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)))
1634 (define-public r-abarray
1640 (uri (bioconductor-uri "ABarray" version))
1643 "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
1644 (properties `((upstream-name . "ABarray")))
1645 (build-system r-build-system)
1646 (propagated-inputs (list r-biobase r-multtest))
1647 (home-page "https://bioconductor.org/packages/ABarray")
1649 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
1651 "The package @code{ABarray} is designed to work with Applied Biosystems
1652 whole genome microarray platform, as well as any other platform whose data can
1653 be transformed into expression data matrix. Functions include data
1654 preprocessing, filtering, control probe analysis, statistical analysis in one
1655 single function. A @dfn{graphical user interface} (GUI) is also provided. The
1656 raw data, processed data, graphics output and statistical results are organized
1657 into folders according to the analysis settings used.")
1658 (license license:gpl2+)))
1660 (define-public r-absseq
1666 (uri (bioconductor-uri "ABSSeq" version))
1669 "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
1670 (properties `((upstream-name . "ABSSeq")))
1671 (build-system r-build-system)
1672 (propagated-inputs (list r-limma r-locfit))
1673 (home-page "https://bioconductor.org/packages/ABSSeq")
1675 "RNA-Seq analysis based on modelling absolute expression differences")
1677 "This package implements a new RNA-Seq analysis method and integrates two
1678 modules: a basic model for pairwise comparison and a linear model for complex
1679 design. RNA-Seq quantifies gene expression with reads count, which usually
1680 consists of conditions (or treatments) and several replicates for each
1681 condition. This software infers differential expression directly by the
1682 counts difference between conditions. It assumes that the sum counts
1683 difference between conditions follow a negative binomial distribution. In
1684 addition, @code{ABSSeq} moderates the fold-changes by two steps: the
1685 expression level and gene-specific dispersion, that might facilitate the gene
1686 ranking by fold-change and visualization.")
1687 (license license:gpl3+)))
1689 (define-public r-adam
1695 (uri (bioconductor-uri "ADAM" version))
1698 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
1699 (properties `((upstream-name . "ADAM")))
1700 (build-system r-build-system)
1701 (propagated-inputs (list r-dplyr
1709 r-summarizedexperiment))
1710 (native-inputs (list r-knitr))
1711 (home-page "https://bioconductor.org/packages/ADAM")
1712 (synopsis "Gene activity and diversity analysis module")
1714 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
1715 package created to group a set of genes from comparative samples (control
1716 versus experiment) belonging to different species according to their respective
1717 functions. The corresponding roles are extracted from the default collections
1718 like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
1719 @code{ADAM} show their significance by calculating the p-values referring to
1720 gene diversity and activity. Each group of genes is called @dfn{Group of
1721 functionally associated genes} (GFAG).")
1722 (license license:gpl2+)))
1724 (define-public r-adamgui
1730 (uri (bioconductor-uri "ADAMgui" version))
1733 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
1734 (properties `((upstream-name . "ADAMgui")))
1735 (build-system r-build-system)
1757 (native-inputs (list r-knitr))
1758 (home-page "https://bioconductor.org/packages/ADAMgui/")
1759 (synopsis "GUI for gene activity and diversity analysis")
1761 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
1762 for the @code{ADAM} package. The @code{ADAMgui} package provides two
1763 shiny-based applications that allows the user to study the output of the
1764 @code{ADAM} package files through different plots. It's possible, for
1765 example, to choose a specific @dfn{group of functionally associated
1766 genes} (GFAG) and observe the gene expression behavior with the plots created
1767 with the @code{GFAGtargetUi} function. Features such as differential
1768 expression and fold change can be easily seen with aid of the plots made with
1769 the @code{GFAGpathUi} function.")
1770 (license license:gpl2+)))
1772 (define-public r-adimpute
1778 (uri (bioconductor-uri "ADImpute" version))
1781 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
1782 (properties `((upstream-name . "ADImpute")))
1783 (build-system r-build-system)
1785 (list r-biocparallel
1795 r-singlecellexperiment
1796 r-summarizedexperiment))
1797 (native-inputs (list r-knitr))
1798 (home-page "https://bioconductor.org/packages/ADImpute")
1799 (synopsis "Adaptive computational prediction for dropout imputations")
1801 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
1802 unable to quantify the expression levels of all genes in a cell, creating a
1803 need for the computational prediction of missing values (dropout imputation).
1804 Most existing dropout imputation methods are limited in the sense that they
1805 exclusively use the scRNA-seq dataset at hand and do not exploit external
1806 gene-gene relationship information. The @code{ADImpute} package proposes two
1807 methods to address this issue:
1810 @item a gene regulatory network-based approach using gene-gene relationships
1811 learnt from external data;
1812 @item a baseline approach corresponding to a sample-wide average.
1815 @code{ADImpute} implements these novel methods and also combines them with
1816 existing imputation methods like @code{DrImpute} and @code{SAVER}.
1817 @code{ADImpute} can learn the best performing method per gene and combine the
1818 results from different methods into an ensemble.")
1819 (license license:gpl3+)))
1821 (define-public r-adsplit
1827 (uri (bioconductor-uri "adSplit" version))
1830 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
1831 (properties `((upstream-name . "adSplit")))
1832 (build-system r-build-system)
1834 (list r-annotationdbi
1840 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
1841 (synopsis "Annotation-driven splits in microarray data")
1843 "This package implements clustering of microarray gene expression
1844 profiles according to functional annotations. For each term genes are
1845 annotated to, splits into two subclasses are computed and a significance of
1846 the supporting gene set is determined.")
1847 (license license:gpl2+)))
1849 (define-public r-affixcan
1855 (uri (bioconductor-uri "AffiXcan" version))
1858 "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
1859 (properties `((upstream-name . "AffiXcan")))
1860 (build-system r-build-system)
1862 (list r-biocparallel
1864 r-multiassayexperiment
1865 r-summarizedexperiment))
1866 (native-inputs (list r-knitr))
1867 (home-page "https://bioconductor.org/packages/AffiXcan")
1868 (synopsis "Functional approach to impute genetically regulated expression")
1870 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
1871 expression} (GReX) for a set of genes in a sample of individuals, using a
1872 method based on the @dfn{total binding affinity} (TBA). Statistical models to
1873 impute GReX can be trained with a training dataset where the real total
1874 expression values are known.")
1875 (license license:gpl3)))
1877 (define-public r-affyrnadegradation
1879 (name "r-affyrnadegradation")
1883 (uri (bioconductor-uri "AffyRNADegradation" version))
1886 "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
1887 (properties `((upstream-name . "AffyRNADegradation")))
1888 (build-system r-build-system)
1889 (propagated-inputs (list r-affy))
1890 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
1892 "Analyze and correct probe positional bias in data due to RNA degradation")
1894 "The @code{AffyRNADegradation} package helps with the assessment and
1895 correction of RNA degradation effects in Affymetrix 3 expression arrays. The
1896 parameter @code{d} gives a robust and accurate measure of RNA integrity. The
1897 correction removes the probe positional bias, and thus improves comparability
1898 of samples that are affected by RNA degradation.")
1899 ;; the R file header specifies GPL2 or later
1900 (license license:gpl2+)))
1902 (define-public r-agdex
1908 (uri (bioconductor-uri "AGDEX" version))
1911 "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
1912 (properties `((upstream-name . "AGDEX")))
1913 (build-system r-build-system)
1914 (propagated-inputs (list r-biobase r-gseabase))
1915 (home-page "https://bioconductor.org/packages/AGDEX")
1917 "Evaluate agreement of differential expression for cross-species genomics")
1919 "The objective of @code{AGDEX} is to evaluate whether the results of a
1920 pair of two-group differential expression analysis comparisons show a level of
1921 agreement that is greater than expected if the group labels for each two-group
1922 comparison are randomly assigned. The agreement is evaluated for the entire
1923 transcriptome and (optionally) for a collection of pre-defined gene-sets.
1924 Additionally, the procedure performs permutation-based differential expression
1925 and meta analysis at both gene and gene-set levels of the data from each
1927 (license license:gpl2+)))
1929 (define-public r-aggregatebiovar
1931 (name "r-aggregatebiovar")
1935 (uri (bioconductor-uri "aggregateBioVar" version))
1938 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
1939 (properties `((upstream-name . "aggregateBioVar")))
1940 (build-system r-build-system)
1945 r-singlecellexperiment
1946 r-summarizedexperiment
1948 (native-inputs (list r-knitr))
1949 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
1950 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
1952 "This package @code{aggregateBioVar} contains tools to summarize single
1953 cell gene expression profiles at the level of subject for single cell RNA-seq
1954 data collected from more than one subject (e.g. biological sample or technical
1955 replicates). A @code{SingleCellExperiment} object is taken as input and
1956 converted to a list of @code{SummarizedExperiment} objects, where each list
1957 element corresponds to an assigned cell type. The @code{SummarizedExperiment}
1958 objects contain aggregate gene-by-subject count matrices and inter-subject
1959 column metadata for individual subjects that can be processed using downstream
1960 bulk RNA-seq tools.")
1961 (license license:gpl3)))
1963 (define-public r-agilp
1969 (uri (bioconductor-uri "agilp" version))
1972 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
1973 (properties `((upstream-name . "agilp")))
1974 (build-system r-build-system)
1975 (home-page "https://bioconductor.org/packages/agilp")
1976 (synopsis "Processing of Agilent expression array")
1978 "This package aims to provide a pipeline for the low-level analysis of
1979 gene expression microarray data, primarily focused on the Agilent platform,
1980 but which also provides utilities which may be useful for other platforms.")
1981 ;; Some files are under GPLv2+ but the combined work is released under the
1983 (license license:gpl3)))
1985 (define-public r-adductomicsr
1987 (name "r-adductomicsr")
1991 (uri (bioconductor-uri "adductomicsR" version))
1994 "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
1995 (properties `((upstream-name . "adductomicsR")))
1996 (build-system r-build-system)
2019 (native-inputs (list r-knitr))
2020 (home-page "https://bioconductor.org/packages/adductomicsR")
2021 (synopsis "Processing of adductomic mass spectral datasets")
2023 "This package @code{adductomicsR} processes data generated by the
2024 @dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
2025 peptides from spectra that has been corrected for mass drift and retention
2026 time drift and quantifies level mass spectral peaks from @dfn{first stage of
2027 mass spectrometry} (MS1) data.")
2028 (license license:artistic2.0)))
2030 (define-public r-agimicrorna
2032 (name "r-agimicrorna")
2036 (uri (bioconductor-uri "AgiMicroRna" version))
2039 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
2040 (properties `((upstream-name . "AgiMicroRna")))
2041 (build-system r-build-system)
2048 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
2050 "Processing and differential expression analysis of Agilent microRNA chips")
2052 "@code{AgiMicroRna} provides useful functionality for the processing,
2053 quality assessment and differential expression analysis of Agilent microRNA
2054 array data. The package uses a limma-like structure to generate the processed
2055 data in order to make statistical inferences about differential expression
2056 using the linear model features implemented in limma. Standard Bioconductor
2057 objects are used so that other packages could be used as well.")
2058 (license license:gpl3)))
2060 (define-public r-amountain
2062 (name "r-amountain")
2066 (uri (bioconductor-uri "AMOUNTAIN" version))
2069 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
2070 (properties `((upstream-name . "AMOUNTAIN")))
2071 (build-system r-build-system)
2073 (native-inputs (list r-knitr))
2074 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
2075 (synopsis "Modules for multilayer weighted gene co-expression networks")
2077 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
2078 gene co-expression network) could be constructed only from expression profile.
2079 Different layers in such networks may represent different time points, multiple
2080 conditions or various species. @code{AMOUNTAIN} aims to search active modules
2081 in multi-layer WGCN using a continuous optimization approach.")
2082 (license license:gpl2+)))
2084 (define-public r-amaretto
2090 (uri (bioconductor-uri "AMARETTO" version))
2093 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
2094 (properties `((upstream-name . "AMARETTO")))
2095 (build-system r-build-system)
2097 (list r-biocfilecache
2115 r-multiassayexperiment
2121 (native-inputs (list r-knitr))
2122 (home-page "https://bioconductor.org/packages/AMARETTO")
2123 (synopsis "Regulatory network inference and driver gene evaluation")
2125 "This package @code{AMARETTO} represents an algorithm that integrates copy
2126 number, DNA methylation and gene expression data to identify a set of driver
2127 genes by analyzing cancer samples and connects them to clusters of co-expressed
2128 genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
2129 setting to identify cancer driver genes and their modules on multiple cancer
2130 sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
2131 and EMT, and modules that accurately predict survival and molecular subtypes.
2132 This allows @code{AMARETTO} to identify novel cancer driver genes directing
2133 canonical cancer pathways.")
2134 (license license:asl2.0)))
2136 (define-public r-anaquin
2142 (uri (bioconductor-uri "Anaquin" version))
2145 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
2146 (properties `((upstream-name . "Anaquin")))
2147 (build-system r-build-system)
2156 (native-inputs (list r-knitr))
2157 (home-page "https://www.sequinstandards.com/")
2158 (synopsis "Statistical analysis of sequins")
2160 "The project is intended to support the use of @dfn{sequins}(synthetic
2161 sequencing spike-in controls) owned and made available by the Garvan Institute
2162 of Medical Research. The goal is to provide a standard library for quantitative
2163 analysis, modelling, and visualization of spike-in controls.")
2164 (license license:bsd-3)))
2166 (define-public r-aneufinder
2168 (name "r-aneufinder")
2172 (uri (bioconductor-uri "AneuFinder" version))
2175 "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
2176 (build-system r-build-system)
2180 (list r-genomicranges
2201 (home-page "https://bioconductor.org/packages/AneuFinder/")
2202 (synopsis "Copy number variation analysis in single-cell-sequencing data")
2203 (description "This package implements functions for copy number variant
2204 calling, plotting, export and analysis from whole-genome single cell
2206 (license license:artistic2.0)))
2208 (define-public r-anf
2214 (uri (bioconductor-uri "ANF" version))
2217 "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
2218 (properties `((upstream-name . "ANF")))
2219 (build-system r-build-system)
2226 (native-inputs (list r-knitr))
2227 (home-page "https://bioconductor.org/packages/ANF")
2228 (synopsis "Affinity network fusion for complex patient clustering")
2230 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
2231 matrix construction and fusion as well as spectral clustering. This package is
2232 used for complex patient clustering by integrating multi-omic data through affinity
2234 (license license:gpl3)))
2236 (define-public r-annmap
2242 (uri (bioconductor-uri "annmap" version))
2245 "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
2246 (properties `((upstream-name . "annmap")))
2247 (build-system r-build-system)
2259 (home-page "https://github.com/cruk-mi/annmap")
2261 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
2263 "This package @code{annmap} provides annotation mappings for Affymetrix exon
2264 arrays and coordinate based queries to support deep sequencing data analysis.
2265 Database access is hidden behind the API which provides a set of functions such
2266 as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
2267 Functions to plot gene architecture and BAM file data are also provided.")
2268 (license license:gpl2)))
2270 (define-public r-antiprofiles
2272 (name "r-antiprofiles")
2276 (uri (bioconductor-uri "antiProfiles" version))
2279 "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
2280 (properties `((upstream-name . "antiProfiles")))
2281 (build-system r-build-system)
2285 (home-page "https://github.com/HCBravoLab/antiProfiles")
2286 (synopsis "Implementation of gene expression anti-profiles")
2288 "This package implements the gene expression anti-profiles method.
2289 Anti-profiles are a new approach for developing cancer genomic signatures that
2290 specifically take advantage of gene expression heterogeneity. They explicitly
2291 model increased gene expression variability in cancer to define robust and
2292 reproducible gene expression signatures capable of accurately distinguishing
2293 tumor samples from healthy controls.")
2294 (license license:artistic2.0)))
2296 (define-public r-baalchip
2302 (uri (bioconductor-uri "BaalChIP" version))
2305 "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
2306 (properties `((upstream-name . "BaalChIP")))
2307 (build-system r-build-system)
2308 (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
2322 (native-inputs (list r-knitr))
2323 (home-page "https://bioconductor.org/packages/BaalChIP")
2325 "Analysis of allele-specific transcription factor binding in cancer genomes")
2327 "This package offers functions to process multiple @code{ChIP-seq BAM}
2328 files and detect allele-specific events. It computes allele counts at
2329 individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
2330 control) steps to remove problematic variants, and utilizes a Bayesian
2331 framework to identify statistically significant allele-specific events.
2332 BaalChIP is able to account for copy number differences between the two
2333 alleles, a known phenotypical feature of cancer samples.")
2334 (license license:artistic2.0)))
2336 (define-public r-biocversion
2338 (name "r-biocversion")
2343 (uri (bioconductor-uri "BiocVersion" version))
2346 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
2347 (properties `((upstream-name . "BiocVersion")))
2348 (build-system r-build-system)
2349 (home-page "https://bioconductor.org/packages/BiocVersion/")
2350 (synopsis "Set the appropriate version of Bioconductor packages")
2352 "This package provides repository information for the appropriate version
2354 (license license:artistic2.0)))
2356 (define-public r-biocgenerics
2358 (name "r-biocgenerics")
2362 (uri (bioconductor-uri "BiocGenerics" version))
2365 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
2367 `((upstream-name . "BiocGenerics")))
2368 (build-system r-build-system)
2369 (home-page "https://bioconductor.org/packages/BiocGenerics")
2370 (synopsis "S4 generic functions for Bioconductor")
2372 "This package provides S4 generic functions needed by many Bioconductor
2374 (license license:artistic2.0)))
2376 (define-public r-coverageview
2378 (name "r-coverageview")
2382 (uri (bioconductor-uri "CoverageView" version))
2385 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
2386 (build-system r-build-system)
2394 (home-page "https://bioconductor.org/packages/CoverageView/")
2395 (synopsis "Coverage visualization package for R")
2396 (description "This package provides a framework for the visualization of
2397 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
2398 be also used for genome-wide nucleosome positioning experiments or other
2399 experiment types where it is important to have a framework in order to inspect
2400 how the coverage distributed across the genome.")
2401 (license license:artistic2.0)))
2403 (define-public r-cummerbund
2405 (name "r-cummerbund")
2409 (uri (bioconductor-uri "cummeRbund" version))
2412 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
2413 (build-system r-build-system)
2425 (home-page "https://bioconductor.org/packages/cummeRbund/")
2426 (synopsis "Analyze Cufflinks high-throughput sequencing data")
2427 (description "This package allows for persistent storage, access,
2428 exploration, and manipulation of Cufflinks high-throughput sequencing
2429 data. In addition, provides numerous plotting functions for commonly
2430 used visualizations.")
2431 (license license:artistic2.0)))
2433 (define-public r-dearseq
2440 (uri (bioconductor-uri "dearseq" version))
2443 "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl"))))
2444 (build-system r-build-system)
2446 (list r-compquadform
2462 (home-page "https://github.com/borishejblum/dearseq")
2463 (synopsis "DEA for RNA-seq data through a robust variance component test")
2465 "This is a package for Differential Expression Analysis of RNA-seq data.
2466 It features a variance component score test accounting for data
2467 heteroscedasticity through precision weights. Perform both gene-wise and gene
2468 set analyses, and can deal with repeated or longitudinal data.")
2469 (license license:gpl2)))
2471 (define-public r-decipher
2477 (uri (bioconductor-uri "DECIPHER" version))
2480 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
2481 (build-system r-build-system)
2489 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
2490 (synopsis "Tools for deciphering and managing biological sequences")
2491 (description "This package provides a toolset for deciphering and managing
2492 biological sequences.")
2493 (license license:gpl3)))
2495 (define-public r-deconvr
2501 (uri (bioconductor-uri "deconvR" version))
2504 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
2505 (properties `((upstream-name . "deconvR")))
2506 (build-system r-build-system)
2525 (native-inputs (list r-knitr))
2526 (home-page "https://github.com/BIMSBbioinfo/deconvR")
2527 (synopsis "Simulation and deconvolution of omic profiles")
2529 "This package provides a collection of functions designed for analyzing
2530 deconvolution of the bulk sample(s) using an atlas of reference omic signature
2531 profiles and a user-selected model. Users are given the option to create or
2532 extend a reference atlas and,also simulate the desired size of the bulk
2533 signature profile of the reference cell types. The package includes the
2534 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
2535 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
2536 make mapping WGBS data to their probe IDs easier.")
2537 (license license:artistic2.0)))
2539 (define-public r-decoupler
2541 (name "r-decoupler")
2546 (uri (bioconductor-uri "decoupleR" version))
2548 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
2549 (properties `((upstream-name . "decoupleR")))
2550 (build-system r-build-system)
2563 (native-inputs (list r-knitr))
2564 (home-page "https://saezlab.github.io/decoupleR/")
2565 (synopsis "Computational methods to infer biological activities from omics data")
2567 "Many methods allow us to extract biological activities from omics data using
2568 information from prior knowledge resources, reducing the dimensionality for
2569 increased statistical power and better interpretability. decoupleR is a
2570 Bioconductor package containing different statistical methods to extract these
2571 signatures within a unified framework. decoupleR allows the user to flexibly
2572 test any method with any resource. It incorporates methods that take into
2573 account the sign and weight of network interactions. decoupleR can be used
2574 with any omic, as long as its features can be linked to a biological process
2575 based on prior knowledge. For example, in transcriptomics gene sets regulated
2576 by a transcription factor, or in phospho-proteomics phosphosites that are
2577 targeted by a kinase.")
2578 (license license:gpl3)))
2580 (define-public r-deepsnv
2586 (uri (bioconductor-uri "deepSNV" version))
2589 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
2590 (properties `((upstream-name . "deepSNV")))
2591 (build-system r-build-system)
2597 r-summarizedexperiment
2602 (home-page "https://github.com/gerstung-lab/deepSNV/")
2603 (synopsis "Detection of subclonal SNVs in deep sequencing data")
2605 "This package provides quantitative variant callers for detecting
2606 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
2607 The deepSNV algorithm is used for a comparative setup with a control experiment
2608 of the same loci and uses a beta-binomial model and a likelihood ratio test to
2609 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
2610 computes a Bayes classifier based on a beta-binomial model for variant calling
2611 with multiple samples for precisely estimating model parameters - such as local
2612 error rates and dispersion - and prior knowledge, e.g. from variation data
2613 bases such as COSMIC.")
2614 (license license:gpl3)))
2616 (define-public r-delayedarray
2618 (name "r-delayedarray")
2622 (uri (bioconductor-uri "DelayedArray" version))
2625 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
2627 `((upstream-name . "DelayedArray")))
2628 (build-system r-build-system)
2630 (list r-biocgenerics r-s4vectors r-iranges r-matrix
2634 (home-page "https://bioconductor.org/packages/DelayedArray")
2635 (synopsis "Delayed operations on array-like objects")
2637 "Wrapping an array-like object (typically an on-disk object) in a
2638 @code{DelayedArray} object allows one to perform common array operations on it
2639 without loading the object in memory. In order to reduce memory usage and
2640 optimize performance, operations on the object are either delayed or executed
2641 using a block processing mechanism. Note that this also works on in-memory
2642 array-like objects like @code{DataFrame} objects (typically with Rle columns),
2643 @code{Matrix} objects, and ordinary arrays and data frames.")
2644 (license license:artistic2.0)))
2646 (define-public r-derfinderhelper
2648 (name "r-derfinderhelper")
2653 (uri (bioconductor-uri "derfinderHelper" version))
2655 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
2656 (properties `((upstream-name . "derfinderHelper")))
2657 (build-system r-build-system)
2659 (list r-iranges r-matrix r-s4vectors))
2662 (home-page "https://github.com/leekgroup/derfinderHelper")
2663 (synopsis "Helper for derfinder")
2665 "This package speeds up the derfinder package when using multiple cores.
2666 It is particularly useful when using BiocParallel and it helps reduce the time
2667 spent loading the full derfinder package when running the F-statistics
2668 calculation in parallel.")
2669 (license license:artistic2.0)))
2671 (define-public r-drimseq
2678 (uri (bioconductor-uri "DRIMSeq" version))
2680 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
2681 (properties `((upstream-name . "DRIMSeq")))
2682 (build-system r-build-system)
2684 (list r-biocgenerics
2694 (native-inputs (list r-knitr))
2695 (home-page "https://bioconductor.org/packages/DRIMSeq")
2696 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
2698 "The package provides two frameworks. One for the differential
2699 transcript usage analysis between different conditions and one for the tuQTL
2700 analysis. Both are based on modeling the counts of genomic features (i.e.,
2701 transcripts) with the Dirichlet-multinomial distribution. The package also
2702 makes available functions for visualization and exploration of the data and
2704 (license license:gpl3+)))
2706 (define-public r-bluster
2712 (uri (bioconductor-uri "bluster" version))
2715 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
2716 (properties `((upstream-name . "bluster")))
2717 (build-system r-build-system)
2719 (list r-biocneighbors
2728 (home-page "https://bioconductor.org/packages/bluster")
2729 (synopsis "Clustering algorithms for Bioconductor")
2730 (description"This package wraps common clustering algorithms in an easily
2731 extended S4 framework. Backends are implemented for hierarchical, k-means
2732 and graph-based clustering. Several utilities are also provided to compare
2733 and evaluate clustering results.")
2734 (license license:gpl3)))
2736 (define-public r-ideoviz
2742 (uri (bioconductor-uri "IdeoViz" version))
2745 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
2746 (build-system r-build-system)
2754 (home-page "https://bioconductor.org/packages/IdeoViz/")
2755 (synopsis "Plots data along a chromosomal ideogram")
2756 (description "This package provides functions to plot data associated with
2757 arbitrary genomic intervals along chromosomal ideogram.")
2758 (license license:gpl2)))
2760 (define-public r-infercnv
2767 (uri (bioconductor-uri "infercnv" version))
2770 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
2771 (properties `((upstream-name . "infercnv")))
2772 (build-system r-build-system)
2773 (inputs (list python))
2802 r-singlecellexperiment
2803 r-summarizedexperiment
2805 (native-inputs (list r-knitr))
2806 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
2807 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
2809 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
2810 evidence for somatic large-scale chromosomal copy number alterations, such as gains
2811 or deletions of entire chromosomes or large segments of chromosomes. This is done
2812 by exploring expression intensity of genes across positions of a tumor genome in
2813 comparison to a set of reference \"normal\" cells. A heatmap is generated
2814 illustrating the relative expression intensities across each chromosome, and it
2815 often becomes readily apparent as to which regions of the tumor genome are
2816 over-abundant or less-abundant as compared to that of normal cells.")
2817 (license license:bsd-3)))
2819 (define-public r-iranges
2825 (uri (bioconductor-uri "IRanges" version))
2828 "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
2830 `((upstream-name . "IRanges")))
2831 (build-system r-build-system)
2833 (list r-biocgenerics r-s4vectors))
2834 (home-page "https://bioconductor.org/packages/IRanges")
2835 (synopsis "Infrastructure for manipulating intervals on sequences")
2837 "This package provides efficient low-level and highly reusable S4 classes
2838 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
2839 generally, data that can be organized sequentially (formally defined as
2840 @code{Vector} objects), as well as views on these @code{Vector} objects.
2841 Efficient list-like classes are also provided for storing big collections of
2842 instances of the basic classes. All classes in the package use consistent
2843 naming and share the same rich and consistent \"Vector API\" as much as
2845 (license license:artistic2.0)))
2847 (define-public r-isoformswitchanalyzer
2849 (name "r-isoformswitchanalyzer")
2854 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
2856 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
2857 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
2858 (build-system r-build-system)
2891 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
2892 (synopsis "Analyze alternative splicing in RNA-seq data")
2894 "This is a package for the analysis of alternative splicing and isoform
2895 switches with predicted functional consequences (e.g. gain/loss of protein
2896 domains etc.) from quantification of all types of RNASeq by tools such as
2897 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
2898 (license license:gpl2+)))
2900 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
2901 (define-public r-absfiltergsea
2903 (name "r-absfiltergsea")
2908 (uri (cran-uri "AbsFilterGSEA" version))
2910 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
2911 (properties `((upstream-name . "AbsFilterGSEA")))
2912 (build-system r-build-system)
2914 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
2915 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
2916 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
2918 "This package provides a function that performs gene-permuting of a gene-set
2919 enrichment analysis (GSEA) calculation with or without the absolute filtering.
2920 Without filtering, users can perform (original) two-tailed or one-tailed
2922 (license license:gpl2)))
2924 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
2925 (define-public r-bisquerna
2927 (name "r-bisquerna")
2931 (uri (cran-uri "BisqueRNA" version))
2934 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
2935 (properties `((upstream-name . "BisqueRNA")))
2936 (build-system r-build-system)
2938 (list r-biobase r-limsolve))
2941 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2942 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2943 (description "This package provides tools to accurately estimate cell type
2944 abundances from heterogeneous bulk expression. A reference-based method
2945 utilizes single-cell information to generate a signature matrix and
2946 transformation of bulk expression for accurate regression based estimates.
2947 A marker-based method utilizes known cell-specific marker genes to measure
2948 relative abundances across samples.")
2949 (license license:gpl3)))
2951 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
2952 ;; from Bioconductor.
2953 (define-public r-deconstructsigs
2955 (name "r-deconstructsigs")
2959 (uri (cran-uri "deconstructSigs" version))
2962 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
2964 `((upstream-name . "deconstructSigs")))
2965 (build-system r-build-system)
2967 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
2969 (home-page "https://github.com/raerose01/deconstructSigs")
2970 (synopsis "Identifies signatures present in a tumor sample")
2971 (description "This package takes sample information in the form of the
2972 fraction of mutations in each of 96 trinucleotide contexts and identifies
2973 the weighted combination of published signatures that, when summed, most
2974 closely reconstructs the mutational profile.")
2975 (license license:gpl2+)))
2977 ;; This is a CRAN package, but it depends on Bioconductor packages.
2978 (define-public r-jetset
2985 (uri (cran-uri "jetset" version))
2987 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
2988 (properties `((upstream-name . "jetset")))
2989 (build-system r-build-system)
2990 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
2991 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
2992 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
2994 "This package provides a one-to-one mapping from gene to \"best\" probe
2995 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
2996 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
2997 gene may be measured by multiple probe sets. This can present a mild
2998 conundrum when attempting to evaluate a gene \"signature\" that is defined by
2999 gene names rather than by specific probe sets. This package also includes the
3000 pre-calculated probe set quality scores that were used to define the
3002 (license license:artistic2.0)))
3004 ;; This is a CRAN package, but it depends on Bioconductor packages.
3005 (define-public r-nmf
3012 (uri (cran-uri "NMF" version))
3015 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
3016 (properties `((upstream-name . "NMF")))
3017 (build-system r-build-system)
3022 r-bigmemory ; suggested
3023 r-synchronicity ; suggested
3038 (home-page "http://renozao.github.io/NMF")
3039 (synopsis "Algorithms and framework for nonnegative matrix factorization")
3041 "This package provides a framework to perform Non-negative Matrix
3042 Factorization (NMF). The package implements a set of already published
3043 algorithms and seeding methods, and provides a framework to test, develop and
3044 plug new or custom algorithms. Most of the built-in algorithms have been
3045 optimized in C++, and the main interface function provides an easy way of
3046 performing parallel computations on multicore machines.")
3047 (license license:gpl2+)))
3049 (define-public r-affy
3056 (uri (bioconductor-uri "affy" version))
3059 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
3060 (build-system r-build-system)
3070 (home-page "https://bioconductor.org/packages/affy")
3071 (synopsis "Methods for affymetrix oligonucleotide arrays")
3073 "This package contains functions for exploratory oligonucleotide array
3075 (license license:lgpl2.0+)))
3077 (define-public r-affycomp
3084 (uri (bioconductor-uri "affycomp" version))
3087 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
3088 (properties `((upstream-name . "affycomp")))
3089 (build-system r-build-system)
3090 (propagated-inputs (list r-biobase))
3091 (home-page "https://bioconductor.org/packages/affycomp/")
3092 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
3094 "The package contains functions that can be used to compare expression
3095 measures for Affymetrix Oligonucleotide Arrays.")
3096 (license license:gpl2+)))
3098 (define-public r-affycompatible
3100 (name "r-affycompatible")
3105 (uri (bioconductor-uri "AffyCompatible" version))
3108 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
3110 `((upstream-name . "AffyCompatible")))
3111 (build-system r-build-system)
3115 `(modify-phases %standard-phases
3116 (add-after 'unpack 'make-reproducible
3118 ;; Order DTD elements before generating R code from them.
3119 (substitute* "R/methods-AffyCompatible.R"
3122 elements <- dtd$elements
3123 ordered <- elements[order(names(elements))]\n"))
3124 (("elt in dtd\\$elements")
3126 ;; Use a predictable directory name for code generation.
3127 (mkdir-p "/tmp/NetAffxResourcePrototype")
3128 (substitute* "R/DataClasses.R"
3129 (("directory=tempdir\\(\\)")
3130 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
3132 (list r-biostrings r-rcurl r-xml))
3133 (home-page "https://bioconductor.org/packages/AffyCompatible/")
3134 (synopsis "Work with Affymetrix GeneChip files")
3136 "This package provides an interface to Affymetrix chip annotation and
3137 sample attribute files. The package allows an easy way for users to download
3138 and manage local data bases of Affynmetrix NetAffx annotation files. It also
3139 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
3140 Command Console} (AGCC)-compatible sample annotation files.")
3141 (license license:artistic2.0)))
3143 (define-public r-affycontam
3145 (name "r-affycontam")
3150 (uri (bioconductor-uri "affyContam" version))
3153 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
3154 (properties `((upstream-name . "affyContam")))
3155 (build-system r-build-system)
3157 (list r-affy r-affydata r-biobase))
3158 (home-page "https://bioconductor.org/packages/affyContam/")
3159 (synopsis "Structured corruption of Affymetrix CEL file data")
3161 "Microarray quality assessment is a major concern of microarray analysts.
3162 This package provides some simple approaches to in silico creation of quality
3163 problems in CEL-level data to help evaluate performance of quality metrics.")
3164 (license license:artistic2.0)))
3166 (define-public r-affycoretools
3168 (name "r-affycoretools")
3173 (uri (bioconductor-uri "affycoretools" version))
3176 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
3177 (properties `((upstream-name . "affycoretools")))
3178 (build-system r-build-system)
3201 (home-page "https://bioconductor.org/packages/affycoretools/")
3202 (synopsis "Functions for analyses with Affymetrix GeneChips")
3204 "This package provides various wrapper functions that have been written
3205 to streamline the more common analyses that a Biostatistician might see.")
3206 (license license:artistic2.0)))
3208 (define-public r-affyio
3215 (uri (bioconductor-uri "affyio" version))
3218 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
3219 (build-system r-build-system)
3224 (home-page "https://github.com/bmbolstad/affyio")
3225 (synopsis "Tools for parsing Affymetrix data files")
3227 "This package provides routines for parsing Affymetrix data files based
3228 upon file format information. The primary focus is on accessing the CEL and
3230 (license license:lgpl2.0+)))
3232 (define-public r-affxparser
3234 (name "r-affxparser")
3239 (uri (bioconductor-uri "affxparser" version))
3242 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
3243 (properties `((upstream-name . "affxparser")))
3244 (build-system r-build-system)
3245 (home-page "https://github.com/HenrikBengtsson/affxparser")
3246 (synopsis "Affymetrix File Parsing SDK")
3248 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
3249 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
3250 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
3251 are supported. Currently, there are methods for reading @dfn{chip definition
3252 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
3253 either in full or in part. For example, probe signals from a few probesets
3254 can be extracted very quickly from a set of CEL files into a convenient list
3256 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
3258 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
3260 (define-public r-annotate
3267 (uri (bioconductor-uri "annotate" version))
3270 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
3271 (build-system r-build-system)
3273 (list r-annotationdbi
3281 "https://bioconductor.org/packages/annotate")
3282 (synopsis "Annotation for microarrays")
3283 (description "This package provides R environments for the annotation of
3285 (license license:artistic2.0)))
3287 (define-public r-annotationdbi
3289 (name "r-annotationdbi")
3293 (uri (bioconductor-uri "AnnotationDbi" version))
3296 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
3298 `((upstream-name . "AnnotationDbi")))
3299 (build-system r-build-system)
3310 (home-page "https://bioconductor.org/packages/AnnotationDbi")
3311 (synopsis "Annotation database interface")
3313 "This package provides user interface and database connection code for
3314 annotation data packages using SQLite data storage.")
3315 (license license:artistic2.0)))
3317 (define-public r-annotationfilter
3319 (name "r-annotationfilter")
3323 (uri (bioconductor-uri "AnnotationFilter" version))
3326 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
3328 `((upstream-name . "AnnotationFilter")))
3329 (build-system r-build-system)
3331 (list r-genomicranges r-lazyeval))
3334 (home-page "https://github.com/Bioconductor/AnnotationFilter")
3335 (synopsis "Facilities for filtering Bioconductor annotation resources")
3337 "This package provides classes and other infrastructure to implement
3338 filters for manipulating Bioconductor annotation resources. The filters are
3339 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
3340 (license license:artistic2.0)))
3342 (define-public r-annotationforge
3344 (name "r-annotationforge")
3349 (uri (bioconductor-uri "AnnotationForge" version))
3352 "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v"))))
3354 `((upstream-name . "AnnotationForge")))
3355 (build-system r-build-system)
3357 (list r-annotationdbi
3367 (home-page "https://bioconductor.org/packages/AnnotationForge")
3368 (synopsis "Code for building annotation database packages")
3370 "This package provides code for generating Annotation packages and their
3371 databases. Packages produced are intended to be used with AnnotationDbi.")
3372 (license license:artistic2.0)))
3374 (define-public r-annotationhub
3376 (name "r-annotationhub")
3381 (uri (bioconductor-uri "AnnotationHub" version))
3384 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
3385 (properties `((upstream-name . "AnnotationHub")))
3386 (build-system r-build-system)
3388 (list r-annotationdbi
3396 r-interactivedisplaybase
3403 (home-page "https://bioconductor.org/packages/AnnotationHub")
3404 (synopsis "Client to access AnnotationHub resources")
3406 "This package provides a client for the Bioconductor AnnotationHub web
3407 resource. The AnnotationHub web resource provides a central location where
3408 genomic files (e.g. VCF, bed, wig) and other resources from standard
3409 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
3410 metadata about each resource, e.g., a textual description, tags, and date of
3411 modification. The client creates and manages a local cache of files retrieved
3412 by the user, helping with quick and reproducible access.")
3413 (license license:artistic2.0)))
3415 (define-public r-aroma-light
3417 (name "r-aroma-light")
3422 (uri (bioconductor-uri "aroma.light" version))
3425 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
3426 (properties `((upstream-name . "aroma.light")))
3427 (build-system r-build-system)
3429 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
3430 (home-page "https://github.com/HenrikBengtsson/aroma.light")
3431 (synopsis "Methods for normalization and visualization of microarray data")
3433 "This package provides methods for microarray analysis that take basic
3434 data types such as matrices and lists of vectors. These methods can be used
3435 standalone, be utilized in other packages, or be wrapped up in higher-level
3437 (license license:gpl2+)))
3439 (define-public r-bamsignals
3441 (name "r-bamsignals")
3446 (uri (bioconductor-uri "bamsignals" version))
3449 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
3450 (build-system r-build-system)
3452 (list r-biocgenerics
3460 (home-page "https://bioconductor.org/packages/bamsignals")
3461 (synopsis "Extract read count signals from bam files")
3463 "This package efficiently obtains count vectors from indexed bam
3464 files. It counts the number of nucleotide sequence reads in given genomic
3465 ranges and it computes reads profiles and coverage profiles. It also handles
3467 (license license:gpl2+)))
3469 (define-public r-biobase
3475 (uri (bioconductor-uri "Biobase" version))
3478 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
3480 `((upstream-name . "Biobase")))
3481 (build-system r-build-system)
3483 (list r-biocgenerics))
3484 (home-page "https://bioconductor.org/packages/Biobase")
3485 (synopsis "Base functions for Bioconductor")
3487 "This package provides functions that are needed by many other packages
3488 on Bioconductor or which replace R functions.")
3489 (license license:artistic2.0)))
3491 (define-public r-biomart
3497 (uri (bioconductor-uri "biomaRt" version))
3500 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
3502 `((upstream-name . "biomaRt")))
3503 (build-system r-build-system)
3505 (list r-annotationdbi
3516 (home-page "https://bioconductor.org/packages/biomaRt")
3517 (synopsis "Interface to BioMart databases")
3519 "biomaRt provides an interface to a growing collection of databases
3520 implementing the @url{BioMart software suite, http://www.biomart.org}. The
3521 package enables retrieval of large amounts of data in a uniform way without
3522 the need to know the underlying database schemas or write complex SQL queries.
3523 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
3524 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
3525 users direct access to a diverse set of data and enable a wide range of
3526 powerful online queries from gene annotation to database mining.")
3527 (license license:artistic2.0)))
3529 ;; This is a CRAN package, but it depends on a Bioconductor package:
3531 (define-public r-biomartr
3537 (uri (cran-uri "biomartr" version))
3540 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
3541 (properties `((upstream-name . "biomartr")))
3542 (build-system r-build-system)
3562 (native-inputs (list r-knitr))
3563 (home-page "https://docs.ropensci.org/biomartr/")
3564 (synopsis "Genomic data retrieval")
3566 "Perform large scale genomic data retrieval and functional annotation
3567 retrieval. This package aims to provide users with a standardized way to
3568 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
3569 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
3570 Furthermore, an interface to the BioMart database allows users to retrieve
3571 functional annotation for genomic loci. In addition, users can download
3572 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
3574 (license license:gpl2)))
3576 (define-public r-biocparallel
3578 (name "r-biocparallel")
3582 (uri (bioconductor-uri "BiocParallel" version))
3585 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
3587 `((upstream-name . "BiocParallel")))
3588 (build-system r-build-system)
3591 (modify-phases %standard-phases
3592 (add-after 'unpack 'make-reproducible
3594 ;; Remove generated documentation.
3595 (for-each delete-file
3596 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
3597 "inst/doc/Introduction_To_BiocParallel.pdf"
3598 "inst/doc/Errors_Logs_And_Debugging.pdf"
3599 "inst/doc/BiocParallel_BatchtoolsParam.R"
3600 "inst/doc/Introduction_To_BiocParallel.R"
3601 "inst/doc/Errors_Logs_And_Debugging.R"))
3603 ;; Remove time-dependent macro
3604 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
3605 "inst/doc/Introduction_To_BiocParallel.Rnw"
3606 "inst/doc/Errors_Logs_And_Debugging.Rnw"
3607 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
3608 "vignettes/Introduction_To_BiocParallel.Rnw"
3609 "vignettes/Errors_Logs_And_Debugging.Rnw")
3610 (("\\today") "later"))
3612 ;; Initialize the random number generator seed when building.
3613 (substitute* "R/rng.R"
3614 (("\"L'Ecuyer-CMRG\"\\)" m)
3616 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
3618 (list r-bh r-codetools r-futile-logger r-snow))
3621 (home-page "https://bioconductor.org/packages/BiocParallel")
3622 (synopsis "Bioconductor facilities for parallel evaluation")
3624 "This package provides modified versions and novel implementation of
3625 functions for parallel evaluation, tailored to use with Bioconductor
3627 (license (list license:gpl2+ license:gpl3+))))
3629 (define-public r-biostrings
3631 (name "r-biostrings")
3635 (uri (bioconductor-uri "Biostrings" version))
3638 "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"))))
3640 `((upstream-name . "Biostrings")))
3641 (build-system r-build-system)
3643 (list r-biocgenerics
3649 (home-page "https://bioconductor.org/packages/Biostrings")
3650 (synopsis "String objects and algorithms for biological sequences")
3652 "This package provides memory efficient string containers, string
3653 matching algorithms, and other utilities, for fast manipulation of large
3654 biological sequences or sets of sequences.")
3655 (license license:artistic2.0)))
3657 (define-public r-biovizbase
3659 (name "r-biovizbase")
3664 (uri (bioconductor-uri "biovizBase" version))
3667 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
3668 (properties `((upstream-name . "biovizBase")))
3669 (build-system r-build-system)
3671 (list r-annotationdbi
3688 r-summarizedexperiment
3689 r-variantannotation))
3690 (home-page "https://bioconductor.org/packages/biovizBase")
3691 (synopsis "Basic graphic utilities for visualization of genomic data")
3693 "The biovizBase package is designed to provide a set of utilities, color
3694 schemes and conventions for genomic data. It serves as the base for various
3695 high-level packages for biological data visualization. This saves development
3696 effort and encourages consistency.")
3697 (license license:artistic2.0)))
3699 (define-public r-bsgenome
3705 (uri (bioconductor-uri "BSgenome" version))
3708 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
3710 `((upstream-name . "BSgenome")))
3711 (build-system r-build-system)
3713 (list r-biocgenerics
3723 (home-page "https://bioconductor.org/packages/BSgenome")
3724 (synopsis "Infrastructure for Biostrings-based genome data packages")
3726 "This package provides infrastructure shared by all Biostrings-based
3727 genome data packages and support for efficient SNP representation.")
3728 (license license:artistic2.0)))
3730 (define-public r-category
3737 (uri (bioconductor-uri "Category" version))
3740 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
3741 (properties `((upstream-name . "Category")))
3742 (build-system r-build-system)
3754 (home-page "https://bioconductor.org/packages/Category")
3755 (synopsis "Category analysis")
3757 "This package provides a collection of tools for performing category
3759 (license license:artistic2.0)))
3761 (define-public r-chipseeker
3763 (name "r-chipseeker")
3767 (uri (bioconductor-uri "ChIPseeker" version))
3770 "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"))))
3771 (build-system r-build-system)
3775 (list r-annotationdbi
3794 r-txdb-hsapiens-ucsc-hg19-knowngene))
3795 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
3796 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
3797 (description "This package implements functions to retrieve the nearest
3798 genes around the peak, annotate genomic region of the peak, statstical methods
3799 for estimate the significance of overlap among ChIP peak data sets, and
3800 incorporate GEO database for user to compare the own dataset with those
3801 deposited in database. The comparison can be used to infer cooperative
3802 regulation and thus can be used to generate hypotheses. Several visualization
3803 functions are implemented to summarize the coverage of the peak experiment,
3804 average profile and heatmap of peaks binding to TSS regions, genomic
3805 annotation, distance to TSS, and overlap of peaks or genes.")
3806 (license license:artistic2.0)))
3808 (define-public r-chipseq
3815 (uri (bioconductor-uri "chipseq" version))
3818 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
3819 (build-system r-build-system)
3821 (list r-biocgenerics
3827 (home-page "https://bioconductor.org/packages/chipseq")
3828 (synopsis "Package for analyzing ChIPseq data")
3830 "This package provides tools for processing short read data from ChIPseq
3832 (license license:artistic2.0)))
3834 (define-public r-complexheatmap
3836 (name "r-complexheatmap")
3841 (uri (bioconductor-uri "ComplexHeatmap" version))
3844 "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"))))
3846 `((upstream-name . "ComplexHeatmap")))
3847 (build-system r-build-system)
3865 "https://github.com/jokergoo/ComplexHeatmap")
3866 (synopsis "Making Complex Heatmaps")
3868 "Complex heatmaps are efficient to visualize associations between
3869 different sources of data sets and reveal potential structures. This package
3870 provides a highly flexible way to arrange multiple heatmaps and supports
3871 self-defined annotation graphics.")
3872 (license license:gpl2+)))
3874 (define-public r-copywriter
3876 (name "r-copywriter")
3881 (uri (bioconductor-uri "CopywriteR" version))
3884 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
3885 (properties `((upstream-name . "CopywriteR")))
3886 (build-system r-build-system)
3888 (list r-biocparallel
3902 (home-page "https://github.com/PeeperLab/CopywriteR")
3903 (synopsis "Copy number information from targeted sequencing")
3905 "CopywriteR extracts DNA copy number information from targeted sequencing
3906 by utilizing off-target reads. It allows for extracting uniformly distributed
3907 copy number information, can be used without reference, and can be applied to
3908 sequencing data obtained from various techniques including chromatin
3909 immunoprecipitation and target enrichment on small gene panels. Thereby,
3910 CopywriteR constitutes a widely applicable alternative to available copy
3911 number detection tools.")
3912 (license license:gpl2)))
3914 (define-public r-deseq
3921 (uri (bioconductor-uri "DESeq" version))
3924 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
3925 (properties `((upstream-name . "DESeq")))
3926 (build-system r-build-system)
3936 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
3937 (synopsis "Differential gene expression analysis")
3939 "This package provides tools for estimating variance-mean dependence in
3940 count data from high-throughput genetic sequencing assays and for testing for
3941 differential expression based on a model using the negative binomial
3943 (license license:gpl3+)))
3945 (define-public r-deseq2
3952 (uri (bioconductor-uri "DESeq2" version))
3955 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
3956 (properties `((upstream-name . "DESeq2")))
3957 (build-system r-build-system)
3971 r-summarizedexperiment))
3974 (home-page "https://bioconductor.org/packages/DESeq2")
3975 (synopsis "Differential gene expression analysis")
3977 "This package provides functions to estimate variance-mean dependence in
3978 count data from high-throughput nucleotide sequencing assays and test for
3979 differential expression based on a model using the negative binomial
3981 (license license:lgpl3+)))
3983 (define-public r-dexseq
3990 (uri (bioconductor-uri "DEXSeq" version))
3993 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
3994 (properties `((upstream-name . "DEXSeq")))
3995 (build-system r-build-system)
3997 (list r-annotationdbi
4013 r-summarizedexperiment))
4016 (home-page "https://bioconductor.org/packages/DEXSeq")
4017 (synopsis "Inference of differential exon usage in RNA-Seq")
4019 "This package is focused on finding differential exon usage using RNA-seq
4020 exon counts between samples with different experimental designs. It provides
4021 functions that allows the user to make the necessary statistical tests based
4022 on a model that uses the negative binomial distribution to estimate the
4023 variance between biological replicates and generalized linear models for
4024 testing. The package also provides functions for the visualization and
4025 exploration of the results.")
4026 (license license:gpl3+)))
4028 (define-public r-diffcyt
4035 (uri (bioconductor-uri "diffcyt" version))
4037 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
4038 (properties `((upstream-name . "diffcyt")))
4039 (build-system r-build-system)
4053 r-summarizedexperiment
4055 (native-inputs (list r-knitr))
4056 (home-page "https://github.com/lmweber/diffcyt")
4057 (synopsis "Differential discovery in high-dimensional cytometry")
4059 "This package provides statistical methods for differential discovery
4060 analyses in high-dimensional cytometry data (including flow cytometry, mass
4061 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
4062 combination of high-resolution clustering and empirical Bayes moderated tests
4063 adapted from transcriptomics.")
4064 (license license:expat)))
4066 (define-public r-dirichletmultinomial
4068 (name "r-dirichletmultinomial")
4073 (uri (bioconductor-uri "DirichletMultinomial" version))
4076 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
4078 `((upstream-name . "DirichletMultinomial")))
4079 (build-system r-build-system)
4083 (list r-biocgenerics r-iranges r-s4vectors))
4084 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
4085 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
4087 "Dirichlet-multinomial mixture models can be used to describe variability
4088 in microbial metagenomic data. This package is an interface to code
4089 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
4091 (license license:lgpl3)))
4093 (define-public r-dittoseq
4099 (uri (bioconductor-uri "dittoSeq" version))
4102 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
4103 (properties `((upstream-name . "dittoSeq")))
4104 (build-system r-build-system)
4115 r-singlecellexperiment
4116 r-summarizedexperiment))
4117 (native-inputs (list r-knitr))
4118 (home-page "https://bioconductor.org/packages/dittoSeq")
4119 (synopsis "Single-cell and bulk RNA sequencing visualization")
4121 "This package provides a universal, user friendly, single-cell and bulk RNA
4122 sequencing visualization toolkit that allows highly customizable creation of
4123 color blindness friendly, publication-quality figures. dittoSeq accepts both
4124 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
4125 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
4126 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
4127 percent composition or expression across groups, and more. Customizations
4128 range from size and title adjustments to automatic generation of annotations
4129 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
4130 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
4131 many more. All with simple, discrete inputs. Color blindness friendliness is
4132 powered by legend adjustments (enlarged keys), and by allowing the use of
4133 shapes or letter-overlay in addition to the carefully selected
4134 code{dittoColors()}.")
4135 (license license:expat)))
4137 (define-public r-edaseq
4144 (uri (bioconductor-uri "EDASeq" version))
4147 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
4148 (properties `((upstream-name . "EDASeq")))
4149 (build-system r-build-system)
4151 (list r-annotationdbi
4165 (home-page "https://github.com/drisso/EDASeq")
4166 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
4168 "This package provides support for numerical and graphical summaries of
4169 RNA-Seq genomic read data. Provided within-lane normalization procedures to
4170 adjust for GC-content effect (or other gene-level effects) on read counts:
4171 loess robust local regression, global-scaling, and full-quantile
4172 normalization. Between-lane normalization procedures to adjust for
4173 distributional differences between lanes (e.g., sequencing depth):
4174 global-scaling and full-quantile normalization.")
4175 (license license:artistic2.0)))
4177 (define-public r-edger
4183 (uri (bioconductor-uri "edgeR" version))
4186 "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
4187 (properties `((upstream-name . "edgeR")))
4188 (build-system r-build-system)
4190 (list r-limma r-locfit r-rcpp))
4191 (home-page "http://bioinf.wehi.edu.au/edgeR")
4192 (synopsis "EdgeR does empirical analysis of digital gene expression data")
4193 (description "This package can do differential expression analysis of
4194 RNA-seq expression profiles with biological replication. It implements a range
4195 of statistical methodology based on the negative binomial distributions,
4196 including empirical Bayes estimation, exact tests, generalized linear models
4197 and quasi-likelihood tests. It be applied to differential signal analysis of
4198 other types of genomic data that produce counts, including ChIP-seq, SAGE and
4200 (license license:gpl2+)))
4202 (define-public r-ensembldb
4204 (name "r-ensembldb")
4209 (uri (bioconductor-uri "ensembldb" version))
4212 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
4213 (build-system r-build-system)
4215 (list r-annotationdbi
4233 (home-page "https://github.com/jotsetung/ensembldb")
4234 (synopsis "Utilities to create and use Ensembl-based annotation databases")
4236 "The package provides functions to create and use transcript-centric
4237 annotation databases/packages. The annotation for the databases are directly
4238 fetched from Ensembl using their Perl API. The functionality and data is
4239 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
4240 but, in addition to retrieve all gene/transcript models and annotations from
4241 the database, the @code{ensembldb} package also provides a filter framework
4242 allowing to retrieve annotations for specific entries like genes encoded on a
4243 chromosome region or transcript models of lincRNA genes.")
4244 ;; No version specified
4245 (license license:lgpl3+)))
4247 (define-public r-fastseg
4254 (uri (bioconductor-uri "fastseg" version))
4257 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
4258 (build-system r-build-system)
4260 (list r-biobase r-biocgenerics r-genomicranges r-iranges
4262 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
4263 (synopsis "Fast segmentation algorithm for genetic sequencing data")
4265 "Fastseg implements a very fast and efficient segmentation algorithm.
4266 It can segment data from DNA microarrays and data from next generation
4267 sequencing for example to detect copy number segments. Further it can segment
4268 data from RNA microarrays like tiling arrays to identify transcripts. Most
4269 generally, it can segment data given as a matrix or as a vector. Various data
4270 formats can be used as input to fastseg like expression set objects for
4271 microarrays or GRanges for sequencing data.")
4272 (license license:lgpl2.0+)))
4274 (define-public r-gage
4281 (uri (bioconductor-uri "gage" version))
4284 "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"))))
4285 (build-system r-build-system)
4287 (list r-annotationdbi r-go-db r-graph r-keggrest))
4288 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
4289 "articles/10.1186/1471-2105-10-161"))
4290 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
4292 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
4293 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
4294 data attributes including sample sizes, experimental designs, assay platforms,
4295 and other types of heterogeneity. The gage package provides functions for
4296 basic GAGE analysis, result processing and presentation. In addition, it
4297 provides demo microarray data and commonly used gene set data based on KEGG
4298 pathways and GO terms. These functions and data are also useful for gene set
4299 analysis using other methods.")
4300 (license license:gpl2+)))
4302 (define-public r-genefilter
4304 (name "r-genefilter")
4309 (uri (bioconductor-uri "genefilter" version))
4312 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
4313 (build-system r-build-system)
4315 (list gfortran r-knitr))
4317 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
4319 (home-page "https://bioconductor.org/packages/genefilter")
4320 (synopsis "Filter genes from high-throughput experiments")
4322 "This package provides basic functions for filtering genes from
4323 high-throughput sequencing experiments.")
4324 (license license:artistic2.0)))
4326 (define-public r-geneoverlap
4328 (name "r-geneoverlap")
4332 (uri (bioconductor-uri "GeneOverlap" version))
4335 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
4336 (build-system r-build-system)
4338 (list r-rcolorbrewer r-gplots))
4339 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
4340 (synopsis "Test and visualize gene overlaps")
4341 (description "This package can be used to test two sets of gene lists
4342 and visualize the results.")
4343 (license license:gpl3)))
4345 (define-public r-genomation
4347 (name "r-genomation")
4351 (uri (bioconductor-uri "genomation" version))
4354 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
4355 (build-system r-build-system)
4379 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
4380 (synopsis "Summary, annotation and visualization of genomic data")
4382 "This package provides a package for summary and annotation of genomic
4383 intervals. Users can visualize and quantify genomic intervals over
4384 pre-defined functional regions, such as promoters, exons, introns, etc. The
4385 genomic intervals represent regions with a defined chromosome position, which
4386 may be associated with a score, such as aligned reads from HT-seq experiments,
4387 TF binding sites, methylation scores, etc. The package can use any tabular
4388 genomic feature data as long as it has minimal information on the locations of
4389 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4390 (license license:artistic2.0)))
4392 (define-public r-genomeinfodb
4394 (name "r-genomeinfodb")
4398 (uri (bioconductor-uri "GenomeInfoDb" version))
4401 "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"))))
4403 `((upstream-name . "GenomeInfoDb")))
4404 (build-system r-build-system)
4406 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
4410 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
4411 (synopsis "Utilities for manipulating chromosome identifiers")
4413 "This package contains data and functions that define and allow
4414 translation between different chromosome sequence naming conventions (e.g.,
4415 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4416 names in their natural, rather than lexicographic, order.")
4417 (license license:artistic2.0)))
4419 (define-public r-genomicalignments
4421 (name "r-genomicalignments")
4425 (uri (bioconductor-uri "GenomicAlignments" version))
4428 "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
4430 `((upstream-name . "GenomicAlignments")))
4431 (build-system r-build-system)
4433 (list r-biocgenerics
4441 r-summarizedexperiment))
4442 (home-page "https://bioconductor.org/packages/GenomicAlignments")
4443 (synopsis "Representation and manipulation of short genomic alignments")
4445 "This package provides efficient containers for storing and manipulating
4446 short genomic alignments (typically obtained by aligning short reads to a
4447 reference genome). This includes read counting, computing the coverage,
4448 junction detection, and working with the nucleotide content of the
4450 (license license:artistic2.0)))
4452 (define-public r-genomicfeatures
4454 (name "r-genomicfeatures")
4458 (uri (bioconductor-uri "GenomicFeatures" version))
4461 "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"))))
4463 `((upstream-name . "GenomicFeatures")))
4464 (build-system r-build-system)
4466 (list r-annotationdbi
4483 (home-page "https://bioconductor.org/packages/GenomicFeatures")
4484 (synopsis "Tools for working with transcript centric annotations")
4486 "This package provides a set of tools and methods for making and
4487 manipulating transcript centric annotations. With these tools the user can
4488 easily download the genomic locations of the transcripts, exons and cds of a
4489 given organism, from either the UCSC Genome Browser or a BioMart
4490 database (more sources will be supported in the future). This information is
4491 then stored in a local database that keeps track of the relationship between
4492 transcripts, exons, cds and genes. Flexible methods are provided for
4493 extracting the desired features in a convenient format.")
4494 (license license:artistic2.0)))
4496 (define-public r-genomicfiles
4498 (name "r-genomicfiles")
4503 (uri (bioconductor-uri "GenomicFiles" version))
4506 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
4507 (properties `((upstream-name . "GenomicFiles")))
4508 (build-system r-build-system)
4510 (list r-biocgenerics
4520 r-summarizedexperiment
4521 r-variantannotation))
4522 (home-page "https://bioconductor.org/packages/GenomicFiles")
4523 (synopsis "Distributed computing by file or by range")
4525 "This package provides infrastructure for parallel computations
4526 distributed by file or by range. User defined mapper and reducer functions
4527 provide added flexibility for data combination and manipulation.")
4528 (license license:artistic2.0)))
4530 (define-public r-genomicranges
4532 (name "r-genomicranges")
4536 (uri (bioconductor-uri "GenomicRanges" version))
4539 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
4541 `((upstream-name . "GenomicRanges")))
4542 (build-system r-build-system)
4544 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
4547 (home-page "https://bioconductor.org/packages/GenomicRanges")
4548 (synopsis "Representation and manipulation of genomic intervals")
4550 "This package provides tools to efficiently represent and manipulate
4551 genomic annotations and alignments is playing a central role when it comes to
4552 analyzing high-throughput sequencing data (a.k.a. NGS data). The
4553 GenomicRanges package defines general purpose containers for storing and
4554 manipulating genomic intervals and variables defined along a genome.")
4555 (license license:artistic2.0)))
4557 (define-public r-gostats
4564 (uri (bioconductor-uri "GOstats" version))
4567 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
4568 (properties `((upstream-name . "GOstats")))
4569 (build-system r-build-system)
4580 (home-page "https://bioconductor.org/packages/GOstats")
4581 (synopsis "Tools for manipulating GO and microarrays")
4583 "This package provides a set of tools for interacting with GO and
4584 microarray data. A variety of basic manipulation tools for graphs, hypothesis
4585 testing and other simple calculations.")
4586 (license license:artistic2.0)))
4588 (define-public r-gseabase
4595 (uri (bioconductor-uri "GSEABase" version))
4598 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
4599 (properties `((upstream-name . "GSEABase")))
4600 (build-system r-build-system)
4610 (home-page "https://bioconductor.org/packages/GSEABase")
4611 (synopsis "Gene set enrichment data structures and methods")
4613 "This package provides classes and methods to support @dfn{Gene Set
4614 Enrichment Analysis} (GSEA).")
4615 (license license:artistic2.0)))
4617 (define-public r-hpar
4624 (uri (bioconductor-uri "hpar" version))
4627 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
4628 (build-system r-build-system)
4631 (home-page "https://bioconductor.org/packages/hpar/")
4632 (synopsis "Human Protein Atlas in R")
4633 (description "This package provides a simple interface to and data from
4634 the Human Protein Atlas project.")
4635 (license license:artistic2.0)))
4637 (define-public r-rhtslib
4644 (uri (bioconductor-uri "Rhtslib" version))
4647 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
4648 (properties `((upstream-name . "Rhtslib")))
4649 (build-system r-build-system)
4650 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
4651 ;; which makes R abort the build.
4652 (arguments '(#:configure-flags '("--no-staged-install")))
4654 (list curl zlib ; packages using rhtslib need to link with zlib
4657 (list pkg-config r-knitr))
4658 (home-page "https://github.com/nhayden/Rhtslib")
4659 (synopsis "High-throughput sequencing library as an R package")
4661 "This package provides the HTSlib C library for high-throughput
4662 nucleotide sequence analysis. The package is primarily useful to developers
4663 of other R packages who wish to make use of HTSlib.")
4664 (license license:lgpl2.0+)))
4666 (define-public r-impute
4672 (uri (bioconductor-uri "impute" version))
4675 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
4678 (build-system r-build-system)
4679 (home-page "https://bioconductor.org/packages/impute")
4680 (synopsis "Imputation for microarray data")
4682 "This package provides a function to impute missing gene expression
4683 microarray data, using nearest neighbor averaging.")
4684 (license license:gpl2+)))
4686 (define-public r-interactivedisplaybase
4688 (name "r-interactivedisplaybase")
4693 (uri (bioconductor-uri "interactiveDisplayBase" version))
4696 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
4698 `((upstream-name . "interactiveDisplayBase")))
4699 (build-system r-build-system)
4701 (list r-biocgenerics r-dt r-shiny))
4704 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
4705 (synopsis "Base package for web displays of Bioconductor objects")
4707 "This package contains the basic methods needed to generate interactive
4708 Shiny-based display methods for Bioconductor objects.")
4709 (license license:artistic2.0)))
4711 (define-public r-keggrest
4718 (uri (bioconductor-uri "KEGGREST" version))
4721 "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
4722 (properties `((upstream-name . "KEGGREST")))
4723 (build-system r-build-system)
4725 (list r-biostrings r-httr r-png))
4728 (home-page "https://bioconductor.org/packages/KEGGREST")
4729 (synopsis "Client-side REST access to KEGG")
4731 "This package provides a package that provides a client interface to the
4732 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
4733 (license license:artistic2.0)))
4735 (define-public r-lfa
4742 (uri (bioconductor-uri "lfa" version))
4744 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
4745 (properties `((upstream-name . "lfa")))
4746 (build-system r-build-system)
4747 (propagated-inputs (list r-corpcor))
4748 (native-inputs (list r-knitr))
4749 (home-page "https://github.com/StoreyLab/lfa")
4750 (synopsis "Logistic Factor Analysis for categorical data")
4752 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
4753 Binomial data via estimation of latent structure in the natural parameter.")
4754 (license license:gpl3)))
4756 (define-public r-limma
4762 (uri (bioconductor-uri "limma" version))
4765 "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"))))
4766 (build-system r-build-system)
4767 (home-page "http://bioinf.wehi.edu.au/limma")
4768 (synopsis "Package for linear models for microarray and RNA-seq data")
4769 (description "This package can be used for the analysis of gene expression
4770 studies, especially the use of linear models for analysing designed experiments
4771 and the assessment of differential expression. The analysis methods apply to
4772 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
4773 (license license:gpl2+)))
4775 (define-public r-made4
4781 (uri (bioconductor-uri "made4" version))
4784 "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
4785 (properties `((upstream-name . "made4")))
4786 (build-system r-build-system)
4793 r-summarizedexperiment))
4794 (native-inputs (list r-knitr))
4795 (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
4796 (synopsis "Multivariate analysis of microarray data using ADE4")
4798 "This is a package for multivariate data analysis and graphical display
4799 of microarray data. Functions are included for supervised dimension
4800 reduction (between group analysis) and joint dimension reduction of two
4801 datasets (coinertia analysis).")
4802 (license license:artistic2.0)))
4804 (define-public r-methylkit
4806 (name "r-methylkit")
4810 (uri (bioconductor-uri "methylKit" version))
4813 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
4814 (properties `((upstream-name . "methylKit")))
4815 (build-system r-build-system)
4837 (list r-knitr)) ; for vignettes
4838 (home-page "https://github.com/al2na/methylKit")
4840 "DNA methylation analysis from high-throughput bisulfite sequencing results")
4842 "MethylKit is an R package for DNA methylation analysis and annotation
4843 from high-throughput bisulfite sequencing. The package is designed to deal
4844 with sequencing data from @dfn{Reduced representation bisulfite
4845 sequencing} (RRBS) and its variants, but also target-capture methods and whole
4846 genome bisulfite sequencing. It also has functions to analyze base-pair
4847 resolution 5hmC data from experimental protocols such as oxBS-Seq and
4849 (license license:artistic2.0)))
4851 (define-public r-motifrg
4858 (uri (bioconductor-uri "motifRG" version))
4861 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
4862 (properties `((upstream-name . "motifRG")))
4863 (build-system r-build-system)
4867 r-bsgenome-hsapiens-ucsc-hg19
4871 (home-page "https://bioconductor.org/packages/motifRG")
4872 (synopsis "Discover motifs in high throughput sequencing data")
4874 "This package provides tools for discriminative motif discovery in high
4875 throughput genetic sequencing data sets using regression methods.")
4876 (license license:artistic2.0)))
4878 (define-public r-muscat
4885 (uri (bioconductor-uri "muscat" version))
4888 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
4889 (properties `((upstream-name . "muscat")))
4890 (build-system r-build-system)
4892 (list r-biocparallel
4913 r-singlecellexperiment
4914 r-summarizedexperiment
4917 (native-inputs (list r-knitr))
4918 (home-page "https://github.com/HelenaLC/muscat")
4919 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
4921 "This package @code{muscat} provides various methods and visualization tools
4922 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
4923 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
4924 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
4925 platform that mimics both single and multi-sample scRNA-seq data.")
4926 (license license:gpl3)))
4928 (define-public r-mutationalpatterns
4930 (name "r-mutationalpatterns")
4935 (uri (bioconductor-uri "MutationalPatterns" version))
4938 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
4939 (build-system r-build-system)
4943 (list r-biocgenerics
4946 ;; These two packages are suggested packages
4947 r-bsgenome-hsapiens-1000genomes-hs37d5
4948 r-bsgenome-hsapiens-ucsc-hg19
4966 r-variantannotation))
4967 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
4968 (synopsis "Extract and visualize mutational patterns in genomic data")
4969 (description "This package provides an extensive toolset for the
4970 characterization and visualization of a wide range of mutational patterns
4971 in SNV base substitution data.")
4972 (license license:expat)))
4974 (define-public r-msnbase
4981 (uri (bioconductor-uri "MSnbase" version))
4984 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
4985 (properties `((upstream-name . "MSnbase")))
4986 (build-system r-build-system)
5012 (home-page "https://github.com/lgatto/MSnbase")
5013 (synopsis "Base functions and classes for MS-based proteomics")
5015 "This package provides basic plotting, data manipulation and processing
5016 of mass spectrometry based proteomics data.")
5017 (license license:artistic2.0)))
5019 (define-public r-msnid
5026 (uri (bioconductor-uri "MSnID" version))
5029 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
5030 (properties `((upstream-name . "MSnID")))
5031 (build-system r-build-system)
5034 (modify-phases %standard-phases
5035 (add-after 'unpack 'set-HOME
5036 (lambda _ (setenv "HOME" "/tmp"))))))
5038 (list r-annotationdbi
5064 (home-page "https://bioconductor.org/packages/MSnID")
5065 (synopsis "Utilities for LC-MSn proteomics identifications")
5067 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
5068 from mzIdentML (leveraging the mzID package) or text files. After collating
5069 the search results from multiple datasets it assesses their identification
5070 quality and optimize filtering criteria to achieve the maximum number of
5071 identifications while not exceeding a specified false discovery rate. It also
5072 contains a number of utilities to explore the MS/MS results and assess missed
5073 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
5074 (license license:artistic2.0)))
5076 (define-public r-mzid
5083 (uri (bioconductor-uri "mzID" version))
5086 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
5087 (properties `((upstream-name . "mzID")))
5088 (build-system r-build-system)
5098 (home-page "https://bioconductor.org/packages/mzID")
5099 (synopsis "Parser for mzIdentML files")
5101 "This package provides a parser for mzIdentML files implemented using the
5102 XML package. The parser tries to be general and able to handle all types of
5103 mzIdentML files with the drawback of having less pretty output than a vendor
5105 (license license:gpl2+)))
5107 (define-public r-mzr
5114 (uri (bioconductor-uri "mzR" version))
5117 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
5118 (modules '((guix build utils)))
5120 '(delete-file-recursively "src/boost"))))
5121 (properties `((upstream-name . "mzR")))
5122 (build-system r-build-system)
5125 (modify-phases %standard-phases
5126 (add-after 'unpack 'use-system-boost
5128 (substitute* "src/Makevars"
5129 (("\\./boost/libs.*") "")
5130 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
5131 (("\\ARCH_OBJS=" line)
5133 "\nBOOST_LIBS=-lboost_system -lboost_regex \
5134 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
5136 (list boost ; use this instead of the bundled boost sources
5147 (home-page "https://github.com/sneumann/mzR/")
5148 (synopsis "Parser for mass spectrometry data files")
5150 "The mzR package provides a unified API to the common file formats and
5151 parsers available for mass spectrometry data. It comes with a wrapper for the
5152 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
5153 The package contains the original code written by the ISB, and a subset of the
5154 proteowizard library for mzML and mzIdentML. The netCDF reading code has
5155 previously been used in XCMS.")
5156 (license license:artistic2.0)))
5158 (define-public r-organism-dplyr
5160 (name "r-organism-dplyr")
5165 (uri (bioconductor-uri "Organism.dplyr" version))
5168 "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
5169 (properties `((upstream-name . "Organism.dplyr")))
5170 (build-system r-build-system)
5172 (list r-annotationdbi
5186 (native-inputs (list r-knitr))
5187 (home-page "https://bioconductor.org/packages/Organism.dplyr")
5188 (synopsis "Dplyr-based access to Bioconductor annotation resources")
5190 "This package provides an alternative interface to Bioconductor @code{
5191 annotation} resources, in particular the gene identifier mapping functionality
5192 of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
5193 functionality of the @code{TxDb} packages (e.g.,
5194 @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
5195 (license license:artistic2.0)))
5197 (define-public r-organismdbi
5199 (name "r-organismdbi")
5204 (uri (bioconductor-uri "OrganismDbi" version))
5207 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
5208 (properties `((upstream-name . "OrganismDbi")))
5209 (build-system r-build-system)
5211 (list r-annotationdbi
5222 (home-page "https://bioconductor.org/packages/OrganismDbi")
5223 (synopsis "Software to enable the smooth interfacing of database packages")
5224 (description "The package enables a simple unified interface to several
5225 annotation packages each of which has its own schema by taking advantage of
5226 the fact that each of these packages implements a select methods.")
5227 (license license:artistic2.0)))
5229 (define-public r-pcaexplorer
5231 (name "r-pcaexplorer")
5236 (uri (bioconductor-uri "pcaExplorer" version))
5239 "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
5240 (properties `((upstream-name . "pcaExplorer")))
5241 (build-system r-build-system)
5243 (list r-annotationdbi
5269 r-summarizedexperiment
5273 (native-inputs (list r-knitr))
5274 (home-page "https://github.com/federicomarini/pcaExplorer")
5276 "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
5278 "This package provides functionality for interactive visualization of RNA-seq
5279 datasets based on Principal Components Analysis. The methods provided allow for
5280 quick information extraction and effective data exploration. A Shiny
5281 application encapsulates the whole analysis.")
5282 (license license:expat)))
5284 (define-public r-pcamethods
5286 (name "r-pcamethods")
5291 (uri (bioconductor-uri "pcaMethods" version))
5294 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
5295 (properties `((upstream-name . "pcaMethods")))
5296 (build-system r-build-system)
5298 (list r-biobase r-biocgenerics r-mass r-rcpp))
5299 (home-page "https://github.com/hredestig/pcamethods")
5300 (synopsis "Collection of PCA methods")
5302 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
5303 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
5304 for missing value estimation is included for comparison. BPCA, PPCA and
5305 NipalsPCA may be used to perform PCA on incomplete data as well as for
5306 accurate missing value estimation. A set of methods for printing and plotting
5307 the results is also provided. All PCA methods make use of the same data
5308 structure (pcaRes) to provide a common interface to the PCA results.")
5309 (license license:gpl3+)))
5311 ;; This is a CRAN package, but it depends on a Bioconductor package:
5312 ;; r-aroma-light, r-dnacopy..
5313 (define-public r-pscbs
5320 (uri (cran-uri "PSCBS" version))
5322 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
5323 (properties `((upstream-name . "PSCBS")))
5324 (build-system r-build-system)
5327 (modify-phases %standard-phases
5328 (add-before 'install 'change-home-dir
5330 ;; Change from /homeless-shelter to /tmp for write permission.
5331 (setenv "HOME" "/tmp"))))))
5343 (list r-r-rsp ;used to build vignettes
5345 (home-page "https://github.com/HenrikBengtsson/PSCBS")
5346 (synopsis "Analysis of parent-specific DNA copy numbers")
5348 "This is a package for segmentation of allele-specific DNA copy number
5349 data and detection of regions with abnormal copy number within each parental
5350 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
5351 (license license:gpl2+)))
5353 (define-public r-protgenerics
5355 (name "r-protgenerics")
5360 (uri (bioconductor-uri "ProtGenerics" version))
5363 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
5364 (properties `((upstream-name . "ProtGenerics")))
5365 (build-system r-build-system)
5366 (home-page "https://github.com/lgatto/ProtGenerics")
5367 (synopsis "S4 generic functions for proteomics infrastructure")
5369 "This package provides S4 generic functions needed by Bioconductor
5370 proteomics packages.")
5371 (license license:artistic2.0)))
5373 (define-public r-rbgl
5380 (uri (bioconductor-uri "RBGL" version))
5383 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
5384 (properties `((upstream-name . "RBGL")))
5385 (build-system r-build-system)
5387 (list r-bh r-graph))
5388 (home-page "https://www.bioconductor.org/packages/RBGL")
5389 (synopsis "Interface to the Boost graph library")
5391 "This package provides a fairly extensive and comprehensive interface to
5392 the graph algorithms contained in the Boost library.")
5393 (license license:artistic2.0)))
5395 (define-public r-rcas
5401 (uri (bioconductor-uri "RCAS" version))
5404 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
5405 (properties `((upstream-name . "RCAS")))
5406 (build-system r-build-system)
5408 (list r-biocgenerics
5411 r-bsgenome-hsapiens-ucsc-hg19
5437 (synopsis "RNA-centric annotation system")
5439 "RCAS aims to be a standalone RNA-centric annotation system that provides
5440 intuitive reports and publication-ready graphics. This package provides the R
5441 library implementing most of the pipeline's features.")
5442 (home-page "https://github.com/BIMSBbioinfo/RCAS")
5443 (license license:artistic2.0)))
5445 (define-public r-regioner
5452 (uri (bioconductor-uri "regioneR" version))
5455 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
5456 (properties `((upstream-name . "regioneR")))
5457 (build-system r-build-system)
5469 (home-page "https://bioconductor.org/packages/regioneR/")
5470 (synopsis "Association analysis of genomic regions")
5471 (description "This package offers a statistical framework based on
5472 customizable permutation tests to assess the association between genomic
5473 region sets and other genomic features.")
5474 (license license:artistic2.0)))
5476 (define-public r-reportingtools
5478 (name "r-reportingtools")
5483 (uri (bioconductor-uri "ReportingTools" version))
5486 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
5488 `((upstream-name . "ReportingTools")))
5489 (build-system r-build-system)
5512 (home-page "https://bioconductor.org/packages/ReportingTools/")
5513 (synopsis "Tools for making reports in various formats")
5515 "The ReportingTools package enables users to easily display reports of
5516 analysis results generated from sources such as microarray and sequencing
5517 data. The package allows users to create HTML pages that may be viewed on a
5518 web browser, or in other formats. Users can generate tables with sortable and
5519 filterable columns, make and display plots, and link table entries to other
5520 data sources such as NCBI or larger plots within the HTML page. Using the
5521 package, users can also produce a table of contents page to link various
5522 reports together for a particular project that can be viewed in a web
5524 (license license:artistic2.0)))
5526 (define-public r-rhdf5
5532 (uri (bioconductor-uri "rhdf5" version))
5535 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
5536 (build-system r-build-system)
5538 (list r-rhdf5filters r-rhdf5lib))
5541 (home-page "https://bioconductor.org/packages/rhdf5")
5542 (synopsis "HDF5 interface to R")
5544 "This R/Bioconductor package provides an interface between HDF5 and R.
5545 HDF5's main features are the ability to store and access very large and/or
5546 complex datasets and a wide variety of metadata on mass storage (disk) through
5547 a completely portable file format. The rhdf5 package is thus suited for the
5548 exchange of large and/or complex datasets between R and other software
5549 package, and for letting R applications work on datasets that are larger than
5550 the available RAM.")
5551 (license license:artistic2.0)))
5553 (define-public r-rhdf5filters
5555 (name "r-rhdf5filters")
5560 (uri (bioconductor-uri "rhdf5filters" version))
5563 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
5564 (properties `((upstream-name . "rhdf5filters")))
5565 (build-system r-build-system)
5572 (home-page "https://github.com/grimbough/rhdf5filters")
5573 (synopsis "HDF5 compression filters")
5575 "This package provides a collection of compression filters for use with
5577 (license license:bsd-2)))
5579 (define-public r-rsamtools
5581 (name "r-rsamtools")
5585 (uri (bioconductor-uri "Rsamtools" version))
5588 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
5590 `((upstream-name . "Rsamtools")))
5591 (build-system r-build-system)
5594 (modify-phases %standard-phases
5595 (add-after 'unpack 'use-system-zlib
5597 (substitute* "DESCRIPTION"
5598 (("zlibbioc, ") ""))
5599 (substitute* "NAMESPACE"
5600 (("import\\(zlibbioc\\)") "")))))))
5602 (list r-biocgenerics
5612 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
5613 (synopsis "Interface to samtools, bcftools, and tabix")
5615 "This package provides an interface to the @code{samtools},
5616 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
5617 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
5618 tab-delimited (tabix) files.")
5619 (license license:expat)))
5621 ;; This is a CRAN package, but it depends on a Bioconductor package:
5623 (define-public r-restfulr
5630 (uri (cran-uri "restfulr" version))
5633 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
5634 (properties `((upstream-name . "restfulr")))
5635 (build-system r-build-system)
5637 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
5638 (home-page "https://cran.r-project.org/package=restfulr")
5639 (synopsis "R interface to RESTful web services")
5641 "This package models a RESTful service as if it were a nested R list.")
5642 (license license:artistic2.0)))
5644 (define-public r-rtracklayer
5646 (name "r-rtracklayer")
5650 (uri (bioconductor-uri "rtracklayer" version))
5653 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
5654 (build-system r-build-system)
5657 (modify-phases %standard-phases
5658 (add-after 'unpack 'use-system-zlib
5660 (substitute* "DESCRIPTION"
5661 ((" zlibbioc,") ""))
5662 (substitute* "NAMESPACE"
5663 (("import\\(zlibbioc\\)") "")))))))
5669 (list r-biocgenerics
5683 (home-page "https://bioconductor.org/packages/rtracklayer")
5684 (synopsis "R interface to genome browsers and their annotation tracks")
5686 "rtracklayer is an extensible framework for interacting with multiple
5687 genome browsers (currently UCSC built-in) and manipulating annotation tracks
5688 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
5689 built-in). The user may export/import tracks to/from the supported browsers,
5690 as well as query and modify the browser state, such as the current viewport.")
5691 (license license:artistic2.0)))
5693 ;; This is a CRAN package, but it depends on a Bioconductor package.
5694 (define-public r-samr
5701 (uri (cran-uri "samr" version))
5704 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
5705 (properties `((upstream-name . "samr")))
5706 (build-system r-build-system)
5714 (native-inputs (list gfortran))
5715 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
5716 (synopsis "Significance analysis of Microarrays")
5718 "This is a package for significance analysis of Microarrays for
5719 differential expression analysis, RNAseq data and related problems.")
5720 ;; Any version of the LGPL
5721 (license license:lgpl3+)))
5723 (define-public r-scannotatr
5725 (name "r-scannotatr")
5730 (uri (bioconductor-uri "scAnnotatR" version))
5732 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
5733 (properties `((upstream-name . "scAnnotatR")))
5734 (build-system r-build-system)
5736 (list r-annotationhub
5747 r-singlecellexperiment
5748 r-summarizedexperiment))
5749 (native-inputs (list r-knitr))
5750 (home-page "https://github.com/grisslab/scAnnotatR")
5751 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
5753 "This package comprises a set of pretrained machine learning models to
5754 predict basic immune cell types. This enables to quickly get a first
5755 annotation of the cell types present in the dataset without requiring prior
5756 knowledge. The package also lets you train using own models to predict new
5757 cell types based on specific research needs.")
5758 (license license:expat)))
5760 (define-public r-scdblfinder
5762 (name "r-scdblfinder")
5767 (uri (bioconductor-uri "scDblFinder" version))
5769 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
5770 (properties `((upstream-name . "scDblFinder")))
5771 (build-system r-build-system)
5773 (list r-biocgenerics
5791 r-singlecellexperiment
5792 r-summarizedexperiment
5794 (native-inputs (list r-knitr))
5795 (home-page "https://github.com/plger/scDblFinder")
5796 (synopsis "Detect multiplets in single-cell RNA sequencing data")
5798 "The scDblFinder package gathers various methods for the detection and
5799 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
5800 multiple cells captured within the same droplet or reaction volume). It
5801 includes methods formerly found in the scran package, and the new fast and
5802 comprehensive scDblFinder method.")
5803 (license license:gpl3)))
5805 (define-public r-scmap
5812 (uri (bioconductor-uri "scmap" version))
5814 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
5815 (properties `((upstream-name . "scmap")))
5816 (build-system r-build-system)
5831 r-singlecellexperiment
5832 r-summarizedexperiment))
5833 (native-inputs (list r-knitr))
5834 (home-page "https://github.com/hemberg-lab/scmap")
5835 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
5837 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
5838 composition of complex tissues since the technology allows researchers to
5839 define cell-types using unsupervised clustering of the transcriptome.
5840 However, due to differences in experimental methods and computational
5841 analyses, it is often challenging to directly compare the cells identified in
5842 two different experiments. @code{scmap} is a method for projecting cells from
5843 a scRNA-seq experiment onto the cell-types or individual cells identified in a
5844 different experiment.")
5845 (license license:gpl3)))
5847 (define-public r-scry
5853 (uri (bioconductor-uri "scry" version))
5856 "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
5857 (properties `((upstream-name . "scry")))
5858 (build-system r-build-system)
5860 (list r-biocsingular
5865 r-singlecellexperiment
5866 r-summarizedexperiment))
5867 (native-inputs (list r-knitr))
5868 (home-page "https://bioconductor.org/packages/scry.html")
5869 (synopsis "Small-count analysis methods for high-dimensional data")
5871 "Many modern biological datasets consist of small counts that are not
5872 well fit by standard linear-Gaussian methods such as principal component
5873 analysis. This package provides implementations of count-based feature
5874 selection and dimension reduction algorithms. These methods can be used to
5875 facilitate unsupervised analysis of any high-dimensional data such as
5876 single-cell RNA-seq.")
5877 (license license:artistic2.0)))
5879 (define-public r-seqlogo
5886 (uri (bioconductor-uri "seqLogo" version))
5889 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
5890 (properties `((upstream-name . "seqLogo")))
5891 (build-system r-build-system)
5894 (home-page "https://bioconductor.org/packages/seqLogo")
5895 (synopsis "Sequence logos for DNA sequence alignments")
5897 "seqLogo takes the position weight matrix of a DNA sequence motif and
5898 plots the corresponding sequence logo as introduced by Schneider and
5900 (license license:lgpl2.0+)))
5902 (define-public r-seqpattern
5904 (name "r-seqpattern")
5908 (uri (bioconductor-uri "seqPattern" version))
5911 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
5913 `((upstream-name . "seqPattern")))
5914 (build-system r-build-system)
5916 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
5917 (home-page "https://bioconductor.org/packages/seqPattern")
5918 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
5920 "This package provides tools to visualize oligonucleotide patterns and
5921 sequence motif occurrences across a large set of sequences centred at a common
5922 reference point and sorted by a user defined feature.")
5923 (license license:gpl3+)))
5925 (define-public r-shortread
5927 (name "r-shortread")
5932 (uri (bioconductor-uri "ShortRead" version))
5935 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
5936 (properties `((upstream-name . "ShortRead")))
5937 (build-system r-build-system)
5957 (home-page "https://bioconductor.org/packages/ShortRead")
5958 (synopsis "FASTQ input and manipulation tools")
5960 "This package implements sampling, iteration, and input of FASTQ files.
5961 It includes functions for filtering and trimming reads, and for generating a
5962 quality assessment report. Data are represented as
5963 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
5964 purposes. The package also contains legacy support for early single-end,
5965 ungapped alignment formats.")
5966 (license license:artistic2.0)))
5968 (define-public r-simplifyenrichment
5970 (name "r-simplifyenrichment")
5975 (uri (bioconductor-uri "simplifyEnrichment" version))
5978 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
5980 `((upstream-name . "simplifyEnrichment")))
5981 (build-system r-build-system)
5983 (list r-annotationdbi
6000 (native-inputs (list r-knitr))
6001 (home-page "https://github.com/jokergoo/simplifyEnrichment")
6002 (synopsis "Simplify functional enrichment results")
6003 (description "This package provides a new clustering algorithm, binary
6004 cut, for clustering similarity matrices of functional terms is implemented in
6005 this package. It also provides functionalities for visualizing, summarizing
6006 and comparing the clusterings.")
6007 (license license:expat)))
6009 (define-public r-transcriptr
6011 (name "r-transcriptr")
6016 (uri (bioconductor-uri "transcriptR" version))
6018 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
6019 (properties `((upstream-name . "transcriptR")))
6020 (build-system r-build-system)
6022 (list r-biocgenerics
6037 (native-inputs (list r-knitr))
6038 (home-page "https://bioconductor.org/packages/transcriptR")
6039 (synopsis "Primary transcripts detection and quantification")
6041 "The differences in the RNA types being sequenced have an impact on the
6042 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
6043 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
6044 broader coverage of both exonic and intronic regions. The presence of
6045 intronic reads in GRO-seq type of data makes it possible to use it to
6046 computationally identify and quantify all de novo continuous regions of
6047 transcription distributed across the genome. This type of data, however, is
6048 more challenging to interpret and less common practice compared to mRNA-seq.
6049 One of the challenges for primary transcript detection concerns the
6050 simultaneous transcription of closely spaced genes, which needs to be properly
6051 divided into individually transcribed units. The R package transcriptR
6052 combines RNA-seq data with ChIP-seq data of histone modifications that mark
6053 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
6054 overcome this challenge. The advantage of this approach over the use of, for
6055 example, gene annotations is that this approach is data driven and therefore
6056 able to deal also with novel and case specific events.")
6057 (license license:gpl3)))
6059 (define-public r-trajectoryutils
6061 (name "r-trajectoryutils")
6066 (uri (bioconductor-uri "TrajectoryUtils" version))
6069 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
6071 `((upstream-name . "TrajectoryUtils")))
6072 (build-system r-build-system)
6074 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
6075 r-summarizedexperiment))
6076 (native-inputs (list r-knitr))
6077 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
6078 (synopsis "Single-cell trajectory analysis utilities")
6080 "This package implements low-level utilities for single-cell trajectory
6081 analysis, primarily intended for re-use inside higher-level packages. It
6082 includes a function to create a cluster-level minimum spanning tree and data
6083 structures to hold pseudotime inference results.")
6084 (license license:gpl3)))
6086 (define-public r-slingshot
6088 (name "r-slingshot")
6092 (uri (bioconductor-uri "slingshot" version))
6095 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
6096 (build-system r-build-system)
6102 r-singlecellexperiment
6103 r-summarizedexperiment
6107 (home-page "https://bioconductor.org/packages/slingshot")
6108 (synopsis "Tools for ordering single-cell sequencing")
6109 (description "This package provides functions for inferring continuous,
6110 branching lineage structures in low-dimensional data. Slingshot was designed
6111 to model developmental trajectories in single-cell RNA sequencing data and
6112 serve as a component in an analysis pipeline after dimensionality reduction
6113 and clustering. It is flexible enough to handle arbitrarily many branching
6114 events and allows for the incorporation of prior knowledge through supervised
6115 graph construction.")
6116 (license license:artistic2.0)))
6118 (define-public r-stager
6125 (uri (bioconductor-uri "stageR" version))
6127 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
6128 (properties `((upstream-name . "stageR")))
6129 (build-system r-build-system)
6130 (propagated-inputs (list r-summarizedexperiment))
6131 (native-inputs (list r-knitr))
6132 (home-page "https://bioconductor.org/packages/stageR")
6133 (synopsis "Stage-wise analysis of high throughput gene expression data")
6135 "The stageR package allows automated stage-wise analysis of
6136 high-throughput gene expression data. The method is published in Genome
6138 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
6139 (license license:gpl3)))
6141 (define-public r-stringdb
6148 (uri (bioconductor-uri "STRINGdb" version))
6150 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
6151 (properties `((upstream-name . "STRINGdb")))
6152 (build-system r-build-system)
6163 (home-page "https://git.bioconductor.org/packages/STRINGdb")
6164 (synopsis "Search tool for the retrieval of interacting proteins database")
6166 "The @code{STRINGdb} package provides an R interface to the STRING
6167 protein-protein interactions database. @url{https://www.string-db.org,
6168 STRING} is a database of known and predicted protein-protein interactions.
6169 The interactions include direct (physical) and indirect (functional)
6170 associations. Each interaction is associated with a combined confidence score
6171 that integrates the various evidences.")
6172 (license license:gpl2)))
6174 (define-public r-structuralvariantannotation
6176 (name "r-structuralvariantannotation")
6181 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
6183 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
6184 (build-system r-build-system)
6198 r-summarizedexperiment
6199 r-variantannotation))
6202 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
6203 (synopsis "R package designed to simplify structural variant analysis")
6205 "This package contains useful helper functions for dealing with structural
6206 variants in VCF format. The packages contains functions for parsing VCFs from
6207 a number of popular callers as well as functions for dealing with breakpoints
6208 involving two separate genomic loci encoded as GRanges objects.")
6209 (license license:gpl3)))
6211 (define-public r-summarizedexperiment
6213 (name "r-summarizedexperiment")
6217 (uri (bioconductor-uri "SummarizedExperiment" version))
6220 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
6222 `((upstream-name . "SummarizedExperiment")))
6223 (build-system r-build-system)
6236 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
6237 (synopsis "Container for representing genomic ranges by sample")
6239 "The SummarizedExperiment container contains one or more assays, each
6240 represented by a matrix-like object of numeric or other mode. The rows
6241 typically represent genomic ranges of interest and the columns represent
6243 (license license:artistic2.0)))
6245 (define-public r-sva
6252 (uri (bioconductor-uri "sva" version))
6255 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
6256 (build-system r-build-system)
6264 (home-page "https://bioconductor.org/packages/sva")
6265 (synopsis "Surrogate variable analysis")
6267 "This package contains functions for removing batch effects and other
6268 unwanted variation in high-throughput experiment. It also contains functions
6269 for identifying and building surrogate variables for high-dimensional data
6270 sets. Surrogate variables are covariates constructed directly from
6271 high-dimensional data like gene expression/RNA sequencing/methylation/brain
6272 imaging data that can be used in subsequent analyses to adjust for unknown,
6273 unmodeled, or latent sources of noise.")
6274 (license license:artistic2.0)))
6276 (define-public r-systempiper
6278 (name "r-systempiper")
6283 (uri (bioconductor-uri "systemPipeR" version))
6286 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
6287 (properties `((upstream-name . "systemPipeR")))
6288 (build-system r-build-system)
6290 (list r-biocgenerics
6301 r-summarizedexperiment
6305 (home-page "https://github.com/tgirke/systemPipeR")
6306 (synopsis "Next generation sequencing workflow and reporting environment")
6308 "This R package provides tools for building and running automated
6309 end-to-end analysis workflows for a wide range of @dfn{next generation
6310 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6311 Important features include a uniform workflow interface across different NGS
6312 applications, automated report generation, and support for running both R and
6313 command-line software, such as NGS aligners or peak/variant callers, on local
6314 computers or compute clusters. Efficient handling of complex sample sets and
6315 experimental designs is facilitated by a consistently implemented sample
6316 annotation infrastructure.")
6317 (license license:artistic2.0)))
6319 (define-public r-topgo
6325 (uri (bioconductor-uri "topGO" version))
6328 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
6330 `((upstream-name . "topGO")))
6331 (build-system r-build-system)
6333 (list r-annotationdbi
6342 (home-page "https://bioconductor.org/packages/topGO")
6343 (synopsis "Enrichment analysis for gene ontology")
6345 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6346 terms while accounting for the topology of the GO graph. Different test
6347 statistics and different methods for eliminating local similarities and
6348 dependencies between GO terms can be implemented and applied.")
6349 ;; Any version of the LGPL applies.
6350 (license license:lgpl2.1+)))
6352 (define-public r-tximport
6358 (uri (bioconductor-uri "tximport" version))
6361 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
6362 (build-system r-build-system)
6365 (home-page "https://bioconductor.org/packages/tximport")
6366 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
6368 "This package provides tools to import transcript-level abundance,
6369 estimated counts and transcript lengths, and to summarize them into matrices
6370 for use with downstream gene-level analysis packages. Average transcript
6371 length, weighted by sample-specific transcript abundance estimates, is
6372 provided as a matrix which can be used as an offset for different expression
6373 of gene-level counts.")
6374 (license license:gpl2+)))
6376 ;; This is a CRAN package, but it depends on a Bioconductor package.
6377 (define-public r-valr
6384 (uri (cran-uri "valr" version))
6387 "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
6388 (build-system r-build-system)
6396 r-rtracklayer ;bioconductor package
6401 (home-page "https://github.com/rnabioco/valr")
6402 (synopsis "Genome interval arithmetic in R")
6404 "This package enables you to read and manipulate genome intervals and
6405 signals. It provides functionality similar to command-line tool suites within
6406 R, enabling interactive analysis and visualization of genome-scale data.")
6407 (license license:expat)))
6409 (define-public r-variantannotation
6411 (name "r-variantannotation")
6415 (uri (bioconductor-uri "VariantAnnotation" version))
6418 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
6420 `((upstream-name . "VariantAnnotation")))
6422 (list r-annotationdbi
6433 r-summarizedexperiment
6440 (build-system r-build-system)
6441 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6442 (synopsis "Package for annotation of genetic variants")
6443 (description "This R package can annotate variants, compute amino acid
6444 coding changes and predict coding outcomes.")
6445 (license license:artistic2.0)))
6447 (define-public r-vsn
6454 (uri (bioconductor-uri "vsn" version))
6457 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
6458 (build-system r-build-system)
6460 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
6462 (list r-knitr)) ; for vignettes
6463 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
6464 (synopsis "Variance stabilization and calibration for microarray data")
6466 "The package implements a method for normalising microarray intensities,
6467 and works for single- and multiple-color arrays. It can also be used for data
6468 from other technologies, as long as they have similar format. The method uses
6469 a robust variant of the maximum-likelihood estimator for an
6470 additive-multiplicative error model and affine calibration. The model
6471 incorporates data calibration step (a.k.a. normalization), a model for the
6472 dependence of the variance on the mean intensity and a variance stabilizing
6473 data transformation. Differences between transformed intensities are
6474 analogous to \"normalized log-ratios\". However, in contrast to the latter,
6475 their variance is independent of the mean, and they are usually more sensitive
6476 and specific in detecting differential transcription.")
6477 (license license:artistic2.0)))
6479 ;; There is no source tarball, so we fetch the code from the Bioconductor git
6481 (define-public r-xcir
6482 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
6486 (version (git-version "1.8.0" revision commit))
6490 (url "https://git.bioconductor.org/packages/XCIR")
6492 (file-name (git-file-name name version))
6495 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
6496 (properties `((upstream-name . "XCIR")))
6497 (build-system r-build-system)
6498 (propagated-inputs (list r-biomart
6506 r-variantannotation))
6507 (native-inputs (list r-knitr))
6508 (home-page "https://github.com/SRenan/XCIR")
6509 (synopsis "Analysis of X chromosome inactivation")
6511 "This package is an R package that offers models and tools for subject
6512 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
6514 (license license:gpl2))))
6516 (define-public r-xina
6523 (uri (bioconductor-uri "XINA" version))
6525 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
6526 (properties `((upstream-name . "XINA")))
6527 (build-system r-build-system)
6536 (native-inputs (list r-knitr))
6537 (home-page "https://git.bioconductor.org/packages/XINA")
6538 (synopsis "Identifying proteins that exhibit similar patterns")
6540 "The aim of @code{XINA} is to determine which proteins exhibit similar
6541 patterns within and across experimental conditions, since proteins with
6542 co-abundance patterns may have common molecular functions. @code{XINA} imports
6543 multiple datasets, tags dataset in silico, and combines the data for subsequent
6544 subgrouping into multiple clusters. The result is a single output depicting
6545 the variation across all conditions. @code{XINA} not only extracts
6546 coabundance profiles within and across experiments, but also incorporates
6547 protein-protein interaction databases and integrative resources such as
6548 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
6549 molecular functions, respectively, and produces intuitive graphical outputs.")
6550 (license license:gpl3)))
6552 (define-public r-xmapbridge
6554 (name "r-xmapbridge")
6559 (uri (bioconductor-uri "xmapbridge" version))
6561 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
6562 (properties `((upstream-name . "xmapbridge")))
6563 (build-system r-build-system)
6564 (home-page "https://git.bioconductor.org/packages/xmapbridge")
6565 (synopsis "Display numeric data in the web based genome browser X:MAP")
6567 "The package @code{xmapbridge} can plot graphs in the X:Map genome
6568 browser. X:Map uses the Google Maps API to provide a scrollable view of the
6569 genome. It supports a number of species, and can be accessed at
6570 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
6571 suitable format. Graph plotting in R is done using calls to the functions
6572 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
6573 similar to those used by the standard plot methods in R. These result in data
6574 being written to a set of files (in a specific directory structure) that
6575 contain the data to be displayed, as well as some additional meta-data
6576 describing each of the graphs.")
6577 (license license:lgpl3)))
6579 (define-public r-xvector
6585 (uri (bioconductor-uri "XVector" version))
6588 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
6590 `((upstream-name . "XVector")))
6591 (build-system r-build-system)
6594 (modify-phases %standard-phases
6595 (add-after 'unpack 'use-system-zlib
6597 (substitute* "DESCRIPTION"
6598 (("zlibbioc, ") ""))
6599 (substitute* "NAMESPACE"
6600 (("import\\(zlibbioc\\)") ""))
6605 (list r-biocgenerics r-iranges r-s4vectors))
6606 (home-page "https://bioconductor.org/packages/XVector")
6607 (synopsis "Representation and manpulation of external sequences")
6609 "This package provides memory efficient S4 classes for storing sequences
6610 \"externally\" (behind an R external pointer, or on disk).")
6611 (license license:artistic2.0)))
6613 (define-public r-zlibbioc
6619 (uri (bioconductor-uri "zlibbioc" version))
6622 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
6624 `((upstream-name . "zlibbioc")))
6625 (build-system r-build-system)
6626 (home-page "https://bioconductor.org/packages/zlibbioc")
6627 (synopsis "Provider for zlib-1.2.5 to R packages")
6628 (description "This package uses the source code of zlib-1.2.5 to create
6629 libraries for systems that do not have these available via other means.")
6630 (license license:artistic2.0)))
6632 (define-public r-zellkonverter
6634 (name "r-zellkonverter")
6639 (uri (bioconductor-uri "zellkonverter" version))
6641 (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"))))
6642 (properties `((upstream-name . "zellkonverter")))
6643 (build-system r-build-system)
6651 r-singlecellexperiment
6652 r-summarizedexperiment))
6653 (native-inputs (list r-knitr))
6654 (home-page "https://github.com/theislab/zellkonverter")
6655 (synopsis "Conversion between AnnData and single-cell experiments objects")
6657 "This package provides methods to convert between Python AnnData objects
6658 and SingleCellExperiment objects. These are primarily intended for use by
6659 downstream Bioconductor packages that wrap Python methods for single-cell data
6660 analysis. It also includes functions to read and write H5AD files used for
6661 saving AnnData objects to disk.")
6662 (license license:expat)))
6664 (define-public r-geneplotter
6666 (name "r-geneplotter")
6671 (uri (bioconductor-uri "geneplotter" version))
6674 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
6675 (build-system r-build-system)
6683 (home-page "https://bioconductor.org/packages/geneplotter")
6684 (synopsis "Graphics functions for genomic data")
6686 "This package provides functions for plotting genomic data.")
6687 (license license:artistic2.0)))
6689 (define-public r-oligoclasses
6691 (name "r-oligoclasses")
6696 (uri (bioconductor-uri "oligoClasses" version))
6699 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
6700 (properties `((upstream-name . "oligoClasses")))
6701 (build-system r-build-system)
6715 r-summarizedexperiment))
6716 (home-page "https://bioconductor.org/packages/oligoClasses/")
6717 (synopsis "Classes for high-throughput arrays")
6719 "This package contains class definitions, validity checks, and
6720 initialization methods for classes used by the @code{oligo} and @code{crlmm}
6722 (license license:gpl2+)))
6724 (define-public r-oligo
6731 (uri (bioconductor-uri "oligo" version))
6734 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
6735 (properties `((upstream-name . "oligo")))
6736 (build-system r-build-system)
6737 (inputs (list zlib))
6752 (home-page "https://bioconductor.org/packages/oligo/")
6753 (synopsis "Preprocessing tools for oligonucleotide arrays")
6755 "This package provides a package to analyze oligonucleotide
6756 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
6757 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
6758 (license license:lgpl2.0+)))
6760 (define-public r-qvalue
6767 (uri (bioconductor-uri "qvalue" version))
6770 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
6771 (build-system r-build-system)
6773 (list r-ggplot2 r-reshape2))
6776 (home-page "https://github.com/StoreyLab/qvalue")
6777 (synopsis "Q-value estimation for false discovery rate control")
6779 "This package takes a list of p-values resulting from the simultaneous
6780 testing of many hypotheses and estimates their q-values and local @dfn{false
6781 discovery rate} (FDR) values. The q-value of a test measures the proportion
6782 of false positives incurred when that particular test is called significant.
6783 The local FDR measures the posterior probability the null hypothesis is true
6784 given the test's p-value. Various plots are automatically generated, allowing
6785 one to make sensible significance cut-offs. The software can be applied to
6786 problems in genomics, brain imaging, astrophysics, and data mining.")
6787 ;; Any version of the LGPL.
6788 (license license:lgpl3+)))
6790 (define r-rcppnumerical
6792 (name "r-rcppnumerical")
6796 (uri (cran-uri "RcppNumerical" version))
6799 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
6800 (properties `((upstream-name . "RcppNumerical")))
6801 (build-system r-build-system)
6803 `(("r-rcpp" ,r-rcpp)
6804 ("r-rcppeigen" ,r-rcppeigen)))
6806 `(("r-knitr" ,r-knitr)))
6807 (home-page "https://github.com/yixuan/RcppNumerical")
6808 (synopsis "Rcpp integration for numerical computing libraries")
6810 "This package provides a collection of libraries for numerical computing
6811 (numerical integration, optimization, etc.) and their integration with
6813 (license license:gpl2+)))
6815 (define-public r-apeglm
6821 (uri (bioconductor-uri "apeglm" version))
6824 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
6825 (properties `((upstream-name . "apeglm")))
6826 (build-system r-build-system)
6833 r-summarizedexperiment))
6834 (native-inputs (list r-knitr))
6835 (home-page "https://bioconductor.org/packages/apeglm")
6836 (synopsis "Approximate posterior estimation for GLM coefficients")
6837 (description "This package provides Bayesian shrinkage estimators for
6838 effect sizes for a variety of GLM models, using approximation of the
6839 posterior for individual coefficients.")
6840 (license license:gpl2)))
6842 (define-public r-greylistchip
6844 (name "r-greylistchip")
6848 (uri (bioconductor-uri "GreyListChIP" version))
6851 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
6852 (properties `((upstream-name . "GreyListChIP")))
6853 (build-system r-build-system)
6862 r-summarizedexperiment))
6863 (home-page "https://bioconductor.org/packages/GreyListChIP")
6864 (synopsis "Greylist artefact regions based on ChIP inputs")
6865 (description "This package identifies regions of ChIP experiments with high
6866 signal in the input, that lead to spurious peaks during peak calling.")
6867 (license license:artistic2.0)))
6869 (define-public r-diffbind
6876 (uri (bioconductor-uri "DiffBind" version))
6879 "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr"))))
6880 (properties `((upstream-name . "DiffBind")))
6881 (build-system r-build-system)
6904 r-summarizedexperiment
6906 (home-page "https://bioconductor.org/packages/DiffBind")
6907 (synopsis "Differential binding analysis of ChIP-Seq peak data")
6909 "This package computes differentially bound sites from multiple
6910 ChIP-seq experiments using affinity (quantitative) data. Also enables
6911 occupancy (overlap) analysis and plotting functions.")
6912 (license license:artistic2.0)))
6914 (define-public r-ripseeker
6916 (name "r-ripseeker")
6921 (uri (bioconductor-uri "RIPSeeker" version))
6924 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
6925 (properties `((upstream-name . "RIPSeeker")))
6926 (build-system r-build-system)
6931 r-summarizedexperiment
6935 (home-page "https://bioconductor.org/packages/RIPSeeker")
6937 "Identifying protein-associated transcripts from RIP-seq experiments")
6939 "This package infers and discriminates RIP peaks from RIP-seq alignments
6940 using two-state HMM with negative binomial emission probability. While
6941 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
6942 a suite of bioinformatics tools integrated within this self-contained software
6943 package comprehensively addressing issues ranging from post-alignments
6944 processing to visualization and annotation.")
6945 (license license:gpl2)))
6947 (define-public r-mbkmeans
6953 (uri (bioconductor-uri "mbkmeans" version))
6956 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
6957 (build-system r-build-system)
6971 r-singlecellexperiment
6972 r-summarizedexperiment))
6973 (home-page "https://bioconductor.org/packages/mbkmeans")
6974 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
6975 (description "This package implements the mini-batch k-means algorithm for
6976 large datasets, including support for on-disk data representation.")
6977 (license license:expat)))
6979 (define-public r-multtest
6986 (uri (bioconductor-uri "multtest" version))
6989 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
6990 (build-system r-build-system)
6992 (list r-survival r-biocgenerics r-biobase r-mass))
6993 (home-page "https://bioconductor.org/packages/multtest")
6994 (synopsis "Resampling-based multiple hypothesis testing")
6996 "This package can do non-parametric bootstrap and permutation
6997 resampling-based multiple testing procedures (including empirical Bayes
6998 methods) for controlling the family-wise error rate (FWER), generalized
6999 family-wise error rate (gFWER), tail probability of the proportion of
7000 false positives (TPPFP), and false discovery rate (FDR). Several choices
7001 of bootstrap-based null distribution are implemented (centered, centered
7002 and scaled, quantile-transformed). Single-step and step-wise methods are
7003 available. Tests based on a variety of T- and F-statistics (including
7004 T-statistics based on regression parameters from linear and survival models
7005 as well as those based on correlation parameters) are included. When probing
7006 hypotheses with T-statistics, users may also select a potentially faster null
7007 distribution which is multivariate normal with mean zero and variance
7008 covariance matrix derived from the vector influence function. Results are
7009 reported in terms of adjusted P-values, confidence regions and test statistic
7010 cutoffs. The procedures are directly applicable to identifying differentially
7011 expressed genes in DNA microarray experiments.")
7012 (license license:lgpl3)))
7014 (define-public r-graph
7020 (uri (bioconductor-uri "graph" version))
7023 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
7024 (build-system r-build-system)
7026 (list r-biocgenerics))
7027 (home-page "https://bioconductor.org/packages/graph")
7028 (synopsis "Handle graph data structures in R")
7030 "This package implements some simple graph handling capabilities for R.")
7031 (license license:artistic2.0)))
7033 ;; This is a CRAN package, but it depends on a Bioconductor package.
7034 (define-public r-ggm
7041 (uri (cran-uri "ggm" version))
7044 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
7045 (properties `((upstream-name . "ggm")))
7046 (build-system r-build-system)
7048 (list r-graph r-igraph))
7049 (home-page "https://cran.r-project.org/package=ggm")
7050 (synopsis "Functions for graphical Markov models")
7052 "This package provides functions and datasets for maximum likelihood
7053 fitting of some classes of graphical Markov models.")
7054 (license license:gpl2+)))
7056 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
7057 (define-public r-perfmeas
7064 (uri (cran-uri "PerfMeas" version))
7067 "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
7068 (properties `((upstream-name . "PerfMeas")))
7069 (build-system r-build-system)
7071 (list r-graph r-limma r-rbgl))
7072 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
7073 (synopsis "Performance measures for ranking and classification tasks")
7075 "This package implements different performance measures for
7076 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
7077 a given recall, F-score for single and multiple classes are available.")
7078 (license license:gpl2+)))
7080 ;; This is a CRAN package, but it depends on a Bioconductor package.
7081 (define-public r-codedepends
7083 (name "r-codedepends")
7088 (uri (cran-uri "CodeDepends" version))
7091 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
7092 (properties `((upstream-name . "CodeDepends")))
7093 (build-system r-build-system)
7095 (list r-codetools r-graph r-xml))
7096 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
7097 (synopsis "Analysis of R code for reproducible research and code comprehension")
7099 "This package provides tools for analyzing R expressions or blocks of
7100 code and determining the dependencies between them. It focuses on R scripts,
7101 but can be used on the bodies of functions. There are many facilities
7102 including the ability to summarize or get a high-level view of code,
7103 determining dependencies between variables, code improvement suggestions.")
7104 ;; Any version of the GPL
7105 (license (list license:gpl2+ license:gpl3+))))
7107 (define-public r-chippeakanno
7109 (name "r-chippeakanno")
7114 (uri (bioconductor-uri "ChIPpeakAnno" version))
7117 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
7118 (properties `((upstream-name . "ChIPpeakAnno")))
7119 (build-system r-build-system)
7121 (list r-annotationdbi
7144 r-summarizedexperiment
7148 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
7149 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
7151 "The package includes functions to retrieve the sequences around the peak,
7152 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
7153 custom features such as most conserved elements and other transcription factor
7154 binding sites supplied by users. Starting 2.0.5, new functions have been added
7155 for finding the peaks with bi-directional promoters with summary statistics
7156 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
7157 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
7158 enrichedGO (addGeneIDs).")
7159 (license license:gpl2+)))
7161 (define-public r-matrixgenerics
7163 (name "r-matrixgenerics")
7167 (uri (bioconductor-uri "MatrixGenerics" version))
7170 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
7172 `((upstream-name . "MatrixGenerics")))
7173 (build-system r-build-system)
7175 (list r-matrixstats))
7176 (home-page "https://bioconductor.org/packages/MatrixGenerics")
7177 (synopsis "S4 generic summary statistic functions for matrix-like objects")
7179 "This package provides S4 generic functions modeled after the
7180 @code{matrixStats} API for alternative matrix implementations. Packages with
7181 alternative matrix implementation can depend on this package and implement the
7182 generic functions that are defined here for a useful set of row and column
7183 summary statistics. Other package developers can import this package and
7184 handle a different matrix implementations without worrying about
7185 incompatibilities.")
7186 (license license:artistic2.0)))
7188 (define-public r-marray
7194 (uri (bioconductor-uri "marray" version))
7196 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
7197 (build-system r-build-system)
7200 (home-page "https://bioconductor.org/packages/marray")
7201 (synopsis "Exploratory analysis for two-color spotted microarray data")
7202 (description "This package contains class definitions for two-color spotted
7203 microarray data. It also includes functions for data input, diagnostic plots,
7204 normalization and quality checking.")
7205 (license license:lgpl2.0+)))
7207 (define-public r-cghbase
7213 (uri (bioconductor-uri "CGHbase" version))
7215 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
7216 (properties `((upstream-name . "CGHbase")))
7217 (build-system r-build-system)
7219 (list r-biobase r-marray))
7220 (home-page "https://bioconductor.org/packages/CGHbase")
7221 (synopsis "Base functions and classes for arrayCGH data analysis")
7222 (description "This package contains functions and classes that are needed by
7223 the @code{arrayCGH} packages.")
7224 (license license:gpl2+)))
7226 (define-public r-cghcall
7232 (uri (bioconductor-uri "CGHcall" version))
7234 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
7235 (properties `((upstream-name . "CGHcall")))
7236 (build-system r-build-system)
7238 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
7239 (home-page "https://bioconductor.org/packages/CGHcall")
7240 (synopsis "Base functions and classes for arrayCGH data analysis")
7241 (description "This package contains functions and classes that are needed by
7242 @code{arrayCGH} packages.")
7243 (license license:gpl2+)))
7245 (define-public r-qdnaseq
7251 (uri (bioconductor-uri "QDNAseq" version))
7253 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
7254 (properties `((upstream-name . "QDNAseq")))
7255 (build-system r-build-system)
7267 (home-page "https://bioconductor.org/packages/QDNAseq")
7268 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
7269 (description "The genome is divided into non-overlapping fixed-sized bins,
7270 number of sequence reads in each counted, adjusted with a simultaneous
7271 two-dimensional loess correction for sequence mappability and GC content, and
7272 filtered to remove spurious regions in the genome. Downstream steps of
7273 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
7275 (license license:gpl2+)))
7277 (define-public r-bayseq
7284 (uri (bioconductor-uri "baySeq" version))
7287 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
7288 (properties `((upstream-name . "baySeq")))
7289 (build-system r-build-system)
7291 (list r-abind r-edger r-genomicranges))
7292 (home-page "https://bioconductor.org/packages/baySeq/")
7293 (synopsis "Bayesian analysis of differential expression patterns in count data")
7295 "This package identifies differential expression in high-throughput count
7296 data, such as that derived from next-generation sequencing machines,
7297 calculating estimated posterior likelihoods of differential expression (or
7298 more complex hypotheses) via empirical Bayesian methods.")
7299 (license license:gpl3)))
7301 (define-public r-chipcomp
7308 (uri (bioconductor-uri "ChIPComp" version))
7311 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
7312 (properties `((upstream-name . "ChIPComp")))
7313 (build-system r-build-system)
7315 (list r-biocgenerics
7316 r-bsgenome-hsapiens-ucsc-hg19
7317 r-bsgenome-mmusculus-ucsc-mm9
7325 (home-page "https://bioconductor.org/packages/ChIPComp")
7326 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
7328 "ChIPComp implements a statistical method for quantitative comparison of
7329 multiple ChIP-seq datasets. It detects differentially bound sharp binding
7330 sites across multiple conditions considering matching control in ChIP-seq
7332 ;; Any version of the GPL.
7333 (license license:gpl3+)))
7335 (define-public r-riboprofiling
7337 (name "r-riboprofiling")
7342 (uri (bioconductor-uri "RiboProfiling" version))
7345 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
7346 (properties `((upstream-name . "RiboProfiling")))
7347 (build-system r-build-system)
7349 (list r-biocgenerics
7367 (home-page "https://bioconductor.org/packages/RiboProfiling/")
7368 (synopsis "Ribosome profiling data analysis")
7369 (description "Starting with a BAM file, this package provides the
7370 necessary functions for quality assessment, read start position recalibration,
7371 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
7372 of count data: pairs, log fold-change, codon frequency and coverage
7373 assessment, principal component analysis on codon coverage.")
7374 (license license:gpl3)))
7376 (define-public r-riboseqr
7383 (uri (bioconductor-uri "riboSeqR" version))
7386 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
7387 (properties `((upstream-name . "riboSeqR")))
7388 (build-system r-build-system)
7397 (home-page "https://bioconductor.org/packages/riboSeqR/")
7398 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
7400 "This package provides plotting functions, frameshift detection and
7401 parsing of genetic sequencing data from ribosome profiling experiments.")
7402 (license license:gpl3)))
7404 (define-public r-interactionset
7406 (name "r-interactionset")
7411 (uri (bioconductor-uri "InteractionSet" version))
7414 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
7416 `((upstream-name . "InteractionSet")))
7417 (build-system r-build-system)
7419 (list r-biocgenerics
7426 r-summarizedexperiment))
7429 (home-page "https://bioconductor.org/packages/InteractionSet")
7430 (synopsis "Base classes for storing genomic interaction data")
7432 "This package provides the @code{GInteractions},
7433 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
7434 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
7436 (license license:gpl3)))
7438 (define-public r-genomicinteractions
7440 (name "r-genomicinteractions")
7445 (uri (bioconductor-uri "GenomicInteractions" version))
7448 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
7450 `((upstream-name . "GenomicInteractions")))
7451 (build-system r-build-system)
7471 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
7472 (synopsis "R package for handling genomic interaction data")
7474 "This R package provides tools for handling genomic interaction data,
7475 such as ChIA-PET/Hi-C, annotating genomic features with interaction
7476 information and producing various plots and statistics.")
7477 (license license:gpl3)))
7479 (define-public r-ctc
7486 (uri (bioconductor-uri "ctc" version))
7489 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
7490 (build-system r-build-system)
7491 (propagated-inputs (list r-amap))
7492 (home-page "https://bioconductor.org/packages/ctc/")
7493 (synopsis "Cluster and tree conversion")
7495 "This package provides tools for exporting and importing classification
7496 trees and clusters to other programs.")
7497 (license license:gpl2)))
7499 (define-public r-goseq
7506 (uri (bioconductor-uri "goseq" version))
7509 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
7510 (build-system r-build-system)
7512 (list r-annotationdbi
7518 (home-page "https://bioconductor.org/packages/goseq/")
7519 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
7521 "This package provides tools to detect Gene Ontology and/or other user
7522 defined categories which are over/under represented in RNA-seq data.")
7523 (license license:lgpl2.0+)))
7525 (define-public r-glimma
7532 (uri (bioconductor-uri "Glimma" version))
7535 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
7536 (properties `((upstream-name . "Glimma")))
7537 (build-system r-build-system)
7545 r-summarizedexperiment))
7548 (home-page "https://github.com/Shians/Glimma")
7549 (synopsis "Interactive HTML graphics")
7551 "This package generates interactive visualisations for analysis of
7552 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
7553 HTML page. The interactions are built on top of the popular static
7554 representations of analysis results in order to provide additional
7556 (license license:lgpl3)))
7558 (define-public r-rots
7565 (uri (bioconductor-uri "ROTS" version))
7568 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
7569 (properties `((upstream-name . "ROTS")))
7570 (build-system r-build-system)
7572 (list r-biobase r-rcpp))
7573 (home-page "https://bioconductor.org/packages/ROTS/")
7574 (synopsis "Reproducibility-Optimized Test Statistic")
7576 "This package provides tools for calculating the
7577 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
7579 (license license:gpl2+)))
7581 (define-public r-plgem
7588 (uri (bioconductor-uri "plgem" version))
7591 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
7592 (build-system r-build-system)
7594 (list r-biobase r-mass))
7595 (home-page "http://www.genopolis.it")
7596 (synopsis "Detect differential expression in microarray and proteomics datasets")
7598 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
7599 model the variance-versus-mean dependence that exists in a variety of
7600 genome-wide datasets, including microarray and proteomics data. The use of
7601 PLGEM has been shown to improve the detection of differentially expressed
7602 genes or proteins in these datasets.")
7603 (license license:gpl2)))
7605 (define-public r-inspect
7612 (uri (bioconductor-uri "INSPEcT" version))
7615 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
7616 (properties `((upstream-name . "INSPEcT")))
7617 (build-system r-build-system)
7638 r-summarizedexperiment
7639 r-txdb-mmusculus-ucsc-mm9-knowngene))
7642 (home-page "https://bioconductor.org/packages/INSPEcT")
7643 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
7645 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
7646 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
7647 order to evaluate synthesis, processing and degradation rates and assess via
7648 modeling the rates that determines changes in mature mRNA levels.")
7649 (license license:gpl2)))
7651 (define-public r-dnabarcodes
7653 (name "r-dnabarcodes")
7658 (uri (bioconductor-uri "DNABarcodes" version))
7661 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
7662 (properties `((upstream-name . "DNABarcodes")))
7663 (build-system r-build-system)
7665 (list r-bh r-matrix r-rcpp))
7668 (home-page "https://bioconductor.org/packages/DNABarcodes")
7669 (synopsis "Create and analyze DNA barcodes")
7671 "This package offers tools to create DNA barcode sets capable of
7672 correcting insertion, deletion, and substitution errors. Existing barcodes
7673 can be analyzed regarding their minimal, maximal and average distances between
7674 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
7675 demultiplexed, i.e. assigned to their original reference barcode.")
7676 (license license:gpl2)))
7678 (define-public r-ruvseq
7685 (uri (bioconductor-uri "RUVSeq" version))
7688 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
7689 (properties `((upstream-name . "RUVSeq")))
7690 (build-system r-build-system)
7692 (list r-biobase r-edaseq r-edger r-mass))
7695 (home-page "https://github.com/drisso/RUVSeq")
7696 (synopsis "Remove unwanted variation from RNA-Seq data")
7698 "This package implements methods to @dfn{remove unwanted variation} (RUV)
7699 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
7701 (license license:artistic2.0)))
7703 (define-public r-biocneighbors
7705 (name "r-biocneighbors")
7710 (uri (bioconductor-uri "BiocNeighbors" version))
7713 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
7714 (properties `((upstream-name . "BiocNeighbors")))
7715 (build-system r-build-system)
7717 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
7720 (home-page "https://bioconductor.org/packages/BiocNeighbors")
7721 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
7723 "This package implements exact and approximate methods for nearest
7724 neighbor detection, in a framework that allows them to be easily switched
7725 within Bioconductor packages or workflows. The exact algorithm is implemented
7726 using pre-clustering with the k-means algorithm. Functions are also provided
7727 to search for all neighbors within a given distance. Parallelization is
7728 achieved for all methods using the BiocParallel framework.")
7729 (license license:gpl3)))
7731 (define-public r-scaledmatrix
7733 (name "r-scaledmatrix")
7738 (uri (bioconductor-uri "ScaledMatrix" version))
7741 "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"))))
7742 (properties `((upstream-name . "ScaledMatrix")))
7743 (build-system r-build-system)
7745 (list r-delayedarray r-matrix r-s4vectors))
7746 (native-inputs (list r-knitr))
7747 (home-page "https://github.com/LTLA/ScaledMatrix")
7748 (synopsis "Create a DelayedMatrix of scaled and centered values")
7750 "This package provides delayed computation of a matrix of scaled and
7751 centered values. The result is equivalent to using the @code{scale} function
7752 but avoids explicit realization of a dense matrix during block processing.
7753 This permits greater efficiency in common operations, most notably matrix
7755 (license license:gpl3)))
7757 (define-public r-treeio
7764 (uri (bioconductor-uri "treeio" version))
7767 "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"))))
7768 (properties `((upstream-name . "treeio")))
7769 (build-system r-build-system)
7778 (native-inputs (list r-knitr))
7779 (home-page "https://github.com/YuLab-SMU/treeio")
7780 (synopsis "Base classes and functions for Phylogenetic tree input and output")
7782 "This is an R package to make it easier to import and store phylogenetic
7783 trees with associated data; and to link external data from different sources
7784 to phylogeny. It also supports exporting phylogenetic trees with
7785 heterogeneous associated data to a single tree file and can be served as a
7786 platform for merging tree with associated data and converting file formats.")
7787 (license license:artistic2.0)))
7789 (define-public r-ggtree
7796 (uri (bioconductor-uri "ggtree" version))
7799 "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"))))
7800 (properties `((upstream-name . "ggtree")))
7801 (build-system r-build-system)
7816 (native-inputs (list r-knitr))
7817 (home-page "https://yulab-smu.top/treedata-book/")
7818 (synopsis "R package for visualization of trees and annotation data")
7820 "This package extends the ggplot2 plotting system which implements a
7821 grammar of graphics. ggtree is designed for visualization and annotation of
7822 phylogenetic trees and other tree-like structures with their annotation
7824 (license license:artistic2.0)))
7826 (define-public r-metapod
7833 (uri (bioconductor-uri "metapod" version))
7836 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
7837 (properties `((upstream-name . "metapod")))
7838 (build-system r-build-system)
7843 (home-page "https://bioconductor.org/packages/metapod")
7844 (synopsis "Meta-analyses on p-values of differential analyses")
7846 "This package implements a variety of methods for combining p-values in
7847 differential analyses of genome-scale datasets. Functions can combine
7848 p-values across different tests in the same analysis (e.g., genomic windows in
7849 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
7850 analyses (e.g., replicated comparisons, effect of different treatment
7851 conditions). Support is provided for handling log-transformed input p-values,
7852 missing values and weighting where appropriate.")
7853 (license license:gpl3)))
7855 (define-public r-biocsingular
7857 (name "r-biocsingular")
7862 (uri (bioconductor-uri "BiocSingular" version))
7865 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
7866 (properties `((upstream-name . "BiocSingular")))
7867 (build-system r-build-system)
7881 (home-page "https://github.com/LTLA/BiocSingular")
7882 (synopsis "Singular value decomposition for Bioconductor packages")
7884 "This package implements exact and approximate methods for singular value
7885 decomposition and principal components analysis, in a framework that allows
7886 them to be easily switched within Bioconductor packages or workflows. Where
7887 possible, parallelization is achieved using the BiocParallel framework.")
7888 (license license:gpl3)))
7890 (define-public r-destiny
7897 (uri (bioconductor-uri "destiny" version))
7900 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
7901 (build-system r-build-system)
7919 r-singlecellexperiment
7921 r-summarizedexperiment
7926 (list r-knitr r-nbconvertr)) ; for vignettes
7927 (home-page "https://bioconductor.org/packages/destiny/")
7928 (synopsis "Create and plot diffusion maps")
7929 (description "This package provides tools to create and plot diffusion
7931 ;; Any version of the GPL
7932 (license license:gpl3+)))
7934 (define-public r-savr
7941 (uri (bioconductor-uri "savR" version))
7944 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
7945 (properties `((upstream-name . "savR")))
7946 (build-system r-build-system)
7948 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
7949 (home-page "https://github.com/bcalder/savR")
7950 (synopsis "Parse and analyze Illumina SAV files")
7952 "This package provides tools to parse Illumina Sequence Analysis
7953 Viewer (SAV) files, access data, and generate QC plots.")
7954 (license license:agpl3+)))
7956 (define-public r-chipexoqual
7958 (name "r-chipexoqual")
7963 (uri (bioconductor-uri "ChIPexoQual" version))
7966 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
7967 (properties `((upstream-name . "ChIPexoQual")))
7968 (build-system r-build-system)
7970 (list r-biocparallel
7989 (home-page "https://github.com/keleslab/ChIPexoQual")
7990 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
7992 "This package provides a quality control pipeline for ChIP-exo/nexus
7994 (license license:gpl2+)))
7996 (define-public r-copynumber
7998 (name "r-copynumber")
8002 (uri (bioconductor-uri "copynumber" version))
8005 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
8006 (build-system r-build-system)
8008 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
8009 (home-page "https://bioconductor.org/packages/copynumber")
8010 (synopsis "Segmentation of single- and multi-track copy number data")
8012 "This package segments single- and multi-track copy number data by a
8013 penalized least squares regression method.")
8014 (license license:artistic2.0)))
8016 (define-public r-dnacopy
8023 (uri (bioconductor-uri "DNAcopy" version))
8026 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
8027 (properties `((upstream-name . "DNAcopy")))
8028 (build-system r-build-system)
8029 (native-inputs (list gfortran))
8030 (home-page "https://bioconductor.org/packages/DNAcopy")
8031 (synopsis "DNA copy number data analysis")
8033 "This package implements the @dfn{circular binary segmentation} (CBS)
8034 algorithm to segment DNA copy number data and identify genomic regions with
8035 abnormal copy number.")
8036 (license license:gpl2+)))
8038 ;; This is a CRAN package, but it uncharacteristically depends on a
8039 ;; Bioconductor package.
8040 (define-public r-htscluster
8042 (name "r-htscluster")
8047 (uri (cran-uri "HTSCluster" version))
8050 "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
8051 (properties `((upstream-name . "HTSCluster")))
8052 (build-system r-build-system)
8054 (list r-capushe r-edger r-plotrix))
8055 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
8056 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
8058 "This package provides a Poisson mixture model is implemented to cluster
8059 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
8060 estimation is performed using either the EM or CEM algorithm, and the slope
8061 heuristics are used for model selection (i.e., to choose the number of
8063 (license license:gpl3+)))
8065 (define-public r-deds
8072 (uri (bioconductor-uri "DEDS" version))
8075 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
8076 (properties `((upstream-name . "DEDS")))
8077 (build-system r-build-system)
8078 (home-page "https://bioconductor.org/packages/DEDS/")
8079 (synopsis "Differential expression via distance summary for microarray data")
8081 "This library contains functions that calculate various statistics of
8082 differential expression for microarray data, including t statistics, fold
8083 change, F statistics, SAM, moderated t and F statistics and B statistics. It
8084 also implements a new methodology called DEDS (Differential Expression via
8085 Distance Summary), which selects differentially expressed genes by integrating
8086 and summarizing a set of statistics using a weighted distance approach.")
8087 ;; Any version of the LGPL.
8088 (license license:lgpl3+)))
8090 ;; This is a CRAN package, but since it depends on a Bioconductor package we
8092 (define-public r-nbpseq
8099 (uri (cran-uri "NBPSeq" version))
8102 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
8103 (properties `((upstream-name . "NBPSeq")))
8104 (build-system r-build-system)
8107 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
8108 (synopsis "Negative binomial models for RNA-Seq data")
8110 "This package provides negative binomial models for two-group comparisons
8111 and regression inferences from RNA-sequencing data.")
8112 (license license:gpl2)))
8114 (define-public r-ebseq
8121 (uri (bioconductor-uri "EBSeq" version))
8124 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
8125 (properties `((upstream-name . "EBSeq")))
8126 (build-system r-build-system)
8128 (list r-blockmodeling r-gplots r-testthat))
8129 (home-page "https://bioconductor.org/packages/EBSeq")
8130 (synopsis "Differential expression analysis of RNA-seq data")
8132 "This package provides tools for differential expression analysis at both
8133 gene and isoform level using RNA-seq data")
8134 (license license:artistic2.0)))
8136 (define-public r-karyoploter
8138 (name "r-karyoploter")
8142 (uri (bioconductor-uri "karyoploteR" version))
8145 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
8146 (build-system r-build-system)
8148 (list r-annotationdbi
8162 r-variantannotation))
8165 (home-page "https://bioconductor.org/packages/karyoploteR/")
8166 (synopsis "Plot customizable linear genomes displaying arbitrary data")
8167 (description "This package creates karyotype plots of arbitrary genomes and
8168 offers a complete set of functions to plot arbitrary data on them. It mimics
8169 many R base graphics functions coupling them with a coordinate change function
8170 automatically mapping the chromosome and data coordinates into the plot
8172 (license license:artistic2.0)))
8174 (define-public r-lpsymphony
8176 (name "r-lpsymphony")
8181 (uri (bioconductor-uri "lpsymphony" version))
8184 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
8185 (build-system r-build-system)
8189 '(modify-phases %standard-phases
8190 (add-after 'unpack 'make-build-order-reproducible
8192 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
8193 "src/SYMPHONY/Cgl/configure")
8194 (("for file in `ls \\*/Makefile.in`")
8195 "for file in `ls */Makefile.in | sort`")))))))
8199 (list pkg-config r-knitr))
8200 (home-page "https://r-forge.r-project.org/projects/rsymphony")
8201 (synopsis "Symphony integer linear programming solver in R")
8203 "This package was derived from Rsymphony. The package provides an R
8204 interface to SYMPHONY, a linear programming solver written in C++. The main
8205 difference between this package and Rsymphony is that it includes the solver
8206 source code, while Rsymphony expects to find header and library files on the
8207 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
8208 to install interface to SYMPHONY.")
8209 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
8210 ;; lpsimphony is released under the same terms.
8211 (license license:epl1.0)))
8213 (define-public r-ihw
8220 (uri (bioconductor-uri "IHW" version))
8223 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
8224 (properties `((upstream-name . "IHW")))
8225 (build-system r-build-system)
8227 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
8230 (home-page "https://bioconductor.org/packages/IHW")
8231 (synopsis "Independent hypothesis weighting")
8233 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
8234 procedure that increases power compared to the method of Benjamini and
8235 Hochberg by assigning data-driven weights to each hypothesis. The input to
8236 IHW is a two-column table of p-values and covariates. The covariate can be
8237 any continuous-valued or categorical variable that is thought to be
8238 informative on the statistical properties of each hypothesis test, while it is
8239 independent of the p-value under the null hypothesis.")
8240 (license license:artistic2.0)))
8242 (define-public r-icobra
8249 (uri (bioconductor-uri "iCOBRA" version))
8252 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
8253 (properties `((upstream-name . "iCOBRA")))
8254 (build-system r-build-system)
8270 (home-page "https://bioconductor.org/packages/iCOBRA")
8271 (synopsis "Comparison and visualization of ranking and assignment methods")
8273 "This package provides functions for calculation and visualization of
8274 performance metrics for evaluation of ranking and binary
8275 classification (assignment) methods. It also contains a Shiny application for
8276 interactive exploration of results.")
8277 (license license:gpl2+)))
8279 (define-public r-residualmatrix
8281 (name "r-residualmatrix")
8286 (uri (bioconductor-uri "ResidualMatrix" version))
8289 "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"))))
8291 `((upstream-name . "ResidualMatrix")))
8292 (build-system r-build-system)
8294 (list r-delayedarray r-matrix r-s4vectors))
8297 (home-page "https://github.com/LTLA/ResidualMatrix")
8298 (synopsis "Create a DelayedMatrix of regression residuals")
8300 "This package implements tools for delayed computation of a matrix of
8301 residuals after fitting a linear model to each column of an input matrix. It
8302 also supports partial computation of residuals where selected factors are to
8303 be preserved in the output matrix. It implements a number of efficient
8304 methods for operating on the delayed matrix of residuals, most notably matrix
8305 multiplication and calculation of row/column sums or means.")
8306 (license license:gpl3)))
8308 (define-public r-batchelor
8310 (name "r-batchelor")
8315 (uri (bioconductor-uri "batchelor" version))
8318 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
8319 (properties `((upstream-name . "batchelor")))
8320 (build-system r-build-system)
8328 r-delayedmatrixstats
8336 r-singlecellexperiment
8337 r-summarizedexperiment))
8338 (native-inputs (list r-knitr))
8339 (home-page "https://bioconductor.org/packages/batchelor")
8340 (synopsis "Single-Cell Batch Correction Methods")
8342 "This package implements a variety of methods for batch correction of
8343 single-cell (RNA sequencing) data. This includes methods based on detecting
8344 mutually nearest neighbors, as well as several efficient variants of linear
8345 regression of the log-expression values. Functions are also provided to
8346 perform global rescaling to remove differences in depth between batches, and
8347 to perform a principal components analysis that is robust to differences in
8348 the numbers of cells across batches.")
8349 (license license:gpl3)))
8351 (define-public r-mast
8358 (uri (bioconductor-uri "MAST" version))
8361 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
8362 (properties `((upstream-name . "MAST")))
8363 (build-system r-build-system)
8374 r-singlecellexperiment
8376 r-summarizedexperiment))
8379 (home-page "https://github.com/RGLab/MAST/")
8380 (synopsis "Model-based analysis of single cell transcriptomics")
8382 "This package provides methods and models for handling zero-inflated
8383 single cell assay data.")
8384 (license license:gpl2+)))
8386 (define-public r-monocle
8393 (uri (bioconductor-uri "monocle" version))
8396 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
8397 (build-system r-build-system)
8431 (home-page "https://bioconductor.org/packages/monocle")
8432 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
8434 "Monocle performs differential expression and time-series analysis for
8435 single-cell expression experiments. It orders individual cells according to
8436 progress through a biological process, without knowing ahead of time which
8437 genes define progress through that process. Monocle also performs
8438 differential expression analysis, clustering, visualization, and other useful
8439 tasks on single cell expression data. It is designed to work with RNA-Seq and
8440 qPCR data, but could be used with other types as well.")
8441 (license license:artistic2.0)))
8443 (define-public r-leidenbase
8444 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
8447 (name "r-leidenbase")
8448 (version (git-version "0.1.9" revision commit))
8453 (url "https://github.com/cole-trapnell-lab/leidenbase")
8455 (file-name (git-file-name name version))
8458 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
8459 (properties `((upstream-name . "leidenbase")))
8460 (build-system r-build-system)
8467 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
8468 (synopsis "R and C wrappers to run the Leiden find_partition function")
8470 "This package provides an R to C interface that runs the Leiden
8471 community detection algorithm to find a basic partition. It runs the
8472 equivalent of the @code{find_partition} function. This package includes the
8473 required source code files from the official Leidenalg distribution and
8474 several functions from the R igraph package.")
8475 (license license:gpl3+))))
8477 (define-public r-sanssouci
8478 ;; sansscouci doesn't have a (versioned) release yet.
8479 ;; This is the latest commit as of packaging for Guix.
8480 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
8483 (name "r-sanssouci")
8484 (version (git-version "0" revision commit))
8488 (url "https://github.com/pneuvial/sanssouci.git")
8490 (file-name (git-file-name name version))
8493 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
8494 (build-system r-build-system)
8496 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
8497 (home-page "https://pneuvial.github.io/sanssouci")
8498 (synopsis "Post Hoc multiple testing inference")
8500 "The goal of sansSouci is to perform post hoc inference: in a multiple
8501 testing context, sansSouci provides statistical guarantees on possibly
8502 user-defined and/or data-driven sets of hypotheses.")
8503 (license license:gpl3))))
8505 (define-public r-monocle3
8513 (url "https://github.com/cole-trapnell-lab/monocle3")
8515 (file-name (git-file-name name version))
8518 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
8519 (build-system r-build-system)
8525 r-delayedmatrixstats
8560 r-singlecellexperiment
8565 (home-page "https://github.com/cole-trapnell-lab/monocle3")
8566 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
8568 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
8569 (license license:expat)))
8571 (define-public r-noiseq
8578 (uri (bioconductor-uri "NOISeq" version))
8581 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
8582 (properties `((upstream-name . "NOISeq")))
8583 (build-system r-build-system)
8585 (list r-biobase r-matrix))
8586 (home-page "https://bioconductor.org/packages/NOISeq")
8587 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
8589 "This package provides tools to support the analysis of RNA-seq
8590 expression data or other similar kind of data. It provides exploratory plots
8591 to evaluate saturation, count distribution, expression per chromosome, type of
8592 detected features, features length, etc. It also supports the analysis of
8593 differential expression between two experimental conditions with no parametric
8595 (license license:artistic2.0)))
8597 (define-public r-scdd
8604 (uri (bioconductor-uri "scDD" version))
8607 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
8608 (properties `((upstream-name . "scDD")))
8609 (build-system r-build-system)
8620 r-singlecellexperiment
8621 r-summarizedexperiment))
8624 (home-page "https://github.com/kdkorthauer/scDD")
8625 (synopsis "Mixture modeling of single-cell RNA-seq data")
8627 "This package implements a method to analyze single-cell RNA-seq data
8628 utilizing flexible Dirichlet Process mixture models. Genes with differential
8629 distributions of expression are classified into several interesting patterns
8630 of differences between two conditions. The package also includes functions
8631 for simulating data with these patterns from negative binomial
8633 (license license:gpl2)))
8635 (define-public r-scone
8642 (uri (bioconductor-uri "scone" version))
8645 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
8646 (build-system r-build-system)
8667 r-singlecellexperiment
8668 r-summarizedexperiment))
8671 (home-page "https://bioconductor.org/packages/scone")
8672 (synopsis "Single cell overview of normalized expression data")
8674 "SCONE is an R package for comparing and ranking the performance of
8675 different normalization schemes for single-cell RNA-seq and other
8676 high-throughput analyses.")
8677 (license license:artistic2.0)))
8679 (define-public r-geoquery
8686 (uri (bioconductor-uri "GEOquery" version))
8689 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
8690 (properties `((upstream-name . "GEOquery")))
8691 (build-system r-build-system)
8705 (home-page "https://github.com/seandavi/GEOquery/")
8706 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
8708 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
8709 microarray data. Given the rich and varied nature of this resource, it is
8710 only natural to want to apply BioConductor tools to these data. GEOquery is
8711 the bridge between GEO and BioConductor.")
8712 (license license:gpl2)))
8714 (define-public r-illuminaio
8716 (name "r-illuminaio")
8721 (uri (bioconductor-uri "illuminaio" version))
8724 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
8725 (build-system r-build-system)
8728 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
8729 (synopsis "Parse Illumina microarray output files")
8731 "This package provides tools for parsing Illumina's microarray output
8732 files, including IDAT.")
8733 (license license:gpl2)))
8735 (define-public r-siggenes
8742 (uri (bioconductor-uri "siggenes" version))
8745 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
8746 (build-system r-build-system)
8748 (list r-biobase r-multtest r-scrime))
8749 (home-page "https://bioconductor.org/packages/siggenes/")
8751 "Multiple testing using SAM and Efron's empirical Bayes approaches")
8753 "This package provides tools for the identification of differentially
8754 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
8755 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
8756 Bayes Analyses of Microarrays} (EBAM).")
8757 (license license:lgpl2.0+)))
8759 (define-public r-bumphunter
8761 (name "r-bumphunter")
8766 (uri (bioconductor-uri "bumphunter" version))
8769 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
8770 (build-system r-build-system)
8772 (list r-annotationdbi
8785 (home-page "https://github.com/ririzarr/bumphunter")
8786 (synopsis "Find bumps in genomic data")
8788 "This package provides tools for finding bumps in genomic data in order
8789 to identify differentially methylated regions in epigenetic epidemiology
8791 (license license:artistic2.0)))
8793 (define-public r-milor
8799 (uri (bioconductor-uri "miloR" version))
8802 "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
8803 (properties `((upstream-name . "miloR")))
8804 (build-system r-build-system)
8806 (list r-biocgenerics
8826 r-singlecellexperiment
8828 r-summarizedexperiment
8831 (native-inputs (list r-knitr))
8832 (home-page "https://marionilab.github.io/miloR")
8833 (synopsis "Differential neighbourhood abundance testing on a graph")
8835 "Milo performs single-cell differential abundance testing. Cell states
8836 are modelled as representative neighbourhoods on a nearest neighbour graph.
8837 Hypothesis testing is performed using a negative bionomial generalized linear
8839 (license license:gpl3)))
8841 (define-public r-minfi
8848 (uri (bioconductor-uri "minfi" version))
8851 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
8852 (build-system r-build-system)
8862 r-delayedmatrixstats
8882 r-summarizedexperiment))
8885 (home-page "https://github.com/hansenlab/minfi")
8886 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
8888 "This package provides tools to analyze and visualize Illumina Infinium
8889 methylation arrays.")
8890 (license license:artistic2.0)))
8892 (define-public r-methylumi
8894 (name "r-methylumi")
8899 (uri (bioconductor-uri "methylumi" version))
8902 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
8903 (build-system r-build-system)
8909 r-fdb-infiniummethylation-hg19
8923 r-summarizedexperiment))
8926 (home-page "https://bioconductor.org/packages/methylumi")
8927 (synopsis "Handle Illumina methylation data")
8929 "This package provides classes for holding and manipulating Illumina
8930 methylation data. Based on eSet, it can contain MIAME information, sample
8931 information, feature information, and multiple matrices of data. An
8932 \"intelligent\" import function, methylumiR can read the Illumina text files
8933 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
8934 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
8935 background correction, and quality control features for GoldenGate, Infinium,
8936 and Infinium HD arrays are also included.")
8937 (license license:gpl2)))
8939 (define-public r-lumi
8946 (uri (bioconductor-uri "lumi" version))
8949 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
8950 (build-system r-build-system)
8967 (home-page "https://bioconductor.org/packages/lumi")
8968 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
8970 "The lumi package provides an integrated solution for the Illumina
8971 microarray data analysis. It includes functions of Illumina
8972 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
8973 variance stabilization, normalization and gene annotation at the probe level.
8974 It also includes the functions of processing Illumina methylation microarrays,
8975 especially Illumina Infinium methylation microarrays.")
8976 (license license:lgpl2.0+)))
8978 (define-public r-linnorm
8985 (uri (bioconductor-uri "Linnorm" version))
8988 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
8989 (properties `((upstream-name . "Linnorm")))
8990 (build-system r-build-system)
9012 (home-page "http://www.jjwanglab.org/Linnorm/")
9013 (synopsis "Linear model and normality based transformation method")
9015 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
9016 count data or any large scale count data. It transforms such datasets for
9017 parametric tests. In addition to the transformtion function (@code{Linnorm}),
9018 the following pipelines are implemented:
9021 @item Library size/batch effect normalization (@code{Linnorm.Norm})
9022 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
9023 clustering or hierarchical clustering (@code{Linnorm.tSNE},
9024 @code{Linnorm.PCA}, @code{Linnorm.HClust})
9025 @item Differential expression analysis or differential peak detection using
9026 limma (@code{Linnorm.limma})
9027 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
9028 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
9029 @item Stable gene selection for scRNA-seq data; for users without or who do
9030 not want to rely on spike-in genes (@code{Linnorm.SGenes})
9031 @item Data imputation (@code{Linnorm.DataImput}).
9034 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
9035 @code{RnaXSim} function is included for simulating RNA-seq data for the
9036 evaluation of DEG analysis methods.")
9037 (license license:expat)))
9039 (define-public r-ioniser
9046 (uri (bioconductor-uri "IONiseR" version))
9049 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
9050 (properties `((upstream-name . "IONiseR")))
9051 (build-system r-build-system)
9053 (list r-biocgenerics
9068 (home-page "https://bioconductor.org/packages/IONiseR/")
9069 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
9071 "IONiseR provides tools for the quality assessment of Oxford Nanopore
9072 MinION data. It extracts summary statistics from a set of fast5 files and can
9073 be used either before or after base calling. In addition to standard
9074 summaries of the read-types produced, it provides a number of plots for
9075 visualising metrics relative to experiment run time or spatially over the
9076 surface of a flowcell.")
9077 (license license:expat)))
9079 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
9080 (define-public r-mutoss
9087 (uri (cran-uri "mutoss" version))
9090 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
9091 (properties `((upstream-name . "mutoss")))
9092 (build-system r-build-system)
9094 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
9095 (home-page "https://github.com/kornl/mutoss/")
9096 (synopsis "Unified multiple testing procedures")
9098 "This package is designed to ease the application and comparison of
9099 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
9100 are standardized and usable by the accompanying mutossGUI package.")
9101 ;; Any version of the GPL.
9102 (license (list license:gpl2+ license:gpl3+))))
9104 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
9105 ;; from Bioconductor, so we put it here.
9106 (define-public r-metap
9113 (uri (cran-uri "metap" version))
9116 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
9117 (build-system r-build-system)
9125 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
9126 (synopsis "Meta-analysis of significance values")
9128 "The canonical way to perform meta-analysis involves using effect sizes.
9129 When they are not available this package provides a number of methods for
9130 meta-analysis of significance values including the methods of Edgington,
9131 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
9132 published results; and a routine for graphical display.")
9133 (license license:gpl2)))
9135 (define-public r-tradeseq
9141 (uri (bioconductor-uri "tradeSeq" version))
9144 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
9145 (build-system r-build-system)
9161 r-singlecellexperiment
9163 r-summarizedexperiment
9169 (home-page "https://statomics.github.io/tradeSeq/index.html")
9170 (synopsis "Trajectory-based differential expression analysis")
9172 "This package provides a flexible method for fitting regression models that
9173 can be used to find genes that are differentially expressed along one or
9174 multiple lineages in a trajectory. Based on the fitted models, it uses a
9175 variety of tests suited to answer different questions of interest, e.g. the
9176 discovery of genes for which expression is associated with pseudotime, or which
9177 are differentially expressed (in a specific region) along the trajectory. It
9178 fits a negative binomial generalized additive model (GAM) for each gene, and
9179 performs inference on the parameters of the GAM.")
9180 (license license:expat)))
9182 (define-public r-triform
9189 (uri (bioconductor-uri "triform" version))
9192 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
9193 (build-system r-build-system)
9195 (list r-biocgenerics r-iranges r-yaml))
9196 (home-page "https://bioconductor.org/packages/triform/")
9197 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
9199 "The Triform algorithm uses model-free statistics to identify peak-like
9200 distributions of TF ChIP sequencing reads, taking advantage of an improved
9201 peak definition in combination with known profile characteristics.")
9202 (license license:gpl2)))
9204 (define-public r-varianttools
9206 (name "r-varianttools")
9211 (uri (bioconductor-uri "VariantTools" version))
9214 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
9215 (properties `((upstream-name . "VariantTools")))
9216 (build-system r-build-system)
9231 r-variantannotation))
9232 (home-page "https://bioconductor.org/packages/VariantTools/")
9233 (synopsis "Tools for exploratory analysis of variant calls")
9235 "Explore, diagnose, and compare variant calls using filters. The
9236 VariantTools package supports a workflow for loading data, calling single
9237 sample variants and tumor-specific somatic mutations or other sample-specific
9238 variant types (e.g., RNA editing). Most of the functions operate on
9239 alignments (BAM files) or datasets of called variants. The user is expected
9240 to have already aligned the reads with a separate tool, e.g., GSNAP via
9242 (license license:artistic2.0)))
9244 (define-public r-heatplus
9251 (uri (bioconductor-uri "Heatplus" version))
9254 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
9255 (properties `((upstream-name . "Heatplus")))
9256 (build-system r-build-system)
9258 (list r-rcolorbrewer))
9259 (home-page "https://github.com/alexploner/Heatplus")
9260 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
9262 "This package provides tools to display a rectangular heatmap (intensity
9263 plot) of a data matrix. By default, both samples (columns) and features (row)
9264 of the matrix are sorted according to a hierarchical clustering, and the
9265 corresponding dendrogram is plotted. Optionally, panels with additional
9266 information about samples and features can be added to the plot.")
9267 (license license:gpl2+)))
9269 (define-public r-gosemsim
9276 (uri (bioconductor-uri "GOSemSim" version))
9279 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
9280 (properties `((upstream-name . "GOSemSim")))
9281 (build-system r-build-system)
9283 (list r-annotationdbi r-go-db r-rcpp))
9286 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
9287 (synopsis "GO-terms semantic similarity measures")
9289 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
9290 quantitative ways to compute similarities between genes and gene groups, and
9291 have became important basis for many bioinformatics analysis approaches.
9292 GOSemSim is an R package for semantic similarity computation among GO terms,
9293 sets of GO terms, gene products and gene clusters.")
9294 (license license:artistic2.0)))
9296 (define-public r-anota
9303 (uri (bioconductor-uri "anota" version))
9306 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
9307 (build-system r-build-system)
9309 (list r-multtest r-qvalue))
9310 (home-page "https://bioconductor.org/packages/anota/")
9311 (synopsis "Analysis of translational activity")
9313 "Genome wide studies of translational control is emerging as a tool to
9314 study various biological conditions. The output from such analysis is both
9315 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
9316 involved in translation (the actively translating mRNA level) for each mRNA.
9317 The standard analysis of such data strives towards identifying differential
9318 translational between two or more sample classes - i.e., differences in
9319 actively translated mRNA levels that are independent of underlying differences
9320 in cytosolic mRNA levels. This package allows for such analysis using partial
9321 variances and the random variance model. As 10s of thousands of mRNAs are
9322 analyzed in parallel the library performs a number of tests to assure that
9323 the data set is suitable for such analysis.")
9324 (license license:gpl3)))
9326 (define-public r-sigpathway
9328 (name "r-sigpathway")
9333 (uri (bioconductor-uri "sigPathway" version))
9336 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
9337 (properties `((upstream-name . "sigPathway")))
9338 (build-system r-build-system)
9339 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
9340 (synopsis "Pathway analysis")
9342 "This package is used to conduct pathway analysis by calculating the NT_k
9343 and NE_k statistics in a statistical framework for determining whether a
9344 specified group of genes for a pathway has a coordinated association with a
9345 phenotype of interest.")
9346 (license license:gpl2)))
9348 (define-public r-fcscan
9355 (uri (bioconductor-uri "fcScan" version))
9357 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
9358 (properties `((upstream-name . "fcScan")))
9359 (build-system r-build-system)
9367 r-summarizedexperiment
9368 r-variantannotation))
9369 (native-inputs (list r-knitr))
9370 (home-page "https://bioconductor.org/packages/fcScan")
9371 (synopsis "Detect clusters of coordinates with user defined options")
9373 "This package is used to detect combination of genomic coordinates
9374 falling within a user defined window size along with user defined overlap
9375 between identified neighboring clusters. It can be used for genomic data
9376 where the clusters are built on a specific chromosome or specific strand.
9377 Clustering can be performed with a \"greedy\" option allowing thus the
9378 presence of additional sites within the allowed window size.")
9379 (license license:artistic2.0)))
9381 (define-public r-fgsea
9388 (uri (bioconductor-uri "fgsea" version))
9391 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
9392 (build-system r-build-system)
9404 (home-page "https://github.com/ctlab/fgsea/")
9405 (synopsis "Fast gene set enrichment analysis")
9407 "The package implements an algorithm for fast gene set enrichment
9408 analysis. Using the fast algorithm makes more permutations and gets
9409 more fine grained p-values, which allows using accurate standard approaches
9410 to multiple hypothesis correction.")
9411 (license license:expat)))
9413 (define-public r-dose
9420 (uri (bioconductor-uri "DOSE" version))
9423 "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"))))
9424 (properties `((upstream-name . "DOSE")))
9425 (build-system r-build-system)
9427 (list r-annotationdbi
9437 (home-page "https://guangchuangyu.github.io/software/DOSE/")
9438 (synopsis "Disease ontology semantic and enrichment analysis")
9440 "This package implements five methods proposed by Resnik, Schlicker,
9441 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
9442 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
9443 including hypergeometric model and gene set enrichment analysis are also
9444 implemented for discovering disease associations of high-throughput biological
9446 (license license:artistic2.0)))
9448 (define-public r-enrichplot
9450 (name "r-enrichplot")
9455 (uri (bioconductor-uri "enrichplot" version))
9458 "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"))))
9459 (build-system r-build-system)
9478 (home-page "https://github.com/GuangchuangYu/enrichplot")
9479 (synopsis "Visualization of functional enrichment result")
9481 "The enrichplot package implements several visualization methods for
9482 interpreting functional enrichment results obtained from ORA or GSEA analyses.
9483 All the visualization methods are developed based on ggplot2 graphics.")
9484 (license license:artistic2.0)))
9486 (define-public r-clusterprofiler
9488 (name "r-clusterprofiler")
9493 (uri (bioconductor-uri "clusterProfiler" version))
9496 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
9498 `((upstream-name . "clusterProfiler")))
9499 (build-system r-build-system)
9501 (list r-annotationdbi
9516 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
9517 (synopsis "Analysis and visualization of functional profiles for gene clusters")
9519 "This package implements methods to analyze and visualize functional
9520 profiles (GO and KEGG) of gene and gene clusters.")
9521 (license license:artistic2.0)))
9523 (define-public r-clusterexperiment
9525 (name "r-clusterexperiment")
9529 (uri (bioconductor-uri "clusterExperiment" version))
9532 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
9533 (build-system r-build-system)
9558 r-singlecellexperiment
9560 r-summarizedexperiment
9562 (home-page "https://bioconductor.org/packages/clusterExperiment/")
9563 (synopsis "Compare clusterings for single-cell sequencing")
9564 (description "This package provides functionality for running and comparing
9565 many different clusterings of single-cell sequencing data or other large mRNA
9566 expression data sets.")
9567 (license license:artistic2.0)))
9569 (define-public r-mlinterfaces
9571 (name "r-mlinterfaces")
9576 (uri (bioconductor-uri "MLInterfaces" version))
9579 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
9580 (properties `((upstream-name . "MLInterfaces")))
9581 (build-system r-build-system)
9603 (home-page "https://bioconductor.org/packages/MLInterfaces/")
9604 (synopsis "Interfaces to R machine learning procedures")
9606 "This package provides uniform interfaces to machine learning code for
9607 data in R and Bioconductor containers.")
9608 ;; Any version of the LGPL.
9609 (license license:lgpl2.1+)))
9611 (define-public r-annaffy
9618 (uri (bioconductor-uri "annaffy" version))
9621 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
9622 (build-system r-build-system)
9625 (modify-phases %standard-phases
9626 (add-after 'unpack 'remove-reference-to-non-free-data
9628 (substitute* "DESCRIPTION"
9629 ((", KEGG.db") "")))))))
9631 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
9632 (home-page "https://bioconductor.org/packages/annaffy/")
9633 (synopsis "Annotation tools for Affymetrix biological metadata")
9635 "This package provides functions for handling data from Bioconductor
9636 Affymetrix annotation data packages. It produces compact HTML and text
9637 reports including experimental data and URL links to many online databases.
9638 It allows searching of biological metadata using various criteria.")
9639 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
9640 ;; the LGPL 2.1 is included.
9641 (license license:lgpl2.1+)))
9643 (define-public r-a4core
9650 (uri (bioconductor-uri "a4Core" version))
9653 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
9654 (properties `((upstream-name . "a4Core")))
9655 (build-system r-build-system)
9657 (list r-biobase r-glmnet))
9660 (home-page "https://bioconductor.org/packages/a4Core")
9661 (synopsis "Automated Affymetrix array analysis core package")
9663 "This is the core package for the automated analysis of Affymetrix
9665 (license license:gpl3)))
9667 (define-public r-a4classif
9669 (name "r-a4classif")
9674 (uri (bioconductor-uri "a4Classif" version))
9677 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
9678 (properties `((upstream-name . "a4Classif")))
9679 (build-system r-build-system)
9690 (home-page "https://bioconductor.org/packages/a4Classif/")
9691 (synopsis "Automated Affymetrix array analysis classification package")
9693 "This is the classification package for the automated analysis of
9694 Affymetrix arrays.")
9695 (license license:gpl3)))
9697 (define-public r-a4preproc
9699 (name "r-a4preproc")
9704 (uri (bioconductor-uri "a4Preproc" version))
9707 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
9708 (properties `((upstream-name . "a4Preproc")))
9709 (build-system r-build-system)
9711 (list r-biobase r-biocgenerics))
9714 (home-page "https://bioconductor.org/packages/a4Preproc/")
9715 (synopsis "Automated Affymetrix array analysis preprocessing package")
9717 "This is a package for the automated analysis of Affymetrix arrays. It
9718 is used for preprocessing the arrays.")
9719 (license license:gpl3)))
9721 (define-public r-a4reporting
9723 (name "r-a4reporting")
9728 (uri (bioconductor-uri "a4Reporting" version))
9731 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
9732 (properties `((upstream-name . "a4Reporting")))
9733 (build-system r-build-system)
9738 (home-page "https://bioconductor.org/packages/a4Reporting/")
9739 (synopsis "Automated Affymetrix array analysis reporting package")
9741 "This is a package for the automated analysis of Affymetrix arrays. It
9742 provides reporting features.")
9743 (license license:gpl3)))
9745 (define-public r-a4base
9752 (uri (bioconductor-uri "a4Base" version))
9755 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
9756 (properties `((upstream-name . "a4Base")))
9757 (build-system r-build-system)
9769 (home-page "https://bioconductor.org/packages/a4Base/")
9770 (synopsis "Automated Affymetrix array analysis base package")
9772 "This package provides basic features for the automated analysis of
9773 Affymetrix arrays.")
9774 (license license:gpl3)))
9783 (uri (bioconductor-uri "a4" version))
9786 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
9787 (build-system r-build-system)
9789 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
9790 (home-page "https://bioconductor.org/packages/a4/")
9791 (synopsis "Automated Affymetrix array analysis umbrella package")
9793 "This package provides a software suite for the automated analysis of
9794 Affymetrix arrays.")
9795 (license license:gpl3)))
9797 (define-public r-abseqr
9804 (uri (bioconductor-uri "abseqR" version))
9807 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
9808 (properties `((upstream-name . "abseqR")))
9809 (build-system r-build-system)
9813 (list r-biocparallel
9833 (home-page "https://github.com/malhamdoosh/abseqR")
9834 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
9836 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
9837 sequencing datasets generated from antibody libraries and abseqR is one of its
9838 packages. AbseqR empowers the users of abseqPy with plotting and reporting
9839 capabilities and allows them to generate interactive HTML reports for the
9840 convenience of viewing and sharing with other researchers. Additionally,
9841 abseqR extends abseqPy to compare multiple repertoire analyses and perform
9842 further downstream analysis on its output.")
9843 (license license:gpl3)))
9845 (define-public r-bacon
9852 (uri (bioconductor-uri "bacon" version))
9855 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
9856 (build-system r-build-system)
9858 (list r-biocparallel r-ellipse r-ggplot2))
9861 (home-page "https://bioconductor.org/packages/bacon/")
9862 (synopsis "Controlling bias and inflation in association studies")
9864 "Bacon can be used to remove inflation and bias often observed in
9865 epigenome- and transcriptome-wide association studies. To this end bacon
9866 constructs an empirical null distribution using a Gibbs Sampling algorithm by
9867 fitting a three-component normal mixture on z-scores.")
9868 (license license:gpl2+)))
9870 (define-public r-rgadem
9877 (uri (bioconductor-uri "rGADEM" version))
9880 "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"))))
9881 (properties `((upstream-name . "rGADEM")))
9882 (build-system r-build-system)
9884 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
9885 (home-page "https://bioconductor.org/packages/rGADEM/")
9886 (synopsis "De novo sequence motif discovery")
9888 "rGADEM is an efficient de novo motif discovery tool for large-scale
9889 genomic sequence data.")
9890 (license license:artistic2.0)))
9892 (define-public r-motiv
9899 (uri (bioconductor-uri "MotIV" version))
9902 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
9903 (properties `((upstream-name . "MotIV")))
9904 (build-system r-build-system)
9908 (list r-biocgenerics
9915 (home-page "https://bioconductor.org/packages/MotIV/")
9916 (synopsis "Motif identification and validation")
9918 "This package is used for the identification and validation of sequence
9919 motifs. It makes use of STAMP for comparing a set of motifs to a given
9920 database (e.g. JASPAR). It can also be used to visualize motifs, motif
9921 distributions, modules and filter motifs.")
9922 (license license:gpl2)))
9924 (define-public r-motifdb
9930 (uri (bioconductor-uri "MotifDb" version))
9932 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
9933 (properties `((upstream-name . "MotifDb")))
9934 (build-system r-build-system)
9936 (list r-biocgenerics
9945 (home-page "https://www.bioconductor.org/packages/MotifDb/")
9946 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
9947 (description "This package provides more than 2000 annotated position
9948 frequency matrices from nine public sources, for multiple organisms.")
9949 (license license:artistic2.0)))
9951 (define-public r-motifbreakr
9953 (name "r-motifbreakr")
9957 (uri (bioconductor-uri "motifbreakR" version))
9959 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
9960 (properties `((upstream-name . "motifbreakR")))
9961 (build-system r-build-system)
9963 (list r-biocgenerics
9977 r-summarizedexperiment
9979 r-variantannotation))
9982 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
9983 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
9984 (description "This package allows biologists to judge in the first place
9985 whether the sequence surrounding the polymorphism is a good match, and in
9986 the second place how much information is gained or lost in one allele of
9987 the polymorphism relative to another. This package gives a choice of
9988 algorithms for interrogation of genomes with motifs from public sources:
9990 @item a weighted-sum probability matrix;
9991 @item log-probabilities;
9992 @item weighted by relative entropy.
9995 This package can predict effects for novel or previously described variants in
9996 public databases, making it suitable for tasks beyond the scope of its original
9997 design. Lastly, it can be used to interrogate any genome curated within
9999 (license license:gpl2+)))
10001 (define-public r-motifstack
10003 (name "r-motifstack")
10008 (uri (bioconductor-uri "motifStack" version))
10011 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
10012 (properties `((upstream-name . "motifStack")))
10013 (build-system r-build-system)
10023 (home-page "https://bioconductor.org/packages/motifStack/")
10024 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
10026 "The motifStack package is designed for graphic representation of
10027 multiple motifs with different similarity scores. It works with both DNA/RNA
10028 sequence motifs and amino acid sequence motifs. In addition, it provides the
10029 flexibility for users to customize the graphic parameters such as the font
10030 type and symbol colors.")
10031 (license license:gpl2+)))
10033 (define-public r-genomicscores
10035 (name "r-genomicscores")
10040 (uri (bioconductor-uri "GenomicScores" version))
10043 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
10044 (properties `((upstream-name . "GenomicScores")))
10045 (build-system r-build-system)
10047 (list r-annotationhub
10064 (home-page "https://github.com/rcastelo/GenomicScores/")
10065 (synopsis "Work with genome-wide position-specific scores")
10067 "This package provides infrastructure to store and access genome-wide
10068 position-specific scores within R and Bioconductor.")
10069 (license license:artistic2.0)))
10071 (define-public r-atacseqqc
10073 (name "r-atacseqqc")
10078 (uri (bioconductor-uri "ATACseqQC" version))
10081 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
10082 (properties `((upstream-name . "ATACseqQC")))
10083 (build-system r-build-system)
10085 (list r-biocgenerics
10091 r-genomicalignments
10105 (home-page "https://bioconductor.org/packages/ATACseqQC/")
10106 (synopsis "ATAC-seq quality control")
10108 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
10109 sequencing, is a rapid and sensitive method for chromatin accessibility
10110 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
10111 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
10112 assess whether their ATAC-seq experiment is successful. It includes
10113 diagnostic plots of fragment size distribution, proportion of mitochondria
10114 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
10116 (license license:gpl2+)))
10118 (define-public r-gofuncr
10125 (uri (bioconductor-uri "GOfuncR" version))
10128 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
10129 (properties `((upstream-name . "GOfuncR")))
10130 (build-system r-build-system)
10132 (list r-annotationdbi
10141 (home-page "https://bioconductor.org/packages/GOfuncR/")
10142 (synopsis "Gene ontology enrichment using FUNC")
10144 "GOfuncR performs a gene ontology enrichment analysis based on the
10145 ontology enrichment software FUNC. GO-annotations are obtained from
10146 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
10147 included in the package and updated regularly. GOfuncR provides the standard
10148 candidate vs background enrichment analysis using the hypergeometric test, as
10149 well as three additional tests:
10152 @item the Wilcoxon rank-sum test that is used when genes are ranked,
10153 @item a binomial test that is used when genes are associated with two counts,
10155 @item a Chi-square or Fisher's exact test that is used in cases when genes are
10156 associated with four counts.
10159 To correct for multiple testing and interdependency of the tests, family-wise
10160 error rates are computed based on random permutations of the gene-associated
10161 variables. GOfuncR also provides tools for exploring the ontology graph and
10162 the annotations, and options to take gene-length or spatial clustering of
10163 genes into account. It is also possible to provide custom gene coordinates,
10164 annotations and ontologies.")
10165 (license license:gpl2+)))
10167 (define-public r-abaenrichment
10169 (name "r-abaenrichment")
10174 (uri (bioconductor-uri "ABAEnrichment" version))
10177 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
10178 (properties `((upstream-name . "ABAEnrichment")))
10179 (build-system r-build-system)
10189 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
10190 (synopsis "Gene expression enrichment in human brain regions")
10192 "The package ABAEnrichment is designed to test for enrichment of user
10193 defined candidate genes in the set of expressed genes in different human brain
10194 regions. The core function @code{aba_enrich} integrates the expression of the
10195 candidate gene set (averaged across donors) and the structural information of
10196 the brain using an ontology, both provided by the Allen Brain Atlas project.")
10197 (license license:gpl2+)))
10199 (define-public r-annotationfuncs
10201 (name "r-annotationfuncs")
10206 (uri (bioconductor-uri "AnnotationFuncs" version))
10209 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
10211 `((upstream-name . "AnnotationFuncs")))
10212 (build-system r-build-system)
10214 (list r-annotationdbi r-dbi))
10215 (home-page "https://www.iysik.com/r/annotationfuncs")
10216 (synopsis "Annotation translation functions")
10218 "This package provides functions for handling translating between
10219 different identifieres using the Biocore Data Team data-packages (e.g.
10220 @code{org.Bt.eg.db}).")
10221 (license license:gpl2)))
10223 (define-public r-annotationtools
10225 (name "r-annotationtools")
10230 (uri (bioconductor-uri "annotationTools" version))
10233 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
10235 `((upstream-name . "annotationTools")))
10236 (build-system r-build-system)
10237 (propagated-inputs (list r-biobase))
10238 (home-page "https://bioconductor.org/packages/annotationTools/")
10239 (synopsis "Annotate microarrays and perform gene expression analyses")
10241 "This package provides functions to annotate microarrays, find orthologs,
10242 and integrate heterogeneous gene expression profiles using annotation and
10243 other molecular biology information available as flat file database (plain
10245 ;; Any version of the GPL.
10246 (license (list license:gpl2+))))
10248 (define-public r-allelicimbalance
10250 (name "r-allelicimbalance")
10255 (uri (bioconductor-uri "AllelicImbalance" version))
10258 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
10260 `((upstream-name . "AllelicImbalance")))
10261 (build-system r-build-system)
10263 (list r-annotationdbi
10268 r-genomicalignments
10280 r-summarizedexperiment
10281 r-variantannotation))
10284 (home-page "https://github.com/pappewaio/AllelicImbalance")
10285 (synopsis "Investigate allele-specific expression")
10287 "This package provides a framework for allele-specific expression
10288 investigation using RNA-seq data.")
10289 (license license:gpl3)))
10291 (define-public r-aucell
10298 (uri (bioconductor-uri "AUCell" version))
10301 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
10302 (properties `((upstream-name . "AUCell")))
10303 (build-system r-build-system)
10305 (list r-biocgenerics
10308 r-delayedmatrixstats
10313 r-summarizedexperiment))
10316 (home-page "https://bioconductor.org/packages/AUCell/")
10317 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
10319 "AUCell identifies cells with active gene sets (e.g. signatures,
10320 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
10321 Under the Curve} (AUC) to calculate whether a critical subset of the input
10322 gene set is enriched within the expressed genes for each cell. The
10323 distribution of AUC scores across all the cells allows exploring the relative
10324 expression of the signature. Since the scoring method is ranking-based,
10325 AUCell is independent of the gene expression units and the normalization
10326 procedure. In addition, since the cells are evaluated individually, it can
10327 easily be applied to bigger datasets, subsetting the expression matrix if
10329 (license license:gpl3)))
10331 (define-public r-ebimage
10338 (uri (bioconductor-uri "EBImage" version))
10341 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
10342 (properties `((upstream-name . "EBImage")))
10343 (build-system r-build-system)
10356 (list r-knitr)) ; for vignettes
10357 (home-page "https://github.com/aoles/EBImage")
10358 (synopsis "Image processing and analysis toolbox for R")
10360 "EBImage provides general purpose functionality for image processing and
10361 analysis. In the context of (high-throughput) microscopy-based cellular
10362 assays, EBImage offers tools to segment cells and extract quantitative
10363 cellular descriptors. This allows the automation of such tasks using the R
10364 programming language and facilitates the use of other tools in the R
10365 environment for signal processing, statistical modeling, machine learning and
10366 visualization with image data.")
10367 ;; Any version of the LGPL.
10368 (license license:lgpl2.1+)))
10370 (define-public r-yamss
10377 (uri (bioconductor-uri "yamss" version))
10380 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
10381 (build-system r-build-system)
10383 (list r-biocgenerics
10391 r-summarizedexperiment))
10394 (home-page "https://github.com/hansenlab/yamss")
10395 (synopsis "Tools for high-throughput metabolomics")
10397 "This package provides tools to analyze and visualize high-throughput
10398 metabolomics data acquired using chromatography-mass spectrometry. These tools
10399 preprocess data in a way that enables reliable and powerful differential
10401 (license license:artistic2.0)))
10403 (define-public r-gtrellis
10405 (name "r-gtrellis")
10410 (uri (bioconductor-uri "gtrellis" version))
10413 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
10414 (build-system r-build-system)
10416 (list r-circlize r-genomicranges r-getoptlong r-iranges))
10419 (home-page "https://github.com/jokergoo/gtrellis")
10420 (synopsis "Genome level Trellis layout")
10422 "Genome level Trellis graph visualizes genomic data conditioned by
10423 genomic categories (e.g. chromosomes). For each genomic category, multiple
10424 dimensional data which are represented as tracks describe different features
10425 from different aspects. This package provides high flexibility to arrange
10426 genomic categories and to add self-defined graphics in the plot.")
10427 (license license:expat)))
10429 (define-public r-somaticsignatures
10431 (name "r-somaticsignatures")
10436 (uri (bioconductor-uri "SomaticSignatures" version))
10439 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
10441 `((upstream-name . "SomaticSignatures")))
10442 (build-system r-build-system)
10456 r-variantannotation))
10459 (home-page "https://github.com/juliangehring/SomaticSignatures")
10460 (synopsis "Somatic signatures")
10462 "This package identifies mutational signatures of @dfn{single nucleotide
10463 variants} (SNVs). It provides a infrastructure related to the methodology
10464 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
10465 decomposition algorithms.")
10466 (license license:expat)))
10468 (define-public r-yapsa
10475 (uri (bioconductor-uri "YAPSA" version))
10478 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
10479 (properties `((upstream-name . "YAPSA")))
10480 (build-system r-build-system)
10483 r-bsgenome-hsapiens-ucsc-hg19
10503 r-somaticsignatures
10504 r-variantannotation))
10507 (home-page "https://bioconductor.org/packages/YAPSA/")
10508 (synopsis "Yet another package for signature analysis")
10510 "This package provides functions and routines useful in the analysis of
10511 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
10512 functions to perform a signature analysis with known signatures and a
10513 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
10515 (license license:gpl3)))
10517 (define-public r-gcrma
10524 (uri (bioconductor-uri "gcrma" version))
10527 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
10528 (build-system r-build-system)
10536 (home-page "https://bioconductor.org/packages/gcrma/")
10537 (synopsis "Background adjustment using sequence information")
10539 "Gcrma adjusts for background intensities in Affymetrix array data which
10540 include optical noise and @dfn{non-specific binding} (NSB). The main function
10541 @code{gcrma} converts background adjusted probe intensities to expression
10542 measures using the same normalization and summarization methods as a
10543 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
10544 to estimate probe affinity to NSB. The sequence information is summarized in
10545 a more complex way than the simple GC content. Instead, the base types (A, T,
10546 G or C) at each position along the probe determine the affinity of each probe.
10547 The parameters of the position-specific base contributions to the probe
10548 affinity is estimated in an NSB experiment in which only NSB but no
10549 gene-specific binding is expected.")
10550 ;; Any version of the LGPL
10551 (license license:lgpl2.1+)))
10553 (define-public r-simpleaffy
10555 (name "r-simpleaffy")
10560 (uri (bioconductor-uri "simpleaffy" version))
10563 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
10564 (build-system r-build-system)
10566 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
10567 (home-page "https://bioconductor.org/packages/simpleaffy/")
10568 (synopsis "Very simple high level analysis of Affymetrix data")
10570 "This package provides high level functions for reading Affy @file{.CEL}
10571 files, phenotypic data, and then computing simple things with it, such as
10572 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
10573 library. It also has some basic scatter plot functions and mechanisms for
10574 generating high resolution journal figures.")
10575 (license license:gpl2+)))
10577 (define-public r-yaqcaffy
10579 (name "r-yaqcaffy")
10584 (uri (bioconductor-uri "yaqcaffy" version))
10587 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
10588 (build-system r-build-system)
10590 (list r-simpleaffy))
10591 (home-page "https://bioconductor.org/packages/yaqcaffy/")
10592 (synopsis "Affymetrix quality control and reproducibility analysis")
10594 "This is a package that can be used for quality control of Affymetrix
10595 GeneChip expression data and reproducibility analysis of human whole genome
10596 chips with the MAQC reference datasets.")
10597 (license license:artistic2.0)))
10599 (define-public r-quantro
10606 (uri (bioconductor-uri "quantro" version))
10609 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
10610 (build-system r-build-system)
10621 (home-page "https://bioconductor.org/packages/quantro/")
10622 (synopsis "Test for when to use quantile normalization")
10624 "This package provides a data-driven test for the assumptions of quantile
10625 normalization using raw data such as objects that inherit eSets (e.g.
10626 ExpressionSet, MethylSet). Group level information about each sample (such as
10627 Tumor / Normal status) must also be provided because the test assesses if
10628 there are global differences in the distributions between the user-defined
10630 (license license:gpl3+)))
10632 (define-public r-yarn
10639 (uri (bioconductor-uri "yarn" version))
10642 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
10643 (build-system r-build-system)
10658 (home-page "https://bioconductor.org/packages/yarn/")
10659 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
10661 "Expedite large RNA-Seq analyses using a combination of previously
10662 developed tools. YARN is meant to make it easier for the user in performing
10663 basic mis-annotation quality control, filtering, and condition-aware
10664 normalization. YARN leverages many Bioconductor tools and statistical
10665 techniques to account for the large heterogeneity and sparsity found in very
10666 large RNA-seq experiments.")
10667 (license license:artistic2.0)))
10669 (define-public r-roar
10676 (uri (bioconductor-uri "roar" version))
10679 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
10680 (build-system r-build-system)
10682 (list r-biocgenerics
10684 r-genomicalignments
10689 r-summarizedexperiment))
10690 (home-page "https://github.com/vodkatad/roar/")
10691 (synopsis "Identify differential APA usage from RNA-seq alignments")
10693 "This package provides tools for identifying preferential usage of APA
10694 sites, comparing two biological conditions, starting from known alternative
10695 sites and alignments obtained from standard RNA-seq experiments.")
10696 (license license:gpl3)))
10698 (define-public r-xbseq
10705 (uri (bioconductor-uri "XBSeq" version))
10708 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
10709 (properties `((upstream-name . "XBSeq")))
10710 (build-system r-build-system)
10723 (home-page "https://github.com/Liuy12/XBSeq")
10724 (synopsis "Test for differential expression for RNA-seq data")
10726 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
10727 expression} (DE), where a statistical model was established based on the
10728 assumption that observed signals are the convolution of true expression
10729 signals and sequencing noises. The mapped reads in non-exonic regions are
10730 considered as sequencing noises, which follows a Poisson distribution. Given
10731 measurable observed signal and background noise from RNA-seq data, true
10732 expression signals, assuming governed by the negative binomial distribution,
10733 can be delineated and thus the accurate detection of differential expressed
10735 (license license:gpl3+)))
10737 (define-public r-massspecwavelet
10739 (name "r-massspecwavelet")
10744 (uri (bioconductor-uri "MassSpecWavelet" version))
10747 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
10749 `((upstream-name . "MassSpecWavelet")))
10750 (build-system r-build-system)
10753 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
10754 (synopsis "Mass spectrum processing by wavelet-based algorithms")
10756 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
10757 data mainly through the use of wavelet transforms. It supports peak detection
10758 based on @dfn{Continuous Wavelet Transform} (CWT).")
10759 (license license:lgpl2.0+)))
10761 (define-public r-xcms
10768 (uri (bioconductor-uri "xcms" version))
10771 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
10772 (build-system r-build-system)
10790 r-summarizedexperiment))
10793 (home-page "https://bioconductor.org/packages/xcms/")
10794 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
10796 "This package provides a framework for processing and visualization of
10797 chromatographically separated and single-spectra mass spectral data. It
10798 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
10799 data for high-throughput, untargeted analyte profiling.")
10800 (license license:gpl2+)))
10802 (define-public r-wppi
10808 (uri (bioconductor-uri "wppi" version))
10811 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
10812 (properties `((upstream-name . "wppi")))
10813 (build-system r-build-system)
10814 ;; This is necessary because omnipathr attempts to write a configuration
10818 (modify-phases %standard-phases
10819 (add-after 'unpack 'set-HOME
10820 (lambda _ (setenv "HOME" "/tmp"))))))
10821 (propagated-inputs (list r-dplyr
10833 (native-inputs (list r-knitr))
10834 (home-page "https://github.com/AnaGalhoz37/wppi")
10835 (synopsis "Weighting protein-protein interactions")
10837 "This package predicts functional relevance of protein-protein
10838 interactions based on functional annotations such as Human Protein Ontology
10839 and Gene Ontology, and prioritizes genes based on network topology, functional
10840 scores and a path search algorithm.")
10841 (license license:expat)))
10843 (define-public r-wrench
10850 (uri (bioconductor-uri "Wrench" version))
10853 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
10854 (properties `((upstream-name . "Wrench")))
10855 (build-system r-build-system)
10857 (list r-limma r-locfit r-matrixstats))
10860 (home-page "https://github.com/HCBravoLab/Wrench")
10861 (synopsis "Wrench normalization for sparse count data")
10863 "Wrench is a package for normalization sparse genomic count data, like
10864 that arising from 16s metagenomic surveys.")
10865 (license license:artistic2.0)))
10867 (define-public r-wiggleplotr
10869 (name "r-wiggleplotr")
10874 (uri (bioconductor-uri "wiggleplotr" version))
10877 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
10878 (build-system r-build-system)
10892 (home-page "https://bioconductor.org/packages/wiggleplotr/")
10893 (synopsis "Make read coverage plots from BigWig files")
10895 "This package provides tools to visualize read coverage from sequencing
10896 experiments together with genomic annotations (genes, transcripts, peaks).
10897 Introns of long transcripts can be rescaled to a fixed length for better
10898 visualization of exonic read coverage.")
10899 (license license:asl2.0)))
10901 (define-public r-widgettools
10903 (name "r-widgettools")
10908 (uri (bioconductor-uri "widgetTools" version))
10911 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
10912 (properties `((upstream-name . "widgetTools")))
10913 (build-system r-build-system)
10914 (home-page "https://bioconductor.org/packages/widgetTools/")
10915 (synopsis "Tools for creating interactive tcltk widgets")
10917 "This package contains tools to support the construction of tcltk
10919 ;; Any version of the LGPL.
10920 (license license:lgpl3+)))
10922 (define-public r-webbioc
10929 (uri (bioconductor-uri "webbioc" version))
10932 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
10933 (build-system r-build-system)
10935 (list netpbm perl))
10945 (home-page "https://www.bioconductor.org/")
10946 (synopsis "Bioconductor web interface")
10948 "This package provides an integrated web interface for doing microarray
10949 analysis using several of the Bioconductor packages. It is intended to be
10950 deployed as a centralized bioinformatics resource for use by many users.
10951 Currently only Affymetrix oligonucleotide analysis is supported.")
10952 (license license:gpl2+)))
10954 (define-public r-zinbwave
10956 (name "r-zinbwave")
10961 (uri (bioconductor-uri "zinbwave" version))
10964 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
10965 (build-system r-build-system)
10967 (list r-biocparallel
10971 r-singlecellexperiment
10973 r-summarizedexperiment))
10976 (home-page "https://bioconductor.org/packages/zinbwave")
10977 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
10978 (description "This package implements a general and flexible zero-inflated
10979 negative binomial model that can be used to provide a low-dimensional
10980 representations of single-cell RNA-seq data. The model accounts for zero
10981 inflation (dropouts), over-dispersion, and the count nature of the data.
10982 The model also accounts for the difference in library sizes and optionally
10983 for batch effects and/or other covariates, avoiding the need for pre-normalize
10985 (license license:artistic2.0)))
10987 (define-public r-zfpkm
10994 (uri (bioconductor-uri "zFPKM" version))
10997 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
10998 (properties `((upstream-name . "zFPKM")))
10999 (build-system r-build-system)
11001 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
11004 (home-page "https://github.com/ronammar/zFPKM/")
11005 (synopsis "Functions to facilitate zFPKM transformations")
11007 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
11008 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
11010 (license license:gpl3)))
11012 (define-public r-rbowtie2
11014 (name "r-rbowtie2")
11019 (uri (bioconductor-uri "Rbowtie2" version))
11022 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
11023 (properties `((upstream-name . "Rbowtie2")))
11024 (build-system r-build-system)
11026 (list r-magrittr r-rsamtools))
11028 (list samtools zlib))
11031 (home-page "https://bioconductor.org/packages/Rbowtie2/")
11032 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
11034 "This package provides an R wrapper of the popular @code{bowtie2}
11035 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
11036 rapid adapter trimming, identification, and read merging.")
11037 (license license:gpl3+)))
11039 (define-public r-progeny
11046 (uri (bioconductor-uri "progeny" version))
11049 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
11050 (build-system r-build-system)
11062 (home-page "https://github.com/saezlab/progeny")
11063 (synopsis "Pathway responsive gene activity inference")
11065 "This package provides a function to infer pathway activity from gene
11066 expression. It contains the linear model inferred in the publication
11067 \"Perturbation-response genes reveal signaling footprints in cancer gene
11069 (license license:asl2.0)))
11071 (define-public r-arrmnormalization
11073 (name "r-arrmnormalization")
11078 (uri (bioconductor-uri "ARRmNormalization" version))
11081 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
11083 `((upstream-name . "ARRmNormalization")))
11084 (build-system r-build-system)
11085 (propagated-inputs (list r-arrmdata))
11086 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
11087 (synopsis "Adaptive robust regression normalization for methylation data")
11089 "This is a package to perform the @dfn{Adaptive Robust Regression
11090 method} (ARRm) for the normalization of methylation data from the Illumina
11091 Infinium HumanMethylation 450k assay.")
11092 (license license:artistic2.0)))
11094 (define-public r-biocfilecache
11096 (name "r-biocfilecache")
11101 (uri (bioconductor-uri "BiocFileCache" version))
11104 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
11105 (properties `((upstream-name . "BiocFileCache")))
11106 (build-system r-build-system)
11118 (home-page "https://bioconductor.org/packages/BiocFileCache/")
11119 (synopsis "Manage files across sessions")
11121 "This package creates a persistent on-disk cache of files that the user
11122 can add, update, and retrieve. It is useful for managing resources (such as
11123 custom Txdb objects) that are costly or difficult to create, web resources,
11124 and data files used across sessions.")
11125 (license license:artistic2.0)))
11127 (define-public r-iclusterplus
11129 (name "r-iclusterplus")
11134 (uri (bioconductor-uri "iClusterPlus" version))
11137 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
11138 (properties `((upstream-name . "iClusterPlus")))
11139 (build-system r-build-system)
11140 (native-inputs (list gfortran))
11141 (home-page "https://bioconductor.org/packages/iClusterPlus/")
11142 (synopsis "Integrative clustering of multi-type genomic data")
11144 "iClusterPlus is developed for integrative clustering analysis of
11145 multi-type genomic data and is an enhanced version of iCluster proposed and
11146 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
11147 from the experiments where biological samples (e.g. tumor samples) are
11148 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
11149 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
11150 on. In the iClusterPlus model, binary observations such as somatic mutation
11151 are modeled as Binomial processes; categorical observations such as copy
11152 number states are realizations of Multinomial random variables; counts are
11153 modeled as Poisson random processes; and continuous measures are modeled by
11154 Gaussian distributions.")
11155 (license license:gpl2+)))
11157 (define-public r-rbowtie
11164 (uri (bioconductor-uri "Rbowtie" version))
11167 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
11168 (properties `((upstream-name . "Rbowtie")))
11169 (build-system r-build-system)
11172 ;; Disable unsupported `popcnt' instructions on
11173 ;; architectures other than x86_64
11174 ,(if (string-prefix? "x86_64"
11175 (or (%current-target-system)
11176 (%current-system)))
11178 '(modify-phases %standard-phases
11179 (add-after 'unpack 'patch-sources
11181 (setenv "POPCNT_CAPABILITY" "0")))))))
11182 (inputs (list zlib))
11185 (home-page "https://bioconductor.org/packages/Rbowtie/")
11186 (synopsis "R bowtie wrapper")
11188 "This package provides an R wrapper around the popular bowtie short read
11189 aligner and around SpliceMap, a de novo splice junction discovery and
11191 (license license:artistic2.0)))
11193 (define-public r-sgseq
11200 (uri (bioconductor-uri "SGSeq" version))
11203 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
11204 (properties `((upstream-name . "SGSeq")))
11205 (build-system r-build-system)
11207 (list r-annotationdbi
11211 r-genomicalignments
11220 r-summarizedexperiment))
11223 (home-page "https://bioconductor.org/packages/SGSeq/")
11224 (synopsis "Splice event prediction and quantification from RNA-seq data")
11226 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
11227 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
11228 represented as a splice graph, which can be obtained from existing annotation
11229 or predicted from the mapped sequence reads. Splice events are identified
11230 from the graph and are quantified locally using structurally compatible reads
11231 at the start or end of each splice variant. The software includes functions
11232 for splice event prediction, quantification, visualization and
11234 (license license:artistic2.0)))
11236 (define-public r-rhisat2
11243 (uri (bioconductor-uri "Rhisat2" version))
11246 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
11247 (properties `((upstream-name . "Rhisat2")))
11248 (build-system r-build-system)
11251 (modify-phases %standard-phases
11252 (add-after 'unpack 'make-reproducible
11254 (substitute* "src/Makefile"
11255 (("`hostname`") "guix")
11257 ;; Avoid shelling out to "which".
11258 (("^CC =.*") (which "gcc"))
11259 (("^CPP =.*") (which "g++")))
11262 (list r-genomicfeatures r-genomicranges r-sgseq))
11265 (home-page "https://github.com/fmicompbio/Rhisat2")
11266 (synopsis "R Wrapper for HISAT2 sequence aligner")
11268 "This package provides an R interface to the HISAT2 spliced short-read
11269 aligner by Kim et al. (2015). The package contains wrapper functions to
11270 create a genome index and to perform the read alignment to the generated
11272 (license license:gpl3)))
11274 (define-public r-quasr
11281 (uri (bioconductor-uri "QuasR" version))
11284 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
11285 (properties `((upstream-name . "QuasR")))
11286 (build-system r-build-system)
11288 (list r-annotationdbi
11307 (home-page "https://bioconductor.org/packages/QuasR/")
11308 (synopsis "Quantify and annotate short reads in R")
11310 "This package provides a framework for the quantification and analysis of
11311 short genomic reads. It covers a complete workflow starting from raw sequence
11312 reads, over creation of alignments and quality control plots, to the
11313 quantification of genomic regions of interest.")
11314 (license license:gpl2)))
11316 (define-public r-rqc
11323 (uri (bioconductor-uri "Rqc" version))
11326 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
11327 (properties `((upstream-name . "Rqc")))
11328 (build-system r-build-system)
11330 (list r-biocgenerics
11335 r-genomicalignments
11350 (home-page "https://github.com/labbcb/Rqc")
11351 (synopsis "Quality control tool for high-throughput sequencing data")
11353 "Rqc is an optimized tool designed for quality control and assessment of
11354 high-throughput sequencing data. It performs parallel processing of entire
11355 files and produces a report which contains a set of high-resolution
11357 (license license:gpl2+)))
11359 (define-public r-birewire
11361 (name "r-birewire")
11366 (uri (bioconductor-uri "BiRewire" version))
11369 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
11370 (properties `((upstream-name . "BiRewire")))
11371 (build-system r-build-system)
11373 (list r-igraph r-matrix r-rtsne r-slam))
11374 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
11375 (synopsis "Tools for randomization of bipartite graphs")
11377 "This package provides functions for bipartite network rewiring through N
11378 consecutive switching steps and for the computation of the minimal number of
11379 switching steps to be performed in order to maximise the dissimilarity with
11380 respect to the original network. It includes functions for the analysis of
11381 the introduced randomness across the switching steps and several other
11382 routines to analyse the resulting networks and their natural projections.")
11383 (license license:gpl3)))
11385 (define-public r-birta
11392 (uri (bioconductor-uri "birta" version))
11395 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
11396 (build-system r-build-system)
11398 (list r-biobase r-limma r-mass))
11399 (home-page "https://bioconductor.org/packages/birta")
11400 (synopsis "Bayesian inference of regulation of transcriptional activity")
11402 "Expression levels of mRNA molecules are regulated by different
11403 processes, comprising inhibition or activation by transcription factors and
11404 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
11405 Inference of Regulation of Transcriptional Activity) uses the regulatory
11406 networks of transcription factors and miRNAs together with mRNA and miRNA
11407 expression data to predict switches in regulatory activity between two
11408 conditions. A Bayesian network is used to model the regulatory structure and
11409 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
11410 (license license:gpl2+)))
11412 (define-public r-multidataset
11414 (name "r-multidataset")
11419 (uri (bioconductor-uri "MultiDataSet" version))
11422 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
11423 (properties `((upstream-name . "MultiDataSet")))
11424 (build-system r-build-system)
11435 r-summarizedexperiment))
11438 (home-page "https://bioconductor.org/packages/MultiDataSet/")
11439 (synopsis "Implementation of MultiDataSet and ResultSet")
11441 "This package provides an implementation of the BRGE's (Bioinformatic
11442 Research Group in Epidemiology from Center for Research in Environmental
11443 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
11444 integrating multi omics data sets and ResultSet is a container for omics
11445 results. This package contains base classes for MEAL and rexposome
11447 (license license:expat)))
11449 (define-public r-ropls
11456 (uri (bioconductor-uri "ropls" version))
11459 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
11460 (build-system r-build-system)
11463 r-multiassayexperiment
11465 r-summarizedexperiment))
11467 (list r-knitr)) ; for vignettes
11468 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
11469 (synopsis "Multivariate analysis and feature selection of omics data")
11471 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
11472 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
11473 regression, classification, and feature selection of omics data where the
11474 number of variables exceeds the number of samples and with multicollinearity
11475 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
11476 separately model the variation correlated (predictive) to the factor of
11477 interest and the uncorrelated (orthogonal) variation. While performing
11478 similarly to PLS, OPLS facilitates interpretation.
11480 This package provides imlementations of PCA, PLS, and OPLS for multivariate
11481 analysis and feature selection of omics data. In addition to scores, loadings
11482 and weights plots, the package provides metrics and graphics to determine the
11483 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
11484 validity of the model by permutation testing, detect outliers, and perform
11485 feature selection (e.g. with Variable Importance in Projection or regression
11487 (license license:cecill)))
11489 (define-public r-biosigner
11491 (name "r-biosigner")
11496 (uri (bioconductor-uri "biosigner" version))
11499 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
11500 (build-system r-build-system)
11504 r-multiassayexperiment
11508 r-summarizedexperiment))
11511 (home-page "https://bioconductor.org/packages/biosigner/")
11512 (synopsis "Signature discovery from omics data")
11514 "Feature selection is critical in omics data analysis to extract
11515 restricted and meaningful molecular signatures from complex and high-dimension
11516 data, and to build robust classifiers. This package implements a method to
11517 assess the relevance of the variables for the prediction performances of the
11518 classifier. The approach can be run in parallel with the PLS-DA, Random
11519 Forest, and SVM binary classifiers. The signatures and the corresponding
11520 'restricted' models are returned, enabling future predictions on new
11522 (license license:cecill)))
11524 (define-public r-annotatr
11526 (name "r-annotatr")
11531 (uri (bioconductor-uri "annotatr" version))
11534 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
11535 (build-system r-build-system)
11537 (list r-annotationdbi
11552 (home-page "https://bioconductor.org/packages/annotatr/")
11553 (synopsis "Annotation of genomic regions to genomic annotations")
11555 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
11556 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
11557 to investigate the intersecting genomic annotations. Such annotations include
11558 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
11559 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
11560 enhancers. The annotatr package provides an easy way to summarize and
11561 visualize the intersection of genomic sites/regions with genomic
11563 (license license:gpl3)))
11565 (define-public r-rsubread
11567 (name "r-rsubread")
11572 (uri (bioconductor-uri "Rsubread" version))
11575 "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2"))))
11576 (properties `((upstream-name . "Rsubread")))
11577 (build-system r-build-system)
11578 (inputs (list zlib))
11581 (home-page "https://bioconductor.org/packages/Rsubread/")
11582 (synopsis "Subread sequence alignment and counting for R")
11584 "This package provides tools for alignment, quantification and analysis
11585 of second and third generation sequencing data. It includes functionality for
11586 read mapping, read counting, SNP calling, structural variant detection and
11587 gene fusion discovery. It can be applied to all major sequencing techologies
11588 and to both short and long sequence reads.")
11589 (license license:gpl3)))
11591 (define-public r-flowutils
11593 (name "r-flowutils")
11598 (uri (bioconductor-uri "flowUtils" version))
11601 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
11602 (properties `((upstream-name . "flowUtils")))
11603 (build-system r-build-system)
11611 (home-page "https://github.com/jspidlen/flowUtils")
11612 (synopsis "Utilities for flow cytometry")
11614 "This package provides utilities for flow cytometry data.")
11615 (license license:artistic2.0)))
11617 (define-public r-consensusclusterplus
11619 (name "r-consensusclusterplus")
11624 (uri (bioconductor-uri "ConsensusClusterPlus" version))
11627 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
11629 `((upstream-name . "ConsensusClusterPlus")))
11630 (build-system r-build-system)
11632 (list r-all r-biobase r-cluster))
11633 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
11634 (synopsis "Clustering algorithm")
11636 "This package provides an implementation of an algorithm for determining
11637 cluster count and membership by stability evidence in unsupervised analysis.")
11638 (license license:gpl2)))
11640 ;; This is the latest commit and it solves a bug from the latest release.
11641 (define-public r-cycombine
11642 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
11644 (name "r-cycombine")
11645 (version (git-version "0.2.6" revision commit))
11648 (uri (git-reference
11649 (url "https://github.com/biosurf/cyCombine")
11651 (file-name (git-file-name name version))
11654 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
11655 (properties `((upstream-name . "cyCombine")))
11656 (build-system r-build-system)
11674 (native-inputs (list r-knitr))
11675 (home-page "https://github.com/biosurf/cyCombine")
11676 (synopsis "Integration of single-cell cytometry datasets")
11678 "This package provides a method for combining single-cell cytometry
11679 datasets, which increases the analytical flexibility and the statistical power
11680 of the analyses while minimizing technical noise.")
11681 (license license:expat))))
11683 (define-public r-cytolib
11690 (uri (bioconductor-uri "cytolib" version))
11693 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
11694 (properties `((upstream-name . "cytolib")))
11695 (build-system r-build-system)
11705 (home-page "https://bioconductor.org/packages/cytolib/")
11706 (synopsis "C++ infrastructure for working with gated cytometry")
11708 "This package provides the core data structure and API to represent and
11709 interact with gated cytometry data.")
11710 (license license:artistic2.0)))
11712 (define-public r-flowcore
11714 (name "r-flowcore")
11719 (uri (bioconductor-uri "flowCore" version))
11722 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
11723 (properties `((upstream-name . "flowCore")))
11724 (build-system r-build-system)
11737 (home-page "https://bioconductor.org/packages/flowCore")
11738 (synopsis "Basic structures for flow cytometry data")
11740 "This package provides S4 data structures and basic functions to deal
11741 with flow cytometry data.")
11742 (license license:artistic2.0)))
11744 (define-public r-flowmeans
11746 (name "r-flowmeans")
11751 (uri (bioconductor-uri "flowMeans" version))
11754 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
11755 (properties `((upstream-name . "flowMeans")))
11756 (build-system r-build-system)
11758 (list r-biobase r-feature r-flowcore r-rrcov))
11759 (home-page "https://bioconductor.org/packages/flowMeans")
11760 (synopsis "Non-parametric flow cytometry data gating")
11762 "This package provides tools to identify cell populations in Flow
11763 Cytometry data using non-parametric clustering and segmented-regression-based
11764 change point detection.")
11765 (license license:artistic2.0)))
11767 (define-public r-ncdfflow
11769 (name "r-ncdfflow")
11774 (uri (bioconductor-uri "ncdfFlow" version))
11777 "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7"))))
11778 (properties `((upstream-name . "ncdfFlow")))
11779 (build-system r-build-system)
11791 (home-page "https://bioconductor.org/packages/ncdfFlow/")
11792 (synopsis "HDF5 based storage for flow cytometry data")
11794 "This package provides HDF5 storage based methods and functions for
11795 manipulation of flow cytometry data.")
11796 (license license:artistic2.0)))
11798 (define-public r-ggcyto
11805 (uri (bioconductor-uri "ggcyto" version))
11808 "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325"))))
11809 (properties `((upstream-name . "ggcyto")))
11810 (build-system r-build-system)
11825 (home-page "https://github.com/RGLab/ggcyto/issues")
11826 (synopsis "Visualize Cytometry data with ggplot")
11828 "With the dedicated fortify method implemented for @code{flowSet},
11829 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
11830 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
11831 and some custom layers also make it easy to add gates and population
11832 statistics to the plot.")
11833 (license license:artistic2.0)))
11835 (define-public r-flowviz
11842 (uri (bioconductor-uri "flowViz" version))
11845 "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95"))))
11846 (properties `((upstream-name . "flowViz")))
11847 (build-system r-build-system)
11860 (home-page "https://bioconductor.org/packages/flowViz/")
11861 (synopsis "Visualization for flow cytometry")
11863 "This package provides visualization tools for flow cytometry data.")
11864 (license license:artistic2.0)))
11866 (define-public r-flowclust
11868 (name "r-flowclust")
11873 (uri (bioconductor-uri "flowClust" version))
11876 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
11877 (properties `((upstream-name . "flowClust")))
11878 (build-system r-build-system)
11880 `(#:configure-flags
11881 (list "--configure-args=--enable-bundled-gsl=no")))
11890 (list pkg-config r-knitr))
11891 (home-page "https://bioconductor.org/packages/flowClust")
11892 (synopsis "Clustering for flow cytometry")
11894 "This package provides robust model-based clustering using a t-mixture
11895 model with Box-Cox transformation.")
11896 (license license:artistic2.0)))
11898 ;; TODO: this package bundles an old version of protobuf. It's not easy to
11899 ;; make it use our protobuf package instead.
11900 (define-public r-rprotobuflib
11902 (name "r-rprotobuflib")
11907 (uri (bioconductor-uri "RProtoBufLib" version))
11910 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
11911 (properties `((upstream-name . "RProtoBufLib")))
11912 (build-system r-build-system)
11915 (modify-phases %standard-phases
11916 (add-after 'unpack 'unpack-bundled-sources
11918 (with-directory-excursion "src"
11919 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
11922 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
11923 (synopsis "C++ headers and static libraries of Protocol buffers")
11925 "This package provides the headers and static library of Protocol buffers
11926 for other R packages to compile and link against.")
11927 (license license:bsd-3)))
11929 (define-public r-flowworkspace
11931 (name "r-flowworkspace")
11936 (uri (bioconductor-uri "flowWorkspace" version))
11939 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
11940 (properties `((upstream-name . "flowWorkspace")))
11941 (build-system r-build-system)
11972 (home-page "https://bioconductor.org/packages/flowWorkspace/")
11973 (synopsis "Infrastructure for working with cytometry data")
11975 "This package is designed to facilitate comparison of automated gating
11976 methods against manual gating done in flowJo. This package allows you to
11977 import basic flowJo workspaces into BioConductor and replicate the gating from
11978 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
11979 samples, compensation, and transformation are performed so that the output
11980 matches the flowJo analysis.")
11981 (license license:artistic2.0)))
11983 (define-public r-flowstats
11985 (name "r-flowstats")
11990 (uri (bioconductor-uri "flowStats" version))
11993 "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc"))))
11994 (properties `((upstream-name . "flowStats")))
11995 (build-system r-build-system)
12013 (home-page "http://www.github.com/RGLab/flowStats")
12014 (synopsis "Statistical methods for the analysis of flow cytometry data")
12016 "This package provides methods and functionality to analyze flow data
12017 that is beyond the basic infrastructure provided by the @code{flowCore}
12019 (license license:artistic2.0)))
12021 (define-public r-opencyto
12023 (name "r-opencyto")
12028 (uri (bioconductor-uri "openCyto" version))
12031 "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0"))))
12032 (properties `((upstream-name . "openCyto")))
12033 (build-system r-build-system)
12058 (home-page "https://bioconductor.org/packages/openCyto")
12059 (synopsis "Hierarchical gating pipeline for flow cytometry data")
12061 "This package is designed to facilitate the automated gating methods in a
12062 sequential way to mimic the manual gating strategy.")
12063 (license license:artistic2.0)))
12065 (define-public r-cytoml
12072 (uri (bioconductor-uri "CytoML" version))
12075 "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw"))))
12076 (properties `((upstream-name . "CytoML")))
12077 (build-system r-build-system)
12079 (list libxml2 zlib))
12110 (home-page "https://github.com/RGLab/CytoML")
12111 (synopsis "GatingML interface for cross platform cytometry data sharing")
12113 "This package provides an interface to implementations of the GatingML2.0
12114 standard to exchange gated cytometry data with other software platforms.")
12115 (license license:artistic2.0)))
12117 (define-public r-flowsom
12124 (uri (bioconductor-uri "FlowSOM" version))
12127 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
12128 (properties `((upstream-name . "FlowSOM")))
12129 (build-system r-build-system)
12131 (list r-biocgenerics
12133 r-consensusclusterplus
12153 (home-page "https://bioconductor.org/packages/FlowSOM/")
12154 (synopsis "Visualize and interpret cytometry data")
12156 "FlowSOM offers visualization options for cytometry data, by using
12157 self-organizing map clustering and minimal spanning trees.")
12158 (license license:gpl2+)))
12160 (define-public r-mixomics
12162 (name "r-mixomics")
12167 (uri (bioconductor-uri "mixOmics" version))
12170 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
12171 (properties `((upstream-name . "mixOmics")))
12172 (build-system r-build-system)
12174 (list r-biocparallel
12191 (home-page "http://www.mixOmics.org")
12192 (synopsis "Multivariate methods for exploration of biological datasets")
12194 "mixOmics offers a wide range of multivariate methods for the exploration
12195 and integration of biological datasets with a particular focus on variable
12196 selection. The package proposes several sparse multivariate models we have
12197 developed to identify the key variables that are highly correlated, and/or
12198 explain the biological outcome of interest. The data that can be analysed
12199 with mixOmics may come from high throughput sequencing technologies, such as
12200 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
12201 also beyond the realm of omics (e.g. spectral imaging). The methods
12202 implemented in mixOmics can also handle missing values without having to
12203 delete entire rows with missing data.")
12204 (license license:gpl2+)))
12206 (define-public r-depecher
12207 (package ;Source/Weave error
12208 (name "r-depecher")
12213 (uri (bioconductor-uri "DepecheR" version))
12216 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
12217 (properties `((upstream-name . "DepecheR")))
12218 (build-system r-build-system)
12239 (home-page "https://bioconductor.org/packages/DepecheR/")
12240 (synopsis "Identify traits of clusters in high-dimensional entities")
12242 "The purpose of this package is to identify traits in a dataset that can
12243 separate groups. This is done on two levels. First, clustering is performed,
12244 using an implementation of sparse K-means. Secondly, the generated clusters
12245 are used to predict outcomes of groups of individuals based on their
12246 distribution of observations in the different clusters. As certain clusters
12247 with separating information will be identified, and these clusters are defined
12248 by a sparse number of variables, this method can reduce the complexity of
12249 data, to only emphasize the data that actually matters.")
12250 (license license:expat)))
12252 (define-public r-rcistarget
12254 (name "r-rcistarget")
12259 (uri (bioconductor-uri "RcisTarget" version))
12262 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
12263 (properties `((upstream-name . "RcisTarget")))
12264 (build-system r-build-system)
12276 r-summarizedexperiment
12280 (home-page "https://aertslab.org/#scenic")
12281 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
12283 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
12284 over-represented on a gene list. In a first step, RcisTarget selects DNA
12285 motifs that are significantly over-represented in the surroundings of the
12286 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
12287 achieved by using a database that contains genome-wide cross-species rankings
12288 for each motif. The motifs that are then annotated to TFs and those that have
12289 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
12290 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
12291 genes in the gene-set that are ranked above the leading edge).")
12292 (license license:gpl3)))
12294 (define-public r-chicago
12301 (uri (bioconductor-uri "Chicago" version))
12304 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
12305 (properties `((upstream-name . "Chicago")))
12306 (build-system r-build-system)
12308 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
12309 (native-inputs (list r-knitr))
12310 (home-page "https://bioconductor.org/packages/Chicago")
12311 (synopsis "Capture Hi-C analysis of genomic organization")
12313 "This package provides a pipeline for analysing Capture Hi-C data.")
12314 (license license:artistic2.0)))
12316 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12318 (define-public r-ciara
12324 (uri (cran-uri "CIARA" version))
12327 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
12328 (properties `((upstream-name . "CIARA")))
12329 (build-system r-build-system)
12330 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
12331 (native-inputs (list r-knitr))
12332 (home-page "https://cran.r-project.org/package=CIARA")
12333 (synopsis "Cluster-independent algorithm for rare cell types identification")
12335 "This is a package to support identification of markers of rare cell
12336 types by looking at genes whose expression is confined in small regions of the
12337 expression space.")
12338 (license license:artistic2.0)))
12340 (define-public r-cicero
12347 (uri (bioconductor-uri "cicero" version))
12350 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
12351 (build-system r-build-system)
12377 (home-page "https://bioconductor.org/packages/cicero/")
12378 (synopsis "Predict cis-co-accessibility from single-cell data")
12380 "Cicero computes putative cis-regulatory maps from single-cell chromatin
12381 accessibility data. It also extends the monocle package for use in chromatin
12382 accessibility data.")
12383 (license license:expat)))
12385 ;; This is the latest commit on the "monocle3" branch.
12386 (define-public r-cicero-monocle3
12387 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
12389 (package (inherit r-cicero)
12390 (name "r-cicero-monocle3")
12391 (version (git-version "1.3.2" revision commit))
12395 (uri (git-reference
12396 (url "https://github.com/cole-trapnell-lab/cicero-release")
12398 (file-name (git-file-name name version))
12401 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
12403 (modify-inputs (package-propagated-inputs r-cicero)
12404 (delete "r-monocle")
12405 (prepend r-monocle3))))))
12407 (define-public r-circrnaprofiler
12409 (name "r-circrnaprofiler")
12414 (uri (bioconductor-uri "circRNAprofiler" version))
12417 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
12419 `((upstream-name . "circRNAprofiler")))
12420 (build-system r-build-system)
12422 (list r-annotationhub
12425 r-bsgenome-hsapiens-ucsc-hg19
12448 "https://github.com/Aufiero/circRNAprofiler")
12450 "Computational framework for the downstream analysis of circular RNA's")
12452 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
12453 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
12454 framework allows combining and analyzing circRNAs previously detected by
12455 multiple publicly available annotation-based circRNA detection tools. It
12456 covers different aspects of circRNAs analysis from differential expression
12457 analysis, evolutionary conservation, biogenesis to functional analysis.")
12458 (license license:gpl3)))
12460 (define-public r-cistopic
12462 (name "r-cistopic")
12467 (uri (git-reference
12468 (url "https://github.com/aertslab/cisTopic")
12469 (commit (string-append "v" version))))
12470 (file-name (git-file-name name version))
12473 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
12474 (build-system r-build-system)
12491 (home-page "https://github.com/aertslab/cisTopic")
12492 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
12494 "The sparse nature of single cell epigenomics data can be overruled using
12495 probabilistic modelling methods such as @dfn{Latent Dirichlet
12496 Allocation} (LDA). This package allows the probabilistic modelling of
12497 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
12498 includes functionalities to identify cell states based on the contribution of
12499 cisTopics and explore the nature and regulatory proteins driving them.")
12500 (license license:gpl3)))
12502 (define-public r-cistopic-next
12503 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
12506 (inherit r-cistopic)
12507 (name "r-cistopic-next")
12508 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
12509 ;; since the previous release is 2.1.0. Oh well.
12510 (version (git-version "0.3.0" revision commit))
12514 (uri (git-reference
12515 (url "https://github.com/aertslab/cisTopic")
12517 (file-name (git-file-name name version))
12520 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
12521 (properties `((upstream-name . "cisTopic")))
12542 (define-public r-genie3
12549 (uri (bioconductor-uri "GENIE3" version))
12552 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
12553 (properties `((upstream-name . "GENIE3")))
12554 (build-system r-build-system)
12556 (list r-dplyr r-reshape2))
12559 (home-page "https://bioconductor.org/packages/GENIE3")
12560 (synopsis "Gene network inference with ensemble of trees")
12562 "This package implements the GENIE3 algorithm for inferring gene
12563 regulatory networks from expression data.")
12564 (license license:gpl2+)))
12566 (define-public r-roc
12573 (uri (bioconductor-uri "ROC" version))
12576 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
12577 (properties `((upstream-name . "ROC")))
12578 (build-system r-build-system)
12581 (home-page "https://www.bioconductor.org/packages/ROC/")
12582 (synopsis "Utilities for ROC curves")
12584 "This package provides utilities for @dfn{Receiver Operating
12585 Characteristic} (ROC) curves, with a focus on micro arrays.")
12586 (license license:artistic2.0)))
12588 (define-public r-watermelon
12590 (name "r-watermelon")
12595 (uri (bioconductor-uri "wateRmelon" version))
12598 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
12599 (properties `((upstream-name . "wateRmelon")))
12600 (build-system r-build-system)
12603 r-illuminahumanmethylation450kanno-ilmn12-hg19
12612 (home-page "https://bioconductor.org/packages/wateRmelon/")
12613 (synopsis "Illumina 450 methylation array normalization and metrics")
12615 "The standard index of DNA methylation (beta) is computed from methylated
12616 and unmethylated signal intensities. Betas calculated from raw signal
12617 intensities perform well, but using 11 methylomic datasets we demonstrate that
12618 quantile normalization methods produce marked improvement. The commonly used
12619 procedure of normalizing betas is inferior to the separate normalization of M
12620 and U, and it is also advantageous to normalize Type I and Type II assays
12621 separately. This package provides 15 flavours of betas and three performance
12622 metrics, with methods for objects produced by the @code{methylumi} and
12623 @code{minfi} packages.")
12624 (license license:gpl3)))
12626 (define-public r-gdsfmt
12633 (uri (bioconductor-uri "gdsfmt" version))
12636 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
12637 (modules '((guix build utils)))
12638 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
12639 ;; them and link with system libraries instead.
12642 (for-each delete-file-recursively
12646 (substitute* "src/Makevars"
12647 (("all: \\$\\(SHLIB\\)") "all:")
12648 (("\\$\\(SHLIB\\): liblzma.a") "")
12649 (("^ (ZLIB|LZ4)/.*") "")
12650 (("CoreArray/dVLIntGDS.cpp.*")
12651 "CoreArray/dVLIntGDS.cpp")
12652 (("CoreArray/dVLIntGDS.o.*")
12653 "CoreArray/dVLIntGDS.o")
12654 (("PKG_LIBS = ./liblzma.a")
12655 "PKG_LIBS = -llz4"))
12656 (substitute* "src/CoreArray/dStream.h"
12657 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
12658 (string-append "include <" header ">")))))))
12659 (properties `((upstream-name . "gdsfmt")))
12660 (build-system r-build-system)
12662 (list lz4 xz zlib))
12665 (home-page "http://corearray.sourceforge.net/")
12667 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
12669 "This package provides a high-level R interface to CoreArray @dfn{Genomic
12670 Data Structure} (GDS) data files, which are portable across platforms with
12671 hierarchical structure to store multiple scalable array-oriented data sets
12672 with metadata information. It is suited for large-scale datasets, especially
12673 for data which are much larger than the available random-access memory. The
12674 @code{gdsfmt} package offers efficient operations specifically designed for
12675 integers of less than 8 bits, since a diploid genotype, like
12676 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
12677 byte. Data compression and decompression are available with relatively
12678 efficient random access. It is also allowed to read a GDS file in parallel
12679 with multiple R processes supported by the package @code{parallel}.")
12680 (license license:lgpl3)))
12682 (define-public r-bigmelon
12684 (name "r-bigmelon")
12689 (uri (bioconductor-uri "bigmelon" version))
12692 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
12693 (properties `((upstream-name . "bigmelon")))
12694 (build-system r-build-system)
12706 (home-page "https://bioconductor.org/packages/bigmelon/")
12707 (synopsis "Illumina methylation array analysis for large experiments")
12709 "This package provides methods for working with Illumina arrays using the
12710 @code{gdsfmt} package.")
12711 (license license:gpl3)))
12713 (define-public r-seqbias
12720 (uri (bioconductor-uri "seqbias" version))
12723 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
12724 (properties `((upstream-name . "seqbias")))
12725 (build-system r-build-system)
12727 (list r-biostrings r-genomicranges r-rhtslib))
12728 (home-page "https://bioconductor.org/packages/seqbias/")
12729 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
12731 "This package implements a model of per-position sequencing bias in
12732 high-throughput sequencing data using a simple Bayesian network, the structure
12733 and parameters of which are trained on a set of aligned reads and a reference
12735 (license license:lgpl3)))
12737 (define-public r-reqon
12744 (uri (bioconductor-uri "ReQON" version))
12747 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
12748 (properties `((upstream-name . "ReQON")))
12749 (build-system r-build-system)
12751 (list r-rjava r-rsamtools r-seqbias))
12752 (home-page "https://bioconductor.org/packages/ReQON/")
12753 (synopsis "Recalibrating quality of nucleotides")
12755 "This package provides an implementation of an algorithm for
12756 recalibrating the base quality scores for aligned sequencing data in BAM
12758 (license license:gpl2)))
12760 (define-public r-wavcluster
12762 (name "r-wavcluster")
12767 (uri (bioconductor-uri "wavClusteR" version))
12770 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
12771 (properties `((upstream-name . "wavClusteR")))
12772 (build-system r-build-system)
12774 (list r-biocgenerics
12790 (home-page "https://bioconductor.org/packages/wavClusteR/")
12791 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
12793 "This package provides an integrated pipeline for the analysis of
12794 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
12795 sequencing errors, SNPs and additional non-experimental sources by a non-
12796 parametric mixture model. The protein binding sites (clusters) are then
12797 resolved at high resolution and cluster statistics are estimated using a
12798 rigorous Bayesian framework. Post-processing of the results, data export for
12799 UCSC genome browser visualization and motif search analysis are provided. In
12800 addition, the package integrates RNA-Seq data to estimate the False
12801 Discovery Rate of cluster detection. Key functions support parallel multicore
12802 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
12803 be applied to the analysis of other NGS data obtained from experimental
12804 procedures that induce nucleotide substitutions (e.g. BisSeq).")
12805 (license license:gpl2)))
12807 (define-public r-timeseriesexperiment
12809 (name "r-timeseriesexperiment")
12814 (uri (bioconductor-uri "TimeSeriesExperiment" version))
12817 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
12819 `((upstream-name . "TimeSeriesExperiment")))
12820 (build-system r-build-system)
12832 r-summarizedexperiment
12839 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
12840 (synopsis "Analysis for short time-series data")
12842 "This package is a visualization and analysis toolbox for short time
12843 course data which includes dimensionality reduction, clustering, two-sample
12844 differential expression testing and gene ranking techniques. The package also
12845 provides methods for retrieving enriched pathways.")
12846 (license license:lgpl3+)))
12848 (define-public r-variantfiltering
12850 (name "r-variantfiltering")
12855 (uri (bioconductor-uri "VariantFiltering" version))
12858 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
12860 `((upstream-name . "VariantFiltering")))
12861 (build-system r-build-system)
12863 (list r-annotationdbi
12884 r-summarizedexperiment
12885 r-variantannotation
12887 (home-page "https://github.com/rcastelo/VariantFiltering")
12888 (synopsis "Filtering of coding and non-coding genetic variants")
12890 "Filter genetic variants using different criteria such as inheritance
12891 model, amino acid change consequence, minor allele frequencies across human
12892 populations, splice site strength, conservation, etc.")
12893 (license license:artistic2.0)))
12895 (define-public r-genomegraphs
12897 (name "r-genomegraphs")
12902 (uri (bioconductor-uri "GenomeGraphs" version))
12905 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
12906 (properties `((upstream-name . "GenomeGraphs")))
12907 (build-system r-build-system)
12910 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
12911 (synopsis "Plotting genomic information from Ensembl")
12913 "Genomic data analyses requires integrated visualization of known genomic
12914 information and new experimental data. GenomeGraphs uses the biomaRt package
12915 to perform live annotation queries to Ensembl and translates this to e.g.
12916 gene/transcript structures in viewports of the grid graphics package. This
12917 results in genomic information plotted together with your data. Another
12918 strength of GenomeGraphs is to plot different data types such as array CGH,
12919 gene expression, sequencing and other data, together in one plot using the
12920 same genome coordinate system.")
12921 (license license:artistic2.0)))
12923 (define-public r-wavetiling
12925 (name "r-wavetiling")
12930 (uri (bioconductor-uri "waveTiling" version))
12933 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
12934 (properties `((upstream-name . "waveTiling")))
12935 (build-system r-build-system)
12947 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
12948 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
12950 "This package is designed to conduct transcriptome analysis for tiling
12951 arrays based on fast wavelet-based functional models.")
12952 (license license:gpl2+)))
12954 (define-public r-variancepartition
12956 (name "r-variancepartition")
12961 (uri (bioconductor-uri "variancePartition" version))
12964 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
12966 `((upstream-name . "variancePartition")))
12967 (build-system r-build-system)
12991 (home-page "https://bioconductor.org/packages/variancePartition/")
12992 (synopsis "Analyze variation in gene expression experiments")
12994 "This is a package providing tools to quantify and interpret multiple
12995 sources of biological and technical variation in gene expression experiments.
12996 It uses a linear mixed model to quantify variation in gene expression
12997 attributable to individual, tissue, time point, or technical variables. The
12998 package includes dream differential expression analysis for repeated
13000 (license license:gpl2+)))
13002 (define-public r-htqpcr
13009 (uri (bioconductor-uri "HTqPCR" version))
13012 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
13013 (properties `((upstream-name . "HTqPCR")))
13014 (build-system r-build-system)
13016 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
13017 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
13018 "groups/bertone/software/HTqPCR.pdf"))
13019 (synopsis "Automated analysis of high-throughput qPCR data")
13021 "Analysis of Ct values from high throughput quantitative real-time
13022 PCR (qPCR) assays across multiple conditions or replicates. The input data
13023 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
13024 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
13025 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
13026 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
13027 loading, quality assessment, normalization, visualization and parametric or
13028 non-parametric testing for statistical significance in Ct values between
13029 features (e.g. genes, microRNAs).")
13030 (license license:artistic2.0)))
13032 (define-public r-unifiedwmwqpcr
13034 (name "r-unifiedwmwqpcr")
13039 (uri (bioconductor-uri "unifiedWMWqPCR" version))
13042 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
13044 `((upstream-name . "unifiedWMWqPCR")))
13045 (build-system r-build-system)
13047 (list r-biocgenerics r-htqpcr))
13048 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
13049 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
13051 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
13052 data. This modified test allows for testing differential expression in qPCR
13054 (license license:gpl2+)))
13056 (define-public r-universalmotif
13058 (name "r-universalmotif")
13063 (uri (bioconductor-uri "universalmotif" version))
13066 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
13068 `((upstream-name . "universalmotif")))
13069 (build-system r-build-system)
13072 (modify-phases %standard-phases
13073 (add-after 'unpack 'fix-reference-to-strip
13075 (substitute* "src/Makevars"
13076 (("/usr/bin/strip") (which "strip"))))))))
13078 (list r-biocgenerics
13091 "https://bioconductor.org/packages/universalmotif/")
13093 "Specific structures importer, modifier, and exporter for R")
13095 "This package allows importing most common @dfn{specific structure}
13096 (motif) types into R for use by functions provided by other Bioconductor
13097 motif-related packages. Motifs can be exported into most major motif formats
13098 from various classes as defined by other Bioconductor packages. A suite of
13099 motif and sequence manipulation and analysis functions are included, including
13100 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
13101 motifs, and others.")
13102 (license license:gpl3)))
13104 (define-public r-ace
13110 (uri (bioconductor-uri "ACE" version))
13113 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
13114 (properties `((upstream-name . "ACE")))
13115 (build-system r-build-system)
13116 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
13117 (native-inputs (list r-knitr))
13118 (home-page "https://github.com/tgac-vumc/ACE")
13120 "Absolute copy number estimation from low-coverage whole genome sequencing")
13122 "This package uses segmented copy number data to estimate tumor cell
13123 percentage and produce copy number plots displaying absolute copy numbers. For
13124 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
13125 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
13126 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
13127 subsequently run through all samples in the object(s), for which it will create
13128 individual subdirectories. For each sample, it will calculate how well the
13129 segments fit (the relative error) to integer copy numbers for each percentage
13130 of @dfn{tumor cells} (cells with divergent segments).")
13131 (license license:gpl2)))
13133 (define-public r-acgh
13139 (uri (bioconductor-uri "aCGH" version))
13142 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
13143 (properties `((upstream-name . "aCGH")))
13144 (build-system r-build-system)
13145 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
13146 (home-page "https://bioconductor.org/packages/aCGH")
13148 "Classes and functions for array comparative genomic hybridization data")
13150 "This package provides functions for reading
13151 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
13152 output files and clone information files, creation of @code{aCGH} objects for
13153 storing these data. Basic methods are accessing/replacing, subsetting,
13154 printing and plotting @code{aCGH} objects.")
13155 (license license:gpl2)))
13157 (define-public r-acme
13163 (uri (bioconductor-uri "ACME" version))
13166 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
13167 (properties `((upstream-name . "ACME")))
13168 (build-system r-build-system)
13169 (propagated-inputs (list r-biobase r-biocgenerics))
13170 (home-page "https://bioconductor.org/packages/aCGH/")
13171 (synopsis "Calculating microarray enrichment")
13173 "This package implements @dfn{algorithms for calculating microarray
13174 enrichment} (ACME), and it is a set of tools for analysing tiling array of
13175 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
13176 DNAse hypersensitivity, or other experiments that result in regions of the
13177 genome showing enrichment. It does not rely on a specific array technology
13178 (although the array should be a tiling array), is very general (can be applied
13179 in experiments resulting in regions of enrichment), and is very insensitive to
13180 array noise or normalization methods. It is also very fast and can be applied
13181 on whole-genome tiling array experiments quite easily with enough memory.")
13182 (license license:gpl2+)))
13184 (define-public r-acde
13190 (uri (bioconductor-uri "acde" version))
13193 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
13194 (properties `((upstream-name . "acde")))
13195 (build-system r-build-system)
13196 (propagated-inputs (list r-boot))
13197 (home-page "https://bioconductor.org/packages/acde")
13199 "Identification of differentially expressed genes with artificial components")
13201 "This package provides a multivariate inferential analysis method for
13202 detecting differentially expressed genes in gene expression data. It uses
13203 artificial components, close to the data's principal components but with an
13204 exact interpretation in terms of differential genetic expression, to identify
13205 differentially expressed genes while controlling the @dfn{false discovery
13207 (license license:gpl3)))
13209 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13211 (define-public r-activedriverwgs
13213 (name "r-activedriverwgs")
13218 (uri (cran-uri "ActiveDriverWGS" version))
13221 "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
13223 `((upstream-name . "ActiveDriverWGS")))
13224 (build-system r-build-system)
13228 r-bsgenome-hsapiens-ucsc-hg19
13229 r-bsgenome-hsapiens-ucsc-hg38
13230 r-bsgenome-mmusculus-ucsc-mm9
13231 r-bsgenome-mmusculus-ucsc-mm10
13238 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
13239 (synopsis "Driver discovery tool for cancer whole genomes")
13241 "This package provides a method for finding an enrichment of cancer
13242 simple somatic mutations (SNVs and Indels) in functional elements across the
13243 human genome. ActiveDriverWGS detects coding and noncoding driver elements
13244 using whole genome sequencing data.")
13245 (license license:gpl3)))
13247 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13249 (define-public r-activepathways
13251 (name "r-activepathways")
13256 (uri (cran-uri "ActivePathways" version))
13259 "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
13261 `((upstream-name . "ActivePathways")))
13262 (build-system r-build-system)
13264 (list r-data-table r-ggplot2))
13267 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
13268 (synopsis "Multivariate pathway enrichment analysis")
13270 "This package represents an integrative method of analyzing multi omics
13271 data that conducts enrichment analysis of annotated gene sets. ActivePathways
13272 uses a statistical data fusion approach, rationalizes contributing evidence
13273 and highlights associated genes, improving systems-level understanding of
13274 cellular organization in health and disease.")
13275 (license license:gpl3)))
13277 (define-public r-bgmix
13284 (uri (bioconductor-uri "BGmix" version))
13287 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
13288 (properties `((upstream-name . "BGmix")))
13289 (build-system r-build-system)
13291 (list r-kernsmooth))
13292 (home-page "https://bioconductor.org/packages/BGmix/")
13293 (synopsis "Bayesian models for differential gene expression")
13295 "This package provides fully Bayesian mixture models for differential
13297 (license license:gpl2)))
13299 (define-public r-bgx
13306 (uri (bioconductor-uri "bgx" version))
13309 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
13310 (properties `((upstream-name . "bgx")))
13311 (build-system r-build-system)
13315 '(modify-phases %standard-phases
13316 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
13318 (substitute* "configure.ac"
13319 (("AX_GCC_ARCHFLAG.*") ""))
13320 (delete-file "configure")
13321 (invoke "autoreconf" "-vif"))))))
13325 (list r-affy r-biobase r-gcrma r-rcpp))
13327 (list autoconf automake))
13328 (home-page "https://bioconductor.org/packages/bgx/")
13329 (synopsis "Bayesian gene expression")
13331 "This package provides tools for Bayesian integrated analysis of
13332 Affymetrix GeneChips.")
13333 (license license:gpl2)))
13335 (define-public r-bhc
13342 (uri (bioconductor-uri "BHC" version))
13345 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
13346 (properties `((upstream-name . "BHC")))
13347 (build-system r-build-system)
13348 (home-page "https://bioconductor.org/packages/BHC/")
13349 (synopsis "Bayesian hierarchical clustering")
13351 "The method implemented in this package performs bottom-up hierarchical
13352 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
13353 in the data and Bayesian model selection to decide at each step which clusters
13354 to merge. This avoids several limitations of traditional methods, for example
13355 how many clusters there should be and how to choose a principled distance
13356 metric. This implementation accepts multinomial (i.e. discrete, with 2+
13357 categories) or time-series data. This version also includes a randomised
13358 algorithm which is more efficient for larger data sets.")
13359 (license license:gpl3)))
13361 (define-public r-bicare
13368 (uri (bioconductor-uri "BicARE" version))
13371 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
13372 (properties `((upstream-name . "BicARE")))
13373 (build-system r-build-system)
13375 (list r-biobase r-gseabase r-multtest))
13376 (home-page "http://bioinfo.curie.fr")
13377 (synopsis "Biclustering analysis and results exploration")
13379 "This is a package for biclustering analysis and exploration of
13381 (license license:gpl2)))
13383 (define-public r-bifet
13390 (uri (bioconductor-uri "BiFET" version))
13393 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
13394 (properties `((upstream-name . "BiFET")))
13395 (build-system r-build-system)
13397 (list r-genomicranges r-poibin))
13400 (home-page "https://bioconductor.org/packages/BiFET")
13401 (synopsis "Bias-free footprint enrichment test")
13403 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
13404 over-represented in target regions compared to background regions after
13405 correcting for the bias arising from the imbalance in read counts and GC
13406 contents between the target and background regions. For a given TF k, BiFET
13407 tests the null hypothesis that the target regions have the same probability of
13408 having footprints for the TF k as the background regions while correcting for
13409 the read count and GC content bias.")
13410 (license license:gpl3)))
13412 (define-public r-rsbml
13419 (uri (bioconductor-uri "rsbml" version))
13422 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
13423 (properties `((upstream-name . "rsbml")))
13424 (build-system r-build-system)
13428 (list r-biocgenerics r-graph))
13431 (home-page "http://www.sbml.org")
13432 (synopsis "R support for SBML")
13434 "This package provides an R interface to libsbml for SBML parsing,
13435 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
13436 (license license:artistic2.0)))
13438 (define-public r-hypergraph
13440 (name "r-hypergraph")
13445 (uri (bioconductor-uri "hypergraph" version))
13448 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
13449 (properties `((upstream-name . "hypergraph")))
13450 (build-system r-build-system)
13453 (home-page "https://bioconductor.org/packages/hypergraph")
13454 (synopsis "Hypergraph data structures")
13456 "This package implements some simple capabilities for representing and
13457 manipulating hypergraphs.")
13458 (license license:artistic2.0)))
13460 (define-public r-hyperdraw
13462 (name "r-hyperdraw")
13467 (uri (bioconductor-uri "hyperdraw" version))
13470 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
13471 (properties `((upstream-name . "hyperdraw")))
13472 (build-system r-build-system)
13473 (inputs (list graphviz))
13475 (list r-graph r-hypergraph r-rgraphviz))
13476 (home-page "https://bioconductor.org/packages/hyperdraw")
13477 (synopsis "Visualizing hypergraphs")
13479 "This package provides functions for visualizing hypergraphs.")
13480 (license license:gpl2+)))
13482 (define-public r-biggr
13489 (uri (bioconductor-uri "BiGGR" version))
13492 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
13493 (properties `((upstream-name . "BiGGR")))
13494 (build-system r-build-system)
13502 (home-page "https://bioconductor.org/packages/BiGGR/")
13503 (synopsis "Constraint based modeling using metabolic reconstruction databases")
13505 "This package provides an interface to simulate metabolic reconstruction
13506 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
13507 reconstruction databases. The package facilitates @dfn{flux balance
13508 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
13509 networks and estimated fluxes can be visualized with hypergraphs.")
13510 (license license:gpl3+)))
13512 (define-public r-bigmemoryextras
13514 (name "r-bigmemoryextras")
13519 (uri (bioconductor-uri "bigmemoryExtras" version))
13522 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
13524 `((upstream-name . "bigmemoryExtras")))
13525 (build-system r-build-system)
13527 (list r-bigmemory))
13530 (home-page "https://github.com/phaverty/bigmemoryExtras")
13531 (synopsis "Extension of the bigmemory package")
13533 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
13534 safety and convenience features to the @code{filebacked.big.matrix} class from
13535 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
13536 monitoring and gracefully restoring the connection to on-disk data and it also
13537 protects against accidental data modification with a file-system-based
13538 permissions system. Utilities are provided for using @code{BigMatrix}-derived
13539 classes as @code{assayData} matrices within the @code{Biobase} package's
13540 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
13541 related to attaching to, and indexing into, file-backed matrices with
13542 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
13543 a file-backed matrix with factor properties.")
13544 (license license:artistic2.0)))
13546 (define-public r-bigpint
13553 (uri (bioconductor-uri "bigPint" version))
13556 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
13557 (properties `((upstream-name . "bigPint")))
13558 (build-system r-build-system)
13560 (list r-delayedarray
13576 r-summarizedexperiment
13580 (home-page "https://github.com/lindsayrutter/bigPint")
13581 (synopsis "Big multivariate data plotted interactively")
13583 "This package provides methods for visualizing large multivariate
13584 datasets using static and interactive scatterplot matrices, parallel
13585 coordinate plots, volcano plots, and litre plots. It includes examples for
13586 visualizing RNA-sequencing datasets and differentially expressed genes.")
13587 (license license:gpl3)))
13589 (define-public r-chemminer
13591 (name "r-chemminer")
13596 (uri (bioconductor-uri "ChemmineR" version))
13599 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
13600 (properties `((upstream-name . "ChemmineR")))
13601 (build-system r-build-system)
13620 (home-page "https://github.com/girke-lab/ChemmineR")
13621 (synopsis "Cheminformatics toolkit for R")
13623 "ChemmineR is a cheminformatics package for analyzing drug-like small
13624 molecule data in R. It contains functions for efficient processing of large
13625 numbers of molecules, physicochemical/structural property predictions,
13626 structural similarity searching, classification and clustering of compound
13627 libraries with a wide spectrum of algorithms. In addition, it offers
13628 visualization functions for compound clustering results and chemical
13630 (license license:artistic2.0)))
13632 (define-public r-fmcsr
13639 (uri (bioconductor-uri "fmcsR" version))
13641 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
13642 (properties `((upstream-name . "fmcsR")))
13643 (build-system r-build-system)
13645 (list r-biocgenerics r-chemminer r-runit))
13646 (native-inputs (list r-knitr))
13647 (home-page "https://github.com/girke-lab/fmcsR")
13648 (synopsis "Mismatch tolerant maximum common substructure searching")
13650 "The fmcsR package introduces an efficient @dfn{maximum common
13651 substructure} (MCS) algorithms combined with a novel matching strategy that
13652 allows for atom and/or bond mismatches in the substructures shared among two
13653 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
13654 strict MCSs, resulting in the identification of more common features in their
13655 source structures, as well as a higher sensitivity in finding compounds with
13656 weak structural similarities. The fmcsR package provides several utilities to
13657 use the FMCS algorithm for pairwise compound comparisons, structure similarity
13658 searching and clustering.")
13659 (license license:artistic2.0)))
13661 (define-public r-bioassayr
13663 (name "r-bioassayr")
13668 (uri (bioconductor-uri "bioassayR" version))
13671 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
13672 (properties `((upstream-name . "bioassayR")))
13673 (build-system r-build-system)
13675 (list r-biocgenerics
13684 (home-page "https://github.com/girke-lab/bioassayR")
13685 (synopsis "Cross-target analysis of small molecule bioactivity")
13687 "bioassayR is a computational tool that enables simultaneous analysis of
13688 thousands of bioassay experiments performed over a diverse set of compounds
13689 and biological targets. Unique features include support for large-scale
13690 cross-target analyses of both public and custom bioassays, generation of
13691 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
13692 preloaded database that provides access to a substantial portion of publicly
13693 available bioactivity data.")
13694 (license license:artistic2.0)))
13696 (define-public r-biobroom
13698 (name "r-biobroom")
13703 (uri (bioconductor-uri "biobroom" version))
13706 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
13707 (properties `((upstream-name . "biobroom")))
13708 (build-system r-build-system)
13710 (list r-biobase r-broom r-dplyr r-tidyr))
13713 (home-page "https://github.com/StoreyLab/biobroom")
13714 (synopsis "Turn Bioconductor objects into tidy data frames")
13716 "This package contains methods for converting standard objects
13717 constructed by bioinformatics packages, especially those in Bioconductor, and
13718 converting them to @code{tidy} data. It thus serves as a complement to the
13719 @code{broom} package, and follows the same tidy, augment, glance division of
13720 tidying methods. Tidying data makes it easy to recombine, reshape and
13721 visualize bioinformatics analyses.")
13722 ;; Any version of the LGPL.
13723 (license license:lgpl3+)))
13725 (define-public r-graphite
13727 (name "r-graphite")
13732 (uri (bioconductor-uri "graphite" version))
13735 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
13736 (properties `((upstream-name . "graphite")))
13737 (build-system r-build-system)
13739 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
13740 (home-page "https://bioconductor.org/packages/graphite/")
13741 (synopsis "Networks from pathway databases")
13743 "Graphite provides networks derived from eight public pathway databases,
13744 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
13746 (license license:agpl3+)))
13748 (define-public r-reactomepa
13750 (name "r-reactomepa")
13755 (uri (bioconductor-uri "ReactomePA" version))
13758 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
13759 (properties `((upstream-name . "ReactomePA")))
13760 (build-system r-build-system)
13762 (list r-annotationdbi
13772 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
13773 (synopsis "Reactome pathway analysis")
13775 "This package provides functions for pathway analysis based on the
13776 REACTOME pathway database. It implements enrichment analysis, gene set
13777 enrichment analysis and several functions for visualization.")
13778 (license license:gpl2)))
13780 (define-public r-ebarrays
13782 (name "r-ebarrays")
13787 (uri (bioconductor-uri "EBarrays" version))
13790 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
13791 (properties `((upstream-name . "EBarrays")))
13792 (build-system r-build-system)
13794 (list r-biobase r-cluster r-lattice))
13795 (home-page "https://bioconductor.org/packages/EBarrays/")
13796 (synopsis "Gene clustering and differential expression identification")
13798 "EBarrays provides tools for the analysis of replicated/unreplicated
13800 (license license:gpl2+)))
13802 (define-public r-bioccasestudies
13804 (name "r-bioccasestudies")
13809 (uri (bioconductor-uri "BiocCaseStudies" version))
13812 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
13814 `((upstream-name . "BiocCaseStudies")))
13815 (build-system r-build-system)
13816 (propagated-inputs (list r-biobase))
13817 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
13818 (synopsis "Support for the case studies monograph")
13820 "This package provides software and data to support the case studies
13822 (license license:artistic2.0)))
13824 (define-public r-bioccheck
13826 (name "r-bioccheck")
13830 (uri (bioconductor-uri "BiocCheck" version))
13833 "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw"))))
13835 `((upstream-name . "BiocCheck")))
13836 (build-system r-build-system)
13847 (home-page "https://bioconductor.org/packages/BiocCheck")
13848 (synopsis "Executes Bioconductor-specific package checks")
13849 (description "This package contains tools to perform additional quality
13850 checks on R packages that are to be submitted to the Bioconductor repository.")
13851 (license license:artistic2.0)))
13853 (define-public r-biocgraph
13855 (name "r-biocgraph")
13860 (uri (bioconductor-uri "biocGraph" version))
13863 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
13864 (properties `((upstream-name . "biocGraph")))
13865 (build-system r-build-system)
13867 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
13868 (home-page "https://bioconductor.org/packages/biocGraph/")
13869 (synopsis "Graph examples and use cases in Bioinformatics")
13871 "This package provides examples and code that make use of the
13872 different graph related packages produced by Bioconductor.")
13873 (license license:artistic2.0)))
13875 (define-public r-biocstyle
13877 (name "r-biocstyle")
13881 (uri (bioconductor-uri "BiocStyle" version))
13884 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
13886 `((upstream-name . "BiocStyle")))
13887 (build-system r-build-system)
13889 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
13892 (home-page "https://bioconductor.org/packages/BiocStyle")
13893 (synopsis "Bioconductor formatting styles")
13894 (description "This package provides standard formatting styles for
13895 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
13897 (license license:artistic2.0)))
13899 (define-public r-biocviews
13901 (name "r-biocviews")
13905 (uri (bioconductor-uri "biocViews" version))
13908 "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38"))))
13910 `((upstream-name . "biocViews")))
13911 (build-system r-build-system)
13920 (home-page "https://bioconductor.org/packages/biocViews")
13921 (synopsis "Bioconductor package categorization helper")
13922 (description "The purpose of biocViews is to create HTML pages that
13923 categorize packages in a Bioconductor package repository according to keywords,
13924 also known as views, in a controlled vocabulary.")
13925 (license license:artistic2.0)))
13927 (define-public r-experimenthub
13929 (name "r-experimenthub")
13934 (uri (bioconductor-uri "ExperimentHub" version))
13937 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
13938 (properties `((upstream-name . "ExperimentHub")))
13939 (build-system r-build-system)
13941 (list r-annotationhub
13950 (home-page "https://bioconductor.org/packages/ExperimentHub/")
13951 (synopsis "Client to access ExperimentHub resources")
13953 "This package provides a client for the Bioconductor ExperimentHub web
13954 resource. ExperimentHub provides a central location where curated data from
13955 experiments, publications or training courses can be accessed. Each resource
13956 has associated metadata, tags and date of modification. The client creates
13957 and manages a local cache of files retrieved enabling quick and reproducible
13959 (license license:artistic2.0)))
13961 (define-public r-grohmm
13968 (uri (bioconductor-uri "groHMM" version))
13971 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
13972 (properties `((upstream-name . "groHMM")))
13973 (build-system r-build-system)
13975 (list r-genomeinfodb
13976 r-genomicalignments
13982 (home-page "https://github.com/Kraus-Lab/groHMM")
13983 (synopsis "GRO-seq analysis pipeline")
13985 "This package provides a pipeline for the analysis of GRO-seq data.")
13986 (license license:gpl3+)))
13988 (define-public r-multiassayexperiment
13990 (name "r-multiassayexperiment")
13995 (uri (bioconductor-uri "MultiAssayExperiment" version))
13998 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
14000 `((upstream-name . "MultiAssayExperiment")))
14001 (build-system r-build-system)
14008 r-summarizedexperiment
14012 (home-page "https://waldronlab.io/MultiAssayExperiment/")
14013 (synopsis "Integration of multi-omics experiments in Bioconductor")
14015 "MultiAssayExperiment harmonizes data management of multiple assays
14016 performed on an overlapping set of specimens. It provides a familiar
14017 Bioconductor user experience by extending concepts from
14018 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
14019 classes for individual assays, and allowing subsetting by genomic ranges or
14021 (license license:artistic2.0)))
14023 (define-public r-bioconcotk
14025 (name "r-bioconcotk")
14030 (uri (bioconductor-uri "BiocOncoTK" version))
14033 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
14034 (properties `((upstream-name . "BiocOncoTK")))
14035 (build-system r-build-system)
14058 r-summarizedexperiment))
14061 (home-page "https://bioconductor.org/packages/BiocOncoTK")
14062 (synopsis "Bioconductor components for general cancer genomics")
14064 "The purpose of this package is to provide a central interface to various
14065 tools for genome-scale analysis of cancer studies.")
14066 (license license:artistic2.0)))
14068 (define-public r-biocor
14075 (uri (bioconductor-uri "BioCor" version))
14078 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
14079 (properties `((upstream-name . "BioCor")))
14080 (build-system r-build-system)
14082 (list r-biocparallel r-gseabase r-matrix))
14085 (home-page "https://llrs.github.io/BioCor/")
14086 (synopsis "Functional similarities")
14088 "This package provides tools to calculate functional similarities based
14089 on the pathways described on KEGG and REACTOME or in gene sets. These
14090 similarities can be calculated for pathways or gene sets, genes, or clusters
14091 and combined with other similarities. They can be used to improve networks,
14092 gene selection, testing relationships, and so on.")
14093 (license license:expat)))
14095 (define-public r-biocpkgtools
14097 (name "r-biocpkgtools")
14102 (uri (bioconductor-uri "BiocPkgTools" version))
14105 "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd"))))
14106 (properties `((upstream-name . "BiocPkgTools")))
14107 (build-system r-build-system)
14109 (list r-biocfilecache
14133 (home-page "https://github.com/seandavi/BiocPkgTools")
14134 (synopsis "Collection of tools for learning about Bioconductor packages")
14136 "Bioconductor has a rich ecosystem of metadata around packages, usage,
14137 and build status. This package is a simple collection of functions to access
14138 that metadata from R. The goal is to expose metadata for data mining and
14139 value-added functionality such as package searching, text mining, and
14140 analytics on packages.")
14141 (license license:expat)))
14143 (define-public r-biocset
14150 (uri (bioconductor-uri "BiocSet" version))
14153 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
14154 (properties `((upstream-name . "BiocSet")))
14155 (build-system r-build-system)
14157 (list r-annotationdbi
14170 "https://bioconductor.org/packages/BiocSet")
14172 "Representing Different Biological Sets")
14174 "BiocSet displays different biological sets in a triple tibble format.
14175 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
14176 The user has the ability to activate one of these three tibbles to perform
14177 common functions from the @code{dplyr} package. Mapping functionality and
14178 accessing web references for elements/sets are also available in BiocSet.")
14179 (license license:artistic2.0)))
14181 (define-public r-biocworkflowtools
14183 (name "r-biocworkflowtools")
14188 (uri (bioconductor-uri "BiocWorkflowTools" version))
14191 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
14193 `((upstream-name . "BiocWorkflowTools")))
14194 (build-system r-build-system)
14207 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
14208 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
14210 "This package provides functions to ease the transition between
14211 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
14212 (license license:expat)))
14214 (define-public r-biodist
14221 (uri (bioconductor-uri "bioDist" version))
14224 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
14225 (properties `((upstream-name . "bioDist")))
14226 (build-system r-build-system)
14228 (list r-biobase r-kernsmooth))
14229 (home-page "https://bioconductor.org/packages/bioDist/")
14230 (synopsis "Different distance measures")
14232 "This package provides a collection of software tools for calculating
14233 distance measures.")
14234 (license license:artistic2.0)))
14236 (define-public r-pcatools
14238 (name "r-pcatools")
14243 (uri (bioconductor-uri "PCAtools" version))
14246 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
14247 (properties `((upstream-name . "PCAtools")))
14248 (build-system r-build-system)
14256 r-delayedmatrixstats
14264 (native-inputs (list r-knitr))
14265 (home-page "https://github.com/kevinblighe/PCAtools")
14266 (synopsis "PCAtools: everything Principal Components Analysis")
14268 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
14269 structure of the data without the need to build any model to represent it.
14270 This \"summary\" of the data is arrived at through a process of reduction that
14271 can transform the large number of variables into a lesser number that are
14272 uncorrelated (i.e. the 'principal components'), while at the same time being
14273 capable of easy interpretation on the original data. PCAtools provides
14274 functions for data exploration via PCA, and allows the user to generate
14275 publication-ready figures. PCA is performed via @code{BiocSingular}; users
14276 can also identify an optimal number of principal components via different
14277 metrics, such as the elbow method and Horn's parallel analysis, which has
14278 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
14279 dimensional mass cytometry data.")
14280 (license license:gpl3)))
14282 (define-public r-rgreat
14289 (uri (bioconductor-uri "rGREAT" version))
14292 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
14293 (properties `((upstream-name . "rGREAT")))
14294 (build-system r-build-system)
14296 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
14297 (native-inputs (list r-knitr))
14298 (home-page "https://github.com/jokergoo/rGREAT")
14299 (synopsis "Client for GREAT analysis")
14301 "This package makes GREAT (Genomic Regions Enrichment of Annotations
14302 Tool) analysis automatic by constructing a HTTP POST request according to
14303 user's input and automatically retrieving results from GREAT web server.")
14304 (license license:expat)))
14306 (define-public r-m3c
14313 (uri (bioconductor-uri "M3C" version))
14316 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
14317 (properties `((upstream-name . "M3C")))
14318 (build-system r-build-system)
14330 (native-inputs (list r-knitr))
14331 (home-page "https://bioconductor.org/packages/M3C")
14332 (synopsis "Monte Carlo reference-based consensus clustering")
14334 "M3C is a consensus clustering algorithm that uses a Monte Carlo
14335 simulation to eliminate overestimation of @code{K} and can reject the null
14336 hypothesis @code{K=1}.")
14337 (license license:agpl3+)))
14339 (define-public r-icens
14346 (uri (bioconductor-uri "Icens" version))
14349 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
14350 (properties `((upstream-name . "Icens")))
14351 (build-system r-build-system)
14354 (home-page "https://bioconductor.org/packages/Icens")
14355 (synopsis "NPMLE for censored and truncated data")
14357 "This package provides many functions for computing the
14358 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
14360 (license license:artistic2.0)))
14362 ;; This is a CRAN package but it depends on r-icens, which is published on
14364 (define-public r-interval
14366 (name "r-interval")
14367 (version "1.1-0.8")
14371 (uri (cran-uri "interval" version))
14374 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
14375 (properties `((upstream-name . "interval")))
14376 (build-system r-build-system)
14378 (list r-icens r-mlecens r-perm r-survival))
14379 (home-page "https://cran.r-project.org/web/packages/interval/")
14380 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
14382 "This package provides functions to fit nonparametric survival curves,
14383 plot them, and perform logrank or Wilcoxon type tests.")
14384 (license license:gpl2+)))
14386 ;; This is a CRAN package, but it depends on r-interval, which depends on a
14387 ;; Bioconductor package.
14388 (define-public r-fhtest
14395 (uri (cran-uri "FHtest" version))
14398 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
14399 (properties `((upstream-name . "FHtest")))
14400 (build-system r-build-system)
14402 (list r-interval r-kmsurv r-mass r-perm r-survival))
14403 (home-page "https://cran.r-project.org/web/packages/FHtest/")
14404 (synopsis "Tests for survival data based on the Fleming-Harrington class")
14406 "This package provides functions to compare two or more survival curves
14410 @item The Fleming-Harrington test for right-censored data based on
14411 permutations and on counting processes.
14412 @item An extension of the Fleming-Harrington test for interval-censored data
14413 based on a permutation distribution and on a score vector distribution.
14416 (license license:gpl2+)))
14418 (define-public r-fourcseq
14420 (name "r-fourcseq")
14425 (uri (bioconductor-uri "FourCSeq" version))
14427 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
14428 (properties `((upstream-name . "FourCSeq")))
14429 (build-system r-build-system)
14435 r-genomicalignments
14445 r-summarizedexperiment))
14449 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
14450 (synopsis "Analysis of multiplexed 4C sequencing data")
14452 "This package is an R package dedicated to the analysis of (multiplexed)
14453 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
14454 interactions between DNA elements and identify differential interactions
14455 between conditions. The statistical analysis in R starts with individual bam
14456 files for each sample as inputs. To obtain these files, the package contains
14457 a Python script to demultiplex libraries and trim off primer sequences. With
14458 a standard alignment software the required bam files can be then be
14460 (license license:gpl3+)))
14462 (define-public r-preprocesscore
14464 (name "r-preprocesscore")
14469 (uri (bioconductor-uri "preprocessCore" version))
14472 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
14474 `((upstream-name . "preprocessCore")))
14475 (build-system r-build-system)
14476 (home-page "https://github.com/bmbolstad/preprocessCore")
14477 (synopsis "Collection of pre-processing functions")
14479 "This package provides a library of core pre-processing and normalization
14481 (license license:lgpl2.0+)))
14483 (define-public r-s4vectors
14485 (name "r-s4vectors")
14489 (uri (bioconductor-uri "S4Vectors" version))
14492 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
14494 `((upstream-name . "S4Vectors")))
14495 (build-system r-build-system)
14497 (list r-biocgenerics))
14498 (home-page "https://bioconductor.org/packages/S4Vectors")
14499 (synopsis "S4 implementation of vectors and lists")
14501 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
14502 classes and a set of generic functions that extend the semantic of ordinary
14503 vectors and lists in R. Package developers can easily implement vector-like
14504 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
14505 In addition, a few low-level concrete subclasses of general interest (e.g.
14506 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
14507 S4Vectors package itself.")
14508 (license license:artistic2.0)))
14510 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
14511 ;; Bioconductor package.
14512 (define-public r-wgcna
14519 (uri (cran-uri "WGCNA" version))
14522 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
14523 (properties `((upstream-name . "WGCNA")))
14524 (build-system r-build-system)
14526 (list r-annotationdbi
14539 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14540 (synopsis "Weighted correlation network analysis")
14542 "This package provides functions necessary to perform Weighted
14543 Correlation Network Analysis on high-dimensional data. It includes functions
14544 for rudimentary data cleaning, construction and summarization of correlation
14545 networks, module identification and functions for relating both variables and
14546 modules to sample traits. It also includes a number of utility functions for
14547 data manipulation and visualization.")
14548 (license license:gpl2+)))
14550 (define-public r-rgraphviz
14552 (name "r-rgraphviz")
14557 (uri (bioconductor-uri "Rgraphviz" version))
14560 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
14561 (properties `((upstream-name . "Rgraphviz")))
14562 (build-system r-build-system)
14565 (modify-phases %standard-phases
14566 (add-after 'unpack 'make-reproducible
14568 ;; The replacement value is taken from src/graphviz/builddate.h
14569 (substitute* "src/graphviz/configure"
14570 (("VERSION_DATE=.*")
14571 "VERSION_DATE=20200427.2341\n"))
14573 ;; FIXME: Rgraphviz bundles the sources of an older variant of
14574 ;; graphviz. It does not build with the latest version of graphviz, so
14575 ;; we do not add graphviz to the inputs.
14576 (inputs (list zlib))
14581 (home-page "https://bioconductor.org/packages/Rgraphviz")
14582 (synopsis "Plotting capabilities for R graph objects")
14584 "This package interfaces R with the graphviz library for plotting R graph
14585 objects from the @code{graph} package.")
14586 (license license:epl1.0)))
14588 (define-public r-fithic
14594 (uri (bioconductor-uri "FitHiC" version))
14597 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
14598 (properties `((upstream-name . "FitHiC")))
14599 (build-system r-build-system)
14601 (list r-data-table r-fdrtool r-rcpp))
14604 (home-page "https://bioconductor.org/packages/FitHiC")
14605 (synopsis "Confidence estimation for intra-chromosomal contact maps")
14607 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
14608 intra-chromosomal contact maps produced by genome-wide genome architecture
14609 assays such as Hi-C.")
14610 (license license:gpl2+)))
14612 (define-public r-hitc
14618 (uri (bioconductor-uri "HiTC" version))
14621 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
14622 (properties `((upstream-name . "HiTC")))
14623 (build-system r-build-system)
14632 (home-page "https://bioconductor.org/packages/HiTC")
14633 (synopsis "High throughput chromosome conformation capture analysis")
14635 "The HiTC package was developed to explore high-throughput \"C\" data
14636 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
14637 quality controls, normalization, visualization, and further analysis are also
14639 (license license:artistic2.0)))
14641 (define-public r-hdf5array
14643 (name "r-hdf5array")
14648 (uri (bioconductor-uri "HDF5Array" version))
14651 "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9"))))
14652 (properties `((upstream-name . "HDF5Array")))
14653 (build-system r-build-system)
14657 (list r-biocgenerics
14665 (home-page "https://bioconductor.org/packages/HDF5Array")
14666 (synopsis "HDF5 back end for DelayedArray objects")
14667 (description "This package provides an array-like container for convenient
14668 access and manipulation of HDF5 datasets. It supports delayed operations and
14669 block processing.")
14670 (license license:artistic2.0)))
14672 (define-public r-rhdf5lib
14674 (name "r-rhdf5lib")
14679 (uri (bioconductor-uri "Rhdf5lib" version))
14682 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
14683 (modules '((guix build utils)))
14686 ;; Delete bundled binaries
14687 (delete-file-recursively "src/wininclude/")
14688 (delete-file-recursively "src/winlib/")
14689 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
14690 (properties `((upstream-name . "Rhdf5lib")))
14691 (build-system r-build-system)
14694 (modify-phases %standard-phases
14695 (add-after 'unpack 'do-not-use-bundled-hdf5
14696 (lambda* (#:key inputs #:allow-other-keys)
14697 (for-each delete-file '("configure" "configure.ac"))
14698 (substitute* "R/zzz.R"
14699 (("return\\(links\\)") "return(\" -lz\")"))
14700 (with-directory-excursion "src"
14701 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
14702 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
14704 ;; Remove timestamp and host system information to make
14705 ;; the build reproducible.
14706 (substitute* "hdf5/src/libhdf5.settings.in"
14707 (("Configured on: @CONFIG_DATE@")
14708 "Configured on: Guix")
14709 (("Uname information:.*")
14710 "Uname information: Linux\n")
14711 ;; Remove unnecessary store reference.
14713 "C Compiler: GCC\n"))
14714 (rename-file "hdf5/src/libhdf5.settings.in"
14715 "hdf5/src/libhdf5.settings")
14716 (rename-file "Makevars.in" "Makevars")
14717 (substitute* "Makevars"
14718 (("@BUILD_HDF5@") "")
14719 (("@COPY_SZIP@") "")
14720 (("@ZLIB_LIB@") "-lz")
14721 (("@ZLIB_INCLUDE@") "")
14722 (("HDF5_CXX_LIB=.*")
14723 (string-append "HDF5_CXX_LIB="
14724 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
14726 (string-append "HDF5_LIB="
14727 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
14728 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
14729 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
14730 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
14731 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
14732 (("HDF5_HL_LIB=.*")
14733 (string-append "HDF5_HL_LIB="
14734 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
14735 (("HDF5_HL_CXX_LIB=.*")
14736 (string-append "HDF5_HL_CXX_LIB="
14737 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
14738 ;; szip is non-free software
14739 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
14740 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
14742 (list hdf5-1.10 zlib))
14744 `(("hdf5-source" ,(package-source hdf5-1.10))
14745 ("r-knitr" ,r-knitr)))
14746 (home-page "https://bioconductor.org/packages/Rhdf5lib")
14747 (synopsis "HDF5 library as an R package")
14748 (description "This package provides C and C++ HDF5 libraries for use in R
14750 (license license:artistic2.0)))
14752 (define-public r-beachmat
14754 (name "r-beachmat")
14759 (uri (bioconductor-uri "beachmat" version))
14762 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
14763 (build-system r-build-system)
14765 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
14768 (home-page "https://bioconductor.org/packages/beachmat")
14769 (synopsis "Compiling Bioconductor to handle each matrix type")
14770 (description "This package provides a consistent C++ class interface for a
14771 variety of commonly used matrix types, including sparse and HDF5-backed
14773 (license license:gpl3)))
14775 ;; This package includes files that have been taken from kentutils. Some
14776 ;; parts of kentutils are not released under a free license, but this package
14777 ;; only uses files that are also found in the free parts of kentutils.
14778 (define-public r-cner
14785 (uri (bioconductor-uri "CNEr" version))
14787 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
14788 (properties `((upstream-name . "CNEr")))
14789 (build-system r-build-system)
14790 (inputs (list zlib))
14797 r-genomicalignments
14813 (home-page "https://github.com/ge11232002/CNEr")
14814 (synopsis "CNE Detection and Visualization")
14816 "This package provides tools for large-scale identification and
14817 advanced visualization of sets of conserved noncoding elements.")
14818 ;; For all files in src/ucsc "license is hereby granted for all use -
14819 ;; public, private or commercial"; this includes those files that don't
14820 ;; have a license header, because they are included in the free parts of
14821 ;; the kentutils package.
14822 (license (list license:gpl2
14823 (license:non-copyleft
14824 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
14826 (define-public r-tfbstools
14828 (name "r-tfbstools")
14833 (uri (bioconductor-uri "TFBSTools" version))
14836 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
14837 (properties `((upstream-name . "TFBSTools")))
14838 (build-system r-build-system)
14848 r-dirichletmultinomial
14860 (native-inputs (list r-knitr))
14861 (home-page "https://github.com/ge11232002/TFBSTools")
14862 (synopsis "Transcription factor binding site (TFBS) analysis")
14864 "TFBSTools is a package for the analysis and manipulation of
14865 transcription factor binding sites. It includes matrices conversion
14866 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
14867 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
14868 scan putative TFBS from sequence/alignment, query JASPAR database and
14869 provides a wrapper of de novo motif discovery software.")
14870 (license license:gpl2)))
14872 (define-public r-maftools
14874 (name "r-maftools")
14879 (uri (bioconductor-uri "maftools" version))
14881 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
14882 (properties `((upstream-name . "maftools")))
14883 (build-system r-build-system)
14891 (native-inputs (list r-knitr))
14892 (home-page "https://github.com/PoisonAlien/maftools")
14893 (synopsis "Summarize, analyze and visualize MAF files")
14895 "Analyze and visualize Mutation Annotation Format (MAF) files from large
14896 scale sequencing studies. This package provides various functions to perform
14897 most commonly used analyses in cancer genomics and to create feature rich
14898 customizable visualzations with minimal effort.")
14899 (license license:expat)))
14901 (define-public r-motifmatchr
14903 (name "r-motifmatchr")
14908 (uri (bioconductor-uri "motifmatchr" version))
14911 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
14912 (properties `((upstream-name . "motifmatchr")))
14913 (build-system r-build-system)
14925 r-summarizedexperiment
14927 (native-inputs (list r-knitr))
14928 (home-page "https://bioconductor.org/packages/motifmatchr")
14929 (synopsis "Fast motif matching in R")
14931 "Quickly find motif matches for many motifs and many sequences.
14932 This package wraps C++ code from the MOODS motif calling library.")
14933 (license license:gpl3)))
14935 (define-public r-chromvar
14937 (name "r-chromvar")
14942 (uri (bioconductor-uri "chromVAR" version))
14944 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
14945 (properties `((upstream-name . "chromVAR")))
14946 (build-system r-build-system)
14948 (list r-biocgenerics
14968 r-summarizedexperiment
14970 (native-inputs (list r-knitr))
14971 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
14972 (synopsis "Determine chromatin variation across regions")
14974 "This package @code{r-chromvar} determines variation in chromatin
14975 accessibility across sets of annotations or peaks. @code{r-chromvar} is
14976 designed primarily for single-cell or sparse chromatin accessibility data like
14977 single cell assay for transposase-accessible chromatin using
14978 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
14979 sequence (@code{DNAse-seq}) experiments.")
14980 (license license:expat)))
14982 (define-public r-singlecellexperiment
14984 (name "r-singlecellexperiment")
14989 (uri (bioconductor-uri "SingleCellExperiment" version))
14992 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
14994 `((upstream-name . "SingleCellExperiment")))
14995 (build-system r-build-system)
14997 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
14998 r-summarizedexperiment))
15001 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
15002 (synopsis "S4 classes for single cell data")
15003 (description "This package defines an S4 class for storing data from
15004 single-cell experiments. This includes specialized methods to store and
15005 retrieve spike-in information, dimensionality reduction coordinates and size
15006 factors for each cell, along with the usual metadata for genes and
15008 (license license:gpl3)))
15010 (define-public r-singler
15017 (uri (bioconductor-uri "SingleR" version))
15019 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
15020 (properties `((upstream-name . "SingleR")))
15021 (build-system r-build-system)
15028 r-delayedmatrixstats
15032 r-summarizedexperiment))
15033 (native-inputs (list r-knitr))
15034 (home-page "https://github.com/LTLA/SingleR")
15035 (synopsis "Reference-based single-cell RNA-seq annotation")
15037 "This package performs unbiased cell type recognition from single-cell
15038 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
15039 cell types to infer the cell of origin of each single cell independently.")
15040 (license license:gpl3)))
15042 (define-public r-scuttle
15049 (uri (bioconductor-uri "scuttle" version))
15052 "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671"))))
15053 (properties `((upstream-name . "scuttle")))
15054 (build-system r-build-system)
15060 r-delayedmatrixstats
15065 r-singlecellexperiment
15066 r-summarizedexperiment))
15067 (native-inputs (list r-knitr))
15068 (home-page "https://bioconductor.org/packages/scuttle")
15069 (synopsis "Single-cell RNA-Seq analysis utilities")
15071 "This package provides basic utility functions for performing single-cell
15072 analyses, focusing on simple normalization, quality control and data
15073 transformations. It also provides some helper functions to assist development
15074 of other packages.")
15075 (license license:gpl3)))
15077 (define-public r-scater
15083 (uri (bioconductor-uri "scater" version))
15086 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
15087 (build-system r-build-system)
15095 r-delayedmatrixstats
15107 r-singlecellexperiment
15108 r-summarizedexperiment
15112 (home-page "https://github.com/davismcc/scater")
15113 (synopsis "Single-cell analysis toolkit for gene expression data in R")
15114 (description "This package provides a collection of tools for doing
15115 various analyses of single-cell RNA-seq gene expression data, with a focus on
15117 (license license:gpl2+)))
15119 (define-public r-scran
15126 (uri (bioconductor-uri "scran" version))
15129 "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni"))))
15130 (build-system r-build-system)
15139 r-delayedmatrixstats
15149 r-singlecellexperiment
15151 r-summarizedexperiment))
15154 (home-page "https://bioconductor.org/packages/scran")
15155 (synopsis "Methods for single-cell RNA-Seq data analysis")
15156 (description "This package implements a variety of low-level analyses of
15157 single-cell RNA-seq data. Methods are provided for normalization of
15158 cell-specific biases, assignment of cell cycle phase, and detection of highly
15159 variable and significantly correlated genes.")
15160 (license license:gpl3)))
15162 (define-public r-sparsematrixstats
15164 (name "r-sparsematrixstats")
15169 (uri (bioconductor-uri "sparseMatrixStats" version))
15172 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
15174 `((upstream-name . "sparseMatrixStats")))
15175 (build-system r-build-system)
15177 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
15178 (native-inputs (list r-knitr))
15179 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
15180 (synopsis "Summary statistics for rows and columns of sparse matrices")
15182 "This package provides high performance functions for row and column
15183 operations on sparse matrices. Currently, the optimizations are limited to
15184 data in the column sparse format.")
15185 (license license:expat)))
15187 (define-public r-delayedmatrixstats
15189 (name "r-delayedmatrixstats")
15194 (uri (bioconductor-uri "DelayedMatrixStats" version))
15197 "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv"))))
15199 `((upstream-name . "DelayedMatrixStats")))
15200 (build-system r-build-system)
15202 (list r-delayedarray
15208 r-sparsematrixstats))
15211 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
15212 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
15214 "This package provides a port of the @code{matrixStats} API for use with
15215 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
15216 contains high-performing functions operating on rows and columns of
15217 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
15218 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
15219 are optimized per data type and for subsetted calculations such that both
15220 memory usage and processing time is minimized.")
15221 (license license:expat)))
15223 (define-public r-mscoreutils
15225 (name "r-mscoreutils")
15230 (uri (bioconductor-uri "MsCoreUtils" version))
15233 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
15234 (properties `((upstream-name . "MsCoreUtils")))
15235 (build-system r-build-system)
15237 (list r-clue r-mass r-rcpp r-s4vectors))
15240 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
15241 (synopsis "Core utils for mass spectrometry data")
15243 "This package defines low-level functions for mass spectrometry data and
15244 is independent of any high-level data structures. These functions include
15245 mass spectra processing functions (noise estimation, smoothing, binning),
15246 quantitative aggregation functions (median polish, robust summarisation,
15247 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
15248 well as misc helper functions, that are used across high-level data structure
15249 within the R for Mass Spectrometry packages.")
15250 (license license:artistic2.0)))
15252 (define-public r-msfeatures
15254 (name "r-msfeatures")
15259 (uri (bioconductor-uri "MsFeatures" version))
15261 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
15262 (properties `((upstream-name . "MsFeatures")))
15263 (build-system r-build-system)
15265 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
15268 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
15269 (synopsis "Functionality for mass spectrometry features")
15271 "The MsFeature package defines functionality for Mass Spectrometry
15272 features. This includes functions to group (LC-MS) features based on some of
15273 their properties, such as retention time (coeluting features), or correlation
15274 of signals across samples. This package hence can be used to group features, and
15275 its results can be used as an input for the @code{QFeatures} package which
15276 allows aggregating abundance levels of features within each group. This
15277 package defines concepts and functions for base and common data types,
15278 implementations for more specific data types are expected to be implemented in
15279 the respective packages (such as e.g. @code{xcms}).")
15280 (license license:artistic2.0)))
15282 (define-public r-biocio
15289 (uri (bioconductor-uri "BiocIO" version))
15292 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
15293 (properties `((upstream-name . "BiocIO")))
15294 (build-system r-build-system)
15296 (list r-biocgenerics r-s4vectors))
15299 (home-page "https://bioconductor.org/packages/BiocIO")
15300 (synopsis "Standard input and output for Bioconductor packages")
15302 "This package implements `import()` and `export()` standard generics for
15303 importing and exporting biological data formats. `import()` supports
15304 whole-file as well as chunk-wise iterative import. The `import()` interface
15305 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
15306 row or element-like components of the file resource), `select()` (on
15307 column-like components of the file resource) and `collect()`. The `import()`
15308 interface optionally provides transparent access to remote (e.g. via https)
15309 as well as local access. Developers can register a file extension, e.g.,
15310 `.loom` for dispatch from character-based URIs to specific `import()` /
15311 `export()` methods based on classes representing file types, e.g.,
15313 (license license:artistic2.0)))
15315 (define-public r-msmseda
15322 (uri (bioconductor-uri "msmsEDA" version))
15325 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
15326 (properties `((upstream-name . "msmsEDA")))
15327 (build-system r-build-system)
15329 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
15331 "https://bioconductor.org/packages/msmsEDA")
15332 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
15334 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
15335 experiments, and visualize de influence of the involved factors.")
15336 (license license:gpl2)))
15338 (define-public r-msmstests
15340 (name "r-msmstests")
15345 (uri (bioconductor-uri "msmsTests" version))
15348 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
15349 (properties `((upstream-name . "msmsTests")))
15350 (build-system r-build-system)
15352 (list r-edger r-msmseda r-msnbase r-qvalue))
15354 "https://bioconductor.org/packages/msmsTests")
15355 (synopsis "Differential LC-MS/MS expression tests")
15357 "This package provides statistical tests for label-free LC-MS/MS data
15358 by spectral counts, to discover differentially expressed proteins between two
15359 biological conditions. Three tests are available: Poisson GLM regression,
15360 quasi-likelihood GLM regression, and the negative binomial of the edgeR
15361 package. The three models admit blocking factors to control for nuisance
15362 variables. To assure a good level of reproducibility a post-test filter is
15363 available, where we may set the minimum effect size considered biologicaly
15364 relevant, and the minimum expression of the most abundant condition.")
15365 (license license:gpl2)))
15367 (define-public r-catalyst
15369 (name "r-catalyst")
15374 (uri (bioconductor-uri "CATALYST" version))
15377 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
15378 (properties `((upstream-name . "CATALYST")))
15379 (build-system r-build-system)
15383 r-consensusclusterplus
15405 r-singlecellexperiment
15406 r-summarizedexperiment))
15409 (home-page "https://github.com/HelenaLC/CATALYST")
15410 (synopsis "Cytometry data analysis tools")
15412 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
15413 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
15414 isotopes rather than fluorescent tags as reporters to label antibodies,
15415 thereby substantially decreasing spectral overlap and allowing for examination
15416 of over 50 parameters at the single cell level. While spectral overlap is
15417 significantly less pronounced in CyTOF than flow cytometry, spillover due to
15418 detection sensitivity, isotopic impurities, and oxide formation can impede
15419 data interpretability. @code{CATALYST} was designed to provide a pipeline for
15420 preprocessing of cytometry data, including:
15423 @item normalization using bead standards;
15424 @item single-cell deconvolution;
15425 @item bead-based compensation.
15428 (license license:gpl2+)))
15430 (define-public r-erma
15437 (uri (bioconductor-uri "erma" version))
15440 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
15441 (build-system r-build-system)
15443 (list r-annotationdbi
15456 r-summarizedexperiment))
15459 (home-page "https://bioconductor.org/packages/erma")
15460 (synopsis "Epigenomic road map adventures")
15462 "The epigenomics road map describes locations of epigenetic marks in DNA
15463 from a variety of cell types. Of interest are locations of histone
15464 modifications, sites of DNA methylation, and regions of accessible chromatin.
15465 This package presents a selection of elements of the road map including
15466 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
15467 by Ernst and Kellis.")
15468 (license license:artistic2.0)))
15470 (define-public r-ggbio
15477 (uri (bioconductor-uri "ggbio" version))
15480 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
15481 (build-system r-build-system)
15484 (modify-phases %standard-phases
15485 ;; See https://github.com/tengfei/ggbio/issues/117
15486 ;; This fix will be included in the next release.
15487 (add-after 'unpack 'fix-typo
15489 (substitute* "R/GGbio-class.R"
15490 (("fechable") "fetchable"))
15493 (list r-annotationdbi
15502 r-genomicalignments
15518 r-summarizedexperiment
15519 r-variantannotation))
15522 (home-page "http://www.tengfei.name/ggbio/")
15523 (synopsis "Visualization tools for genomic data")
15525 "The ggbio package extends and specializes the grammar of graphics for
15526 biological data. The graphics are designed to answer common scientific
15527 questions, in particular those often asked of high throughput genomics data.
15528 All core Bioconductor data structures are supported, where appropriate. The
15529 package supports detailed views of particular genomic regions, as well as
15530 genome-wide overviews. Supported overviews include ideograms and grand linear
15531 views. High-level plots include sequence fragment length, edge-linked
15532 interval to data view, mismatch pileup, and several splicing summaries.")
15533 (license license:artistic2.0)))
15535 (define-public r-gqtlbase
15537 (name "r-gqtlbase")
15542 (uri (bioconductor-uri "gQTLBase" version))
15545 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
15546 (properties `((upstream-name . "gQTLBase")))
15547 (build-system r-build-system)
15550 (modify-phases %standard-phases
15551 ;; This is an upstream bug.
15552 (add-after 'unpack 'fix-imports
15554 (substitute* "NAMESPACE"
15555 ((".*maxffmode.*") "")
15556 (("importFrom\\(ff,.*") "import(ff)\n"))
15571 r-summarizedexperiment))
15574 (home-page "https://bioconductor.org/packages/gQTLBase")
15575 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
15577 "The purpose of this package is to simplify the storage and interrogation
15578 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
15580 (license license:artistic2.0)))
15582 (define-public r-gqtlstats
15584 (name "r-gqtlstats")
15589 (uri (bioconductor-uri "gQTLstats" version))
15592 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
15593 (properties `((upstream-name . "gQTLstats")))
15594 (build-system r-build-system)
15596 (list r-annotationdbi
15624 r-summarizedexperiment
15625 r-variantannotation))
15628 (home-page "https://bioconductor.org/packages/gQTLstats")
15629 (synopsis "Computationally efficient analysis for eQTL and allied studies")
15631 "This package provides tools for the computationally efficient analysis
15632 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
15633 The software in this package aims to support refinements and functional
15634 interpretation of members of a collection of association statistics on a
15635 family of feature/genome hypotheses.")
15636 (license license:artistic2.0)))
15638 (define-public r-gviz
15645 (uri (bioconductor-uri "Gviz" version))
15648 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
15649 (properties `((upstream-name . "Gviz")))
15650 (build-system r-build-system)
15652 (list r-annotationdbi
15662 r-genomicalignments
15676 (home-page "https://bioconductor.org/packages/Gviz")
15677 (synopsis "Plotting data and annotation information along genomic coordinates")
15679 "Genomic data analyses requires integrated visualization of known genomic
15680 information and new experimental data. Gviz uses the biomaRt and the
15681 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
15682 and translates this to e.g. gene/transcript structures in viewports of the
15683 grid graphics package. This results in genomic information plotted together
15685 (license license:artistic2.0)))
15687 (define-public r-gwascat
15694 (uri (bioconductor-uri "gwascat" version))
15697 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
15698 (build-system r-build-system)
15700 (list r-annotationdbi
15711 r-variantannotation))
15714 (home-page "https://bioconductor.org/packages/gwascat")
15715 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
15717 "This package provides tools for representing and modeling data in the
15718 EMBL-EBI GWAS catalog.")
15719 (license license:artistic2.0)))
15721 (define-public r-kegggraph
15723 (name "r-kegggraph")
15728 (uri (bioconductor-uri "KEGGgraph" version))
15730 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
15731 (properties `((upstream-name . "KEGGgraph")))
15732 (build-system r-build-system)
15734 (list r-graph r-rcurl r-rgraphviz r-xml))
15735 (home-page "https://bioconductor.org/packages/KEGGgraph")
15736 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
15738 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
15739 object as well as a collection of tools to analyze, dissect and visualize these
15740 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
15741 maintaining all essential pathway attributes. The package offers
15742 functionalities including parsing, graph operation, visualization and etc.")
15743 (license license:gpl2+)))
15745 (define-public r-ldblock
15752 (uri (bioconductor-uri "ldblock" version))
15755 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
15756 (build-system r-build-system)
15758 (list r-biocgenerics
15759 r-ensdb-hsapiens-v75
15767 r-variantannotation))
15770 (home-page "https://bioconductor.org/packages/ldblock")
15771 (synopsis "Data structures for linkage disequilibrium measures in populations")
15773 "This package defines data structures for @dfn{linkage
15774 disequilibrium} (LD) measures in populations. Its purpose is to simplify
15775 handling of existing population-level data for the purpose of flexibly
15776 defining LD blocks.")
15777 (license license:artistic2.0)))
15779 ;; This is a CRAN package, but it depends on r-snpstats, which is a
15780 ;; Bioconductor package.
15781 (define-public r-ldheatmap
15783 (name "r-ldheatmap")
15788 (uri (cran-uri "LDheatmap" version))
15791 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
15792 (properties `((upstream-name . "LDheatmap")))
15793 (build-system r-build-system)
15795 (list r-genetics r-rcpp r-snpstats))
15796 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
15797 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
15799 "This package provides tools to produce a graphical display, as a heat
15800 map, of measures of pairwise linkage disequilibria between SNPs. Users may
15801 optionally include the physical locations or genetic map distances of each SNP
15803 (license license:gpl3)))
15805 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
15806 ;; Bioconductor package.
15807 (define-public r-abn
15814 (uri (cran-uri "abn" version))
15817 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
15818 (build-system r-build-system)
15831 (home-page "https://r-bayesian-networks.org/")
15832 (synopsis "Modelling multivariate data with additive bayesian networks")
15834 "Bayesian network analysis is a form of probabilistic graphical models
15835 which derives from empirical data a directed acyclic graph, DAG, describing
15836 the dependency structure between random variables. An additive Bayesian
15837 network model consists of a form of a DAG where each node comprises a
15838 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
15839 equivalent to Bayesian multivariate regression using graphical modelling, they
15840 generalises the usual multivariable regression, GLM, to multiple dependent
15841 variables. This package provides routines to help determine optimal Bayesian
15842 network models for a given data set, where these models are used to identify
15843 statistical dependencies in messy, complex data.")
15844 (license license:gpl2+)))
15846 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
15847 ;; Bioconductor package.
15848 (define-public r-spp
15854 (uri (cran-uri "spp" version))
15857 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
15858 (build-system r-build-system)
15862 (list r-bh r-catools r-rcpp r-rsamtools))
15863 (home-page "https://cran.r-project.org/web/packages/spp/")
15864 (synopsis "ChIP-Seq processing pipeline")
15865 (description "This package provides tools for analysis of ChIP-seq and
15866 other functional sequencing data.")
15867 (license license:gpl2)))
15869 (define-public r-pathview
15871 (name "r-pathview")
15876 (uri (bioconductor-uri "pathview" version))
15878 (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71"))))
15879 (properties `((upstream-name . "pathview")))
15880 (build-system r-build-system)
15882 (list r-annotationdbi
15890 (home-page "https://pathview.uncc.edu/")
15891 (synopsis "Tool set for pathway based data integration and visualization")
15893 "@code{r-pathview} is a tool set for pathway based data integration and
15894 visualization. It maps and renders a wide variety of biological data on
15895 relevant pathway graphs. All users need is to supply their data and specify
15896 the target pathway. This package automatically downloads the pathway graph
15897 data, parses the data file, maps user data to the pathway, and render pathway
15898 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
15899 integrates with pathway and gene set (enrichment) analysis tools for
15900 large-scale and fully automated analysis.")
15901 (license license:gpl3+)))
15903 (define-public r-snpstats
15905 (name "r-snpstats")
15910 (uri (bioconductor-uri "snpStats" version))
15913 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
15914 (properties `((upstream-name . "snpStats")))
15915 (build-system r-build-system)
15916 (inputs (list zlib))
15918 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
15919 (home-page "https://bioconductor.org/packages/snpStats")
15920 (synopsis "Methods for SNP association studies")
15922 "This package provides classes and statistical methods for large
15923 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
15924 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
15925 (license license:gpl3)))
15927 (define-public r-chromstar
15929 (name "r-chromstar")
15934 (uri (bioconductor-uri "chromstaR" version))
15937 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
15938 (properties `((upstream-name . "chromstaR")))
15939 (build-system r-build-system)
15947 r-genomicalignments
15955 (native-inputs (list r-knitr))
15956 (home-page "https://github.com/ataudt/chromstaR")
15957 (synopsis "Chromatin state analysis for ChIP-Seq data")
15959 "This package implements functions for combinatorial and differential
15960 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
15961 export to genome browser viewable files, and functions for enrichment
15963 (license license:artistic2.0)))
15965 (define-public r-guitar
15972 (uri (bioconductor-uri "Guitar" version))
15975 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
15976 (properties `((upstream-name . "Guitar")))
15977 (build-system r-build-system)
15979 (list r-annotationdbi
15989 (home-page "https://bioconductor.org/packages/Guitar")
15990 (synopsis "Visualize genomic features")
15992 "This package is designed for visualization of RNA-related genomic
15993 features with respect to the landmarks of RNA transcripts, i.e., transcription
15994 starting site, start codon, stop codon and transcription ending site.")
15995 (license license:gpl2)))
15997 (define-public r-sushi
16003 (uri (bioconductor-uri "Sushi" version))
16006 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
16007 (properties `((upstream-name . "Sushi")))
16008 (build-system r-build-system)
16010 (list r-biomart r-zoo))
16011 (home-page "https://bioconductor.org/packages/Sushi")
16012 (synopsis "Tools for visualizing genomics data")
16014 "This package provides flexible, quantitative, and integrative genomic
16015 visualizations for publication-quality multi-panel figures.")
16016 (license license:gpl2+)))
16018 (define-public r-ballgown
16020 (name "r-ballgown")
16025 (uri (bioconductor-uri "ballgown" version))
16028 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
16029 (properties `((upstream-name . "ballgown")))
16030 (build-system r-build-system)
16043 (home-page "https://bioconductor.org/packages/ballgown")
16044 (synopsis "Flexible, isoform-level differential expression analysis")
16046 "This package provides tools for statistical analysis of assembled
16047 transcriptomes, including flexible differential expression analysis,
16048 visualization of transcript structures, and matching of assembled transcripts
16050 (license license:artistic2.0)))
16052 (define-public r-megadepth
16054 (name "r-megadepth")
16059 (uri (bioconductor-uri "megadepth" version))
16062 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
16063 (properties `((upstream-name . "megadepth")))
16064 (build-system r-build-system)
16065 (inputs (list megadepth))
16076 (home-page "https://github.com/LieberInstitute/megadepth")
16077 (synopsis "BigWig and BAM related utilities")
16079 "This package provides an R interface to Megadepth. It is particularly
16080 useful for computing the coverage of a set of genomic regions across bigWig or
16081 BAM files. With this package, you can build base-pair coverage matrices for
16082 regions or annotations of your choice from BigWig files.")
16083 (license license:artistic2.0)))
16085 (define-public r-beclear
16092 (uri (bioconductor-uri "BEclear" version))
16095 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
16096 (properties `((upstream-name . "BEclear")))
16097 (build-system r-build-system)
16109 (home-page "https://github.com/uds-helms/BEclear")
16110 (synopsis "Correction of batch effects in DNA methylation data")
16112 "This package provides functions to detect and correct for batch effects
16113 in DNA methylation data. The core function is based on latent factor models
16114 and can also be used to predict missing values in any other matrix containing
16116 (license license:gpl3)))
16118 (define-public r-bgeecall
16120 (name "r-bgeecall")
16125 (uri (bioconductor-uri "BgeeCall" version))
16128 "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil"))))
16129 (properties `((upstream-name . "BgeeCall")))
16130 (build-system r-build-system)
16144 (native-inputs (list r-knitr))
16145 (home-page "https://github.com/BgeeDB/BgeeCall")
16146 (synopsis "RNA-Seq present/absent gene expression calls generation")
16148 "BgeeCall allows generating present/absent gene expression calls without
16149 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
16150 intergenic sequences. These sequences are generated based on expression of
16151 all RNA-Seq libraries of each species integrated in Bgee.")
16152 (license license:gpl3)))
16154 (define-public r-bgeedb
16161 (uri (bioconductor-uri "BgeeDB" version))
16164 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
16165 (properties `((upstream-name . "BgeeDB")))
16166 (build-system r-build-system)
16179 (native-inputs (list r-knitr))
16180 (home-page "https://github.com/BgeeDB/BgeeDB_R")
16181 (synopsis "Annotation and gene expression data retrieval from Bgee database")
16183 "This package provides a package for the annotation and gene expression
16184 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
16185 anatomical terms, mapped to genes by expression patterns.")
16186 (license license:gpl3)))
16188 (define-public r-biobtreer
16190 (name "r-biobtreer")
16195 (uri (bioconductor-uri "biobtreeR" version))
16198 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
16199 (properties `((upstream-name . "biobtreeR")))
16200 (build-system r-build-system)
16202 (list r-httpuv r-httr r-jsonlite r-stringi))
16203 (native-inputs (list r-knitr))
16204 (home-page "https://github.com/tamerh/biobtreeR")
16205 (synopsis "Use biobtree tool from R")
16207 "The biobtreeR package provides an interface to biobtree, a tool which
16208 covers large sets of bioinformatics datasets and allows search and chain
16209 mappings functionalities.")
16210 (license license:expat)))
16212 (define-public r-minet
16219 (uri (bioconductor-uri "minet" version))
16222 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
16223 (properties `((upstream-name . "minet")))
16224 (build-system r-build-system)
16227 (home-page "http://minet.meyerp.com")
16228 (synopsis "Mutual information networks")
16230 "This package implements various algorithms for inferring mutual
16231 information networks from data.")
16232 (license license:artistic2.0)))
16234 (define-public r-genetclassifier
16236 (name "r-genetclassifier")
16241 (uri (bioconductor-uri "geNetClassifier" version))
16244 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
16246 `((upstream-name . "geNetClassifier")))
16247 (build-system r-build-system)
16249 (list r-biobase r-e1071 r-ebarrays r-minet))
16250 (home-page "https://www.cicancer.org")
16251 (synopsis "Classify diseases and build gene networks using expression profiles")
16253 "This is a comprehensive package to automatically train and validate a
16254 multi-class SVM classifier based on gene expression data. It provides
16255 transparent selection of gene markers, their coexpression networks, and an
16256 interface to query the classifier.")
16257 (license license:gpl2+)))
16259 (define-public r-dir-expiry
16261 (name "r-dir-expiry")
16266 (uri (bioconductor-uri "dir.expiry" version))
16269 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
16270 (properties `((upstream-name . "dir.expiry")))
16271 (build-system r-build-system)
16272 (propagated-inputs (list r-filelock))
16273 (native-inputs (list r-knitr))
16274 (home-page "https://bioconductor.org/packages/dir.expiry")
16275 (synopsis "Managing expiration for cache directories")
16277 "This package implements an expiration system for access to versioned
16278 directories. Directories that have not been accessed by a registered function
16279 within a certain time frame are deleted. This aims to reduce disk usage by
16280 eliminating obsolete caches generated by old versions of packages.")
16281 (license license:gpl3)))
16283 (define-public r-basilisk-utils
16285 (name "r-basilisk-utils")
16290 (uri (bioconductor-uri "basilisk.utils" version))
16293 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
16295 `((upstream-name . "basilisk.utils")))
16296 (build-system r-build-system)
16298 (list r-dir-expiry))
16299 (native-inputs (list r-knitr))
16300 (home-page "https://bioconductor.org/packages/basilisk.utils")
16301 (synopsis "Basilisk installation utilities")
16303 "This package implements utilities for installation of the basilisk
16304 package, primarily for creation of the underlying Conda instance.")
16305 (license license:gpl3)))
16307 (define-public r-basilisk
16309 (name "r-basilisk")
16314 (uri (bioconductor-uri "basilisk" version))
16317 "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk"))))
16318 (properties `((upstream-name . "basilisk")))
16319 (build-system r-build-system)
16321 (list r-basilisk-utils r-dir-expiry r-reticulate))
16322 (native-inputs (list r-knitr))
16323 (home-page "https://bioconductor.org/packages/basilisk")
16324 (synopsis "Freeze Python dependencies inside Bioconductor packages")
16326 "This package installs a self-contained Conda instance that is managed by
16327 the R/Bioconductor installation machinery. This aims to provide a consistent
16328 Python environment that can be used reliably by Bioconductor packages.
16329 Functions are also provided to enable smooth interoperability of multiple
16330 Python environments in a single R session.")
16331 (license license:gpl3)))
16333 (define-public r-biocthis
16335 (name "r-biocthis")
16340 (uri (bioconductor-uri "biocthis" version))
16343 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
16344 (properties `((upstream-name . "biocthis")))
16345 (build-system r-build-system)
16348 (modify-phases %standard-phases
16349 (add-after 'unpack 'set-HOME
16350 (lambda _ (setenv "HOME" "/tmp"))))))
16352 (list r-biocmanager
16358 (native-inputs (list r-knitr))
16359 (home-page "https://github.com/lcolladotor/biocthis")
16360 (synopsis "Automate package and project setup for Bioconductor packages")
16362 "This package expands the @code{usethis} package with the goal of helping
16363 automate the process of creating R packages for Bioconductor or making them
16364 Bioconductor-friendly.")
16365 (license license:artistic2.0)))
16367 (define-public r-biocdockermanager
16369 (name "r-biocdockermanager")
16374 (uri (bioconductor-uri "BiocDockerManager" version))
16377 "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d"))))
16379 `((upstream-name . "BiocDockerManager")))
16380 (build-system r-build-system)
16388 (native-inputs (list r-knitr))
16389 (home-page "https://bioconductor.org/packages/BiocDockerManager")
16390 (synopsis "Access and manage Bioconductor Docker images")
16392 "This package works analogous to BiocManager but for Docker images. Use
16393 the BiocDockerManager package to install and manage Docker images provided by
16394 the Bioconductor project.")
16395 (license license:artistic2.0)))
16397 (define-public r-biodb
16404 (uri (bioconductor-uri "biodb" version))
16407 "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1"))))
16408 (properties `((upstream-name . "biodb")))
16409 (build-system r-build-system)
16411 (list r-biocfilecache
16429 (native-inputs (list r-knitr))
16430 (home-page "https://bioconductor.org/packages/biodb")
16431 (synopsis "Library for connecting to chemical and biological databases")
16433 "The biodb package provides access to standard remote chemical and
16434 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
16435 database files (CSV, SQLite), with easy retrieval of entries, access to web
16436 services, search of compounds by mass and/or name, and mass spectra matching
16437 for LCMS and MSMS. Its architecture as a development framework facilitates
16438 the development of new database connectors for local projects or inside
16439 separate published packages.")
16440 (license license:agpl3+)))
16442 (define-public r-biomformat
16444 (name "r-biomformat")
16449 (uri (bioconductor-uri "biomformat" version))
16452 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
16453 (properties `((upstream-name . "biomformat")))
16454 (build-system r-build-system)
16456 (list r-jsonlite r-matrix r-plyr r-rhdf5))
16457 (native-inputs (list r-knitr))
16458 (home-page "https://github.com/joey711/biomformat/")
16459 (synopsis "Interface package for the BIOM file format")
16461 "This is an R package for interfacing with the BIOM format. This package
16462 includes basic tools for reading biom-format files, accessing and subsetting
16463 data tables from a biom object (which is more complex than a single table), as
16464 well as limited support for writing a biom-object back to a biom-format file.
16465 The design of this API is intended to match the Python API and other tools
16466 included with the biom-format project, but with a decidedly \"R flavor\" that
16467 should be familiar to R users. This includes S4 classes and methods, as well
16468 as extensions of common core functions/methods.")
16469 (license license:gpl2)))
16471 (define-public r-mvcclass
16473 (name "r-mvcclass")
16478 (uri (bioconductor-uri "MVCClass" version))
16481 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
16482 (properties `((upstream-name . "MVCClass")))
16483 (build-system r-build-system)
16484 (home-page "https://bioconductor.org/packages/MVCClass")
16485 (synopsis "Model-View-Controller (MVC) classes")
16487 "This package contains classes used in model-view-controller (MVC)
16489 (license license:lgpl2.1+)))
16491 (define-public r-biomvcclass
16493 (name "r-biomvcclass")
16498 (uri (bioconductor-uri "BioMVCClass" version))
16501 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
16502 (properties `((upstream-name . "BioMVCClass")))
16503 (build-system r-build-system)
16505 (list r-biobase r-graph r-mvcclass r-rgraphviz))
16506 (home-page "https://bioconductor.org/packages/BioMVCClass")
16507 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
16509 "This package contains classes used in model-view-controller (MVC)
16511 (license license:lgpl2.1+)))
16513 (define-public r-biomvrcns
16515 (name "r-biomvrcns")
16520 (uri (bioconductor-uri "biomvRCNS" version))
16523 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
16524 (properties `((upstream-name . "biomvRCNS")))
16525 (build-system r-build-system)
16527 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
16528 (home-page "https://bioconductor.org/packages/biomvRCNS")
16529 (synopsis "Copy number study and segmentation for multivariate biological data")
16531 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
16532 homogeneous segmentation model are designed and implemented for segmentation
16533 genomic data, with the aim of assisting in transcripts detection using high
16534 throughput technology like RNA-seq or tiling array, and copy number analysis
16535 using aCGH or sequencing.")
16536 (license license:gpl2+)))
16538 (define-public r-bionero
16545 (uri (bioconductor-uri "BioNERO" version))
16548 "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp"))))
16549 (properties `((upstream-name . "BioNERO")))
16550 (build-system r-build-system)
16552 (list r-biocparallel
16569 r-summarizedexperiment
16574 (home-page "https://github.com/almeidasilvaf/BioNERO")
16575 (synopsis "Biological network reconstruction omnibus")
16577 "BioNERO aims to integrate all aspects of biological network inference in
16578 a single package, including data preprocessing, exploratory analyses, network
16579 inference, and analyses for biological interpretations. BioNERO can be used
16580 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
16581 from gene expression data. Additionally, it can be used to explore
16582 topological properties of protein-protein interaction (PPI) networks. GCN
16583 inference relies on the popular WGCNA algorithm. GRN inference is based on
16584 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
16585 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
16586 rank for each interaction pair. As all steps of network analyses are included
16587 in this package, BioNERO makes users avoid having to learn the syntaxes of
16588 several packages and how to communicate between them. Finally, users can also
16589 identify consensus modules across independent expression sets and calculate
16590 intra and interspecies module preservation statistics between different
16592 (license license:gpl3)))
16594 (define-public r-bionet
16601 (uri (bioconductor-uri "BioNet" version))
16604 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
16605 (properties `((upstream-name . "BioNet")))
16606 (build-system r-build-system)
16608 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
16609 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
16610 (synopsis "Functional analysis of biological networks")
16612 "This package provides functions for the integrated analysis of
16613 protein-protein interaction networks and the detection of functional modules.
16614 Different datasets can be integrated into the network by assigning p-values of
16615 statistical tests to the nodes of the network. E.g. p-values obtained from
16616 the differential expression of the genes from an Affymetrix array are assigned
16617 to the nodes of the network. By fitting a beta-uniform mixture model and
16618 calculating scores from the p-values, overall scores of network regions can be
16619 calculated and an integer linear programming algorithm identifies the maximum
16620 scoring subnetwork.")
16621 (license license:gpl2+)))
16623 (define-public r-bionetstat
16625 (name "r-bionetstat")
16630 (uri (bioconductor-uri "BioNetStat" version))
16633 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
16634 (properties `((upstream-name . "BioNetStat")))
16635 (build-system r-build-system)
16637 (list r-biocparallel
16657 (home-page "https://github.com/jardimViniciusC/BioNetStat")
16658 (synopsis "Biological network analysis")
16660 "This package provides a package to perform differential network
16661 analysis, differential node analysis (differential coexpression analysis),
16662 network and metabolic pathways view.")
16663 (license license:gpl3+)))
16665 (define-public r-bioqc
16672 (uri (bioconductor-uri "BioQC" version))
16675 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
16676 (properties `((upstream-name . "BioQC")))
16677 (build-system r-build-system)
16679 (list r-biobase r-edger r-rcpp))
16682 (home-page "https://accio.github.io/BioQC/")
16683 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
16685 "BioQC performs quality control of high-throughput expression data based
16686 on tissue gene signatures. It can detect tissue heterogeneity in gene
16687 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
16688 optimised for high performance.")
16689 (license license:gpl3+)))
16691 (define-public r-biotip
16698 (uri (bioconductor-uri "BioTIP" version))
16701 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
16702 (properties `((upstream-name . "BioTIP")))
16703 (build-system r-build-system)
16714 (home-page "https://github.com/xyang2uchicago/BioTIP")
16715 (synopsis "R package for characterization of biological tipping-point")
16717 "This package adopts tipping-point theory to transcriptome profiles to
16718 help unravel disease regulatory trajectory.")
16719 (license license:gpl2)))
16721 (define-public r-biotmle
16728 (uri (bioconductor-uri "biotmle" version))
16731 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
16732 (properties `((upstream-name . "biotmle")))
16733 (build-system r-build-system)
16744 r-summarizedexperiment
16749 (home-page "https://code.nimahejazi.org/biotmle/")
16750 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
16752 "This package provides tools for differential expression biomarker
16753 discovery based on microarray and next-generation sequencing data that
16754 leverage efficient semiparametric estimators of the average treatment effect
16755 for variable importance analysis. Estimation and inference of the (marginal)
16756 average treatment effects of potential biomarkers are computed by targeted
16757 minimum loss-based estimation, with joint, stable inference constructed across
16758 all biomarkers using a generalization of moderated statistics for use with the
16759 estimated efficient influence function. The procedure accommodates the use of
16760 ensemble machine learning for the estimation of nuisance functions.")
16761 (license license:expat)))
16763 (define-public r-bsseq
16770 (uri (bioconductor-uri "bsseq" version))
16773 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
16774 (properties `((upstream-name . "bsseq")))
16775 (build-system r-build-system)
16785 r-delayedmatrixstats
16799 r-summarizedexperiment))
16802 (home-page "https://github.com/hansenlab/bsseq")
16803 (synopsis "Analyze, manage and store bisulfite sequencing data")
16805 "This package provides a collection of tools for analyzing and
16806 visualizing bisulfite sequencing data.")
16807 (license license:artistic2.0)))
16809 (define-public r-dada2
16815 (uri (bioconductor-uri "dada2" version))
16818 "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x"))))
16819 (properties `((upstream-name . "dada2")))
16820 (build-system r-build-system)
16822 (list r-biocgenerics
16831 (native-inputs (list r-knitr))
16832 (home-page "https://benjjneb.github.io/dada2/")
16834 "Accurate, high-resolution sample inference from amplicon sequencing data")
16836 "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
16837 from high-throughput amplicon sequencing data, replacing the coarser and less
16838 accurate OTU clustering approach. The dada2 pipeline takes as input
16839 demultiplexed fastq files, and outputs the sequence variants and their
16840 sample-wise abundances after removing substitution and chimera errors.
16841 Taxonomic classification is available via a native implementation of the RDP
16842 naive Bayesian classifier, and species-level assignment to 16S rRNA gene
16843 fragments by exact matching.")
16844 (license license:lgpl2.0)))
16846 (define-public r-dmrseq
16853 (uri (bioconductor-uri "dmrseq" version))
16856 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
16857 (properties `((upstream-name . "dmrseq")))
16858 (build-system r-build-system)
16860 (list r-annotationhub
16865 r-delayedmatrixstats
16879 (home-page "https://bioconductor.org/packages/dmrseq")
16880 (synopsis "Detection and inference of differentially methylated regions")
16882 "This package implements an approach for scanning the genome to detect
16883 and perform accurate inference on differentially methylated regions from Whole
16884 Genome Bisulfite Sequencing data. The method is based on comparing detected
16885 regions to a pooled null distribution, that can be implemented even when as
16886 few as two samples per population are available. Region-level statistics are
16887 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
16888 with a nested autoregressive correlated error structure for the effect of
16889 interest on transformed methylation proportions.")
16890 (license license:expat)))
16892 (define-public r-omicade4
16894 (name "r-omicade4")
16898 (uri (bioconductor-uri "omicade4" version))
16901 "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
16902 (properties `((upstream-name . "omicade4")))
16903 (build-system r-build-system)
16904 (propagated-inputs (list r-ade4 r-biobase r-made4))
16905 (home-page "https://bioconductor.org/packages/omicade4")
16906 (synopsis "Multiple co-inertia analysis of omics datasets")
16908 "This package performes multiple co-inertia analysis of omics datasets.")
16909 (license license:gpl2)))
16911 (define-public r-omnipathr
16913 (name "r-omnipathr")
16918 (uri (bioconductor-uri "OmnipathR" version))
16920 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
16921 (properties `((upstream-name . "OmnipathR")))
16922 (build-system r-build-system)
16925 (modify-phases %standard-phases
16926 (add-after 'unpack 'set-HOME
16927 (lambda _ (setenv "HOME" "/tmp"))))))
16953 (native-inputs (list r-knitr))
16954 (home-page "https://saezlab.github.io/OmnipathR/")
16955 (synopsis "OmniPath web service client and more")
16957 "This package provides a client for the OmniPath web service and many
16958 other resources. It also includes functions to transform and pretty print
16959 some of the downloaded data, functions to access a number of other resources.
16960 Furthermore, OmnipathR features a close integration with the NicheNet method
16961 for ligand activity prediction from transcriptomics data.")
16962 (license license:expat)))
16964 (define-public r-biscuiteer
16966 (name "r-biscuiteer")
16971 (uri (bioconductor-uri "biscuiteer" version))
16974 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
16975 (properties `((upstream-name . "biscuiteer")))
16976 (build-system r-build-system)
16984 r-delayedmatrixstats
17003 r-summarizedexperiment
17004 r-variantannotation))
17007 (home-page "https://github.com/trichelab/biscuiteer")
17008 (synopsis "Convenience functions for the Biscuit package")
17010 "This package provides a test harness for bsseq loading of Biscuit
17011 output, summarization of WGBS data over defined regions and in mappable
17012 samples, with or without imputation, dropping of mostly-NA rows, age
17014 (license license:gpl3)))
17016 (define-public r-tcgabiolinks
17018 (name "r-tcgabiolinks")
17023 (uri (bioconductor-uri "TCGAbiolinks" version))
17025 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
17026 (properties `((upstream-name . "TCGAbiolinks")))
17027 (build-system r-build-system)
17046 r-summarizedexperiment
17047 r-tcgabiolinksgui-data
17052 (native-inputs (list r-knitr))
17053 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
17054 (synopsis "Integrative analysis with GDC data")
17056 "The aim of TCGAbiolinks is:
17059 @item facilitate GDC open-access data retrieval;
17060 @item prepare the data using the appropriate pre-processing strategies;
17061 @item provide the means to carry out different standard analyses, and;
17062 @item to easily reproduce earlier research results.
17065 In more detail, the package provides multiple methods for analysis (e.g.,
17066 differential expression analysis, identifying differentially methylated
17067 regions) and methods for visualization (e.g., survival plots, volcano plots,
17068 starburst plots) in order to easily develop complete analysis pipelines.")
17069 (license license:gpl3+)))
17071 (define-public r-tricycle
17073 (name "r-tricycle")
17077 (uri (bioconductor-uri "tricycle" version))
17080 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
17081 (properties `((upstream-name . "tricycle")))
17082 (build-system r-build-system)
17084 (list r-annotationdbi
17095 r-singlecellexperiment
17096 r-summarizedexperiment))
17097 (native-inputs (list r-knitr))
17098 (home-page "https://github.com/hansenlab/tricycle")
17099 (synopsis "Transferable representation and inference of cell cycle")
17101 "The package contains functions to infer and visualize cell cycle process
17102 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
17103 projecting new data to the previous learned biologically interpretable space.
17104 The @code{tricycle} provides a pre-learned cell cycle space, which could be
17105 used to infer cell cycle time of human and mouse single cell samples. In
17106 addition, it also offer functions to visualize cell cycle time on different
17107 embeddings and functions to build new reference.")
17108 (license license:gpl3)))
17110 (define-public r-tximeta
17117 (uri (bioconductor-uri "tximeta" version))
17120 "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8"))))
17121 (properties `((upstream-name . "tximeta")))
17122 (build-system r-build-system)
17124 (list r-annotationdbi
17136 r-summarizedexperiment
17141 (home-page "https://github.com/mikelove/tximeta")
17142 (synopsis "Transcript quantification import with automatic metadata")
17144 "This package implements transcript quantification import from Salmon and
17145 alevin with automatic attachment of transcript ranges and release information,
17146 and other associated metadata. De novo transcriptomes can be linked to the
17147 appropriate sources with linkedTxomes and shared for computational
17149 (license license:gpl2)))
17151 (define-public r-phyloseq
17153 (name "r-phyloseq")
17158 (uri (bioconductor-uri "phyloseq" version))
17160 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
17161 (properties `((upstream-name . "phyloseq")))
17162 (build-system r-build-system)
17182 (home-page "https://github.com/joey711/phyloseq")
17183 (synopsis "Handling and analysis of high-throughput microbiome census data")
17185 "Phyloseq provides a set of classes and tools to facilitate the import,
17186 storage, analysis, and graphical display of microbiome census data.")
17187 (license license:agpl3)))
17190 ;;; Avoid adding new packages to the end of this file. To reduce the chances
17191 ;;; of a merge conflict, place them above by existing packages with similar
17192 ;;; functionality or similar names.