7090 custom features such as most conserved elements and other transcription factor
7091 binding sites supplied by users. Starting 2.0.5, new functions have been added
7092 for finding the peaks with bi-directional promoters with summary statistics
7093 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
7094 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
7095 enrichedGO (addGeneIDs).")
7096 (license license:gpl2+)))
7098 (define-public r-matrixgenerics
7100 (name "r-matrixgenerics")
7104 (uri (bioconductor-uri "MatrixGenerics" version))
7107 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
7109 `((upstream-name . "MatrixGenerics")))
7110 (build-system r-build-system)
7112 (list r-matrixstats))
7113 (home-page "https://bioconductor.org/packages/MatrixGenerics")
7114 (synopsis "S4 generic summary statistic functions for matrix-like objects")
7116 "This package provides S4 generic functions modeled after the
7117 @code{matrixStats} API for alternative matrix implementations. Packages with
7118 alternative matrix implementation can depend on this package and implement the
7119 generic functions that are defined here for a useful set of row and column
7120 summary statistics. Other package developers can import this package and
7121 handle a different matrix implementations without worrying about
7122 incompatibilities.")
7123 (license license:artistic2.0)))
7125 (define-public r-marray
7131 (uri (bioconductor-uri "marray" version))
7133 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
7134 (build-system r-build-system)
7137 (home-page "https://bioconductor.org/packages/marray")
7138 (synopsis "Exploratory analysis for two-color spotted microarray data")
7139 (description "This package contains class definitions for two-color spotted
7140 microarray data. It also includes functions for data input, diagnostic plots,
7141 normalization and quality checking.")
7142 (license license:lgpl2.0+)))
7144 (define-public r-cghbase
7150 (uri (bioconductor-uri "CGHbase" version))
7152 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
7153 (properties `((upstream-name . "CGHbase")))
7154 (build-system r-build-system)
7156 (list r-biobase r-marray))
7157 (home-page "https://bioconductor.org/packages/CGHbase")
7158 (synopsis "Base functions and classes for arrayCGH data analysis")
7159 (description "This package contains functions and classes that are needed by
7160 the @code{arrayCGH} packages.")
7161 (license license:gpl2+)))
7163 (define-public r-cghcall
7169 (uri (bioconductor-uri "CGHcall" version))
7171 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
7172 (properties `((upstream-name . "CGHcall")))
7173 (build-system r-build-system)
7175 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
7176 (home-page "https://bioconductor.org/packages/CGHcall")
7177 (synopsis "Base functions and classes for arrayCGH data analysis")
7178 (description "This package contains functions and classes that are needed by
7179 @code{arrayCGH} packages.")
7180 (license license:gpl2+)))
7182 (define-public r-qdnaseq
7188 (uri (bioconductor-uri "QDNAseq" version))
7190 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
7191 (properties `((upstream-name . "QDNAseq")))
7192 (build-system r-build-system)
7204 (home-page "https://bioconductor.org/packages/QDNAseq")
7205 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
7206 (description "The genome is divided into non-overlapping fixed-sized bins,
7207 number of sequence reads in each counted, adjusted with a simultaneous
7208 two-dimensional loess correction for sequence mappability and GC content, and
7209 filtered to remove spurious regions in the genome. Downstream steps of
7210 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
7212 (license license:gpl2+)))
7214 (define-public r-bayseq
7221 (uri (bioconductor-uri "baySeq" version))
7224 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
7225 (properties `((upstream-name . "baySeq")))
7226 (build-system r-build-system)
7228 (list r-abind r-edger r-genomicranges))
7229 (home-page "https://bioconductor.org/packages/baySeq/")
7230 (synopsis "Bayesian analysis of differential expression patterns in count data")
7232 "This package identifies differential expression in high-throughput count
7233 data, such as that derived from next-generation sequencing machines,
7234 calculating estimated posterior likelihoods of differential expression (or
7235 more complex hypotheses) via empirical Bayesian methods.")
7236 (license license:gpl3)))
7238 (define-public r-chipcomp
7245 (uri (bioconductor-uri "ChIPComp" version))
7248 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
7249 (properties `((upstream-name . "ChIPComp")))
7250 (build-system r-build-system)
7252 (list r-biocgenerics
7253 r-bsgenome-hsapiens-ucsc-hg19
7254 r-bsgenome-mmusculus-ucsc-mm9
7262 (home-page "https://bioconductor.org/packages/ChIPComp")
7263 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
7265 "ChIPComp implements a statistical method for quantitative comparison of
7266 multiple ChIP-seq datasets. It detects differentially bound sharp binding
7267 sites across multiple conditions considering matching control in ChIP-seq
7269 ;; Any version of the GPL.
7270 (license license:gpl3+)))
7272 (define-public r-riboprofiling
7274 (name "r-riboprofiling")
7279 (uri (bioconductor-uri "RiboProfiling" version))
7282 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
7283 (properties `((upstream-name . "RiboProfiling")))
7284 (build-system r-build-system)
7286 (list r-biocgenerics
7304 (home-page "https://bioconductor.org/packages/RiboProfiling/")
7305 (synopsis "Ribosome profiling data analysis")
7306 (description "Starting with a BAM file, this package provides the
7307 necessary functions for quality assessment, read start position recalibration,
7308 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
7309 of count data: pairs, log fold-change, codon frequency and coverage
7310 assessment, principal component analysis on codon coverage.")
7311 (license license:gpl3)))
7313 (define-public r-riboseqr
7320 (uri (bioconductor-uri "riboSeqR" version))
7323 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
7324 (properties `((upstream-name . "riboSeqR")))
7325 (build-system r-build-system)
7334 (home-page "https://bioconductor.org/packages/riboSeqR/")
7335 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
7337 "This package provides plotting functions, frameshift detection and
7338 parsing of genetic sequencing data from ribosome profiling experiments.")
7339 (license license:gpl3)))
7341 (define-public r-interactionset
7343 (name "r-interactionset")
7348 (uri (bioconductor-uri "InteractionSet" version))
7351 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
7353 `((upstream-name . "InteractionSet")))
7354 (build-system r-build-system)
7356 (list r-biocgenerics
7363 r-summarizedexperiment))
7366 (home-page "https://bioconductor.org/packages/InteractionSet")
7367 (synopsis "Base classes for storing genomic interaction data")
7369 "This package provides the @code{GInteractions},
7370 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
7371 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
7373 (license license:gpl3)))
7375 (define-public r-genomicinteractions
7377 (name "r-genomicinteractions")
7382 (uri (bioconductor-uri "GenomicInteractions" version))
7385 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
7387 `((upstream-name . "GenomicInteractions")))
7388 (build-system r-build-system)
7408 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
7409 (synopsis "R package for handling genomic interaction data")
7411 "This R package provides tools for handling genomic interaction data,
7412 such as ChIA-PET/Hi-C, annotating genomic features with interaction
7413 information and producing various plots and statistics.")
7414 (license license:gpl3)))
7416 (define-public r-ctc
7423 (uri (bioconductor-uri "ctc" version))
7426 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
7427 (build-system r-build-system)
7428 (propagated-inputs (list r-amap))
7429 (home-page "https://bioconductor.org/packages/ctc/")
7430 (synopsis "Cluster and tree conversion")
7432 "This package provides tools for exporting and importing classification
7433 trees and clusters to other programs.")
7434 (license license:gpl2)))
7436 (define-public r-goseq
7443 (uri (bioconductor-uri "goseq" version))
7446 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
7447 (build-system r-build-system)
7449 (list r-annotationdbi
7455 (home-page "https://bioconductor.org/packages/goseq/")
7456 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
7458 "This package provides tools to detect Gene Ontology and/or other user
7459 defined categories which are over/under represented in RNA-seq data.")
7460 (license license:lgpl2.0+)))
7462 (define-public r-glimma
7469 (uri (bioconductor-uri "Glimma" version))
7472 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
7473 (properties `((upstream-name . "Glimma")))
7474 (build-system r-build-system)
7482 r-summarizedexperiment))
7485 (home-page "https://github.com/Shians/Glimma")
7486 (synopsis "Interactive HTML graphics")
7488 "This package generates interactive visualisations for analysis of
7489 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
7490 HTML page. The interactions are built on top of the popular static
7491 representations of analysis results in order to provide additional
7493 (license license:lgpl3)))
7495 (define-public r-rots
7502 (uri (bioconductor-uri "ROTS" version))
7505 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
7506 (properties `((upstream-name . "ROTS")))
7507 (build-system r-build-system)
7509 (list r-biobase r-rcpp))
7510 (home-page "https://bioconductor.org/packages/ROTS/")
7511 (synopsis "Reproducibility-Optimized Test Statistic")
7513 "This package provides tools for calculating the
7514 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
7516 (license license:gpl2+)))
7518 (define-public r-plgem
7525 (uri (bioconductor-uri "plgem" version))
7528 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
7529 (build-system r-build-system)
7531 (list r-biobase r-mass))
7532 (home-page "http://www.genopolis.it")
7533 (synopsis "Detect differential expression in microarray and proteomics datasets")
7535 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
7536 model the variance-versus-mean dependence that exists in a variety of
7537 genome-wide datasets, including microarray and proteomics data. The use of
7538 PLGEM has been shown to improve the detection of differentially expressed
7539 genes or proteins in these datasets.")
7540 (license license:gpl2)))
7542 (define-public r-inspect
7549 (uri (bioconductor-uri "INSPEcT" version))
7552 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
7553 (properties `((upstream-name . "INSPEcT")))
7554 (build-system r-build-system)
7575 r-summarizedexperiment
7576 r-txdb-mmusculus-ucsc-mm9-knowngene))
7579 (home-page "https://bioconductor.org/packages/INSPEcT")
7580 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
7582 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
7583 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
7584 order to evaluate synthesis, processing and degradation rates and assess via
7585 modeling the rates that determines changes in mature mRNA levels.")
7586 (license license:gpl2)))
7588 (define-public r-dnabarcodes
7590 (name "r-dnabarcodes")
7595 (uri (bioconductor-uri "DNABarcodes" version))
7598 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
7599 (properties `((upstream-name . "DNABarcodes")))
7600 (build-system r-build-system)
7602 (list r-bh r-matrix r-rcpp))
7605 (home-page "https://bioconductor.org/packages/DNABarcodes")
7606 (synopsis "Create and analyze DNA barcodes")
7608 "This package offers tools to create DNA barcode sets capable of
7609 correcting insertion, deletion, and substitution errors. Existing barcodes
7610 can be analyzed regarding their minimal, maximal and average distances between
7611 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
7612 demultiplexed, i.e. assigned to their original reference barcode.")
7613 (license license:gpl2)))
7615 (define-public r-ruvseq
7622 (uri (bioconductor-uri "RUVSeq" version))
7625 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
7626 (properties `((upstream-name . "RUVSeq")))
7627 (build-system r-build-system)
7629 (list r-biobase r-edaseq r-edger r-mass))
7632 (home-page "https://github.com/drisso/RUVSeq")
7633 (synopsis "Remove unwanted variation from RNA-Seq data")
7635 "This package implements methods to @dfn{remove unwanted variation} (RUV)
7636 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
7638 (license license:artistic2.0)))
7640 (define-public r-biocneighbors
7642 (name "r-biocneighbors")
7647 (uri (bioconductor-uri "BiocNeighbors" version))
7650 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
7651 (properties `((upstream-name . "BiocNeighbors")))
7652 (build-system r-build-system)
7654 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
7657 (home-page "https://bioconductor.org/packages/BiocNeighbors")
7658 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
7660 "This package implements exact and approximate methods for nearest
7661 neighbor detection, in a framework that allows them to be easily switched
7662 within Bioconductor packages or workflows. The exact algorithm is implemented
7663 using pre-clustering with the k-means algorithm. Functions are also provided
7664 to search for all neighbors within a given distance. Parallelization is
7665 achieved for all methods using the BiocParallel framework.")
7666 (license license:gpl3)))
7668 (define-public r-scaledmatrix
7670 (name "r-scaledmatrix")
7675 (uri (bioconductor-uri "ScaledMatrix" version))
7678 "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"))))
7679 (properties `((upstream-name . "ScaledMatrix")))
7680 (build-system r-build-system)
7682 (list r-delayedarray r-matrix r-s4vectors))
7683 (native-inputs (list r-knitr))
7684 (home-page "https://github.com/LTLA/ScaledMatrix")
7685 (synopsis "Create a DelayedMatrix of scaled and centered values")
7687 "This package provides delayed computation of a matrix of scaled and
7688 centered values. The result is equivalent to using the @code{scale} function
7689 but avoids explicit realization of a dense matrix during block processing.
7690 This permits greater efficiency in common operations, most notably matrix
7692 (license license:gpl3)))
7694 (define-public r-treeio
7701 (uri (bioconductor-uri "treeio" version))
7704 "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"))))
7705 (properties `((upstream-name . "treeio")))
7706 (build-system r-build-system)
7715 (native-inputs (list r-knitr))
7716 (home-page "https://github.com/YuLab-SMU/treeio")
7717 (synopsis "Base classes and functions for Phylogenetic tree input and output")
7719 "This is an R package to make it easier to import and store phylogenetic
7720 trees with associated data; and to link external data from different sources
7721 to phylogeny. It also supports exporting phylogenetic trees with
7722 heterogeneous associated data to a single tree file and can be served as a
7723 platform for merging tree with associated data and converting file formats.")
7724 (license license:artistic2.0)))
7726 (define-public r-ggtree
7733 (uri (bioconductor-uri "ggtree" version))
7736 "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"))))
7737 (properties `((upstream-name . "ggtree")))
7738 (build-system r-build-system)
7753 (native-inputs (list r-knitr))
7754 (home-page "https://yulab-smu.top/treedata-book/")
7755 (synopsis "R package for visualization of trees and annotation data")
7757 "This package extends the ggplot2 plotting system which implements a
7758 grammar of graphics. ggtree is designed for visualization and annotation of
7759 phylogenetic trees and other tree-like structures with their annotation
7761 (license license:artistic2.0)))
7763 (define-public r-metapod
7770 (uri (bioconductor-uri "metapod" version))
7773 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
7774 (properties `((upstream-name . "metapod")))
7775 (build-system r-build-system)
7780 (home-page "https://bioconductor.org/packages/metapod")
7781 (synopsis "Meta-analyses on p-values of differential analyses")
7783 "This package implements a variety of methods for combining p-values in
7784 differential analyses of genome-scale datasets. Functions can combine
7785 p-values across different tests in the same analysis (e.g., genomic windows in
7786 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
7787 analyses (e.g., replicated comparisons, effect of different treatment
7788 conditions). Support is provided for handling log-transformed input p-values,
7789 missing values and weighting where appropriate.")
7790 (license license:gpl3)))
7792 (define-public r-biocsingular
7794 (name "r-biocsingular")
7799 (uri (bioconductor-uri "BiocSingular" version))
7802 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
7803 (properties `((upstream-name . "BiocSingular")))
7804 (build-system r-build-system)
7818 (home-page "https://github.com/LTLA/BiocSingular")
7819 (synopsis "Singular value decomposition for Bioconductor packages")
7821 "This package implements exact and approximate methods for singular value
7822 decomposition and principal components analysis, in a framework that allows
7823 them to be easily switched within Bioconductor packages or workflows. Where
7824 possible, parallelization is achieved using the BiocParallel framework.")
7825 (license license:gpl3)))
7827 (define-public r-destiny
7834 (uri (bioconductor-uri "destiny" version))
7837 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
7838 (build-system r-build-system)
7856 r-singlecellexperiment
7858 r-summarizedexperiment
7863 (list r-knitr r-nbconvertr)) ; for vignettes
7864 (home-page "https://bioconductor.org/packages/destiny/")
7865 (synopsis "Create and plot diffusion maps")
7866 (description "This package provides tools to create and plot diffusion
7868 ;; Any version of the GPL
7869 (license license:gpl3+)))
7871 (define-public r-savr
7878 (uri (bioconductor-uri "savR" version))
7881 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
7882 (properties `((upstream-name . "savR")))
7883 (build-system r-build-system)
7885 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
7886 (home-page "https://github.com/bcalder/savR")
7887 (synopsis "Parse and analyze Illumina SAV files")
7889 "This package provides tools to parse Illumina Sequence Analysis
7890 Viewer (SAV) files, access data, and generate QC plots.")
7891 (license license:agpl3+)))
7893 (define-public r-chipexoqual
7895 (name "r-chipexoqual")
7900 (uri (bioconductor-uri "ChIPexoQual" version))
7903 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
7904 (properties `((upstream-name . "ChIPexoQual")))
7905 (build-system r-build-system)
7907 (list r-biocparallel
7926 (home-page "https://github.com/keleslab/ChIPexoQual")
7927 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
7929 "This package provides a quality control pipeline for ChIP-exo/nexus
7931 (license license:gpl2+)))
7933 (define-public r-copynumber
7935 (name "r-copynumber")
7939 (uri (bioconductor-uri "copynumber" version))
7942 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
7943 (build-system r-build-system)
7945 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
7946 (home-page "https://bioconductor.org/packages/copynumber")
7947 (synopsis "Segmentation of single- and multi-track copy number data")
7949 "This package segments single- and multi-track copy number data by a
7950 penalized least squares regression method.")
7951 (license license:artistic2.0)))
7953 (define-public r-dnacopy
7960 (uri (bioconductor-uri "DNAcopy" version))
7963 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
7964 (properties `((upstream-name . "DNAcopy")))
7965 (build-system r-build-system)
7966 (native-inputs (list gfortran))
7967 (home-page "https://bioconductor.org/packages/DNAcopy")
7968 (synopsis "DNA copy number data analysis")
7970 "This package implements the @dfn{circular binary segmentation} (CBS)
7971 algorithm to segment DNA copy number data and identify genomic regions with
7972 abnormal copy number.")
7973 (license license:gpl2+)))
7975 ;; This is a CRAN package, but it uncharacteristically depends on a
7976 ;; Bioconductor package.
7977 (define-public r-htscluster
7979 (name "r-htscluster")
7984 (uri (cran-uri "HTSCluster" version))
7987 "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
7988 (properties `((upstream-name . "HTSCluster")))
7989 (build-system r-build-system)
7991 (list r-capushe r-edger r-plotrix))
7992 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
7993 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
7995 "This package provides a Poisson mixture model is implemented to cluster
7996 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
7997 estimation is performed using either the EM or CEM algorithm, and the slope
7998 heuristics are used for model selection (i.e., to choose the number of
8000 (license license:gpl3+)))
8002 (define-public r-deds
8009 (uri (bioconductor-uri "DEDS" version))
8012 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
8013 (properties `((upstream-name . "DEDS")))
8014 (build-system r-build-system)
8015 (home-page "https://bioconductor.org/packages/DEDS/")
8016 (synopsis "Differential expression via distance summary for microarray data")
8018 "This library contains functions that calculate various statistics of
8019 differential expression for microarray data, including t statistics, fold
8020 change, F statistics, SAM, moderated t and F statistics and B statistics. It
8021 also implements a new methodology called DEDS (Differential Expression via
8022 Distance Summary), which selects differentially expressed genes by integrating
8023 and summarizing a set of statistics using a weighted distance approach.")
8024 ;; Any version of the LGPL.
8025 (license license:lgpl3+)))
8027 ;; This is a CRAN package, but since it depends on a Bioconductor package we
8029 (define-public r-nbpseq
8036 (uri (cran-uri "NBPSeq" version))
8039 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
8040 (properties `((upstream-name . "NBPSeq")))
8041 (build-system r-build-system)
8044 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
8045 (synopsis "Negative binomial models for RNA-Seq data")
8047 "This package provides negative binomial models for two-group comparisons
8048 and regression inferences from RNA-sequencing data.")
8049 (license license:gpl2)))
8051 (define-public r-ebseq
8058 (uri (bioconductor-uri "EBSeq" version))
8061 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
8062 (properties `((upstream-name . "EBSeq")))
8063 (build-system r-build-system)
8065 (list r-blockmodeling r-gplots r-testthat))
8066 (home-page "https://bioconductor.org/packages/EBSeq")
8067 (synopsis "Differential expression analysis of RNA-seq data")
8069 "This package provides tools for differential expression analysis at both
8070 gene and isoform level using RNA-seq data")
8071 (license license:artistic2.0)))
8073 (define-public r-karyoploter
8075 (name "r-karyoploter")
8079 (uri (bioconductor-uri "karyoploteR" version))
8082 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
8083 (build-system r-build-system)
8085 (list r-annotationdbi
8099 r-variantannotation))
8102 (home-page "https://bioconductor.org/packages/karyoploteR/")
8103 (synopsis "Plot customizable linear genomes displaying arbitrary data")
8104 (description "This package creates karyotype plots of arbitrary genomes and
8105 offers a complete set of functions to plot arbitrary data on them. It mimics
8106 many R base graphics functions coupling them with a coordinate change function
8107 automatically mapping the chromosome and data coordinates into the plot
8109 (license license:artistic2.0)))
8111 (define-public r-lpsymphony
8113 (name "r-lpsymphony")
8118 (uri (bioconductor-uri "lpsymphony" version))
8121 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
8122 (build-system r-build-system)
8126 '(modify-phases %standard-phases
8127 (add-after 'unpack 'make-build-order-reproducible
8129 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
8130 "src/SYMPHONY/Cgl/configure")
8131 (("for file in `ls \\*/Makefile.in`")
8132 "for file in `ls */Makefile.in | sort`")))))))
8136 (list pkg-config r-knitr))
8137 (home-page "https://r-forge.r-project.org/projects/rsymphony")
8138 (synopsis "Symphony integer linear programming solver in R")
8140 "This package was derived from Rsymphony. The package provides an R
8141 interface to SYMPHONY, a linear programming solver written in C++. The main
8142 difference between this package and Rsymphony is that it includes the solver
8143 source code, while Rsymphony expects to find header and library files on the
8144 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
8145 to install interface to SYMPHONY.")
8146 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
8147 ;; lpsimphony is released under the same terms.
8148 (license license:epl1.0)))
8150 (define-public r-ihw
8157 (uri (bioconductor-uri "IHW" version))
8160 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
8161 (properties `((upstream-name . "IHW")))
8162 (build-system r-build-system)
8164 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
8167 (home-page "https://bioconductor.org/packages/IHW")
8168 (synopsis "Independent hypothesis weighting")
8170 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
8171 procedure that increases power compared to the method of Benjamini and
8172 Hochberg by assigning data-driven weights to each hypothesis. The input to
8173 IHW is a two-column table of p-values and covariates. The covariate can be
8174 any continuous-valued or categorical variable that is thought to be
8175 informative on the statistical properties of each hypothesis test, while it is
8176 independent of the p-value under the null hypothesis.")
8177 (license license:artistic2.0)))
8179 (define-public r-icobra
8186 (uri (bioconductor-uri "iCOBRA" version))
8189 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
8190 (properties `((upstream-name . "iCOBRA")))
8191 (build-system r-build-system)
8207 (home-page "https://bioconductor.org/packages/iCOBRA")
8208 (synopsis "Comparison and visualization of ranking and assignment methods")
8210 "This package provides functions for calculation and visualization of
8211 performance metrics for evaluation of ranking and binary
8212 classification (assignment) methods. It also contains a Shiny application for
8213 interactive exploration of results.")
8214 (license license:gpl2+)))
8216 (define-public r-residualmatrix
8218 (name "r-residualmatrix")
8223 (uri (bioconductor-uri "ResidualMatrix" version))
8226 "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"))))
8228 `((upstream-name . "ResidualMatrix")))
8229 (build-system r-build-system)
8231 (list r-delayedarray r-matrix r-s4vectors))
8234 (home-page "https://github.com/LTLA/ResidualMatrix")
8235 (synopsis "Create a DelayedMatrix of regression residuals")
8237 "This package implements tools for delayed computation of a matrix of
8238 residuals after fitting a linear model to each column of an input matrix. It
8239 also supports partial computation of residuals where selected factors are to
8240 be preserved in the output matrix. It implements a number of efficient
8241 methods for operating on the delayed matrix of residuals, most notably matrix
8242 multiplication and calculation of row/column sums or means.")
8243 (license license:gpl3)))
8245 (define-public r-batchelor
8247 (name "r-batchelor")
8252 (uri (bioconductor-uri "batchelor" version))
8255 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
8256 (properties `((upstream-name . "batchelor")))
8257 (build-system r-build-system)
8265 r-delayedmatrixstats
8273 r-singlecellexperiment
8274 r-summarizedexperiment))
8275 (native-inputs (list r-knitr))
8276 (home-page "https://bioconductor.org/packages/batchelor")
8277 (synopsis "Single-Cell Batch Correction Methods")
8279 "This package implements a variety of methods for batch correction of
8280 single-cell (RNA sequencing) data. This includes methods based on detecting
8281 mutually nearest neighbors, as well as several efficient variants of linear
8282 regression of the log-expression values. Functions are also provided to
8283 perform global rescaling to remove differences in depth between batches, and
8284 to perform a principal components analysis that is robust to differences in
8285 the numbers of cells across batches.")
8286 (license license:gpl3)))
8288 (define-public r-mast
8295 (uri (bioconductor-uri "MAST" version))
8298 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
8299 (properties `((upstream-name . "MAST")))
8300 (build-system r-build-system)
8311 r-singlecellexperiment
8313 r-summarizedexperiment))
8316 (home-page "https://github.com/RGLab/MAST/")
8317 (synopsis "Model-based analysis of single cell transcriptomics")
8319 "This package provides methods and models for handling zero-inflated
8320 single cell assay data.")
8321 (license license:gpl2+)))
8323 (define-public r-monocle
8330 (uri (bioconductor-uri "monocle" version))
8333 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
8334 (build-system r-build-system)
8368 (home-page "https://bioconductor.org/packages/monocle")
8369 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
8371 "Monocle performs differential expression and time-series analysis for
8372 single-cell expression experiments. It orders individual cells according to
8373 progress through a biological process, without knowing ahead of time which
8374 genes define progress through that process. Monocle also performs
8375 differential expression analysis, clustering, visualization, and other useful
8376 tasks on single cell expression data. It is designed to work with RNA-Seq and
8377 qPCR data, but could be used with other types as well.")
8378 (license license:artistic2.0)))
8380 (define-public r-leidenbase
8381 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
8384 (name "r-leidenbase")
8385 (version (git-version "0.1.9" revision commit))
8390 (url "https://github.com/cole-trapnell-lab/leidenbase")
8392 (file-name (git-file-name name version))
8395 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
8396 (properties `((upstream-name . "leidenbase")))
8397 (build-system r-build-system)
8404 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
8405 (synopsis "R and C wrappers to run the Leiden find_partition function")
8407 "This package provides an R to C interface that runs the Leiden
8408 community detection algorithm to find a basic partition. It runs the
8409 equivalent of the @code{find_partition} function. This package includes the
8410 required source code files from the official Leidenalg distribution and
8411 several functions from the R igraph package.")
8412 (license license:gpl3+))))
8414 (define-public r-sanssouci
8415 ;; sansscouci doesn't have a (versioned) release yet.
8416 ;; This is the latest commit as of packaging for Guix.
8417 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
8420 (name "r-sanssouci")
8421 (version (git-version "0" revision commit))
8425 (url "https://github.com/pneuvial/sanssouci.git")
8427 (file-name (git-file-name name version))
8430 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
8431 (build-system r-build-system)
8433 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
8434 (home-page "https://pneuvial.github.io/sanssouci")
8435 (synopsis "Post Hoc multiple testing inference")
8437 "The goal of sansSouci is to perform post hoc inference: in a multiple
8438 testing context, sansSouci provides statistical guarantees on possibly
8439 user-defined and/or data-driven sets of hypotheses.")
8440 (license license:gpl3))))
8442 (define-public r-monocle3
8450 (url "https://github.com/cole-trapnell-lab/monocle3")
8452 (file-name (git-file-name name version))
8455 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
8456 (build-system r-build-system)
8462 r-delayedmatrixstats
8497 r-singlecellexperiment
8502 (home-page "https://github.com/cole-trapnell-lab/monocle3")
8503 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
8505 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
8506 (license license:expat)))
8508 (define-public r-noiseq
8515 (uri (bioconductor-uri "NOISeq" version))
8518 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
8519 (properties `((upstream-name . "NOISeq")))
8520 (build-system r-build-system)
8522 (list r-biobase r-matrix))
8523 (home-page "https://bioconductor.org/packages/NOISeq")
8524 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
8526 "This package provides tools to support the analysis of RNA-seq
8527 expression data or other similar kind of data. It provides exploratory plots
8528 to evaluate saturation, count distribution, expression per chromosome, type of
8529 detected features, features length, etc. It also supports the analysis of
8530 differential expression between two experimental conditions with no parametric
8532 (license license:artistic2.0)))
8534 (define-public r-scdd
8541 (uri (bioconductor-uri "scDD" version))
8544 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
8545 (properties `((upstream-name . "scDD")))
8546 (build-system r-build-system)
8557 r-singlecellexperiment
8558 r-summarizedexperiment))
8561 (home-page "https://github.com/kdkorthauer/scDD")
8562 (synopsis "Mixture modeling of single-cell RNA-seq data")
8564 "This package implements a method to analyze single-cell RNA-seq data
8565 utilizing flexible Dirichlet Process mixture models. Genes with differential
8566 distributions of expression are classified into several interesting patterns
8567 of differences between two conditions. The package also includes functions
8568 for simulating data with these patterns from negative binomial
8570 (license license:gpl2)))
8572 (define-public r-scone
8579 (uri (bioconductor-uri "scone" version))
8582 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
8583 (build-system r-build-system)
8604 r-singlecellexperiment
8605 r-summarizedexperiment))
8608 (home-page "https://bioconductor.org/packages/scone")
8609 (synopsis "Single cell overview of normalized expression data")
8611 "SCONE is an R package for comparing and ranking the performance of
8612 different normalization schemes for single-cell RNA-seq and other
8613 high-throughput analyses.")
8614 (license license:artistic2.0)))
8616 (define-public r-geoquery
8623 (uri (bioconductor-uri "GEOquery" version))
8626 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
8627 (properties `((upstream-name . "GEOquery")))
8628 (build-system r-build-system)
8642 (home-page "https://github.com/seandavi/GEOquery/")
8643 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
8645 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
8646 microarray data. Given the rich and varied nature of this resource, it is
8647 only natural to want to apply BioConductor tools to these data. GEOquery is
8648 the bridge between GEO and BioConductor.")
8649 (license license:gpl2)))
8651 (define-public r-illuminaio
8653 (name "r-illuminaio")
8658 (uri (bioconductor-uri "illuminaio" version))
8661 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
8662 (build-system r-build-system)
8665 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
8666 (synopsis "Parse Illumina microarray output files")
8668 "This package provides tools for parsing Illumina's microarray output
8669 files, including IDAT.")
8670 (license license:gpl2)))
8672 (define-public r-siggenes
8679 (uri (bioconductor-uri "siggenes" version))
8682 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
8683 (build-system r-build-system)
8685 (list r-biobase r-multtest r-scrime))
8686 (home-page "https://bioconductor.org/packages/siggenes/")
8688 "Multiple testing using SAM and Efron's empirical Bayes approaches")
8690 "This package provides tools for the identification of differentially
8691 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
8692 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
8693 Bayes Analyses of Microarrays} (EBAM).")
8694 (license license:lgpl2.0+)))
8696 (define-public r-bumphunter
8698 (name "r-bumphunter")
8703 (uri (bioconductor-uri "bumphunter" version))
8706 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
8707 (build-system r-build-system)
8709 (list r-annotationdbi
8722 (home-page "https://github.com/ririzarr/bumphunter")
8723 (synopsis "Find bumps in genomic data")
8725 "This package provides tools for finding bumps in genomic data in order
8726 to identify differentially methylated regions in epigenetic epidemiology
8728 (license license:artistic2.0)))
8730 (define-public r-milor
8736 (uri (bioconductor-uri "miloR" version))
8739 "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
8740 (properties `((upstream-name . "miloR")))
8741 (build-system r-build-system)
8743 (list r-biocgenerics
8763 r-singlecellexperiment
8765 r-summarizedexperiment
8768 (native-inputs (list r-knitr))
8769 (home-page "https://marionilab.github.io/miloR")
8770 (synopsis "Differential neighbourhood abundance testing on a graph")
8772 "Milo performs single-cell differential abundance testing. Cell states
8773 are modelled as representative neighbourhoods on a nearest neighbour graph.
8774 Hypothesis testing is performed using a negative bionomial generalized linear
8776 (license license:gpl3)))
8778 (define-public r-minfi
8785 (uri (bioconductor-uri "minfi" version))
8788 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
8789 (build-system r-build-system)
8799 r-delayedmatrixstats
8819 r-summarizedexperiment))
8822 (home-page "https://github.com/hansenlab/minfi")
8823 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
8825 "This package provides tools to analyze and visualize Illumina Infinium
8826 methylation arrays.")
8827 (license license:artistic2.0)))
8829 (define-public r-methylumi
8831 (name "r-methylumi")
8836 (uri (bioconductor-uri "methylumi" version))
8839 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
8840 (build-system r-build-system)
8846 r-fdb-infiniummethylation-hg19
8860 r-summarizedexperiment))
8863 (home-page "https://bioconductor.org/packages/methylumi")
8864 (synopsis "Handle Illumina methylation data")
8866 "This package provides classes for holding and manipulating Illumina
8867 methylation data. Based on eSet, it can contain MIAME information, sample
8868 information, feature information, and multiple matrices of data. An
8869 \"intelligent\" import function, methylumiR can read the Illumina text files
8870 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
8871 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
8872 background correction, and quality control features for GoldenGate, Infinium,
8873 and Infinium HD arrays are also included.")
8874 (license license:gpl2)))
8876 (define-public r-lumi
8883 (uri (bioconductor-uri "lumi" version))
8886 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
8887 (build-system r-build-system)
8904 (home-page "https://bioconductor.org/packages/lumi")
8905 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
8907 "The lumi package provides an integrated solution for the Illumina
8908 microarray data analysis. It includes functions of Illumina
8909 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
8910 variance stabilization, normalization and gene annotation at the probe level.
8911 It also includes the functions of processing Illumina methylation microarrays,
8912 especially Illumina Infinium methylation microarrays.")
8913 (license license:lgpl2.0+)))
8915 (define-public r-linnorm
8922 (uri (bioconductor-uri "Linnorm" version))
8925 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
8926 (properties `((upstream-name . "Linnorm")))
8927 (build-system r-build-system)
8949 (home-page "http://www.jjwanglab.org/Linnorm/")
8950 (synopsis "Linear model and normality based transformation method")
8952 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
8953 count data or any large scale count data. It transforms such datasets for
8954 parametric tests. In addition to the transformtion function (@code{Linnorm}),
8955 the following pipelines are implemented:
8958 @item Library size/batch effect normalization (@code{Linnorm.Norm})
8959 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
8960 clustering or hierarchical clustering (@code{Linnorm.tSNE},
8961 @code{Linnorm.PCA}, @code{Linnorm.HClust})
8962 @item Differential expression analysis or differential peak detection using
8963 limma (@code{Linnorm.limma})
8964 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
8965 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
8966 @item Stable gene selection for scRNA-seq data; for users without or who do
8967 not want to rely on spike-in genes (@code{Linnorm.SGenes})
8968 @item Data imputation (@code{Linnorm.DataImput}).
8971 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
8972 @code{RnaXSim} function is included for simulating RNA-seq data for the
8973 evaluation of DEG analysis methods.")
8974 (license license:expat)))
8976 (define-public r-ioniser
8983 (uri (bioconductor-uri "IONiseR" version))
8986 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
8987 (properties `((upstream-name . "IONiseR")))
8988 (build-system r-build-system)
8990 (list r-biocgenerics
9005 (home-page "https://bioconductor.org/packages/IONiseR/")
9006 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
9008 "IONiseR provides tools for the quality assessment of Oxford Nanopore
9009 MinION data. It extracts summary statistics from a set of fast5 files and can
9010 be used either before or after base calling. In addition to standard
9011 summaries of the read-types produced, it provides a number of plots for
9012 visualising metrics relative to experiment run time or spatially over the
9013 surface of a flowcell.")
9014 (license license:expat)))
9016 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
9017 (define-public r-mutoss
9024 (uri (cran-uri "mutoss" version))
9027 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
9028 (properties `((upstream-name . "mutoss")))
9029 (build-system r-build-system)
9031 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
9032 (home-page "https://github.com/kornl/mutoss/")
9033 (synopsis "Unified multiple testing procedures")
9035 "This package is designed to ease the application and comparison of
9036 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
9037 are standardized and usable by the accompanying mutossGUI package.")
9038 ;; Any version of the GPL.
9039 (license (list license:gpl2+ license:gpl3+))))
9041 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
9042 ;; from Bioconductor, so we put it here.
9043 (define-public r-metap
9050 (uri (cran-uri "metap" version))
9053 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
9054 (build-system r-build-system)
9062 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
9063 (synopsis "Meta-analysis of significance values")
9065 "The canonical way to perform meta-analysis involves using effect sizes.
9066 When they are not available this package provides a number of methods for
9067 meta-analysis of significance values including the methods of Edgington,
9068 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
9069 published results; and a routine for graphical display.")
9070 (license license:gpl2)))
9072 (define-public r-tradeseq
9078 (uri (bioconductor-uri "tradeSeq" version))
9081 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
9082 (build-system r-build-system)
9098 r-singlecellexperiment
9100 r-summarizedexperiment
9106 (home-page "https://statomics.github.io/tradeSeq/index.html")
9107 (synopsis "Trajectory-based differential expression analysis")
9109 "This package provides a flexible method for fitting regression models that
9110 can be used to find genes that are differentially expressed along one or
9111 multiple lineages in a trajectory. Based on the fitted models, it uses a
9112 variety of tests suited to answer different questions of interest, e.g. the
9113 discovery of genes for which expression is associated with pseudotime, or which
9114 are differentially expressed (in a specific region) along the trajectory. It
9115 fits a negative binomial generalized additive model (GAM) for each gene, and
9116 performs inference on the parameters of the GAM.")
9117 (license license:expat)))
9119 (define-public r-triform
9126 (uri (bioconductor-uri "triform" version))
9129 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
9130 (build-system r-build-system)
9132 (list r-biocgenerics r-iranges r-yaml))
9133 (home-page "https://bioconductor.org/packages/triform/")
9134 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
9136 "The Triform algorithm uses model-free statistics to identify peak-like
9137 distributions of TF ChIP sequencing reads, taking advantage of an improved
9138 peak definition in combination with known profile characteristics.")
9139 (license license:gpl2)))
9141 (define-public r-varianttools
9143 (name "r-varianttools")
9148 (uri (bioconductor-uri "VariantTools" version))
9151 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
9152 (properties `((upstream-name . "VariantTools")))
9153 (build-system r-build-system)
9168 r-variantannotation))
9169 (home-page "https://bioconductor.org/packages/VariantTools/")
9170 (synopsis "Tools for exploratory analysis of variant calls")
9172 "Explore, diagnose, and compare variant calls using filters. The
9173 VariantTools package supports a workflow for loading data, calling single
9174 sample variants and tumor-specific somatic mutations or other sample-specific
9175 variant types (e.g., RNA editing). Most of the functions operate on
9176 alignments (BAM files) or datasets of called variants. The user is expected
9177 to have already aligned the reads with a separate tool, e.g., GSNAP via
9179 (license license:artistic2.0)))
9181 (define-public r-heatplus
9188 (uri (bioconductor-uri "Heatplus" version))
9191 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
9192 (properties `((upstream-name . "Heatplus")))
9193 (build-system r-build-system)
9195 (list r-rcolorbrewer))
9196 (home-page "https://github.com/alexploner/Heatplus")
9197 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
9199 "This package provides tools to display a rectangular heatmap (intensity
9200 plot) of a data matrix. By default, both samples (columns) and features (row)
9201 of the matrix are sorted according to a hierarchical clustering, and the
9202 corresponding dendrogram is plotted. Optionally, panels with additional
9203 information about samples and features can be added to the plot.")
9204 (license license:gpl2+)))
9206 (define-public r-gosemsim
9213 (uri (bioconductor-uri "GOSemSim" version))
9216 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
9217 (properties `((upstream-name . "GOSemSim")))
9218 (build-system r-build-system)
9220 (list r-annotationdbi r-go-db r-rcpp))
9223 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
9224 (synopsis "GO-terms semantic similarity measures")
9226 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
9227 quantitative ways to compute similarities between genes and gene groups, and
9228 have became important basis for many bioinformatics analysis approaches.
9229 GOSemSim is an R package for semantic similarity computation among GO terms,
9230 sets of GO terms, gene products and gene clusters.")
9231 (license license:artistic2.0)))
9233 (define-public r-anota
9240 (uri (bioconductor-uri "anota" version))
9243 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
9244 (build-system r-build-system)
9246 (list r-multtest r-qvalue))
9247 (home-page "https://bioconductor.org/packages/anota/")
9248 (synopsis "Analysis of translational activity")
9250 "Genome wide studies of translational control is emerging as a tool to
9251 study various biological conditions. The output from such analysis is both
9252 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
9253 involved in translation (the actively translating mRNA level) for each mRNA.
9254 The standard analysis of such data strives towards identifying differential
9255 translational between two or more sample classes - i.e., differences in
9256 actively translated mRNA levels that are independent of underlying differences
9257 in cytosolic mRNA levels. This package allows for such analysis using partial
9258 variances and the random variance model. As 10s of thousands of mRNAs are
9259 analyzed in parallel the library performs a number of tests to assure that
9260 the data set is suitable for such analysis.")
9261 (license license:gpl3)))
9263 (define-public r-sigpathway
9265 (name "r-sigpathway")
9270 (uri (bioconductor-uri "sigPathway" version))
9273 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
9274 (properties `((upstream-name . "sigPathway")))
9275 (build-system r-build-system)
9276 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
9277 (synopsis "Pathway analysis")
9279 "This package is used to conduct pathway analysis by calculating the NT_k
9280 and NE_k statistics in a statistical framework for determining whether a
9281 specified group of genes for a pathway has a coordinated association with a
9282 phenotype of interest.")
9283 (license license:gpl2)))
9285 (define-public r-fcscan
9292 (uri (bioconductor-uri "fcScan" version))
9294 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
9295 (properties `((upstream-name . "fcScan")))
9296 (build-system r-build-system)
9304 r-summarizedexperiment
9305 r-variantannotation))
9306 (native-inputs (list r-knitr))
9307 (home-page "https://bioconductor.org/packages/fcScan")
9308 (synopsis "Detect clusters of coordinates with user defined options")
9310 "This package is used to detect combination of genomic coordinates
9311 falling within a user defined window size along with user defined overlap
9312 between identified neighboring clusters. It can be used for genomic data
9313 where the clusters are built on a specific chromosome or specific strand.
9314 Clustering can be performed with a \"greedy\" option allowing thus the
9315 presence of additional sites within the allowed window size.")
9316 (license license:artistic2.0)))
9318 (define-public r-fgsea
9325 (uri (bioconductor-uri "fgsea" version))
9328 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
9329 (build-system r-build-system)
9341 (home-page "https://github.com/ctlab/fgsea/")
9342 (synopsis "Fast gene set enrichment analysis")
9344 "The package implements an algorithm for fast gene set enrichment
9345 analysis. Using the fast algorithm makes more permutations and gets
9346 more fine grained p-values, which allows using accurate standard approaches
9347 to multiple hypothesis correction.")
9348 (license license:expat)))
9350 (define-public r-dose
9357 (uri (bioconductor-uri "DOSE" version))
9360 "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"))))
9361 (properties `((upstream-name . "DOSE")))
9362 (build-system r-build-system)
9364 (list r-annotationdbi
9374 (home-page "https://guangchuangyu.github.io/software/DOSE/")
9375 (synopsis "Disease ontology semantic and enrichment analysis")
9377 "This package implements five methods proposed by Resnik, Schlicker,
9378 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
9379 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
9380 including hypergeometric model and gene set enrichment analysis are also
9381 implemented for discovering disease associations of high-throughput biological
9383 (license license:artistic2.0)))
9385 (define-public r-enrichplot
9387 (name "r-enrichplot")
9392 (uri (bioconductor-uri "enrichplot" version))
9395 "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"))))
9396 (build-system r-build-system)
9415 (home-page "https://github.com/GuangchuangYu/enrichplot")
9416 (synopsis "Visualization of functional enrichment result")
9418 "The enrichplot package implements several visualization methods for
9419 interpreting functional enrichment results obtained from ORA or GSEA analyses.
9420 All the visualization methods are developed based on ggplot2 graphics.")
9421 (license license:artistic2.0)))
9423 (define-public r-clusterprofiler
9425 (name "r-clusterprofiler")
9430 (uri (bioconductor-uri "clusterProfiler" version))
9433 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
9435 `((upstream-name . "clusterProfiler")))
9436 (build-system r-build-system)
9438 (list r-annotationdbi
9453 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
9454 (synopsis "Analysis and visualization of functional profiles for gene clusters")
9456 "This package implements methods to analyze and visualize functional
9457 profiles (GO and KEGG) of gene and gene clusters.")
9458 (license license:artistic2.0)))
9460 (define-public r-clusterexperiment
9462 (name "r-clusterexperiment")
9466 (uri (bioconductor-uri "clusterExperiment" version))
9469 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
9470 (build-system r-build-system)
9495 r-singlecellexperiment
9497 r-summarizedexperiment
9499 (home-page "https://bioconductor.org/packages/clusterExperiment/")
9500 (synopsis "Compare clusterings for single-cell sequencing")
9501 (description "This package provides functionality for running and comparing
9502 many different clusterings of single-cell sequencing data or other large mRNA
9503 expression data sets.")
9504 (license license:artistic2.0)))
9506 (define-public r-mlinterfaces
9508 (name "r-mlinterfaces")
9513 (uri (bioconductor-uri "MLInterfaces" version))
9516 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
9517 (properties `((upstream-name . "MLInterfaces")))
9518 (build-system r-build-system)
9540 (home-page "https://bioconductor.org/packages/MLInterfaces/")
9541 (synopsis "Interfaces to R machine learning procedures")
9543 "This package provides uniform interfaces to machine learning code for
9544 data in R and Bioconductor containers.")
9545 ;; Any version of the LGPL.
9546 (license license:lgpl2.1+)))
9548 (define-public r-annaffy
9555 (uri (bioconductor-uri "annaffy" version))
9558 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
9559 (build-system r-build-system)
9562 (modify-phases %standard-phases
9563 (add-after 'unpack 'remove-reference-to-non-free-data
9565 (substitute* "DESCRIPTION"
9566 ((", KEGG.db") "")))))))
9568 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
9569 (home-page "https://bioconductor.org/packages/annaffy/")
9570 (synopsis "Annotation tools for Affymetrix biological metadata")
9572 "This package provides functions for handling data from Bioconductor
9573 Affymetrix annotation data packages. It produces compact HTML and text
9574 reports including experimental data and URL links to many online databases.
9575 It allows searching of biological metadata using various criteria.")
9576 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
9577 ;; the LGPL 2.1 is included.
9578 (license license:lgpl2.1+)))
9580 (define-public r-a4core
9587 (uri (bioconductor-uri "a4Core" version))
9590 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
9591 (properties `((upstream-name . "a4Core")))
9592 (build-system r-build-system)
9594 (list r-biobase r-glmnet))
9597 (home-page "https://bioconductor.org/packages/a4Core")
9598 (synopsis "Automated Affymetrix array analysis core package")
9600 "This is the core package for the automated analysis of Affymetrix
9602 (license license:gpl3)))
9604 (define-public r-a4classif
9606 (name "r-a4classif")
9611 (uri (bioconductor-uri "a4Classif" version))
9614 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
9615 (properties `((upstream-name . "a4Classif")))
9616 (build-system r-build-system)
9627 (home-page "https://bioconductor.org/packages/a4Classif/")
9628 (synopsis "Automated Affymetrix array analysis classification package")
9630 "This is the classification package for the automated analysis of
9631 Affymetrix arrays.")
9632 (license license:gpl3)))
9634 (define-public r-a4preproc
9636 (name "r-a4preproc")
9641 (uri (bioconductor-uri "a4Preproc" version))
9644 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
9645 (properties `((upstream-name . "a4Preproc")))
9646 (build-system r-build-system)
9648 (list r-biobase r-biocgenerics))
9651 (home-page "https://bioconductor.org/packages/a4Preproc/")
9652 (synopsis "Automated Affymetrix array analysis preprocessing package")
9654 "This is a package for the automated analysis of Affymetrix arrays. It
9655 is used for preprocessing the arrays.")
9656 (license license:gpl3)))
9658 (define-public r-a4reporting
9660 (name "r-a4reporting")
9665 (uri (bioconductor-uri "a4Reporting" version))
9668 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
9669 (properties `((upstream-name . "a4Reporting")))
9670 (build-system r-build-system)
9675 (home-page "https://bioconductor.org/packages/a4Reporting/")
9676 (synopsis "Automated Affymetrix array analysis reporting package")
9678 "This is a package for the automated analysis of Affymetrix arrays. It
9679 provides reporting features.")
9680 (license license:gpl3)))
9682 (define-public r-a4base
9689 (uri (bioconductor-uri "a4Base" version))
9692 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
9693 (properties `((upstream-name . "a4Base")))
9694 (build-system r-build-system)
9706 (home-page "https://bioconductor.org/packages/a4Base/")
9707 (synopsis "Automated Affymetrix array analysis base package")
9709 "This package provides basic features for the automated analysis of
9710 Affymetrix arrays.")
9711 (license license:gpl3)))
9720 (uri (bioconductor-uri "a4" version))
9723 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
9724 (build-system r-build-system)
9726 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
9727 (home-page "https://bioconductor.org/packages/a4/")
9728 (synopsis "Automated Affymetrix array analysis umbrella package")
9730 "This package provides a software suite for the automated analysis of
9731 Affymetrix arrays.")
9732 (license license:gpl3)))
9734 (define-public r-abseqr
9741 (uri (bioconductor-uri "abseqR" version))
9744 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
9745 (properties `((upstream-name . "abseqR")))
9746 (build-system r-build-system)
9750 (list r-biocparallel
9770 (home-page "https://github.com/malhamdoosh/abseqR")
9771 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
9773 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
9774 sequencing datasets generated from antibody libraries and abseqR is one of its
9775 packages. AbseqR empowers the users of abseqPy with plotting and reporting
9776 capabilities and allows them to generate interactive HTML reports for the
9777 convenience of viewing and sharing with other researchers. Additionally,
9778 abseqR extends abseqPy to compare multiple repertoire analyses and perform
9779 further downstream analysis on its output.")
9780 (license license:gpl3)))
9782 (define-public r-bacon
9789 (uri (bioconductor-uri "bacon" version))
9792 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
9793 (build-system r-build-system)
9795 (list r-biocparallel r-ellipse r-ggplot2))
9798 (home-page "https://bioconductor.org/packages/bacon/")
9799 (synopsis "Controlling bias and inflation in association studies")
9801 "Bacon can be used to remove inflation and bias often observed in
9802 epigenome- and transcriptome-wide association studies. To this end bacon
9803 constructs an empirical null distribution using a Gibbs Sampling algorithm by
9804 fitting a three-component normal mixture on z-scores.")
9805 (license license:gpl2+)))
9807 (define-public r-rgadem
9814 (uri (bioconductor-uri "rGADEM" version))
9817 "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"))))
9818 (properties `((upstream-name . "rGADEM")))
9819 (build-system r-build-system)
9821 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
9822 (home-page "https://bioconductor.org/packages/rGADEM/")
9823 (synopsis "De novo sequence motif discovery")
9825 "rGADEM is an efficient de novo motif discovery tool for large-scale
9826 genomic sequence data.")
9827 (license license:artistic2.0)))
9829 (define-public r-motiv
9836 (uri (bioconductor-uri "MotIV" version))
9839 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
9840 (properties `((upstream-name . "MotIV")))
9841 (build-system r-build-system)
9845 (list r-biocgenerics
9852 (home-page "https://bioconductor.org/packages/MotIV/")
9853 (synopsis "Motif identification and validation")
9855 "This package is used for the identification and validation of sequence
9856 motifs. It makes use of STAMP for comparing a set of motifs to a given
9857 database (e.g. JASPAR). It can also be used to visualize motifs, motif
9858 distributions, modules and filter motifs.")
9859 (license license:gpl2)))
9861 (define-public r-motifdb
9867 (uri (bioconductor-uri "MotifDb" version))
9869 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
9870 (properties `((upstream-name . "MotifDb")))
9871 (build-system r-build-system)
9873 (list r-biocgenerics
9882 (home-page "https://www.bioconductor.org/packages/MotifDb/")
9883 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
9884 (description "This package provides more than 2000 annotated position
9885 frequency matrices from nine public sources, for multiple organisms.")
9886 (license license:artistic2.0)))
9888 (define-public r-motifbreakr
9890 (name "r-motifbreakr")
9894 (uri (bioconductor-uri "motifbreakR" version))
9896 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
9897 (properties `((upstream-name . "motifbreakR")))
9898 (build-system r-build-system)
9900 (list r-biocgenerics
9914 r-summarizedexperiment
9916 r-variantannotation))
9919 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
9920 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
9921 (description "This package allows biologists to judge in the first place
9922 whether the sequence surrounding the polymorphism is a good match, and in
9923 the second place how much information is gained or lost in one allele of
9924 the polymorphism relative to another. This package gives a choice of
9925 algorithms for interrogation of genomes with motifs from public sources:
9927 @item a weighted-sum probability matrix;
9928 @item log-probabilities;
9929 @item weighted by relative entropy.
9932 This package can predict effects for novel or previously described variants in
9933 public databases, making it suitable for tasks beyond the scope of its original
9934 design. Lastly, it can be used to interrogate any genome curated within
9936 (license license:gpl2+)))
9938 (define-public r-motifstack
9940 (name "r-motifstack")
9945 (uri (bioconductor-uri "motifStack" version))
9948 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
9949 (properties `((upstream-name . "motifStack")))
9950 (build-system r-build-system)
9960 (home-page "https://bioconductor.org/packages/motifStack/")
9961 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
9963 "The motifStack package is designed for graphic representation of
9964 multiple motifs with different similarity scores. It works with both DNA/RNA
9965 sequence motifs and amino acid sequence motifs. In addition, it provides the
9966 flexibility for users to customize the graphic parameters such as the font
9967 type and symbol colors.")
9968 (license license:gpl2+)))
9970 (define-public r-genomicscores
9972 (name "r-genomicscores")
9977 (uri (bioconductor-uri "GenomicScores" version))
9980 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
9981 (properties `((upstream-name . "GenomicScores")))
9982 (build-system r-build-system)
9984 (list r-annotationhub
10001 (home-page "https://github.com/rcastelo/GenomicScores/")
10002 (synopsis "Work with genome-wide position-specific scores")
10004 "This package provides infrastructure to store and access genome-wide
10005 position-specific scores within R and Bioconductor.")
10006 (license license:artistic2.0)))
10008 (define-public r-atacseqqc
10010 (name "r-atacseqqc")
10015 (uri (bioconductor-uri "ATACseqQC" version))
10018 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
10019 (properties `((upstream-name . "ATACseqQC")))
10020 (build-system r-build-system)
10022 (list r-biocgenerics
10028 r-genomicalignments
10042 (home-page "https://bioconductor.org/packages/ATACseqQC/")
10043 (synopsis "ATAC-seq quality control")
10045 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
10046 sequencing, is a rapid and sensitive method for chromatin accessibility
10047 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
10048 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
10049 assess whether their ATAC-seq experiment is successful. It includes
10050 diagnostic plots of fragment size distribution, proportion of mitochondria
10051 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
10053 (license license:gpl2+)))
10055 (define-public r-gofuncr
10062 (uri (bioconductor-uri "GOfuncR" version))
10065 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
10066 (properties `((upstream-name . "GOfuncR")))
10067 (build-system r-build-system)
10069 (list r-annotationdbi
10078 (home-page "https://bioconductor.org/packages/GOfuncR/")
10079 (synopsis "Gene ontology enrichment using FUNC")
10081 "GOfuncR performs a gene ontology enrichment analysis based on the
10082 ontology enrichment software FUNC. GO-annotations are obtained from
10083 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
10084 included in the package and updated regularly. GOfuncR provides the standard
10085 candidate vs background enrichment analysis using the hypergeometric test, as
10086 well as three additional tests:
10089 @item the Wilcoxon rank-sum test that is used when genes are ranked,
10090 @item a binomial test that is used when genes are associated with two counts,
10092 @item a Chi-square or Fisher's exact test that is used in cases when genes are
10093 associated with four counts.
10096 To correct for multiple testing and interdependency of the tests, family-wise
10097 error rates are computed based on random permutations of the gene-associated
10098 variables. GOfuncR also provides tools for exploring the ontology graph and
10099 the annotations, and options to take gene-length or spatial clustering of
10100 genes into account. It is also possible to provide custom gene coordinates,
10101 annotations and ontologies.")
10102 (license license:gpl2+)))
10104 (define-public r-abaenrichment
10106 (name "r-abaenrichment")
10111 (uri (bioconductor-uri "ABAEnrichment" version))
10114 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
10115 (properties `((upstream-name . "ABAEnrichment")))
10116 (build-system r-build-system)
10126 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
10127 (synopsis "Gene expression enrichment in human brain regions")
10129 "The package ABAEnrichment is designed to test for enrichment of user
10130 defined candidate genes in the set of expressed genes in different human brain
10131 regions. The core function @code{aba_enrich} integrates the expression of the
10132 candidate gene set (averaged across donors) and the structural information of
10133 the brain using an ontology, both provided by the Allen Brain Atlas project.")
10134 (license license:gpl2+)))
10136 (define-public r-annotationfuncs
10138 (name "r-annotationfuncs")
10143 (uri (bioconductor-uri "AnnotationFuncs" version))
10146 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
10148 `((upstream-name . "AnnotationFuncs")))
10149 (build-system r-build-system)
10151 (list r-annotationdbi r-dbi))
10152 (home-page "https://www.iysik.com/r/annotationfuncs")
10153 (synopsis "Annotation translation functions")
10155 "This package provides functions for handling translating between
10156 different identifieres using the Biocore Data Team data-packages (e.g.
10157 @code{org.Bt.eg.db}).")
10158 (license license:gpl2)))
10160 (define-public r-annotationtools
10162 (name "r-annotationtools")
10167 (uri (bioconductor-uri "annotationTools" version))
10170 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
10172 `((upstream-name . "annotationTools")))
10173 (build-system r-build-system)
10174 (propagated-inputs (list r-biobase))
10175 (home-page "https://bioconductor.org/packages/annotationTools/")
10176 (synopsis "Annotate microarrays and perform gene expression analyses")
10178 "This package provides functions to annotate microarrays, find orthologs,
10179 and integrate heterogeneous gene expression profiles using annotation and
10180 other molecular biology information available as flat file database (plain
10182 ;; Any version of the GPL.
10183 (license (list license:gpl2+))))
10185 (define-public r-allelicimbalance
10187 (name "r-allelicimbalance")
10192 (uri (bioconductor-uri "AllelicImbalance" version))
10195 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
10197 `((upstream-name . "AllelicImbalance")))
10198 (build-system r-build-system)
10200 (list r-annotationdbi
10205 r-genomicalignments
10217 r-summarizedexperiment
10218 r-variantannotation))
10221 (home-page "https://github.com/pappewaio/AllelicImbalance")
10222 (synopsis "Investigate allele-specific expression")
10224 "This package provides a framework for allele-specific expression
10225 investigation using RNA-seq data.")
10226 (license license:gpl3)))
10228 (define-public r-aucell
10235 (uri (bioconductor-uri "AUCell" version))
10238 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
10239 (properties `((upstream-name . "AUCell")))
10240 (build-system r-build-system)
10242 (list r-biocgenerics
10245 r-delayedmatrixstats
10250 r-summarizedexperiment))
10253 (home-page "https://bioconductor.org/packages/AUCell/")
10254 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
10256 "AUCell identifies cells with active gene sets (e.g. signatures,
10257 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
10258 Under the Curve} (AUC) to calculate whether a critical subset of the input
10259 gene set is enriched within the expressed genes for each cell. The
10260 distribution of AUC scores across all the cells allows exploring the relative
10261 expression of the signature. Since the scoring method is ranking-based,
10262 AUCell is independent of the gene expression units and the normalization
10263 procedure. In addition, since the cells are evaluated individually, it can
10264 easily be applied to bigger datasets, subsetting the expression matrix if
10266 (license license:gpl3)))
10268 (define-public r-ebimage
10275 (uri (bioconductor-uri "EBImage" version))
10278 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
10279 (properties `((upstream-name . "EBImage")))
10280 (build-system r-build-system)
10293 (list r-knitr)) ; for vignettes
10294 (home-page "https://github.com/aoles/EBImage")
10295 (synopsis "Image processing and analysis toolbox for R")
10297 "EBImage provides general purpose functionality for image processing and
10298 analysis. In the context of (high-throughput) microscopy-based cellular
10299 assays, EBImage offers tools to segment cells and extract quantitative
10300 cellular descriptors. This allows the automation of such tasks using the R
10301 programming language and facilitates the use of other tools in the R
10302 environment for signal processing, statistical modeling, machine learning and
10303 visualization with image data.")
10304 ;; Any version of the LGPL.
10305 (license license:lgpl2.1+)))
10307 (define-public r-yamss
10314 (uri (bioconductor-uri "yamss" version))
10317 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
10318 (build-system r-build-system)
10320 (list r-biocgenerics
10328 r-summarizedexperiment))
10331 (home-page "https://github.com/hansenlab/yamss")
10332 (synopsis "Tools for high-throughput metabolomics")
10334 "This package provides tools to analyze and visualize high-throughput
10335 metabolomics data acquired using chromatography-mass spectrometry. These tools
10336 preprocess data in a way that enables reliable and powerful differential
10338 (license license:artistic2.0)))
10340 (define-public r-gtrellis
10342 (name "r-gtrellis")
10347 (uri (bioconductor-uri "gtrellis" version))
10350 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
10351 (build-system r-build-system)
10353 (list r-circlize r-genomicranges r-getoptlong r-iranges))
10356 (home-page "https://github.com/jokergoo/gtrellis")
10357 (synopsis "Genome level Trellis layout")
10359 "Genome level Trellis graph visualizes genomic data conditioned by
10360 genomic categories (e.g. chromosomes). For each genomic category, multiple
10361 dimensional data which are represented as tracks describe different features
10362 from different aspects. This package provides high flexibility to arrange
10363 genomic categories and to add self-defined graphics in the plot.")
10364 (license license:expat)))
10366 (define-public r-somaticsignatures
10368 (name "r-somaticsignatures")
10373 (uri (bioconductor-uri "SomaticSignatures" version))
10376 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
10378 `((upstream-name . "SomaticSignatures")))
10379 (build-system r-build-system)
10393 r-variantannotation))
10396 (home-page "https://github.com/juliangehring/SomaticSignatures")
10397 (synopsis "Somatic signatures")
10399 "This package identifies mutational signatures of @dfn{single nucleotide
10400 variants} (SNVs). It provides a infrastructure related to the methodology
10401 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
10402 decomposition algorithms.")
10403 (license license:expat)))
10405 (define-public r-yapsa
10412 (uri (bioconductor-uri "YAPSA" version))
10415 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
10416 (properties `((upstream-name . "YAPSA")))
10417 (build-system r-build-system)
10420 r-bsgenome-hsapiens-ucsc-hg19
10440 r-somaticsignatures
10441 r-variantannotation))
10444 (home-page "https://bioconductor.org/packages/YAPSA/")
10445 (synopsis "Yet another package for signature analysis")
10447 "This package provides functions and routines useful in the analysis of
10448 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
10449 functions to perform a signature analysis with known signatures and a
10450 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
10452 (license license:gpl3)))
10454 (define-public r-gcrma
10461 (uri (bioconductor-uri "gcrma" version))
10464 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
10465 (build-system r-build-system)
10473 (home-page "https://bioconductor.org/packages/gcrma/")
10474 (synopsis "Background adjustment using sequence information")
10476 "Gcrma adjusts for background intensities in Affymetrix array data which
10477 include optical noise and @dfn{non-specific binding} (NSB). The main function
10478 @code{gcrma} converts background adjusted probe intensities to expression
10479 measures using the same normalization and summarization methods as a
10480 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
10481 to estimate probe affinity to NSB. The sequence information is summarized in
10482 a more complex way than the simple GC content. Instead, the base types (A, T,
10483 G or C) at each position along the probe determine the affinity of each probe.
10484 The parameters of the position-specific base contributions to the probe
10485 affinity is estimated in an NSB experiment in which only NSB but no
10486 gene-specific binding is expected.")
10487 ;; Any version of the LGPL
10488 (license license:lgpl2.1+)))
10490 (define-public r-simpleaffy
10492 (name "r-simpleaffy")
10497 (uri (bioconductor-uri "simpleaffy" version))
10500 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
10501 (build-system r-build-system)
10503 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
10504 (home-page "https://bioconductor.org/packages/simpleaffy/")
10505 (synopsis "Very simple high level analysis of Affymetrix data")
10507 "This package provides high level functions for reading Affy @file{.CEL}
10508 files, phenotypic data, and then computing simple things with it, such as
10509 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
10510 library. It also has some basic scatter plot functions and mechanisms for
10511 generating high resolution journal figures.")
10512 (license license:gpl2+)))
10514 (define-public r-yaqcaffy
10516 (name "r-yaqcaffy")
10521 (uri (bioconductor-uri "yaqcaffy" version))
10524 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
10525 (build-system r-build-system)
10527 (list r-simpleaffy))
10528 (home-page "https://bioconductor.org/packages/yaqcaffy/")
10529 (synopsis "Affymetrix quality control and reproducibility analysis")
10531 "This is a package that can be used for quality control of Affymetrix
10532 GeneChip expression data and reproducibility analysis of human whole genome
10533 chips with the MAQC reference datasets.")
10534 (license license:artistic2.0)))
10536 (define-public r-quantro
10543 (uri (bioconductor-uri "quantro" version))
10546 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
10547 (build-system r-build-system)
10558 (home-page "https://bioconductor.org/packages/quantro/")
10559 (synopsis "Test for when to use quantile normalization")
10561 "This package provides a data-driven test for the assumptions of quantile
10562 normalization using raw data such as objects that inherit eSets (e.g.
10563 ExpressionSet, MethylSet). Group level information about each sample (such as
10564 Tumor / Normal status) must also be provided because the test assesses if
10565 there are global differences in the distributions between the user-defined
10567 (license license:gpl3+)))
10569 (define-public r-yarn
10576 (uri (bioconductor-uri "yarn" version))
10579 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
10580 (build-system r-build-system)
10595 (home-page "https://bioconductor.org/packages/yarn/")
10596 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
10598 "Expedite large RNA-Seq analyses using a combination of previously
10599 developed tools. YARN is meant to make it easier for the user in performing
10600 basic mis-annotation quality control, filtering, and condition-aware
10601 normalization. YARN leverages many Bioconductor tools and statistical
10602 techniques to account for the large heterogeneity and sparsity found in very
10603 large RNA-seq experiments.")
10604 (license license:artistic2.0)))
10606 (define-public r-roar
10613 (uri (bioconductor-uri "roar" version))
10616 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
10617 (build-system r-build-system)
10619 (list r-biocgenerics
10621 r-genomicalignments
10626 r-summarizedexperiment))
10627 (home-page "https://github.com/vodkatad/roar/")
10628 (synopsis "Identify differential APA usage from RNA-seq alignments")
10630 "This package provides tools for identifying preferential usage of APA
10631 sites, comparing two biological conditions, starting from known alternative
10632 sites and alignments obtained from standard RNA-seq experiments.")
10633 (license license:gpl3)))
10635 (define-public r-xbseq
10642 (uri (bioconductor-uri "XBSeq" version))
10645 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
10646 (properties `((upstream-name . "XBSeq")))
10647 (build-system r-build-system)
10660 (home-page "https://github.com/Liuy12/XBSeq")
10661 (synopsis "Test for differential expression for RNA-seq data")
10663 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
10664 expression} (DE), where a statistical model was established based on the
10665 assumption that observed signals are the convolution of true expression
10666 signals and sequencing noises. The mapped reads in non-exonic regions are
10667 considered as sequencing noises, which follows a Poisson distribution. Given
10668 measurable observed signal and background noise from RNA-seq data, true
10669 expression signals, assuming governed by the negative binomial distribution,
10670 can be delineated and thus the accurate detection of differential expressed
10672 (license license:gpl3+)))
10674 (define-public r-massspecwavelet
10676 (name "r-massspecwavelet")
10681 (uri (bioconductor-uri "MassSpecWavelet" version))
10684 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
10686 `((upstream-name . "MassSpecWavelet")))
10687 (build-system r-build-system)
10690 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
10691 (synopsis "Mass spectrum processing by wavelet-based algorithms")
10693 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
10694 data mainly through the use of wavelet transforms. It supports peak detection
10695 based on @dfn{Continuous Wavelet Transform} (CWT).")
10696 (license license:lgpl2.0+)))
10698 (define-public r-xcms
10705 (uri (bioconductor-uri "xcms" version))
10708 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
10709 (build-system r-build-system)
10727 r-summarizedexperiment))
10730 (home-page "https://bioconductor.org/packages/xcms/")
10731 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
10733 "This package provides a framework for processing and visualization of
10734 chromatographically separated and single-spectra mass spectral data. It
10735 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
10736 data for high-throughput, untargeted analyte profiling.")
10737 (license license:gpl2+)))
10739 (define-public r-wppi
10745 (uri (bioconductor-uri "wppi" version))
10748 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
10749 (properties `((upstream-name . "wppi")))
10750 (build-system r-build-system)
10751 ;; This is necessary because omnipathr attempts to write a configuration
10755 (modify-phases %standard-phases
10756 (add-after 'unpack 'set-HOME
10757 (lambda _ (setenv "HOME" "/tmp"))))))
10758 (propagated-inputs (list r-dplyr
10770 (native-inputs (list r-knitr))
10771 (home-page "https://github.com/AnaGalhoz37/wppi")
10772 (synopsis "Weighting protein-protein interactions")
10774 "This package predicts functional relevance of protein-protein
10775 interactions based on functional annotations such as Human Protein Ontology
10776 and Gene Ontology, and prioritizes genes based on network topology, functional
10777 scores and a path search algorithm.")
10778 (license license:expat)))
10780 (define-public r-wrench
10787 (uri (bioconductor-uri "Wrench" version))
10790 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
10791 (properties `((upstream-name . "Wrench")))
10792 (build-system r-build-system)
10794 (list r-limma r-locfit r-matrixstats))
10797 (home-page "https://github.com/HCBravoLab/Wrench")
10798 (synopsis "Wrench normalization for sparse count data")
10800 "Wrench is a package for normalization sparse genomic count data, like
10801 that arising from 16s metagenomic surveys.")
10802 (license license:artistic2.0)))
10804 (define-public r-wiggleplotr
10806 (name "r-wiggleplotr")
10811 (uri (bioconductor-uri "wiggleplotr" version))
10814 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
10815 (build-system r-build-system)
10829 (home-page "https://bioconductor.org/packages/wiggleplotr/")
10830 (synopsis "Make read coverage plots from BigWig files")
10832 "This package provides tools to visualize read coverage from sequencing
10833 experiments together with genomic annotations (genes, transcripts, peaks).
10834 Introns of long transcripts can be rescaled to a fixed length for better
10835 visualization of exonic read coverage.")
10836 (license license:asl2.0)))
10838 (define-public r-widgettools
10840 (name "r-widgettools")
10845 (uri (bioconductor-uri "widgetTools" version))
10848 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
10849 (properties `((upstream-name . "widgetTools")))
10850 (build-system r-build-system)
10851 (home-page "https://bioconductor.org/packages/widgetTools/")
10852 (synopsis "Tools for creating interactive tcltk widgets")
10854 "This package contains tools to support the construction of tcltk
10856 ;; Any version of the LGPL.
10857 (license license:lgpl3+)))
10859 (define-public r-webbioc
10866 (uri (bioconductor-uri "webbioc" version))
10869 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
10870 (build-system r-build-system)
10872 (list netpbm perl))
10882 (home-page "https://www.bioconductor.org/")
10883 (synopsis "Bioconductor web interface")
10885 "This package provides an integrated web interface for doing microarray
10886 analysis using several of the Bioconductor packages. It is intended to be
10887 deployed as a centralized bioinformatics resource for use by many users.
10888 Currently only Affymetrix oligonucleotide analysis is supported.")
10889 (license license:gpl2+)))
10891 (define-public r-zinbwave
10893 (name "r-zinbwave")
10898 (uri (bioconductor-uri "zinbwave" version))
10901 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
10902 (build-system r-build-system)
10904 (list r-biocparallel
10908 r-singlecellexperiment
10910 r-summarizedexperiment))
10913 (home-page "https://bioconductor.org/packages/zinbwave")
10914 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
10915 (description "This package implements a general and flexible zero-inflated
10916 negative binomial model that can be used to provide a low-dimensional
10917 representations of single-cell RNA-seq data. The model accounts for zero
10918 inflation (dropouts), over-dispersion, and the count nature of the data.
10919 The model also accounts for the difference in library sizes and optionally
10920 for batch effects and/or other covariates, avoiding the need for pre-normalize
10922 (license license:artistic2.0)))
10924 (define-public r-zfpkm
10931 (uri (bioconductor-uri "zFPKM" version))
10934 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
10935 (properties `((upstream-name . "zFPKM")))
10936 (build-system r-build-system)
10938 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
10941 (home-page "https://github.com/ronammar/zFPKM/")
10942 (synopsis "Functions to facilitate zFPKM transformations")
10944 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
10945 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
10947 (license license:gpl3)))
10949 (define-public r-rbowtie2
10951 (name "r-rbowtie2")
10956 (uri (bioconductor-uri "Rbowtie2" version))
10959 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
10960 (properties `((upstream-name . "Rbowtie2")))
10961 (build-system r-build-system)
10963 (list r-magrittr r-rsamtools))
10965 (list samtools zlib))
10968 (home-page "https://bioconductor.org/packages/Rbowtie2/")
10969 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
10971 "This package provides an R wrapper of the popular @code{bowtie2}
10972 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
10973 rapid adapter trimming, identification, and read merging.")
10974 (license license:gpl3+)))
10976 (define-public r-progeny
10983 (uri (bioconductor-uri "progeny" version))
10986 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
10987 (build-system r-build-system)
10999 (home-page "https://github.com/saezlab/progeny")
11000 (synopsis "Pathway responsive gene activity inference")
11002 "This package provides a function to infer pathway activity from gene
11003 expression. It contains the linear model inferred in the publication
11004 \"Perturbation-response genes reveal signaling footprints in cancer gene
11006 (license license:asl2.0)))
11008 (define-public r-arrmnormalization
11010 (name "r-arrmnormalization")
11015 (uri (bioconductor-uri "ARRmNormalization" version))
11018 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
11020 `((upstream-name . "ARRmNormalization")))
11021 (build-system r-build-system)
11022 (propagated-inputs (list r-arrmdata))
11023 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
11024 (synopsis "Adaptive robust regression normalization for methylation data")
11026 "This is a package to perform the @dfn{Adaptive Robust Regression
11027 method} (ARRm) for the normalization of methylation data from the Illumina
11028 Infinium HumanMethylation 450k assay.")
11029 (license license:artistic2.0)))
11031 (define-public r-biocfilecache
11033 (name "r-biocfilecache")
11038 (uri (bioconductor-uri "BiocFileCache" version))
11041 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
11042 (properties `((upstream-name . "BiocFileCache")))
11043 (build-system r-build-system)
11055 (home-page "https://bioconductor.org/packages/BiocFileCache/")
11056 (synopsis "Manage files across sessions")
11058 "This package creates a persistent on-disk cache of files that the user
11059 can add, update, and retrieve. It is useful for managing resources (such as
11060 custom Txdb objects) that are costly or difficult to create, web resources,
11061 and data files used across sessions.")
11062 (license license:artistic2.0)))
11064 (define-public r-iclusterplus
11066 (name "r-iclusterplus")
11071 (uri (bioconductor-uri "iClusterPlus" version))
11074 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
11075 (properties `((upstream-name . "iClusterPlus")))
11076 (build-system r-build-system)
11077 (native-inputs (list gfortran))
11078 (home-page "https://bioconductor.org/packages/iClusterPlus/")
11079 (synopsis "Integrative clustering of multi-type genomic data")
11081 "iClusterPlus is developed for integrative clustering analysis of
11082 multi-type genomic data and is an enhanced version of iCluster proposed and
11083 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
11084 from the experiments where biological samples (e.g. tumor samples) are
11085 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
11086 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
11087 on. In the iClusterPlus model, binary observations such as somatic mutation
11088 are modeled as Binomial processes; categorical observations such as copy
11089 number states are realizations of Multinomial random variables; counts are
11090 modeled as Poisson random processes; and continuous measures are modeled by
11091 Gaussian distributions.")
11092 (license license:gpl2+)))
11094 (define-public r-rbowtie
11101 (uri (bioconductor-uri "Rbowtie" version))
11104 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
11105 (properties `((upstream-name . "Rbowtie")))
11106 (build-system r-build-system)
11109 ;; Disable unsupported `popcnt' instructions on
11110 ;; architectures other than x86_64
11111 ,(if (string-prefix? "x86_64"
11112 (or (%current-target-system)
11113 (%current-system)))
11115 '(modify-phases %standard-phases
11116 (add-after 'unpack 'patch-sources
11118 (setenv "POPCNT_CAPABILITY" "0")))))))
11119 (inputs (list zlib))
11122 (home-page "https://bioconductor.org/packages/Rbowtie/")
11123 (synopsis "R bowtie wrapper")
11125 "This package provides an R wrapper around the popular bowtie short read
11126 aligner and around SpliceMap, a de novo splice junction discovery and
11128 (license license:artistic2.0)))
11130 (define-public r-sgseq
11137 (uri (bioconductor-uri "SGSeq" version))
11140 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
11141 (properties `((upstream-name . "SGSeq")))
11142 (build-system r-build-system)
11144 (list r-annotationdbi
11148 r-genomicalignments
11157 r-summarizedexperiment))
11160 (home-page "https://bioconductor.org/packages/SGSeq/")
11161 (synopsis "Splice event prediction and quantification from RNA-seq data")
11163 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
11164 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
11165 represented as a splice graph, which can be obtained from existing annotation
11166 or predicted from the mapped sequence reads. Splice events are identified
11167 from the graph and are quantified locally using structurally compatible reads
11168 at the start or end of each splice variant. The software includes functions
11169 for splice event prediction, quantification, visualization and
11171 (license license:artistic2.0)))
11173 (define-public r-rhisat2
11180 (uri (bioconductor-uri "Rhisat2" version))
11183 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
11184 (properties `((upstream-name . "Rhisat2")))
11185 (build-system r-build-system)
11188 (modify-phases %standard-phases
11189 (add-after 'unpack 'make-reproducible
11191 (substitute* "src/Makefile"
11192 (("`hostname`") "guix")
11194 ;; Avoid shelling out to "which".
11195 (("^CC =.*") (which "gcc"))
11196 (("^CPP =.*") (which "g++")))
11199 (list r-genomicfeatures r-genomicranges r-sgseq))
11202 (home-page "https://github.com/fmicompbio/Rhisat2")
11203 (synopsis "R Wrapper for HISAT2 sequence aligner")
11205 "This package provides an R interface to the HISAT2 spliced short-read
11206 aligner by Kim et al. (2015). The package contains wrapper functions to
11207 create a genome index and to perform the read alignment to the generated
11209 (license license:gpl3)))
11211 (define-public r-quasr
11218 (uri (bioconductor-uri "QuasR" version))
11221 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
11222 (properties `((upstream-name . "QuasR")))
11223 (build-system r-build-system)
11225 (list r-annotationdbi
11244 (home-page "https://bioconductor.org/packages/QuasR/")
11245 (synopsis "Quantify and annotate short reads in R")
11247 "This package provides a framework for the quantification and analysis of
11248 short genomic reads. It covers a complete workflow starting from raw sequence
11249 reads, over creation of alignments and quality control plots, to the
11250 quantification of genomic regions of interest.")
11251 (license license:gpl2)))
11253 (define-public r-rqc
11260 (uri (bioconductor-uri "Rqc" version))
11263 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
11264 (properties `((upstream-name . "Rqc")))
11265 (build-system r-build-system)
11267 (list r-biocgenerics
11272 r-genomicalignments
11287 (home-page "https://github.com/labbcb/Rqc")
11288 (synopsis "Quality control tool for high-throughput sequencing data")
11290 "Rqc is an optimized tool designed for quality control and assessment of
11291 high-throughput sequencing data. It performs parallel processing of entire
11292 files and produces a report which contains a set of high-resolution
11294 (license license:gpl2+)))
11296 (define-public r-birewire
11298 (name "r-birewire")
11303 (uri (bioconductor-uri "BiRewire" version))
11306 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
11307 (properties `((upstream-name . "BiRewire")))
11308 (build-system r-build-system)
11310 (list r-igraph r-matrix r-rtsne r-slam))
11311 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
11312 (synopsis "Tools for randomization of bipartite graphs")
11314 "This package provides functions for bipartite network rewiring through N
11315 consecutive switching steps and for the computation of the minimal number of
11316 switching steps to be performed in order to maximise the dissimilarity with
11317 respect to the original network. It includes functions for the analysis of
11318 the introduced randomness across the switching steps and several other
11319 routines to analyse the resulting networks and their natural projections.")
11320 (license license:gpl3)))
11322 (define-public r-birta
11329 (uri (bioconductor-uri "birta" version))
11332 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
11333 (build-system r-build-system)
11335 (list r-biobase r-limma r-mass))
11336 (home-page "https://bioconductor.org/packages/birta")
11337 (synopsis "Bayesian inference of regulation of transcriptional activity")
11339 "Expression levels of mRNA molecules are regulated by different
11340 processes, comprising inhibition or activation by transcription factors and
11341 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
11342 Inference of Regulation of Transcriptional Activity) uses the regulatory
11343 networks of transcription factors and miRNAs together with mRNA and miRNA
11344 expression data to predict switches in regulatory activity between two
11345 conditions. A Bayesian network is used to model the regulatory structure and
11346 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
11347 (license license:gpl2+)))
11349 (define-public r-multidataset
11351 (name "r-multidataset")
11356 (uri (bioconductor-uri "MultiDataSet" version))
11359 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
11360 (properties `((upstream-name . "MultiDataSet")))
11361 (build-system r-build-system)
11372 r-summarizedexperiment))
11375 (home-page "https://bioconductor.org/packages/MultiDataSet/")
11376 (synopsis "Implementation of MultiDataSet and ResultSet")
11378 "This package provides an implementation of the BRGE's (Bioinformatic
11379 Research Group in Epidemiology from Center for Research in Environmental
11380 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
11381 integrating multi omics data sets and ResultSet is a container for omics
11382 results. This package contains base classes for MEAL and rexposome
11384 (license license:expat)))
11386 (define-public r-ropls
11393 (uri (bioconductor-uri "ropls" version))
11396 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
11397 (build-system r-build-system)
11400 r-multiassayexperiment
11402 r-summarizedexperiment))
11404 (list r-knitr)) ; for vignettes
11405 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
11406 (synopsis "Multivariate analysis and feature selection of omics data")
11408 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
11409 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
11410 regression, classification, and feature selection of omics data where the
11411 number of variables exceeds the number of samples and with multicollinearity
11412 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
11413 separately model the variation correlated (predictive) to the factor of
11414 interest and the uncorrelated (orthogonal) variation. While performing
11415 similarly to PLS, OPLS facilitates interpretation.
11417 This package provides imlementations of PCA, PLS, and OPLS for multivariate
11418 analysis and feature selection of omics data. In addition to scores, loadings
11419 and weights plots, the package provides metrics and graphics to determine the
11420 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
11421 validity of the model by permutation testing, detect outliers, and perform
11422 feature selection (e.g. with Variable Importance in Projection or regression
11424 (license license:cecill)))
11426 (define-public r-biosigner
11428 (name "r-biosigner")
11433 (uri (bioconductor-uri "biosigner" version))
11436 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
11437 (build-system r-build-system)
11441 r-multiassayexperiment
11445 r-summarizedexperiment))
11448 (home-page "https://bioconductor.org/packages/biosigner/")
11449 (synopsis "Signature discovery from omics data")
11451 "Feature selection is critical in omics data analysis to extract
11452 restricted and meaningful molecular signatures from complex and high-dimension
11453 data, and to build robust classifiers. This package implements a method to
11454 assess the relevance of the variables for the prediction performances of the
11455 classifier. The approach can be run in parallel with the PLS-DA, Random
11456 Forest, and SVM binary classifiers. The signatures and the corresponding
11457 'restricted' models are returned, enabling future predictions on new
11459 (license license:cecill)))
11461 (define-public r-annotatr
11463 (name "r-annotatr")
11468 (uri (bioconductor-uri "annotatr" version))
11471 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
11472 (build-system r-build-system)
11474 (list r-annotationdbi
11489 (home-page "https://bioconductor.org/packages/annotatr/")
11490 (synopsis "Annotation of genomic regions to genomic annotations")
11492 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
11493 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
11494 to investigate the intersecting genomic annotations. Such annotations include
11495 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
11496 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
11497 enhancers. The annotatr package provides an easy way to summarize and
11498 visualize the intersection of genomic sites/regions with genomic
11500 (license license:gpl3)))
11502 (define-public r-rsubread
11504 (name "r-rsubread")
11509 (uri (bioconductor-uri "Rsubread" version))
11512 "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2"))))
11513 (properties `((upstream-name . "Rsubread")))
11514 (build-system r-build-system)
11515 (inputs (list zlib))
11518 (home-page "https://bioconductor.org/packages/Rsubread/")
11519 (synopsis "Subread sequence alignment and counting for R")
11521 "This package provides tools for alignment, quantification and analysis
11522 of second and third generation sequencing data. It includes functionality for
11523 read mapping, read counting, SNP calling, structural variant detection and
11524 gene fusion discovery. It can be applied to all major sequencing techologies
11525 and to both short and long sequence reads.")
11526 (license license:gpl3)))
11528 (define-public r-flowutils
11530 (name "r-flowutils")
11535 (uri (bioconductor-uri "flowUtils" version))
11538 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
11539 (properties `((upstream-name . "flowUtils")))
11540 (build-system r-build-system)
11548 (home-page "https://github.com/jspidlen/flowUtils")
11549 (synopsis "Utilities for flow cytometry")
11551 "This package provides utilities for flow cytometry data.")
11552 (license license:artistic2.0)))
11554 (define-public r-consensusclusterplus
11556 (name "r-consensusclusterplus")
11561 (uri (bioconductor-uri "ConsensusClusterPlus" version))
11564 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
11566 `((upstream-name . "ConsensusClusterPlus")))
11567 (build-system r-build-system)
11569 (list r-all r-biobase r-cluster))
11570 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
11571 (synopsis "Clustering algorithm")
11573 "This package provides an implementation of an algorithm for determining
11574 cluster count and membership by stability evidence in unsupervised analysis.")
11575 (license license:gpl2)))
11577 ;; This is the latest commit and it solves a bug from the latest release.
11578 (define-public r-cycombine
11579 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
11581 (name "r-cycombine")
11582 (version (git-version "0.2.6" revision commit))
11585 (uri (git-reference
11586 (url "https://github.com/biosurf/cyCombine")
11588 (file-name (git-file-name name version))
11591 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
11592 (properties `((upstream-name . "cyCombine")))
11593 (build-system r-build-system)
11611 (native-inputs (list r-knitr))
11612 (home-page "https://github.com/biosurf/cyCombine")
11613 (synopsis "Integration of single-cell cytometry datasets")
11615 "This package provides a method for combining single-cell cytometry
11616 datasets, which increases the analytical flexibility and the statistical power
11617 of the analyses while minimizing technical noise.")
11618 (license license:expat))))
11620 (define-public r-cytolib
11627 (uri (bioconductor-uri "cytolib" version))
11630 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
11631 (properties `((upstream-name . "cytolib")))
11632 (build-system r-build-system)
11642 (home-page "https://bioconductor.org/packages/cytolib/")
11643 (synopsis "C++ infrastructure for working with gated cytometry")
11645 "This package provides the core data structure and API to represent and
11646 interact with gated cytometry data.")
11647 (license license:artistic2.0)))
11649 (define-public r-flowcore
11651 (name "r-flowcore")
11656 (uri (bioconductor-uri "flowCore" version))
11659 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
11660 (properties `((upstream-name . "flowCore")))
11661 (build-system r-build-system)
11674 (home-page "https://bioconductor.org/packages/flowCore")
11675 (synopsis "Basic structures for flow cytometry data")
11677 "This package provides S4 data structures and basic functions to deal
11678 with flow cytometry data.")
11679 (license license:artistic2.0)))
11681 (define-public r-flowmeans
11683 (name "r-flowmeans")
11688 (uri (bioconductor-uri "flowMeans" version))
11691 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
11692 (properties `((upstream-name . "flowMeans")))
11693 (build-system r-build-system)
11695 (list r-biobase r-feature r-flowcore r-rrcov))
11696 (home-page "https://bioconductor.org/packages/flowMeans")
11697 (synopsis "Non-parametric flow cytometry data gating")
11699 "This package provides tools to identify cell populations in Flow
11700 Cytometry data using non-parametric clustering and segmented-regression-based
11701 change point detection.")
11702 (license license:artistic2.0)))
11704 (define-public r-ncdfflow
11706 (name "r-ncdfflow")
11711 (uri (bioconductor-uri "ncdfFlow" version))
11714 "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m"))))
11715 (properties `((upstream-name . "ncdfFlow")))
11716 (build-system r-build-system)
11728 (home-page "https://bioconductor.org/packages/ncdfFlow/")
11729 (synopsis "HDF5 based storage for flow cytometry data")
11731 "This package provides HDF5 storage based methods and functions for
11732 manipulation of flow cytometry data.")
11733 (license license:artistic2.0)))
11735 (define-public r-ggcyto
11742 (uri (bioconductor-uri "ggcyto" version))
11745 "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"))))
11746 (properties `((upstream-name . "ggcyto")))
11747 (build-system r-build-system)
11762 (home-page "https://github.com/RGLab/ggcyto/issues")
11763 (synopsis "Visualize Cytometry data with ggplot")
11765 "With the dedicated fortify method implemented for @code{flowSet},
11766 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
11767 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
11768 and some custom layers also make it easy to add gates and population
11769 statistics to the plot.")
11770 (license license:artistic2.0)))
11772 (define-public r-flowviz
11779 (uri (bioconductor-uri "flowViz" version))
11782 "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f"))))
11783 (properties `((upstream-name . "flowViz")))
11784 (build-system r-build-system)
11797 (home-page "https://bioconductor.org/packages/flowViz/")
11798 (synopsis "Visualization for flow cytometry")
11800 "This package provides visualization tools for flow cytometry data.")
11801 (license license:artistic2.0)))
11803 (define-public r-flowclust
11805 (name "r-flowclust")
11810 (uri (bioconductor-uri "flowClust" version))
11813 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
11814 (properties `((upstream-name . "flowClust")))
11815 (build-system r-build-system)
11817 `(#:configure-flags
11818 (list "--configure-args=--enable-bundled-gsl=no")))
11827 (list pkg-config r-knitr))
11828 (home-page "https://bioconductor.org/packages/flowClust")
11829 (synopsis "Clustering for flow cytometry")
11831 "This package provides robust model-based clustering using a t-mixture
11832 model with Box-Cox transformation.")
11833 (license license:artistic2.0)))
11835 ;; TODO: this package bundles an old version of protobuf. It's not easy to
11836 ;; make it use our protobuf package instead.
11837 (define-public r-rprotobuflib
11839 (name "r-rprotobuflib")
11844 (uri (bioconductor-uri "RProtoBufLib" version))
11847 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
11848 (properties `((upstream-name . "RProtoBufLib")))
11849 (build-system r-build-system)
11852 (modify-phases %standard-phases
11853 (add-after 'unpack 'unpack-bundled-sources
11855 (with-directory-excursion "src"
11856 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
11859 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
11860 (synopsis "C++ headers and static libraries of Protocol buffers")
11862 "This package provides the headers and static library of Protocol buffers
11863 for other R packages to compile and link against.")
11864 (license license:bsd-3)))
11866 (define-public r-flowworkspace
11868 (name "r-flowworkspace")
11873 (uri (bioconductor-uri "flowWorkspace" version))
11876 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
11877 (properties `((upstream-name . "flowWorkspace")))
11878 (build-system r-build-system)
11909 (home-page "https://bioconductor.org/packages/flowWorkspace/")
11910 (synopsis "Infrastructure for working with cytometry data")
11912 "This package is designed to facilitate comparison of automated gating
11913 methods against manual gating done in flowJo. This package allows you to
11914 import basic flowJo workspaces into BioConductor and replicate the gating from
11915 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
11916 samples, compensation, and transformation are performed so that the output
11917 matches the flowJo analysis.")
11918 (license license:artistic2.0)))
11920 (define-public r-flowstats
11922 (name "r-flowstats")
11927 (uri (bioconductor-uri "flowStats" version))
11930 "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj"))))
11931 (properties `((upstream-name . "flowStats")))
11932 (build-system r-build-system)
11950 (home-page "http://www.github.com/RGLab/flowStats")
11951 (synopsis "Statistical methods for the analysis of flow cytometry data")
11953 "This package provides methods and functionality to analyze flow data
11954 that is beyond the basic infrastructure provided by the @code{flowCore}
11956 (license license:artistic2.0)))
11958 (define-public r-opencyto
11960 (name "r-opencyto")
11965 (uri (bioconductor-uri "openCyto" version))
11968 "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y"))))
11969 (properties `((upstream-name . "openCyto")))
11970 (build-system r-build-system)
11995 (home-page "https://bioconductor.org/packages/openCyto")
11996 (synopsis "Hierarchical gating pipeline for flow cytometry data")
11998 "This package is designed to facilitate the automated gating methods in a
11999 sequential way to mimic the manual gating strategy.")
12000 (license license:artistic2.0)))
12002 (define-public r-cytoml
12009 (uri (bioconductor-uri "CytoML" version))
12012 "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"))))
12013 (properties `((upstream-name . "CytoML")))
12014 (build-system r-build-system)
12016 (list libxml2 zlib))
12047 (home-page "https://github.com/RGLab/CytoML")
12048 (synopsis "GatingML interface for cross platform cytometry data sharing")
12050 "This package provides an interface to implementations of the GatingML2.0
12051 standard to exchange gated cytometry data with other software platforms.")
12052 (license license:artistic2.0)))
12054 (define-public r-flowsom
12061 (uri (bioconductor-uri "FlowSOM" version))
12064 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
12065 (properties `((upstream-name . "FlowSOM")))
12066 (build-system r-build-system)
12068 (list r-biocgenerics
12070 r-consensusclusterplus
12090 (home-page "https://bioconductor.org/packages/FlowSOM/")
12091 (synopsis "Visualize and interpret cytometry data")
12093 "FlowSOM offers visualization options for cytometry data, by using
12094 self-organizing map clustering and minimal spanning trees.")
12095 (license license:gpl2+)))
12097 (define-public r-mixomics
12099 (name "r-mixomics")
12104 (uri (bioconductor-uri "mixOmics" version))
12107 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
12108 (properties `((upstream-name . "mixOmics")))
12109 (build-system r-build-system)
12111 (list r-biocparallel
12128 (home-page "http://www.mixOmics.org")
12129 (synopsis "Multivariate methods for exploration of biological datasets")
12131 "mixOmics offers a wide range of multivariate methods for the exploration
12132 and integration of biological datasets with a particular focus on variable
12133 selection. The package proposes several sparse multivariate models we have
12134 developed to identify the key variables that are highly correlated, and/or
12135 explain the biological outcome of interest. The data that can be analysed
12136 with mixOmics may come from high throughput sequencing technologies, such as
12137 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
12138 also beyond the realm of omics (e.g. spectral imaging). The methods
12139 implemented in mixOmics can also handle missing values without having to
12140 delete entire rows with missing data.")
12141 (license license:gpl2+)))
12143 (define-public r-depecher
12144 (package ;Source/Weave error
12145 (name "r-depecher")
12150 (uri (bioconductor-uri "DepecheR" version))
12153 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
12154 (properties `((upstream-name . "DepecheR")))
12155 (build-system r-build-system)
12176 (home-page "https://bioconductor.org/packages/DepecheR/")
12177 (synopsis "Identify traits of clusters in high-dimensional entities")
12179 "The purpose of this package is to identify traits in a dataset that can
12180 separate groups. This is done on two levels. First, clustering is performed,
12181 using an implementation of sparse K-means. Secondly, the generated clusters
12182 are used to predict outcomes of groups of individuals based on their
12183 distribution of observations in the different clusters. As certain clusters
12184 with separating information will be identified, and these clusters are defined
12185 by a sparse number of variables, this method can reduce the complexity of
12186 data, to only emphasize the data that actually matters.")
12187 (license license:expat)))
12189 (define-public r-rcistarget
12191 (name "r-rcistarget")
12196 (uri (bioconductor-uri "RcisTarget" version))
12199 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
12200 (properties `((upstream-name . "RcisTarget")))
12201 (build-system r-build-system)
12213 r-summarizedexperiment
12217 (home-page "https://aertslab.org/#scenic")
12218 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
12220 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
12221 over-represented on a gene list. In a first step, RcisTarget selects DNA
12222 motifs that are significantly over-represented in the surroundings of the
12223 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
12224 achieved by using a database that contains genome-wide cross-species rankings
12225 for each motif. The motifs that are then annotated to TFs and those that have
12226 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
12227 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
12228 genes in the gene-set that are ranked above the leading edge).")
12229 (license license:gpl3)))
12231 (define-public r-chicago
12238 (uri (bioconductor-uri "Chicago" version))
12241 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
12242 (properties `((upstream-name . "Chicago")))
12243 (build-system r-build-system)
12245 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
12246 (native-inputs (list r-knitr))
12247 (home-page "https://bioconductor.org/packages/Chicago")
12248 (synopsis "Capture Hi-C analysis of genomic organization")
12250 "This package provides a pipeline for analysing Capture Hi-C data.")
12251 (license license:artistic2.0)))
12253 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12255 (define-public r-ciara
12261 (uri (cran-uri "CIARA" version))
12264 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
12265 (properties `((upstream-name . "CIARA")))
12266 (build-system r-build-system)
12267 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
12268 (native-inputs (list r-knitr))
12269 (home-page "https://cran.r-project.org/package=CIARA")
12270 (synopsis "Cluster-independent algorithm for rare cell types identification")
12272 "This is a package to support identification of markers of rare cell
12273 types by looking at genes whose expression is confined in small regions of the
12274 expression space.")
12275 (license license:artistic2.0)))
12277 (define-public r-cicero
12284 (uri (bioconductor-uri "cicero" version))
12287 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
12288 (build-system r-build-system)
12314 (home-page "https://bioconductor.org/packages/cicero/")
12315 (synopsis "Predict cis-co-accessibility from single-cell data")
12317 "Cicero computes putative cis-regulatory maps from single-cell chromatin
12318 accessibility data. It also extends the monocle package for use in chromatin
12319 accessibility data.")
12320 (license license:expat)))
12322 ;; This is the latest commit on the "monocle3" branch.
12323 (define-public r-cicero-monocle3
12324 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
12326 (package (inherit r-cicero)
12327 (name "r-cicero-monocle3")
12328 (version (git-version "1.3.2" revision commit))
12332 (uri (git-reference
12333 (url "https://github.com/cole-trapnell-lab/cicero-release")
12335 (file-name (git-file-name name version))
12338 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
12340 (modify-inputs (package-propagated-inputs r-cicero)
12341 (delete "r-monocle")
12342 (prepend r-monocle3))))))
12344 (define-public r-circrnaprofiler
12346 (name "r-circrnaprofiler")
12351 (uri (bioconductor-uri "circRNAprofiler" version))
12354 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
12356 `((upstream-name . "circRNAprofiler")))
12357 (build-system r-build-system)
12359 (list r-annotationhub
12362 r-bsgenome-hsapiens-ucsc-hg19
12385 "https://github.com/Aufiero/circRNAprofiler")
12387 "Computational framework for the downstream analysis of circular RNA's")
12389 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
12390 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
12391 framework allows combining and analyzing circRNAs previously detected by
12392 multiple publicly available annotation-based circRNA detection tools. It
12393 covers different aspects of circRNAs analysis from differential expression
12394 analysis, evolutionary conservation, biogenesis to functional analysis.")
12395 (license license:gpl3)))
12397 (define-public r-cistopic
12399 (name "r-cistopic")
12404 (uri (git-reference
12405 (url "https://github.com/aertslab/cisTopic")
12406 (commit (string-append "v" version))))
12407 (file-name (git-file-name name version))
12410 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
12411 (build-system r-build-system)
12428 (home-page "https://github.com/aertslab/cisTopic")
12429 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
12431 "The sparse nature of single cell epigenomics data can be overruled using
12432 probabilistic modelling methods such as @dfn{Latent Dirichlet
12433 Allocation} (LDA). This package allows the probabilistic modelling of
12434 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
12435 includes functionalities to identify cell states based on the contribution of
12436 cisTopics and explore the nature and regulatory proteins driving them.")
12437 (license license:gpl3)))
12439 (define-public r-cistopic-next
12440 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
12443 (inherit r-cistopic)
12444 (name "r-cistopic-next")
12445 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
12446 ;; since the previous release is 2.1.0. Oh well.
12447 (version (git-version "0.3.0" revision commit))
12451 (uri (git-reference
12452 (url "https://github.com/aertslab/cisTopic")
12454 (file-name (git-file-name name version))
12457 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
12458 (properties `((upstream-name . "cisTopic")))
12479 (define-public r-genie3
12486 (uri (bioconductor-uri "GENIE3" version))
12489 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
12490 (properties `((upstream-name . "GENIE3")))
12491 (build-system r-build-system)
12493 (list r-dplyr r-reshape2))
12496 (home-page "https://bioconductor.org/packages/GENIE3")
12497 (synopsis "Gene network inference with ensemble of trees")
12499 "This package implements the GENIE3 algorithm for inferring gene
12500 regulatory networks from expression data.")
12501 (license license:gpl2+)))
12503 (define-public r-roc
12510 (uri (bioconductor-uri "ROC" version))
12513 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
12514 (properties `((upstream-name . "ROC")))
12515 (build-system r-build-system)
12518 (home-page "https://www.bioconductor.org/packages/ROC/")
12519 (synopsis "Utilities for ROC curves")
12521 "This package provides utilities for @dfn{Receiver Operating
12522 Characteristic} (ROC) curves, with a focus on micro arrays.")
12523 (license license:artistic2.0)))
12525 (define-public r-watermelon
12527 (name "r-watermelon")
12532 (uri (bioconductor-uri "wateRmelon" version))
12535 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
12536 (properties `((upstream-name . "wateRmelon")))
12537 (build-system r-build-system)
12540 r-illuminahumanmethylation450kanno-ilmn12-hg19
12549 (home-page "https://bioconductor.org/packages/wateRmelon/")
12550 (synopsis "Illumina 450 methylation array normalization and metrics")
12552 "The standard index of DNA methylation (beta) is computed from methylated
12553 and unmethylated signal intensities. Betas calculated from raw signal
12554 intensities perform well, but using 11 methylomic datasets we demonstrate that
12555 quantile normalization methods produce marked improvement. The commonly used
12556 procedure of normalizing betas is inferior to the separate normalization of M
12557 and U, and it is also advantageous to normalize Type I and Type II assays
12558 separately. This package provides 15 flavours of betas and three performance
12559 metrics, with methods for objects produced by the @code{methylumi} and
12560 @code{minfi} packages.")
12561 (license license:gpl3)))
12563 (define-public r-gdsfmt
12570 (uri (bioconductor-uri "gdsfmt" version))
12573 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
12574 (modules '((guix build utils)))
12575 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
12576 ;; them and link with system libraries instead.
12579 (for-each delete-file-recursively
12583 (substitute* "src/Makevars"
12584 (("all: \\$\\(SHLIB\\)") "all:")
12585 (("\\$\\(SHLIB\\): liblzma.a") "")
12586 (("^ (ZLIB|LZ4)/.*") "")
12587 (("CoreArray/dVLIntGDS.cpp.*")
12588 "CoreArray/dVLIntGDS.cpp")
12589 (("CoreArray/dVLIntGDS.o.*")
12590 "CoreArray/dVLIntGDS.o")
12591 (("PKG_LIBS = ./liblzma.a")
12592 "PKG_LIBS = -llz4"))
12593 (substitute* "src/CoreArray/dStream.h"
12594 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
12595 (string-append "include <" header ">")))))))
12596 (properties `((upstream-name . "gdsfmt")))
12597 (build-system r-build-system)
12599 (list lz4 xz zlib))
12602 (home-page "http://corearray.sourceforge.net/")
12604 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
12606 "This package provides a high-level R interface to CoreArray @dfn{Genomic
12607 Data Structure} (GDS) data files, which are portable across platforms with
12608 hierarchical structure to store multiple scalable array-oriented data sets
12609 with metadata information. It is suited for large-scale datasets, especially
12610 for data which are much larger than the available random-access memory. The
12611 @code{gdsfmt} package offers efficient operations specifically designed for
12612 integers of less than 8 bits, since a diploid genotype, like
12613 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
12614 byte. Data compression and decompression are available with relatively
12615 efficient random access. It is also allowed to read a GDS file in parallel
12616 with multiple R processes supported by the package @code{parallel}.")
12617 (license license:lgpl3)))
12619 (define-public r-bigmelon
12621 (name "r-bigmelon")
12626 (uri (bioconductor-uri "bigmelon" version))
12629 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
12630 (properties `((upstream-name . "bigmelon")))
12631 (build-system r-build-system)
12643 (home-page "https://bioconductor.org/packages/bigmelon/")
12644 (synopsis "Illumina methylation array analysis for large experiments")
12646 "This package provides methods for working with Illumina arrays using the
12647 @code{gdsfmt} package.")
12648 (license license:gpl3)))
12650 (define-public r-seqbias
12657 (uri (bioconductor-uri "seqbias" version))
12660 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
12661 (properties `((upstream-name . "seqbias")))
12662 (build-system r-build-system)
12664 (list r-biostrings r-genomicranges r-rhtslib))
12665 (home-page "https://bioconductor.org/packages/seqbias/")
12666 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
12668 "This package implements a model of per-position sequencing bias in
12669 high-throughput sequencing data using a simple Bayesian network, the structure
12670 and parameters of which are trained on a set of aligned reads and a reference
12672 (license license:lgpl3)))
12674 (define-public r-reqon
12681 (uri (bioconductor-uri "ReQON" version))
12684 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
12685 (properties `((upstream-name . "ReQON")))
12686 (build-system r-build-system)
12688 (list r-rjava r-rsamtools r-seqbias))
12689 (home-page "https://bioconductor.org/packages/ReQON/")
12690 (synopsis "Recalibrating quality of nucleotides")
12692 "This package provides an implementation of an algorithm for
12693 recalibrating the base quality scores for aligned sequencing data in BAM
12695 (license license:gpl2)))
12697 (define-public r-wavcluster
12699 (name "r-wavcluster")
12704 (uri (bioconductor-uri "wavClusteR" version))
12707 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
12708 (properties `((upstream-name . "wavClusteR")))
12709 (build-system r-build-system)
12711 (list r-biocgenerics
12727 (home-page "https://bioconductor.org/packages/wavClusteR/")
12728 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
12730 "This package provides an integrated pipeline for the analysis of
12731 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
12732 sequencing errors, SNPs and additional non-experimental sources by a non-
12733 parametric mixture model. The protein binding sites (clusters) are then
12734 resolved at high resolution and cluster statistics are estimated using a
12735 rigorous Bayesian framework. Post-processing of the results, data export for
12736 UCSC genome browser visualization and motif search analysis are provided. In
12737 addition, the package integrates RNA-Seq data to estimate the False
12738 Discovery Rate of cluster detection. Key functions support parallel multicore
12739 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
12740 be applied to the analysis of other NGS data obtained from experimental
12741 procedures that induce nucleotide substitutions (e.g. BisSeq).")
12742 (license license:gpl2)))
12744 (define-public r-timeseriesexperiment
12746 (name "r-timeseriesexperiment")
12751 (uri (bioconductor-uri "TimeSeriesExperiment" version))
12754 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
12756 `((upstream-name . "TimeSeriesExperiment")))
12757 (build-system r-build-system)
12769 r-summarizedexperiment
12776 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
12777 (synopsis "Analysis for short time-series data")
12779 "This package is a visualization and analysis toolbox for short time
12780 course data which includes dimensionality reduction, clustering, two-sample
12781 differential expression testing and gene ranking techniques. The package also
12782 provides methods for retrieving enriched pathways.")
12783 (license license:lgpl3+)))
12785 (define-public r-variantfiltering
12787 (name "r-variantfiltering")
12792 (uri (bioconductor-uri "VariantFiltering" version))
12795 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
12797 `((upstream-name . "VariantFiltering")))
12798 (build-system r-build-system)
12800 (list r-annotationdbi
12821 r-summarizedexperiment
12822 r-variantannotation
12824 (home-page "https://github.com/rcastelo/VariantFiltering")
12825 (synopsis "Filtering of coding and non-coding genetic variants")
12827 "Filter genetic variants using different criteria such as inheritance
12828 model, amino acid change consequence, minor allele frequencies across human
12829 populations, splice site strength, conservation, etc.")
12830 (license license:artistic2.0)))
12832 (define-public r-genomegraphs
12834 (name "r-genomegraphs")
12839 (uri (bioconductor-uri "GenomeGraphs" version))
12842 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
12843 (properties `((upstream-name . "GenomeGraphs")))
12844 (build-system r-build-system)
12847 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
12848 (synopsis "Plotting genomic information from Ensembl")
12850 "Genomic data analyses requires integrated visualization of known genomic
12851 information and new experimental data. GenomeGraphs uses the biomaRt package
12852 to perform live annotation queries to Ensembl and translates this to e.g.
12853 gene/transcript structures in viewports of the grid graphics package. This
12854 results in genomic information plotted together with your data. Another
12855 strength of GenomeGraphs is to plot different data types such as array CGH,
12856 gene expression, sequencing and other data, together in one plot using the
12857 same genome coordinate system.")
12858 (license license:artistic2.0)))
12860 (define-public r-wavetiling
12862 (name "r-wavetiling")
12867 (uri (bioconductor-uri "waveTiling" version))
12870 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
12871 (properties `((upstream-name . "waveTiling")))
12872 (build-system r-build-system)
12884 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
12885 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
12887 "This package is designed to conduct transcriptome analysis for tiling
12888 arrays based on fast wavelet-based functional models.")
12889 (license license:gpl2+)))
12891 (define-public r-variancepartition
12893 (name "r-variancepartition")
12898 (uri (bioconductor-uri "variancePartition" version))
12901 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
12903 `((upstream-name . "variancePartition")))
12904 (build-system r-build-system)
12928 (home-page "https://bioconductor.org/packages/variancePartition/")
12929 (synopsis "Analyze variation in gene expression experiments")
12931 "This is a package providing tools to quantify and interpret multiple
12932 sources of biological and technical variation in gene expression experiments.
12933 It uses a linear mixed model to quantify variation in gene expression
12934 attributable to individual, tissue, time point, or technical variables. The
12935 package includes dream differential expression analysis for repeated
12937 (license license:gpl2+)))
12939 (define-public r-htqpcr
12946 (uri (bioconductor-uri "HTqPCR" version))
12949 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
12950 (properties `((upstream-name . "HTqPCR")))
12951 (build-system r-build-system)
12953 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
12954 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
12955 "groups/bertone/software/HTqPCR.pdf"))
12956 (synopsis "Automated analysis of high-throughput qPCR data")
12958 "Analysis of Ct values from high throughput quantitative real-time
12959 PCR (qPCR) assays across multiple conditions or replicates. The input data
12960 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
12961 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
12962 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
12963 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
12964 loading, quality assessment, normalization, visualization and parametric or
12965 non-parametric testing for statistical significance in Ct values between
12966 features (e.g. genes, microRNAs).")
12967 (license license:artistic2.0)))
12969 (define-public r-unifiedwmwqpcr
12971 (name "r-unifiedwmwqpcr")
12976 (uri (bioconductor-uri "unifiedWMWqPCR" version))
12979 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
12981 `((upstream-name . "unifiedWMWqPCR")))
12982 (build-system r-build-system)
12984 (list r-biocgenerics r-htqpcr))
12985 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
12986 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
12988 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
12989 data. This modified test allows for testing differential expression in qPCR
12991 (license license:gpl2+)))
12993 (define-public r-universalmotif
12995 (name "r-universalmotif")
13000 (uri (bioconductor-uri "universalmotif" version))
13003 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
13005 `((upstream-name . "universalmotif")))
13006 (build-system r-build-system)
13009 (modify-phases %standard-phases
13010 (add-after 'unpack 'fix-reference-to-strip
13012 (substitute* "src/Makevars"
13013 (("/usr/bin/strip") (which "strip"))))))))
13015 (list r-biocgenerics
13028 "https://bioconductor.org/packages/universalmotif/")
13030 "Specific structures importer, modifier, and exporter for R")
13032 "This package allows importing most common @dfn{specific structure}
13033 (motif) types into R for use by functions provided by other Bioconductor
13034 motif-related packages. Motifs can be exported into most major motif formats
13035 from various classes as defined by other Bioconductor packages. A suite of
13036 motif and sequence manipulation and analysis functions are included, including
13037 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
13038 motifs, and others.")
13039 (license license:gpl3)))
13041 (define-public r-ace
13047 (uri (bioconductor-uri "ACE" version))
13050 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
13051 (properties `((upstream-name . "ACE")))
13052 (build-system r-build-system)
13053 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
13054 (native-inputs (list r-knitr))
13055 (home-page "https://github.com/tgac-vumc/ACE")
13057 "Absolute copy number estimation from low-coverage whole genome sequencing")
13059 "This package uses segmented copy number data to estimate tumor cell
13060 percentage and produce copy number plots displaying absolute copy numbers. For
13061 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
13062 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
13063 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
13064 subsequently run through all samples in the object(s), for which it will create
13065 individual subdirectories. For each sample, it will calculate how well the
13066 segments fit (the relative error) to integer copy numbers for each percentage
13067 of @dfn{tumor cells} (cells with divergent segments).")
13068 (license license:gpl2)))
13070 (define-public r-acgh
13076 (uri (bioconductor-uri "aCGH" version))
13079 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
13080 (properties `((upstream-name . "aCGH")))
13081 (build-system r-build-system)
13082 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
13083 (home-page "https://bioconductor.org/packages/aCGH")
13085 "Classes and functions for array comparative genomic hybridization data")
13087 "This package provides functions for reading
13088 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
13089 output files and clone information files, creation of @code{aCGH} objects for
13090 storing these data. Basic methods are accessing/replacing, subsetting,
13091 printing and plotting @code{aCGH} objects.")
13092 (license license:gpl2)))
13094 (define-public r-acme
13100 (uri (bioconductor-uri "ACME" version))
13103 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
13104 (properties `((upstream-name . "ACME")))
13105 (build-system r-build-system)
13106 (propagated-inputs (list r-biobase r-biocgenerics))
13107 (home-page "https://bioconductor.org/packages/aCGH/")
13108 (synopsis "Calculating microarray enrichment")
13110 "This package implements @dfn{algorithms for calculating microarray
13111 enrichment} (ACME), and it is a set of tools for analysing tiling array of
13112 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
13113 DNAse hypersensitivity, or other experiments that result in regions of the
13114 genome showing enrichment. It does not rely on a specific array technology
13115 (although the array should be a tiling array), is very general (can be applied
13116 in experiments resulting in regions of enrichment), and is very insensitive to
13117 array noise or normalization methods. It is also very fast and can be applied
13118 on whole-genome tiling array experiments quite easily with enough memory.")
13119 (license license:gpl2+)))
13121 (define-public r-acde
13127 (uri (bioconductor-uri "acde" version))
13130 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
13131 (properties `((upstream-name . "acde")))
13132 (build-system r-build-system)
13133 (propagated-inputs (list r-boot))
13134 (home-page "https://bioconductor.org/packages/acde")
13136 "Identification of differentially expressed genes with artificial components")
13138 "This package provides a multivariate inferential analysis method for
13139 detecting differentially expressed genes in gene expression data. It uses
13140 artificial components, close to the data's principal components but with an
13141 exact interpretation in terms of differential genetic expression, to identify
13142 differentially expressed genes while controlling the @dfn{false discovery
13144 (license license:gpl3)))
13146 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13148 (define-public r-activedriverwgs
13150 (name "r-activedriverwgs")
13155 (uri (cran-uri "ActiveDriverWGS" version))
13158 "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
13160 `((upstream-name . "ActiveDriverWGS")))
13161 (build-system r-build-system)
13165 r-bsgenome-hsapiens-ucsc-hg19
13166 r-bsgenome-hsapiens-ucsc-hg38
13167 r-bsgenome-mmusculus-ucsc-mm9
13168 r-bsgenome-mmusculus-ucsc-mm10
13175 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
13176 (synopsis "Driver discovery tool for cancer whole genomes")
13178 "This package provides a method for finding an enrichment of cancer
13179 simple somatic mutations (SNVs and Indels) in functional elements across the
13180 human genome. ActiveDriverWGS detects coding and noncoding driver elements
13181 using whole genome sequencing data.")
13182 (license license:gpl3)))
13184 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13186 (define-public r-activepathways
13188 (name "r-activepathways")
13193 (uri (cran-uri "ActivePathways" version))
13196 "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
13198 `((upstream-name . "ActivePathways")))
13199 (build-system r-build-system)
13201 (list r-data-table r-ggplot2))
13204 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
13205 (synopsis "Multivariate pathway enrichment analysis")
13207 "This package represents an integrative method of analyzing multi omics
13208 data that conducts enrichment analysis of annotated gene sets. ActivePathways
13209 uses a statistical data fusion approach, rationalizes contributing evidence
13210 and highlights associated genes, improving systems-level understanding of
13211 cellular organization in health and disease.")
13212 (license license:gpl3)))
13214 (define-public r-bgmix
13221 (uri (bioconductor-uri "BGmix" version))
13224 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
13225 (properties `((upstream-name . "BGmix")))
13226 (build-system r-build-system)
13228 (list r-kernsmooth))
13229 (home-page "https://bioconductor.org/packages/BGmix/")
13230 (synopsis "Bayesian models for differential gene expression")
13232 "This package provides fully Bayesian mixture models for differential
13234 (license license:gpl2)))
13236 (define-public r-bgx
13243 (uri (bioconductor-uri "bgx" version))
13246 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
13247 (properties `((upstream-name . "bgx")))
13248 (build-system r-build-system)
13252 '(modify-phases %standard-phases
13253 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
13255 (substitute* "configure.ac"
13256 (("AX_GCC_ARCHFLAG.*") ""))
13257 (delete-file "configure")
13258 (invoke "autoreconf" "-vif"))))))
13262 (list r-affy r-biobase r-gcrma r-rcpp))
13264 (list autoconf automake))
13265 (home-page "https://bioconductor.org/packages/bgx/")
13266 (synopsis "Bayesian gene expression")
13268 "This package provides tools for Bayesian integrated analysis of
13269 Affymetrix GeneChips.")
13270 (license license:gpl2)))
13272 (define-public r-bhc
13279 (uri (bioconductor-uri "BHC" version))
13282 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
13283 (properties `((upstream-name . "BHC")))
13284 (build-system r-build-system)
13285 (home-page "https://bioconductor.org/packages/BHC/")
13286 (synopsis "Bayesian hierarchical clustering")
13288 "The method implemented in this package performs bottom-up hierarchical
13289 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
13290 in the data and Bayesian model selection to decide at each step which clusters
13291 to merge. This avoids several limitations of traditional methods, for example
13292 how many clusters there should be and how to choose a principled distance
13293 metric. This implementation accepts multinomial (i.e. discrete, with 2+
13294 categories) or time-series data. This version also includes a randomised
13295 algorithm which is more efficient for larger data sets.")
13296 (license license:gpl3)))
13298 (define-public r-bicare
13305 (uri (bioconductor-uri "BicARE" version))
13308 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
13309 (properties `((upstream-name . "BicARE")))
13310 (build-system r-build-system)
13312 (list r-biobase r-gseabase r-multtest))
13313 (home-page "http://bioinfo.curie.fr")
13314 (synopsis "Biclustering analysis and results exploration")
13316 "This is a package for biclustering analysis and exploration of
13318 (license license:gpl2)))
13320 (define-public r-bifet
13327 (uri (bioconductor-uri "BiFET" version))
13330 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
13331 (properties `((upstream-name . "BiFET")))
13332 (build-system r-build-system)
13334 (list r-genomicranges r-poibin))
13337 (home-page "https://bioconductor.org/packages/BiFET")
13338 (synopsis "Bias-free footprint enrichment test")
13340 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
13341 over-represented in target regions compared to background regions after
13342 correcting for the bias arising from the imbalance in read counts and GC
13343 contents between the target and background regions. For a given TF k, BiFET
13344 tests the null hypothesis that the target regions have the same probability of
13345 having footprints for the TF k as the background regions while correcting for
13346 the read count and GC content bias.")
13347 (license license:gpl3)))
13349 (define-public r-rsbml
13356 (uri (bioconductor-uri "rsbml" version))
13359 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
13360 (properties `((upstream-name . "rsbml")))
13361 (build-system r-build-system)
13365 (list r-biocgenerics r-graph))
13368 (home-page "http://www.sbml.org")
13369 (synopsis "R support for SBML")
13371 "This package provides an R interface to libsbml for SBML parsing,
13372 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
13373 (license license:artistic2.0)))
13375 (define-public r-hypergraph
13377 (name "r-hypergraph")
13382 (uri (bioconductor-uri "hypergraph" version))
13385 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
13386 (properties `((upstream-name . "hypergraph")))
13387 (build-system r-build-system)
13390 (home-page "https://bioconductor.org/packages/hypergraph")
13391 (synopsis "Hypergraph data structures")
13393 "This package implements some simple capabilities for representing and
13394 manipulating hypergraphs.")
13395 (license license:artistic2.0)))
13397 (define-public r-hyperdraw
13399 (name "r-hyperdraw")
13404 (uri (bioconductor-uri "hyperdraw" version))
13407 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
13408 (properties `((upstream-name . "hyperdraw")))
13409 (build-system r-build-system)
13410 (inputs (list graphviz))
13412 (list r-graph r-hypergraph r-rgraphviz))
13413 (home-page "https://bioconductor.org/packages/hyperdraw")
13414 (synopsis "Visualizing hypergraphs")
13416 "This package provides functions for visualizing hypergraphs.")
13417 (license license:gpl2+)))
13419 (define-public r-biggr
13426 (uri (bioconductor-uri "BiGGR" version))
13429 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
13430 (properties `((upstream-name . "BiGGR")))
13431 (build-system r-build-system)
13439 (home-page "https://bioconductor.org/packages/BiGGR/")
13440 (synopsis "Constraint based modeling using metabolic reconstruction databases")
13442 "This package provides an interface to simulate metabolic reconstruction
13443 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
13444 reconstruction databases. The package facilitates @dfn{flux balance
13445 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
13446 networks and estimated fluxes can be visualized with hypergraphs.")
13447 (license license:gpl3+)))
13449 (define-public r-bigmemoryextras
13451 (name "r-bigmemoryextras")
13456 (uri (bioconductor-uri "bigmemoryExtras" version))
13459 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
13461 `((upstream-name . "bigmemoryExtras")))
13462 (build-system r-build-system)
13464 (list r-bigmemory))
13467 (home-page "https://github.com/phaverty/bigmemoryExtras")
13468 (synopsis "Extension of the bigmemory package")
13470 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
13471 safety and convenience features to the @code{filebacked.big.matrix} class from
13472 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
13473 monitoring and gracefully restoring the connection to on-disk data and it also
13474 protects against accidental data modification with a file-system-based
13475 permissions system. Utilities are provided for using @code{BigMatrix}-derived
13476 classes as @code{assayData} matrices within the @code{Biobase} package's
13477 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
13478 related to attaching to, and indexing into, file-backed matrices with
13479 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
13480 a file-backed matrix with factor properties.")
13481 (license license:artistic2.0)))
13483 (define-public r-bigpint
13490 (uri (bioconductor-uri "bigPint" version))
13493 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
13494 (properties `((upstream-name . "bigPint")))
13495 (build-system r-build-system)
13497 (list r-delayedarray
13513 r-summarizedexperiment
13517 (home-page "https://github.com/lindsayrutter/bigPint")
13518 (synopsis "Big multivariate data plotted interactively")
13520 "This package provides methods for visualizing large multivariate
13521 datasets using static and interactive scatterplot matrices, parallel
13522 coordinate plots, volcano plots, and litre plots. It includes examples for
13523 visualizing RNA-sequencing datasets and differentially expressed genes.")
13524 (license license:gpl3)))
13526 (define-public r-chemminer
13528 (name "r-chemminer")
13533 (uri (bioconductor-uri "ChemmineR" version))
13536 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
13537 (properties `((upstream-name . "ChemmineR")))
13538 (build-system r-build-system)
13557 (home-page "https://github.com/girke-lab/ChemmineR")
13558 (synopsis "Cheminformatics toolkit for R")
13560 "ChemmineR is a cheminformatics package for analyzing drug-like small
13561 molecule data in R. It contains functions for efficient processing of large
13562 numbers of molecules, physicochemical/structural property predictions,
13563 structural similarity searching, classification and clustering of compound
13564 libraries with a wide spectrum of algorithms. In addition, it offers
13565 visualization functions for compound clustering results and chemical
13567 (license license:artistic2.0)))
13569 (define-public r-fmcsr
13576 (uri (bioconductor-uri "fmcsR" version))
13578 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
13579 (properties `((upstream-name . "fmcsR")))
13580 (build-system r-build-system)
13582 (list r-biocgenerics r-chemminer r-runit))
13583 (native-inputs (list r-knitr))
13584 (home-page "https://github.com/girke-lab/fmcsR")
13585 (synopsis "Mismatch tolerant maximum common substructure searching")
13587 "The fmcsR package introduces an efficient @dfn{maximum common
13588 substructure} (MCS) algorithms combined with a novel matching strategy that
13589 allows for atom and/or bond mismatches in the substructures shared among two
13590 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
13591 strict MCSs, resulting in the identification of more common features in their
13592 source structures, as well as a higher sensitivity in finding compounds with
13593 weak structural similarities. The fmcsR package provides several utilities to
13594 use the FMCS algorithm for pairwise compound comparisons, structure similarity
13595 searching and clustering.")
13596 (license license:artistic2.0)))
13598 (define-public r-bioassayr
13600 (name "r-bioassayr")
13605 (uri (bioconductor-uri "bioassayR" version))
13608 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
13609 (properties `((upstream-name . "bioassayR")))
13610 (build-system r-build-system)
13612 (list r-biocgenerics
13621 (home-page "https://github.com/girke-lab/bioassayR")
13622 (synopsis "Cross-target analysis of small molecule bioactivity")
13624 "bioassayR is a computational tool that enables simultaneous analysis of
13625 thousands of bioassay experiments performed over a diverse set of compounds
13626 and biological targets. Unique features include support for large-scale
13627 cross-target analyses of both public and custom bioassays, generation of
13628 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
13629 preloaded database that provides access to a substantial portion of publicly
13630 available bioactivity data.")
13631 (license license:artistic2.0)))
13633 (define-public r-biobroom
13635 (name "r-biobroom")
13640 (uri (bioconductor-uri "biobroom" version))
13643 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
13644 (properties `((upstream-name . "biobroom")))
13645 (build-system r-build-system)
13647 (list r-biobase r-broom r-dplyr r-tidyr))
13650 (home-page "https://github.com/StoreyLab/biobroom")
13651 (synopsis "Turn Bioconductor objects into tidy data frames")
13653 "This package contains methods for converting standard objects
13654 constructed by bioinformatics packages, especially those in Bioconductor, and
13655 converting them to @code{tidy} data. It thus serves as a complement to the
13656 @code{broom} package, and follows the same tidy, augment, glance division of
13657 tidying methods. Tidying data makes it easy to recombine, reshape and
13658 visualize bioinformatics analyses.")
13659 ;; Any version of the LGPL.
13660 (license license:lgpl3+)))
13662 (define-public r-graphite
13664 (name "r-graphite")
13669 (uri (bioconductor-uri "graphite" version))
13672 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
13673 (properties `((upstream-name . "graphite")))
13674 (build-system r-build-system)
13676 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
13677 (home-page "https://bioconductor.org/packages/graphite/")
13678 (synopsis "Networks from pathway databases")
13680 "Graphite provides networks derived from eight public pathway databases,
13681 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
13683 (license license:agpl3+)))
13685 (define-public r-reactomepa
13687 (name "r-reactomepa")
13692 (uri (bioconductor-uri "ReactomePA" version))
13695 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
13696 (properties `((upstream-name . "ReactomePA")))
13697 (build-system r-build-system)
13699 (list r-annotationdbi
13709 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
13710 (synopsis "Reactome pathway analysis")
13712 "This package provides functions for pathway analysis based on the
13713 REACTOME pathway database. It implements enrichment analysis, gene set
13714 enrichment analysis and several functions for visualization.")
13715 (license license:gpl2)))
13717 (define-public r-ebarrays
13719 (name "r-ebarrays")
13724 (uri (bioconductor-uri "EBarrays" version))
13727 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
13728 (properties `((upstream-name . "EBarrays")))
13729 (build-system r-build-system)
13731 (list r-biobase r-cluster r-lattice))
13732 (home-page "https://bioconductor.org/packages/EBarrays/")
13733 (synopsis "Gene clustering and differential expression identification")
13735 "EBarrays provides tools for the analysis of replicated/unreplicated
13737 (license license:gpl2+)))
13739 (define-public r-bioccasestudies
13741 (name "r-bioccasestudies")
13746 (uri (bioconductor-uri "BiocCaseStudies" version))
13749 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
13751 `((upstream-name . "BiocCaseStudies")))
13752 (build-system r-build-system)
13753 (propagated-inputs (list r-biobase))
13754 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
13755 (synopsis "Support for the case studies monograph")
13757 "This package provides software and data to support the case studies
13759 (license license:artistic2.0)))
13761 (define-public r-bioccheck
13763 (name "r-bioccheck")
13767 (uri (bioconductor-uri "BiocCheck" version))
13770 "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"))))
13772 `((upstream-name . "BiocCheck")))
13773 (build-system r-build-system)
13784 (home-page "https://bioconductor.org/packages/BiocCheck")
13785 (synopsis "Executes Bioconductor-specific package checks")
13786 (description "This package contains tools to perform additional quality
13787 checks on R packages that are to be submitted to the Bioconductor repository.")
13788 (license license:artistic2.0)))
13790 (define-public r-biocgraph
13792 (name "r-biocgraph")
13797 (uri (bioconductor-uri "biocGraph" version))
13800 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
13801 (properties `((upstream-name . "biocGraph")))
13802 (build-system r-build-system)
13804 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
13805 (home-page "https://bioconductor.org/packages/biocGraph/")
13806 (synopsis "Graph examples and use cases in Bioinformatics")
13808 "This package provides examples and code that make use of the
13809 different graph related packages produced by Bioconductor.")
13810 (license license:artistic2.0)))
13812 (define-public r-biocstyle
13814 (name "r-biocstyle")
13818 (uri (bioconductor-uri "BiocStyle" version))
13821 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
13823 `((upstream-name . "BiocStyle")))
13824 (build-system r-build-system)
13826 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
13829 (home-page "https://bioconductor.org/packages/BiocStyle")
13830 (synopsis "Bioconductor formatting styles")
13831 (description "This package provides standard formatting styles for
13832 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
13834 (license license:artistic2.0)))
13836 (define-public r-biocviews
13838 (name "r-biocviews")
13842 (uri (bioconductor-uri "biocViews" version))
13845 "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126"))))
13847 `((upstream-name . "biocViews")))
13848 (build-system r-build-system)
13857 (home-page "https://bioconductor.org/packages/biocViews")
13858 (synopsis "Bioconductor package categorization helper")
13859 (description "The purpose of biocViews is to create HTML pages that
13860 categorize packages in a Bioconductor package repository according to keywords,
13861 also known as views, in a controlled vocabulary.")
13862 (license license:artistic2.0)))
13864 (define-public r-experimenthub
13866 (name "r-experimenthub")
13871 (uri (bioconductor-uri "ExperimentHub" version))
13874 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
13875 (properties `((upstream-name . "ExperimentHub")))
13876 (build-system r-build-system)
13878 (list r-annotationhub
13887 (home-page "https://bioconductor.org/packages/ExperimentHub/")
13888 (synopsis "Client to access ExperimentHub resources")
13890 "This package provides a client for the Bioconductor ExperimentHub web
13891 resource. ExperimentHub provides a central location where curated data from
13892 experiments, publications or training courses can be accessed. Each resource
13893 has associated metadata, tags and date of modification. The client creates
13894 and manages a local cache of files retrieved enabling quick and reproducible
13896 (license license:artistic2.0)))
13898 (define-public r-grohmm
13905 (uri (bioconductor-uri "groHMM" version))
13908 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
13909 (properties `((upstream-name . "groHMM")))
13910 (build-system r-build-system)
13912 (list r-genomeinfodb
13913 r-genomicalignments
13919 (home-page "https://github.com/Kraus-Lab/groHMM")
13920 (synopsis "GRO-seq analysis pipeline")
13922 "This package provides a pipeline for the analysis of GRO-seq data.")
13923 (license license:gpl3+)))
13925 (define-public r-multiassayexperiment
13927 (name "r-multiassayexperiment")
13932 (uri (bioconductor-uri "MultiAssayExperiment" version))
13935 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
13937 `((upstream-name . "MultiAssayExperiment")))
13938 (build-system r-build-system)
13945 r-summarizedexperiment
13949 (home-page "https://waldronlab.io/MultiAssayExperiment/")
13950 (synopsis "Integration of multi-omics experiments in Bioconductor")
13952 "MultiAssayExperiment harmonizes data management of multiple assays
13953 performed on an overlapping set of specimens. It provides a familiar
13954 Bioconductor user experience by extending concepts from
13955 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
13956 classes for individual assays, and allowing subsetting by genomic ranges or
13958 (license license:artistic2.0)))
13960 (define-public r-bioconcotk
13962 (name "r-bioconcotk")
13967 (uri (bioconductor-uri "BiocOncoTK" version))
13970 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
13971 (properties `((upstream-name . "BiocOncoTK")))
13972 (build-system r-build-system)
13995 r-summarizedexperiment))
13998 (home-page "https://bioconductor.org/packages/BiocOncoTK")
13999 (synopsis "Bioconductor components for general cancer genomics")
14001 "The purpose of this package is to provide a central interface to various
14002 tools for genome-scale analysis of cancer studies.")
14003 (license license:artistic2.0)))
14005 (define-public r-biocor
14012 (uri (bioconductor-uri "BioCor" version))
14015 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
14016 (properties `((upstream-name . "BioCor")))
14017 (build-system r-build-system)
14019 (list r-biocparallel r-gseabase r-matrix))
14022 (home-page "https://llrs.github.io/BioCor/")
14023 (synopsis "Functional similarities")
14025 "This package provides tools to calculate functional similarities based
14026 on the pathways described on KEGG and REACTOME or in gene sets. These
14027 similarities can be calculated for pathways or gene sets, genes, or clusters
14028 and combined with other similarities. They can be used to improve networks,
14029 gene selection, testing relationships, and so on.")
14030 (license license:expat)))
14032 (define-public r-biocpkgtools
14034 (name "r-biocpkgtools")
14039 (uri (bioconductor-uri "BiocPkgTools" version))
14042 "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"))))
14043 (properties `((upstream-name . "BiocPkgTools")))
14044 (build-system r-build-system)
14046 (list r-biocfilecache
14070 (home-page "https://github.com/seandavi/BiocPkgTools")
14071 (synopsis "Collection of tools for learning about Bioconductor packages")
14073 "Bioconductor has a rich ecosystem of metadata around packages, usage,
14074 and build status. This package is a simple collection of functions to access
14075 that metadata from R. The goal is to expose metadata for data mining and
14076 value-added functionality such as package searching, text mining, and
14077 analytics on packages.")
14078 (license license:expat)))
14080 (define-public r-biocset
14087 (uri (bioconductor-uri "BiocSet" version))
14090 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
14091 (properties `((upstream-name . "BiocSet")))
14092 (build-system r-build-system)
14094 (list r-annotationdbi
14107 "https://bioconductor.org/packages/BiocSet")
14109 "Representing Different Biological Sets")
14111 "BiocSet displays different biological sets in a triple tibble format.
14112 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
14113 The user has the ability to activate one of these three tibbles to perform
14114 common functions from the @code{dplyr} package. Mapping functionality and
14115 accessing web references for elements/sets are also available in BiocSet.")
14116 (license license:artistic2.0)))
14118 (define-public r-biocworkflowtools
14120 (name "r-biocworkflowtools")
14125 (uri (bioconductor-uri "BiocWorkflowTools" version))
14128 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
14130 `((upstream-name . "BiocWorkflowTools")))
14131 (build-system r-build-system)
14144 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
14145 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
14147 "This package provides functions to ease the transition between
14148 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
14149 (license license:expat)))
14151 (define-public r-biodist
14158 (uri (bioconductor-uri "bioDist" version))
14161 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
14162 (properties `((upstream-name . "bioDist")))
14163 (build-system r-build-system)
14165 (list r-biobase r-kernsmooth))
14166 (home-page "https://bioconductor.org/packages/bioDist/")
14167 (synopsis "Different distance measures")
14169 "This package provides a collection of software tools for calculating
14170 distance measures.")
14171 (license license:artistic2.0)))
14173 (define-public r-pcatools
14175 (name "r-pcatools")
14180 (uri (bioconductor-uri "PCAtools" version))
14183 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
14184 (properties `((upstream-name . "PCAtools")))
14185 (build-system r-build-system)
14193 r-delayedmatrixstats
14201 (native-inputs (list r-knitr))
14202 (home-page "https://github.com/kevinblighe/PCAtools")
14203 (synopsis "PCAtools: everything Principal Components Analysis")
14205 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
14206 structure of the data without the need to build any model to represent it.
14207 This \"summary\" of the data is arrived at through a process of reduction that
14208 can transform the large number of variables into a lesser number that are
14209 uncorrelated (i.e. the 'principal components'), while at the same time being
14210 capable of easy interpretation on the original data. PCAtools provides
14211 functions for data exploration via PCA, and allows the user to generate
14212 publication-ready figures. PCA is performed via @code{BiocSingular}; users
14213 can also identify an optimal number of principal components via different
14214 metrics, such as the elbow method and Horn's parallel analysis, which has
14215 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
14216 dimensional mass cytometry data.")
14217 (license license:gpl3)))
14219 (define-public r-rgreat
14226 (uri (bioconductor-uri "rGREAT" version))
14229 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
14230 (properties `((upstream-name . "rGREAT")))
14231 (build-system r-build-system)
14233 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
14234 (native-inputs (list r-knitr))
14235 (home-page "https://github.com/jokergoo/rGREAT")
14236 (synopsis "Client for GREAT analysis")
14238 "This package makes GREAT (Genomic Regions Enrichment of Annotations
14239 Tool) analysis automatic by constructing a HTTP POST request according to
14240 user's input and automatically retrieving results from GREAT web server.")
14241 (license license:expat)))
14243 (define-public r-m3c
14250 (uri (bioconductor-uri "M3C" version))
14253 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
14254 (properties `((upstream-name . "M3C")))
14255 (build-system r-build-system)
14267 (native-inputs (list r-knitr))
14268 (home-page "https://bioconductor.org/packages/M3C")
14269 (synopsis "Monte Carlo reference-based consensus clustering")
14271 "M3C is a consensus clustering algorithm that uses a Monte Carlo
14272 simulation to eliminate overestimation of @code{K} and can reject the null
14273 hypothesis @code{K=1}.")
14274 (license license:agpl3+)))
14276 (define-public r-icens
14283 (uri (bioconductor-uri "Icens" version))
14286 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
14287 (properties `((upstream-name . "Icens")))
14288 (build-system r-build-system)
14291 (home-page "https://bioconductor.org/packages/Icens")
14292 (synopsis "NPMLE for censored and truncated data")
14294 "This package provides many functions for computing the
14295 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
14297 (license license:artistic2.0)))
14299 ;; This is a CRAN package but it depends on r-icens, which is published on
14301 (define-public r-interval
14303 (name "r-interval")
14304 (version "1.1-0.8")
14308 (uri (cran-uri "interval" version))
14311 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
14312 (properties `((upstream-name . "interval")))
14313 (build-system r-build-system)
14315 (list r-icens r-mlecens r-perm r-survival))
14316 (home-page "https://cran.r-project.org/web/packages/interval/")
14317 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
14319 "This package provides functions to fit nonparametric survival curves,
14320 plot them, and perform logrank or Wilcoxon type tests.")
14321 (license license:gpl2+)))
14323 ;; This is a CRAN package, but it depends on r-interval, which depends on a
14324 ;; Bioconductor package.
14325 (define-public r-fhtest
14332 (uri (cran-uri "FHtest" version))
14335 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
14336 (properties `((upstream-name . "FHtest")))
14337 (build-system r-build-system)
14339 (list r-interval r-kmsurv r-mass r-perm r-survival))
14340 (home-page "https://cran.r-project.org/web/packages/FHtest/")
14341 (synopsis "Tests for survival data based on the Fleming-Harrington class")
14343 "This package provides functions to compare two or more survival curves
14347 @item The Fleming-Harrington test for right-censored data based on
14348 permutations and on counting processes.
14349 @item An extension of the Fleming-Harrington test for interval-censored data
14350 based on a permutation distribution and on a score vector distribution.
14353 (license license:gpl2+)))
14355 (define-public r-fourcseq
14357 (name "r-fourcseq")
14362 (uri (bioconductor-uri "FourCSeq" version))
14364 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
14365 (properties `((upstream-name . "FourCSeq")))
14366 (build-system r-build-system)
14372 r-genomicalignments
14382 r-summarizedexperiment))
14386 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
14387 (synopsis "Analysis of multiplexed 4C sequencing data")
14389 "This package is an R package dedicated to the analysis of (multiplexed)
14390 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
14391 interactions between DNA elements and identify differential interactions
14392 between conditions. The statistical analysis in R starts with individual bam
14393 files for each sample as inputs. To obtain these files, the package contains
14394 a Python script to demultiplex libraries and trim off primer sequences. With
14395 a standard alignment software the required bam files can be then be
14397 (license license:gpl3+)))
14399 (define-public r-preprocesscore
14401 (name "r-preprocesscore")
14406 (uri (bioconductor-uri "preprocessCore" version))
14409 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
14411 `((upstream-name . "preprocessCore")))
14412 (build-system r-build-system)
14413 (home-page "https://github.com/bmbolstad/preprocessCore")
14414 (synopsis "Collection of pre-processing functions")
14416 "This package provides a library of core pre-processing and normalization
14418 (license license:lgpl2.0+)))
14420 (define-public r-s4vectors
14422 (name "r-s4vectors")
14426 (uri (bioconductor-uri "S4Vectors" version))
14429 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
14431 `((upstream-name . "S4Vectors")))
14432 (build-system r-build-system)
14434 (list r-biocgenerics))
14435 (home-page "https://bioconductor.org/packages/S4Vectors")
14436 (synopsis "S4 implementation of vectors and lists")
14438 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
14439 classes and a set of generic functions that extend the semantic of ordinary
14440 vectors and lists in R. Package developers can easily implement vector-like
14441 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
14442 In addition, a few low-level concrete subclasses of general interest (e.g.
14443 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
14444 S4Vectors package itself.")
14445 (license license:artistic2.0)))
14447 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
14448 ;; Bioconductor package.
14449 (define-public r-wgcna
14456 (uri (cran-uri "WGCNA" version))
14459 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
14460 (properties `((upstream-name . "WGCNA")))
14461 (build-system r-build-system)
14463 (list r-annotationdbi
14476 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14477 (synopsis "Weighted correlation network analysis")
14479 "This package provides functions necessary to perform Weighted
14480 Correlation Network Analysis on high-dimensional data. It includes functions
14481 for rudimentary data cleaning, construction and summarization of correlation
14482 networks, module identification and functions for relating both variables and
14483 modules to sample traits. It also includes a number of utility functions for
14484 data manipulation and visualization.")
14485 (license license:gpl2+)))
14487 (define-public r-rgraphviz
14489 (name "r-rgraphviz")
14494 (uri (bioconductor-uri "Rgraphviz" version))
14497 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
14498 (properties `((upstream-name . "Rgraphviz")))
14499 (build-system r-build-system)
14502 (modify-phases %standard-phases
14503 (add-after 'unpack 'make-reproducible
14505 ;; The replacement value is taken from src/graphviz/builddate.h
14506 (substitute* "src/graphviz/configure"
14507 (("VERSION_DATE=.*")
14508 "VERSION_DATE=20200427.2341\n"))
14510 ;; FIXME: Rgraphviz bundles the sources of an older variant of
14511 ;; graphviz. It does not build with the latest version of graphviz, so
14512 ;; we do not add graphviz to the inputs.
14513 (inputs (list zlib))
14518 (home-page "https://bioconductor.org/packages/Rgraphviz")
14519 (synopsis "Plotting capabilities for R graph objects")
14521 "This package interfaces R with the graphviz library for plotting R graph
14522 objects from the @code{graph} package.")
14523 (license license:epl1.0)))
14525 (define-public r-fithic
14531 (uri (bioconductor-uri "FitHiC" version))
14534 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
14535 (properties `((upstream-name . "FitHiC")))
14536 (build-system r-build-system)
14538 (list r-data-table r-fdrtool r-rcpp))
14541 (home-page "https://bioconductor.org/packages/FitHiC")
14542 (synopsis "Confidence estimation for intra-chromosomal contact maps")
14544 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
14545 intra-chromosomal contact maps produced by genome-wide genome architecture
14546 assays such as Hi-C.")
14547 (license license:gpl2+)))
14549 (define-public r-hitc
14555 (uri (bioconductor-uri "HiTC" version))
14558 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
14559 (properties `((upstream-name . "HiTC")))
14560 (build-system r-build-system)
14569 (home-page "https://bioconductor.org/packages/HiTC")
14570 (synopsis "High throughput chromosome conformation capture analysis")
14572 "The HiTC package was developed to explore high-throughput \"C\" data
14573 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
14574 quality controls, normalization, visualization, and further analysis are also
14576 (license license:artistic2.0)))
14578 (define-public r-hdf5array
14580 (name "r-hdf5array")
14585 (uri (bioconductor-uri "HDF5Array" version))
14588 "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday"))))
14589 (properties `((upstream-name . "HDF5Array")))
14590 (build-system r-build-system)
14594 (list r-biocgenerics
14602 (home-page "https://bioconductor.org/packages/HDF5Array")
14603 (synopsis "HDF5 back end for DelayedArray objects")
14604 (description "This package provides an array-like container for convenient
14605 access and manipulation of HDF5 datasets. It supports delayed operations and
14606 block processing.")
14607 (license license:artistic2.0)))
14609 (define-public r-rhdf5lib
14611 (name "r-rhdf5lib")
14616 (uri (bioconductor-uri "Rhdf5lib" version))
14619 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
14620 (modules '((guix build utils)))
14623 ;; Delete bundled binaries
14624 (delete-file-recursively "src/wininclude/")
14625 (delete-file-recursively "src/winlib/")
14626 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
14627 (properties `((upstream-name . "Rhdf5lib")))
14628 (build-system r-build-system)
14631 (modify-phases %standard-phases
14632 (add-after 'unpack 'do-not-use-bundled-hdf5
14633 (lambda* (#:key inputs #:allow-other-keys)
14634 (for-each delete-file '("configure" "configure.ac"))
14635 (substitute* "R/zzz.R"
14636 (("return\\(links\\)") "return(\" -lz\")"))
14637 (with-directory-excursion "src"
14638 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
14639 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
14641 ;; Remove timestamp and host system information to make
14642 ;; the build reproducible.
14643 (substitute* "hdf5/src/libhdf5.settings.in"
14644 (("Configured on: @CONFIG_DATE@")
14645 "Configured on: Guix")
14646 (("Uname information:.*")
14647 "Uname information: Linux\n")
14648 ;; Remove unnecessary store reference.
14650 "C Compiler: GCC\n"))
14651 (rename-file "hdf5/src/libhdf5.settings.in"
14652 "hdf5/src/libhdf5.settings")
14653 (rename-file "Makevars.in" "Makevars")
14654 (substitute* "Makevars"
14655 (("@BUILD_HDF5@") "")
14656 (("@COPY_SZIP@") "")
14657 (("@ZLIB_LIB@") "-lz")
14658 (("@ZLIB_INCLUDE@") "")
14659 (("HDF5_CXX_LIB=.*")
14660 (string-append "HDF5_CXX_LIB="
14661 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
14663 (string-append "HDF5_LIB="
14664 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
14665 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
14666 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
14667 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
14668 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
14669 (("HDF5_HL_LIB=.*")
14670 (string-append "HDF5_HL_LIB="
14671 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
14672 (("HDF5_HL_CXX_LIB=.*")
14673 (string-append "HDF5_HL_CXX_LIB="
14674 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
14675 ;; szip is non-free software
14676 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
14677 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
14679 (list hdf5-1.10 zlib))
14681 `(("hdf5-source" ,(package-source hdf5-1.10))
14682 ("r-knitr" ,r-knitr)))
14683 (home-page "https://bioconductor.org/packages/Rhdf5lib")
14684 (synopsis "HDF5 library as an R package")
14685 (description "This package provides C and C++ HDF5 libraries for use in R
14687 (license license:artistic2.0)))
14689 (define-public r-beachmat
14691 (name "r-beachmat")
14696 (uri (bioconductor-uri "beachmat" version))
14699 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
14700 (build-system r-build-system)
14702 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
14705 (home-page "https://bioconductor.org/packages/beachmat")
14706 (synopsis "Compiling Bioconductor to handle each matrix type")
14707 (description "This package provides a consistent C++ class interface for a
14708 variety of commonly used matrix types, including sparse and HDF5-backed
14710 (license license:gpl3)))
14712 ;; This package includes files that have been taken from kentutils. Some
14713 ;; parts of kentutils are not released under a free license, but this package
14714 ;; only uses files that are also found in the free parts of kentutils.
14715 (define-public r-cner
14722 (uri (bioconductor-uri "CNEr" version))
14724 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
14725 (properties `((upstream-name . "CNEr")))
14726 (build-system r-build-system)
14727 (inputs (list zlib))
14734 r-genomicalignments
14750 (home-page "https://github.com/ge11232002/CNEr")
14751 (synopsis "CNE Detection and Visualization")
14753 "This package provides tools for large-scale identification and
14754 advanced visualization of sets of conserved noncoding elements.")
14755 ;; For all files in src/ucsc "license is hereby granted for all use -
14756 ;; public, private or commercial"; this includes those files that don't
14757 ;; have a license header, because they are included in the free parts of
14758 ;; the kentutils package.
14759 (license (list license:gpl2
14760 (license:non-copyleft
14761 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
14763 (define-public r-tfbstools
14765 (name "r-tfbstools")
14770 (uri (bioconductor-uri "TFBSTools" version))
14773 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
14774 (properties `((upstream-name . "TFBSTools")))
14775 (build-system r-build-system)
14785 r-dirichletmultinomial
14797 (native-inputs (list r-knitr))
14798 (home-page "https://github.com/ge11232002/TFBSTools")
14799 (synopsis "Transcription factor binding site (TFBS) analysis")
14801 "TFBSTools is a package for the analysis and manipulation of
14802 transcription factor binding sites. It includes matrices conversion
14803 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
14804 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
14805 scan putative TFBS from sequence/alignment, query JASPAR database and
14806 provides a wrapper of de novo motif discovery software.")
14807 (license license:gpl2)))
14809 (define-public r-maftools
14811 (name "r-maftools")
14816 (uri (bioconductor-uri "maftools" version))
14818 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
14819 (properties `((upstream-name . "maftools")))
14820 (build-system r-build-system)
14828 (native-inputs (list r-knitr))
14829 (home-page "https://github.com/PoisonAlien/maftools")
14830 (synopsis "Summarize, analyze and visualize MAF files")
14832 "Analyze and visualize Mutation Annotation Format (MAF) files from large
14833 scale sequencing studies. This package provides various functions to perform
14834 most commonly used analyses in cancer genomics and to create feature rich
14835 customizable visualzations with minimal effort.")
14836 (license license:expat)))
14838 (define-public r-motifmatchr
14840 (name "r-motifmatchr")
14845 (uri (bioconductor-uri "motifmatchr" version))
14848 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
14849 (properties `((upstream-name . "motifmatchr")))
14850 (build-system r-build-system)
14862 r-summarizedexperiment
14864 (native-inputs (list r-knitr))
14865 (home-page "https://bioconductor.org/packages/motifmatchr")
14866 (synopsis "Fast motif matching in R")
14868 "Quickly find motif matches for many motifs and many sequences.
14869 This package wraps C++ code from the MOODS motif calling library.")
14870 (license license:gpl3)))
14872 (define-public r-chromvar
14874 (name "r-chromvar")
14879 (uri (bioconductor-uri "chromVAR" version))
14881 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
14882 (properties `((upstream-name . "chromVAR")))
14883 (build-system r-build-system)
14885 (list r-biocgenerics
14905 r-summarizedexperiment
14907 (native-inputs (list r-knitr))
14908 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
14909 (synopsis "Determine chromatin variation across regions")
14911 "This package @code{r-chromvar} determines variation in chromatin
14912 accessibility across sets of annotations or peaks. @code{r-chromvar} is
14913 designed primarily for single-cell or sparse chromatin accessibility data like
14914 single cell assay for transposase-accessible chromatin using
14915 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
14916 sequence (@code{DNAse-seq}) experiments.")
14917 (license license:expat)))
14919 (define-public r-singlecellexperiment
14921 (name "r-singlecellexperiment")
14926 (uri (bioconductor-uri "SingleCellExperiment" version))
14929 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
14931 `((upstream-name . "SingleCellExperiment")))
14932 (build-system r-build-system)
14934 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
14935 r-summarizedexperiment))
14938 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
14939 (synopsis "S4 classes for single cell data")
14940 (description "This package defines an S4 class for storing data from
14941 single-cell experiments. This includes specialized methods to store and
14942 retrieve spike-in information, dimensionality reduction coordinates and size
14943 factors for each cell, along with the usual metadata for genes and
14945 (license license:gpl3)))
14947 (define-public r-singler
14954 (uri (bioconductor-uri "SingleR" version))
14956 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
14957 (properties `((upstream-name . "SingleR")))
14958 (build-system r-build-system)
14965 r-delayedmatrixstats
14969 r-summarizedexperiment))
14970 (native-inputs (list r-knitr))
14971 (home-page "https://github.com/LTLA/SingleR")
14972 (synopsis "Reference-based single-cell RNA-seq annotation")
14974 "This package performs unbiased cell type recognition from single-cell
14975 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
14976 cell types to infer the cell of origin of each single cell independently.")
14977 (license license:gpl3)))
14979 (define-public r-scuttle
14986 (uri (bioconductor-uri "scuttle" version))
14989 "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"))))
14990 (properties `((upstream-name . "scuttle")))
14991 (build-system r-build-system)
14997 r-delayedmatrixstats
15002 r-singlecellexperiment
15003 r-summarizedexperiment))
15004 (native-inputs (list r-knitr))
15005 (home-page "https://bioconductor.org/packages/scuttle")
15006 (synopsis "Single-cell RNA-Seq analysis utilities")
15008 "This package provides basic utility functions for performing single-cell
15009 analyses, focusing on simple normalization, quality control and data
15010 transformations. It also provides some helper functions to assist development
15011 of other packages.")
15012 (license license:gpl3)))
15014 (define-public r-scater
15020 (uri (bioconductor-uri "scater" version))
15023 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
15024 (build-system r-build-system)
15032 r-delayedmatrixstats
15044 r-singlecellexperiment
15045 r-summarizedexperiment
15049 (home-page "https://github.com/davismcc/scater")
15050 (synopsis "Single-cell analysis toolkit for gene expression data in R")
15051 (description "This package provides a collection of tools for doing
15052 various analyses of single-cell RNA-seq gene expression data, with a focus on
15054 (license license:gpl2+)))
15056 (define-public r-scran
15063 (uri (bioconductor-uri "scran" version))
15066 "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"))))
15067 (build-system r-build-system)
15076 r-delayedmatrixstats
15086 r-singlecellexperiment
15088 r-summarizedexperiment))
15091 (home-page "https://bioconductor.org/packages/scran")
15092 (synopsis "Methods for single-cell RNA-Seq data analysis")
15093 (description "This package implements a variety of low-level analyses of
15094 single-cell RNA-seq data. Methods are provided for normalization of
15095 cell-specific biases, assignment of cell cycle phase, and detection of highly
15096 variable and significantly correlated genes.")
15097 (license license:gpl3)))
15099 (define-public r-sparsematrixstats
15101 (name "r-sparsematrixstats")
15106 (uri (bioconductor-uri "sparseMatrixStats" version))
15109 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
15111 `((upstream-name . "sparseMatrixStats")))
15112 (build-system r-build-system)
15114 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
15115 (native-inputs (list r-knitr))
15116 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
15117 (synopsis "Summary statistics for rows and columns of sparse matrices")
15119 "This package provides high performance functions for row and column
15120 operations on sparse matrices. Currently, the optimizations are limited to
15121 data in the column sparse format.")
15122 (license license:expat)))
15124 (define-public r-delayedmatrixstats
15126 (name "r-delayedmatrixstats")
15131 (uri (bioconductor-uri "DelayedMatrixStats" version))
15134 "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"))))
15136 `((upstream-name . "DelayedMatrixStats")))
15137 (build-system r-build-system)
15139 (list r-delayedarray
15145 r-sparsematrixstats))
15148 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
15149 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
15151 "This package provides a port of the @code{matrixStats} API for use with
15152 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
15153 contains high-performing functions operating on rows and columns of
15154 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
15155 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
15156 are optimized per data type and for subsetted calculations such that both
15157 memory usage and processing time is minimized.")
15158 (license license:expat)))
15160 (define-public r-mscoreutils
15162 (name "r-mscoreutils")
15167 (uri (bioconductor-uri "MsCoreUtils" version))
15170 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
15171 (properties `((upstream-name . "MsCoreUtils")))
15172 (build-system r-build-system)
15174 (list r-clue r-mass r-rcpp r-s4vectors))
15177 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
15178 (synopsis "Core utils for mass spectrometry data")
15180 "This package defines low-level functions for mass spectrometry data and
15181 is independent of any high-level data structures. These functions include
15182 mass spectra processing functions (noise estimation, smoothing, binning),
15183 quantitative aggregation functions (median polish, robust summarisation,
15184 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
15185 well as misc helper functions, that are used across high-level data structure
15186 within the R for Mass Spectrometry packages.")
15187 (license license:artistic2.0)))
15189 (define-public r-msfeatures
15191 (name "r-msfeatures")
15196 (uri (bioconductor-uri "MsFeatures" version))
15198 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
15199 (properties `((upstream-name . "MsFeatures")))
15200 (build-system r-build-system)
15202 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
15205 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
15206 (synopsis "Functionality for mass spectrometry features")
15208 "The MsFeature package defines functionality for Mass Spectrometry
15209 features. This includes functions to group (LC-MS) features based on some of
15210 their properties, such as retention time (coeluting features), or correlation
15211 of signals across samples. This package hence can be used to group features, and
15212 its results can be used as an input for the @code{QFeatures} package which
15213 allows aggregating abundance levels of features within each group. This
15214 package defines concepts and functions for base and common data types,
15215 implementations for more specific data types are expected to be implemented in
15216 the respective packages (such as e.g. @code{xcms}).")
15217 (license license:artistic2.0)))
15219 (define-public r-biocio
15226 (uri (bioconductor-uri "BiocIO" version))
15229 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
15230 (properties `((upstream-name . "BiocIO")))
15231 (build-system r-build-system)
15233 (list r-biocgenerics r-s4vectors))
15236 (home-page "https://bioconductor.org/packages/BiocIO")
15237 (synopsis "Standard input and output for Bioconductor packages")
15239 "This package implements `import()` and `export()` standard generics for
15240 importing and exporting biological data formats. `import()` supports
15241 whole-file as well as chunk-wise iterative import. The `import()` interface
15242 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
15243 row or element-like components of the file resource), `select()` (on
15244 column-like components of the file resource) and `collect()`. The `import()`
15245 interface optionally provides transparent access to remote (e.g. via https)
15246 as well as local access. Developers can register a file extension, e.g.,
15247 `.loom` for dispatch from character-based URIs to specific `import()` /
15248 `export()` methods based on classes representing file types, e.g.,
15250 (license license:artistic2.0)))
15252 (define-public r-msmseda
15259 (uri (bioconductor-uri "msmsEDA" version))
15262 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
15263 (properties `((upstream-name . "msmsEDA")))
15264 (build-system r-build-system)
15266 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
15268 "https://bioconductor.org/packages/msmsEDA")
15269 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
15271 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
15272 experiments, and visualize de influence of the involved factors.")
15273 (license license:gpl2)))
15275 (define-public r-msmstests
15277 (name "r-msmstests")
15282 (uri (bioconductor-uri "msmsTests" version))
15285 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
15286 (properties `((upstream-name . "msmsTests")))
15287 (build-system r-build-system)
15289 (list r-edger r-msmseda r-msnbase r-qvalue))
15291 "https://bioconductor.org/packages/msmsTests")
15292 (synopsis "Differential LC-MS/MS expression tests")
15294 "This package provides statistical tests for label-free LC-MS/MS data
15295 by spectral counts, to discover differentially expressed proteins between two
15296 biological conditions. Three tests are available: Poisson GLM regression,
15297 quasi-likelihood GLM regression, and the negative binomial of the edgeR
15298 package. The three models admit blocking factors to control for nuisance
15299 variables. To assure a good level of reproducibility a post-test filter is
15300 available, where we may set the minimum effect size considered biologicaly
15301 relevant, and the minimum expression of the most abundant condition.")
15302 (license license:gpl2)))
15304 (define-public r-catalyst
15306 (name "r-catalyst")
15311 (uri (bioconductor-uri "CATALYST" version))
15314 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
15315 (properties `((upstream-name . "CATALYST")))
15316 (build-system r-build-system)
15320 r-consensusclusterplus
15342 r-singlecellexperiment
15343 r-summarizedexperiment))
15346 (home-page "https://github.com/HelenaLC/CATALYST")
15347 (synopsis "Cytometry data analysis tools")
15349 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
15350 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
15351 isotopes rather than fluorescent tags as reporters to label antibodies,
15352 thereby substantially decreasing spectral overlap and allowing for examination
15353 of over 50 parameters at the single cell level. While spectral overlap is
15354 significantly less pronounced in CyTOF than flow cytometry, spillover due to
15355 detection sensitivity, isotopic impurities, and oxide formation can impede
15356 data interpretability. @code{CATALYST} was designed to provide a pipeline for
15357 preprocessing of cytometry data, including:
15360 @item normalization using bead standards;
15361 @item single-cell deconvolution;
15362 @item bead-based compensation.
15365 (license license:gpl2+)))
15367 (define-public r-erma
15374 (uri (bioconductor-uri "erma" version))
15377 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
15378 (build-system r-build-system)
15380 (list r-annotationdbi
15393 r-summarizedexperiment))
15396 (home-page "https://bioconductor.org/packages/erma")
15397 (synopsis "Epigenomic road map adventures")
15399 "The epigenomics road map describes locations of epigenetic marks in DNA
15400 from a variety of cell types. Of interest are locations of histone
15401 modifications, sites of DNA methylation, and regions of accessible chromatin.
15402 This package presents a selection of elements of the road map including
15403 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
15404 by Ernst and Kellis.")
15405 (license license:artistic2.0)))
15407 (define-public r-ggbio
15414 (uri (bioconductor-uri "ggbio" version))
15417 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
15418 (build-system r-build-system)
15421 (modify-phases %standard-phases
15422 ;; See https://github.com/tengfei/ggbio/issues/117
15423 ;; This fix will be included in the next release.
15424 (add-after 'unpack 'fix-typo
15426 (substitute* "R/GGbio-class.R"
15427 (("fechable") "fetchable"))
15430 (list r-annotationdbi
15439 r-genomicalignments
15455 r-summarizedexperiment
15456 r-variantannotation))
15459 (home-page "http://www.tengfei.name/ggbio/")
15460 (synopsis "Visualization tools for genomic data")
15462 "The ggbio package extends and specializes the grammar of graphics for
15463 biological data. The graphics are designed to answer common scientific
15464 questions, in particular those often asked of high throughput genomics data.
15465 All core Bioconductor data structures are supported, where appropriate. The
15466 package supports detailed views of particular genomic regions, as well as
15467 genome-wide overviews. Supported overviews include ideograms and grand linear
15468 views. High-level plots include sequence fragment length, edge-linked
15469 interval to data view, mismatch pileup, and several splicing summaries.")
15470 (license license:artistic2.0)))
15472 (define-public r-gqtlbase
15474 (name "r-gqtlbase")
15479 (uri (bioconductor-uri "gQTLBase" version))
15482 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
15483 (properties `((upstream-name . "gQTLBase")))
15484 (build-system r-build-system)
15487 (modify-phases %standard-phases
15488 ;; This is an upstream bug.
15489 (add-after 'unpack 'fix-imports
15491 (substitute* "NAMESPACE"
15492 ((".*maxffmode.*") "")
15493 (("importFrom\\(ff,.*") "import(ff)\n"))
15508 r-summarizedexperiment))
15511 (home-page "https://bioconductor.org/packages/gQTLBase")
15512 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
15514 "The purpose of this package is to simplify the storage and interrogation
15515 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
15517 (license license:artistic2.0)))
15519 (define-public r-gqtlstats
15521 (name "r-gqtlstats")
15526 (uri (bioconductor-uri "gQTLstats" version))
15529 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
15530 (properties `((upstream-name . "gQTLstats")))
15531 (build-system r-build-system)
15533 (list r-annotationdbi
15561 r-summarizedexperiment
15562 r-variantannotation))
15565 (home-page "https://bioconductor.org/packages/gQTLstats")
15566 (synopsis "Computationally efficient analysis for eQTL and allied studies")
15568 "This package provides tools for the computationally efficient analysis
15569 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
15570 The software in this package aims to support refinements and functional
15571 interpretation of members of a collection of association statistics on a
15572 family of feature/genome hypotheses.")
15573 (license license:artistic2.0)))
15575 (define-public r-gviz
15582 (uri (bioconductor-uri "Gviz" version))
15585 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
15586 (properties `((upstream-name . "Gviz")))
15587 (build-system r-build-system)
15589 (list r-annotationdbi
15599 r-genomicalignments
15613 (home-page "https://bioconductor.org/packages/Gviz")
15614 (synopsis "Plotting data and annotation information along genomic coordinates")
15616 "Genomic data analyses requires integrated visualization of known genomic
15617 information and new experimental data. Gviz uses the biomaRt and the
15618 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
15619 and translates this to e.g. gene/transcript structures in viewports of the
15620 grid graphics package. This results in genomic information plotted together
15622 (license license:artistic2.0)))
15624 (define-public r-gwascat
15631 (uri (bioconductor-uri "gwascat" version))
15634 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
15635 (build-system r-build-system)
15637 (list r-annotationdbi
15648 r-variantannotation))
15651 (home-page "https://bioconductor.org/packages/gwascat")
15652 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
15654 "This package provides tools for representing and modeling data in the
15655 EMBL-EBI GWAS catalog.")
15656 (license license:artistic2.0)))
15658 (define-public r-kegggraph
15660 (name "r-kegggraph")
15665 (uri (bioconductor-uri "KEGGgraph" version))
15667 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
15668 (properties `((upstream-name . "KEGGgraph")))
15669 (build-system r-build-system)
15671 (list r-graph r-rcurl r-rgraphviz r-xml))
15672 (home-page "https://bioconductor.org/packages/KEGGgraph")
15673 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
15675 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
15676 object as well as a collection of tools to analyze, dissect and visualize these
15677 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
15678 maintaining all essential pathway attributes. The package offers
15679 functionalities including parsing, graph operation, visualization and etc.")
15680 (license license:gpl2+)))
15682 (define-public r-ldblock
15689 (uri (bioconductor-uri "ldblock" version))
15692 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
15693 (build-system r-build-system)
15695 (list r-biocgenerics
15696 r-ensdb-hsapiens-v75
15704 r-variantannotation))
15707 (home-page "https://bioconductor.org/packages/ldblock")
15708 (synopsis "Data structures for linkage disequilibrium measures in populations")
15710 "This package defines data structures for @dfn{linkage
15711 disequilibrium} (LD) measures in populations. Its purpose is to simplify
15712 handling of existing population-level data for the purpose of flexibly
15713 defining LD blocks.")
15714 (license license:artistic2.0)))
15716 ;; This is a CRAN package, but it depends on r-snpstats, which is a
15717 ;; Bioconductor package.
15718 (define-public r-ldheatmap
15720 (name "r-ldheatmap")
15725 (uri (cran-uri "LDheatmap" version))
15728 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
15729 (properties `((upstream-name . "LDheatmap")))
15730 (build-system r-build-system)
15732 (list r-genetics r-rcpp r-snpstats))
15733 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
15734 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
15736 "This package provides tools to produce a graphical display, as a heat
15737 map, of measures of pairwise linkage disequilibria between SNPs. Users may
15738 optionally include the physical locations or genetic map distances of each SNP
15740 (license license:gpl3)))
15742 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
15743 ;; Bioconductor package.
15744 (define-public r-abn
15751 (uri (cran-uri "abn" version))
15754 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
15755 (build-system r-build-system)
15768 (home-page "https://r-bayesian-networks.org/")
15769 (synopsis "Modelling multivariate data with additive bayesian networks")
15771 "Bayesian network analysis is a form of probabilistic graphical models
15772 which derives from empirical data a directed acyclic graph, DAG, describing
15773 the dependency structure between random variables. An additive Bayesian
15774 network model consists of a form of a DAG where each node comprises a
15775 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
15776 equivalent to Bayesian multivariate regression using graphical modelling, they
15777 generalises the usual multivariable regression, GLM, to multiple dependent
15778 variables. This package provides routines to help determine optimal Bayesian
15779 network models for a given data set, where these models are used to identify
15780 statistical dependencies in messy, complex data.")
15781 (license license:gpl2+)))
15783 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
15784 ;; Bioconductor package.
15785 (define-public r-spp
15791 (uri (cran-uri "spp" version))
15794 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
15795 (build-system r-build-system)
15799 (list r-bh r-catools r-rcpp r-rsamtools))
15800 (home-page "https://cran.r-project.org/web/packages/spp/")
15801 (synopsis "ChIP-Seq processing pipeline")
15802 (description "This package provides tools for analysis of ChIP-seq and
15803 other functional sequencing data.")
15804 (license license:gpl2)))
15806 (define-public r-pathview
15808 (name "r-pathview")
15813 (uri (bioconductor-uri "pathview" version))
15815 (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"))))
15816 (properties `((upstream-name . "pathview")))
15817 (build-system r-build-system)
15819 (list r-annotationdbi
15827 (home-page "https://pathview.uncc.edu/")
15828 (synopsis "Tool set for pathway based data integration and visualization")
15830 "@code{r-pathview} is a tool set for pathway based data integration and
15831 visualization. It maps and renders a wide variety of biological data on
15832 relevant pathway graphs. All users need is to supply their data and specify
15833 the target pathway. This package automatically downloads the pathway graph
15834 data, parses the data file, maps user data to the pathway, and render pathway
15835 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
15836 integrates with pathway and gene set (enrichment) analysis tools for
15837 large-scale and fully automated analysis.")
15838 (license license:gpl3+)))
15840 (define-public r-snpstats
15842 (name "r-snpstats")
15847 (uri (bioconductor-uri "snpStats" version))
15850 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
15851 (properties `((upstream-name . "snpStats")))
15852 (build-system r-build-system)
15853 (inputs (list zlib))
15855 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
15856 (home-page "https://bioconductor.org/packages/snpStats")
15857 (synopsis "Methods for SNP association studies")
15859 "This package provides classes and statistical methods for large
15860 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
15861 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
15862 (license license:gpl3)))
15864 (define-public r-chromstar
15866 (name "r-chromstar")
15871 (uri (bioconductor-uri "chromstaR" version))
15874 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
15875 (properties `((upstream-name . "chromstaR")))
15876 (build-system r-build-system)
15884 r-genomicalignments
15892 (native-inputs (list r-knitr))
15893 (home-page "https://github.com/ataudt/chromstaR")
15894 (synopsis "Chromatin state analysis for ChIP-Seq data")
15896 "This package implements functions for combinatorial and differential
15897 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
15898 export to genome browser viewable files, and functions for enrichment
15900 (license license:artistic2.0)))
15902 (define-public r-guitar
15909 (uri (bioconductor-uri "Guitar" version))
15912 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
15913 (properties `((upstream-name . "Guitar")))
15914 (build-system r-build-system)
15916 (list r-annotationdbi
15926 (home-page "https://bioconductor.org/packages/Guitar")
15927 (synopsis "Visualize genomic features")
15929 "This package is designed for visualization of RNA-related genomic
15930 features with respect to the landmarks of RNA transcripts, i.e., transcription
15931 starting site, start codon, stop codon and transcription ending site.")
15932 (license license:gpl2)))
15934 (define-public r-sushi
15940 (uri (bioconductor-uri "Sushi" version))
15943 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
15944 (properties `((upstream-name . "Sushi")))
15945 (build-system r-build-system)
15947 (list r-biomart r-zoo))
15948 (home-page "https://bioconductor.org/packages/Sushi")
15949 (synopsis "Tools for visualizing genomics data")
15951 "This package provides flexible, quantitative, and integrative genomic
15952 visualizations for publication-quality multi-panel figures.")
15953 (license license:gpl2+)))
15955 (define-public r-ballgown
15957 (name "r-ballgown")
15962 (uri (bioconductor-uri "ballgown" version))
15965 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
15966 (properties `((upstream-name . "ballgown")))
15967 (build-system r-build-system)
15980 (home-page "https://bioconductor.org/packages/ballgown")
15981 (synopsis "Flexible, isoform-level differential expression analysis")
15983 "This package provides tools for statistical analysis of assembled
15984 transcriptomes, including flexible differential expression analysis,
15985 visualization of transcript structures, and matching of assembled transcripts
15987 (license license:artistic2.0)))
15989 (define-public r-megadepth
15991 (name "r-megadepth")
15996 (uri (bioconductor-uri "megadepth" version))
15999 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
16000 (properties `((upstream-name . "megadepth")))
16001 (build-system r-build-system)
16002 (inputs (list megadepth))
16013 (home-page "https://github.com/LieberInstitute/megadepth")
16014 (synopsis "BigWig and BAM related utilities")
16016 "This package provides an R interface to Megadepth. It is particularly
16017 useful for computing the coverage of a set of genomic regions across bigWig or
16018 BAM files. With this package, you can build base-pair coverage matrices for
16019 regions or annotations of your choice from BigWig files.")
16020 (license license:artistic2.0)))
16022 (define-public r-beclear
16029 (uri (bioconductor-uri "BEclear" version))
16032 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
16033 (properties `((upstream-name . "BEclear")))
16034 (build-system r-build-system)
16046 (home-page "https://github.com/uds-helms/BEclear")
16047 (synopsis "Correction of batch effects in DNA methylation data")
16049 "This package provides functions to detect and correct for batch effects
16050 in DNA methylation data. The core function is based on latent factor models
16051 and can also be used to predict missing values in any other matrix containing
16053 (license license:gpl3)))
16055 (define-public r-bgeecall
16057 (name "r-bgeecall")
16062 (uri (bioconductor-uri "BgeeCall" version))
16065 "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"))))
16066 (properties `((upstream-name . "BgeeCall")))
16067 (build-system r-build-system)
16081 (native-inputs (list r-knitr))
16082 (home-page "https://github.com/BgeeDB/BgeeCall")
16083 (synopsis "RNA-Seq present/absent gene expression calls generation")
16085 "BgeeCall allows generating present/absent gene expression calls without
16086 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
16087 intergenic sequences. These sequences are generated based on expression of
16088 all RNA-Seq libraries of each species integrated in Bgee.")
16089 (license license:gpl3)))
16091 (define-public r-bgeedb
16098 (uri (bioconductor-uri "BgeeDB" version))
16101 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
16102 (properties `((upstream-name . "BgeeDB")))
16103 (build-system r-build-system)
16116 (native-inputs (list r-knitr))
16117 (home-page "https://github.com/BgeeDB/BgeeDB_R")
16118 (synopsis "Annotation and gene expression data retrieval from Bgee database")
16120 "This package provides a package for the annotation and gene expression
16121 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
16122 anatomical terms, mapped to genes by expression patterns.")
16123 (license license:gpl3)))
16125 (define-public r-biobtreer
16127 (name "r-biobtreer")
16132 (uri (bioconductor-uri "biobtreeR" version))
16135 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
16136 (properties `((upstream-name . "biobtreeR")))
16137 (build-system r-build-system)
16139 (list r-httpuv r-httr r-jsonlite r-stringi))
16140 (native-inputs (list r-knitr))
16141 (home-page "https://github.com/tamerh/biobtreeR")
16142 (synopsis "Use biobtree tool from R")
16144 "The biobtreeR package provides an interface to biobtree, a tool which
16145 covers large sets of bioinformatics datasets and allows search and chain
16146 mappings functionalities.")
16147 (license license:expat)))
16149 (define-public r-minet
16156 (uri (bioconductor-uri "minet" version))
16159 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
16160 (properties `((upstream-name . "minet")))
16161 (build-system r-build-system)
16164 (home-page "http://minet.meyerp.com")
16165 (synopsis "Mutual information networks")
16167 "This package implements various algorithms for inferring mutual
16168 information networks from data.")
16169 (license license:artistic2.0)))
16171 (define-public r-genetclassifier
16173 (name "r-genetclassifier")
16178 (uri (bioconductor-uri "geNetClassifier" version))
16181 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
16183 `((upstream-name . "geNetClassifier")))
16184 (build-system r-build-system)
16186 (list r-biobase r-e1071 r-ebarrays r-minet))
16187 (home-page "https://www.cicancer.org")
16188 (synopsis "Classify diseases and build gene networks using expression profiles")
16190 "This is a comprehensive package to automatically train and validate a
16191 multi-class SVM classifier based on gene expression data. It provides
16192 transparent selection of gene markers, their coexpression networks, and an
16193 interface to query the classifier.")
16194 (license license:gpl2+)))
16196 (define-public r-dir-expiry
16198 (name "r-dir-expiry")
16203 (uri (bioconductor-uri "dir.expiry" version))
16206 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
16207 (properties `((upstream-name . "dir.expiry")))
16208 (build-system r-build-system)
16209 (propagated-inputs (list r-filelock))
16210 (native-inputs (list r-knitr))
16211 (home-page "https://bioconductor.org/packages/dir.expiry")
16212 (synopsis "Managing expiration for cache directories")
16214 "This package implements an expiration system for access to versioned
16215 directories. Directories that have not been accessed by a registered function
16216 within a certain time frame are deleted. This aims to reduce disk usage by
16217 eliminating obsolete caches generated by old versions of packages.")
16218 (license license:gpl3)))
16220 (define-public r-basilisk-utils
16222 (name "r-basilisk-utils")
16227 (uri (bioconductor-uri "basilisk.utils" version))
16230 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
16232 `((upstream-name . "basilisk.utils")))
16233 (build-system r-build-system)
16235 (list r-dir-expiry))
16236 (native-inputs (list r-knitr))
16237 (home-page "https://bioconductor.org/packages/basilisk.utils")
16238 (synopsis "Basilisk installation utilities")
16240 "This package implements utilities for installation of the basilisk
16241 package, primarily for creation of the underlying Conda instance.")
16242 (license license:gpl3)))
16244 (define-public r-basilisk
16246 (name "r-basilisk")
16251 (uri (bioconductor-uri "basilisk" version))
16254 "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"))))
16255 (properties `((upstream-name . "basilisk")))
16256 (build-system r-build-system)
16258 (list r-basilisk-utils r-dir-expiry r-reticulate))
16259 (native-inputs (list r-knitr))
16260 (home-page "https://bioconductor.org/packages/basilisk")
16261 (synopsis "Freeze Python dependencies inside Bioconductor packages")
16263 "This package installs a self-contained Conda instance that is managed by
16264 the R/Bioconductor installation machinery. This aims to provide a consistent
16265 Python environment that can be used reliably by Bioconductor packages.
16266 Functions are also provided to enable smooth interoperability of multiple
16267 Python environments in a single R session.")
16268 (license license:gpl3)))
16270 (define-public r-biocthis
16272 (name "r-biocthis")
16277 (uri (bioconductor-uri "biocthis" version))
16280 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
16281 (properties `((upstream-name . "biocthis")))
16282 (build-system r-build-system)
16285 (modify-phases %standard-phases
16286 (add-after 'unpack 'set-HOME
16287 (lambda _ (setenv "HOME" "/tmp"))))))
16289 (list r-biocmanager
16295 (native-inputs (list r-knitr))
16296 (home-page "https://github.com/lcolladotor/biocthis")
16297 (synopsis "Automate package and project setup for Bioconductor packages")
16299 "This package expands the @code{usethis} package with the goal of helping
16300 automate the process of creating R packages for Bioconductor or making them
16301 Bioconductor-friendly.")
16302 (license license:artistic2.0)))
16304 (define-public r-biocdockermanager
16306 (name "r-biocdockermanager")
16311 (uri (bioconductor-uri "BiocDockerManager" version))
16314 "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"))))
16316 `((upstream-name . "BiocDockerManager")))
16317 (build-system r-build-system)
16325 (native-inputs (list r-knitr))
16326 (home-page "https://bioconductor.org/packages/BiocDockerManager")
16327 (synopsis "Access and manage Bioconductor Docker images")
16329 "This package works analogous to BiocManager but for Docker images. Use
16330 the BiocDockerManager package to install and manage Docker images provided by
16331 the Bioconductor project.")
16332 (license license:artistic2.0)))
16334 (define-public r-biodb
16341 (uri (bioconductor-uri "biodb" version))
16344 "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"))))
16345 (properties `((upstream-name . "biodb")))
16346 (build-system r-build-system)
16348 (list r-biocfilecache
16366 (native-inputs (list r-knitr))
16367 (home-page "https://bioconductor.org/packages/biodb")
16368 (synopsis "Library for connecting to chemical and biological databases")
16370 "The biodb package provides access to standard remote chemical and
16371 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
16372 database files (CSV, SQLite), with easy retrieval of entries, access to web
16373 services, search of compounds by mass and/or name, and mass spectra matching
16374 for LCMS and MSMS. Its architecture as a development framework facilitates
16375 the development of new database connectors for local projects or inside
16376 separate published packages.")
16377 (license license:agpl3+)))
16379 (define-public r-biomformat
16381 (name "r-biomformat")
16386 (uri (bioconductor-uri "biomformat" version))
16389 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
16390 (properties `((upstream-name . "biomformat")))
16391 (build-system r-build-system)
16393 (list r-jsonlite r-matrix r-plyr r-rhdf5))
16394 (native-inputs (list r-knitr))
16395 (home-page "https://github.com/joey711/biomformat/")
16396 (synopsis "Interface package for the BIOM file format")
16398 "This is an R package for interfacing with the BIOM format. This package
16399 includes basic tools for reading biom-format files, accessing and subsetting
16400 data tables from a biom object (which is more complex than a single table), as
16401 well as limited support for writing a biom-object back to a biom-format file.
16402 The design of this API is intended to match the Python API and other tools
16403 included with the biom-format project, but with a decidedly \"R flavor\" that
16404 should be familiar to R users. This includes S4 classes and methods, as well
16405 as extensions of common core functions/methods.")
16406 (license license:gpl2)))
16408 (define-public r-mvcclass
16410 (name "r-mvcclass")
16415 (uri (bioconductor-uri "MVCClass" version))
16418 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
16419 (properties `((upstream-name . "MVCClass")))
16420 (build-system r-build-system)
16421 (home-page "https://bioconductor.org/packages/MVCClass")
16422 (synopsis "Model-View-Controller (MVC) classes")
16424 "This package contains classes used in model-view-controller (MVC)
16426 (license license:lgpl2.1+)))
16428 (define-public r-biomvcclass
16430 (name "r-biomvcclass")
16435 (uri (bioconductor-uri "BioMVCClass" version))
16438 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
16439 (properties `((upstream-name . "BioMVCClass")))
16440 (build-system r-build-system)
16442 (list r-biobase r-graph r-mvcclass r-rgraphviz))
16443 (home-page "https://bioconductor.org/packages/BioMVCClass")
16444 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
16446 "This package contains classes used in model-view-controller (MVC)
16448 (license license:lgpl2.1+)))
16450 (define-public r-biomvrcns
16452 (name "r-biomvrcns")
16457 (uri (bioconductor-uri "biomvRCNS" version))
16460 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
16461 (properties `((upstream-name . "biomvRCNS")))
16462 (build-system r-build-system)
16464 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
16465 (home-page "https://bioconductor.org/packages/biomvRCNS")
16466 (synopsis "Copy number study and segmentation for multivariate biological data")
16468 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
16469 homogeneous segmentation model are designed and implemented for segmentation
16470 genomic data, with the aim of assisting in transcripts detection using high
16471 throughput technology like RNA-seq or tiling array, and copy number analysis
16472 using aCGH or sequencing.")
16473 (license license:gpl2+)))
16475 (define-public r-bionero
16482 (uri (bioconductor-uri "BioNERO" version))
16485 "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"))))
16486 (properties `((upstream-name . "BioNERO")))
16487 (build-system r-build-system)
16489 (list r-biocparallel
16506 r-summarizedexperiment
16511 (home-page "https://github.com/almeidasilvaf/BioNERO")
16512 (synopsis "Biological network reconstruction omnibus")
16514 "BioNERO aims to integrate all aspects of biological network inference in
16515 a single package, including data preprocessing, exploratory analyses, network
16516 inference, and analyses for biological interpretations. BioNERO can be used
16517 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
16518 from gene expression data. Additionally, it can be used to explore
16519 topological properties of protein-protein interaction (PPI) networks. GCN
16520 inference relies on the popular WGCNA algorithm. GRN inference is based on
16521 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
16522 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
16523 rank for each interaction pair. As all steps of network analyses are included
16524 in this package, BioNERO makes users avoid having to learn the syntaxes of
16525 several packages and how to communicate between them. Finally, users can also
16526 identify consensus modules across independent expression sets and calculate
16527 intra and interspecies module preservation statistics between different
16529 (license license:gpl3)))
16531 (define-public r-bionet
16538 (uri (bioconductor-uri "BioNet" version))
16541 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
16542 (properties `((upstream-name . "BioNet")))
16543 (build-system r-build-system)
16545 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
16546 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
16547 (synopsis "Functional analysis of biological networks")
16549 "This package provides functions for the integrated analysis of
16550 protein-protein interaction networks and the detection of functional modules.
16551 Different datasets can be integrated into the network by assigning p-values of
16552 statistical tests to the nodes of the network. E.g. p-values obtained from
16553 the differential expression of the genes from an Affymetrix array are assigned
16554 to the nodes of the network. By fitting a beta-uniform mixture model and
16555 calculating scores from the p-values, overall scores of network regions can be
16556 calculated and an integer linear programming algorithm identifies the maximum
16557 scoring subnetwork.")
16558 (license license:gpl2+)))
16560 (define-public r-bionetstat
16562 (name "r-bionetstat")
16567 (uri (bioconductor-uri "BioNetStat" version))
16570 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
16571 (properties `((upstream-name . "BioNetStat")))
16572 (build-system r-build-system)
16574 (list r-biocparallel
16594 (home-page "https://github.com/jardimViniciusC/BioNetStat")
16595 (synopsis "Biological network analysis")
16597 "This package provides a package to perform differential network
16598 analysis, differential node analysis (differential coexpression analysis),
16599 network and metabolic pathways view.")
16600 (license license:gpl3+)))
16602 (define-public r-bioqc
16609 (uri (bioconductor-uri "BioQC" version))
16612 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
16613 (properties `((upstream-name . "BioQC")))
16614 (build-system r-build-system)
16616 (list r-biobase r-edger r-rcpp))
16619 (home-page "https://accio.github.io/BioQC/")
16620 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
16622 "BioQC performs quality control of high-throughput expression data based
16623 on tissue gene signatures. It can detect tissue heterogeneity in gene
16624 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
16625 optimised for high performance.")
16626 (license license:gpl3+)))
16628 (define-public r-biotip
16635 (uri (bioconductor-uri "BioTIP" version))
16638 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
16639 (properties `((upstream-name . "BioTIP")))
16640 (build-system r-build-system)
16651 (home-page "https://github.com/xyang2uchicago/BioTIP")
16652 (synopsis "R package for characterization of biological tipping-point")
16654 "This package adopts tipping-point theory to transcriptome profiles to
16655 help unravel disease regulatory trajectory.")
16656 (license license:gpl2)))
16658 (define-public r-biotmle
16665 (uri (bioconductor-uri "biotmle" version))
16668 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
16669 (properties `((upstream-name . "biotmle")))
16670 (build-system r-build-system)
16681 r-summarizedexperiment
16686 (home-page "https://code.nimahejazi.org/biotmle/")
16687 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
16689 "This package provides tools for differential expression biomarker
16690 discovery based on microarray and next-generation sequencing data that
16691 leverage efficient semiparametric estimators of the average treatment effect
16692 for variable importance analysis. Estimation and inference of the (marginal)
16693 average treatment effects of potential biomarkers are computed by targeted
16694 minimum loss-based estimation, with joint, stable inference constructed across
16695 all biomarkers using a generalization of moderated statistics for use with the
16696 estimated efficient influence function. The procedure accommodates the use of
16697 ensemble machine learning for the estimation of nuisance functions.")
16698 (license license:expat)))
16700 (define-public r-bsseq
16707 (uri (bioconductor-uri "bsseq" version))
16710 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
16711 (properties `((upstream-name . "bsseq")))
16712 (build-system r-build-system)
16722 r-delayedmatrixstats
16736 r-summarizedexperiment))
16739 (home-page "https://github.com/hansenlab/bsseq")
16740 (synopsis "Analyze, manage and store bisulfite sequencing data")
16742 "This package provides a collection of tools for analyzing and
16743 visualizing bisulfite sequencing data.")
16744 (license license:artistic2.0)))
16746 (define-public r-dmrseq
16753 (uri (bioconductor-uri "dmrseq" version))
16756 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
16757 (properties `((upstream-name . "dmrseq")))
16758 (build-system r-build-system)
16760 (list r-annotationhub
16765 r-delayedmatrixstats
16779 (home-page "https://bioconductor.org/packages/dmrseq")
16780 (synopsis "Detection and inference of differentially methylated regions")
16782 "This package implements an approach for scanning the genome to detect
16783 and perform accurate inference on differentially methylated regions from Whole
16784 Genome Bisulfite Sequencing data. The method is based on comparing detected
16785 regions to a pooled null distribution, that can be implemented even when as
16786 few as two samples per population are available. Region-level statistics are
16787 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
16788 with a nested autoregressive correlated error structure for the effect of
16789 interest on transformed methylation proportions.")
16790 (license license:expat)))
16792 (define-public r-omicade4
16794 (name "r-omicade4")
16798 (uri (bioconductor-uri "omicade4" version))
16801 "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
16802 (properties `((upstream-name . "omicade4")))
16803 (build-system r-build-system)
16804 (propagated-inputs (list r-ade4 r-biobase r-made4))
16805 (home-page "https://bioconductor.org/packages/omicade4")
16806 (synopsis "Multiple co-inertia analysis of omics datasets")
16808 "This package performes multiple co-inertia analysis of omics datasets.")
16809 (license license:gpl2)))
16811 (define-public r-omnipathr
16813 (name "r-omnipathr")
16818 (uri (bioconductor-uri "OmnipathR" version))
16820 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
16821 (properties `((upstream-name . "OmnipathR")))
16822 (build-system r-build-system)
16825 (modify-phases %standard-phases
16826 (add-after 'unpack 'set-HOME
16827 (lambda _ (setenv "HOME" "/tmp"))))))
16853 (native-inputs (list r-knitr))
16854 (home-page "https://saezlab.github.io/OmnipathR/")
16855 (synopsis "OmniPath web service client and more")
16857 "This package provides a client for the OmniPath web service and many
16858 other resources. It also includes functions to transform and pretty print
16859 some of the downloaded data, functions to access a number of other resources.
16860 Furthermore, OmnipathR features a close integration with the NicheNet method
16861 for ligand activity prediction from transcriptomics data.")
16862 (license license:expat)))
16864 (define-public r-biscuiteer
16866 (name "r-biscuiteer")
16871 (uri (bioconductor-uri "biscuiteer" version))
16874 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
16875 (properties `((upstream-name . "biscuiteer")))
16876 (build-system r-build-system)
16884 r-delayedmatrixstats
16903 r-summarizedexperiment
16904 r-variantannotation))
16907 (home-page "https://github.com/trichelab/biscuiteer")
16908 (synopsis "Convenience functions for the Biscuit package")
16910 "This package provides a test harness for bsseq loading of Biscuit
16911 output, summarization of WGBS data over defined regions and in mappable
16912 samples, with or without imputation, dropping of mostly-NA rows, age
16914 (license license:gpl3)))
16916 (define-public r-tcgabiolinks
16918 (name "r-tcgabiolinks")
16923 (uri (bioconductor-uri "TCGAbiolinks" version))
16925 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
16926 (properties `((upstream-name . "TCGAbiolinks")))
16927 (build-system r-build-system)
16946 r-summarizedexperiment
16947 r-tcgabiolinksgui-data
16952 (native-inputs (list r-knitr))
16953 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
16954 (synopsis "Integrative analysis with GDC data")
16956 "The aim of TCGAbiolinks is:
16959 @item facilitate GDC open-access data retrieval;
16960 @item prepare the data using the appropriate pre-processing strategies;
16961 @item provide the means to carry out different standard analyses, and;
16962 @item to easily reproduce earlier research results.
16965 In more detail, the package provides multiple methods for analysis (e.g.,
16966 differential expression analysis, identifying differentially methylated
16967 regions) and methods for visualization (e.g., survival plots, volcano plots,
16968 starburst plots) in order to easily develop complete analysis pipelines.")
16969 (license license:gpl3+)))
16971 (define-public r-tricycle
16973 (name "r-tricycle")
16977 (uri (bioconductor-uri "tricycle" version))
16980 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
16981 (properties `((upstream-name . "tricycle")))
16982 (build-system r-build-system)
16984 (list r-annotationdbi
16995 r-singlecellexperiment
16996 r-summarizedexperiment))
16997 (native-inputs (list r-knitr))
16998 (home-page "https://github.com/hansenlab/tricycle")
16999 (synopsis "Transferable representation and inference of cell cycle")
17001 "The package contains functions to infer and visualize cell cycle process
17002 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
17003 projecting new data to the previous learned biologically interpretable space.
17004 The @code{tricycle} provides a pre-learned cell cycle space, which could be
17005 used to infer cell cycle time of human and mouse single cell samples. In
17006 addition, it also offer functions to visualize cell cycle time on different
17007 embeddings and functions to build new reference.")
17008 (license license:gpl3)))
17010 (define-public r-tximeta
17017 (uri (bioconductor-uri "tximeta" version))
17020 "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl"))))
17021 (properties `((upstream-name . "tximeta")))
17022 (build-system r-build-system)
17024 (list r-annotationdbi
17036 r-summarizedexperiment
17041 (home-page "https://github.com/mikelove/tximeta")
17042 (synopsis "Transcript quantification import with automatic metadata")
17044 "This package implements transcript quantification import from Salmon and
17045 alevin with automatic attachment of transcript ranges and release information,
17046 and other associated metadata. De novo transcriptomes can be linked to the
17047 appropriate sources with linkedTxomes and shared for computational
17049 (license license:gpl2)))
17051 (define-public r-phyloseq
17053 (name "r-phyloseq")
17058 (uri (bioconductor-uri "phyloseq" version))
17060 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
17061 (properties `((upstream-name . "phyloseq")))
17062 (build-system r-build-system)
17082 (home-page "https://github.com/joey711/phyloseq")
17083 (synopsis "Handling and analysis of high-throughput microbiome census data")
17085 "Phyloseq provides a set of classes and tools to facilitate the import,
17086 storage, analysis, and graphical display of microbiome census data.")
17087 (license license:agpl3)))
17090 ;;; Avoid adding new packages to the end of this file. To reduce the chances
17091 ;;; of a merge conflict, place them above by existing packages with similar
17092 ;;; functionality or similar names.