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-asset
2326 (uri (bioconductor-uri "ASSET" version))
2329 "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg"))))
2330 (properties `((upstream-name . "ASSET")))
2331 (build-system r-build-system)
2332 (propagated-inputs (list r-mass r-msm r-rmeta))
2333 (native-inputs (list r-knitr))
2334 (home-page "https://bioconductor.org/packages/ASSET")
2336 "Subset-based association analysis of heterogeneous traits and subtypes")
2338 "This package is an R program for the subset-based analysis of
2339 heterogeneous traits and disease subtypes. ASSET allows the user to search
2340 through all possible subsets of z-scores to identify the subset of traits
2341 giving the best meta-analyzed z-score. Further, it returns a p-value
2342 adjusting for the multiple-testing involved in the search. It also allows for
2343 searching for the best combination of disease subtypes associated with each
2345 (license license:gpl2)))
2347 (define-public r-atena
2353 (uri (bioconductor-uri "atena" version))
2356 "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp"))))
2357 (properties `((upstream-name . "atena")))
2358 (build-system r-build-system)
2360 (list r-annotationhub
2373 r-summarizedexperiment))
2374 (native-inputs (list r-knitr))
2375 (home-page "https://github.com/functionalgenomics/atena")
2376 (synopsis "Analysis of transposable elements")
2378 "The atena package quantifies expression of @dfn{TEs} (transposable
2379 elements) from RNA-seq data through different methods, including ERVmap,
2380 TEtranscripts and Telescope. A common interface is provided to use each of
2381 these methods, which consists of building a parameter object, calling the
2382 quantification function with this object and getting a
2383 @code{SummarizedExperiment} object as an output container of the quantified
2384 expression profiles. The implementation allows quantifing TEs and gene
2385 transcripts in an integrated manner.")
2386 (license license:artistic2.0)))
2388 (define-public r-atsnp
2394 (uri (bioconductor-uri "atSNP" version))
2397 "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz"))))
2398 (properties `((upstream-name . "atSNP")))
2399 (build-system r-build-system)
2401 (list r-biocfilecache
2411 (native-inputs (list r-knitr))
2412 (home-page "https://github.com/sunyoungshin/atSNP")
2414 "Affinity test for identifying regulatory single nucleotide polymorphisms")
2416 "The atSNP package performs affinity tests of motif matches with the
2417 @dfn{SNP} (single nucleotide polymorphism) or the reference genomes and
2418 SNP-led changes in motif matches.")
2419 (license license:gpl2)))
2421 (define-public r-attract
2427 (uri (bioconductor-uri "attract" version))
2430 "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82"))))
2431 (properties `((upstream-name . "attract")))
2432 (build-system r-build-system)
2434 (list r-annotationdbi
2442 (home-page "https://bioconductor.org/packages/attract")
2443 (synopsis "Finding drivers of Kauffman's attractor landscape")
2445 "This package contains the functions to find the gene expression modules
2446 that represent the drivers of Kauffman's attractor landscape. The modules are
2447 the core attractor pathways that discriminate between different cell types of
2448 groups of interest. Each pathway has a set of synexpression groups, which show
2449 transcriptionally-coordinated changes in gene expression.")
2450 (license license:lgpl2.0+)))
2452 (define-public r-awfisher
2458 (uri (bioconductor-uri "AWFisher" version))
2461 "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1"))))
2462 (properties `((upstream-name . "AWFisher")))
2463 (build-system r-build-system)
2467 (native-inputs (list r-knitr))
2468 (home-page "https://bioconductor.org/packages/AWFisher")
2469 (synopsis "Fast computing for adaptively weighted fisher's method")
2471 "This package is an implementation of the Adaptively Weighted Fisher's
2472 method, including fast p-value computing, variability index, and
2474 (license license:gpl3)))
2476 (define-public r-awst
2482 (uri (bioconductor-uri "awst" version))
2485 "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav"))))
2486 (properties `((upstream-name . "awst")))
2487 (build-system r-build-system)
2488 (propagated-inputs (list r-summarizedexperiment))
2489 (native-inputs (list r-knitr))
2490 (home-page "https://github.com/drisso/awst")
2491 (synopsis "Asymmetric within-sample transformation")
2493 "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that
2494 regularizes RNA-seq read counts and reduces the effect of noise on the
2495 classification of samples. AWST comprises two main steps: standardization and
2496 smoothing. These steps transform gene expression data to reduce the noise of
2497 the lowly expressed features, which suffer from background effects and low
2498 signal-to-noise ratio, and the influence of the highly expressed features,
2499 which may be the result of amplification bias and other experimental
2501 (license license:expat)))
2503 (define-public r-baalchip
2509 (uri (bioconductor-uri "BaalChIP" version))
2512 "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
2513 (properties `((upstream-name . "BaalChIP")))
2514 (build-system r-build-system)
2515 (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
2529 (native-inputs (list r-knitr))
2530 (home-page "https://bioconductor.org/packages/BaalChIP")
2532 "Analysis of allele-specific transcription factor binding in cancer genomes")
2534 "This package offers functions to process multiple @code{ChIP-seq BAM}
2535 files and detect allele-specific events. It computes allele counts at
2536 individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
2537 control) steps to remove problematic variants, and utilizes a Bayesian
2538 framework to identify statistically significant allele-specific events.
2539 BaalChIP is able to account for copy number differences between the two
2540 alleles, a known phenotypical feature of cancer samples.")
2541 (license license:artistic2.0)))
2543 (define-public r-basespacer
2545 (name "r-basespacer")
2549 (uri (bioconductor-uri "BaseSpaceR" version))
2552 "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj"))))
2553 (properties `((upstream-name . "BaseSpaceR")))
2554 (build-system r-build-system)
2555 (propagated-inputs (list r-rcurl r-rjsonio))
2556 (home-page "https://bioconductor.org/packages/BaseSpaceR")
2557 (synopsis "R SDK for BaseSpace RESTful API")
2559 "This package provides an R interface to Illumina's BaseSpace cloud
2560 computing environment, enabling the fast development of data analysis and
2561 visualization tools. Besides providing an easy to use set of tools for
2562 manipulating the data from BaseSpace, it also facilitates the access to R's
2563 rich environment of statistical and data analysis tools.")
2564 (license license:asl2.0)))
2566 (define-public r-bac
2572 (uri (bioconductor-uri "BAC" version))
2575 "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2"))))
2576 (properties `((upstream-name . "BAC")))
2577 (build-system r-build-system)
2578 (home-page "https://bioconductor.org/packages/BAC")
2579 (synopsis "Bayesian analysis of Chip-chip experiment")
2581 "This package uses a Bayesian hierarchical model to detect enriched
2582 regions from ChIP-chip experiments. The common goal in analyzing this
2583 ChIP-chip data is to detect DNA-protein interactions from ChIP-chip
2584 experiments. The BAC package has mainly been tested with Affymetrix tiling
2585 array data. However, we expect it to work with other platforms (e.g. Agilent,
2586 Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so
2587 you will have to normalize your data beforehand.")
2588 (license license:artistic2.0)))
2590 (define-public r-bader
2596 (uri (bioconductor-uri "BADER" version))
2599 "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm"))))
2600 (properties `((upstream-name . "BADER")))
2601 (build-system r-build-system)
2602 (home-page "https://bioconductor.org/packages/BADER")
2604 "Bayesian analysis of differential expression in RNA sequencing data")
2606 "The BADER package is intended for the analysis of RNA sequencing data.
2607 The algorithm fits a Bayesian hierarchical model for RNA sequencing count
2608 data. BADER returns the posterior probability of differential expression for
2609 each gene between two groups A and B. The joint posterior distribution of the
2610 variables in the model can be returned in the form of posterior samples, which
2611 can be used for further down-stream analyses such as gene set enrichment.")
2612 (license license:gpl2)))
2614 (define-public r-badregionfinder
2616 (name "r-badregionfinder")
2620 (uri (bioconductor-uri "BadRegionFinder" version))
2623 "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9"))))
2624 (properties `((upstream-name . "BadRegionFinder")))
2625 (build-system r-build-system)
2631 r-variantannotation))
2632 (home-page "https://bioconductor.org/packages/BadRegionFinder")
2633 (synopsis "Identifying regions with bad coverage in sequence alignment data")
2635 "BadRegionFinder is a package for identifying regions with a bad,
2636 acceptable and good coverage in sequence alignment data available as bam
2637 files. The whole genome may be considered as well as a set of target regions.
2638 Various visual and textual types of output are available.")
2639 (license license:lgpl3)))
2641 (define-public r-bambu
2647 (uri (bioconductor-uri "bambu" version))
2650 "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w"))))
2651 (properties `((upstream-name . "bambu")))
2652 (build-system r-build-system)
2654 (list r-biocgenerics
2668 r-summarizedexperiment
2671 (native-inputs (list r-knitr))
2672 (home-page "https://github.com/GoekeLab/bambu")
2674 "Isoform reconstruction and quantification for long read RNA-Seq data")
2676 "This R package is for multi-sample transcript discovery and
2677 quantification using long read RNA-Seq data. You can use bambu after read
2678 alignment to obtain expression estimates for known and novel transcripts and
2679 genes. The output from bambu can directly be used for visualisation and
2680 downstream analysis, such as differential gene expression or transcript
2682 (license license:gpl3)))
2684 (define-public r-bandits
2690 (uri (bioconductor-uri "BANDITS" version))
2693 "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9"))))
2694 (properties `((upstream-name . "BANDITS")))
2695 (build-system r-build-system)
2697 (list r-biocparallel
2708 (native-inputs (list r-knitr))
2709 (home-page "https://github.com/SimoneTiberi/BANDITS")
2710 (synopsis "Bayesian analysis of differential splicing")
2712 "BANDITS is a Bayesian hierarchical model for detecting differential
2713 splicing of genes and transcripts, via @dfn{DTU} (differential transcript
2714 usage), between two or more conditions. The method uses a Bayesian
2715 hierarchical framework, which allows for sample specific proportions in a
2716 Dirichlet-Multinomial model, and samples the allocation of fragments to the
2717 transcripts. Parameters are inferred via @dfn{MCMC} (Markov chain Monte
2718 Carlo) techniques and a DTU test is performed via a multivariate Wald test on
2719 the posterior densities for the average relative abundance of transcripts.")
2720 (license license:gpl3+)))
2722 (define-public r-banocc
2728 (uri (bioconductor-uri "banocc" version))
2731 "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx"))))
2732 (properties `((upstream-name . "banocc")))
2733 (build-system r-build-system)
2739 (native-inputs (list r-knitr))
2740 (home-page "https://bioconductor.org/packages/banocc")
2741 (synopsis "Bayesian analysis of compositional covariance")
2743 "BAnOCC is a package designed for compositional data, where each sample
2744 sums to one. It infers the approximate covariance of the unconstrained data
2745 using a Bayesian model coded with @code{rstan}. It provides as output the
2746 @code{stanfit} object as well as posterior median and credible interval
2747 estimates for each correlation element.")
2748 (license license:expat)))
2750 (define-public r-barcodetrackr
2752 (name "r-barcodetrackr")
2756 (uri (bioconductor-uri "barcodetrackR" version))
2759 "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3"))))
2760 (properties `((upstream-name . "barcodetrackR")))
2761 (build-system r-build-system)
2777 r-summarizedexperiment
2782 (native-inputs (list r-knitr))
2783 (home-page "https://github.com/dunbarlabNIH/barcodetrackR")
2784 (synopsis "Functions for analyzing cellular barcoding data")
2786 "This package is developed for the analysis and visualization of clonal
2787 tracking data. The required data is formed by samples and tag abundances in
2788 matrix form, usually from cellular barcoding experiments, integration site
2789 retrieval analyses, or similar technologies.")
2790 (license license:cc0)))
2792 (define-public r-biocversion
2794 (name "r-biocversion")
2799 (uri (bioconductor-uri "BiocVersion" version))
2802 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
2803 (properties `((upstream-name . "BiocVersion")))
2804 (build-system r-build-system)
2805 (home-page "https://bioconductor.org/packages/BiocVersion/")
2806 (synopsis "Set the appropriate version of Bioconductor packages")
2808 "This package provides repository information for the appropriate version
2810 (license license:artistic2.0)))
2812 (define-public r-biocgenerics
2814 (name "r-biocgenerics")
2818 (uri (bioconductor-uri "BiocGenerics" version))
2821 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
2823 `((upstream-name . "BiocGenerics")))
2824 (build-system r-build-system)
2825 (home-page "https://bioconductor.org/packages/BiocGenerics")
2826 (synopsis "S4 generic functions for Bioconductor")
2828 "This package provides S4 generic functions needed by many Bioconductor
2830 (license license:artistic2.0)))
2832 (define-public r-coverageview
2834 (name "r-coverageview")
2838 (uri (bioconductor-uri "CoverageView" version))
2841 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
2842 (build-system r-build-system)
2850 (home-page "https://bioconductor.org/packages/CoverageView/")
2851 (synopsis "Coverage visualization package for R")
2852 (description "This package provides a framework for the visualization of
2853 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
2854 be also used for genome-wide nucleosome positioning experiments or other
2855 experiment types where it is important to have a framework in order to inspect
2856 how the coverage distributed across the genome.")
2857 (license license:artistic2.0)))
2859 (define-public r-cummerbund
2861 (name "r-cummerbund")
2865 (uri (bioconductor-uri "cummeRbund" version))
2868 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
2869 (build-system r-build-system)
2881 (home-page "https://bioconductor.org/packages/cummeRbund/")
2882 (synopsis "Analyze Cufflinks high-throughput sequencing data")
2883 (description "This package allows for persistent storage, access,
2884 exploration, and manipulation of Cufflinks high-throughput sequencing
2885 data. In addition, provides numerous plotting functions for commonly
2886 used visualizations.")
2887 (license license:artistic2.0)))
2889 (define-public r-dearseq
2896 (uri (bioconductor-uri "dearseq" version))
2899 "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl"))))
2900 (build-system r-build-system)
2902 (list r-compquadform
2918 (home-page "https://github.com/borishejblum/dearseq")
2919 (synopsis "DEA for RNA-seq data through a robust variance component test")
2921 "This is a package for Differential Expression Analysis of RNA-seq data.
2922 It features a variance component score test accounting for data
2923 heteroscedasticity through precision weights. Perform both gene-wise and gene
2924 set analyses, and can deal with repeated or longitudinal data.")
2925 (license license:gpl2)))
2927 (define-public r-decipher
2933 (uri (bioconductor-uri "DECIPHER" version))
2936 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
2937 (build-system r-build-system)
2945 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
2946 (synopsis "Tools for deciphering and managing biological sequences")
2947 (description "This package provides a toolset for deciphering and managing
2948 biological sequences.")
2949 (license license:gpl3)))
2951 (define-public r-deconvr
2957 (uri (bioconductor-uri "deconvR" version))
2960 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
2961 (properties `((upstream-name . "deconvR")))
2962 (build-system r-build-system)
2981 (native-inputs (list r-knitr))
2982 (home-page "https://github.com/BIMSBbioinfo/deconvR")
2983 (synopsis "Simulation and deconvolution of omic profiles")
2985 "This package provides a collection of functions designed for analyzing
2986 deconvolution of the bulk sample(s) using an atlas of reference omic signature
2987 profiles and a user-selected model. Users are given the option to create or
2988 extend a reference atlas and,also simulate the desired size of the bulk
2989 signature profile of the reference cell types. The package includes the
2990 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
2991 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
2992 make mapping WGBS data to their probe IDs easier.")
2993 (license license:artistic2.0)))
2995 (define-public r-decoupler
2997 (name "r-decoupler")
3002 (uri (bioconductor-uri "decoupleR" version))
3004 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
3005 (properties `((upstream-name . "decoupleR")))
3006 (build-system r-build-system)
3019 (native-inputs (list r-knitr))
3020 (home-page "https://saezlab.github.io/decoupleR/")
3021 (synopsis "Computational methods to infer biological activities from omics data")
3023 "Many methods allow us to extract biological activities from omics data using
3024 information from prior knowledge resources, reducing the dimensionality for
3025 increased statistical power and better interpretability. decoupleR is a
3026 Bioconductor package containing different statistical methods to extract these
3027 signatures within a unified framework. decoupleR allows the user to flexibly
3028 test any method with any resource. It incorporates methods that take into
3029 account the sign and weight of network interactions. decoupleR can be used
3030 with any omic, as long as its features can be linked to a biological process
3031 based on prior knowledge. For example, in transcriptomics gene sets regulated
3032 by a transcription factor, or in phospho-proteomics phosphosites that are
3033 targeted by a kinase.")
3034 (license license:gpl3)))
3036 (define-public r-deepsnv
3042 (uri (bioconductor-uri "deepSNV" version))
3045 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
3046 (properties `((upstream-name . "deepSNV")))
3047 (build-system r-build-system)
3053 r-summarizedexperiment
3058 (home-page "https://github.com/gerstung-lab/deepSNV/")
3059 (synopsis "Detection of subclonal SNVs in deep sequencing data")
3061 "This package provides quantitative variant callers for detecting
3062 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
3063 The deepSNV algorithm is used for a comparative setup with a control experiment
3064 of the same loci and uses a beta-binomial model and a likelihood ratio test to
3065 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
3066 computes a Bayes classifier based on a beta-binomial model for variant calling
3067 with multiple samples for precisely estimating model parameters - such as local
3068 error rates and dispersion - and prior knowledge, e.g. from variation data
3069 bases such as COSMIC.")
3070 (license license:gpl3)))
3072 (define-public r-delayedarray
3074 (name "r-delayedarray")
3078 (uri (bioconductor-uri "DelayedArray" version))
3081 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
3083 `((upstream-name . "DelayedArray")))
3084 (build-system r-build-system)
3086 (list r-biocgenerics r-s4vectors r-iranges r-matrix
3090 (home-page "https://bioconductor.org/packages/DelayedArray")
3091 (synopsis "Delayed operations on array-like objects")
3093 "Wrapping an array-like object (typically an on-disk object) in a
3094 @code{DelayedArray} object allows one to perform common array operations on it
3095 without loading the object in memory. In order to reduce memory usage and
3096 optimize performance, operations on the object are either delayed or executed
3097 using a block processing mechanism. Note that this also works on in-memory
3098 array-like objects like @code{DataFrame} objects (typically with Rle columns),
3099 @code{Matrix} objects, and ordinary arrays and data frames.")
3100 (license license:artistic2.0)))
3102 (define-public r-derfinderhelper
3104 (name "r-derfinderhelper")
3109 (uri (bioconductor-uri "derfinderHelper" version))
3111 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
3112 (properties `((upstream-name . "derfinderHelper")))
3113 (build-system r-build-system)
3115 (list r-iranges r-matrix r-s4vectors))
3118 (home-page "https://github.com/leekgroup/derfinderHelper")
3119 (synopsis "Helper for derfinder")
3121 "This package speeds up the derfinder package when using multiple cores.
3122 It is particularly useful when using BiocParallel and it helps reduce the time
3123 spent loading the full derfinder package when running the F-statistics
3124 calculation in parallel.")
3125 (license license:artistic2.0)))
3127 (define-public r-drimseq
3134 (uri (bioconductor-uri "DRIMSeq" version))
3136 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
3137 (properties `((upstream-name . "DRIMSeq")))
3138 (build-system r-build-system)
3140 (list r-biocgenerics
3150 (native-inputs (list r-knitr))
3151 (home-page "https://bioconductor.org/packages/DRIMSeq")
3152 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
3154 "The package provides two frameworks. One for the differential
3155 transcript usage analysis between different conditions and one for the tuQTL
3156 analysis. Both are based on modeling the counts of genomic features (i.e.,
3157 transcripts) with the Dirichlet-multinomial distribution. The package also
3158 makes available functions for visualization and exploration of the data and
3160 (license license:gpl3+)))
3162 (define-public r-bluster
3168 (uri (bioconductor-uri "bluster" version))
3171 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
3172 (properties `((upstream-name . "bluster")))
3173 (build-system r-build-system)
3175 (list r-biocneighbors
3184 (home-page "https://bioconductor.org/packages/bluster")
3185 (synopsis "Clustering algorithms for Bioconductor")
3186 (description"This package wraps common clustering algorithms in an easily
3187 extended S4 framework. Backends are implemented for hierarchical, k-means
3188 and graph-based clustering. Several utilities are also provided to compare
3189 and evaluate clustering results.")
3190 (license license:gpl3)))
3192 (define-public r-ideoviz
3198 (uri (bioconductor-uri "IdeoViz" version))
3201 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
3202 (build-system r-build-system)
3210 (home-page "https://bioconductor.org/packages/IdeoViz/")
3211 (synopsis "Plots data along a chromosomal ideogram")
3212 (description "This package provides functions to plot data associated with
3213 arbitrary genomic intervals along chromosomal ideogram.")
3214 (license license:gpl2)))
3216 (define-public r-infercnv
3223 (uri (bioconductor-uri "infercnv" version))
3226 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
3227 (properties `((upstream-name . "infercnv")))
3228 (build-system r-build-system)
3229 (inputs (list python))
3258 r-singlecellexperiment
3259 r-summarizedexperiment
3261 (native-inputs (list r-knitr))
3262 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
3263 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
3265 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
3266 evidence for somatic large-scale chromosomal copy number alterations, such as gains
3267 or deletions of entire chromosomes or large segments of chromosomes. This is done
3268 by exploring expression intensity of genes across positions of a tumor genome in
3269 comparison to a set of reference \"normal\" cells. A heatmap is generated
3270 illustrating the relative expression intensities across each chromosome, and it
3271 often becomes readily apparent as to which regions of the tumor genome are
3272 over-abundant or less-abundant as compared to that of normal cells.")
3273 (license license:bsd-3)))
3275 (define-public r-iranges
3281 (uri (bioconductor-uri "IRanges" version))
3284 "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
3286 `((upstream-name . "IRanges")))
3287 (build-system r-build-system)
3289 (list r-biocgenerics r-s4vectors))
3290 (home-page "https://bioconductor.org/packages/IRanges")
3291 (synopsis "Infrastructure for manipulating intervals on sequences")
3293 "This package provides efficient low-level and highly reusable S4 classes
3294 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
3295 generally, data that can be organized sequentially (formally defined as
3296 @code{Vector} objects), as well as views on these @code{Vector} objects.
3297 Efficient list-like classes are also provided for storing big collections of
3298 instances of the basic classes. All classes in the package use consistent
3299 naming and share the same rich and consistent \"Vector API\" as much as
3301 (license license:artistic2.0)))
3303 (define-public r-isoformswitchanalyzer
3305 (name "r-isoformswitchanalyzer")
3310 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
3312 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
3313 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
3314 (build-system r-build-system)
3347 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
3348 (synopsis "Analyze alternative splicing in RNA-seq data")
3350 "This is a package for the analysis of alternative splicing and isoform
3351 switches with predicted functional consequences (e.g. gain/loss of protein
3352 domains etc.) from quantification of all types of RNASeq by tools such as
3353 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
3354 (license license:gpl2+)))
3356 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
3357 (define-public r-absfiltergsea
3359 (name "r-absfiltergsea")
3364 (uri (cran-uri "AbsFilterGSEA" version))
3366 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
3367 (properties `((upstream-name . "AbsFilterGSEA")))
3368 (build-system r-build-system)
3370 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
3371 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
3372 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
3374 "This package provides a function that performs gene-permuting of a gene-set
3375 enrichment analysis (GSEA) calculation with or without the absolute filtering.
3376 Without filtering, users can perform (original) two-tailed or one-tailed
3378 (license license:gpl2)))
3380 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
3381 (define-public r-bisquerna
3383 (name "r-bisquerna")
3387 (uri (cran-uri "BisqueRNA" version))
3390 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
3391 (properties `((upstream-name . "BisqueRNA")))
3392 (build-system r-build-system)
3394 (list r-biobase r-limsolve))
3397 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
3398 (synopsis "Decomposition of bulk expression with single-cell sequencing")
3399 (description "This package provides tools to accurately estimate cell type
3400 abundances from heterogeneous bulk expression. A reference-based method
3401 utilizes single-cell information to generate a signature matrix and
3402 transformation of bulk expression for accurate regression based estimates.
3403 A marker-based method utilizes known cell-specific marker genes to measure
3404 relative abundances across samples.")
3405 (license license:gpl3)))
3407 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
3408 ;; from Bioconductor.
3409 (define-public r-deconstructsigs
3411 (name "r-deconstructsigs")
3415 (uri (cran-uri "deconstructSigs" version))
3418 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
3420 `((upstream-name . "deconstructSigs")))
3421 (build-system r-build-system)
3423 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
3425 (home-page "https://github.com/raerose01/deconstructSigs")
3426 (synopsis "Identifies signatures present in a tumor sample")
3427 (description "This package takes sample information in the form of the
3428 fraction of mutations in each of 96 trinucleotide contexts and identifies
3429 the weighted combination of published signatures that, when summed, most
3430 closely reconstructs the mutational profile.")
3431 (license license:gpl2+)))
3433 ;; This is a CRAN package, but it depends on Bioconductor packages.
3434 (define-public r-jetset
3441 (uri (cran-uri "jetset" version))
3443 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
3444 (properties `((upstream-name . "jetset")))
3445 (build-system r-build-system)
3446 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
3447 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
3448 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
3450 "This package provides a one-to-one mapping from gene to \"best\" probe
3451 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
3452 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
3453 gene may be measured by multiple probe sets. This can present a mild
3454 conundrum when attempting to evaluate a gene \"signature\" that is defined by
3455 gene names rather than by specific probe sets. This package also includes the
3456 pre-calculated probe set quality scores that were used to define the
3458 (license license:artistic2.0)))
3460 ;; This is a CRAN package, but it depends on Bioconductor packages.
3461 (define-public r-nmf
3468 (uri (cran-uri "NMF" version))
3471 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
3472 (properties `((upstream-name . "NMF")))
3473 (build-system r-build-system)
3478 r-bigmemory ; suggested
3479 r-synchronicity ; suggested
3494 (home-page "http://renozao.github.io/NMF")
3495 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3497 "This package provides a framework to perform Non-negative Matrix
3498 Factorization (NMF). The package implements a set of already published
3499 algorithms and seeding methods, and provides a framework to test, develop and
3500 plug new or custom algorithms. Most of the built-in algorithms have been
3501 optimized in C++, and the main interface function provides an easy way of
3502 performing parallel computations on multicore machines.")
3503 (license license:gpl2+)))
3505 (define-public r-affy
3512 (uri (bioconductor-uri "affy" version))
3515 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
3516 (build-system r-build-system)
3526 (home-page "https://bioconductor.org/packages/affy")
3527 (synopsis "Methods for affymetrix oligonucleotide arrays")
3529 "This package contains functions for exploratory oligonucleotide array
3531 (license license:lgpl2.0+)))
3533 (define-public r-affycomp
3540 (uri (bioconductor-uri "affycomp" version))
3543 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
3544 (properties `((upstream-name . "affycomp")))
3545 (build-system r-build-system)
3546 (propagated-inputs (list r-biobase))
3547 (home-page "https://bioconductor.org/packages/affycomp/")
3548 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
3550 "The package contains functions that can be used to compare expression
3551 measures for Affymetrix Oligonucleotide Arrays.")
3552 (license license:gpl2+)))
3554 (define-public r-affycompatible
3556 (name "r-affycompatible")
3561 (uri (bioconductor-uri "AffyCompatible" version))
3564 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
3566 `((upstream-name . "AffyCompatible")))
3567 (build-system r-build-system)
3571 `(modify-phases %standard-phases
3572 (add-after 'unpack 'make-reproducible
3574 ;; Order DTD elements before generating R code from them.
3575 (substitute* "R/methods-AffyCompatible.R"
3578 elements <- dtd$elements
3579 ordered <- elements[order(names(elements))]\n"))
3580 (("elt in dtd\\$elements")
3582 ;; Use a predictable directory name for code generation.
3583 (mkdir-p "/tmp/NetAffxResourcePrototype")
3584 (substitute* "R/DataClasses.R"
3585 (("directory=tempdir\\(\\)")
3586 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
3588 (list r-biostrings r-rcurl r-xml))
3589 (home-page "https://bioconductor.org/packages/AffyCompatible/")
3590 (synopsis "Work with Affymetrix GeneChip files")
3592 "This package provides an interface to Affymetrix chip annotation and
3593 sample attribute files. The package allows an easy way for users to download
3594 and manage local data bases of Affynmetrix NetAffx annotation files. It also
3595 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
3596 Command Console} (AGCC)-compatible sample annotation files.")
3597 (license license:artistic2.0)))
3599 (define-public r-affycontam
3601 (name "r-affycontam")
3606 (uri (bioconductor-uri "affyContam" version))
3609 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
3610 (properties `((upstream-name . "affyContam")))
3611 (build-system r-build-system)
3613 (list r-affy r-affydata r-biobase))
3614 (home-page "https://bioconductor.org/packages/affyContam/")
3615 (synopsis "Structured corruption of Affymetrix CEL file data")
3617 "Microarray quality assessment is a major concern of microarray analysts.
3618 This package provides some simple approaches to in silico creation of quality
3619 problems in CEL-level data to help evaluate performance of quality metrics.")
3620 (license license:artistic2.0)))
3622 (define-public r-affycoretools
3624 (name "r-affycoretools")
3629 (uri (bioconductor-uri "affycoretools" version))
3632 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
3633 (properties `((upstream-name . "affycoretools")))
3634 (build-system r-build-system)
3657 (home-page "https://bioconductor.org/packages/affycoretools/")
3658 (synopsis "Functions for analyses with Affymetrix GeneChips")
3660 "This package provides various wrapper functions that have been written
3661 to streamline the more common analyses that a Biostatistician might see.")
3662 (license license:artistic2.0)))
3664 (define-public r-affyio
3671 (uri (bioconductor-uri "affyio" version))
3674 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
3675 (build-system r-build-system)
3680 (home-page "https://github.com/bmbolstad/affyio")
3681 (synopsis "Tools for parsing Affymetrix data files")
3683 "This package provides routines for parsing Affymetrix data files based
3684 upon file format information. The primary focus is on accessing the CEL and
3686 (license license:lgpl2.0+)))
3688 (define-public r-affxparser
3690 (name "r-affxparser")
3695 (uri (bioconductor-uri "affxparser" version))
3698 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
3699 (properties `((upstream-name . "affxparser")))
3700 (build-system r-build-system)
3701 (home-page "https://github.com/HenrikBengtsson/affxparser")
3702 (synopsis "Affymetrix File Parsing SDK")
3704 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
3705 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
3706 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
3707 are supported. Currently, there are methods for reading @dfn{chip definition
3708 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
3709 either in full or in part. For example, probe signals from a few probesets
3710 can be extracted very quickly from a set of CEL files into a convenient list
3712 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
3714 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
3716 (define-public r-annotate
3723 (uri (bioconductor-uri "annotate" version))
3726 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
3727 (build-system r-build-system)
3729 (list r-annotationdbi
3737 "https://bioconductor.org/packages/annotate")
3738 (synopsis "Annotation for microarrays")
3739 (description "This package provides R environments for the annotation of
3741 (license license:artistic2.0)))
3743 (define-public r-annotationdbi
3745 (name "r-annotationdbi")
3749 (uri (bioconductor-uri "AnnotationDbi" version))
3752 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
3754 `((upstream-name . "AnnotationDbi")))
3755 (build-system r-build-system)
3766 (home-page "https://bioconductor.org/packages/AnnotationDbi")
3767 (synopsis "Annotation database interface")
3769 "This package provides user interface and database connection code for
3770 annotation data packages using SQLite data storage.")
3771 (license license:artistic2.0)))
3773 (define-public r-annotationfilter
3775 (name "r-annotationfilter")
3779 (uri (bioconductor-uri "AnnotationFilter" version))
3782 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
3784 `((upstream-name . "AnnotationFilter")))
3785 (build-system r-build-system)
3787 (list r-genomicranges r-lazyeval))
3790 (home-page "https://github.com/Bioconductor/AnnotationFilter")
3791 (synopsis "Facilities for filtering Bioconductor annotation resources")
3793 "This package provides classes and other infrastructure to implement
3794 filters for manipulating Bioconductor annotation resources. The filters are
3795 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
3796 (license license:artistic2.0)))
3798 (define-public r-annotationforge
3800 (name "r-annotationforge")
3805 (uri (bioconductor-uri "AnnotationForge" version))
3808 "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v"))))
3810 `((upstream-name . "AnnotationForge")))
3811 (build-system r-build-system)
3813 (list r-annotationdbi
3823 (home-page "https://bioconductor.org/packages/AnnotationForge")
3824 (synopsis "Code for building annotation database packages")
3826 "This package provides code for generating Annotation packages and their
3827 databases. Packages produced are intended to be used with AnnotationDbi.")
3828 (license license:artistic2.0)))
3830 (define-public r-annotationhub
3832 (name "r-annotationhub")
3837 (uri (bioconductor-uri "AnnotationHub" version))
3840 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
3841 (properties `((upstream-name . "AnnotationHub")))
3842 (build-system r-build-system)
3844 (list r-annotationdbi
3852 r-interactivedisplaybase
3859 (home-page "https://bioconductor.org/packages/AnnotationHub")
3860 (synopsis "Client to access AnnotationHub resources")
3862 "This package provides a client for the Bioconductor AnnotationHub web
3863 resource. The AnnotationHub web resource provides a central location where
3864 genomic files (e.g. VCF, bed, wig) and other resources from standard
3865 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
3866 metadata about each resource, e.g., a textual description, tags, and date of
3867 modification. The client creates and manages a local cache of files retrieved
3868 by the user, helping with quick and reproducible access.")
3869 (license license:artistic2.0)))
3871 (define-public r-aroma-light
3873 (name "r-aroma-light")
3878 (uri (bioconductor-uri "aroma.light" version))
3881 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
3882 (properties `((upstream-name . "aroma.light")))
3883 (build-system r-build-system)
3885 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
3886 (home-page "https://github.com/HenrikBengtsson/aroma.light")
3887 (synopsis "Methods for normalization and visualization of microarray data")
3889 "This package provides methods for microarray analysis that take basic
3890 data types such as matrices and lists of vectors. These methods can be used
3891 standalone, be utilized in other packages, or be wrapped up in higher-level
3893 (license license:gpl2+)))
3895 (define-public r-bamsignals
3897 (name "r-bamsignals")
3902 (uri (bioconductor-uri "bamsignals" version))
3905 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
3906 (build-system r-build-system)
3908 (list r-biocgenerics
3916 (home-page "https://bioconductor.org/packages/bamsignals")
3917 (synopsis "Extract read count signals from bam files")
3919 "This package efficiently obtains count vectors from indexed bam
3920 files. It counts the number of nucleotide sequence reads in given genomic
3921 ranges and it computes reads profiles and coverage profiles. It also handles
3923 (license license:gpl2+)))
3925 (define-public r-biobase
3931 (uri (bioconductor-uri "Biobase" version))
3934 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
3936 `((upstream-name . "Biobase")))
3937 (build-system r-build-system)
3939 (list r-biocgenerics))
3940 (home-page "https://bioconductor.org/packages/Biobase")
3941 (synopsis "Base functions for Bioconductor")
3943 "This package provides functions that are needed by many other packages
3944 on Bioconductor or which replace R functions.")
3945 (license license:artistic2.0)))
3947 (define-public r-biomart
3953 (uri (bioconductor-uri "biomaRt" version))
3956 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
3958 `((upstream-name . "biomaRt")))
3959 (build-system r-build-system)
3961 (list r-annotationdbi
3972 (home-page "https://bioconductor.org/packages/biomaRt")
3973 (synopsis "Interface to BioMart databases")
3975 "biomaRt provides an interface to a growing collection of databases
3976 implementing the @url{BioMart software suite, http://www.biomart.org}. The
3977 package enables retrieval of large amounts of data in a uniform way without
3978 the need to know the underlying database schemas or write complex SQL queries.
3979 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
3980 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
3981 users direct access to a diverse set of data and enable a wide range of
3982 powerful online queries from gene annotation to database mining.")
3983 (license license:artistic2.0)))
3985 ;; This is a CRAN package, but it depends on a Bioconductor package:
3987 (define-public r-biomartr
3993 (uri (cran-uri "biomartr" version))
3996 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
3997 (properties `((upstream-name . "biomartr")))
3998 (build-system r-build-system)
4018 (native-inputs (list r-knitr))
4019 (home-page "https://docs.ropensci.org/biomartr/")
4020 (synopsis "Genomic data retrieval")
4022 "Perform large scale genomic data retrieval and functional annotation
4023 retrieval. This package aims to provide users with a standardized way to
4024 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
4025 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
4026 Furthermore, an interface to the BioMart database allows users to retrieve
4027 functional annotation for genomic loci. In addition, users can download
4028 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
4030 (license license:gpl2)))
4032 (define-public r-biocparallel
4034 (name "r-biocparallel")
4038 (uri (bioconductor-uri "BiocParallel" version))
4041 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
4043 `((upstream-name . "BiocParallel")))
4044 (build-system r-build-system)
4047 (modify-phases %standard-phases
4048 (add-after 'unpack 'make-reproducible
4050 ;; Remove generated documentation.
4051 (for-each delete-file
4052 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
4053 "inst/doc/Introduction_To_BiocParallel.pdf"
4054 "inst/doc/Errors_Logs_And_Debugging.pdf"
4055 "inst/doc/BiocParallel_BatchtoolsParam.R"
4056 "inst/doc/Introduction_To_BiocParallel.R"
4057 "inst/doc/Errors_Logs_And_Debugging.R"))
4059 ;; Remove time-dependent macro
4060 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
4061 "inst/doc/Introduction_To_BiocParallel.Rnw"
4062 "inst/doc/Errors_Logs_And_Debugging.Rnw"
4063 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
4064 "vignettes/Introduction_To_BiocParallel.Rnw"
4065 "vignettes/Errors_Logs_And_Debugging.Rnw")
4066 (("\\today") "later"))
4068 ;; Initialize the random number generator seed when building.
4069 (substitute* "R/rng.R"
4070 (("\"L'Ecuyer-CMRG\"\\)" m)
4072 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
4074 (list r-bh r-codetools r-futile-logger r-snow))
4077 (home-page "https://bioconductor.org/packages/BiocParallel")
4078 (synopsis "Bioconductor facilities for parallel evaluation")
4080 "This package provides modified versions and novel implementation of
4081 functions for parallel evaluation, tailored to use with Bioconductor
4083 (license (list license:gpl2+ license:gpl3+))))
4085 (define-public r-biostrings
4087 (name "r-biostrings")
4091 (uri (bioconductor-uri "Biostrings" version))
4094 "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"))))
4096 `((upstream-name . "Biostrings")))
4097 (build-system r-build-system)
4099 (list r-biocgenerics
4105 (home-page "https://bioconductor.org/packages/Biostrings")
4106 (synopsis "String objects and algorithms for biological sequences")
4108 "This package provides memory efficient string containers, string
4109 matching algorithms, and other utilities, for fast manipulation of large
4110 biological sequences or sets of sequences.")
4111 (license license:artistic2.0)))
4113 (define-public r-biovizbase
4115 (name "r-biovizbase")
4120 (uri (bioconductor-uri "biovizBase" version))
4123 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
4124 (properties `((upstream-name . "biovizBase")))
4125 (build-system r-build-system)
4127 (list r-annotationdbi
4144 r-summarizedexperiment
4145 r-variantannotation))
4146 (home-page "https://bioconductor.org/packages/biovizBase")
4147 (synopsis "Basic graphic utilities for visualization of genomic data")
4149 "The biovizBase package is designed to provide a set of utilities, color
4150 schemes and conventions for genomic data. It serves as the base for various
4151 high-level packages for biological data visualization. This saves development
4152 effort and encourages consistency.")
4153 (license license:artistic2.0)))
4155 (define-public r-bsgenome
4161 (uri (bioconductor-uri "BSgenome" version))
4164 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
4166 `((upstream-name . "BSgenome")))
4167 (build-system r-build-system)
4169 (list r-biocgenerics
4179 (home-page "https://bioconductor.org/packages/BSgenome")
4180 (synopsis "Infrastructure for Biostrings-based genome data packages")
4182 "This package provides infrastructure shared by all Biostrings-based
4183 genome data packages and support for efficient SNP representation.")
4184 (license license:artistic2.0)))
4186 (define-public r-category
4193 (uri (bioconductor-uri "Category" version))
4196 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
4197 (properties `((upstream-name . "Category")))
4198 (build-system r-build-system)
4210 (home-page "https://bioconductor.org/packages/Category")
4211 (synopsis "Category analysis")
4213 "This package provides a collection of tools for performing category
4215 (license license:artistic2.0)))
4217 (define-public r-chipseeker
4219 (name "r-chipseeker")
4223 (uri (bioconductor-uri "ChIPseeker" version))
4226 "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"))))
4227 (build-system r-build-system)
4231 (list r-annotationdbi
4250 r-txdb-hsapiens-ucsc-hg19-knowngene))
4251 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
4252 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
4253 (description "This package implements functions to retrieve the nearest
4254 genes around the peak, annotate genomic region of the peak, statstical methods
4255 for estimate the significance of overlap among ChIP peak data sets, and
4256 incorporate GEO database for user to compare the own dataset with those
4257 deposited in database. The comparison can be used to infer cooperative
4258 regulation and thus can be used to generate hypotheses. Several visualization
4259 functions are implemented to summarize the coverage of the peak experiment,
4260 average profile and heatmap of peaks binding to TSS regions, genomic
4261 annotation, distance to TSS, and overlap of peaks or genes.")
4262 (license license:artistic2.0)))
4264 (define-public r-chipseq
4271 (uri (bioconductor-uri "chipseq" version))
4274 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
4275 (build-system r-build-system)
4277 (list r-biocgenerics
4283 (home-page "https://bioconductor.org/packages/chipseq")
4284 (synopsis "Package for analyzing ChIPseq data")
4286 "This package provides tools for processing short read data from ChIPseq
4288 (license license:artistic2.0)))
4290 (define-public r-complexheatmap
4292 (name "r-complexheatmap")
4297 (uri (bioconductor-uri "ComplexHeatmap" version))
4300 "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"))))
4302 `((upstream-name . "ComplexHeatmap")))
4303 (build-system r-build-system)
4321 "https://github.com/jokergoo/ComplexHeatmap")
4322 (synopsis "Making Complex Heatmaps")
4324 "Complex heatmaps are efficient to visualize associations between
4325 different sources of data sets and reveal potential structures. This package
4326 provides a highly flexible way to arrange multiple heatmaps and supports
4327 self-defined annotation graphics.")
4328 (license license:gpl2+)))
4330 (define-public r-copywriter
4332 (name "r-copywriter")
4337 (uri (bioconductor-uri "CopywriteR" version))
4340 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
4341 (properties `((upstream-name . "CopywriteR")))
4342 (build-system r-build-system)
4344 (list r-biocparallel
4358 (home-page "https://github.com/PeeperLab/CopywriteR")
4359 (synopsis "Copy number information from targeted sequencing")
4361 "CopywriteR extracts DNA copy number information from targeted sequencing
4362 by utilizing off-target reads. It allows for extracting uniformly distributed
4363 copy number information, can be used without reference, and can be applied to
4364 sequencing data obtained from various techniques including chromatin
4365 immunoprecipitation and target enrichment on small gene panels. Thereby,
4366 CopywriteR constitutes a widely applicable alternative to available copy
4367 number detection tools.")
4368 (license license:gpl2)))
4370 (define-public r-deseq
4377 (uri (bioconductor-uri "DESeq" version))
4380 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
4381 (properties `((upstream-name . "DESeq")))
4382 (build-system r-build-system)
4392 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
4393 (synopsis "Differential gene expression analysis")
4395 "This package provides tools for estimating variance-mean dependence in
4396 count data from high-throughput genetic sequencing assays and for testing for
4397 differential expression based on a model using the negative binomial
4399 (license license:gpl3+)))
4401 (define-public r-deseq2
4408 (uri (bioconductor-uri "DESeq2" version))
4411 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
4412 (properties `((upstream-name . "DESeq2")))
4413 (build-system r-build-system)
4427 r-summarizedexperiment))
4430 (home-page "https://bioconductor.org/packages/DESeq2")
4431 (synopsis "Differential gene expression analysis")
4433 "This package provides functions to estimate variance-mean dependence in
4434 count data from high-throughput nucleotide sequencing assays and test for
4435 differential expression based on a model using the negative binomial
4437 (license license:lgpl3+)))
4439 (define-public r-dexseq
4446 (uri (bioconductor-uri "DEXSeq" version))
4449 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
4450 (properties `((upstream-name . "DEXSeq")))
4451 (build-system r-build-system)
4453 (list r-annotationdbi
4469 r-summarizedexperiment))
4472 (home-page "https://bioconductor.org/packages/DEXSeq")
4473 (synopsis "Inference of differential exon usage in RNA-Seq")
4475 "This package is focused on finding differential exon usage using RNA-seq
4476 exon counts between samples with different experimental designs. It provides
4477 functions that allows the user to make the necessary statistical tests based
4478 on a model that uses the negative binomial distribution to estimate the
4479 variance between biological replicates and generalized linear models for
4480 testing. The package also provides functions for the visualization and
4481 exploration of the results.")
4482 (license license:gpl3+)))
4484 (define-public r-diffcyt
4491 (uri (bioconductor-uri "diffcyt" version))
4493 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
4494 (properties `((upstream-name . "diffcyt")))
4495 (build-system r-build-system)
4509 r-summarizedexperiment
4511 (native-inputs (list r-knitr))
4512 (home-page "https://github.com/lmweber/diffcyt")
4513 (synopsis "Differential discovery in high-dimensional cytometry")
4515 "This package provides statistical methods for differential discovery
4516 analyses in high-dimensional cytometry data (including flow cytometry, mass
4517 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
4518 combination of high-resolution clustering and empirical Bayes moderated tests
4519 adapted from transcriptomics.")
4520 (license license:expat)))
4522 (define-public r-dirichletmultinomial
4524 (name "r-dirichletmultinomial")
4529 (uri (bioconductor-uri "DirichletMultinomial" version))
4532 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
4534 `((upstream-name . "DirichletMultinomial")))
4535 (build-system r-build-system)
4539 (list r-biocgenerics r-iranges r-s4vectors))
4540 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
4541 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
4543 "Dirichlet-multinomial mixture models can be used to describe variability
4544 in microbial metagenomic data. This package is an interface to code
4545 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
4547 (license license:lgpl3)))
4549 (define-public r-dittoseq
4555 (uri (bioconductor-uri "dittoSeq" version))
4558 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
4559 (properties `((upstream-name . "dittoSeq")))
4560 (build-system r-build-system)
4571 r-singlecellexperiment
4572 r-summarizedexperiment))
4573 (native-inputs (list r-knitr))
4574 (home-page "https://bioconductor.org/packages/dittoSeq")
4575 (synopsis "Single-cell and bulk RNA sequencing visualization")
4577 "This package provides a universal, user friendly, single-cell and bulk RNA
4578 sequencing visualization toolkit that allows highly customizable creation of
4579 color blindness friendly, publication-quality figures. dittoSeq accepts both
4580 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
4581 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
4582 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
4583 percent composition or expression across groups, and more. Customizations
4584 range from size and title adjustments to automatic generation of annotations
4585 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
4586 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
4587 many more. All with simple, discrete inputs. Color blindness friendliness is
4588 powered by legend adjustments (enlarged keys), and by allowing the use of
4589 shapes or letter-overlay in addition to the carefully selected
4590 code{dittoColors()}.")
4591 (license license:expat)))
4593 (define-public r-edaseq
4600 (uri (bioconductor-uri "EDASeq" version))
4603 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
4604 (properties `((upstream-name . "EDASeq")))
4605 (build-system r-build-system)
4607 (list r-annotationdbi
4621 (home-page "https://github.com/drisso/EDASeq")
4622 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
4624 "This package provides support for numerical and graphical summaries of
4625 RNA-Seq genomic read data. Provided within-lane normalization procedures to
4626 adjust for GC-content effect (or other gene-level effects) on read counts:
4627 loess robust local regression, global-scaling, and full-quantile
4628 normalization. Between-lane normalization procedures to adjust for
4629 distributional differences between lanes (e.g., sequencing depth):
4630 global-scaling and full-quantile normalization.")
4631 (license license:artistic2.0)))
4633 (define-public r-edger
4639 (uri (bioconductor-uri "edgeR" version))
4642 "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
4643 (properties `((upstream-name . "edgeR")))
4644 (build-system r-build-system)
4646 (list r-limma r-locfit r-rcpp))
4647 (home-page "http://bioinf.wehi.edu.au/edgeR")
4648 (synopsis "EdgeR does empirical analysis of digital gene expression data")
4649 (description "This package can do differential expression analysis of
4650 RNA-seq expression profiles with biological replication. It implements a range
4651 of statistical methodology based on the negative binomial distributions,
4652 including empirical Bayes estimation, exact tests, generalized linear models
4653 and quasi-likelihood tests. It be applied to differential signal analysis of
4654 other types of genomic data that produce counts, including ChIP-seq, SAGE and
4656 (license license:gpl2+)))
4658 (define-public r-ensembldb
4660 (name "r-ensembldb")
4665 (uri (bioconductor-uri "ensembldb" version))
4668 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
4669 (build-system r-build-system)
4671 (list r-annotationdbi
4689 (home-page "https://github.com/jotsetung/ensembldb")
4690 (synopsis "Utilities to create and use Ensembl-based annotation databases")
4692 "The package provides functions to create and use transcript-centric
4693 annotation databases/packages. The annotation for the databases are directly
4694 fetched from Ensembl using their Perl API. The functionality and data is
4695 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
4696 but, in addition to retrieve all gene/transcript models and annotations from
4697 the database, the @code{ensembldb} package also provides a filter framework
4698 allowing to retrieve annotations for specific entries like genes encoded on a
4699 chromosome region or transcript models of lincRNA genes.")
4700 ;; No version specified
4701 (license license:lgpl3+)))
4703 (define-public r-fastseg
4710 (uri (bioconductor-uri "fastseg" version))
4713 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
4714 (build-system r-build-system)
4716 (list r-biobase r-biocgenerics r-genomicranges r-iranges
4718 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
4719 (synopsis "Fast segmentation algorithm for genetic sequencing data")
4721 "Fastseg implements a very fast and efficient segmentation algorithm.
4722 It can segment data from DNA microarrays and data from next generation
4723 sequencing for example to detect copy number segments. Further it can segment
4724 data from RNA microarrays like tiling arrays to identify transcripts. Most
4725 generally, it can segment data given as a matrix or as a vector. Various data
4726 formats can be used as input to fastseg like expression set objects for
4727 microarrays or GRanges for sequencing data.")
4728 (license license:lgpl2.0+)))
4730 (define-public r-gage
4737 (uri (bioconductor-uri "gage" version))
4740 "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"))))
4741 (build-system r-build-system)
4743 (list r-annotationdbi r-go-db r-graph r-keggrest))
4744 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
4745 "articles/10.1186/1471-2105-10-161"))
4746 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
4748 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
4749 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
4750 data attributes including sample sizes, experimental designs, assay platforms,
4751 and other types of heterogeneity. The gage package provides functions for
4752 basic GAGE analysis, result processing and presentation. In addition, it
4753 provides demo microarray data and commonly used gene set data based on KEGG
4754 pathways and GO terms. These functions and data are also useful for gene set
4755 analysis using other methods.")
4756 (license license:gpl2+)))
4758 (define-public r-genefilter
4760 (name "r-genefilter")
4765 (uri (bioconductor-uri "genefilter" version))
4768 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
4769 (build-system r-build-system)
4771 (list gfortran r-knitr))
4773 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
4775 (home-page "https://bioconductor.org/packages/genefilter")
4776 (synopsis "Filter genes from high-throughput experiments")
4778 "This package provides basic functions for filtering genes from
4779 high-throughput sequencing experiments.")
4780 (license license:artistic2.0)))
4782 (define-public r-geneoverlap
4784 (name "r-geneoverlap")
4788 (uri (bioconductor-uri "GeneOverlap" version))
4791 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
4792 (build-system r-build-system)
4794 (list r-rcolorbrewer r-gplots))
4795 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
4796 (synopsis "Test and visualize gene overlaps")
4797 (description "This package can be used to test two sets of gene lists
4798 and visualize the results.")
4799 (license license:gpl3)))
4801 (define-public r-genomation
4803 (name "r-genomation")
4807 (uri (bioconductor-uri "genomation" version))
4810 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
4811 (build-system r-build-system)
4835 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
4836 (synopsis "Summary, annotation and visualization of genomic data")
4838 "This package provides a package for summary and annotation of genomic
4839 intervals. Users can visualize and quantify genomic intervals over
4840 pre-defined functional regions, such as promoters, exons, introns, etc. The
4841 genomic intervals represent regions with a defined chromosome position, which
4842 may be associated with a score, such as aligned reads from HT-seq experiments,
4843 TF binding sites, methylation scores, etc. The package can use any tabular
4844 genomic feature data as long as it has minimal information on the locations of
4845 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4846 (license license:artistic2.0)))
4848 (define-public r-genomeinfodb
4850 (name "r-genomeinfodb")
4854 (uri (bioconductor-uri "GenomeInfoDb" version))
4857 "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"))))
4859 `((upstream-name . "GenomeInfoDb")))
4860 (build-system r-build-system)
4862 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
4866 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
4867 (synopsis "Utilities for manipulating chromosome identifiers")
4869 "This package contains data and functions that define and allow
4870 translation between different chromosome sequence naming conventions (e.g.,
4871 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4872 names in their natural, rather than lexicographic, order.")
4873 (license license:artistic2.0)))
4875 (define-public r-genomicalignments
4877 (name "r-genomicalignments")
4881 (uri (bioconductor-uri "GenomicAlignments" version))
4884 "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
4886 `((upstream-name . "GenomicAlignments")))
4887 (build-system r-build-system)
4889 (list r-biocgenerics
4897 r-summarizedexperiment))
4898 (home-page "https://bioconductor.org/packages/GenomicAlignments")
4899 (synopsis "Representation and manipulation of short genomic alignments")
4901 "This package provides efficient containers for storing and manipulating
4902 short genomic alignments (typically obtained by aligning short reads to a
4903 reference genome). This includes read counting, computing the coverage,
4904 junction detection, and working with the nucleotide content of the
4906 (license license:artistic2.0)))
4908 (define-public r-genomicfeatures
4910 (name "r-genomicfeatures")
4914 (uri (bioconductor-uri "GenomicFeatures" version))
4917 "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"))))
4919 `((upstream-name . "GenomicFeatures")))
4920 (build-system r-build-system)
4922 (list r-annotationdbi
4939 (home-page "https://bioconductor.org/packages/GenomicFeatures")
4940 (synopsis "Tools for working with transcript centric annotations")
4942 "This package provides a set of tools and methods for making and
4943 manipulating transcript centric annotations. With these tools the user can
4944 easily download the genomic locations of the transcripts, exons and cds of a
4945 given organism, from either the UCSC Genome Browser or a BioMart
4946 database (more sources will be supported in the future). This information is
4947 then stored in a local database that keeps track of the relationship between
4948 transcripts, exons, cds and genes. Flexible methods are provided for
4949 extracting the desired features in a convenient format.")
4950 (license license:artistic2.0)))
4952 (define-public r-genomicfiles
4954 (name "r-genomicfiles")
4959 (uri (bioconductor-uri "GenomicFiles" version))
4962 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
4963 (properties `((upstream-name . "GenomicFiles")))
4964 (build-system r-build-system)
4966 (list r-biocgenerics
4976 r-summarizedexperiment
4977 r-variantannotation))
4978 (home-page "https://bioconductor.org/packages/GenomicFiles")
4979 (synopsis "Distributed computing by file or by range")
4981 "This package provides infrastructure for parallel computations
4982 distributed by file or by range. User defined mapper and reducer functions
4983 provide added flexibility for data combination and manipulation.")
4984 (license license:artistic2.0)))
4986 (define-public r-genomicranges
4988 (name "r-genomicranges")
4992 (uri (bioconductor-uri "GenomicRanges" version))
4995 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
4997 `((upstream-name . "GenomicRanges")))
4998 (build-system r-build-system)
5000 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
5003 (home-page "https://bioconductor.org/packages/GenomicRanges")
5004 (synopsis "Representation and manipulation of genomic intervals")
5006 "This package provides tools to efficiently represent and manipulate
5007 genomic annotations and alignments is playing a central role when it comes to
5008 analyzing high-throughput sequencing data (a.k.a. NGS data). The
5009 GenomicRanges package defines general purpose containers for storing and
5010 manipulating genomic intervals and variables defined along a genome.")
5011 (license license:artistic2.0)))
5013 (define-public r-gostats
5020 (uri (bioconductor-uri "GOstats" version))
5023 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
5024 (properties `((upstream-name . "GOstats")))
5025 (build-system r-build-system)
5036 (home-page "https://bioconductor.org/packages/GOstats")
5037 (synopsis "Tools for manipulating GO and microarrays")
5039 "This package provides a set of tools for interacting with GO and
5040 microarray data. A variety of basic manipulation tools for graphs, hypothesis
5041 testing and other simple calculations.")
5042 (license license:artistic2.0)))
5044 (define-public r-gseabase
5051 (uri (bioconductor-uri "GSEABase" version))
5054 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
5055 (properties `((upstream-name . "GSEABase")))
5056 (build-system r-build-system)
5066 (home-page "https://bioconductor.org/packages/GSEABase")
5067 (synopsis "Gene set enrichment data structures and methods")
5069 "This package provides classes and methods to support @dfn{Gene Set
5070 Enrichment Analysis} (GSEA).")
5071 (license license:artistic2.0)))
5073 (define-public r-hpar
5080 (uri (bioconductor-uri "hpar" version))
5083 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
5084 (build-system r-build-system)
5087 (home-page "https://bioconductor.org/packages/hpar/")
5088 (synopsis "Human Protein Atlas in R")
5089 (description "This package provides a simple interface to and data from
5090 the Human Protein Atlas project.")
5091 (license license:artistic2.0)))
5093 (define-public r-rhtslib
5100 (uri (bioconductor-uri "Rhtslib" version))
5103 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
5104 (properties `((upstream-name . "Rhtslib")))
5105 (build-system r-build-system)
5106 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
5107 ;; which makes R abort the build.
5108 (arguments '(#:configure-flags '("--no-staged-install")))
5110 (list curl zlib ; packages using rhtslib need to link with zlib
5113 (list pkg-config r-knitr))
5114 (home-page "https://github.com/nhayden/Rhtslib")
5115 (synopsis "High-throughput sequencing library as an R package")
5117 "This package provides the HTSlib C library for high-throughput
5118 nucleotide sequence analysis. The package is primarily useful to developers
5119 of other R packages who wish to make use of HTSlib.")
5120 (license license:lgpl2.0+)))
5122 (define-public r-impute
5128 (uri (bioconductor-uri "impute" version))
5131 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
5134 (build-system r-build-system)
5135 (home-page "https://bioconductor.org/packages/impute")
5136 (synopsis "Imputation for microarray data")
5138 "This package provides a function to impute missing gene expression
5139 microarray data, using nearest neighbor averaging.")
5140 (license license:gpl2+)))
5142 (define-public r-interactivedisplaybase
5144 (name "r-interactivedisplaybase")
5149 (uri (bioconductor-uri "interactiveDisplayBase" version))
5152 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
5154 `((upstream-name . "interactiveDisplayBase")))
5155 (build-system r-build-system)
5157 (list r-biocgenerics r-dt r-shiny))
5160 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
5161 (synopsis "Base package for web displays of Bioconductor objects")
5163 "This package contains the basic methods needed to generate interactive
5164 Shiny-based display methods for Bioconductor objects.")
5165 (license license:artistic2.0)))
5167 (define-public r-keggrest
5174 (uri (bioconductor-uri "KEGGREST" version))
5177 "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
5178 (properties `((upstream-name . "KEGGREST")))
5179 (build-system r-build-system)
5181 (list r-biostrings r-httr r-png))
5184 (home-page "https://bioconductor.org/packages/KEGGREST")
5185 (synopsis "Client-side REST access to KEGG")
5187 "This package provides a package that provides a client interface to the
5188 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
5189 (license license:artistic2.0)))
5191 (define-public r-lfa
5198 (uri (bioconductor-uri "lfa" version))
5200 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
5201 (properties `((upstream-name . "lfa")))
5202 (build-system r-build-system)
5203 (propagated-inputs (list r-corpcor))
5204 (native-inputs (list r-knitr))
5205 (home-page "https://github.com/StoreyLab/lfa")
5206 (synopsis "Logistic Factor Analysis for categorical data")
5208 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
5209 Binomial data via estimation of latent structure in the natural parameter.")
5210 (license license:gpl3)))
5212 (define-public r-limma
5218 (uri (bioconductor-uri "limma" version))
5221 "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"))))
5222 (build-system r-build-system)
5223 (home-page "http://bioinf.wehi.edu.au/limma")
5224 (synopsis "Package for linear models for microarray and RNA-seq data")
5225 (description "This package can be used for the analysis of gene expression
5226 studies, especially the use of linear models for analysing designed experiments
5227 and the assessment of differential expression. The analysis methods apply to
5228 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
5229 (license license:gpl2+)))
5231 (define-public r-made4
5237 (uri (bioconductor-uri "made4" version))
5240 "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
5241 (properties `((upstream-name . "made4")))
5242 (build-system r-build-system)
5249 r-summarizedexperiment))
5250 (native-inputs (list r-knitr))
5251 (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
5252 (synopsis "Multivariate analysis of microarray data using ADE4")
5254 "This is a package for multivariate data analysis and graphical display
5255 of microarray data. Functions are included for supervised dimension
5256 reduction (between group analysis) and joint dimension reduction of two
5257 datasets (coinertia analysis).")
5258 (license license:artistic2.0)))
5260 (define-public r-methylkit
5262 (name "r-methylkit")
5266 (uri (bioconductor-uri "methylKit" version))
5269 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
5270 (properties `((upstream-name . "methylKit")))
5271 (build-system r-build-system)
5293 (list r-knitr)) ; for vignettes
5294 (home-page "https://github.com/al2na/methylKit")
5296 "DNA methylation analysis from high-throughput bisulfite sequencing results")
5298 "MethylKit is an R package for DNA methylation analysis and annotation
5299 from high-throughput bisulfite sequencing. The package is designed to deal
5300 with sequencing data from @dfn{Reduced representation bisulfite
5301 sequencing} (RRBS) and its variants, but also target-capture methods and whole
5302 genome bisulfite sequencing. It also has functions to analyze base-pair
5303 resolution 5hmC data from experimental protocols such as oxBS-Seq and
5305 (license license:artistic2.0)))
5307 (define-public r-motifrg
5314 (uri (bioconductor-uri "motifRG" version))
5317 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
5318 (properties `((upstream-name . "motifRG")))
5319 (build-system r-build-system)
5323 r-bsgenome-hsapiens-ucsc-hg19
5327 (home-page "https://bioconductor.org/packages/motifRG")
5328 (synopsis "Discover motifs in high throughput sequencing data")
5330 "This package provides tools for discriminative motif discovery in high
5331 throughput genetic sequencing data sets using regression methods.")
5332 (license license:artistic2.0)))
5334 (define-public r-muscat
5341 (uri (bioconductor-uri "muscat" version))
5344 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
5345 (properties `((upstream-name . "muscat")))
5346 (build-system r-build-system)
5348 (list r-biocparallel
5369 r-singlecellexperiment
5370 r-summarizedexperiment
5373 (native-inputs (list r-knitr))
5374 (home-page "https://github.com/HelenaLC/muscat")
5375 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
5377 "This package @code{muscat} provides various methods and visualization tools
5378 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
5379 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
5380 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
5381 platform that mimics both single and multi-sample scRNA-seq data.")
5382 (license license:gpl3)))
5384 (define-public r-mutationalpatterns
5386 (name "r-mutationalpatterns")
5391 (uri (bioconductor-uri "MutationalPatterns" version))
5394 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
5395 (build-system r-build-system)
5399 (list r-biocgenerics
5402 ;; These two packages are suggested packages
5403 r-bsgenome-hsapiens-1000genomes-hs37d5
5404 r-bsgenome-hsapiens-ucsc-hg19
5422 r-variantannotation))
5423 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
5424 (synopsis "Extract and visualize mutational patterns in genomic data")
5425 (description "This package provides an extensive toolset for the
5426 characterization and visualization of a wide range of mutational patterns
5427 in SNV base substitution data.")
5428 (license license:expat)))
5430 (define-public r-msnbase
5437 (uri (bioconductor-uri "MSnbase" version))
5440 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
5441 (properties `((upstream-name . "MSnbase")))
5442 (build-system r-build-system)
5468 (home-page "https://github.com/lgatto/MSnbase")
5469 (synopsis "Base functions and classes for MS-based proteomics")
5471 "This package provides basic plotting, data manipulation and processing
5472 of mass spectrometry based proteomics data.")
5473 (license license:artistic2.0)))
5475 (define-public r-msnid
5482 (uri (bioconductor-uri "MSnID" version))
5485 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
5486 (properties `((upstream-name . "MSnID")))
5487 (build-system r-build-system)
5490 (modify-phases %standard-phases
5491 (add-after 'unpack 'set-HOME
5492 (lambda _ (setenv "HOME" "/tmp"))))))
5494 (list r-annotationdbi
5520 (home-page "https://bioconductor.org/packages/MSnID")
5521 (synopsis "Utilities for LC-MSn proteomics identifications")
5523 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
5524 from mzIdentML (leveraging the mzID package) or text files. After collating
5525 the search results from multiple datasets it assesses their identification
5526 quality and optimize filtering criteria to achieve the maximum number of
5527 identifications while not exceeding a specified false discovery rate. It also
5528 contains a number of utilities to explore the MS/MS results and assess missed
5529 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
5530 (license license:artistic2.0)))
5532 (define-public r-mzid
5539 (uri (bioconductor-uri "mzID" version))
5542 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
5543 (properties `((upstream-name . "mzID")))
5544 (build-system r-build-system)
5554 (home-page "https://bioconductor.org/packages/mzID")
5555 (synopsis "Parser for mzIdentML files")
5557 "This package provides a parser for mzIdentML files implemented using the
5558 XML package. The parser tries to be general and able to handle all types of
5559 mzIdentML files with the drawback of having less pretty output than a vendor
5561 (license license:gpl2+)))
5563 (define-public r-mzr
5570 (uri (bioconductor-uri "mzR" version))
5573 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
5574 (modules '((guix build utils)))
5576 '(delete-file-recursively "src/boost"))))
5577 (properties `((upstream-name . "mzR")))
5578 (build-system r-build-system)
5581 (modify-phases %standard-phases
5582 (add-after 'unpack 'use-system-boost
5584 (substitute* "src/Makevars"
5585 (("\\./boost/libs.*") "")
5586 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
5587 (("\\ARCH_OBJS=" line)
5589 "\nBOOST_LIBS=-lboost_system -lboost_regex \
5590 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
5592 (list boost ; use this instead of the bundled boost sources
5603 (home-page "https://github.com/sneumann/mzR/")
5604 (synopsis "Parser for mass spectrometry data files")
5606 "The mzR package provides a unified API to the common file formats and
5607 parsers available for mass spectrometry data. It comes with a wrapper for the
5608 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
5609 The package contains the original code written by the ISB, and a subset of the
5610 proteowizard library for mzML and mzIdentML. The netCDF reading code has
5611 previously been used in XCMS.")
5612 (license license:artistic2.0)))
5614 (define-public r-organism-dplyr
5616 (name "r-organism-dplyr")
5621 (uri (bioconductor-uri "Organism.dplyr" version))
5624 "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
5625 (properties `((upstream-name . "Organism.dplyr")))
5626 (build-system r-build-system)
5628 (list r-annotationdbi
5642 (native-inputs (list r-knitr))
5643 (home-page "https://bioconductor.org/packages/Organism.dplyr")
5644 (synopsis "Dplyr-based access to Bioconductor annotation resources")
5646 "This package provides an alternative interface to Bioconductor @code{
5647 annotation} resources, in particular the gene identifier mapping functionality
5648 of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
5649 functionality of the @code{TxDb} packages (e.g.,
5650 @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
5651 (license license:artistic2.0)))
5653 (define-public r-organismdbi
5655 (name "r-organismdbi")
5660 (uri (bioconductor-uri "OrganismDbi" version))
5663 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
5664 (properties `((upstream-name . "OrganismDbi")))
5665 (build-system r-build-system)
5667 (list r-annotationdbi
5678 (home-page "https://bioconductor.org/packages/OrganismDbi")
5679 (synopsis "Software to enable the smooth interfacing of database packages")
5680 (description "The package enables a simple unified interface to several
5681 annotation packages each of which has its own schema by taking advantage of
5682 the fact that each of these packages implements a select methods.")
5683 (license license:artistic2.0)))
5685 (define-public r-pcaexplorer
5687 (name "r-pcaexplorer")
5692 (uri (bioconductor-uri "pcaExplorer" version))
5695 "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
5696 (properties `((upstream-name . "pcaExplorer")))
5697 (build-system r-build-system)
5699 (list r-annotationdbi
5725 r-summarizedexperiment
5729 (native-inputs (list r-knitr))
5730 (home-page "https://github.com/federicomarini/pcaExplorer")
5732 "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
5734 "This package provides functionality for interactive visualization of RNA-seq
5735 datasets based on Principal Components Analysis. The methods provided allow for
5736 quick information extraction and effective data exploration. A Shiny
5737 application encapsulates the whole analysis.")
5738 (license license:expat)))
5740 (define-public r-pcamethods
5742 (name "r-pcamethods")
5747 (uri (bioconductor-uri "pcaMethods" version))
5750 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
5751 (properties `((upstream-name . "pcaMethods")))
5752 (build-system r-build-system)
5754 (list r-biobase r-biocgenerics r-mass r-rcpp))
5755 (home-page "https://github.com/hredestig/pcamethods")
5756 (synopsis "Collection of PCA methods")
5758 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
5759 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
5760 for missing value estimation is included for comparison. BPCA, PPCA and
5761 NipalsPCA may be used to perform PCA on incomplete data as well as for
5762 accurate missing value estimation. A set of methods for printing and plotting
5763 the results is also provided. All PCA methods make use of the same data
5764 structure (pcaRes) to provide a common interface to the PCA results.")
5765 (license license:gpl3+)))
5767 ;; This is a CRAN package, but it depends on a Bioconductor package:
5768 ;; r-aroma-light, r-dnacopy..
5769 (define-public r-pscbs
5776 (uri (cran-uri "PSCBS" version))
5778 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
5779 (properties `((upstream-name . "PSCBS")))
5780 (build-system r-build-system)
5783 (modify-phases %standard-phases
5784 (add-before 'install 'change-home-dir
5786 ;; Change from /homeless-shelter to /tmp for write permission.
5787 (setenv "HOME" "/tmp"))))))
5799 (list r-r-rsp ;used to build vignettes
5801 (home-page "https://github.com/HenrikBengtsson/PSCBS")
5802 (synopsis "Analysis of parent-specific DNA copy numbers")
5804 "This is a package for segmentation of allele-specific DNA copy number
5805 data and detection of regions with abnormal copy number within each parental
5806 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
5807 (license license:gpl2+)))
5809 (define-public r-protgenerics
5811 (name "r-protgenerics")
5816 (uri (bioconductor-uri "ProtGenerics" version))
5819 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
5820 (properties `((upstream-name . "ProtGenerics")))
5821 (build-system r-build-system)
5822 (home-page "https://github.com/lgatto/ProtGenerics")
5823 (synopsis "S4 generic functions for proteomics infrastructure")
5825 "This package provides S4 generic functions needed by Bioconductor
5826 proteomics packages.")
5827 (license license:artistic2.0)))
5829 (define-public r-rbgl
5836 (uri (bioconductor-uri "RBGL" version))
5839 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
5840 (properties `((upstream-name . "RBGL")))
5841 (build-system r-build-system)
5843 (list r-bh r-graph))
5844 (home-page "https://www.bioconductor.org/packages/RBGL")
5845 (synopsis "Interface to the Boost graph library")
5847 "This package provides a fairly extensive and comprehensive interface to
5848 the graph algorithms contained in the Boost library.")
5849 (license license:artistic2.0)))
5851 (define-public r-rcas
5857 (uri (bioconductor-uri "RCAS" version))
5860 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
5861 (properties `((upstream-name . "RCAS")))
5862 (build-system r-build-system)
5864 (list r-biocgenerics
5867 r-bsgenome-hsapiens-ucsc-hg19
5893 (synopsis "RNA-centric annotation system")
5895 "RCAS aims to be a standalone RNA-centric annotation system that provides
5896 intuitive reports and publication-ready graphics. This package provides the R
5897 library implementing most of the pipeline's features.")
5898 (home-page "https://github.com/BIMSBbioinfo/RCAS")
5899 (license license:artistic2.0)))
5901 (define-public r-regioner
5908 (uri (bioconductor-uri "regioneR" version))
5911 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
5912 (properties `((upstream-name . "regioneR")))
5913 (build-system r-build-system)
5925 (home-page "https://bioconductor.org/packages/regioneR/")
5926 (synopsis "Association analysis of genomic regions")
5927 (description "This package offers a statistical framework based on
5928 customizable permutation tests to assess the association between genomic
5929 region sets and other genomic features.")
5930 (license license:artistic2.0)))
5932 (define-public r-reportingtools
5934 (name "r-reportingtools")
5939 (uri (bioconductor-uri "ReportingTools" version))
5942 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
5944 `((upstream-name . "ReportingTools")))
5945 (build-system r-build-system)
5968 (home-page "https://bioconductor.org/packages/ReportingTools/")
5969 (synopsis "Tools for making reports in various formats")
5971 "The ReportingTools package enables users to easily display reports of
5972 analysis results generated from sources such as microarray and sequencing
5973 data. The package allows users to create HTML pages that may be viewed on a
5974 web browser, or in other formats. Users can generate tables with sortable and
5975 filterable columns, make and display plots, and link table entries to other
5976 data sources such as NCBI or larger plots within the HTML page. Using the
5977 package, users can also produce a table of contents page to link various
5978 reports together for a particular project that can be viewed in a web
5980 (license license:artistic2.0)))
5982 (define-public r-rhdf5
5988 (uri (bioconductor-uri "rhdf5" version))
5991 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
5992 (build-system r-build-system)
5994 (list r-rhdf5filters r-rhdf5lib))
5997 (home-page "https://bioconductor.org/packages/rhdf5")
5998 (synopsis "HDF5 interface to R")
6000 "This R/Bioconductor package provides an interface between HDF5 and R.
6001 HDF5's main features are the ability to store and access very large and/or
6002 complex datasets and a wide variety of metadata on mass storage (disk) through
6003 a completely portable file format. The rhdf5 package is thus suited for the
6004 exchange of large and/or complex datasets between R and other software
6005 package, and for letting R applications work on datasets that are larger than
6006 the available RAM.")
6007 (license license:artistic2.0)))
6009 (define-public r-rhdf5filters
6011 (name "r-rhdf5filters")
6016 (uri (bioconductor-uri "rhdf5filters" version))
6019 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
6020 (properties `((upstream-name . "rhdf5filters")))
6021 (build-system r-build-system)
6028 (home-page "https://github.com/grimbough/rhdf5filters")
6029 (synopsis "HDF5 compression filters")
6031 "This package provides a collection of compression filters for use with
6033 (license license:bsd-2)))
6035 (define-public r-rsamtools
6037 (name "r-rsamtools")
6041 (uri (bioconductor-uri "Rsamtools" version))
6044 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
6046 `((upstream-name . "Rsamtools")))
6047 (build-system r-build-system)
6050 (modify-phases %standard-phases
6051 (add-after 'unpack 'use-system-zlib
6053 (substitute* "DESCRIPTION"
6054 (("zlibbioc, ") ""))
6055 (substitute* "NAMESPACE"
6056 (("import\\(zlibbioc\\)") "")))))))
6058 (list r-biocgenerics
6068 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
6069 (synopsis "Interface to samtools, bcftools, and tabix")
6071 "This package provides an interface to the @code{samtools},
6072 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
6073 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
6074 tab-delimited (tabix) files.")
6075 (license license:expat)))
6077 ;; This is a CRAN package, but it depends on a Bioconductor package:
6079 (define-public r-restfulr
6086 (uri (cran-uri "restfulr" version))
6089 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
6090 (properties `((upstream-name . "restfulr")))
6091 (build-system r-build-system)
6093 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
6094 (home-page "https://cran.r-project.org/package=restfulr")
6095 (synopsis "R interface to RESTful web services")
6097 "This package models a RESTful service as if it were a nested R list.")
6098 (license license:artistic2.0)))
6100 (define-public r-rtracklayer
6102 (name "r-rtracklayer")
6106 (uri (bioconductor-uri "rtracklayer" version))
6109 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
6110 (build-system r-build-system)
6113 (modify-phases %standard-phases
6114 (add-after 'unpack 'use-system-zlib
6116 (substitute* "DESCRIPTION"
6117 ((" zlibbioc,") ""))
6118 (substitute* "NAMESPACE"
6119 (("import\\(zlibbioc\\)") "")))))))
6125 (list r-biocgenerics
6139 (home-page "https://bioconductor.org/packages/rtracklayer")
6140 (synopsis "R interface to genome browsers and their annotation tracks")
6142 "rtracklayer is an extensible framework for interacting with multiple
6143 genome browsers (currently UCSC built-in) and manipulating annotation tracks
6144 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
6145 built-in). The user may export/import tracks to/from the supported browsers,
6146 as well as query and modify the browser state, such as the current viewport.")
6147 (license license:artistic2.0)))
6149 ;; This is a CRAN package, but it depends on a Bioconductor package.
6150 (define-public r-samr
6157 (uri (cran-uri "samr" version))
6160 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
6161 (properties `((upstream-name . "samr")))
6162 (build-system r-build-system)
6170 (native-inputs (list gfortran))
6171 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
6172 (synopsis "Significance analysis of Microarrays")
6174 "This is a package for significance analysis of Microarrays for
6175 differential expression analysis, RNAseq data and related problems.")
6176 ;; Any version of the LGPL
6177 (license license:lgpl3+)))
6179 (define-public r-scannotatr
6181 (name "r-scannotatr")
6186 (uri (bioconductor-uri "scAnnotatR" version))
6188 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
6189 (properties `((upstream-name . "scAnnotatR")))
6190 (build-system r-build-system)
6192 (list r-annotationhub
6203 r-singlecellexperiment
6204 r-summarizedexperiment))
6205 (native-inputs (list r-knitr))
6206 (home-page "https://github.com/grisslab/scAnnotatR")
6207 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
6209 "This package comprises a set of pretrained machine learning models to
6210 predict basic immune cell types. This enables to quickly get a first
6211 annotation of the cell types present in the dataset without requiring prior
6212 knowledge. The package also lets you train using own models to predict new
6213 cell types based on specific research needs.")
6214 (license license:expat)))
6216 (define-public r-scdblfinder
6218 (name "r-scdblfinder")
6223 (uri (bioconductor-uri "scDblFinder" version))
6225 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
6226 (properties `((upstream-name . "scDblFinder")))
6227 (build-system r-build-system)
6229 (list r-biocgenerics
6247 r-singlecellexperiment
6248 r-summarizedexperiment
6250 (native-inputs (list r-knitr))
6251 (home-page "https://github.com/plger/scDblFinder")
6252 (synopsis "Detect multiplets in single-cell RNA sequencing data")
6254 "The scDblFinder package gathers various methods for the detection and
6255 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
6256 multiple cells captured within the same droplet or reaction volume). It
6257 includes methods formerly found in the scran package, and the new fast and
6258 comprehensive scDblFinder method.")
6259 (license license:gpl3)))
6261 (define-public r-scmap
6268 (uri (bioconductor-uri "scmap" version))
6270 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
6271 (properties `((upstream-name . "scmap")))
6272 (build-system r-build-system)
6287 r-singlecellexperiment
6288 r-summarizedexperiment))
6289 (native-inputs (list r-knitr))
6290 (home-page "https://github.com/hemberg-lab/scmap")
6291 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
6293 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
6294 composition of complex tissues since the technology allows researchers to
6295 define cell-types using unsupervised clustering of the transcriptome.
6296 However, due to differences in experimental methods and computational
6297 analyses, it is often challenging to directly compare the cells identified in
6298 two different experiments. @code{scmap} is a method for projecting cells from
6299 a scRNA-seq experiment onto the cell-types or individual cells identified in a
6300 different experiment.")
6301 (license license:gpl3)))
6303 (define-public r-scry
6309 (uri (bioconductor-uri "scry" version))
6312 "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
6313 (properties `((upstream-name . "scry")))
6314 (build-system r-build-system)
6316 (list r-biocsingular
6321 r-singlecellexperiment
6322 r-summarizedexperiment))
6323 (native-inputs (list r-knitr))
6324 (home-page "https://bioconductor.org/packages/scry.html")
6325 (synopsis "Small-count analysis methods for high-dimensional data")
6327 "Many modern biological datasets consist of small counts that are not
6328 well fit by standard linear-Gaussian methods such as principal component
6329 analysis. This package provides implementations of count-based feature
6330 selection and dimension reduction algorithms. These methods can be used to
6331 facilitate unsupervised analysis of any high-dimensional data such as
6332 single-cell RNA-seq.")
6333 (license license:artistic2.0)))
6335 (define-public r-seqlogo
6342 (uri (bioconductor-uri "seqLogo" version))
6345 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
6346 (properties `((upstream-name . "seqLogo")))
6347 (build-system r-build-system)
6350 (home-page "https://bioconductor.org/packages/seqLogo")
6351 (synopsis "Sequence logos for DNA sequence alignments")
6353 "seqLogo takes the position weight matrix of a DNA sequence motif and
6354 plots the corresponding sequence logo as introduced by Schneider and
6356 (license license:lgpl2.0+)))
6358 (define-public r-seqpattern
6360 (name "r-seqpattern")
6364 (uri (bioconductor-uri "seqPattern" version))
6367 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
6369 `((upstream-name . "seqPattern")))
6370 (build-system r-build-system)
6372 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
6373 (home-page "https://bioconductor.org/packages/seqPattern")
6374 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
6376 "This package provides tools to visualize oligonucleotide patterns and
6377 sequence motif occurrences across a large set of sequences centred at a common
6378 reference point and sorted by a user defined feature.")
6379 (license license:gpl3+)))
6381 (define-public r-shortread
6383 (name "r-shortread")
6388 (uri (bioconductor-uri "ShortRead" version))
6391 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
6392 (properties `((upstream-name . "ShortRead")))
6393 (build-system r-build-system)
6413 (home-page "https://bioconductor.org/packages/ShortRead")
6414 (synopsis "FASTQ input and manipulation tools")
6416 "This package implements sampling, iteration, and input of FASTQ files.
6417 It includes functions for filtering and trimming reads, and for generating a
6418 quality assessment report. Data are represented as
6419 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6420 purposes. The package also contains legacy support for early single-end,
6421 ungapped alignment formats.")
6422 (license license:artistic2.0)))
6424 (define-public r-simplifyenrichment
6426 (name "r-simplifyenrichment")
6431 (uri (bioconductor-uri "simplifyEnrichment" version))
6434 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
6436 `((upstream-name . "simplifyEnrichment")))
6437 (build-system r-build-system)
6439 (list r-annotationdbi
6456 (native-inputs (list r-knitr))
6457 (home-page "https://github.com/jokergoo/simplifyEnrichment")
6458 (synopsis "Simplify functional enrichment results")
6459 (description "This package provides a new clustering algorithm, binary
6460 cut, for clustering similarity matrices of functional terms is implemented in
6461 this package. It also provides functionalities for visualizing, summarizing
6462 and comparing the clusterings.")
6463 (license license:expat)))
6465 (define-public r-transcriptr
6467 (name "r-transcriptr")
6472 (uri (bioconductor-uri "transcriptR" version))
6474 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
6475 (properties `((upstream-name . "transcriptR")))
6476 (build-system r-build-system)
6478 (list r-biocgenerics
6493 (native-inputs (list r-knitr))
6494 (home-page "https://bioconductor.org/packages/transcriptR")
6495 (synopsis "Primary transcripts detection and quantification")
6497 "The differences in the RNA types being sequenced have an impact on the
6498 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
6499 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
6500 broader coverage of both exonic and intronic regions. The presence of
6501 intronic reads in GRO-seq type of data makes it possible to use it to
6502 computationally identify and quantify all de novo continuous regions of
6503 transcription distributed across the genome. This type of data, however, is
6504 more challenging to interpret and less common practice compared to mRNA-seq.
6505 One of the challenges for primary transcript detection concerns the
6506 simultaneous transcription of closely spaced genes, which needs to be properly
6507 divided into individually transcribed units. The R package transcriptR
6508 combines RNA-seq data with ChIP-seq data of histone modifications that mark
6509 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
6510 overcome this challenge. The advantage of this approach over the use of, for
6511 example, gene annotations is that this approach is data driven and therefore
6512 able to deal also with novel and case specific events.")
6513 (license license:gpl3)))
6515 (define-public r-trajectoryutils
6517 (name "r-trajectoryutils")
6522 (uri (bioconductor-uri "TrajectoryUtils" version))
6525 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
6527 `((upstream-name . "TrajectoryUtils")))
6528 (build-system r-build-system)
6530 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
6531 r-summarizedexperiment))
6532 (native-inputs (list r-knitr))
6533 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
6534 (synopsis "Single-cell trajectory analysis utilities")
6536 "This package implements low-level utilities for single-cell trajectory
6537 analysis, primarily intended for re-use inside higher-level packages. It
6538 includes a function to create a cluster-level minimum spanning tree and data
6539 structures to hold pseudotime inference results.")
6540 (license license:gpl3)))
6542 (define-public r-slingshot
6544 (name "r-slingshot")
6548 (uri (bioconductor-uri "slingshot" version))
6551 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
6552 (build-system r-build-system)
6558 r-singlecellexperiment
6559 r-summarizedexperiment
6563 (home-page "https://bioconductor.org/packages/slingshot")
6564 (synopsis "Tools for ordering single-cell sequencing")
6565 (description "This package provides functions for inferring continuous,
6566 branching lineage structures in low-dimensional data. Slingshot was designed
6567 to model developmental trajectories in single-cell RNA sequencing data and
6568 serve as a component in an analysis pipeline after dimensionality reduction
6569 and clustering. It is flexible enough to handle arbitrarily many branching
6570 events and allows for the incorporation of prior knowledge through supervised
6571 graph construction.")
6572 (license license:artistic2.0)))
6574 (define-public r-stager
6581 (uri (bioconductor-uri "stageR" version))
6583 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
6584 (properties `((upstream-name . "stageR")))
6585 (build-system r-build-system)
6586 (propagated-inputs (list r-summarizedexperiment))
6587 (native-inputs (list r-knitr))
6588 (home-page "https://bioconductor.org/packages/stageR")
6589 (synopsis "Stage-wise analysis of high throughput gene expression data")
6591 "The stageR package allows automated stage-wise analysis of
6592 high-throughput gene expression data. The method is published in Genome
6594 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
6595 (license license:gpl3)))
6597 (define-public r-stringdb
6604 (uri (bioconductor-uri "STRINGdb" version))
6606 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
6607 (properties `((upstream-name . "STRINGdb")))
6608 (build-system r-build-system)
6619 (home-page "https://git.bioconductor.org/packages/STRINGdb")
6620 (synopsis "Search tool for the retrieval of interacting proteins database")
6622 "The @code{STRINGdb} package provides an R interface to the STRING
6623 protein-protein interactions database. @url{https://www.string-db.org,
6624 STRING} is a database of known and predicted protein-protein interactions.
6625 The interactions include direct (physical) and indirect (functional)
6626 associations. Each interaction is associated with a combined confidence score
6627 that integrates the various evidences.")
6628 (license license:gpl2)))
6630 (define-public r-structuralvariantannotation
6632 (name "r-structuralvariantannotation")
6637 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
6639 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
6640 (build-system r-build-system)
6654 r-summarizedexperiment
6655 r-variantannotation))
6658 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
6659 (synopsis "R package designed to simplify structural variant analysis")
6661 "This package contains useful helper functions for dealing with structural
6662 variants in VCF format. The packages contains functions for parsing VCFs from
6663 a number of popular callers as well as functions for dealing with breakpoints
6664 involving two separate genomic loci encoded as GRanges objects.")
6665 (license license:gpl3)))
6667 (define-public r-summarizedexperiment
6669 (name "r-summarizedexperiment")
6673 (uri (bioconductor-uri "SummarizedExperiment" version))
6676 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
6678 `((upstream-name . "SummarizedExperiment")))
6679 (build-system r-build-system)
6692 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
6693 (synopsis "Container for representing genomic ranges by sample")
6695 "The SummarizedExperiment container contains one or more assays, each
6696 represented by a matrix-like object of numeric or other mode. The rows
6697 typically represent genomic ranges of interest and the columns represent
6699 (license license:artistic2.0)))
6701 (define-public r-sva
6708 (uri (bioconductor-uri "sva" version))
6711 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
6712 (build-system r-build-system)
6720 (home-page "https://bioconductor.org/packages/sva")
6721 (synopsis "Surrogate variable analysis")
6723 "This package contains functions for removing batch effects and other
6724 unwanted variation in high-throughput experiment. It also contains functions
6725 for identifying and building surrogate variables for high-dimensional data
6726 sets. Surrogate variables are covariates constructed directly from
6727 high-dimensional data like gene expression/RNA sequencing/methylation/brain
6728 imaging data that can be used in subsequent analyses to adjust for unknown,
6729 unmodeled, or latent sources of noise.")
6730 (license license:artistic2.0)))
6732 (define-public r-systempiper
6734 (name "r-systempiper")
6739 (uri (bioconductor-uri "systemPipeR" version))
6742 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
6743 (properties `((upstream-name . "systemPipeR")))
6744 (build-system r-build-system)
6746 (list r-biocgenerics
6757 r-summarizedexperiment
6761 (home-page "https://github.com/tgirke/systemPipeR")
6762 (synopsis "Next generation sequencing workflow and reporting environment")
6764 "This R package provides tools for building and running automated
6765 end-to-end analysis workflows for a wide range of @dfn{next generation
6766 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6767 Important features include a uniform workflow interface across different NGS
6768 applications, automated report generation, and support for running both R and
6769 command-line software, such as NGS aligners or peak/variant callers, on local
6770 computers or compute clusters. Efficient handling of complex sample sets and
6771 experimental designs is facilitated by a consistently implemented sample
6772 annotation infrastructure.")
6773 (license license:artistic2.0)))
6775 (define-public r-topgo
6781 (uri (bioconductor-uri "topGO" version))
6784 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
6786 `((upstream-name . "topGO")))
6787 (build-system r-build-system)
6789 (list r-annotationdbi
6798 (home-page "https://bioconductor.org/packages/topGO")
6799 (synopsis "Enrichment analysis for gene ontology")
6801 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6802 terms while accounting for the topology of the GO graph. Different test
6803 statistics and different methods for eliminating local similarities and
6804 dependencies between GO terms can be implemented and applied.")
6805 ;; Any version of the LGPL applies.
6806 (license license:lgpl2.1+)))
6808 (define-public r-tximport
6814 (uri (bioconductor-uri "tximport" version))
6817 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
6818 (build-system r-build-system)
6821 (home-page "https://bioconductor.org/packages/tximport")
6822 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
6824 "This package provides tools to import transcript-level abundance,
6825 estimated counts and transcript lengths, and to summarize them into matrices
6826 for use with downstream gene-level analysis packages. Average transcript
6827 length, weighted by sample-specific transcript abundance estimates, is
6828 provided as a matrix which can be used as an offset for different expression
6829 of gene-level counts.")
6830 (license license:gpl2+)))
6832 ;; This is a CRAN package, but it depends on a Bioconductor package.
6833 (define-public r-valr
6840 (uri (cran-uri "valr" version))
6843 "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
6844 (build-system r-build-system)
6852 r-rtracklayer ;bioconductor package
6857 (home-page "https://github.com/rnabioco/valr")
6858 (synopsis "Genome interval arithmetic in R")
6860 "This package enables you to read and manipulate genome intervals and
6861 signals. It provides functionality similar to command-line tool suites within
6862 R, enabling interactive analysis and visualization of genome-scale data.")
6863 (license license:expat)))
6865 (define-public r-variantannotation
6867 (name "r-variantannotation")
6871 (uri (bioconductor-uri "VariantAnnotation" version))
6874 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
6876 `((upstream-name . "VariantAnnotation")))
6878 (list r-annotationdbi
6889 r-summarizedexperiment
6896 (build-system r-build-system)
6897 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6898 (synopsis "Package for annotation of genetic variants")
6899 (description "This R package can annotate variants, compute amino acid
6900 coding changes and predict coding outcomes.")
6901 (license license:artistic2.0)))
6903 (define-public r-vsn
6910 (uri (bioconductor-uri "vsn" version))
6913 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
6914 (build-system r-build-system)
6916 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
6918 (list r-knitr)) ; for vignettes
6919 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
6920 (synopsis "Variance stabilization and calibration for microarray data")
6922 "The package implements a method for normalising microarray intensities,
6923 and works for single- and multiple-color arrays. It can also be used for data
6924 from other technologies, as long as they have similar format. The method uses
6925 a robust variant of the maximum-likelihood estimator for an
6926 additive-multiplicative error model and affine calibration. The model
6927 incorporates data calibration step (a.k.a. normalization), a model for the
6928 dependence of the variance on the mean intensity and a variance stabilizing
6929 data transformation. Differences between transformed intensities are
6930 analogous to \"normalized log-ratios\". However, in contrast to the latter,
6931 their variance is independent of the mean, and they are usually more sensitive
6932 and specific in detecting differential transcription.")
6933 (license license:artistic2.0)))
6935 ;; There is no source tarball, so we fetch the code from the Bioconductor git
6937 (define-public r-xcir
6938 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
6942 (version (git-version "1.8.0" revision commit))
6946 (url "https://git.bioconductor.org/packages/XCIR")
6948 (file-name (git-file-name name version))
6951 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
6952 (properties `((upstream-name . "XCIR")))
6953 (build-system r-build-system)
6954 (propagated-inputs (list r-biomart
6962 r-variantannotation))
6963 (native-inputs (list r-knitr))
6964 (home-page "https://github.com/SRenan/XCIR")
6965 (synopsis "Analysis of X chromosome inactivation")
6967 "This package is an R package that offers models and tools for subject
6968 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
6970 (license license:gpl2))))
6972 (define-public r-xina
6979 (uri (bioconductor-uri "XINA" version))
6981 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
6982 (properties `((upstream-name . "XINA")))
6983 (build-system r-build-system)
6992 (native-inputs (list r-knitr))
6993 (home-page "https://git.bioconductor.org/packages/XINA")
6994 (synopsis "Identifying proteins that exhibit similar patterns")
6996 "The aim of @code{XINA} is to determine which proteins exhibit similar
6997 patterns within and across experimental conditions, since proteins with
6998 co-abundance patterns may have common molecular functions. @code{XINA} imports
6999 multiple datasets, tags dataset in silico, and combines the data for subsequent
7000 subgrouping into multiple clusters. The result is a single output depicting
7001 the variation across all conditions. @code{XINA} not only extracts
7002 coabundance profiles within and across experiments, but also incorporates
7003 protein-protein interaction databases and integrative resources such as
7004 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
7005 molecular functions, respectively, and produces intuitive graphical outputs.")
7006 (license license:gpl3)))
7008 (define-public r-xmapbridge
7010 (name "r-xmapbridge")
7015 (uri (bioconductor-uri "xmapbridge" version))
7017 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
7018 (properties `((upstream-name . "xmapbridge")))
7019 (build-system r-build-system)
7020 (home-page "https://git.bioconductor.org/packages/xmapbridge")
7021 (synopsis "Display numeric data in the web based genome browser X:MAP")
7023 "The package @code{xmapbridge} can plot graphs in the X:Map genome
7024 browser. X:Map uses the Google Maps API to provide a scrollable view of the
7025 genome. It supports a number of species, and can be accessed at
7026 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
7027 suitable format. Graph plotting in R is done using calls to the functions
7028 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
7029 similar to those used by the standard plot methods in R. These result in data
7030 being written to a set of files (in a specific directory structure) that
7031 contain the data to be displayed, as well as some additional meta-data
7032 describing each of the graphs.")
7033 (license license:lgpl3)))
7035 (define-public r-xvector
7041 (uri (bioconductor-uri "XVector" version))
7044 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
7046 `((upstream-name . "XVector")))
7047 (build-system r-build-system)
7050 (modify-phases %standard-phases
7051 (add-after 'unpack 'use-system-zlib
7053 (substitute* "DESCRIPTION"
7054 (("zlibbioc, ") ""))
7055 (substitute* "NAMESPACE"
7056 (("import\\(zlibbioc\\)") ""))
7061 (list r-biocgenerics r-iranges r-s4vectors))
7062 (home-page "https://bioconductor.org/packages/XVector")
7063 (synopsis "Representation and manpulation of external sequences")
7065 "This package provides memory efficient S4 classes for storing sequences
7066 \"externally\" (behind an R external pointer, or on disk).")
7067 (license license:artistic2.0)))
7069 (define-public r-zlibbioc
7075 (uri (bioconductor-uri "zlibbioc" version))
7078 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
7080 `((upstream-name . "zlibbioc")))
7081 (build-system r-build-system)
7082 (home-page "https://bioconductor.org/packages/zlibbioc")
7083 (synopsis "Provider for zlib-1.2.5 to R packages")
7084 (description "This package uses the source code of zlib-1.2.5 to create
7085 libraries for systems that do not have these available via other means.")
7086 (license license:artistic2.0)))
7088 (define-public r-zellkonverter
7090 (name "r-zellkonverter")
7095 (uri (bioconductor-uri "zellkonverter" version))
7097 (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"))))
7098 (properties `((upstream-name . "zellkonverter")))
7099 (build-system r-build-system)
7107 r-singlecellexperiment
7108 r-summarizedexperiment))
7109 (native-inputs (list r-knitr))
7110 (home-page "https://github.com/theislab/zellkonverter")
7111 (synopsis "Conversion between AnnData and single-cell experiments objects")
7113 "This package provides methods to convert between Python AnnData objects
7114 and SingleCellExperiment objects. These are primarily intended for use by
7115 downstream Bioconductor packages that wrap Python methods for single-cell data
7116 analysis. It also includes functions to read and write H5AD files used for
7117 saving AnnData objects to disk.")
7118 (license license:expat)))
7120 (define-public r-geneplotter
7122 (name "r-geneplotter")
7127 (uri (bioconductor-uri "geneplotter" version))
7130 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
7131 (build-system r-build-system)
7139 (home-page "https://bioconductor.org/packages/geneplotter")
7140 (synopsis "Graphics functions for genomic data")
7142 "This package provides functions for plotting genomic data.")
7143 (license license:artistic2.0)))
7145 (define-public r-oligoclasses
7147 (name "r-oligoclasses")
7152 (uri (bioconductor-uri "oligoClasses" version))
7155 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
7156 (properties `((upstream-name . "oligoClasses")))
7157 (build-system r-build-system)
7171 r-summarizedexperiment))
7172 (home-page "https://bioconductor.org/packages/oligoClasses/")
7173 (synopsis "Classes for high-throughput arrays")
7175 "This package contains class definitions, validity checks, and
7176 initialization methods for classes used by the @code{oligo} and @code{crlmm}
7178 (license license:gpl2+)))
7180 (define-public r-oligo
7187 (uri (bioconductor-uri "oligo" version))
7190 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
7191 (properties `((upstream-name . "oligo")))
7192 (build-system r-build-system)
7193 (inputs (list zlib))
7208 (home-page "https://bioconductor.org/packages/oligo/")
7209 (synopsis "Preprocessing tools for oligonucleotide arrays")
7211 "This package provides a package to analyze oligonucleotide
7212 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
7213 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
7214 (license license:lgpl2.0+)))
7216 (define-public r-qvalue
7223 (uri (bioconductor-uri "qvalue" version))
7226 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
7227 (build-system r-build-system)
7229 (list r-ggplot2 r-reshape2))
7232 (home-page "https://github.com/StoreyLab/qvalue")
7233 (synopsis "Q-value estimation for false discovery rate control")
7235 "This package takes a list of p-values resulting from the simultaneous
7236 testing of many hypotheses and estimates their q-values and local @dfn{false
7237 discovery rate} (FDR) values. The q-value of a test measures the proportion
7238 of false positives incurred when that particular test is called significant.
7239 The local FDR measures the posterior probability the null hypothesis is true
7240 given the test's p-value. Various plots are automatically generated, allowing
7241 one to make sensible significance cut-offs. The software can be applied to
7242 problems in genomics, brain imaging, astrophysics, and data mining.")
7243 ;; Any version of the LGPL.
7244 (license license:lgpl3+)))
7246 (define r-rcppnumerical
7248 (name "r-rcppnumerical")
7252 (uri (cran-uri "RcppNumerical" version))
7255 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
7256 (properties `((upstream-name . "RcppNumerical")))
7257 (build-system r-build-system)
7259 `(("r-rcpp" ,r-rcpp)
7260 ("r-rcppeigen" ,r-rcppeigen)))
7262 `(("r-knitr" ,r-knitr)))
7263 (home-page "https://github.com/yixuan/RcppNumerical")
7264 (synopsis "Rcpp integration for numerical computing libraries")
7266 "This package provides a collection of libraries for numerical computing
7267 (numerical integration, optimization, etc.) and their integration with
7269 (license license:gpl2+)))
7271 (define-public r-apeglm
7277 (uri (bioconductor-uri "apeglm" version))
7280 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
7281 (properties `((upstream-name . "apeglm")))
7282 (build-system r-build-system)
7289 r-summarizedexperiment))
7290 (native-inputs (list r-knitr))
7291 (home-page "https://bioconductor.org/packages/apeglm")
7292 (synopsis "Approximate posterior estimation for GLM coefficients")
7293 (description "This package provides Bayesian shrinkage estimators for
7294 effect sizes for a variety of GLM models, using approximation of the
7295 posterior for individual coefficients.")
7296 (license license:gpl2)))
7298 (define-public r-greylistchip
7300 (name "r-greylistchip")
7304 (uri (bioconductor-uri "GreyListChIP" version))
7307 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
7308 (properties `((upstream-name . "GreyListChIP")))
7309 (build-system r-build-system)
7318 r-summarizedexperiment))
7319 (home-page "https://bioconductor.org/packages/GreyListChIP")
7320 (synopsis "Greylist artefact regions based on ChIP inputs")
7321 (description "This package identifies regions of ChIP experiments with high
7322 signal in the input, that lead to spurious peaks during peak calling.")
7323 (license license:artistic2.0)))
7325 (define-public r-diffbind
7332 (uri (bioconductor-uri "DiffBind" version))
7335 "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr"))))
7336 (properties `((upstream-name . "DiffBind")))
7337 (build-system r-build-system)
7360 r-summarizedexperiment
7362 (home-page "https://bioconductor.org/packages/DiffBind")
7363 (synopsis "Differential binding analysis of ChIP-Seq peak data")
7365 "This package computes differentially bound sites from multiple
7366 ChIP-seq experiments using affinity (quantitative) data. Also enables
7367 occupancy (overlap) analysis and plotting functions.")
7368 (license license:artistic2.0)))
7370 (define-public r-ripseeker
7372 (name "r-ripseeker")
7377 (uri (bioconductor-uri "RIPSeeker" version))
7380 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
7381 (properties `((upstream-name . "RIPSeeker")))
7382 (build-system r-build-system)
7387 r-summarizedexperiment
7391 (home-page "https://bioconductor.org/packages/RIPSeeker")
7393 "Identifying protein-associated transcripts from RIP-seq experiments")
7395 "This package infers and discriminates RIP peaks from RIP-seq alignments
7396 using two-state HMM with negative binomial emission probability. While
7397 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
7398 a suite of bioinformatics tools integrated within this self-contained software
7399 package comprehensively addressing issues ranging from post-alignments
7400 processing to visualization and annotation.")
7401 (license license:gpl2)))
7403 (define-public r-mbkmeans
7409 (uri (bioconductor-uri "mbkmeans" version))
7412 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
7413 (build-system r-build-system)
7427 r-singlecellexperiment
7428 r-summarizedexperiment))
7429 (home-page "https://bioconductor.org/packages/mbkmeans")
7430 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
7431 (description "This package implements the mini-batch k-means algorithm for
7432 large datasets, including support for on-disk data representation.")
7433 (license license:expat)))
7435 (define-public r-multtest
7442 (uri (bioconductor-uri "multtest" version))
7445 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
7446 (build-system r-build-system)
7448 (list r-survival r-biocgenerics r-biobase r-mass))
7449 (home-page "https://bioconductor.org/packages/multtest")
7450 (synopsis "Resampling-based multiple hypothesis testing")
7452 "This package can do non-parametric bootstrap and permutation
7453 resampling-based multiple testing procedures (including empirical Bayes
7454 methods) for controlling the family-wise error rate (FWER), generalized
7455 family-wise error rate (gFWER), tail probability of the proportion of
7456 false positives (TPPFP), and false discovery rate (FDR). Several choices
7457 of bootstrap-based null distribution are implemented (centered, centered
7458 and scaled, quantile-transformed). Single-step and step-wise methods are
7459 available. Tests based on a variety of T- and F-statistics (including
7460 T-statistics based on regression parameters from linear and survival models
7461 as well as those based on correlation parameters) are included. When probing
7462 hypotheses with T-statistics, users may also select a potentially faster null
7463 distribution which is multivariate normal with mean zero and variance
7464 covariance matrix derived from the vector influence function. Results are
7465 reported in terms of adjusted P-values, confidence regions and test statistic
7466 cutoffs. The procedures are directly applicable to identifying differentially
7467 expressed genes in DNA microarray experiments.")
7468 (license license:lgpl3)))
7470 (define-public r-graph
7476 (uri (bioconductor-uri "graph" version))
7479 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
7480 (build-system r-build-system)
7482 (list r-biocgenerics))
7483 (home-page "https://bioconductor.org/packages/graph")
7484 (synopsis "Handle graph data structures in R")
7486 "This package implements some simple graph handling capabilities for R.")
7487 (license license:artistic2.0)))
7489 ;; This is a CRAN package, but it depends on a Bioconductor package.
7490 (define-public r-ggm
7497 (uri (cran-uri "ggm" version))
7500 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
7501 (properties `((upstream-name . "ggm")))
7502 (build-system r-build-system)
7504 (list r-graph r-igraph))
7505 (home-page "https://cran.r-project.org/package=ggm")
7506 (synopsis "Functions for graphical Markov models")
7508 "This package provides functions and datasets for maximum likelihood
7509 fitting of some classes of graphical Markov models.")
7510 (license license:gpl2+)))
7512 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
7513 (define-public r-perfmeas
7520 (uri (cran-uri "PerfMeas" version))
7523 "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
7524 (properties `((upstream-name . "PerfMeas")))
7525 (build-system r-build-system)
7527 (list r-graph r-limma r-rbgl))
7528 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
7529 (synopsis "Performance measures for ranking and classification tasks")
7531 "This package implements different performance measures for
7532 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
7533 a given recall, F-score for single and multiple classes are available.")
7534 (license license:gpl2+)))
7536 ;; This is a CRAN package, but it depends on a Bioconductor package.
7537 (define-public r-codedepends
7539 (name "r-codedepends")
7544 (uri (cran-uri "CodeDepends" version))
7547 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
7548 (properties `((upstream-name . "CodeDepends")))
7549 (build-system r-build-system)
7551 (list r-codetools r-graph r-xml))
7552 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
7553 (synopsis "Analysis of R code for reproducible research and code comprehension")
7555 "This package provides tools for analyzing R expressions or blocks of
7556 code and determining the dependencies between them. It focuses on R scripts,
7557 but can be used on the bodies of functions. There are many facilities
7558 including the ability to summarize or get a high-level view of code,
7559 determining dependencies between variables, code improvement suggestions.")
7560 ;; Any version of the GPL
7561 (license (list license:gpl2+ license:gpl3+))))
7563 (define-public r-chippeakanno
7565 (name "r-chippeakanno")
7570 (uri (bioconductor-uri "ChIPpeakAnno" version))
7573 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
7574 (properties `((upstream-name . "ChIPpeakAnno")))
7575 (build-system r-build-system)
7577 (list r-annotationdbi
7600 r-summarizedexperiment
7604 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
7605 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
7607 "The package includes functions to retrieve the sequences around the peak,
7608 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
7609 custom features such as most conserved elements and other transcription factor
7610 binding sites supplied by users. Starting 2.0.5, new functions have been added
7611 for finding the peaks with bi-directional promoters with summary statistics
7612 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
7613 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
7614 enrichedGO (addGeneIDs).")
7615 (license license:gpl2+)))
7617 (define-public r-matrixgenerics
7619 (name "r-matrixgenerics")
7623 (uri (bioconductor-uri "MatrixGenerics" version))
7626 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
7628 `((upstream-name . "MatrixGenerics")))
7629 (build-system r-build-system)
7631 (list r-matrixstats))
7632 (home-page "https://bioconductor.org/packages/MatrixGenerics")
7633 (synopsis "S4 generic summary statistic functions for matrix-like objects")
7635 "This package provides S4 generic functions modeled after the
7636 @code{matrixStats} API for alternative matrix implementations. Packages with
7637 alternative matrix implementation can depend on this package and implement the
7638 generic functions that are defined here for a useful set of row and column
7639 summary statistics. Other package developers can import this package and
7640 handle a different matrix implementations without worrying about
7641 incompatibilities.")
7642 (license license:artistic2.0)))
7644 (define-public r-marray
7650 (uri (bioconductor-uri "marray" version))
7652 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
7653 (build-system r-build-system)
7656 (home-page "https://bioconductor.org/packages/marray")
7657 (synopsis "Exploratory analysis for two-color spotted microarray data")
7658 (description "This package contains class definitions for two-color spotted
7659 microarray data. It also includes functions for data input, diagnostic plots,
7660 normalization and quality checking.")
7661 (license license:lgpl2.0+)))
7663 (define-public r-cghbase
7669 (uri (bioconductor-uri "CGHbase" version))
7671 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
7672 (properties `((upstream-name . "CGHbase")))
7673 (build-system r-build-system)
7675 (list r-biobase r-marray))
7676 (home-page "https://bioconductor.org/packages/CGHbase")
7677 (synopsis "Base functions and classes for arrayCGH data analysis")
7678 (description "This package contains functions and classes that are needed by
7679 the @code{arrayCGH} packages.")
7680 (license license:gpl2+)))
7682 (define-public r-cghcall
7688 (uri (bioconductor-uri "CGHcall" version))
7690 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
7691 (properties `((upstream-name . "CGHcall")))
7692 (build-system r-build-system)
7694 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
7695 (home-page "https://bioconductor.org/packages/CGHcall")
7696 (synopsis "Base functions and classes for arrayCGH data analysis")
7697 (description "This package contains functions and classes that are needed by
7698 @code{arrayCGH} packages.")
7699 (license license:gpl2+)))
7701 (define-public r-qdnaseq
7707 (uri (bioconductor-uri "QDNAseq" version))
7709 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
7710 (properties `((upstream-name . "QDNAseq")))
7711 (build-system r-build-system)
7723 (home-page "https://bioconductor.org/packages/QDNAseq")
7724 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
7725 (description "The genome is divided into non-overlapping fixed-sized bins,
7726 number of sequence reads in each counted, adjusted with a simultaneous
7727 two-dimensional loess correction for sequence mappability and GC content, and
7728 filtered to remove spurious regions in the genome. Downstream steps of
7729 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
7731 (license license:gpl2+)))
7733 (define-public r-bayseq
7740 (uri (bioconductor-uri "baySeq" version))
7743 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
7744 (properties `((upstream-name . "baySeq")))
7745 (build-system r-build-system)
7747 (list r-abind r-edger r-genomicranges))
7748 (home-page "https://bioconductor.org/packages/baySeq/")
7749 (synopsis "Bayesian analysis of differential expression patterns in count data")
7751 "This package identifies differential expression in high-throughput count
7752 data, such as that derived from next-generation sequencing machines,
7753 calculating estimated posterior likelihoods of differential expression (or
7754 more complex hypotheses) via empirical Bayesian methods.")
7755 (license license:gpl3)))
7757 (define-public r-chipcomp
7764 (uri (bioconductor-uri "ChIPComp" version))
7767 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
7768 (properties `((upstream-name . "ChIPComp")))
7769 (build-system r-build-system)
7771 (list r-biocgenerics
7772 r-bsgenome-hsapiens-ucsc-hg19
7773 r-bsgenome-mmusculus-ucsc-mm9
7781 (home-page "https://bioconductor.org/packages/ChIPComp")
7782 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
7784 "ChIPComp implements a statistical method for quantitative comparison of
7785 multiple ChIP-seq datasets. It detects differentially bound sharp binding
7786 sites across multiple conditions considering matching control in ChIP-seq
7788 ;; Any version of the GPL.
7789 (license license:gpl3+)))
7791 (define-public r-riboprofiling
7793 (name "r-riboprofiling")
7798 (uri (bioconductor-uri "RiboProfiling" version))
7801 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
7802 (properties `((upstream-name . "RiboProfiling")))
7803 (build-system r-build-system)
7805 (list r-biocgenerics
7823 (home-page "https://bioconductor.org/packages/RiboProfiling/")
7824 (synopsis "Ribosome profiling data analysis")
7825 (description "Starting with a BAM file, this package provides the
7826 necessary functions for quality assessment, read start position recalibration,
7827 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
7828 of count data: pairs, log fold-change, codon frequency and coverage
7829 assessment, principal component analysis on codon coverage.")
7830 (license license:gpl3)))
7832 (define-public r-riboseqr
7839 (uri (bioconductor-uri "riboSeqR" version))
7842 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
7843 (properties `((upstream-name . "riboSeqR")))
7844 (build-system r-build-system)
7853 (home-page "https://bioconductor.org/packages/riboSeqR/")
7854 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
7856 "This package provides plotting functions, frameshift detection and
7857 parsing of genetic sequencing data from ribosome profiling experiments.")
7858 (license license:gpl3)))
7860 (define-public r-interactionset
7862 (name "r-interactionset")
7867 (uri (bioconductor-uri "InteractionSet" version))
7870 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
7872 `((upstream-name . "InteractionSet")))
7873 (build-system r-build-system)
7875 (list r-biocgenerics
7882 r-summarizedexperiment))
7885 (home-page "https://bioconductor.org/packages/InteractionSet")
7886 (synopsis "Base classes for storing genomic interaction data")
7888 "This package provides the @code{GInteractions},
7889 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
7890 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
7892 (license license:gpl3)))
7894 (define-public r-genomicinteractions
7896 (name "r-genomicinteractions")
7901 (uri (bioconductor-uri "GenomicInteractions" version))
7904 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
7906 `((upstream-name . "GenomicInteractions")))
7907 (build-system r-build-system)
7927 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
7928 (synopsis "R package for handling genomic interaction data")
7930 "This R package provides tools for handling genomic interaction data,
7931 such as ChIA-PET/Hi-C, annotating genomic features with interaction
7932 information and producing various plots and statistics.")
7933 (license license:gpl3)))
7935 (define-public r-ctc
7942 (uri (bioconductor-uri "ctc" version))
7945 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
7946 (build-system r-build-system)
7947 (propagated-inputs (list r-amap))
7948 (home-page "https://bioconductor.org/packages/ctc/")
7949 (synopsis "Cluster and tree conversion")
7951 "This package provides tools for exporting and importing classification
7952 trees and clusters to other programs.")
7953 (license license:gpl2)))
7955 (define-public r-goseq
7962 (uri (bioconductor-uri "goseq" version))
7965 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
7966 (build-system r-build-system)
7968 (list r-annotationdbi
7974 (home-page "https://bioconductor.org/packages/goseq/")
7975 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
7977 "This package provides tools to detect Gene Ontology and/or other user
7978 defined categories which are over/under represented in RNA-seq data.")
7979 (license license:lgpl2.0+)))
7981 (define-public r-glimma
7988 (uri (bioconductor-uri "Glimma" version))
7991 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
7992 (properties `((upstream-name . "Glimma")))
7993 (build-system r-build-system)
8001 r-summarizedexperiment))
8004 (home-page "https://github.com/Shians/Glimma")
8005 (synopsis "Interactive HTML graphics")
8007 "This package generates interactive visualisations for analysis of
8008 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
8009 HTML page. The interactions are built on top of the popular static
8010 representations of analysis results in order to provide additional
8012 (license license:lgpl3)))
8014 (define-public r-rots
8021 (uri (bioconductor-uri "ROTS" version))
8024 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
8025 (properties `((upstream-name . "ROTS")))
8026 (build-system r-build-system)
8028 (list r-biobase r-rcpp))
8029 (home-page "https://bioconductor.org/packages/ROTS/")
8030 (synopsis "Reproducibility-Optimized Test Statistic")
8032 "This package provides tools for calculating the
8033 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
8035 (license license:gpl2+)))
8037 (define-public r-plgem
8044 (uri (bioconductor-uri "plgem" version))
8047 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
8048 (build-system r-build-system)
8050 (list r-biobase r-mass))
8051 (home-page "http://www.genopolis.it")
8052 (synopsis "Detect differential expression in microarray and proteomics datasets")
8054 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
8055 model the variance-versus-mean dependence that exists in a variety of
8056 genome-wide datasets, including microarray and proteomics data. The use of
8057 PLGEM has been shown to improve the detection of differentially expressed
8058 genes or proteins in these datasets.")
8059 (license license:gpl2)))
8061 (define-public r-inspect
8068 (uri (bioconductor-uri "INSPEcT" version))
8071 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
8072 (properties `((upstream-name . "INSPEcT")))
8073 (build-system r-build-system)
8094 r-summarizedexperiment
8095 r-txdb-mmusculus-ucsc-mm9-knowngene))
8098 (home-page "https://bioconductor.org/packages/INSPEcT")
8099 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
8101 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
8102 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
8103 order to evaluate synthesis, processing and degradation rates and assess via
8104 modeling the rates that determines changes in mature mRNA levels.")
8105 (license license:gpl2)))
8107 (define-public r-dnabarcodes
8109 (name "r-dnabarcodes")
8114 (uri (bioconductor-uri "DNABarcodes" version))
8117 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
8118 (properties `((upstream-name . "DNABarcodes")))
8119 (build-system r-build-system)
8121 (list r-bh r-matrix r-rcpp))
8124 (home-page "https://bioconductor.org/packages/DNABarcodes")
8125 (synopsis "Create and analyze DNA barcodes")
8127 "This package offers tools to create DNA barcode sets capable of
8128 correcting insertion, deletion, and substitution errors. Existing barcodes
8129 can be analyzed regarding their minimal, maximal and average distances between
8130 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
8131 demultiplexed, i.e. assigned to their original reference barcode.")
8132 (license license:gpl2)))
8134 (define-public r-ruvseq
8141 (uri (bioconductor-uri "RUVSeq" version))
8144 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
8145 (properties `((upstream-name . "RUVSeq")))
8146 (build-system r-build-system)
8148 (list r-biobase r-edaseq r-edger r-mass))
8151 (home-page "https://github.com/drisso/RUVSeq")
8152 (synopsis "Remove unwanted variation from RNA-Seq data")
8154 "This package implements methods to @dfn{remove unwanted variation} (RUV)
8155 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
8157 (license license:artistic2.0)))
8159 (define-public r-biocneighbors
8161 (name "r-biocneighbors")
8166 (uri (bioconductor-uri "BiocNeighbors" version))
8169 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
8170 (properties `((upstream-name . "BiocNeighbors")))
8171 (build-system r-build-system)
8173 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
8176 (home-page "https://bioconductor.org/packages/BiocNeighbors")
8177 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
8179 "This package implements exact and approximate methods for nearest
8180 neighbor detection, in a framework that allows them to be easily switched
8181 within Bioconductor packages or workflows. The exact algorithm is implemented
8182 using pre-clustering with the k-means algorithm. Functions are also provided
8183 to search for all neighbors within a given distance. Parallelization is
8184 achieved for all methods using the BiocParallel framework.")
8185 (license license:gpl3)))
8187 (define-public r-scaledmatrix
8189 (name "r-scaledmatrix")
8194 (uri (bioconductor-uri "ScaledMatrix" version))
8197 "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"))))
8198 (properties `((upstream-name . "ScaledMatrix")))
8199 (build-system r-build-system)
8201 (list r-delayedarray r-matrix r-s4vectors))
8202 (native-inputs (list r-knitr))
8203 (home-page "https://github.com/LTLA/ScaledMatrix")
8204 (synopsis "Create a DelayedMatrix of scaled and centered values")
8206 "This package provides delayed computation of a matrix of scaled and
8207 centered values. The result is equivalent to using the @code{scale} function
8208 but avoids explicit realization of a dense matrix during block processing.
8209 This permits greater efficiency in common operations, most notably matrix
8211 (license license:gpl3)))
8213 (define-public r-treeio
8220 (uri (bioconductor-uri "treeio" version))
8223 "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"))))
8224 (properties `((upstream-name . "treeio")))
8225 (build-system r-build-system)
8234 (native-inputs (list r-knitr))
8235 (home-page "https://github.com/YuLab-SMU/treeio")
8236 (synopsis "Base classes and functions for Phylogenetic tree input and output")
8238 "This is an R package to make it easier to import and store phylogenetic
8239 trees with associated data; and to link external data from different sources
8240 to phylogeny. It also supports exporting phylogenetic trees with
8241 heterogeneous associated data to a single tree file and can be served as a
8242 platform for merging tree with associated data and converting file formats.")
8243 (license license:artistic2.0)))
8245 (define-public r-ggtree
8252 (uri (bioconductor-uri "ggtree" version))
8255 "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"))))
8256 (properties `((upstream-name . "ggtree")))
8257 (build-system r-build-system)
8272 (native-inputs (list r-knitr))
8273 (home-page "https://yulab-smu.top/treedata-book/")
8274 (synopsis "R package for visualization of trees and annotation data")
8276 "This package extends the ggplot2 plotting system which implements a
8277 grammar of graphics. ggtree is designed for visualization and annotation of
8278 phylogenetic trees and other tree-like structures with their annotation
8280 (license license:artistic2.0)))
8282 (define-public r-metapod
8289 (uri (bioconductor-uri "metapod" version))
8292 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
8293 (properties `((upstream-name . "metapod")))
8294 (build-system r-build-system)
8299 (home-page "https://bioconductor.org/packages/metapod")
8300 (synopsis "Meta-analyses on p-values of differential analyses")
8302 "This package implements a variety of methods for combining p-values in
8303 differential analyses of genome-scale datasets. Functions can combine
8304 p-values across different tests in the same analysis (e.g., genomic windows in
8305 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
8306 analyses (e.g., replicated comparisons, effect of different treatment
8307 conditions). Support is provided for handling log-transformed input p-values,
8308 missing values and weighting where appropriate.")
8309 (license license:gpl3)))
8311 (define-public r-biocsingular
8313 (name "r-biocsingular")
8318 (uri (bioconductor-uri "BiocSingular" version))
8321 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
8322 (properties `((upstream-name . "BiocSingular")))
8323 (build-system r-build-system)
8337 (home-page "https://github.com/LTLA/BiocSingular")
8338 (synopsis "Singular value decomposition for Bioconductor packages")
8340 "This package implements exact and approximate methods for singular value
8341 decomposition and principal components analysis, in a framework that allows
8342 them to be easily switched within Bioconductor packages or workflows. Where
8343 possible, parallelization is achieved using the BiocParallel framework.")
8344 (license license:gpl3)))
8346 (define-public r-destiny
8353 (uri (bioconductor-uri "destiny" version))
8356 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
8357 (build-system r-build-system)
8375 r-singlecellexperiment
8377 r-summarizedexperiment
8382 (list r-knitr r-nbconvertr)) ; for vignettes
8383 (home-page "https://bioconductor.org/packages/destiny/")
8384 (synopsis "Create and plot diffusion maps")
8385 (description "This package provides tools to create and plot diffusion
8387 ;; Any version of the GPL
8388 (license license:gpl3+)))
8390 (define-public r-savr
8397 (uri (bioconductor-uri "savR" version))
8400 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
8401 (properties `((upstream-name . "savR")))
8402 (build-system r-build-system)
8404 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
8405 (home-page "https://github.com/bcalder/savR")
8406 (synopsis "Parse and analyze Illumina SAV files")
8408 "This package provides tools to parse Illumina Sequence Analysis
8409 Viewer (SAV) files, access data, and generate QC plots.")
8410 (license license:agpl3+)))
8412 (define-public r-chipexoqual
8414 (name "r-chipexoqual")
8419 (uri (bioconductor-uri "ChIPexoQual" version))
8422 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
8423 (properties `((upstream-name . "ChIPexoQual")))
8424 (build-system r-build-system)
8426 (list r-biocparallel
8445 (home-page "https://github.com/keleslab/ChIPexoQual")
8446 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
8448 "This package provides a quality control pipeline for ChIP-exo/nexus
8450 (license license:gpl2+)))
8452 (define-public r-copynumber
8454 (name "r-copynumber")
8458 (uri (bioconductor-uri "copynumber" version))
8461 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
8462 (build-system r-build-system)
8464 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
8465 (home-page "https://bioconductor.org/packages/copynumber")
8466 (synopsis "Segmentation of single- and multi-track copy number data")
8468 "This package segments single- and multi-track copy number data by a
8469 penalized least squares regression method.")
8470 (license license:artistic2.0)))
8472 (define-public r-dnacopy
8479 (uri (bioconductor-uri "DNAcopy" version))
8482 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
8483 (properties `((upstream-name . "DNAcopy")))
8484 (build-system r-build-system)
8485 (native-inputs (list gfortran))
8486 (home-page "https://bioconductor.org/packages/DNAcopy")
8487 (synopsis "DNA copy number data analysis")
8489 "This package implements the @dfn{circular binary segmentation} (CBS)
8490 algorithm to segment DNA copy number data and identify genomic regions with
8491 abnormal copy number.")
8492 (license license:gpl2+)))
8494 ;; This is a CRAN package, but it uncharacteristically depends on a
8495 ;; Bioconductor package.
8496 (define-public r-htscluster
8498 (name "r-htscluster")
8503 (uri (cran-uri "HTSCluster" version))
8506 "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
8507 (properties `((upstream-name . "HTSCluster")))
8508 (build-system r-build-system)
8510 (list r-capushe r-edger r-plotrix))
8511 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
8512 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
8514 "This package provides a Poisson mixture model is implemented to cluster
8515 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
8516 estimation is performed using either the EM or CEM algorithm, and the slope
8517 heuristics are used for model selection (i.e., to choose the number of
8519 (license license:gpl3+)))
8521 (define-public r-deds
8528 (uri (bioconductor-uri "DEDS" version))
8531 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
8532 (properties `((upstream-name . "DEDS")))
8533 (build-system r-build-system)
8534 (home-page "https://bioconductor.org/packages/DEDS/")
8535 (synopsis "Differential expression via distance summary for microarray data")
8537 "This library contains functions that calculate various statistics of
8538 differential expression for microarray data, including t statistics, fold
8539 change, F statistics, SAM, moderated t and F statistics and B statistics. It
8540 also implements a new methodology called DEDS (Differential Expression via
8541 Distance Summary), which selects differentially expressed genes by integrating
8542 and summarizing a set of statistics using a weighted distance approach.")
8543 ;; Any version of the LGPL.
8544 (license license:lgpl3+)))
8546 ;; This is a CRAN package, but since it depends on a Bioconductor package we
8548 (define-public r-nbpseq
8555 (uri (cran-uri "NBPSeq" version))
8558 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
8559 (properties `((upstream-name . "NBPSeq")))
8560 (build-system r-build-system)
8563 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
8564 (synopsis "Negative binomial models for RNA-Seq data")
8566 "This package provides negative binomial models for two-group comparisons
8567 and regression inferences from RNA-sequencing data.")
8568 (license license:gpl2)))
8570 (define-public r-ebseq
8577 (uri (bioconductor-uri "EBSeq" version))
8580 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
8581 (properties `((upstream-name . "EBSeq")))
8582 (build-system r-build-system)
8584 (list r-blockmodeling r-gplots r-testthat))
8585 (home-page "https://bioconductor.org/packages/EBSeq")
8586 (synopsis "Differential expression analysis of RNA-seq data")
8588 "This package provides tools for differential expression analysis at both
8589 gene and isoform level using RNA-seq data")
8590 (license license:artistic2.0)))
8592 (define-public r-karyoploter
8594 (name "r-karyoploter")
8598 (uri (bioconductor-uri "karyoploteR" version))
8601 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
8602 (build-system r-build-system)
8604 (list r-annotationdbi
8618 r-variantannotation))
8621 (home-page "https://bioconductor.org/packages/karyoploteR/")
8622 (synopsis "Plot customizable linear genomes displaying arbitrary data")
8623 (description "This package creates karyotype plots of arbitrary genomes and
8624 offers a complete set of functions to plot arbitrary data on them. It mimics
8625 many R base graphics functions coupling them with a coordinate change function
8626 automatically mapping the chromosome and data coordinates into the plot
8628 (license license:artistic2.0)))
8630 (define-public r-lpsymphony
8632 (name "r-lpsymphony")
8637 (uri (bioconductor-uri "lpsymphony" version))
8640 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
8641 (build-system r-build-system)
8645 '(modify-phases %standard-phases
8646 (add-after 'unpack 'make-build-order-reproducible
8648 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
8649 "src/SYMPHONY/Cgl/configure")
8650 (("for file in `ls \\*/Makefile.in`")
8651 "for file in `ls */Makefile.in | sort`")))))))
8655 (list pkg-config r-knitr))
8656 (home-page "https://r-forge.r-project.org/projects/rsymphony")
8657 (synopsis "Symphony integer linear programming solver in R")
8659 "This package was derived from Rsymphony. The package provides an R
8660 interface to SYMPHONY, a linear programming solver written in C++. The main
8661 difference between this package and Rsymphony is that it includes the solver
8662 source code, while Rsymphony expects to find header and library files on the
8663 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
8664 to install interface to SYMPHONY.")
8665 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
8666 ;; lpsimphony is released under the same terms.
8667 (license license:epl1.0)))
8669 (define-public r-ihw
8676 (uri (bioconductor-uri "IHW" version))
8679 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
8680 (properties `((upstream-name . "IHW")))
8681 (build-system r-build-system)
8683 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
8686 (home-page "https://bioconductor.org/packages/IHW")
8687 (synopsis "Independent hypothesis weighting")
8689 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
8690 procedure that increases power compared to the method of Benjamini and
8691 Hochberg by assigning data-driven weights to each hypothesis. The input to
8692 IHW is a two-column table of p-values and covariates. The covariate can be
8693 any continuous-valued or categorical variable that is thought to be
8694 informative on the statistical properties of each hypothesis test, while it is
8695 independent of the p-value under the null hypothesis.")
8696 (license license:artistic2.0)))
8698 (define-public r-icobra
8705 (uri (bioconductor-uri "iCOBRA" version))
8708 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
8709 (properties `((upstream-name . "iCOBRA")))
8710 (build-system r-build-system)
8726 (home-page "https://bioconductor.org/packages/iCOBRA")
8727 (synopsis "Comparison and visualization of ranking and assignment methods")
8729 "This package provides functions for calculation and visualization of
8730 performance metrics for evaluation of ranking and binary
8731 classification (assignment) methods. It also contains a Shiny application for
8732 interactive exploration of results.")
8733 (license license:gpl2+)))
8735 (define-public r-residualmatrix
8737 (name "r-residualmatrix")
8742 (uri (bioconductor-uri "ResidualMatrix" version))
8745 "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"))))
8747 `((upstream-name . "ResidualMatrix")))
8748 (build-system r-build-system)
8750 (list r-delayedarray r-matrix r-s4vectors))
8753 (home-page "https://github.com/LTLA/ResidualMatrix")
8754 (synopsis "Create a DelayedMatrix of regression residuals")
8756 "This package implements tools for delayed computation of a matrix of
8757 residuals after fitting a linear model to each column of an input matrix. It
8758 also supports partial computation of residuals where selected factors are to
8759 be preserved in the output matrix. It implements a number of efficient
8760 methods for operating on the delayed matrix of residuals, most notably matrix
8761 multiplication and calculation of row/column sums or means.")
8762 (license license:gpl3)))
8764 (define-public r-batchelor
8766 (name "r-batchelor")
8771 (uri (bioconductor-uri "batchelor" version))
8774 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
8775 (properties `((upstream-name . "batchelor")))
8776 (build-system r-build-system)
8784 r-delayedmatrixstats
8792 r-singlecellexperiment
8793 r-summarizedexperiment))
8794 (native-inputs (list r-knitr))
8795 (home-page "https://bioconductor.org/packages/batchelor")
8796 (synopsis "Single-Cell Batch Correction Methods")
8798 "This package implements a variety of methods for batch correction of
8799 single-cell (RNA sequencing) data. This includes methods based on detecting
8800 mutually nearest neighbors, as well as several efficient variants of linear
8801 regression of the log-expression values. Functions are also provided to
8802 perform global rescaling to remove differences in depth between batches, and
8803 to perform a principal components analysis that is robust to differences in
8804 the numbers of cells across batches.")
8805 (license license:gpl3)))
8807 (define-public r-mast
8814 (uri (bioconductor-uri "MAST" version))
8817 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
8818 (properties `((upstream-name . "MAST")))
8819 (build-system r-build-system)
8830 r-singlecellexperiment
8832 r-summarizedexperiment))
8835 (home-page "https://github.com/RGLab/MAST/")
8836 (synopsis "Model-based analysis of single cell transcriptomics")
8838 "This package provides methods and models for handling zero-inflated
8839 single cell assay data.")
8840 (license license:gpl2+)))
8842 (define-public r-monocle
8849 (uri (bioconductor-uri "monocle" version))
8852 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
8853 (build-system r-build-system)
8887 (home-page "https://bioconductor.org/packages/monocle")
8888 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
8890 "Monocle performs differential expression and time-series analysis for
8891 single-cell expression experiments. It orders individual cells according to
8892 progress through a biological process, without knowing ahead of time which
8893 genes define progress through that process. Monocle also performs
8894 differential expression analysis, clustering, visualization, and other useful
8895 tasks on single cell expression data. It is designed to work with RNA-Seq and
8896 qPCR data, but could be used with other types as well.")
8897 (license license:artistic2.0)))
8899 (define-public r-leidenbase
8900 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
8903 (name "r-leidenbase")
8904 (version (git-version "0.1.9" revision commit))
8909 (url "https://github.com/cole-trapnell-lab/leidenbase")
8911 (file-name (git-file-name name version))
8914 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
8915 (properties `((upstream-name . "leidenbase")))
8916 (build-system r-build-system)
8923 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
8924 (synopsis "R and C wrappers to run the Leiden find_partition function")
8926 "This package provides an R to C interface that runs the Leiden
8927 community detection algorithm to find a basic partition. It runs the
8928 equivalent of the @code{find_partition} function. This package includes the
8929 required source code files from the official Leidenalg distribution and
8930 several functions from the R igraph package.")
8931 (license license:gpl3+))))
8933 (define-public r-sanssouci
8934 ;; sansscouci doesn't have a (versioned) release yet.
8935 ;; This is the latest commit as of packaging for Guix.
8936 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
8939 (name "r-sanssouci")
8940 (version (git-version "0" revision commit))
8944 (url "https://github.com/pneuvial/sanssouci.git")
8946 (file-name (git-file-name name version))
8949 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
8950 (build-system r-build-system)
8952 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
8953 (home-page "https://pneuvial.github.io/sanssouci")
8954 (synopsis "Post Hoc multiple testing inference")
8956 "The goal of sansSouci is to perform post hoc inference: in a multiple
8957 testing context, sansSouci provides statistical guarantees on possibly
8958 user-defined and/or data-driven sets of hypotheses.")
8959 (license license:gpl3))))
8961 (define-public r-monocle3
8969 (url "https://github.com/cole-trapnell-lab/monocle3")
8971 (file-name (git-file-name name version))
8974 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
8975 (build-system r-build-system)
8981 r-delayedmatrixstats
9016 r-singlecellexperiment
9021 (home-page "https://github.com/cole-trapnell-lab/monocle3")
9022 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
9024 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
9025 (license license:expat)))
9027 (define-public r-noiseq
9034 (uri (bioconductor-uri "NOISeq" version))
9037 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
9038 (properties `((upstream-name . "NOISeq")))
9039 (build-system r-build-system)
9041 (list r-biobase r-matrix))
9042 (home-page "https://bioconductor.org/packages/NOISeq")
9043 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
9045 "This package provides tools to support the analysis of RNA-seq
9046 expression data or other similar kind of data. It provides exploratory plots
9047 to evaluate saturation, count distribution, expression per chromosome, type of
9048 detected features, features length, etc. It also supports the analysis of
9049 differential expression between two experimental conditions with no parametric
9051 (license license:artistic2.0)))
9053 (define-public r-scdd
9060 (uri (bioconductor-uri "scDD" version))
9063 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
9064 (properties `((upstream-name . "scDD")))
9065 (build-system r-build-system)
9076 r-singlecellexperiment
9077 r-summarizedexperiment))
9080 (home-page "https://github.com/kdkorthauer/scDD")
9081 (synopsis "Mixture modeling of single-cell RNA-seq data")
9083 "This package implements a method to analyze single-cell RNA-seq data
9084 utilizing flexible Dirichlet Process mixture models. Genes with differential
9085 distributions of expression are classified into several interesting patterns
9086 of differences between two conditions. The package also includes functions
9087 for simulating data with these patterns from negative binomial
9089 (license license:gpl2)))
9091 (define-public r-scone
9098 (uri (bioconductor-uri "scone" version))
9101 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
9102 (build-system r-build-system)
9123 r-singlecellexperiment
9124 r-summarizedexperiment))
9127 (home-page "https://bioconductor.org/packages/scone")
9128 (synopsis "Single cell overview of normalized expression data")
9130 "SCONE is an R package for comparing and ranking the performance of
9131 different normalization schemes for single-cell RNA-seq and other
9132 high-throughput analyses.")
9133 (license license:artistic2.0)))
9135 (define-public r-geoquery
9142 (uri (bioconductor-uri "GEOquery" version))
9145 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
9146 (properties `((upstream-name . "GEOquery")))
9147 (build-system r-build-system)
9161 (home-page "https://github.com/seandavi/GEOquery/")
9162 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
9164 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
9165 microarray data. Given the rich and varied nature of this resource, it is
9166 only natural to want to apply BioConductor tools to these data. GEOquery is
9167 the bridge between GEO and BioConductor.")
9168 (license license:gpl2)))
9170 (define-public r-illuminaio
9172 (name "r-illuminaio")
9177 (uri (bioconductor-uri "illuminaio" version))
9180 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
9181 (build-system r-build-system)
9184 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
9185 (synopsis "Parse Illumina microarray output files")
9187 "This package provides tools for parsing Illumina's microarray output
9188 files, including IDAT.")
9189 (license license:gpl2)))
9191 (define-public r-siggenes
9198 (uri (bioconductor-uri "siggenes" version))
9201 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
9202 (build-system r-build-system)
9204 (list r-biobase r-multtest r-scrime))
9205 (home-page "https://bioconductor.org/packages/siggenes/")
9207 "Multiple testing using SAM and Efron's empirical Bayes approaches")
9209 "This package provides tools for the identification of differentially
9210 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
9211 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
9212 Bayes Analyses of Microarrays} (EBAM).")
9213 (license license:lgpl2.0+)))
9215 (define-public r-bumphunter
9217 (name "r-bumphunter")
9222 (uri (bioconductor-uri "bumphunter" version))
9225 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
9226 (build-system r-build-system)
9228 (list r-annotationdbi
9241 (home-page "https://github.com/ririzarr/bumphunter")
9242 (synopsis "Find bumps in genomic data")
9244 "This package provides tools for finding bumps in genomic data in order
9245 to identify differentially methylated regions in epigenetic epidemiology
9247 (license license:artistic2.0)))
9249 (define-public r-milor
9255 (uri (bioconductor-uri "miloR" version))
9258 "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
9259 (properties `((upstream-name . "miloR")))
9260 (build-system r-build-system)
9262 (list r-biocgenerics
9282 r-singlecellexperiment
9284 r-summarizedexperiment
9287 (native-inputs (list r-knitr))
9288 (home-page "https://marionilab.github.io/miloR")
9289 (synopsis "Differential neighbourhood abundance testing on a graph")
9291 "Milo performs single-cell differential abundance testing. Cell states
9292 are modelled as representative neighbourhoods on a nearest neighbour graph.
9293 Hypothesis testing is performed using a negative bionomial generalized linear
9295 (license license:gpl3)))
9297 (define-public r-minfi
9304 (uri (bioconductor-uri "minfi" version))
9307 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
9308 (build-system r-build-system)
9318 r-delayedmatrixstats
9338 r-summarizedexperiment))
9341 (home-page "https://github.com/hansenlab/minfi")
9342 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
9344 "This package provides tools to analyze and visualize Illumina Infinium
9345 methylation arrays.")
9346 (license license:artistic2.0)))
9348 (define-public r-methylumi
9350 (name "r-methylumi")
9355 (uri (bioconductor-uri "methylumi" version))
9358 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
9359 (build-system r-build-system)
9365 r-fdb-infiniummethylation-hg19
9379 r-summarizedexperiment))
9382 (home-page "https://bioconductor.org/packages/methylumi")
9383 (synopsis "Handle Illumina methylation data")
9385 "This package provides classes for holding and manipulating Illumina
9386 methylation data. Based on eSet, it can contain MIAME information, sample
9387 information, feature information, and multiple matrices of data. An
9388 \"intelligent\" import function, methylumiR can read the Illumina text files
9389 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
9390 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
9391 background correction, and quality control features for GoldenGate, Infinium,
9392 and Infinium HD arrays are also included.")
9393 (license license:gpl2)))
9395 (define-public r-lumi
9402 (uri (bioconductor-uri "lumi" version))
9405 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
9406 (build-system r-build-system)
9423 (home-page "https://bioconductor.org/packages/lumi")
9424 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
9426 "The lumi package provides an integrated solution for the Illumina
9427 microarray data analysis. It includes functions of Illumina
9428 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
9429 variance stabilization, normalization and gene annotation at the probe level.
9430 It also includes the functions of processing Illumina methylation microarrays,
9431 especially Illumina Infinium methylation microarrays.")
9432 (license license:lgpl2.0+)))
9434 (define-public r-linnorm
9441 (uri (bioconductor-uri "Linnorm" version))
9444 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
9445 (properties `((upstream-name . "Linnorm")))
9446 (build-system r-build-system)
9468 (home-page "http://www.jjwanglab.org/Linnorm/")
9469 (synopsis "Linear model and normality based transformation method")
9471 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
9472 count data or any large scale count data. It transforms such datasets for
9473 parametric tests. In addition to the transformtion function (@code{Linnorm}),
9474 the following pipelines are implemented:
9477 @item Library size/batch effect normalization (@code{Linnorm.Norm})
9478 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
9479 clustering or hierarchical clustering (@code{Linnorm.tSNE},
9480 @code{Linnorm.PCA}, @code{Linnorm.HClust})
9481 @item Differential expression analysis or differential peak detection using
9482 limma (@code{Linnorm.limma})
9483 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
9484 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
9485 @item Stable gene selection for scRNA-seq data; for users without or who do
9486 not want to rely on spike-in genes (@code{Linnorm.SGenes})
9487 @item Data imputation (@code{Linnorm.DataImput}).
9490 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
9491 @code{RnaXSim} function is included for simulating RNA-seq data for the
9492 evaluation of DEG analysis methods.")
9493 (license license:expat)))
9495 (define-public r-ioniser
9502 (uri (bioconductor-uri "IONiseR" version))
9505 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
9506 (properties `((upstream-name . "IONiseR")))
9507 (build-system r-build-system)
9509 (list r-biocgenerics
9524 (home-page "https://bioconductor.org/packages/IONiseR/")
9525 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
9527 "IONiseR provides tools for the quality assessment of Oxford Nanopore
9528 MinION data. It extracts summary statistics from a set of fast5 files and can
9529 be used either before or after base calling. In addition to standard
9530 summaries of the read-types produced, it provides a number of plots for
9531 visualising metrics relative to experiment run time or spatially over the
9532 surface of a flowcell.")
9533 (license license:expat)))
9535 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
9536 (define-public r-mutoss
9543 (uri (cran-uri "mutoss" version))
9546 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
9547 (properties `((upstream-name . "mutoss")))
9548 (build-system r-build-system)
9550 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
9551 (home-page "https://github.com/kornl/mutoss/")
9552 (synopsis "Unified multiple testing procedures")
9554 "This package is designed to ease the application and comparison of
9555 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
9556 are standardized and usable by the accompanying mutossGUI package.")
9557 ;; Any version of the GPL.
9558 (license (list license:gpl2+ license:gpl3+))))
9560 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
9561 ;; from Bioconductor, so we put it here.
9562 (define-public r-metap
9569 (uri (cran-uri "metap" version))
9572 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
9573 (build-system r-build-system)
9581 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
9582 (synopsis "Meta-analysis of significance values")
9584 "The canonical way to perform meta-analysis involves using effect sizes.
9585 When they are not available this package provides a number of methods for
9586 meta-analysis of significance values including the methods of Edgington,
9587 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
9588 published results; and a routine for graphical display.")
9589 (license license:gpl2)))
9591 (define-public r-tradeseq
9597 (uri (bioconductor-uri "tradeSeq" version))
9600 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
9601 (build-system r-build-system)
9617 r-singlecellexperiment
9619 r-summarizedexperiment
9625 (home-page "https://statomics.github.io/tradeSeq/index.html")
9626 (synopsis "Trajectory-based differential expression analysis")
9628 "This package provides a flexible method for fitting regression models that
9629 can be used to find genes that are differentially expressed along one or
9630 multiple lineages in a trajectory. Based on the fitted models, it uses a
9631 variety of tests suited to answer different questions of interest, e.g. the
9632 discovery of genes for which expression is associated with pseudotime, or which
9633 are differentially expressed (in a specific region) along the trajectory. It
9634 fits a negative binomial generalized additive model (GAM) for each gene, and
9635 performs inference on the parameters of the GAM.")
9636 (license license:expat)))
9638 (define-public r-triform
9645 (uri (bioconductor-uri "triform" version))
9648 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
9649 (build-system r-build-system)
9651 (list r-biocgenerics r-iranges r-yaml))
9652 (home-page "https://bioconductor.org/packages/triform/")
9653 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
9655 "The Triform algorithm uses model-free statistics to identify peak-like
9656 distributions of TF ChIP sequencing reads, taking advantage of an improved
9657 peak definition in combination with known profile characteristics.")
9658 (license license:gpl2)))
9660 (define-public r-varianttools
9662 (name "r-varianttools")
9667 (uri (bioconductor-uri "VariantTools" version))
9670 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
9671 (properties `((upstream-name . "VariantTools")))
9672 (build-system r-build-system)
9687 r-variantannotation))
9688 (home-page "https://bioconductor.org/packages/VariantTools/")
9689 (synopsis "Tools for exploratory analysis of variant calls")
9691 "Explore, diagnose, and compare variant calls using filters. The
9692 VariantTools package supports a workflow for loading data, calling single
9693 sample variants and tumor-specific somatic mutations or other sample-specific
9694 variant types (e.g., RNA editing). Most of the functions operate on
9695 alignments (BAM files) or datasets of called variants. The user is expected
9696 to have already aligned the reads with a separate tool, e.g., GSNAP via
9698 (license license:artistic2.0)))
9700 (define-public r-heatplus
9707 (uri (bioconductor-uri "Heatplus" version))
9710 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
9711 (properties `((upstream-name . "Heatplus")))
9712 (build-system r-build-system)
9714 (list r-rcolorbrewer))
9715 (home-page "https://github.com/alexploner/Heatplus")
9716 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
9718 "This package provides tools to display a rectangular heatmap (intensity
9719 plot) of a data matrix. By default, both samples (columns) and features (row)
9720 of the matrix are sorted according to a hierarchical clustering, and the
9721 corresponding dendrogram is plotted. Optionally, panels with additional
9722 information about samples and features can be added to the plot.")
9723 (license license:gpl2+)))
9725 (define-public r-gosemsim
9732 (uri (bioconductor-uri "GOSemSim" version))
9735 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
9736 (properties `((upstream-name . "GOSemSim")))
9737 (build-system r-build-system)
9739 (list r-annotationdbi r-go-db r-rcpp))
9742 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
9743 (synopsis "GO-terms semantic similarity measures")
9745 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
9746 quantitative ways to compute similarities between genes and gene groups, and
9747 have became important basis for many bioinformatics analysis approaches.
9748 GOSemSim is an R package for semantic similarity computation among GO terms,
9749 sets of GO terms, gene products and gene clusters.")
9750 (license license:artistic2.0)))
9752 (define-public r-anota
9759 (uri (bioconductor-uri "anota" version))
9762 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
9763 (build-system r-build-system)
9765 (list r-multtest r-qvalue))
9766 (home-page "https://bioconductor.org/packages/anota/")
9767 (synopsis "Analysis of translational activity")
9769 "Genome wide studies of translational control is emerging as a tool to
9770 study various biological conditions. The output from such analysis is both
9771 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
9772 involved in translation (the actively translating mRNA level) for each mRNA.
9773 The standard analysis of such data strives towards identifying differential
9774 translational between two or more sample classes - i.e., differences in
9775 actively translated mRNA levels that are independent of underlying differences
9776 in cytosolic mRNA levels. This package allows for such analysis using partial
9777 variances and the random variance model. As 10s of thousands of mRNAs are
9778 analyzed in parallel the library performs a number of tests to assure that
9779 the data set is suitable for such analysis.")
9780 (license license:gpl3)))
9782 (define-public r-sigpathway
9784 (name "r-sigpathway")
9789 (uri (bioconductor-uri "sigPathway" version))
9792 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
9793 (properties `((upstream-name . "sigPathway")))
9794 (build-system r-build-system)
9795 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
9796 (synopsis "Pathway analysis")
9798 "This package is used to conduct pathway analysis by calculating the NT_k
9799 and NE_k statistics in a statistical framework for determining whether a
9800 specified group of genes for a pathway has a coordinated association with a
9801 phenotype of interest.")
9802 (license license:gpl2)))
9804 (define-public r-fcscan
9811 (uri (bioconductor-uri "fcScan" version))
9813 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
9814 (properties `((upstream-name . "fcScan")))
9815 (build-system r-build-system)
9823 r-summarizedexperiment
9824 r-variantannotation))
9825 (native-inputs (list r-knitr))
9826 (home-page "https://bioconductor.org/packages/fcScan")
9827 (synopsis "Detect clusters of coordinates with user defined options")
9829 "This package is used to detect combination of genomic coordinates
9830 falling within a user defined window size along with user defined overlap
9831 between identified neighboring clusters. It can be used for genomic data
9832 where the clusters are built on a specific chromosome or specific strand.
9833 Clustering can be performed with a \"greedy\" option allowing thus the
9834 presence of additional sites within the allowed window size.")
9835 (license license:artistic2.0)))
9837 (define-public r-fgsea
9844 (uri (bioconductor-uri "fgsea" version))
9847 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
9848 (build-system r-build-system)
9860 (home-page "https://github.com/ctlab/fgsea/")
9861 (synopsis "Fast gene set enrichment analysis")
9863 "The package implements an algorithm for fast gene set enrichment
9864 analysis. Using the fast algorithm makes more permutations and gets
9865 more fine grained p-values, which allows using accurate standard approaches
9866 to multiple hypothesis correction.")
9867 (license license:expat)))
9869 (define-public r-dose
9876 (uri (bioconductor-uri "DOSE" version))
9879 "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"))))
9880 (properties `((upstream-name . "DOSE")))
9881 (build-system r-build-system)
9883 (list r-annotationdbi
9893 (home-page "https://guangchuangyu.github.io/software/DOSE/")
9894 (synopsis "Disease ontology semantic and enrichment analysis")
9896 "This package implements five methods proposed by Resnik, Schlicker,
9897 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
9898 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
9899 including hypergeometric model and gene set enrichment analysis are also
9900 implemented for discovering disease associations of high-throughput biological
9902 (license license:artistic2.0)))
9904 (define-public r-enrichplot
9906 (name "r-enrichplot")
9911 (uri (bioconductor-uri "enrichplot" version))
9914 "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"))))
9915 (build-system r-build-system)
9934 (home-page "https://github.com/GuangchuangYu/enrichplot")
9935 (synopsis "Visualization of functional enrichment result")
9937 "The enrichplot package implements several visualization methods for
9938 interpreting functional enrichment results obtained from ORA or GSEA analyses.
9939 All the visualization methods are developed based on ggplot2 graphics.")
9940 (license license:artistic2.0)))
9942 (define-public r-clusterprofiler
9944 (name "r-clusterprofiler")
9949 (uri (bioconductor-uri "clusterProfiler" version))
9952 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
9954 `((upstream-name . "clusterProfiler")))
9955 (build-system r-build-system)
9957 (list r-annotationdbi
9972 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
9973 (synopsis "Analysis and visualization of functional profiles for gene clusters")
9975 "This package implements methods to analyze and visualize functional
9976 profiles (GO and KEGG) of gene and gene clusters.")
9977 (license license:artistic2.0)))
9979 (define-public r-clusterexperiment
9981 (name "r-clusterexperiment")
9985 (uri (bioconductor-uri "clusterExperiment" version))
9988 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
9989 (build-system r-build-system)
10014 r-singlecellexperiment
10016 r-summarizedexperiment
10018 (home-page "https://bioconductor.org/packages/clusterExperiment/")
10019 (synopsis "Compare clusterings for single-cell sequencing")
10020 (description "This package provides functionality for running and comparing
10021 many different clusterings of single-cell sequencing data or other large mRNA
10022 expression data sets.")
10023 (license license:artistic2.0)))
10025 (define-public r-mlinterfaces
10027 (name "r-mlinterfaces")
10032 (uri (bioconductor-uri "MLInterfaces" version))
10035 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
10036 (properties `((upstream-name . "MLInterfaces")))
10037 (build-system r-build-system)
10059 (home-page "https://bioconductor.org/packages/MLInterfaces/")
10060 (synopsis "Interfaces to R machine learning procedures")
10062 "This package provides uniform interfaces to machine learning code for
10063 data in R and Bioconductor containers.")
10064 ;; Any version of the LGPL.
10065 (license license:lgpl2.1+)))
10067 (define-public r-annaffy
10074 (uri (bioconductor-uri "annaffy" version))
10077 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
10078 (build-system r-build-system)
10081 (modify-phases %standard-phases
10082 (add-after 'unpack 'remove-reference-to-non-free-data
10084 (substitute* "DESCRIPTION"
10085 ((", KEGG.db") "")))))))
10087 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
10088 (home-page "https://bioconductor.org/packages/annaffy/")
10089 (synopsis "Annotation tools for Affymetrix biological metadata")
10091 "This package provides functions for handling data from Bioconductor
10092 Affymetrix annotation data packages. It produces compact HTML and text
10093 reports including experimental data and URL links to many online databases.
10094 It allows searching of biological metadata using various criteria.")
10095 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
10096 ;; the LGPL 2.1 is included.
10097 (license license:lgpl2.1+)))
10099 (define-public r-a4core
10106 (uri (bioconductor-uri "a4Core" version))
10109 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
10110 (properties `((upstream-name . "a4Core")))
10111 (build-system r-build-system)
10113 (list r-biobase r-glmnet))
10116 (home-page "https://bioconductor.org/packages/a4Core")
10117 (synopsis "Automated Affymetrix array analysis core package")
10119 "This is the core package for the automated analysis of Affymetrix
10121 (license license:gpl3)))
10123 (define-public r-a4classif
10125 (name "r-a4classif")
10130 (uri (bioconductor-uri "a4Classif" version))
10133 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
10134 (properties `((upstream-name . "a4Classif")))
10135 (build-system r-build-system)
10146 (home-page "https://bioconductor.org/packages/a4Classif/")
10147 (synopsis "Automated Affymetrix array analysis classification package")
10149 "This is the classification package for the automated analysis of
10150 Affymetrix arrays.")
10151 (license license:gpl3)))
10153 (define-public r-a4preproc
10155 (name "r-a4preproc")
10160 (uri (bioconductor-uri "a4Preproc" version))
10163 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
10164 (properties `((upstream-name . "a4Preproc")))
10165 (build-system r-build-system)
10167 (list r-biobase r-biocgenerics))
10170 (home-page "https://bioconductor.org/packages/a4Preproc/")
10171 (synopsis "Automated Affymetrix array analysis preprocessing package")
10173 "This is a package for the automated analysis of Affymetrix arrays. It
10174 is used for preprocessing the arrays.")
10175 (license license:gpl3)))
10177 (define-public r-a4reporting
10179 (name "r-a4reporting")
10184 (uri (bioconductor-uri "a4Reporting" version))
10187 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
10188 (properties `((upstream-name . "a4Reporting")))
10189 (build-system r-build-system)
10194 (home-page "https://bioconductor.org/packages/a4Reporting/")
10195 (synopsis "Automated Affymetrix array analysis reporting package")
10197 "This is a package for the automated analysis of Affymetrix arrays. It
10198 provides reporting features.")
10199 (license license:gpl3)))
10201 (define-public r-a4base
10208 (uri (bioconductor-uri "a4Base" version))
10211 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
10212 (properties `((upstream-name . "a4Base")))
10213 (build-system r-build-system)
10225 (home-page "https://bioconductor.org/packages/a4Base/")
10226 (synopsis "Automated Affymetrix array analysis base package")
10228 "This package provides basic features for the automated analysis of
10229 Affymetrix arrays.")
10230 (license license:gpl3)))
10232 (define-public r-a4
10239 (uri (bioconductor-uri "a4" version))
10242 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
10243 (build-system r-build-system)
10245 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
10246 (home-page "https://bioconductor.org/packages/a4/")
10247 (synopsis "Automated Affymetrix array analysis umbrella package")
10249 "This package provides a software suite for the automated analysis of
10250 Affymetrix arrays.")
10251 (license license:gpl3)))
10253 (define-public r-abseqr
10260 (uri (bioconductor-uri "abseqR" version))
10263 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
10264 (properties `((upstream-name . "abseqR")))
10265 (build-system r-build-system)
10269 (list r-biocparallel
10289 (home-page "https://github.com/malhamdoosh/abseqR")
10290 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
10292 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
10293 sequencing datasets generated from antibody libraries and abseqR is one of its
10294 packages. AbseqR empowers the users of abseqPy with plotting and reporting
10295 capabilities and allows them to generate interactive HTML reports for the
10296 convenience of viewing and sharing with other researchers. Additionally,
10297 abseqR extends abseqPy to compare multiple repertoire analyses and perform
10298 further downstream analysis on its output.")
10299 (license license:gpl3)))
10301 (define-public r-bacon
10308 (uri (bioconductor-uri "bacon" version))
10311 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
10312 (build-system r-build-system)
10314 (list r-biocparallel r-ellipse r-ggplot2))
10317 (home-page "https://bioconductor.org/packages/bacon/")
10318 (synopsis "Controlling bias and inflation in association studies")
10320 "Bacon can be used to remove inflation and bias often observed in
10321 epigenome- and transcriptome-wide association studies. To this end bacon
10322 constructs an empirical null distribution using a Gibbs Sampling algorithm by
10323 fitting a three-component normal mixture on z-scores.")
10324 (license license:gpl2+)))
10326 (define-public r-rgadem
10333 (uri (bioconductor-uri "rGADEM" version))
10336 "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"))))
10337 (properties `((upstream-name . "rGADEM")))
10338 (build-system r-build-system)
10340 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
10341 (home-page "https://bioconductor.org/packages/rGADEM/")
10342 (synopsis "De novo sequence motif discovery")
10344 "rGADEM is an efficient de novo motif discovery tool for large-scale
10345 genomic sequence data.")
10346 (license license:artistic2.0)))
10348 (define-public r-motiv
10355 (uri (bioconductor-uri "MotIV" version))
10358 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
10359 (properties `((upstream-name . "MotIV")))
10360 (build-system r-build-system)
10364 (list r-biocgenerics
10371 (home-page "https://bioconductor.org/packages/MotIV/")
10372 (synopsis "Motif identification and validation")
10374 "This package is used for the identification and validation of sequence
10375 motifs. It makes use of STAMP for comparing a set of motifs to a given
10376 database (e.g. JASPAR). It can also be used to visualize motifs, motif
10377 distributions, modules and filter motifs.")
10378 (license license:gpl2)))
10380 (define-public r-motifdb
10386 (uri (bioconductor-uri "MotifDb" version))
10388 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
10389 (properties `((upstream-name . "MotifDb")))
10390 (build-system r-build-system)
10392 (list r-biocgenerics
10398 r-splitstackshape))
10401 (home-page "https://www.bioconductor.org/packages/MotifDb/")
10402 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
10403 (description "This package provides more than 2000 annotated position
10404 frequency matrices from nine public sources, for multiple organisms.")
10405 (license license:artistic2.0)))
10407 (define-public r-motifbreakr
10409 (name "r-motifbreakr")
10413 (uri (bioconductor-uri "motifbreakR" version))
10415 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
10416 (properties `((upstream-name . "motifbreakR")))
10417 (build-system r-build-system)
10419 (list r-biocgenerics
10433 r-summarizedexperiment
10435 r-variantannotation))
10438 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
10439 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
10440 (description "This package allows biologists to judge in the first place
10441 whether the sequence surrounding the polymorphism is a good match, and in
10442 the second place how much information is gained or lost in one allele of
10443 the polymorphism relative to another. This package gives a choice of
10444 algorithms for interrogation of genomes with motifs from public sources:
10446 @item a weighted-sum probability matrix;
10447 @item log-probabilities;
10448 @item weighted by relative entropy.
10451 This package can predict effects for novel or previously described variants in
10452 public databases, making it suitable for tasks beyond the scope of its original
10453 design. Lastly, it can be used to interrogate any genome curated within
10455 (license license:gpl2+)))
10457 (define-public r-motifstack
10459 (name "r-motifstack")
10464 (uri (bioconductor-uri "motifStack" version))
10467 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
10468 (properties `((upstream-name . "motifStack")))
10469 (build-system r-build-system)
10479 (home-page "https://bioconductor.org/packages/motifStack/")
10480 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
10482 "The motifStack package is designed for graphic representation of
10483 multiple motifs with different similarity scores. It works with both DNA/RNA
10484 sequence motifs and amino acid sequence motifs. In addition, it provides the
10485 flexibility for users to customize the graphic parameters such as the font
10486 type and symbol colors.")
10487 (license license:gpl2+)))
10489 (define-public r-genomicscores
10491 (name "r-genomicscores")
10496 (uri (bioconductor-uri "GenomicScores" version))
10499 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
10500 (properties `((upstream-name . "GenomicScores")))
10501 (build-system r-build-system)
10503 (list r-annotationhub
10520 (home-page "https://github.com/rcastelo/GenomicScores/")
10521 (synopsis "Work with genome-wide position-specific scores")
10523 "This package provides infrastructure to store and access genome-wide
10524 position-specific scores within R and Bioconductor.")
10525 (license license:artistic2.0)))
10527 (define-public r-atacseqqc
10529 (name "r-atacseqqc")
10534 (uri (bioconductor-uri "ATACseqQC" version))
10537 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
10538 (properties `((upstream-name . "ATACseqQC")))
10539 (build-system r-build-system)
10541 (list r-biocgenerics
10547 r-genomicalignments
10561 (home-page "https://bioconductor.org/packages/ATACseqQC/")
10562 (synopsis "ATAC-seq quality control")
10564 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
10565 sequencing, is a rapid and sensitive method for chromatin accessibility
10566 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
10567 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
10568 assess whether their ATAC-seq experiment is successful. It includes
10569 diagnostic plots of fragment size distribution, proportion of mitochondria
10570 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
10572 (license license:gpl2+)))
10574 (define-public r-gofuncr
10581 (uri (bioconductor-uri "GOfuncR" version))
10584 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
10585 (properties `((upstream-name . "GOfuncR")))
10586 (build-system r-build-system)
10588 (list r-annotationdbi
10597 (home-page "https://bioconductor.org/packages/GOfuncR/")
10598 (synopsis "Gene ontology enrichment using FUNC")
10600 "GOfuncR performs a gene ontology enrichment analysis based on the
10601 ontology enrichment software FUNC. GO-annotations are obtained from
10602 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
10603 included in the package and updated regularly. GOfuncR provides the standard
10604 candidate vs background enrichment analysis using the hypergeometric test, as
10605 well as three additional tests:
10608 @item the Wilcoxon rank-sum test that is used when genes are ranked,
10609 @item a binomial test that is used when genes are associated with two counts,
10611 @item a Chi-square or Fisher's exact test that is used in cases when genes are
10612 associated with four counts.
10615 To correct for multiple testing and interdependency of the tests, family-wise
10616 error rates are computed based on random permutations of the gene-associated
10617 variables. GOfuncR also provides tools for exploring the ontology graph and
10618 the annotations, and options to take gene-length or spatial clustering of
10619 genes into account. It is also possible to provide custom gene coordinates,
10620 annotations and ontologies.")
10621 (license license:gpl2+)))
10623 (define-public r-abaenrichment
10625 (name "r-abaenrichment")
10630 (uri (bioconductor-uri "ABAEnrichment" version))
10633 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
10634 (properties `((upstream-name . "ABAEnrichment")))
10635 (build-system r-build-system)
10645 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
10646 (synopsis "Gene expression enrichment in human brain regions")
10648 "The package ABAEnrichment is designed to test for enrichment of user
10649 defined candidate genes in the set of expressed genes in different human brain
10650 regions. The core function @code{aba_enrich} integrates the expression of the
10651 candidate gene set (averaged across donors) and the structural information of
10652 the brain using an ontology, both provided by the Allen Brain Atlas project.")
10653 (license license:gpl2+)))
10655 (define-public r-annotationfuncs
10657 (name "r-annotationfuncs")
10662 (uri (bioconductor-uri "AnnotationFuncs" version))
10665 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
10667 `((upstream-name . "AnnotationFuncs")))
10668 (build-system r-build-system)
10670 (list r-annotationdbi r-dbi))
10671 (home-page "https://www.iysik.com/r/annotationfuncs")
10672 (synopsis "Annotation translation functions")
10674 "This package provides functions for handling translating between
10675 different identifieres using the Biocore Data Team data-packages (e.g.
10676 @code{org.Bt.eg.db}).")
10677 (license license:gpl2)))
10679 (define-public r-annotationtools
10681 (name "r-annotationtools")
10686 (uri (bioconductor-uri "annotationTools" version))
10689 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
10691 `((upstream-name . "annotationTools")))
10692 (build-system r-build-system)
10693 (propagated-inputs (list r-biobase))
10694 (home-page "https://bioconductor.org/packages/annotationTools/")
10695 (synopsis "Annotate microarrays and perform gene expression analyses")
10697 "This package provides functions to annotate microarrays, find orthologs,
10698 and integrate heterogeneous gene expression profiles using annotation and
10699 other molecular biology information available as flat file database (plain
10701 ;; Any version of the GPL.
10702 (license (list license:gpl2+))))
10704 (define-public r-allelicimbalance
10706 (name "r-allelicimbalance")
10711 (uri (bioconductor-uri "AllelicImbalance" version))
10714 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
10716 `((upstream-name . "AllelicImbalance")))
10717 (build-system r-build-system)
10719 (list r-annotationdbi
10724 r-genomicalignments
10736 r-summarizedexperiment
10737 r-variantannotation))
10740 (home-page "https://github.com/pappewaio/AllelicImbalance")
10741 (synopsis "Investigate allele-specific expression")
10743 "This package provides a framework for allele-specific expression
10744 investigation using RNA-seq data.")
10745 (license license:gpl3)))
10747 (define-public r-aucell
10754 (uri (bioconductor-uri "AUCell" version))
10757 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
10758 (properties `((upstream-name . "AUCell")))
10759 (build-system r-build-system)
10761 (list r-biocgenerics
10764 r-delayedmatrixstats
10769 r-summarizedexperiment))
10772 (home-page "https://bioconductor.org/packages/AUCell/")
10773 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
10775 "AUCell identifies cells with active gene sets (e.g. signatures,
10776 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
10777 Under the Curve} (AUC) to calculate whether a critical subset of the input
10778 gene set is enriched within the expressed genes for each cell. The
10779 distribution of AUC scores across all the cells allows exploring the relative
10780 expression of the signature. Since the scoring method is ranking-based,
10781 AUCell is independent of the gene expression units and the normalization
10782 procedure. In addition, since the cells are evaluated individually, it can
10783 easily be applied to bigger datasets, subsetting the expression matrix if
10785 (license license:gpl3)))
10787 (define-public r-ebimage
10794 (uri (bioconductor-uri "EBImage" version))
10797 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
10798 (properties `((upstream-name . "EBImage")))
10799 (build-system r-build-system)
10812 (list r-knitr)) ; for vignettes
10813 (home-page "https://github.com/aoles/EBImage")
10814 (synopsis "Image processing and analysis toolbox for R")
10816 "EBImage provides general purpose functionality for image processing and
10817 analysis. In the context of (high-throughput) microscopy-based cellular
10818 assays, EBImage offers tools to segment cells and extract quantitative
10819 cellular descriptors. This allows the automation of such tasks using the R
10820 programming language and facilitates the use of other tools in the R
10821 environment for signal processing, statistical modeling, machine learning and
10822 visualization with image data.")
10823 ;; Any version of the LGPL.
10824 (license license:lgpl2.1+)))
10826 (define-public r-yamss
10833 (uri (bioconductor-uri "yamss" version))
10836 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
10837 (build-system r-build-system)
10839 (list r-biocgenerics
10847 r-summarizedexperiment))
10850 (home-page "https://github.com/hansenlab/yamss")
10851 (synopsis "Tools for high-throughput metabolomics")
10853 "This package provides tools to analyze and visualize high-throughput
10854 metabolomics data acquired using chromatography-mass spectrometry. These tools
10855 preprocess data in a way that enables reliable and powerful differential
10857 (license license:artistic2.0)))
10859 (define-public r-gtrellis
10861 (name "r-gtrellis")
10866 (uri (bioconductor-uri "gtrellis" version))
10869 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
10870 (build-system r-build-system)
10872 (list r-circlize r-genomicranges r-getoptlong r-iranges))
10875 (home-page "https://github.com/jokergoo/gtrellis")
10876 (synopsis "Genome level Trellis layout")
10878 "Genome level Trellis graph visualizes genomic data conditioned by
10879 genomic categories (e.g. chromosomes). For each genomic category, multiple
10880 dimensional data which are represented as tracks describe different features
10881 from different aspects. This package provides high flexibility to arrange
10882 genomic categories and to add self-defined graphics in the plot.")
10883 (license license:expat)))
10885 (define-public r-somaticsignatures
10887 (name "r-somaticsignatures")
10892 (uri (bioconductor-uri "SomaticSignatures" version))
10895 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
10897 `((upstream-name . "SomaticSignatures")))
10898 (build-system r-build-system)
10912 r-variantannotation))
10915 (home-page "https://github.com/juliangehring/SomaticSignatures")
10916 (synopsis "Somatic signatures")
10918 "This package identifies mutational signatures of @dfn{single nucleotide
10919 variants} (SNVs). It provides a infrastructure related to the methodology
10920 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
10921 decomposition algorithms.")
10922 (license license:expat)))
10924 (define-public r-yapsa
10931 (uri (bioconductor-uri "YAPSA" version))
10934 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
10935 (properties `((upstream-name . "YAPSA")))
10936 (build-system r-build-system)
10939 r-bsgenome-hsapiens-ucsc-hg19
10959 r-somaticsignatures
10960 r-variantannotation))
10963 (home-page "https://bioconductor.org/packages/YAPSA/")
10964 (synopsis "Yet another package for signature analysis")
10966 "This package provides functions and routines useful in the analysis of
10967 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
10968 functions to perform a signature analysis with known signatures and a
10969 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
10971 (license license:gpl3)))
10973 (define-public r-gcrma
10980 (uri (bioconductor-uri "gcrma" version))
10983 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
10984 (build-system r-build-system)
10992 (home-page "https://bioconductor.org/packages/gcrma/")
10993 (synopsis "Background adjustment using sequence information")
10995 "Gcrma adjusts for background intensities in Affymetrix array data which
10996 include optical noise and @dfn{non-specific binding} (NSB). The main function
10997 @code{gcrma} converts background adjusted probe intensities to expression
10998 measures using the same normalization and summarization methods as a
10999 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
11000 to estimate probe affinity to NSB. The sequence information is summarized in
11001 a more complex way than the simple GC content. Instead, the base types (A, T,
11002 G or C) at each position along the probe determine the affinity of each probe.
11003 The parameters of the position-specific base contributions to the probe
11004 affinity is estimated in an NSB experiment in which only NSB but no
11005 gene-specific binding is expected.")
11006 ;; Any version of the LGPL
11007 (license license:lgpl2.1+)))
11009 (define-public r-simpleaffy
11011 (name "r-simpleaffy")
11016 (uri (bioconductor-uri "simpleaffy" version))
11019 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
11020 (build-system r-build-system)
11022 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
11023 (home-page "https://bioconductor.org/packages/simpleaffy/")
11024 (synopsis "Very simple high level analysis of Affymetrix data")
11026 "This package provides high level functions for reading Affy @file{.CEL}
11027 files, phenotypic data, and then computing simple things with it, such as
11028 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
11029 library. It also has some basic scatter plot functions and mechanisms for
11030 generating high resolution journal figures.")
11031 (license license:gpl2+)))
11033 (define-public r-yaqcaffy
11035 (name "r-yaqcaffy")
11040 (uri (bioconductor-uri "yaqcaffy" version))
11043 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
11044 (build-system r-build-system)
11046 (list r-simpleaffy))
11047 (home-page "https://bioconductor.org/packages/yaqcaffy/")
11048 (synopsis "Affymetrix quality control and reproducibility analysis")
11050 "This is a package that can be used for quality control of Affymetrix
11051 GeneChip expression data and reproducibility analysis of human whole genome
11052 chips with the MAQC reference datasets.")
11053 (license license:artistic2.0)))
11055 (define-public r-quantro
11062 (uri (bioconductor-uri "quantro" version))
11065 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
11066 (build-system r-build-system)
11077 (home-page "https://bioconductor.org/packages/quantro/")
11078 (synopsis "Test for when to use quantile normalization")
11080 "This package provides a data-driven test for the assumptions of quantile
11081 normalization using raw data such as objects that inherit eSets (e.g.
11082 ExpressionSet, MethylSet). Group level information about each sample (such as
11083 Tumor / Normal status) must also be provided because the test assesses if
11084 there are global differences in the distributions between the user-defined
11086 (license license:gpl3+)))
11088 (define-public r-yarn
11095 (uri (bioconductor-uri "yarn" version))
11098 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
11099 (build-system r-build-system)
11114 (home-page "https://bioconductor.org/packages/yarn/")
11115 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
11117 "Expedite large RNA-Seq analyses using a combination of previously
11118 developed tools. YARN is meant to make it easier for the user in performing
11119 basic mis-annotation quality control, filtering, and condition-aware
11120 normalization. YARN leverages many Bioconductor tools and statistical
11121 techniques to account for the large heterogeneity and sparsity found in very
11122 large RNA-seq experiments.")
11123 (license license:artistic2.0)))
11125 (define-public r-roar
11132 (uri (bioconductor-uri "roar" version))
11135 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
11136 (build-system r-build-system)
11138 (list r-biocgenerics
11140 r-genomicalignments
11145 r-summarizedexperiment))
11146 (home-page "https://github.com/vodkatad/roar/")
11147 (synopsis "Identify differential APA usage from RNA-seq alignments")
11149 "This package provides tools for identifying preferential usage of APA
11150 sites, comparing two biological conditions, starting from known alternative
11151 sites and alignments obtained from standard RNA-seq experiments.")
11152 (license license:gpl3)))
11154 (define-public r-xbseq
11161 (uri (bioconductor-uri "XBSeq" version))
11164 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
11165 (properties `((upstream-name . "XBSeq")))
11166 (build-system r-build-system)
11179 (home-page "https://github.com/Liuy12/XBSeq")
11180 (synopsis "Test for differential expression for RNA-seq data")
11182 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
11183 expression} (DE), where a statistical model was established based on the
11184 assumption that observed signals are the convolution of true expression
11185 signals and sequencing noises. The mapped reads in non-exonic regions are
11186 considered as sequencing noises, which follows a Poisson distribution. Given
11187 measurable observed signal and background noise from RNA-seq data, true
11188 expression signals, assuming governed by the negative binomial distribution,
11189 can be delineated and thus the accurate detection of differential expressed
11191 (license license:gpl3+)))
11193 (define-public r-massspecwavelet
11195 (name "r-massspecwavelet")
11200 (uri (bioconductor-uri "MassSpecWavelet" version))
11203 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
11205 `((upstream-name . "MassSpecWavelet")))
11206 (build-system r-build-system)
11209 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
11210 (synopsis "Mass spectrum processing by wavelet-based algorithms")
11212 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
11213 data mainly through the use of wavelet transforms. It supports peak detection
11214 based on @dfn{Continuous Wavelet Transform} (CWT).")
11215 (license license:lgpl2.0+)))
11217 (define-public r-xcms
11224 (uri (bioconductor-uri "xcms" version))
11227 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
11228 (build-system r-build-system)
11246 r-summarizedexperiment))
11249 (home-page "https://bioconductor.org/packages/xcms/")
11250 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
11252 "This package provides a framework for processing and visualization of
11253 chromatographically separated and single-spectra mass spectral data. It
11254 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
11255 data for high-throughput, untargeted analyte profiling.")
11256 (license license:gpl2+)))
11258 (define-public r-wppi
11264 (uri (bioconductor-uri "wppi" version))
11267 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
11268 (properties `((upstream-name . "wppi")))
11269 (build-system r-build-system)
11270 ;; This is necessary because omnipathr attempts to write a configuration
11274 (modify-phases %standard-phases
11275 (add-after 'unpack 'set-HOME
11276 (lambda _ (setenv "HOME" "/tmp"))))))
11277 (propagated-inputs (list r-dplyr
11289 (native-inputs (list r-knitr))
11290 (home-page "https://github.com/AnaGalhoz37/wppi")
11291 (synopsis "Weighting protein-protein interactions")
11293 "This package predicts functional relevance of protein-protein
11294 interactions based on functional annotations such as Human Protein Ontology
11295 and Gene Ontology, and prioritizes genes based on network topology, functional
11296 scores and a path search algorithm.")
11297 (license license:expat)))
11299 (define-public r-wrench
11306 (uri (bioconductor-uri "Wrench" version))
11309 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
11310 (properties `((upstream-name . "Wrench")))
11311 (build-system r-build-system)
11313 (list r-limma r-locfit r-matrixstats))
11316 (home-page "https://github.com/HCBravoLab/Wrench")
11317 (synopsis "Wrench normalization for sparse count data")
11319 "Wrench is a package for normalization sparse genomic count data, like
11320 that arising from 16s metagenomic surveys.")
11321 (license license:artistic2.0)))
11323 (define-public r-wiggleplotr
11325 (name "r-wiggleplotr")
11330 (uri (bioconductor-uri "wiggleplotr" version))
11333 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
11334 (build-system r-build-system)
11348 (home-page "https://bioconductor.org/packages/wiggleplotr/")
11349 (synopsis "Make read coverage plots from BigWig files")
11351 "This package provides tools to visualize read coverage from sequencing
11352 experiments together with genomic annotations (genes, transcripts, peaks).
11353 Introns of long transcripts can be rescaled to a fixed length for better
11354 visualization of exonic read coverage.")
11355 (license license:asl2.0)))
11357 (define-public r-widgettools
11359 (name "r-widgettools")
11364 (uri (bioconductor-uri "widgetTools" version))
11367 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
11368 (properties `((upstream-name . "widgetTools")))
11369 (build-system r-build-system)
11370 (home-page "https://bioconductor.org/packages/widgetTools/")
11371 (synopsis "Tools for creating interactive tcltk widgets")
11373 "This package contains tools to support the construction of tcltk
11375 ;; Any version of the LGPL.
11376 (license license:lgpl3+)))
11378 (define-public r-webbioc
11385 (uri (bioconductor-uri "webbioc" version))
11388 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
11389 (build-system r-build-system)
11391 (list netpbm perl))
11401 (home-page "https://www.bioconductor.org/")
11402 (synopsis "Bioconductor web interface")
11404 "This package provides an integrated web interface for doing microarray
11405 analysis using several of the Bioconductor packages. It is intended to be
11406 deployed as a centralized bioinformatics resource for use by many users.
11407 Currently only Affymetrix oligonucleotide analysis is supported.")
11408 (license license:gpl2+)))
11410 (define-public r-zinbwave
11412 (name "r-zinbwave")
11417 (uri (bioconductor-uri "zinbwave" version))
11420 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
11421 (build-system r-build-system)
11423 (list r-biocparallel
11427 r-singlecellexperiment
11429 r-summarizedexperiment))
11432 (home-page "https://bioconductor.org/packages/zinbwave")
11433 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
11434 (description "This package implements a general and flexible zero-inflated
11435 negative binomial model that can be used to provide a low-dimensional
11436 representations of single-cell RNA-seq data. The model accounts for zero
11437 inflation (dropouts), over-dispersion, and the count nature of the data.
11438 The model also accounts for the difference in library sizes and optionally
11439 for batch effects and/or other covariates, avoiding the need for pre-normalize
11441 (license license:artistic2.0)))
11443 (define-public r-zfpkm
11450 (uri (bioconductor-uri "zFPKM" version))
11453 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
11454 (properties `((upstream-name . "zFPKM")))
11455 (build-system r-build-system)
11457 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
11460 (home-page "https://github.com/ronammar/zFPKM/")
11461 (synopsis "Functions to facilitate zFPKM transformations")
11463 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
11464 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
11466 (license license:gpl3)))
11468 (define-public r-rbowtie2
11470 (name "r-rbowtie2")
11475 (uri (bioconductor-uri "Rbowtie2" version))
11478 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
11479 (properties `((upstream-name . "Rbowtie2")))
11480 (build-system r-build-system)
11482 (list r-magrittr r-rsamtools))
11484 (list samtools zlib))
11487 (home-page "https://bioconductor.org/packages/Rbowtie2/")
11488 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
11490 "This package provides an R wrapper of the popular @code{bowtie2}
11491 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
11492 rapid adapter trimming, identification, and read merging.")
11493 (license license:gpl3+)))
11495 (define-public r-progeny
11502 (uri (bioconductor-uri "progeny" version))
11505 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
11506 (build-system r-build-system)
11518 (home-page "https://github.com/saezlab/progeny")
11519 (synopsis "Pathway responsive gene activity inference")
11521 "This package provides a function to infer pathway activity from gene
11522 expression. It contains the linear model inferred in the publication
11523 \"Perturbation-response genes reveal signaling footprints in cancer gene
11525 (license license:asl2.0)))
11527 (define-public r-arrmnormalization
11529 (name "r-arrmnormalization")
11534 (uri (bioconductor-uri "ARRmNormalization" version))
11537 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
11539 `((upstream-name . "ARRmNormalization")))
11540 (build-system r-build-system)
11541 (propagated-inputs (list r-arrmdata))
11542 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
11543 (synopsis "Adaptive robust regression normalization for methylation data")
11545 "This is a package to perform the @dfn{Adaptive Robust Regression
11546 method} (ARRm) for the normalization of methylation data from the Illumina
11547 Infinium HumanMethylation 450k assay.")
11548 (license license:artistic2.0)))
11550 (define-public r-biocfilecache
11552 (name "r-biocfilecache")
11557 (uri (bioconductor-uri "BiocFileCache" version))
11560 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
11561 (properties `((upstream-name . "BiocFileCache")))
11562 (build-system r-build-system)
11574 (home-page "https://bioconductor.org/packages/BiocFileCache/")
11575 (synopsis "Manage files across sessions")
11577 "This package creates a persistent on-disk cache of files that the user
11578 can add, update, and retrieve. It is useful for managing resources (such as
11579 custom Txdb objects) that are costly or difficult to create, web resources,
11580 and data files used across sessions.")
11581 (license license:artistic2.0)))
11583 (define-public r-iclusterplus
11585 (name "r-iclusterplus")
11590 (uri (bioconductor-uri "iClusterPlus" version))
11593 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
11594 (properties `((upstream-name . "iClusterPlus")))
11595 (build-system r-build-system)
11596 (native-inputs (list gfortran))
11597 (home-page "https://bioconductor.org/packages/iClusterPlus/")
11598 (synopsis "Integrative clustering of multi-type genomic data")
11600 "iClusterPlus is developed for integrative clustering analysis of
11601 multi-type genomic data and is an enhanced version of iCluster proposed and
11602 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
11603 from the experiments where biological samples (e.g. tumor samples) are
11604 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
11605 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
11606 on. In the iClusterPlus model, binary observations such as somatic mutation
11607 are modeled as Binomial processes; categorical observations such as copy
11608 number states are realizations of Multinomial random variables; counts are
11609 modeled as Poisson random processes; and continuous measures are modeled by
11610 Gaussian distributions.")
11611 (license license:gpl2+)))
11613 (define-public r-rbowtie
11620 (uri (bioconductor-uri "Rbowtie" version))
11623 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
11624 (properties `((upstream-name . "Rbowtie")))
11625 (build-system r-build-system)
11628 ;; Disable unsupported `popcnt' instructions on
11629 ;; architectures other than x86_64
11630 ,(if (string-prefix? "x86_64"
11631 (or (%current-target-system)
11632 (%current-system)))
11634 '(modify-phases %standard-phases
11635 (add-after 'unpack 'patch-sources
11637 (setenv "POPCNT_CAPABILITY" "0")))))))
11638 (inputs (list zlib))
11641 (home-page "https://bioconductor.org/packages/Rbowtie/")
11642 (synopsis "R bowtie wrapper")
11644 "This package provides an R wrapper around the popular bowtie short read
11645 aligner and around SpliceMap, a de novo splice junction discovery and
11647 (license license:artistic2.0)))
11649 (define-public r-sgseq
11656 (uri (bioconductor-uri "SGSeq" version))
11659 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
11660 (properties `((upstream-name . "SGSeq")))
11661 (build-system r-build-system)
11663 (list r-annotationdbi
11667 r-genomicalignments
11676 r-summarizedexperiment))
11679 (home-page "https://bioconductor.org/packages/SGSeq/")
11680 (synopsis "Splice event prediction and quantification from RNA-seq data")
11682 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
11683 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
11684 represented as a splice graph, which can be obtained from existing annotation
11685 or predicted from the mapped sequence reads. Splice events are identified
11686 from the graph and are quantified locally using structurally compatible reads
11687 at the start or end of each splice variant. The software includes functions
11688 for splice event prediction, quantification, visualization and
11690 (license license:artistic2.0)))
11692 (define-public r-rhisat2
11699 (uri (bioconductor-uri "Rhisat2" version))
11702 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
11703 (properties `((upstream-name . "Rhisat2")))
11704 (build-system r-build-system)
11707 (modify-phases %standard-phases
11708 (add-after 'unpack 'make-reproducible
11710 (substitute* "src/Makefile"
11711 (("`hostname`") "guix")
11713 ;; Avoid shelling out to "which".
11714 (("^CC =.*") (which "gcc"))
11715 (("^CPP =.*") (which "g++")))
11718 (list r-genomicfeatures r-genomicranges r-sgseq))
11721 (home-page "https://github.com/fmicompbio/Rhisat2")
11722 (synopsis "R Wrapper for HISAT2 sequence aligner")
11724 "This package provides an R interface to the HISAT2 spliced short-read
11725 aligner by Kim et al. (2015). The package contains wrapper functions to
11726 create a genome index and to perform the read alignment to the generated
11728 (license license:gpl3)))
11730 (define-public r-quasr
11737 (uri (bioconductor-uri "QuasR" version))
11740 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
11741 (properties `((upstream-name . "QuasR")))
11742 (build-system r-build-system)
11744 (list r-annotationdbi
11763 (home-page "https://bioconductor.org/packages/QuasR/")
11764 (synopsis "Quantify and annotate short reads in R")
11766 "This package provides a framework for the quantification and analysis of
11767 short genomic reads. It covers a complete workflow starting from raw sequence
11768 reads, over creation of alignments and quality control plots, to the
11769 quantification of genomic regions of interest.")
11770 (license license:gpl2)))
11772 (define-public r-rqc
11779 (uri (bioconductor-uri "Rqc" version))
11782 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
11783 (properties `((upstream-name . "Rqc")))
11784 (build-system r-build-system)
11786 (list r-biocgenerics
11791 r-genomicalignments
11806 (home-page "https://github.com/labbcb/Rqc")
11807 (synopsis "Quality control tool for high-throughput sequencing data")
11809 "Rqc is an optimized tool designed for quality control and assessment of
11810 high-throughput sequencing data. It performs parallel processing of entire
11811 files and produces a report which contains a set of high-resolution
11813 (license license:gpl2+)))
11815 (define-public r-birewire
11817 (name "r-birewire")
11822 (uri (bioconductor-uri "BiRewire" version))
11825 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
11826 (properties `((upstream-name . "BiRewire")))
11827 (build-system r-build-system)
11829 (list r-igraph r-matrix r-rtsne r-slam))
11830 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
11831 (synopsis "Tools for randomization of bipartite graphs")
11833 "This package provides functions for bipartite network rewiring through N
11834 consecutive switching steps and for the computation of the minimal number of
11835 switching steps to be performed in order to maximise the dissimilarity with
11836 respect to the original network. It includes functions for the analysis of
11837 the introduced randomness across the switching steps and several other
11838 routines to analyse the resulting networks and their natural projections.")
11839 (license license:gpl3)))
11841 (define-public r-birta
11848 (uri (bioconductor-uri "birta" version))
11851 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
11852 (build-system r-build-system)
11854 (list r-biobase r-limma r-mass))
11855 (home-page "https://bioconductor.org/packages/birta")
11856 (synopsis "Bayesian inference of regulation of transcriptional activity")
11858 "Expression levels of mRNA molecules are regulated by different
11859 processes, comprising inhibition or activation by transcription factors and
11860 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
11861 Inference of Regulation of Transcriptional Activity) uses the regulatory
11862 networks of transcription factors and miRNAs together with mRNA and miRNA
11863 expression data to predict switches in regulatory activity between two
11864 conditions. A Bayesian network is used to model the regulatory structure and
11865 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
11866 (license license:gpl2+)))
11868 (define-public r-multidataset
11870 (name "r-multidataset")
11875 (uri (bioconductor-uri "MultiDataSet" version))
11878 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
11879 (properties `((upstream-name . "MultiDataSet")))
11880 (build-system r-build-system)
11891 r-summarizedexperiment))
11894 (home-page "https://bioconductor.org/packages/MultiDataSet/")
11895 (synopsis "Implementation of MultiDataSet and ResultSet")
11897 "This package provides an implementation of the BRGE's (Bioinformatic
11898 Research Group in Epidemiology from Center for Research in Environmental
11899 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
11900 integrating multi omics data sets and ResultSet is a container for omics
11901 results. This package contains base classes for MEAL and rexposome
11903 (license license:expat)))
11905 (define-public r-ropls
11912 (uri (bioconductor-uri "ropls" version))
11915 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
11916 (build-system r-build-system)
11919 r-multiassayexperiment
11921 r-summarizedexperiment))
11923 (list r-knitr)) ; for vignettes
11924 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
11925 (synopsis "Multivariate analysis and feature selection of omics data")
11927 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
11928 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
11929 regression, classification, and feature selection of omics data where the
11930 number of variables exceeds the number of samples and with multicollinearity
11931 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
11932 separately model the variation correlated (predictive) to the factor of
11933 interest and the uncorrelated (orthogonal) variation. While performing
11934 similarly to PLS, OPLS facilitates interpretation.
11936 This package provides imlementations of PCA, PLS, and OPLS for multivariate
11937 analysis and feature selection of omics data. In addition to scores, loadings
11938 and weights plots, the package provides metrics and graphics to determine the
11939 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
11940 validity of the model by permutation testing, detect outliers, and perform
11941 feature selection (e.g. with Variable Importance in Projection or regression
11943 (license license:cecill)))
11945 (define-public r-biosigner
11947 (name "r-biosigner")
11952 (uri (bioconductor-uri "biosigner" version))
11955 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
11956 (build-system r-build-system)
11960 r-multiassayexperiment
11964 r-summarizedexperiment))
11967 (home-page "https://bioconductor.org/packages/biosigner/")
11968 (synopsis "Signature discovery from omics data")
11970 "Feature selection is critical in omics data analysis to extract
11971 restricted and meaningful molecular signatures from complex and high-dimension
11972 data, and to build robust classifiers. This package implements a method to
11973 assess the relevance of the variables for the prediction performances of the
11974 classifier. The approach can be run in parallel with the PLS-DA, Random
11975 Forest, and SVM binary classifiers. The signatures and the corresponding
11976 'restricted' models are returned, enabling future predictions on new
11978 (license license:cecill)))
11980 (define-public r-annotatr
11982 (name "r-annotatr")
11987 (uri (bioconductor-uri "annotatr" version))
11990 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
11991 (build-system r-build-system)
11993 (list r-annotationdbi
12008 (home-page "https://bioconductor.org/packages/annotatr/")
12009 (synopsis "Annotation of genomic regions to genomic annotations")
12011 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
12012 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
12013 to investigate the intersecting genomic annotations. Such annotations include
12014 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
12015 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
12016 enhancers. The annotatr package provides an easy way to summarize and
12017 visualize the intersection of genomic sites/regions with genomic
12019 (license license:gpl3)))
12021 (define-public r-rsubread
12023 (name "r-rsubread")
12028 (uri (bioconductor-uri "Rsubread" version))
12031 "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2"))))
12032 (properties `((upstream-name . "Rsubread")))
12033 (build-system r-build-system)
12034 (inputs (list zlib))
12037 (home-page "https://bioconductor.org/packages/Rsubread/")
12038 (synopsis "Subread sequence alignment and counting for R")
12040 "This package provides tools for alignment, quantification and analysis
12041 of second and third generation sequencing data. It includes functionality for
12042 read mapping, read counting, SNP calling, structural variant detection and
12043 gene fusion discovery. It can be applied to all major sequencing techologies
12044 and to both short and long sequence reads.")
12045 (license license:gpl3)))
12047 (define-public r-flowutils
12049 (name "r-flowutils")
12054 (uri (bioconductor-uri "flowUtils" version))
12057 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
12058 (properties `((upstream-name . "flowUtils")))
12059 (build-system r-build-system)
12067 (home-page "https://github.com/jspidlen/flowUtils")
12068 (synopsis "Utilities for flow cytometry")
12070 "This package provides utilities for flow cytometry data.")
12071 (license license:artistic2.0)))
12073 (define-public r-consensusclusterplus
12075 (name "r-consensusclusterplus")
12080 (uri (bioconductor-uri "ConsensusClusterPlus" version))
12083 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
12085 `((upstream-name . "ConsensusClusterPlus")))
12086 (build-system r-build-system)
12088 (list r-all r-biobase r-cluster))
12089 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
12090 (synopsis "Clustering algorithm")
12092 "This package provides an implementation of an algorithm for determining
12093 cluster count and membership by stability evidence in unsupervised analysis.")
12094 (license license:gpl2)))
12096 ;; This is the latest commit and it solves a bug from the latest release.
12097 (define-public r-cycombine
12098 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
12100 (name "r-cycombine")
12101 (version (git-version "0.2.6" revision commit))
12104 (uri (git-reference
12105 (url "https://github.com/biosurf/cyCombine")
12107 (file-name (git-file-name name version))
12110 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
12111 (properties `((upstream-name . "cyCombine")))
12112 (build-system r-build-system)
12130 (native-inputs (list r-knitr))
12131 (home-page "https://github.com/biosurf/cyCombine")
12132 (synopsis "Integration of single-cell cytometry datasets")
12134 "This package provides a method for combining single-cell cytometry
12135 datasets, which increases the analytical flexibility and the statistical power
12136 of the analyses while minimizing technical noise.")
12137 (license license:expat))))
12139 (define-public r-cytolib
12146 (uri (bioconductor-uri "cytolib" version))
12149 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
12150 (properties `((upstream-name . "cytolib")))
12151 (build-system r-build-system)
12161 (home-page "https://bioconductor.org/packages/cytolib/")
12162 (synopsis "C++ infrastructure for working with gated cytometry")
12164 "This package provides the core data structure and API to represent and
12165 interact with gated cytometry data.")
12166 (license license:artistic2.0)))
12168 (define-public r-flowcore
12170 (name "r-flowcore")
12175 (uri (bioconductor-uri "flowCore" version))
12178 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
12179 (properties `((upstream-name . "flowCore")))
12180 (build-system r-build-system)
12193 (home-page "https://bioconductor.org/packages/flowCore")
12194 (synopsis "Basic structures for flow cytometry data")
12196 "This package provides S4 data structures and basic functions to deal
12197 with flow cytometry data.")
12198 (license license:artistic2.0)))
12200 (define-public r-flowmeans
12202 (name "r-flowmeans")
12207 (uri (bioconductor-uri "flowMeans" version))
12210 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
12211 (properties `((upstream-name . "flowMeans")))
12212 (build-system r-build-system)
12214 (list r-biobase r-feature r-flowcore r-rrcov))
12215 (home-page "https://bioconductor.org/packages/flowMeans")
12216 (synopsis "Non-parametric flow cytometry data gating")
12218 "This package provides tools to identify cell populations in Flow
12219 Cytometry data using non-parametric clustering and segmented-regression-based
12220 change point detection.")
12221 (license license:artistic2.0)))
12223 (define-public r-ncdfflow
12225 (name "r-ncdfflow")
12230 (uri (bioconductor-uri "ncdfFlow" version))
12233 "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7"))))
12234 (properties `((upstream-name . "ncdfFlow")))
12235 (build-system r-build-system)
12247 (home-page "https://bioconductor.org/packages/ncdfFlow/")
12248 (synopsis "HDF5 based storage for flow cytometry data")
12250 "This package provides HDF5 storage based methods and functions for
12251 manipulation of flow cytometry data.")
12252 (license license:artistic2.0)))
12254 (define-public r-ggcyto
12261 (uri (bioconductor-uri "ggcyto" version))
12264 "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325"))))
12265 (properties `((upstream-name . "ggcyto")))
12266 (build-system r-build-system)
12281 (home-page "https://github.com/RGLab/ggcyto/issues")
12282 (synopsis "Visualize Cytometry data with ggplot")
12284 "With the dedicated fortify method implemented for @code{flowSet},
12285 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
12286 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
12287 and some custom layers also make it easy to add gates and population
12288 statistics to the plot.")
12289 (license license:artistic2.0)))
12291 (define-public r-flowviz
12298 (uri (bioconductor-uri "flowViz" version))
12301 "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95"))))
12302 (properties `((upstream-name . "flowViz")))
12303 (build-system r-build-system)
12316 (home-page "https://bioconductor.org/packages/flowViz/")
12317 (synopsis "Visualization for flow cytometry")
12319 "This package provides visualization tools for flow cytometry data.")
12320 (license license:artistic2.0)))
12322 (define-public r-flowclust
12324 (name "r-flowclust")
12329 (uri (bioconductor-uri "flowClust" version))
12332 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
12333 (properties `((upstream-name . "flowClust")))
12334 (build-system r-build-system)
12336 `(#:configure-flags
12337 (list "--configure-args=--enable-bundled-gsl=no")))
12346 (list pkg-config r-knitr))
12347 (home-page "https://bioconductor.org/packages/flowClust")
12348 (synopsis "Clustering for flow cytometry")
12350 "This package provides robust model-based clustering using a t-mixture
12351 model with Box-Cox transformation.")
12352 (license license:artistic2.0)))
12354 ;; TODO: this package bundles an old version of protobuf. It's not easy to
12355 ;; make it use our protobuf package instead.
12356 (define-public r-rprotobuflib
12358 (name "r-rprotobuflib")
12363 (uri (bioconductor-uri "RProtoBufLib" version))
12366 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
12367 (properties `((upstream-name . "RProtoBufLib")))
12368 (build-system r-build-system)
12371 (modify-phases %standard-phases
12372 (add-after 'unpack 'unpack-bundled-sources
12374 (with-directory-excursion "src"
12375 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
12378 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
12379 (synopsis "C++ headers and static libraries of Protocol buffers")
12381 "This package provides the headers and static library of Protocol buffers
12382 for other R packages to compile and link against.")
12383 (license license:bsd-3)))
12385 (define-public r-flowworkspace
12387 (name "r-flowworkspace")
12392 (uri (bioconductor-uri "flowWorkspace" version))
12395 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
12396 (properties `((upstream-name . "flowWorkspace")))
12397 (build-system r-build-system)
12428 (home-page "https://bioconductor.org/packages/flowWorkspace/")
12429 (synopsis "Infrastructure for working with cytometry data")
12431 "This package is designed to facilitate comparison of automated gating
12432 methods against manual gating done in flowJo. This package allows you to
12433 import basic flowJo workspaces into BioConductor and replicate the gating from
12434 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
12435 samples, compensation, and transformation are performed so that the output
12436 matches the flowJo analysis.")
12437 (license license:artistic2.0)))
12439 (define-public r-flowstats
12441 (name "r-flowstats")
12446 (uri (bioconductor-uri "flowStats" version))
12449 "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc"))))
12450 (properties `((upstream-name . "flowStats")))
12451 (build-system r-build-system)
12469 (home-page "http://www.github.com/RGLab/flowStats")
12470 (synopsis "Statistical methods for the analysis of flow cytometry data")
12472 "This package provides methods and functionality to analyze flow data
12473 that is beyond the basic infrastructure provided by the @code{flowCore}
12475 (license license:artistic2.0)))
12477 (define-public r-opencyto
12479 (name "r-opencyto")
12484 (uri (bioconductor-uri "openCyto" version))
12487 "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0"))))
12488 (properties `((upstream-name . "openCyto")))
12489 (build-system r-build-system)
12514 (home-page "https://bioconductor.org/packages/openCyto")
12515 (synopsis "Hierarchical gating pipeline for flow cytometry data")
12517 "This package is designed to facilitate the automated gating methods in a
12518 sequential way to mimic the manual gating strategy.")
12519 (license license:artistic2.0)))
12521 (define-public r-cytoml
12528 (uri (bioconductor-uri "CytoML" version))
12531 "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw"))))
12532 (properties `((upstream-name . "CytoML")))
12533 (build-system r-build-system)
12535 (list libxml2 zlib))
12566 (home-page "https://github.com/RGLab/CytoML")
12567 (synopsis "GatingML interface for cross platform cytometry data sharing")
12569 "This package provides an interface to implementations of the GatingML2.0
12570 standard to exchange gated cytometry data with other software platforms.")
12571 (license license:artistic2.0)))
12573 (define-public r-flowsom
12580 (uri (bioconductor-uri "FlowSOM" version))
12583 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
12584 (properties `((upstream-name . "FlowSOM")))
12585 (build-system r-build-system)
12587 (list r-biocgenerics
12589 r-consensusclusterplus
12609 (home-page "https://bioconductor.org/packages/FlowSOM/")
12610 (synopsis "Visualize and interpret cytometry data")
12612 "FlowSOM offers visualization options for cytometry data, by using
12613 self-organizing map clustering and minimal spanning trees.")
12614 (license license:gpl2+)))
12616 (define-public r-mixomics
12618 (name "r-mixomics")
12623 (uri (bioconductor-uri "mixOmics" version))
12626 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
12627 (properties `((upstream-name . "mixOmics")))
12628 (build-system r-build-system)
12630 (list r-biocparallel
12647 (home-page "http://www.mixOmics.org")
12648 (synopsis "Multivariate methods for exploration of biological datasets")
12650 "mixOmics offers a wide range of multivariate methods for the exploration
12651 and integration of biological datasets with a particular focus on variable
12652 selection. The package proposes several sparse multivariate models we have
12653 developed to identify the key variables that are highly correlated, and/or
12654 explain the biological outcome of interest. The data that can be analysed
12655 with mixOmics may come from high throughput sequencing technologies, such as
12656 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
12657 also beyond the realm of omics (e.g. spectral imaging). The methods
12658 implemented in mixOmics can also handle missing values without having to
12659 delete entire rows with missing data.")
12660 (license license:gpl2+)))
12662 (define-public r-depecher
12663 (package ;Source/Weave error
12664 (name "r-depecher")
12669 (uri (bioconductor-uri "DepecheR" version))
12672 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
12673 (properties `((upstream-name . "DepecheR")))
12674 (build-system r-build-system)
12695 (home-page "https://bioconductor.org/packages/DepecheR/")
12696 (synopsis "Identify traits of clusters in high-dimensional entities")
12698 "The purpose of this package is to identify traits in a dataset that can
12699 separate groups. This is done on two levels. First, clustering is performed,
12700 using an implementation of sparse K-means. Secondly, the generated clusters
12701 are used to predict outcomes of groups of individuals based on their
12702 distribution of observations in the different clusters. As certain clusters
12703 with separating information will be identified, and these clusters are defined
12704 by a sparse number of variables, this method can reduce the complexity of
12705 data, to only emphasize the data that actually matters.")
12706 (license license:expat)))
12708 (define-public r-rcistarget
12710 (name "r-rcistarget")
12715 (uri (bioconductor-uri "RcisTarget" version))
12718 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
12719 (properties `((upstream-name . "RcisTarget")))
12720 (build-system r-build-system)
12732 r-summarizedexperiment
12736 (home-page "https://aertslab.org/#scenic")
12737 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
12739 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
12740 over-represented on a gene list. In a first step, RcisTarget selects DNA
12741 motifs that are significantly over-represented in the surroundings of the
12742 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
12743 achieved by using a database that contains genome-wide cross-species rankings
12744 for each motif. The motifs that are then annotated to TFs and those that have
12745 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
12746 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
12747 genes in the gene-set that are ranked above the leading edge).")
12748 (license license:gpl3)))
12750 (define-public r-chicago
12757 (uri (bioconductor-uri "Chicago" version))
12760 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
12761 (properties `((upstream-name . "Chicago")))
12762 (build-system r-build-system)
12764 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
12765 (native-inputs (list r-knitr))
12766 (home-page "https://bioconductor.org/packages/Chicago")
12767 (synopsis "Capture Hi-C analysis of genomic organization")
12769 "This package provides a pipeline for analysing Capture Hi-C data.")
12770 (license license:artistic2.0)))
12772 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12774 (define-public r-ciara
12780 (uri (cran-uri "CIARA" version))
12783 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
12784 (properties `((upstream-name . "CIARA")))
12785 (build-system r-build-system)
12786 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
12787 (native-inputs (list r-knitr))
12788 (home-page "https://cran.r-project.org/package=CIARA")
12789 (synopsis "Cluster-independent algorithm for rare cell types identification")
12791 "This is a package to support identification of markers of rare cell
12792 types by looking at genes whose expression is confined in small regions of the
12793 expression space.")
12794 (license license:artistic2.0)))
12796 (define-public r-cicero
12803 (uri (bioconductor-uri "cicero" version))
12806 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
12807 (build-system r-build-system)
12833 (home-page "https://bioconductor.org/packages/cicero/")
12834 (synopsis "Predict cis-co-accessibility from single-cell data")
12836 "Cicero computes putative cis-regulatory maps from single-cell chromatin
12837 accessibility data. It also extends the monocle package for use in chromatin
12838 accessibility data.")
12839 (license license:expat)))
12841 ;; This is the latest commit on the "monocle3" branch.
12842 (define-public r-cicero-monocle3
12843 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
12845 (package (inherit r-cicero)
12846 (name "r-cicero-monocle3")
12847 (version (git-version "1.3.2" revision commit))
12851 (uri (git-reference
12852 (url "https://github.com/cole-trapnell-lab/cicero-release")
12854 (file-name (git-file-name name version))
12857 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
12859 (modify-inputs (package-propagated-inputs r-cicero)
12860 (delete "r-monocle")
12861 (prepend r-monocle3))))))
12863 (define-public r-circrnaprofiler
12865 (name "r-circrnaprofiler")
12870 (uri (bioconductor-uri "circRNAprofiler" version))
12873 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
12875 `((upstream-name . "circRNAprofiler")))
12876 (build-system r-build-system)
12878 (list r-annotationhub
12881 r-bsgenome-hsapiens-ucsc-hg19
12904 "https://github.com/Aufiero/circRNAprofiler")
12906 "Computational framework for the downstream analysis of circular RNA's")
12908 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
12909 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
12910 framework allows combining and analyzing circRNAs previously detected by
12911 multiple publicly available annotation-based circRNA detection tools. It
12912 covers different aspects of circRNAs analysis from differential expression
12913 analysis, evolutionary conservation, biogenesis to functional analysis.")
12914 (license license:gpl3)))
12916 (define-public r-cistopic
12918 (name "r-cistopic")
12923 (uri (git-reference
12924 (url "https://github.com/aertslab/cisTopic")
12925 (commit (string-append "v" version))))
12926 (file-name (git-file-name name version))
12929 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
12930 (build-system r-build-system)
12947 (home-page "https://github.com/aertslab/cisTopic")
12948 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
12950 "The sparse nature of single cell epigenomics data can be overruled using
12951 probabilistic modelling methods such as @dfn{Latent Dirichlet
12952 Allocation} (LDA). This package allows the probabilistic modelling of
12953 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
12954 includes functionalities to identify cell states based on the contribution of
12955 cisTopics and explore the nature and regulatory proteins driving them.")
12956 (license license:gpl3)))
12958 (define-public r-cistopic-next
12959 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
12962 (inherit r-cistopic)
12963 (name "r-cistopic-next")
12964 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
12965 ;; since the previous release is 2.1.0. Oh well.
12966 (version (git-version "0.3.0" revision commit))
12970 (uri (git-reference
12971 (url "https://github.com/aertslab/cisTopic")
12973 (file-name (git-file-name name version))
12976 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
12977 (properties `((upstream-name . "cisTopic")))
12998 (define-public r-genie3
13005 (uri (bioconductor-uri "GENIE3" version))
13008 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
13009 (properties `((upstream-name . "GENIE3")))
13010 (build-system r-build-system)
13012 (list r-dplyr r-reshape2))
13015 (home-page "https://bioconductor.org/packages/GENIE3")
13016 (synopsis "Gene network inference with ensemble of trees")
13018 "This package implements the GENIE3 algorithm for inferring gene
13019 regulatory networks from expression data.")
13020 (license license:gpl2+)))
13022 (define-public r-roc
13029 (uri (bioconductor-uri "ROC" version))
13032 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
13033 (properties `((upstream-name . "ROC")))
13034 (build-system r-build-system)
13037 (home-page "https://www.bioconductor.org/packages/ROC/")
13038 (synopsis "Utilities for ROC curves")
13040 "This package provides utilities for @dfn{Receiver Operating
13041 Characteristic} (ROC) curves, with a focus on micro arrays.")
13042 (license license:artistic2.0)))
13044 (define-public r-watermelon
13046 (name "r-watermelon")
13051 (uri (bioconductor-uri "wateRmelon" version))
13054 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
13055 (properties `((upstream-name . "wateRmelon")))
13056 (build-system r-build-system)
13059 r-illuminahumanmethylation450kanno-ilmn12-hg19
13068 (home-page "https://bioconductor.org/packages/wateRmelon/")
13069 (synopsis "Illumina 450 methylation array normalization and metrics")
13071 "The standard index of DNA methylation (beta) is computed from methylated
13072 and unmethylated signal intensities. Betas calculated from raw signal
13073 intensities perform well, but using 11 methylomic datasets we demonstrate that
13074 quantile normalization methods produce marked improvement. The commonly used
13075 procedure of normalizing betas is inferior to the separate normalization of M
13076 and U, and it is also advantageous to normalize Type I and Type II assays
13077 separately. This package provides 15 flavours of betas and three performance
13078 metrics, with methods for objects produced by the @code{methylumi} and
13079 @code{minfi} packages.")
13080 (license license:gpl3)))
13082 (define-public r-gdsfmt
13089 (uri (bioconductor-uri "gdsfmt" version))
13092 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
13093 (modules '((guix build utils)))
13094 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
13095 ;; them and link with system libraries instead.
13098 (for-each delete-file-recursively
13102 (substitute* "src/Makevars"
13103 (("all: \\$\\(SHLIB\\)") "all:")
13104 (("\\$\\(SHLIB\\): liblzma.a") "")
13105 (("^ (ZLIB|LZ4)/.*") "")
13106 (("CoreArray/dVLIntGDS.cpp.*")
13107 "CoreArray/dVLIntGDS.cpp")
13108 (("CoreArray/dVLIntGDS.o.*")
13109 "CoreArray/dVLIntGDS.o")
13110 (("PKG_LIBS = ./liblzma.a")
13111 "PKG_LIBS = -llz4"))
13112 (substitute* "src/CoreArray/dStream.h"
13113 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
13114 (string-append "include <" header ">")))))))
13115 (properties `((upstream-name . "gdsfmt")))
13116 (build-system r-build-system)
13118 (list lz4 xz zlib))
13121 (home-page "http://corearray.sourceforge.net/")
13123 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
13125 "This package provides a high-level R interface to CoreArray @dfn{Genomic
13126 Data Structure} (GDS) data files, which are portable across platforms with
13127 hierarchical structure to store multiple scalable array-oriented data sets
13128 with metadata information. It is suited for large-scale datasets, especially
13129 for data which are much larger than the available random-access memory. The
13130 @code{gdsfmt} package offers efficient operations specifically designed for
13131 integers of less than 8 bits, since a diploid genotype, like
13132 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
13133 byte. Data compression and decompression are available with relatively
13134 efficient random access. It is also allowed to read a GDS file in parallel
13135 with multiple R processes supported by the package @code{parallel}.")
13136 (license license:lgpl3)))
13138 (define-public r-bigmelon
13140 (name "r-bigmelon")
13145 (uri (bioconductor-uri "bigmelon" version))
13148 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
13149 (properties `((upstream-name . "bigmelon")))
13150 (build-system r-build-system)
13162 (home-page "https://bioconductor.org/packages/bigmelon/")
13163 (synopsis "Illumina methylation array analysis for large experiments")
13165 "This package provides methods for working with Illumina arrays using the
13166 @code{gdsfmt} package.")
13167 (license license:gpl3)))
13169 (define-public r-seqbias
13176 (uri (bioconductor-uri "seqbias" version))
13179 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
13180 (properties `((upstream-name . "seqbias")))
13181 (build-system r-build-system)
13183 (list r-biostrings r-genomicranges r-rhtslib))
13184 (home-page "https://bioconductor.org/packages/seqbias/")
13185 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
13187 "This package implements a model of per-position sequencing bias in
13188 high-throughput sequencing data using a simple Bayesian network, the structure
13189 and parameters of which are trained on a set of aligned reads and a reference
13191 (license license:lgpl3)))
13193 (define-public r-reqon
13200 (uri (bioconductor-uri "ReQON" version))
13203 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
13204 (properties `((upstream-name . "ReQON")))
13205 (build-system r-build-system)
13207 (list r-rjava r-rsamtools r-seqbias))
13208 (home-page "https://bioconductor.org/packages/ReQON/")
13209 (synopsis "Recalibrating quality of nucleotides")
13211 "This package provides an implementation of an algorithm for
13212 recalibrating the base quality scores for aligned sequencing data in BAM
13214 (license license:gpl2)))
13216 (define-public r-wavcluster
13218 (name "r-wavcluster")
13223 (uri (bioconductor-uri "wavClusteR" version))
13226 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
13227 (properties `((upstream-name . "wavClusteR")))
13228 (build-system r-build-system)
13230 (list r-biocgenerics
13246 (home-page "https://bioconductor.org/packages/wavClusteR/")
13247 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
13249 "This package provides an integrated pipeline for the analysis of
13250 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
13251 sequencing errors, SNPs and additional non-experimental sources by a non-
13252 parametric mixture model. The protein binding sites (clusters) are then
13253 resolved at high resolution and cluster statistics are estimated using a
13254 rigorous Bayesian framework. Post-processing of the results, data export for
13255 UCSC genome browser visualization and motif search analysis are provided. In
13256 addition, the package integrates RNA-Seq data to estimate the False
13257 Discovery Rate of cluster detection. Key functions support parallel multicore
13258 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
13259 be applied to the analysis of other NGS data obtained from experimental
13260 procedures that induce nucleotide substitutions (e.g. BisSeq).")
13261 (license license:gpl2)))
13263 (define-public r-timeseriesexperiment
13265 (name "r-timeseriesexperiment")
13270 (uri (bioconductor-uri "TimeSeriesExperiment" version))
13273 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
13275 `((upstream-name . "TimeSeriesExperiment")))
13276 (build-system r-build-system)
13288 r-summarizedexperiment
13295 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
13296 (synopsis "Analysis for short time-series data")
13298 "This package is a visualization and analysis toolbox for short time
13299 course data which includes dimensionality reduction, clustering, two-sample
13300 differential expression testing and gene ranking techniques. The package also
13301 provides methods for retrieving enriched pathways.")
13302 (license license:lgpl3+)))
13304 (define-public r-variantfiltering
13306 (name "r-variantfiltering")
13311 (uri (bioconductor-uri "VariantFiltering" version))
13314 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
13316 `((upstream-name . "VariantFiltering")))
13317 (build-system r-build-system)
13319 (list r-annotationdbi
13340 r-summarizedexperiment
13341 r-variantannotation
13343 (home-page "https://github.com/rcastelo/VariantFiltering")
13344 (synopsis "Filtering of coding and non-coding genetic variants")
13346 "Filter genetic variants using different criteria such as inheritance
13347 model, amino acid change consequence, minor allele frequencies across human
13348 populations, splice site strength, conservation, etc.")
13349 (license license:artistic2.0)))
13351 (define-public r-genomegraphs
13353 (name "r-genomegraphs")
13358 (uri (bioconductor-uri "GenomeGraphs" version))
13361 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
13362 (properties `((upstream-name . "GenomeGraphs")))
13363 (build-system r-build-system)
13366 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
13367 (synopsis "Plotting genomic information from Ensembl")
13369 "Genomic data analyses requires integrated visualization of known genomic
13370 information and new experimental data. GenomeGraphs uses the biomaRt package
13371 to perform live annotation queries to Ensembl and translates this to e.g.
13372 gene/transcript structures in viewports of the grid graphics package. This
13373 results in genomic information plotted together with your data. Another
13374 strength of GenomeGraphs is to plot different data types such as array CGH,
13375 gene expression, sequencing and other data, together in one plot using the
13376 same genome coordinate system.")
13377 (license license:artistic2.0)))
13379 (define-public r-wavetiling
13381 (name "r-wavetiling")
13386 (uri (bioconductor-uri "waveTiling" version))
13389 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
13390 (properties `((upstream-name . "waveTiling")))
13391 (build-system r-build-system)
13403 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
13404 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
13406 "This package is designed to conduct transcriptome analysis for tiling
13407 arrays based on fast wavelet-based functional models.")
13408 (license license:gpl2+)))
13410 (define-public r-variancepartition
13412 (name "r-variancepartition")
13417 (uri (bioconductor-uri "variancePartition" version))
13420 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
13422 `((upstream-name . "variancePartition")))
13423 (build-system r-build-system)
13447 (home-page "https://bioconductor.org/packages/variancePartition/")
13448 (synopsis "Analyze variation in gene expression experiments")
13450 "This is a package providing tools to quantify and interpret multiple
13451 sources of biological and technical variation in gene expression experiments.
13452 It uses a linear mixed model to quantify variation in gene expression
13453 attributable to individual, tissue, time point, or technical variables. The
13454 package includes dream differential expression analysis for repeated
13456 (license license:gpl2+)))
13458 (define-public r-htqpcr
13465 (uri (bioconductor-uri "HTqPCR" version))
13468 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
13469 (properties `((upstream-name . "HTqPCR")))
13470 (build-system r-build-system)
13472 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
13473 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
13474 "groups/bertone/software/HTqPCR.pdf"))
13475 (synopsis "Automated analysis of high-throughput qPCR data")
13477 "Analysis of Ct values from high throughput quantitative real-time
13478 PCR (qPCR) assays across multiple conditions or replicates. The input data
13479 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
13480 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
13481 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
13482 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
13483 loading, quality assessment, normalization, visualization and parametric or
13484 non-parametric testing for statistical significance in Ct values between
13485 features (e.g. genes, microRNAs).")
13486 (license license:artistic2.0)))
13488 (define-public r-unifiedwmwqpcr
13490 (name "r-unifiedwmwqpcr")
13495 (uri (bioconductor-uri "unifiedWMWqPCR" version))
13498 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
13500 `((upstream-name . "unifiedWMWqPCR")))
13501 (build-system r-build-system)
13503 (list r-biocgenerics r-htqpcr))
13504 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
13505 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
13507 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
13508 data. This modified test allows for testing differential expression in qPCR
13510 (license license:gpl2+)))
13512 (define-public r-universalmotif
13514 (name "r-universalmotif")
13519 (uri (bioconductor-uri "universalmotif" version))
13522 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
13524 `((upstream-name . "universalmotif")))
13525 (build-system r-build-system)
13528 (modify-phases %standard-phases
13529 (add-after 'unpack 'fix-reference-to-strip
13531 (substitute* "src/Makevars"
13532 (("/usr/bin/strip") (which "strip"))))))))
13534 (list r-biocgenerics
13547 "https://bioconductor.org/packages/universalmotif/")
13549 "Specific structures importer, modifier, and exporter for R")
13551 "This package allows importing most common @dfn{specific structure}
13552 (motif) types into R for use by functions provided by other Bioconductor
13553 motif-related packages. Motifs can be exported into most major motif formats
13554 from various classes as defined by other Bioconductor packages. A suite of
13555 motif and sequence manipulation and analysis functions are included, including
13556 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
13557 motifs, and others.")
13558 (license license:gpl3)))
13560 (define-public r-ace
13566 (uri (bioconductor-uri "ACE" version))
13569 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
13570 (properties `((upstream-name . "ACE")))
13571 (build-system r-build-system)
13572 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
13573 (native-inputs (list r-knitr))
13574 (home-page "https://github.com/tgac-vumc/ACE")
13576 "Absolute copy number estimation from low-coverage whole genome sequencing")
13578 "This package uses segmented copy number data to estimate tumor cell
13579 percentage and produce copy number plots displaying absolute copy numbers. For
13580 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
13581 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
13582 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
13583 subsequently run through all samples in the object(s), for which it will create
13584 individual subdirectories. For each sample, it will calculate how well the
13585 segments fit (the relative error) to integer copy numbers for each percentage
13586 of @dfn{tumor cells} (cells with divergent segments).")
13587 (license license:gpl2)))
13589 (define-public r-acgh
13595 (uri (bioconductor-uri "aCGH" version))
13598 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
13599 (properties `((upstream-name . "aCGH")))
13600 (build-system r-build-system)
13601 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
13602 (home-page "https://bioconductor.org/packages/aCGH")
13604 "Classes and functions for array comparative genomic hybridization data")
13606 "This package provides functions for reading
13607 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
13608 output files and clone information files, creation of @code{aCGH} objects for
13609 storing these data. Basic methods are accessing/replacing, subsetting,
13610 printing and plotting @code{aCGH} objects.")
13611 (license license:gpl2)))
13613 (define-public r-acme
13619 (uri (bioconductor-uri "ACME" version))
13622 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
13623 (properties `((upstream-name . "ACME")))
13624 (build-system r-build-system)
13625 (propagated-inputs (list r-biobase r-biocgenerics))
13626 (home-page "https://bioconductor.org/packages/aCGH/")
13627 (synopsis "Calculating microarray enrichment")
13629 "This package implements @dfn{algorithms for calculating microarray
13630 enrichment} (ACME), and it is a set of tools for analysing tiling array of
13631 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
13632 DNAse hypersensitivity, or other experiments that result in regions of the
13633 genome showing enrichment. It does not rely on a specific array technology
13634 (although the array should be a tiling array), is very general (can be applied
13635 in experiments resulting in regions of enrichment), and is very insensitive to
13636 array noise or normalization methods. It is also very fast and can be applied
13637 on whole-genome tiling array experiments quite easily with enough memory.")
13638 (license license:gpl2+)))
13640 (define-public r-acde
13646 (uri (bioconductor-uri "acde" version))
13649 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
13650 (properties `((upstream-name . "acde")))
13651 (build-system r-build-system)
13652 (propagated-inputs (list r-boot))
13653 (home-page "https://bioconductor.org/packages/acde")
13655 "Identification of differentially expressed genes with artificial components")
13657 "This package provides a multivariate inferential analysis method for
13658 detecting differentially expressed genes in gene expression data. It uses
13659 artificial components, close to the data's principal components but with an
13660 exact interpretation in terms of differential genetic expression, to identify
13661 differentially expressed genes while controlling the @dfn{false discovery
13663 (license license:gpl3)))
13665 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13667 (define-public r-activedriverwgs
13669 (name "r-activedriverwgs")
13674 (uri (cran-uri "ActiveDriverWGS" version))
13677 "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
13679 `((upstream-name . "ActiveDriverWGS")))
13680 (build-system r-build-system)
13684 r-bsgenome-hsapiens-ucsc-hg19
13685 r-bsgenome-hsapiens-ucsc-hg38
13686 r-bsgenome-mmusculus-ucsc-mm9
13687 r-bsgenome-mmusculus-ucsc-mm10
13694 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
13695 (synopsis "Driver discovery tool for cancer whole genomes")
13697 "This package provides a method for finding an enrichment of cancer
13698 simple somatic mutations (SNVs and Indels) in functional elements across the
13699 human genome. ActiveDriverWGS detects coding and noncoding driver elements
13700 using whole genome sequencing data.")
13701 (license license:gpl3)))
13703 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13705 (define-public r-activepathways
13707 (name "r-activepathways")
13712 (uri (cran-uri "ActivePathways" version))
13715 "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
13717 `((upstream-name . "ActivePathways")))
13718 (build-system r-build-system)
13720 (list r-data-table r-ggplot2))
13723 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
13724 (synopsis "Multivariate pathway enrichment analysis")
13726 "This package represents an integrative method of analyzing multi omics
13727 data that conducts enrichment analysis of annotated gene sets. ActivePathways
13728 uses a statistical data fusion approach, rationalizes contributing evidence
13729 and highlights associated genes, improving systems-level understanding of
13730 cellular organization in health and disease.")
13731 (license license:gpl3)))
13733 (define-public r-bgmix
13740 (uri (bioconductor-uri "BGmix" version))
13743 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
13744 (properties `((upstream-name . "BGmix")))
13745 (build-system r-build-system)
13747 (list r-kernsmooth))
13748 (home-page "https://bioconductor.org/packages/BGmix/")
13749 (synopsis "Bayesian models for differential gene expression")
13751 "This package provides fully Bayesian mixture models for differential
13753 (license license:gpl2)))
13755 (define-public r-bgx
13762 (uri (bioconductor-uri "bgx" version))
13765 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
13766 (properties `((upstream-name . "bgx")))
13767 (build-system r-build-system)
13771 '(modify-phases %standard-phases
13772 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
13774 (substitute* "configure.ac"
13775 (("AX_GCC_ARCHFLAG.*") ""))
13776 (delete-file "configure")
13777 (invoke "autoreconf" "-vif"))))))
13781 (list r-affy r-biobase r-gcrma r-rcpp))
13783 (list autoconf automake))
13784 (home-page "https://bioconductor.org/packages/bgx/")
13785 (synopsis "Bayesian gene expression")
13787 "This package provides tools for Bayesian integrated analysis of
13788 Affymetrix GeneChips.")
13789 (license license:gpl2)))
13791 (define-public r-bhc
13798 (uri (bioconductor-uri "BHC" version))
13801 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
13802 (properties `((upstream-name . "BHC")))
13803 (build-system r-build-system)
13804 (home-page "https://bioconductor.org/packages/BHC/")
13805 (synopsis "Bayesian hierarchical clustering")
13807 "The method implemented in this package performs bottom-up hierarchical
13808 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
13809 in the data and Bayesian model selection to decide at each step which clusters
13810 to merge. This avoids several limitations of traditional methods, for example
13811 how many clusters there should be and how to choose a principled distance
13812 metric. This implementation accepts multinomial (i.e. discrete, with 2+
13813 categories) or time-series data. This version also includes a randomised
13814 algorithm which is more efficient for larger data sets.")
13815 (license license:gpl3)))
13817 (define-public r-bicare
13824 (uri (bioconductor-uri "BicARE" version))
13827 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
13828 (properties `((upstream-name . "BicARE")))
13829 (build-system r-build-system)
13831 (list r-biobase r-gseabase r-multtest))
13832 (home-page "http://bioinfo.curie.fr")
13833 (synopsis "Biclustering analysis and results exploration")
13835 "This is a package for biclustering analysis and exploration of
13837 (license license:gpl2)))
13839 (define-public r-bifet
13846 (uri (bioconductor-uri "BiFET" version))
13849 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
13850 (properties `((upstream-name . "BiFET")))
13851 (build-system r-build-system)
13853 (list r-genomicranges r-poibin))
13856 (home-page "https://bioconductor.org/packages/BiFET")
13857 (synopsis "Bias-free footprint enrichment test")
13859 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
13860 over-represented in target regions compared to background regions after
13861 correcting for the bias arising from the imbalance in read counts and GC
13862 contents between the target and background regions. For a given TF k, BiFET
13863 tests the null hypothesis that the target regions have the same probability of
13864 having footprints for the TF k as the background regions while correcting for
13865 the read count and GC content bias.")
13866 (license license:gpl3)))
13868 (define-public r-rsbml
13875 (uri (bioconductor-uri "rsbml" version))
13878 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
13879 (properties `((upstream-name . "rsbml")))
13880 (build-system r-build-system)
13884 (list r-biocgenerics r-graph))
13887 (home-page "http://www.sbml.org")
13888 (synopsis "R support for SBML")
13890 "This package provides an R interface to libsbml for SBML parsing,
13891 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
13892 (license license:artistic2.0)))
13894 (define-public r-hypergraph
13896 (name "r-hypergraph")
13901 (uri (bioconductor-uri "hypergraph" version))
13904 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
13905 (properties `((upstream-name . "hypergraph")))
13906 (build-system r-build-system)
13909 (home-page "https://bioconductor.org/packages/hypergraph")
13910 (synopsis "Hypergraph data structures")
13912 "This package implements some simple capabilities for representing and
13913 manipulating hypergraphs.")
13914 (license license:artistic2.0)))
13916 (define-public r-hyperdraw
13918 (name "r-hyperdraw")
13923 (uri (bioconductor-uri "hyperdraw" version))
13926 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
13927 (properties `((upstream-name . "hyperdraw")))
13928 (build-system r-build-system)
13929 (inputs (list graphviz))
13931 (list r-graph r-hypergraph r-rgraphviz))
13932 (home-page "https://bioconductor.org/packages/hyperdraw")
13933 (synopsis "Visualizing hypergraphs")
13935 "This package provides functions for visualizing hypergraphs.")
13936 (license license:gpl2+)))
13938 (define-public r-biggr
13945 (uri (bioconductor-uri "BiGGR" version))
13948 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
13949 (properties `((upstream-name . "BiGGR")))
13950 (build-system r-build-system)
13958 (home-page "https://bioconductor.org/packages/BiGGR/")
13959 (synopsis "Constraint based modeling using metabolic reconstruction databases")
13961 "This package provides an interface to simulate metabolic reconstruction
13962 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
13963 reconstruction databases. The package facilitates @dfn{flux balance
13964 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
13965 networks and estimated fluxes can be visualized with hypergraphs.")
13966 (license license:gpl3+)))
13968 (define-public r-bigmemoryextras
13970 (name "r-bigmemoryextras")
13975 (uri (bioconductor-uri "bigmemoryExtras" version))
13978 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
13980 `((upstream-name . "bigmemoryExtras")))
13981 (build-system r-build-system)
13983 (list r-bigmemory))
13986 (home-page "https://github.com/phaverty/bigmemoryExtras")
13987 (synopsis "Extension of the bigmemory package")
13989 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
13990 safety and convenience features to the @code{filebacked.big.matrix} class from
13991 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
13992 monitoring and gracefully restoring the connection to on-disk data and it also
13993 protects against accidental data modification with a file-system-based
13994 permissions system. Utilities are provided for using @code{BigMatrix}-derived
13995 classes as @code{assayData} matrices within the @code{Biobase} package's
13996 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
13997 related to attaching to, and indexing into, file-backed matrices with
13998 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
13999 a file-backed matrix with factor properties.")
14000 (license license:artistic2.0)))
14002 (define-public r-bigpint
14009 (uri (bioconductor-uri "bigPint" version))
14012 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
14013 (properties `((upstream-name . "bigPint")))
14014 (build-system r-build-system)
14016 (list r-delayedarray
14032 r-summarizedexperiment
14036 (home-page "https://github.com/lindsayrutter/bigPint")
14037 (synopsis "Big multivariate data plotted interactively")
14039 "This package provides methods for visualizing large multivariate
14040 datasets using static and interactive scatterplot matrices, parallel
14041 coordinate plots, volcano plots, and litre plots. It includes examples for
14042 visualizing RNA-sequencing datasets and differentially expressed genes.")
14043 (license license:gpl3)))
14045 (define-public r-chemminer
14047 (name "r-chemminer")
14052 (uri (bioconductor-uri "ChemmineR" version))
14055 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
14056 (properties `((upstream-name . "ChemmineR")))
14057 (build-system r-build-system)
14076 (home-page "https://github.com/girke-lab/ChemmineR")
14077 (synopsis "Cheminformatics toolkit for R")
14079 "ChemmineR is a cheminformatics package for analyzing drug-like small
14080 molecule data in R. It contains functions for efficient processing of large
14081 numbers of molecules, physicochemical/structural property predictions,
14082 structural similarity searching, classification and clustering of compound
14083 libraries with a wide spectrum of algorithms. In addition, it offers
14084 visualization functions for compound clustering results and chemical
14086 (license license:artistic2.0)))
14088 (define-public r-fmcsr
14095 (uri (bioconductor-uri "fmcsR" version))
14097 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
14098 (properties `((upstream-name . "fmcsR")))
14099 (build-system r-build-system)
14101 (list r-biocgenerics r-chemminer r-runit))
14102 (native-inputs (list r-knitr))
14103 (home-page "https://github.com/girke-lab/fmcsR")
14104 (synopsis "Mismatch tolerant maximum common substructure searching")
14106 "The fmcsR package introduces an efficient @dfn{maximum common
14107 substructure} (MCS) algorithms combined with a novel matching strategy that
14108 allows for atom and/or bond mismatches in the substructures shared among two
14109 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
14110 strict MCSs, resulting in the identification of more common features in their
14111 source structures, as well as a higher sensitivity in finding compounds with
14112 weak structural similarities. The fmcsR package provides several utilities to
14113 use the FMCS algorithm for pairwise compound comparisons, structure similarity
14114 searching and clustering.")
14115 (license license:artistic2.0)))
14117 (define-public r-bioassayr
14119 (name "r-bioassayr")
14124 (uri (bioconductor-uri "bioassayR" version))
14127 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
14128 (properties `((upstream-name . "bioassayR")))
14129 (build-system r-build-system)
14131 (list r-biocgenerics
14140 (home-page "https://github.com/girke-lab/bioassayR")
14141 (synopsis "Cross-target analysis of small molecule bioactivity")
14143 "bioassayR is a computational tool that enables simultaneous analysis of
14144 thousands of bioassay experiments performed over a diverse set of compounds
14145 and biological targets. Unique features include support for large-scale
14146 cross-target analyses of both public and custom bioassays, generation of
14147 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
14148 preloaded database that provides access to a substantial portion of publicly
14149 available bioactivity data.")
14150 (license license:artistic2.0)))
14152 (define-public r-biobroom
14154 (name "r-biobroom")
14159 (uri (bioconductor-uri "biobroom" version))
14162 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
14163 (properties `((upstream-name . "biobroom")))
14164 (build-system r-build-system)
14166 (list r-biobase r-broom r-dplyr r-tidyr))
14169 (home-page "https://github.com/StoreyLab/biobroom")
14170 (synopsis "Turn Bioconductor objects into tidy data frames")
14172 "This package contains methods for converting standard objects
14173 constructed by bioinformatics packages, especially those in Bioconductor, and
14174 converting them to @code{tidy} data. It thus serves as a complement to the
14175 @code{broom} package, and follows the same tidy, augment, glance division of
14176 tidying methods. Tidying data makes it easy to recombine, reshape and
14177 visualize bioinformatics analyses.")
14178 ;; Any version of the LGPL.
14179 (license license:lgpl3+)))
14181 (define-public r-graphite
14183 (name "r-graphite")
14188 (uri (bioconductor-uri "graphite" version))
14191 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
14192 (properties `((upstream-name . "graphite")))
14193 (build-system r-build-system)
14195 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
14196 (home-page "https://bioconductor.org/packages/graphite/")
14197 (synopsis "Networks from pathway databases")
14199 "Graphite provides networks derived from eight public pathway databases,
14200 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
14202 (license license:agpl3+)))
14204 (define-public r-reactomepa
14206 (name "r-reactomepa")
14211 (uri (bioconductor-uri "ReactomePA" version))
14214 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
14215 (properties `((upstream-name . "ReactomePA")))
14216 (build-system r-build-system)
14218 (list r-annotationdbi
14228 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
14229 (synopsis "Reactome pathway analysis")
14231 "This package provides functions for pathway analysis based on the
14232 REACTOME pathway database. It implements enrichment analysis, gene set
14233 enrichment analysis and several functions for visualization.")
14234 (license license:gpl2)))
14236 (define-public r-ebarrays
14238 (name "r-ebarrays")
14243 (uri (bioconductor-uri "EBarrays" version))
14246 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
14247 (properties `((upstream-name . "EBarrays")))
14248 (build-system r-build-system)
14250 (list r-biobase r-cluster r-lattice))
14251 (home-page "https://bioconductor.org/packages/EBarrays/")
14252 (synopsis "Gene clustering and differential expression identification")
14254 "EBarrays provides tools for the analysis of replicated/unreplicated
14256 (license license:gpl2+)))
14258 (define-public r-bioccasestudies
14260 (name "r-bioccasestudies")
14265 (uri (bioconductor-uri "BiocCaseStudies" version))
14268 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
14270 `((upstream-name . "BiocCaseStudies")))
14271 (build-system r-build-system)
14272 (propagated-inputs (list r-biobase))
14273 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
14274 (synopsis "Support for the case studies monograph")
14276 "This package provides software and data to support the case studies
14278 (license license:artistic2.0)))
14280 (define-public r-bioccheck
14282 (name "r-bioccheck")
14286 (uri (bioconductor-uri "BiocCheck" version))
14289 "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw"))))
14291 `((upstream-name . "BiocCheck")))
14292 (build-system r-build-system)
14303 (home-page "https://bioconductor.org/packages/BiocCheck")
14304 (synopsis "Executes Bioconductor-specific package checks")
14305 (description "This package contains tools to perform additional quality
14306 checks on R packages that are to be submitted to the Bioconductor repository.")
14307 (license license:artistic2.0)))
14309 (define-public r-biocgraph
14311 (name "r-biocgraph")
14316 (uri (bioconductor-uri "biocGraph" version))
14319 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
14320 (properties `((upstream-name . "biocGraph")))
14321 (build-system r-build-system)
14323 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
14324 (home-page "https://bioconductor.org/packages/biocGraph/")
14325 (synopsis "Graph examples and use cases in Bioinformatics")
14327 "This package provides examples and code that make use of the
14328 different graph related packages produced by Bioconductor.")
14329 (license license:artistic2.0)))
14331 (define-public r-biocstyle
14333 (name "r-biocstyle")
14337 (uri (bioconductor-uri "BiocStyle" version))
14340 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
14342 `((upstream-name . "BiocStyle")))
14343 (build-system r-build-system)
14345 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
14348 (home-page "https://bioconductor.org/packages/BiocStyle")
14349 (synopsis "Bioconductor formatting styles")
14350 (description "This package provides standard formatting styles for
14351 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
14353 (license license:artistic2.0)))
14355 (define-public r-biocviews
14357 (name "r-biocviews")
14361 (uri (bioconductor-uri "biocViews" version))
14364 "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38"))))
14366 `((upstream-name . "biocViews")))
14367 (build-system r-build-system)
14376 (home-page "https://bioconductor.org/packages/biocViews")
14377 (synopsis "Bioconductor package categorization helper")
14378 (description "The purpose of biocViews is to create HTML pages that
14379 categorize packages in a Bioconductor package repository according to keywords,
14380 also known as views, in a controlled vocabulary.")
14381 (license license:artistic2.0)))
14383 (define-public r-experimenthub
14385 (name "r-experimenthub")
14390 (uri (bioconductor-uri "ExperimentHub" version))
14393 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
14394 (properties `((upstream-name . "ExperimentHub")))
14395 (build-system r-build-system)
14397 (list r-annotationhub
14406 (home-page "https://bioconductor.org/packages/ExperimentHub/")
14407 (synopsis "Client to access ExperimentHub resources")
14409 "This package provides a client for the Bioconductor ExperimentHub web
14410 resource. ExperimentHub provides a central location where curated data from
14411 experiments, publications or training courses can be accessed. Each resource
14412 has associated metadata, tags and date of modification. The client creates
14413 and manages a local cache of files retrieved enabling quick and reproducible
14415 (license license:artistic2.0)))
14417 (define-public r-grohmm
14424 (uri (bioconductor-uri "groHMM" version))
14427 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
14428 (properties `((upstream-name . "groHMM")))
14429 (build-system r-build-system)
14431 (list r-genomeinfodb
14432 r-genomicalignments
14438 (home-page "https://github.com/Kraus-Lab/groHMM")
14439 (synopsis "GRO-seq analysis pipeline")
14441 "This package provides a pipeline for the analysis of GRO-seq data.")
14442 (license license:gpl3+)))
14444 (define-public r-multiassayexperiment
14446 (name "r-multiassayexperiment")
14451 (uri (bioconductor-uri "MultiAssayExperiment" version))
14454 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
14456 `((upstream-name . "MultiAssayExperiment")))
14457 (build-system r-build-system)
14464 r-summarizedexperiment
14468 (home-page "https://waldronlab.io/MultiAssayExperiment/")
14469 (synopsis "Integration of multi-omics experiments in Bioconductor")
14471 "MultiAssayExperiment harmonizes data management of multiple assays
14472 performed on an overlapping set of specimens. It provides a familiar
14473 Bioconductor user experience by extending concepts from
14474 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
14475 classes for individual assays, and allowing subsetting by genomic ranges or
14477 (license license:artistic2.0)))
14479 (define-public r-bioconcotk
14481 (name "r-bioconcotk")
14486 (uri (bioconductor-uri "BiocOncoTK" version))
14489 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
14490 (properties `((upstream-name . "BiocOncoTK")))
14491 (build-system r-build-system)
14514 r-summarizedexperiment))
14517 (home-page "https://bioconductor.org/packages/BiocOncoTK")
14518 (synopsis "Bioconductor components for general cancer genomics")
14520 "The purpose of this package is to provide a central interface to various
14521 tools for genome-scale analysis of cancer studies.")
14522 (license license:artistic2.0)))
14524 (define-public r-biocor
14531 (uri (bioconductor-uri "BioCor" version))
14534 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
14535 (properties `((upstream-name . "BioCor")))
14536 (build-system r-build-system)
14538 (list r-biocparallel r-gseabase r-matrix))
14541 (home-page "https://llrs.github.io/BioCor/")
14542 (synopsis "Functional similarities")
14544 "This package provides tools to calculate functional similarities based
14545 on the pathways described on KEGG and REACTOME or in gene sets. These
14546 similarities can be calculated for pathways or gene sets, genes, or clusters
14547 and combined with other similarities. They can be used to improve networks,
14548 gene selection, testing relationships, and so on.")
14549 (license license:expat)))
14551 (define-public r-biocpkgtools
14553 (name "r-biocpkgtools")
14558 (uri (bioconductor-uri "BiocPkgTools" version))
14561 "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd"))))
14562 (properties `((upstream-name . "BiocPkgTools")))
14563 (build-system r-build-system)
14565 (list r-biocfilecache
14589 (home-page "https://github.com/seandavi/BiocPkgTools")
14590 (synopsis "Collection of tools for learning about Bioconductor packages")
14592 "Bioconductor has a rich ecosystem of metadata around packages, usage,
14593 and build status. This package is a simple collection of functions to access
14594 that metadata from R. The goal is to expose metadata for data mining and
14595 value-added functionality such as package searching, text mining, and
14596 analytics on packages.")
14597 (license license:expat)))
14599 (define-public r-biocset
14606 (uri (bioconductor-uri "BiocSet" version))
14609 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
14610 (properties `((upstream-name . "BiocSet")))
14611 (build-system r-build-system)
14613 (list r-annotationdbi
14626 "https://bioconductor.org/packages/BiocSet")
14628 "Representing Different Biological Sets")
14630 "BiocSet displays different biological sets in a triple tibble format.
14631 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
14632 The user has the ability to activate one of these three tibbles to perform
14633 common functions from the @code{dplyr} package. Mapping functionality and
14634 accessing web references for elements/sets are also available in BiocSet.")
14635 (license license:artistic2.0)))
14637 (define-public r-biocworkflowtools
14639 (name "r-biocworkflowtools")
14644 (uri (bioconductor-uri "BiocWorkflowTools" version))
14647 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
14649 `((upstream-name . "BiocWorkflowTools")))
14650 (build-system r-build-system)
14663 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
14664 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
14666 "This package provides functions to ease the transition between
14667 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
14668 (license license:expat)))
14670 (define-public r-biodist
14677 (uri (bioconductor-uri "bioDist" version))
14680 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
14681 (properties `((upstream-name . "bioDist")))
14682 (build-system r-build-system)
14684 (list r-biobase r-kernsmooth))
14685 (home-page "https://bioconductor.org/packages/bioDist/")
14686 (synopsis "Different distance measures")
14688 "This package provides a collection of software tools for calculating
14689 distance measures.")
14690 (license license:artistic2.0)))
14692 (define-public r-pcatools
14694 (name "r-pcatools")
14699 (uri (bioconductor-uri "PCAtools" version))
14702 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
14703 (properties `((upstream-name . "PCAtools")))
14704 (build-system r-build-system)
14712 r-delayedmatrixstats
14720 (native-inputs (list r-knitr))
14721 (home-page "https://github.com/kevinblighe/PCAtools")
14722 (synopsis "PCAtools: everything Principal Components Analysis")
14724 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
14725 structure of the data without the need to build any model to represent it.
14726 This \"summary\" of the data is arrived at through a process of reduction that
14727 can transform the large number of variables into a lesser number that are
14728 uncorrelated (i.e. the 'principal components'), while at the same time being
14729 capable of easy interpretation on the original data. PCAtools provides
14730 functions for data exploration via PCA, and allows the user to generate
14731 publication-ready figures. PCA is performed via @code{BiocSingular}; users
14732 can also identify an optimal number of principal components via different
14733 metrics, such as the elbow method and Horn's parallel analysis, which has
14734 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
14735 dimensional mass cytometry data.")
14736 (license license:gpl3)))
14738 (define-public r-rgreat
14745 (uri (bioconductor-uri "rGREAT" version))
14748 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
14749 (properties `((upstream-name . "rGREAT")))
14750 (build-system r-build-system)
14752 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
14753 (native-inputs (list r-knitr))
14754 (home-page "https://github.com/jokergoo/rGREAT")
14755 (synopsis "Client for GREAT analysis")
14757 "This package makes GREAT (Genomic Regions Enrichment of Annotations
14758 Tool) analysis automatic by constructing a HTTP POST request according to
14759 user's input and automatically retrieving results from GREAT web server.")
14760 (license license:expat)))
14762 (define-public r-m3c
14769 (uri (bioconductor-uri "M3C" version))
14772 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
14773 (properties `((upstream-name . "M3C")))
14774 (build-system r-build-system)
14786 (native-inputs (list r-knitr))
14787 (home-page "https://bioconductor.org/packages/M3C")
14788 (synopsis "Monte Carlo reference-based consensus clustering")
14790 "M3C is a consensus clustering algorithm that uses a Monte Carlo
14791 simulation to eliminate overestimation of @code{K} and can reject the null
14792 hypothesis @code{K=1}.")
14793 (license license:agpl3+)))
14795 (define-public r-icens
14802 (uri (bioconductor-uri "Icens" version))
14805 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
14806 (properties `((upstream-name . "Icens")))
14807 (build-system r-build-system)
14810 (home-page "https://bioconductor.org/packages/Icens")
14811 (synopsis "NPMLE for censored and truncated data")
14813 "This package provides many functions for computing the
14814 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
14816 (license license:artistic2.0)))
14818 ;; This is a CRAN package but it depends on r-icens, which is published on
14820 (define-public r-interval
14822 (name "r-interval")
14823 (version "1.1-0.8")
14827 (uri (cran-uri "interval" version))
14830 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
14831 (properties `((upstream-name . "interval")))
14832 (build-system r-build-system)
14834 (list r-icens r-mlecens r-perm r-survival))
14835 (home-page "https://cran.r-project.org/web/packages/interval/")
14836 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
14838 "This package provides functions to fit nonparametric survival curves,
14839 plot them, and perform logrank or Wilcoxon type tests.")
14840 (license license:gpl2+)))
14842 ;; This is a CRAN package, but it depends on r-interval, which depends on a
14843 ;; Bioconductor package.
14844 (define-public r-fhtest
14851 (uri (cran-uri "FHtest" version))
14854 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
14855 (properties `((upstream-name . "FHtest")))
14856 (build-system r-build-system)
14858 (list r-interval r-kmsurv r-mass r-perm r-survival))
14859 (home-page "https://cran.r-project.org/web/packages/FHtest/")
14860 (synopsis "Tests for survival data based on the Fleming-Harrington class")
14862 "This package provides functions to compare two or more survival curves
14866 @item The Fleming-Harrington test for right-censored data based on
14867 permutations and on counting processes.
14868 @item An extension of the Fleming-Harrington test for interval-censored data
14869 based on a permutation distribution and on a score vector distribution.
14872 (license license:gpl2+)))
14874 (define-public r-fourcseq
14876 (name "r-fourcseq")
14881 (uri (bioconductor-uri "FourCSeq" version))
14883 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
14884 (properties `((upstream-name . "FourCSeq")))
14885 (build-system r-build-system)
14891 r-genomicalignments
14901 r-summarizedexperiment))
14905 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
14906 (synopsis "Analysis of multiplexed 4C sequencing data")
14908 "This package is an R package dedicated to the analysis of (multiplexed)
14909 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
14910 interactions between DNA elements and identify differential interactions
14911 between conditions. The statistical analysis in R starts with individual bam
14912 files for each sample as inputs. To obtain these files, the package contains
14913 a Python script to demultiplex libraries and trim off primer sequences. With
14914 a standard alignment software the required bam files can be then be
14916 (license license:gpl3+)))
14918 (define-public r-preprocesscore
14920 (name "r-preprocesscore")
14925 (uri (bioconductor-uri "preprocessCore" version))
14928 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
14930 `((upstream-name . "preprocessCore")))
14931 (build-system r-build-system)
14932 (home-page "https://github.com/bmbolstad/preprocessCore")
14933 (synopsis "Collection of pre-processing functions")
14935 "This package provides a library of core pre-processing and normalization
14937 (license license:lgpl2.0+)))
14939 (define-public r-s4vectors
14941 (name "r-s4vectors")
14945 (uri (bioconductor-uri "S4Vectors" version))
14948 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
14950 `((upstream-name . "S4Vectors")))
14951 (build-system r-build-system)
14953 (list r-biocgenerics))
14954 (home-page "https://bioconductor.org/packages/S4Vectors")
14955 (synopsis "S4 implementation of vectors and lists")
14957 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
14958 classes and a set of generic functions that extend the semantic of ordinary
14959 vectors and lists in R. Package developers can easily implement vector-like
14960 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
14961 In addition, a few low-level concrete subclasses of general interest (e.g.
14962 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
14963 S4Vectors package itself.")
14964 (license license:artistic2.0)))
14966 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
14967 ;; Bioconductor package.
14968 (define-public r-wgcna
14975 (uri (cran-uri "WGCNA" version))
14978 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
14979 (properties `((upstream-name . "WGCNA")))
14980 (build-system r-build-system)
14982 (list r-annotationdbi
14995 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14996 (synopsis "Weighted correlation network analysis")
14998 "This package provides functions necessary to perform Weighted
14999 Correlation Network Analysis on high-dimensional data. It includes functions
15000 for rudimentary data cleaning, construction and summarization of correlation
15001 networks, module identification and functions for relating both variables and
15002 modules to sample traits. It also includes a number of utility functions for
15003 data manipulation and visualization.")
15004 (license license:gpl2+)))
15006 (define-public r-rgraphviz
15008 (name "r-rgraphviz")
15013 (uri (bioconductor-uri "Rgraphviz" version))
15016 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
15017 (properties `((upstream-name . "Rgraphviz")))
15018 (build-system r-build-system)
15021 (modify-phases %standard-phases
15022 (add-after 'unpack 'make-reproducible
15024 ;; The replacement value is taken from src/graphviz/builddate.h
15025 (substitute* "src/graphviz/configure"
15026 (("VERSION_DATE=.*")
15027 "VERSION_DATE=20200427.2341\n"))
15029 ;; FIXME: Rgraphviz bundles the sources of an older variant of
15030 ;; graphviz. It does not build with the latest version of graphviz, so
15031 ;; we do not add graphviz to the inputs.
15032 (inputs (list zlib))
15037 (home-page "https://bioconductor.org/packages/Rgraphviz")
15038 (synopsis "Plotting capabilities for R graph objects")
15040 "This package interfaces R with the graphviz library for plotting R graph
15041 objects from the @code{graph} package.")
15042 (license license:epl1.0)))
15044 (define-public r-fishpond
15046 (name "r-fishpond")
15050 (uri (bioconductor-uri "fishpond" version))
15053 "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym"))))
15054 (properties `((upstream-name . "fishpond")))
15055 (build-system r-build-system)
15056 (inputs (list zlib))
15068 r-singlecellexperiment
15069 r-summarizedexperiment
15071 (native-inputs (list r-knitr))
15072 (home-page "https://github.com/mikelove/fishpond")
15073 (synopsis "Downstream methods and tools for expression data")
15075 "The @code{fishpond} package contains methods for differential transcript
15076 and gene expression analysis of RNA-seq data using inferential replicates for
15077 uncertainty of abundance quantification, as generated by Gibbs sampling or
15078 bootstrap sampling. Also the package contains a number of utilities for
15079 working with Salmon and Alevin quantification files.")
15080 (license license:gpl2)))
15082 (define-public r-fithic
15088 (uri (bioconductor-uri "FitHiC" version))
15091 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
15092 (properties `((upstream-name . "FitHiC")))
15093 (build-system r-build-system)
15095 (list r-data-table r-fdrtool r-rcpp))
15098 (home-page "https://bioconductor.org/packages/FitHiC")
15099 (synopsis "Confidence estimation for intra-chromosomal contact maps")
15101 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
15102 intra-chromosomal contact maps produced by genome-wide genome architecture
15103 assays such as Hi-C.")
15104 (license license:gpl2+)))
15106 (define-public r-hitc
15112 (uri (bioconductor-uri "HiTC" version))
15115 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
15116 (properties `((upstream-name . "HiTC")))
15117 (build-system r-build-system)
15126 (home-page "https://bioconductor.org/packages/HiTC")
15127 (synopsis "High throughput chromosome conformation capture analysis")
15129 "The HiTC package was developed to explore high-throughput \"C\" data
15130 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
15131 quality controls, normalization, visualization, and further analysis are also
15133 (license license:artistic2.0)))
15135 (define-public r-hdf5array
15137 (name "r-hdf5array")
15142 (uri (bioconductor-uri "HDF5Array" version))
15145 "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9"))))
15146 (properties `((upstream-name . "HDF5Array")))
15147 (build-system r-build-system)
15151 (list r-biocgenerics
15159 (home-page "https://bioconductor.org/packages/HDF5Array")
15160 (synopsis "HDF5 back end for DelayedArray objects")
15161 (description "This package provides an array-like container for convenient
15162 access and manipulation of HDF5 datasets. It supports delayed operations and
15163 block processing.")
15164 (license license:artistic2.0)))
15166 (define-public r-rhdf5lib
15168 (name "r-rhdf5lib")
15173 (uri (bioconductor-uri "Rhdf5lib" version))
15176 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
15177 (modules '((guix build utils)))
15180 ;; Delete bundled binaries
15181 (delete-file-recursively "src/wininclude/")
15182 (delete-file-recursively "src/winlib/")
15183 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
15184 (properties `((upstream-name . "Rhdf5lib")))
15185 (build-system r-build-system)
15188 (modify-phases %standard-phases
15189 (add-after 'unpack 'do-not-use-bundled-hdf5
15190 (lambda* (#:key inputs #:allow-other-keys)
15191 (for-each delete-file '("configure" "configure.ac"))
15192 (substitute* "R/zzz.R"
15193 (("return\\(links\\)") "return(\" -lz\")"))
15194 (with-directory-excursion "src"
15195 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
15196 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
15198 ;; Remove timestamp and host system information to make
15199 ;; the build reproducible.
15200 (substitute* "hdf5/src/libhdf5.settings.in"
15201 (("Configured on: @CONFIG_DATE@")
15202 "Configured on: Guix")
15203 (("Uname information:.*")
15204 "Uname information: Linux\n")
15205 ;; Remove unnecessary store reference.
15207 "C Compiler: GCC\n"))
15208 (rename-file "hdf5/src/libhdf5.settings.in"
15209 "hdf5/src/libhdf5.settings")
15210 (rename-file "Makevars.in" "Makevars")
15211 (substitute* "Makevars"
15212 (("@BUILD_HDF5@") "")
15213 (("@COPY_SZIP@") "")
15214 (("@ZLIB_LIB@") "-lz")
15215 (("@ZLIB_INCLUDE@") "")
15216 (("HDF5_CXX_LIB=.*")
15217 (string-append "HDF5_CXX_LIB="
15218 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
15220 (string-append "HDF5_LIB="
15221 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
15222 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
15223 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
15224 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
15225 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
15226 (("HDF5_HL_LIB=.*")
15227 (string-append "HDF5_HL_LIB="
15228 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
15229 (("HDF5_HL_CXX_LIB=.*")
15230 (string-append "HDF5_HL_CXX_LIB="
15231 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
15232 ;; szip is non-free software
15233 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
15234 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
15236 (list hdf5-1.10 zlib))
15238 `(("hdf5-source" ,(package-source hdf5-1.10))
15239 ("r-knitr" ,r-knitr)))
15240 (home-page "https://bioconductor.org/packages/Rhdf5lib")
15241 (synopsis "HDF5 library as an R package")
15242 (description "This package provides C and C++ HDF5 libraries for use in R
15244 (license license:artistic2.0)))
15246 (define-public r-beachmat
15248 (name "r-beachmat")
15253 (uri (bioconductor-uri "beachmat" version))
15256 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
15257 (build-system r-build-system)
15259 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
15262 (home-page "https://bioconductor.org/packages/beachmat")
15263 (synopsis "Compiling Bioconductor to handle each matrix type")
15264 (description "This package provides a consistent C++ class interface for a
15265 variety of commonly used matrix types, including sparse and HDF5-backed
15267 (license license:gpl3)))
15269 ;; This package includes files that have been taken from kentutils. Some
15270 ;; parts of kentutils are not released under a free license, but this package
15271 ;; only uses files that are also found in the free parts of kentutils.
15272 (define-public r-cner
15279 (uri (bioconductor-uri "CNEr" version))
15281 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
15282 (properties `((upstream-name . "CNEr")))
15283 (build-system r-build-system)
15284 (inputs (list zlib))
15291 r-genomicalignments
15307 (home-page "https://github.com/ge11232002/CNEr")
15308 (synopsis "CNE Detection and Visualization")
15310 "This package provides tools for large-scale identification and
15311 advanced visualization of sets of conserved noncoding elements.")
15312 ;; For all files in src/ucsc "license is hereby granted for all use -
15313 ;; public, private or commercial"; this includes those files that don't
15314 ;; have a license header, because they are included in the free parts of
15315 ;; the kentutils package.
15316 (license (list license:gpl2
15317 (license:non-copyleft
15318 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
15320 (define-public r-tfbstools
15322 (name "r-tfbstools")
15327 (uri (bioconductor-uri "TFBSTools" version))
15330 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
15331 (properties `((upstream-name . "TFBSTools")))
15332 (build-system r-build-system)
15342 r-dirichletmultinomial
15354 (native-inputs (list r-knitr))
15355 (home-page "https://github.com/ge11232002/TFBSTools")
15356 (synopsis "Transcription factor binding site (TFBS) analysis")
15358 "TFBSTools is a package for the analysis and manipulation of
15359 transcription factor binding sites. It includes matrices conversion
15360 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
15361 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
15362 scan putative TFBS from sequence/alignment, query JASPAR database and
15363 provides a wrapper of de novo motif discovery software.")
15364 (license license:gpl2)))
15366 (define-public r-maftools
15368 (name "r-maftools")
15373 (uri (bioconductor-uri "maftools" version))
15375 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
15376 (properties `((upstream-name . "maftools")))
15377 (build-system r-build-system)
15385 (native-inputs (list r-knitr))
15386 (home-page "https://github.com/PoisonAlien/maftools")
15387 (synopsis "Summarize, analyze and visualize MAF files")
15389 "Analyze and visualize Mutation Annotation Format (MAF) files from large
15390 scale sequencing studies. This package provides various functions to perform
15391 most commonly used analyses in cancer genomics and to create feature rich
15392 customizable visualzations with minimal effort.")
15393 (license license:expat)))
15395 (define-public r-motifmatchr
15397 (name "r-motifmatchr")
15402 (uri (bioconductor-uri "motifmatchr" version))
15405 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
15406 (properties `((upstream-name . "motifmatchr")))
15407 (build-system r-build-system)
15419 r-summarizedexperiment
15421 (native-inputs (list r-knitr))
15422 (home-page "https://bioconductor.org/packages/motifmatchr")
15423 (synopsis "Fast motif matching in R")
15425 "Quickly find motif matches for many motifs and many sequences.
15426 This package wraps C++ code from the MOODS motif calling library.")
15427 (license license:gpl3)))
15429 (define-public r-chromvar
15431 (name "r-chromvar")
15436 (uri (bioconductor-uri "chromVAR" version))
15438 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
15439 (properties `((upstream-name . "chromVAR")))
15440 (build-system r-build-system)
15442 (list r-biocgenerics
15462 r-summarizedexperiment
15464 (native-inputs (list r-knitr))
15465 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
15466 (synopsis "Determine chromatin variation across regions")
15468 "This package @code{r-chromvar} determines variation in chromatin
15469 accessibility across sets of annotations or peaks. @code{r-chromvar} is
15470 designed primarily for single-cell or sparse chromatin accessibility data like
15471 single cell assay for transposase-accessible chromatin using
15472 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
15473 sequence (@code{DNAse-seq}) experiments.")
15474 (license license:expat)))
15476 (define-public r-singlecellexperiment
15478 (name "r-singlecellexperiment")
15483 (uri (bioconductor-uri "SingleCellExperiment" version))
15486 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
15488 `((upstream-name . "SingleCellExperiment")))
15489 (build-system r-build-system)
15491 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
15492 r-summarizedexperiment))
15495 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
15496 (synopsis "S4 classes for single cell data")
15497 (description "This package defines an S4 class for storing data from
15498 single-cell experiments. This includes specialized methods to store and
15499 retrieve spike-in information, dimensionality reduction coordinates and size
15500 factors for each cell, along with the usual metadata for genes and
15502 (license license:gpl3)))
15504 (define-public r-singler
15511 (uri (bioconductor-uri "SingleR" version))
15513 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
15514 (properties `((upstream-name . "SingleR")))
15515 (build-system r-build-system)
15522 r-delayedmatrixstats
15526 r-summarizedexperiment))
15527 (native-inputs (list r-knitr))
15528 (home-page "https://github.com/LTLA/SingleR")
15529 (synopsis "Reference-based single-cell RNA-seq annotation")
15531 "This package performs unbiased cell type recognition from single-cell
15532 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
15533 cell types to infer the cell of origin of each single cell independently.")
15534 (license license:gpl3)))
15536 (define-public r-scuttle
15543 (uri (bioconductor-uri "scuttle" version))
15546 "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671"))))
15547 (properties `((upstream-name . "scuttle")))
15548 (build-system r-build-system)
15554 r-delayedmatrixstats
15559 r-singlecellexperiment
15560 r-summarizedexperiment))
15561 (native-inputs (list r-knitr))
15562 (home-page "https://bioconductor.org/packages/scuttle")
15563 (synopsis "Single-cell RNA-Seq analysis utilities")
15565 "This package provides basic utility functions for performing single-cell
15566 analyses, focusing on simple normalization, quality control and data
15567 transformations. It also provides some helper functions to assist development
15568 of other packages.")
15569 (license license:gpl3)))
15571 (define-public r-scater
15577 (uri (bioconductor-uri "scater" version))
15580 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
15581 (build-system r-build-system)
15589 r-delayedmatrixstats
15601 r-singlecellexperiment
15602 r-summarizedexperiment
15606 (home-page "https://github.com/davismcc/scater")
15607 (synopsis "Single-cell analysis toolkit for gene expression data in R")
15608 (description "This package provides a collection of tools for doing
15609 various analyses of single-cell RNA-seq gene expression data, with a focus on
15611 (license license:gpl2+)))
15613 (define-public r-scran
15620 (uri (bioconductor-uri "scran" version))
15623 "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni"))))
15624 (build-system r-build-system)
15633 r-delayedmatrixstats
15643 r-singlecellexperiment
15645 r-summarizedexperiment))
15648 (home-page "https://bioconductor.org/packages/scran")
15649 (synopsis "Methods for single-cell RNA-Seq data analysis")
15650 (description "This package implements a variety of low-level analyses of
15651 single-cell RNA-seq data. Methods are provided for normalization of
15652 cell-specific biases, assignment of cell cycle phase, and detection of highly
15653 variable and significantly correlated genes.")
15654 (license license:gpl3)))
15656 (define-public r-sparsematrixstats
15658 (name "r-sparsematrixstats")
15663 (uri (bioconductor-uri "sparseMatrixStats" version))
15666 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
15668 `((upstream-name . "sparseMatrixStats")))
15669 (build-system r-build-system)
15671 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
15672 (native-inputs (list r-knitr))
15673 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
15674 (synopsis "Summary statistics for rows and columns of sparse matrices")
15676 "This package provides high performance functions for row and column
15677 operations on sparse matrices. Currently, the optimizations are limited to
15678 data in the column sparse format.")
15679 (license license:expat)))
15681 (define-public r-delayedmatrixstats
15683 (name "r-delayedmatrixstats")
15688 (uri (bioconductor-uri "DelayedMatrixStats" version))
15691 "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv"))))
15693 `((upstream-name . "DelayedMatrixStats")))
15694 (build-system r-build-system)
15696 (list r-delayedarray
15702 r-sparsematrixstats))
15705 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
15706 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
15708 "This package provides a port of the @code{matrixStats} API for use with
15709 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
15710 contains high-performing functions operating on rows and columns of
15711 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
15712 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
15713 are optimized per data type and for subsetted calculations such that both
15714 memory usage and processing time is minimized.")
15715 (license license:expat)))
15717 (define-public r-mscoreutils
15719 (name "r-mscoreutils")
15724 (uri (bioconductor-uri "MsCoreUtils" version))
15727 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
15728 (properties `((upstream-name . "MsCoreUtils")))
15729 (build-system r-build-system)
15731 (list r-clue r-mass r-rcpp r-s4vectors))
15734 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
15735 (synopsis "Core utils for mass spectrometry data")
15737 "This package defines low-level functions for mass spectrometry data and
15738 is independent of any high-level data structures. These functions include
15739 mass spectra processing functions (noise estimation, smoothing, binning),
15740 quantitative aggregation functions (median polish, robust summarisation,
15741 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
15742 well as misc helper functions, that are used across high-level data structure
15743 within the R for Mass Spectrometry packages.")
15744 (license license:artistic2.0)))
15746 (define-public r-msfeatures
15748 (name "r-msfeatures")
15753 (uri (bioconductor-uri "MsFeatures" version))
15755 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
15756 (properties `((upstream-name . "MsFeatures")))
15757 (build-system r-build-system)
15759 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
15762 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
15763 (synopsis "Functionality for mass spectrometry features")
15765 "The MsFeature package defines functionality for Mass Spectrometry
15766 features. This includes functions to group (LC-MS) features based on some of
15767 their properties, such as retention time (coeluting features), or correlation
15768 of signals across samples. This package hence can be used to group features, and
15769 its results can be used as an input for the @code{QFeatures} package which
15770 allows aggregating abundance levels of features within each group. This
15771 package defines concepts and functions for base and common data types,
15772 implementations for more specific data types are expected to be implemented in
15773 the respective packages (such as e.g. @code{xcms}).")
15774 (license license:artistic2.0)))
15776 (define-public r-biocio
15783 (uri (bioconductor-uri "BiocIO" version))
15786 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
15787 (properties `((upstream-name . "BiocIO")))
15788 (build-system r-build-system)
15790 (list r-biocgenerics r-s4vectors))
15793 (home-page "https://bioconductor.org/packages/BiocIO")
15794 (synopsis "Standard input and output for Bioconductor packages")
15796 "This package implements `import()` and `export()` standard generics for
15797 importing and exporting biological data formats. `import()` supports
15798 whole-file as well as chunk-wise iterative import. The `import()` interface
15799 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
15800 row or element-like components of the file resource), `select()` (on
15801 column-like components of the file resource) and `collect()`. The `import()`
15802 interface optionally provides transparent access to remote (e.g. via https)
15803 as well as local access. Developers can register a file extension, e.g.,
15804 `.loom` for dispatch from character-based URIs to specific `import()` /
15805 `export()` methods based on classes representing file types, e.g.,
15807 (license license:artistic2.0)))
15809 (define-public r-msmseda
15816 (uri (bioconductor-uri "msmsEDA" version))
15819 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
15820 (properties `((upstream-name . "msmsEDA")))
15821 (build-system r-build-system)
15823 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
15825 "https://bioconductor.org/packages/msmsEDA")
15826 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
15828 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
15829 experiments, and visualize de influence of the involved factors.")
15830 (license license:gpl2)))
15832 (define-public r-msmstests
15834 (name "r-msmstests")
15839 (uri (bioconductor-uri "msmsTests" version))
15842 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
15843 (properties `((upstream-name . "msmsTests")))
15844 (build-system r-build-system)
15846 (list r-edger r-msmseda r-msnbase r-qvalue))
15848 "https://bioconductor.org/packages/msmsTests")
15849 (synopsis "Differential LC-MS/MS expression tests")
15851 "This package provides statistical tests for label-free LC-MS/MS data
15852 by spectral counts, to discover differentially expressed proteins between two
15853 biological conditions. Three tests are available: Poisson GLM regression,
15854 quasi-likelihood GLM regression, and the negative binomial of the edgeR
15855 package. The three models admit blocking factors to control for nuisance
15856 variables. To assure a good level of reproducibility a post-test filter is
15857 available, where we may set the minimum effect size considered biologicaly
15858 relevant, and the minimum expression of the most abundant condition.")
15859 (license license:gpl2)))
15861 (define-public r-catalyst
15863 (name "r-catalyst")
15868 (uri (bioconductor-uri "CATALYST" version))
15871 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
15872 (properties `((upstream-name . "CATALYST")))
15873 (build-system r-build-system)
15877 r-consensusclusterplus
15899 r-singlecellexperiment
15900 r-summarizedexperiment))
15903 (home-page "https://github.com/HelenaLC/CATALYST")
15904 (synopsis "Cytometry data analysis tools")
15906 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
15907 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
15908 isotopes rather than fluorescent tags as reporters to label antibodies,
15909 thereby substantially decreasing spectral overlap and allowing for examination
15910 of over 50 parameters at the single cell level. While spectral overlap is
15911 significantly less pronounced in CyTOF than flow cytometry, spillover due to
15912 detection sensitivity, isotopic impurities, and oxide formation can impede
15913 data interpretability. @code{CATALYST} was designed to provide a pipeline for
15914 preprocessing of cytometry data, including:
15917 @item normalization using bead standards;
15918 @item single-cell deconvolution;
15919 @item bead-based compensation.
15922 (license license:gpl2+)))
15924 (define-public r-erma
15931 (uri (bioconductor-uri "erma" version))
15934 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
15935 (build-system r-build-system)
15937 (list r-annotationdbi
15950 r-summarizedexperiment))
15953 (home-page "https://bioconductor.org/packages/erma")
15954 (synopsis "Epigenomic road map adventures")
15956 "The epigenomics road map describes locations of epigenetic marks in DNA
15957 from a variety of cell types. Of interest are locations of histone
15958 modifications, sites of DNA methylation, and regions of accessible chromatin.
15959 This package presents a selection of elements of the road map including
15960 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
15961 by Ernst and Kellis.")
15962 (license license:artistic2.0)))
15964 (define-public r-ggbio
15971 (uri (bioconductor-uri "ggbio" version))
15974 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
15975 (build-system r-build-system)
15978 (modify-phases %standard-phases
15979 ;; See https://github.com/tengfei/ggbio/issues/117
15980 ;; This fix will be included in the next release.
15981 (add-after 'unpack 'fix-typo
15983 (substitute* "R/GGbio-class.R"
15984 (("fechable") "fetchable"))
15987 (list r-annotationdbi
15996 r-genomicalignments
16012 r-summarizedexperiment
16013 r-variantannotation))
16016 (home-page "http://www.tengfei.name/ggbio/")
16017 (synopsis "Visualization tools for genomic data")
16019 "The ggbio package extends and specializes the grammar of graphics for
16020 biological data. The graphics are designed to answer common scientific
16021 questions, in particular those often asked of high throughput genomics data.
16022 All core Bioconductor data structures are supported, where appropriate. The
16023 package supports detailed views of particular genomic regions, as well as
16024 genome-wide overviews. Supported overviews include ideograms and grand linear
16025 views. High-level plots include sequence fragment length, edge-linked
16026 interval to data view, mismatch pileup, and several splicing summaries.")
16027 (license license:artistic2.0)))
16029 (define-public r-gqtlbase
16031 (name "r-gqtlbase")
16036 (uri (bioconductor-uri "gQTLBase" version))
16039 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
16040 (properties `((upstream-name . "gQTLBase")))
16041 (build-system r-build-system)
16044 (modify-phases %standard-phases
16045 ;; This is an upstream bug.
16046 (add-after 'unpack 'fix-imports
16048 (substitute* "NAMESPACE"
16049 ((".*maxffmode.*") "")
16050 (("importFrom\\(ff,.*") "import(ff)\n"))
16065 r-summarizedexperiment))
16068 (home-page "https://bioconductor.org/packages/gQTLBase")
16069 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
16071 "The purpose of this package is to simplify the storage and interrogation
16072 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
16074 (license license:artistic2.0)))
16076 (define-public r-gqtlstats
16078 (name "r-gqtlstats")
16083 (uri (bioconductor-uri "gQTLstats" version))
16086 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
16087 (properties `((upstream-name . "gQTLstats")))
16088 (build-system r-build-system)
16090 (list r-annotationdbi
16118 r-summarizedexperiment
16119 r-variantannotation))
16122 (home-page "https://bioconductor.org/packages/gQTLstats")
16123 (synopsis "Computationally efficient analysis for eQTL and allied studies")
16125 "This package provides tools for the computationally efficient analysis
16126 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
16127 The software in this package aims to support refinements and functional
16128 interpretation of members of a collection of association statistics on a
16129 family of feature/genome hypotheses.")
16130 (license license:artistic2.0)))
16132 (define-public r-gviz
16139 (uri (bioconductor-uri "Gviz" version))
16142 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
16143 (properties `((upstream-name . "Gviz")))
16144 (build-system r-build-system)
16146 (list r-annotationdbi
16156 r-genomicalignments
16170 (home-page "https://bioconductor.org/packages/Gviz")
16171 (synopsis "Plotting data and annotation information along genomic coordinates")
16173 "Genomic data analyses requires integrated visualization of known genomic
16174 information and new experimental data. Gviz uses the biomaRt and the
16175 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
16176 and translates this to e.g. gene/transcript structures in viewports of the
16177 grid graphics package. This results in genomic information plotted together
16179 (license license:artistic2.0)))
16181 (define-public r-gwascat
16188 (uri (bioconductor-uri "gwascat" version))
16191 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
16192 (build-system r-build-system)
16194 (list r-annotationdbi
16205 r-variantannotation))
16208 (home-page "https://bioconductor.org/packages/gwascat")
16209 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
16211 "This package provides tools for representing and modeling data in the
16212 EMBL-EBI GWAS catalog.")
16213 (license license:artistic2.0)))
16215 (define-public r-kegggraph
16217 (name "r-kegggraph")
16222 (uri (bioconductor-uri "KEGGgraph" version))
16224 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
16225 (properties `((upstream-name . "KEGGgraph")))
16226 (build-system r-build-system)
16228 (list r-graph r-rcurl r-rgraphviz r-xml))
16229 (home-page "https://bioconductor.org/packages/KEGGgraph")
16230 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
16232 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
16233 object as well as a collection of tools to analyze, dissect and visualize these
16234 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
16235 maintaining all essential pathway attributes. The package offers
16236 functionalities including parsing, graph operation, visualization and etc.")
16237 (license license:gpl2+)))
16239 (define-public r-ldblock
16246 (uri (bioconductor-uri "ldblock" version))
16249 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
16250 (build-system r-build-system)
16252 (list r-biocgenerics
16253 r-ensdb-hsapiens-v75
16261 r-variantannotation))
16264 (home-page "https://bioconductor.org/packages/ldblock")
16265 (synopsis "Data structures for linkage disequilibrium measures in populations")
16267 "This package defines data structures for @dfn{linkage
16268 disequilibrium} (LD) measures in populations. Its purpose is to simplify
16269 handling of existing population-level data for the purpose of flexibly
16270 defining LD blocks.")
16271 (license license:artistic2.0)))
16273 ;; This is a CRAN package, but it depends on r-snpstats, which is a
16274 ;; Bioconductor package.
16275 (define-public r-ldheatmap
16277 (name "r-ldheatmap")
16282 (uri (cran-uri "LDheatmap" version))
16285 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
16286 (properties `((upstream-name . "LDheatmap")))
16287 (build-system r-build-system)
16289 (list r-genetics r-rcpp r-snpstats))
16290 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
16291 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
16293 "This package provides tools to produce a graphical display, as a heat
16294 map, of measures of pairwise linkage disequilibria between SNPs. Users may
16295 optionally include the physical locations or genetic map distances of each SNP
16297 (license license:gpl3)))
16299 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
16300 ;; Bioconductor package.
16301 (define-public r-abn
16308 (uri (cran-uri "abn" version))
16311 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
16312 (build-system r-build-system)
16325 (home-page "https://r-bayesian-networks.org/")
16326 (synopsis "Modelling multivariate data with additive bayesian networks")
16328 "Bayesian network analysis is a form of probabilistic graphical models
16329 which derives from empirical data a directed acyclic graph, DAG, describing
16330 the dependency structure between random variables. An additive Bayesian
16331 network model consists of a form of a DAG where each node comprises a
16332 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
16333 equivalent to Bayesian multivariate regression using graphical modelling, they
16334 generalises the usual multivariable regression, GLM, to multiple dependent
16335 variables. This package provides routines to help determine optimal Bayesian
16336 network models for a given data set, where these models are used to identify
16337 statistical dependencies in messy, complex data.")
16338 (license license:gpl2+)))
16340 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
16341 ;; Bioconductor package.
16342 (define-public r-spp
16348 (uri (cran-uri "spp" version))
16351 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
16352 (build-system r-build-system)
16356 (list r-bh r-catools r-rcpp r-rsamtools))
16357 (home-page "https://cran.r-project.org/web/packages/spp/")
16358 (synopsis "ChIP-Seq processing pipeline")
16359 (description "This package provides tools for analysis of ChIP-seq and
16360 other functional sequencing data.")
16361 (license license:gpl2)))
16363 (define-public r-pathview
16365 (name "r-pathview")
16370 (uri (bioconductor-uri "pathview" version))
16372 (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71"))))
16373 (properties `((upstream-name . "pathview")))
16374 (build-system r-build-system)
16376 (list r-annotationdbi
16384 (home-page "https://pathview.uncc.edu/")
16385 (synopsis "Tool set for pathway based data integration and visualization")
16387 "@code{r-pathview} is a tool set for pathway based data integration and
16388 visualization. It maps and renders a wide variety of biological data on
16389 relevant pathway graphs. All users need is to supply their data and specify
16390 the target pathway. This package automatically downloads the pathway graph
16391 data, parses the data file, maps user data to the pathway, and render pathway
16392 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
16393 integrates with pathway and gene set (enrichment) analysis tools for
16394 large-scale and fully automated analysis.")
16395 (license license:gpl3+)))
16397 (define-public r-snpstats
16399 (name "r-snpstats")
16404 (uri (bioconductor-uri "snpStats" version))
16407 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
16408 (properties `((upstream-name . "snpStats")))
16409 (build-system r-build-system)
16410 (inputs (list zlib))
16412 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
16413 (home-page "https://bioconductor.org/packages/snpStats")
16414 (synopsis "Methods for SNP association studies")
16416 "This package provides classes and statistical methods for large
16417 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
16418 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
16419 (license license:gpl3)))
16421 (define-public r-chromstar
16423 (name "r-chromstar")
16428 (uri (bioconductor-uri "chromstaR" version))
16431 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
16432 (properties `((upstream-name . "chromstaR")))
16433 (build-system r-build-system)
16441 r-genomicalignments
16449 (native-inputs (list r-knitr))
16450 (home-page "https://github.com/ataudt/chromstaR")
16451 (synopsis "Chromatin state analysis for ChIP-Seq data")
16453 "This package implements functions for combinatorial and differential
16454 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
16455 export to genome browser viewable files, and functions for enrichment
16457 (license license:artistic2.0)))
16459 (define-public r-guitar
16466 (uri (bioconductor-uri "Guitar" version))
16469 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
16470 (properties `((upstream-name . "Guitar")))
16471 (build-system r-build-system)
16473 (list r-annotationdbi
16483 (home-page "https://bioconductor.org/packages/Guitar")
16484 (synopsis "Visualize genomic features")
16486 "This package is designed for visualization of RNA-related genomic
16487 features with respect to the landmarks of RNA transcripts, i.e., transcription
16488 starting site, start codon, stop codon and transcription ending site.")
16489 (license license:gpl2)))
16491 (define-public r-sushi
16497 (uri (bioconductor-uri "Sushi" version))
16500 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
16501 (properties `((upstream-name . "Sushi")))
16502 (build-system r-build-system)
16504 (list r-biomart r-zoo))
16505 (home-page "https://bioconductor.org/packages/Sushi")
16506 (synopsis "Tools for visualizing genomics data")
16508 "This package provides flexible, quantitative, and integrative genomic
16509 visualizations for publication-quality multi-panel figures.")
16510 (license license:gpl2+)))
16512 (define-public r-ballgown
16514 (name "r-ballgown")
16519 (uri (bioconductor-uri "ballgown" version))
16522 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
16523 (properties `((upstream-name . "ballgown")))
16524 (build-system r-build-system)
16537 (home-page "https://bioconductor.org/packages/ballgown")
16538 (synopsis "Flexible, isoform-level differential expression analysis")
16540 "This package provides tools for statistical analysis of assembled
16541 transcriptomes, including flexible differential expression analysis,
16542 visualization of transcript structures, and matching of assembled transcripts
16544 (license license:artistic2.0)))
16546 (define-public r-megadepth
16548 (name "r-megadepth")
16553 (uri (bioconductor-uri "megadepth" version))
16556 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
16557 (properties `((upstream-name . "megadepth")))
16558 (build-system r-build-system)
16559 (inputs (list megadepth))
16570 (home-page "https://github.com/LieberInstitute/megadepth")
16571 (synopsis "BigWig and BAM related utilities")
16573 "This package provides an R interface to Megadepth. It is particularly
16574 useful for computing the coverage of a set of genomic regions across bigWig or
16575 BAM files. With this package, you can build base-pair coverage matrices for
16576 regions or annotations of your choice from BigWig files.")
16577 (license license:artistic2.0)))
16579 (define-public r-beclear
16586 (uri (bioconductor-uri "BEclear" version))
16589 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
16590 (properties `((upstream-name . "BEclear")))
16591 (build-system r-build-system)
16603 (home-page "https://github.com/uds-helms/BEclear")
16604 (synopsis "Correction of batch effects in DNA methylation data")
16606 "This package provides functions to detect and correct for batch effects
16607 in DNA methylation data. The core function is based on latent factor models
16608 and can also be used to predict missing values in any other matrix containing
16610 (license license:gpl3)))
16612 (define-public r-bgeecall
16614 (name "r-bgeecall")
16619 (uri (bioconductor-uri "BgeeCall" version))
16622 "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil"))))
16623 (properties `((upstream-name . "BgeeCall")))
16624 (build-system r-build-system)
16638 (native-inputs (list r-knitr))
16639 (home-page "https://github.com/BgeeDB/BgeeCall")
16640 (synopsis "RNA-Seq present/absent gene expression calls generation")
16642 "BgeeCall allows generating present/absent gene expression calls without
16643 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
16644 intergenic sequences. These sequences are generated based on expression of
16645 all RNA-Seq libraries of each species integrated in Bgee.")
16646 (license license:gpl3)))
16648 (define-public r-bgeedb
16655 (uri (bioconductor-uri "BgeeDB" version))
16658 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
16659 (properties `((upstream-name . "BgeeDB")))
16660 (build-system r-build-system)
16673 (native-inputs (list r-knitr))
16674 (home-page "https://github.com/BgeeDB/BgeeDB_R")
16675 (synopsis "Annotation and gene expression data retrieval from Bgee database")
16677 "This package provides a package for the annotation and gene expression
16678 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
16679 anatomical terms, mapped to genes by expression patterns.")
16680 (license license:gpl3)))
16682 (define-public r-biobtreer
16684 (name "r-biobtreer")
16689 (uri (bioconductor-uri "biobtreeR" version))
16692 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
16693 (properties `((upstream-name . "biobtreeR")))
16694 (build-system r-build-system)
16696 (list r-httpuv r-httr r-jsonlite r-stringi))
16697 (native-inputs (list r-knitr))
16698 (home-page "https://github.com/tamerh/biobtreeR")
16699 (synopsis "Use biobtree tool from R")
16701 "The biobtreeR package provides an interface to biobtree, a tool which
16702 covers large sets of bioinformatics datasets and allows search and chain
16703 mappings functionalities.")
16704 (license license:expat)))
16706 (define-public r-minet
16713 (uri (bioconductor-uri "minet" version))
16716 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
16717 (properties `((upstream-name . "minet")))
16718 (build-system r-build-system)
16721 (home-page "http://minet.meyerp.com")
16722 (synopsis "Mutual information networks")
16724 "This package implements various algorithms for inferring mutual
16725 information networks from data.")
16726 (license license:artistic2.0)))
16728 (define-public r-genetclassifier
16730 (name "r-genetclassifier")
16735 (uri (bioconductor-uri "geNetClassifier" version))
16738 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
16740 `((upstream-name . "geNetClassifier")))
16741 (build-system r-build-system)
16743 (list r-biobase r-e1071 r-ebarrays r-minet))
16744 (home-page "https://www.cicancer.org")
16745 (synopsis "Classify diseases and build gene networks using expression profiles")
16747 "This is a comprehensive package to automatically train and validate a
16748 multi-class SVM classifier based on gene expression data. It provides
16749 transparent selection of gene markers, their coexpression networks, and an
16750 interface to query the classifier.")
16751 (license license:gpl2+)))
16753 (define-public r-dir-expiry
16755 (name "r-dir-expiry")
16760 (uri (bioconductor-uri "dir.expiry" version))
16763 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
16764 (properties `((upstream-name . "dir.expiry")))
16765 (build-system r-build-system)
16766 (propagated-inputs (list r-filelock))
16767 (native-inputs (list r-knitr))
16768 (home-page "https://bioconductor.org/packages/dir.expiry")
16769 (synopsis "Managing expiration for cache directories")
16771 "This package implements an expiration system for access to versioned
16772 directories. Directories that have not been accessed by a registered function
16773 within a certain time frame are deleted. This aims to reduce disk usage by
16774 eliminating obsolete caches generated by old versions of packages.")
16775 (license license:gpl3)))
16777 (define-public r-basilisk-utils
16779 (name "r-basilisk-utils")
16784 (uri (bioconductor-uri "basilisk.utils" version))
16787 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
16789 `((upstream-name . "basilisk.utils")))
16790 (build-system r-build-system)
16792 (list r-dir-expiry))
16793 (native-inputs (list r-knitr))
16794 (home-page "https://bioconductor.org/packages/basilisk.utils")
16795 (synopsis "Basilisk installation utilities")
16797 "This package implements utilities for installation of the basilisk
16798 package, primarily for creation of the underlying Conda instance.")
16799 (license license:gpl3)))
16801 (define-public r-basilisk
16803 (name "r-basilisk")
16808 (uri (bioconductor-uri "basilisk" version))
16811 "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk"))))
16812 (properties `((upstream-name . "basilisk")))
16813 (build-system r-build-system)
16815 (list r-basilisk-utils r-dir-expiry r-reticulate))
16816 (native-inputs (list r-knitr))
16817 (home-page "https://bioconductor.org/packages/basilisk")
16818 (synopsis "Freeze Python dependencies inside Bioconductor packages")
16820 "This package installs a self-contained Conda instance that is managed by
16821 the R/Bioconductor installation machinery. This aims to provide a consistent
16822 Python environment that can be used reliably by Bioconductor packages.
16823 Functions are also provided to enable smooth interoperability of multiple
16824 Python environments in a single R session.")
16825 (license license:gpl3)))
16827 (define-public r-biocthis
16829 (name "r-biocthis")
16834 (uri (bioconductor-uri "biocthis" version))
16837 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
16838 (properties `((upstream-name . "biocthis")))
16839 (build-system r-build-system)
16842 (modify-phases %standard-phases
16843 (add-after 'unpack 'set-HOME
16844 (lambda _ (setenv "HOME" "/tmp"))))))
16846 (list r-biocmanager
16852 (native-inputs (list r-knitr))
16853 (home-page "https://github.com/lcolladotor/biocthis")
16854 (synopsis "Automate package and project setup for Bioconductor packages")
16856 "This package expands the @code{usethis} package with the goal of helping
16857 automate the process of creating R packages for Bioconductor or making them
16858 Bioconductor-friendly.")
16859 (license license:artistic2.0)))
16861 (define-public r-biocdockermanager
16863 (name "r-biocdockermanager")
16868 (uri (bioconductor-uri "BiocDockerManager" version))
16871 "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d"))))
16873 `((upstream-name . "BiocDockerManager")))
16874 (build-system r-build-system)
16882 (native-inputs (list r-knitr))
16883 (home-page "https://bioconductor.org/packages/BiocDockerManager")
16884 (synopsis "Access and manage Bioconductor Docker images")
16886 "This package works analogous to BiocManager but for Docker images. Use
16887 the BiocDockerManager package to install and manage Docker images provided by
16888 the Bioconductor project.")
16889 (license license:artistic2.0)))
16891 (define-public r-biodb
16898 (uri (bioconductor-uri "biodb" version))
16901 "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1"))))
16902 (properties `((upstream-name . "biodb")))
16903 (build-system r-build-system)
16905 (list r-biocfilecache
16923 (native-inputs (list r-knitr))
16924 (home-page "https://bioconductor.org/packages/biodb")
16925 (synopsis "Library for connecting to chemical and biological databases")
16927 "The biodb package provides access to standard remote chemical and
16928 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
16929 database files (CSV, SQLite), with easy retrieval of entries, access to web
16930 services, search of compounds by mass and/or name, and mass spectra matching
16931 for LCMS and MSMS. Its architecture as a development framework facilitates
16932 the development of new database connectors for local projects or inside
16933 separate published packages.")
16934 (license license:agpl3+)))
16936 (define-public r-biomformat
16938 (name "r-biomformat")
16943 (uri (bioconductor-uri "biomformat" version))
16946 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
16947 (properties `((upstream-name . "biomformat")))
16948 (build-system r-build-system)
16950 (list r-jsonlite r-matrix r-plyr r-rhdf5))
16951 (native-inputs (list r-knitr))
16952 (home-page "https://github.com/joey711/biomformat/")
16953 (synopsis "Interface package for the BIOM file format")
16955 "This is an R package for interfacing with the BIOM format. This package
16956 includes basic tools for reading biom-format files, accessing and subsetting
16957 data tables from a biom object (which is more complex than a single table), as
16958 well as limited support for writing a biom-object back to a biom-format file.
16959 The design of this API is intended to match the Python API and other tools
16960 included with the biom-format project, but with a decidedly \"R flavor\" that
16961 should be familiar to R users. This includes S4 classes and methods, as well
16962 as extensions of common core functions/methods.")
16963 (license license:gpl2)))
16965 (define-public r-mvcclass
16967 (name "r-mvcclass")
16972 (uri (bioconductor-uri "MVCClass" version))
16975 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
16976 (properties `((upstream-name . "MVCClass")))
16977 (build-system r-build-system)
16978 (home-page "https://bioconductor.org/packages/MVCClass")
16979 (synopsis "Model-View-Controller (MVC) classes")
16981 "This package contains classes used in model-view-controller (MVC)
16983 (license license:lgpl2.1+)))
16985 (define-public r-biomvcclass
16987 (name "r-biomvcclass")
16992 (uri (bioconductor-uri "BioMVCClass" version))
16995 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
16996 (properties `((upstream-name . "BioMVCClass")))
16997 (build-system r-build-system)
16999 (list r-biobase r-graph r-mvcclass r-rgraphviz))
17000 (home-page "https://bioconductor.org/packages/BioMVCClass")
17001 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
17003 "This package contains classes used in model-view-controller (MVC)
17005 (license license:lgpl2.1+)))
17007 (define-public r-biomvrcns
17009 (name "r-biomvrcns")
17014 (uri (bioconductor-uri "biomvRCNS" version))
17017 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
17018 (properties `((upstream-name . "biomvRCNS")))
17019 (build-system r-build-system)
17021 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
17022 (home-page "https://bioconductor.org/packages/biomvRCNS")
17023 (synopsis "Copy number study and segmentation for multivariate biological data")
17025 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
17026 homogeneous segmentation model are designed and implemented for segmentation
17027 genomic data, with the aim of assisting in transcripts detection using high
17028 throughput technology like RNA-seq or tiling array, and copy number analysis
17029 using aCGH or sequencing.")
17030 (license license:gpl2+)))
17032 (define-public r-bionero
17039 (uri (bioconductor-uri "BioNERO" version))
17042 "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp"))))
17043 (properties `((upstream-name . "BioNERO")))
17044 (build-system r-build-system)
17046 (list r-biocparallel
17063 r-summarizedexperiment
17068 (home-page "https://github.com/almeidasilvaf/BioNERO")
17069 (synopsis "Biological network reconstruction omnibus")
17071 "BioNERO aims to integrate all aspects of biological network inference in
17072 a single package, including data preprocessing, exploratory analyses, network
17073 inference, and analyses for biological interpretations. BioNERO can be used
17074 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
17075 from gene expression data. Additionally, it can be used to explore
17076 topological properties of protein-protein interaction (PPI) networks. GCN
17077 inference relies on the popular WGCNA algorithm. GRN inference is based on
17078 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
17079 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
17080 rank for each interaction pair. As all steps of network analyses are included
17081 in this package, BioNERO makes users avoid having to learn the syntaxes of
17082 several packages and how to communicate between them. Finally, users can also
17083 identify consensus modules across independent expression sets and calculate
17084 intra and interspecies module preservation statistics between different
17086 (license license:gpl3)))
17088 (define-public r-bionet
17095 (uri (bioconductor-uri "BioNet" version))
17098 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
17099 (properties `((upstream-name . "BioNet")))
17100 (build-system r-build-system)
17102 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
17103 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
17104 (synopsis "Functional analysis of biological networks")
17106 "This package provides functions for the integrated analysis of
17107 protein-protein interaction networks and the detection of functional modules.
17108 Different datasets can be integrated into the network by assigning p-values of
17109 statistical tests to the nodes of the network. E.g. p-values obtained from
17110 the differential expression of the genes from an Affymetrix array are assigned
17111 to the nodes of the network. By fitting a beta-uniform mixture model and
17112 calculating scores from the p-values, overall scores of network regions can be
17113 calculated and an integer linear programming algorithm identifies the maximum
17114 scoring subnetwork.")
17115 (license license:gpl2+)))
17117 (define-public r-bionetstat
17119 (name "r-bionetstat")
17124 (uri (bioconductor-uri "BioNetStat" version))
17127 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
17128 (properties `((upstream-name . "BioNetStat")))
17129 (build-system r-build-system)
17131 (list r-biocparallel
17151 (home-page "https://github.com/jardimViniciusC/BioNetStat")
17152 (synopsis "Biological network analysis")
17154 "This package provides a package to perform differential network
17155 analysis, differential node analysis (differential coexpression analysis),
17156 network and metabolic pathways view.")
17157 (license license:gpl3+)))
17159 (define-public r-bioqc
17166 (uri (bioconductor-uri "BioQC" version))
17169 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
17170 (properties `((upstream-name . "BioQC")))
17171 (build-system r-build-system)
17173 (list r-biobase r-edger r-rcpp))
17176 (home-page "https://accio.github.io/BioQC/")
17177 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
17179 "BioQC performs quality control of high-throughput expression data based
17180 on tissue gene signatures. It can detect tissue heterogeneity in gene
17181 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
17182 optimised for high performance.")
17183 (license license:gpl3+)))
17185 (define-public r-biotip
17192 (uri (bioconductor-uri "BioTIP" version))
17195 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
17196 (properties `((upstream-name . "BioTIP")))
17197 (build-system r-build-system)
17208 (home-page "https://github.com/xyang2uchicago/BioTIP")
17209 (synopsis "R package for characterization of biological tipping-point")
17211 "This package adopts tipping-point theory to transcriptome profiles to
17212 help unravel disease regulatory trajectory.")
17213 (license license:gpl2)))
17215 (define-public r-biotmle
17222 (uri (bioconductor-uri "biotmle" version))
17225 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
17226 (properties `((upstream-name . "biotmle")))
17227 (build-system r-build-system)
17238 r-summarizedexperiment
17243 (home-page "https://code.nimahejazi.org/biotmle/")
17244 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
17246 "This package provides tools for differential expression biomarker
17247 discovery based on microarray and next-generation sequencing data that
17248 leverage efficient semiparametric estimators of the average treatment effect
17249 for variable importance analysis. Estimation and inference of the (marginal)
17250 average treatment effects of potential biomarkers are computed by targeted
17251 minimum loss-based estimation, with joint, stable inference constructed across
17252 all biomarkers using a generalization of moderated statistics for use with the
17253 estimated efficient influence function. The procedure accommodates the use of
17254 ensemble machine learning for the estimation of nuisance functions.")
17255 (license license:expat)))
17257 (define-public r-bsseq
17264 (uri (bioconductor-uri "bsseq" version))
17267 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
17268 (properties `((upstream-name . "bsseq")))
17269 (build-system r-build-system)
17279 r-delayedmatrixstats
17293 r-summarizedexperiment))
17296 (home-page "https://github.com/hansenlab/bsseq")
17297 (synopsis "Analyze, manage and store bisulfite sequencing data")
17299 "This package provides a collection of tools for analyzing and
17300 visualizing bisulfite sequencing data.")
17301 (license license:artistic2.0)))
17303 (define-public r-dada2
17309 (uri (bioconductor-uri "dada2" version))
17312 "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x"))))
17313 (properties `((upstream-name . "dada2")))
17314 (build-system r-build-system)
17316 (list r-biocgenerics
17325 (native-inputs (list r-knitr))
17326 (home-page "https://benjjneb.github.io/dada2/")
17328 "Accurate, high-resolution sample inference from amplicon sequencing data")
17330 "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
17331 from high-throughput amplicon sequencing data, replacing the coarser and less
17332 accurate OTU clustering approach. The dada2 pipeline takes as input
17333 demultiplexed fastq files, and outputs the sequence variants and their
17334 sample-wise abundances after removing substitution and chimera errors.
17335 Taxonomic classification is available via a native implementation of the RDP
17336 naive Bayesian classifier, and species-level assignment to 16S rRNA gene
17337 fragments by exact matching.")
17338 (license license:lgpl2.0)))
17340 (define-public r-dmrseq
17347 (uri (bioconductor-uri "dmrseq" version))
17350 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
17351 (properties `((upstream-name . "dmrseq")))
17352 (build-system r-build-system)
17354 (list r-annotationhub
17359 r-delayedmatrixstats
17373 (home-page "https://bioconductor.org/packages/dmrseq")
17374 (synopsis "Detection and inference of differentially methylated regions")
17376 "This package implements an approach for scanning the genome to detect
17377 and perform accurate inference on differentially methylated regions from Whole
17378 Genome Bisulfite Sequencing data. The method is based on comparing detected
17379 regions to a pooled null distribution, that can be implemented even when as
17380 few as two samples per population are available. Region-level statistics are
17381 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
17382 with a nested autoregressive correlated error structure for the effect of
17383 interest on transformed methylation proportions.")
17384 (license license:expat)))
17386 (define-public r-omicade4
17388 (name "r-omicade4")
17392 (uri (bioconductor-uri "omicade4" version))
17395 "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
17396 (properties `((upstream-name . "omicade4")))
17397 (build-system r-build-system)
17398 (propagated-inputs (list r-ade4 r-biobase r-made4))
17399 (home-page "https://bioconductor.org/packages/omicade4")
17400 (synopsis "Multiple co-inertia analysis of omics datasets")
17402 "This package performes multiple co-inertia analysis of omics datasets.")
17403 (license license:gpl2)))
17405 (define-public r-omnipathr
17407 (name "r-omnipathr")
17412 (uri (bioconductor-uri "OmnipathR" version))
17414 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
17415 (properties `((upstream-name . "OmnipathR")))
17416 (build-system r-build-system)
17419 (modify-phases %standard-phases
17420 (add-after 'unpack 'set-HOME
17421 (lambda _ (setenv "HOME" "/tmp"))))))
17447 (native-inputs (list r-knitr))
17448 (home-page "https://saezlab.github.io/OmnipathR/")
17449 (synopsis "OmniPath web service client and more")
17451 "This package provides a client for the OmniPath web service and many
17452 other resources. It also includes functions to transform and pretty print
17453 some of the downloaded data, functions to access a number of other resources.
17454 Furthermore, OmnipathR features a close integration with the NicheNet method
17455 for ligand activity prediction from transcriptomics data.")
17456 (license license:expat)))
17458 (define-public r-biscuiteer
17460 (name "r-biscuiteer")
17465 (uri (bioconductor-uri "biscuiteer" version))
17468 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
17469 (properties `((upstream-name . "biscuiteer")))
17470 (build-system r-build-system)
17478 r-delayedmatrixstats
17497 r-summarizedexperiment
17498 r-variantannotation))
17501 (home-page "https://github.com/trichelab/biscuiteer")
17502 (synopsis "Convenience functions for the Biscuit package")
17504 "This package provides a test harness for bsseq loading of Biscuit
17505 output, summarization of WGBS data over defined regions and in mappable
17506 samples, with or without imputation, dropping of mostly-NA rows, age
17508 (license license:gpl3)))
17510 (define-public r-tcgabiolinks
17512 (name "r-tcgabiolinks")
17517 (uri (bioconductor-uri "TCGAbiolinks" version))
17519 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
17520 (properties `((upstream-name . "TCGAbiolinks")))
17521 (build-system r-build-system)
17540 r-summarizedexperiment
17541 r-tcgabiolinksgui-data
17546 (native-inputs (list r-knitr))
17547 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
17548 (synopsis "Integrative analysis with GDC data")
17550 "The aim of TCGAbiolinks is:
17553 @item facilitate GDC open-access data retrieval;
17554 @item prepare the data using the appropriate pre-processing strategies;
17555 @item provide the means to carry out different standard analyses, and;
17556 @item to easily reproduce earlier research results.
17559 In more detail, the package provides multiple methods for analysis (e.g.,
17560 differential expression analysis, identifying differentially methylated
17561 regions) and methods for visualization (e.g., survival plots, volcano plots,
17562 starburst plots) in order to easily develop complete analysis pipelines.")
17563 (license license:gpl3+)))
17565 (define-public r-tricycle
17567 (name "r-tricycle")
17571 (uri (bioconductor-uri "tricycle" version))
17574 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
17575 (properties `((upstream-name . "tricycle")))
17576 (build-system r-build-system)
17578 (list r-annotationdbi
17589 r-singlecellexperiment
17590 r-summarizedexperiment))
17591 (native-inputs (list r-knitr))
17592 (home-page "https://github.com/hansenlab/tricycle")
17593 (synopsis "Transferable representation and inference of cell cycle")
17595 "The package contains functions to infer and visualize cell cycle process
17596 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
17597 projecting new data to the previous learned biologically interpretable space.
17598 The @code{tricycle} provides a pre-learned cell cycle space, which could be
17599 used to infer cell cycle time of human and mouse single cell samples. In
17600 addition, it also offer functions to visualize cell cycle time on different
17601 embeddings and functions to build new reference.")
17602 (license license:gpl3)))
17604 (define-public r-tximeta
17611 (uri (bioconductor-uri "tximeta" version))
17614 "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8"))))
17615 (properties `((upstream-name . "tximeta")))
17616 (build-system r-build-system)
17618 (list r-annotationdbi
17630 r-summarizedexperiment
17635 (home-page "https://github.com/mikelove/tximeta")
17636 (synopsis "Transcript quantification import with automatic metadata")
17638 "This package implements transcript quantification import from Salmon and
17639 alevin with automatic attachment of transcript ranges and release information,
17640 and other associated metadata. De novo transcriptomes can be linked to the
17641 appropriate sources with linkedTxomes and shared for computational
17643 (license license:gpl2)))
17645 (define-public r-phyloseq
17647 (name "r-phyloseq")
17652 (uri (bioconductor-uri "phyloseq" version))
17654 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
17655 (properties `((upstream-name . "phyloseq")))
17656 (build-system r-build-system)
17676 (home-page "https://github.com/joey711/phyloseq")
17677 (synopsis "Handling and analysis of high-throughput microbiome census data")
17679 "Phyloseq provides a set of classes and tools to facilitate the import,
17680 storage, analysis, and graphical display of microbiome census data.")
17681 (license license:agpl3)))
17684 ;;; Avoid adding new packages to the end of this file. To reduce the chances
17685 ;;; of a merge conflict, place them above by existing packages with similar
17686 ;;; functionality or similar names.
HCoop / jackhill / guix / guix.git / blob