1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
11 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
12 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
13 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
14 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
16 ;;; This file is part of GNU Guix.
18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
19 ;;; under the terms of the GNU General Public License as published by
20 ;;; the Free Software Foundation; either version 3 of the License, or (at
21 ;;; your option) any later version.
23 ;;; GNU Guix is distributed in the hope that it will be useful, but
24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 ;;; GNU General Public License for more details.
28 ;;; You should have received a copy of the GNU General Public License
29 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
31 (define-module (gnu packages bioconductor)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix download)
35 #:use-module (guix git-download)
36 #:use-module (guix build-system r)
37 #:use-module (gnu packages)
38 #:use-module (gnu packages autotools)
39 #:use-module (gnu packages base)
40 #:use-module (gnu packages bioinformatics)
41 #:use-module (gnu packages boost)
42 #:use-module (gnu packages cran)
43 #:use-module (gnu packages compression)
44 #:use-module (gnu packages curl)
45 #:use-module (gnu packages docker)
46 #:use-module (gnu packages gcc)
47 #:use-module (gnu packages graph)
48 #:use-module (gnu packages graphviz)
49 #:use-module (gnu packages haskell-xyz)
50 #:use-module (gnu packages image)
51 #:use-module (gnu packages maths)
52 #:use-module (gnu packages netpbm)
53 #:use-module (gnu packages python)
54 #:use-module (gnu packages perl)
55 #:use-module (gnu packages pkg-config)
56 #:use-module (gnu packages statistics)
57 #:use-module (gnu packages web)
58 #:use-module (gnu packages xml)
59 #:use-module (srfi srfi-1))
64 (define-public r-org-eck12-eg-db
66 (name "r-org-eck12-eg-db")
71 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
73 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
75 `((upstream-name . "org.EcK12.eg.db")))
76 (build-system r-build-system)
78 (list r-annotationdbi))
79 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
80 (synopsis "Genome wide annotation for E coli strain K12")
82 "This package provides genome wide annotation for E coli strain K12,
83 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
84 National Center for Biotechnology Information (NCBI)’s database for
85 gene-specific information. Entrez Gene maintains records from genomes which
86 have been completely sequenced, which have an active research community to
87 submit gene-specific information, or which are scheduled for intense sequence
89 (license license:artistic2.0)))
91 (define-public r-org-bt-eg-db
93 (name "r-org-bt-eg-db")
98 (uri (bioconductor-uri
104 "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi"))))
105 (properties `((upstream-name . "org.Bt.eg.db")))
106 (build-system r-build-system)
108 (list r-annotationdbi))
109 (home-page "https://bioconductor.org/packages/org.Bt.eg.db")
110 (synopsis "Genome wide annotation for Bovine")
112 "This package provides genome wide annotations for Bovine, primarily
113 based on mapping using Entrez Gene identifiers.")
114 (license license:artistic2.0)))
116 (define-public r-reactome-db
118 (name "r-reactome-db")
123 (uri (bioconductor-uri "reactome.db" version 'annotation))
126 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
127 (properties `((upstream-name . "reactome.db")))
128 (build-system r-build-system)
130 (list r-annotationdbi))
131 (home-page "https://bioconductor.org/packages/reactome.db/")
132 (synopsis "Annotation maps for reactome")
134 "This package provides a set of annotation maps for the REACTOME
135 database, assembled using data from REACTOME.")
136 (license license:cc-by4.0)))
138 (define-public r-bsgenome-btaurus-ucsc-bostau8
140 (name "r-bsgenome-btaurus-ucsc-bostau8")
144 (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
145 version 'annotation))
148 "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
150 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
151 (build-system r-build-system)
155 "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
156 (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
157 (description "This package provides the full genome sequences for Bos
158 taurus (UCSC version bosTau8).")
159 (license license:artistic2.0)))
161 (define-public r-bsgenome-celegans-ucsc-ce6
163 (name "r-bsgenome-celegans-ucsc-ce6")
167 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
168 version 'annotation))
171 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
173 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
174 (build-system r-build-system)
178 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
179 (synopsis "Full genome sequences for Worm")
181 "This package provides full genome sequences for Caenorhabditis
182 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
184 (license license:artistic2.0)))
186 (define-public r-bsgenome-celegans-ucsc-ce10
188 (name "r-bsgenome-celegans-ucsc-ce10")
192 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
193 version 'annotation))
196 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
198 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
199 (build-system r-build-system)
203 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
204 (synopsis "Full genome sequences for Worm")
206 "This package provides full genome sequences for Caenorhabditis
207 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
209 (license license:artistic2.0)))
211 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
213 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
217 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
218 version 'annotation))
221 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
223 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
224 (build-system r-build-system)
228 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
229 (synopsis "Full genome sequences for Fly")
231 "This package provides full genome sequences for Drosophila
232 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
234 (license license:artistic2.0)))
236 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
238 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
242 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
243 version 'annotation))
246 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
248 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
249 (build-system r-build-system)
253 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
254 (synopsis "Full genome sequences for Fly")
256 "This package provides full genome sequences for Drosophila
257 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
258 Biostrings objects.")
259 (license license:artistic2.0)))
261 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
263 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
267 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
268 version 'annotation))
271 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
273 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
274 (build-system r-build-system)
276 (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
277 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
278 (synopsis "Full masked genome sequences for Fly")
280 "This package provides full masked genome sequences for Drosophila
281 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
282 Biostrings objects. The sequences are the same as in
283 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
284 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
285 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
286 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
287 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
288 (license license:artistic2.0)))
290 (define-public r-bsgenome-drerio-ucsc-danrer11
292 (name "r-bsgenome-drerio-ucsc-danrer11")
297 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
298 version 'annotation))
300 (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
301 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
302 (build-system r-build-system)
305 (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
306 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
308 "This package provides full genome sequences for Danio rerio (Zebrafish)
309 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
310 (license license:artistic2.0)))
312 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
314 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
318 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
319 version 'annotation))
322 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
324 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
325 (build-system r-build-system)
329 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
330 (synopsis "Full genome sequences for Homo sapiens")
332 "This package provides full genome sequences for Homo sapiens from
333 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
334 (license license:artistic2.0)))
336 (define-public r-bsgenome-hsapiens-ncbi-grch38
338 (name "r-bsgenome-hsapiens-ncbi-grch38")
343 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
344 version 'annotation))
347 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
348 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
349 (build-system r-build-system)
350 (propagated-inputs (list r-bsgenome))
352 "https://bioconductor.org/packages/release/data/annotation/html/\
353 BSgenome.Hsapiens.NCBI.GRCh38.html")
354 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
356 "This package provides full genome sequences for Homo sapiens (Human) as
357 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
358 (license license:artistic2.0)))
360 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
362 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
367 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
368 version 'annotation))
370 (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
372 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
373 (build-system r-build-system)
375 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
376 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
377 (synopsis "Full masked genome sequences for Homo sapiens")
379 "This package provides full genome sequences for Homo sapiens (Human) as
380 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
381 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
382 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
383 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
384 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
385 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
387 (license license:artistic2.0)))
389 (define-public r-bsgenome-mmusculus-ucsc-mm9
391 (name "r-bsgenome-mmusculus-ucsc-mm9")
395 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
396 version 'annotation))
399 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
401 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
402 (build-system r-build-system)
406 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
407 (synopsis "Full genome sequences for Mouse")
409 "This package provides full genome sequences for Mus musculus (Mouse) as
410 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
411 (license license:artistic2.0)))
413 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
415 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
419 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
420 version 'annotation))
423 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
425 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
426 (build-system r-build-system)
428 (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
429 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
430 (synopsis "Full masked genome sequences for Mouse")
432 "This package provides full genome sequences for Mus musculus (Mouse) as
433 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
434 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
435 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
436 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
437 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
438 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
440 (license license:artistic2.0)))
442 (define-public r-bsgenome-mmusculus-ucsc-mm10
444 (name "r-bsgenome-mmusculus-ucsc-mm10")
448 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
449 version 'annotation))
452 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
454 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
455 (build-system r-build-system)
459 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
460 (synopsis "Full genome sequences for Mouse")
462 "This package provides full genome sequences for Mus
463 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
464 in Biostrings objects.")
465 (license license:artistic2.0)))
467 (define-public r-genomeinfodbdata
469 (name "r-genomeinfodbdata")
473 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
476 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
478 `((upstream-name . "GenomeInfoDbData")))
479 (build-system r-build-system)
480 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
481 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
482 (description "This package contains data for mapping between NCBI taxonomy
483 ID and species. It is used by functions in the GenomeInfoDb package.")
484 (license license:artistic2.0)))
486 (define-public r-go-db
492 (uri (bioconductor-uri "GO.db" version 'annotation))
495 "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
497 `((upstream-name . "GO.db")))
498 (build-system r-build-system)
500 (list r-annotationdbi))
501 (home-page "https://bioconductor.org/packages/GO.db")
502 (synopsis "Annotation maps describing the entire Gene Ontology")
504 "The purpose of this GO.db annotation package is to provide detailed
505 information about the latest version of the Gene Ontologies.")
506 (license license:artistic2.0)))
508 (define-public r-homo-sapiens
510 (name "r-homo-sapiens")
514 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
517 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
519 `((upstream-name . "Homo.sapiens")))
520 (build-system r-build-system)
522 (list r-genomicfeatures
525 r-txdb-hsapiens-ucsc-hg19-knowngene
528 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
529 (synopsis "Annotation package for the Homo.sapiens object")
531 "This package contains the Homo.sapiens object to access data from
532 several related annotation packages.")
533 (license license:artistic2.0)))
535 (define-public r-mus-musculus
537 (name "r-mus-musculus")
542 (uri (bioconductor-uri "Mus.musculus" version 'annotation))
545 "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"))))
546 (properties `((upstream-name . "Mus.musculus")))
547 (build-system r-build-system)
549 (list r-annotationdbi
554 r-txdb-mmusculus-ucsc-mm10-knowngene))
555 (home-page "https://bioconductor.org/packages/Mus.musculus")
556 (synopsis "Annotation package for the Mus.musculus object")
558 "This package contains the @code{Mus.musculus} object to access data
559 from several related annotation packages.")
560 (license license:artistic2.0)))
562 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
564 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
569 (uri (bioconductor-uri
570 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
571 version 'annotation))
574 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
577 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
578 (build-system r-build-system)
579 (propagated-inputs (list r-minfi))
581 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
582 (synopsis "Annotation for Illumina's 450k methylation arrays")
584 "This package provides manifests and annotation for Illumina's 450k array
586 (license license:artistic2.0)))
588 (define-public r-org-ce-eg-db
590 (name "r-org-ce-eg-db")
594 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
597 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
599 `((upstream-name . "org.Ce.eg.db")))
600 (build-system r-build-system)
602 (list r-annotationdbi))
603 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
604 (synopsis "Genome wide annotation for Worm")
606 "This package provides mappings from Entrez gene identifiers to various
607 annotations for the genome of the model worm Caenorhabditis elegans.")
608 (license license:artistic2.0)))
610 (define-public r-org-dm-eg-db
612 (name "r-org-dm-eg-db")
616 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
619 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
621 `((upstream-name . "org.Dm.eg.db")))
622 (build-system r-build-system)
624 (list r-annotationdbi))
625 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
626 (synopsis "Genome wide annotation for Fly")
628 "This package provides mappings from Entrez gene identifiers to various
629 annotations for the genome of the model fruit fly Drosophila melanogaster.")
630 (license license:artistic2.0)))
632 (define-public r-org-dr-eg-db
634 (name "r-org-dr-eg-db")
638 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
641 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
643 `((upstream-name . "org.Dr.eg.db")))
644 (build-system r-build-system)
646 (list r-annotationdbi))
647 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
648 (synopsis "Annotation for Zebrafish")
650 "This package provides genome wide annotations for Zebrafish, primarily
651 based on mapping using Entrez Gene identifiers.")
652 (license license:artistic2.0)))
654 (define-public r-org-hs-eg-db
656 (name "r-org-hs-eg-db")
660 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
663 "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
665 `((upstream-name . "org.Hs.eg.db")))
666 (build-system r-build-system)
668 (list r-annotationdbi))
669 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
670 (synopsis "Genome wide annotation for Human")
672 "This package contains genome-wide annotations for Human, primarily based
673 on mapping using Entrez Gene identifiers.")
674 (license license:artistic2.0)))
676 (define-public r-org-mm-eg-db
678 (name "r-org-mm-eg-db")
682 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
685 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
687 `((upstream-name . "org.Mm.eg.db")))
688 (build-system r-build-system)
690 (list r-annotationdbi))
691 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
692 (synopsis "Genome wide annotation for Mouse")
694 "This package provides mappings from Entrez gene identifiers to various
695 annotations for the genome of the model mouse Mus musculus.")
696 (license license:artistic2.0)))
698 (define-public r-bsgenome-hsapiens-ucsc-hg19
700 (name "r-bsgenome-hsapiens-ucsc-hg19")
704 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
705 version 'annotation))
708 "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
710 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
711 (build-system r-build-system)
715 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
716 (synopsis "Full genome sequences for Homo sapiens")
718 "This package provides full genome sequences for Homo sapiens as provided
719 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
720 (license license:artistic2.0)))
722 (define-public r-bsgenome-hsapiens-ucsc-hg38
724 (name "r-bsgenome-hsapiens-ucsc-hg38")
728 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
729 version 'annotation))
731 (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"))))
733 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
734 (build-system r-build-system)
738 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
739 (synopsis "Full genome sequences for Homo sapiens")
741 "This package provides full genome sequences for Homo sapiens (Human)
742 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
743 (license license:artistic2.0)))
745 (define-public r-ensdb-hsapiens-v75
747 (name "r-ensdb-hsapiens-v75")
752 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
755 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
757 `((upstream-name . "EnsDb.Hsapiens.v75")))
758 (build-system r-build-system)
761 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
762 (synopsis "Ensembl based annotation package")
764 "This package exposes an annotation database generated from Ensembl.")
765 (license license:artistic2.0)))
767 (define-public r-ensdb-hsapiens-v86
769 (name "r-ensdb-hsapiens-v86")
774 (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation))
776 (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"))))
777 (properties `((upstream-name . "EnsDb.Hsapiens.v86")))
778 (build-system r-build-system)
779 (propagated-inputs (list r-ensembldb))
780 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86")
781 (synopsis "Ensembl based annotation package")
782 (description "This package exposes an annotation database generated from
784 (license license:artistic2.0)))
786 (define-public r-ensdb-mmusculus-v79
788 (name "r-ensdb-mmusculus-v79")
793 (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation))
795 (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7"))))
796 (properties `((upstream-name . "EnsDb.Mmusculus.v79")))
797 (build-system r-build-system)
798 (propagated-inputs (list r-ensembldb))
799 (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79")
800 (synopsis "Ensembl based annotation package")
801 (description "This package exposes an annotation database generated from
803 (license license:artistic2.0)))
805 (define-public r-snplocs-hsapiens-dbsnp144-grch37
807 (name "r-snplocs-hsapiens-dbsnp144-grch37")
811 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
812 version 'annotation))
815 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
816 (build-system r-build-system)
817 ;; As this package provides little more than a very large data file it
818 ;; doesn't make sense to build substitutes.
819 (arguments `(#:substitutable? #f))
829 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
830 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
831 (description "This package provides SNP locations and alleles for Homo
832 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
833 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
834 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
835 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
836 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
837 the mitochondrion chromosome. Therefore, the SNPs in this package can be
838 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
839 correct position but this injection will exclude chrM (i.e. nothing will be
840 injected in that sequence).")
841 (license license:artistic2.0)))
843 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
845 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
850 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
851 version 'annotation))
854 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
856 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
857 (build-system r-build-system)
859 (list r-annotationdbi r-genomicfeatures))
861 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
862 (synopsis "Annotation package for TxDb object(s)")
864 "This package exposes an annotation databases generated from UCSC by
865 exposing these as TxDb objects.")
866 (license license:artistic2.0)))
868 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
870 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
874 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
875 version 'annotation))
878 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
880 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
881 (build-system r-build-system)
883 (list r-genomicfeatures))
885 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
886 (synopsis "Annotation package for human genome in TxDb format")
888 "This package provides an annotation database of Homo sapiens genome
889 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
890 track. The database is exposed as a @code{TxDb} object.")
891 (license license:artistic2.0)))
893 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
895 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
899 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
900 version 'annotation))
902 (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879"))))
904 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
905 (build-system r-build-system)
907 (list r-annotationdbi r-genomicfeatures))
909 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
910 (synopsis "Annotation package for human genome in TxDb format")
912 "This package provides an annotation database of Homo sapiens genome
913 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
914 track. The database is exposed as a @code{TxDb} object.")
915 (license license:artistic2.0)))
917 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
919 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
923 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
924 version 'annotation))
927 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
929 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
930 (build-system r-build-system)
932 (list r-genomicfeatures r-annotationdbi))
934 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
935 (synopsis "Annotation package for mouse genome in TxDb format")
937 "This package provides an annotation database of Mouse genome data. It
938 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
939 database is exposed as a @code{TxDb} object.")
940 (license license:artistic2.0)))
942 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
944 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
948 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
949 version 'annotation))
952 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
954 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
955 (build-system r-build-system)
957 (list r-bsgenome r-genomicfeatures r-annotationdbi))
959 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
960 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
962 "This package loads a TxDb object, which is an R interface to
963 prefabricated databases contained in this package. This package provides
964 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
965 based on the knownGene track.")
966 (license license:artistic2.0)))
968 (define-public r-txdb-celegans-ucsc-ce6-ensgene
970 (name "r-txdb-celegans-ucsc-ce6-ensgene")
975 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
976 version 'annotation))
979 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
981 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
982 (build-system r-build-system)
984 (list r-annotationdbi r-genomicfeatures))
985 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
986 (synopsis "Annotation package for C elegans TxDb objects")
988 "This package exposes a C elegans annotation database generated from UCSC
989 by exposing these as TxDb objects.")
990 (license license:artistic2.0)))
992 (define-public r-fdb-infiniummethylation-hg19
994 (name "r-fdb-infiniummethylation-hg19")
998 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
999 version 'annotation))
1002 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
1004 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
1005 (build-system r-build-system)
1007 (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db
1008 r-txdb-hsapiens-ucsc-hg19-knowngene))
1009 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
1010 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
1012 "This is an annotation package for Illumina Infinium DNA methylation
1013 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
1015 (license license:artistic2.0)))
1017 (define-public r-illuminahumanmethylationepicmanifest
1019 (name "r-illuminahumanmethylationepicmanifest")
1023 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
1024 version 'annotation))
1027 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
1029 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
1030 (build-system r-build-system)
1033 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
1034 (synopsis "Manifest for Illumina's EPIC methylation arrays")
1036 "This is a manifest package for Illumina's EPIC methylation arrays.")
1037 (license license:artistic2.0)))
1039 (define-public r-do-db
1045 (uri (bioconductor-uri "DO.db" version 'annotation))
1048 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
1050 `((upstream-name . "DO.db")))
1051 (build-system r-build-system)
1053 (list r-annotationdbi))
1054 (home-page "https://www.bioconductor.org/packages/DO.db/")
1055 (synopsis "Annotation maps describing the entire Disease Ontology")
1057 "This package provides a set of annotation maps describing the entire
1059 (license license:artistic2.0)))
1061 (define-public r-hgu133plus2-db
1063 (name "r-hgu133plus2-db")
1068 (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
1070 (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
1071 (properties `((upstream-name . "hgu133plus2.db")))
1072 (build-system r-build-system)
1073 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
1074 (home-page "https://bioconductor.org/packages/hgu133plus2.db")
1075 (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
1077 "This package provides Affymetrix HG-U133_Plus_2 array annotation
1078 data (chip hgu133plus2) assembled using data from public repositories.")
1079 (license license:artistic2.0)))
1081 (define-public r-pfam-db
1088 (uri (bioconductor-uri "PFAM.db" version 'annotation))
1090 (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7"))))
1091 (properties `((upstream-name . "PFAM.db")))
1092 (build-system r-build-system)
1094 (list r-annotationdbi))
1095 (home-page "https://bioconductor.org/packages/PFAM.db")
1096 (synopsis "Set of protein ID mappings for PFAM")
1098 "This package provides a set of protein ID mappings for PFAM, assembled
1099 using data from public repositories.")
1100 (license license:artistic2.0)))
1102 (define-public r-phastcons100way-ucsc-hg19
1104 (name "r-phastcons100way-ucsc-hg19")
1109 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
1110 version 'annotation))
1113 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
1115 `((upstream-name . "phastCons100way.UCSC.hg19")))
1116 (build-system r-build-system)
1124 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
1125 (synopsis "UCSC phastCons conservation scores for hg19")
1127 "This package provides UCSC phastCons conservation scores for the human
1128 genome (hg19) calculated from multiple alignments with other 99 vertebrate
1130 (license license:artistic2.0)))
1135 (define-public r-abadata
1141 (uri (bioconductor-uri "ABAData" version 'experiment))
1144 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
1146 `((upstream-name . "ABAData")))
1147 (build-system r-build-system)
1149 (list r-annotationdbi))
1150 (home-page "https://www.bioconductor.org/packages/ABAData/")
1151 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
1153 "This package provides the data for the gene expression enrichment
1154 analysis conducted in the package ABAEnrichment. The package includes three
1155 datasets which are derived from the Allen Brain Atlas:
1158 @item Gene expression data from Human Brain (adults) averaged across donors,
1159 @item Gene expression data from the Developing Human Brain pooled into five
1160 age categories and averaged across donors, and
1161 @item a developmental effect score based on the Developing Human Brain
1165 All datasets are restricted to protein coding genes.")
1166 (license license:gpl2+)))
1168 (define-public r-adductdata
1170 (name "r-adductdata")
1174 (uri (bioconductor-uri "adductData" version 'experiment))
1176 (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48"))))
1177 (properties `((upstream-name . "adductData")))
1178 (build-system r-build-system)
1179 (propagated-inputs (list r-annotationhub r-experimenthub))
1180 (native-inputs (list r-knitr))
1181 (home-page "https://bioconductor.org/packages/adductData")
1182 (synopsis "Data from untargeted mass spectrometry of modifications to Cys34")
1184 "This package contains data from untargeted @dfn{mass spectrometry} (MS)
1185 of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
1187 (license license:artistic2.0)))
1189 (define-public r-aneufinderdata
1191 (name "r-aneufinderdata")
1195 (uri (bioconductor-uri "AneuFinderData" version 'experiment))
1197 (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7"))))
1198 (build-system r-build-system)
1199 (home-page "https://bioconductor.org/packages/AneuFinderData/")
1200 (synopsis "Data package for @code{AneuFinder}")
1201 (description "This package contains whole-genome single cell sequencing data for
1202 demonstration purposes in the @code{AneuFinder} package.")
1203 (license license:artistic2.0)))
1205 (define-public r-arrmdata
1211 (uri (bioconductor-uri "ARRmData" version 'experiment))
1213 (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p"))))
1215 `((upstream-name . "ARRmData")))
1216 (build-system r-build-system)
1217 (home-page "https://www.bioconductor.org/packages/ARRmData/")
1218 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
1220 "This package provides raw beta values from 36 samples across 3 groups
1221 from Illumina 450k methylation arrays.")
1222 (license license:artistic2.0)))
1224 (define-public r-bladderbatch
1226 (name "r-bladderbatch")
1230 (uri (bioconductor-uri "bladderbatch" version
1234 "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k"))))
1235 (properties `((upstream-name . "bladderbatch")))
1236 (build-system r-build-system)
1237 (propagated-inputs (list r-biobase))
1238 (home-page "https://bioconductor.org/packages/bladderbatch")
1239 (synopsis "Bladder gene expression data illustrating batch effects")
1241 "This package contains microarray gene expression data on 57 bladder samples from
1242 5 batches. The data are used as an illustrative example for the sva package.")
1243 (license license:artistic2.0)))
1245 (define-public r-biscuiteerdata
1247 (name "r-biscuiteerdata")
1252 (uri (bioconductor-uri "biscuiteerData" version 'experiment))
1254 (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
1256 `((upstream-name . "biscuiteerData")))
1257 (build-system r-build-system)
1259 (list r-annotationhub r-curl r-experimenthub))
1260 (native-inputs (list r-knitr))
1261 (home-page "https://bioconductor.org/packages/biscuiteerData")
1262 (synopsis "Data package for Biscuiteer")
1264 "This package contains default datasets used by the Bioconductor package
1266 (license license:gpl3)))
1268 (define-public r-celldex
1275 (uri (bioconductor-uri "celldex" version 'experiment))
1277 (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
1278 (properties `((upstream-name . "celldex")))
1279 (build-system r-build-system)
1281 (list r-annotationdbi
1284 r-delayedmatrixstats
1287 r-summarizedexperiment))
1288 (native-inputs (list r-knitr))
1289 (home-page "https://github.com/LTLA/celldex")
1290 (synopsis "Reference index for cell types")
1292 "This package provides a collection of reference expression datasets with
1293 curated cell type labels, for use in procedures like automated annotation of
1294 single-cell data or deconvolution of bulk RNA-seq.")
1295 (license license:gpl3)))
1297 (define-public r-chromstardata
1299 (name "r-chromstardata")
1304 (uri (bioconductor-uri "chromstaRData" version 'experiment))
1306 (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
1307 (properties `((upstream-name . "chromstaRData")))
1308 (build-system r-build-system)
1309 (home-page "https://bioconductor.org/packages/chromstaRData/")
1310 (synopsis "ChIP-seq data for demonstration purposes")
1312 "This package provides ChIP-seq data for demonstration purposes in the
1313 chromstaR package.")
1314 (license license:gpl3)))
1316 (define-public r-copyhelper
1318 (name "r-copyhelper")
1323 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
1325 (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
1326 (properties `((upstream-name . "CopyhelpeR")))
1327 (build-system r-build-system)
1328 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
1329 (synopsis "Helper files for CopywriteR")
1331 "This package contains the helper files that are required to run the
1332 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
1333 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
1334 mm10. In addition, it contains a blacklist filter to remove regions that
1335 display copy number variation. Files are stored as GRanges objects from the
1336 GenomicRanges Bioconductor package.")
1337 (license license:gpl2)))
1339 (define-public r-genelendatabase
1341 (name "r-genelendatabase")
1346 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
1348 (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
1350 `((upstream-name . "geneLenDataBase")))
1351 (build-system r-build-system)
1353 (list r-rtracklayer r-genomicfeatures))
1354 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
1355 (synopsis "Lengths of mRNA transcripts for a number of genomes")
1357 "This package provides the lengths of mRNA transcripts for a number of
1358 genomes and gene ID formats, largely based on the UCSC table browser.")
1359 (license license:lgpl2.0+)))
1361 (define-public r-genomationdata
1363 (name "r-genomationdata")
1368 (uri (bioconductor-uri "genomationData" version 'experiment))
1370 (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
1372 `((upstream-name . "genomationData")))
1373 (build-system r-build-system)
1374 ;; As this package provides little more than large data files, it doesn't
1375 ;; make sense to build substitutes.
1376 (arguments `(#:substitutable? #f))
1379 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
1380 (synopsis "Experimental data for use with the genomation package")
1382 "This package contains experimental genetic data for use with the
1383 genomation package. Included are Chip Seq, Methylation and Cage data,
1384 downloaded from Encode.")
1385 (license license:gpl3+)))
1387 (define-public r-macrophage
1389 (name "r-macrophage")
1393 (uri (bioconductor-uri "macrophage" version
1397 "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms"))))
1398 (properties `((upstream-name . "macrophage")))
1399 (build-system r-build-system)
1400 (native-inputs (list r-knitr))
1401 (home-page "https://bioconductor.org/packages/macrophage")
1402 (synopsis "Human macrophage immune response data")
1404 "This package provides the output of running @code{Salmon} on a set of 24
1405 RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and
1406 gene expression indicate a role for enhancer priming in immune response\", published
1407 in Nature Genetics, January 2018.")
1408 (license license:gpl2+)))
1410 (define-public r-msdata
1417 (uri (bioconductor-uri "msdata" version 'experiment))
1419 (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
1420 (properties `((upstream-name . "msdata")))
1421 (build-system r-build-system)
1422 (home-page "https://bioconductor.org/packages/msdata")
1423 (synopsis "Various Mass Spectrometry raw data example files")
1425 "This package provides Ion Trap positive ionization mode data in mzML file
1426 format. It includes a subset from 500-850 m/z and 1190-1310 seconds,
1427 including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
1428 III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
1429 LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
1430 files for various search engines.")
1431 (license license:gpl2+)))
1433 (define-public r-pasilla
1440 (uri (bioconductor-uri "pasilla" version 'experiment))
1442 (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
1443 (build-system r-build-system)
1444 (propagated-inputs (list r-dexseq))
1445 (native-inputs (list r-knitr))
1446 (home-page "https://www.bioconductor.org/packages/pasilla/")
1447 (synopsis "Data package with per-exon and per-gene read counts")
1448 (description "This package provides per-exon and per-gene read counts
1449 computed for selected genes from RNA-seq data that were presented in the
1450 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1451 by Brooks et al., Genome Research 2011.")
1452 (license license:lgpl2.1+)))
1454 (define-public r-hsmmsinglecell
1456 (name "r-hsmmsinglecell")
1461 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1463 (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
1465 `((upstream-name . "HSMMSingleCell")))
1466 (build-system r-build-system)
1467 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1468 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1470 "Skeletal myoblasts undergo a well-characterized sequence of
1471 morphological and transcriptional changes during differentiation. In this
1472 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1473 under high mitogen conditions (GM) and then differentiated by switching to
1474 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1475 hundred cells taken over a time-course of serum-induced differentiation.
1476 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1477 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1478 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1479 which were then sequenced to a depth of ~4 million reads per library,
1480 resulting in a complete gene expression profile for each cell.")
1481 (license license:artistic2.0)))
1483 (define-public r-all
1490 (uri (bioconductor-uri "ALL" version 'experiment))
1492 (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
1493 (properties `((upstream-name . "ALL")))
1494 (build-system r-build-system)
1497 (home-page "https://bioconductor.org/packages/ALL")
1498 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1500 "The data consist of microarrays from 128 different individuals with
1501 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1502 are available. The data have been normalized (using rma) and it is the
1503 jointly normalized data that are available here. The data are presented in
1504 the form of an @code{exprSet} object.")
1505 (license license:artistic2.0)))
1507 (define-public r-affydata
1514 (uri (bioconductor-uri "affydata" version 'experiment))
1516 (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
1517 (properties `((upstream-name . "affydata")))
1518 (build-system r-build-system)
1521 (home-page "https://bioconductor.org/packages/affydata/")
1522 (synopsis "Affymetrix data for demonstration purposes")
1524 "This package provides example datasets that represent 'real world
1525 examples' of Affymetrix data, unlike the artificial examples included in the
1526 package @code{affy}.")
1527 (license license:gpl2+)))
1529 (define-public r-gagedata
1536 (uri (bioconductor-uri "gageData" version 'experiment))
1538 (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
1539 (properties `((upstream-name . "gageData")))
1540 (build-system r-build-system)
1541 (home-page "https://bioconductor.org/packages/gageData")
1542 (synopsis "Auxiliary data for the gage package")
1544 "This is a supportive data package for the software package @code{gage}.
1545 However, the data supplied here are also useful for gene set or pathway
1546 analysis or microarray data analysis in general. In this package, we provide
1547 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1548 BMP6 (originally published as an demo dataset for GAGE, also registered as
1549 GSE13604 in GEO). This package also includes commonly used gene set data based
1550 on KEGG pathways and GO terms for major research species, including human,
1551 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1552 yeast are also included.")
1553 (license license:gpl2+)))
1555 (define-public r-curatedtcgadata
1557 (name "r-curatedtcgadata")
1562 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1564 (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
1566 `((upstream-name . "curatedTCGAData")))
1567 (build-system r-build-system)
1569 (list r-annotationhub
1572 r-multiassayexperiment
1574 r-summarizedexperiment))
1575 (native-inputs (list r-knitr))
1576 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1577 (synopsis "Curated data from The Cancer Genome Atlas")
1579 "This package provides publicly available data from The Cancer Genome
1580 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1581 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1582 number, mutation, microRNA, protein, and others) with clinical / pathological
1583 data. It also links assay barcodes with patient identifiers, enabling
1584 harmonized subsetting of rows (features) and columns (patients / samples)
1585 across the entire multi-'omics experiment.")
1586 (license license:artistic2.0)))
1588 (define-public r-parathyroidse
1590 (name "r-parathyroidse")
1594 (uri (bioconductor-uri "parathyroidSE" version
1598 "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16"))))
1599 (properties `((upstream-name . "parathyroidSE")))
1600 (build-system r-build-system)
1601 (propagated-inputs (list r-summarizedexperiment))
1602 (home-page "https://bioconductor.org/packages/parathyroidSE")
1603 (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors")
1605 "This package provides @code{RangedSummarizedExperiment} objects of read
1606 counts in genes and exonic parts for paired-end RNA-Seq data from experiments on
1607 primary cultures of parathyroid tumors. The sequencing was performed on tumor
1608 cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).")
1609 ;; The author(s) mentions only LGPL without any specific version.
1610 (license license:lgpl2.1+)))
1612 (define-public r-tcgabiolinksgui-data
1614 (name "r-tcgabiolinksgui-data")
1619 (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
1621 (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
1622 (properties `((upstream-name . "TCGAbiolinksGUI.data")))
1623 (build-system r-build-system)
1624 (native-inputs (list r-knitr))
1625 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
1626 (synopsis "Data for the TCGAbiolinksGUI package")
1627 (description "This package provides supporting data for the
1628 TCGAbiolinksGUI package.")
1629 (license license:gpl3)))
1631 (define-public r-tximportdata
1633 (name "r-tximportdata")
1637 (uri (bioconductor-uri "tximportData" version
1641 "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy"))))
1642 (properties `((upstream-name . "tximportData")))
1643 (build-system r-build-system)
1644 (native-inputs (list r-knitr))
1645 (home-page "https://bioconductor.org/packages/tximportData")
1646 (synopsis "Data for the tximport package")
1648 "This package provides the output of running various transcript abundance
1649 quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The
1650 quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon}
1651 and @code{Sailfish}. Alevin example output is also included.")
1652 (license license:gpl2+)))
1658 (define-public r-abarray
1664 (uri (bioconductor-uri "ABarray" version))
1667 "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
1668 (properties `((upstream-name . "ABarray")))
1669 (build-system r-build-system)
1670 (propagated-inputs (list r-biobase r-multtest))
1671 (home-page "https://bioconductor.org/packages/ABarray")
1673 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
1675 "The package @code{ABarray} is designed to work with Applied Biosystems
1676 whole genome microarray platform, as well as any other platform whose data can
1677 be transformed into expression data matrix. Functions include data
1678 preprocessing, filtering, control probe analysis, statistical analysis in one
1679 single function. A @dfn{graphical user interface} (GUI) is also provided. The
1680 raw data, processed data, graphics output and statistical results are organized
1681 into folders according to the analysis settings used.")
1682 (license license:gpl2+)))
1684 (define-public r-absseq
1690 (uri (bioconductor-uri "ABSSeq" version))
1693 "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
1694 (properties `((upstream-name . "ABSSeq")))
1695 (build-system r-build-system)
1696 (propagated-inputs (list r-limma r-locfit))
1697 (home-page "https://bioconductor.org/packages/ABSSeq")
1699 "RNA-Seq analysis based on modelling absolute expression differences")
1701 "This package implements a new RNA-Seq analysis method and integrates two
1702 modules: a basic model for pairwise comparison and a linear model for complex
1703 design. RNA-Seq quantifies gene expression with reads count, which usually
1704 consists of conditions (or treatments) and several replicates for each
1705 condition. This software infers differential expression directly by the
1706 counts difference between conditions. It assumes that the sum counts
1707 difference between conditions follow a negative binomial distribution. In
1708 addition, @code{ABSSeq} moderates the fold-changes by two steps: the
1709 expression level and gene-specific dispersion, that might facilitate the gene
1710 ranking by fold-change and visualization.")
1711 (license license:gpl3+)))
1713 (define-public r-adam
1719 (uri (bioconductor-uri "ADAM" version))
1722 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
1723 (properties `((upstream-name . "ADAM")))
1724 (build-system r-build-system)
1725 (propagated-inputs (list r-dplyr
1733 r-summarizedexperiment))
1734 (native-inputs (list r-knitr))
1735 (home-page "https://bioconductor.org/packages/ADAM")
1736 (synopsis "Gene activity and diversity analysis module")
1738 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
1739 package created to group a set of genes from comparative samples (control
1740 versus experiment) belonging to different species according to their respective
1741 functions. The corresponding roles are extracted from the default collections
1742 like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
1743 @code{ADAM} show their significance by calculating the p-values referring to
1744 gene diversity and activity. Each group of genes is called @dfn{Group of
1745 functionally associated genes} (GFAG).")
1746 (license license:gpl2+)))
1748 (define-public r-adamgui
1754 (uri (bioconductor-uri "ADAMgui" version))
1757 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
1758 (properties `((upstream-name . "ADAMgui")))
1759 (build-system r-build-system)
1781 (native-inputs (list r-knitr))
1782 (home-page "https://bioconductor.org/packages/ADAMgui/")
1783 (synopsis "GUI for gene activity and diversity analysis")
1785 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
1786 for the @code{ADAM} package. The @code{ADAMgui} package provides two
1787 shiny-based applications that allows the user to study the output of the
1788 @code{ADAM} package files through different plots. It's possible, for
1789 example, to choose a specific @dfn{group of functionally associated
1790 genes} (GFAG) and observe the gene expression behavior with the plots created
1791 with the @code{GFAGtargetUi} function. Features such as differential
1792 expression and fold change can be easily seen with aid of the plots made with
1793 the @code{GFAGpathUi} function.")
1794 (license license:gpl2+)))
1796 (define-public r-adimpute
1802 (uri (bioconductor-uri "ADImpute" version))
1805 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
1806 (properties `((upstream-name . "ADImpute")))
1807 (build-system r-build-system)
1809 (list r-biocparallel
1819 r-singlecellexperiment
1820 r-summarizedexperiment))
1821 (native-inputs (list r-knitr))
1822 (home-page "https://bioconductor.org/packages/ADImpute")
1823 (synopsis "Adaptive computational prediction for dropout imputations")
1825 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
1826 unable to quantify the expression levels of all genes in a cell, creating a
1827 need for the computational prediction of missing values (dropout imputation).
1828 Most existing dropout imputation methods are limited in the sense that they
1829 exclusively use the scRNA-seq dataset at hand and do not exploit external
1830 gene-gene relationship information. The @code{ADImpute} package proposes two
1831 methods to address this issue:
1834 @item a gene regulatory network-based approach using gene-gene relationships
1835 learnt from external data;
1836 @item a baseline approach corresponding to a sample-wide average.
1839 @code{ADImpute} implements these novel methods and also combines them with
1840 existing imputation methods like @code{DrImpute} and @code{SAVER}.
1841 @code{ADImpute} can learn the best performing method per gene and combine the
1842 results from different methods into an ensemble.")
1843 (license license:gpl3+)))
1845 (define-public r-adsplit
1851 (uri (bioconductor-uri "adSplit" version))
1854 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
1855 (properties `((upstream-name . "adSplit")))
1856 (build-system r-build-system)
1858 (list r-annotationdbi
1864 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
1865 (synopsis "Annotation-driven splits in microarray data")
1867 "This package implements clustering of microarray gene expression
1868 profiles according to functional annotations. For each term genes are
1869 annotated to, splits into two subclasses are computed and a significance of
1870 the supporting gene set is determined.")
1871 (license license:gpl2+)))
1873 (define-public r-affixcan
1879 (uri (bioconductor-uri "AffiXcan" version))
1882 "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
1883 (properties `((upstream-name . "AffiXcan")))
1884 (build-system r-build-system)
1886 (list r-biocparallel
1888 r-multiassayexperiment
1889 r-summarizedexperiment))
1890 (native-inputs (list r-knitr))
1891 (home-page "https://bioconductor.org/packages/AffiXcan")
1892 (synopsis "Functional approach to impute genetically regulated expression")
1894 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
1895 expression} (GReX) for a set of genes in a sample of individuals, using a
1896 method based on the @dfn{total binding affinity} (TBA). Statistical models to
1897 impute GReX can be trained with a training dataset where the real total
1898 expression values are known.")
1899 (license license:gpl3)))
1901 (define-public r-affyrnadegradation
1903 (name "r-affyrnadegradation")
1907 (uri (bioconductor-uri "AffyRNADegradation" version))
1910 "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
1911 (properties `((upstream-name . "AffyRNADegradation")))
1912 (build-system r-build-system)
1913 (propagated-inputs (list r-affy))
1914 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
1916 "Analyze and correct probe positional bias in data due to RNA degradation")
1918 "The @code{AffyRNADegradation} package helps with the assessment and
1919 correction of RNA degradation effects in Affymetrix 3 expression arrays. The
1920 parameter @code{d} gives a robust and accurate measure of RNA integrity. The
1921 correction removes the probe positional bias, and thus improves comparability
1922 of samples that are affected by RNA degradation.")
1923 ;; the R file header specifies GPL2 or later
1924 (license license:gpl2+)))
1926 (define-public r-agdex
1932 (uri (bioconductor-uri "AGDEX" version))
1935 "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
1936 (properties `((upstream-name . "AGDEX")))
1937 (build-system r-build-system)
1938 (propagated-inputs (list r-biobase r-gseabase))
1939 (home-page "https://bioconductor.org/packages/AGDEX")
1941 "Evaluate agreement of differential expression for cross-species genomics")
1943 "The objective of @code{AGDEX} is to evaluate whether the results of a
1944 pair of two-group differential expression analysis comparisons show a level of
1945 agreement that is greater than expected if the group labels for each two-group
1946 comparison are randomly assigned. The agreement is evaluated for the entire
1947 transcriptome and (optionally) for a collection of pre-defined gene-sets.
1948 Additionally, the procedure performs permutation-based differential expression
1949 and meta analysis at both gene and gene-set levels of the data from each
1951 (license license:gpl2+)))
1953 (define-public r-aggregatebiovar
1955 (name "r-aggregatebiovar")
1959 (uri (bioconductor-uri "aggregateBioVar" version))
1962 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
1963 (properties `((upstream-name . "aggregateBioVar")))
1964 (build-system r-build-system)
1969 r-singlecellexperiment
1970 r-summarizedexperiment
1972 (native-inputs (list r-knitr))
1973 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
1974 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
1976 "This package @code{aggregateBioVar} contains tools to summarize single
1977 cell gene expression profiles at the level of subject for single cell RNA-seq
1978 data collected from more than one subject (e.g. biological sample or technical
1979 replicates). A @code{SingleCellExperiment} object is taken as input and
1980 converted to a list of @code{SummarizedExperiment} objects, where each list
1981 element corresponds to an assigned cell type. The @code{SummarizedExperiment}
1982 objects contain aggregate gene-by-subject count matrices and inter-subject
1983 column metadata for individual subjects that can be processed using downstream
1984 bulk RNA-seq tools.")
1985 (license license:gpl3)))
1987 (define-public r-agilp
1993 (uri (bioconductor-uri "agilp" version))
1996 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
1997 (properties `((upstream-name . "agilp")))
1998 (build-system r-build-system)
1999 (home-page "https://bioconductor.org/packages/agilp")
2000 (synopsis "Processing of Agilent expression array")
2002 "This package aims to provide a pipeline for the low-level analysis of
2003 gene expression microarray data, primarily focused on the Agilent platform,
2004 but which also provides utilities which may be useful for other platforms.")
2005 ;; Some files are under GPLv2+ but the combined work is released under the
2007 (license license:gpl3)))
2009 (define-public r-adductomicsr
2011 (name "r-adductomicsr")
2015 (uri (bioconductor-uri "adductomicsR" version))
2018 "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
2019 (properties `((upstream-name . "adductomicsR")))
2020 (build-system r-build-system)
2043 (native-inputs (list r-knitr))
2044 (home-page "https://bioconductor.org/packages/adductomicsR")
2045 (synopsis "Processing of adductomic mass spectral datasets")
2047 "This package @code{adductomicsR} processes data generated by the
2048 @dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
2049 peptides from spectra that has been corrected for mass drift and retention
2050 time drift and quantifies level mass spectral peaks from @dfn{first stage of
2051 mass spectrometry} (MS1) data.")
2052 (license license:artistic2.0)))
2054 (define-public r-agimicrorna
2056 (name "r-agimicrorna")
2060 (uri (bioconductor-uri "AgiMicroRna" version))
2063 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
2064 (properties `((upstream-name . "AgiMicroRna")))
2065 (build-system r-build-system)
2072 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
2074 "Processing and differential expression analysis of Agilent microRNA chips")
2076 "@code{AgiMicroRna} provides useful functionality for the processing,
2077 quality assessment and differential expression analysis of Agilent microRNA
2078 array data. The package uses a limma-like structure to generate the processed
2079 data in order to make statistical inferences about differential expression
2080 using the linear model features implemented in limma. Standard Bioconductor
2081 objects are used so that other packages could be used as well.")
2082 (license license:gpl3)))
2084 (define-public r-amountain
2086 (name "r-amountain")
2090 (uri (bioconductor-uri "AMOUNTAIN" version))
2093 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
2094 (properties `((upstream-name . "AMOUNTAIN")))
2095 (build-system r-build-system)
2097 (native-inputs (list r-knitr))
2098 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
2099 (synopsis "Modules for multilayer weighted gene co-expression networks")
2101 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
2102 gene co-expression network) could be constructed only from expression profile.
2103 Different layers in such networks may represent different time points, multiple
2104 conditions or various species. @code{AMOUNTAIN} aims to search active modules
2105 in multi-layer WGCN using a continuous optimization approach.")
2106 (license license:gpl2+)))
2108 (define-public r-amaretto
2114 (uri (bioconductor-uri "AMARETTO" version))
2117 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
2118 (properties `((upstream-name . "AMARETTO")))
2119 (build-system r-build-system)
2121 (list r-biocfilecache
2139 r-multiassayexperiment
2145 (native-inputs (list r-knitr))
2146 (home-page "https://bioconductor.org/packages/AMARETTO")
2147 (synopsis "Regulatory network inference and driver gene evaluation")
2149 "This package @code{AMARETTO} represents an algorithm that integrates copy
2150 number, DNA methylation and gene expression data to identify a set of driver
2151 genes by analyzing cancer samples and connects them to clusters of co-expressed
2152 genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
2153 setting to identify cancer driver genes and their modules on multiple cancer
2154 sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
2155 and EMT, and modules that accurately predict survival and molecular subtypes.
2156 This allows @code{AMARETTO} to identify novel cancer driver genes directing
2157 canonical cancer pathways.")
2158 (license license:asl2.0)))
2160 (define-public r-anaquin
2166 (uri (bioconductor-uri "Anaquin" version))
2169 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
2170 (properties `((upstream-name . "Anaquin")))
2171 (build-system r-build-system)
2180 (native-inputs (list r-knitr))
2181 (home-page "https://www.sequinstandards.com/")
2182 (synopsis "Statistical analysis of sequins")
2184 "The project is intended to support the use of @dfn{sequins}(synthetic
2185 sequencing spike-in controls) owned and made available by the Garvan Institute
2186 of Medical Research. The goal is to provide a standard library for quantitative
2187 analysis, modelling, and visualization of spike-in controls.")
2188 (license license:bsd-3)))
2190 (define-public r-aneufinder
2192 (name "r-aneufinder")
2196 (uri (bioconductor-uri "AneuFinder" version))
2199 "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
2200 (build-system r-build-system)
2204 (list r-genomicranges
2225 (home-page "https://bioconductor.org/packages/AneuFinder/")
2226 (synopsis "Copy number variation analysis in single-cell-sequencing data")
2227 (description "This package implements functions for copy number variant
2228 calling, plotting, export and analysis from whole-genome single cell
2230 (license license:artistic2.0)))
2232 (define-public r-anf
2238 (uri (bioconductor-uri "ANF" version))
2241 "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
2242 (properties `((upstream-name . "ANF")))
2243 (build-system r-build-system)
2250 (native-inputs (list r-knitr))
2251 (home-page "https://bioconductor.org/packages/ANF")
2252 (synopsis "Affinity network fusion for complex patient clustering")
2254 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
2255 matrix construction and fusion as well as spectral clustering. This package is
2256 used for complex patient clustering by integrating multi-omic data through affinity
2258 (license license:gpl3)))
2260 (define-public r-annmap
2266 (uri (bioconductor-uri "annmap" version))
2269 "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
2270 (properties `((upstream-name . "annmap")))
2271 (build-system r-build-system)
2283 (home-page "https://github.com/cruk-mi/annmap")
2285 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
2287 "This package @code{annmap} provides annotation mappings for Affymetrix exon
2288 arrays and coordinate based queries to support deep sequencing data analysis.
2289 Database access is hidden behind the API which provides a set of functions such
2290 as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
2291 Functions to plot gene architecture and BAM file data are also provided.")
2292 (license license:gpl2)))
2294 (define-public r-antiprofiles
2296 (name "r-antiprofiles")
2300 (uri (bioconductor-uri "antiProfiles" version))
2303 "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
2304 (properties `((upstream-name . "antiProfiles")))
2305 (build-system r-build-system)
2309 (home-page "https://github.com/HCBravoLab/antiProfiles")
2310 (synopsis "Implementation of gene expression anti-profiles")
2312 "This package implements the gene expression anti-profiles method.
2313 Anti-profiles are a new approach for developing cancer genomic signatures that
2314 specifically take advantage of gene expression heterogeneity. They explicitly
2315 model increased gene expression variability in cancer to define robust and
2316 reproducible gene expression signatures capable of accurately distinguishing
2317 tumor samples from healthy controls.")
2318 (license license:artistic2.0)))
2320 (define-public r-atsnp
2326 (uri (bioconductor-uri "atSNP" version))
2329 "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz"))))
2330 (properties `((upstream-name . "atSNP")))
2331 (build-system r-build-system)
2333 (list r-biocfilecache
2343 (native-inputs (list r-knitr))
2344 (home-page "https://github.com/sunyoungshin/atSNP")
2346 "Affinity test for identifying regulatory single nucleotide polymorphisms")
2348 "The atSNP package performs affinity tests of motif matches with the
2349 @dfn{SNP} (single nucleotide polymorphism) or the reference genomes and
2350 SNP-led changes in motif matches.")
2351 (license license:gpl2)))
2353 (define-public r-attract
2359 (uri (bioconductor-uri "attract" version))
2362 "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82"))))
2363 (properties `((upstream-name . "attract")))
2364 (build-system r-build-system)
2366 (list r-annotationdbi
2374 (home-page "https://bioconductor.org/packages/attract")
2375 (synopsis "Finding drivers of Kauffman's attractor landscape")
2377 "This package contains the functions to find the gene expression modules
2378 that represent the drivers of Kauffman's attractor landscape. The modules are
2379 the core attractor pathways that discriminate between different cell types of
2380 groups of interest. Each pathway has a set of synexpression groups, which show
2381 transcriptionally-coordinated changes in gene expression.")
2382 (license license:lgpl2.0+)))
2384 (define-public r-awfisher
2390 (uri (bioconductor-uri "AWFisher" version))
2393 "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1"))))
2394 (properties `((upstream-name . "AWFisher")))
2395 (build-system r-build-system)
2399 (native-inputs (list r-knitr))
2400 (home-page "https://bioconductor.org/packages/AWFisher")
2401 (synopsis "Fast computing for adaptively weighted fisher's method")
2403 "This package is an implementation of the Adaptively Weighted Fisher's
2404 method, including fast p-value computing, variability index, and
2406 (license license:gpl3)))
2408 (define-public r-awst
2414 (uri (bioconductor-uri "awst" version))
2417 "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav"))))
2418 (properties `((upstream-name . "awst")))
2419 (build-system r-build-system)
2420 (propagated-inputs (list r-summarizedexperiment))
2421 (native-inputs (list r-knitr))
2422 (home-page "https://github.com/drisso/awst")
2423 (synopsis "Asymmetric within-sample transformation")
2425 "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that
2426 regularizes RNA-seq read counts and reduces the effect of noise on the
2427 classification of samples. AWST comprises two main steps: standardization and
2428 smoothing. These steps transform gene expression data to reduce the noise of
2429 the lowly expressed features, which suffer from background effects and low
2430 signal-to-noise ratio, and the influence of the highly expressed features,
2431 which may be the result of amplification bias and other experimental
2433 (license license:expat)))
2435 (define-public r-baalchip
2441 (uri (bioconductor-uri "BaalChIP" version))
2444 "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
2445 (properties `((upstream-name . "BaalChIP")))
2446 (build-system r-build-system)
2447 (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
2461 (native-inputs (list r-knitr))
2462 (home-page "https://bioconductor.org/packages/BaalChIP")
2464 "Analysis of allele-specific transcription factor binding in cancer genomes")
2466 "This package offers functions to process multiple @code{ChIP-seq BAM}
2467 files and detect allele-specific events. It computes allele counts at
2468 individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
2469 control) steps to remove problematic variants, and utilizes a Bayesian
2470 framework to identify statistically significant allele-specific events.
2471 BaalChIP is able to account for copy number differences between the two
2472 alleles, a known phenotypical feature of cancer samples.")
2473 (license license:artistic2.0)))
2475 (define-public r-basespacer
2477 (name "r-basespacer")
2481 (uri (bioconductor-uri "BaseSpaceR" version))
2484 "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj"))))
2485 (properties `((upstream-name . "BaseSpaceR")))
2486 (build-system r-build-system)
2487 (propagated-inputs (list r-rcurl r-rjsonio))
2488 (home-page "https://bioconductor.org/packages/BaseSpaceR")
2489 (synopsis "R SDK for BaseSpace RESTful API")
2491 "This package provides an R interface to Illumina's BaseSpace cloud
2492 computing environment, enabling the fast development of data analysis and
2493 visualization tools. Besides providing an easy to use set of tools for
2494 manipulating the data from BaseSpace, it also facilitates the access to R's
2495 rich environment of statistical and data analysis tools.")
2496 (license license:asl2.0)))
2498 (define-public r-bac
2504 (uri (bioconductor-uri "BAC" version))
2507 "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2"))))
2508 (properties `((upstream-name . "BAC")))
2509 (build-system r-build-system)
2510 (home-page "https://bioconductor.org/packages/BAC")
2511 (synopsis "Bayesian analysis of Chip-chip experiment")
2513 "This package uses a Bayesian hierarchical model to detect enriched
2514 regions from ChIP-chip experiments. The common goal in analyzing this
2515 ChIP-chip data is to detect DNA-protein interactions from ChIP-chip
2516 experiments. The BAC package has mainly been tested with Affymetrix tiling
2517 array data. However, we expect it to work with other platforms (e.g. Agilent,
2518 Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so
2519 you will have to normalize your data beforehand.")
2520 (license license:artistic2.0)))
2522 (define-public r-bader
2528 (uri (bioconductor-uri "BADER" version))
2531 "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm"))))
2532 (properties `((upstream-name . "BADER")))
2533 (build-system r-build-system)
2534 (home-page "https://bioconductor.org/packages/BADER")
2536 "Bayesian analysis of differential expression in RNA sequencing data")
2538 "The BADER package is intended for the analysis of RNA sequencing data.
2539 The algorithm fits a Bayesian hierarchical model for RNA sequencing count
2540 data. BADER returns the posterior probability of differential expression for
2541 each gene between two groups A and B. The joint posterior distribution of the
2542 variables in the model can be returned in the form of posterior samples, which
2543 can be used for further down-stream analyses such as gene set enrichment.")
2544 (license license:gpl2)))
2546 (define-public r-badregionfinder
2548 (name "r-badregionfinder")
2552 (uri (bioconductor-uri "BadRegionFinder" version))
2555 "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9"))))
2556 (properties `((upstream-name . "BadRegionFinder")))
2557 (build-system r-build-system)
2563 r-variantannotation))
2564 (home-page "https://bioconductor.org/packages/BadRegionFinder")
2565 (synopsis "Identifying regions with bad coverage in sequence alignment data")
2567 "BadRegionFinder is a package for identifying regions with a bad,
2568 acceptable and good coverage in sequence alignment data available as bam
2569 files. The whole genome may be considered as well as a set of target regions.
2570 Various visual and textual types of output are available.")
2571 (license license:lgpl3)))
2573 (define-public r-bambu
2579 (uri (bioconductor-uri "bambu" version))
2582 "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w"))))
2583 (properties `((upstream-name . "bambu")))
2584 (build-system r-build-system)
2586 (list r-biocgenerics
2600 r-summarizedexperiment
2603 (native-inputs (list r-knitr))
2604 (home-page "https://github.com/GoekeLab/bambu")
2606 "Isoform reconstruction and quantification for long read RNA-Seq data")
2608 "This R package is for multi-sample transcript discovery and
2609 quantification using long read RNA-Seq data. You can use bambu after read
2610 alignment to obtain expression estimates for known and novel transcripts and
2611 genes. The output from bambu can directly be used for visualisation and
2612 downstream analysis, such as differential gene expression or transcript
2614 (license license:gpl3)))
2616 (define-public r-bandits
2622 (uri (bioconductor-uri "BANDITS" version))
2625 "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9"))))
2626 (properties `((upstream-name . "BANDITS")))
2627 (build-system r-build-system)
2629 (list r-biocparallel
2640 (native-inputs (list r-knitr))
2641 (home-page "https://github.com/SimoneTiberi/BANDITS")
2642 (synopsis "Bayesian analysis of differential splicing")
2644 "BANDITS is a Bayesian hierarchical model for detecting differential
2645 splicing of genes and transcripts, via @dfn{DTU} (differential transcript
2646 usage), between two or more conditions. The method uses a Bayesian
2647 hierarchical framework, which allows for sample specific proportions in a
2648 Dirichlet-Multinomial model, and samples the allocation of fragments to the
2649 transcripts. Parameters are inferred via @dfn{MCMC} (Markov chain Monte
2650 Carlo) techniques and a DTU test is performed via a multivariate Wald test on
2651 the posterior densities for the average relative abundance of transcripts.")
2652 (license license:gpl3+)))
2654 (define-public r-banocc
2660 (uri (bioconductor-uri "banocc" version))
2663 "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx"))))
2664 (properties `((upstream-name . "banocc")))
2665 (build-system r-build-system)
2671 (native-inputs (list r-knitr))
2672 (home-page "https://bioconductor.org/packages/banocc")
2673 (synopsis "Bayesian analysis of compositional covariance")
2675 "BAnOCC is a package designed for compositional data, where each sample
2676 sums to one. It infers the approximate covariance of the unconstrained data
2677 using a Bayesian model coded with @code{rstan}. It provides as output the
2678 @code{stanfit} object as well as posterior median and credible interval
2679 estimates for each correlation element.")
2680 (license license:expat)))
2682 (define-public r-barcodetrackr
2684 (name "r-barcodetrackr")
2688 (uri (bioconductor-uri "barcodetrackR" version))
2691 "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3"))))
2692 (properties `((upstream-name . "barcodetrackR")))
2693 (build-system r-build-system)
2709 r-summarizedexperiment
2714 (native-inputs (list r-knitr))
2715 (home-page "https://github.com/dunbarlabNIH/barcodetrackR")
2716 (synopsis "Functions for analyzing cellular barcoding data")
2718 "This package is developed for the analysis and visualization of clonal
2719 tracking data. The required data is formed by samples and tag abundances in
2720 matrix form, usually from cellular barcoding experiments, integration site
2721 retrieval analyses, or similar technologies.")
2722 (license license:cc0)))
2724 (define-public r-biocversion
2726 (name "r-biocversion")
2731 (uri (bioconductor-uri "BiocVersion" version))
2734 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
2735 (properties `((upstream-name . "BiocVersion")))
2736 (build-system r-build-system)
2737 (home-page "https://bioconductor.org/packages/BiocVersion/")
2738 (synopsis "Set the appropriate version of Bioconductor packages")
2740 "This package provides repository information for the appropriate version
2742 (license license:artistic2.0)))
2744 (define-public r-biocgenerics
2746 (name "r-biocgenerics")
2750 (uri (bioconductor-uri "BiocGenerics" version))
2753 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
2755 `((upstream-name . "BiocGenerics")))
2756 (build-system r-build-system)
2757 (home-page "https://bioconductor.org/packages/BiocGenerics")
2758 (synopsis "S4 generic functions for Bioconductor")
2760 "This package provides S4 generic functions needed by many Bioconductor
2762 (license license:artistic2.0)))
2764 (define-public r-coverageview
2766 (name "r-coverageview")
2770 (uri (bioconductor-uri "CoverageView" version))
2773 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
2774 (build-system r-build-system)
2782 (home-page "https://bioconductor.org/packages/CoverageView/")
2783 (synopsis "Coverage visualization package for R")
2784 (description "This package provides a framework for the visualization of
2785 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
2786 be also used for genome-wide nucleosome positioning experiments or other
2787 experiment types where it is important to have a framework in order to inspect
2788 how the coverage distributed across the genome.")
2789 (license license:artistic2.0)))
2791 (define-public r-cummerbund
2793 (name "r-cummerbund")
2797 (uri (bioconductor-uri "cummeRbund" version))
2800 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
2801 (build-system r-build-system)
2813 (home-page "https://bioconductor.org/packages/cummeRbund/")
2814 (synopsis "Analyze Cufflinks high-throughput sequencing data")
2815 (description "This package allows for persistent storage, access,
2816 exploration, and manipulation of Cufflinks high-throughput sequencing
2817 data. In addition, provides numerous plotting functions for commonly
2818 used visualizations.")
2819 (license license:artistic2.0)))
2821 (define-public r-dearseq
2828 (uri (bioconductor-uri "dearseq" version))
2831 "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl"))))
2832 (build-system r-build-system)
2834 (list r-compquadform
2850 (home-page "https://github.com/borishejblum/dearseq")
2851 (synopsis "DEA for RNA-seq data through a robust variance component test")
2853 "This is a package for Differential Expression Analysis of RNA-seq data.
2854 It features a variance component score test accounting for data
2855 heteroscedasticity through precision weights. Perform both gene-wise and gene
2856 set analyses, and can deal with repeated or longitudinal data.")
2857 (license license:gpl2)))
2859 (define-public r-decipher
2865 (uri (bioconductor-uri "DECIPHER" version))
2868 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
2869 (build-system r-build-system)
2877 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
2878 (synopsis "Tools for deciphering and managing biological sequences")
2879 (description "This package provides a toolset for deciphering and managing
2880 biological sequences.")
2881 (license license:gpl3)))
2883 (define-public r-deconvr
2889 (uri (bioconductor-uri "deconvR" version))
2892 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
2893 (properties `((upstream-name . "deconvR")))
2894 (build-system r-build-system)
2913 (native-inputs (list r-knitr))
2914 (home-page "https://github.com/BIMSBbioinfo/deconvR")
2915 (synopsis "Simulation and deconvolution of omic profiles")
2917 "This package provides a collection of functions designed for analyzing
2918 deconvolution of the bulk sample(s) using an atlas of reference omic signature
2919 profiles and a user-selected model. Users are given the option to create or
2920 extend a reference atlas and,also simulate the desired size of the bulk
2921 signature profile of the reference cell types. The package includes the
2922 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
2923 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
2924 make mapping WGBS data to their probe IDs easier.")
2925 (license license:artistic2.0)))
2927 (define-public r-decoupler
2929 (name "r-decoupler")
2934 (uri (bioconductor-uri "decoupleR" version))
2936 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
2937 (properties `((upstream-name . "decoupleR")))
2938 (build-system r-build-system)
2951 (native-inputs (list r-knitr))
2952 (home-page "https://saezlab.github.io/decoupleR/")
2953 (synopsis "Computational methods to infer biological activities from omics data")
2955 "Many methods allow us to extract biological activities from omics data using
2956 information from prior knowledge resources, reducing the dimensionality for
2957 increased statistical power and better interpretability. decoupleR is a
2958 Bioconductor package containing different statistical methods to extract these
2959 signatures within a unified framework. decoupleR allows the user to flexibly
2960 test any method with any resource. It incorporates methods that take into
2961 account the sign and weight of network interactions. decoupleR can be used
2962 with any omic, as long as its features can be linked to a biological process
2963 based on prior knowledge. For example, in transcriptomics gene sets regulated
2964 by a transcription factor, or in phospho-proteomics phosphosites that are
2965 targeted by a kinase.")
2966 (license license:gpl3)))
2968 (define-public r-deepsnv
2974 (uri (bioconductor-uri "deepSNV" version))
2977 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
2978 (properties `((upstream-name . "deepSNV")))
2979 (build-system r-build-system)
2985 r-summarizedexperiment
2990 (home-page "https://github.com/gerstung-lab/deepSNV/")
2991 (synopsis "Detection of subclonal SNVs in deep sequencing data")
2993 "This package provides quantitative variant callers for detecting
2994 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
2995 The deepSNV algorithm is used for a comparative setup with a control experiment
2996 of the same loci and uses a beta-binomial model and a likelihood ratio test to
2997 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
2998 computes a Bayes classifier based on a beta-binomial model for variant calling
2999 with multiple samples for precisely estimating model parameters - such as local
3000 error rates and dispersion - and prior knowledge, e.g. from variation data
3001 bases such as COSMIC.")
3002 (license license:gpl3)))
3004 (define-public r-delayedarray
3006 (name "r-delayedarray")
3010 (uri (bioconductor-uri "DelayedArray" version))
3013 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
3015 `((upstream-name . "DelayedArray")))
3016 (build-system r-build-system)
3018 (list r-biocgenerics r-s4vectors r-iranges r-matrix
3022 (home-page "https://bioconductor.org/packages/DelayedArray")
3023 (synopsis "Delayed operations on array-like objects")
3025 "Wrapping an array-like object (typically an on-disk object) in a
3026 @code{DelayedArray} object allows one to perform common array operations on it
3027 without loading the object in memory. In order to reduce memory usage and
3028 optimize performance, operations on the object are either delayed or executed
3029 using a block processing mechanism. Note that this also works on in-memory
3030 array-like objects like @code{DataFrame} objects (typically with Rle columns),
3031 @code{Matrix} objects, and ordinary arrays and data frames.")
3032 (license license:artistic2.0)))
3034 (define-public r-derfinderhelper
3036 (name "r-derfinderhelper")
3041 (uri (bioconductor-uri "derfinderHelper" version))
3043 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
3044 (properties `((upstream-name . "derfinderHelper")))
3045 (build-system r-build-system)
3047 (list r-iranges r-matrix r-s4vectors))
3050 (home-page "https://github.com/leekgroup/derfinderHelper")
3051 (synopsis "Helper for derfinder")
3053 "This package speeds up the derfinder package when using multiple cores.
3054 It is particularly useful when using BiocParallel and it helps reduce the time
3055 spent loading the full derfinder package when running the F-statistics
3056 calculation in parallel.")
3057 (license license:artistic2.0)))
3059 (define-public r-drimseq
3066 (uri (bioconductor-uri "DRIMSeq" version))
3068 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
3069 (properties `((upstream-name . "DRIMSeq")))
3070 (build-system r-build-system)
3072 (list r-biocgenerics
3082 (native-inputs (list r-knitr))
3083 (home-page "https://bioconductor.org/packages/DRIMSeq")
3084 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
3086 "The package provides two frameworks. One for the differential
3087 transcript usage analysis between different conditions and one for the tuQTL
3088 analysis. Both are based on modeling the counts of genomic features (i.e.,
3089 transcripts) with the Dirichlet-multinomial distribution. The package also
3090 makes available functions for visualization and exploration of the data and
3092 (license license:gpl3+)))
3094 (define-public r-bluster
3100 (uri (bioconductor-uri "bluster" version))
3103 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
3104 (properties `((upstream-name . "bluster")))
3105 (build-system r-build-system)
3107 (list r-biocneighbors
3116 (home-page "https://bioconductor.org/packages/bluster")
3117 (synopsis "Clustering algorithms for Bioconductor")
3118 (description"This package wraps common clustering algorithms in an easily
3119 extended S4 framework. Backends are implemented for hierarchical, k-means
3120 and graph-based clustering. Several utilities are also provided to compare
3121 and evaluate clustering results.")
3122 (license license:gpl3)))
3124 (define-public r-ideoviz
3130 (uri (bioconductor-uri "IdeoViz" version))
3133 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
3134 (build-system r-build-system)
3142 (home-page "https://bioconductor.org/packages/IdeoViz/")
3143 (synopsis "Plots data along a chromosomal ideogram")
3144 (description "This package provides functions to plot data associated with
3145 arbitrary genomic intervals along chromosomal ideogram.")
3146 (license license:gpl2)))
3148 (define-public r-infercnv
3155 (uri (bioconductor-uri "infercnv" version))
3158 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
3159 (properties `((upstream-name . "infercnv")))
3160 (build-system r-build-system)
3161 (inputs (list python))
3190 r-singlecellexperiment
3191 r-summarizedexperiment
3193 (native-inputs (list r-knitr))
3194 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
3195 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
3197 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
3198 evidence for somatic large-scale chromosomal copy number alterations, such as gains
3199 or deletions of entire chromosomes or large segments of chromosomes. This is done
3200 by exploring expression intensity of genes across positions of a tumor genome in
3201 comparison to a set of reference \"normal\" cells. A heatmap is generated
3202 illustrating the relative expression intensities across each chromosome, and it
3203 often becomes readily apparent as to which regions of the tumor genome are
3204 over-abundant or less-abundant as compared to that of normal cells.")
3205 (license license:bsd-3)))
3207 (define-public r-iranges
3213 (uri (bioconductor-uri "IRanges" version))
3216 "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
3218 `((upstream-name . "IRanges")))
3219 (build-system r-build-system)
3221 (list r-biocgenerics r-s4vectors))
3222 (home-page "https://bioconductor.org/packages/IRanges")
3223 (synopsis "Infrastructure for manipulating intervals on sequences")
3225 "This package provides efficient low-level and highly reusable S4 classes
3226 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
3227 generally, data that can be organized sequentially (formally defined as
3228 @code{Vector} objects), as well as views on these @code{Vector} objects.
3229 Efficient list-like classes are also provided for storing big collections of
3230 instances of the basic classes. All classes in the package use consistent
3231 naming and share the same rich and consistent \"Vector API\" as much as
3233 (license license:artistic2.0)))
3235 (define-public r-isoformswitchanalyzer
3237 (name "r-isoformswitchanalyzer")
3242 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
3244 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
3245 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
3246 (build-system r-build-system)
3279 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
3280 (synopsis "Analyze alternative splicing in RNA-seq data")
3282 "This is a package for the analysis of alternative splicing and isoform
3283 switches with predicted functional consequences (e.g. gain/loss of protein
3284 domains etc.) from quantification of all types of RNASeq by tools such as
3285 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
3286 (license license:gpl2+)))
3288 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
3289 (define-public r-absfiltergsea
3291 (name "r-absfiltergsea")
3296 (uri (cran-uri "AbsFilterGSEA" version))
3298 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
3299 (properties `((upstream-name . "AbsFilterGSEA")))
3300 (build-system r-build-system)
3302 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
3303 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
3304 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
3306 "This package provides a function that performs gene-permuting of a gene-set
3307 enrichment analysis (GSEA) calculation with or without the absolute filtering.
3308 Without filtering, users can perform (original) two-tailed or one-tailed
3310 (license license:gpl2)))
3312 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
3313 (define-public r-bisquerna
3315 (name "r-bisquerna")
3319 (uri (cran-uri "BisqueRNA" version))
3322 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
3323 (properties `((upstream-name . "BisqueRNA")))
3324 (build-system r-build-system)
3326 (list r-biobase r-limsolve))
3329 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
3330 (synopsis "Decomposition of bulk expression with single-cell sequencing")
3331 (description "This package provides tools to accurately estimate cell type
3332 abundances from heterogeneous bulk expression. A reference-based method
3333 utilizes single-cell information to generate a signature matrix and
3334 transformation of bulk expression for accurate regression based estimates.
3335 A marker-based method utilizes known cell-specific marker genes to measure
3336 relative abundances across samples.")
3337 (license license:gpl3)))
3339 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
3340 ;; from Bioconductor.
3341 (define-public r-deconstructsigs
3343 (name "r-deconstructsigs")
3347 (uri (cran-uri "deconstructSigs" version))
3350 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
3352 `((upstream-name . "deconstructSigs")))
3353 (build-system r-build-system)
3355 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
3357 (home-page "https://github.com/raerose01/deconstructSigs")
3358 (synopsis "Identifies signatures present in a tumor sample")
3359 (description "This package takes sample information in the form of the
3360 fraction of mutations in each of 96 trinucleotide contexts and identifies
3361 the weighted combination of published signatures that, when summed, most
3362 closely reconstructs the mutational profile.")
3363 (license license:gpl2+)))
3365 ;; This is a CRAN package, but it depends on Bioconductor packages.
3366 (define-public r-jetset
3373 (uri (cran-uri "jetset" version))
3375 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
3376 (properties `((upstream-name . "jetset")))
3377 (build-system r-build-system)
3378 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
3379 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
3380 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
3382 "This package provides a one-to-one mapping from gene to \"best\" probe
3383 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
3384 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
3385 gene may be measured by multiple probe sets. This can present a mild
3386 conundrum when attempting to evaluate a gene \"signature\" that is defined by
3387 gene names rather than by specific probe sets. This package also includes the
3388 pre-calculated probe set quality scores that were used to define the
3390 (license license:artistic2.0)))
3392 ;; This is a CRAN package, but it depends on Bioconductor packages.
3393 (define-public r-nmf
3400 (uri (cran-uri "NMF" version))
3403 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
3404 (properties `((upstream-name . "NMF")))
3405 (build-system r-build-system)
3410 r-bigmemory ; suggested
3411 r-synchronicity ; suggested
3426 (home-page "http://renozao.github.io/NMF")
3427 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3429 "This package provides a framework to perform Non-negative Matrix
3430 Factorization (NMF). The package implements a set of already published
3431 algorithms and seeding methods, and provides a framework to test, develop and
3432 plug new or custom algorithms. Most of the built-in algorithms have been
3433 optimized in C++, and the main interface function provides an easy way of
3434 performing parallel computations on multicore machines.")
3435 (license license:gpl2+)))
3437 (define-public r-affy
3444 (uri (bioconductor-uri "affy" version))
3447 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
3448 (build-system r-build-system)
3458 (home-page "https://bioconductor.org/packages/affy")
3459 (synopsis "Methods for affymetrix oligonucleotide arrays")
3461 "This package contains functions for exploratory oligonucleotide array
3463 (license license:lgpl2.0+)))
3465 (define-public r-affycomp
3472 (uri (bioconductor-uri "affycomp" version))
3475 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
3476 (properties `((upstream-name . "affycomp")))
3477 (build-system r-build-system)
3478 (propagated-inputs (list r-biobase))
3479 (home-page "https://bioconductor.org/packages/affycomp/")
3480 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
3482 "The package contains functions that can be used to compare expression
3483 measures for Affymetrix Oligonucleotide Arrays.")
3484 (license license:gpl2+)))
3486 (define-public r-affycompatible
3488 (name "r-affycompatible")
3493 (uri (bioconductor-uri "AffyCompatible" version))
3496 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
3498 `((upstream-name . "AffyCompatible")))
3499 (build-system r-build-system)
3503 `(modify-phases %standard-phases
3504 (add-after 'unpack 'make-reproducible
3506 ;; Order DTD elements before generating R code from them.
3507 (substitute* "R/methods-AffyCompatible.R"
3510 elements <- dtd$elements
3511 ordered <- elements[order(names(elements))]\n"))
3512 (("elt in dtd\\$elements")
3514 ;; Use a predictable directory name for code generation.
3515 (mkdir-p "/tmp/NetAffxResourcePrototype")
3516 (substitute* "R/DataClasses.R"
3517 (("directory=tempdir\\(\\)")
3518 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
3520 (list r-biostrings r-rcurl r-xml))
3521 (home-page "https://bioconductor.org/packages/AffyCompatible/")
3522 (synopsis "Work with Affymetrix GeneChip files")
3524 "This package provides an interface to Affymetrix chip annotation and
3525 sample attribute files. The package allows an easy way for users to download
3526 and manage local data bases of Affynmetrix NetAffx annotation files. It also
3527 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
3528 Command Console} (AGCC)-compatible sample annotation files.")
3529 (license license:artistic2.0)))
3531 (define-public r-affycontam
3533 (name "r-affycontam")
3538 (uri (bioconductor-uri "affyContam" version))
3541 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
3542 (properties `((upstream-name . "affyContam")))
3543 (build-system r-build-system)
3545 (list r-affy r-affydata r-biobase))
3546 (home-page "https://bioconductor.org/packages/affyContam/")
3547 (synopsis "Structured corruption of Affymetrix CEL file data")
3549 "Microarray quality assessment is a major concern of microarray analysts.
3550 This package provides some simple approaches to in silico creation of quality
3551 problems in CEL-level data to help evaluate performance of quality metrics.")
3552 (license license:artistic2.0)))
3554 (define-public r-affycoretools
3556 (name "r-affycoretools")
3561 (uri (bioconductor-uri "affycoretools" version))
3564 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
3565 (properties `((upstream-name . "affycoretools")))
3566 (build-system r-build-system)
3589 (home-page "https://bioconductor.org/packages/affycoretools/")
3590 (synopsis "Functions for analyses with Affymetrix GeneChips")
3592 "This package provides various wrapper functions that have been written
3593 to streamline the more common analyses that a Biostatistician might see.")
3594 (license license:artistic2.0)))
3596 (define-public r-affyio
3603 (uri (bioconductor-uri "affyio" version))
3606 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
3607 (build-system r-build-system)
3612 (home-page "https://github.com/bmbolstad/affyio")
3613 (synopsis "Tools for parsing Affymetrix data files")
3615 "This package provides routines for parsing Affymetrix data files based
3616 upon file format information. The primary focus is on accessing the CEL and
3618 (license license:lgpl2.0+)))
3620 (define-public r-affxparser
3622 (name "r-affxparser")
3627 (uri (bioconductor-uri "affxparser" version))
3630 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
3631 (properties `((upstream-name . "affxparser")))
3632 (build-system r-build-system)
3633 (home-page "https://github.com/HenrikBengtsson/affxparser")
3634 (synopsis "Affymetrix File Parsing SDK")
3636 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
3637 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
3638 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
3639 are supported. Currently, there are methods for reading @dfn{chip definition
3640 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
3641 either in full or in part. For example, probe signals from a few probesets
3642 can be extracted very quickly from a set of CEL files into a convenient list
3644 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
3646 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
3648 (define-public r-annotate
3655 (uri (bioconductor-uri "annotate" version))
3658 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
3659 (build-system r-build-system)
3661 (list r-annotationdbi
3669 "https://bioconductor.org/packages/annotate")
3670 (synopsis "Annotation for microarrays")
3671 (description "This package provides R environments for the annotation of
3673 (license license:artistic2.0)))
3675 (define-public r-annotationdbi
3677 (name "r-annotationdbi")
3681 (uri (bioconductor-uri "AnnotationDbi" version))
3684 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
3686 `((upstream-name . "AnnotationDbi")))
3687 (build-system r-build-system)
3698 (home-page "https://bioconductor.org/packages/AnnotationDbi")
3699 (synopsis "Annotation database interface")
3701 "This package provides user interface and database connection code for
3702 annotation data packages using SQLite data storage.")
3703 (license license:artistic2.0)))
3705 (define-public r-annotationfilter
3707 (name "r-annotationfilter")
3711 (uri (bioconductor-uri "AnnotationFilter" version))
3714 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
3716 `((upstream-name . "AnnotationFilter")))
3717 (build-system r-build-system)
3719 (list r-genomicranges r-lazyeval))
3722 (home-page "https://github.com/Bioconductor/AnnotationFilter")
3723 (synopsis "Facilities for filtering Bioconductor annotation resources")
3725 "This package provides classes and other infrastructure to implement
3726 filters for manipulating Bioconductor annotation resources. The filters are
3727 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
3728 (license license:artistic2.0)))
3730 (define-public r-annotationforge
3732 (name "r-annotationforge")
3737 (uri (bioconductor-uri "AnnotationForge" version))
3740 "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v"))))
3742 `((upstream-name . "AnnotationForge")))
3743 (build-system r-build-system)
3745 (list r-annotationdbi
3755 (home-page "https://bioconductor.org/packages/AnnotationForge")
3756 (synopsis "Code for building annotation database packages")
3758 "This package provides code for generating Annotation packages and their
3759 databases. Packages produced are intended to be used with AnnotationDbi.")
3760 (license license:artistic2.0)))
3762 (define-public r-annotationhub
3764 (name "r-annotationhub")
3769 (uri (bioconductor-uri "AnnotationHub" version))
3772 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
3773 (properties `((upstream-name . "AnnotationHub")))
3774 (build-system r-build-system)
3776 (list r-annotationdbi
3784 r-interactivedisplaybase
3791 (home-page "https://bioconductor.org/packages/AnnotationHub")
3792 (synopsis "Client to access AnnotationHub resources")
3794 "This package provides a client for the Bioconductor AnnotationHub web
3795 resource. The AnnotationHub web resource provides a central location where
3796 genomic files (e.g. VCF, bed, wig) and other resources from standard
3797 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
3798 metadata about each resource, e.g., a textual description, tags, and date of
3799 modification. The client creates and manages a local cache of files retrieved
3800 by the user, helping with quick and reproducible access.")
3801 (license license:artistic2.0)))
3803 (define-public r-aroma-light
3805 (name "r-aroma-light")
3810 (uri (bioconductor-uri "aroma.light" version))
3813 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
3814 (properties `((upstream-name . "aroma.light")))
3815 (build-system r-build-system)
3817 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
3818 (home-page "https://github.com/HenrikBengtsson/aroma.light")
3819 (synopsis "Methods for normalization and visualization of microarray data")
3821 "This package provides methods for microarray analysis that take basic
3822 data types such as matrices and lists of vectors. These methods can be used
3823 standalone, be utilized in other packages, or be wrapped up in higher-level
3825 (license license:gpl2+)))
3827 (define-public r-bamsignals
3829 (name "r-bamsignals")
3834 (uri (bioconductor-uri "bamsignals" version))
3837 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
3838 (build-system r-build-system)
3840 (list r-biocgenerics
3848 (home-page "https://bioconductor.org/packages/bamsignals")
3849 (synopsis "Extract read count signals from bam files")
3851 "This package efficiently obtains count vectors from indexed bam
3852 files. It counts the number of nucleotide sequence reads in given genomic
3853 ranges and it computes reads profiles and coverage profiles. It also handles
3855 (license license:gpl2+)))
3857 (define-public r-biobase
3863 (uri (bioconductor-uri "Biobase" version))
3866 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
3868 `((upstream-name . "Biobase")))
3869 (build-system r-build-system)
3871 (list r-biocgenerics))
3872 (home-page "https://bioconductor.org/packages/Biobase")
3873 (synopsis "Base functions for Bioconductor")
3875 "This package provides functions that are needed by many other packages
3876 on Bioconductor or which replace R functions.")
3877 (license license:artistic2.0)))
3879 (define-public r-biomart
3885 (uri (bioconductor-uri "biomaRt" version))
3888 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
3890 `((upstream-name . "biomaRt")))
3891 (build-system r-build-system)
3893 (list r-annotationdbi
3904 (home-page "https://bioconductor.org/packages/biomaRt")
3905 (synopsis "Interface to BioMart databases")
3907 "biomaRt provides an interface to a growing collection of databases
3908 implementing the @url{BioMart software suite, http://www.biomart.org}. The
3909 package enables retrieval of large amounts of data in a uniform way without
3910 the need to know the underlying database schemas or write complex SQL queries.
3911 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
3912 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
3913 users direct access to a diverse set of data and enable a wide range of
3914 powerful online queries from gene annotation to database mining.")
3915 (license license:artistic2.0)))
3917 ;; This is a CRAN package, but it depends on a Bioconductor package:
3919 (define-public r-biomartr
3925 (uri (cran-uri "biomartr" version))
3928 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
3929 (properties `((upstream-name . "biomartr")))
3930 (build-system r-build-system)
3950 (native-inputs (list r-knitr))
3951 (home-page "https://docs.ropensci.org/biomartr/")
3952 (synopsis "Genomic data retrieval")
3954 "Perform large scale genomic data retrieval and functional annotation
3955 retrieval. This package aims to provide users with a standardized way to
3956 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
3957 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
3958 Furthermore, an interface to the BioMart database allows users to retrieve
3959 functional annotation for genomic loci. In addition, users can download
3960 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
3962 (license license:gpl2)))
3964 (define-public r-biocparallel
3966 (name "r-biocparallel")
3970 (uri (bioconductor-uri "BiocParallel" version))
3973 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
3975 `((upstream-name . "BiocParallel")))
3976 (build-system r-build-system)
3979 (modify-phases %standard-phases
3980 (add-after 'unpack 'make-reproducible
3982 ;; Remove generated documentation.
3983 (for-each delete-file
3984 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
3985 "inst/doc/Introduction_To_BiocParallel.pdf"
3986 "inst/doc/Errors_Logs_And_Debugging.pdf"
3987 "inst/doc/BiocParallel_BatchtoolsParam.R"
3988 "inst/doc/Introduction_To_BiocParallel.R"
3989 "inst/doc/Errors_Logs_And_Debugging.R"))
3991 ;; Remove time-dependent macro
3992 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
3993 "inst/doc/Introduction_To_BiocParallel.Rnw"
3994 "inst/doc/Errors_Logs_And_Debugging.Rnw"
3995 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
3996 "vignettes/Introduction_To_BiocParallel.Rnw"
3997 "vignettes/Errors_Logs_And_Debugging.Rnw")
3998 (("\\today") "later"))
4000 ;; Initialize the random number generator seed when building.
4001 (substitute* "R/rng.R"
4002 (("\"L'Ecuyer-CMRG\"\\)" m)
4004 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
4006 (list r-bh r-codetools r-futile-logger r-snow))
4009 (home-page "https://bioconductor.org/packages/BiocParallel")
4010 (synopsis "Bioconductor facilities for parallel evaluation")
4012 "This package provides modified versions and novel implementation of
4013 functions for parallel evaluation, tailored to use with Bioconductor
4015 (license (list license:gpl2+ license:gpl3+))))
4017 (define-public r-biostrings
4019 (name "r-biostrings")
4023 (uri (bioconductor-uri "Biostrings" version))
4026 "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"))))
4028 `((upstream-name . "Biostrings")))
4029 (build-system r-build-system)
4031 (list r-biocgenerics
4037 (home-page "https://bioconductor.org/packages/Biostrings")
4038 (synopsis "String objects and algorithms for biological sequences")
4040 "This package provides memory efficient string containers, string
4041 matching algorithms, and other utilities, for fast manipulation of large
4042 biological sequences or sets of sequences.")
4043 (license license:artistic2.0)))
4045 (define-public r-biovizbase
4047 (name "r-biovizbase")
4052 (uri (bioconductor-uri "biovizBase" version))
4055 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
4056 (properties `((upstream-name . "biovizBase")))
4057 (build-system r-build-system)
4059 (list r-annotationdbi
4076 r-summarizedexperiment
4077 r-variantannotation))
4078 (home-page "https://bioconductor.org/packages/biovizBase")
4079 (synopsis "Basic graphic utilities for visualization of genomic data")
4081 "The biovizBase package is designed to provide a set of utilities, color
4082 schemes and conventions for genomic data. It serves as the base for various
4083 high-level packages for biological data visualization. This saves development
4084 effort and encourages consistency.")
4085 (license license:artistic2.0)))
4087 (define-public r-bsgenome
4093 (uri (bioconductor-uri "BSgenome" version))
4096 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
4098 `((upstream-name . "BSgenome")))
4099 (build-system r-build-system)
4101 (list r-biocgenerics
4111 (home-page "https://bioconductor.org/packages/BSgenome")
4112 (synopsis "Infrastructure for Biostrings-based genome data packages")
4114 "This package provides infrastructure shared by all Biostrings-based
4115 genome data packages and support for efficient SNP representation.")
4116 (license license:artistic2.0)))
4118 (define-public r-category
4125 (uri (bioconductor-uri "Category" version))
4128 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
4129 (properties `((upstream-name . "Category")))
4130 (build-system r-build-system)
4142 (home-page "https://bioconductor.org/packages/Category")
4143 (synopsis "Category analysis")
4145 "This package provides a collection of tools for performing category
4147 (license license:artistic2.0)))
4149 (define-public r-chipseeker
4151 (name "r-chipseeker")
4155 (uri (bioconductor-uri "ChIPseeker" version))
4158 "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"))))
4159 (build-system r-build-system)
4163 (list r-annotationdbi
4182 r-txdb-hsapiens-ucsc-hg19-knowngene))
4183 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
4184 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
4185 (description "This package implements functions to retrieve the nearest
4186 genes around the peak, annotate genomic region of the peak, statstical methods
4187 for estimate the significance of overlap among ChIP peak data sets, and
4188 incorporate GEO database for user to compare the own dataset with those
4189 deposited in database. The comparison can be used to infer cooperative
4190 regulation and thus can be used to generate hypotheses. Several visualization
4191 functions are implemented to summarize the coverage of the peak experiment,
4192 average profile and heatmap of peaks binding to TSS regions, genomic
4193 annotation, distance to TSS, and overlap of peaks or genes.")
4194 (license license:artistic2.0)))
4196 (define-public r-chipseq
4203 (uri (bioconductor-uri "chipseq" version))
4206 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
4207 (build-system r-build-system)
4209 (list r-biocgenerics
4215 (home-page "https://bioconductor.org/packages/chipseq")
4216 (synopsis "Package for analyzing ChIPseq data")
4218 "This package provides tools for processing short read data from ChIPseq
4220 (license license:artistic2.0)))
4222 (define-public r-complexheatmap
4224 (name "r-complexheatmap")
4229 (uri (bioconductor-uri "ComplexHeatmap" version))
4232 "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"))))
4234 `((upstream-name . "ComplexHeatmap")))
4235 (build-system r-build-system)
4253 "https://github.com/jokergoo/ComplexHeatmap")
4254 (synopsis "Making Complex Heatmaps")
4256 "Complex heatmaps are efficient to visualize associations between
4257 different sources of data sets and reveal potential structures. This package
4258 provides a highly flexible way to arrange multiple heatmaps and supports
4259 self-defined annotation graphics.")
4260 (license license:gpl2+)))
4262 (define-public r-copywriter
4264 (name "r-copywriter")
4269 (uri (bioconductor-uri "CopywriteR" version))
4272 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
4273 (properties `((upstream-name . "CopywriteR")))
4274 (build-system r-build-system)
4276 (list r-biocparallel
4290 (home-page "https://github.com/PeeperLab/CopywriteR")
4291 (synopsis "Copy number information from targeted sequencing")
4293 "CopywriteR extracts DNA copy number information from targeted sequencing
4294 by utilizing off-target reads. It allows for extracting uniformly distributed
4295 copy number information, can be used without reference, and can be applied to
4296 sequencing data obtained from various techniques including chromatin
4297 immunoprecipitation and target enrichment on small gene panels. Thereby,
4298 CopywriteR constitutes a widely applicable alternative to available copy
4299 number detection tools.")
4300 (license license:gpl2)))
4302 (define-public r-deseq
4309 (uri (bioconductor-uri "DESeq" version))
4312 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
4313 (properties `((upstream-name . "DESeq")))
4314 (build-system r-build-system)
4324 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
4325 (synopsis "Differential gene expression analysis")
4327 "This package provides tools for estimating variance-mean dependence in
4328 count data from high-throughput genetic sequencing assays and for testing for
4329 differential expression based on a model using the negative binomial
4331 (license license:gpl3+)))
4333 (define-public r-deseq2
4340 (uri (bioconductor-uri "DESeq2" version))
4343 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
4344 (properties `((upstream-name . "DESeq2")))
4345 (build-system r-build-system)
4359 r-summarizedexperiment))
4362 (home-page "https://bioconductor.org/packages/DESeq2")
4363 (synopsis "Differential gene expression analysis")
4365 "This package provides functions to estimate variance-mean dependence in
4366 count data from high-throughput nucleotide sequencing assays and test for
4367 differential expression based on a model using the negative binomial
4369 (license license:lgpl3+)))
4371 (define-public r-dexseq
4378 (uri (bioconductor-uri "DEXSeq" version))
4381 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
4382 (properties `((upstream-name . "DEXSeq")))
4383 (build-system r-build-system)
4385 (list r-annotationdbi
4401 r-summarizedexperiment))
4404 (home-page "https://bioconductor.org/packages/DEXSeq")
4405 (synopsis "Inference of differential exon usage in RNA-Seq")
4407 "This package is focused on finding differential exon usage using RNA-seq
4408 exon counts between samples with different experimental designs. It provides
4409 functions that allows the user to make the necessary statistical tests based
4410 on a model that uses the negative binomial distribution to estimate the
4411 variance between biological replicates and generalized linear models for
4412 testing. The package also provides functions for the visualization and
4413 exploration of the results.")
4414 (license license:gpl3+)))
4416 (define-public r-diffcyt
4423 (uri (bioconductor-uri "diffcyt" version))
4425 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
4426 (properties `((upstream-name . "diffcyt")))
4427 (build-system r-build-system)
4441 r-summarizedexperiment
4443 (native-inputs (list r-knitr))
4444 (home-page "https://github.com/lmweber/diffcyt")
4445 (synopsis "Differential discovery in high-dimensional cytometry")
4447 "This package provides statistical methods for differential discovery
4448 analyses in high-dimensional cytometry data (including flow cytometry, mass
4449 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
4450 combination of high-resolution clustering and empirical Bayes moderated tests
4451 adapted from transcriptomics.")
4452 (license license:expat)))
4454 (define-public r-dirichletmultinomial
4456 (name "r-dirichletmultinomial")
4461 (uri (bioconductor-uri "DirichletMultinomial" version))
4464 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
4466 `((upstream-name . "DirichletMultinomial")))
4467 (build-system r-build-system)
4471 (list r-biocgenerics r-iranges r-s4vectors))
4472 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
4473 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
4475 "Dirichlet-multinomial mixture models can be used to describe variability
4476 in microbial metagenomic data. This package is an interface to code
4477 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
4479 (license license:lgpl3)))
4481 (define-public r-dittoseq
4487 (uri (bioconductor-uri "dittoSeq" version))
4490 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
4491 (properties `((upstream-name . "dittoSeq")))
4492 (build-system r-build-system)
4503 r-singlecellexperiment
4504 r-summarizedexperiment))
4505 (native-inputs (list r-knitr))
4506 (home-page "https://bioconductor.org/packages/dittoSeq")
4507 (synopsis "Single-cell and bulk RNA sequencing visualization")
4509 "This package provides a universal, user friendly, single-cell and bulk RNA
4510 sequencing visualization toolkit that allows highly customizable creation of
4511 color blindness friendly, publication-quality figures. dittoSeq accepts both
4512 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
4513 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
4514 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
4515 percent composition or expression across groups, and more. Customizations
4516 range from size and title adjustments to automatic generation of annotations
4517 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
4518 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
4519 many more. All with simple, discrete inputs. Color blindness friendliness is
4520 powered by legend adjustments (enlarged keys), and by allowing the use of
4521 shapes or letter-overlay in addition to the carefully selected
4522 code{dittoColors()}.")
4523 (license license:expat)))
4525 (define-public r-edaseq
4532 (uri (bioconductor-uri "EDASeq" version))
4535 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
4536 (properties `((upstream-name . "EDASeq")))
4537 (build-system r-build-system)
4539 (list r-annotationdbi
4553 (home-page "https://github.com/drisso/EDASeq")
4554 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
4556 "This package provides support for numerical and graphical summaries of
4557 RNA-Seq genomic read data. Provided within-lane normalization procedures to
4558 adjust for GC-content effect (or other gene-level effects) on read counts:
4559 loess robust local regression, global-scaling, and full-quantile
4560 normalization. Between-lane normalization procedures to adjust for
4561 distributional differences between lanes (e.g., sequencing depth):
4562 global-scaling and full-quantile normalization.")
4563 (license license:artistic2.0)))
4565 (define-public r-edger
4571 (uri (bioconductor-uri "edgeR" version))
4574 "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
4575 (properties `((upstream-name . "edgeR")))
4576 (build-system r-build-system)
4578 (list r-limma r-locfit r-rcpp))
4579 (home-page "http://bioinf.wehi.edu.au/edgeR")
4580 (synopsis "EdgeR does empirical analysis of digital gene expression data")
4581 (description "This package can do differential expression analysis of
4582 RNA-seq expression profiles with biological replication. It implements a range
4583 of statistical methodology based on the negative binomial distributions,
4584 including empirical Bayes estimation, exact tests, generalized linear models
4585 and quasi-likelihood tests. It be applied to differential signal analysis of
4586 other types of genomic data that produce counts, including ChIP-seq, SAGE and
4588 (license license:gpl2+)))
4590 (define-public r-ensembldb
4592 (name "r-ensembldb")
4597 (uri (bioconductor-uri "ensembldb" version))
4600 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
4601 (build-system r-build-system)
4603 (list r-annotationdbi
4621 (home-page "https://github.com/jotsetung/ensembldb")
4622 (synopsis "Utilities to create and use Ensembl-based annotation databases")
4624 "The package provides functions to create and use transcript-centric
4625 annotation databases/packages. The annotation for the databases are directly
4626 fetched from Ensembl using their Perl API. The functionality and data is
4627 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
4628 but, in addition to retrieve all gene/transcript models and annotations from
4629 the database, the @code{ensembldb} package also provides a filter framework
4630 allowing to retrieve annotations for specific entries like genes encoded on a
4631 chromosome region or transcript models of lincRNA genes.")
4632 ;; No version specified
4633 (license license:lgpl3+)))
4635 (define-public r-fastseg
4642 (uri (bioconductor-uri "fastseg" version))
4645 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
4646 (build-system r-build-system)
4648 (list r-biobase r-biocgenerics r-genomicranges r-iranges
4650 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
4651 (synopsis "Fast segmentation algorithm for genetic sequencing data")
4653 "Fastseg implements a very fast and efficient segmentation algorithm.
4654 It can segment data from DNA microarrays and data from next generation
4655 sequencing for example to detect copy number segments. Further it can segment
4656 data from RNA microarrays like tiling arrays to identify transcripts. Most
4657 generally, it can segment data given as a matrix or as a vector. Various data
4658 formats can be used as input to fastseg like expression set objects for
4659 microarrays or GRanges for sequencing data.")
4660 (license license:lgpl2.0+)))
4662 (define-public r-gage
4669 (uri (bioconductor-uri "gage" version))
4672 "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"))))
4673 (build-system r-build-system)
4675 (list r-annotationdbi r-go-db r-graph r-keggrest))
4676 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
4677 "articles/10.1186/1471-2105-10-161"))
4678 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
4680 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
4681 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
4682 data attributes including sample sizes, experimental designs, assay platforms,
4683 and other types of heterogeneity. The gage package provides functions for
4684 basic GAGE analysis, result processing and presentation. In addition, it
4685 provides demo microarray data and commonly used gene set data based on KEGG
4686 pathways and GO terms. These functions and data are also useful for gene set
4687 analysis using other methods.")
4688 (license license:gpl2+)))
4690 (define-public r-genefilter
4692 (name "r-genefilter")
4697 (uri (bioconductor-uri "genefilter" version))
4700 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
4701 (build-system r-build-system)
4703 (list gfortran r-knitr))
4705 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
4707 (home-page "https://bioconductor.org/packages/genefilter")
4708 (synopsis "Filter genes from high-throughput experiments")
4710 "This package provides basic functions for filtering genes from
4711 high-throughput sequencing experiments.")
4712 (license license:artistic2.0)))
4714 (define-public r-geneoverlap
4716 (name "r-geneoverlap")
4720 (uri (bioconductor-uri "GeneOverlap" version))
4723 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
4724 (build-system r-build-system)
4726 (list r-rcolorbrewer r-gplots))
4727 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
4728 (synopsis "Test and visualize gene overlaps")
4729 (description "This package can be used to test two sets of gene lists
4730 and visualize the results.")
4731 (license license:gpl3)))
4733 (define-public r-genomation
4735 (name "r-genomation")
4739 (uri (bioconductor-uri "genomation" version))
4742 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
4743 (build-system r-build-system)
4767 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
4768 (synopsis "Summary, annotation and visualization of genomic data")
4770 "This package provides a package for summary and annotation of genomic
4771 intervals. Users can visualize and quantify genomic intervals over
4772 pre-defined functional regions, such as promoters, exons, introns, etc. The
4773 genomic intervals represent regions with a defined chromosome position, which
4774 may be associated with a score, such as aligned reads from HT-seq experiments,
4775 TF binding sites, methylation scores, etc. The package can use any tabular
4776 genomic feature data as long as it has minimal information on the locations of
4777 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4778 (license license:artistic2.0)))
4780 (define-public r-genomeinfodb
4782 (name "r-genomeinfodb")
4786 (uri (bioconductor-uri "GenomeInfoDb" version))
4789 "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"))))
4791 `((upstream-name . "GenomeInfoDb")))
4792 (build-system r-build-system)
4794 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
4798 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
4799 (synopsis "Utilities for manipulating chromosome identifiers")
4801 "This package contains data and functions that define and allow
4802 translation between different chromosome sequence naming conventions (e.g.,
4803 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4804 names in their natural, rather than lexicographic, order.")
4805 (license license:artistic2.0)))
4807 (define-public r-genomicalignments
4809 (name "r-genomicalignments")
4813 (uri (bioconductor-uri "GenomicAlignments" version))
4816 "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
4818 `((upstream-name . "GenomicAlignments")))
4819 (build-system r-build-system)
4821 (list r-biocgenerics
4829 r-summarizedexperiment))
4830 (home-page "https://bioconductor.org/packages/GenomicAlignments")
4831 (synopsis "Representation and manipulation of short genomic alignments")
4833 "This package provides efficient containers for storing and manipulating
4834 short genomic alignments (typically obtained by aligning short reads to a
4835 reference genome). This includes read counting, computing the coverage,
4836 junction detection, and working with the nucleotide content of the
4838 (license license:artistic2.0)))
4840 (define-public r-genomicfeatures
4842 (name "r-genomicfeatures")
4846 (uri (bioconductor-uri "GenomicFeatures" version))
4849 "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"))))
4851 `((upstream-name . "GenomicFeatures")))
4852 (build-system r-build-system)
4854 (list r-annotationdbi
4871 (home-page "https://bioconductor.org/packages/GenomicFeatures")
4872 (synopsis "Tools for working with transcript centric annotations")
4874 "This package provides a set of tools and methods for making and
4875 manipulating transcript centric annotations. With these tools the user can
4876 easily download the genomic locations of the transcripts, exons and cds of a
4877 given organism, from either the UCSC Genome Browser or a BioMart
4878 database (more sources will be supported in the future). This information is
4879 then stored in a local database that keeps track of the relationship between
4880 transcripts, exons, cds and genes. Flexible methods are provided for
4881 extracting the desired features in a convenient format.")
4882 (license license:artistic2.0)))
4884 (define-public r-genomicfiles
4886 (name "r-genomicfiles")
4891 (uri (bioconductor-uri "GenomicFiles" version))
4894 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
4895 (properties `((upstream-name . "GenomicFiles")))
4896 (build-system r-build-system)
4898 (list r-biocgenerics
4908 r-summarizedexperiment
4909 r-variantannotation))
4910 (home-page "https://bioconductor.org/packages/GenomicFiles")
4911 (synopsis "Distributed computing by file or by range")
4913 "This package provides infrastructure for parallel computations
4914 distributed by file or by range. User defined mapper and reducer functions
4915 provide added flexibility for data combination and manipulation.")
4916 (license license:artistic2.0)))
4918 (define-public r-genomicranges
4920 (name "r-genomicranges")
4924 (uri (bioconductor-uri "GenomicRanges" version))
4927 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
4929 `((upstream-name . "GenomicRanges")))
4930 (build-system r-build-system)
4932 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
4935 (home-page "https://bioconductor.org/packages/GenomicRanges")
4936 (synopsis "Representation and manipulation of genomic intervals")
4938 "This package provides tools to efficiently represent and manipulate
4939 genomic annotations and alignments is playing a central role when it comes to
4940 analyzing high-throughput sequencing data (a.k.a. NGS data). The
4941 GenomicRanges package defines general purpose containers for storing and
4942 manipulating genomic intervals and variables defined along a genome.")
4943 (license license:artistic2.0)))
4945 (define-public r-gostats
4952 (uri (bioconductor-uri "GOstats" version))
4955 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
4956 (properties `((upstream-name . "GOstats")))
4957 (build-system r-build-system)
4968 (home-page "https://bioconductor.org/packages/GOstats")
4969 (synopsis "Tools for manipulating GO and microarrays")
4971 "This package provides a set of tools for interacting with GO and
4972 microarray data. A variety of basic manipulation tools for graphs, hypothesis
4973 testing and other simple calculations.")
4974 (license license:artistic2.0)))
4976 (define-public r-gseabase
4983 (uri (bioconductor-uri "GSEABase" version))
4986 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
4987 (properties `((upstream-name . "GSEABase")))
4988 (build-system r-build-system)
4998 (home-page "https://bioconductor.org/packages/GSEABase")
4999 (synopsis "Gene set enrichment data structures and methods")
5001 "This package provides classes and methods to support @dfn{Gene Set
5002 Enrichment Analysis} (GSEA).")
5003 (license license:artistic2.0)))
5005 (define-public r-hpar
5012 (uri (bioconductor-uri "hpar" version))
5015 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
5016 (build-system r-build-system)
5019 (home-page "https://bioconductor.org/packages/hpar/")
5020 (synopsis "Human Protein Atlas in R")
5021 (description "This package provides a simple interface to and data from
5022 the Human Protein Atlas project.")
5023 (license license:artistic2.0)))
5025 (define-public r-rhtslib
5032 (uri (bioconductor-uri "Rhtslib" version))
5035 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
5036 (properties `((upstream-name . "Rhtslib")))
5037 (build-system r-build-system)
5038 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
5039 ;; which makes R abort the build.
5040 (arguments '(#:configure-flags '("--no-staged-install")))
5042 (list curl zlib ; packages using rhtslib need to link with zlib
5045 (list pkg-config r-knitr))
5046 (home-page "https://github.com/nhayden/Rhtslib")
5047 (synopsis "High-throughput sequencing library as an R package")
5049 "This package provides the HTSlib C library for high-throughput
5050 nucleotide sequence analysis. The package is primarily useful to developers
5051 of other R packages who wish to make use of HTSlib.")
5052 (license license:lgpl2.0+)))
5054 (define-public r-impute
5060 (uri (bioconductor-uri "impute" version))
5063 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
5066 (build-system r-build-system)
5067 (home-page "https://bioconductor.org/packages/impute")
5068 (synopsis "Imputation for microarray data")
5070 "This package provides a function to impute missing gene expression
5071 microarray data, using nearest neighbor averaging.")
5072 (license license:gpl2+)))
5074 (define-public r-interactivedisplaybase
5076 (name "r-interactivedisplaybase")
5081 (uri (bioconductor-uri "interactiveDisplayBase" version))
5084 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
5086 `((upstream-name . "interactiveDisplayBase")))
5087 (build-system r-build-system)
5089 (list r-biocgenerics r-dt r-shiny))
5092 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
5093 (synopsis "Base package for web displays of Bioconductor objects")
5095 "This package contains the basic methods needed to generate interactive
5096 Shiny-based display methods for Bioconductor objects.")
5097 (license license:artistic2.0)))
5099 (define-public r-keggrest
5106 (uri (bioconductor-uri "KEGGREST" version))
5109 "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
5110 (properties `((upstream-name . "KEGGREST")))
5111 (build-system r-build-system)
5113 (list r-biostrings r-httr r-png))
5116 (home-page "https://bioconductor.org/packages/KEGGREST")
5117 (synopsis "Client-side REST access to KEGG")
5119 "This package provides a package that provides a client interface to the
5120 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
5121 (license license:artistic2.0)))
5123 (define-public r-lfa
5130 (uri (bioconductor-uri "lfa" version))
5132 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
5133 (properties `((upstream-name . "lfa")))
5134 (build-system r-build-system)
5135 (propagated-inputs (list r-corpcor))
5136 (native-inputs (list r-knitr))
5137 (home-page "https://github.com/StoreyLab/lfa")
5138 (synopsis "Logistic Factor Analysis for categorical data")
5140 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
5141 Binomial data via estimation of latent structure in the natural parameter.")
5142 (license license:gpl3)))
5144 (define-public r-limma
5150 (uri (bioconductor-uri "limma" version))
5153 "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"))))
5154 (build-system r-build-system)
5155 (home-page "http://bioinf.wehi.edu.au/limma")
5156 (synopsis "Package for linear models for microarray and RNA-seq data")
5157 (description "This package can be used for the analysis of gene expression
5158 studies, especially the use of linear models for analysing designed experiments
5159 and the assessment of differential expression. The analysis methods apply to
5160 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
5161 (license license:gpl2+)))
5163 (define-public r-made4
5169 (uri (bioconductor-uri "made4" version))
5172 "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
5173 (properties `((upstream-name . "made4")))
5174 (build-system r-build-system)
5181 r-summarizedexperiment))
5182 (native-inputs (list r-knitr))
5183 (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
5184 (synopsis "Multivariate analysis of microarray data using ADE4")
5186 "This is a package for multivariate data analysis and graphical display
5187 of microarray data. Functions are included for supervised dimension
5188 reduction (between group analysis) and joint dimension reduction of two
5189 datasets (coinertia analysis).")
5190 (license license:artistic2.0)))
5192 (define-public r-methylkit
5194 (name "r-methylkit")
5198 (uri (bioconductor-uri "methylKit" version))
5201 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
5202 (properties `((upstream-name . "methylKit")))
5203 (build-system r-build-system)
5225 (list r-knitr)) ; for vignettes
5226 (home-page "https://github.com/al2na/methylKit")
5228 "DNA methylation analysis from high-throughput bisulfite sequencing results")
5230 "MethylKit is an R package for DNA methylation analysis and annotation
5231 from high-throughput bisulfite sequencing. The package is designed to deal
5232 with sequencing data from @dfn{Reduced representation bisulfite
5233 sequencing} (RRBS) and its variants, but also target-capture methods and whole
5234 genome bisulfite sequencing. It also has functions to analyze base-pair
5235 resolution 5hmC data from experimental protocols such as oxBS-Seq and
5237 (license license:artistic2.0)))
5239 (define-public r-motifrg
5246 (uri (bioconductor-uri "motifRG" version))
5249 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
5250 (properties `((upstream-name . "motifRG")))
5251 (build-system r-build-system)
5255 r-bsgenome-hsapiens-ucsc-hg19
5259 (home-page "https://bioconductor.org/packages/motifRG")
5260 (synopsis "Discover motifs in high throughput sequencing data")
5262 "This package provides tools for discriminative motif discovery in high
5263 throughput genetic sequencing data sets using regression methods.")
5264 (license license:artistic2.0)))
5266 (define-public r-muscat
5273 (uri (bioconductor-uri "muscat" version))
5276 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
5277 (properties `((upstream-name . "muscat")))
5278 (build-system r-build-system)
5280 (list r-biocparallel
5301 r-singlecellexperiment
5302 r-summarizedexperiment
5305 (native-inputs (list r-knitr))
5306 (home-page "https://github.com/HelenaLC/muscat")
5307 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
5309 "This package @code{muscat} provides various methods and visualization tools
5310 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
5311 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
5312 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
5313 platform that mimics both single and multi-sample scRNA-seq data.")
5314 (license license:gpl3)))
5316 (define-public r-mutationalpatterns
5318 (name "r-mutationalpatterns")
5323 (uri (bioconductor-uri "MutationalPatterns" version))
5326 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
5327 (build-system r-build-system)
5331 (list r-biocgenerics
5334 ;; These two packages are suggested packages
5335 r-bsgenome-hsapiens-1000genomes-hs37d5
5336 r-bsgenome-hsapiens-ucsc-hg19
5354 r-variantannotation))
5355 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
5356 (synopsis "Extract and visualize mutational patterns in genomic data")
5357 (description "This package provides an extensive toolset for the
5358 characterization and visualization of a wide range of mutational patterns
5359 in SNV base substitution data.")
5360 (license license:expat)))
5362 (define-public r-msnbase
5369 (uri (bioconductor-uri "MSnbase" version))
5372 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
5373 (properties `((upstream-name . "MSnbase")))
5374 (build-system r-build-system)
5400 (home-page "https://github.com/lgatto/MSnbase")
5401 (synopsis "Base functions and classes for MS-based proteomics")
5403 "This package provides basic plotting, data manipulation and processing
5404 of mass spectrometry based proteomics data.")
5405 (license license:artistic2.0)))
5407 (define-public r-msnid
5414 (uri (bioconductor-uri "MSnID" version))
5417 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
5418 (properties `((upstream-name . "MSnID")))
5419 (build-system r-build-system)
5422 (modify-phases %standard-phases
5423 (add-after 'unpack 'set-HOME
5424 (lambda _ (setenv "HOME" "/tmp"))))))
5426 (list r-annotationdbi
5452 (home-page "https://bioconductor.org/packages/MSnID")
5453 (synopsis "Utilities for LC-MSn proteomics identifications")
5455 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
5456 from mzIdentML (leveraging the mzID package) or text files. After collating
5457 the search results from multiple datasets it assesses their identification
5458 quality and optimize filtering criteria to achieve the maximum number of
5459 identifications while not exceeding a specified false discovery rate. It also
5460 contains a number of utilities to explore the MS/MS results and assess missed
5461 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
5462 (license license:artistic2.0)))
5464 (define-public r-mzid
5471 (uri (bioconductor-uri "mzID" version))
5474 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
5475 (properties `((upstream-name . "mzID")))
5476 (build-system r-build-system)
5486 (home-page "https://bioconductor.org/packages/mzID")
5487 (synopsis "Parser for mzIdentML files")
5489 "This package provides a parser for mzIdentML files implemented using the
5490 XML package. The parser tries to be general and able to handle all types of
5491 mzIdentML files with the drawback of having less pretty output than a vendor
5493 (license license:gpl2+)))
5495 (define-public r-mzr
5502 (uri (bioconductor-uri "mzR" version))
5505 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
5506 (modules '((guix build utils)))
5508 '(delete-file-recursively "src/boost"))))
5509 (properties `((upstream-name . "mzR")))
5510 (build-system r-build-system)
5513 (modify-phases %standard-phases
5514 (add-after 'unpack 'use-system-boost
5516 (substitute* "src/Makevars"
5517 (("\\./boost/libs.*") "")
5518 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
5519 (("\\ARCH_OBJS=" line)
5521 "\nBOOST_LIBS=-lboost_system -lboost_regex \
5522 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
5524 (list boost ; use this instead of the bundled boost sources
5535 (home-page "https://github.com/sneumann/mzR/")
5536 (synopsis "Parser for mass spectrometry data files")
5538 "The mzR package provides a unified API to the common file formats and
5539 parsers available for mass spectrometry data. It comes with a wrapper for the
5540 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
5541 The package contains the original code written by the ISB, and a subset of the
5542 proteowizard library for mzML and mzIdentML. The netCDF reading code has
5543 previously been used in XCMS.")
5544 (license license:artistic2.0)))
5546 (define-public r-organism-dplyr
5548 (name "r-organism-dplyr")
5553 (uri (bioconductor-uri "Organism.dplyr" version))
5556 "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
5557 (properties `((upstream-name . "Organism.dplyr")))
5558 (build-system r-build-system)
5560 (list r-annotationdbi
5574 (native-inputs (list r-knitr))
5575 (home-page "https://bioconductor.org/packages/Organism.dplyr")
5576 (synopsis "Dplyr-based access to Bioconductor annotation resources")
5578 "This package provides an alternative interface to Bioconductor @code{
5579 annotation} resources, in particular the gene identifier mapping functionality
5580 of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
5581 functionality of the @code{TxDb} packages (e.g.,
5582 @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
5583 (license license:artistic2.0)))
5585 (define-public r-organismdbi
5587 (name "r-organismdbi")
5592 (uri (bioconductor-uri "OrganismDbi" version))
5595 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
5596 (properties `((upstream-name . "OrganismDbi")))
5597 (build-system r-build-system)
5599 (list r-annotationdbi
5610 (home-page "https://bioconductor.org/packages/OrganismDbi")
5611 (synopsis "Software to enable the smooth interfacing of database packages")
5612 (description "The package enables a simple unified interface to several
5613 annotation packages each of which has its own schema by taking advantage of
5614 the fact that each of these packages implements a select methods.")
5615 (license license:artistic2.0)))
5617 (define-public r-pcaexplorer
5619 (name "r-pcaexplorer")
5624 (uri (bioconductor-uri "pcaExplorer" version))
5627 "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
5628 (properties `((upstream-name . "pcaExplorer")))
5629 (build-system r-build-system)
5631 (list r-annotationdbi
5657 r-summarizedexperiment
5661 (native-inputs (list r-knitr))
5662 (home-page "https://github.com/federicomarini/pcaExplorer")
5664 "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
5666 "This package provides functionality for interactive visualization of RNA-seq
5667 datasets based on Principal Components Analysis. The methods provided allow for
5668 quick information extraction and effective data exploration. A Shiny
5669 application encapsulates the whole analysis.")
5670 (license license:expat)))
5672 (define-public r-pcamethods
5674 (name "r-pcamethods")
5679 (uri (bioconductor-uri "pcaMethods" version))
5682 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
5683 (properties `((upstream-name . "pcaMethods")))
5684 (build-system r-build-system)
5686 (list r-biobase r-biocgenerics r-mass r-rcpp))
5687 (home-page "https://github.com/hredestig/pcamethods")
5688 (synopsis "Collection of PCA methods")
5690 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
5691 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
5692 for missing value estimation is included for comparison. BPCA, PPCA and
5693 NipalsPCA may be used to perform PCA on incomplete data as well as for
5694 accurate missing value estimation. A set of methods for printing and plotting
5695 the results is also provided. All PCA methods make use of the same data
5696 structure (pcaRes) to provide a common interface to the PCA results.")
5697 (license license:gpl3+)))
5699 ;; This is a CRAN package, but it depends on a Bioconductor package:
5700 ;; r-aroma-light, r-dnacopy..
5701 (define-public r-pscbs
5708 (uri (cran-uri "PSCBS" version))
5710 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
5711 (properties `((upstream-name . "PSCBS")))
5712 (build-system r-build-system)
5715 (modify-phases %standard-phases
5716 (add-before 'install 'change-home-dir
5718 ;; Change from /homeless-shelter to /tmp for write permission.
5719 (setenv "HOME" "/tmp"))))))
5731 (list r-r-rsp ;used to build vignettes
5733 (home-page "https://github.com/HenrikBengtsson/PSCBS")
5734 (synopsis "Analysis of parent-specific DNA copy numbers")
5736 "This is a package for segmentation of allele-specific DNA copy number
5737 data and detection of regions with abnormal copy number within each parental
5738 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
5739 (license license:gpl2+)))
5741 (define-public r-protgenerics
5743 (name "r-protgenerics")
5748 (uri (bioconductor-uri "ProtGenerics" version))
5751 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
5752 (properties `((upstream-name . "ProtGenerics")))
5753 (build-system r-build-system)
5754 (home-page "https://github.com/lgatto/ProtGenerics")
5755 (synopsis "S4 generic functions for proteomics infrastructure")
5757 "This package provides S4 generic functions needed by Bioconductor
5758 proteomics packages.")
5759 (license license:artistic2.0)))
5761 (define-public r-rbgl
5768 (uri (bioconductor-uri "RBGL" version))
5771 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
5772 (properties `((upstream-name . "RBGL")))
5773 (build-system r-build-system)
5775 (list r-bh r-graph))
5776 (home-page "https://www.bioconductor.org/packages/RBGL")
5777 (synopsis "Interface to the Boost graph library")
5779 "This package provides a fairly extensive and comprehensive interface to
5780 the graph algorithms contained in the Boost library.")
5781 (license license:artistic2.0)))
5783 (define-public r-rcas
5789 (uri (bioconductor-uri "RCAS" version))
5792 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
5793 (properties `((upstream-name . "RCAS")))
5794 (build-system r-build-system)
5796 (list r-biocgenerics
5799 r-bsgenome-hsapiens-ucsc-hg19
5825 (synopsis "RNA-centric annotation system")
5827 "RCAS aims to be a standalone RNA-centric annotation system that provides
5828 intuitive reports and publication-ready graphics. This package provides the R
5829 library implementing most of the pipeline's features.")
5830 (home-page "https://github.com/BIMSBbioinfo/RCAS")
5831 (license license:artistic2.0)))
5833 (define-public r-regioner
5840 (uri (bioconductor-uri "regioneR" version))
5843 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
5844 (properties `((upstream-name . "regioneR")))
5845 (build-system r-build-system)
5857 (home-page "https://bioconductor.org/packages/regioneR/")
5858 (synopsis "Association analysis of genomic regions")
5859 (description "This package offers a statistical framework based on
5860 customizable permutation tests to assess the association between genomic
5861 region sets and other genomic features.")
5862 (license license:artistic2.0)))
5864 (define-public r-reportingtools
5866 (name "r-reportingtools")
5871 (uri (bioconductor-uri "ReportingTools" version))
5874 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
5876 `((upstream-name . "ReportingTools")))
5877 (build-system r-build-system)
5900 (home-page "https://bioconductor.org/packages/ReportingTools/")
5901 (synopsis "Tools for making reports in various formats")
5903 "The ReportingTools package enables users to easily display reports of
5904 analysis results generated from sources such as microarray and sequencing
5905 data. The package allows users to create HTML pages that may be viewed on a
5906 web browser, or in other formats. Users can generate tables with sortable and
5907 filterable columns, make and display plots, and link table entries to other
5908 data sources such as NCBI or larger plots within the HTML page. Using the
5909 package, users can also produce a table of contents page to link various
5910 reports together for a particular project that can be viewed in a web
5912 (license license:artistic2.0)))
5914 (define-public r-rhdf5
5920 (uri (bioconductor-uri "rhdf5" version))
5923 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
5924 (build-system r-build-system)
5926 (list r-rhdf5filters r-rhdf5lib))
5929 (home-page "https://bioconductor.org/packages/rhdf5")
5930 (synopsis "HDF5 interface to R")
5932 "This R/Bioconductor package provides an interface between HDF5 and R.
5933 HDF5's main features are the ability to store and access very large and/or
5934 complex datasets and a wide variety of metadata on mass storage (disk) through
5935 a completely portable file format. The rhdf5 package is thus suited for the
5936 exchange of large and/or complex datasets between R and other software
5937 package, and for letting R applications work on datasets that are larger than
5938 the available RAM.")
5939 (license license:artistic2.0)))
5941 (define-public r-rhdf5filters
5943 (name "r-rhdf5filters")
5948 (uri (bioconductor-uri "rhdf5filters" version))
5951 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
5952 (properties `((upstream-name . "rhdf5filters")))
5953 (build-system r-build-system)
5960 (home-page "https://github.com/grimbough/rhdf5filters")
5961 (synopsis "HDF5 compression filters")
5963 "This package provides a collection of compression filters for use with
5965 (license license:bsd-2)))
5967 (define-public r-rsamtools
5969 (name "r-rsamtools")
5973 (uri (bioconductor-uri "Rsamtools" version))
5976 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
5978 `((upstream-name . "Rsamtools")))
5979 (build-system r-build-system)
5982 (modify-phases %standard-phases
5983 (add-after 'unpack 'use-system-zlib
5985 (substitute* "DESCRIPTION"
5986 (("zlibbioc, ") ""))
5987 (substitute* "NAMESPACE"
5988 (("import\\(zlibbioc\\)") "")))))))
5990 (list r-biocgenerics
6000 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
6001 (synopsis "Interface to samtools, bcftools, and tabix")
6003 "This package provides an interface to the @code{samtools},
6004 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
6005 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
6006 tab-delimited (tabix) files.")
6007 (license license:expat)))
6009 ;; This is a CRAN package, but it depends on a Bioconductor package:
6011 (define-public r-restfulr
6018 (uri (cran-uri "restfulr" version))
6021 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
6022 (properties `((upstream-name . "restfulr")))
6023 (build-system r-build-system)
6025 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
6026 (home-page "https://cran.r-project.org/package=restfulr")
6027 (synopsis "R interface to RESTful web services")
6029 "This package models a RESTful service as if it were a nested R list.")
6030 (license license:artistic2.0)))
6032 (define-public r-rtracklayer
6034 (name "r-rtracklayer")
6038 (uri (bioconductor-uri "rtracklayer" version))
6041 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
6042 (build-system r-build-system)
6045 (modify-phases %standard-phases
6046 (add-after 'unpack 'use-system-zlib
6048 (substitute* "DESCRIPTION"
6049 ((" zlibbioc,") ""))
6050 (substitute* "NAMESPACE"
6051 (("import\\(zlibbioc\\)") "")))))))
6057 (list r-biocgenerics
6071 (home-page "https://bioconductor.org/packages/rtracklayer")
6072 (synopsis "R interface to genome browsers and their annotation tracks")
6074 "rtracklayer is an extensible framework for interacting with multiple
6075 genome browsers (currently UCSC built-in) and manipulating annotation tracks
6076 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
6077 built-in). The user may export/import tracks to/from the supported browsers,
6078 as well as query and modify the browser state, such as the current viewport.")
6079 (license license:artistic2.0)))
6081 ;; This is a CRAN package, but it depends on a Bioconductor package.
6082 (define-public r-samr
6089 (uri (cran-uri "samr" version))
6092 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
6093 (properties `((upstream-name . "samr")))
6094 (build-system r-build-system)
6102 (native-inputs (list gfortran))
6103 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
6104 (synopsis "Significance analysis of Microarrays")
6106 "This is a package for significance analysis of Microarrays for
6107 differential expression analysis, RNAseq data and related problems.")
6108 ;; Any version of the LGPL
6109 (license license:lgpl3+)))
6111 (define-public r-scannotatr
6113 (name "r-scannotatr")
6118 (uri (bioconductor-uri "scAnnotatR" version))
6120 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
6121 (properties `((upstream-name . "scAnnotatR")))
6122 (build-system r-build-system)
6124 (list r-annotationhub
6135 r-singlecellexperiment
6136 r-summarizedexperiment))
6137 (native-inputs (list r-knitr))
6138 (home-page "https://github.com/grisslab/scAnnotatR")
6139 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
6141 "This package comprises a set of pretrained machine learning models to
6142 predict basic immune cell types. This enables to quickly get a first
6143 annotation of the cell types present in the dataset without requiring prior
6144 knowledge. The package also lets you train using own models to predict new
6145 cell types based on specific research needs.")
6146 (license license:expat)))
6148 (define-public r-scdblfinder
6150 (name "r-scdblfinder")
6155 (uri (bioconductor-uri "scDblFinder" version))
6157 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
6158 (properties `((upstream-name . "scDblFinder")))
6159 (build-system r-build-system)
6161 (list r-biocgenerics
6179 r-singlecellexperiment
6180 r-summarizedexperiment
6182 (native-inputs (list r-knitr))
6183 (home-page "https://github.com/plger/scDblFinder")
6184 (synopsis "Detect multiplets in single-cell RNA sequencing data")
6186 "The scDblFinder package gathers various methods for the detection and
6187 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
6188 multiple cells captured within the same droplet or reaction volume). It
6189 includes methods formerly found in the scran package, and the new fast and
6190 comprehensive scDblFinder method.")
6191 (license license:gpl3)))
6193 (define-public r-scmap
6200 (uri (bioconductor-uri "scmap" version))
6202 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
6203 (properties `((upstream-name . "scmap")))
6204 (build-system r-build-system)
6219 r-singlecellexperiment
6220 r-summarizedexperiment))
6221 (native-inputs (list r-knitr))
6222 (home-page "https://github.com/hemberg-lab/scmap")
6223 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
6225 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
6226 composition of complex tissues since the technology allows researchers to
6227 define cell-types using unsupervised clustering of the transcriptome.
6228 However, due to differences in experimental methods and computational
6229 analyses, it is often challenging to directly compare the cells identified in
6230 two different experiments. @code{scmap} is a method for projecting cells from
6231 a scRNA-seq experiment onto the cell-types or individual cells identified in a
6232 different experiment.")
6233 (license license:gpl3)))
6235 (define-public r-scry
6241 (uri (bioconductor-uri "scry" version))
6244 "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
6245 (properties `((upstream-name . "scry")))
6246 (build-system r-build-system)
6248 (list r-biocsingular
6253 r-singlecellexperiment
6254 r-summarizedexperiment))
6255 (native-inputs (list r-knitr))
6256 (home-page "https://bioconductor.org/packages/scry.html")
6257 (synopsis "Small-count analysis methods for high-dimensional data")
6259 "Many modern biological datasets consist of small counts that are not
6260 well fit by standard linear-Gaussian methods such as principal component
6261 analysis. This package provides implementations of count-based feature
6262 selection and dimension reduction algorithms. These methods can be used to
6263 facilitate unsupervised analysis of any high-dimensional data such as
6264 single-cell RNA-seq.")
6265 (license license:artistic2.0)))
6267 (define-public r-seqlogo
6274 (uri (bioconductor-uri "seqLogo" version))
6277 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
6278 (properties `((upstream-name . "seqLogo")))
6279 (build-system r-build-system)
6282 (home-page "https://bioconductor.org/packages/seqLogo")
6283 (synopsis "Sequence logos for DNA sequence alignments")
6285 "seqLogo takes the position weight matrix of a DNA sequence motif and
6286 plots the corresponding sequence logo as introduced by Schneider and
6288 (license license:lgpl2.0+)))
6290 (define-public r-seqpattern
6292 (name "r-seqpattern")
6296 (uri (bioconductor-uri "seqPattern" version))
6299 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
6301 `((upstream-name . "seqPattern")))
6302 (build-system r-build-system)
6304 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
6305 (home-page "https://bioconductor.org/packages/seqPattern")
6306 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
6308 "This package provides tools to visualize oligonucleotide patterns and
6309 sequence motif occurrences across a large set of sequences centred at a common
6310 reference point and sorted by a user defined feature.")
6311 (license license:gpl3+)))
6313 (define-public r-shortread
6315 (name "r-shortread")
6320 (uri (bioconductor-uri "ShortRead" version))
6323 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
6324 (properties `((upstream-name . "ShortRead")))
6325 (build-system r-build-system)
6345 (home-page "https://bioconductor.org/packages/ShortRead")
6346 (synopsis "FASTQ input and manipulation tools")
6348 "This package implements sampling, iteration, and input of FASTQ files.
6349 It includes functions for filtering and trimming reads, and for generating a
6350 quality assessment report. Data are represented as
6351 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6352 purposes. The package also contains legacy support for early single-end,
6353 ungapped alignment formats.")
6354 (license license:artistic2.0)))
6356 (define-public r-simplifyenrichment
6358 (name "r-simplifyenrichment")
6363 (uri (bioconductor-uri "simplifyEnrichment" version))
6366 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
6368 `((upstream-name . "simplifyEnrichment")))
6369 (build-system r-build-system)
6371 (list r-annotationdbi
6388 (native-inputs (list r-knitr))
6389 (home-page "https://github.com/jokergoo/simplifyEnrichment")
6390 (synopsis "Simplify functional enrichment results")
6391 (description "This package provides a new clustering algorithm, binary
6392 cut, for clustering similarity matrices of functional terms is implemented in
6393 this package. It also provides functionalities for visualizing, summarizing
6394 and comparing the clusterings.")
6395 (license license:expat)))
6397 (define-public r-transcriptr
6399 (name "r-transcriptr")
6404 (uri (bioconductor-uri "transcriptR" version))
6406 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
6407 (properties `((upstream-name . "transcriptR")))
6408 (build-system r-build-system)
6410 (list r-biocgenerics
6425 (native-inputs (list r-knitr))
6426 (home-page "https://bioconductor.org/packages/transcriptR")
6427 (synopsis "Primary transcripts detection and quantification")
6429 "The differences in the RNA types being sequenced have an impact on the
6430 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
6431 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
6432 broader coverage of both exonic and intronic regions. The presence of
6433 intronic reads in GRO-seq type of data makes it possible to use it to
6434 computationally identify and quantify all de novo continuous regions of
6435 transcription distributed across the genome. This type of data, however, is
6436 more challenging to interpret and less common practice compared to mRNA-seq.
6437 One of the challenges for primary transcript detection concerns the
6438 simultaneous transcription of closely spaced genes, which needs to be properly
6439 divided into individually transcribed units. The R package transcriptR
6440 combines RNA-seq data with ChIP-seq data of histone modifications that mark
6441 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
6442 overcome this challenge. The advantage of this approach over the use of, for
6443 example, gene annotations is that this approach is data driven and therefore
6444 able to deal also with novel and case specific events.")
6445 (license license:gpl3)))
6447 (define-public r-trajectoryutils
6449 (name "r-trajectoryutils")
6454 (uri (bioconductor-uri "TrajectoryUtils" version))
6457 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
6459 `((upstream-name . "TrajectoryUtils")))
6460 (build-system r-build-system)
6462 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
6463 r-summarizedexperiment))
6464 (native-inputs (list r-knitr))
6465 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
6466 (synopsis "Single-cell trajectory analysis utilities")
6468 "This package implements low-level utilities for single-cell trajectory
6469 analysis, primarily intended for re-use inside higher-level packages. It
6470 includes a function to create a cluster-level minimum spanning tree and data
6471 structures to hold pseudotime inference results.")
6472 (license license:gpl3)))
6474 (define-public r-slingshot
6476 (name "r-slingshot")
6480 (uri (bioconductor-uri "slingshot" version))
6483 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
6484 (build-system r-build-system)
6490 r-singlecellexperiment
6491 r-summarizedexperiment
6495 (home-page "https://bioconductor.org/packages/slingshot")
6496 (synopsis "Tools for ordering single-cell sequencing")
6497 (description "This package provides functions for inferring continuous,
6498 branching lineage structures in low-dimensional data. Slingshot was designed
6499 to model developmental trajectories in single-cell RNA sequencing data and
6500 serve as a component in an analysis pipeline after dimensionality reduction
6501 and clustering. It is flexible enough to handle arbitrarily many branching
6502 events and allows for the incorporation of prior knowledge through supervised
6503 graph construction.")
6504 (license license:artistic2.0)))
6506 (define-public r-stager
6513 (uri (bioconductor-uri "stageR" version))
6515 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
6516 (properties `((upstream-name . "stageR")))
6517 (build-system r-build-system)
6518 (propagated-inputs (list r-summarizedexperiment))
6519 (native-inputs (list r-knitr))
6520 (home-page "https://bioconductor.org/packages/stageR")
6521 (synopsis "Stage-wise analysis of high throughput gene expression data")
6523 "The stageR package allows automated stage-wise analysis of
6524 high-throughput gene expression data. The method is published in Genome
6526 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
6527 (license license:gpl3)))
6529 (define-public r-stringdb
6536 (uri (bioconductor-uri "STRINGdb" version))
6538 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
6539 (properties `((upstream-name . "STRINGdb")))
6540 (build-system r-build-system)
6551 (home-page "https://git.bioconductor.org/packages/STRINGdb")
6552 (synopsis "Search tool for the retrieval of interacting proteins database")
6554 "The @code{STRINGdb} package provides an R interface to the STRING
6555 protein-protein interactions database. @url{https://www.string-db.org,
6556 STRING} is a database of known and predicted protein-protein interactions.
6557 The interactions include direct (physical) and indirect (functional)
6558 associations. Each interaction is associated with a combined confidence score
6559 that integrates the various evidences.")
6560 (license license:gpl2)))
6562 (define-public r-structuralvariantannotation
6564 (name "r-structuralvariantannotation")
6569 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
6571 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
6572 (build-system r-build-system)
6586 r-summarizedexperiment
6587 r-variantannotation))
6590 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
6591 (synopsis "R package designed to simplify structural variant analysis")
6593 "This package contains useful helper functions for dealing with structural
6594 variants in VCF format. The packages contains functions for parsing VCFs from
6595 a number of popular callers as well as functions for dealing with breakpoints
6596 involving two separate genomic loci encoded as GRanges objects.")
6597 (license license:gpl3)))
6599 (define-public r-summarizedexperiment
6601 (name "r-summarizedexperiment")
6605 (uri (bioconductor-uri "SummarizedExperiment" version))
6608 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
6610 `((upstream-name . "SummarizedExperiment")))
6611 (build-system r-build-system)
6624 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
6625 (synopsis "Container for representing genomic ranges by sample")
6627 "The SummarizedExperiment container contains one or more assays, each
6628 represented by a matrix-like object of numeric or other mode. The rows
6629 typically represent genomic ranges of interest and the columns represent
6631 (license license:artistic2.0)))
6633 (define-public r-sva
6640 (uri (bioconductor-uri "sva" version))
6643 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
6644 (build-system r-build-system)
6652 (home-page "https://bioconductor.org/packages/sva")
6653 (synopsis "Surrogate variable analysis")
6655 "This package contains functions for removing batch effects and other
6656 unwanted variation in high-throughput experiment. It also contains functions
6657 for identifying and building surrogate variables for high-dimensional data
6658 sets. Surrogate variables are covariates constructed directly from
6659 high-dimensional data like gene expression/RNA sequencing/methylation/brain
6660 imaging data that can be used in subsequent analyses to adjust for unknown,
6661 unmodeled, or latent sources of noise.")
6662 (license license:artistic2.0)))
6664 (define-public r-systempiper
6666 (name "r-systempiper")
6671 (uri (bioconductor-uri "systemPipeR" version))
6674 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
6675 (properties `((upstream-name . "systemPipeR")))
6676 (build-system r-build-system)
6678 (list r-biocgenerics
6689 r-summarizedexperiment
6693 (home-page "https://github.com/tgirke/systemPipeR")
6694 (synopsis "Next generation sequencing workflow and reporting environment")
6696 "This R package provides tools for building and running automated
6697 end-to-end analysis workflows for a wide range of @dfn{next generation
6698 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6699 Important features include a uniform workflow interface across different NGS
6700 applications, automated report generation, and support for running both R and
6701 command-line software, such as NGS aligners or peak/variant callers, on local
6702 computers or compute clusters. Efficient handling of complex sample sets and
6703 experimental designs is facilitated by a consistently implemented sample
6704 annotation infrastructure.")
6705 (license license:artistic2.0)))
6707 (define-public r-topgo
6713 (uri (bioconductor-uri "topGO" version))
6716 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
6718 `((upstream-name . "topGO")))
6719 (build-system r-build-system)
6721 (list r-annotationdbi
6730 (home-page "https://bioconductor.org/packages/topGO")
6731 (synopsis "Enrichment analysis for gene ontology")
6733 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6734 terms while accounting for the topology of the GO graph. Different test
6735 statistics and different methods for eliminating local similarities and
6736 dependencies between GO terms can be implemented and applied.")
6737 ;; Any version of the LGPL applies.
6738 (license license:lgpl2.1+)))
6740 (define-public r-tximport
6746 (uri (bioconductor-uri "tximport" version))
6749 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
6750 (build-system r-build-system)
6753 (home-page "https://bioconductor.org/packages/tximport")
6754 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
6756 "This package provides tools to import transcript-level abundance,
6757 estimated counts and transcript lengths, and to summarize them into matrices
6758 for use with downstream gene-level analysis packages. Average transcript
6759 length, weighted by sample-specific transcript abundance estimates, is
6760 provided as a matrix which can be used as an offset for different expression
6761 of gene-level counts.")
6762 (license license:gpl2+)))
6764 ;; This is a CRAN package, but it depends on a Bioconductor package.
6765 (define-public r-valr
6772 (uri (cran-uri "valr" version))
6775 "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
6776 (build-system r-build-system)
6784 r-rtracklayer ;bioconductor package
6789 (home-page "https://github.com/rnabioco/valr")
6790 (synopsis "Genome interval arithmetic in R")
6792 "This package enables you to read and manipulate genome intervals and
6793 signals. It provides functionality similar to command-line tool suites within
6794 R, enabling interactive analysis and visualization of genome-scale data.")
6795 (license license:expat)))
6797 (define-public r-variantannotation
6799 (name "r-variantannotation")
6803 (uri (bioconductor-uri "VariantAnnotation" version))
6806 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
6808 `((upstream-name . "VariantAnnotation")))
6810 (list r-annotationdbi
6821 r-summarizedexperiment
6828 (build-system r-build-system)
6829 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6830 (synopsis "Package for annotation of genetic variants")
6831 (description "This R package can annotate variants, compute amino acid
6832 coding changes and predict coding outcomes.")
6833 (license license:artistic2.0)))
6835 (define-public r-vsn
6842 (uri (bioconductor-uri "vsn" version))
6845 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
6846 (build-system r-build-system)
6848 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
6850 (list r-knitr)) ; for vignettes
6851 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
6852 (synopsis "Variance stabilization and calibration for microarray data")
6854 "The package implements a method for normalising microarray intensities,
6855 and works for single- and multiple-color arrays. It can also be used for data
6856 from other technologies, as long as they have similar format. The method uses
6857 a robust variant of the maximum-likelihood estimator for an
6858 additive-multiplicative error model and affine calibration. The model
6859 incorporates data calibration step (a.k.a. normalization), a model for the
6860 dependence of the variance on the mean intensity and a variance stabilizing
6861 data transformation. Differences between transformed intensities are
6862 analogous to \"normalized log-ratios\". However, in contrast to the latter,
6863 their variance is independent of the mean, and they are usually more sensitive
6864 and specific in detecting differential transcription.")
6865 (license license:artistic2.0)))
6867 ;; There is no source tarball, so we fetch the code from the Bioconductor git
6869 (define-public r-xcir
6870 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
6874 (version (git-version "1.8.0" revision commit))
6878 (url "https://git.bioconductor.org/packages/XCIR")
6880 (file-name (git-file-name name version))
6883 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
6884 (properties `((upstream-name . "XCIR")))
6885 (build-system r-build-system)
6886 (propagated-inputs (list r-biomart
6894 r-variantannotation))
6895 (native-inputs (list r-knitr))
6896 (home-page "https://github.com/SRenan/XCIR")
6897 (synopsis "Analysis of X chromosome inactivation")
6899 "This package is an R package that offers models and tools for subject
6900 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
6902 (license license:gpl2))))
6904 (define-public r-xina
6911 (uri (bioconductor-uri "XINA" version))
6913 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
6914 (properties `((upstream-name . "XINA")))
6915 (build-system r-build-system)
6924 (native-inputs (list r-knitr))
6925 (home-page "https://git.bioconductor.org/packages/XINA")
6926 (synopsis "Identifying proteins that exhibit similar patterns")
6928 "The aim of @code{XINA} is to determine which proteins exhibit similar
6929 patterns within and across experimental conditions, since proteins with
6930 co-abundance patterns may have common molecular functions. @code{XINA} imports
6931 multiple datasets, tags dataset in silico, and combines the data for subsequent
6932 subgrouping into multiple clusters. The result is a single output depicting
6933 the variation across all conditions. @code{XINA} not only extracts
6934 coabundance profiles within and across experiments, but also incorporates
6935 protein-protein interaction databases and integrative resources such as
6936 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
6937 molecular functions, respectively, and produces intuitive graphical outputs.")
6938 (license license:gpl3)))
6940 (define-public r-xmapbridge
6942 (name "r-xmapbridge")
6947 (uri (bioconductor-uri "xmapbridge" version))
6949 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
6950 (properties `((upstream-name . "xmapbridge")))
6951 (build-system r-build-system)
6952 (home-page "https://git.bioconductor.org/packages/xmapbridge")
6953 (synopsis "Display numeric data in the web based genome browser X:MAP")
6955 "The package @code{xmapbridge} can plot graphs in the X:Map genome
6956 browser. X:Map uses the Google Maps API to provide a scrollable view of the
6957 genome. It supports a number of species, and can be accessed at
6958 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
6959 suitable format. Graph plotting in R is done using calls to the functions
6960 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
6961 similar to those used by the standard plot methods in R. These result in data
6962 being written to a set of files (in a specific directory structure) that
6963 contain the data to be displayed, as well as some additional meta-data
6964 describing each of the graphs.")
6965 (license license:lgpl3)))
6967 (define-public r-xvector
6973 (uri (bioconductor-uri "XVector" version))
6976 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
6978 `((upstream-name . "XVector")))
6979 (build-system r-build-system)
6982 (modify-phases %standard-phases
6983 (add-after 'unpack 'use-system-zlib
6985 (substitute* "DESCRIPTION"
6986 (("zlibbioc, ") ""))
6987 (substitute* "NAMESPACE"
6988 (("import\\(zlibbioc\\)") ""))
6993 (list r-biocgenerics r-iranges r-s4vectors))
6994 (home-page "https://bioconductor.org/packages/XVector")
6995 (synopsis "Representation and manpulation of external sequences")
6997 "This package provides memory efficient S4 classes for storing sequences
6998 \"externally\" (behind an R external pointer, or on disk).")
6999 (license license:artistic2.0)))
7001 (define-public r-zlibbioc
7007 (uri (bioconductor-uri "zlibbioc" version))
7010 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
7012 `((upstream-name . "zlibbioc")))
7013 (build-system r-build-system)
7014 (home-page "https://bioconductor.org/packages/zlibbioc")
7015 (synopsis "Provider for zlib-1.2.5 to R packages")
7016 (description "This package uses the source code of zlib-1.2.5 to create
7017 libraries for systems that do not have these available via other means.")
7018 (license license:artistic2.0)))
7020 (define-public r-zellkonverter
7022 (name "r-zellkonverter")
7027 (uri (bioconductor-uri "zellkonverter" version))
7029 (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"))))
7030 (properties `((upstream-name . "zellkonverter")))
7031 (build-system r-build-system)
7039 r-singlecellexperiment
7040 r-summarizedexperiment))
7041 (native-inputs (list r-knitr))
7042 (home-page "https://github.com/theislab/zellkonverter")
7043 (synopsis "Conversion between AnnData and single-cell experiments objects")
7045 "This package provides methods to convert between Python AnnData objects
7046 and SingleCellExperiment objects. These are primarily intended for use by
7047 downstream Bioconductor packages that wrap Python methods for single-cell data
7048 analysis. It also includes functions to read and write H5AD files used for
7049 saving AnnData objects to disk.")
7050 (license license:expat)))
7052 (define-public r-geneplotter
7054 (name "r-geneplotter")
7059 (uri (bioconductor-uri "geneplotter" version))
7062 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
7063 (build-system r-build-system)
7071 (home-page "https://bioconductor.org/packages/geneplotter")
7072 (synopsis "Graphics functions for genomic data")
7074 "This package provides functions for plotting genomic data.")
7075 (license license:artistic2.0)))
7077 (define-public r-oligoclasses
7079 (name "r-oligoclasses")
7084 (uri (bioconductor-uri "oligoClasses" version))
7087 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
7088 (properties `((upstream-name . "oligoClasses")))
7089 (build-system r-build-system)
7103 r-summarizedexperiment))
7104 (home-page "https://bioconductor.org/packages/oligoClasses/")
7105 (synopsis "Classes for high-throughput arrays")
7107 "This package contains class definitions, validity checks, and
7108 initialization methods for classes used by the @code{oligo} and @code{crlmm}
7110 (license license:gpl2+)))
7112 (define-public r-oligo
7119 (uri (bioconductor-uri "oligo" version))
7122 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
7123 (properties `((upstream-name . "oligo")))
7124 (build-system r-build-system)
7125 (inputs (list zlib))
7140 (home-page "https://bioconductor.org/packages/oligo/")
7141 (synopsis "Preprocessing tools for oligonucleotide arrays")
7143 "This package provides a package to analyze oligonucleotide
7144 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
7145 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
7146 (license license:lgpl2.0+)))
7148 (define-public r-qvalue
7155 (uri (bioconductor-uri "qvalue" version))
7158 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
7159 (build-system r-build-system)
7161 (list r-ggplot2 r-reshape2))
7164 (home-page "https://github.com/StoreyLab/qvalue")
7165 (synopsis "Q-value estimation for false discovery rate control")
7167 "This package takes a list of p-values resulting from the simultaneous
7168 testing of many hypotheses and estimates their q-values and local @dfn{false
7169 discovery rate} (FDR) values. The q-value of a test measures the proportion
7170 of false positives incurred when that particular test is called significant.
7171 The local FDR measures the posterior probability the null hypothesis is true
7172 given the test's p-value. Various plots are automatically generated, allowing
7173 one to make sensible significance cut-offs. The software can be applied to
7174 problems in genomics, brain imaging, astrophysics, and data mining.")
7175 ;; Any version of the LGPL.
7176 (license license:lgpl3+)))
7178 (define r-rcppnumerical
7180 (name "r-rcppnumerical")
7184 (uri (cran-uri "RcppNumerical" version))
7187 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
7188 (properties `((upstream-name . "RcppNumerical")))
7189 (build-system r-build-system)
7191 `(("r-rcpp" ,r-rcpp)
7192 ("r-rcppeigen" ,r-rcppeigen)))
7194 `(("r-knitr" ,r-knitr)))
7195 (home-page "https://github.com/yixuan/RcppNumerical")
7196 (synopsis "Rcpp integration for numerical computing libraries")
7198 "This package provides a collection of libraries for numerical computing
7199 (numerical integration, optimization, etc.) and their integration with
7201 (license license:gpl2+)))
7203 (define-public r-apeglm
7209 (uri (bioconductor-uri "apeglm" version))
7212 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
7213 (properties `((upstream-name . "apeglm")))
7214 (build-system r-build-system)
7221 r-summarizedexperiment))
7222 (native-inputs (list r-knitr))
7223 (home-page "https://bioconductor.org/packages/apeglm")
7224 (synopsis "Approximate posterior estimation for GLM coefficients")
7225 (description "This package provides Bayesian shrinkage estimators for
7226 effect sizes for a variety of GLM models, using approximation of the
7227 posterior for individual coefficients.")
7228 (license license:gpl2)))
7230 (define-public r-greylistchip
7232 (name "r-greylistchip")
7236 (uri (bioconductor-uri "GreyListChIP" version))
7239 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
7240 (properties `((upstream-name . "GreyListChIP")))
7241 (build-system r-build-system)
7250 r-summarizedexperiment))
7251 (home-page "https://bioconductor.org/packages/GreyListChIP")
7252 (synopsis "Greylist artefact regions based on ChIP inputs")
7253 (description "This package identifies regions of ChIP experiments with high
7254 signal in the input, that lead to spurious peaks during peak calling.")
7255 (license license:artistic2.0)))
7257 (define-public r-diffbind
7264 (uri (bioconductor-uri "DiffBind" version))
7267 "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr"))))
7268 (properties `((upstream-name . "DiffBind")))
7269 (build-system r-build-system)
7292 r-summarizedexperiment
7294 (home-page "https://bioconductor.org/packages/DiffBind")
7295 (synopsis "Differential binding analysis of ChIP-Seq peak data")
7297 "This package computes differentially bound sites from multiple
7298 ChIP-seq experiments using affinity (quantitative) data. Also enables
7299 occupancy (overlap) analysis and plotting functions.")
7300 (license license:artistic2.0)))
7302 (define-public r-ripseeker
7304 (name "r-ripseeker")
7309 (uri (bioconductor-uri "RIPSeeker" version))
7312 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
7313 (properties `((upstream-name . "RIPSeeker")))
7314 (build-system r-build-system)
7319 r-summarizedexperiment
7323 (home-page "https://bioconductor.org/packages/RIPSeeker")
7325 "Identifying protein-associated transcripts from RIP-seq experiments")
7327 "This package infers and discriminates RIP peaks from RIP-seq alignments
7328 using two-state HMM with negative binomial emission probability. While
7329 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
7330 a suite of bioinformatics tools integrated within this self-contained software
7331 package comprehensively addressing issues ranging from post-alignments
7332 processing to visualization and annotation.")
7333 (license license:gpl2)))
7335 (define-public r-mbkmeans
7341 (uri (bioconductor-uri "mbkmeans" version))
7344 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
7345 (build-system r-build-system)
7359 r-singlecellexperiment
7360 r-summarizedexperiment))
7361 (home-page "https://bioconductor.org/packages/mbkmeans")
7362 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
7363 (description "This package implements the mini-batch k-means algorithm for
7364 large datasets, including support for on-disk data representation.")
7365 (license license:expat)))
7367 (define-public r-multtest
7374 (uri (bioconductor-uri "multtest" version))
7377 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
7378 (build-system r-build-system)
7380 (list r-survival r-biocgenerics r-biobase r-mass))
7381 (home-page "https://bioconductor.org/packages/multtest")
7382 (synopsis "Resampling-based multiple hypothesis testing")
7384 "This package can do non-parametric bootstrap and permutation
7385 resampling-based multiple testing procedures (including empirical Bayes
7386 methods) for controlling the family-wise error rate (FWER), generalized
7387 family-wise error rate (gFWER), tail probability of the proportion of
7388 false positives (TPPFP), and false discovery rate (FDR). Several choices
7389 of bootstrap-based null distribution are implemented (centered, centered
7390 and scaled, quantile-transformed). Single-step and step-wise methods are
7391 available. Tests based on a variety of T- and F-statistics (including
7392 T-statistics based on regression parameters from linear and survival models
7393 as well as those based on correlation parameters) are included. When probing
7394 hypotheses with T-statistics, users may also select a potentially faster null
7395 distribution which is multivariate normal with mean zero and variance
7396 covariance matrix derived from the vector influence function. Results are
7397 reported in terms of adjusted P-values, confidence regions and test statistic
7398 cutoffs. The procedures are directly applicable to identifying differentially
7399 expressed genes in DNA microarray experiments.")
7400 (license license:lgpl3)))
7402 (define-public r-graph
7408 (uri (bioconductor-uri "graph" version))
7411 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
7412 (build-system r-build-system)
7414 (list r-biocgenerics))
7415 (home-page "https://bioconductor.org/packages/graph")
7416 (synopsis "Handle graph data structures in R")
7418 "This package implements some simple graph handling capabilities for R.")
7419 (license license:artistic2.0)))
7421 ;; This is a CRAN package, but it depends on a Bioconductor package.
7422 (define-public r-ggm
7429 (uri (cran-uri "ggm" version))
7432 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
7433 (properties `((upstream-name . "ggm")))
7434 (build-system r-build-system)
7436 (list r-graph r-igraph))
7437 (home-page "https://cran.r-project.org/package=ggm")
7438 (synopsis "Functions for graphical Markov models")
7440 "This package provides functions and datasets for maximum likelihood
7441 fitting of some classes of graphical Markov models.")
7442 (license license:gpl2+)))
7444 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
7445 (define-public r-perfmeas
7452 (uri (cran-uri "PerfMeas" version))
7455 "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
7456 (properties `((upstream-name . "PerfMeas")))
7457 (build-system r-build-system)
7459 (list r-graph r-limma r-rbgl))
7460 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
7461 (synopsis "Performance measures for ranking and classification tasks")
7463 "This package implements different performance measures for
7464 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
7465 a given recall, F-score for single and multiple classes are available.")
7466 (license license:gpl2+)))
7468 ;; This is a CRAN package, but it depends on a Bioconductor package.
7469 (define-public r-codedepends
7471 (name "r-codedepends")
7476 (uri (cran-uri "CodeDepends" version))
7479 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
7480 (properties `((upstream-name . "CodeDepends")))
7481 (build-system r-build-system)
7483 (list r-codetools r-graph r-xml))
7484 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
7485 (synopsis "Analysis of R code for reproducible research and code comprehension")
7487 "This package provides tools for analyzing R expressions or blocks of
7488 code and determining the dependencies between them. It focuses on R scripts,
7489 but can be used on the bodies of functions. There are many facilities
7490 including the ability to summarize or get a high-level view of code,
7491 determining dependencies between variables, code improvement suggestions.")
7492 ;; Any version of the GPL
7493 (license (list license:gpl2+ license:gpl3+))))
7495 (define-public r-chippeakanno
7497 (name "r-chippeakanno")
7502 (uri (bioconductor-uri "ChIPpeakAnno" version))
7505 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
7506 (properties `((upstream-name . "ChIPpeakAnno")))
7507 (build-system r-build-system)
7509 (list r-annotationdbi
7532 r-summarizedexperiment
7536 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
7537 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
7539 "The package includes functions to retrieve the sequences around the peak,
7540 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
7541 custom features such as most conserved elements and other transcription factor
7542 binding sites supplied by users. Starting 2.0.5, new functions have been added
7543 for finding the peaks with bi-directional promoters with summary statistics
7544 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
7545 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
7546 enrichedGO (addGeneIDs).")
7547 (license license:gpl2+)))
7549 (define-public r-matrixgenerics
7551 (name "r-matrixgenerics")
7555 (uri (bioconductor-uri "MatrixGenerics" version))
7558 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
7560 `((upstream-name . "MatrixGenerics")))
7561 (build-system r-build-system)
7563 (list r-matrixstats))
7564 (home-page "https://bioconductor.org/packages/MatrixGenerics")
7565 (synopsis "S4 generic summary statistic functions for matrix-like objects")
7567 "This package provides S4 generic functions modeled after the
7568 @code{matrixStats} API for alternative matrix implementations. Packages with
7569 alternative matrix implementation can depend on this package and implement the
7570 generic functions that are defined here for a useful set of row and column
7571 summary statistics. Other package developers can import this package and
7572 handle a different matrix implementations without worrying about
7573 incompatibilities.")
7574 (license license:artistic2.0)))
7576 (define-public r-marray
7582 (uri (bioconductor-uri "marray" version))
7584 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
7585 (build-system r-build-system)
7588 (home-page "https://bioconductor.org/packages/marray")
7589 (synopsis "Exploratory analysis for two-color spotted microarray data")
7590 (description "This package contains class definitions for two-color spotted
7591 microarray data. It also includes functions for data input, diagnostic plots,
7592 normalization and quality checking.")
7593 (license license:lgpl2.0+)))
7595 (define-public r-cghbase
7601 (uri (bioconductor-uri "CGHbase" version))
7603 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
7604 (properties `((upstream-name . "CGHbase")))
7605 (build-system r-build-system)
7607 (list r-biobase r-marray))
7608 (home-page "https://bioconductor.org/packages/CGHbase")
7609 (synopsis "Base functions and classes for arrayCGH data analysis")
7610 (description "This package contains functions and classes that are needed by
7611 the @code{arrayCGH} packages.")
7612 (license license:gpl2+)))
7614 (define-public r-cghcall
7620 (uri (bioconductor-uri "CGHcall" version))
7622 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
7623 (properties `((upstream-name . "CGHcall")))
7624 (build-system r-build-system)
7626 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
7627 (home-page "https://bioconductor.org/packages/CGHcall")
7628 (synopsis "Base functions and classes for arrayCGH data analysis")
7629 (description "This package contains functions and classes that are needed by
7630 @code{arrayCGH} packages.")
7631 (license license:gpl2+)))
7633 (define-public r-qdnaseq
7639 (uri (bioconductor-uri "QDNAseq" version))
7641 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
7642 (properties `((upstream-name . "QDNAseq")))
7643 (build-system r-build-system)
7655 (home-page "https://bioconductor.org/packages/QDNAseq")
7656 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
7657 (description "The genome is divided into non-overlapping fixed-sized bins,
7658 number of sequence reads in each counted, adjusted with a simultaneous
7659 two-dimensional loess correction for sequence mappability and GC content, and
7660 filtered to remove spurious regions in the genome. Downstream steps of
7661 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
7663 (license license:gpl2+)))
7665 (define-public r-bayseq
7672 (uri (bioconductor-uri "baySeq" version))
7675 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
7676 (properties `((upstream-name . "baySeq")))
7677 (build-system r-build-system)
7679 (list r-abind r-edger r-genomicranges))
7680 (home-page "https://bioconductor.org/packages/baySeq/")
7681 (synopsis "Bayesian analysis of differential expression patterns in count data")
7683 "This package identifies differential expression in high-throughput count
7684 data, such as that derived from next-generation sequencing machines,
7685 calculating estimated posterior likelihoods of differential expression (or
7686 more complex hypotheses) via empirical Bayesian methods.")
7687 (license license:gpl3)))
7689 (define-public r-chipcomp
7696 (uri (bioconductor-uri "ChIPComp" version))
7699 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
7700 (properties `((upstream-name . "ChIPComp")))
7701 (build-system r-build-system)
7703 (list r-biocgenerics
7704 r-bsgenome-hsapiens-ucsc-hg19
7705 r-bsgenome-mmusculus-ucsc-mm9
7713 (home-page "https://bioconductor.org/packages/ChIPComp")
7714 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
7716 "ChIPComp implements a statistical method for quantitative comparison of
7717 multiple ChIP-seq datasets. It detects differentially bound sharp binding
7718 sites across multiple conditions considering matching control in ChIP-seq
7720 ;; Any version of the GPL.
7721 (license license:gpl3+)))
7723 (define-public r-riboprofiling
7725 (name "r-riboprofiling")
7730 (uri (bioconductor-uri "RiboProfiling" version))
7733 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
7734 (properties `((upstream-name . "RiboProfiling")))
7735 (build-system r-build-system)
7737 (list r-biocgenerics
7755 (home-page "https://bioconductor.org/packages/RiboProfiling/")
7756 (synopsis "Ribosome profiling data analysis")
7757 (description "Starting with a BAM file, this package provides the
7758 necessary functions for quality assessment, read start position recalibration,
7759 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
7760 of count data: pairs, log fold-change, codon frequency and coverage
7761 assessment, principal component analysis on codon coverage.")
7762 (license license:gpl3)))
7764 (define-public r-riboseqr
7771 (uri (bioconductor-uri "riboSeqR" version))
7774 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
7775 (properties `((upstream-name . "riboSeqR")))
7776 (build-system r-build-system)
7785 (home-page "https://bioconductor.org/packages/riboSeqR/")
7786 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
7788 "This package provides plotting functions, frameshift detection and
7789 parsing of genetic sequencing data from ribosome profiling experiments.")
7790 (license license:gpl3)))
7792 (define-public r-interactionset
7794 (name "r-interactionset")
7799 (uri (bioconductor-uri "InteractionSet" version))
7802 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
7804 `((upstream-name . "InteractionSet")))
7805 (build-system r-build-system)
7807 (list r-biocgenerics
7814 r-summarizedexperiment))
7817 (home-page "https://bioconductor.org/packages/InteractionSet")
7818 (synopsis "Base classes for storing genomic interaction data")
7820 "This package provides the @code{GInteractions},
7821 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
7822 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
7824 (license license:gpl3)))
7826 (define-public r-genomicinteractions
7828 (name "r-genomicinteractions")
7833 (uri (bioconductor-uri "GenomicInteractions" version))
7836 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
7838 `((upstream-name . "GenomicInteractions")))
7839 (build-system r-build-system)
7859 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
7860 (synopsis "R package for handling genomic interaction data")
7862 "This R package provides tools for handling genomic interaction data,
7863 such as ChIA-PET/Hi-C, annotating genomic features with interaction
7864 information and producing various plots and statistics.")
7865 (license license:gpl3)))
7867 (define-public r-ctc
7874 (uri (bioconductor-uri "ctc" version))
7877 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
7878 (build-system r-build-system)
7879 (propagated-inputs (list r-amap))
7880 (home-page "https://bioconductor.org/packages/ctc/")
7881 (synopsis "Cluster and tree conversion")
7883 "This package provides tools for exporting and importing classification
7884 trees and clusters to other programs.")
7885 (license license:gpl2)))
7887 (define-public r-goseq
7894 (uri (bioconductor-uri "goseq" version))
7897 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
7898 (build-system r-build-system)
7900 (list r-annotationdbi
7906 (home-page "https://bioconductor.org/packages/goseq/")
7907 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
7909 "This package provides tools to detect Gene Ontology and/or other user
7910 defined categories which are over/under represented in RNA-seq data.")
7911 (license license:lgpl2.0+)))
7913 (define-public r-glimma
7920 (uri (bioconductor-uri "Glimma" version))
7923 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
7924 (properties `((upstream-name . "Glimma")))
7925 (build-system r-build-system)
7933 r-summarizedexperiment))
7936 (home-page "https://github.com/Shians/Glimma")
7937 (synopsis "Interactive HTML graphics")
7939 "This package generates interactive visualisations for analysis of
7940 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
7941 HTML page. The interactions are built on top of the popular static
7942 representations of analysis results in order to provide additional
7944 (license license:lgpl3)))
7946 (define-public r-rots
7953 (uri (bioconductor-uri "ROTS" version))
7956 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
7957 (properties `((upstream-name . "ROTS")))
7958 (build-system r-build-system)
7960 (list r-biobase r-rcpp))
7961 (home-page "https://bioconductor.org/packages/ROTS/")
7962 (synopsis "Reproducibility-Optimized Test Statistic")
7964 "This package provides tools for calculating the
7965 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
7967 (license license:gpl2+)))
7969 (define-public r-plgem
7976 (uri (bioconductor-uri "plgem" version))
7979 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
7980 (build-system r-build-system)
7982 (list r-biobase r-mass))
7983 (home-page "http://www.genopolis.it")
7984 (synopsis "Detect differential expression in microarray and proteomics datasets")
7986 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
7987 model the variance-versus-mean dependence that exists in a variety of
7988 genome-wide datasets, including microarray and proteomics data. The use of
7989 PLGEM has been shown to improve the detection of differentially expressed
7990 genes or proteins in these datasets.")
7991 (license license:gpl2)))
7993 (define-public r-inspect
8000 (uri (bioconductor-uri "INSPEcT" version))
8003 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
8004 (properties `((upstream-name . "INSPEcT")))
8005 (build-system r-build-system)
8026 r-summarizedexperiment
8027 r-txdb-mmusculus-ucsc-mm9-knowngene))
8030 (home-page "https://bioconductor.org/packages/INSPEcT")
8031 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
8033 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
8034 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
8035 order to evaluate synthesis, processing and degradation rates and assess via
8036 modeling the rates that determines changes in mature mRNA levels.")
8037 (license license:gpl2)))
8039 (define-public r-dnabarcodes
8041 (name "r-dnabarcodes")
8046 (uri (bioconductor-uri "DNABarcodes" version))
8049 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
8050 (properties `((upstream-name . "DNABarcodes")))
8051 (build-system r-build-system)
8053 (list r-bh r-matrix r-rcpp))
8056 (home-page "https://bioconductor.org/packages/DNABarcodes")
8057 (synopsis "Create and analyze DNA barcodes")
8059 "This package offers tools to create DNA barcode sets capable of
8060 correcting insertion, deletion, and substitution errors. Existing barcodes
8061 can be analyzed regarding their minimal, maximal and average distances between
8062 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
8063 demultiplexed, i.e. assigned to their original reference barcode.")
8064 (license license:gpl2)))
8066 (define-public r-ruvseq
8073 (uri (bioconductor-uri "RUVSeq" version))
8076 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
8077 (properties `((upstream-name . "RUVSeq")))
8078 (build-system r-build-system)
8080 (list r-biobase r-edaseq r-edger r-mass))
8083 (home-page "https://github.com/drisso/RUVSeq")
8084 (synopsis "Remove unwanted variation from RNA-Seq data")
8086 "This package implements methods to @dfn{remove unwanted variation} (RUV)
8087 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
8089 (license license:artistic2.0)))
8091 (define-public r-biocneighbors
8093 (name "r-biocneighbors")
8098 (uri (bioconductor-uri "BiocNeighbors" version))
8101 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
8102 (properties `((upstream-name . "BiocNeighbors")))
8103 (build-system r-build-system)
8105 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
8108 (home-page "https://bioconductor.org/packages/BiocNeighbors")
8109 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
8111 "This package implements exact and approximate methods for nearest
8112 neighbor detection, in a framework that allows them to be easily switched
8113 within Bioconductor packages or workflows. The exact algorithm is implemented
8114 using pre-clustering with the k-means algorithm. Functions are also provided
8115 to search for all neighbors within a given distance. Parallelization is
8116 achieved for all methods using the BiocParallel framework.")
8117 (license license:gpl3)))
8119 (define-public r-scaledmatrix
8121 (name "r-scaledmatrix")
8126 (uri (bioconductor-uri "ScaledMatrix" version))
8129 "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"))))
8130 (properties `((upstream-name . "ScaledMatrix")))
8131 (build-system r-build-system)
8133 (list r-delayedarray r-matrix r-s4vectors))
8134 (native-inputs (list r-knitr))
8135 (home-page "https://github.com/LTLA/ScaledMatrix")
8136 (synopsis "Create a DelayedMatrix of scaled and centered values")
8138 "This package provides delayed computation of a matrix of scaled and
8139 centered values. The result is equivalent to using the @code{scale} function
8140 but avoids explicit realization of a dense matrix during block processing.
8141 This permits greater efficiency in common operations, most notably matrix
8143 (license license:gpl3)))
8145 (define-public r-treeio
8152 (uri (bioconductor-uri "treeio" version))
8155 "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"))))
8156 (properties `((upstream-name . "treeio")))
8157 (build-system r-build-system)
8166 (native-inputs (list r-knitr))
8167 (home-page "https://github.com/YuLab-SMU/treeio")
8168 (synopsis "Base classes and functions for Phylogenetic tree input and output")
8170 "This is an R package to make it easier to import and store phylogenetic
8171 trees with associated data; and to link external data from different sources
8172 to phylogeny. It also supports exporting phylogenetic trees with
8173 heterogeneous associated data to a single tree file and can be served as a
8174 platform for merging tree with associated data and converting file formats.")
8175 (license license:artistic2.0)))
8177 (define-public r-ggtree
8184 (uri (bioconductor-uri "ggtree" version))
8187 "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"))))
8188 (properties `((upstream-name . "ggtree")))
8189 (build-system r-build-system)
8204 (native-inputs (list r-knitr))
8205 (home-page "https://yulab-smu.top/treedata-book/")
8206 (synopsis "R package for visualization of trees and annotation data")
8208 "This package extends the ggplot2 plotting system which implements a
8209 grammar of graphics. ggtree is designed for visualization and annotation of
8210 phylogenetic trees and other tree-like structures with their annotation
8212 (license license:artistic2.0)))
8214 (define-public r-metapod
8221 (uri (bioconductor-uri "metapod" version))
8224 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
8225 (properties `((upstream-name . "metapod")))
8226 (build-system r-build-system)
8231 (home-page "https://bioconductor.org/packages/metapod")
8232 (synopsis "Meta-analyses on p-values of differential analyses")
8234 "This package implements a variety of methods for combining p-values in
8235 differential analyses of genome-scale datasets. Functions can combine
8236 p-values across different tests in the same analysis (e.g., genomic windows in
8237 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
8238 analyses (e.g., replicated comparisons, effect of different treatment
8239 conditions). Support is provided for handling log-transformed input p-values,
8240 missing values and weighting where appropriate.")
8241 (license license:gpl3)))
8243 (define-public r-biocsingular
8245 (name "r-biocsingular")
8250 (uri (bioconductor-uri "BiocSingular" version))
8253 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
8254 (properties `((upstream-name . "BiocSingular")))
8255 (build-system r-build-system)
8269 (home-page "https://github.com/LTLA/BiocSingular")
8270 (synopsis "Singular value decomposition for Bioconductor packages")
8272 "This package implements exact and approximate methods for singular value
8273 decomposition and principal components analysis, in a framework that allows
8274 them to be easily switched within Bioconductor packages or workflows. Where
8275 possible, parallelization is achieved using the BiocParallel framework.")
8276 (license license:gpl3)))
8278 (define-public r-destiny
8285 (uri (bioconductor-uri "destiny" version))
8288 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
8289 (build-system r-build-system)
8307 r-singlecellexperiment
8309 r-summarizedexperiment
8314 (list r-knitr r-nbconvertr)) ; for vignettes
8315 (home-page "https://bioconductor.org/packages/destiny/")
8316 (synopsis "Create and plot diffusion maps")
8317 (description "This package provides tools to create and plot diffusion
8319 ;; Any version of the GPL
8320 (license license:gpl3+)))
8322 (define-public r-savr
8329 (uri (bioconductor-uri "savR" version))
8332 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
8333 (properties `((upstream-name . "savR")))
8334 (build-system r-build-system)
8336 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
8337 (home-page "https://github.com/bcalder/savR")
8338 (synopsis "Parse and analyze Illumina SAV files")
8340 "This package provides tools to parse Illumina Sequence Analysis
8341 Viewer (SAV) files, access data, and generate QC plots.")
8342 (license license:agpl3+)))
8344 (define-public r-chipexoqual
8346 (name "r-chipexoqual")
8351 (uri (bioconductor-uri "ChIPexoQual" version))
8354 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
8355 (properties `((upstream-name . "ChIPexoQual")))
8356 (build-system r-build-system)
8358 (list r-biocparallel
8377 (home-page "https://github.com/keleslab/ChIPexoQual")
8378 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
8380 "This package provides a quality control pipeline for ChIP-exo/nexus
8382 (license license:gpl2+)))
8384 (define-public r-copynumber
8386 (name "r-copynumber")
8390 (uri (bioconductor-uri "copynumber" version))
8393 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
8394 (build-system r-build-system)
8396 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
8397 (home-page "https://bioconductor.org/packages/copynumber")
8398 (synopsis "Segmentation of single- and multi-track copy number data")
8400 "This package segments single- and multi-track copy number data by a
8401 penalized least squares regression method.")
8402 (license license:artistic2.0)))
8404 (define-public r-dnacopy
8411 (uri (bioconductor-uri "DNAcopy" version))
8414 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
8415 (properties `((upstream-name . "DNAcopy")))
8416 (build-system r-build-system)
8417 (native-inputs (list gfortran))
8418 (home-page "https://bioconductor.org/packages/DNAcopy")
8419 (synopsis "DNA copy number data analysis")
8421 "This package implements the @dfn{circular binary segmentation} (CBS)
8422 algorithm to segment DNA copy number data and identify genomic regions with
8423 abnormal copy number.")
8424 (license license:gpl2+)))
8426 ;; This is a CRAN package, but it uncharacteristically depends on a
8427 ;; Bioconductor package.
8428 (define-public r-htscluster
8430 (name "r-htscluster")
8435 (uri (cran-uri "HTSCluster" version))
8438 "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
8439 (properties `((upstream-name . "HTSCluster")))
8440 (build-system r-build-system)
8442 (list r-capushe r-edger r-plotrix))
8443 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
8444 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
8446 "This package provides a Poisson mixture model is implemented to cluster
8447 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
8448 estimation is performed using either the EM or CEM algorithm, and the slope
8449 heuristics are used for model selection (i.e., to choose the number of
8451 (license license:gpl3+)))
8453 (define-public r-deds
8460 (uri (bioconductor-uri "DEDS" version))
8463 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
8464 (properties `((upstream-name . "DEDS")))
8465 (build-system r-build-system)
8466 (home-page "https://bioconductor.org/packages/DEDS/")
8467 (synopsis "Differential expression via distance summary for microarray data")
8469 "This library contains functions that calculate various statistics of
8470 differential expression for microarray data, including t statistics, fold
8471 change, F statistics, SAM, moderated t and F statistics and B statistics. It
8472 also implements a new methodology called DEDS (Differential Expression via
8473 Distance Summary), which selects differentially expressed genes by integrating
8474 and summarizing a set of statistics using a weighted distance approach.")
8475 ;; Any version of the LGPL.
8476 (license license:lgpl3+)))
8478 ;; This is a CRAN package, but since it depends on a Bioconductor package we
8480 (define-public r-nbpseq
8487 (uri (cran-uri "NBPSeq" version))
8490 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
8491 (properties `((upstream-name . "NBPSeq")))
8492 (build-system r-build-system)
8495 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
8496 (synopsis "Negative binomial models for RNA-Seq data")
8498 "This package provides negative binomial models for two-group comparisons
8499 and regression inferences from RNA-sequencing data.")
8500 (license license:gpl2)))
8502 (define-public r-ebseq
8509 (uri (bioconductor-uri "EBSeq" version))
8512 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
8513 (properties `((upstream-name . "EBSeq")))
8514 (build-system r-build-system)
8516 (list r-blockmodeling r-gplots r-testthat))
8517 (home-page "https://bioconductor.org/packages/EBSeq")
8518 (synopsis "Differential expression analysis of RNA-seq data")
8520 "This package provides tools for differential expression analysis at both
8521 gene and isoform level using RNA-seq data")
8522 (license license:artistic2.0)))
8524 (define-public r-karyoploter
8526 (name "r-karyoploter")
8530 (uri (bioconductor-uri "karyoploteR" version))
8533 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
8534 (build-system r-build-system)
8536 (list r-annotationdbi
8550 r-variantannotation))
8553 (home-page "https://bioconductor.org/packages/karyoploteR/")
8554 (synopsis "Plot customizable linear genomes displaying arbitrary data")
8555 (description "This package creates karyotype plots of arbitrary genomes and
8556 offers a complete set of functions to plot arbitrary data on them. It mimics
8557 many R base graphics functions coupling them with a coordinate change function
8558 automatically mapping the chromosome and data coordinates into the plot
8560 (license license:artistic2.0)))
8562 (define-public r-lpsymphony
8564 (name "r-lpsymphony")
8569 (uri (bioconductor-uri "lpsymphony" version))
8572 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
8573 (build-system r-build-system)
8577 '(modify-phases %standard-phases
8578 (add-after 'unpack 'make-build-order-reproducible
8580 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
8581 "src/SYMPHONY/Cgl/configure")
8582 (("for file in `ls \\*/Makefile.in`")
8583 "for file in `ls */Makefile.in | sort`")))))))
8587 (list pkg-config r-knitr))
8588 (home-page "https://r-forge.r-project.org/projects/rsymphony")
8589 (synopsis "Symphony integer linear programming solver in R")
8591 "This package was derived from Rsymphony. The package provides an R
8592 interface to SYMPHONY, a linear programming solver written in C++. The main
8593 difference between this package and Rsymphony is that it includes the solver
8594 source code, while Rsymphony expects to find header and library files on the
8595 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
8596 to install interface to SYMPHONY.")
8597 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
8598 ;; lpsimphony is released under the same terms.
8599 (license license:epl1.0)))
8601 (define-public r-ihw
8608 (uri (bioconductor-uri "IHW" version))
8611 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
8612 (properties `((upstream-name . "IHW")))
8613 (build-system r-build-system)
8615 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
8618 (home-page "https://bioconductor.org/packages/IHW")
8619 (synopsis "Independent hypothesis weighting")
8621 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
8622 procedure that increases power compared to the method of Benjamini and
8623 Hochberg by assigning data-driven weights to each hypothesis. The input to
8624 IHW is a two-column table of p-values and covariates. The covariate can be
8625 any continuous-valued or categorical variable that is thought to be
8626 informative on the statistical properties of each hypothesis test, while it is
8627 independent of the p-value under the null hypothesis.")
8628 (license license:artistic2.0)))
8630 (define-public r-icobra
8637 (uri (bioconductor-uri "iCOBRA" version))
8640 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
8641 (properties `((upstream-name . "iCOBRA")))
8642 (build-system r-build-system)
8658 (home-page "https://bioconductor.org/packages/iCOBRA")
8659 (synopsis "Comparison and visualization of ranking and assignment methods")
8661 "This package provides functions for calculation and visualization of
8662 performance metrics for evaluation of ranking and binary
8663 classification (assignment) methods. It also contains a Shiny application for
8664 interactive exploration of results.")
8665 (license license:gpl2+)))
8667 (define-public r-residualmatrix
8669 (name "r-residualmatrix")
8674 (uri (bioconductor-uri "ResidualMatrix" version))
8677 "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"))))
8679 `((upstream-name . "ResidualMatrix")))
8680 (build-system r-build-system)
8682 (list r-delayedarray r-matrix r-s4vectors))
8685 (home-page "https://github.com/LTLA/ResidualMatrix")
8686 (synopsis "Create a DelayedMatrix of regression residuals")
8688 "This package implements tools for delayed computation of a matrix of
8689 residuals after fitting a linear model to each column of an input matrix. It
8690 also supports partial computation of residuals where selected factors are to
8691 be preserved in the output matrix. It implements a number of efficient
8692 methods for operating on the delayed matrix of residuals, most notably matrix
8693 multiplication and calculation of row/column sums or means.")
8694 (license license:gpl3)))
8696 (define-public r-batchelor
8698 (name "r-batchelor")
8703 (uri (bioconductor-uri "batchelor" version))
8706 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
8707 (properties `((upstream-name . "batchelor")))
8708 (build-system r-build-system)
8716 r-delayedmatrixstats
8724 r-singlecellexperiment
8725 r-summarizedexperiment))
8726 (native-inputs (list r-knitr))
8727 (home-page "https://bioconductor.org/packages/batchelor")
8728 (synopsis "Single-Cell Batch Correction Methods")
8730 "This package implements a variety of methods for batch correction of
8731 single-cell (RNA sequencing) data. This includes methods based on detecting
8732 mutually nearest neighbors, as well as several efficient variants of linear
8733 regression of the log-expression values. Functions are also provided to
8734 perform global rescaling to remove differences in depth between batches, and
8735 to perform a principal components analysis that is robust to differences in
8736 the numbers of cells across batches.")
8737 (license license:gpl3)))
8739 (define-public r-mast
8746 (uri (bioconductor-uri "MAST" version))
8749 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
8750 (properties `((upstream-name . "MAST")))
8751 (build-system r-build-system)
8762 r-singlecellexperiment
8764 r-summarizedexperiment))
8767 (home-page "https://github.com/RGLab/MAST/")
8768 (synopsis "Model-based analysis of single cell transcriptomics")
8770 "This package provides methods and models for handling zero-inflated
8771 single cell assay data.")
8772 (license license:gpl2+)))
8774 (define-public r-monocle
8781 (uri (bioconductor-uri "monocle" version))
8784 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
8785 (build-system r-build-system)
8819 (home-page "https://bioconductor.org/packages/monocle")
8820 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
8822 "Monocle performs differential expression and time-series analysis for
8823 single-cell expression experiments. It orders individual cells according to
8824 progress through a biological process, without knowing ahead of time which
8825 genes define progress through that process. Monocle also performs
8826 differential expression analysis, clustering, visualization, and other useful
8827 tasks on single cell expression data. It is designed to work with RNA-Seq and
8828 qPCR data, but could be used with other types as well.")
8829 (license license:artistic2.0)))
8831 (define-public r-leidenbase
8832 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
8835 (name "r-leidenbase")
8836 (version (git-version "0.1.9" revision commit))
8841 (url "https://github.com/cole-trapnell-lab/leidenbase")
8843 (file-name (git-file-name name version))
8846 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
8847 (properties `((upstream-name . "leidenbase")))
8848 (build-system r-build-system)
8855 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
8856 (synopsis "R and C wrappers to run the Leiden find_partition function")
8858 "This package provides an R to C interface that runs the Leiden
8859 community detection algorithm to find a basic partition. It runs the
8860 equivalent of the @code{find_partition} function. This package includes the
8861 required source code files from the official Leidenalg distribution and
8862 several functions from the R igraph package.")
8863 (license license:gpl3+))))
8865 (define-public r-sanssouci
8866 ;; sansscouci doesn't have a (versioned) release yet.
8867 ;; This is the latest commit as of packaging for Guix.
8868 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
8871 (name "r-sanssouci")
8872 (version (git-version "0" revision commit))
8876 (url "https://github.com/pneuvial/sanssouci.git")
8878 (file-name (git-file-name name version))
8881 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
8882 (build-system r-build-system)
8884 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
8885 (home-page "https://pneuvial.github.io/sanssouci")
8886 (synopsis "Post Hoc multiple testing inference")
8888 "The goal of sansSouci is to perform post hoc inference: in a multiple
8889 testing context, sansSouci provides statistical guarantees on possibly
8890 user-defined and/or data-driven sets of hypotheses.")
8891 (license license:gpl3))))
8893 (define-public r-monocle3
8901 (url "https://github.com/cole-trapnell-lab/monocle3")
8903 (file-name (git-file-name name version))
8906 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
8907 (build-system r-build-system)
8913 r-delayedmatrixstats
8948 r-singlecellexperiment
8953 (home-page "https://github.com/cole-trapnell-lab/monocle3")
8954 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
8956 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
8957 (license license:expat)))
8959 (define-public r-noiseq
8966 (uri (bioconductor-uri "NOISeq" version))
8969 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
8970 (properties `((upstream-name . "NOISeq")))
8971 (build-system r-build-system)
8973 (list r-biobase r-matrix))
8974 (home-page "https://bioconductor.org/packages/NOISeq")
8975 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
8977 "This package provides tools to support the analysis of RNA-seq
8978 expression data or other similar kind of data. It provides exploratory plots
8979 to evaluate saturation, count distribution, expression per chromosome, type of
8980 detected features, features length, etc. It also supports the analysis of
8981 differential expression between two experimental conditions with no parametric
8983 (license license:artistic2.0)))
8985 (define-public r-scdd
8992 (uri (bioconductor-uri "scDD" version))
8995 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
8996 (properties `((upstream-name . "scDD")))
8997 (build-system r-build-system)
9008 r-singlecellexperiment
9009 r-summarizedexperiment))
9012 (home-page "https://github.com/kdkorthauer/scDD")
9013 (synopsis "Mixture modeling of single-cell RNA-seq data")
9015 "This package implements a method to analyze single-cell RNA-seq data
9016 utilizing flexible Dirichlet Process mixture models. Genes with differential
9017 distributions of expression are classified into several interesting patterns
9018 of differences between two conditions. The package also includes functions
9019 for simulating data with these patterns from negative binomial
9021 (license license:gpl2)))
9023 (define-public r-scone
9030 (uri (bioconductor-uri "scone" version))
9033 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
9034 (build-system r-build-system)
9055 r-singlecellexperiment
9056 r-summarizedexperiment))
9059 (home-page "https://bioconductor.org/packages/scone")
9060 (synopsis "Single cell overview of normalized expression data")
9062 "SCONE is an R package for comparing and ranking the performance of
9063 different normalization schemes for single-cell RNA-seq and other
9064 high-throughput analyses.")
9065 (license license:artistic2.0)))
9067 (define-public r-geoquery
9074 (uri (bioconductor-uri "GEOquery" version))
9077 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
9078 (properties `((upstream-name . "GEOquery")))
9079 (build-system r-build-system)
9093 (home-page "https://github.com/seandavi/GEOquery/")
9094 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
9096 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
9097 microarray data. Given the rich and varied nature of this resource, it is
9098 only natural to want to apply BioConductor tools to these data. GEOquery is
9099 the bridge between GEO and BioConductor.")
9100 (license license:gpl2)))
9102 (define-public r-illuminaio
9104 (name "r-illuminaio")
9109 (uri (bioconductor-uri "illuminaio" version))
9112 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
9113 (build-system r-build-system)
9116 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
9117 (synopsis "Parse Illumina microarray output files")
9119 "This package provides tools for parsing Illumina's microarray output
9120 files, including IDAT.")
9121 (license license:gpl2)))
9123 (define-public r-siggenes
9130 (uri (bioconductor-uri "siggenes" version))
9133 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
9134 (build-system r-build-system)
9136 (list r-biobase r-multtest r-scrime))
9137 (home-page "https://bioconductor.org/packages/siggenes/")
9139 "Multiple testing using SAM and Efron's empirical Bayes approaches")
9141 "This package provides tools for the identification of differentially
9142 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
9143 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
9144 Bayes Analyses of Microarrays} (EBAM).")
9145 (license license:lgpl2.0+)))
9147 (define-public r-bumphunter
9149 (name "r-bumphunter")
9154 (uri (bioconductor-uri "bumphunter" version))
9157 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
9158 (build-system r-build-system)
9160 (list r-annotationdbi
9173 (home-page "https://github.com/ririzarr/bumphunter")
9174 (synopsis "Find bumps in genomic data")
9176 "This package provides tools for finding bumps in genomic data in order
9177 to identify differentially methylated regions in epigenetic epidemiology
9179 (license license:artistic2.0)))
9181 (define-public r-milor
9187 (uri (bioconductor-uri "miloR" version))
9190 "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
9191 (properties `((upstream-name . "miloR")))
9192 (build-system r-build-system)
9194 (list r-biocgenerics
9214 r-singlecellexperiment
9216 r-summarizedexperiment
9219 (native-inputs (list r-knitr))
9220 (home-page "https://marionilab.github.io/miloR")
9221 (synopsis "Differential neighbourhood abundance testing on a graph")
9223 "Milo performs single-cell differential abundance testing. Cell states
9224 are modelled as representative neighbourhoods on a nearest neighbour graph.
9225 Hypothesis testing is performed using a negative bionomial generalized linear
9227 (license license:gpl3)))
9229 (define-public r-minfi
9236 (uri (bioconductor-uri "minfi" version))
9239 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
9240 (build-system r-build-system)
9250 r-delayedmatrixstats
9270 r-summarizedexperiment))
9273 (home-page "https://github.com/hansenlab/minfi")
9274 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
9276 "This package provides tools to analyze and visualize Illumina Infinium
9277 methylation arrays.")
9278 (license license:artistic2.0)))
9280 (define-public r-methylumi
9282 (name "r-methylumi")
9287 (uri (bioconductor-uri "methylumi" version))
9290 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
9291 (build-system r-build-system)
9297 r-fdb-infiniummethylation-hg19
9311 r-summarizedexperiment))
9314 (home-page "https://bioconductor.org/packages/methylumi")
9315 (synopsis "Handle Illumina methylation data")
9317 "This package provides classes for holding and manipulating Illumina
9318 methylation data. Based on eSet, it can contain MIAME information, sample
9319 information, feature information, and multiple matrices of data. An
9320 \"intelligent\" import function, methylumiR can read the Illumina text files
9321 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
9322 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
9323 background correction, and quality control features for GoldenGate, Infinium,
9324 and Infinium HD arrays are also included.")
9325 (license license:gpl2)))
9327 (define-public r-lumi
9334 (uri (bioconductor-uri "lumi" version))
9337 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
9338 (build-system r-build-system)
9355 (home-page "https://bioconductor.org/packages/lumi")
9356 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
9358 "The lumi package provides an integrated solution for the Illumina
9359 microarray data analysis. It includes functions of Illumina
9360 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
9361 variance stabilization, normalization and gene annotation at the probe level.
9362 It also includes the functions of processing Illumina methylation microarrays,
9363 especially Illumina Infinium methylation microarrays.")
9364 (license license:lgpl2.0+)))
9366 (define-public r-linnorm
9373 (uri (bioconductor-uri "Linnorm" version))
9376 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
9377 (properties `((upstream-name . "Linnorm")))
9378 (build-system r-build-system)
9400 (home-page "http://www.jjwanglab.org/Linnorm/")
9401 (synopsis "Linear model and normality based transformation method")
9403 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
9404 count data or any large scale count data. It transforms such datasets for
9405 parametric tests. In addition to the transformtion function (@code{Linnorm}),
9406 the following pipelines are implemented:
9409 @item Library size/batch effect normalization (@code{Linnorm.Norm})
9410 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
9411 clustering or hierarchical clustering (@code{Linnorm.tSNE},
9412 @code{Linnorm.PCA}, @code{Linnorm.HClust})
9413 @item Differential expression analysis or differential peak detection using
9414 limma (@code{Linnorm.limma})
9415 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
9416 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
9417 @item Stable gene selection for scRNA-seq data; for users without or who do
9418 not want to rely on spike-in genes (@code{Linnorm.SGenes})
9419 @item Data imputation (@code{Linnorm.DataImput}).
9422 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
9423 @code{RnaXSim} function is included for simulating RNA-seq data for the
9424 evaluation of DEG analysis methods.")
9425 (license license:expat)))
9427 (define-public r-ioniser
9434 (uri (bioconductor-uri "IONiseR" version))
9437 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
9438 (properties `((upstream-name . "IONiseR")))
9439 (build-system r-build-system)
9441 (list r-biocgenerics
9456 (home-page "https://bioconductor.org/packages/IONiseR/")
9457 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
9459 "IONiseR provides tools for the quality assessment of Oxford Nanopore
9460 MinION data. It extracts summary statistics from a set of fast5 files and can
9461 be used either before or after base calling. In addition to standard
9462 summaries of the read-types produced, it provides a number of plots for
9463 visualising metrics relative to experiment run time or spatially over the
9464 surface of a flowcell.")
9465 (license license:expat)))
9467 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
9468 (define-public r-mutoss
9475 (uri (cran-uri "mutoss" version))
9478 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
9479 (properties `((upstream-name . "mutoss")))
9480 (build-system r-build-system)
9482 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
9483 (home-page "https://github.com/kornl/mutoss/")
9484 (synopsis "Unified multiple testing procedures")
9486 "This package is designed to ease the application and comparison of
9487 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
9488 are standardized and usable by the accompanying mutossGUI package.")
9489 ;; Any version of the GPL.
9490 (license (list license:gpl2+ license:gpl3+))))
9492 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
9493 ;; from Bioconductor, so we put it here.
9494 (define-public r-metap
9501 (uri (cran-uri "metap" version))
9504 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
9505 (build-system r-build-system)
9513 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
9514 (synopsis "Meta-analysis of significance values")
9516 "The canonical way to perform meta-analysis involves using effect sizes.
9517 When they are not available this package provides a number of methods for
9518 meta-analysis of significance values including the methods of Edgington,
9519 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
9520 published results; and a routine for graphical display.")
9521 (license license:gpl2)))
9523 (define-public r-tradeseq
9529 (uri (bioconductor-uri "tradeSeq" version))
9532 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
9533 (build-system r-build-system)
9549 r-singlecellexperiment
9551 r-summarizedexperiment
9557 (home-page "https://statomics.github.io/tradeSeq/index.html")
9558 (synopsis "Trajectory-based differential expression analysis")
9560 "This package provides a flexible method for fitting regression models that
9561 can be used to find genes that are differentially expressed along one or
9562 multiple lineages in a trajectory. Based on the fitted models, it uses a
9563 variety of tests suited to answer different questions of interest, e.g. the
9564 discovery of genes for which expression is associated with pseudotime, or which
9565 are differentially expressed (in a specific region) along the trajectory. It
9566 fits a negative binomial generalized additive model (GAM) for each gene, and
9567 performs inference on the parameters of the GAM.")
9568 (license license:expat)))
9570 (define-public r-triform
9577 (uri (bioconductor-uri "triform" version))
9580 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
9581 (build-system r-build-system)
9583 (list r-biocgenerics r-iranges r-yaml))
9584 (home-page "https://bioconductor.org/packages/triform/")
9585 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
9587 "The Triform algorithm uses model-free statistics to identify peak-like
9588 distributions of TF ChIP sequencing reads, taking advantage of an improved
9589 peak definition in combination with known profile characteristics.")
9590 (license license:gpl2)))
9592 (define-public r-varianttools
9594 (name "r-varianttools")
9599 (uri (bioconductor-uri "VariantTools" version))
9602 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
9603 (properties `((upstream-name . "VariantTools")))
9604 (build-system r-build-system)
9619 r-variantannotation))
9620 (home-page "https://bioconductor.org/packages/VariantTools/")
9621 (synopsis "Tools for exploratory analysis of variant calls")
9623 "Explore, diagnose, and compare variant calls using filters. The
9624 VariantTools package supports a workflow for loading data, calling single
9625 sample variants and tumor-specific somatic mutations or other sample-specific
9626 variant types (e.g., RNA editing). Most of the functions operate on
9627 alignments (BAM files) or datasets of called variants. The user is expected
9628 to have already aligned the reads with a separate tool, e.g., GSNAP via
9630 (license license:artistic2.0)))
9632 (define-public r-heatplus
9639 (uri (bioconductor-uri "Heatplus" version))
9642 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
9643 (properties `((upstream-name . "Heatplus")))
9644 (build-system r-build-system)
9646 (list r-rcolorbrewer))
9647 (home-page "https://github.com/alexploner/Heatplus")
9648 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
9650 "This package provides tools to display a rectangular heatmap (intensity
9651 plot) of a data matrix. By default, both samples (columns) and features (row)
9652 of the matrix are sorted according to a hierarchical clustering, and the
9653 corresponding dendrogram is plotted. Optionally, panels with additional
9654 information about samples and features can be added to the plot.")
9655 (license license:gpl2+)))
9657 (define-public r-gosemsim
9664 (uri (bioconductor-uri "GOSemSim" version))
9667 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
9668 (properties `((upstream-name . "GOSemSim")))
9669 (build-system r-build-system)
9671 (list r-annotationdbi r-go-db r-rcpp))
9674 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
9675 (synopsis "GO-terms semantic similarity measures")
9677 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
9678 quantitative ways to compute similarities between genes and gene groups, and
9679 have became important basis for many bioinformatics analysis approaches.
9680 GOSemSim is an R package for semantic similarity computation among GO terms,
9681 sets of GO terms, gene products and gene clusters.")
9682 (license license:artistic2.0)))
9684 (define-public r-anota
9691 (uri (bioconductor-uri "anota" version))
9694 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
9695 (build-system r-build-system)
9697 (list r-multtest r-qvalue))
9698 (home-page "https://bioconductor.org/packages/anota/")
9699 (synopsis "Analysis of translational activity")
9701 "Genome wide studies of translational control is emerging as a tool to
9702 study various biological conditions. The output from such analysis is both
9703 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
9704 involved in translation (the actively translating mRNA level) for each mRNA.
9705 The standard analysis of such data strives towards identifying differential
9706 translational between two or more sample classes - i.e., differences in
9707 actively translated mRNA levels that are independent of underlying differences
9708 in cytosolic mRNA levels. This package allows for such analysis using partial
9709 variances and the random variance model. As 10s of thousands of mRNAs are
9710 analyzed in parallel the library performs a number of tests to assure that
9711 the data set is suitable for such analysis.")
9712 (license license:gpl3)))
9714 (define-public r-sigpathway
9716 (name "r-sigpathway")
9721 (uri (bioconductor-uri "sigPathway" version))
9724 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
9725 (properties `((upstream-name . "sigPathway")))
9726 (build-system r-build-system)
9727 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
9728 (synopsis "Pathway analysis")
9730 "This package is used to conduct pathway analysis by calculating the NT_k
9731 and NE_k statistics in a statistical framework for determining whether a
9732 specified group of genes for a pathway has a coordinated association with a
9733 phenotype of interest.")
9734 (license license:gpl2)))
9736 (define-public r-fcscan
9743 (uri (bioconductor-uri "fcScan" version))
9745 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
9746 (properties `((upstream-name . "fcScan")))
9747 (build-system r-build-system)
9755 r-summarizedexperiment
9756 r-variantannotation))
9757 (native-inputs (list r-knitr))
9758 (home-page "https://bioconductor.org/packages/fcScan")
9759 (synopsis "Detect clusters of coordinates with user defined options")
9761 "This package is used to detect combination of genomic coordinates
9762 falling within a user defined window size along with user defined overlap
9763 between identified neighboring clusters. It can be used for genomic data
9764 where the clusters are built on a specific chromosome or specific strand.
9765 Clustering can be performed with a \"greedy\" option allowing thus the
9766 presence of additional sites within the allowed window size.")
9767 (license license:artistic2.0)))
9769 (define-public r-fgsea
9776 (uri (bioconductor-uri "fgsea" version))
9779 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
9780 (build-system r-build-system)
9792 (home-page "https://github.com/ctlab/fgsea/")
9793 (synopsis "Fast gene set enrichment analysis")
9795 "The package implements an algorithm for fast gene set enrichment
9796 analysis. Using the fast algorithm makes more permutations and gets
9797 more fine grained p-values, which allows using accurate standard approaches
9798 to multiple hypothesis correction.")
9799 (license license:expat)))
9801 (define-public r-dose
9808 (uri (bioconductor-uri "DOSE" version))
9811 "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"))))
9812 (properties `((upstream-name . "DOSE")))
9813 (build-system r-build-system)
9815 (list r-annotationdbi
9825 (home-page "https://guangchuangyu.github.io/software/DOSE/")
9826 (synopsis "Disease ontology semantic and enrichment analysis")
9828 "This package implements five methods proposed by Resnik, Schlicker,
9829 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
9830 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
9831 including hypergeometric model and gene set enrichment analysis are also
9832 implemented for discovering disease associations of high-throughput biological
9834 (license license:artistic2.0)))
9836 (define-public r-enrichplot
9838 (name "r-enrichplot")
9843 (uri (bioconductor-uri "enrichplot" version))
9846 "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"))))
9847 (build-system r-build-system)
9866 (home-page "https://github.com/GuangchuangYu/enrichplot")
9867 (synopsis "Visualization of functional enrichment result")
9869 "The enrichplot package implements several visualization methods for
9870 interpreting functional enrichment results obtained from ORA or GSEA analyses.
9871 All the visualization methods are developed based on ggplot2 graphics.")
9872 (license license:artistic2.0)))
9874 (define-public r-clusterprofiler
9876 (name "r-clusterprofiler")
9881 (uri (bioconductor-uri "clusterProfiler" version))
9884 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
9886 `((upstream-name . "clusterProfiler")))
9887 (build-system r-build-system)
9889 (list r-annotationdbi
9904 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
9905 (synopsis "Analysis and visualization of functional profiles for gene clusters")
9907 "This package implements methods to analyze and visualize functional
9908 profiles (GO and KEGG) of gene and gene clusters.")
9909 (license license:artistic2.0)))
9911 (define-public r-clusterexperiment
9913 (name "r-clusterexperiment")
9917 (uri (bioconductor-uri "clusterExperiment" version))
9920 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
9921 (build-system r-build-system)
9946 r-singlecellexperiment
9948 r-summarizedexperiment
9950 (home-page "https://bioconductor.org/packages/clusterExperiment/")
9951 (synopsis "Compare clusterings for single-cell sequencing")
9952 (description "This package provides functionality for running and comparing
9953 many different clusterings of single-cell sequencing data or other large mRNA
9954 expression data sets.")
9955 (license license:artistic2.0)))
9957 (define-public r-mlinterfaces
9959 (name "r-mlinterfaces")
9964 (uri (bioconductor-uri "MLInterfaces" version))
9967 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
9968 (properties `((upstream-name . "MLInterfaces")))
9969 (build-system r-build-system)
9991 (home-page "https://bioconductor.org/packages/MLInterfaces/")
9992 (synopsis "Interfaces to R machine learning procedures")
9994 "This package provides uniform interfaces to machine learning code for
9995 data in R and Bioconductor containers.")
9996 ;; Any version of the LGPL.
9997 (license license:lgpl2.1+)))
9999 (define-public r-annaffy
10006 (uri (bioconductor-uri "annaffy" version))
10009 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
10010 (build-system r-build-system)
10013 (modify-phases %standard-phases
10014 (add-after 'unpack 'remove-reference-to-non-free-data
10016 (substitute* "DESCRIPTION"
10017 ((", KEGG.db") "")))))))
10019 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
10020 (home-page "https://bioconductor.org/packages/annaffy/")
10021 (synopsis "Annotation tools for Affymetrix biological metadata")
10023 "This package provides functions for handling data from Bioconductor
10024 Affymetrix annotation data packages. It produces compact HTML and text
10025 reports including experimental data and URL links to many online databases.
10026 It allows searching of biological metadata using various criteria.")
10027 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
10028 ;; the LGPL 2.1 is included.
10029 (license license:lgpl2.1+)))
10031 (define-public r-a4core
10038 (uri (bioconductor-uri "a4Core" version))
10041 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
10042 (properties `((upstream-name . "a4Core")))
10043 (build-system r-build-system)
10045 (list r-biobase r-glmnet))
10048 (home-page "https://bioconductor.org/packages/a4Core")
10049 (synopsis "Automated Affymetrix array analysis core package")
10051 "This is the core package for the automated analysis of Affymetrix
10053 (license license:gpl3)))
10055 (define-public r-a4classif
10057 (name "r-a4classif")
10062 (uri (bioconductor-uri "a4Classif" version))
10065 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
10066 (properties `((upstream-name . "a4Classif")))
10067 (build-system r-build-system)
10078 (home-page "https://bioconductor.org/packages/a4Classif/")
10079 (synopsis "Automated Affymetrix array analysis classification package")
10081 "This is the classification package for the automated analysis of
10082 Affymetrix arrays.")
10083 (license license:gpl3)))
10085 (define-public r-a4preproc
10087 (name "r-a4preproc")
10092 (uri (bioconductor-uri "a4Preproc" version))
10095 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
10096 (properties `((upstream-name . "a4Preproc")))
10097 (build-system r-build-system)
10099 (list r-biobase r-biocgenerics))
10102 (home-page "https://bioconductor.org/packages/a4Preproc/")
10103 (synopsis "Automated Affymetrix array analysis preprocessing package")
10105 "This is a package for the automated analysis of Affymetrix arrays. It
10106 is used for preprocessing the arrays.")
10107 (license license:gpl3)))
10109 (define-public r-a4reporting
10111 (name "r-a4reporting")
10116 (uri (bioconductor-uri "a4Reporting" version))
10119 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
10120 (properties `((upstream-name . "a4Reporting")))
10121 (build-system r-build-system)
10126 (home-page "https://bioconductor.org/packages/a4Reporting/")
10127 (synopsis "Automated Affymetrix array analysis reporting package")
10129 "This is a package for the automated analysis of Affymetrix arrays. It
10130 provides reporting features.")
10131 (license license:gpl3)))
10133 (define-public r-a4base
10140 (uri (bioconductor-uri "a4Base" version))
10143 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
10144 (properties `((upstream-name . "a4Base")))
10145 (build-system r-build-system)
10157 (home-page "https://bioconductor.org/packages/a4Base/")
10158 (synopsis "Automated Affymetrix array analysis base package")
10160 "This package provides basic features for the automated analysis of
10161 Affymetrix arrays.")
10162 (license license:gpl3)))
10164 (define-public r-a4
10171 (uri (bioconductor-uri "a4" version))
10174 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
10175 (build-system r-build-system)
10177 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
10178 (home-page "https://bioconductor.org/packages/a4/")
10179 (synopsis "Automated Affymetrix array analysis umbrella package")
10181 "This package provides a software suite for the automated analysis of
10182 Affymetrix arrays.")
10183 (license license:gpl3)))
10185 (define-public r-abseqr
10192 (uri (bioconductor-uri "abseqR" version))
10195 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
10196 (properties `((upstream-name . "abseqR")))
10197 (build-system r-build-system)
10201 (list r-biocparallel
10221 (home-page "https://github.com/malhamdoosh/abseqR")
10222 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
10224 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
10225 sequencing datasets generated from antibody libraries and abseqR is one of its
10226 packages. AbseqR empowers the users of abseqPy with plotting and reporting
10227 capabilities and allows them to generate interactive HTML reports for the
10228 convenience of viewing and sharing with other researchers. Additionally,
10229 abseqR extends abseqPy to compare multiple repertoire analyses and perform
10230 further downstream analysis on its output.")
10231 (license license:gpl3)))
10233 (define-public r-bacon
10240 (uri (bioconductor-uri "bacon" version))
10243 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
10244 (build-system r-build-system)
10246 (list r-biocparallel r-ellipse r-ggplot2))
10249 (home-page "https://bioconductor.org/packages/bacon/")
10250 (synopsis "Controlling bias and inflation in association studies")
10252 "Bacon can be used to remove inflation and bias often observed in
10253 epigenome- and transcriptome-wide association studies. To this end bacon
10254 constructs an empirical null distribution using a Gibbs Sampling algorithm by
10255 fitting a three-component normal mixture on z-scores.")
10256 (license license:gpl2+)))
10258 (define-public r-rgadem
10265 (uri (bioconductor-uri "rGADEM" version))
10268 "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"))))
10269 (properties `((upstream-name . "rGADEM")))
10270 (build-system r-build-system)
10272 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
10273 (home-page "https://bioconductor.org/packages/rGADEM/")
10274 (synopsis "De novo sequence motif discovery")
10276 "rGADEM is an efficient de novo motif discovery tool for large-scale
10277 genomic sequence data.")
10278 (license license:artistic2.0)))
10280 (define-public r-motiv
10287 (uri (bioconductor-uri "MotIV" version))
10290 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
10291 (properties `((upstream-name . "MotIV")))
10292 (build-system r-build-system)
10296 (list r-biocgenerics
10303 (home-page "https://bioconductor.org/packages/MotIV/")
10304 (synopsis "Motif identification and validation")
10306 "This package is used for the identification and validation of sequence
10307 motifs. It makes use of STAMP for comparing a set of motifs to a given
10308 database (e.g. JASPAR). It can also be used to visualize motifs, motif
10309 distributions, modules and filter motifs.")
10310 (license license:gpl2)))
10312 (define-public r-motifdb
10318 (uri (bioconductor-uri "MotifDb" version))
10320 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
10321 (properties `((upstream-name . "MotifDb")))
10322 (build-system r-build-system)
10324 (list r-biocgenerics
10330 r-splitstackshape))
10333 (home-page "https://www.bioconductor.org/packages/MotifDb/")
10334 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
10335 (description "This package provides more than 2000 annotated position
10336 frequency matrices from nine public sources, for multiple organisms.")
10337 (license license:artistic2.0)))
10339 (define-public r-motifbreakr
10341 (name "r-motifbreakr")
10345 (uri (bioconductor-uri "motifbreakR" version))
10347 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
10348 (properties `((upstream-name . "motifbreakR")))
10349 (build-system r-build-system)
10351 (list r-biocgenerics
10365 r-summarizedexperiment
10367 r-variantannotation))
10370 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
10371 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
10372 (description "This package allows biologists to judge in the first place
10373 whether the sequence surrounding the polymorphism is a good match, and in
10374 the second place how much information is gained or lost in one allele of
10375 the polymorphism relative to another. This package gives a choice of
10376 algorithms for interrogation of genomes with motifs from public sources:
10378 @item a weighted-sum probability matrix;
10379 @item log-probabilities;
10380 @item weighted by relative entropy.
10383 This package can predict effects for novel or previously described variants in
10384 public databases, making it suitable for tasks beyond the scope of its original
10385 design. Lastly, it can be used to interrogate any genome curated within
10387 (license license:gpl2+)))
10389 (define-public r-motifstack
10391 (name "r-motifstack")
10396 (uri (bioconductor-uri "motifStack" version))
10399 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
10400 (properties `((upstream-name . "motifStack")))
10401 (build-system r-build-system)
10411 (home-page "https://bioconductor.org/packages/motifStack/")
10412 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
10414 "The motifStack package is designed for graphic representation of
10415 multiple motifs with different similarity scores. It works with both DNA/RNA
10416 sequence motifs and amino acid sequence motifs. In addition, it provides the
10417 flexibility for users to customize the graphic parameters such as the font
10418 type and symbol colors.")
10419 (license license:gpl2+)))
10421 (define-public r-genomicscores
10423 (name "r-genomicscores")
10428 (uri (bioconductor-uri "GenomicScores" version))
10431 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
10432 (properties `((upstream-name . "GenomicScores")))
10433 (build-system r-build-system)
10435 (list r-annotationhub
10452 (home-page "https://github.com/rcastelo/GenomicScores/")
10453 (synopsis "Work with genome-wide position-specific scores")
10455 "This package provides infrastructure to store and access genome-wide
10456 position-specific scores within R and Bioconductor.")
10457 (license license:artistic2.0)))
10459 (define-public r-atacseqqc
10461 (name "r-atacseqqc")
10466 (uri (bioconductor-uri "ATACseqQC" version))
10469 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
10470 (properties `((upstream-name . "ATACseqQC")))
10471 (build-system r-build-system)
10473 (list r-biocgenerics
10479 r-genomicalignments
10493 (home-page "https://bioconductor.org/packages/ATACseqQC/")
10494 (synopsis "ATAC-seq quality control")
10496 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
10497 sequencing, is a rapid and sensitive method for chromatin accessibility
10498 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
10499 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
10500 assess whether their ATAC-seq experiment is successful. It includes
10501 diagnostic plots of fragment size distribution, proportion of mitochondria
10502 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
10504 (license license:gpl2+)))
10506 (define-public r-gofuncr
10513 (uri (bioconductor-uri "GOfuncR" version))
10516 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
10517 (properties `((upstream-name . "GOfuncR")))
10518 (build-system r-build-system)
10520 (list r-annotationdbi
10529 (home-page "https://bioconductor.org/packages/GOfuncR/")
10530 (synopsis "Gene ontology enrichment using FUNC")
10532 "GOfuncR performs a gene ontology enrichment analysis based on the
10533 ontology enrichment software FUNC. GO-annotations are obtained from
10534 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
10535 included in the package and updated regularly. GOfuncR provides the standard
10536 candidate vs background enrichment analysis using the hypergeometric test, as
10537 well as three additional tests:
10540 @item the Wilcoxon rank-sum test that is used when genes are ranked,
10541 @item a binomial test that is used when genes are associated with two counts,
10543 @item a Chi-square or Fisher's exact test that is used in cases when genes are
10544 associated with four counts.
10547 To correct for multiple testing and interdependency of the tests, family-wise
10548 error rates are computed based on random permutations of the gene-associated
10549 variables. GOfuncR also provides tools for exploring the ontology graph and
10550 the annotations, and options to take gene-length or spatial clustering of
10551 genes into account. It is also possible to provide custom gene coordinates,
10552 annotations and ontologies.")
10553 (license license:gpl2+)))
10555 (define-public r-abaenrichment
10557 (name "r-abaenrichment")
10562 (uri (bioconductor-uri "ABAEnrichment" version))
10565 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
10566 (properties `((upstream-name . "ABAEnrichment")))
10567 (build-system r-build-system)
10577 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
10578 (synopsis "Gene expression enrichment in human brain regions")
10580 "The package ABAEnrichment is designed to test for enrichment of user
10581 defined candidate genes in the set of expressed genes in different human brain
10582 regions. The core function @code{aba_enrich} integrates the expression of the
10583 candidate gene set (averaged across donors) and the structural information of
10584 the brain using an ontology, both provided by the Allen Brain Atlas project.")
10585 (license license:gpl2+)))
10587 (define-public r-annotationfuncs
10589 (name "r-annotationfuncs")
10594 (uri (bioconductor-uri "AnnotationFuncs" version))
10597 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
10599 `((upstream-name . "AnnotationFuncs")))
10600 (build-system r-build-system)
10602 (list r-annotationdbi r-dbi))
10603 (home-page "https://www.iysik.com/r/annotationfuncs")
10604 (synopsis "Annotation translation functions")
10606 "This package provides functions for handling translating between
10607 different identifieres using the Biocore Data Team data-packages (e.g.
10608 @code{org.Bt.eg.db}).")
10609 (license license:gpl2)))
10611 (define-public r-annotationtools
10613 (name "r-annotationtools")
10618 (uri (bioconductor-uri "annotationTools" version))
10621 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
10623 `((upstream-name . "annotationTools")))
10624 (build-system r-build-system)
10625 (propagated-inputs (list r-biobase))
10626 (home-page "https://bioconductor.org/packages/annotationTools/")
10627 (synopsis "Annotate microarrays and perform gene expression analyses")
10629 "This package provides functions to annotate microarrays, find orthologs,
10630 and integrate heterogeneous gene expression profiles using annotation and
10631 other molecular biology information available as flat file database (plain
10633 ;; Any version of the GPL.
10634 (license (list license:gpl2+))))
10636 (define-public r-allelicimbalance
10638 (name "r-allelicimbalance")
10643 (uri (bioconductor-uri "AllelicImbalance" version))
10646 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
10648 `((upstream-name . "AllelicImbalance")))
10649 (build-system r-build-system)
10651 (list r-annotationdbi
10656 r-genomicalignments
10668 r-summarizedexperiment
10669 r-variantannotation))
10672 (home-page "https://github.com/pappewaio/AllelicImbalance")
10673 (synopsis "Investigate allele-specific expression")
10675 "This package provides a framework for allele-specific expression
10676 investigation using RNA-seq data.")
10677 (license license:gpl3)))
10679 (define-public r-aucell
10686 (uri (bioconductor-uri "AUCell" version))
10689 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
10690 (properties `((upstream-name . "AUCell")))
10691 (build-system r-build-system)
10693 (list r-biocgenerics
10696 r-delayedmatrixstats
10701 r-summarizedexperiment))
10704 (home-page "https://bioconductor.org/packages/AUCell/")
10705 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
10707 "AUCell identifies cells with active gene sets (e.g. signatures,
10708 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
10709 Under the Curve} (AUC) to calculate whether a critical subset of the input
10710 gene set is enriched within the expressed genes for each cell. The
10711 distribution of AUC scores across all the cells allows exploring the relative
10712 expression of the signature. Since the scoring method is ranking-based,
10713 AUCell is independent of the gene expression units and the normalization
10714 procedure. In addition, since the cells are evaluated individually, it can
10715 easily be applied to bigger datasets, subsetting the expression matrix if
10717 (license license:gpl3)))
10719 (define-public r-ebimage
10726 (uri (bioconductor-uri "EBImage" version))
10729 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
10730 (properties `((upstream-name . "EBImage")))
10731 (build-system r-build-system)
10744 (list r-knitr)) ; for vignettes
10745 (home-page "https://github.com/aoles/EBImage")
10746 (synopsis "Image processing and analysis toolbox for R")
10748 "EBImage provides general purpose functionality for image processing and
10749 analysis. In the context of (high-throughput) microscopy-based cellular
10750 assays, EBImage offers tools to segment cells and extract quantitative
10751 cellular descriptors. This allows the automation of such tasks using the R
10752 programming language and facilitates the use of other tools in the R
10753 environment for signal processing, statistical modeling, machine learning and
10754 visualization with image data.")
10755 ;; Any version of the LGPL.
10756 (license license:lgpl2.1+)))
10758 (define-public r-yamss
10765 (uri (bioconductor-uri "yamss" version))
10768 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
10769 (build-system r-build-system)
10771 (list r-biocgenerics
10779 r-summarizedexperiment))
10782 (home-page "https://github.com/hansenlab/yamss")
10783 (synopsis "Tools for high-throughput metabolomics")
10785 "This package provides tools to analyze and visualize high-throughput
10786 metabolomics data acquired using chromatography-mass spectrometry. These tools
10787 preprocess data in a way that enables reliable and powerful differential
10789 (license license:artistic2.0)))
10791 (define-public r-gtrellis
10793 (name "r-gtrellis")
10798 (uri (bioconductor-uri "gtrellis" version))
10801 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
10802 (build-system r-build-system)
10804 (list r-circlize r-genomicranges r-getoptlong r-iranges))
10807 (home-page "https://github.com/jokergoo/gtrellis")
10808 (synopsis "Genome level Trellis layout")
10810 "Genome level Trellis graph visualizes genomic data conditioned by
10811 genomic categories (e.g. chromosomes). For each genomic category, multiple
10812 dimensional data which are represented as tracks describe different features
10813 from different aspects. This package provides high flexibility to arrange
10814 genomic categories and to add self-defined graphics in the plot.")
10815 (license license:expat)))
10817 (define-public r-somaticsignatures
10819 (name "r-somaticsignatures")
10824 (uri (bioconductor-uri "SomaticSignatures" version))
10827 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
10829 `((upstream-name . "SomaticSignatures")))
10830 (build-system r-build-system)
10844 r-variantannotation))
10847 (home-page "https://github.com/juliangehring/SomaticSignatures")
10848 (synopsis "Somatic signatures")
10850 "This package identifies mutational signatures of @dfn{single nucleotide
10851 variants} (SNVs). It provides a infrastructure related to the methodology
10852 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
10853 decomposition algorithms.")
10854 (license license:expat)))
10856 (define-public r-yapsa
10863 (uri (bioconductor-uri "YAPSA" version))
10866 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
10867 (properties `((upstream-name . "YAPSA")))
10868 (build-system r-build-system)
10871 r-bsgenome-hsapiens-ucsc-hg19
10891 r-somaticsignatures
10892 r-variantannotation))
10895 (home-page "https://bioconductor.org/packages/YAPSA/")
10896 (synopsis "Yet another package for signature analysis")
10898 "This package provides functions and routines useful in the analysis of
10899 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
10900 functions to perform a signature analysis with known signatures and a
10901 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
10903 (license license:gpl3)))
10905 (define-public r-gcrma
10912 (uri (bioconductor-uri "gcrma" version))
10915 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
10916 (build-system r-build-system)
10924 (home-page "https://bioconductor.org/packages/gcrma/")
10925 (synopsis "Background adjustment using sequence information")
10927 "Gcrma adjusts for background intensities in Affymetrix array data which
10928 include optical noise and @dfn{non-specific binding} (NSB). The main function
10929 @code{gcrma} converts background adjusted probe intensities to expression
10930 measures using the same normalization and summarization methods as a
10931 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
10932 to estimate probe affinity to NSB. The sequence information is summarized in
10933 a more complex way than the simple GC content. Instead, the base types (A, T,
10934 G or C) at each position along the probe determine the affinity of each probe.
10935 The parameters of the position-specific base contributions to the probe
10936 affinity is estimated in an NSB experiment in which only NSB but no
10937 gene-specific binding is expected.")
10938 ;; Any version of the LGPL
10939 (license license:lgpl2.1+)))
10941 (define-public r-simpleaffy
10943 (name "r-simpleaffy")
10948 (uri (bioconductor-uri "simpleaffy" version))
10951 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
10952 (build-system r-build-system)
10954 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
10955 (home-page "https://bioconductor.org/packages/simpleaffy/")
10956 (synopsis "Very simple high level analysis of Affymetrix data")
10958 "This package provides high level functions for reading Affy @file{.CEL}
10959 files, phenotypic data, and then computing simple things with it, such as
10960 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
10961 library. It also has some basic scatter plot functions and mechanisms for
10962 generating high resolution journal figures.")
10963 (license license:gpl2+)))
10965 (define-public r-yaqcaffy
10967 (name "r-yaqcaffy")
10972 (uri (bioconductor-uri "yaqcaffy" version))
10975 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
10976 (build-system r-build-system)
10978 (list r-simpleaffy))
10979 (home-page "https://bioconductor.org/packages/yaqcaffy/")
10980 (synopsis "Affymetrix quality control and reproducibility analysis")
10982 "This is a package that can be used for quality control of Affymetrix
10983 GeneChip expression data and reproducibility analysis of human whole genome
10984 chips with the MAQC reference datasets.")
10985 (license license:artistic2.0)))
10987 (define-public r-quantro
10994 (uri (bioconductor-uri "quantro" version))
10997 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
10998 (build-system r-build-system)
11009 (home-page "https://bioconductor.org/packages/quantro/")
11010 (synopsis "Test for when to use quantile normalization")
11012 "This package provides a data-driven test for the assumptions of quantile
11013 normalization using raw data such as objects that inherit eSets (e.g.
11014 ExpressionSet, MethylSet). Group level information about each sample (such as
11015 Tumor / Normal status) must also be provided because the test assesses if
11016 there are global differences in the distributions between the user-defined
11018 (license license:gpl3+)))
11020 (define-public r-yarn
11027 (uri (bioconductor-uri "yarn" version))
11030 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
11031 (build-system r-build-system)
11046 (home-page "https://bioconductor.org/packages/yarn/")
11047 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
11049 "Expedite large RNA-Seq analyses using a combination of previously
11050 developed tools. YARN is meant to make it easier for the user in performing
11051 basic mis-annotation quality control, filtering, and condition-aware
11052 normalization. YARN leverages many Bioconductor tools and statistical
11053 techniques to account for the large heterogeneity and sparsity found in very
11054 large RNA-seq experiments.")
11055 (license license:artistic2.0)))
11057 (define-public r-roar
11064 (uri (bioconductor-uri "roar" version))
11067 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
11068 (build-system r-build-system)
11070 (list r-biocgenerics
11072 r-genomicalignments
11077 r-summarizedexperiment))
11078 (home-page "https://github.com/vodkatad/roar/")
11079 (synopsis "Identify differential APA usage from RNA-seq alignments")
11081 "This package provides tools for identifying preferential usage of APA
11082 sites, comparing two biological conditions, starting from known alternative
11083 sites and alignments obtained from standard RNA-seq experiments.")
11084 (license license:gpl3)))
11086 (define-public r-xbseq
11093 (uri (bioconductor-uri "XBSeq" version))
11096 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
11097 (properties `((upstream-name . "XBSeq")))
11098 (build-system r-build-system)
11111 (home-page "https://github.com/Liuy12/XBSeq")
11112 (synopsis "Test for differential expression for RNA-seq data")
11114 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
11115 expression} (DE), where a statistical model was established based on the
11116 assumption that observed signals are the convolution of true expression
11117 signals and sequencing noises. The mapped reads in non-exonic regions are
11118 considered as sequencing noises, which follows a Poisson distribution. Given
11119 measurable observed signal and background noise from RNA-seq data, true
11120 expression signals, assuming governed by the negative binomial distribution,
11121 can be delineated and thus the accurate detection of differential expressed
11123 (license license:gpl3+)))
11125 (define-public r-massspecwavelet
11127 (name "r-massspecwavelet")
11132 (uri (bioconductor-uri "MassSpecWavelet" version))
11135 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
11137 `((upstream-name . "MassSpecWavelet")))
11138 (build-system r-build-system)
11141 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
11142 (synopsis "Mass spectrum processing by wavelet-based algorithms")
11144 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
11145 data mainly through the use of wavelet transforms. It supports peak detection
11146 based on @dfn{Continuous Wavelet Transform} (CWT).")
11147 (license license:lgpl2.0+)))
11149 (define-public r-xcms
11156 (uri (bioconductor-uri "xcms" version))
11159 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
11160 (build-system r-build-system)
11178 r-summarizedexperiment))
11181 (home-page "https://bioconductor.org/packages/xcms/")
11182 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
11184 "This package provides a framework for processing and visualization of
11185 chromatographically separated and single-spectra mass spectral data. It
11186 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
11187 data for high-throughput, untargeted analyte profiling.")
11188 (license license:gpl2+)))
11190 (define-public r-wppi
11196 (uri (bioconductor-uri "wppi" version))
11199 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
11200 (properties `((upstream-name . "wppi")))
11201 (build-system r-build-system)
11202 ;; This is necessary because omnipathr attempts to write a configuration
11206 (modify-phases %standard-phases
11207 (add-after 'unpack 'set-HOME
11208 (lambda _ (setenv "HOME" "/tmp"))))))
11209 (propagated-inputs (list r-dplyr
11221 (native-inputs (list r-knitr))
11222 (home-page "https://github.com/AnaGalhoz37/wppi")
11223 (synopsis "Weighting protein-protein interactions")
11225 "This package predicts functional relevance of protein-protein
11226 interactions based on functional annotations such as Human Protein Ontology
11227 and Gene Ontology, and prioritizes genes based on network topology, functional
11228 scores and a path search algorithm.")
11229 (license license:expat)))
11231 (define-public r-wrench
11238 (uri (bioconductor-uri "Wrench" version))
11241 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
11242 (properties `((upstream-name . "Wrench")))
11243 (build-system r-build-system)
11245 (list r-limma r-locfit r-matrixstats))
11248 (home-page "https://github.com/HCBravoLab/Wrench")
11249 (synopsis "Wrench normalization for sparse count data")
11251 "Wrench is a package for normalization sparse genomic count data, like
11252 that arising from 16s metagenomic surveys.")
11253 (license license:artistic2.0)))
11255 (define-public r-wiggleplotr
11257 (name "r-wiggleplotr")
11262 (uri (bioconductor-uri "wiggleplotr" version))
11265 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
11266 (build-system r-build-system)
11280 (home-page "https://bioconductor.org/packages/wiggleplotr/")
11281 (synopsis "Make read coverage plots from BigWig files")
11283 "This package provides tools to visualize read coverage from sequencing
11284 experiments together with genomic annotations (genes, transcripts, peaks).
11285 Introns of long transcripts can be rescaled to a fixed length for better
11286 visualization of exonic read coverage.")
11287 (license license:asl2.0)))
11289 (define-public r-widgettools
11291 (name "r-widgettools")
11296 (uri (bioconductor-uri "widgetTools" version))
11299 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
11300 (properties `((upstream-name . "widgetTools")))
11301 (build-system r-build-system)
11302 (home-page "https://bioconductor.org/packages/widgetTools/")
11303 (synopsis "Tools for creating interactive tcltk widgets")
11305 "This package contains tools to support the construction of tcltk
11307 ;; Any version of the LGPL.
11308 (license license:lgpl3+)))
11310 (define-public r-webbioc
11317 (uri (bioconductor-uri "webbioc" version))
11320 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
11321 (build-system r-build-system)
11323 (list netpbm perl))
11333 (home-page "https://www.bioconductor.org/")
11334 (synopsis "Bioconductor web interface")
11336 "This package provides an integrated web interface for doing microarray
11337 analysis using several of the Bioconductor packages. It is intended to be
11338 deployed as a centralized bioinformatics resource for use by many users.
11339 Currently only Affymetrix oligonucleotide analysis is supported.")
11340 (license license:gpl2+)))
11342 (define-public r-zinbwave
11344 (name "r-zinbwave")
11349 (uri (bioconductor-uri "zinbwave" version))
11352 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
11353 (build-system r-build-system)
11355 (list r-biocparallel
11359 r-singlecellexperiment
11361 r-summarizedexperiment))
11364 (home-page "https://bioconductor.org/packages/zinbwave")
11365 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
11366 (description "This package implements a general and flexible zero-inflated
11367 negative binomial model that can be used to provide a low-dimensional
11368 representations of single-cell RNA-seq data. The model accounts for zero
11369 inflation (dropouts), over-dispersion, and the count nature of the data.
11370 The model also accounts for the difference in library sizes and optionally
11371 for batch effects and/or other covariates, avoiding the need for pre-normalize
11373 (license license:artistic2.0)))
11375 (define-public r-zfpkm
11382 (uri (bioconductor-uri "zFPKM" version))
11385 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
11386 (properties `((upstream-name . "zFPKM")))
11387 (build-system r-build-system)
11389 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
11392 (home-page "https://github.com/ronammar/zFPKM/")
11393 (synopsis "Functions to facilitate zFPKM transformations")
11395 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
11396 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
11398 (license license:gpl3)))
11400 (define-public r-rbowtie2
11402 (name "r-rbowtie2")
11407 (uri (bioconductor-uri "Rbowtie2" version))
11410 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
11411 (properties `((upstream-name . "Rbowtie2")))
11412 (build-system r-build-system)
11414 (list r-magrittr r-rsamtools))
11416 (list samtools zlib))
11419 (home-page "https://bioconductor.org/packages/Rbowtie2/")
11420 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
11422 "This package provides an R wrapper of the popular @code{bowtie2}
11423 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
11424 rapid adapter trimming, identification, and read merging.")
11425 (license license:gpl3+)))
11427 (define-public r-progeny
11434 (uri (bioconductor-uri "progeny" version))
11437 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
11438 (build-system r-build-system)
11450 (home-page "https://github.com/saezlab/progeny")
11451 (synopsis "Pathway responsive gene activity inference")
11453 "This package provides a function to infer pathway activity from gene
11454 expression. It contains the linear model inferred in the publication
11455 \"Perturbation-response genes reveal signaling footprints in cancer gene
11457 (license license:asl2.0)))
11459 (define-public r-arrmnormalization
11461 (name "r-arrmnormalization")
11466 (uri (bioconductor-uri "ARRmNormalization" version))
11469 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
11471 `((upstream-name . "ARRmNormalization")))
11472 (build-system r-build-system)
11473 (propagated-inputs (list r-arrmdata))
11474 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
11475 (synopsis "Adaptive robust regression normalization for methylation data")
11477 "This is a package to perform the @dfn{Adaptive Robust Regression
11478 method} (ARRm) for the normalization of methylation data from the Illumina
11479 Infinium HumanMethylation 450k assay.")
11480 (license license:artistic2.0)))
11482 (define-public r-biocfilecache
11484 (name "r-biocfilecache")
11489 (uri (bioconductor-uri "BiocFileCache" version))
11492 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
11493 (properties `((upstream-name . "BiocFileCache")))
11494 (build-system r-build-system)
11506 (home-page "https://bioconductor.org/packages/BiocFileCache/")
11507 (synopsis "Manage files across sessions")
11509 "This package creates a persistent on-disk cache of files that the user
11510 can add, update, and retrieve. It is useful for managing resources (such as
11511 custom Txdb objects) that are costly or difficult to create, web resources,
11512 and data files used across sessions.")
11513 (license license:artistic2.0)))
11515 (define-public r-iclusterplus
11517 (name "r-iclusterplus")
11522 (uri (bioconductor-uri "iClusterPlus" version))
11525 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
11526 (properties `((upstream-name . "iClusterPlus")))
11527 (build-system r-build-system)
11528 (native-inputs (list gfortran))
11529 (home-page "https://bioconductor.org/packages/iClusterPlus/")
11530 (synopsis "Integrative clustering of multi-type genomic data")
11532 "iClusterPlus is developed for integrative clustering analysis of
11533 multi-type genomic data and is an enhanced version of iCluster proposed and
11534 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
11535 from the experiments where biological samples (e.g. tumor samples) are
11536 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
11537 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
11538 on. In the iClusterPlus model, binary observations such as somatic mutation
11539 are modeled as Binomial processes; categorical observations such as copy
11540 number states are realizations of Multinomial random variables; counts are
11541 modeled as Poisson random processes; and continuous measures are modeled by
11542 Gaussian distributions.")
11543 (license license:gpl2+)))
11545 (define-public r-rbowtie
11552 (uri (bioconductor-uri "Rbowtie" version))
11555 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
11556 (properties `((upstream-name . "Rbowtie")))
11557 (build-system r-build-system)
11560 ;; Disable unsupported `popcnt' instructions on
11561 ;; architectures other than x86_64
11562 ,(if (string-prefix? "x86_64"
11563 (or (%current-target-system)
11564 (%current-system)))
11566 '(modify-phases %standard-phases
11567 (add-after 'unpack 'patch-sources
11569 (setenv "POPCNT_CAPABILITY" "0")))))))
11570 (inputs (list zlib))
11573 (home-page "https://bioconductor.org/packages/Rbowtie/")
11574 (synopsis "R bowtie wrapper")
11576 "This package provides an R wrapper around the popular bowtie short read
11577 aligner and around SpliceMap, a de novo splice junction discovery and
11579 (license license:artistic2.0)))
11581 (define-public r-sgseq
11588 (uri (bioconductor-uri "SGSeq" version))
11591 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
11592 (properties `((upstream-name . "SGSeq")))
11593 (build-system r-build-system)
11595 (list r-annotationdbi
11599 r-genomicalignments
11608 r-summarizedexperiment))
11611 (home-page "https://bioconductor.org/packages/SGSeq/")
11612 (synopsis "Splice event prediction and quantification from RNA-seq data")
11614 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
11615 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
11616 represented as a splice graph, which can be obtained from existing annotation
11617 or predicted from the mapped sequence reads. Splice events are identified
11618 from the graph and are quantified locally using structurally compatible reads
11619 at the start or end of each splice variant. The software includes functions
11620 for splice event prediction, quantification, visualization and
11622 (license license:artistic2.0)))
11624 (define-public r-rhisat2
11631 (uri (bioconductor-uri "Rhisat2" version))
11634 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
11635 (properties `((upstream-name . "Rhisat2")))
11636 (build-system r-build-system)
11639 (modify-phases %standard-phases
11640 (add-after 'unpack 'make-reproducible
11642 (substitute* "src/Makefile"
11643 (("`hostname`") "guix")
11645 ;; Avoid shelling out to "which".
11646 (("^CC =.*") (which "gcc"))
11647 (("^CPP =.*") (which "g++")))
11650 (list r-genomicfeatures r-genomicranges r-sgseq))
11653 (home-page "https://github.com/fmicompbio/Rhisat2")
11654 (synopsis "R Wrapper for HISAT2 sequence aligner")
11656 "This package provides an R interface to the HISAT2 spliced short-read
11657 aligner by Kim et al. (2015). The package contains wrapper functions to
11658 create a genome index and to perform the read alignment to the generated
11660 (license license:gpl3)))
11662 (define-public r-quasr
11669 (uri (bioconductor-uri "QuasR" version))
11672 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
11673 (properties `((upstream-name . "QuasR")))
11674 (build-system r-build-system)
11676 (list r-annotationdbi
11695 (home-page "https://bioconductor.org/packages/QuasR/")
11696 (synopsis "Quantify and annotate short reads in R")
11698 "This package provides a framework for the quantification and analysis of
11699 short genomic reads. It covers a complete workflow starting from raw sequence
11700 reads, over creation of alignments and quality control plots, to the
11701 quantification of genomic regions of interest.")
11702 (license license:gpl2)))
11704 (define-public r-rqc
11711 (uri (bioconductor-uri "Rqc" version))
11714 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
11715 (properties `((upstream-name . "Rqc")))
11716 (build-system r-build-system)
11718 (list r-biocgenerics
11723 r-genomicalignments
11738 (home-page "https://github.com/labbcb/Rqc")
11739 (synopsis "Quality control tool for high-throughput sequencing data")
11741 "Rqc is an optimized tool designed for quality control and assessment of
11742 high-throughput sequencing data. It performs parallel processing of entire
11743 files and produces a report which contains a set of high-resolution
11745 (license license:gpl2+)))
11747 (define-public r-birewire
11749 (name "r-birewire")
11754 (uri (bioconductor-uri "BiRewire" version))
11757 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
11758 (properties `((upstream-name . "BiRewire")))
11759 (build-system r-build-system)
11761 (list r-igraph r-matrix r-rtsne r-slam))
11762 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
11763 (synopsis "Tools for randomization of bipartite graphs")
11765 "This package provides functions for bipartite network rewiring through N
11766 consecutive switching steps and for the computation of the minimal number of
11767 switching steps to be performed in order to maximise the dissimilarity with
11768 respect to the original network. It includes functions for the analysis of
11769 the introduced randomness across the switching steps and several other
11770 routines to analyse the resulting networks and their natural projections.")
11771 (license license:gpl3)))
11773 (define-public r-birta
11780 (uri (bioconductor-uri "birta" version))
11783 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
11784 (build-system r-build-system)
11786 (list r-biobase r-limma r-mass))
11787 (home-page "https://bioconductor.org/packages/birta")
11788 (synopsis "Bayesian inference of regulation of transcriptional activity")
11790 "Expression levels of mRNA molecules are regulated by different
11791 processes, comprising inhibition or activation by transcription factors and
11792 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
11793 Inference of Regulation of Transcriptional Activity) uses the regulatory
11794 networks of transcription factors and miRNAs together with mRNA and miRNA
11795 expression data to predict switches in regulatory activity between two
11796 conditions. A Bayesian network is used to model the regulatory structure and
11797 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
11798 (license license:gpl2+)))
11800 (define-public r-multidataset
11802 (name "r-multidataset")
11807 (uri (bioconductor-uri "MultiDataSet" version))
11810 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
11811 (properties `((upstream-name . "MultiDataSet")))
11812 (build-system r-build-system)
11823 r-summarizedexperiment))
11826 (home-page "https://bioconductor.org/packages/MultiDataSet/")
11827 (synopsis "Implementation of MultiDataSet and ResultSet")
11829 "This package provides an implementation of the BRGE's (Bioinformatic
11830 Research Group in Epidemiology from Center for Research in Environmental
11831 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
11832 integrating multi omics data sets and ResultSet is a container for omics
11833 results. This package contains base classes for MEAL and rexposome
11835 (license license:expat)))
11837 (define-public r-ropls
11844 (uri (bioconductor-uri "ropls" version))
11847 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
11848 (build-system r-build-system)
11851 r-multiassayexperiment
11853 r-summarizedexperiment))
11855 (list r-knitr)) ; for vignettes
11856 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
11857 (synopsis "Multivariate analysis and feature selection of omics data")
11859 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
11860 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
11861 regression, classification, and feature selection of omics data where the
11862 number of variables exceeds the number of samples and with multicollinearity
11863 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
11864 separately model the variation correlated (predictive) to the factor of
11865 interest and the uncorrelated (orthogonal) variation. While performing
11866 similarly to PLS, OPLS facilitates interpretation.
11868 This package provides imlementations of PCA, PLS, and OPLS for multivariate
11869 analysis and feature selection of omics data. In addition to scores, loadings
11870 and weights plots, the package provides metrics and graphics to determine the
11871 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
11872 validity of the model by permutation testing, detect outliers, and perform
11873 feature selection (e.g. with Variable Importance in Projection or regression
11875 (license license:cecill)))
11877 (define-public r-biosigner
11879 (name "r-biosigner")
11884 (uri (bioconductor-uri "biosigner" version))
11887 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
11888 (build-system r-build-system)
11892 r-multiassayexperiment
11896 r-summarizedexperiment))
11899 (home-page "https://bioconductor.org/packages/biosigner/")
11900 (synopsis "Signature discovery from omics data")
11902 "Feature selection is critical in omics data analysis to extract
11903 restricted and meaningful molecular signatures from complex and high-dimension
11904 data, and to build robust classifiers. This package implements a method to
11905 assess the relevance of the variables for the prediction performances of the
11906 classifier. The approach can be run in parallel with the PLS-DA, Random
11907 Forest, and SVM binary classifiers. The signatures and the corresponding
11908 'restricted' models are returned, enabling future predictions on new
11910 (license license:cecill)))
11912 (define-public r-annotatr
11914 (name "r-annotatr")
11919 (uri (bioconductor-uri "annotatr" version))
11922 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
11923 (build-system r-build-system)
11925 (list r-annotationdbi
11940 (home-page "https://bioconductor.org/packages/annotatr/")
11941 (synopsis "Annotation of genomic regions to genomic annotations")
11943 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
11944 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
11945 to investigate the intersecting genomic annotations. Such annotations include
11946 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
11947 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
11948 enhancers. The annotatr package provides an easy way to summarize and
11949 visualize the intersection of genomic sites/regions with genomic
11951 (license license:gpl3)))
11953 (define-public r-rsubread
11955 (name "r-rsubread")
11960 (uri (bioconductor-uri "Rsubread" version))
11963 "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2"))))
11964 (properties `((upstream-name . "Rsubread")))
11965 (build-system r-build-system)
11966 (inputs (list zlib))
11969 (home-page "https://bioconductor.org/packages/Rsubread/")
11970 (synopsis "Subread sequence alignment and counting for R")
11972 "This package provides tools for alignment, quantification and analysis
11973 of second and third generation sequencing data. It includes functionality for
11974 read mapping, read counting, SNP calling, structural variant detection and
11975 gene fusion discovery. It can be applied to all major sequencing techologies
11976 and to both short and long sequence reads.")
11977 (license license:gpl3)))
11979 (define-public r-flowutils
11981 (name "r-flowutils")
11986 (uri (bioconductor-uri "flowUtils" version))
11989 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
11990 (properties `((upstream-name . "flowUtils")))
11991 (build-system r-build-system)
11999 (home-page "https://github.com/jspidlen/flowUtils")
12000 (synopsis "Utilities for flow cytometry")
12002 "This package provides utilities for flow cytometry data.")
12003 (license license:artistic2.0)))
12005 (define-public r-consensusclusterplus
12007 (name "r-consensusclusterplus")
12012 (uri (bioconductor-uri "ConsensusClusterPlus" version))
12015 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
12017 `((upstream-name . "ConsensusClusterPlus")))
12018 (build-system r-build-system)
12020 (list r-all r-biobase r-cluster))
12021 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
12022 (synopsis "Clustering algorithm")
12024 "This package provides an implementation of an algorithm for determining
12025 cluster count and membership by stability evidence in unsupervised analysis.")
12026 (license license:gpl2)))
12028 ;; This is the latest commit and it solves a bug from the latest release.
12029 (define-public r-cycombine
12030 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
12032 (name "r-cycombine")
12033 (version (git-version "0.2.6" revision commit))
12036 (uri (git-reference
12037 (url "https://github.com/biosurf/cyCombine")
12039 (file-name (git-file-name name version))
12042 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
12043 (properties `((upstream-name . "cyCombine")))
12044 (build-system r-build-system)
12062 (native-inputs (list r-knitr))
12063 (home-page "https://github.com/biosurf/cyCombine")
12064 (synopsis "Integration of single-cell cytometry datasets")
12066 "This package provides a method for combining single-cell cytometry
12067 datasets, which increases the analytical flexibility and the statistical power
12068 of the analyses while minimizing technical noise.")
12069 (license license:expat))))
12071 (define-public r-cytolib
12078 (uri (bioconductor-uri "cytolib" version))
12081 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
12082 (properties `((upstream-name . "cytolib")))
12083 (build-system r-build-system)
12093 (home-page "https://bioconductor.org/packages/cytolib/")
12094 (synopsis "C++ infrastructure for working with gated cytometry")
12096 "This package provides the core data structure and API to represent and
12097 interact with gated cytometry data.")
12098 (license license:artistic2.0)))
12100 (define-public r-flowcore
12102 (name "r-flowcore")
12107 (uri (bioconductor-uri "flowCore" version))
12110 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
12111 (properties `((upstream-name . "flowCore")))
12112 (build-system r-build-system)
12125 (home-page "https://bioconductor.org/packages/flowCore")
12126 (synopsis "Basic structures for flow cytometry data")
12128 "This package provides S4 data structures and basic functions to deal
12129 with flow cytometry data.")
12130 (license license:artistic2.0)))
12132 (define-public r-flowmeans
12134 (name "r-flowmeans")
12139 (uri (bioconductor-uri "flowMeans" version))
12142 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
12143 (properties `((upstream-name . "flowMeans")))
12144 (build-system r-build-system)
12146 (list r-biobase r-feature r-flowcore r-rrcov))
12147 (home-page "https://bioconductor.org/packages/flowMeans")
12148 (synopsis "Non-parametric flow cytometry data gating")
12150 "This package provides tools to identify cell populations in Flow
12151 Cytometry data using non-parametric clustering and segmented-regression-based
12152 change point detection.")
12153 (license license:artistic2.0)))
12155 (define-public r-ncdfflow
12157 (name "r-ncdfflow")
12162 (uri (bioconductor-uri "ncdfFlow" version))
12165 "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7"))))
12166 (properties `((upstream-name . "ncdfFlow")))
12167 (build-system r-build-system)
12179 (home-page "https://bioconductor.org/packages/ncdfFlow/")
12180 (synopsis "HDF5 based storage for flow cytometry data")
12182 "This package provides HDF5 storage based methods and functions for
12183 manipulation of flow cytometry data.")
12184 (license license:artistic2.0)))
12186 (define-public r-ggcyto
12193 (uri (bioconductor-uri "ggcyto" version))
12196 "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325"))))
12197 (properties `((upstream-name . "ggcyto")))
12198 (build-system r-build-system)
12213 (home-page "https://github.com/RGLab/ggcyto/issues")
12214 (synopsis "Visualize Cytometry data with ggplot")
12216 "With the dedicated fortify method implemented for @code{flowSet},
12217 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
12218 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
12219 and some custom layers also make it easy to add gates and population
12220 statistics to the plot.")
12221 (license license:artistic2.0)))
12223 (define-public r-flowviz
12230 (uri (bioconductor-uri "flowViz" version))
12233 "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95"))))
12234 (properties `((upstream-name . "flowViz")))
12235 (build-system r-build-system)
12248 (home-page "https://bioconductor.org/packages/flowViz/")
12249 (synopsis "Visualization for flow cytometry")
12251 "This package provides visualization tools for flow cytometry data.")
12252 (license license:artistic2.0)))
12254 (define-public r-flowclust
12256 (name "r-flowclust")
12261 (uri (bioconductor-uri "flowClust" version))
12264 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
12265 (properties `((upstream-name . "flowClust")))
12266 (build-system r-build-system)
12268 `(#:configure-flags
12269 (list "--configure-args=--enable-bundled-gsl=no")))
12278 (list pkg-config r-knitr))
12279 (home-page "https://bioconductor.org/packages/flowClust")
12280 (synopsis "Clustering for flow cytometry")
12282 "This package provides robust model-based clustering using a t-mixture
12283 model with Box-Cox transformation.")
12284 (license license:artistic2.0)))
12286 ;; TODO: this package bundles an old version of protobuf. It's not easy to
12287 ;; make it use our protobuf package instead.
12288 (define-public r-rprotobuflib
12290 (name "r-rprotobuflib")
12295 (uri (bioconductor-uri "RProtoBufLib" version))
12298 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
12299 (properties `((upstream-name . "RProtoBufLib")))
12300 (build-system r-build-system)
12303 (modify-phases %standard-phases
12304 (add-after 'unpack 'unpack-bundled-sources
12306 (with-directory-excursion "src"
12307 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
12310 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
12311 (synopsis "C++ headers and static libraries of Protocol buffers")
12313 "This package provides the headers and static library of Protocol buffers
12314 for other R packages to compile and link against.")
12315 (license license:bsd-3)))
12317 (define-public r-flowworkspace
12319 (name "r-flowworkspace")
12324 (uri (bioconductor-uri "flowWorkspace" version))
12327 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
12328 (properties `((upstream-name . "flowWorkspace")))
12329 (build-system r-build-system)
12360 (home-page "https://bioconductor.org/packages/flowWorkspace/")
12361 (synopsis "Infrastructure for working with cytometry data")
12363 "This package is designed to facilitate comparison of automated gating
12364 methods against manual gating done in flowJo. This package allows you to
12365 import basic flowJo workspaces into BioConductor and replicate the gating from
12366 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
12367 samples, compensation, and transformation are performed so that the output
12368 matches the flowJo analysis.")
12369 (license license:artistic2.0)))
12371 (define-public r-flowstats
12373 (name "r-flowstats")
12378 (uri (bioconductor-uri "flowStats" version))
12381 "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc"))))
12382 (properties `((upstream-name . "flowStats")))
12383 (build-system r-build-system)
12401 (home-page "http://www.github.com/RGLab/flowStats")
12402 (synopsis "Statistical methods for the analysis of flow cytometry data")
12404 "This package provides methods and functionality to analyze flow data
12405 that is beyond the basic infrastructure provided by the @code{flowCore}
12407 (license license:artistic2.0)))
12409 (define-public r-opencyto
12411 (name "r-opencyto")
12416 (uri (bioconductor-uri "openCyto" version))
12419 "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0"))))
12420 (properties `((upstream-name . "openCyto")))
12421 (build-system r-build-system)
12446 (home-page "https://bioconductor.org/packages/openCyto")
12447 (synopsis "Hierarchical gating pipeline for flow cytometry data")
12449 "This package is designed to facilitate the automated gating methods in a
12450 sequential way to mimic the manual gating strategy.")
12451 (license license:artistic2.0)))
12453 (define-public r-cytoml
12460 (uri (bioconductor-uri "CytoML" version))
12463 "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw"))))
12464 (properties `((upstream-name . "CytoML")))
12465 (build-system r-build-system)
12467 (list libxml2 zlib))
12498 (home-page "https://github.com/RGLab/CytoML")
12499 (synopsis "GatingML interface for cross platform cytometry data sharing")
12501 "This package provides an interface to implementations of the GatingML2.0
12502 standard to exchange gated cytometry data with other software platforms.")
12503 (license license:artistic2.0)))
12505 (define-public r-flowsom
12512 (uri (bioconductor-uri "FlowSOM" version))
12515 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
12516 (properties `((upstream-name . "FlowSOM")))
12517 (build-system r-build-system)
12519 (list r-biocgenerics
12521 r-consensusclusterplus
12541 (home-page "https://bioconductor.org/packages/FlowSOM/")
12542 (synopsis "Visualize and interpret cytometry data")
12544 "FlowSOM offers visualization options for cytometry data, by using
12545 self-organizing map clustering and minimal spanning trees.")
12546 (license license:gpl2+)))
12548 (define-public r-mixomics
12550 (name "r-mixomics")
12555 (uri (bioconductor-uri "mixOmics" version))
12558 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
12559 (properties `((upstream-name . "mixOmics")))
12560 (build-system r-build-system)
12562 (list r-biocparallel
12579 (home-page "http://www.mixOmics.org")
12580 (synopsis "Multivariate methods for exploration of biological datasets")
12582 "mixOmics offers a wide range of multivariate methods for the exploration
12583 and integration of biological datasets with a particular focus on variable
12584 selection. The package proposes several sparse multivariate models we have
12585 developed to identify the key variables that are highly correlated, and/or
12586 explain the biological outcome of interest. The data that can be analysed
12587 with mixOmics may come from high throughput sequencing technologies, such as
12588 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
12589 also beyond the realm of omics (e.g. spectral imaging). The methods
12590 implemented in mixOmics can also handle missing values without having to
12591 delete entire rows with missing data.")
12592 (license license:gpl2+)))
12594 (define-public r-depecher
12595 (package ;Source/Weave error
12596 (name "r-depecher")
12601 (uri (bioconductor-uri "DepecheR" version))
12604 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
12605 (properties `((upstream-name . "DepecheR")))
12606 (build-system r-build-system)
12627 (home-page "https://bioconductor.org/packages/DepecheR/")
12628 (synopsis "Identify traits of clusters in high-dimensional entities")
12630 "The purpose of this package is to identify traits in a dataset that can
12631 separate groups. This is done on two levels. First, clustering is performed,
12632 using an implementation of sparse K-means. Secondly, the generated clusters
12633 are used to predict outcomes of groups of individuals based on their
12634 distribution of observations in the different clusters. As certain clusters
12635 with separating information will be identified, and these clusters are defined
12636 by a sparse number of variables, this method can reduce the complexity of
12637 data, to only emphasize the data that actually matters.")
12638 (license license:expat)))
12640 (define-public r-rcistarget
12642 (name "r-rcistarget")
12647 (uri (bioconductor-uri "RcisTarget" version))
12650 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
12651 (properties `((upstream-name . "RcisTarget")))
12652 (build-system r-build-system)
12664 r-summarizedexperiment
12668 (home-page "https://aertslab.org/#scenic")
12669 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
12671 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
12672 over-represented on a gene list. In a first step, RcisTarget selects DNA
12673 motifs that are significantly over-represented in the surroundings of the
12674 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
12675 achieved by using a database that contains genome-wide cross-species rankings
12676 for each motif. The motifs that are then annotated to TFs and those that have
12677 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
12678 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
12679 genes in the gene-set that are ranked above the leading edge).")
12680 (license license:gpl3)))
12682 (define-public r-chicago
12689 (uri (bioconductor-uri "Chicago" version))
12692 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
12693 (properties `((upstream-name . "Chicago")))
12694 (build-system r-build-system)
12696 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
12697 (native-inputs (list r-knitr))
12698 (home-page "https://bioconductor.org/packages/Chicago")
12699 (synopsis "Capture Hi-C analysis of genomic organization")
12701 "This package provides a pipeline for analysing Capture Hi-C data.")
12702 (license license:artistic2.0)))
12704 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12706 (define-public r-ciara
12712 (uri (cran-uri "CIARA" version))
12715 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
12716 (properties `((upstream-name . "CIARA")))
12717 (build-system r-build-system)
12718 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
12719 (native-inputs (list r-knitr))
12720 (home-page "https://cran.r-project.org/package=CIARA")
12721 (synopsis "Cluster-independent algorithm for rare cell types identification")
12723 "This is a package to support identification of markers of rare cell
12724 types by looking at genes whose expression is confined in small regions of the
12725 expression space.")
12726 (license license:artistic2.0)))
12728 (define-public r-cicero
12735 (uri (bioconductor-uri "cicero" version))
12738 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
12739 (build-system r-build-system)
12765 (home-page "https://bioconductor.org/packages/cicero/")
12766 (synopsis "Predict cis-co-accessibility from single-cell data")
12768 "Cicero computes putative cis-regulatory maps from single-cell chromatin
12769 accessibility data. It also extends the monocle package for use in chromatin
12770 accessibility data.")
12771 (license license:expat)))
12773 ;; This is the latest commit on the "monocle3" branch.
12774 (define-public r-cicero-monocle3
12775 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
12777 (package (inherit r-cicero)
12778 (name "r-cicero-monocle3")
12779 (version (git-version "1.3.2" revision commit))
12783 (uri (git-reference
12784 (url "https://github.com/cole-trapnell-lab/cicero-release")
12786 (file-name (git-file-name name version))
12789 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
12791 (modify-inputs (package-propagated-inputs r-cicero)
12792 (delete "r-monocle")
12793 (prepend r-monocle3))))))
12795 (define-public r-circrnaprofiler
12797 (name "r-circrnaprofiler")
12802 (uri (bioconductor-uri "circRNAprofiler" version))
12805 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
12807 `((upstream-name . "circRNAprofiler")))
12808 (build-system r-build-system)
12810 (list r-annotationhub
12813 r-bsgenome-hsapiens-ucsc-hg19
12836 "https://github.com/Aufiero/circRNAprofiler")
12838 "Computational framework for the downstream analysis of circular RNA's")
12840 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
12841 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
12842 framework allows combining and analyzing circRNAs previously detected by
12843 multiple publicly available annotation-based circRNA detection tools. It
12844 covers different aspects of circRNAs analysis from differential expression
12845 analysis, evolutionary conservation, biogenesis to functional analysis.")
12846 (license license:gpl3)))
12848 (define-public r-cistopic
12850 (name "r-cistopic")
12855 (uri (git-reference
12856 (url "https://github.com/aertslab/cisTopic")
12857 (commit (string-append "v" version))))
12858 (file-name (git-file-name name version))
12861 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
12862 (build-system r-build-system)
12879 (home-page "https://github.com/aertslab/cisTopic")
12880 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
12882 "The sparse nature of single cell epigenomics data can be overruled using
12883 probabilistic modelling methods such as @dfn{Latent Dirichlet
12884 Allocation} (LDA). This package allows the probabilistic modelling of
12885 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
12886 includes functionalities to identify cell states based on the contribution of
12887 cisTopics and explore the nature and regulatory proteins driving them.")
12888 (license license:gpl3)))
12890 (define-public r-cistopic-next
12891 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
12894 (inherit r-cistopic)
12895 (name "r-cistopic-next")
12896 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
12897 ;; since the previous release is 2.1.0. Oh well.
12898 (version (git-version "0.3.0" revision commit))
12902 (uri (git-reference
12903 (url "https://github.com/aertslab/cisTopic")
12905 (file-name (git-file-name name version))
12908 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
12909 (properties `((upstream-name . "cisTopic")))
12930 (define-public r-genie3
12937 (uri (bioconductor-uri "GENIE3" version))
12940 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
12941 (properties `((upstream-name . "GENIE3")))
12942 (build-system r-build-system)
12944 (list r-dplyr r-reshape2))
12947 (home-page "https://bioconductor.org/packages/GENIE3")
12948 (synopsis "Gene network inference with ensemble of trees")
12950 "This package implements the GENIE3 algorithm for inferring gene
12951 regulatory networks from expression data.")
12952 (license license:gpl2+)))
12954 (define-public r-roc
12961 (uri (bioconductor-uri "ROC" version))
12964 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
12965 (properties `((upstream-name . "ROC")))
12966 (build-system r-build-system)
12969 (home-page "https://www.bioconductor.org/packages/ROC/")
12970 (synopsis "Utilities for ROC curves")
12972 "This package provides utilities for @dfn{Receiver Operating
12973 Characteristic} (ROC) curves, with a focus on micro arrays.")
12974 (license license:artistic2.0)))
12976 (define-public r-watermelon
12978 (name "r-watermelon")
12983 (uri (bioconductor-uri "wateRmelon" version))
12986 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
12987 (properties `((upstream-name . "wateRmelon")))
12988 (build-system r-build-system)
12991 r-illuminahumanmethylation450kanno-ilmn12-hg19
13000 (home-page "https://bioconductor.org/packages/wateRmelon/")
13001 (synopsis "Illumina 450 methylation array normalization and metrics")
13003 "The standard index of DNA methylation (beta) is computed from methylated
13004 and unmethylated signal intensities. Betas calculated from raw signal
13005 intensities perform well, but using 11 methylomic datasets we demonstrate that
13006 quantile normalization methods produce marked improvement. The commonly used
13007 procedure of normalizing betas is inferior to the separate normalization of M
13008 and U, and it is also advantageous to normalize Type I and Type II assays
13009 separately. This package provides 15 flavours of betas and three performance
13010 metrics, with methods for objects produced by the @code{methylumi} and
13011 @code{minfi} packages.")
13012 (license license:gpl3)))
13014 (define-public r-gdsfmt
13021 (uri (bioconductor-uri "gdsfmt" version))
13024 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
13025 (modules '((guix build utils)))
13026 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
13027 ;; them and link with system libraries instead.
13030 (for-each delete-file-recursively
13034 (substitute* "src/Makevars"
13035 (("all: \\$\\(SHLIB\\)") "all:")
13036 (("\\$\\(SHLIB\\): liblzma.a") "")
13037 (("^ (ZLIB|LZ4)/.*") "")
13038 (("CoreArray/dVLIntGDS.cpp.*")
13039 "CoreArray/dVLIntGDS.cpp")
13040 (("CoreArray/dVLIntGDS.o.*")
13041 "CoreArray/dVLIntGDS.o")
13042 (("PKG_LIBS = ./liblzma.a")
13043 "PKG_LIBS = -llz4"))
13044 (substitute* "src/CoreArray/dStream.h"
13045 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
13046 (string-append "include <" header ">")))))))
13047 (properties `((upstream-name . "gdsfmt")))
13048 (build-system r-build-system)
13050 (list lz4 xz zlib))
13053 (home-page "http://corearray.sourceforge.net/")
13055 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
13057 "This package provides a high-level R interface to CoreArray @dfn{Genomic
13058 Data Structure} (GDS) data files, which are portable across platforms with
13059 hierarchical structure to store multiple scalable array-oriented data sets
13060 with metadata information. It is suited for large-scale datasets, especially
13061 for data which are much larger than the available random-access memory. The
13062 @code{gdsfmt} package offers efficient operations specifically designed for
13063 integers of less than 8 bits, since a diploid genotype, like
13064 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
13065 byte. Data compression and decompression are available with relatively
13066 efficient random access. It is also allowed to read a GDS file in parallel
13067 with multiple R processes supported by the package @code{parallel}.")
13068 (license license:lgpl3)))
13070 (define-public r-bigmelon
13072 (name "r-bigmelon")
13077 (uri (bioconductor-uri "bigmelon" version))
13080 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
13081 (properties `((upstream-name . "bigmelon")))
13082 (build-system r-build-system)
13094 (home-page "https://bioconductor.org/packages/bigmelon/")
13095 (synopsis "Illumina methylation array analysis for large experiments")
13097 "This package provides methods for working with Illumina arrays using the
13098 @code{gdsfmt} package.")
13099 (license license:gpl3)))
13101 (define-public r-seqbias
13108 (uri (bioconductor-uri "seqbias" version))
13111 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
13112 (properties `((upstream-name . "seqbias")))
13113 (build-system r-build-system)
13115 (list r-biostrings r-genomicranges r-rhtslib))
13116 (home-page "https://bioconductor.org/packages/seqbias/")
13117 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
13119 "This package implements a model of per-position sequencing bias in
13120 high-throughput sequencing data using a simple Bayesian network, the structure
13121 and parameters of which are trained on a set of aligned reads and a reference
13123 (license license:lgpl3)))
13125 (define-public r-reqon
13132 (uri (bioconductor-uri "ReQON" version))
13135 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
13136 (properties `((upstream-name . "ReQON")))
13137 (build-system r-build-system)
13139 (list r-rjava r-rsamtools r-seqbias))
13140 (home-page "https://bioconductor.org/packages/ReQON/")
13141 (synopsis "Recalibrating quality of nucleotides")
13143 "This package provides an implementation of an algorithm for
13144 recalibrating the base quality scores for aligned sequencing data in BAM
13146 (license license:gpl2)))
13148 (define-public r-wavcluster
13150 (name "r-wavcluster")
13155 (uri (bioconductor-uri "wavClusteR" version))
13158 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
13159 (properties `((upstream-name . "wavClusteR")))
13160 (build-system r-build-system)
13162 (list r-biocgenerics
13178 (home-page "https://bioconductor.org/packages/wavClusteR/")
13179 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
13181 "This package provides an integrated pipeline for the analysis of
13182 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
13183 sequencing errors, SNPs and additional non-experimental sources by a non-
13184 parametric mixture model. The protein binding sites (clusters) are then
13185 resolved at high resolution and cluster statistics are estimated using a
13186 rigorous Bayesian framework. Post-processing of the results, data export for
13187 UCSC genome browser visualization and motif search analysis are provided. In
13188 addition, the package integrates RNA-Seq data to estimate the False
13189 Discovery Rate of cluster detection. Key functions support parallel multicore
13190 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
13191 be applied to the analysis of other NGS data obtained from experimental
13192 procedures that induce nucleotide substitutions (e.g. BisSeq).")
13193 (license license:gpl2)))
13195 (define-public r-timeseriesexperiment
13197 (name "r-timeseriesexperiment")
13202 (uri (bioconductor-uri "TimeSeriesExperiment" version))
13205 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
13207 `((upstream-name . "TimeSeriesExperiment")))
13208 (build-system r-build-system)
13220 r-summarizedexperiment
13227 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
13228 (synopsis "Analysis for short time-series data")
13230 "This package is a visualization and analysis toolbox for short time
13231 course data which includes dimensionality reduction, clustering, two-sample
13232 differential expression testing and gene ranking techniques. The package also
13233 provides methods for retrieving enriched pathways.")
13234 (license license:lgpl3+)))
13236 (define-public r-variantfiltering
13238 (name "r-variantfiltering")
13243 (uri (bioconductor-uri "VariantFiltering" version))
13246 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
13248 `((upstream-name . "VariantFiltering")))
13249 (build-system r-build-system)
13251 (list r-annotationdbi
13272 r-summarizedexperiment
13273 r-variantannotation
13275 (home-page "https://github.com/rcastelo/VariantFiltering")
13276 (synopsis "Filtering of coding and non-coding genetic variants")
13278 "Filter genetic variants using different criteria such as inheritance
13279 model, amino acid change consequence, minor allele frequencies across human
13280 populations, splice site strength, conservation, etc.")
13281 (license license:artistic2.0)))
13283 (define-public r-genomegraphs
13285 (name "r-genomegraphs")
13290 (uri (bioconductor-uri "GenomeGraphs" version))
13293 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
13294 (properties `((upstream-name . "GenomeGraphs")))
13295 (build-system r-build-system)
13298 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
13299 (synopsis "Plotting genomic information from Ensembl")
13301 "Genomic data analyses requires integrated visualization of known genomic
13302 information and new experimental data. GenomeGraphs uses the biomaRt package
13303 to perform live annotation queries to Ensembl and translates this to e.g.
13304 gene/transcript structures in viewports of the grid graphics package. This
13305 results in genomic information plotted together with your data. Another
13306 strength of GenomeGraphs is to plot different data types such as array CGH,
13307 gene expression, sequencing and other data, together in one plot using the
13308 same genome coordinate system.")
13309 (license license:artistic2.0)))
13311 (define-public r-wavetiling
13313 (name "r-wavetiling")
13318 (uri (bioconductor-uri "waveTiling" version))
13321 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
13322 (properties `((upstream-name . "waveTiling")))
13323 (build-system r-build-system)
13335 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
13336 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
13338 "This package is designed to conduct transcriptome analysis for tiling
13339 arrays based on fast wavelet-based functional models.")
13340 (license license:gpl2+)))
13342 (define-public r-variancepartition
13344 (name "r-variancepartition")
13349 (uri (bioconductor-uri "variancePartition" version))
13352 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
13354 `((upstream-name . "variancePartition")))
13355 (build-system r-build-system)
13379 (home-page "https://bioconductor.org/packages/variancePartition/")
13380 (synopsis "Analyze variation in gene expression experiments")
13382 "This is a package providing tools to quantify and interpret multiple
13383 sources of biological and technical variation in gene expression experiments.
13384 It uses a linear mixed model to quantify variation in gene expression
13385 attributable to individual, tissue, time point, or technical variables. The
13386 package includes dream differential expression analysis for repeated
13388 (license license:gpl2+)))
13390 (define-public r-htqpcr
13397 (uri (bioconductor-uri "HTqPCR" version))
13400 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
13401 (properties `((upstream-name . "HTqPCR")))
13402 (build-system r-build-system)
13404 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
13405 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
13406 "groups/bertone/software/HTqPCR.pdf"))
13407 (synopsis "Automated analysis of high-throughput qPCR data")
13409 "Analysis of Ct values from high throughput quantitative real-time
13410 PCR (qPCR) assays across multiple conditions or replicates. The input data
13411 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
13412 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
13413 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
13414 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
13415 loading, quality assessment, normalization, visualization and parametric or
13416 non-parametric testing for statistical significance in Ct values between
13417 features (e.g. genes, microRNAs).")
13418 (license license:artistic2.0)))
13420 (define-public r-unifiedwmwqpcr
13422 (name "r-unifiedwmwqpcr")
13427 (uri (bioconductor-uri "unifiedWMWqPCR" version))
13430 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
13432 `((upstream-name . "unifiedWMWqPCR")))
13433 (build-system r-build-system)
13435 (list r-biocgenerics r-htqpcr))
13436 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
13437 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
13439 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
13440 data. This modified test allows for testing differential expression in qPCR
13442 (license license:gpl2+)))
13444 (define-public r-universalmotif
13446 (name "r-universalmotif")
13451 (uri (bioconductor-uri "universalmotif" version))
13454 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
13456 `((upstream-name . "universalmotif")))
13457 (build-system r-build-system)
13460 (modify-phases %standard-phases
13461 (add-after 'unpack 'fix-reference-to-strip
13463 (substitute* "src/Makevars"
13464 (("/usr/bin/strip") (which "strip"))))))))
13466 (list r-biocgenerics
13479 "https://bioconductor.org/packages/universalmotif/")
13481 "Specific structures importer, modifier, and exporter for R")
13483 "This package allows importing most common @dfn{specific structure}
13484 (motif) types into R for use by functions provided by other Bioconductor
13485 motif-related packages. Motifs can be exported into most major motif formats
13486 from various classes as defined by other Bioconductor packages. A suite of
13487 motif and sequence manipulation and analysis functions are included, including
13488 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
13489 motifs, and others.")
13490 (license license:gpl3)))
13492 (define-public r-ace
13498 (uri (bioconductor-uri "ACE" version))
13501 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
13502 (properties `((upstream-name . "ACE")))
13503 (build-system r-build-system)
13504 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
13505 (native-inputs (list r-knitr))
13506 (home-page "https://github.com/tgac-vumc/ACE")
13508 "Absolute copy number estimation from low-coverage whole genome sequencing")
13510 "This package uses segmented copy number data to estimate tumor cell
13511 percentage and produce copy number plots displaying absolute copy numbers. For
13512 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
13513 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
13514 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
13515 subsequently run through all samples in the object(s), for which it will create
13516 individual subdirectories. For each sample, it will calculate how well the
13517 segments fit (the relative error) to integer copy numbers for each percentage
13518 of @dfn{tumor cells} (cells with divergent segments).")
13519 (license license:gpl2)))
13521 (define-public r-acgh
13527 (uri (bioconductor-uri "aCGH" version))
13530 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
13531 (properties `((upstream-name . "aCGH")))
13532 (build-system r-build-system)
13533 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
13534 (home-page "https://bioconductor.org/packages/aCGH")
13536 "Classes and functions for array comparative genomic hybridization data")
13538 "This package provides functions for reading
13539 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
13540 output files and clone information files, creation of @code{aCGH} objects for
13541 storing these data. Basic methods are accessing/replacing, subsetting,
13542 printing and plotting @code{aCGH} objects.")
13543 (license license:gpl2)))
13545 (define-public r-acme
13551 (uri (bioconductor-uri "ACME" version))
13554 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
13555 (properties `((upstream-name . "ACME")))
13556 (build-system r-build-system)
13557 (propagated-inputs (list r-biobase r-biocgenerics))
13558 (home-page "https://bioconductor.org/packages/aCGH/")
13559 (synopsis "Calculating microarray enrichment")
13561 "This package implements @dfn{algorithms for calculating microarray
13562 enrichment} (ACME), and it is a set of tools for analysing tiling array of
13563 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
13564 DNAse hypersensitivity, or other experiments that result in regions of the
13565 genome showing enrichment. It does not rely on a specific array technology
13566 (although the array should be a tiling array), is very general (can be applied
13567 in experiments resulting in regions of enrichment), and is very insensitive to
13568 array noise or normalization methods. It is also very fast and can be applied
13569 on whole-genome tiling array experiments quite easily with enough memory.")
13570 (license license:gpl2+)))
13572 (define-public r-acde
13578 (uri (bioconductor-uri "acde" version))
13581 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
13582 (properties `((upstream-name . "acde")))
13583 (build-system r-build-system)
13584 (propagated-inputs (list r-boot))
13585 (home-page "https://bioconductor.org/packages/acde")
13587 "Identification of differentially expressed genes with artificial components")
13589 "This package provides a multivariate inferential analysis method for
13590 detecting differentially expressed genes in gene expression data. It uses
13591 artificial components, close to the data's principal components but with an
13592 exact interpretation in terms of differential genetic expression, to identify
13593 differentially expressed genes while controlling the @dfn{false discovery
13595 (license license:gpl3)))
13597 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13599 (define-public r-activedriverwgs
13601 (name "r-activedriverwgs")
13606 (uri (cran-uri "ActiveDriverWGS" version))
13609 "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
13611 `((upstream-name . "ActiveDriverWGS")))
13612 (build-system r-build-system)
13616 r-bsgenome-hsapiens-ucsc-hg19
13617 r-bsgenome-hsapiens-ucsc-hg38
13618 r-bsgenome-mmusculus-ucsc-mm9
13619 r-bsgenome-mmusculus-ucsc-mm10
13626 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
13627 (synopsis "Driver discovery tool for cancer whole genomes")
13629 "This package provides a method for finding an enrichment of cancer
13630 simple somatic mutations (SNVs and Indels) in functional elements across the
13631 human genome. ActiveDriverWGS detects coding and noncoding driver elements
13632 using whole genome sequencing data.")
13633 (license license:gpl3)))
13635 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13637 (define-public r-activepathways
13639 (name "r-activepathways")
13644 (uri (cran-uri "ActivePathways" version))
13647 "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
13649 `((upstream-name . "ActivePathways")))
13650 (build-system r-build-system)
13652 (list r-data-table r-ggplot2))
13655 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
13656 (synopsis "Multivariate pathway enrichment analysis")
13658 "This package represents an integrative method of analyzing multi omics
13659 data that conducts enrichment analysis of annotated gene sets. ActivePathways
13660 uses a statistical data fusion approach, rationalizes contributing evidence
13661 and highlights associated genes, improving systems-level understanding of
13662 cellular organization in health and disease.")
13663 (license license:gpl3)))
13665 (define-public r-bgmix
13672 (uri (bioconductor-uri "BGmix" version))
13675 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
13676 (properties `((upstream-name . "BGmix")))
13677 (build-system r-build-system)
13679 (list r-kernsmooth))
13680 (home-page "https://bioconductor.org/packages/BGmix/")
13681 (synopsis "Bayesian models for differential gene expression")
13683 "This package provides fully Bayesian mixture models for differential
13685 (license license:gpl2)))
13687 (define-public r-bgx
13694 (uri (bioconductor-uri "bgx" version))
13697 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
13698 (properties `((upstream-name . "bgx")))
13699 (build-system r-build-system)
13703 '(modify-phases %standard-phases
13704 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
13706 (substitute* "configure.ac"
13707 (("AX_GCC_ARCHFLAG.*") ""))
13708 (delete-file "configure")
13709 (invoke "autoreconf" "-vif"))))))
13713 (list r-affy r-biobase r-gcrma r-rcpp))
13715 (list autoconf automake))
13716 (home-page "https://bioconductor.org/packages/bgx/")
13717 (synopsis "Bayesian gene expression")
13719 "This package provides tools for Bayesian integrated analysis of
13720 Affymetrix GeneChips.")
13721 (license license:gpl2)))
13723 (define-public r-bhc
13730 (uri (bioconductor-uri "BHC" version))
13733 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
13734 (properties `((upstream-name . "BHC")))
13735 (build-system r-build-system)
13736 (home-page "https://bioconductor.org/packages/BHC/")
13737 (synopsis "Bayesian hierarchical clustering")
13739 "The method implemented in this package performs bottom-up hierarchical
13740 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
13741 in the data and Bayesian model selection to decide at each step which clusters
13742 to merge. This avoids several limitations of traditional methods, for example
13743 how many clusters there should be and how to choose a principled distance
13744 metric. This implementation accepts multinomial (i.e. discrete, with 2+
13745 categories) or time-series data. This version also includes a randomised
13746 algorithm which is more efficient for larger data sets.")
13747 (license license:gpl3)))
13749 (define-public r-bicare
13756 (uri (bioconductor-uri "BicARE" version))
13759 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
13760 (properties `((upstream-name . "BicARE")))
13761 (build-system r-build-system)
13763 (list r-biobase r-gseabase r-multtest))
13764 (home-page "http://bioinfo.curie.fr")
13765 (synopsis "Biclustering analysis and results exploration")
13767 "This is a package for biclustering analysis and exploration of
13769 (license license:gpl2)))
13771 (define-public r-bifet
13778 (uri (bioconductor-uri "BiFET" version))
13781 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
13782 (properties `((upstream-name . "BiFET")))
13783 (build-system r-build-system)
13785 (list r-genomicranges r-poibin))
13788 (home-page "https://bioconductor.org/packages/BiFET")
13789 (synopsis "Bias-free footprint enrichment test")
13791 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
13792 over-represented in target regions compared to background regions after
13793 correcting for the bias arising from the imbalance in read counts and GC
13794 contents between the target and background regions. For a given TF k, BiFET
13795 tests the null hypothesis that the target regions have the same probability of
13796 having footprints for the TF k as the background regions while correcting for
13797 the read count and GC content bias.")
13798 (license license:gpl3)))
13800 (define-public r-rsbml
13807 (uri (bioconductor-uri "rsbml" version))
13810 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
13811 (properties `((upstream-name . "rsbml")))
13812 (build-system r-build-system)
13816 (list r-biocgenerics r-graph))
13819 (home-page "http://www.sbml.org")
13820 (synopsis "R support for SBML")
13822 "This package provides an R interface to libsbml for SBML parsing,
13823 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
13824 (license license:artistic2.0)))
13826 (define-public r-hypergraph
13828 (name "r-hypergraph")
13833 (uri (bioconductor-uri "hypergraph" version))
13836 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
13837 (properties `((upstream-name . "hypergraph")))
13838 (build-system r-build-system)
13841 (home-page "https://bioconductor.org/packages/hypergraph")
13842 (synopsis "Hypergraph data structures")
13844 "This package implements some simple capabilities for representing and
13845 manipulating hypergraphs.")
13846 (license license:artistic2.0)))
13848 (define-public r-hyperdraw
13850 (name "r-hyperdraw")
13855 (uri (bioconductor-uri "hyperdraw" version))
13858 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
13859 (properties `((upstream-name . "hyperdraw")))
13860 (build-system r-build-system)
13861 (inputs (list graphviz))
13863 (list r-graph r-hypergraph r-rgraphviz))
13864 (home-page "https://bioconductor.org/packages/hyperdraw")
13865 (synopsis "Visualizing hypergraphs")
13867 "This package provides functions for visualizing hypergraphs.")
13868 (license license:gpl2+)))
13870 (define-public r-biggr
13877 (uri (bioconductor-uri "BiGGR" version))
13880 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
13881 (properties `((upstream-name . "BiGGR")))
13882 (build-system r-build-system)
13890 (home-page "https://bioconductor.org/packages/BiGGR/")
13891 (synopsis "Constraint based modeling using metabolic reconstruction databases")
13893 "This package provides an interface to simulate metabolic reconstruction
13894 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
13895 reconstruction databases. The package facilitates @dfn{flux balance
13896 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
13897 networks and estimated fluxes can be visualized with hypergraphs.")
13898 (license license:gpl3+)))
13900 (define-public r-bigmemoryextras
13902 (name "r-bigmemoryextras")
13907 (uri (bioconductor-uri "bigmemoryExtras" version))
13910 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
13912 `((upstream-name . "bigmemoryExtras")))
13913 (build-system r-build-system)
13915 (list r-bigmemory))
13918 (home-page "https://github.com/phaverty/bigmemoryExtras")
13919 (synopsis "Extension of the bigmemory package")
13921 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
13922 safety and convenience features to the @code{filebacked.big.matrix} class from
13923 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
13924 monitoring and gracefully restoring the connection to on-disk data and it also
13925 protects against accidental data modification with a file-system-based
13926 permissions system. Utilities are provided for using @code{BigMatrix}-derived
13927 classes as @code{assayData} matrices within the @code{Biobase} package's
13928 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
13929 related to attaching to, and indexing into, file-backed matrices with
13930 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
13931 a file-backed matrix with factor properties.")
13932 (license license:artistic2.0)))
13934 (define-public r-bigpint
13941 (uri (bioconductor-uri "bigPint" version))
13944 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
13945 (properties `((upstream-name . "bigPint")))
13946 (build-system r-build-system)
13948 (list r-delayedarray
13964 r-summarizedexperiment
13968 (home-page "https://github.com/lindsayrutter/bigPint")
13969 (synopsis "Big multivariate data plotted interactively")
13971 "This package provides methods for visualizing large multivariate
13972 datasets using static and interactive scatterplot matrices, parallel
13973 coordinate plots, volcano plots, and litre plots. It includes examples for
13974 visualizing RNA-sequencing datasets and differentially expressed genes.")
13975 (license license:gpl3)))
13977 (define-public r-chemminer
13979 (name "r-chemminer")
13984 (uri (bioconductor-uri "ChemmineR" version))
13987 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
13988 (properties `((upstream-name . "ChemmineR")))
13989 (build-system r-build-system)
14008 (home-page "https://github.com/girke-lab/ChemmineR")
14009 (synopsis "Cheminformatics toolkit for R")
14011 "ChemmineR is a cheminformatics package for analyzing drug-like small
14012 molecule data in R. It contains functions for efficient processing of large
14013 numbers of molecules, physicochemical/structural property predictions,
14014 structural similarity searching, classification and clustering of compound
14015 libraries with a wide spectrum of algorithms. In addition, it offers
14016 visualization functions for compound clustering results and chemical
14018 (license license:artistic2.0)))
14020 (define-public r-fmcsr
14027 (uri (bioconductor-uri "fmcsR" version))
14029 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
14030 (properties `((upstream-name . "fmcsR")))
14031 (build-system r-build-system)
14033 (list r-biocgenerics r-chemminer r-runit))
14034 (native-inputs (list r-knitr))
14035 (home-page "https://github.com/girke-lab/fmcsR")
14036 (synopsis "Mismatch tolerant maximum common substructure searching")
14038 "The fmcsR package introduces an efficient @dfn{maximum common
14039 substructure} (MCS) algorithms combined with a novel matching strategy that
14040 allows for atom and/or bond mismatches in the substructures shared among two
14041 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
14042 strict MCSs, resulting in the identification of more common features in their
14043 source structures, as well as a higher sensitivity in finding compounds with
14044 weak structural similarities. The fmcsR package provides several utilities to
14045 use the FMCS algorithm for pairwise compound comparisons, structure similarity
14046 searching and clustering.")
14047 (license license:artistic2.0)))
14049 (define-public r-bioassayr
14051 (name "r-bioassayr")
14056 (uri (bioconductor-uri "bioassayR" version))
14059 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
14060 (properties `((upstream-name . "bioassayR")))
14061 (build-system r-build-system)
14063 (list r-biocgenerics
14072 (home-page "https://github.com/girke-lab/bioassayR")
14073 (synopsis "Cross-target analysis of small molecule bioactivity")
14075 "bioassayR is a computational tool that enables simultaneous analysis of
14076 thousands of bioassay experiments performed over a diverse set of compounds
14077 and biological targets. Unique features include support for large-scale
14078 cross-target analyses of both public and custom bioassays, generation of
14079 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
14080 preloaded database that provides access to a substantial portion of publicly
14081 available bioactivity data.")
14082 (license license:artistic2.0)))
14084 (define-public r-biobroom
14086 (name "r-biobroom")
14091 (uri (bioconductor-uri "biobroom" version))
14094 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
14095 (properties `((upstream-name . "biobroom")))
14096 (build-system r-build-system)
14098 (list r-biobase r-broom r-dplyr r-tidyr))
14101 (home-page "https://github.com/StoreyLab/biobroom")
14102 (synopsis "Turn Bioconductor objects into tidy data frames")
14104 "This package contains methods for converting standard objects
14105 constructed by bioinformatics packages, especially those in Bioconductor, and
14106 converting them to @code{tidy} data. It thus serves as a complement to the
14107 @code{broom} package, and follows the same tidy, augment, glance division of
14108 tidying methods. Tidying data makes it easy to recombine, reshape and
14109 visualize bioinformatics analyses.")
14110 ;; Any version of the LGPL.
14111 (license license:lgpl3+)))
14113 (define-public r-graphite
14115 (name "r-graphite")
14120 (uri (bioconductor-uri "graphite" version))
14123 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
14124 (properties `((upstream-name . "graphite")))
14125 (build-system r-build-system)
14127 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
14128 (home-page "https://bioconductor.org/packages/graphite/")
14129 (synopsis "Networks from pathway databases")
14131 "Graphite provides networks derived from eight public pathway databases,
14132 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
14134 (license license:agpl3+)))
14136 (define-public r-reactomepa
14138 (name "r-reactomepa")
14143 (uri (bioconductor-uri "ReactomePA" version))
14146 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
14147 (properties `((upstream-name . "ReactomePA")))
14148 (build-system r-build-system)
14150 (list r-annotationdbi
14160 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
14161 (synopsis "Reactome pathway analysis")
14163 "This package provides functions for pathway analysis based on the
14164 REACTOME pathway database. It implements enrichment analysis, gene set
14165 enrichment analysis and several functions for visualization.")
14166 (license license:gpl2)))
14168 (define-public r-ebarrays
14170 (name "r-ebarrays")
14175 (uri (bioconductor-uri "EBarrays" version))
14178 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
14179 (properties `((upstream-name . "EBarrays")))
14180 (build-system r-build-system)
14182 (list r-biobase r-cluster r-lattice))
14183 (home-page "https://bioconductor.org/packages/EBarrays/")
14184 (synopsis "Gene clustering and differential expression identification")
14186 "EBarrays provides tools for the analysis of replicated/unreplicated
14188 (license license:gpl2+)))
14190 (define-public r-bioccasestudies
14192 (name "r-bioccasestudies")
14197 (uri (bioconductor-uri "BiocCaseStudies" version))
14200 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
14202 `((upstream-name . "BiocCaseStudies")))
14203 (build-system r-build-system)
14204 (propagated-inputs (list r-biobase))
14205 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
14206 (synopsis "Support for the case studies monograph")
14208 "This package provides software and data to support the case studies
14210 (license license:artistic2.0)))
14212 (define-public r-bioccheck
14214 (name "r-bioccheck")
14218 (uri (bioconductor-uri "BiocCheck" version))
14221 "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw"))))
14223 `((upstream-name . "BiocCheck")))
14224 (build-system r-build-system)
14235 (home-page "https://bioconductor.org/packages/BiocCheck")
14236 (synopsis "Executes Bioconductor-specific package checks")
14237 (description "This package contains tools to perform additional quality
14238 checks on R packages that are to be submitted to the Bioconductor repository.")
14239 (license license:artistic2.0)))
14241 (define-public r-biocgraph
14243 (name "r-biocgraph")
14248 (uri (bioconductor-uri "biocGraph" version))
14251 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
14252 (properties `((upstream-name . "biocGraph")))
14253 (build-system r-build-system)
14255 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
14256 (home-page "https://bioconductor.org/packages/biocGraph/")
14257 (synopsis "Graph examples and use cases in Bioinformatics")
14259 "This package provides examples and code that make use of the
14260 different graph related packages produced by Bioconductor.")
14261 (license license:artistic2.0)))
14263 (define-public r-biocstyle
14265 (name "r-biocstyle")
14269 (uri (bioconductor-uri "BiocStyle" version))
14272 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
14274 `((upstream-name . "BiocStyle")))
14275 (build-system r-build-system)
14277 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
14280 (home-page "https://bioconductor.org/packages/BiocStyle")
14281 (synopsis "Bioconductor formatting styles")
14282 (description "This package provides standard formatting styles for
14283 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
14285 (license license:artistic2.0)))
14287 (define-public r-biocviews
14289 (name "r-biocviews")
14293 (uri (bioconductor-uri "biocViews" version))
14296 "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38"))))
14298 `((upstream-name . "biocViews")))
14299 (build-system r-build-system)
14308 (home-page "https://bioconductor.org/packages/biocViews")
14309 (synopsis "Bioconductor package categorization helper")
14310 (description "The purpose of biocViews is to create HTML pages that
14311 categorize packages in a Bioconductor package repository according to keywords,
14312 also known as views, in a controlled vocabulary.")
14313 (license license:artistic2.0)))
14315 (define-public r-experimenthub
14317 (name "r-experimenthub")
14322 (uri (bioconductor-uri "ExperimentHub" version))
14325 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
14326 (properties `((upstream-name . "ExperimentHub")))
14327 (build-system r-build-system)
14329 (list r-annotationhub
14338 (home-page "https://bioconductor.org/packages/ExperimentHub/")
14339 (synopsis "Client to access ExperimentHub resources")
14341 "This package provides a client for the Bioconductor ExperimentHub web
14342 resource. ExperimentHub provides a central location where curated data from
14343 experiments, publications or training courses can be accessed. Each resource
14344 has associated metadata, tags and date of modification. The client creates
14345 and manages a local cache of files retrieved enabling quick and reproducible
14347 (license license:artistic2.0)))
14349 (define-public r-grohmm
14356 (uri (bioconductor-uri "groHMM" version))
14359 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
14360 (properties `((upstream-name . "groHMM")))
14361 (build-system r-build-system)
14363 (list r-genomeinfodb
14364 r-genomicalignments
14370 (home-page "https://github.com/Kraus-Lab/groHMM")
14371 (synopsis "GRO-seq analysis pipeline")
14373 "This package provides a pipeline for the analysis of GRO-seq data.")
14374 (license license:gpl3+)))
14376 (define-public r-multiassayexperiment
14378 (name "r-multiassayexperiment")
14383 (uri (bioconductor-uri "MultiAssayExperiment" version))
14386 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
14388 `((upstream-name . "MultiAssayExperiment")))
14389 (build-system r-build-system)
14396 r-summarizedexperiment
14400 (home-page "https://waldronlab.io/MultiAssayExperiment/")
14401 (synopsis "Integration of multi-omics experiments in Bioconductor")
14403 "MultiAssayExperiment harmonizes data management of multiple assays
14404 performed on an overlapping set of specimens. It provides a familiar
14405 Bioconductor user experience by extending concepts from
14406 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
14407 classes for individual assays, and allowing subsetting by genomic ranges or
14409 (license license:artistic2.0)))
14411 (define-public r-bioconcotk
14413 (name "r-bioconcotk")
14418 (uri (bioconductor-uri "BiocOncoTK" version))
14421 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
14422 (properties `((upstream-name . "BiocOncoTK")))
14423 (build-system r-build-system)
14446 r-summarizedexperiment))
14449 (home-page "https://bioconductor.org/packages/BiocOncoTK")
14450 (synopsis "Bioconductor components for general cancer genomics")
14452 "The purpose of this package is to provide a central interface to various
14453 tools for genome-scale analysis of cancer studies.")
14454 (license license:artistic2.0)))
14456 (define-public r-biocor
14463 (uri (bioconductor-uri "BioCor" version))
14466 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
14467 (properties `((upstream-name . "BioCor")))
14468 (build-system r-build-system)
14470 (list r-biocparallel r-gseabase r-matrix))
14473 (home-page "https://llrs.github.io/BioCor/")
14474 (synopsis "Functional similarities")
14476 "This package provides tools to calculate functional similarities based
14477 on the pathways described on KEGG and REACTOME or in gene sets. These
14478 similarities can be calculated for pathways or gene sets, genes, or clusters
14479 and combined with other similarities. They can be used to improve networks,
14480 gene selection, testing relationships, and so on.")
14481 (license license:expat)))
14483 (define-public r-biocpkgtools
14485 (name "r-biocpkgtools")
14490 (uri (bioconductor-uri "BiocPkgTools" version))
14493 "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd"))))
14494 (properties `((upstream-name . "BiocPkgTools")))
14495 (build-system r-build-system)
14497 (list r-biocfilecache
14521 (home-page "https://github.com/seandavi/BiocPkgTools")
14522 (synopsis "Collection of tools for learning about Bioconductor packages")
14524 "Bioconductor has a rich ecosystem of metadata around packages, usage,
14525 and build status. This package is a simple collection of functions to access
14526 that metadata from R. The goal is to expose metadata for data mining and
14527 value-added functionality such as package searching, text mining, and
14528 analytics on packages.")
14529 (license license:expat)))
14531 (define-public r-biocset
14538 (uri (bioconductor-uri "BiocSet" version))
14541 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
14542 (properties `((upstream-name . "BiocSet")))
14543 (build-system r-build-system)
14545 (list r-annotationdbi
14558 "https://bioconductor.org/packages/BiocSet")
14560 "Representing Different Biological Sets")
14562 "BiocSet displays different biological sets in a triple tibble format.
14563 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
14564 The user has the ability to activate one of these three tibbles to perform
14565 common functions from the @code{dplyr} package. Mapping functionality and
14566 accessing web references for elements/sets are also available in BiocSet.")
14567 (license license:artistic2.0)))
14569 (define-public r-biocworkflowtools
14571 (name "r-biocworkflowtools")
14576 (uri (bioconductor-uri "BiocWorkflowTools" version))
14579 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
14581 `((upstream-name . "BiocWorkflowTools")))
14582 (build-system r-build-system)
14595 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
14596 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
14598 "This package provides functions to ease the transition between
14599 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
14600 (license license:expat)))
14602 (define-public r-biodist
14609 (uri (bioconductor-uri "bioDist" version))
14612 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
14613 (properties `((upstream-name . "bioDist")))
14614 (build-system r-build-system)
14616 (list r-biobase r-kernsmooth))
14617 (home-page "https://bioconductor.org/packages/bioDist/")
14618 (synopsis "Different distance measures")
14620 "This package provides a collection of software tools for calculating
14621 distance measures.")
14622 (license license:artistic2.0)))
14624 (define-public r-pcatools
14626 (name "r-pcatools")
14631 (uri (bioconductor-uri "PCAtools" version))
14634 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
14635 (properties `((upstream-name . "PCAtools")))
14636 (build-system r-build-system)
14644 r-delayedmatrixstats
14652 (native-inputs (list r-knitr))
14653 (home-page "https://github.com/kevinblighe/PCAtools")
14654 (synopsis "PCAtools: everything Principal Components Analysis")
14656 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
14657 structure of the data without the need to build any model to represent it.
14658 This \"summary\" of the data is arrived at through a process of reduction that
14659 can transform the large number of variables into a lesser number that are
14660 uncorrelated (i.e. the 'principal components'), while at the same time being
14661 capable of easy interpretation on the original data. PCAtools provides
14662 functions for data exploration via PCA, and allows the user to generate
14663 publication-ready figures. PCA is performed via @code{BiocSingular}; users
14664 can also identify an optimal number of principal components via different
14665 metrics, such as the elbow method and Horn's parallel analysis, which has
14666 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
14667 dimensional mass cytometry data.")
14668 (license license:gpl3)))
14670 (define-public r-rgreat
14677 (uri (bioconductor-uri "rGREAT" version))
14680 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
14681 (properties `((upstream-name . "rGREAT")))
14682 (build-system r-build-system)
14684 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
14685 (native-inputs (list r-knitr))
14686 (home-page "https://github.com/jokergoo/rGREAT")
14687 (synopsis "Client for GREAT analysis")
14689 "This package makes GREAT (Genomic Regions Enrichment of Annotations
14690 Tool) analysis automatic by constructing a HTTP POST request according to
14691 user's input and automatically retrieving results from GREAT web server.")
14692 (license license:expat)))
14694 (define-public r-m3c
14701 (uri (bioconductor-uri "M3C" version))
14704 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
14705 (properties `((upstream-name . "M3C")))
14706 (build-system r-build-system)
14718 (native-inputs (list r-knitr))
14719 (home-page "https://bioconductor.org/packages/M3C")
14720 (synopsis "Monte Carlo reference-based consensus clustering")
14722 "M3C is a consensus clustering algorithm that uses a Monte Carlo
14723 simulation to eliminate overestimation of @code{K} and can reject the null
14724 hypothesis @code{K=1}.")
14725 (license license:agpl3+)))
14727 (define-public r-icens
14734 (uri (bioconductor-uri "Icens" version))
14737 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
14738 (properties `((upstream-name . "Icens")))
14739 (build-system r-build-system)
14742 (home-page "https://bioconductor.org/packages/Icens")
14743 (synopsis "NPMLE for censored and truncated data")
14745 "This package provides many functions for computing the
14746 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
14748 (license license:artistic2.0)))
14750 ;; This is a CRAN package but it depends on r-icens, which is published on
14752 (define-public r-interval
14754 (name "r-interval")
14755 (version "1.1-0.8")
14759 (uri (cran-uri "interval" version))
14762 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
14763 (properties `((upstream-name . "interval")))
14764 (build-system r-build-system)
14766 (list r-icens r-mlecens r-perm r-survival))
14767 (home-page "https://cran.r-project.org/web/packages/interval/")
14768 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
14770 "This package provides functions to fit nonparametric survival curves,
14771 plot them, and perform logrank or Wilcoxon type tests.")
14772 (license license:gpl2+)))
14774 ;; This is a CRAN package, but it depends on r-interval, which depends on a
14775 ;; Bioconductor package.
14776 (define-public r-fhtest
14783 (uri (cran-uri "FHtest" version))
14786 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
14787 (properties `((upstream-name . "FHtest")))
14788 (build-system r-build-system)
14790 (list r-interval r-kmsurv r-mass r-perm r-survival))
14791 (home-page "https://cran.r-project.org/web/packages/FHtest/")
14792 (synopsis "Tests for survival data based on the Fleming-Harrington class")
14794 "This package provides functions to compare two or more survival curves
14798 @item The Fleming-Harrington test for right-censored data based on
14799 permutations and on counting processes.
14800 @item An extension of the Fleming-Harrington test for interval-censored data
14801 based on a permutation distribution and on a score vector distribution.
14804 (license license:gpl2+)))
14806 (define-public r-fourcseq
14808 (name "r-fourcseq")
14813 (uri (bioconductor-uri "FourCSeq" version))
14815 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
14816 (properties `((upstream-name . "FourCSeq")))
14817 (build-system r-build-system)
14823 r-genomicalignments
14833 r-summarizedexperiment))
14837 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
14838 (synopsis "Analysis of multiplexed 4C sequencing data")
14840 "This package is an R package dedicated to the analysis of (multiplexed)
14841 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
14842 interactions between DNA elements and identify differential interactions
14843 between conditions. The statistical analysis in R starts with individual bam
14844 files for each sample as inputs. To obtain these files, the package contains
14845 a Python script to demultiplex libraries and trim off primer sequences. With
14846 a standard alignment software the required bam files can be then be
14848 (license license:gpl3+)))
14850 (define-public r-preprocesscore
14852 (name "r-preprocesscore")
14857 (uri (bioconductor-uri "preprocessCore" version))
14860 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
14862 `((upstream-name . "preprocessCore")))
14863 (build-system r-build-system)
14864 (home-page "https://github.com/bmbolstad/preprocessCore")
14865 (synopsis "Collection of pre-processing functions")
14867 "This package provides a library of core pre-processing and normalization
14869 (license license:lgpl2.0+)))
14871 (define-public r-s4vectors
14873 (name "r-s4vectors")
14877 (uri (bioconductor-uri "S4Vectors" version))
14880 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
14882 `((upstream-name . "S4Vectors")))
14883 (build-system r-build-system)
14885 (list r-biocgenerics))
14886 (home-page "https://bioconductor.org/packages/S4Vectors")
14887 (synopsis "S4 implementation of vectors and lists")
14889 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
14890 classes and a set of generic functions that extend the semantic of ordinary
14891 vectors and lists in R. Package developers can easily implement vector-like
14892 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
14893 In addition, a few low-level concrete subclasses of general interest (e.g.
14894 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
14895 S4Vectors package itself.")
14896 (license license:artistic2.0)))
14898 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
14899 ;; Bioconductor package.
14900 (define-public r-wgcna
14907 (uri (cran-uri "WGCNA" version))
14910 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
14911 (properties `((upstream-name . "WGCNA")))
14912 (build-system r-build-system)
14914 (list r-annotationdbi
14927 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14928 (synopsis "Weighted correlation network analysis")
14930 "This package provides functions necessary to perform Weighted
14931 Correlation Network Analysis on high-dimensional data. It includes functions
14932 for rudimentary data cleaning, construction and summarization of correlation
14933 networks, module identification and functions for relating both variables and
14934 modules to sample traits. It also includes a number of utility functions for
14935 data manipulation and visualization.")
14936 (license license:gpl2+)))
14938 (define-public r-rgraphviz
14940 (name "r-rgraphviz")
14945 (uri (bioconductor-uri "Rgraphviz" version))
14948 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
14949 (properties `((upstream-name . "Rgraphviz")))
14950 (build-system r-build-system)
14953 (modify-phases %standard-phases
14954 (add-after 'unpack 'make-reproducible
14956 ;; The replacement value is taken from src/graphviz/builddate.h
14957 (substitute* "src/graphviz/configure"
14958 (("VERSION_DATE=.*")
14959 "VERSION_DATE=20200427.2341\n"))
14961 ;; FIXME: Rgraphviz bundles the sources of an older variant of
14962 ;; graphviz. It does not build with the latest version of graphviz, so
14963 ;; we do not add graphviz to the inputs.
14964 (inputs (list zlib))
14969 (home-page "https://bioconductor.org/packages/Rgraphviz")
14970 (synopsis "Plotting capabilities for R graph objects")
14972 "This package interfaces R with the graphviz library for plotting R graph
14973 objects from the @code{graph} package.")
14974 (license license:epl1.0)))
14976 (define-public r-fishpond
14978 (name "r-fishpond")
14982 (uri (bioconductor-uri "fishpond" version))
14985 "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym"))))
14986 (properties `((upstream-name . "fishpond")))
14987 (build-system r-build-system)
14988 (inputs (list zlib))
15000 r-singlecellexperiment
15001 r-summarizedexperiment
15003 (native-inputs (list r-knitr))
15004 (home-page "https://github.com/mikelove/fishpond")
15005 (synopsis "Downstream methods and tools for expression data")
15007 "The @code{fishpond} package contains methods for differential transcript
15008 and gene expression analysis of RNA-seq data using inferential replicates for
15009 uncertainty of abundance quantification, as generated by Gibbs sampling or
15010 bootstrap sampling. Also the package contains a number of utilities for
15011 working with Salmon and Alevin quantification files.")
15012 (license license:gpl2)))
15014 (define-public r-fithic
15020 (uri (bioconductor-uri "FitHiC" version))
15023 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
15024 (properties `((upstream-name . "FitHiC")))
15025 (build-system r-build-system)
15027 (list r-data-table r-fdrtool r-rcpp))
15030 (home-page "https://bioconductor.org/packages/FitHiC")
15031 (synopsis "Confidence estimation for intra-chromosomal contact maps")
15033 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
15034 intra-chromosomal contact maps produced by genome-wide genome architecture
15035 assays such as Hi-C.")
15036 (license license:gpl2+)))
15038 (define-public r-hitc
15044 (uri (bioconductor-uri "HiTC" version))
15047 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
15048 (properties `((upstream-name . "HiTC")))
15049 (build-system r-build-system)
15058 (home-page "https://bioconductor.org/packages/HiTC")
15059 (synopsis "High throughput chromosome conformation capture analysis")
15061 "The HiTC package was developed to explore high-throughput \"C\" data
15062 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
15063 quality controls, normalization, visualization, and further analysis are also
15065 (license license:artistic2.0)))
15067 (define-public r-hdf5array
15069 (name "r-hdf5array")
15074 (uri (bioconductor-uri "HDF5Array" version))
15077 "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9"))))
15078 (properties `((upstream-name . "HDF5Array")))
15079 (build-system r-build-system)
15083 (list r-biocgenerics
15091 (home-page "https://bioconductor.org/packages/HDF5Array")
15092 (synopsis "HDF5 back end for DelayedArray objects")
15093 (description "This package provides an array-like container for convenient
15094 access and manipulation of HDF5 datasets. It supports delayed operations and
15095 block processing.")
15096 (license license:artistic2.0)))
15098 (define-public r-rhdf5lib
15100 (name "r-rhdf5lib")
15105 (uri (bioconductor-uri "Rhdf5lib" version))
15108 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
15109 (modules '((guix build utils)))
15112 ;; Delete bundled binaries
15113 (delete-file-recursively "src/wininclude/")
15114 (delete-file-recursively "src/winlib/")
15115 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
15116 (properties `((upstream-name . "Rhdf5lib")))
15117 (build-system r-build-system)
15120 (modify-phases %standard-phases
15121 (add-after 'unpack 'do-not-use-bundled-hdf5
15122 (lambda* (#:key inputs #:allow-other-keys)
15123 (for-each delete-file '("configure" "configure.ac"))
15124 (substitute* "R/zzz.R"
15125 (("return\\(links\\)") "return(\" -lz\")"))
15126 (with-directory-excursion "src"
15127 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
15128 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
15130 ;; Remove timestamp and host system information to make
15131 ;; the build reproducible.
15132 (substitute* "hdf5/src/libhdf5.settings.in"
15133 (("Configured on: @CONFIG_DATE@")
15134 "Configured on: Guix")
15135 (("Uname information:.*")
15136 "Uname information: Linux\n")
15137 ;; Remove unnecessary store reference.
15139 "C Compiler: GCC\n"))
15140 (rename-file "hdf5/src/libhdf5.settings.in"
15141 "hdf5/src/libhdf5.settings")
15142 (rename-file "Makevars.in" "Makevars")
15143 (substitute* "Makevars"
15144 (("@BUILD_HDF5@") "")
15145 (("@COPY_SZIP@") "")
15146 (("@ZLIB_LIB@") "-lz")
15147 (("@ZLIB_INCLUDE@") "")
15148 (("HDF5_CXX_LIB=.*")
15149 (string-append "HDF5_CXX_LIB="
15150 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
15152 (string-append "HDF5_LIB="
15153 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
15154 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
15155 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
15156 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
15157 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
15158 (("HDF5_HL_LIB=.*")
15159 (string-append "HDF5_HL_LIB="
15160 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
15161 (("HDF5_HL_CXX_LIB=.*")
15162 (string-append "HDF5_HL_CXX_LIB="
15163 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
15164 ;; szip is non-free software
15165 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
15166 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
15168 (list hdf5-1.10 zlib))
15170 `(("hdf5-source" ,(package-source hdf5-1.10))
15171 ("r-knitr" ,r-knitr)))
15172 (home-page "https://bioconductor.org/packages/Rhdf5lib")
15173 (synopsis "HDF5 library as an R package")
15174 (description "This package provides C and C++ HDF5 libraries for use in R
15176 (license license:artistic2.0)))
15178 (define-public r-beachmat
15180 (name "r-beachmat")
15185 (uri (bioconductor-uri "beachmat" version))
15188 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
15189 (build-system r-build-system)
15191 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
15194 (home-page "https://bioconductor.org/packages/beachmat")
15195 (synopsis "Compiling Bioconductor to handle each matrix type")
15196 (description "This package provides a consistent C++ class interface for a
15197 variety of commonly used matrix types, including sparse and HDF5-backed
15199 (license license:gpl3)))
15201 ;; This package includes files that have been taken from kentutils. Some
15202 ;; parts of kentutils are not released under a free license, but this package
15203 ;; only uses files that are also found in the free parts of kentutils.
15204 (define-public r-cner
15211 (uri (bioconductor-uri "CNEr" version))
15213 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
15214 (properties `((upstream-name . "CNEr")))
15215 (build-system r-build-system)
15216 (inputs (list zlib))
15223 r-genomicalignments
15239 (home-page "https://github.com/ge11232002/CNEr")
15240 (synopsis "CNE Detection and Visualization")
15242 "This package provides tools for large-scale identification and
15243 advanced visualization of sets of conserved noncoding elements.")
15244 ;; For all files in src/ucsc "license is hereby granted for all use -
15245 ;; public, private or commercial"; this includes those files that don't
15246 ;; have a license header, because they are included in the free parts of
15247 ;; the kentutils package.
15248 (license (list license:gpl2
15249 (license:non-copyleft
15250 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
15252 (define-public r-tfbstools
15254 (name "r-tfbstools")
15259 (uri (bioconductor-uri "TFBSTools" version))
15262 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
15263 (properties `((upstream-name . "TFBSTools")))
15264 (build-system r-build-system)
15274 r-dirichletmultinomial
15286 (native-inputs (list r-knitr))
15287 (home-page "https://github.com/ge11232002/TFBSTools")
15288 (synopsis "Transcription factor binding site (TFBS) analysis")
15290 "TFBSTools is a package for the analysis and manipulation of
15291 transcription factor binding sites. It includes matrices conversion
15292 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
15293 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
15294 scan putative TFBS from sequence/alignment, query JASPAR database and
15295 provides a wrapper of de novo motif discovery software.")
15296 (license license:gpl2)))
15298 (define-public r-maftools
15300 (name "r-maftools")
15305 (uri (bioconductor-uri "maftools" version))
15307 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
15308 (properties `((upstream-name . "maftools")))
15309 (build-system r-build-system)
15317 (native-inputs (list r-knitr))
15318 (home-page "https://github.com/PoisonAlien/maftools")
15319 (synopsis "Summarize, analyze and visualize MAF files")
15321 "Analyze and visualize Mutation Annotation Format (MAF) files from large
15322 scale sequencing studies. This package provides various functions to perform
15323 most commonly used analyses in cancer genomics and to create feature rich
15324 customizable visualzations with minimal effort.")
15325 (license license:expat)))
15327 (define-public r-motifmatchr
15329 (name "r-motifmatchr")
15334 (uri (bioconductor-uri "motifmatchr" version))
15337 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
15338 (properties `((upstream-name . "motifmatchr")))
15339 (build-system r-build-system)
15351 r-summarizedexperiment
15353 (native-inputs (list r-knitr))
15354 (home-page "https://bioconductor.org/packages/motifmatchr")
15355 (synopsis "Fast motif matching in R")
15357 "Quickly find motif matches for many motifs and many sequences.
15358 This package wraps C++ code from the MOODS motif calling library.")
15359 (license license:gpl3)))
15361 (define-public r-chromvar
15363 (name "r-chromvar")
15368 (uri (bioconductor-uri "chromVAR" version))
15370 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
15371 (properties `((upstream-name . "chromVAR")))
15372 (build-system r-build-system)
15374 (list r-biocgenerics
15394 r-summarizedexperiment
15396 (native-inputs (list r-knitr))
15397 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
15398 (synopsis "Determine chromatin variation across regions")
15400 "This package @code{r-chromvar} determines variation in chromatin
15401 accessibility across sets of annotations or peaks. @code{r-chromvar} is
15402 designed primarily for single-cell or sparse chromatin accessibility data like
15403 single cell assay for transposase-accessible chromatin using
15404 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
15405 sequence (@code{DNAse-seq}) experiments.")
15406 (license license:expat)))
15408 (define-public r-singlecellexperiment
15410 (name "r-singlecellexperiment")
15415 (uri (bioconductor-uri "SingleCellExperiment" version))
15418 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
15420 `((upstream-name . "SingleCellExperiment")))
15421 (build-system r-build-system)
15423 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
15424 r-summarizedexperiment))
15427 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
15428 (synopsis "S4 classes for single cell data")
15429 (description "This package defines an S4 class for storing data from
15430 single-cell experiments. This includes specialized methods to store and
15431 retrieve spike-in information, dimensionality reduction coordinates and size
15432 factors for each cell, along with the usual metadata for genes and
15434 (license license:gpl3)))
15436 (define-public r-singler
15443 (uri (bioconductor-uri "SingleR" version))
15445 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
15446 (properties `((upstream-name . "SingleR")))
15447 (build-system r-build-system)
15454 r-delayedmatrixstats
15458 r-summarizedexperiment))
15459 (native-inputs (list r-knitr))
15460 (home-page "https://github.com/LTLA/SingleR")
15461 (synopsis "Reference-based single-cell RNA-seq annotation")
15463 "This package performs unbiased cell type recognition from single-cell
15464 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
15465 cell types to infer the cell of origin of each single cell independently.")
15466 (license license:gpl3)))
15468 (define-public r-scuttle
15475 (uri (bioconductor-uri "scuttle" version))
15478 "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671"))))
15479 (properties `((upstream-name . "scuttle")))
15480 (build-system r-build-system)
15486 r-delayedmatrixstats
15491 r-singlecellexperiment
15492 r-summarizedexperiment))
15493 (native-inputs (list r-knitr))
15494 (home-page "https://bioconductor.org/packages/scuttle")
15495 (synopsis "Single-cell RNA-Seq analysis utilities")
15497 "This package provides basic utility functions for performing single-cell
15498 analyses, focusing on simple normalization, quality control and data
15499 transformations. It also provides some helper functions to assist development
15500 of other packages.")
15501 (license license:gpl3)))
15503 (define-public r-scater
15509 (uri (bioconductor-uri "scater" version))
15512 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
15513 (build-system r-build-system)
15521 r-delayedmatrixstats
15533 r-singlecellexperiment
15534 r-summarizedexperiment
15538 (home-page "https://github.com/davismcc/scater")
15539 (synopsis "Single-cell analysis toolkit for gene expression data in R")
15540 (description "This package provides a collection of tools for doing
15541 various analyses of single-cell RNA-seq gene expression data, with a focus on
15543 (license license:gpl2+)))
15545 (define-public r-scran
15552 (uri (bioconductor-uri "scran" version))
15555 "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni"))))
15556 (build-system r-build-system)
15565 r-delayedmatrixstats
15575 r-singlecellexperiment
15577 r-summarizedexperiment))
15580 (home-page "https://bioconductor.org/packages/scran")
15581 (synopsis "Methods for single-cell RNA-Seq data analysis")
15582 (description "This package implements a variety of low-level analyses of
15583 single-cell RNA-seq data. Methods are provided for normalization of
15584 cell-specific biases, assignment of cell cycle phase, and detection of highly
15585 variable and significantly correlated genes.")
15586 (license license:gpl3)))
15588 (define-public r-sparsematrixstats
15590 (name "r-sparsematrixstats")
15595 (uri (bioconductor-uri "sparseMatrixStats" version))
15598 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
15600 `((upstream-name . "sparseMatrixStats")))
15601 (build-system r-build-system)
15603 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
15604 (native-inputs (list r-knitr))
15605 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
15606 (synopsis "Summary statistics for rows and columns of sparse matrices")
15608 "This package provides high performance functions for row and column
15609 operations on sparse matrices. Currently, the optimizations are limited to
15610 data in the column sparse format.")
15611 (license license:expat)))
15613 (define-public r-delayedmatrixstats
15615 (name "r-delayedmatrixstats")
15620 (uri (bioconductor-uri "DelayedMatrixStats" version))
15623 "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv"))))
15625 `((upstream-name . "DelayedMatrixStats")))
15626 (build-system r-build-system)
15628 (list r-delayedarray
15634 r-sparsematrixstats))
15637 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
15638 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
15640 "This package provides a port of the @code{matrixStats} API for use with
15641 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
15642 contains high-performing functions operating on rows and columns of
15643 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
15644 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
15645 are optimized per data type and for subsetted calculations such that both
15646 memory usage and processing time is minimized.")
15647 (license license:expat)))
15649 (define-public r-mscoreutils
15651 (name "r-mscoreutils")
15656 (uri (bioconductor-uri "MsCoreUtils" version))
15659 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
15660 (properties `((upstream-name . "MsCoreUtils")))
15661 (build-system r-build-system)
15663 (list r-clue r-mass r-rcpp r-s4vectors))
15666 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
15667 (synopsis "Core utils for mass spectrometry data")
15669 "This package defines low-level functions for mass spectrometry data and
15670 is independent of any high-level data structures. These functions include
15671 mass spectra processing functions (noise estimation, smoothing, binning),
15672 quantitative aggregation functions (median polish, robust summarisation,
15673 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
15674 well as misc helper functions, that are used across high-level data structure
15675 within the R for Mass Spectrometry packages.")
15676 (license license:artistic2.0)))
15678 (define-public r-msfeatures
15680 (name "r-msfeatures")
15685 (uri (bioconductor-uri "MsFeatures" version))
15687 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
15688 (properties `((upstream-name . "MsFeatures")))
15689 (build-system r-build-system)
15691 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
15694 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
15695 (synopsis "Functionality for mass spectrometry features")
15697 "The MsFeature package defines functionality for Mass Spectrometry
15698 features. This includes functions to group (LC-MS) features based on some of
15699 their properties, such as retention time (coeluting features), or correlation
15700 of signals across samples. This package hence can be used to group features, and
15701 its results can be used as an input for the @code{QFeatures} package which
15702 allows aggregating abundance levels of features within each group. This
15703 package defines concepts and functions for base and common data types,
15704 implementations for more specific data types are expected to be implemented in
15705 the respective packages (such as e.g. @code{xcms}).")
15706 (license license:artistic2.0)))
15708 (define-public r-biocio
15715 (uri (bioconductor-uri "BiocIO" version))
15718 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
15719 (properties `((upstream-name . "BiocIO")))
15720 (build-system r-build-system)
15722 (list r-biocgenerics r-s4vectors))
15725 (home-page "https://bioconductor.org/packages/BiocIO")
15726 (synopsis "Standard input and output for Bioconductor packages")
15728 "This package implements `import()` and `export()` standard generics for
15729 importing and exporting biological data formats. `import()` supports
15730 whole-file as well as chunk-wise iterative import. The `import()` interface
15731 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
15732 row or element-like components of the file resource), `select()` (on
15733 column-like components of the file resource) and `collect()`. The `import()`
15734 interface optionally provides transparent access to remote (e.g. via https)
15735 as well as local access. Developers can register a file extension, e.g.,
15736 `.loom` for dispatch from character-based URIs to specific `import()` /
15737 `export()` methods based on classes representing file types, e.g.,
15739 (license license:artistic2.0)))
15741 (define-public r-msmseda
15748 (uri (bioconductor-uri "msmsEDA" version))
15751 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
15752 (properties `((upstream-name . "msmsEDA")))
15753 (build-system r-build-system)
15755 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
15757 "https://bioconductor.org/packages/msmsEDA")
15758 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
15760 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
15761 experiments, and visualize de influence of the involved factors.")
15762 (license license:gpl2)))
15764 (define-public r-msmstests
15766 (name "r-msmstests")
15771 (uri (bioconductor-uri "msmsTests" version))
15774 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
15775 (properties `((upstream-name . "msmsTests")))
15776 (build-system r-build-system)
15778 (list r-edger r-msmseda r-msnbase r-qvalue))
15780 "https://bioconductor.org/packages/msmsTests")
15781 (synopsis "Differential LC-MS/MS expression tests")
15783 "This package provides statistical tests for label-free LC-MS/MS data
15784 by spectral counts, to discover differentially expressed proteins between two
15785 biological conditions. Three tests are available: Poisson GLM regression,
15786 quasi-likelihood GLM regression, and the negative binomial of the edgeR
15787 package. The three models admit blocking factors to control for nuisance
15788 variables. To assure a good level of reproducibility a post-test filter is
15789 available, where we may set the minimum effect size considered biologicaly
15790 relevant, and the minimum expression of the most abundant condition.")
15791 (license license:gpl2)))
15793 (define-public r-catalyst
15795 (name "r-catalyst")
15800 (uri (bioconductor-uri "CATALYST" version))
15803 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
15804 (properties `((upstream-name . "CATALYST")))
15805 (build-system r-build-system)
15809 r-consensusclusterplus
15831 r-singlecellexperiment
15832 r-summarizedexperiment))
15835 (home-page "https://github.com/HelenaLC/CATALYST")
15836 (synopsis "Cytometry data analysis tools")
15838 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
15839 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
15840 isotopes rather than fluorescent tags as reporters to label antibodies,
15841 thereby substantially decreasing spectral overlap and allowing for examination
15842 of over 50 parameters at the single cell level. While spectral overlap is
15843 significantly less pronounced in CyTOF than flow cytometry, spillover due to
15844 detection sensitivity, isotopic impurities, and oxide formation can impede
15845 data interpretability. @code{CATALYST} was designed to provide a pipeline for
15846 preprocessing of cytometry data, including:
15849 @item normalization using bead standards;
15850 @item single-cell deconvolution;
15851 @item bead-based compensation.
15854 (license license:gpl2+)))
15856 (define-public r-erma
15863 (uri (bioconductor-uri "erma" version))
15866 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
15867 (build-system r-build-system)
15869 (list r-annotationdbi
15882 r-summarizedexperiment))
15885 (home-page "https://bioconductor.org/packages/erma")
15886 (synopsis "Epigenomic road map adventures")
15888 "The epigenomics road map describes locations of epigenetic marks in DNA
15889 from a variety of cell types. Of interest are locations of histone
15890 modifications, sites of DNA methylation, and regions of accessible chromatin.
15891 This package presents a selection of elements of the road map including
15892 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
15893 by Ernst and Kellis.")
15894 (license license:artistic2.0)))
15896 (define-public r-ggbio
15903 (uri (bioconductor-uri "ggbio" version))
15906 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
15907 (build-system r-build-system)
15910 (modify-phases %standard-phases
15911 ;; See https://github.com/tengfei/ggbio/issues/117
15912 ;; This fix will be included in the next release.
15913 (add-after 'unpack 'fix-typo
15915 (substitute* "R/GGbio-class.R"
15916 (("fechable") "fetchable"))
15919 (list r-annotationdbi
15928 r-genomicalignments
15944 r-summarizedexperiment
15945 r-variantannotation))
15948 (home-page "http://www.tengfei.name/ggbio/")
15949 (synopsis "Visualization tools for genomic data")
15951 "The ggbio package extends and specializes the grammar of graphics for
15952 biological data. The graphics are designed to answer common scientific
15953 questions, in particular those often asked of high throughput genomics data.
15954 All core Bioconductor data structures are supported, where appropriate. The
15955 package supports detailed views of particular genomic regions, as well as
15956 genome-wide overviews. Supported overviews include ideograms and grand linear
15957 views. High-level plots include sequence fragment length, edge-linked
15958 interval to data view, mismatch pileup, and several splicing summaries.")
15959 (license license:artistic2.0)))
15961 (define-public r-gqtlbase
15963 (name "r-gqtlbase")
15968 (uri (bioconductor-uri "gQTLBase" version))
15971 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
15972 (properties `((upstream-name . "gQTLBase")))
15973 (build-system r-build-system)
15976 (modify-phases %standard-phases
15977 ;; This is an upstream bug.
15978 (add-after 'unpack 'fix-imports
15980 (substitute* "NAMESPACE"
15981 ((".*maxffmode.*") "")
15982 (("importFrom\\(ff,.*") "import(ff)\n"))
15997 r-summarizedexperiment))
16000 (home-page "https://bioconductor.org/packages/gQTLBase")
16001 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
16003 "The purpose of this package is to simplify the storage and interrogation
16004 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
16006 (license license:artistic2.0)))
16008 (define-public r-gqtlstats
16010 (name "r-gqtlstats")
16015 (uri (bioconductor-uri "gQTLstats" version))
16018 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
16019 (properties `((upstream-name . "gQTLstats")))
16020 (build-system r-build-system)
16022 (list r-annotationdbi
16050 r-summarizedexperiment
16051 r-variantannotation))
16054 (home-page "https://bioconductor.org/packages/gQTLstats")
16055 (synopsis "Computationally efficient analysis for eQTL and allied studies")
16057 "This package provides tools for the computationally efficient analysis
16058 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
16059 The software in this package aims to support refinements and functional
16060 interpretation of members of a collection of association statistics on a
16061 family of feature/genome hypotheses.")
16062 (license license:artistic2.0)))
16064 (define-public r-gviz
16071 (uri (bioconductor-uri "Gviz" version))
16074 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
16075 (properties `((upstream-name . "Gviz")))
16076 (build-system r-build-system)
16078 (list r-annotationdbi
16088 r-genomicalignments
16102 (home-page "https://bioconductor.org/packages/Gviz")
16103 (synopsis "Plotting data and annotation information along genomic coordinates")
16105 "Genomic data analyses requires integrated visualization of known genomic
16106 information and new experimental data. Gviz uses the biomaRt and the
16107 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
16108 and translates this to e.g. gene/transcript structures in viewports of the
16109 grid graphics package. This results in genomic information plotted together
16111 (license license:artistic2.0)))
16113 (define-public r-gwascat
16120 (uri (bioconductor-uri "gwascat" version))
16123 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
16124 (build-system r-build-system)
16126 (list r-annotationdbi
16137 r-variantannotation))
16140 (home-page "https://bioconductor.org/packages/gwascat")
16141 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
16143 "This package provides tools for representing and modeling data in the
16144 EMBL-EBI GWAS catalog.")
16145 (license license:artistic2.0)))
16147 (define-public r-kegggraph
16149 (name "r-kegggraph")
16154 (uri (bioconductor-uri "KEGGgraph" version))
16156 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
16157 (properties `((upstream-name . "KEGGgraph")))
16158 (build-system r-build-system)
16160 (list r-graph r-rcurl r-rgraphviz r-xml))
16161 (home-page "https://bioconductor.org/packages/KEGGgraph")
16162 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
16164 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
16165 object as well as a collection of tools to analyze, dissect and visualize these
16166 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
16167 maintaining all essential pathway attributes. The package offers
16168 functionalities including parsing, graph operation, visualization and etc.")
16169 (license license:gpl2+)))
16171 (define-public r-ldblock
16178 (uri (bioconductor-uri "ldblock" version))
16181 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
16182 (build-system r-build-system)
16184 (list r-biocgenerics
16185 r-ensdb-hsapiens-v75
16193 r-variantannotation))
16196 (home-page "https://bioconductor.org/packages/ldblock")
16197 (synopsis "Data structures for linkage disequilibrium measures in populations")
16199 "This package defines data structures for @dfn{linkage
16200 disequilibrium} (LD) measures in populations. Its purpose is to simplify
16201 handling of existing population-level data for the purpose of flexibly
16202 defining LD blocks.")
16203 (license license:artistic2.0)))
16205 ;; This is a CRAN package, but it depends on r-snpstats, which is a
16206 ;; Bioconductor package.
16207 (define-public r-ldheatmap
16209 (name "r-ldheatmap")
16214 (uri (cran-uri "LDheatmap" version))
16217 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
16218 (properties `((upstream-name . "LDheatmap")))
16219 (build-system r-build-system)
16221 (list r-genetics r-rcpp r-snpstats))
16222 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
16223 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
16225 "This package provides tools to produce a graphical display, as a heat
16226 map, of measures of pairwise linkage disequilibria between SNPs. Users may
16227 optionally include the physical locations or genetic map distances of each SNP
16229 (license license:gpl3)))
16231 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
16232 ;; Bioconductor package.
16233 (define-public r-abn
16240 (uri (cran-uri "abn" version))
16243 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
16244 (build-system r-build-system)
16257 (home-page "https://r-bayesian-networks.org/")
16258 (synopsis "Modelling multivariate data with additive bayesian networks")
16260 "Bayesian network analysis is a form of probabilistic graphical models
16261 which derives from empirical data a directed acyclic graph, DAG, describing
16262 the dependency structure between random variables. An additive Bayesian
16263 network model consists of a form of a DAG where each node comprises a
16264 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
16265 equivalent to Bayesian multivariate regression using graphical modelling, they
16266 generalises the usual multivariable regression, GLM, to multiple dependent
16267 variables. This package provides routines to help determine optimal Bayesian
16268 network models for a given data set, where these models are used to identify
16269 statistical dependencies in messy, complex data.")
16270 (license license:gpl2+)))
16272 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
16273 ;; Bioconductor package.
16274 (define-public r-spp
16280 (uri (cran-uri "spp" version))
16283 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
16284 (build-system r-build-system)
16288 (list r-bh r-catools r-rcpp r-rsamtools))
16289 (home-page "https://cran.r-project.org/web/packages/spp/")
16290 (synopsis "ChIP-Seq processing pipeline")
16291 (description "This package provides tools for analysis of ChIP-seq and
16292 other functional sequencing data.")
16293 (license license:gpl2)))
16295 (define-public r-pathview
16297 (name "r-pathview")
16302 (uri (bioconductor-uri "pathview" version))
16304 (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71"))))
16305 (properties `((upstream-name . "pathview")))
16306 (build-system r-build-system)
16308 (list r-annotationdbi
16316 (home-page "https://pathview.uncc.edu/")
16317 (synopsis "Tool set for pathway based data integration and visualization")
16319 "@code{r-pathview} is a tool set for pathway based data integration and
16320 visualization. It maps and renders a wide variety of biological data on
16321 relevant pathway graphs. All users need is to supply their data and specify
16322 the target pathway. This package automatically downloads the pathway graph
16323 data, parses the data file, maps user data to the pathway, and render pathway
16324 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
16325 integrates with pathway and gene set (enrichment) analysis tools for
16326 large-scale and fully automated analysis.")
16327 (license license:gpl3+)))
16329 (define-public r-snpstats
16331 (name "r-snpstats")
16336 (uri (bioconductor-uri "snpStats" version))
16339 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
16340 (properties `((upstream-name . "snpStats")))
16341 (build-system r-build-system)
16342 (inputs (list zlib))
16344 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
16345 (home-page "https://bioconductor.org/packages/snpStats")
16346 (synopsis "Methods for SNP association studies")
16348 "This package provides classes and statistical methods for large
16349 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
16350 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
16351 (license license:gpl3)))
16353 (define-public r-chromstar
16355 (name "r-chromstar")
16360 (uri (bioconductor-uri "chromstaR" version))
16363 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
16364 (properties `((upstream-name . "chromstaR")))
16365 (build-system r-build-system)
16373 r-genomicalignments
16381 (native-inputs (list r-knitr))
16382 (home-page "https://github.com/ataudt/chromstaR")
16383 (synopsis "Chromatin state analysis for ChIP-Seq data")
16385 "This package implements functions for combinatorial and differential
16386 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
16387 export to genome browser viewable files, and functions for enrichment
16389 (license license:artistic2.0)))
16391 (define-public r-guitar
16398 (uri (bioconductor-uri "Guitar" version))
16401 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
16402 (properties `((upstream-name . "Guitar")))
16403 (build-system r-build-system)
16405 (list r-annotationdbi
16415 (home-page "https://bioconductor.org/packages/Guitar")
16416 (synopsis "Visualize genomic features")
16418 "This package is designed for visualization of RNA-related genomic
16419 features with respect to the landmarks of RNA transcripts, i.e., transcription
16420 starting site, start codon, stop codon and transcription ending site.")
16421 (license license:gpl2)))
16423 (define-public r-sushi
16429 (uri (bioconductor-uri "Sushi" version))
16432 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
16433 (properties `((upstream-name . "Sushi")))
16434 (build-system r-build-system)
16436 (list r-biomart r-zoo))
16437 (home-page "https://bioconductor.org/packages/Sushi")
16438 (synopsis "Tools for visualizing genomics data")
16440 "This package provides flexible, quantitative, and integrative genomic
16441 visualizations for publication-quality multi-panel figures.")
16442 (license license:gpl2+)))
16444 (define-public r-ballgown
16446 (name "r-ballgown")
16451 (uri (bioconductor-uri "ballgown" version))
16454 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
16455 (properties `((upstream-name . "ballgown")))
16456 (build-system r-build-system)
16469 (home-page "https://bioconductor.org/packages/ballgown")
16470 (synopsis "Flexible, isoform-level differential expression analysis")
16472 "This package provides tools for statistical analysis of assembled
16473 transcriptomes, including flexible differential expression analysis,
16474 visualization of transcript structures, and matching of assembled transcripts
16476 (license license:artistic2.0)))
16478 (define-public r-megadepth
16480 (name "r-megadepth")
16485 (uri (bioconductor-uri "megadepth" version))
16488 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
16489 (properties `((upstream-name . "megadepth")))
16490 (build-system r-build-system)
16491 (inputs (list megadepth))
16502 (home-page "https://github.com/LieberInstitute/megadepth")
16503 (synopsis "BigWig and BAM related utilities")
16505 "This package provides an R interface to Megadepth. It is particularly
16506 useful for computing the coverage of a set of genomic regions across bigWig or
16507 BAM files. With this package, you can build base-pair coverage matrices for
16508 regions or annotations of your choice from BigWig files.")
16509 (license license:artistic2.0)))
16511 (define-public r-beclear
16518 (uri (bioconductor-uri "BEclear" version))
16521 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
16522 (properties `((upstream-name . "BEclear")))
16523 (build-system r-build-system)
16535 (home-page "https://github.com/uds-helms/BEclear")
16536 (synopsis "Correction of batch effects in DNA methylation data")
16538 "This package provides functions to detect and correct for batch effects
16539 in DNA methylation data. The core function is based on latent factor models
16540 and can also be used to predict missing values in any other matrix containing
16542 (license license:gpl3)))
16544 (define-public r-bgeecall
16546 (name "r-bgeecall")
16551 (uri (bioconductor-uri "BgeeCall" version))
16554 "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil"))))
16555 (properties `((upstream-name . "BgeeCall")))
16556 (build-system r-build-system)
16570 (native-inputs (list r-knitr))
16571 (home-page "https://github.com/BgeeDB/BgeeCall")
16572 (synopsis "RNA-Seq present/absent gene expression calls generation")
16574 "BgeeCall allows generating present/absent gene expression calls without
16575 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
16576 intergenic sequences. These sequences are generated based on expression of
16577 all RNA-Seq libraries of each species integrated in Bgee.")
16578 (license license:gpl3)))
16580 (define-public r-bgeedb
16587 (uri (bioconductor-uri "BgeeDB" version))
16590 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
16591 (properties `((upstream-name . "BgeeDB")))
16592 (build-system r-build-system)
16605 (native-inputs (list r-knitr))
16606 (home-page "https://github.com/BgeeDB/BgeeDB_R")
16607 (synopsis "Annotation and gene expression data retrieval from Bgee database")
16609 "This package provides a package for the annotation and gene expression
16610 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
16611 anatomical terms, mapped to genes by expression patterns.")
16612 (license license:gpl3)))
16614 (define-public r-biobtreer
16616 (name "r-biobtreer")
16621 (uri (bioconductor-uri "biobtreeR" version))
16624 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
16625 (properties `((upstream-name . "biobtreeR")))
16626 (build-system r-build-system)
16628 (list r-httpuv r-httr r-jsonlite r-stringi))
16629 (native-inputs (list r-knitr))
16630 (home-page "https://github.com/tamerh/biobtreeR")
16631 (synopsis "Use biobtree tool from R")
16633 "The biobtreeR package provides an interface to biobtree, a tool which
16634 covers large sets of bioinformatics datasets and allows search and chain
16635 mappings functionalities.")
16636 (license license:expat)))
16638 (define-public r-minet
16645 (uri (bioconductor-uri "minet" version))
16648 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
16649 (properties `((upstream-name . "minet")))
16650 (build-system r-build-system)
16653 (home-page "http://minet.meyerp.com")
16654 (synopsis "Mutual information networks")
16656 "This package implements various algorithms for inferring mutual
16657 information networks from data.")
16658 (license license:artistic2.0)))
16660 (define-public r-genetclassifier
16662 (name "r-genetclassifier")
16667 (uri (bioconductor-uri "geNetClassifier" version))
16670 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
16672 `((upstream-name . "geNetClassifier")))
16673 (build-system r-build-system)
16675 (list r-biobase r-e1071 r-ebarrays r-minet))
16676 (home-page "https://www.cicancer.org")
16677 (synopsis "Classify diseases and build gene networks using expression profiles")
16679 "This is a comprehensive package to automatically train and validate a
16680 multi-class SVM classifier based on gene expression data. It provides
16681 transparent selection of gene markers, their coexpression networks, and an
16682 interface to query the classifier.")
16683 (license license:gpl2+)))
16685 (define-public r-dir-expiry
16687 (name "r-dir-expiry")
16692 (uri (bioconductor-uri "dir.expiry" version))
16695 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
16696 (properties `((upstream-name . "dir.expiry")))
16697 (build-system r-build-system)
16698 (propagated-inputs (list r-filelock))
16699 (native-inputs (list r-knitr))
16700 (home-page "https://bioconductor.org/packages/dir.expiry")
16701 (synopsis "Managing expiration for cache directories")
16703 "This package implements an expiration system for access to versioned
16704 directories. Directories that have not been accessed by a registered function
16705 within a certain time frame are deleted. This aims to reduce disk usage by
16706 eliminating obsolete caches generated by old versions of packages.")
16707 (license license:gpl3)))
16709 (define-public r-basilisk-utils
16711 (name "r-basilisk-utils")
16716 (uri (bioconductor-uri "basilisk.utils" version))
16719 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
16721 `((upstream-name . "basilisk.utils")))
16722 (build-system r-build-system)
16724 (list r-dir-expiry))
16725 (native-inputs (list r-knitr))
16726 (home-page "https://bioconductor.org/packages/basilisk.utils")
16727 (synopsis "Basilisk installation utilities")
16729 "This package implements utilities for installation of the basilisk
16730 package, primarily for creation of the underlying Conda instance.")
16731 (license license:gpl3)))
16733 (define-public r-basilisk
16735 (name "r-basilisk")
16740 (uri (bioconductor-uri "basilisk" version))
16743 "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk"))))
16744 (properties `((upstream-name . "basilisk")))
16745 (build-system r-build-system)
16747 (list r-basilisk-utils r-dir-expiry r-reticulate))
16748 (native-inputs (list r-knitr))
16749 (home-page "https://bioconductor.org/packages/basilisk")
16750 (synopsis "Freeze Python dependencies inside Bioconductor packages")
16752 "This package installs a self-contained Conda instance that is managed by
16753 the R/Bioconductor installation machinery. This aims to provide a consistent
16754 Python environment that can be used reliably by Bioconductor packages.
16755 Functions are also provided to enable smooth interoperability of multiple
16756 Python environments in a single R session.")
16757 (license license:gpl3)))
16759 (define-public r-biocthis
16761 (name "r-biocthis")
16766 (uri (bioconductor-uri "biocthis" version))
16769 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
16770 (properties `((upstream-name . "biocthis")))
16771 (build-system r-build-system)
16774 (modify-phases %standard-phases
16775 (add-after 'unpack 'set-HOME
16776 (lambda _ (setenv "HOME" "/tmp"))))))
16778 (list r-biocmanager
16784 (native-inputs (list r-knitr))
16785 (home-page "https://github.com/lcolladotor/biocthis")
16786 (synopsis "Automate package and project setup for Bioconductor packages")
16788 "This package expands the @code{usethis} package with the goal of helping
16789 automate the process of creating R packages for Bioconductor or making them
16790 Bioconductor-friendly.")
16791 (license license:artistic2.0)))
16793 (define-public r-biocdockermanager
16795 (name "r-biocdockermanager")
16800 (uri (bioconductor-uri "BiocDockerManager" version))
16803 "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d"))))
16805 `((upstream-name . "BiocDockerManager")))
16806 (build-system r-build-system)
16814 (native-inputs (list r-knitr))
16815 (home-page "https://bioconductor.org/packages/BiocDockerManager")
16816 (synopsis "Access and manage Bioconductor Docker images")
16818 "This package works analogous to BiocManager but for Docker images. Use
16819 the BiocDockerManager package to install and manage Docker images provided by
16820 the Bioconductor project.")
16821 (license license:artistic2.0)))
16823 (define-public r-biodb
16830 (uri (bioconductor-uri "biodb" version))
16833 "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1"))))
16834 (properties `((upstream-name . "biodb")))
16835 (build-system r-build-system)
16837 (list r-biocfilecache
16855 (native-inputs (list r-knitr))
16856 (home-page "https://bioconductor.org/packages/biodb")
16857 (synopsis "Library for connecting to chemical and biological databases")
16859 "The biodb package provides access to standard remote chemical and
16860 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
16861 database files (CSV, SQLite), with easy retrieval of entries, access to web
16862 services, search of compounds by mass and/or name, and mass spectra matching
16863 for LCMS and MSMS. Its architecture as a development framework facilitates
16864 the development of new database connectors for local projects or inside
16865 separate published packages.")
16866 (license license:agpl3+)))
16868 (define-public r-biomformat
16870 (name "r-biomformat")
16875 (uri (bioconductor-uri "biomformat" version))
16878 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
16879 (properties `((upstream-name . "biomformat")))
16880 (build-system r-build-system)
16882 (list r-jsonlite r-matrix r-plyr r-rhdf5))
16883 (native-inputs (list r-knitr))
16884 (home-page "https://github.com/joey711/biomformat/")
16885 (synopsis "Interface package for the BIOM file format")
16887 "This is an R package for interfacing with the BIOM format. This package
16888 includes basic tools for reading biom-format files, accessing and subsetting
16889 data tables from a biom object (which is more complex than a single table), as
16890 well as limited support for writing a biom-object back to a biom-format file.
16891 The design of this API is intended to match the Python API and other tools
16892 included with the biom-format project, but with a decidedly \"R flavor\" that
16893 should be familiar to R users. This includes S4 classes and methods, as well
16894 as extensions of common core functions/methods.")
16895 (license license:gpl2)))
16897 (define-public r-mvcclass
16899 (name "r-mvcclass")
16904 (uri (bioconductor-uri "MVCClass" version))
16907 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
16908 (properties `((upstream-name . "MVCClass")))
16909 (build-system r-build-system)
16910 (home-page "https://bioconductor.org/packages/MVCClass")
16911 (synopsis "Model-View-Controller (MVC) classes")
16913 "This package contains classes used in model-view-controller (MVC)
16915 (license license:lgpl2.1+)))
16917 (define-public r-biomvcclass
16919 (name "r-biomvcclass")
16924 (uri (bioconductor-uri "BioMVCClass" version))
16927 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
16928 (properties `((upstream-name . "BioMVCClass")))
16929 (build-system r-build-system)
16931 (list r-biobase r-graph r-mvcclass r-rgraphviz))
16932 (home-page "https://bioconductor.org/packages/BioMVCClass")
16933 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
16935 "This package contains classes used in model-view-controller (MVC)
16937 (license license:lgpl2.1+)))
16939 (define-public r-biomvrcns
16941 (name "r-biomvrcns")
16946 (uri (bioconductor-uri "biomvRCNS" version))
16949 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
16950 (properties `((upstream-name . "biomvRCNS")))
16951 (build-system r-build-system)
16953 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
16954 (home-page "https://bioconductor.org/packages/biomvRCNS")
16955 (synopsis "Copy number study and segmentation for multivariate biological data")
16957 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
16958 homogeneous segmentation model are designed and implemented for segmentation
16959 genomic data, with the aim of assisting in transcripts detection using high
16960 throughput technology like RNA-seq or tiling array, and copy number analysis
16961 using aCGH or sequencing.")
16962 (license license:gpl2+)))
16964 (define-public r-bionero
16971 (uri (bioconductor-uri "BioNERO" version))
16974 "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp"))))
16975 (properties `((upstream-name . "BioNERO")))
16976 (build-system r-build-system)
16978 (list r-biocparallel
16995 r-summarizedexperiment
17000 (home-page "https://github.com/almeidasilvaf/BioNERO")
17001 (synopsis "Biological network reconstruction omnibus")
17003 "BioNERO aims to integrate all aspects of biological network inference in
17004 a single package, including data preprocessing, exploratory analyses, network
17005 inference, and analyses for biological interpretations. BioNERO can be used
17006 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
17007 from gene expression data. Additionally, it can be used to explore
17008 topological properties of protein-protein interaction (PPI) networks. GCN
17009 inference relies on the popular WGCNA algorithm. GRN inference is based on
17010 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
17011 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
17012 rank for each interaction pair. As all steps of network analyses are included
17013 in this package, BioNERO makes users avoid having to learn the syntaxes of
17014 several packages and how to communicate between them. Finally, users can also
17015 identify consensus modules across independent expression sets and calculate
17016 intra and interspecies module preservation statistics between different
17018 (license license:gpl3)))
17020 (define-public r-bionet
17027 (uri (bioconductor-uri "BioNet" version))
17030 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
17031 (properties `((upstream-name . "BioNet")))
17032 (build-system r-build-system)
17034 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
17035 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
17036 (synopsis "Functional analysis of biological networks")
17038 "This package provides functions for the integrated analysis of
17039 protein-protein interaction networks and the detection of functional modules.
17040 Different datasets can be integrated into the network by assigning p-values of
17041 statistical tests to the nodes of the network. E.g. p-values obtained from
17042 the differential expression of the genes from an Affymetrix array are assigned
17043 to the nodes of the network. By fitting a beta-uniform mixture model and
17044 calculating scores from the p-values, overall scores of network regions can be
17045 calculated and an integer linear programming algorithm identifies the maximum
17046 scoring subnetwork.")
17047 (license license:gpl2+)))
17049 (define-public r-bionetstat
17051 (name "r-bionetstat")
17056 (uri (bioconductor-uri "BioNetStat" version))
17059 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
17060 (properties `((upstream-name . "BioNetStat")))
17061 (build-system r-build-system)
17063 (list r-biocparallel
17083 (home-page "https://github.com/jardimViniciusC/BioNetStat")
17084 (synopsis "Biological network analysis")
17086 "This package provides a package to perform differential network
17087 analysis, differential node analysis (differential coexpression analysis),
17088 network and metabolic pathways view.")
17089 (license license:gpl3+)))
17091 (define-public r-bioqc
17098 (uri (bioconductor-uri "BioQC" version))
17101 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
17102 (properties `((upstream-name . "BioQC")))
17103 (build-system r-build-system)
17105 (list r-biobase r-edger r-rcpp))
17108 (home-page "https://accio.github.io/BioQC/")
17109 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
17111 "BioQC performs quality control of high-throughput expression data based
17112 on tissue gene signatures. It can detect tissue heterogeneity in gene
17113 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
17114 optimised for high performance.")
17115 (license license:gpl3+)))
17117 (define-public r-biotip
17124 (uri (bioconductor-uri "BioTIP" version))
17127 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
17128 (properties `((upstream-name . "BioTIP")))
17129 (build-system r-build-system)
17140 (home-page "https://github.com/xyang2uchicago/BioTIP")
17141 (synopsis "R package for characterization of biological tipping-point")
17143 "This package adopts tipping-point theory to transcriptome profiles to
17144 help unravel disease regulatory trajectory.")
17145 (license license:gpl2)))
17147 (define-public r-biotmle
17154 (uri (bioconductor-uri "biotmle" version))
17157 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
17158 (properties `((upstream-name . "biotmle")))
17159 (build-system r-build-system)
17170 r-summarizedexperiment
17175 (home-page "https://code.nimahejazi.org/biotmle/")
17176 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
17178 "This package provides tools for differential expression biomarker
17179 discovery based on microarray and next-generation sequencing data that
17180 leverage efficient semiparametric estimators of the average treatment effect
17181 for variable importance analysis. Estimation and inference of the (marginal)
17182 average treatment effects of potential biomarkers are computed by targeted
17183 minimum loss-based estimation, with joint, stable inference constructed across
17184 all biomarkers using a generalization of moderated statistics for use with the
17185 estimated efficient influence function. The procedure accommodates the use of
17186 ensemble machine learning for the estimation of nuisance functions.")
17187 (license license:expat)))
17189 (define-public r-bsseq
17196 (uri (bioconductor-uri "bsseq" version))
17199 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
17200 (properties `((upstream-name . "bsseq")))
17201 (build-system r-build-system)
17211 r-delayedmatrixstats
17225 r-summarizedexperiment))
17228 (home-page "https://github.com/hansenlab/bsseq")
17229 (synopsis "Analyze, manage and store bisulfite sequencing data")
17231 "This package provides a collection of tools for analyzing and
17232 visualizing bisulfite sequencing data.")
17233 (license license:artistic2.0)))
17235 (define-public r-dada2
17241 (uri (bioconductor-uri "dada2" version))
17244 "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x"))))
17245 (properties `((upstream-name . "dada2")))
17246 (build-system r-build-system)
17248 (list r-biocgenerics
17257 (native-inputs (list r-knitr))
17258 (home-page "https://benjjneb.github.io/dada2/")
17260 "Accurate, high-resolution sample inference from amplicon sequencing data")
17262 "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
17263 from high-throughput amplicon sequencing data, replacing the coarser and less
17264 accurate OTU clustering approach. The dada2 pipeline takes as input
17265 demultiplexed fastq files, and outputs the sequence variants and their
17266 sample-wise abundances after removing substitution and chimera errors.
17267 Taxonomic classification is available via a native implementation of the RDP
17268 naive Bayesian classifier, and species-level assignment to 16S rRNA gene
17269 fragments by exact matching.")
17270 (license license:lgpl2.0)))
17272 (define-public r-dmrseq
17279 (uri (bioconductor-uri "dmrseq" version))
17282 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
17283 (properties `((upstream-name . "dmrseq")))
17284 (build-system r-build-system)
17286 (list r-annotationhub
17291 r-delayedmatrixstats
17305 (home-page "https://bioconductor.org/packages/dmrseq")
17306 (synopsis "Detection and inference of differentially methylated regions")
17308 "This package implements an approach for scanning the genome to detect
17309 and perform accurate inference on differentially methylated regions from Whole
17310 Genome Bisulfite Sequencing data. The method is based on comparing detected
17311 regions to a pooled null distribution, that can be implemented even when as
17312 few as two samples per population are available. Region-level statistics are
17313 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
17314 with a nested autoregressive correlated error structure for the effect of
17315 interest on transformed methylation proportions.")
17316 (license license:expat)))
17318 (define-public r-omicade4
17320 (name "r-omicade4")
17324 (uri (bioconductor-uri "omicade4" version))
17327 "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
17328 (properties `((upstream-name . "omicade4")))
17329 (build-system r-build-system)
17330 (propagated-inputs (list r-ade4 r-biobase r-made4))
17331 (home-page "https://bioconductor.org/packages/omicade4")
17332 (synopsis "Multiple co-inertia analysis of omics datasets")
17334 "This package performes multiple co-inertia analysis of omics datasets.")
17335 (license license:gpl2)))
17337 (define-public r-omnipathr
17339 (name "r-omnipathr")
17344 (uri (bioconductor-uri "OmnipathR" version))
17346 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
17347 (properties `((upstream-name . "OmnipathR")))
17348 (build-system r-build-system)
17351 (modify-phases %standard-phases
17352 (add-after 'unpack 'set-HOME
17353 (lambda _ (setenv "HOME" "/tmp"))))))
17379 (native-inputs (list r-knitr))
17380 (home-page "https://saezlab.github.io/OmnipathR/")
17381 (synopsis "OmniPath web service client and more")
17383 "This package provides a client for the OmniPath web service and many
17384 other resources. It also includes functions to transform and pretty print
17385 some of the downloaded data, functions to access a number of other resources.
17386 Furthermore, OmnipathR features a close integration with the NicheNet method
17387 for ligand activity prediction from transcriptomics data.")
17388 (license license:expat)))
17390 (define-public r-biscuiteer
17392 (name "r-biscuiteer")
17397 (uri (bioconductor-uri "biscuiteer" version))
17400 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
17401 (properties `((upstream-name . "biscuiteer")))
17402 (build-system r-build-system)
17410 r-delayedmatrixstats
17429 r-summarizedexperiment
17430 r-variantannotation))
17433 (home-page "https://github.com/trichelab/biscuiteer")
17434 (synopsis "Convenience functions for the Biscuit package")
17436 "This package provides a test harness for bsseq loading of Biscuit
17437 output, summarization of WGBS data over defined regions and in mappable
17438 samples, with or without imputation, dropping of mostly-NA rows, age
17440 (license license:gpl3)))
17442 (define-public r-tcgabiolinks
17444 (name "r-tcgabiolinks")
17449 (uri (bioconductor-uri "TCGAbiolinks" version))
17451 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
17452 (properties `((upstream-name . "TCGAbiolinks")))
17453 (build-system r-build-system)
17472 r-summarizedexperiment
17473 r-tcgabiolinksgui-data
17478 (native-inputs (list r-knitr))
17479 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
17480 (synopsis "Integrative analysis with GDC data")
17482 "The aim of TCGAbiolinks is:
17485 @item facilitate GDC open-access data retrieval;
17486 @item prepare the data using the appropriate pre-processing strategies;
17487 @item provide the means to carry out different standard analyses, and;
17488 @item to easily reproduce earlier research results.
17491 In more detail, the package provides multiple methods for analysis (e.g.,
17492 differential expression analysis, identifying differentially methylated
17493 regions) and methods for visualization (e.g., survival plots, volcano plots,
17494 starburst plots) in order to easily develop complete analysis pipelines.")
17495 (license license:gpl3+)))
17497 (define-public r-tricycle
17499 (name "r-tricycle")
17503 (uri (bioconductor-uri "tricycle" version))
17506 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
17507 (properties `((upstream-name . "tricycle")))
17508 (build-system r-build-system)
17510 (list r-annotationdbi
17521 r-singlecellexperiment
17522 r-summarizedexperiment))
17523 (native-inputs (list r-knitr))
17524 (home-page "https://github.com/hansenlab/tricycle")
17525 (synopsis "Transferable representation and inference of cell cycle")
17527 "The package contains functions to infer and visualize cell cycle process
17528 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
17529 projecting new data to the previous learned biologically interpretable space.
17530 The @code{tricycle} provides a pre-learned cell cycle space, which could be
17531 used to infer cell cycle time of human and mouse single cell samples. In
17532 addition, it also offer functions to visualize cell cycle time on different
17533 embeddings and functions to build new reference.")
17534 (license license:gpl3)))
17536 (define-public r-tximeta
17543 (uri (bioconductor-uri "tximeta" version))
17546 "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8"))))
17547 (properties `((upstream-name . "tximeta")))
17548 (build-system r-build-system)
17550 (list r-annotationdbi
17562 r-summarizedexperiment
17567 (home-page "https://github.com/mikelove/tximeta")
17568 (synopsis "Transcript quantification import with automatic metadata")
17570 "This package implements transcript quantification import from Salmon and
17571 alevin with automatic attachment of transcript ranges and release information,
17572 and other associated metadata. De novo transcriptomes can be linked to the
17573 appropriate sources with linkedTxomes and shared for computational
17575 (license license:gpl2)))
17577 (define-public r-phyloseq
17579 (name "r-phyloseq")
17584 (uri (bioconductor-uri "phyloseq" version))
17586 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
17587 (properties `((upstream-name . "phyloseq")))
17588 (build-system r-build-system)
17608 (home-page "https://github.com/joey711/phyloseq")
17609 (synopsis "Handling and analysis of high-throughput microbiome census data")
17611 "Phyloseq provides a set of classes and tools to facilitate the import,
17612 storage, analysis, and graphical display of microbiome census data.")
17613 (license license:agpl3)))
17616 ;;; Avoid adding new packages to the end of this file. To reduce the chances
17617 ;;; of a merge conflict, place them above by existing packages with similar
17618 ;;; functionality or similar names.