1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
11 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
12 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
13 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
14 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
16 ;;; This file is part of GNU Guix.
18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
19 ;;; under the terms of the GNU General Public License as published by
20 ;;; the Free Software Foundation; either version 3 of the License, or (at
21 ;;; your option) any later version.
23 ;;; GNU Guix is distributed in the hope that it will be useful, but
24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 ;;; GNU General Public License for more details.
28 ;;; You should have received a copy of the GNU General Public License
29 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
31 (define-module (gnu packages bioconductor)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix download)
35 #:use-module (guix git-download)
36 #:use-module (guix build-system r)
37 #:use-module (gnu packages)
38 #:use-module (gnu packages base)
39 #:use-module (gnu packages bioinformatics)
40 #:use-module (gnu packages boost)
41 #:use-module (gnu packages cran)
42 #:use-module (gnu packages compression)
43 #:use-module (gnu packages curl)
44 #:use-module (gnu packages docker)
45 #:use-module (gnu packages gcc)
46 #:use-module (gnu packages graph)
47 #:use-module (gnu packages graphviz)
48 #:use-module (gnu packages haskell-xyz)
49 #:use-module (gnu packages image)
50 #:use-module (gnu packages maths)
51 #:use-module (gnu packages netpbm)
52 #:use-module (gnu packages python)
53 #:use-module (gnu packages perl)
54 #:use-module (gnu packages pkg-config)
55 #:use-module (gnu packages statistics)
56 #:use-module (gnu packages web)
57 #:use-module (gnu packages xml)
58 #:use-module (srfi srfi-1))
63 (define-public r-org-eck12-eg-db
65 (name "r-org-eck12-eg-db")
70 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
72 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
74 `((upstream-name . "org.EcK12.eg.db")))
75 (build-system r-build-system)
77 (list r-annotationdbi))
78 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
79 (synopsis "Genome wide annotation for E coli strain K12")
81 "This package provides genome wide annotation for E coli strain K12,
82 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
83 National Center for Biotechnology Information (NCBI)’s database for
84 gene-specific information. Entrez Gene maintains records from genomes which
85 have been completely sequenced, which have an active research community to
86 submit gene-specific information, or which are scheduled for intense sequence
88 (license license:artistic2.0)))
90 (define-public r-org-bt-eg-db
92 (name "r-org-bt-eg-db")
97 (uri (bioconductor-uri
103 "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi"))))
104 (properties `((upstream-name . "org.Bt.eg.db")))
105 (build-system r-build-system)
107 (list r-annotationdbi))
108 (home-page "https://bioconductor.org/packages/org.Bt.eg.db")
109 (synopsis "Genome wide annotation for Bovine")
111 "This package provides genome wide annotations for Bovine, primarily
112 based on mapping using Entrez Gene identifiers.")
113 (license license:artistic2.0)))
115 (define-public r-reactome-db
117 (name "r-reactome-db")
122 (uri (bioconductor-uri "reactome.db" version 'annotation))
125 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
126 (properties `((upstream-name . "reactome.db")))
127 (build-system r-build-system)
129 (list r-annotationdbi))
130 (home-page "https://bioconductor.org/packages/reactome.db/")
131 (synopsis "Annotation maps for reactome")
133 "This package provides a set of annotation maps for the REACTOME
134 database, assembled using data from REACTOME.")
135 (license license:cc-by4.0)))
137 (define-public r-bsgenome-btaurus-ucsc-bostau8
139 (name "r-bsgenome-btaurus-ucsc-bostau8")
143 (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
144 version 'annotation))
147 "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
149 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
150 (build-system r-build-system)
154 "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
155 (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
156 (description "This package provides the full genome sequences for Bos
157 taurus (UCSC version bosTau8).")
158 (license license:artistic2.0)))
160 (define-public r-bsgenome-celegans-ucsc-ce6
162 (name "r-bsgenome-celegans-ucsc-ce6")
166 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
167 version 'annotation))
170 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
172 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
173 (build-system r-build-system)
177 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
178 (synopsis "Full genome sequences for Worm")
180 "This package provides full genome sequences for Caenorhabditis
181 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
183 (license license:artistic2.0)))
185 (define-public r-bsgenome-celegans-ucsc-ce10
187 (name "r-bsgenome-celegans-ucsc-ce10")
191 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
192 version 'annotation))
195 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
197 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
198 (build-system r-build-system)
202 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
203 (synopsis "Full genome sequences for Worm")
205 "This package provides full genome sequences for Caenorhabditis
206 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
208 (license license:artistic2.0)))
210 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
212 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
216 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
217 version 'annotation))
220 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
222 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
223 (build-system r-build-system)
227 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
228 (synopsis "Full genome sequences for Fly")
230 "This package provides full genome sequences for Drosophila
231 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
233 (license license:artistic2.0)))
235 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
237 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
241 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
242 version 'annotation))
245 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
247 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
248 (build-system r-build-system)
252 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
253 (synopsis "Full genome sequences for Fly")
255 "This package provides full genome sequences for Drosophila
256 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
257 Biostrings objects.")
258 (license license:artistic2.0)))
260 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
262 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
266 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
267 version 'annotation))
270 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
272 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
273 (build-system r-build-system)
275 (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
276 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
277 (synopsis "Full masked genome sequences for Fly")
279 "This package provides full masked genome sequences for Drosophila
280 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
281 Biostrings objects. The sequences are the same as in
282 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
283 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
284 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
285 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
286 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
287 (license license:artistic2.0)))
289 (define-public r-bsgenome-drerio-ucsc-danrer11
291 (name "r-bsgenome-drerio-ucsc-danrer11")
296 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
297 version 'annotation))
299 (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
300 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
301 (build-system r-build-system)
304 (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
305 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
307 "This package provides full genome sequences for Danio rerio (Zebrafish)
308 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
309 (license license:artistic2.0)))
311 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
313 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
317 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
318 version 'annotation))
321 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
323 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
324 (build-system r-build-system)
328 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
329 (synopsis "Full genome sequences for Homo sapiens")
331 "This package provides full genome sequences for Homo sapiens from
332 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
333 (license license:artistic2.0)))
335 (define-public r-bsgenome-hsapiens-ncbi-grch38
337 (name "r-bsgenome-hsapiens-ncbi-grch38")
342 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
343 version 'annotation))
346 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
347 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
348 (build-system r-build-system)
349 (propagated-inputs (list r-bsgenome))
351 "https://bioconductor.org/packages/release/data/annotation/html/\
352 BSgenome.Hsapiens.NCBI.GRCh38.html")
353 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
355 "This package provides full genome sequences for Homo sapiens (Human) as
356 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
357 (license license:artistic2.0)))
359 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
361 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
366 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
367 version 'annotation))
369 (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
371 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
372 (build-system r-build-system)
374 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
375 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
376 (synopsis "Full masked genome sequences for Homo sapiens")
378 "This package provides full genome sequences for Homo sapiens (Human) as
379 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
380 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
381 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
382 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
383 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
384 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
386 (license license:artistic2.0)))
388 (define-public r-bsgenome-mmusculus-ucsc-mm9
390 (name "r-bsgenome-mmusculus-ucsc-mm9")
394 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
395 version 'annotation))
398 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
400 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
401 (build-system r-build-system)
405 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
406 (synopsis "Full genome sequences for Mouse")
408 "This package provides full genome sequences for Mus musculus (Mouse) as
409 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
410 (license license:artistic2.0)))
412 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
414 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
418 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
419 version 'annotation))
422 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
424 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
425 (build-system r-build-system)
427 (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
428 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
429 (synopsis "Full masked genome sequences for Mouse")
431 "This package provides full genome sequences for Mus musculus (Mouse) as
432 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
433 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
434 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
435 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
436 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
437 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
439 (license license:artistic2.0)))
441 (define-public r-bsgenome-mmusculus-ucsc-mm10
443 (name "r-bsgenome-mmusculus-ucsc-mm10")
447 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
448 version 'annotation))
451 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
453 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
454 (build-system r-build-system)
458 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
459 (synopsis "Full genome sequences for Mouse")
461 "This package provides full genome sequences for Mus
462 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
463 in Biostrings objects.")
464 (license license:artistic2.0)))
466 (define-public r-genomeinfodbdata
468 (name "r-genomeinfodbdata")
472 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
475 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
477 `((upstream-name . "GenomeInfoDbData")))
478 (build-system r-build-system)
479 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
480 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
481 (description "This package contains data for mapping between NCBI taxonomy
482 ID and species. It is used by functions in the GenomeInfoDb package.")
483 (license license:artistic2.0)))
485 (define-public r-go-db
491 (uri (bioconductor-uri "GO.db" version 'annotation))
494 "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
496 `((upstream-name . "GO.db")))
497 (build-system r-build-system)
499 (list r-annotationdbi))
500 (home-page "https://bioconductor.org/packages/GO.db")
501 (synopsis "Annotation maps describing the entire Gene Ontology")
503 "The purpose of this GO.db annotation package is to provide detailed
504 information about the latest version of the Gene Ontologies.")
505 (license license:artistic2.0)))
507 (define-public r-homo-sapiens
509 (name "r-homo-sapiens")
513 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
516 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
518 `((upstream-name . "Homo.sapiens")))
519 (build-system r-build-system)
521 (list r-genomicfeatures
524 r-txdb-hsapiens-ucsc-hg19-knowngene
527 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
528 (synopsis "Annotation package for the Homo.sapiens object")
530 "This package contains the Homo.sapiens object to access data from
531 several related annotation packages.")
532 (license license:artistic2.0)))
534 (define-public r-mus-musculus
536 (name "r-mus-musculus")
541 (uri (bioconductor-uri "Mus.musculus" version 'annotation))
544 "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"))))
545 (properties `((upstream-name . "Mus.musculus")))
546 (build-system r-build-system)
548 (list r-annotationdbi
553 r-txdb-mmusculus-ucsc-mm10-knowngene))
554 (home-page "https://bioconductor.org/packages/Mus.musculus")
555 (synopsis "Annotation package for the Mus.musculus object")
557 "This package contains the @code{Mus.musculus} object to access data
558 from several related annotation packages.")
559 (license license:artistic2.0)))
561 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
563 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
568 (uri (bioconductor-uri
569 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
570 version 'annotation))
573 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
576 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
577 (build-system r-build-system)
578 (propagated-inputs (list r-minfi))
580 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
581 (synopsis "Annotation for Illumina's 450k methylation arrays")
583 "This package provides manifests and annotation for Illumina's 450k array
585 (license license:artistic2.0)))
587 (define-public r-org-ce-eg-db
589 (name "r-org-ce-eg-db")
593 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
596 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
598 `((upstream-name . "org.Ce.eg.db")))
599 (build-system r-build-system)
601 (list r-annotationdbi))
602 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
603 (synopsis "Genome wide annotation for Worm")
605 "This package provides mappings from Entrez gene identifiers to various
606 annotations for the genome of the model worm Caenorhabditis elegans.")
607 (license license:artistic2.0)))
609 (define-public r-org-dm-eg-db
611 (name "r-org-dm-eg-db")
615 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
618 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
620 `((upstream-name . "org.Dm.eg.db")))
621 (build-system r-build-system)
623 (list r-annotationdbi))
624 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
625 (synopsis "Genome wide annotation for Fly")
627 "This package provides mappings from Entrez gene identifiers to various
628 annotations for the genome of the model fruit fly Drosophila melanogaster.")
629 (license license:artistic2.0)))
631 (define-public r-org-dr-eg-db
633 (name "r-org-dr-eg-db")
637 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
640 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
642 `((upstream-name . "org.Dr.eg.db")))
643 (build-system r-build-system)
645 (list r-annotationdbi))
646 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
647 (synopsis "Annotation for Zebrafish")
649 "This package provides genome wide annotations for Zebrafish, primarily
650 based on mapping using Entrez Gene identifiers.")
651 (license license:artistic2.0)))
653 (define-public r-org-hs-eg-db
655 (name "r-org-hs-eg-db")
659 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
662 "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
664 `((upstream-name . "org.Hs.eg.db")))
665 (build-system r-build-system)
667 (list r-annotationdbi))
668 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
669 (synopsis "Genome wide annotation for Human")
671 "This package contains genome-wide annotations for Human, primarily based
672 on mapping using Entrez Gene identifiers.")
673 (license license:artistic2.0)))
675 (define-public r-org-mm-eg-db
677 (name "r-org-mm-eg-db")
681 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
684 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
686 `((upstream-name . "org.Mm.eg.db")))
687 (build-system r-build-system)
689 (list r-annotationdbi))
690 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
691 (synopsis "Genome wide annotation for Mouse")
693 "This package provides mappings from Entrez gene identifiers to various
694 annotations for the genome of the model mouse Mus musculus.")
695 (license license:artistic2.0)))
697 (define-public r-bsgenome-hsapiens-ucsc-hg19
699 (name "r-bsgenome-hsapiens-ucsc-hg19")
703 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
704 version 'annotation))
707 "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
709 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
710 (build-system r-build-system)
714 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
715 (synopsis "Full genome sequences for Homo sapiens")
717 "This package provides full genome sequences for Homo sapiens as provided
718 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
719 (license license:artistic2.0)))
721 (define-public r-bsgenome-hsapiens-ucsc-hg38
723 (name "r-bsgenome-hsapiens-ucsc-hg38")
727 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
728 version 'annotation))
730 (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"))))
732 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
733 (build-system r-build-system)
737 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
738 (synopsis "Full genome sequences for Homo sapiens")
740 "This package provides full genome sequences for Homo sapiens (Human)
741 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
742 (license license:artistic2.0)))
744 (define-public r-ensdb-hsapiens-v75
746 (name "r-ensdb-hsapiens-v75")
751 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
754 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
756 `((upstream-name . "EnsDb.Hsapiens.v75")))
757 (build-system r-build-system)
760 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
761 (synopsis "Ensembl based annotation package")
763 "This package exposes an annotation database generated from Ensembl.")
764 (license license:artistic2.0)))
766 (define-public r-ensdb-hsapiens-v86
768 (name "r-ensdb-hsapiens-v86")
773 (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation))
775 (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"))))
776 (properties `((upstream-name . "EnsDb.Hsapiens.v86")))
777 (build-system r-build-system)
778 (propagated-inputs (list r-ensembldb))
779 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86")
780 (synopsis "Ensembl based annotation package")
781 (description "This package exposes an annotation database generated from
783 (license license:artistic2.0)))
785 (define-public r-ensdb-mmusculus-v79
787 (name "r-ensdb-mmusculus-v79")
792 (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation))
794 (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7"))))
795 (properties `((upstream-name . "EnsDb.Mmusculus.v79")))
796 (build-system r-build-system)
797 (propagated-inputs (list r-ensembldb))
798 (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79")
799 (synopsis "Ensembl based annotation package")
800 (description "This package exposes an annotation database generated from
802 (license license:artistic2.0)))
804 (define-public r-snplocs-hsapiens-dbsnp144-grch37
806 (name "r-snplocs-hsapiens-dbsnp144-grch37")
810 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
811 version 'annotation))
814 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
815 (build-system r-build-system)
816 ;; As this package provides little more than a very large data file it
817 ;; doesn't make sense to build substitutes.
818 (arguments `(#:substitutable? #f))
828 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
829 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
830 (description "This package provides SNP locations and alleles for Homo
831 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
832 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
833 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
834 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
835 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
836 the mitochondrion chromosome. Therefore, the SNPs in this package can be
837 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
838 correct position but this injection will exclude chrM (i.e. nothing will be
839 injected in that sequence).")
840 (license license:artistic2.0)))
842 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
844 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
849 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
850 version 'annotation))
853 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
855 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
856 (build-system r-build-system)
858 (list r-annotationdbi r-genomicfeatures))
860 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
861 (synopsis "Annotation package for TxDb object(s)")
863 "This package exposes an annotation databases generated from UCSC by
864 exposing these as TxDb objects.")
865 (license license:artistic2.0)))
867 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
869 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
873 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
874 version 'annotation))
877 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
879 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
880 (build-system r-build-system)
882 (list r-genomicfeatures))
884 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
885 (synopsis "Annotation package for human genome in TxDb format")
887 "This package provides an annotation database of Homo sapiens genome
888 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
889 track. The database is exposed as a @code{TxDb} object.")
890 (license license:artistic2.0)))
892 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
894 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
898 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
899 version 'annotation))
901 (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879"))))
903 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
904 (build-system r-build-system)
906 (list r-annotationdbi r-genomicfeatures))
908 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
909 (synopsis "Annotation package for human genome in TxDb format")
911 "This package provides an annotation database of Homo sapiens genome
912 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
913 track. The database is exposed as a @code{TxDb} object.")
914 (license license:artistic2.0)))
916 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
918 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
922 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
923 version 'annotation))
926 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
928 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
929 (build-system r-build-system)
931 (list r-genomicfeatures r-annotationdbi))
933 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
934 (synopsis "Annotation package for mouse genome in TxDb format")
936 "This package provides an annotation database of Mouse genome data. It
937 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
938 database is exposed as a @code{TxDb} object.")
939 (license license:artistic2.0)))
941 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
943 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
947 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
948 version 'annotation))
951 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
953 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
954 (build-system r-build-system)
956 (list r-bsgenome r-genomicfeatures r-annotationdbi))
958 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
959 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
961 "This package loads a TxDb object, which is an R interface to
962 prefabricated databases contained in this package. This package provides
963 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
964 based on the knownGene track.")
965 (license license:artistic2.0)))
967 (define-public r-txdb-celegans-ucsc-ce6-ensgene
969 (name "r-txdb-celegans-ucsc-ce6-ensgene")
974 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
975 version 'annotation))
978 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
980 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
981 (build-system r-build-system)
983 (list r-annotationdbi r-genomicfeatures))
984 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
985 (synopsis "Annotation package for C elegans TxDb objects")
987 "This package exposes a C elegans annotation database generated from UCSC
988 by exposing these as TxDb objects.")
989 (license license:artistic2.0)))
991 (define-public r-fdb-infiniummethylation-hg19
993 (name "r-fdb-infiniummethylation-hg19")
997 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
998 version 'annotation))
1001 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
1003 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
1004 (build-system r-build-system)
1006 (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db
1007 r-txdb-hsapiens-ucsc-hg19-knowngene))
1008 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
1009 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
1011 "This is an annotation package for Illumina Infinium DNA methylation
1012 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
1014 (license license:artistic2.0)))
1016 (define-public r-illuminahumanmethylationepicmanifest
1018 (name "r-illuminahumanmethylationepicmanifest")
1022 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
1023 version 'annotation))
1026 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
1028 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
1029 (build-system r-build-system)
1032 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
1033 (synopsis "Manifest for Illumina's EPIC methylation arrays")
1035 "This is a manifest package for Illumina's EPIC methylation arrays.")
1036 (license license:artistic2.0)))
1038 (define-public r-do-db
1044 (uri (bioconductor-uri "DO.db" version 'annotation))
1047 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
1049 `((upstream-name . "DO.db")))
1050 (build-system r-build-system)
1052 (list r-annotationdbi))
1053 (home-page "https://www.bioconductor.org/packages/DO.db/")
1054 (synopsis "Annotation maps describing the entire Disease Ontology")
1056 "This package provides a set of annotation maps describing the entire
1058 (license license:artistic2.0)))
1060 (define-public r-hgu133plus2-db
1062 (name "r-hgu133plus2-db")
1067 (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
1069 (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
1070 (properties `((upstream-name . "hgu133plus2.db")))
1071 (build-system r-build-system)
1072 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
1073 (home-page "https://bioconductor.org/packages/hgu133plus2.db")
1074 (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
1076 "This package provides Affymetrix HG-U133_Plus_2 array annotation
1077 data (chip hgu133plus2) assembled using data from public repositories.")
1078 (license license:artistic2.0)))
1080 (define-public r-pfam-db
1087 (uri (bioconductor-uri "PFAM.db" version 'annotation))
1089 (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7"))))
1090 (properties `((upstream-name . "PFAM.db")))
1091 (build-system r-build-system)
1093 (list r-annotationdbi))
1094 (home-page "https://bioconductor.org/packages/PFAM.db")
1095 (synopsis "Set of protein ID mappings for PFAM")
1097 "This package provides a set of protein ID mappings for PFAM, assembled
1098 using data from public repositories.")
1099 (license license:artistic2.0)))
1101 (define-public r-phastcons100way-ucsc-hg19
1103 (name "r-phastcons100way-ucsc-hg19")
1108 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
1109 version 'annotation))
1112 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
1114 `((upstream-name . "phastCons100way.UCSC.hg19")))
1115 (build-system r-build-system)
1123 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
1124 (synopsis "UCSC phastCons conservation scores for hg19")
1126 "This package provides UCSC phastCons conservation scores for the human
1127 genome (hg19) calculated from multiple alignments with other 99 vertebrate
1129 (license license:artistic2.0)))
1134 (define-public r-abadata
1140 (uri (bioconductor-uri "ABAData" version 'experiment))
1143 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
1145 `((upstream-name . "ABAData")))
1146 (build-system r-build-system)
1148 (list r-annotationdbi))
1149 (home-page "https://www.bioconductor.org/packages/ABAData/")
1150 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
1152 "This package provides the data for the gene expression enrichment
1153 analysis conducted in the package ABAEnrichment. The package includes three
1154 datasets which are derived from the Allen Brain Atlas:
1157 @item Gene expression data from Human Brain (adults) averaged across donors,
1158 @item Gene expression data from the Developing Human Brain pooled into five
1159 age categories and averaged across donors, and
1160 @item a developmental effect score based on the Developing Human Brain
1164 All datasets are restricted to protein coding genes.")
1165 (license license:gpl2+)))
1167 (define-public r-adductdata
1169 (name "r-adductdata")
1173 (uri (bioconductor-uri "adductData" version 'experiment))
1175 (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48"))))
1176 (properties `((upstream-name . "adductData")))
1177 (build-system r-build-system)
1178 (propagated-inputs (list r-annotationhub r-experimenthub))
1179 (native-inputs (list r-knitr))
1180 (home-page "https://bioconductor.org/packages/adductData")
1181 (synopsis "Data from untargeted mass spectrometry of modifications to Cys34")
1183 "This package contains data from untargeted @dfn{mass spectrometry} (MS)
1184 of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
1186 (license license:artistic2.0)))
1188 (define-public r-aneufinderdata
1190 (name "r-aneufinderdata")
1194 (uri (bioconductor-uri "AneuFinderData" version 'experiment))
1196 (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7"))))
1197 (build-system r-build-system)
1198 (home-page "https://bioconductor.org/packages/AneuFinderData/")
1199 (synopsis "Data package for @code{AneuFinder}")
1200 (description "This package contains whole-genome single cell sequencing data for
1201 demonstration purposes in the @code{AneuFinder} package.")
1202 (license license:artistic2.0)))
1204 (define-public r-arrmdata
1210 (uri (bioconductor-uri "ARRmData" version 'experiment))
1212 (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p"))))
1214 `((upstream-name . "ARRmData")))
1215 (build-system r-build-system)
1216 (home-page "https://www.bioconductor.org/packages/ARRmData/")
1217 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
1219 "This package provides raw beta values from 36 samples across 3 groups
1220 from Illumina 450k methylation arrays.")
1221 (license license:artistic2.0)))
1223 (define-public r-biscuiteerdata
1225 (name "r-biscuiteerdata")
1230 (uri (bioconductor-uri "biscuiteerData" version 'experiment))
1232 (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
1234 `((upstream-name . "biscuiteerData")))
1235 (build-system r-build-system)
1237 (list r-annotationhub r-curl r-experimenthub))
1238 (native-inputs (list r-knitr))
1239 (home-page "https://bioconductor.org/packages/biscuiteerData")
1240 (synopsis "Data package for Biscuiteer")
1242 "This package contains default datasets used by the Bioconductor package
1244 (license license:gpl3)))
1246 (define-public r-celldex
1253 (uri (bioconductor-uri "celldex" version 'experiment))
1255 (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
1256 (properties `((upstream-name . "celldex")))
1257 (build-system r-build-system)
1259 (list r-annotationdbi
1262 r-delayedmatrixstats
1265 r-summarizedexperiment))
1266 (native-inputs (list r-knitr))
1267 (home-page "https://github.com/LTLA/celldex")
1268 (synopsis "Reference index for cell types")
1270 "This package provides a collection of reference expression datasets with
1271 curated cell type labels, for use in procedures like automated annotation of
1272 single-cell data or deconvolution of bulk RNA-seq.")
1273 (license license:gpl3)))
1275 (define-public r-chromstardata
1277 (name "r-chromstardata")
1282 (uri (bioconductor-uri "chromstaRData" version 'experiment))
1284 (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
1285 (properties `((upstream-name . "chromstaRData")))
1286 (build-system r-build-system)
1287 (home-page "https://bioconductor.org/packages/chromstaRData/")
1288 (synopsis "ChIP-seq data for demonstration purposes")
1290 "This package provides ChIP-seq data for demonstration purposes in the
1291 chromstaR package.")
1292 (license license:gpl3)))
1294 (define-public r-copyhelper
1296 (name "r-copyhelper")
1301 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
1303 (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
1304 (properties `((upstream-name . "CopyhelpeR")))
1305 (build-system r-build-system)
1306 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
1307 (synopsis "Helper files for CopywriteR")
1309 "This package contains the helper files that are required to run the
1310 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
1311 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
1312 mm10. In addition, it contains a blacklist filter to remove regions that
1313 display copy number variation. Files are stored as GRanges objects from the
1314 GenomicRanges Bioconductor package.")
1315 (license license:gpl2)))
1317 (define-public r-genelendatabase
1319 (name "r-genelendatabase")
1324 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
1326 (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
1328 `((upstream-name . "geneLenDataBase")))
1329 (build-system r-build-system)
1331 (list r-rtracklayer r-genomicfeatures))
1332 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
1333 (synopsis "Lengths of mRNA transcripts for a number of genomes")
1335 "This package provides the lengths of mRNA transcripts for a number of
1336 genomes and gene ID formats, largely based on the UCSC table browser.")
1337 (license license:lgpl2.0+)))
1339 (define-public r-genomationdata
1341 (name "r-genomationdata")
1346 (uri (bioconductor-uri "genomationData" version 'experiment))
1348 (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
1350 `((upstream-name . "genomationData")))
1351 (build-system r-build-system)
1352 ;; As this package provides little more than large data files, it doesn't
1353 ;; make sense to build substitutes.
1354 (arguments `(#:substitutable? #f))
1357 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
1358 (synopsis "Experimental data for use with the genomation package")
1360 "This package contains experimental genetic data for use with the
1361 genomation package. Included are Chip Seq, Methylation and Cage data,
1362 downloaded from Encode.")
1363 (license license:gpl3+)))
1365 (define-public r-msdata
1372 (uri (bioconductor-uri "msdata" version 'experiment))
1374 (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
1375 (properties `((upstream-name . "msdata")))
1376 (build-system r-build-system)
1377 (home-page "https://bioconductor.org/packages/msdata")
1378 (synopsis "Various Mass Spectrometry raw data example files")
1380 "This package provides Ion Trap positive ionization mode data in mzML file
1381 format. It includes a subset from 500-850 m/z and 1190-1310 seconds,
1382 including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
1383 III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
1384 LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
1385 files for various search engines.")
1386 (license license:gpl2+)))
1388 (define-public r-pasilla
1395 (uri (bioconductor-uri "pasilla" version 'experiment))
1397 (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
1398 (build-system r-build-system)
1399 (propagated-inputs (list r-dexseq))
1400 (native-inputs (list r-knitr))
1401 (home-page "https://www.bioconductor.org/packages/pasilla/")
1402 (synopsis "Data package with per-exon and per-gene read counts")
1403 (description "This package provides per-exon and per-gene read counts
1404 computed for selected genes from RNA-seq data that were presented in the
1405 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1406 by Brooks et al., Genome Research 2011.")
1407 (license license:lgpl2.1+)))
1409 (define-public r-hsmmsinglecell
1411 (name "r-hsmmsinglecell")
1416 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1418 (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
1420 `((upstream-name . "HSMMSingleCell")))
1421 (build-system r-build-system)
1422 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1423 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1425 "Skeletal myoblasts undergo a well-characterized sequence of
1426 morphological and transcriptional changes during differentiation. In this
1427 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1428 under high mitogen conditions (GM) and then differentiated by switching to
1429 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1430 hundred cells taken over a time-course of serum-induced differentiation.
1431 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1432 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1433 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1434 which were then sequenced to a depth of ~4 million reads per library,
1435 resulting in a complete gene expression profile for each cell.")
1436 (license license:artistic2.0)))
1438 (define-public r-all
1445 (uri (bioconductor-uri "ALL" version 'experiment))
1447 (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
1448 (properties `((upstream-name . "ALL")))
1449 (build-system r-build-system)
1452 (home-page "https://bioconductor.org/packages/ALL")
1453 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1455 "The data consist of microarrays from 128 different individuals with
1456 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1457 are available. The data have been normalized (using rma) and it is the
1458 jointly normalized data that are available here. The data are presented in
1459 the form of an @code{exprSet} object.")
1460 (license license:artistic2.0)))
1462 (define-public r-affydata
1469 (uri (bioconductor-uri "affydata" version 'experiment))
1471 (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
1472 (properties `((upstream-name . "affydata")))
1473 (build-system r-build-system)
1476 (home-page "https://bioconductor.org/packages/affydata/")
1477 (synopsis "Affymetrix data for demonstration purposes")
1479 "This package provides example datasets that represent 'real world
1480 examples' of Affymetrix data, unlike the artificial examples included in the
1481 package @code{affy}.")
1482 (license license:gpl2+)))
1484 (define-public r-gagedata
1491 (uri (bioconductor-uri "gageData" version 'experiment))
1493 (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
1494 (properties `((upstream-name . "gageData")))
1495 (build-system r-build-system)
1496 (home-page "https://bioconductor.org/packages/gageData")
1497 (synopsis "Auxiliary data for the gage package")
1499 "This is a supportive data package for the software package @code{gage}.
1500 However, the data supplied here are also useful for gene set or pathway
1501 analysis or microarray data analysis in general. In this package, we provide
1502 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1503 BMP6 (originally published as an demo dataset for GAGE, also registered as
1504 GSE13604 in GEO). This package also includes commonly used gene set data based
1505 on KEGG pathways and GO terms for major research species, including human,
1506 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1507 yeast are also included.")
1508 (license license:gpl2+)))
1510 (define-public r-curatedtcgadata
1512 (name "r-curatedtcgadata")
1517 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1519 (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
1521 `((upstream-name . "curatedTCGAData")))
1522 (build-system r-build-system)
1524 (list r-annotationhub
1527 r-multiassayexperiment
1529 r-summarizedexperiment))
1530 (native-inputs (list r-knitr))
1531 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1532 (synopsis "Curated data from The Cancer Genome Atlas")
1534 "This package provides publicly available data from The Cancer Genome
1535 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1536 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1537 number, mutation, microRNA, protein, and others) with clinical / pathological
1538 data. It also links assay barcodes with patient identifiers, enabling
1539 harmonized subsetting of rows (features) and columns (patients / samples)
1540 across the entire multi-'omics experiment.")
1541 (license license:artistic2.0)))
1543 (define-public r-tcgabiolinksgui-data
1545 (name "r-tcgabiolinksgui-data")
1550 (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
1552 (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
1553 (properties `((upstream-name . "TCGAbiolinksGUI.data")))
1554 (build-system r-build-system)
1555 (native-inputs (list r-knitr))
1556 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
1557 (synopsis "Data for the TCGAbiolinksGUI package")
1558 (description "This package provides supporting data for the
1559 TCGAbiolinksGUI package.")
1560 (license license:gpl3)))
1565 (define-public r-abarray
1571 (uri (bioconductor-uri "ABarray" version))
1574 "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
1575 (properties `((upstream-name . "ABarray")))
1576 (build-system r-build-system)
1577 (propagated-inputs (list r-biobase r-multtest))
1578 (home-page "https://bioconductor.org/packages/ABarray")
1580 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
1582 "The package @code{ABarray} is designed to work with Applied Biosystems
1583 whole genome microarray platform, as well as any other platform whose data can
1584 be transformed into expression data matrix. Functions include data
1585 preprocessing, filtering, control probe analysis, statistical analysis in one
1586 single function. A @dfn{graphical user interface} (GUI) is also provided. The
1587 raw data, processed data, graphics output and statistical results are organized
1588 into folders according to the analysis settings used.")
1589 (license license:gpl2+)))
1591 (define-public r-absseq
1597 (uri (bioconductor-uri "ABSSeq" version))
1600 "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
1601 (properties `((upstream-name . "ABSSeq")))
1602 (build-system r-build-system)
1603 (propagated-inputs (list r-limma r-locfit))
1604 (home-page "https://bioconductor.org/packages/ABSSeq")
1606 "RNA-Seq analysis based on modelling absolute expression differences")
1608 "This package implements a new RNA-Seq analysis method and integrates two
1609 modules: a basic model for pairwise comparison and a linear model for complex
1610 design. RNA-Seq quantifies gene expression with reads count, which usually
1611 consists of conditions (or treatments) and several replicates for each
1612 condition. This software infers differential expression directly by the
1613 counts difference between conditions. It assumes that the sum counts
1614 difference between conditions follow a negative binomial distribution. In
1615 addition, @code{ABSSeq} moderates the fold-changes by two steps: the
1616 expression level and gene-specific dispersion, that might facilitate the gene
1617 ranking by fold-change and visualization.")
1618 (license license:gpl3+)))
1620 (define-public r-adam
1626 (uri (bioconductor-uri "ADAM" version))
1629 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
1630 (properties `((upstream-name . "ADAM")))
1631 (build-system r-build-system)
1632 (propagated-inputs (list r-dplyr
1640 r-summarizedexperiment))
1641 (native-inputs (list r-knitr))
1642 (home-page "https://bioconductor.org/packages/ADAM")
1643 (synopsis "Gene activity and diversity analysis module")
1645 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
1646 package created to group a set of genes from comparative samples (control
1647 versus experiment) belonging to different species according to their respective
1648 functions. The corresponding roles are extracted from the default collections
1649 like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
1650 @code{ADAM} show their significance by calculating the p-values referring to
1651 gene diversity and activity. Each group of genes is called @dfn{Group of
1652 functionally associated genes} (GFAG).")
1653 (license license:gpl2+)))
1655 (define-public r-adamgui
1661 (uri (bioconductor-uri "ADAMgui" version))
1664 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
1665 (properties `((upstream-name . "ADAMgui")))
1666 (build-system r-build-system)
1688 (native-inputs (list r-knitr))
1689 (home-page "https://bioconductor.org/packages/ADAMgui/")
1690 (synopsis "GUI for gene activity and diversity analysis")
1692 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
1693 for the @code{ADAM} package. The @code{ADAMgui} package provides two
1694 shiny-based applications that allows the user to study the output of the
1695 @code{ADAM} package files through different plots. It's possible, for
1696 example, to choose a specific @dfn{group of functionally associated
1697 genes} (GFAG) and observe the gene expression behavior with the plots created
1698 with the @code{GFAGtargetUi} function. Features such as differential
1699 expression and fold change can be easily seen with aid of the plots made with
1700 the @code{GFAGpathUi} function.")
1701 (license license:gpl2+)))
1703 (define-public r-adimpute
1709 (uri (bioconductor-uri "ADImpute" version))
1712 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
1713 (properties `((upstream-name . "ADImpute")))
1714 (build-system r-build-system)
1716 (list r-biocparallel
1726 r-singlecellexperiment
1727 r-summarizedexperiment))
1728 (native-inputs (list r-knitr))
1729 (home-page "https://bioconductor.org/packages/ADImpute")
1730 (synopsis "Adaptive computational prediction for dropout imputations")
1732 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
1733 unable to quantify the expression levels of all genes in a cell, creating a
1734 need for the computational prediction of missing values (dropout imputation).
1735 Most existing dropout imputation methods are limited in the sense that they
1736 exclusively use the scRNA-seq dataset at hand and do not exploit external
1737 gene-gene relationship information. The @code{ADImpute} package proposes two
1738 methods to address this issue:
1741 @item a gene regulatory network-based approach using gene-gene relationships
1742 learnt from external data;
1743 @item a baseline approach corresponding to a sample-wide average.
1746 @code{ADImpute} implements these novel methods and also combines them with
1747 existing imputation methods like @code{DrImpute} and @code{SAVER}.
1748 @code{ADImpute} can learn the best performing method per gene and combine the
1749 results from different methods into an ensemble.")
1750 (license license:gpl3+)))
1752 (define-public r-adsplit
1758 (uri (bioconductor-uri "adSplit" version))
1761 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
1762 (properties `((upstream-name . "adSplit")))
1763 (build-system r-build-system)
1765 (list r-annotationdbi
1771 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
1772 (synopsis "Annotation-driven splits in microarray data")
1774 "This package implements clustering of microarray gene expression
1775 profiles according to functional annotations. For each term genes are
1776 annotated to, splits into two subclasses are computed and a significance of
1777 the supporting gene set is determined.")
1778 (license license:gpl2+)))
1780 (define-public r-affixcan
1786 (uri (bioconductor-uri "AffiXcan" version))
1789 "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
1790 (properties `((upstream-name . "AffiXcan")))
1791 (build-system r-build-system)
1793 (list r-biocparallel
1795 r-multiassayexperiment
1796 r-summarizedexperiment))
1797 (native-inputs (list r-knitr))
1798 (home-page "https://bioconductor.org/packages/AffiXcan")
1799 (synopsis "Functional approach to impute genetically regulated expression")
1801 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
1802 expression} (GReX) for a set of genes in a sample of individuals, using a
1803 method based on the @dfn{total binding affinity} (TBA). Statistical models to
1804 impute GReX can be trained with a training dataset where the real total
1805 expression values are known.")
1806 (license license:gpl3)))
1808 (define-public r-affyrnadegradation
1810 (name "r-affyrnadegradation")
1814 (uri (bioconductor-uri "AffyRNADegradation" version))
1817 "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
1818 (properties `((upstream-name . "AffyRNADegradation")))
1819 (build-system r-build-system)
1820 (propagated-inputs (list r-affy))
1821 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
1823 "Analyze and correct probe positional bias in data due to RNA degradation")
1825 "The @code{AffyRNADegradation} package helps with the assessment and
1826 correction of RNA degradation effects in Affymetrix 3 expression arrays. The
1827 parameter @code{d} gives a robust and accurate measure of RNA integrity. The
1828 correction removes the probe positional bias, and thus improves comparability
1829 of samples that are affected by RNA degradation.")
1830 ;; the R file header specifies GPL2 or later
1831 (license license:gpl2+)))
1833 (define-public r-agdex
1839 (uri (bioconductor-uri "AGDEX" version))
1842 "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
1843 (properties `((upstream-name . "AGDEX")))
1844 (build-system r-build-system)
1845 (propagated-inputs (list r-biobase r-gseabase))
1846 (home-page "https://bioconductor.org/packages/AGDEX")
1848 "Evaluate agreement of differential expression for cross-species genomics")
1850 "The objective of @code{AGDEX} is to evaluate whether the results of a
1851 pair of two-group differential expression analysis comparisons show a level of
1852 agreement that is greater than expected if the group labels for each two-group
1853 comparison are randomly assigned. The agreement is evaluated for the entire
1854 transcriptome and (optionally) for a collection of pre-defined gene-sets.
1855 Additionally, the procedure performs permutation-based differential expression
1856 and meta analysis at both gene and gene-set levels of the data from each
1858 (license license:gpl2+)))
1860 (define-public r-aggregatebiovar
1862 (name "r-aggregatebiovar")
1866 (uri (bioconductor-uri "aggregateBioVar" version))
1869 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
1870 (properties `((upstream-name . "aggregateBioVar")))
1871 (build-system r-build-system)
1876 r-singlecellexperiment
1877 r-summarizedexperiment
1879 (native-inputs (list r-knitr))
1880 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
1881 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
1883 "This package @code{aggregateBioVar} contains tools to summarize single
1884 cell gene expression profiles at the level of subject for single cell RNA-seq
1885 data collected from more than one subject (e.g. biological sample or technical
1886 replicates). A @code{SingleCellExperiment} object is taken as input and
1887 converted to a list of @code{SummarizedExperiment} objects, where each list
1888 element corresponds to an assigned cell type. The @code{SummarizedExperiment}
1889 objects contain aggregate gene-by-subject count matrices and inter-subject
1890 column metadata for individual subjects that can be processed using downstream
1891 bulk RNA-seq tools.")
1892 (license license:gpl3)))
1894 (define-public r-agilp
1900 (uri (bioconductor-uri "agilp" version))
1903 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
1904 (properties `((upstream-name . "agilp")))
1905 (build-system r-build-system)
1906 (home-page "https://bioconductor.org/packages/agilp")
1907 (synopsis "Processing of Agilent expression array")
1909 "This package aims to provide a pipeline for the low-level analysis of
1910 gene expression microarray data, primarily focused on the Agilent platform,
1911 but which also provides utilities which may be useful for other platforms.")
1912 ;; Some files are under GPLv2+ but the combined work is released under the
1914 (license license:gpl3)))
1916 (define-public r-adductomicsr
1918 (name "r-adductomicsr")
1922 (uri (bioconductor-uri "adductomicsR" version))
1925 "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
1926 (properties `((upstream-name . "adductomicsR")))
1927 (build-system r-build-system)
1950 (native-inputs (list r-knitr))
1951 (home-page "https://bioconductor.org/packages/adductomicsR")
1952 (synopsis "Processing of adductomic mass spectral datasets")
1954 "This package @code{adductomicsR} processes data generated by the
1955 @dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
1956 peptides from spectra that has been corrected for mass drift and retention
1957 time drift and quantifies level mass spectral peaks from @dfn{first stage of
1958 mass spectrometry} (MS1) data.")
1959 (license license:artistic2.0)))
1961 (define-public r-agimicrorna
1963 (name "r-agimicrorna")
1967 (uri (bioconductor-uri "AgiMicroRna" version))
1970 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
1971 (properties `((upstream-name . "AgiMicroRna")))
1972 (build-system r-build-system)
1979 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
1981 "Processing and differential expression analysis of Agilent microRNA chips")
1983 "@code{AgiMicroRna} provides useful functionality for the processing,
1984 quality assessment and differential expression analysis of Agilent microRNA
1985 array data. The package uses a limma-like structure to generate the processed
1986 data in order to make statistical inferences about differential expression
1987 using the linear model features implemented in limma. Standard Bioconductor
1988 objects are used so that other packages could be used as well.")
1989 (license license:gpl3)))
1991 (define-public r-amountain
1993 (name "r-amountain")
1997 (uri (bioconductor-uri "AMOUNTAIN" version))
2000 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
2001 (properties `((upstream-name . "AMOUNTAIN")))
2002 (build-system r-build-system)
2004 (native-inputs (list r-knitr))
2005 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
2006 (synopsis "Modules for multilayer weighted gene co-expression networks")
2008 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
2009 gene co-expression network) could be constructed only from expression profile.
2010 Different layers in such networks may represent different time points, multiple
2011 conditions or various species. @code{AMOUNTAIN} aims to search active modules
2012 in multi-layer WGCN using a continuous optimization approach.")
2013 (license license:gpl2+)))
2015 (define-public r-amaretto
2021 (uri (bioconductor-uri "AMARETTO" version))
2024 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
2025 (properties `((upstream-name . "AMARETTO")))
2026 (build-system r-build-system)
2028 (list r-biocfilecache
2046 r-multiassayexperiment
2052 (native-inputs (list r-knitr))
2053 (home-page "https://bioconductor.org/packages/AMARETTO")
2054 (synopsis "Regulatory network inference and driver gene evaluation")
2056 "This package @code{AMARETTO} represents an algorithm that integrates copy
2057 number, DNA methylation and gene expression data to identify a set of driver
2058 genes by analyzing cancer samples and connects them to clusters of co-expressed
2059 genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
2060 setting to identify cancer driver genes and their modules on multiple cancer
2061 sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
2062 and EMT, and modules that accurately predict survival and molecular subtypes.
2063 This allows @code{AMARETTO} to identify novel cancer driver genes directing
2064 canonical cancer pathways.")
2065 (license license:asl2.0)))
2067 (define-public r-anaquin
2073 (uri (bioconductor-uri "Anaquin" version))
2076 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
2077 (properties `((upstream-name . "Anaquin")))
2078 (build-system r-build-system)
2087 (native-inputs (list r-knitr))
2088 (home-page "https://www.sequinstandards.com/")
2089 (synopsis "Statistical analysis of sequins")
2091 "The project is intended to support the use of @dfn{sequins}(synthetic
2092 sequencing spike-in controls) owned and made available by the Garvan Institute
2093 of Medical Research. The goal is to provide a standard open source library for
2094 quantitative analysis, modelling and visualization of spike-in controls.")
2095 (license license:bsd-3)))
2097 (define-public r-aneufinder
2099 (name "r-aneufinder")
2103 (uri (bioconductor-uri "AneuFinder" version))
2106 "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
2107 (build-system r-build-system)
2111 (list r-genomicranges
2132 (home-page "https://bioconductor.org/packages/AneuFinder/")
2133 (synopsis "Copy number variation analysis in single-cell-sequencing data")
2134 (description "This package implements functions for copy number variant
2135 calling, plotting, export and analysis from whole-genome single cell
2137 (license license:artistic2.0)))
2139 (define-public r-anf
2145 (uri (bioconductor-uri "ANF" version))
2148 "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
2149 (properties `((upstream-name . "ANF")))
2150 (build-system r-build-system)
2157 (native-inputs (list r-knitr))
2158 (home-page "https://bioconductor.org/packages/ANF")
2159 (synopsis "Affinity network fusion for complex patient clustering")
2161 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
2162 matrix construction and fusion as well as spectral clustering. This package is
2163 used for complex patient clustering by integrating multi-omic data through affinity
2165 (license license:gpl3)))
2167 (define-public r-annmap
2173 (uri (bioconductor-uri "annmap" version))
2176 "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
2177 (properties `((upstream-name . "annmap")))
2178 (build-system r-build-system)
2190 (home-page "https://github.com/cruk-mi/annmap")
2192 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
2194 "This package @code{annmap} provides annotation mappings for Affymetrix exon
2195 arrays and coordinate based queries to support deep sequencing data analysis.
2196 Database access is hidden behind the API which provides a set of functions such
2197 as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
2198 Functions to plot gene architecture and BAM file data are also provided.")
2199 (license license:gpl2)))
2201 (define-public r-antiprofiles
2203 (name "r-antiprofiles")
2207 (uri (bioconductor-uri "antiProfiles" version))
2210 "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
2211 (properties `((upstream-name . "antiProfiles")))
2212 (build-system r-build-system)
2216 (home-page "https://github.com/HCBravoLab/antiProfiles")
2217 (synopsis "Implementation of gene expression anti-profiles")
2219 "This package implements the gene expression anti-profiles method.
2220 Anti-profiles are a new approach for developing cancer genomic signatures that
2221 specifically take advantage of gene expression heterogeneity. They explicitly
2222 model increased gene expression variability in cancer to define robust and
2223 reproducible gene expression signatures capable of accurately distinguishing
2224 tumor samples from healthy controls.")
2225 (license license:artistic2.0)))
2227 (define-public r-biocversion
2229 (name "r-biocversion")
2234 (uri (bioconductor-uri "BiocVersion" version))
2237 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
2238 (properties `((upstream-name . "BiocVersion")))
2239 (build-system r-build-system)
2240 (home-page "https://bioconductor.org/packages/BiocVersion/")
2241 (synopsis "Set the appropriate version of Bioconductor packages")
2243 "This package provides repository information for the appropriate version
2245 (license license:artistic2.0)))
2247 (define-public r-biocgenerics
2249 (name "r-biocgenerics")
2253 (uri (bioconductor-uri "BiocGenerics" version))
2256 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
2258 `((upstream-name . "BiocGenerics")))
2259 (build-system r-build-system)
2260 (home-page "https://bioconductor.org/packages/BiocGenerics")
2261 (synopsis "S4 generic functions for Bioconductor")
2263 "This package provides S4 generic functions needed by many Bioconductor
2265 (license license:artistic2.0)))
2267 (define-public r-coverageview
2269 (name "r-coverageview")
2273 (uri (bioconductor-uri "CoverageView" version))
2276 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
2277 (build-system r-build-system)
2285 (home-page "https://bioconductor.org/packages/CoverageView/")
2286 (synopsis "Coverage visualization package for R")
2287 (description "This package provides a framework for the visualization of
2288 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
2289 be also used for genome-wide nucleosome positioning experiments or other
2290 experiment types where it is important to have a framework in order to inspect
2291 how the coverage distributed across the genome.")
2292 (license license:artistic2.0)))
2294 (define-public r-cummerbund
2296 (name "r-cummerbund")
2300 (uri (bioconductor-uri "cummeRbund" version))
2303 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
2304 (build-system r-build-system)
2316 (home-page "https://bioconductor.org/packages/cummeRbund/")
2317 (synopsis "Analyze Cufflinks high-throughput sequencing data")
2318 (description "This package allows for persistent storage, access,
2319 exploration, and manipulation of Cufflinks high-throughput sequencing
2320 data. In addition, provides numerous plotting functions for commonly
2321 used visualizations.")
2322 (license license:artistic2.0)))
2324 (define-public r-dearseq
2331 (uri (bioconductor-uri "dearseq" version))
2334 "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1"))))
2335 (build-system r-build-system)
2337 (list r-compquadform
2353 (home-page "https://github.com/borishejblum/dearseq")
2354 (synopsis "DEA for RNA-seq data through a robust variance component test")
2356 "This is a package for Differential Expression Analysis of RNA-seq data.
2357 It features a variance component score test accounting for data
2358 heteroscedasticity through precision weights. Perform both gene-wise and gene
2359 set analyses, and can deal with repeated or longitudinal data.")
2360 (license license:gpl2)))
2362 (define-public r-decipher
2368 (uri (bioconductor-uri "DECIPHER" version))
2371 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
2372 (build-system r-build-system)
2380 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
2381 (synopsis "Tools for deciphering and managing biological sequences")
2382 (description "This package provides a toolset for deciphering and managing
2383 biological sequences.")
2384 (license license:gpl3)))
2386 (define-public r-deconvr
2392 (uri (bioconductor-uri "deconvR" version))
2395 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
2396 (properties `((upstream-name . "deconvR")))
2397 (build-system r-build-system)
2416 (native-inputs (list r-knitr))
2417 (home-page "https://github.com/BIMSBbioinfo/deconvR")
2418 (synopsis "Simulation and deconvolution of omic profiles")
2420 "This package provides a collection of functions designed for analyzing
2421 deconvolution of the bulk sample(s) using an atlas of reference omic signature
2422 profiles and a user-selected model. Users are given the option to create or
2423 extend a reference atlas and,also simulate the desired size of the bulk
2424 signature profile of the reference cell types. The package includes the
2425 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
2426 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
2427 make mapping WGBS data to their probe IDs easier.")
2428 (license license:artistic2.0)))
2430 (define-public r-decoupler
2432 (name "r-decoupler")
2437 (uri (bioconductor-uri "decoupleR" version))
2439 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
2440 (properties `((upstream-name . "decoupleR")))
2441 (build-system r-build-system)
2454 (native-inputs (list r-knitr))
2455 (home-page "https://saezlab.github.io/decoupleR/")
2456 (synopsis "Computational methods to infer biological activities from omics data")
2458 "Many methods allow us to extract biological activities from omics data using
2459 information from prior knowledge resources, reducing the dimensionality for
2460 increased statistical power and better interpretability. decoupleR is a
2461 Bioconductor package containing different statistical methods to extract these
2462 signatures within a unified framework. decoupleR allows the user to flexibly
2463 test any method with any resource. It incorporates methods that take into
2464 account the sign and weight of network interactions. decoupleR can be used
2465 with any omic, as long as its features can be linked to a biological process
2466 based on prior knowledge. For example, in transcriptomics gene sets regulated
2467 by a transcription factor, or in phospho-proteomics phosphosites that are
2468 targeted by a kinase.")
2469 (license license:gpl3)))
2471 (define-public r-deepsnv
2477 (uri (bioconductor-uri "deepSNV" version))
2480 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
2481 (properties `((upstream-name . "deepSNV")))
2482 (build-system r-build-system)
2488 r-summarizedexperiment
2493 (home-page "https://github.com/gerstung-lab/deepSNV/")
2494 (synopsis "Detection of subclonal SNVs in deep sequencing data")
2496 "This package provides quantitative variant callers for detecting
2497 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
2498 The deepSNV algorithm is used for a comparative setup with a control experiment
2499 of the same loci and uses a beta-binomial model and a likelihood ratio test to
2500 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
2501 computes a Bayes classifier based on a beta-binomial model for variant calling
2502 with multiple samples for precisely estimating model parameters - such as local
2503 error rates and dispersion - and prior knowledge, e.g. from variation data
2504 bases such as COSMIC.")
2505 (license license:gpl3)))
2507 (define-public r-delayedarray
2509 (name "r-delayedarray")
2513 (uri (bioconductor-uri "DelayedArray" version))
2516 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
2518 `((upstream-name . "DelayedArray")))
2519 (build-system r-build-system)
2521 (list r-biocgenerics r-s4vectors r-iranges r-matrix
2525 (home-page "https://bioconductor.org/packages/DelayedArray")
2526 (synopsis "Delayed operations on array-like objects")
2528 "Wrapping an array-like object (typically an on-disk object) in a
2529 @code{DelayedArray} object allows one to perform common array operations on it
2530 without loading the object in memory. In order to reduce memory usage and
2531 optimize performance, operations on the object are either delayed or executed
2532 using a block processing mechanism. Note that this also works on in-memory
2533 array-like objects like @code{DataFrame} objects (typically with Rle columns),
2534 @code{Matrix} objects, and ordinary arrays and data frames.")
2535 (license license:artistic2.0)))
2537 (define-public r-derfinderhelper
2539 (name "r-derfinderhelper")
2544 (uri (bioconductor-uri "derfinderHelper" version))
2546 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
2547 (properties `((upstream-name . "derfinderHelper")))
2548 (build-system r-build-system)
2550 (list r-iranges r-matrix r-s4vectors))
2553 (home-page "https://github.com/leekgroup/derfinderHelper")
2554 (synopsis "Helper for derfinder")
2556 "This package speeds up the derfinder package when using multiple cores.
2557 It is particularly useful when using BiocParallel and it helps reduce the time
2558 spent loading the full derfinder package when running the F-statistics
2559 calculation in parallel.")
2560 (license license:artistic2.0)))
2562 (define-public r-drimseq
2569 (uri (bioconductor-uri "DRIMSeq" version))
2571 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
2572 (properties `((upstream-name . "DRIMSeq")))
2573 (build-system r-build-system)
2575 (list r-biocgenerics
2585 (native-inputs (list r-knitr))
2586 (home-page "https://bioconductor.org/packages/DRIMSeq")
2587 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
2589 "The package provides two frameworks. One for the differential
2590 transcript usage analysis between different conditions and one for the tuQTL
2591 analysis. Both are based on modeling the counts of genomic features (i.e.,
2592 transcripts) with the Dirichlet-multinomial distribution. The package also
2593 makes available functions for visualization and exploration of the data and
2595 (license license:gpl3+)))
2597 (define-public r-bluster
2603 (uri (bioconductor-uri "bluster" version))
2606 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
2607 (properties `((upstream-name . "bluster")))
2608 (build-system r-build-system)
2610 (list r-biocneighbors
2619 (home-page "https://bioconductor.org/packages/bluster")
2620 (synopsis "Clustering algorithms for Bioconductor")
2621 (description"This package wraps common clustering algorithms in an easily
2622 extended S4 framework. Backends are implemented for hierarchical, k-means
2623 and graph-based clustering. Several utilities are also provided to compare
2624 and evaluate clustering results.")
2625 (license license:gpl3)))
2627 (define-public r-ideoviz
2633 (uri (bioconductor-uri "IdeoViz" version))
2636 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
2637 (build-system r-build-system)
2645 (home-page "https://bioconductor.org/packages/IdeoViz/")
2646 (synopsis "Plots data along a chromosomal ideogram")
2647 (description "This package provides functions to plot data associated with
2648 arbitrary genomic intervals along chromosomal ideogram.")
2649 (license license:gpl2)))
2651 (define-public r-infercnv
2658 (uri (bioconductor-uri "infercnv" version))
2661 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
2662 (properties `((upstream-name . "infercnv")))
2663 (build-system r-build-system)
2664 (inputs (list python))
2693 r-singlecellexperiment
2694 r-summarizedexperiment
2696 (native-inputs (list r-knitr))
2697 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
2698 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
2700 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
2701 evidence for somatic large-scale chromosomal copy number alterations, such as gains
2702 or deletions of entire chromosomes or large segments of chromosomes. This is done
2703 by exploring expression intensity of genes across positions of a tumor genome in
2704 comparison to a set of reference \"normal\" cells. A heatmap is generated
2705 illustrating the relative expression intensities across each chromosome, and it
2706 often becomes readily apparent as to which regions of the tumor genome are
2707 over-abundant or less-abundant as compared to that of normal cells.")
2708 (license license:bsd-3)))
2710 (define-public r-iranges
2716 (uri (bioconductor-uri "IRanges" version))
2719 "0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k"))))
2721 `((upstream-name . "IRanges")))
2722 (build-system r-build-system)
2724 (list r-biocgenerics r-s4vectors))
2725 (home-page "https://bioconductor.org/packages/IRanges")
2726 (synopsis "Infrastructure for manipulating intervals on sequences")
2728 "This package provides efficient low-level and highly reusable S4 classes
2729 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
2730 generally, data that can be organized sequentially (formally defined as
2731 @code{Vector} objects), as well as views on these @code{Vector} objects.
2732 Efficient list-like classes are also provided for storing big collections of
2733 instances of the basic classes. All classes in the package use consistent
2734 naming and share the same rich and consistent \"Vector API\" as much as
2736 (license license:artistic2.0)))
2738 (define-public r-isoformswitchanalyzer
2740 (name "r-isoformswitchanalyzer")
2745 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
2747 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
2748 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
2749 (build-system r-build-system)
2782 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
2783 (synopsis "Analyze alternative splicing in RNA-seq data")
2785 "This is a package for the analysis of alternative splicing and isoform
2786 switches with predicted functional consequences (e.g. gain/loss of protein
2787 domains etc.) from quantification of all types of RNASeq by tools such as
2788 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
2789 (license license:gpl2+)))
2791 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
2792 (define-public r-absfiltergsea
2794 (name "r-absfiltergsea")
2799 (uri (cran-uri "AbsFilterGSEA" version))
2801 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
2802 (properties `((upstream-name . "AbsFilterGSEA")))
2803 (build-system r-build-system)
2805 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
2806 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
2807 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
2809 "This package provides a function that performs gene-permuting of a gene-set
2810 enrichment analysis (GSEA) calculation with or without the absolute filtering.
2811 Without filtering, users can perform (original) two-tailed or one-tailed
2813 (license license:gpl2)))
2815 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
2816 (define-public r-bisquerna
2818 (name "r-bisquerna")
2822 (uri (cran-uri "BisqueRNA" version))
2825 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
2826 (properties `((upstream-name . "BisqueRNA")))
2827 (build-system r-build-system)
2829 (list r-biobase r-limsolve))
2832 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
2833 (synopsis "Decomposition of bulk expression with single-cell sequencing")
2834 (description "This package provides tools to accurately estimate cell type
2835 abundances from heterogeneous bulk expression. A reference-based method
2836 utilizes single-cell information to generate a signature matrix and
2837 transformation of bulk expression for accurate regression based estimates.
2838 A marker-based method utilizes known cell-specific marker genes to measure
2839 relative abundances across samples.")
2840 (license license:gpl3)))
2842 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
2843 ;; from Bioconductor.
2844 (define-public r-deconstructsigs
2846 (name "r-deconstructsigs")
2850 (uri (cran-uri "deconstructSigs" version))
2853 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
2855 `((upstream-name . "deconstructSigs")))
2856 (build-system r-build-system)
2858 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
2860 (home-page "https://github.com/raerose01/deconstructSigs")
2861 (synopsis "Identifies signatures present in a tumor sample")
2862 (description "This package takes sample information in the form of the
2863 fraction of mutations in each of 96 trinucleotide contexts and identifies
2864 the weighted combination of published signatures that, when summed, most
2865 closely reconstructs the mutational profile.")
2866 (license license:gpl2+)))
2868 ;; This is a CRAN package, but it depends on Bioconductor packages.
2869 (define-public r-jetset
2876 (uri (cran-uri "jetset" version))
2878 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
2879 (properties `((upstream-name . "jetset")))
2880 (build-system r-build-system)
2881 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
2882 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
2883 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
2885 "This package provides a one-to-one mapping from gene to \"best\" probe
2886 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
2887 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
2888 gene may be measured by multiple probe sets. This can present a mild
2889 conundrum when attempting to evaluate a gene \"signature\" that is defined by
2890 gene names rather than by specific probe sets. This package also includes the
2891 pre-calculated probe set quality scores that were used to define the
2893 (license license:artistic2.0)))
2895 ;; This is a CRAN package, but it depends on Bioconductor packages.
2896 (define-public r-nmf
2903 (uri (cran-uri "NMF" version))
2906 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
2907 (properties `((upstream-name . "NMF")))
2908 (build-system r-build-system)
2913 r-bigmemory ; suggested
2914 r-synchronicity ; suggested
2929 (home-page "http://renozao.github.io/NMF")
2930 (synopsis "Algorithms and framework for nonnegative matrix factorization")
2932 "This package provides a framework to perform Non-negative Matrix
2933 Factorization (NMF). The package implements a set of already published
2934 algorithms and seeding methods, and provides a framework to test, develop and
2935 plug new or custom algorithms. Most of the built-in algorithms have been
2936 optimized in C++, and the main interface function provides an easy way of
2937 performing parallel computations on multicore machines.")
2938 (license license:gpl2+)))
2940 (define-public r-affy
2947 (uri (bioconductor-uri "affy" version))
2950 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
2951 (build-system r-build-system)
2961 (home-page "https://bioconductor.org/packages/affy")
2962 (synopsis "Methods for affymetrix oligonucleotide arrays")
2964 "This package contains functions for exploratory oligonucleotide array
2966 (license license:lgpl2.0+)))
2968 (define-public r-affycomp
2975 (uri (bioconductor-uri "affycomp" version))
2978 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
2979 (properties `((upstream-name . "affycomp")))
2980 (build-system r-build-system)
2981 (propagated-inputs (list r-biobase))
2982 (home-page "https://bioconductor.org/packages/affycomp/")
2983 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
2985 "The package contains functions that can be used to compare expression
2986 measures for Affymetrix Oligonucleotide Arrays.")
2987 (license license:gpl2+)))
2989 (define-public r-affycompatible
2991 (name "r-affycompatible")
2996 (uri (bioconductor-uri "AffyCompatible" version))
2999 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
3001 `((upstream-name . "AffyCompatible")))
3002 (build-system r-build-system)
3006 `(modify-phases %standard-phases
3007 (add-after 'unpack 'make-reproducible
3009 ;; Order DTD elements before generating R code from them.
3010 (substitute* "R/methods-AffyCompatible.R"
3013 elements <- dtd$elements
3014 ordered <- elements[order(names(elements))]\n"))
3015 (("elt in dtd\\$elements")
3017 ;; Use a predictable directory name for code generation.
3018 (mkdir-p "/tmp/NetAffxResourcePrototype")
3019 (substitute* "R/DataClasses.R"
3020 (("directory=tempdir\\(\\)")
3021 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
3023 (list r-biostrings r-rcurl r-xml))
3024 (home-page "https://bioconductor.org/packages/AffyCompatible/")
3025 (synopsis "Work with Affymetrix GeneChip files")
3027 "This package provides an interface to Affymetrix chip annotation and
3028 sample attribute files. The package allows an easy way for users to download
3029 and manage local data bases of Affynmetrix NetAffx annotation files. It also
3030 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
3031 Command Console} (AGCC)-compatible sample annotation files.")
3032 (license license:artistic2.0)))
3034 (define-public r-affycontam
3036 (name "r-affycontam")
3041 (uri (bioconductor-uri "affyContam" version))
3044 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
3045 (properties `((upstream-name . "affyContam")))
3046 (build-system r-build-system)
3048 (list r-affy r-affydata r-biobase))
3049 (home-page "https://bioconductor.org/packages/affyContam/")
3050 (synopsis "Structured corruption of Affymetrix CEL file data")
3052 "Microarray quality assessment is a major concern of microarray analysts.
3053 This package provides some simple approaches to in silico creation of quality
3054 problems in CEL-level data to help evaluate performance of quality metrics.")
3055 (license license:artistic2.0)))
3057 (define-public r-affycoretools
3059 (name "r-affycoretools")
3064 (uri (bioconductor-uri "affycoretools" version))
3067 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
3068 (properties `((upstream-name . "affycoretools")))
3069 (build-system r-build-system)
3092 (home-page "https://bioconductor.org/packages/affycoretools/")
3093 (synopsis "Functions for analyses with Affymetrix GeneChips")
3095 "This package provides various wrapper functions that have been written
3096 to streamline the more common analyses that a Biostatistician might see.")
3097 (license license:artistic2.0)))
3099 (define-public r-affyio
3106 (uri (bioconductor-uri "affyio" version))
3109 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
3110 (build-system r-build-system)
3115 (home-page "https://github.com/bmbolstad/affyio")
3116 (synopsis "Tools for parsing Affymetrix data files")
3118 "This package provides routines for parsing Affymetrix data files based
3119 upon file format information. The primary focus is on accessing the CEL and
3121 (license license:lgpl2.0+)))
3123 (define-public r-affxparser
3125 (name "r-affxparser")
3130 (uri (bioconductor-uri "affxparser" version))
3133 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
3134 (properties `((upstream-name . "affxparser")))
3135 (build-system r-build-system)
3136 (home-page "https://github.com/HenrikBengtsson/affxparser")
3137 (synopsis "Affymetrix File Parsing SDK")
3139 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
3140 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
3141 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
3142 are supported. Currently, there are methods for reading @dfn{chip definition
3143 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
3144 either in full or in part. For example, probe signals from a few probesets
3145 can be extracted very quickly from a set of CEL files into a convenient list
3147 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
3149 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
3151 (define-public r-annotate
3158 (uri (bioconductor-uri "annotate" version))
3161 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
3162 (build-system r-build-system)
3164 (list r-annotationdbi
3172 "https://bioconductor.org/packages/annotate")
3173 (synopsis "Annotation for microarrays")
3174 (description "This package provides R environments for the annotation of
3176 (license license:artistic2.0)))
3178 (define-public r-annotationdbi
3180 (name "r-annotationdbi")
3184 (uri (bioconductor-uri "AnnotationDbi" version))
3187 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
3189 `((upstream-name . "AnnotationDbi")))
3190 (build-system r-build-system)
3201 (home-page "https://bioconductor.org/packages/AnnotationDbi")
3202 (synopsis "Annotation database interface")
3204 "This package provides user interface and database connection code for
3205 annotation data packages using SQLite data storage.")
3206 (license license:artistic2.0)))
3208 (define-public r-annotationfilter
3210 (name "r-annotationfilter")
3214 (uri (bioconductor-uri "AnnotationFilter" version))
3217 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
3219 `((upstream-name . "AnnotationFilter")))
3220 (build-system r-build-system)
3222 (list r-genomicranges r-lazyeval))
3225 (home-page "https://github.com/Bioconductor/AnnotationFilter")
3226 (synopsis "Facilities for filtering Bioconductor annotation resources")
3228 "This package provides classes and other infrastructure to implement
3229 filters for manipulating Bioconductor annotation resources. The filters are
3230 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
3231 (license license:artistic2.0)))
3233 (define-public r-annotationforge
3235 (name "r-annotationforge")
3240 (uri (bioconductor-uri "AnnotationForge" version))
3243 "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8"))))
3245 `((upstream-name . "AnnotationForge")))
3246 (build-system r-build-system)
3248 (list r-annotationdbi
3258 (home-page "https://bioconductor.org/packages/AnnotationForge")
3259 (synopsis "Code for building annotation database packages")
3261 "This package provides code for generating Annotation packages and their
3262 databases. Packages produced are intended to be used with AnnotationDbi.")
3263 (license license:artistic2.0)))
3265 (define-public r-annotationhub
3267 (name "r-annotationhub")
3272 (uri (bioconductor-uri "AnnotationHub" version))
3275 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
3276 (properties `((upstream-name . "AnnotationHub")))
3277 (build-system r-build-system)
3279 (list r-annotationdbi
3287 r-interactivedisplaybase
3294 (home-page "https://bioconductor.org/packages/AnnotationHub")
3295 (synopsis "Client to access AnnotationHub resources")
3297 "This package provides a client for the Bioconductor AnnotationHub web
3298 resource. The AnnotationHub web resource provides a central location where
3299 genomic files (e.g. VCF, bed, wig) and other resources from standard
3300 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
3301 metadata about each resource, e.g., a textual description, tags, and date of
3302 modification. The client creates and manages a local cache of files retrieved
3303 by the user, helping with quick and reproducible access.")
3304 (license license:artistic2.0)))
3306 (define-public r-aroma-light
3308 (name "r-aroma-light")
3313 (uri (bioconductor-uri "aroma.light" version))
3316 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
3317 (properties `((upstream-name . "aroma.light")))
3318 (build-system r-build-system)
3320 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
3321 (home-page "https://github.com/HenrikBengtsson/aroma.light")
3322 (synopsis "Methods for normalization and visualization of microarray data")
3324 "This package provides methods for microarray analysis that take basic
3325 data types such as matrices and lists of vectors. These methods can be used
3326 standalone, be utilized in other packages, or be wrapped up in higher-level
3328 (license license:gpl2+)))
3330 (define-public r-bamsignals
3332 (name "r-bamsignals")
3337 (uri (bioconductor-uri "bamsignals" version))
3340 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
3341 (build-system r-build-system)
3343 (list r-biocgenerics
3351 (home-page "https://bioconductor.org/packages/bamsignals")
3352 (synopsis "Extract read count signals from bam files")
3354 "This package efficiently obtains count vectors from indexed bam
3355 files. It counts the number of nucleotide sequence reads in given genomic
3356 ranges and it computes reads profiles and coverage profiles. It also handles
3358 (license license:gpl2+)))
3360 (define-public r-biobase
3366 (uri (bioconductor-uri "Biobase" version))
3369 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
3371 `((upstream-name . "Biobase")))
3372 (build-system r-build-system)
3374 (list r-biocgenerics))
3375 (home-page "https://bioconductor.org/packages/Biobase")
3376 (synopsis "Base functions for Bioconductor")
3378 "This package provides functions that are needed by many other packages
3379 on Bioconductor or which replace R functions.")
3380 (license license:artistic2.0)))
3382 (define-public r-biomart
3388 (uri (bioconductor-uri "biomaRt" version))
3391 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
3393 `((upstream-name . "biomaRt")))
3394 (build-system r-build-system)
3396 (list r-annotationdbi
3407 (home-page "https://bioconductor.org/packages/biomaRt")
3408 (synopsis "Interface to BioMart databases")
3410 "biomaRt provides an interface to a growing collection of databases
3411 implementing the @url{BioMart software suite, http://www.biomart.org}. The
3412 package enables retrieval of large amounts of data in a uniform way without
3413 the need to know the underlying database schemas or write complex SQL queries.
3414 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
3415 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
3416 users direct access to a diverse set of data and enable a wide range of
3417 powerful online queries from gene annotation to database mining.")
3418 (license license:artistic2.0)))
3420 ;; This is a CRAN package, but it depends on a Bioconductor package:
3422 (define-public r-biomartr
3428 (uri (cran-uri "biomartr" version))
3431 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
3432 (properties `((upstream-name . "biomartr")))
3433 (build-system r-build-system)
3453 (native-inputs (list r-knitr))
3454 (home-page "https://docs.ropensci.org/biomartr/")
3455 (synopsis "Genomic data retrieval")
3457 "Perform large scale genomic data retrieval and functional annotation
3458 retrieval. This package aims to provide users with a standardized way to
3459 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
3460 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
3461 Furthermore, an interface to the BioMart database allows users to retrieve
3462 functional annotation for genomic loci. In addition, users can download
3463 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
3465 (license license:gpl2)))
3467 (define-public r-biocparallel
3469 (name "r-biocparallel")
3473 (uri (bioconductor-uri "BiocParallel" version))
3476 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
3478 `((upstream-name . "BiocParallel")))
3479 (build-system r-build-system)
3482 (modify-phases %standard-phases
3483 (add-after 'unpack 'make-reproducible
3485 ;; Remove generated documentation.
3486 (for-each delete-file
3487 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
3488 "inst/doc/Introduction_To_BiocParallel.pdf"
3489 "inst/doc/Errors_Logs_And_Debugging.pdf"
3490 "inst/doc/BiocParallel_BatchtoolsParam.R"
3491 "inst/doc/Introduction_To_BiocParallel.R"
3492 "inst/doc/Errors_Logs_And_Debugging.R"))
3494 ;; Remove time-dependent macro
3495 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
3496 "inst/doc/Introduction_To_BiocParallel.Rnw"
3497 "inst/doc/Errors_Logs_And_Debugging.Rnw"
3498 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
3499 "vignettes/Introduction_To_BiocParallel.Rnw"
3500 "vignettes/Errors_Logs_And_Debugging.Rnw")
3501 (("\\today") "later"))
3503 ;; Initialize the random number generator seed when building.
3504 (substitute* "R/rng.R"
3505 (("\"L'Ecuyer-CMRG\"\\)" m)
3507 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
3509 (list r-bh r-codetools r-futile-logger r-snow))
3512 (home-page "https://bioconductor.org/packages/BiocParallel")
3513 (synopsis "Bioconductor facilities for parallel evaluation")
3515 "This package provides modified versions and novel implementation of
3516 functions for parallel evaluation, tailored to use with Bioconductor
3518 (license (list license:gpl2+ license:gpl3+))))
3520 (define-public r-biostrings
3522 (name "r-biostrings")
3526 (uri (bioconductor-uri "Biostrings" version))
3529 "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8"))))
3531 `((upstream-name . "Biostrings")))
3532 (build-system r-build-system)
3534 (list r-biocgenerics
3540 (home-page "https://bioconductor.org/packages/Biostrings")
3541 (synopsis "String objects and algorithms for biological sequences")
3543 "This package provides memory efficient string containers, string
3544 matching algorithms, and other utilities, for fast manipulation of large
3545 biological sequences or sets of sequences.")
3546 (license license:artistic2.0)))
3548 (define-public r-biovizbase
3550 (name "r-biovizbase")
3555 (uri (bioconductor-uri "biovizBase" version))
3558 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
3559 (properties `((upstream-name . "biovizBase")))
3560 (build-system r-build-system)
3562 (list r-annotationdbi
3579 r-summarizedexperiment
3580 r-variantannotation))
3581 (home-page "https://bioconductor.org/packages/biovizBase")
3582 (synopsis "Basic graphic utilities for visualization of genomic data")
3584 "The biovizBase package is designed to provide a set of utilities, color
3585 schemes and conventions for genomic data. It serves as the base for various
3586 high-level packages for biological data visualization. This saves development
3587 effort and encourages consistency.")
3588 (license license:artistic2.0)))
3590 (define-public r-bsgenome
3596 (uri (bioconductor-uri "BSgenome" version))
3599 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
3601 `((upstream-name . "BSgenome")))
3602 (build-system r-build-system)
3604 (list r-biocgenerics
3614 (home-page "https://bioconductor.org/packages/BSgenome")
3615 (synopsis "Infrastructure for Biostrings-based genome data packages")
3617 "This package provides infrastructure shared by all Biostrings-based
3618 genome data packages and support for efficient SNP representation.")
3619 (license license:artistic2.0)))
3621 (define-public r-category
3628 (uri (bioconductor-uri "Category" version))
3631 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
3632 (properties `((upstream-name . "Category")))
3633 (build-system r-build-system)
3645 (home-page "https://bioconductor.org/packages/Category")
3646 (synopsis "Category analysis")
3648 "This package provides a collection of tools for performing category
3650 (license license:artistic2.0)))
3652 (define-public r-chipseeker
3654 (name "r-chipseeker")
3658 (uri (bioconductor-uri "ChIPseeker" version))
3661 "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"))))
3662 (build-system r-build-system)
3666 (list r-annotationdbi
3684 r-txdb-hsapiens-ucsc-hg19-knowngene))
3685 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
3686 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
3687 (description "This package implements functions to retrieve the nearest
3688 genes around the peak, annotate genomic region of the peak, statstical methods
3689 for estimate the significance of overlap among ChIP peak data sets, and
3690 incorporate GEO database for user to compare the own dataset with those
3691 deposited in database. The comparison can be used to infer cooperative
3692 regulation and thus can be used to generate hypotheses. Several visualization
3693 functions are implemented to summarize the coverage of the peak experiment,
3694 average profile and heatmap of peaks binding to TSS regions, genomic
3695 annotation, distance to TSS, and overlap of peaks or genes.")
3696 (license license:artistic2.0)))
3698 (define-public r-chipseq
3705 (uri (bioconductor-uri "chipseq" version))
3708 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
3709 (build-system r-build-system)
3711 (list r-biocgenerics
3717 (home-page "https://bioconductor.org/packages/chipseq")
3718 (synopsis "Package for analyzing ChIPseq data")
3720 "This package provides tools for processing short read data from ChIPseq
3722 (license license:artistic2.0)))
3724 (define-public r-complexheatmap
3726 (name "r-complexheatmap")
3731 (uri (bioconductor-uri "ComplexHeatmap" version))
3734 "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65"))))
3736 `((upstream-name . "ComplexHeatmap")))
3737 (build-system r-build-system)
3755 "https://github.com/jokergoo/ComplexHeatmap")
3756 (synopsis "Making Complex Heatmaps")
3758 "Complex heatmaps are efficient to visualize associations between
3759 different sources of data sets and reveal potential structures. This package
3760 provides a highly flexible way to arrange multiple heatmaps and supports
3761 self-defined annotation graphics.")
3762 (license license:gpl2+)))
3764 (define-public r-copywriter
3766 (name "r-copywriter")
3771 (uri (bioconductor-uri "CopywriteR" version))
3774 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
3775 (properties `((upstream-name . "CopywriteR")))
3776 (build-system r-build-system)
3778 (list r-biocparallel
3792 (home-page "https://github.com/PeeperLab/CopywriteR")
3793 (synopsis "Copy number information from targeted sequencing")
3795 "CopywriteR extracts DNA copy number information from targeted sequencing
3796 by utilizing off-target reads. It allows for extracting uniformly distributed
3797 copy number information, can be used without reference, and can be applied to
3798 sequencing data obtained from various techniques including chromatin
3799 immunoprecipitation and target enrichment on small gene panels. Thereby,
3800 CopywriteR constitutes a widely applicable alternative to available copy
3801 number detection tools.")
3802 (license license:gpl2)))
3804 (define-public r-deseq
3811 (uri (bioconductor-uri "DESeq" version))
3814 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
3815 (properties `((upstream-name . "DESeq")))
3816 (build-system r-build-system)
3826 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
3827 (synopsis "Differential gene expression analysis")
3829 "This package provides tools for estimating variance-mean dependence in
3830 count data from high-throughput genetic sequencing assays and for testing for
3831 differential expression based on a model using the negative binomial
3833 (license license:gpl3+)))
3835 (define-public r-deseq2
3842 (uri (bioconductor-uri "DESeq2" version))
3845 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
3846 (properties `((upstream-name . "DESeq2")))
3847 (build-system r-build-system)
3861 r-summarizedexperiment))
3864 (home-page "https://bioconductor.org/packages/DESeq2")
3865 (synopsis "Differential gene expression analysis")
3867 "This package provides functions to estimate variance-mean dependence in
3868 count data from high-throughput nucleotide sequencing assays and test for
3869 differential expression based on a model using the negative binomial
3871 (license license:lgpl3+)))
3873 (define-public r-dexseq
3880 (uri (bioconductor-uri "DEXSeq" version))
3883 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
3884 (properties `((upstream-name . "DEXSeq")))
3885 (build-system r-build-system)
3887 (list r-annotationdbi
3903 r-summarizedexperiment))
3906 (home-page "https://bioconductor.org/packages/DEXSeq")
3907 (synopsis "Inference of differential exon usage in RNA-Seq")
3909 "This package is focused on finding differential exon usage using RNA-seq
3910 exon counts between samples with different experimental designs. It provides
3911 functions that allows the user to make the necessary statistical tests based
3912 on a model that uses the negative binomial distribution to estimate the
3913 variance between biological replicates and generalized linear models for
3914 testing. The package also provides functions for the visualization and
3915 exploration of the results.")
3916 (license license:gpl3+)))
3918 (define-public r-diffcyt
3925 (uri (bioconductor-uri "diffcyt" version))
3927 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
3928 (properties `((upstream-name . "diffcyt")))
3929 (build-system r-build-system)
3943 r-summarizedexperiment
3945 (native-inputs (list r-knitr))
3946 (home-page "https://github.com/lmweber/diffcyt")
3947 (synopsis "Differential discovery in high-dimensional cytometry")
3949 "This package provides statistical methods for differential discovery
3950 analyses in high-dimensional cytometry data (including flow cytometry, mass
3951 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
3952 combination of high-resolution clustering and empirical Bayes moderated tests
3953 adapted from transcriptomics.")
3954 (license license:expat)))
3956 (define-public r-dirichletmultinomial
3958 (name "r-dirichletmultinomial")
3963 (uri (bioconductor-uri "DirichletMultinomial" version))
3966 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
3968 `((upstream-name . "DirichletMultinomial")))
3969 (build-system r-build-system)
3973 (list r-biocgenerics r-iranges r-s4vectors))
3974 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
3975 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
3977 "Dirichlet-multinomial mixture models can be used to describe variability
3978 in microbial metagenomic data. This package is an interface to code
3979 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
3981 (license license:lgpl3)))
3983 (define-public r-dittoseq
3989 (uri (bioconductor-uri "dittoSeq" version))
3992 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
3993 (properties `((upstream-name . "dittoSeq")))
3994 (build-system r-build-system)
4005 r-singlecellexperiment
4006 r-summarizedexperiment))
4007 (native-inputs (list r-knitr))
4008 (home-page "https://bioconductor.org/packages/dittoSeq")
4009 (synopsis "Single-cell and bulk RNA sequencing visualization")
4011 "This package provides a universal, user friendly, single-cell and bulk RNA
4012 sequencing visualization toolkit that allows highly customizable creation of
4013 color blindness friendly, publication-quality figures. dittoSeq accepts both
4014 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
4015 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
4016 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
4017 percent composition or expression across groups, and more. Customizations
4018 range from size and title adjustments to automatic generation of annotations
4019 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
4020 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
4021 many more. All with simple, discrete inputs. Color blindness friendliness is
4022 powered by legend adjustments (enlarged keys), and by allowing the use of
4023 shapes or letter-overlay in addition to the carefully selected
4024 code{dittoColors()}.")
4025 (license license:expat)))
4027 (define-public r-edaseq
4034 (uri (bioconductor-uri "EDASeq" version))
4037 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
4038 (properties `((upstream-name . "EDASeq")))
4039 (build-system r-build-system)
4041 (list r-annotationdbi
4055 (home-page "https://github.com/drisso/EDASeq")
4056 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
4058 "This package provides support for numerical and graphical summaries of
4059 RNA-Seq genomic read data. Provided within-lane normalization procedures to
4060 adjust for GC-content effect (or other gene-level effects) on read counts:
4061 loess robust local regression, global-scaling, and full-quantile
4062 normalization. Between-lane normalization procedures to adjust for
4063 distributional differences between lanes (e.g., sequencing depth):
4064 global-scaling and full-quantile normalization.")
4065 (license license:artistic2.0)))
4067 (define-public r-edger
4073 (uri (bioconductor-uri "edgeR" version))
4076 "1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik"))))
4077 (properties `((upstream-name . "edgeR")))
4078 (build-system r-build-system)
4080 (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp
4081 (home-page "http://bioinf.wehi.edu.au/edgeR")
4082 (synopsis "EdgeR does empirical analysis of digital gene expression data")
4083 (description "This package can do differential expression analysis of
4084 RNA-seq expression profiles with biological replication. It implements a range
4085 of statistical methodology based on the negative binomial distributions,
4086 including empirical Bayes estimation, exact tests, generalized linear models
4087 and quasi-likelihood tests. It be applied to differential signal analysis of
4088 other types of genomic data that produce counts, including ChIP-seq, SAGE and
4090 (license license:gpl2+)))
4092 (define-public r-ensembldb
4094 (name "r-ensembldb")
4099 (uri (bioconductor-uri "ensembldb" version))
4102 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
4103 (build-system r-build-system)
4105 (list r-annotationdbi
4123 (home-page "https://github.com/jotsetung/ensembldb")
4124 (synopsis "Utilities to create and use Ensembl-based annotation databases")
4126 "The package provides functions to create and use transcript-centric
4127 annotation databases/packages. The annotation for the databases are directly
4128 fetched from Ensembl using their Perl API. The functionality and data is
4129 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
4130 but, in addition to retrieve all gene/transcript models and annotations from
4131 the database, the @code{ensembldb} package also provides a filter framework
4132 allowing to retrieve annotations for specific entries like genes encoded on a
4133 chromosome region or transcript models of lincRNA genes.")
4134 ;; No version specified
4135 (license license:lgpl3+)))
4137 (define-public r-fastseg
4144 (uri (bioconductor-uri "fastseg" version))
4147 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
4148 (build-system r-build-system)
4150 (list r-biobase r-biocgenerics r-genomicranges r-iranges
4152 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
4153 (synopsis "Fast segmentation algorithm for genetic sequencing data")
4155 "Fastseg implements a very fast and efficient segmentation algorithm.
4156 It can segment data from DNA microarrays and data from next generation
4157 sequencing for example to detect copy number segments. Further it can segment
4158 data from RNA microarrays like tiling arrays to identify transcripts. Most
4159 generally, it can segment data given as a matrix or as a vector. Various data
4160 formats can be used as input to fastseg like expression set objects for
4161 microarrays or GRanges for sequencing data.")
4162 (license license:lgpl2.0+)))
4164 (define-public r-gage
4171 (uri (bioconductor-uri "gage" version))
4174 "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"))))
4175 (build-system r-build-system)
4177 (list r-annotationdbi r-go-db r-graph r-keggrest))
4178 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
4179 "articles/10.1186/1471-2105-10-161"))
4180 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
4182 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
4183 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
4184 data attributes including sample sizes, experimental designs, assay platforms,
4185 and other types of heterogeneity. The gage package provides functions for
4186 basic GAGE analysis, result processing and presentation. In addition, it
4187 provides demo microarray data and commonly used gene set data based on KEGG
4188 pathways and GO terms. These functions and data are also useful for gene set
4189 analysis using other methods.")
4190 (license license:gpl2+)))
4192 (define-public r-genefilter
4194 (name "r-genefilter")
4199 (uri (bioconductor-uri "genefilter" version))
4202 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
4203 (build-system r-build-system)
4205 (list gfortran r-knitr))
4207 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
4209 (home-page "https://bioconductor.org/packages/genefilter")
4210 (synopsis "Filter genes from high-throughput experiments")
4212 "This package provides basic functions for filtering genes from
4213 high-throughput sequencing experiments.")
4214 (license license:artistic2.0)))
4216 (define-public r-geneoverlap
4218 (name "r-geneoverlap")
4222 (uri (bioconductor-uri "GeneOverlap" version))
4225 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
4226 (build-system r-build-system)
4228 (list r-rcolorbrewer r-gplots))
4229 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
4230 (synopsis "Test and visualize gene overlaps")
4231 (description "This package can be used to test two sets of gene lists
4232 and visualize the results.")
4233 (license license:gpl3)))
4235 (define-public r-genomation
4237 (name "r-genomation")
4241 (uri (bioconductor-uri "genomation" version))
4244 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
4245 (build-system r-build-system)
4269 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
4270 (synopsis "Summary, annotation and visualization of genomic data")
4272 "This package provides a package for summary and annotation of genomic
4273 intervals. Users can visualize and quantify genomic intervals over
4274 pre-defined functional regions, such as promoters, exons, introns, etc. The
4275 genomic intervals represent regions with a defined chromosome position, which
4276 may be associated with a score, such as aligned reads from HT-seq experiments,
4277 TF binding sites, methylation scores, etc. The package can use any tabular
4278 genomic feature data as long as it has minimal information on the locations of
4279 genomic intervals. In addition, it can use BAM or BigWig files as input.")
4280 (license license:artistic2.0)))
4282 (define-public r-genomeinfodb
4284 (name "r-genomeinfodb")
4288 (uri (bioconductor-uri "GenomeInfoDb" version))
4291 "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh"))))
4293 `((upstream-name . "GenomeInfoDb")))
4294 (build-system r-build-system)
4296 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
4300 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
4301 (synopsis "Utilities for manipulating chromosome identifiers")
4303 "This package contains data and functions that define and allow
4304 translation between different chromosome sequence naming conventions (e.g.,
4305 \"chr1\" versus \"1\"), including a function that attempts to place sequence
4306 names in their natural, rather than lexicographic, order.")
4307 (license license:artistic2.0)))
4309 (define-public r-genomicalignments
4311 (name "r-genomicalignments")
4315 (uri (bioconductor-uri "GenomicAlignments" version))
4318 "1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi"))))
4320 `((upstream-name . "GenomicAlignments")))
4321 (build-system r-build-system)
4323 (list r-biocgenerics
4331 r-summarizedexperiment))
4332 (home-page "https://bioconductor.org/packages/GenomicAlignments")
4333 (synopsis "Representation and manipulation of short genomic alignments")
4335 "This package provides efficient containers for storing and manipulating
4336 short genomic alignments (typically obtained by aligning short reads to a
4337 reference genome). This includes read counting, computing the coverage,
4338 junction detection, and working with the nucleotide content of the
4340 (license license:artistic2.0)))
4342 (define-public r-genomicfeatures
4344 (name "r-genomicfeatures")
4348 (uri (bioconductor-uri "GenomicFeatures" version))
4351 "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1"))))
4353 `((upstream-name . "GenomicFeatures")))
4354 (build-system r-build-system)
4356 (list r-annotationdbi
4373 (home-page "https://bioconductor.org/packages/GenomicFeatures")
4374 (synopsis "Tools for working with transcript centric annotations")
4376 "This package provides a set of tools and methods for making and
4377 manipulating transcript centric annotations. With these tools the user can
4378 easily download the genomic locations of the transcripts, exons and cds of a
4379 given organism, from either the UCSC Genome Browser or a BioMart
4380 database (more sources will be supported in the future). This information is
4381 then stored in a local database that keeps track of the relationship between
4382 transcripts, exons, cds and genes. Flexible methods are provided for
4383 extracting the desired features in a convenient format.")
4384 (license license:artistic2.0)))
4386 (define-public r-genomicfiles
4388 (name "r-genomicfiles")
4393 (uri (bioconductor-uri "GenomicFiles" version))
4396 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
4397 (properties `((upstream-name . "GenomicFiles")))
4398 (build-system r-build-system)
4400 (list r-biocgenerics
4410 r-summarizedexperiment
4411 r-variantannotation))
4412 (home-page "https://bioconductor.org/packages/GenomicFiles")
4413 (synopsis "Distributed computing by file or by range")
4415 "This package provides infrastructure for parallel computations
4416 distributed by file or by range. User defined mapper and reducer functions
4417 provide added flexibility for data combination and manipulation.")
4418 (license license:artistic2.0)))
4420 (define-public r-genomicranges
4422 (name "r-genomicranges")
4426 (uri (bioconductor-uri "GenomicRanges" version))
4429 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
4431 `((upstream-name . "GenomicRanges")))
4432 (build-system r-build-system)
4434 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
4437 (home-page "https://bioconductor.org/packages/GenomicRanges")
4438 (synopsis "Representation and manipulation of genomic intervals")
4440 "This package provides tools to efficiently represent and manipulate
4441 genomic annotations and alignments is playing a central role when it comes to
4442 analyzing high-throughput sequencing data (a.k.a. NGS data). The
4443 GenomicRanges package defines general purpose containers for storing and
4444 manipulating genomic intervals and variables defined along a genome.")
4445 (license license:artistic2.0)))
4447 (define-public r-gostats
4454 (uri (bioconductor-uri "GOstats" version))
4457 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
4458 (properties `((upstream-name . "GOstats")))
4459 (build-system r-build-system)
4470 (home-page "https://bioconductor.org/packages/GOstats")
4471 (synopsis "Tools for manipulating GO and microarrays")
4473 "This package provides a set of tools for interacting with GO and
4474 microarray data. A variety of basic manipulation tools for graphs, hypothesis
4475 testing and other simple calculations.")
4476 (license license:artistic2.0)))
4478 (define-public r-gseabase
4485 (uri (bioconductor-uri "GSEABase" version))
4488 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
4489 (properties `((upstream-name . "GSEABase")))
4490 (build-system r-build-system)
4500 (home-page "https://bioconductor.org/packages/GSEABase")
4501 (synopsis "Gene set enrichment data structures and methods")
4503 "This package provides classes and methods to support @dfn{Gene Set
4504 Enrichment Analysis} (GSEA).")
4505 (license license:artistic2.0)))
4507 (define-public r-hpar
4514 (uri (bioconductor-uri "hpar" version))
4517 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
4518 (build-system r-build-system)
4521 (home-page "https://bioconductor.org/packages/hpar/")
4522 (synopsis "Human Protein Atlas in R")
4523 (description "This package provides a simple interface to and data from
4524 the Human Protein Atlas project.")
4525 (license license:artistic2.0)))
4527 (define-public r-rhtslib
4534 (uri (bioconductor-uri "Rhtslib" version))
4537 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
4538 (properties `((upstream-name . "Rhtslib")))
4539 (build-system r-build-system)
4540 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
4541 ;; which makes R abort the build.
4542 (arguments '(#:configure-flags '("--no-staged-install")))
4544 (list curl zlib ; packages using rhtslib need to link with zlib
4547 (list pkg-config r-knitr))
4548 (home-page "https://github.com/nhayden/Rhtslib")
4549 (synopsis "High-throughput sequencing library as an R package")
4551 "This package provides the HTSlib C library for high-throughput
4552 nucleotide sequence analysis. The package is primarily useful to developers
4553 of other R packages who wish to make use of HTSlib.")
4554 (license license:lgpl2.0+)))
4556 (define-public r-impute
4562 (uri (bioconductor-uri "impute" version))
4565 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
4568 (build-system r-build-system)
4569 (home-page "https://bioconductor.org/packages/impute")
4570 (synopsis "Imputation for microarray data")
4572 "This package provides a function to impute missing gene expression
4573 microarray data, using nearest neighbor averaging.")
4574 (license license:gpl2+)))
4576 (define-public r-interactivedisplaybase
4578 (name "r-interactivedisplaybase")
4583 (uri (bioconductor-uri "interactiveDisplayBase" version))
4586 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
4588 `((upstream-name . "interactiveDisplayBase")))
4589 (build-system r-build-system)
4591 (list r-biocgenerics r-dt r-shiny))
4594 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
4595 (synopsis "Base package for web displays of Bioconductor objects")
4597 "This package contains the basic methods needed to generate interactive
4598 Shiny-based display methods for Bioconductor objects.")
4599 (license license:artistic2.0)))
4601 (define-public r-keggrest
4608 (uri (bioconductor-uri "KEGGREST" version))
4611 "1rn03w8y80prbvzahkvf8275haiymnjj1ijcgn55p3d0sb54yzgw"))))
4612 (properties `((upstream-name . "KEGGREST")))
4613 (build-system r-build-system)
4615 (list r-biostrings r-httr r-png))
4618 (home-page "https://bioconductor.org/packages/KEGGREST")
4619 (synopsis "Client-side REST access to KEGG")
4621 "This package provides a package that provides a client interface to the
4622 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
4623 (license license:artistic2.0)))
4625 (define-public r-lfa
4632 (uri (bioconductor-uri "lfa" version))
4634 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
4635 (properties `((upstream-name . "lfa")))
4636 (build-system r-build-system)
4637 (propagated-inputs (list r-corpcor))
4638 (native-inputs (list r-knitr))
4639 (home-page "https://github.com/StoreyLab/lfa")
4640 (synopsis "Logistic Factor Analysis for categorical data")
4642 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
4643 Binomial data via estimation of latent structure in the natural parameter.")
4644 (license license:gpl3)))
4646 (define-public r-limma
4652 (uri (bioconductor-uri "limma" version))
4655 "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65"))))
4656 (build-system r-build-system)
4657 (home-page "http://bioinf.wehi.edu.au/limma")
4658 (synopsis "Package for linear models for microarray and RNA-seq data")
4659 (description "This package can be used for the analysis of gene expression
4660 studies, especially the use of linear models for analysing designed experiments
4661 and the assessment of differential expression. The analysis methods apply to
4662 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
4663 (license license:gpl2+)))
4665 (define-public r-methylkit
4667 (name "r-methylkit")
4671 (uri (bioconductor-uri "methylKit" version))
4674 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
4675 (properties `((upstream-name . "methylKit")))
4676 (build-system r-build-system)
4698 (list r-knitr)) ; for vignettes
4699 (home-page "https://github.com/al2na/methylKit")
4701 "DNA methylation analysis from high-throughput bisulfite sequencing results")
4703 "MethylKit is an R package for DNA methylation analysis and annotation
4704 from high-throughput bisulfite sequencing. The package is designed to deal
4705 with sequencing data from @dfn{Reduced representation bisulfite
4706 sequencing} (RRBS) and its variants, but also target-capture methods and whole
4707 genome bisulfite sequencing. It also has functions to analyze base-pair
4708 resolution 5hmC data from experimental protocols such as oxBS-Seq and
4710 (license license:artistic2.0)))
4712 (define-public r-motifrg
4719 (uri (bioconductor-uri "motifRG" version))
4722 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
4723 (properties `((upstream-name . "motifRG")))
4724 (build-system r-build-system)
4728 r-bsgenome-hsapiens-ucsc-hg19
4732 (home-page "https://bioconductor.org/packages/motifRG")
4733 (synopsis "Discover motifs in high throughput sequencing data")
4735 "This package provides tools for discriminative motif discovery in high
4736 throughput genetic sequencing data sets using regression methods.")
4737 (license license:artistic2.0)))
4739 (define-public r-muscat
4746 (uri (bioconductor-uri "muscat" version))
4749 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
4750 (properties `((upstream-name . "muscat")))
4751 (build-system r-build-system)
4753 (list r-biocparallel
4774 r-singlecellexperiment
4775 r-summarizedexperiment
4778 (native-inputs (list r-knitr))
4779 (home-page "https://github.com/HelenaLC/muscat")
4780 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
4782 "This package @code{muscat} provides various methods and visualization tools
4783 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
4784 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
4785 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
4786 platform that mimics both single and multi-sample scRNA-seq data.")
4787 (license license:gpl3)))
4789 (define-public r-mutationalpatterns
4791 (name "r-mutationalpatterns")
4796 (uri (bioconductor-uri "MutationalPatterns" version))
4799 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
4800 (build-system r-build-system)
4804 (list r-biocgenerics
4807 ;; These two packages are suggested packages
4808 r-bsgenome-hsapiens-1000genomes-hs37d5
4809 r-bsgenome-hsapiens-ucsc-hg19
4827 r-variantannotation))
4828 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
4829 (synopsis "Extract and visualize mutational patterns in genomic data")
4830 (description "This package provides an extensive toolset for the
4831 characterization and visualization of a wide range of mutational patterns
4832 in SNV base substitution data.")
4833 (license license:expat)))
4835 (define-public r-msnbase
4842 (uri (bioconductor-uri "MSnbase" version))
4845 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
4846 (properties `((upstream-name . "MSnbase")))
4847 (build-system r-build-system)
4873 (home-page "https://github.com/lgatto/MSnbase")
4874 (synopsis "Base functions and classes for MS-based proteomics")
4876 "This package provides basic plotting, data manipulation and processing
4877 of mass spectrometry based proteomics data.")
4878 (license license:artistic2.0)))
4880 (define-public r-msnid
4887 (uri (bioconductor-uri "MSnID" version))
4890 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
4891 (properties `((upstream-name . "MSnID")))
4892 (build-system r-build-system)
4895 (modify-phases %standard-phases
4896 (add-after 'unpack 'set-HOME
4897 (lambda _ (setenv "HOME" "/tmp"))))))
4899 (list r-annotationdbi
4925 (home-page "https://bioconductor.org/packages/MSnID")
4926 (synopsis "Utilities for LC-MSn proteomics identifications")
4928 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
4929 from mzIdentML (leveraging the mzID package) or text files. After collating
4930 the search results from multiple datasets it assesses their identification
4931 quality and optimize filtering criteria to achieve the maximum number of
4932 identifications while not exceeding a specified false discovery rate. It also
4933 contains a number of utilities to explore the MS/MS results and assess missed
4934 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
4935 (license license:artistic2.0)))
4937 (define-public r-mzid
4944 (uri (bioconductor-uri "mzID" version))
4947 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
4948 (properties `((upstream-name . "mzID")))
4949 (build-system r-build-system)
4959 (home-page "https://bioconductor.org/packages/mzID")
4960 (synopsis "Parser for mzIdentML files")
4962 "This package provides a parser for mzIdentML files implemented using the
4963 XML package. The parser tries to be general and able to handle all types of
4964 mzIdentML files with the drawback of having less pretty output than a vendor
4966 (license license:gpl2+)))
4968 (define-public r-mzr
4975 (uri (bioconductor-uri "mzR" version))
4978 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
4979 (modules '((guix build utils)))
4981 '(delete-file-recursively "src/boost"))))
4982 (properties `((upstream-name . "mzR")))
4983 (build-system r-build-system)
4986 (modify-phases %standard-phases
4987 (add-after 'unpack 'use-system-boost
4989 (substitute* "src/Makevars"
4990 (("\\./boost/libs.*") "")
4991 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
4992 (("\\ARCH_OBJS=" line)
4994 "\nBOOST_LIBS=-lboost_system -lboost_regex \
4995 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
4997 (list boost ; use this instead of the bundled boost sources
5008 (home-page "https://github.com/sneumann/mzR/")
5009 (synopsis "Parser for mass spectrometry data files")
5011 "The mzR package provides a unified API to the common file formats and
5012 parsers available for mass spectrometry data. It comes with a wrapper for the
5013 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
5014 The package contains the original code written by the ISB, and a subset of the
5015 proteowizard library for mzML and mzIdentML. The netCDF reading code has
5016 previously been used in XCMS.")
5017 (license license:artistic2.0)))
5019 (define-public r-organismdbi
5021 (name "r-organismdbi")
5026 (uri (bioconductor-uri "OrganismDbi" version))
5029 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
5030 (properties `((upstream-name . "OrganismDbi")))
5031 (build-system r-build-system)
5033 (list r-annotationdbi
5044 (home-page "https://bioconductor.org/packages/OrganismDbi")
5045 (synopsis "Software to enable the smooth interfacing of database packages")
5046 (description "The package enables a simple unified interface to several
5047 annotation packages each of which has its own schema by taking advantage of
5048 the fact that each of these packages implements a select methods.")
5049 (license license:artistic2.0)))
5051 (define-public r-pcamethods
5053 (name "r-pcamethods")
5058 (uri (bioconductor-uri "pcaMethods" version))
5061 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
5062 (properties `((upstream-name . "pcaMethods")))
5063 (build-system r-build-system)
5065 (list r-biobase r-biocgenerics r-mass r-rcpp))
5066 (home-page "https://github.com/hredestig/pcamethods")
5067 (synopsis "Collection of PCA methods")
5069 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
5070 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
5071 for missing value estimation is included for comparison. BPCA, PPCA and
5072 NipalsPCA may be used to perform PCA on incomplete data as well as for
5073 accurate missing value estimation. A set of methods for printing and plotting
5074 the results is also provided. All PCA methods make use of the same data
5075 structure (pcaRes) to provide a common interface to the PCA results.")
5076 (license license:gpl3+)))
5078 ;; This is a CRAN package, but it depends on a Bioconductor package:
5079 ;; r-aroma-light, r-dnacopy..
5080 (define-public r-pscbs
5087 (uri (cran-uri "PSCBS" version))
5089 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
5090 (properties `((upstream-name . "PSCBS")))
5091 (build-system r-build-system)
5094 (modify-phases %standard-phases
5095 (add-before 'install 'change-home-dir
5097 ;; Change from /homeless-shelter to /tmp for write permission.
5098 (setenv "HOME" "/tmp"))))))
5110 (list r-r-rsp ;used to build vignettes
5112 (home-page "https://github.com/HenrikBengtsson/PSCBS")
5113 (synopsis "Analysis of parent-specific DNA copy numbers")
5115 "This is a package for segmentation of allele-specific DNA copy number
5116 data and detection of regions with abnormal copy number within each parental
5117 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
5118 (license license:gpl2+)))
5120 (define-public r-protgenerics
5122 (name "r-protgenerics")
5127 (uri (bioconductor-uri "ProtGenerics" version))
5130 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
5131 (properties `((upstream-name . "ProtGenerics")))
5132 (build-system r-build-system)
5133 (home-page "https://github.com/lgatto/ProtGenerics")
5134 (synopsis "S4 generic functions for proteomics infrastructure")
5136 "This package provides S4 generic functions needed by Bioconductor
5137 proteomics packages.")
5138 (license license:artistic2.0)))
5140 (define-public r-rbgl
5147 (uri (bioconductor-uri "RBGL" version))
5150 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
5151 (properties `((upstream-name . "RBGL")))
5152 (build-system r-build-system)
5154 (list r-bh r-graph))
5155 (home-page "https://www.bioconductor.org/packages/RBGL")
5156 (synopsis "Interface to the Boost graph library")
5158 "This package provides a fairly extensive and comprehensive interface to
5159 the graph algorithms contained in the Boost library.")
5160 (license license:artistic2.0)))
5162 (define-public r-rcas
5168 (uri (bioconductor-uri "RCAS" version))
5171 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
5172 (properties `((upstream-name . "RCAS")))
5173 (build-system r-build-system)
5175 (list r-biocgenerics
5178 r-bsgenome-hsapiens-ucsc-hg19
5204 (synopsis "RNA-centric annotation system")
5206 "RCAS aims to be a standalone RNA-centric annotation system that provides
5207 intuitive reports and publication-ready graphics. This package provides the R
5208 library implementing most of the pipeline's features.")
5209 (home-page "https://github.com/BIMSBbioinfo/RCAS")
5210 (license license:artistic2.0)))
5212 (define-public r-regioner
5219 (uri (bioconductor-uri "regioneR" version))
5222 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
5223 (properties `((upstream-name . "regioneR")))
5224 (build-system r-build-system)
5236 (home-page "https://bioconductor.org/packages/regioneR/")
5237 (synopsis "Association analysis of genomic regions")
5238 (description "This package offers a statistical framework based on
5239 customizable permutation tests to assess the association between genomic
5240 region sets and other genomic features.")
5241 (license license:artistic2.0)))
5243 (define-public r-reportingtools
5245 (name "r-reportingtools")
5250 (uri (bioconductor-uri "ReportingTools" version))
5253 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
5255 `((upstream-name . "ReportingTools")))
5256 (build-system r-build-system)
5279 (home-page "https://bioconductor.org/packages/ReportingTools/")
5280 (synopsis "Tools for making reports in various formats")
5282 "The ReportingTools package enables users to easily display reports of
5283 analysis results generated from sources such as microarray and sequencing
5284 data. The package allows users to create HTML pages that may be viewed on a
5285 web browser, or in other formats. Users can generate tables with sortable and
5286 filterable columns, make and display plots, and link table entries to other
5287 data sources such as NCBI or larger plots within the HTML page. Using the
5288 package, users can also produce a table of contents page to link various
5289 reports together for a particular project that can be viewed in a web
5291 (license license:artistic2.0)))
5293 (define-public r-rhdf5
5299 (uri (bioconductor-uri "rhdf5" version))
5302 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
5303 (build-system r-build-system)
5305 (list r-rhdf5filters r-rhdf5lib))
5308 (home-page "https://bioconductor.org/packages/rhdf5")
5309 (synopsis "HDF5 interface to R")
5311 "This R/Bioconductor package provides an interface between HDF5 and R.
5312 HDF5's main features are the ability to store and access very large and/or
5313 complex datasets and a wide variety of metadata on mass storage (disk) through
5314 a completely portable file format. The rhdf5 package is thus suited for the
5315 exchange of large and/or complex datasets between R and other software
5316 package, and for letting R applications work on datasets that are larger than
5317 the available RAM.")
5318 (license license:artistic2.0)))
5320 (define-public r-rhdf5filters
5322 (name "r-rhdf5filters")
5327 (uri (bioconductor-uri "rhdf5filters" version))
5330 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
5331 (properties `((upstream-name . "rhdf5filters")))
5332 (build-system r-build-system)
5339 (home-page "https://github.com/grimbough/rhdf5filters")
5340 (synopsis "HDF5 compression filters")
5342 "This package provides a collection of compression filters for use with
5344 (license license:bsd-2)))
5346 (define-public r-rsamtools
5348 (name "r-rsamtools")
5352 (uri (bioconductor-uri "Rsamtools" version))
5355 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
5357 `((upstream-name . "Rsamtools")))
5358 (build-system r-build-system)
5361 (modify-phases %standard-phases
5362 (add-after 'unpack 'use-system-zlib
5364 (substitute* "DESCRIPTION"
5365 (("zlibbioc, ") ""))
5366 (substitute* "NAMESPACE"
5367 (("import\\(zlibbioc\\)") "")))))))
5369 (list r-biocgenerics
5379 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
5380 (synopsis "Interface to samtools, bcftools, and tabix")
5382 "This package provides an interface to the @code{samtools},
5383 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
5384 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
5385 tab-delimited (tabix) files.")
5386 (license license:expat)))
5388 ;; This is a CRAN package, but it depends on a Bioconductor package:
5390 (define-public r-restfulr
5397 (uri (cran-uri "restfulr" version))
5400 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
5401 (properties `((upstream-name . "restfulr")))
5402 (build-system r-build-system)
5404 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
5405 (home-page "https://cran.r-project.org/package=restfulr")
5406 (synopsis "R interface to RESTful web services")
5408 "This package models a RESTful service as if it were a nested R list.")
5409 (license license:artistic2.0)))
5411 (define-public r-rtracklayer
5413 (name "r-rtracklayer")
5417 (uri (bioconductor-uri "rtracklayer" version))
5420 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
5421 (build-system r-build-system)
5424 (modify-phases %standard-phases
5425 (add-after 'unpack 'use-system-zlib
5427 (substitute* "DESCRIPTION"
5428 ((" zlibbioc,") ""))
5429 (substitute* "NAMESPACE"
5430 (("import\\(zlibbioc\\)") "")))))))
5436 (list r-biocgenerics
5450 (home-page "https://bioconductor.org/packages/rtracklayer")
5451 (synopsis "R interface to genome browsers and their annotation tracks")
5453 "rtracklayer is an extensible framework for interacting with multiple
5454 genome browsers (currently UCSC built-in) and manipulating annotation tracks
5455 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
5456 built-in). The user may export/import tracks to/from the supported browsers,
5457 as well as query and modify the browser state, such as the current viewport.")
5458 (license license:artistic2.0)))
5460 ;; This is a CRAN package, but it depends on a Bioconductor package.
5461 (define-public r-samr
5468 (uri (cran-uri "samr" version))
5471 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
5472 (properties `((upstream-name . "samr")))
5473 (build-system r-build-system)
5481 (native-inputs (list gfortran))
5482 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
5483 (synopsis "Significance analysis of Microarrays")
5485 "This is a package for significance analysis of Microarrays for
5486 differential expression analysis, RNAseq data and related problems.")
5487 ;; Any version of the LGPL
5488 (license license:lgpl3+)))
5490 (define-public r-scannotatr
5492 (name "r-scannotatr")
5497 (uri (bioconductor-uri "scAnnotatR" version))
5499 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
5500 (properties `((upstream-name . "scAnnotatR")))
5501 (build-system r-build-system)
5503 (list r-annotationhub
5514 r-singlecellexperiment
5515 r-summarizedexperiment))
5516 (native-inputs (list r-knitr))
5517 (home-page "https://github.com/grisslab/scAnnotatR")
5518 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
5520 "This package comprises a set of pretrained machine learning models to
5521 predict basic immune cell types. This enables to quickly get a first
5522 annotation of the cell types present in the dataset without requiring prior
5523 knowledge. The package also lets you train using own models to predict new
5524 cell types based on specific research needs.")
5525 (license license:expat)))
5527 (define-public r-scdblfinder
5529 (name "r-scdblfinder")
5534 (uri (bioconductor-uri "scDblFinder" version))
5536 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
5537 (properties `((upstream-name . "scDblFinder")))
5538 (build-system r-build-system)
5540 (list r-biocgenerics
5558 r-singlecellexperiment
5559 r-summarizedexperiment
5561 (native-inputs (list r-knitr))
5562 (home-page "https://github.com/plger/scDblFinder")
5563 (synopsis "Detect multiplets in single-cell RNA sequencing data")
5565 "The scDblFinder package gathers various methods for the detection and
5566 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
5567 multiple cells captured within the same droplet or reaction volume). It
5568 includes methods formerly found in the scran package, and the new fast and
5569 comprehensive scDblFinder method.")
5570 (license license:gpl3)))
5572 (define-public r-scmap
5579 (uri (bioconductor-uri "scmap" version))
5581 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
5582 (properties `((upstream-name . "scmap")))
5583 (build-system r-build-system)
5598 r-singlecellexperiment
5599 r-summarizedexperiment))
5600 (native-inputs (list r-knitr))
5601 (home-page "https://github.com/hemberg-lab/scmap")
5602 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
5604 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
5605 composition of complex tissues since the technology allows researchers to
5606 define cell-types using unsupervised clustering of the transcriptome.
5607 However, due to differences in experimental methods and computational
5608 analyses, it is often challenging to directly compare the cells identified in
5609 two different experiments. @code{scmap} is a method for projecting cells from
5610 a scRNA-seq experiment onto the cell-types or individual cells identified in a
5611 different experiment.")
5612 (license license:gpl3)))
5614 (define-public r-seqlogo
5621 (uri (bioconductor-uri "seqLogo" version))
5624 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
5625 (properties `((upstream-name . "seqLogo")))
5626 (build-system r-build-system)
5629 (home-page "https://bioconductor.org/packages/seqLogo")
5630 (synopsis "Sequence logos for DNA sequence alignments")
5632 "seqLogo takes the position weight matrix of a DNA sequence motif and
5633 plots the corresponding sequence logo as introduced by Schneider and
5635 (license license:lgpl2.0+)))
5637 (define-public r-seqpattern
5639 (name "r-seqpattern")
5643 (uri (bioconductor-uri "seqPattern" version))
5646 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
5648 `((upstream-name . "seqPattern")))
5649 (build-system r-build-system)
5651 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
5652 (home-page "https://bioconductor.org/packages/seqPattern")
5653 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
5655 "This package provides tools to visualize oligonucleotide patterns and
5656 sequence motif occurrences across a large set of sequences centred at a common
5657 reference point and sorted by a user defined feature.")
5658 (license license:gpl3+)))
5660 (define-public r-shortread
5662 (name "r-shortread")
5667 (uri (bioconductor-uri "ShortRead" version))
5670 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
5671 (properties `((upstream-name . "ShortRead")))
5672 (build-system r-build-system)
5692 (home-page "https://bioconductor.org/packages/ShortRead")
5693 (synopsis "FASTQ input and manipulation tools")
5695 "This package implements sampling, iteration, and input of FASTQ files.
5696 It includes functions for filtering and trimming reads, and for generating a
5697 quality assessment report. Data are represented as
5698 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
5699 purposes. The package also contains legacy support for early single-end,
5700 ungapped alignment formats.")
5701 (license license:artistic2.0)))
5703 (define-public r-simplifyenrichment
5705 (name "r-simplifyenrichment")
5710 (uri (bioconductor-uri "simplifyEnrichment" version))
5713 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
5715 `((upstream-name . "simplifyEnrichment")))
5716 (build-system r-build-system)
5718 (list r-annotationdbi
5735 (native-inputs (list r-knitr))
5736 (home-page "https://github.com/jokergoo/simplifyEnrichment")
5737 (synopsis "Simplify functional enrichment results")
5738 (description "This package provides a new clustering algorithm, binary
5739 cut, for clustering similarity matrices of functional terms is implemented in
5740 this package. It also provides functionalities for visualizing, summarizing
5741 and comparing the clusterings.")
5742 (license license:expat)))
5744 (define-public r-transcriptr
5746 (name "r-transcriptr")
5751 (uri (bioconductor-uri "transcriptR" version))
5753 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
5754 (properties `((upstream-name . "transcriptR")))
5755 (build-system r-build-system)
5757 (list r-biocgenerics
5772 (native-inputs (list r-knitr))
5773 (home-page "https://bioconductor.org/packages/transcriptR")
5774 (synopsis "Primary transcripts detection and quantification")
5776 "The differences in the RNA types being sequenced have an impact on the
5777 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
5778 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
5779 broader coverage of both exonic and intronic regions. The presence of
5780 intronic reads in GRO-seq type of data makes it possible to use it to
5781 computationally identify and quantify all de novo continuous regions of
5782 transcription distributed across the genome. This type of data, however, is
5783 more challenging to interpret and less common practice compared to mRNA-seq.
5784 One of the challenges for primary transcript detection concerns the
5785 simultaneous transcription of closely spaced genes, which needs to be properly
5786 divided into individually transcribed units. The R package transcriptR
5787 combines RNA-seq data with ChIP-seq data of histone modifications that mark
5788 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
5789 overcome this challenge. The advantage of this approach over the use of, for
5790 example, gene annotations is that this approach is data driven and therefore
5791 able to deal also with novel and case specific events.")
5792 (license license:gpl3)))
5794 (define-public r-trajectoryutils
5796 (name "r-trajectoryutils")
5801 (uri (bioconductor-uri "TrajectoryUtils" version))
5804 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
5806 `((upstream-name . "TrajectoryUtils")))
5807 (build-system r-build-system)
5809 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
5810 r-summarizedexperiment))
5811 (native-inputs (list r-knitr))
5812 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
5813 (synopsis "Single-cell trajectory analysis utilities")
5815 "This package implements low-level utilities for single-cell trajectory
5816 analysis, primarily intended for re-use inside higher-level packages. It
5817 includes a function to create a cluster-level minimum spanning tree and data
5818 structures to hold pseudotime inference results.")
5819 (license license:gpl3)))
5821 (define-public r-slingshot
5823 (name "r-slingshot")
5827 (uri (bioconductor-uri "slingshot" version))
5830 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
5831 (build-system r-build-system)
5837 r-singlecellexperiment
5838 r-summarizedexperiment
5842 (home-page "https://bioconductor.org/packages/slingshot")
5843 (synopsis "Tools for ordering single-cell sequencing")
5844 (description "This package provides functions for inferring continuous,
5845 branching lineage structures in low-dimensional data. Slingshot was designed
5846 to model developmental trajectories in single-cell RNA sequencing data and
5847 serve as a component in an analysis pipeline after dimensionality reduction
5848 and clustering. It is flexible enough to handle arbitrarily many branching
5849 events and allows for the incorporation of prior knowledge through supervised
5850 graph construction.")
5851 (license license:artistic2.0)))
5853 (define-public r-stager
5860 (uri (bioconductor-uri "stageR" version))
5862 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
5863 (properties `((upstream-name . "stageR")))
5864 (build-system r-build-system)
5865 (propagated-inputs (list r-summarizedexperiment))
5866 (native-inputs (list r-knitr))
5867 (home-page "https://bioconductor.org/packages/stageR")
5868 (synopsis "Stage-wise analysis of high throughput gene expression data")
5870 "The stageR package allows automated stage-wise analysis of
5871 high-throughput gene expression data. The method is published in Genome
5873 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
5874 (license license:gpl3)))
5876 (define-public r-stringdb
5883 (uri (bioconductor-uri "STRINGdb" version))
5885 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
5886 (properties `((upstream-name . "STRINGdb")))
5887 (build-system r-build-system)
5898 (home-page "https://git.bioconductor.org/packages/STRINGdb")
5899 (synopsis "Search tool for the retrieval of interacting proteins database")
5901 "The @code{STRINGdb} package provides an R interface to the STRING
5902 protein-protein interactions database. @url{https://www.string-db.org,
5903 STRING} is a database of known and predicted protein-protein interactions.
5904 The interactions include direct (physical) and indirect (functional)
5905 associations. Each interaction is associated with a combined confidence score
5906 that integrates the various evidences.")
5907 (license license:gpl2)))
5909 (define-public r-structuralvariantannotation
5911 (name "r-structuralvariantannotation")
5916 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
5918 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
5919 (build-system r-build-system)
5933 r-summarizedexperiment
5934 r-variantannotation))
5937 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
5938 (synopsis "R package designed to simplify structural variant analysis")
5940 "This package contains useful helper functions for dealing with structural
5941 variants in VCF format. The packages contains functions for parsing VCFs from
5942 a number of popular callers as well as functions for dealing with breakpoints
5943 involving two separate genomic loci encoded as GRanges objects.")
5944 (license license:gpl3)))
5946 (define-public r-summarizedexperiment
5948 (name "r-summarizedexperiment")
5952 (uri (bioconductor-uri "SummarizedExperiment" version))
5955 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
5957 `((upstream-name . "SummarizedExperiment")))
5958 (build-system r-build-system)
5971 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
5972 (synopsis "Container for representing genomic ranges by sample")
5974 "The SummarizedExperiment container contains one or more assays, each
5975 represented by a matrix-like object of numeric or other mode. The rows
5976 typically represent genomic ranges of interest and the columns represent
5978 (license license:artistic2.0)))
5980 (define-public r-sva
5987 (uri (bioconductor-uri "sva" version))
5990 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
5991 (build-system r-build-system)
5999 (home-page "https://bioconductor.org/packages/sva")
6000 (synopsis "Surrogate variable analysis")
6002 "This package contains functions for removing batch effects and other
6003 unwanted variation in high-throughput experiment. It also contains functions
6004 for identifying and building surrogate variables for high-dimensional data
6005 sets. Surrogate variables are covariates constructed directly from
6006 high-dimensional data like gene expression/RNA sequencing/methylation/brain
6007 imaging data that can be used in subsequent analyses to adjust for unknown,
6008 unmodeled, or latent sources of noise.")
6009 (license license:artistic2.0)))
6011 (define-public r-systempiper
6013 (name "r-systempiper")
6018 (uri (bioconductor-uri "systemPipeR" version))
6021 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
6022 (properties `((upstream-name . "systemPipeR")))
6023 (build-system r-build-system)
6025 (list r-biocgenerics
6036 r-summarizedexperiment
6040 (home-page "https://github.com/tgirke/systemPipeR")
6041 (synopsis "Next generation sequencing workflow and reporting environment")
6043 "This R package provides tools for building and running automated
6044 end-to-end analysis workflows for a wide range of @dfn{next generation
6045 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
6046 Important features include a uniform workflow interface across different NGS
6047 applications, automated report generation, and support for running both R and
6048 command-line software, such as NGS aligners or peak/variant callers, on local
6049 computers or compute clusters. Efficient handling of complex sample sets and
6050 experimental designs is facilitated by a consistently implemented sample
6051 annotation infrastructure.")
6052 (license license:artistic2.0)))
6054 (define-public r-topgo
6060 (uri (bioconductor-uri "topGO" version))
6063 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
6065 `((upstream-name . "topGO")))
6066 (build-system r-build-system)
6068 (list r-annotationdbi
6077 (home-page "https://bioconductor.org/packages/topGO")
6078 (synopsis "Enrichment analysis for gene ontology")
6080 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
6081 terms while accounting for the topology of the GO graph. Different test
6082 statistics and different methods for eliminating local similarities and
6083 dependencies between GO terms can be implemented and applied.")
6084 ;; Any version of the LGPL applies.
6085 (license license:lgpl2.1+)))
6087 (define-public r-tximport
6093 (uri (bioconductor-uri "tximport" version))
6096 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
6097 (build-system r-build-system)
6100 (home-page "https://bioconductor.org/packages/tximport")
6101 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
6103 "This package provides tools to import transcript-level abundance,
6104 estimated counts and transcript lengths, and to summarize them into matrices
6105 for use with downstream gene-level analysis packages. Average transcript
6106 length, weighted by sample-specific transcript abundance estimates, is
6107 provided as a matrix which can be used as an offset for different expression
6108 of gene-level counts.")
6109 (license license:gpl2+)))
6111 ;; This is a CRAN package, but it depends on a Bioconductor package.
6112 (define-public r-valr
6119 (uri (cran-uri "valr" version))
6122 "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k"))))
6123 (build-system r-build-system)
6131 r-rtracklayer ;bioconductor package
6136 (home-page "https://github.com/rnabioco/valr")
6137 (synopsis "Genome interval arithmetic in R")
6139 "This package enables you to read and manipulate genome intervals and
6140 signals. It provides functionality similar to command-line tool suites within
6141 R, enabling interactive analysis and visualization of genome-scale data.")
6142 (license license:expat)))
6144 (define-public r-variantannotation
6146 (name "r-variantannotation")
6150 (uri (bioconductor-uri "VariantAnnotation" version))
6153 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
6155 `((upstream-name . "VariantAnnotation")))
6157 (list r-annotationdbi
6168 r-summarizedexperiment
6175 (build-system r-build-system)
6176 (home-page "https://bioconductor.org/packages/VariantAnnotation")
6177 (synopsis "Package for annotation of genetic variants")
6178 (description "This R package can annotate variants, compute amino acid
6179 coding changes and predict coding outcomes.")
6180 (license license:artistic2.0)))
6182 (define-public r-vsn
6189 (uri (bioconductor-uri "vsn" version))
6192 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
6193 (build-system r-build-system)
6195 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
6197 (list r-knitr)) ; for vignettes
6198 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
6199 (synopsis "Variance stabilization and calibration for microarray data")
6201 "The package implements a method for normalising microarray intensities,
6202 and works for single- and multiple-color arrays. It can also be used for data
6203 from other technologies, as long as they have similar format. The method uses
6204 a robust variant of the maximum-likelihood estimator for an
6205 additive-multiplicative error model and affine calibration. The model
6206 incorporates data calibration step (a.k.a. normalization), a model for the
6207 dependence of the variance on the mean intensity and a variance stabilizing
6208 data transformation. Differences between transformed intensities are
6209 analogous to \"normalized log-ratios\". However, in contrast to the latter,
6210 their variance is independent of the mean, and they are usually more sensitive
6211 and specific in detecting differential transcription.")
6212 (license license:artistic2.0)))
6214 ;; There is no source tarball, so we fetch the code from the Bioconductor git
6216 (define-public r-xcir
6217 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
6221 (version (git-version "1.8.0" revision commit))
6225 (url "https://git.bioconductor.org/packages/XCIR")
6227 (file-name (git-file-name name version))
6230 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
6231 (properties `((upstream-name . "XCIR")))
6232 (build-system r-build-system)
6233 (propagated-inputs (list r-biomart
6241 r-variantannotation))
6242 (native-inputs (list r-knitr))
6243 (home-page "https://github.com/SRenan/XCIR")
6244 (synopsis "Analysis of X chromosome inactivation")
6246 "This package is an R package that offers models and tools for subject
6247 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
6249 (license license:gpl2))))
6251 (define-public r-xina
6258 (uri (bioconductor-uri "XINA" version))
6260 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
6261 (properties `((upstream-name . "XINA")))
6262 (build-system r-build-system)
6271 (native-inputs (list r-knitr))
6272 (home-page "https://git.bioconductor.org/packages/XINA")
6273 (synopsis "Identifying proteins that exhibit similar patterns")
6275 "The aim of @code{XINA} is to determine which proteins exhibit similar
6276 patterns within and across experimental conditions, since proteins with
6277 co-abundance patterns may have common molecular functions. @code{XINA} imports
6278 multiple datasets, tags dataset in silico, and combines the data for subsequent
6279 subgrouping into multiple clusters. The result is a single output depicting
6280 the variation across all conditions. @code{XINA} not only extracts
6281 coabundance profiles within and across experiments, but also incorporates
6282 protein-protein interaction databases and integrative resources such as
6283 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
6284 molecular functions, respectively, and produces intuitive graphical outputs.")
6285 (license license:gpl3)))
6287 (define-public r-xmapbridge
6289 (name "r-xmapbridge")
6294 (uri (bioconductor-uri "xmapbridge" version))
6296 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
6297 (properties `((upstream-name . "xmapbridge")))
6298 (build-system r-build-system)
6299 (home-page "https://git.bioconductor.org/packages/xmapbridge")
6300 (synopsis "Display numeric data in the web based genome browser X:MAP")
6302 "The package @code{xmapbridge} can plot graphs in the X:Map genome
6303 browser. X:Map uses the Google Maps API to provide a scrollable view of the
6304 genome. It supports a number of species, and can be accessed at
6305 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
6306 suitable format. Graph plotting in R is done using calls to the functions
6307 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
6308 similar to those used by the standard plot methods in R. These result in data
6309 being written to a set of files (in a specific directory structure) that
6310 contain the data to be displayed, as well as some additional meta-data
6311 describing each of the graphs.")
6312 (license license:lgpl3)))
6314 (define-public r-xvector
6320 (uri (bioconductor-uri "XVector" version))
6323 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
6325 `((upstream-name . "XVector")))
6326 (build-system r-build-system)
6329 (modify-phases %standard-phases
6330 (add-after 'unpack 'use-system-zlib
6332 (substitute* "DESCRIPTION"
6333 (("zlibbioc, ") ""))
6334 (substitute* "NAMESPACE"
6335 (("import\\(zlibbioc\\)") ""))
6340 (list r-biocgenerics r-iranges r-s4vectors))
6341 (home-page "https://bioconductor.org/packages/XVector")
6342 (synopsis "Representation and manpulation of external sequences")
6344 "This package provides memory efficient S4 classes for storing sequences
6345 \"externally\" (behind an R external pointer, or on disk).")
6346 (license license:artistic2.0)))
6348 (define-public r-zlibbioc
6354 (uri (bioconductor-uri "zlibbioc" version))
6357 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
6359 `((upstream-name . "zlibbioc")))
6360 (build-system r-build-system)
6361 (home-page "https://bioconductor.org/packages/zlibbioc")
6362 (synopsis "Provider for zlib-1.2.5 to R packages")
6363 (description "This package uses the source code of zlib-1.2.5 to create
6364 libraries for systems that do not have these available via other means.")
6365 (license license:artistic2.0)))
6367 (define-public r-zellkonverter
6369 (name "r-zellkonverter")
6374 (uri (bioconductor-uri "zellkonverter" version))
6376 (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz"))))
6377 (properties `((upstream-name . "zellkonverter")))
6378 (build-system r-build-system)
6386 r-singlecellexperiment
6387 r-summarizedexperiment))
6388 (native-inputs (list r-knitr))
6389 (home-page "https://github.com/theislab/zellkonverter")
6390 (synopsis "Conversion between AnnData and single-cell experiments objects")
6392 "This package provides methods to convert between Python AnnData objects
6393 and SingleCellExperiment objects. These are primarily intended for use by
6394 downstream Bioconductor packages that wrap Python methods for single-cell data
6395 analysis. It also includes functions to read and write H5AD files used for
6396 saving AnnData objects to disk.")
6397 (license license:expat)))
6399 (define-public r-geneplotter
6401 (name "r-geneplotter")
6406 (uri (bioconductor-uri "geneplotter" version))
6409 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
6410 (build-system r-build-system)
6418 (home-page "https://bioconductor.org/packages/geneplotter")
6419 (synopsis "Graphics functions for genomic data")
6421 "This package provides functions for plotting genomic data.")
6422 (license license:artistic2.0)))
6424 (define-public r-oligoclasses
6426 (name "r-oligoclasses")
6431 (uri (bioconductor-uri "oligoClasses" version))
6434 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
6435 (properties `((upstream-name . "oligoClasses")))
6436 (build-system r-build-system)
6450 r-summarizedexperiment))
6451 (home-page "https://bioconductor.org/packages/oligoClasses/")
6452 (synopsis "Classes for high-throughput arrays")
6454 "This package contains class definitions, validity checks, and
6455 initialization methods for classes used by the @code{oligo} and @code{crlmm}
6457 (license license:gpl2+)))
6459 (define-public r-oligo
6466 (uri (bioconductor-uri "oligo" version))
6469 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
6470 (properties `((upstream-name . "oligo")))
6471 (build-system r-build-system)
6472 (inputs (list zlib))
6487 (home-page "https://bioconductor.org/packages/oligo/")
6488 (synopsis "Preprocessing tools for oligonucleotide arrays")
6490 "This package provides a package to analyze oligonucleotide
6491 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
6492 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
6493 (license license:lgpl2.0+)))
6495 (define-public r-qvalue
6502 (uri (bioconductor-uri "qvalue" version))
6505 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
6506 (build-system r-build-system)
6508 (list r-ggplot2 r-reshape2))
6511 (home-page "https://github.com/StoreyLab/qvalue")
6512 (synopsis "Q-value estimation for false discovery rate control")
6514 "This package takes a list of p-values resulting from the simultaneous
6515 testing of many hypotheses and estimates their q-values and local @dfn{false
6516 discovery rate} (FDR) values. The q-value of a test measures the proportion
6517 of false positives incurred when that particular test is called significant.
6518 The local FDR measures the posterior probability the null hypothesis is true
6519 given the test's p-value. Various plots are automatically generated, allowing
6520 one to make sensible significance cut-offs. The software can be applied to
6521 problems in genomics, brain imaging, astrophysics, and data mining.")
6522 ;; Any version of the LGPL.
6523 (license license:lgpl3+)))
6525 (define r-rcppnumerical
6527 (name "r-rcppnumerical")
6531 (uri (cran-uri "RcppNumerical" version))
6534 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
6535 (properties `((upstream-name . "RcppNumerical")))
6536 (build-system r-build-system)
6538 `(("r-rcpp" ,r-rcpp)
6539 ("r-rcppeigen" ,r-rcppeigen)))
6541 `(("r-knitr" ,r-knitr)))
6542 (home-page "https://github.com/yixuan/RcppNumerical")
6543 (synopsis "Rcpp integration for numerical computing libraries")
6544 (description "This package provides a collection of open source libraries
6545 for numerical computing (numerical integration, optimization, etc.) and their
6546 integration with @code{Rcpp}.")
6547 (license license:gpl2+)))
6549 (define-public r-apeglm
6555 (uri (bioconductor-uri "apeglm" version))
6558 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
6559 (properties `((upstream-name . "apeglm")))
6560 (build-system r-build-system)
6567 r-summarizedexperiment))
6568 (native-inputs (list r-knitr))
6569 (home-page "https://bioconductor.org/packages/apeglm")
6570 (synopsis "Approximate posterior estimation for GLM coefficients")
6571 (description "This package provides Bayesian shrinkage estimators for
6572 effect sizes for a variety of GLM models, using approximation of the
6573 posterior for individual coefficients.")
6574 (license license:gpl2)))
6576 (define-public r-greylistchip
6578 (name "r-greylistchip")
6582 (uri (bioconductor-uri "GreyListChIP" version))
6585 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
6586 (properties `((upstream-name . "GreyListChIP")))
6587 (build-system r-build-system)
6596 r-summarizedexperiment))
6597 (home-page "https://bioconductor.org/packages/GreyListChIP")
6598 (synopsis "Greylist artefact regions based on ChIP inputs")
6599 (description "This package identifies regions of ChIP experiments with high
6600 signal in the input, that lead to spurious peaks during peak calling.")
6601 (license license:artistic2.0)))
6603 (define-public r-diffbind
6610 (uri (bioconductor-uri "DiffBind" version))
6613 "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr"))))
6614 (properties `((upstream-name . "DiffBind")))
6615 (build-system r-build-system)
6638 r-summarizedexperiment
6640 (home-page "https://bioconductor.org/packages/DiffBind")
6641 (synopsis "Differential binding analysis of ChIP-Seq peak data")
6643 "This package computes differentially bound sites from multiple
6644 ChIP-seq experiments using affinity (quantitative) data. Also enables
6645 occupancy (overlap) analysis and plotting functions.")
6646 (license license:artistic2.0)))
6648 (define-public r-ripseeker
6650 (name "r-ripseeker")
6655 (uri (bioconductor-uri "RIPSeeker" version))
6658 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
6659 (properties `((upstream-name . "RIPSeeker")))
6660 (build-system r-build-system)
6665 r-summarizedexperiment
6669 (home-page "https://bioconductor.org/packages/RIPSeeker")
6671 "Identifying protein-associated transcripts from RIP-seq experiments")
6673 "This package infers and discriminates RIP peaks from RIP-seq alignments
6674 using two-state HMM with negative binomial emission probability. While
6675 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
6676 a suite of bioinformatics tools integrated within this self-contained software
6677 package comprehensively addressing issues ranging from post-alignments
6678 processing to visualization and annotation.")
6679 (license license:gpl2)))
6681 (define-public r-mbkmeans
6687 (uri (bioconductor-uri "mbkmeans" version))
6690 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
6691 (build-system r-build-system)
6705 r-singlecellexperiment
6706 r-summarizedexperiment))
6707 (home-page "https://bioconductor.org/packages/mbkmeans")
6708 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
6709 (description "This package implements the mini-batch k-means algorithm for
6710 large datasets, including support for on-disk data representation.")
6711 (license license:expat)))
6713 (define-public r-multtest
6720 (uri (bioconductor-uri "multtest" version))
6723 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
6724 (build-system r-build-system)
6726 (list r-survival r-biocgenerics r-biobase r-mass))
6727 (home-page "https://bioconductor.org/packages/multtest")
6728 (synopsis "Resampling-based multiple hypothesis testing")
6730 "This package can do non-parametric bootstrap and permutation
6731 resampling-based multiple testing procedures (including empirical Bayes
6732 methods) for controlling the family-wise error rate (FWER), generalized
6733 family-wise error rate (gFWER), tail probability of the proportion of
6734 false positives (TPPFP), and false discovery rate (FDR). Several choices
6735 of bootstrap-based null distribution are implemented (centered, centered
6736 and scaled, quantile-transformed). Single-step and step-wise methods are
6737 available. Tests based on a variety of T- and F-statistics (including
6738 T-statistics based on regression parameters from linear and survival models
6739 as well as those based on correlation parameters) are included. When probing
6740 hypotheses with T-statistics, users may also select a potentially faster null
6741 distribution which is multivariate normal with mean zero and variance
6742 covariance matrix derived from the vector influence function. Results are
6743 reported in terms of adjusted P-values, confidence regions and test statistic
6744 cutoffs. The procedures are directly applicable to identifying differentially
6745 expressed genes in DNA microarray experiments.")
6746 (license license:lgpl3)))
6748 (define-public r-graph
6754 (uri (bioconductor-uri "graph" version))
6757 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
6758 (build-system r-build-system)
6760 (list r-biocgenerics))
6761 (home-page "https://bioconductor.org/packages/graph")
6762 (synopsis "Handle graph data structures in R")
6764 "This package implements some simple graph handling capabilities for R.")
6765 (license license:artistic2.0)))
6767 ;; This is a CRAN package, but it depends on a Bioconductor package.
6768 (define-public r-ggm
6775 (uri (cran-uri "ggm" version))
6778 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
6779 (properties `((upstream-name . "ggm")))
6780 (build-system r-build-system)
6782 (list r-graph r-igraph))
6783 (home-page "https://cran.r-project.org/package=ggm")
6784 (synopsis "Functions for graphical Markov models")
6786 "This package provides functions and datasets for maximum likelihood
6787 fitting of some classes of graphical Markov models.")
6788 (license license:gpl2+)))
6790 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
6791 (define-public r-perfmeas
6798 (uri (cran-uri "PerfMeas" version))
6801 "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
6802 (properties `((upstream-name . "PerfMeas")))
6803 (build-system r-build-system)
6805 (list r-graph r-limma r-rbgl))
6806 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
6807 (synopsis "Performance measures for ranking and classification tasks")
6809 "This package implements different performance measures for
6810 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
6811 a given recall, F-score for single and multiple classes are available.")
6812 (license license:gpl2+)))
6814 ;; This is a CRAN package, but it depends on a Bioconductor package.
6815 (define-public r-codedepends
6817 (name "r-codedepends")
6822 (uri (cran-uri "CodeDepends" version))
6825 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
6826 (properties `((upstream-name . "CodeDepends")))
6827 (build-system r-build-system)
6829 (list r-codetools r-graph r-xml))
6830 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
6831 (synopsis "Analysis of R code for reproducible research and code comprehension")
6833 "This package provides tools for analyzing R expressions or blocks of
6834 code and determining the dependencies between them. It focuses on R scripts,
6835 but can be used on the bodies of functions. There are many facilities
6836 including the ability to summarize or get a high-level view of code,
6837 determining dependencies between variables, code improvement suggestions.")
6838 ;; Any version of the GPL
6839 (license (list license:gpl2+ license:gpl3+))))
6841 (define-public r-chippeakanno
6843 (name "r-chippeakanno")
6848 (uri (bioconductor-uri "ChIPpeakAnno" version))
6851 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
6852 (properties `((upstream-name . "ChIPpeakAnno")))
6853 (build-system r-build-system)
6855 (list r-annotationdbi
6878 r-summarizedexperiment
6882 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
6883 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
6885 "The package includes functions to retrieve the sequences around the peak,
6886 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
6887 custom features such as most conserved elements and other transcription factor
6888 binding sites supplied by users. Starting 2.0.5, new functions have been added
6889 for finding the peaks with bi-directional promoters with summary statistics
6890 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
6891 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
6892 enrichedGO (addGeneIDs).")
6893 (license license:gpl2+)))
6895 (define-public r-matrixgenerics
6897 (name "r-matrixgenerics")
6901 (uri (bioconductor-uri "MatrixGenerics" version))
6904 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
6906 `((upstream-name . "MatrixGenerics")))
6907 (build-system r-build-system)
6909 (list r-matrixstats))
6910 (home-page "https://bioconductor.org/packages/MatrixGenerics")
6911 (synopsis "S4 generic summary statistic functions for matrix-like objects")
6913 "This package provides S4 generic functions modeled after the
6914 @code{matrixStats} API for alternative matrix implementations. Packages with
6915 alternative matrix implementation can depend on this package and implement the
6916 generic functions that are defined here for a useful set of row and column
6917 summary statistics. Other package developers can import this package and
6918 handle a different matrix implementations without worrying about
6919 incompatibilities.")
6920 (license license:artistic2.0)))
6922 (define-public r-marray
6928 (uri (bioconductor-uri "marray" version))
6930 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
6931 (build-system r-build-system)
6934 (home-page "https://bioconductor.org/packages/marray")
6935 (synopsis "Exploratory analysis for two-color spotted microarray data")
6936 (description "This package contains class definitions for two-color spotted
6937 microarray data. It also includes functions for data input, diagnostic plots,
6938 normalization and quality checking.")
6939 (license license:lgpl2.0+)))
6941 (define-public r-cghbase
6947 (uri (bioconductor-uri "CGHbase" version))
6949 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
6950 (properties `((upstream-name . "CGHbase")))
6951 (build-system r-build-system)
6953 (list r-biobase r-marray))
6954 (home-page "https://bioconductor.org/packages/CGHbase")
6955 (synopsis "Base functions and classes for arrayCGH data analysis")
6956 (description "This package contains functions and classes that are needed by
6957 the @code{arrayCGH} packages.")
6958 (license license:gpl2+)))
6960 (define-public r-cghcall
6966 (uri (bioconductor-uri "CGHcall" version))
6968 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
6969 (properties `((upstream-name . "CGHcall")))
6970 (build-system r-build-system)
6972 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
6973 (home-page "https://bioconductor.org/packages/CGHcall")
6974 (synopsis "Base functions and classes for arrayCGH data analysis")
6975 (description "This package contains functions and classes that are needed by
6976 @code{arrayCGH} packages.")
6977 (license license:gpl2+)))
6979 (define-public r-qdnaseq
6985 (uri (bioconductor-uri "QDNAseq" version))
6987 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
6988 (properties `((upstream-name . "QDNAseq")))
6989 (build-system r-build-system)
7001 (home-page "https://bioconductor.org/packages/QDNAseq")
7002 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
7003 (description "The genome is divided into non-overlapping fixed-sized bins,
7004 number of sequence reads in each counted, adjusted with a simultaneous
7005 two-dimensional loess correction for sequence mappability and GC content, and
7006 filtered to remove spurious regions in the genome. Downstream steps of
7007 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
7009 (license license:gpl2+)))
7011 (define-public r-bayseq
7018 (uri (bioconductor-uri "baySeq" version))
7021 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
7022 (properties `((upstream-name . "baySeq")))
7023 (build-system r-build-system)
7025 (list r-abind r-edger r-genomicranges))
7026 (home-page "https://bioconductor.org/packages/baySeq/")
7027 (synopsis "Bayesian analysis of differential expression patterns in count data")
7029 "This package identifies differential expression in high-throughput count
7030 data, such as that derived from next-generation sequencing machines,
7031 calculating estimated posterior likelihoods of differential expression (or
7032 more complex hypotheses) via empirical Bayesian methods.")
7033 (license license:gpl3)))
7035 (define-public r-chipcomp
7042 (uri (bioconductor-uri "ChIPComp" version))
7045 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
7046 (properties `((upstream-name . "ChIPComp")))
7047 (build-system r-build-system)
7049 (list r-biocgenerics
7050 r-bsgenome-hsapiens-ucsc-hg19
7051 r-bsgenome-mmusculus-ucsc-mm9
7059 (home-page "https://bioconductor.org/packages/ChIPComp")
7060 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
7062 "ChIPComp implements a statistical method for quantitative comparison of
7063 multiple ChIP-seq datasets. It detects differentially bound sharp binding
7064 sites across multiple conditions considering matching control in ChIP-seq
7066 ;; Any version of the GPL.
7067 (license license:gpl3+)))
7069 (define-public r-riboprofiling
7071 (name "r-riboprofiling")
7076 (uri (bioconductor-uri "RiboProfiling" version))
7079 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
7080 (properties `((upstream-name . "RiboProfiling")))
7081 (build-system r-build-system)
7083 (list r-biocgenerics
7101 (home-page "https://bioconductor.org/packages/RiboProfiling/")
7102 (synopsis "Ribosome profiling data analysis")
7103 (description "Starting with a BAM file, this package provides the
7104 necessary functions for quality assessment, read start position recalibration,
7105 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
7106 of count data: pairs, log fold-change, codon frequency and coverage
7107 assessment, principal component analysis on codon coverage.")
7108 (license license:gpl3)))
7110 (define-public r-riboseqr
7117 (uri (bioconductor-uri "riboSeqR" version))
7120 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
7121 (properties `((upstream-name . "riboSeqR")))
7122 (build-system r-build-system)
7131 (home-page "https://bioconductor.org/packages/riboSeqR/")
7132 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
7134 "This package provides plotting functions, frameshift detection and
7135 parsing of genetic sequencing data from ribosome profiling experiments.")
7136 (license license:gpl3)))
7138 (define-public r-interactionset
7140 (name "r-interactionset")
7145 (uri (bioconductor-uri "InteractionSet" version))
7148 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
7150 `((upstream-name . "InteractionSet")))
7151 (build-system r-build-system)
7153 (list r-biocgenerics
7160 r-summarizedexperiment))
7163 (home-page "https://bioconductor.org/packages/InteractionSet")
7164 (synopsis "Base classes for storing genomic interaction data")
7166 "This package provides the @code{GInteractions},
7167 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
7168 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
7170 (license license:gpl3)))
7172 (define-public r-genomicinteractions
7174 (name "r-genomicinteractions")
7179 (uri (bioconductor-uri "GenomicInteractions" version))
7182 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
7184 `((upstream-name . "GenomicInteractions")))
7185 (build-system r-build-system)
7205 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
7206 (synopsis "R package for handling genomic interaction data")
7208 "This R package provides tools for handling genomic interaction data,
7209 such as ChIA-PET/Hi-C, annotating genomic features with interaction
7210 information and producing various plots and statistics.")
7211 (license license:gpl3)))
7213 (define-public r-ctc
7220 (uri (bioconductor-uri "ctc" version))
7223 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
7224 (build-system r-build-system)
7225 (propagated-inputs (list r-amap))
7226 (home-page "https://bioconductor.org/packages/ctc/")
7227 (synopsis "Cluster and tree conversion")
7229 "This package provides tools for exporting and importing classification
7230 trees and clusters to other programs.")
7231 (license license:gpl2)))
7233 (define-public r-goseq
7240 (uri (bioconductor-uri "goseq" version))
7243 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
7244 (build-system r-build-system)
7246 (list r-annotationdbi
7252 (home-page "https://bioconductor.org/packages/goseq/")
7253 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
7255 "This package provides tools to detect Gene Ontology and/or other user
7256 defined categories which are over/under represented in RNA-seq data.")
7257 (license license:lgpl2.0+)))
7259 (define-public r-glimma
7266 (uri (bioconductor-uri "Glimma" version))
7269 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
7270 (properties `((upstream-name . "Glimma")))
7271 (build-system r-build-system)
7279 r-summarizedexperiment))
7282 (home-page "https://github.com/Shians/Glimma")
7283 (synopsis "Interactive HTML graphics")
7285 "This package generates interactive visualisations for analysis of
7286 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
7287 HTML page. The interactions are built on top of the popular static
7288 representations of analysis results in order to provide additional
7290 (license license:lgpl3)))
7292 (define-public r-rots
7299 (uri (bioconductor-uri "ROTS" version))
7302 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
7303 (properties `((upstream-name . "ROTS")))
7304 (build-system r-build-system)
7306 (list r-biobase r-rcpp))
7307 (home-page "https://bioconductor.org/packages/ROTS/")
7308 (synopsis "Reproducibility-Optimized Test Statistic")
7310 "This package provides tools for calculating the
7311 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
7313 (license license:gpl2+)))
7315 (define-public r-plgem
7322 (uri (bioconductor-uri "plgem" version))
7325 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
7326 (build-system r-build-system)
7328 (list r-biobase r-mass))
7329 (home-page "http://www.genopolis.it")
7330 (synopsis "Detect differential expression in microarray and proteomics datasets")
7332 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
7333 model the variance-versus-mean dependence that exists in a variety of
7334 genome-wide datasets, including microarray and proteomics data. The use of
7335 PLGEM has been shown to improve the detection of differentially expressed
7336 genes or proteins in these datasets.")
7337 (license license:gpl2)))
7339 (define-public r-inspect
7346 (uri (bioconductor-uri "INSPEcT" version))
7349 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
7350 (properties `((upstream-name . "INSPEcT")))
7351 (build-system r-build-system)
7372 r-summarizedexperiment
7373 r-txdb-mmusculus-ucsc-mm9-knowngene))
7376 (home-page "https://bioconductor.org/packages/INSPEcT")
7377 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
7379 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
7380 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
7381 order to evaluate synthesis, processing and degradation rates and assess via
7382 modeling the rates that determines changes in mature mRNA levels.")
7383 (license license:gpl2)))
7385 (define-public r-dnabarcodes
7387 (name "r-dnabarcodes")
7392 (uri (bioconductor-uri "DNABarcodes" version))
7395 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
7396 (properties `((upstream-name . "DNABarcodes")))
7397 (build-system r-build-system)
7399 (list r-bh r-matrix r-rcpp))
7402 (home-page "https://bioconductor.org/packages/DNABarcodes")
7403 (synopsis "Create and analyze DNA barcodes")
7405 "This package offers tools to create DNA barcode sets capable of
7406 correcting insertion, deletion, and substitution errors. Existing barcodes
7407 can be analyzed regarding their minimal, maximal and average distances between
7408 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
7409 demultiplexed, i.e. assigned to their original reference barcode.")
7410 (license license:gpl2)))
7412 (define-public r-ruvseq
7419 (uri (bioconductor-uri "RUVSeq" version))
7422 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
7423 (properties `((upstream-name . "RUVSeq")))
7424 (build-system r-build-system)
7426 (list r-biobase r-edaseq r-edger r-mass))
7429 (home-page "https://github.com/drisso/RUVSeq")
7430 (synopsis "Remove unwanted variation from RNA-Seq data")
7432 "This package implements methods to @dfn{remove unwanted variation} (RUV)
7433 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
7435 (license license:artistic2.0)))
7437 (define-public r-biocneighbors
7439 (name "r-biocneighbors")
7444 (uri (bioconductor-uri "BiocNeighbors" version))
7447 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
7448 (properties `((upstream-name . "BiocNeighbors")))
7449 (build-system r-build-system)
7451 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
7454 (home-page "https://bioconductor.org/packages/BiocNeighbors")
7455 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
7457 "This package implements exact and approximate methods for nearest
7458 neighbor detection, in a framework that allows them to be easily switched
7459 within Bioconductor packages or workflows. The exact algorithm is implemented
7460 using pre-clustering with the k-means algorithm. Functions are also provided
7461 to search for all neighbors within a given distance. Parallelization is
7462 achieved for all methods using the BiocParallel framework.")
7463 (license license:gpl3)))
7465 (define-public r-scaledmatrix
7467 (name "r-scaledmatrix")
7472 (uri (bioconductor-uri "ScaledMatrix" version))
7475 "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl"))))
7476 (properties `((upstream-name . "ScaledMatrix")))
7477 (build-system r-build-system)
7479 (list r-delayedarray r-matrix r-s4vectors))
7480 (native-inputs (list r-knitr))
7481 (home-page "https://github.com/LTLA/ScaledMatrix")
7482 (synopsis "Create a DelayedMatrix of scaled and centered values")
7484 "This package provides delayed computation of a matrix of scaled and
7485 centered values. The result is equivalent to using the @code{scale} function
7486 but avoids explicit realization of a dense matrix during block processing.
7487 This permits greater efficiency in common operations, most notably matrix
7489 (license license:gpl3)))
7491 (define-public r-treeio
7498 (uri (bioconductor-uri "treeio" version))
7501 "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla"))))
7502 (properties `((upstream-name . "treeio")))
7503 (build-system r-build-system)
7512 (native-inputs (list r-knitr))
7513 (home-page "https://github.com/YuLab-SMU/treeio")
7514 (synopsis "Base classes and functions for Phylogenetic tree input and output")
7516 "This is an R package to make it easier to import and store phylogenetic
7517 trees with associated data; and to link external data from different sources
7518 to phylogeny. It also supports exporting phylogenetic trees with
7519 heterogeneous associated data to a single tree file and can be served as a
7520 platform for merging tree with associated data and converting file formats.")
7521 (license license:artistic2.0)))
7523 (define-public r-ggtree
7530 (uri (bioconductor-uri "ggtree" version))
7533 "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4"))))
7534 (properties `((upstream-name . "ggtree")))
7535 (build-system r-build-system)
7550 (native-inputs (list r-knitr))
7551 (home-page "https://yulab-smu.top/treedata-book/")
7552 (synopsis "R package for visualization of trees and annotation data")
7554 "This package extends the ggplot2 plotting system which implements a
7555 grammar of graphics. ggtree is designed for visualization and annotation of
7556 phylogenetic trees and other tree-like structures with their annotation
7558 (license license:artistic2.0)))
7560 (define-public r-metapod
7567 (uri (bioconductor-uri "metapod" version))
7570 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
7571 (properties `((upstream-name . "metapod")))
7572 (build-system r-build-system)
7577 (home-page "https://bioconductor.org/packages/metapod")
7578 (synopsis "Meta-analyses on p-values of differential analyses")
7580 "This package implements a variety of methods for combining p-values in
7581 differential analyses of genome-scale datasets. Functions can combine
7582 p-values across different tests in the same analysis (e.g., genomic windows in
7583 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
7584 analyses (e.g., replicated comparisons, effect of different treatment
7585 conditions). Support is provided for handling log-transformed input p-values,
7586 missing values and weighting where appropriate.")
7587 (license license:gpl3)))
7589 (define-public r-biocsingular
7591 (name "r-biocsingular")
7596 (uri (bioconductor-uri "BiocSingular" version))
7599 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
7600 (properties `((upstream-name . "BiocSingular")))
7601 (build-system r-build-system)
7615 (home-page "https://github.com/LTLA/BiocSingular")
7616 (synopsis "Singular value decomposition for Bioconductor packages")
7618 "This package implements exact and approximate methods for singular value
7619 decomposition and principal components analysis, in a framework that allows
7620 them to be easily switched within Bioconductor packages or workflows. Where
7621 possible, parallelization is achieved using the BiocParallel framework.")
7622 (license license:gpl3)))
7624 (define-public r-destiny
7631 (uri (bioconductor-uri "destiny" version))
7634 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
7635 (build-system r-build-system)
7653 r-singlecellexperiment
7655 r-summarizedexperiment
7660 (list r-knitr r-nbconvertr)) ; for vignettes
7661 (home-page "https://bioconductor.org/packages/destiny/")
7662 (synopsis "Create and plot diffusion maps")
7663 (description "This package provides tools to create and plot diffusion
7665 ;; Any version of the GPL
7666 (license license:gpl3+)))
7668 (define-public r-savr
7675 (uri (bioconductor-uri "savR" version))
7678 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
7679 (properties `((upstream-name . "savR")))
7680 (build-system r-build-system)
7682 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
7683 (home-page "https://github.com/bcalder/savR")
7684 (synopsis "Parse and analyze Illumina SAV files")
7686 "This package provides tools to parse Illumina Sequence Analysis
7687 Viewer (SAV) files, access data, and generate QC plots.")
7688 (license license:agpl3+)))
7690 (define-public r-chipexoqual
7692 (name "r-chipexoqual")
7697 (uri (bioconductor-uri "ChIPexoQual" version))
7700 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
7701 (properties `((upstream-name . "ChIPexoQual")))
7702 (build-system r-build-system)
7704 (list r-biocparallel
7723 (home-page "https://github.com/keleslab/ChIPexoQual")
7724 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
7726 "This package provides a quality control pipeline for ChIP-exo/nexus
7728 (license license:gpl2+)))
7730 (define-public r-copynumber
7732 (name "r-copynumber")
7736 (uri (bioconductor-uri "copynumber" version))
7739 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
7740 (build-system r-build-system)
7742 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
7743 (home-page "https://bioconductor.org/packages/copynumber")
7744 (synopsis "Segmentation of single- and multi-track copy number data")
7746 "This package segments single- and multi-track copy number data by a
7747 penalized least squares regression method.")
7748 (license license:artistic2.0)))
7750 (define-public r-dnacopy
7757 (uri (bioconductor-uri "DNAcopy" version))
7760 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
7761 (properties `((upstream-name . "DNAcopy")))
7762 (build-system r-build-system)
7763 (native-inputs (list gfortran))
7764 (home-page "https://bioconductor.org/packages/DNAcopy")
7765 (synopsis "DNA copy number data analysis")
7767 "This package implements the @dfn{circular binary segmentation} (CBS)
7768 algorithm to segment DNA copy number data and identify genomic regions with
7769 abnormal copy number.")
7770 (license license:gpl2+)))
7772 ;; This is a CRAN package, but it uncharacteristically depends on a
7773 ;; Bioconductor package.
7774 (define-public r-htscluster
7776 (name "r-htscluster")
7781 (uri (cran-uri "HTSCluster" version))
7784 "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
7785 (properties `((upstream-name . "HTSCluster")))
7786 (build-system r-build-system)
7788 (list r-capushe r-edger r-plotrix))
7789 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
7790 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
7792 "This package provides a Poisson mixture model is implemented to cluster
7793 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
7794 estimation is performed using either the EM or CEM algorithm, and the slope
7795 heuristics are used for model selection (i.e., to choose the number of
7797 (license license:gpl3+)))
7799 (define-public r-deds
7806 (uri (bioconductor-uri "DEDS" version))
7809 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
7810 (properties `((upstream-name . "DEDS")))
7811 (build-system r-build-system)
7812 (home-page "https://bioconductor.org/packages/DEDS/")
7813 (synopsis "Differential expression via distance summary for microarray data")
7815 "This library contains functions that calculate various statistics of
7816 differential expression for microarray data, including t statistics, fold
7817 change, F statistics, SAM, moderated t and F statistics and B statistics. It
7818 also implements a new methodology called DEDS (Differential Expression via
7819 Distance Summary), which selects differentially expressed genes by integrating
7820 and summarizing a set of statistics using a weighted distance approach.")
7821 ;; Any version of the LGPL.
7822 (license license:lgpl3+)))
7824 ;; This is a CRAN package, but since it depends on a Bioconductor package we
7826 (define-public r-nbpseq
7833 (uri (cran-uri "NBPSeq" version))
7836 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
7837 (properties `((upstream-name . "NBPSeq")))
7838 (build-system r-build-system)
7841 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
7842 (synopsis "Negative binomial models for RNA-Seq data")
7844 "This package provides negative binomial models for two-group comparisons
7845 and regression inferences from RNA-sequencing data.")
7846 (license license:gpl2)))
7848 (define-public r-ebseq
7855 (uri (bioconductor-uri "EBSeq" version))
7858 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
7859 (properties `((upstream-name . "EBSeq")))
7860 (build-system r-build-system)
7862 (list r-blockmodeling r-gplots r-testthat))
7863 (home-page "https://bioconductor.org/packages/EBSeq")
7864 (synopsis "Differential expression analysis of RNA-seq data")
7866 "This package provides tools for differential expression analysis at both
7867 gene and isoform level using RNA-seq data")
7868 (license license:artistic2.0)))
7870 (define-public r-karyoploter
7872 (name "r-karyoploter")
7876 (uri (bioconductor-uri "karyoploteR" version))
7879 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
7880 (build-system r-build-system)
7882 (list r-annotationdbi
7896 r-variantannotation))
7899 (home-page "https://bioconductor.org/packages/karyoploteR/")
7900 (synopsis "Plot customizable linear genomes displaying arbitrary data")
7901 (description "This package creates karyotype plots of arbitrary genomes and
7902 offers a complete set of functions to plot arbitrary data on them. It mimics
7903 many R base graphics functions coupling them with a coordinate change function
7904 automatically mapping the chromosome and data coordinates into the plot
7906 (license license:artistic2.0)))
7908 (define-public r-lpsymphony
7910 (name "r-lpsymphony")
7915 (uri (bioconductor-uri "lpsymphony" version))
7918 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
7919 (build-system r-build-system)
7923 (list pkg-config r-knitr))
7924 (home-page "https://r-forge.r-project.org/projects/rsymphony")
7925 (synopsis "Symphony integer linear programming solver in R")
7927 "This package was derived from Rsymphony. The package provides an R
7928 interface to SYMPHONY, a linear programming solver written in C++. The main
7929 difference between this package and Rsymphony is that it includes the solver
7930 source code, while Rsymphony expects to find header and library files on the
7931 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
7932 to install interface to SYMPHONY.")
7933 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
7934 ;; lpsimphony is released under the same terms.
7935 (license license:epl1.0)))
7937 (define-public r-ihw
7944 (uri (bioconductor-uri "IHW" version))
7947 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
7948 (properties `((upstream-name . "IHW")))
7949 (build-system r-build-system)
7951 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
7954 (home-page "https://bioconductor.org/packages/IHW")
7955 (synopsis "Independent hypothesis weighting")
7957 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
7958 procedure that increases power compared to the method of Benjamini and
7959 Hochberg by assigning data-driven weights to each hypothesis. The input to
7960 IHW is a two-column table of p-values and covariates. The covariate can be
7961 any continuous-valued or categorical variable that is thought to be
7962 informative on the statistical properties of each hypothesis test, while it is
7963 independent of the p-value under the null hypothesis.")
7964 (license license:artistic2.0)))
7966 (define-public r-icobra
7973 (uri (bioconductor-uri "iCOBRA" version))
7976 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
7977 (properties `((upstream-name . "iCOBRA")))
7978 (build-system r-build-system)
7994 (home-page "https://bioconductor.org/packages/iCOBRA")
7995 (synopsis "Comparison and visualization of ranking and assignment methods")
7997 "This package provides functions for calculation and visualization of
7998 performance metrics for evaluation of ranking and binary
7999 classification (assignment) methods. It also contains a Shiny application for
8000 interactive exploration of results.")
8001 (license license:gpl2+)))
8003 (define-public r-residualmatrix
8005 (name "r-residualmatrix")
8010 (uri (bioconductor-uri "ResidualMatrix" version))
8013 "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4"))))
8015 `((upstream-name . "ResidualMatrix")))
8016 (build-system r-build-system)
8018 (list r-delayedarray r-matrix r-s4vectors))
8021 (home-page "https://github.com/LTLA/ResidualMatrix")
8022 (synopsis "Create a DelayedMatrix of regression residuals")
8024 "This package implements tools for delayed computation of a matrix of
8025 residuals after fitting a linear model to each column of an input matrix. It
8026 also supports partial computation of residuals where selected factors are to
8027 be preserved in the output matrix. It implements a number of efficient
8028 methods for operating on the delayed matrix of residuals, most notably matrix
8029 multiplication and calculation of row/column sums or means.")
8030 (license license:gpl3)))
8032 (define-public r-batchelor
8034 (name "r-batchelor")
8039 (uri (bioconductor-uri "batchelor" version))
8042 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
8043 (properties `((upstream-name . "batchelor")))
8044 (build-system r-build-system)
8052 r-delayedmatrixstats
8060 r-singlecellexperiment
8061 r-summarizedexperiment))
8062 (native-inputs (list r-knitr))
8063 (home-page "https://bioconductor.org/packages/batchelor")
8064 (synopsis "Single-Cell Batch Correction Methods")
8066 "This package implements a variety of methods for batch correction of
8067 single-cell (RNA sequencing) data. This includes methods based on detecting
8068 mutually nearest neighbors, as well as several efficient variants of linear
8069 regression of the log-expression values. Functions are also provided to
8070 perform global rescaling to remove differences in depth between batches, and
8071 to perform a principal components analysis that is robust to differences in
8072 the numbers of cells across batches.")
8073 (license license:gpl3)))
8075 (define-public r-mast
8082 (uri (bioconductor-uri "MAST" version))
8085 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
8086 (properties `((upstream-name . "MAST")))
8087 (build-system r-build-system)
8098 r-singlecellexperiment
8100 r-summarizedexperiment))
8103 (home-page "https://github.com/RGLab/MAST/")
8104 (synopsis "Model-based analysis of single cell transcriptomics")
8106 "This package provides methods and models for handling zero-inflated
8107 single cell assay data.")
8108 (license license:gpl2+)))
8110 (define-public r-monocle
8117 (uri (bioconductor-uri "monocle" version))
8120 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
8121 (build-system r-build-system)
8155 (home-page "https://bioconductor.org/packages/monocle")
8156 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
8158 "Monocle performs differential expression and time-series analysis for
8159 single-cell expression experiments. It orders individual cells according to
8160 progress through a biological process, without knowing ahead of time which
8161 genes define progress through that process. Monocle also performs
8162 differential expression analysis, clustering, visualization, and other useful
8163 tasks on single cell expression data. It is designed to work with RNA-Seq and
8164 qPCR data, but could be used with other types as well.")
8165 (license license:artistic2.0)))
8167 (define-public r-leidenbase
8168 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
8171 (name "r-leidenbase")
8172 (version (git-version "0.1.9" revision commit))
8177 (url "https://github.com/cole-trapnell-lab/leidenbase")
8179 (file-name (git-file-name name version))
8182 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
8183 (properties `((upstream-name . "leidenbase")))
8184 (build-system r-build-system)
8191 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
8192 (synopsis "R and C wrappers to run the Leiden find_partition function")
8194 "This package provides an R to C interface that runs the Leiden
8195 community detection algorithm to find a basic partition. It runs the
8196 equivalent of the @code{find_partition} function. This package includes the
8197 required source code files from the official Leidenalg distribution and
8198 several functions from the R igraph package.")
8199 (license license:gpl3+))))
8201 (define-public r-sanssouci
8202 ;; sansscouci doesn't have a (versioned) release yet.
8203 ;; This is the latest commit as of packaging for Guix.
8204 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
8207 (name "r-sanssouci")
8208 (version (git-version "0" revision commit))
8212 (url "https://github.com/pneuvial/sanssouci.git")
8214 (file-name (git-file-name name version))
8217 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
8218 (build-system r-build-system)
8220 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
8221 (home-page "https://pneuvial.github.io/sanssouci")
8222 (synopsis "Post Hoc multiple testing inference")
8224 "The goal of sansSouci is to perform post hoc inference: in a multiple
8225 testing context, sansSouci provides statistical guarantees on possibly
8226 user-defined and/or data-driven sets of hypotheses.")
8227 (license license:gpl3))))
8229 (define-public r-monocle3
8237 (url "https://github.com/cole-trapnell-lab/monocle3")
8239 (file-name (git-file-name name version))
8242 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
8243 (build-system r-build-system)
8249 r-delayedmatrixstats
8284 r-singlecellexperiment
8289 (home-page "https://github.com/cole-trapnell-lab/monocle3")
8290 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
8292 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
8293 (license license:expat)))
8295 (define-public r-noiseq
8302 (uri (bioconductor-uri "NOISeq" version))
8305 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
8306 (properties `((upstream-name . "NOISeq")))
8307 (build-system r-build-system)
8309 (list r-biobase r-matrix))
8310 (home-page "https://bioconductor.org/packages/NOISeq")
8311 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
8313 "This package provides tools to support the analysis of RNA-seq
8314 expression data or other similar kind of data. It provides exploratory plots
8315 to evaluate saturation, count distribution, expression per chromosome, type of
8316 detected features, features length, etc. It also supports the analysis of
8317 differential expression between two experimental conditions with no parametric
8319 (license license:artistic2.0)))
8321 (define-public r-scdd
8328 (uri (bioconductor-uri "scDD" version))
8331 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
8332 (properties `((upstream-name . "scDD")))
8333 (build-system r-build-system)
8344 r-singlecellexperiment
8345 r-summarizedexperiment))
8348 (home-page "https://github.com/kdkorthauer/scDD")
8349 (synopsis "Mixture modeling of single-cell RNA-seq data")
8351 "This package implements a method to analyze single-cell RNA-seq data
8352 utilizing flexible Dirichlet Process mixture models. Genes with differential
8353 distributions of expression are classified into several interesting patterns
8354 of differences between two conditions. The package also includes functions
8355 for simulating data with these patterns from negative binomial
8357 (license license:gpl2)))
8359 (define-public r-scone
8366 (uri (bioconductor-uri "scone" version))
8369 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
8370 (build-system r-build-system)
8391 r-singlecellexperiment
8392 r-summarizedexperiment))
8395 (home-page "https://bioconductor.org/packages/scone")
8396 (synopsis "Single cell overview of normalized expression data")
8398 "SCONE is an R package for comparing and ranking the performance of
8399 different normalization schemes for single-cell RNA-seq and other
8400 high-throughput analyses.")
8401 (license license:artistic2.0)))
8403 (define-public r-geoquery
8410 (uri (bioconductor-uri "GEOquery" version))
8413 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
8414 (properties `((upstream-name . "GEOquery")))
8415 (build-system r-build-system)
8429 (home-page "https://github.com/seandavi/GEOquery/")
8430 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
8432 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
8433 microarray data. Given the rich and varied nature of this resource, it is
8434 only natural to want to apply BioConductor tools to these data. GEOquery is
8435 the bridge between GEO and BioConductor.")
8436 (license license:gpl2)))
8438 (define-public r-illuminaio
8440 (name "r-illuminaio")
8445 (uri (bioconductor-uri "illuminaio" version))
8448 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
8449 (build-system r-build-system)
8452 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
8453 (synopsis "Parse Illumina microarray output files")
8455 "This package provides tools for parsing Illumina's microarray output
8456 files, including IDAT.")
8457 (license license:gpl2)))
8459 (define-public r-siggenes
8466 (uri (bioconductor-uri "siggenes" version))
8469 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
8470 (build-system r-build-system)
8472 (list r-biobase r-multtest r-scrime))
8473 (home-page "https://bioconductor.org/packages/siggenes/")
8475 "Multiple testing using SAM and Efron's empirical Bayes approaches")
8477 "This package provides tools for the identification of differentially
8478 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
8479 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
8480 Bayes Analyses of Microarrays} (EBAM).")
8481 (license license:lgpl2.0+)))
8483 (define-public r-bumphunter
8485 (name "r-bumphunter")
8490 (uri (bioconductor-uri "bumphunter" version))
8493 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
8494 (build-system r-build-system)
8496 (list r-annotationdbi
8509 (home-page "https://github.com/ririzarr/bumphunter")
8510 (synopsis "Find bumps in genomic data")
8512 "This package provides tools for finding bumps in genomic data in order
8513 to identify differentially methylated regions in epigenetic epidemiology
8515 (license license:artistic2.0)))
8517 (define-public r-minfi
8524 (uri (bioconductor-uri "minfi" version))
8527 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
8528 (build-system r-build-system)
8538 r-delayedmatrixstats
8558 r-summarizedexperiment))
8561 (home-page "https://github.com/hansenlab/minfi")
8562 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
8564 "This package provides tools to analyze and visualize Illumina Infinium
8565 methylation arrays.")
8566 (license license:artistic2.0)))
8568 (define-public r-methylumi
8570 (name "r-methylumi")
8575 (uri (bioconductor-uri "methylumi" version))
8578 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
8579 (build-system r-build-system)
8585 r-fdb-infiniummethylation-hg19
8599 r-summarizedexperiment))
8602 (home-page "https://bioconductor.org/packages/methylumi")
8603 (synopsis "Handle Illumina methylation data")
8605 "This package provides classes for holding and manipulating Illumina
8606 methylation data. Based on eSet, it can contain MIAME information, sample
8607 information, feature information, and multiple matrices of data. An
8608 \"intelligent\" import function, methylumiR can read the Illumina text files
8609 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
8610 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
8611 background correction, and quality control features for GoldenGate, Infinium,
8612 and Infinium HD arrays are also included.")
8613 (license license:gpl2)))
8615 (define-public r-lumi
8622 (uri (bioconductor-uri "lumi" version))
8625 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
8626 (build-system r-build-system)
8643 (home-page "https://bioconductor.org/packages/lumi")
8644 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
8646 "The lumi package provides an integrated solution for the Illumina
8647 microarray data analysis. It includes functions of Illumina
8648 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
8649 variance stabilization, normalization and gene annotation at the probe level.
8650 It also includes the functions of processing Illumina methylation microarrays,
8651 especially Illumina Infinium methylation microarrays.")
8652 (license license:lgpl2.0+)))
8654 (define-public r-linnorm
8661 (uri (bioconductor-uri "Linnorm" version))
8664 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
8665 (properties `((upstream-name . "Linnorm")))
8666 (build-system r-build-system)
8688 (home-page "http://www.jjwanglab.org/Linnorm/")
8689 (synopsis "Linear model and normality based transformation method")
8691 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
8692 count data or any large scale count data. It transforms such datasets for
8693 parametric tests. In addition to the transformtion function (@code{Linnorm}),
8694 the following pipelines are implemented:
8697 @item Library size/batch effect normalization (@code{Linnorm.Norm})
8698 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
8699 clustering or hierarchical clustering (@code{Linnorm.tSNE},
8700 @code{Linnorm.PCA}, @code{Linnorm.HClust})
8701 @item Differential expression analysis or differential peak detection using
8702 limma (@code{Linnorm.limma})
8703 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
8704 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
8705 @item Stable gene selection for scRNA-seq data; for users without or who do
8706 not want to rely on spike-in genes (@code{Linnorm.SGenes})
8707 @item Data imputation (@code{Linnorm.DataImput}).
8710 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
8711 @code{RnaXSim} function is included for simulating RNA-seq data for the
8712 evaluation of DEG analysis methods.")
8713 (license license:expat)))
8715 (define-public r-ioniser
8722 (uri (bioconductor-uri "IONiseR" version))
8725 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
8726 (properties `((upstream-name . "IONiseR")))
8727 (build-system r-build-system)
8729 (list r-biocgenerics
8744 (home-page "https://bioconductor.org/packages/IONiseR/")
8745 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
8747 "IONiseR provides tools for the quality assessment of Oxford Nanopore
8748 MinION data. It extracts summary statistics from a set of fast5 files and can
8749 be used either before or after base calling. In addition to standard
8750 summaries of the read-types produced, it provides a number of plots for
8751 visualising metrics relative to experiment run time or spatially over the
8752 surface of a flowcell.")
8753 (license license:expat)))
8755 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
8756 (define-public r-mutoss
8763 (uri (cran-uri "mutoss" version))
8766 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
8767 (properties `((upstream-name . "mutoss")))
8768 (build-system r-build-system)
8770 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
8771 (home-page "https://github.com/kornl/mutoss/")
8772 (synopsis "Unified multiple testing procedures")
8774 "This package is designed to ease the application and comparison of
8775 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
8776 are standardized and usable by the accompanying mutossGUI package.")
8777 ;; Any version of the GPL.
8778 (license (list license:gpl2+ license:gpl3+))))
8780 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
8781 ;; from Bioconductor, so we put it here.
8782 (define-public r-metap
8789 (uri (cran-uri "metap" version))
8792 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
8793 (build-system r-build-system)
8801 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
8802 (synopsis "Meta-analysis of significance values")
8804 "The canonical way to perform meta-analysis involves using effect sizes.
8805 When they are not available this package provides a number of methods for
8806 meta-analysis of significance values including the methods of Edgington,
8807 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
8808 published results; and a routine for graphical display.")
8809 (license license:gpl2)))
8811 (define-public r-tradeseq
8817 (uri (bioconductor-uri "tradeSeq" version))
8820 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
8821 (build-system r-build-system)
8837 r-singlecellexperiment
8839 r-summarizedexperiment
8845 (home-page "https://statomics.github.io/tradeSeq/index.html")
8846 (synopsis "Trajectory-based differential expression analysis")
8848 "This package provides a flexible method for fitting regression models that
8849 can be used to find genes that are differentially expressed along one or
8850 multiple lineages in a trajectory. Based on the fitted models, it uses a
8851 variety of tests suited to answer different questions of interest, e.g. the
8852 discovery of genes for which expression is associated with pseudotime, or which
8853 are differentially expressed (in a specific region) along the trajectory. It
8854 fits a negative binomial generalized additive model (GAM) for each gene, and
8855 performs inference on the parameters of the GAM.")
8856 (license license:expat)))
8858 (define-public r-triform
8865 (uri (bioconductor-uri "triform" version))
8868 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
8869 (build-system r-build-system)
8871 (list r-biocgenerics r-iranges r-yaml))
8872 (home-page "https://bioconductor.org/packages/triform/")
8873 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
8875 "The Triform algorithm uses model-free statistics to identify peak-like
8876 distributions of TF ChIP sequencing reads, taking advantage of an improved
8877 peak definition in combination with known profile characteristics.")
8878 (license license:gpl2)))
8880 (define-public r-varianttools
8882 (name "r-varianttools")
8887 (uri (bioconductor-uri "VariantTools" version))
8890 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
8891 (properties `((upstream-name . "VariantTools")))
8892 (build-system r-build-system)
8907 r-variantannotation))
8908 (home-page "https://bioconductor.org/packages/VariantTools/")
8909 (synopsis "Tools for exploratory analysis of variant calls")
8911 "Explore, diagnose, and compare variant calls using filters. The
8912 VariantTools package supports a workflow for loading data, calling single
8913 sample variants and tumor-specific somatic mutations or other sample-specific
8914 variant types (e.g., RNA editing). Most of the functions operate on
8915 alignments (BAM files) or datasets of called variants. The user is expected
8916 to have already aligned the reads with a separate tool, e.g., GSNAP via
8918 (license license:artistic2.0)))
8920 (define-public r-heatplus
8927 (uri (bioconductor-uri "Heatplus" version))
8930 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
8931 (properties `((upstream-name . "Heatplus")))
8932 (build-system r-build-system)
8934 (list r-rcolorbrewer))
8935 (home-page "https://github.com/alexploner/Heatplus")
8936 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
8938 "This package provides tools to display a rectangular heatmap (intensity
8939 plot) of a data matrix. By default, both samples (columns) and features (row)
8940 of the matrix are sorted according to a hierarchical clustering, and the
8941 corresponding dendrogram is plotted. Optionally, panels with additional
8942 information about samples and features can be added to the plot.")
8943 (license license:gpl2+)))
8945 (define-public r-gosemsim
8952 (uri (bioconductor-uri "GOSemSim" version))
8955 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
8956 (properties `((upstream-name . "GOSemSim")))
8957 (build-system r-build-system)
8959 (list r-annotationdbi r-go-db r-rcpp))
8962 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
8963 (synopsis "GO-terms semantic similarity measures")
8965 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
8966 quantitative ways to compute similarities between genes and gene groups, and
8967 have became important basis for many bioinformatics analysis approaches.
8968 GOSemSim is an R package for semantic similarity computation among GO terms,
8969 sets of GO terms, gene products and gene clusters.")
8970 (license license:artistic2.0)))
8972 (define-public r-anota
8979 (uri (bioconductor-uri "anota" version))
8982 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
8983 (build-system r-build-system)
8985 (list r-multtest r-qvalue))
8986 (home-page "https://bioconductor.org/packages/anota/")
8987 (synopsis "Analysis of translational activity")
8989 "Genome wide studies of translational control is emerging as a tool to
8990 study various biological conditions. The output from such analysis is both
8991 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
8992 involved in translation (the actively translating mRNA level) for each mRNA.
8993 The standard analysis of such data strives towards identifying differential
8994 translational between two or more sample classes - i.e., differences in
8995 actively translated mRNA levels that are independent of underlying differences
8996 in cytosolic mRNA levels. This package allows for such analysis using partial
8997 variances and the random variance model. As 10s of thousands of mRNAs are
8998 analyzed in parallel the library performs a number of tests to assure that
8999 the data set is suitable for such analysis.")
9000 (license license:gpl3)))
9002 (define-public r-sigpathway
9004 (name "r-sigpathway")
9009 (uri (bioconductor-uri "sigPathway" version))
9012 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
9013 (properties `((upstream-name . "sigPathway")))
9014 (build-system r-build-system)
9015 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
9016 (synopsis "Pathway analysis")
9018 "This package is used to conduct pathway analysis by calculating the NT_k
9019 and NE_k statistics in a statistical framework for determining whether a
9020 specified group of genes for a pathway has a coordinated association with a
9021 phenotype of interest.")
9022 (license license:gpl2)))
9024 (define-public r-fcscan
9031 (uri (bioconductor-uri "fcScan" version))
9033 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
9034 (properties `((upstream-name . "fcScan")))
9035 (build-system r-build-system)
9043 r-summarizedexperiment
9044 r-variantannotation))
9045 (native-inputs (list r-knitr))
9046 (home-page "https://bioconductor.org/packages/fcScan")
9047 (synopsis "Detect clusters of coordinates with user defined options")
9049 "This package is used to detect combination of genomic coordinates
9050 falling within a user defined window size along with user defined overlap
9051 between identified neighboring clusters. It can be used for genomic data
9052 where the clusters are built on a specific chromosome or specific strand.
9053 Clustering can be performed with a \"greedy\" option allowing thus the
9054 presence of additional sites within the allowed window size.")
9055 (license license:artistic2.0)))
9057 (define-public r-fgsea
9064 (uri (bioconductor-uri "fgsea" version))
9067 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
9068 (build-system r-build-system)
9080 (home-page "https://github.com/ctlab/fgsea/")
9081 (synopsis "Fast gene set enrichment analysis")
9083 "The package implements an algorithm for fast gene set enrichment
9084 analysis. Using the fast algorithm makes more permutations and gets
9085 more fine grained p-values, which allows using accurate standard approaches
9086 to multiple hypothesis correction.")
9087 (license license:expat)))
9089 (define-public r-dose
9096 (uri (bioconductor-uri "DOSE" version))
9099 "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp"))))
9100 (properties `((upstream-name . "DOSE")))
9101 (build-system r-build-system)
9103 (list r-annotationdbi
9113 (home-page "https://guangchuangyu.github.io/software/DOSE/")
9114 (synopsis "Disease ontology semantic and enrichment analysis")
9116 "This package implements five methods proposed by Resnik, Schlicker,
9117 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
9118 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
9119 including hypergeometric model and gene set enrichment analysis are also
9120 implemented for discovering disease associations of high-throughput biological
9122 (license license:artistic2.0)))
9124 (define-public r-enrichplot
9126 (name "r-enrichplot")
9131 (uri (bioconductor-uri "enrichplot" version))
9134 "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"))))
9135 (build-system r-build-system)
9154 (home-page "https://github.com/GuangchuangYu/enrichplot")
9155 (synopsis "Visualization of functional enrichment result")
9157 "The enrichplot package implements several visualization methods for
9158 interpreting functional enrichment results obtained from ORA or GSEA analyses.
9159 All the visualization methods are developed based on ggplot2 graphics.")
9160 (license license:artistic2.0)))
9162 (define-public r-clusterprofiler
9164 (name "r-clusterprofiler")
9169 (uri (bioconductor-uri "clusterProfiler" version))
9172 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
9174 `((upstream-name . "clusterProfiler")))
9175 (build-system r-build-system)
9177 (list r-annotationdbi
9192 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
9193 (synopsis "Analysis and visualization of functional profiles for gene clusters")
9195 "This package implements methods to analyze and visualize functional
9196 profiles (GO and KEGG) of gene and gene clusters.")
9197 (license license:artistic2.0)))
9199 (define-public r-clusterexperiment
9201 (name "r-clusterexperiment")
9205 (uri (bioconductor-uri "clusterExperiment" version))
9208 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
9209 (build-system r-build-system)
9234 r-singlecellexperiment
9236 r-summarizedexperiment
9238 (home-page "https://bioconductor.org/packages/clusterExperiment/")
9239 (synopsis "Compare clusterings for single-cell sequencing")
9240 (description "This package provides functionality for running and comparing
9241 many different clusterings of single-cell sequencing data or other large mRNA
9242 expression data sets.")
9243 (license license:artistic2.0)))
9245 (define-public r-mlinterfaces
9247 (name "r-mlinterfaces")
9252 (uri (bioconductor-uri "MLInterfaces" version))
9255 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
9256 (properties `((upstream-name . "MLInterfaces")))
9257 (build-system r-build-system)
9279 (home-page "https://bioconductor.org/packages/MLInterfaces/")
9280 (synopsis "Interfaces to R machine learning procedures")
9282 "This package provides uniform interfaces to machine learning code for
9283 data in R and Bioconductor containers.")
9284 ;; Any version of the LGPL.
9285 (license license:lgpl2.1+)))
9287 (define-public r-annaffy
9294 (uri (bioconductor-uri "annaffy" version))
9297 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
9298 (build-system r-build-system)
9301 (modify-phases %standard-phases
9302 (add-after 'unpack 'remove-reference-to-non-free-data
9304 (substitute* "DESCRIPTION"
9305 ((", KEGG.db") "")))))))
9307 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
9308 (home-page "https://bioconductor.org/packages/annaffy/")
9309 (synopsis "Annotation tools for Affymetrix biological metadata")
9311 "This package provides functions for handling data from Bioconductor
9312 Affymetrix annotation data packages. It produces compact HTML and text
9313 reports including experimental data and URL links to many online databases.
9314 It allows searching of biological metadata using various criteria.")
9315 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
9316 ;; the LGPL 2.1 is included.
9317 (license license:lgpl2.1+)))
9319 (define-public r-a4core
9326 (uri (bioconductor-uri "a4Core" version))
9329 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
9330 (properties `((upstream-name . "a4Core")))
9331 (build-system r-build-system)
9333 (list r-biobase r-glmnet))
9336 (home-page "https://bioconductor.org/packages/a4Core")
9337 (synopsis "Automated Affymetrix array analysis core package")
9339 "This is the core package for the automated analysis of Affymetrix
9341 (license license:gpl3)))
9343 (define-public r-a4classif
9345 (name "r-a4classif")
9350 (uri (bioconductor-uri "a4Classif" version))
9353 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
9354 (properties `((upstream-name . "a4Classif")))
9355 (build-system r-build-system)
9366 (home-page "https://bioconductor.org/packages/a4Classif/")
9367 (synopsis "Automated Affymetrix array analysis classification package")
9369 "This is the classification package for the automated analysis of
9370 Affymetrix arrays.")
9371 (license license:gpl3)))
9373 (define-public r-a4preproc
9375 (name "r-a4preproc")
9380 (uri (bioconductor-uri "a4Preproc" version))
9383 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
9384 (properties `((upstream-name . "a4Preproc")))
9385 (build-system r-build-system)
9387 (list r-biobase r-biocgenerics))
9390 (home-page "https://bioconductor.org/packages/a4Preproc/")
9391 (synopsis "Automated Affymetrix array analysis preprocessing package")
9393 "This is a package for the automated analysis of Affymetrix arrays. It
9394 is used for preprocessing the arrays.")
9395 (license license:gpl3)))
9397 (define-public r-a4reporting
9399 (name "r-a4reporting")
9404 (uri (bioconductor-uri "a4Reporting" version))
9407 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
9408 (properties `((upstream-name . "a4Reporting")))
9409 (build-system r-build-system)
9414 (home-page "https://bioconductor.org/packages/a4Reporting/")
9415 (synopsis "Automated Affymetrix array analysis reporting package")
9417 "This is a package for the automated analysis of Affymetrix arrays. It
9418 provides reporting features.")
9419 (license license:gpl3)))
9421 (define-public r-a4base
9428 (uri (bioconductor-uri "a4Base" version))
9431 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
9432 (properties `((upstream-name . "a4Base")))
9433 (build-system r-build-system)
9445 (home-page "https://bioconductor.org/packages/a4Base/")
9446 (synopsis "Automated Affymetrix array analysis base package")
9448 "This package provides basic features for the automated analysis of
9449 Affymetrix arrays.")
9450 (license license:gpl3)))
9459 (uri (bioconductor-uri "a4" version))
9462 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
9463 (build-system r-build-system)
9465 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
9466 (home-page "https://bioconductor.org/packages/a4/")
9467 (synopsis "Automated Affymetrix array analysis umbrella package")
9469 "This package provides a software suite for the automated analysis of
9470 Affymetrix arrays.")
9471 (license license:gpl3)))
9473 (define-public r-abseqr
9480 (uri (bioconductor-uri "abseqR" version))
9483 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
9484 (properties `((upstream-name . "abseqR")))
9485 (build-system r-build-system)
9489 (list r-biocparallel
9509 (home-page "https://github.com/malhamdoosh/abseqR")
9510 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
9512 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
9513 sequencing datasets generated from antibody libraries and abseqR is one of its
9514 packages. AbseqR empowers the users of abseqPy with plotting and reporting
9515 capabilities and allows them to generate interactive HTML reports for the
9516 convenience of viewing and sharing with other researchers. Additionally,
9517 abseqR extends abseqPy to compare multiple repertoire analyses and perform
9518 further downstream analysis on its output.")
9519 (license license:gpl3)))
9521 (define-public r-bacon
9528 (uri (bioconductor-uri "bacon" version))
9531 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
9532 (build-system r-build-system)
9534 (list r-biocparallel r-ellipse r-ggplot2))
9537 (home-page "https://bioconductor.org/packages/bacon/")
9538 (synopsis "Controlling bias and inflation in association studies")
9540 "Bacon can be used to remove inflation and bias often observed in
9541 epigenome- and transcriptome-wide association studies. To this end bacon
9542 constructs an empirical null distribution using a Gibbs Sampling algorithm by
9543 fitting a three-component normal mixture on z-scores.")
9544 (license license:gpl2+)))
9546 (define-public r-rgadem
9553 (uri (bioconductor-uri "rGADEM" version))
9556 "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4"))))
9557 (properties `((upstream-name . "rGADEM")))
9558 (build-system r-build-system)
9560 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
9561 (home-page "https://bioconductor.org/packages/rGADEM/")
9562 (synopsis "De novo sequence motif discovery")
9564 "rGADEM is an efficient de novo motif discovery tool for large-scale
9565 genomic sequence data.")
9566 (license license:artistic2.0)))
9568 (define-public r-motiv
9575 (uri (bioconductor-uri "MotIV" version))
9578 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
9579 (properties `((upstream-name . "MotIV")))
9580 (build-system r-build-system)
9584 (list r-biocgenerics
9591 (home-page "https://bioconductor.org/packages/MotIV/")
9592 (synopsis "Motif identification and validation")
9594 "This package is used for the identification and validation of sequence
9595 motifs. It makes use of STAMP for comparing a set of motifs to a given
9596 database (e.g. JASPAR). It can also be used to visualize motifs, motif
9597 distributions, modules and filter motifs.")
9598 (license license:gpl2)))
9600 (define-public r-motifdb
9606 (uri (bioconductor-uri "MotifDb" version))
9608 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
9609 (properties `((upstream-name . "MotifDb")))
9610 (build-system r-build-system)
9612 (list r-biocgenerics
9621 (home-page "https://www.bioconductor.org/packages/MotifDb/")
9622 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
9623 (description "This package provides more than 2000 annotated position
9624 frequency matrices from nine public sources, for multiple organisms.")
9625 (license license:artistic2.0)))
9627 (define-public r-motifbreakr
9629 (name "r-motifbreakr")
9633 (uri (bioconductor-uri "motifbreakR" version))
9635 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
9636 (properties `((upstream-name . "motifbreakR")))
9637 (build-system r-build-system)
9639 (list r-biocgenerics
9653 r-summarizedexperiment
9655 r-variantannotation))
9658 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
9659 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
9660 (description "This package allows biologists to judge in the first place
9661 whether the sequence surrounding the polymorphism is a good match, and in
9662 the second place how much information is gained or lost in one allele of
9663 the polymorphism relative to another. This package gives a choice of
9664 algorithms for interrogation of genomes with motifs from public sources:
9666 @item a weighted-sum probability matrix;
9667 @item log-probabilities;
9668 @item weighted by relative entropy.
9671 This package can predict effects for novel or previously described variants in
9672 public databases, making it suitable for tasks beyond the scope of its original
9673 design. Lastly, it can be used to interrogate any genome curated within
9675 (license license:gpl2+)))
9677 (define-public r-motifstack
9679 (name "r-motifstack")
9684 (uri (bioconductor-uri "motifStack" version))
9687 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
9688 (properties `((upstream-name . "motifStack")))
9689 (build-system r-build-system)
9699 (home-page "https://bioconductor.org/packages/motifStack/")
9700 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
9702 "The motifStack package is designed for graphic representation of
9703 multiple motifs with different similarity scores. It works with both DNA/RNA
9704 sequence motifs and amino acid sequence motifs. In addition, it provides the
9705 flexibility for users to customize the graphic parameters such as the font
9706 type and symbol colors.")
9707 (license license:gpl2+)))
9709 (define-public r-genomicscores
9711 (name "r-genomicscores")
9716 (uri (bioconductor-uri "GenomicScores" version))
9719 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
9720 (properties `((upstream-name . "GenomicScores")))
9721 (build-system r-build-system)
9723 (list r-annotationhub
9740 (home-page "https://github.com/rcastelo/GenomicScores/")
9741 (synopsis "Work with genome-wide position-specific scores")
9743 "This package provides infrastructure to store and access genome-wide
9744 position-specific scores within R and Bioconductor.")
9745 (license license:artistic2.0)))
9747 (define-public r-atacseqqc
9749 (name "r-atacseqqc")
9754 (uri (bioconductor-uri "ATACseqQC" version))
9757 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
9758 (properties `((upstream-name . "ATACseqQC")))
9759 (build-system r-build-system)
9761 (list r-biocgenerics
9781 (home-page "https://bioconductor.org/packages/ATACseqQC/")
9782 (synopsis "ATAC-seq quality control")
9784 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
9785 sequencing, is a rapid and sensitive method for chromatin accessibility
9786 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
9787 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
9788 assess whether their ATAC-seq experiment is successful. It includes
9789 diagnostic plots of fragment size distribution, proportion of mitochondria
9790 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
9792 (license license:gpl2+)))
9794 (define-public r-gofuncr
9801 (uri (bioconductor-uri "GOfuncR" version))
9804 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
9805 (properties `((upstream-name . "GOfuncR")))
9806 (build-system r-build-system)
9808 (list r-annotationdbi
9817 (home-page "https://bioconductor.org/packages/GOfuncR/")
9818 (synopsis "Gene ontology enrichment using FUNC")
9820 "GOfuncR performs a gene ontology enrichment analysis based on the
9821 ontology enrichment software FUNC. GO-annotations are obtained from
9822 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
9823 included in the package and updated regularly. GOfuncR provides the standard
9824 candidate vs background enrichment analysis using the hypergeometric test, as
9825 well as three additional tests:
9828 @item the Wilcoxon rank-sum test that is used when genes are ranked,
9829 @item a binomial test that is used when genes are associated with two counts,
9831 @item a Chi-square or Fisher's exact test that is used in cases when genes are
9832 associated with four counts.
9835 To correct for multiple testing and interdependency of the tests, family-wise
9836 error rates are computed based on random permutations of the gene-associated
9837 variables. GOfuncR also provides tools for exploring the ontology graph and
9838 the annotations, and options to take gene-length or spatial clustering of
9839 genes into account. It is also possible to provide custom gene coordinates,
9840 annotations and ontologies.")
9841 (license license:gpl2+)))
9843 (define-public r-abaenrichment
9845 (name "r-abaenrichment")
9850 (uri (bioconductor-uri "ABAEnrichment" version))
9853 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
9854 (properties `((upstream-name . "ABAEnrichment")))
9855 (build-system r-build-system)
9865 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
9866 (synopsis "Gene expression enrichment in human brain regions")
9868 "The package ABAEnrichment is designed to test for enrichment of user
9869 defined candidate genes in the set of expressed genes in different human brain
9870 regions. The core function @code{aba_enrich} integrates the expression of the
9871 candidate gene set (averaged across donors) and the structural information of
9872 the brain using an ontology, both provided by the Allen Brain Atlas project.")
9873 (license license:gpl2+)))
9875 (define-public r-annotationfuncs
9877 (name "r-annotationfuncs")
9882 (uri (bioconductor-uri "AnnotationFuncs" version))
9885 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
9887 `((upstream-name . "AnnotationFuncs")))
9888 (build-system r-build-system)
9890 (list r-annotationdbi r-dbi))
9891 (home-page "https://www.iysik.com/r/annotationfuncs")
9892 (synopsis "Annotation translation functions")
9894 "This package provides functions for handling translating between
9895 different identifieres using the Biocore Data Team data-packages (e.g.
9896 @code{org.Bt.eg.db}).")
9897 (license license:gpl2)))
9899 (define-public r-annotationtools
9901 (name "r-annotationtools")
9906 (uri (bioconductor-uri "annotationTools" version))
9909 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
9911 `((upstream-name . "annotationTools")))
9912 (build-system r-build-system)
9913 (propagated-inputs (list r-biobase))
9914 (home-page "https://bioconductor.org/packages/annotationTools/")
9915 (synopsis "Annotate microarrays and perform gene expression analyses")
9917 "This package provides functions to annotate microarrays, find orthologs,
9918 and integrate heterogeneous gene expression profiles using annotation and
9919 other molecular biology information available as flat file database (plain
9921 ;; Any version of the GPL.
9922 (license (list license:gpl2+))))
9924 (define-public r-allelicimbalance
9926 (name "r-allelicimbalance")
9931 (uri (bioconductor-uri "AllelicImbalance" version))
9934 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
9936 `((upstream-name . "AllelicImbalance")))
9937 (build-system r-build-system)
9939 (list r-annotationdbi
9956 r-summarizedexperiment
9957 r-variantannotation))
9960 (home-page "https://github.com/pappewaio/AllelicImbalance")
9961 (synopsis "Investigate allele-specific expression")
9963 "This package provides a framework for allele-specific expression
9964 investigation using RNA-seq data.")
9965 (license license:gpl3)))
9967 (define-public r-aucell
9974 (uri (bioconductor-uri "AUCell" version))
9977 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
9978 (properties `((upstream-name . "AUCell")))
9979 (build-system r-build-system)
9981 (list r-biocgenerics
9984 r-delayedmatrixstats
9989 r-summarizedexperiment))
9992 (home-page "https://bioconductor.org/packages/AUCell/")
9993 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
9995 "AUCell identifies cells with active gene sets (e.g. signatures,
9996 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
9997 Under the Curve} (AUC) to calculate whether a critical subset of the input
9998 gene set is enriched within the expressed genes for each cell. The
9999 distribution of AUC scores across all the cells allows exploring the relative
10000 expression of the signature. Since the scoring method is ranking-based,
10001 AUCell is independent of the gene expression units and the normalization
10002 procedure. In addition, since the cells are evaluated individually, it can
10003 easily be applied to bigger datasets, subsetting the expression matrix if
10005 (license license:gpl3)))
10007 (define-public r-ebimage
10014 (uri (bioconductor-uri "EBImage" version))
10017 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
10018 (properties `((upstream-name . "EBImage")))
10019 (build-system r-build-system)
10032 (list r-knitr)) ; for vignettes
10033 (home-page "https://github.com/aoles/EBImage")
10034 (synopsis "Image processing and analysis toolbox for R")
10036 "EBImage provides general purpose functionality for image processing and
10037 analysis. In the context of (high-throughput) microscopy-based cellular
10038 assays, EBImage offers tools to segment cells and extract quantitative
10039 cellular descriptors. This allows the automation of such tasks using the R
10040 programming language and facilitates the use of other tools in the R
10041 environment for signal processing, statistical modeling, machine learning and
10042 visualization with image data.")
10043 ;; Any version of the LGPL.
10044 (license license:lgpl2.1+)))
10046 (define-public r-yamss
10053 (uri (bioconductor-uri "yamss" version))
10056 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
10057 (build-system r-build-system)
10059 (list r-biocgenerics
10067 r-summarizedexperiment))
10070 (home-page "https://github.com/hansenlab/yamss")
10071 (synopsis "Tools for high-throughput metabolomics")
10073 "This package provides tools to analyze and visualize high-throughput
10074 metabolomics data acquired using chromatography-mass spectrometry. These tools
10075 preprocess data in a way that enables reliable and powerful differential
10077 (license license:artistic2.0)))
10079 (define-public r-gtrellis
10081 (name "r-gtrellis")
10086 (uri (bioconductor-uri "gtrellis" version))
10089 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
10090 (build-system r-build-system)
10092 (list r-circlize r-genomicranges r-getoptlong r-iranges))
10095 (home-page "https://github.com/jokergoo/gtrellis")
10096 (synopsis "Genome level Trellis layout")
10098 "Genome level Trellis graph visualizes genomic data conditioned by
10099 genomic categories (e.g. chromosomes). For each genomic category, multiple
10100 dimensional data which are represented as tracks describe different features
10101 from different aspects. This package provides high flexibility to arrange
10102 genomic categories and to add self-defined graphics in the plot.")
10103 (license license:expat)))
10105 (define-public r-somaticsignatures
10107 (name "r-somaticsignatures")
10112 (uri (bioconductor-uri "SomaticSignatures" version))
10115 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
10117 `((upstream-name . "SomaticSignatures")))
10118 (build-system r-build-system)
10132 r-variantannotation))
10135 (home-page "https://github.com/juliangehring/SomaticSignatures")
10136 (synopsis "Somatic signatures")
10138 "This package identifies mutational signatures of @dfn{single nucleotide
10139 variants} (SNVs). It provides a infrastructure related to the methodology
10140 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
10141 decomposition algorithms.")
10142 (license license:expat)))
10144 (define-public r-yapsa
10151 (uri (bioconductor-uri "YAPSA" version))
10154 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
10155 (properties `((upstream-name . "YAPSA")))
10156 (build-system r-build-system)
10159 r-bsgenome-hsapiens-ucsc-hg19
10179 r-somaticsignatures
10180 r-variantannotation))
10183 (home-page "https://bioconductor.org/packages/YAPSA/")
10184 (synopsis "Yet another package for signature analysis")
10186 "This package provides functions and routines useful in the analysis of
10187 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
10188 functions to perform a signature analysis with known signatures and a
10189 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
10191 (license license:gpl3)))
10193 (define-public r-gcrma
10200 (uri (bioconductor-uri "gcrma" version))
10203 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
10204 (build-system r-build-system)
10212 (home-page "https://bioconductor.org/packages/gcrma/")
10213 (synopsis "Background adjustment using sequence information")
10215 "Gcrma adjusts for background intensities in Affymetrix array data which
10216 include optical noise and @dfn{non-specific binding} (NSB). The main function
10217 @code{gcrma} converts background adjusted probe intensities to expression
10218 measures using the same normalization and summarization methods as a
10219 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
10220 to estimate probe affinity to NSB. The sequence information is summarized in
10221 a more complex way than the simple GC content. Instead, the base types (A, T,
10222 G or C) at each position along the probe determine the affinity of each probe.
10223 The parameters of the position-specific base contributions to the probe
10224 affinity is estimated in an NSB experiment in which only NSB but no
10225 gene-specific binding is expected.")
10226 ;; Any version of the LGPL
10227 (license license:lgpl2.1+)))
10229 (define-public r-simpleaffy
10231 (name "r-simpleaffy")
10236 (uri (bioconductor-uri "simpleaffy" version))
10239 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
10240 (build-system r-build-system)
10242 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
10243 (home-page "https://bioconductor.org/packages/simpleaffy/")
10244 (synopsis "Very simple high level analysis of Affymetrix data")
10246 "This package provides high level functions for reading Affy @file{.CEL}
10247 files, phenotypic data, and then computing simple things with it, such as
10248 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
10249 library. It also has some basic scatter plot functions and mechanisms for
10250 generating high resolution journal figures.")
10251 (license license:gpl2+)))
10253 (define-public r-yaqcaffy
10255 (name "r-yaqcaffy")
10260 (uri (bioconductor-uri "yaqcaffy" version))
10263 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
10264 (build-system r-build-system)
10266 (list r-simpleaffy))
10267 (home-page "https://bioconductor.org/packages/yaqcaffy/")
10268 (synopsis "Affymetrix quality control and reproducibility analysis")
10270 "This is a package that can be used for quality control of Affymetrix
10271 GeneChip expression data and reproducibility analysis of human whole genome
10272 chips with the MAQC reference datasets.")
10273 (license license:artistic2.0)))
10275 (define-public r-quantro
10282 (uri (bioconductor-uri "quantro" version))
10285 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
10286 (build-system r-build-system)
10297 (home-page "https://bioconductor.org/packages/quantro/")
10298 (synopsis "Test for when to use quantile normalization")
10300 "This package provides a data-driven test for the assumptions of quantile
10301 normalization using raw data such as objects that inherit eSets (e.g.
10302 ExpressionSet, MethylSet). Group level information about each sample (such as
10303 Tumor / Normal status) must also be provided because the test assesses if
10304 there are global differences in the distributions between the user-defined
10306 (license license:gpl3+)))
10308 (define-public r-yarn
10315 (uri (bioconductor-uri "yarn" version))
10318 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
10319 (build-system r-build-system)
10334 (home-page "https://bioconductor.org/packages/yarn/")
10335 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
10337 "Expedite large RNA-Seq analyses using a combination of previously
10338 developed tools. YARN is meant to make it easier for the user in performing
10339 basic mis-annotation quality control, filtering, and condition-aware
10340 normalization. YARN leverages many Bioconductor tools and statistical
10341 techniques to account for the large heterogeneity and sparsity found in very
10342 large RNA-seq experiments.")
10343 (license license:artistic2.0)))
10345 (define-public r-roar
10352 (uri (bioconductor-uri "roar" version))
10355 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
10356 (build-system r-build-system)
10358 (list r-biocgenerics
10360 r-genomicalignments
10365 r-summarizedexperiment))
10366 (home-page "https://github.com/vodkatad/roar/")
10367 (synopsis "Identify differential APA usage from RNA-seq alignments")
10369 "This package provides tools for identifying preferential usage of APA
10370 sites, comparing two biological conditions, starting from known alternative
10371 sites and alignments obtained from standard RNA-seq experiments.")
10372 (license license:gpl3)))
10374 (define-public r-xbseq
10381 (uri (bioconductor-uri "XBSeq" version))
10384 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
10385 (properties `((upstream-name . "XBSeq")))
10386 (build-system r-build-system)
10399 (home-page "https://github.com/Liuy12/XBSeq")
10400 (synopsis "Test for differential expression for RNA-seq data")
10402 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
10403 expression} (DE), where a statistical model was established based on the
10404 assumption that observed signals are the convolution of true expression
10405 signals and sequencing noises. The mapped reads in non-exonic regions are
10406 considered as sequencing noises, which follows a Poisson distribution. Given
10407 measurable observed signal and background noise from RNA-seq data, true
10408 expression signals, assuming governed by the negative binomial distribution,
10409 can be delineated and thus the accurate detection of differential expressed
10411 (license license:gpl3+)))
10413 (define-public r-massspecwavelet
10415 (name "r-massspecwavelet")
10420 (uri (bioconductor-uri "MassSpecWavelet" version))
10423 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
10425 `((upstream-name . "MassSpecWavelet")))
10426 (build-system r-build-system)
10429 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
10430 (synopsis "Mass spectrum processing by wavelet-based algorithms")
10432 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
10433 data mainly through the use of wavelet transforms. It supports peak detection
10434 based on @dfn{Continuous Wavelet Transform} (CWT).")
10435 (license license:lgpl2.0+)))
10437 (define-public r-xcms
10444 (uri (bioconductor-uri "xcms" version))
10447 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
10448 (build-system r-build-system)
10466 r-summarizedexperiment))
10469 (home-page "https://bioconductor.org/packages/xcms/")
10470 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
10472 "This package provides a framework for processing and visualization of
10473 chromatographically separated and single-spectra mass spectral data. It
10474 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
10475 data for high-throughput, untargeted analyte profiling.")
10476 (license license:gpl2+)))
10478 (define-public r-wppi
10484 (uri (bioconductor-uri "wppi" version))
10487 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
10488 (properties `((upstream-name . "wppi")))
10489 (build-system r-build-system)
10490 ;; This is necessary because omnipathr attempts to write a configuration
10494 (modify-phases %standard-phases
10495 (add-after 'unpack 'set-HOME
10496 (lambda _ (setenv "HOME" "/tmp"))))))
10497 (propagated-inputs (list r-dplyr
10509 (native-inputs (list r-knitr))
10510 (home-page "https://github.com/AnaGalhoz37/wppi")
10511 (synopsis "Weighting protein-protein interactions")
10513 "This package predicts functional relevance of protein-protein
10514 interactions based on functional annotations such as Human Protein Ontology
10515 and Gene Ontology, and prioritizes genes based on network topology, functional
10516 scores and a path search algorithm.")
10517 (license license:expat)))
10519 (define-public r-wrench
10526 (uri (bioconductor-uri "Wrench" version))
10529 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
10530 (properties `((upstream-name . "Wrench")))
10531 (build-system r-build-system)
10533 (list r-limma r-locfit r-matrixstats))
10536 (home-page "https://github.com/HCBravoLab/Wrench")
10537 (synopsis "Wrench normalization for sparse count data")
10539 "Wrench is a package for normalization sparse genomic count data, like
10540 that arising from 16s metagenomic surveys.")
10541 (license license:artistic2.0)))
10543 (define-public r-wiggleplotr
10545 (name "r-wiggleplotr")
10550 (uri (bioconductor-uri "wiggleplotr" version))
10553 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
10554 (build-system r-build-system)
10568 (home-page "https://bioconductor.org/packages/wiggleplotr/")
10569 (synopsis "Make read coverage plots from BigWig files")
10571 "This package provides tools to visualize read coverage from sequencing
10572 experiments together with genomic annotations (genes, transcripts, peaks).
10573 Introns of long transcripts can be rescaled to a fixed length for better
10574 visualization of exonic read coverage.")
10575 (license license:asl2.0)))
10577 (define-public r-widgettools
10579 (name "r-widgettools")
10584 (uri (bioconductor-uri "widgetTools" version))
10587 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
10588 (properties `((upstream-name . "widgetTools")))
10589 (build-system r-build-system)
10590 (home-page "https://bioconductor.org/packages/widgetTools/")
10591 (synopsis "Tools for creating interactive tcltk widgets")
10593 "This package contains tools to support the construction of tcltk
10595 ;; Any version of the LGPL.
10596 (license license:lgpl3+)))
10598 (define-public r-webbioc
10605 (uri (bioconductor-uri "webbioc" version))
10608 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
10609 (build-system r-build-system)
10611 (list netpbm perl))
10621 (home-page "https://www.bioconductor.org/")
10622 (synopsis "Bioconductor web interface")
10624 "This package provides an integrated web interface for doing microarray
10625 analysis using several of the Bioconductor packages. It is intended to be
10626 deployed as a centralized bioinformatics resource for use by many users.
10627 Currently only Affymetrix oligonucleotide analysis is supported.")
10628 (license license:gpl2+)))
10630 (define-public r-zinbwave
10632 (name "r-zinbwave")
10637 (uri (bioconductor-uri "zinbwave" version))
10640 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
10641 (build-system r-build-system)
10643 (list r-biocparallel
10647 r-singlecellexperiment
10649 r-summarizedexperiment))
10652 (home-page "https://bioconductor.org/packages/zinbwave")
10653 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
10654 (description "This package implements a general and flexible zero-inflated
10655 negative binomial model that can be used to provide a low-dimensional
10656 representations of single-cell RNA-seq data. The model accounts for zero
10657 inflation (dropouts), over-dispersion, and the count nature of the data.
10658 The model also accounts for the difference in library sizes and optionally
10659 for batch effects and/or other covariates, avoiding the need for pre-normalize
10661 (license license:artistic2.0)))
10663 (define-public r-zfpkm
10670 (uri (bioconductor-uri "zFPKM" version))
10673 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
10674 (properties `((upstream-name . "zFPKM")))
10675 (build-system r-build-system)
10677 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
10680 (home-page "https://github.com/ronammar/zFPKM/")
10681 (synopsis "Functions to facilitate zFPKM transformations")
10683 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
10684 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
10686 (license license:gpl3)))
10688 (define-public r-rbowtie2
10690 (name "r-rbowtie2")
10695 (uri (bioconductor-uri "Rbowtie2" version))
10698 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
10699 (properties `((upstream-name . "Rbowtie2")))
10700 (build-system r-build-system)
10702 (list r-magrittr r-rsamtools))
10704 (list samtools zlib))
10707 (home-page "https://bioconductor.org/packages/Rbowtie2/")
10708 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
10710 "This package provides an R wrapper of the popular @code{bowtie2}
10711 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
10712 rapid adapter trimming, identification, and read merging.")
10713 (license license:gpl3+)))
10715 (define-public r-progeny
10722 (uri (bioconductor-uri "progeny" version))
10725 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
10726 (build-system r-build-system)
10738 (home-page "https://github.com/saezlab/progeny")
10739 (synopsis "Pathway responsive gene activity inference")
10741 "This package provides a function to infer pathway activity from gene
10742 expression. It contains the linear model inferred in the publication
10743 \"Perturbation-response genes reveal signaling footprints in cancer gene
10745 (license license:asl2.0)))
10747 (define-public r-arrmnormalization
10749 (name "r-arrmnormalization")
10754 (uri (bioconductor-uri "ARRmNormalization" version))
10757 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
10759 `((upstream-name . "ARRmNormalization")))
10760 (build-system r-build-system)
10761 (propagated-inputs (list r-arrmdata))
10762 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
10763 (synopsis "Adaptive robust regression normalization for methylation data")
10765 "This is a package to perform the @dfn{Adaptive Robust Regression
10766 method} (ARRm) for the normalization of methylation data from the Illumina
10767 Infinium HumanMethylation 450k assay.")
10768 (license license:artistic2.0)))
10770 (define-public r-biocfilecache
10772 (name "r-biocfilecache")
10777 (uri (bioconductor-uri "BiocFileCache" version))
10780 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
10781 (properties `((upstream-name . "BiocFileCache")))
10782 (build-system r-build-system)
10794 (home-page "https://bioconductor.org/packages/BiocFileCache/")
10795 (synopsis "Manage files across sessions")
10797 "This package creates a persistent on-disk cache of files that the user
10798 can add, update, and retrieve. It is useful for managing resources (such as
10799 custom Txdb objects) that are costly or difficult to create, web resources,
10800 and data files used across sessions.")
10801 (license license:artistic2.0)))
10803 (define-public r-iclusterplus
10805 (name "r-iclusterplus")
10810 (uri (bioconductor-uri "iClusterPlus" version))
10813 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
10814 (properties `((upstream-name . "iClusterPlus")))
10815 (build-system r-build-system)
10816 (native-inputs (list gfortran))
10817 (home-page "https://bioconductor.org/packages/iClusterPlus/")
10818 (synopsis "Integrative clustering of multi-type genomic data")
10820 "iClusterPlus is developed for integrative clustering analysis of
10821 multi-type genomic data and is an enhanced version of iCluster proposed and
10822 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
10823 from the experiments where biological samples (e.g. tumor samples) are
10824 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
10825 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
10826 on. In the iClusterPlus model, binary observations such as somatic mutation
10827 are modeled as Binomial processes; categorical observations such as copy
10828 number states are realizations of Multinomial random variables; counts are
10829 modeled as Poisson random processes; and continuous measures are modeled by
10830 Gaussian distributions.")
10831 (license license:gpl2+)))
10833 (define-public r-rbowtie
10840 (uri (bioconductor-uri "Rbowtie" version))
10843 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
10844 (properties `((upstream-name . "Rbowtie")))
10845 (build-system r-build-system)
10848 ;; Disable unsupported `popcnt' instructions on
10849 ;; architectures other than x86_64
10850 ,(if (string-prefix? "x86_64"
10851 (or (%current-target-system)
10852 (%current-system)))
10854 '(modify-phases %standard-phases
10855 (add-after 'unpack 'patch-sources
10857 (setenv "POPCNT_CAPABILITY" "0")))))))
10858 (inputs (list zlib))
10861 (home-page "https://bioconductor.org/packages/Rbowtie/")
10862 (synopsis "R bowtie wrapper")
10864 "This package provides an R wrapper around the popular bowtie short read
10865 aligner and around SpliceMap, a de novo splice junction discovery and
10867 (license license:artistic2.0)))
10869 (define-public r-sgseq
10876 (uri (bioconductor-uri "SGSeq" version))
10879 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
10880 (properties `((upstream-name . "SGSeq")))
10881 (build-system r-build-system)
10883 (list r-annotationdbi
10887 r-genomicalignments
10896 r-summarizedexperiment))
10899 (home-page "https://bioconductor.org/packages/SGSeq/")
10900 (synopsis "Splice event prediction and quantification from RNA-seq data")
10902 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
10903 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
10904 represented as a splice graph, which can be obtained from existing annotation
10905 or predicted from the mapped sequence reads. Splice events are identified
10906 from the graph and are quantified locally using structurally compatible reads
10907 at the start or end of each splice variant. The software includes functions
10908 for splice event prediction, quantification, visualization and
10910 (license license:artistic2.0)))
10912 (define-public r-rhisat2
10919 (uri (bioconductor-uri "Rhisat2" version))
10922 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
10923 (properties `((upstream-name . "Rhisat2")))
10924 (build-system r-build-system)
10927 (modify-phases %standard-phases
10928 (add-after 'unpack 'make-reproducible
10930 (substitute* "src/Makefile"
10931 (("`hostname`") "guix")
10933 ;; Avoid shelling out to "which".
10934 (("^CC =.*") (which "gcc"))
10935 (("^CPP =.*") (which "g++")))
10938 (list r-genomicfeatures r-genomicranges r-sgseq))
10941 (home-page "https://github.com/fmicompbio/Rhisat2")
10942 (synopsis "R Wrapper for HISAT2 sequence aligner")
10944 "This package provides an R interface to the HISAT2 spliced short-read
10945 aligner by Kim et al. (2015). The package contains wrapper functions to
10946 create a genome index and to perform the read alignment to the generated
10948 (license license:gpl3)))
10950 (define-public r-quasr
10957 (uri (bioconductor-uri "QuasR" version))
10960 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
10961 (properties `((upstream-name . "QuasR")))
10962 (build-system r-build-system)
10964 (list r-annotationdbi
10983 (home-page "https://bioconductor.org/packages/QuasR/")
10984 (synopsis "Quantify and annotate short reads in R")
10986 "This package provides a framework for the quantification and analysis of
10987 short genomic reads. It covers a complete workflow starting from raw sequence
10988 reads, over creation of alignments and quality control plots, to the
10989 quantification of genomic regions of interest.")
10990 (license license:gpl2)))
10992 (define-public r-rqc
10999 (uri (bioconductor-uri "Rqc" version))
11002 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
11003 (properties `((upstream-name . "Rqc")))
11004 (build-system r-build-system)
11006 (list r-biocgenerics
11011 r-genomicalignments
11026 (home-page "https://github.com/labbcb/Rqc")
11027 (synopsis "Quality control tool for high-throughput sequencing data")
11029 "Rqc is an optimized tool designed for quality control and assessment of
11030 high-throughput sequencing data. It performs parallel processing of entire
11031 files and produces a report which contains a set of high-resolution
11033 (license license:gpl2+)))
11035 (define-public r-birewire
11037 (name "r-birewire")
11042 (uri (bioconductor-uri "BiRewire" version))
11045 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
11046 (properties `((upstream-name . "BiRewire")))
11047 (build-system r-build-system)
11049 (list r-igraph r-matrix r-rtsne r-slam))
11050 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
11051 (synopsis "Tools for randomization of bipartite graphs")
11053 "This package provides functions for bipartite network rewiring through N
11054 consecutive switching steps and for the computation of the minimal number of
11055 switching steps to be performed in order to maximise the dissimilarity with
11056 respect to the original network. It includes functions for the analysis of
11057 the introduced randomness across the switching steps and several other
11058 routines to analyse the resulting networks and their natural projections.")
11059 (license license:gpl3)))
11061 (define-public r-birta
11068 (uri (bioconductor-uri "birta" version))
11071 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
11072 (build-system r-build-system)
11074 (list r-biobase r-limma r-mass))
11075 (home-page "https://bioconductor.org/packages/birta")
11076 (synopsis "Bayesian inference of regulation of transcriptional activity")
11078 "Expression levels of mRNA molecules are regulated by different
11079 processes, comprising inhibition or activation by transcription factors and
11080 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
11081 Inference of Regulation of Transcriptional Activity) uses the regulatory
11082 networks of transcription factors and miRNAs together with mRNA and miRNA
11083 expression data to predict switches in regulatory activity between two
11084 conditions. A Bayesian network is used to model the regulatory structure and
11085 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
11086 (license license:gpl2+)))
11088 (define-public r-multidataset
11090 (name "r-multidataset")
11095 (uri (bioconductor-uri "MultiDataSet" version))
11098 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
11099 (properties `((upstream-name . "MultiDataSet")))
11100 (build-system r-build-system)
11111 r-summarizedexperiment))
11114 (home-page "https://bioconductor.org/packages/MultiDataSet/")
11115 (synopsis "Implementation of MultiDataSet and ResultSet")
11117 "This package provides an implementation of the BRGE's (Bioinformatic
11118 Research Group in Epidemiology from Center for Research in Environmental
11119 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
11120 integrating multi omics data sets and ResultSet is a container for omics
11121 results. This package contains base classes for MEAL and rexposome
11123 (license license:expat)))
11125 (define-public r-ropls
11132 (uri (bioconductor-uri "ropls" version))
11135 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
11136 (build-system r-build-system)
11139 r-multiassayexperiment
11141 r-summarizedexperiment))
11143 (list r-knitr)) ; for vignettes
11144 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
11145 (synopsis "Multivariate analysis and feature selection of omics data")
11147 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
11148 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
11149 regression, classification, and feature selection of omics data where the
11150 number of variables exceeds the number of samples and with multicollinearity
11151 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
11152 separately model the variation correlated (predictive) to the factor of
11153 interest and the uncorrelated (orthogonal) variation. While performing
11154 similarly to PLS, OPLS facilitates interpretation.
11156 This package provides imlementations of PCA, PLS, and OPLS for multivariate
11157 analysis and feature selection of omics data. In addition to scores, loadings
11158 and weights plots, the package provides metrics and graphics to determine the
11159 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
11160 validity of the model by permutation testing, detect outliers, and perform
11161 feature selection (e.g. with Variable Importance in Projection or regression
11163 (license license:cecill)))
11165 (define-public r-biosigner
11167 (name "r-biosigner")
11172 (uri (bioconductor-uri "biosigner" version))
11175 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
11176 (build-system r-build-system)
11180 r-multiassayexperiment
11184 r-summarizedexperiment))
11187 (home-page "https://bioconductor.org/packages/biosigner/")
11188 (synopsis "Signature discovery from omics data")
11190 "Feature selection is critical in omics data analysis to extract
11191 restricted and meaningful molecular signatures from complex and high-dimension
11192 data, and to build robust classifiers. This package implements a method to
11193 assess the relevance of the variables for the prediction performances of the
11194 classifier. The approach can be run in parallel with the PLS-DA, Random
11195 Forest, and SVM binary classifiers. The signatures and the corresponding
11196 'restricted' models are returned, enabling future predictions on new
11198 (license license:cecill)))
11200 (define-public r-annotatr
11202 (name "r-annotatr")
11207 (uri (bioconductor-uri "annotatr" version))
11210 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
11211 (build-system r-build-system)
11213 (list r-annotationdbi
11228 (home-page "https://bioconductor.org/packages/annotatr/")
11229 (synopsis "Annotation of genomic regions to genomic annotations")
11231 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
11232 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
11233 to investigate the intersecting genomic annotations. Such annotations include
11234 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
11235 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
11236 enhancers. The annotatr package provides an easy way to summarize and
11237 visualize the intersection of genomic sites/regions with genomic
11239 (license license:gpl3)))
11241 (define-public r-rsubread
11243 (name "r-rsubread")
11248 (uri (bioconductor-uri "Rsubread" version))
11251 "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl"))))
11252 (properties `((upstream-name . "Rsubread")))
11253 (build-system r-build-system)
11254 (inputs (list zlib))
11257 (home-page "https://bioconductor.org/packages/Rsubread/")
11258 (synopsis "Subread sequence alignment and counting for R")
11260 "This package provides tools for alignment, quantification and analysis
11261 of second and third generation sequencing data. It includes functionality for
11262 read mapping, read counting, SNP calling, structural variant detection and
11263 gene fusion discovery. It can be applied to all major sequencing techologies
11264 and to both short and long sequence reads.")
11265 (license license:gpl3)))
11267 (define-public r-flowutils
11269 (name "r-flowutils")
11274 (uri (bioconductor-uri "flowUtils" version))
11277 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
11278 (properties `((upstream-name . "flowUtils")))
11279 (build-system r-build-system)
11287 (home-page "https://github.com/jspidlen/flowUtils")
11288 (synopsis "Utilities for flow cytometry")
11290 "This package provides utilities for flow cytometry data.")
11291 (license license:artistic2.0)))
11293 (define-public r-consensusclusterplus
11295 (name "r-consensusclusterplus")
11300 (uri (bioconductor-uri "ConsensusClusterPlus" version))
11303 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
11305 `((upstream-name . "ConsensusClusterPlus")))
11306 (build-system r-build-system)
11308 (list r-all r-biobase r-cluster))
11309 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
11310 (synopsis "Clustering algorithm")
11312 "This package provides an implementation of an algorithm for determining
11313 cluster count and membership by stability evidence in unsupervised analysis.")
11314 (license license:gpl2)))
11316 ;; This is the latest commit and it solves a bug from the latest release.
11317 (define-public r-cycombine
11318 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
11320 (name "r-cycombine")
11321 (version (git-version "0.2.6" revision commit))
11324 (uri (git-reference
11325 (url "https://github.com/biosurf/cyCombine")
11327 (file-name (git-file-name name version))
11330 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
11331 (properties `((upstream-name . "cyCombine")))
11332 (build-system r-build-system)
11350 (native-inputs (list r-knitr))
11351 (home-page "https://github.com/biosurf/cyCombine")
11352 (synopsis "Integration of single-cell cytometry datasets")
11354 "This package provides a method for combining single-cell cytometry
11355 datasets, which increases the analytical flexibility and the statistical power
11356 of the analyses while minimizing technical noise.")
11357 (license license:expat))))
11359 (define-public r-cytolib
11366 (uri (bioconductor-uri "cytolib" version))
11369 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
11370 (properties `((upstream-name . "cytolib")))
11371 (build-system r-build-system)
11381 (home-page "https://bioconductor.org/packages/cytolib/")
11382 (synopsis "C++ infrastructure for working with gated cytometry")
11384 "This package provides the core data structure and API to represent and
11385 interact with gated cytometry data.")
11386 (license license:artistic2.0)))
11388 (define-public r-flowcore
11390 (name "r-flowcore")
11395 (uri (bioconductor-uri "flowCore" version))
11398 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
11399 (properties `((upstream-name . "flowCore")))
11400 (build-system r-build-system)
11413 (home-page "https://bioconductor.org/packages/flowCore")
11414 (synopsis "Basic structures for flow cytometry data")
11416 "This package provides S4 data structures and basic functions to deal
11417 with flow cytometry data.")
11418 (license license:artistic2.0)))
11420 (define-public r-flowmeans
11422 (name "r-flowmeans")
11427 (uri (bioconductor-uri "flowMeans" version))
11430 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
11431 (properties `((upstream-name . "flowMeans")))
11432 (build-system r-build-system)
11434 (list r-biobase r-feature r-flowcore r-rrcov))
11435 (home-page "https://bioconductor.org/packages/flowMeans")
11436 (synopsis "Non-parametric flow cytometry data gating")
11438 "This package provides tools to identify cell populations in Flow
11439 Cytometry data using non-parametric clustering and segmented-regression-based
11440 change point detection.")
11441 (license license:artistic2.0)))
11443 (define-public r-ncdfflow
11445 (name "r-ncdfflow")
11450 (uri (bioconductor-uri "ncdfFlow" version))
11453 "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m"))))
11454 (properties `((upstream-name . "ncdfFlow")))
11455 (build-system r-build-system)
11467 (home-page "https://bioconductor.org/packages/ncdfFlow/")
11468 (synopsis "HDF5 based storage for flow cytometry data")
11470 "This package provides HDF5 storage based methods and functions for
11471 manipulation of flow cytometry data.")
11472 (license license:artistic2.0)))
11474 (define-public r-ggcyto
11481 (uri (bioconductor-uri "ggcyto" version))
11484 "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"))))
11485 (properties `((upstream-name . "ggcyto")))
11486 (build-system r-build-system)
11501 (home-page "https://github.com/RGLab/ggcyto/issues")
11502 (synopsis "Visualize Cytometry data with ggplot")
11504 "With the dedicated fortify method implemented for @code{flowSet},
11505 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
11506 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
11507 and some custom layers also make it easy to add gates and population
11508 statistics to the plot.")
11509 (license license:artistic2.0)))
11511 (define-public r-flowviz
11518 (uri (bioconductor-uri "flowViz" version))
11521 "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f"))))
11522 (properties `((upstream-name . "flowViz")))
11523 (build-system r-build-system)
11536 (home-page "https://bioconductor.org/packages/flowViz/")
11537 (synopsis "Visualization for flow cytometry")
11539 "This package provides visualization tools for flow cytometry data.")
11540 (license license:artistic2.0)))
11542 (define-public r-flowclust
11544 (name "r-flowclust")
11549 (uri (bioconductor-uri "flowClust" version))
11552 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
11553 (properties `((upstream-name . "flowClust")))
11554 (build-system r-build-system)
11556 `(#:configure-flags
11557 (list "--configure-args=--enable-bundled-gsl=no")))
11566 (list pkg-config r-knitr))
11567 (home-page "https://bioconductor.org/packages/flowClust")
11568 (synopsis "Clustering for flow cytometry")
11570 "This package provides robust model-based clustering using a t-mixture
11571 model with Box-Cox transformation.")
11572 (license license:artistic2.0)))
11574 ;; TODO: this package bundles an old version of protobuf. It's not easy to
11575 ;; make it use our protobuf package instead.
11576 (define-public r-rprotobuflib
11578 (name "r-rprotobuflib")
11583 (uri (bioconductor-uri "RProtoBufLib" version))
11586 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
11587 (properties `((upstream-name . "RProtoBufLib")))
11588 (build-system r-build-system)
11591 (modify-phases %standard-phases
11592 (add-after 'unpack 'unpack-bundled-sources
11594 (with-directory-excursion "src"
11595 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
11598 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
11599 (synopsis "C++ headers and static libraries of Protocol buffers")
11601 "This package provides the headers and static library of Protocol buffers
11602 for other R packages to compile and link against.")
11603 (license license:bsd-3)))
11605 (define-public r-flowworkspace
11607 (name "r-flowworkspace")
11612 (uri (bioconductor-uri "flowWorkspace" version))
11615 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
11616 (properties `((upstream-name . "flowWorkspace")))
11617 (build-system r-build-system)
11648 (home-page "https://bioconductor.org/packages/flowWorkspace/")
11649 (synopsis "Infrastructure for working with cytometry data")
11651 "This package is designed to facilitate comparison of automated gating
11652 methods against manual gating done in flowJo. This package allows you to
11653 import basic flowJo workspaces into BioConductor and replicate the gating from
11654 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
11655 samples, compensation, and transformation are performed so that the output
11656 matches the flowJo analysis.")
11657 (license license:artistic2.0)))
11659 (define-public r-flowstats
11661 (name "r-flowstats")
11666 (uri (bioconductor-uri "flowStats" version))
11669 "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj"))))
11670 (properties `((upstream-name . "flowStats")))
11671 (build-system r-build-system)
11689 (home-page "http://www.github.com/RGLab/flowStats")
11690 (synopsis "Statistical methods for the analysis of flow cytometry data")
11692 "This package provides methods and functionality to analyze flow data
11693 that is beyond the basic infrastructure provided by the @code{flowCore}
11695 (license license:artistic2.0)))
11697 (define-public r-opencyto
11699 (name "r-opencyto")
11704 (uri (bioconductor-uri "openCyto" version))
11707 "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y"))))
11708 (properties `((upstream-name . "openCyto")))
11709 (build-system r-build-system)
11734 (home-page "https://bioconductor.org/packages/openCyto")
11735 (synopsis "Hierarchical gating pipeline for flow cytometry data")
11737 "This package is designed to facilitate the automated gating methods in a
11738 sequential way to mimic the manual gating strategy.")
11739 (license license:artistic2.0)))
11741 (define-public r-cytoml
11748 (uri (bioconductor-uri "CytoML" version))
11751 "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"))))
11752 (properties `((upstream-name . "CytoML")))
11753 (build-system r-build-system)
11755 (list libxml2 zlib))
11786 (home-page "https://github.com/RGLab/CytoML")
11787 (synopsis "GatingML interface for cross platform cytometry data sharing")
11789 "This package provides an interface to implementations of the GatingML2.0
11790 standard to exchange gated cytometry data with other software platforms.")
11791 (license license:artistic2.0)))
11793 (define-public r-flowsom
11800 (uri (bioconductor-uri "FlowSOM" version))
11803 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
11804 (properties `((upstream-name . "FlowSOM")))
11805 (build-system r-build-system)
11807 (list r-biocgenerics
11809 r-consensusclusterplus
11829 (home-page "https://bioconductor.org/packages/FlowSOM/")
11830 (synopsis "Visualize and interpret cytometry data")
11832 "FlowSOM offers visualization options for cytometry data, by using
11833 self-organizing map clustering and minimal spanning trees.")
11834 (license license:gpl2+)))
11836 (define-public r-mixomics
11838 (name "r-mixomics")
11843 (uri (bioconductor-uri "mixOmics" version))
11846 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
11847 (properties `((upstream-name . "mixOmics")))
11848 (build-system r-build-system)
11850 (list r-biocparallel
11867 (home-page "http://www.mixOmics.org")
11868 (synopsis "Multivariate methods for exploration of biological datasets")
11870 "mixOmics offers a wide range of multivariate methods for the exploration
11871 and integration of biological datasets with a particular focus on variable
11872 selection. The package proposes several sparse multivariate models we have
11873 developed to identify the key variables that are highly correlated, and/or
11874 explain the biological outcome of interest. The data that can be analysed
11875 with mixOmics may come from high throughput sequencing technologies, such as
11876 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
11877 also beyond the realm of omics (e.g. spectral imaging). The methods
11878 implemented in mixOmics can also handle missing values without having to
11879 delete entire rows with missing data.")
11880 (license license:gpl2+)))
11882 (define-public r-depecher
11883 (package ;Source/Weave error
11884 (name "r-depecher")
11889 (uri (bioconductor-uri "DepecheR" version))
11892 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
11893 (properties `((upstream-name . "DepecheR")))
11894 (build-system r-build-system)
11915 (home-page "https://bioconductor.org/packages/DepecheR/")
11916 (synopsis "Identify traits of clusters in high-dimensional entities")
11918 "The purpose of this package is to identify traits in a dataset that can
11919 separate groups. This is done on two levels. First, clustering is performed,
11920 using an implementation of sparse K-means. Secondly, the generated clusters
11921 are used to predict outcomes of groups of individuals based on their
11922 distribution of observations in the different clusters. As certain clusters
11923 with separating information will be identified, and these clusters are defined
11924 by a sparse number of variables, this method can reduce the complexity of
11925 data, to only emphasize the data that actually matters.")
11926 (license license:expat)))
11928 (define-public r-rcistarget
11930 (name "r-rcistarget")
11935 (uri (bioconductor-uri "RcisTarget" version))
11938 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
11939 (properties `((upstream-name . "RcisTarget")))
11940 (build-system r-build-system)
11952 r-summarizedexperiment
11956 (home-page "https://aertslab.org/#scenic")
11957 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
11959 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
11960 over-represented on a gene list. In a first step, RcisTarget selects DNA
11961 motifs that are significantly over-represented in the surroundings of the
11962 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
11963 achieved by using a database that contains genome-wide cross-species rankings
11964 for each motif. The motifs that are then annotated to TFs and those that have
11965 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
11966 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
11967 genes in the gene-set that are ranked above the leading edge).")
11968 (license license:gpl3)))
11970 (define-public r-chicago
11977 (uri (bioconductor-uri "Chicago" version))
11980 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
11981 (properties `((upstream-name . "Chicago")))
11982 (build-system r-build-system)
11984 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
11985 (native-inputs (list r-knitr))
11986 (home-page "https://bioconductor.org/packages/Chicago")
11987 (synopsis "Capture Hi-C analysis of genomic organization")
11989 "This package provides a pipeline for analysing Capture Hi-C data.")
11990 (license license:artistic2.0)))
11992 (define-public r-cicero
11999 (uri (bioconductor-uri "cicero" version))
12002 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
12003 (build-system r-build-system)
12029 (home-page "https://bioconductor.org/packages/cicero/")
12030 (synopsis "Predict cis-co-accessibility from single-cell data")
12032 "Cicero computes putative cis-regulatory maps from single-cell chromatin
12033 accessibility data. It also extends the monocle package for use in chromatin
12034 accessibility data.")
12035 (license license:expat)))
12037 ;; This is the latest commit on the "monocle3" branch.
12038 (define-public r-cicero-monocle3
12039 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
12041 (package (inherit r-cicero)
12042 (name "r-cicero-monocle3")
12043 (version (git-version "1.3.2" revision commit))
12047 (uri (git-reference
12048 (url "https://github.com/cole-trapnell-lab/cicero-release")
12050 (file-name (git-file-name name version))
12053 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
12055 (modify-inputs (package-propagated-inputs r-cicero)
12056 (delete "r-monocle")
12057 (prepend r-monocle3))))))
12059 (define-public r-circrnaprofiler
12061 (name "r-circrnaprofiler")
12066 (uri (bioconductor-uri "circRNAprofiler" version))
12069 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
12071 `((upstream-name . "circRNAprofiler")))
12072 (build-system r-build-system)
12074 (list r-annotationhub
12077 r-bsgenome-hsapiens-ucsc-hg19
12100 "https://github.com/Aufiero/circRNAprofiler")
12102 "Computational framework for the downstream analysis of circular RNA's")
12104 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
12105 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
12106 framework allows combining and analyzing circRNAs previously detected by
12107 multiple publicly available annotation-based circRNA detection tools. It
12108 covers different aspects of circRNAs analysis from differential expression
12109 analysis, evolutionary conservation, biogenesis to functional analysis.")
12110 (license license:gpl3)))
12112 (define-public r-cistopic
12114 (name "r-cistopic")
12119 (uri (git-reference
12120 (url "https://github.com/aertslab/cisTopic")
12121 (commit (string-append "v" version))))
12122 (file-name (git-file-name name version))
12125 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
12126 (build-system r-build-system)
12143 (home-page "https://github.com/aertslab/cisTopic")
12144 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
12146 "The sparse nature of single cell epigenomics data can be overruled using
12147 probabilistic modelling methods such as @dfn{Latent Dirichlet
12148 Allocation} (LDA). This package allows the probabilistic modelling of
12149 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
12150 includes functionalities to identify cell states based on the contribution of
12151 cisTopics and explore the nature and regulatory proteins driving them.")
12152 (license license:gpl3)))
12154 (define-public r-cistopic-next
12155 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
12158 (inherit r-cistopic)
12159 (name "r-cistopic-next")
12160 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
12161 ;; since the previous release is 2.1.0. Oh well.
12162 (version (git-version "0.3.0" revision commit))
12166 (uri (git-reference
12167 (url "https://github.com/aertslab/cisTopic")
12169 (file-name (git-file-name name version))
12172 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
12173 (properties `((upstream-name . "cisTopic")))
12194 (define-public r-genie3
12201 (uri (bioconductor-uri "GENIE3" version))
12204 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
12205 (properties `((upstream-name . "GENIE3")))
12206 (build-system r-build-system)
12208 (list r-dplyr r-reshape2))
12211 (home-page "https://bioconductor.org/packages/GENIE3")
12212 (synopsis "Gene network inference with ensemble of trees")
12214 "This package implements the GENIE3 algorithm for inferring gene
12215 regulatory networks from expression data.")
12216 (license license:gpl2+)))
12218 (define-public r-roc
12225 (uri (bioconductor-uri "ROC" version))
12228 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
12229 (properties `((upstream-name . "ROC")))
12230 (build-system r-build-system)
12233 (home-page "https://www.bioconductor.org/packages/ROC/")
12234 (synopsis "Utilities for ROC curves")
12236 "This package provides utilities for @dfn{Receiver Operating
12237 Characteristic} (ROC) curves, with a focus on micro arrays.")
12238 (license license:artistic2.0)))
12240 (define-public r-watermelon
12242 (name "r-watermelon")
12247 (uri (bioconductor-uri "wateRmelon" version))
12250 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
12251 (properties `((upstream-name . "wateRmelon")))
12252 (build-system r-build-system)
12255 r-illuminahumanmethylation450kanno-ilmn12-hg19
12264 (home-page "https://bioconductor.org/packages/wateRmelon/")
12265 (synopsis "Illumina 450 methylation array normalization and metrics")
12267 "The standard index of DNA methylation (beta) is computed from methylated
12268 and unmethylated signal intensities. Betas calculated from raw signal
12269 intensities perform well, but using 11 methylomic datasets we demonstrate that
12270 quantile normalization methods produce marked improvement. The commonly used
12271 procedure of normalizing betas is inferior to the separate normalization of M
12272 and U, and it is also advantageous to normalize Type I and Type II assays
12273 separately. This package provides 15 flavours of betas and three performance
12274 metrics, with methods for objects produced by the @code{methylumi} and
12275 @code{minfi} packages.")
12276 (license license:gpl3)))
12278 (define-public r-gdsfmt
12285 (uri (bioconductor-uri "gdsfmt" version))
12288 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
12289 (modules '((guix build utils)))
12290 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
12291 ;; them and link with system libraries instead.
12294 (for-each delete-file-recursively
12298 (substitute* "src/Makevars"
12299 (("all: \\$\\(SHLIB\\)") "all:")
12300 (("\\$\\(SHLIB\\): liblzma.a") "")
12301 (("^ (ZLIB|LZ4)/.*") "")
12302 (("CoreArray/dVLIntGDS.cpp.*")
12303 "CoreArray/dVLIntGDS.cpp")
12304 (("CoreArray/dVLIntGDS.o.*")
12305 "CoreArray/dVLIntGDS.o")
12306 (("PKG_LIBS = ./liblzma.a")
12307 "PKG_LIBS = -llz4"))
12308 (substitute* "src/CoreArray/dStream.h"
12309 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
12310 (string-append "include <" header ">")))))))
12311 (properties `((upstream-name . "gdsfmt")))
12312 (build-system r-build-system)
12314 (list lz4 xz zlib))
12317 (home-page "http://corearray.sourceforge.net/")
12319 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
12321 "This package provides a high-level R interface to CoreArray @dfn{Genomic
12322 Data Structure} (GDS) data files, which are portable across platforms with
12323 hierarchical structure to store multiple scalable array-oriented data sets
12324 with metadata information. It is suited for large-scale datasets, especially
12325 for data which are much larger than the available random-access memory. The
12326 @code{gdsfmt} package offers efficient operations specifically designed for
12327 integers of less than 8 bits, since a diploid genotype, like
12328 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
12329 byte. Data compression and decompression are available with relatively
12330 efficient random access. It is also allowed to read a GDS file in parallel
12331 with multiple R processes supported by the package @code{parallel}.")
12332 (license license:lgpl3)))
12334 (define-public r-bigmelon
12336 (name "r-bigmelon")
12341 (uri (bioconductor-uri "bigmelon" version))
12344 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
12345 (properties `((upstream-name . "bigmelon")))
12346 (build-system r-build-system)
12358 (home-page "https://bioconductor.org/packages/bigmelon/")
12359 (synopsis "Illumina methylation array analysis for large experiments")
12361 "This package provides methods for working with Illumina arrays using the
12362 @code{gdsfmt} package.")
12363 (license license:gpl3)))
12365 (define-public r-seqbias
12372 (uri (bioconductor-uri "seqbias" version))
12375 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
12376 (properties `((upstream-name . "seqbias")))
12377 (build-system r-build-system)
12379 (list r-biostrings r-genomicranges r-rhtslib))
12380 (home-page "https://bioconductor.org/packages/seqbias/")
12381 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
12383 "This package implements a model of per-position sequencing bias in
12384 high-throughput sequencing data using a simple Bayesian network, the structure
12385 and parameters of which are trained on a set of aligned reads and a reference
12387 (license license:lgpl3)))
12389 (define-public r-reqon
12396 (uri (bioconductor-uri "ReQON" version))
12399 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
12400 (properties `((upstream-name . "ReQON")))
12401 (build-system r-build-system)
12403 (list r-rjava r-rsamtools r-seqbias))
12404 (home-page "https://bioconductor.org/packages/ReQON/")
12405 (synopsis "Recalibrating quality of nucleotides")
12407 "This package provides an implementation of an algorithm for
12408 recalibrating the base quality scores for aligned sequencing data in BAM
12410 (license license:gpl2)))
12412 (define-public r-wavcluster
12414 (name "r-wavcluster")
12419 (uri (bioconductor-uri "wavClusteR" version))
12422 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
12423 (properties `((upstream-name . "wavClusteR")))
12424 (build-system r-build-system)
12426 (list r-biocgenerics
12442 (home-page "https://bioconductor.org/packages/wavClusteR/")
12443 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
12445 "This package provides an integrated pipeline for the analysis of
12446 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
12447 sequencing errors, SNPs and additional non-experimental sources by a non-
12448 parametric mixture model. The protein binding sites (clusters) are then
12449 resolved at high resolution and cluster statistics are estimated using a
12450 rigorous Bayesian framework. Post-processing of the results, data export for
12451 UCSC genome browser visualization and motif search analysis are provided. In
12452 addition, the package integrates RNA-Seq data to estimate the False
12453 Discovery Rate of cluster detection. Key functions support parallel multicore
12454 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
12455 be applied to the analysis of other NGS data obtained from experimental
12456 procedures that induce nucleotide substitutions (e.g. BisSeq).")
12457 (license license:gpl2)))
12459 (define-public r-timeseriesexperiment
12461 (name "r-timeseriesexperiment")
12466 (uri (bioconductor-uri "TimeSeriesExperiment" version))
12469 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
12471 `((upstream-name . "TimeSeriesExperiment")))
12472 (build-system r-build-system)
12484 r-summarizedexperiment
12491 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
12492 (synopsis "Analysis for short time-series data")
12494 "This package is a visualization and analysis toolbox for short time
12495 course data which includes dimensionality reduction, clustering, two-sample
12496 differential expression testing and gene ranking techniques. The package also
12497 provides methods for retrieving enriched pathways.")
12498 (license license:lgpl3+)))
12500 (define-public r-variantfiltering
12502 (name "r-variantfiltering")
12507 (uri (bioconductor-uri "VariantFiltering" version))
12510 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
12512 `((upstream-name . "VariantFiltering")))
12513 (build-system r-build-system)
12515 (list r-annotationdbi
12536 r-summarizedexperiment
12537 r-variantannotation
12539 (home-page "https://github.com/rcastelo/VariantFiltering")
12540 (synopsis "Filtering of coding and non-coding genetic variants")
12542 "Filter genetic variants using different criteria such as inheritance
12543 model, amino acid change consequence, minor allele frequencies across human
12544 populations, splice site strength, conservation, etc.")
12545 (license license:artistic2.0)))
12547 (define-public r-genomegraphs
12549 (name "r-genomegraphs")
12554 (uri (bioconductor-uri "GenomeGraphs" version))
12557 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
12558 (properties `((upstream-name . "GenomeGraphs")))
12559 (build-system r-build-system)
12562 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
12563 (synopsis "Plotting genomic information from Ensembl")
12565 "Genomic data analyses requires integrated visualization of known genomic
12566 information and new experimental data. GenomeGraphs uses the biomaRt package
12567 to perform live annotation queries to Ensembl and translates this to e.g.
12568 gene/transcript structures in viewports of the grid graphics package. This
12569 results in genomic information plotted together with your data. Another
12570 strength of GenomeGraphs is to plot different data types such as array CGH,
12571 gene expression, sequencing and other data, together in one plot using the
12572 same genome coordinate system.")
12573 (license license:artistic2.0)))
12575 (define-public r-wavetiling
12577 (name "r-wavetiling")
12582 (uri (bioconductor-uri "waveTiling" version))
12585 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
12586 (properties `((upstream-name . "waveTiling")))
12587 (build-system r-build-system)
12599 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
12600 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
12602 "This package is designed to conduct transcriptome analysis for tiling
12603 arrays based on fast wavelet-based functional models.")
12604 (license license:gpl2+)))
12606 (define-public r-variancepartition
12608 (name "r-variancepartition")
12613 (uri (bioconductor-uri "variancePartition" version))
12616 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
12618 `((upstream-name . "variancePartition")))
12619 (build-system r-build-system)
12643 (home-page "https://bioconductor.org/packages/variancePartition/")
12644 (synopsis "Analyze variation in gene expression experiments")
12646 "This is a package providing tools to quantify and interpret multiple
12647 sources of biological and technical variation in gene expression experiments.
12648 It uses a linear mixed model to quantify variation in gene expression
12649 attributable to individual, tissue, time point, or technical variables. The
12650 package includes dream differential expression analysis for repeated
12652 (license license:gpl2+)))
12654 (define-public r-htqpcr
12661 (uri (bioconductor-uri "HTqPCR" version))
12664 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
12665 (properties `((upstream-name . "HTqPCR")))
12666 (build-system r-build-system)
12668 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
12669 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
12670 "groups/bertone/software/HTqPCR.pdf"))
12671 (synopsis "Automated analysis of high-throughput qPCR data")
12673 "Analysis of Ct values from high throughput quantitative real-time
12674 PCR (qPCR) assays across multiple conditions or replicates. The input data
12675 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
12676 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
12677 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
12678 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
12679 loading, quality assessment, normalization, visualization and parametric or
12680 non-parametric testing for statistical significance in Ct values between
12681 features (e.g. genes, microRNAs).")
12682 (license license:artistic2.0)))
12684 (define-public r-unifiedwmwqpcr
12686 (name "r-unifiedwmwqpcr")
12691 (uri (bioconductor-uri "unifiedWMWqPCR" version))
12694 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
12696 `((upstream-name . "unifiedWMWqPCR")))
12697 (build-system r-build-system)
12699 (list r-biocgenerics r-htqpcr))
12700 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
12701 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
12703 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
12704 data. This modified test allows for testing differential expression in qPCR
12706 (license license:gpl2+)))
12708 (define-public r-universalmotif
12710 (name "r-universalmotif")
12715 (uri (bioconductor-uri "universalmotif" version))
12718 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
12720 `((upstream-name . "universalmotif")))
12721 (build-system r-build-system)
12724 (modify-phases %standard-phases
12725 (add-after 'unpack 'fix-reference-to-strip
12727 (substitute* "src/Makevars"
12728 (("/usr/bin/strip") (which "strip"))))))))
12730 (list r-biocgenerics
12743 "https://bioconductor.org/packages/universalmotif/")
12745 "Specific structures importer, modifier, and exporter for R")
12747 "This package allows importing most common @dfn{specific structure}
12748 (motif) types into R for use by functions provided by other Bioconductor
12749 motif-related packages. Motifs can be exported into most major motif formats
12750 from various classes as defined by other Bioconductor packages. A suite of
12751 motif and sequence manipulation and analysis functions are included, including
12752 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
12753 motifs, and others.")
12754 (license license:gpl3)))
12756 (define-public r-ace
12762 (uri (bioconductor-uri "ACE" version))
12765 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
12766 (properties `((upstream-name . "ACE")))
12767 (build-system r-build-system)
12768 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
12769 (native-inputs (list r-knitr))
12770 (home-page "https://github.com/tgac-vumc/ACE")
12772 "Absolute copy number estimation from low-coverage whole genome sequencing")
12774 "This package uses segmented copy number data to estimate tumor cell
12775 percentage and produce copy number plots displaying absolute copy numbers. For
12776 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
12777 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
12778 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
12779 subsequently run through all samples in the object(s), for which it will create
12780 individual subdirectories. For each sample, it will calculate how well the
12781 segments fit (the relative error) to integer copy numbers for each percentage
12782 of @dfn{tumor cells} (cells with divergent segments).")
12783 (license license:gpl2)))
12785 (define-public r-acgh
12791 (uri (bioconductor-uri "aCGH" version))
12794 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
12795 (properties `((upstream-name . "aCGH")))
12796 (build-system r-build-system)
12797 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
12798 (home-page "https://bioconductor.org/packages/aCGH")
12800 "Classes and functions for array comparative genomic hybridization data")
12802 "This package provides functions for reading
12803 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
12804 output files and clone information files, creation of @code{aCGH} objects for
12805 storing these data. Basic methods are accessing/replacing, subsetting,
12806 printing and plotting @code{aCGH} objects.")
12807 (license license:gpl2)))
12809 (define-public r-acme
12815 (uri (bioconductor-uri "ACME" version))
12818 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
12819 (properties `((upstream-name . "ACME")))
12820 (build-system r-build-system)
12821 (propagated-inputs (list r-biobase r-biocgenerics))
12822 (home-page "https://bioconductor.org/packages/aCGH/")
12823 (synopsis "Calculating microarray enrichment")
12825 "This package implements @dfn{algorithms for calculating microarray
12826 enrichment} (ACME), and it is a set of tools for analysing tiling array of
12827 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
12828 DNAse hypersensitivity, or other experiments that result in regions of the
12829 genome showing enrichment. It does not rely on a specific array technology
12830 (although the array should be a tiling array), is very general (can be applied
12831 in experiments resulting in regions of enrichment), and is very insensitive to
12832 array noise or normalization methods. It is also very fast and can be applied
12833 on whole-genome tiling array experiments quite easily with enough memory.")
12834 (license license:gpl2+)))
12836 (define-public r-acde
12842 (uri (bioconductor-uri "acde" version))
12845 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
12846 (properties `((upstream-name . "acde")))
12847 (build-system r-build-system)
12848 (propagated-inputs (list r-boot))
12849 (home-page "https://bioconductor.org/packages/acde")
12851 "Identification of differentially expressed genes with artificial components")
12853 "This package provides a multivariate inferential analysis method for
12854 detecting differentially expressed genes in gene expression data. It uses
12855 artificial components, close to the data's principal components but with an
12856 exact interpretation in terms of differential genetic expression, to identify
12857 differentially expressed genes while controlling the @dfn{false discovery
12859 (license license:gpl3)))
12861 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12863 (define-public r-activedriverwgs
12865 (name "r-activedriverwgs")
12870 (uri (cran-uri "ActiveDriverWGS" version))
12873 "13b5yazgv9kckcp6gck183mh1m0q8lc5ixagmcy9s8kv2wz7wq45"))))
12875 `((upstream-name . "ActiveDriverWGS")))
12876 (build-system r-build-system)
12880 r-bsgenome-hsapiens-ucsc-hg19
12881 r-bsgenome-hsapiens-ucsc-hg38
12882 r-bsgenome-mmusculus-ucsc-mm9
12883 r-bsgenome-mmusculus-ucsc-mm10
12890 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
12891 (synopsis "Driver discovery tool for cancer whole genomes")
12893 "This package provides a method for finding an enrichment of cancer
12894 simple somatic mutations (SNVs and Indels) in functional elements across the
12895 human genome. ActiveDriverWGS detects coding and noncoding driver elements
12896 using whole genome sequencing data.")
12897 (license license:gpl3)))
12899 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
12901 (define-public r-activepathways
12903 (name "r-activepathways")
12908 (uri (cran-uri "ActivePathways" version))
12911 "0zbrgz91mlik7j8j11wsdswqqqfsijj8jkgd5fx1ar3mc6rqsmbg"))))
12913 `((upstream-name . "ActivePathways")))
12914 (build-system r-build-system)
12916 (list r-data-table r-ggplot2))
12919 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
12920 (synopsis "Multivariate pathway enrichment analysis")
12922 "This package represents an integrative method of analyzing multi omics
12923 data that conducts enrichment analysis of annotated gene sets. ActivePathways
12924 uses a statistical data fusion approach, rationalizes contributing evidence
12925 and highlights associated genes, improving systems-level understanding of
12926 cellular organization in health and disease.")
12927 (license license:gpl3)))
12929 (define-public r-bgmix
12936 (uri (bioconductor-uri "BGmix" version))
12939 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
12940 (properties `((upstream-name . "BGmix")))
12941 (build-system r-build-system)
12943 (list r-kernsmooth))
12944 (home-page "https://bioconductor.org/packages/BGmix/")
12945 (synopsis "Bayesian models for differential gene expression")
12947 "This package provides fully Bayesian mixture models for differential
12949 (license license:gpl2)))
12951 (define-public r-bgx
12958 (uri (bioconductor-uri "bgx" version))
12961 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
12962 (properties `((upstream-name . "bgx")))
12963 (build-system r-build-system)
12965 (list r-affy r-biobase r-gcrma r-rcpp))
12966 (home-page "https://bioconductor.org/packages/bgx/")
12967 (synopsis "Bayesian gene expression")
12969 "This package provides tools for Bayesian integrated analysis of
12970 Affymetrix GeneChips.")
12971 (license license:gpl2)))
12973 (define-public r-bhc
12980 (uri (bioconductor-uri "BHC" version))
12983 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
12984 (properties `((upstream-name . "BHC")))
12985 (build-system r-build-system)
12986 (home-page "https://bioconductor.org/packages/BHC/")
12987 (synopsis "Bayesian hierarchical clustering")
12989 "The method implemented in this package performs bottom-up hierarchical
12990 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
12991 in the data and Bayesian model selection to decide at each step which clusters
12992 to merge. This avoids several limitations of traditional methods, for example
12993 how many clusters there should be and how to choose a principled distance
12994 metric. This implementation accepts multinomial (i.e. discrete, with 2+
12995 categories) or time-series data. This version also includes a randomised
12996 algorithm which is more efficient for larger data sets.")
12997 (license license:gpl3)))
12999 (define-public r-bicare
13006 (uri (bioconductor-uri "BicARE" version))
13009 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
13010 (properties `((upstream-name . "BicARE")))
13011 (build-system r-build-system)
13013 (list r-biobase r-gseabase r-multtest))
13014 (home-page "http://bioinfo.curie.fr")
13015 (synopsis "Biclustering analysis and results exploration")
13017 "This is a package for biclustering analysis and exploration of
13019 (license license:gpl2)))
13021 (define-public r-bifet
13028 (uri (bioconductor-uri "BiFET" version))
13031 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
13032 (properties `((upstream-name . "BiFET")))
13033 (build-system r-build-system)
13035 (list r-genomicranges r-poibin))
13038 (home-page "https://bioconductor.org/packages/BiFET")
13039 (synopsis "Bias-free footprint enrichment test")
13041 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
13042 over-represented in target regions compared to background regions after
13043 correcting for the bias arising from the imbalance in read counts and GC
13044 contents between the target and background regions. For a given TF k, BiFET
13045 tests the null hypothesis that the target regions have the same probability of
13046 having footprints for the TF k as the background regions while correcting for
13047 the read count and GC content bias.")
13048 (license license:gpl3)))
13050 (define-public r-rsbml
13057 (uri (bioconductor-uri "rsbml" version))
13060 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
13061 (properties `((upstream-name . "rsbml")))
13062 (build-system r-build-system)
13066 (list r-biocgenerics r-graph))
13069 (home-page "http://www.sbml.org")
13070 (synopsis "R support for SBML")
13072 "This package provides an R interface to libsbml for SBML parsing,
13073 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
13074 (license license:artistic2.0)))
13076 (define-public r-hypergraph
13078 (name "r-hypergraph")
13083 (uri (bioconductor-uri "hypergraph" version))
13086 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
13087 (properties `((upstream-name . "hypergraph")))
13088 (build-system r-build-system)
13091 (home-page "https://bioconductor.org/packages/hypergraph")
13092 (synopsis "Hypergraph data structures")
13094 "This package implements some simple capabilities for representing and
13095 manipulating hypergraphs.")
13096 (license license:artistic2.0)))
13098 (define-public r-hyperdraw
13100 (name "r-hyperdraw")
13105 (uri (bioconductor-uri "hyperdraw" version))
13108 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
13109 (properties `((upstream-name . "hyperdraw")))
13110 (build-system r-build-system)
13111 (inputs (list graphviz))
13113 (list r-graph r-hypergraph r-rgraphviz))
13114 (home-page "https://bioconductor.org/packages/hyperdraw")
13115 (synopsis "Visualizing hypergraphs")
13117 "This package provides functions for visualizing hypergraphs.")
13118 (license license:gpl2+)))
13120 (define-public r-biggr
13127 (uri (bioconductor-uri "BiGGR" version))
13130 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
13131 (properties `((upstream-name . "BiGGR")))
13132 (build-system r-build-system)
13140 (home-page "https://bioconductor.org/packages/BiGGR/")
13141 (synopsis "Constraint based modeling using metabolic reconstruction databases")
13143 "This package provides an interface to simulate metabolic reconstruction
13144 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
13145 reconstruction databases. The package facilitates @dfn{flux balance
13146 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
13147 networks and estimated fluxes can be visualized with hypergraphs.")
13148 (license license:gpl3+)))
13150 (define-public r-bigmemoryextras
13152 (name "r-bigmemoryextras")
13157 (uri (bioconductor-uri "bigmemoryExtras" version))
13160 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
13162 `((upstream-name . "bigmemoryExtras")))
13163 (build-system r-build-system)
13165 (list r-bigmemory))
13168 (home-page "https://github.com/phaverty/bigmemoryExtras")
13169 (synopsis "Extension of the bigmemory package")
13171 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
13172 safety and convenience features to the @code{filebacked.big.matrix} class from
13173 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
13174 monitoring and gracefully restoring the connection to on-disk data and it also
13175 protects against accidental data modification with a file-system-based
13176 permissions system. Utilities are provided for using @code{BigMatrix}-derived
13177 classes as @code{assayData} matrices within the @code{Biobase} package's
13178 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
13179 related to attaching to, and indexing into, file-backed matrices with
13180 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
13181 a file-backed matrix with factor properties.")
13182 (license license:artistic2.0)))
13184 (define-public r-bigpint
13191 (uri (bioconductor-uri "bigPint" version))
13194 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
13195 (properties `((upstream-name . "bigPint")))
13196 (build-system r-build-system)
13198 (list r-delayedarray
13214 r-summarizedexperiment
13218 (home-page "https://github.com/lindsayrutter/bigPint")
13219 (synopsis "Big multivariate data plotted interactively")
13221 "This package provides methods for visualizing large multivariate
13222 datasets using static and interactive scatterplot matrices, parallel
13223 coordinate plots, volcano plots, and litre plots. It includes examples for
13224 visualizing RNA-sequencing datasets and differentially expressed genes.")
13225 (license license:gpl3)))
13227 (define-public r-chemminer
13229 (name "r-chemminer")
13234 (uri (bioconductor-uri "ChemmineR" version))
13237 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
13238 (properties `((upstream-name . "ChemmineR")))
13239 (build-system r-build-system)
13258 (home-page "https://github.com/girke-lab/ChemmineR")
13259 (synopsis "Cheminformatics toolkit for R")
13261 "ChemmineR is a cheminformatics package for analyzing drug-like small
13262 molecule data in R. It contains functions for efficient processing of large
13263 numbers of molecules, physicochemical/structural property predictions,
13264 structural similarity searching, classification and clustering of compound
13265 libraries with a wide spectrum of algorithms. In addition, it offers
13266 visualization functions for compound clustering results and chemical
13268 (license license:artistic2.0)))
13270 (define-public r-fmcsr
13277 (uri (bioconductor-uri "fmcsR" version))
13279 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
13280 (properties `((upstream-name . "fmcsR")))
13281 (build-system r-build-system)
13283 (list r-biocgenerics r-chemminer r-runit))
13284 (native-inputs (list r-knitr))
13285 (home-page "https://github.com/girke-lab/fmcsR")
13286 (synopsis "Mismatch tolerant maximum common substructure searching")
13288 "The fmcsR package introduces an efficient @dfn{maximum common
13289 substructure} (MCS) algorithms combined with a novel matching strategy that
13290 allows for atom and/or bond mismatches in the substructures shared among two
13291 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
13292 strict MCSs, resulting in the identification of more common features in their
13293 source structures, as well as a higher sensitivity in finding compounds with
13294 weak structural similarities. The fmcsR package provides several utilities to
13295 use the FMCS algorithm for pairwise compound comparisons, structure similarity
13296 searching and clustering.")
13297 (license license:artistic2.0)))
13299 (define-public r-bioassayr
13301 (name "r-bioassayr")
13306 (uri (bioconductor-uri "bioassayR" version))
13309 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
13310 (properties `((upstream-name . "bioassayR")))
13311 (build-system r-build-system)
13313 (list r-biocgenerics
13322 (home-page "https://github.com/girke-lab/bioassayR")
13323 (synopsis "Cross-target analysis of small molecule bioactivity")
13325 "bioassayR is a computational tool that enables simultaneous analysis of
13326 thousands of bioassay experiments performed over a diverse set of compounds
13327 and biological targets. Unique features include support for large-scale
13328 cross-target analyses of both public and custom bioassays, generation of
13329 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
13330 preloaded database that provides access to a substantial portion of publicly
13331 available bioactivity data.")
13332 (license license:artistic2.0)))
13334 (define-public r-biobroom
13336 (name "r-biobroom")
13341 (uri (bioconductor-uri "biobroom" version))
13344 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
13345 (properties `((upstream-name . "biobroom")))
13346 (build-system r-build-system)
13348 (list r-biobase r-broom r-dplyr r-tidyr))
13351 (home-page "https://github.com/StoreyLab/biobroom")
13352 (synopsis "Turn Bioconductor objects into tidy data frames")
13354 "This package contains methods for converting standard objects
13355 constructed by bioinformatics packages, especially those in Bioconductor, and
13356 converting them to @code{tidy} data. It thus serves as a complement to the
13357 @code{broom} package, and follows the same tidy, augment, glance division of
13358 tidying methods. Tidying data makes it easy to recombine, reshape and
13359 visualize bioinformatics analyses.")
13360 ;; Any version of the LGPL.
13361 (license license:lgpl3+)))
13363 (define-public r-graphite
13365 (name "r-graphite")
13370 (uri (bioconductor-uri "graphite" version))
13373 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
13374 (properties `((upstream-name . "graphite")))
13375 (build-system r-build-system)
13377 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
13378 (home-page "https://bioconductor.org/packages/graphite/")
13379 (synopsis "Networks from pathway databases")
13381 "Graphite provides networks derived from eight public pathway databases,
13382 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
13384 (license license:agpl3+)))
13386 (define-public r-reactomepa
13388 (name "r-reactomepa")
13393 (uri (bioconductor-uri "ReactomePA" version))
13396 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
13397 (properties `((upstream-name . "ReactomePA")))
13398 (build-system r-build-system)
13400 (list r-annotationdbi
13410 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
13411 (synopsis "Reactome pathway analysis")
13413 "This package provides functions for pathway analysis based on the
13414 REACTOME pathway database. It implements enrichment analysis, gene set
13415 enrichment analysis and several functions for visualization.")
13416 (license license:gpl2)))
13418 (define-public r-ebarrays
13420 (name "r-ebarrays")
13425 (uri (bioconductor-uri "EBarrays" version))
13428 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
13429 (properties `((upstream-name . "EBarrays")))
13430 (build-system r-build-system)
13432 (list r-biobase r-cluster r-lattice))
13433 (home-page "https://bioconductor.org/packages/EBarrays/")
13434 (synopsis "Gene clustering and differential expression identification")
13436 "EBarrays provides tools for the analysis of replicated/unreplicated
13438 (license license:gpl2+)))
13440 (define-public r-bioccasestudies
13442 (name "r-bioccasestudies")
13447 (uri (bioconductor-uri "BiocCaseStudies" version))
13450 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
13452 `((upstream-name . "BiocCaseStudies")))
13453 (build-system r-build-system)
13454 (propagated-inputs (list r-biobase))
13455 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
13456 (synopsis "Support for the case studies monograph")
13458 "This package provides software and data to support the case studies
13460 (license license:artistic2.0)))
13462 (define-public r-bioccheck
13464 (name "r-bioccheck")
13468 (uri (bioconductor-uri "BiocCheck" version))
13471 "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"))))
13473 `((upstream-name . "BiocCheck")))
13474 (build-system r-build-system)
13485 (home-page "https://bioconductor.org/packages/BiocCheck")
13486 (synopsis "Executes Bioconductor-specific package checks")
13487 (description "This package contains tools to perform additional quality
13488 checks on R packages that are to be submitted to the Bioconductor repository.")
13489 (license license:artistic2.0)))
13491 (define-public r-biocgraph
13493 (name "r-biocgraph")
13498 (uri (bioconductor-uri "biocGraph" version))
13501 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
13502 (properties `((upstream-name . "biocGraph")))
13503 (build-system r-build-system)
13505 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
13506 (home-page "https://bioconductor.org/packages/biocGraph/")
13507 (synopsis "Graph examples and use cases in Bioinformatics")
13509 "This package provides examples and code that make use of the
13510 different graph related packages produced by Bioconductor.")
13511 (license license:artistic2.0)))
13513 (define-public r-biocstyle
13515 (name "r-biocstyle")
13519 (uri (bioconductor-uri "BiocStyle" version))
13522 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
13524 `((upstream-name . "BiocStyle")))
13525 (build-system r-build-system)
13527 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
13530 (home-page "https://bioconductor.org/packages/BiocStyle")
13531 (synopsis "Bioconductor formatting styles")
13532 (description "This package provides standard formatting styles for
13533 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
13535 (license license:artistic2.0)))
13537 (define-public r-biocviews
13539 (name "r-biocviews")
13543 (uri (bioconductor-uri "biocViews" version))
13546 "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126"))))
13548 `((upstream-name . "biocViews")))
13549 (build-system r-build-system)
13558 (home-page "https://bioconductor.org/packages/biocViews")
13559 (synopsis "Bioconductor package categorization helper")
13560 (description "The purpose of biocViews is to create HTML pages that
13561 categorize packages in a Bioconductor package repository according to keywords,
13562 also known as views, in a controlled vocabulary.")
13563 (license license:artistic2.0)))
13565 (define-public r-experimenthub
13567 (name "r-experimenthub")
13572 (uri (bioconductor-uri "ExperimentHub" version))
13575 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
13576 (properties `((upstream-name . "ExperimentHub")))
13577 (build-system r-build-system)
13579 (list r-annotationhub
13588 (home-page "https://bioconductor.org/packages/ExperimentHub/")
13589 (synopsis "Client to access ExperimentHub resources")
13591 "This package provides a client for the Bioconductor ExperimentHub web
13592 resource. ExperimentHub provides a central location where curated data from
13593 experiments, publications or training courses can be accessed. Each resource
13594 has associated metadata, tags and date of modification. The client creates
13595 and manages a local cache of files retrieved enabling quick and reproducible
13597 (license license:artistic2.0)))
13599 (define-public r-grohmm
13606 (uri (bioconductor-uri "groHMM" version))
13609 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
13610 (properties `((upstream-name . "groHMM")))
13611 (build-system r-build-system)
13613 (list r-genomeinfodb
13614 r-genomicalignments
13620 (home-page "https://github.com/Kraus-Lab/groHMM")
13621 (synopsis "GRO-seq analysis pipeline")
13623 "This package provides a pipeline for the analysis of GRO-seq data.")
13624 (license license:gpl3+)))
13626 (define-public r-multiassayexperiment
13628 (name "r-multiassayexperiment")
13633 (uri (bioconductor-uri "MultiAssayExperiment" version))
13636 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
13638 `((upstream-name . "MultiAssayExperiment")))
13639 (build-system r-build-system)
13646 r-summarizedexperiment
13650 (home-page "https://waldronlab.io/MultiAssayExperiment/")
13651 (synopsis "Integration of multi-omics experiments in Bioconductor")
13653 "MultiAssayExperiment harmonizes data management of multiple assays
13654 performed on an overlapping set of specimens. It provides a familiar
13655 Bioconductor user experience by extending concepts from
13656 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
13657 classes for individual assays, and allowing subsetting by genomic ranges or
13659 (license license:artistic2.0)))
13661 (define-public r-bioconcotk
13663 (name "r-bioconcotk")
13668 (uri (bioconductor-uri "BiocOncoTK" version))
13671 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
13672 (properties `((upstream-name . "BiocOncoTK")))
13673 (build-system r-build-system)
13696 r-summarizedexperiment))
13699 (home-page "https://bioconductor.org/packages/BiocOncoTK")
13700 (synopsis "Bioconductor components for general cancer genomics")
13702 "The purpose of this package is to provide a central interface to various
13703 tools for genome-scale analysis of cancer studies.")
13704 (license license:artistic2.0)))
13706 (define-public r-biocor
13713 (uri (bioconductor-uri "BioCor" version))
13716 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
13717 (properties `((upstream-name . "BioCor")))
13718 (build-system r-build-system)
13720 (list r-biocparallel r-gseabase r-matrix))
13723 (home-page "https://llrs.github.io/BioCor/")
13724 (synopsis "Functional similarities")
13726 "This package provides tools to calculate functional similarities based
13727 on the pathways described on KEGG and REACTOME or in gene sets. These
13728 similarities can be calculated for pathways or gene sets, genes, or clusters
13729 and combined with other similarities. They can be used to improve networks,
13730 gene selection, testing relationships, and so on.")
13731 (license license:expat)))
13733 (define-public r-biocpkgtools
13735 (name "r-biocpkgtools")
13740 (uri (bioconductor-uri "BiocPkgTools" version))
13743 "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"))))
13744 (properties `((upstream-name . "BiocPkgTools")))
13745 (build-system r-build-system)
13747 (list r-biocfilecache
13771 (home-page "https://github.com/seandavi/BiocPkgTools")
13772 (synopsis "Collection of tools for learning about Bioconductor packages")
13774 "Bioconductor has a rich ecosystem of metadata around packages, usage,
13775 and build status. This package is a simple collection of functions to access
13776 that metadata from R. The goal is to expose metadata for data mining and
13777 value-added functionality such as package searching, text mining, and
13778 analytics on packages.")
13779 (license license:expat)))
13781 (define-public r-biocset
13788 (uri (bioconductor-uri "BiocSet" version))
13791 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
13792 (properties `((upstream-name . "BiocSet")))
13793 (build-system r-build-system)
13795 (list r-annotationdbi
13808 "https://bioconductor.org/packages/BiocSet")
13810 "Representing Different Biological Sets")
13812 "BiocSet displays different biological sets in a triple tibble format.
13813 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
13814 The user has the ability to activate one of these three tibbles to perform
13815 common functions from the @code{dplyr} package. Mapping functionality and
13816 accessing web references for elements/sets are also available in BiocSet.")
13817 (license license:artistic2.0)))
13819 (define-public r-biocworkflowtools
13821 (name "r-biocworkflowtools")
13826 (uri (bioconductor-uri "BiocWorkflowTools" version))
13829 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
13831 `((upstream-name . "BiocWorkflowTools")))
13832 (build-system r-build-system)
13845 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
13846 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
13848 "This package provides functions to ease the transition between
13849 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
13850 (license license:expat)))
13852 (define-public r-biodist
13859 (uri (bioconductor-uri "bioDist" version))
13862 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
13863 (properties `((upstream-name . "bioDist")))
13864 (build-system r-build-system)
13866 (list r-biobase r-kernsmooth))
13867 (home-page "https://bioconductor.org/packages/bioDist/")
13868 (synopsis "Different distance measures")
13870 "This package provides a collection of software tools for calculating
13871 distance measures.")
13872 (license license:artistic2.0)))
13874 (define-public r-pcatools
13876 (name "r-pcatools")
13881 (uri (bioconductor-uri "PCAtools" version))
13884 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
13885 (properties `((upstream-name . "PCAtools")))
13886 (build-system r-build-system)
13894 r-delayedmatrixstats
13902 (native-inputs (list r-knitr))
13903 (home-page "https://github.com/kevinblighe/PCAtools")
13904 (synopsis "PCAtools: everything Principal Components Analysis")
13906 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
13907 structure of the data without the need to build any model to represent it.
13908 This \"summary\" of the data is arrived at through a process of reduction that
13909 can transform the large number of variables into a lesser number that are
13910 uncorrelated (i.e. the 'principal components'), while at the same time being
13911 capable of easy interpretation on the original data. PCAtools provides
13912 functions for data exploration via PCA, and allows the user to generate
13913 publication-ready figures. PCA is performed via @code{BiocSingular}; users
13914 can also identify an optimal number of principal components via different
13915 metrics, such as the elbow method and Horn's parallel analysis, which has
13916 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
13917 dimensional mass cytometry data.")
13918 (license license:gpl3)))
13920 (define-public r-rgreat
13927 (uri (bioconductor-uri "rGREAT" version))
13930 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
13931 (properties `((upstream-name . "rGREAT")))
13932 (build-system r-build-system)
13934 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
13935 (native-inputs (list r-knitr))
13936 (home-page "https://github.com/jokergoo/rGREAT")
13937 (synopsis "Client for GREAT analysis")
13939 "This package makes GREAT (Genomic Regions Enrichment of Annotations
13940 Tool) analysis automatic by constructing a HTTP POST request according to
13941 user's input and automatically retrieving results from GREAT web server.")
13942 (license license:expat)))
13944 (define-public r-m3c
13951 (uri (bioconductor-uri "M3C" version))
13954 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
13955 (properties `((upstream-name . "M3C")))
13956 (build-system r-build-system)
13968 (native-inputs (list r-knitr))
13969 (home-page "https://bioconductor.org/packages/M3C")
13970 (synopsis "Monte Carlo reference-based consensus clustering")
13972 "M3C is a consensus clustering algorithm that uses a Monte Carlo
13973 simulation to eliminate overestimation of @code{K} and can reject the null
13974 hypothesis @code{K=1}.")
13975 (license license:agpl3+)))
13977 (define-public r-icens
13984 (uri (bioconductor-uri "Icens" version))
13987 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
13988 (properties `((upstream-name . "Icens")))
13989 (build-system r-build-system)
13992 (home-page "https://bioconductor.org/packages/Icens")
13993 (synopsis "NPMLE for censored and truncated data")
13995 "This package provides many functions for computing the
13996 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
13998 (license license:artistic2.0)))
14000 ;; This is a CRAN package but it depends on r-icens, which is published on
14002 (define-public r-interval
14004 (name "r-interval")
14005 (version "1.1-0.8")
14009 (uri (cran-uri "interval" version))
14012 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
14013 (properties `((upstream-name . "interval")))
14014 (build-system r-build-system)
14016 (list r-icens r-mlecens r-perm r-survival))
14017 (home-page "https://cran.r-project.org/web/packages/interval/")
14018 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
14020 "This package provides functions to fit nonparametric survival curves,
14021 plot them, and perform logrank or Wilcoxon type tests.")
14022 (license license:gpl2+)))
14024 ;; This is a CRAN package, but it depends on r-interval, which depends on a
14025 ;; Bioconductor package.
14026 (define-public r-fhtest
14033 (uri (cran-uri "FHtest" version))
14036 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
14037 (properties `((upstream-name . "FHtest")))
14038 (build-system r-build-system)
14040 (list r-interval r-kmsurv r-mass r-perm r-survival))
14041 (home-page "https://cran.r-project.org/web/packages/FHtest/")
14042 (synopsis "Tests for survival data based on the Fleming-Harrington class")
14044 "This package provides functions to compare two or more survival curves
14048 @item The Fleming-Harrington test for right-censored data based on
14049 permutations and on counting processes.
14050 @item An extension of the Fleming-Harrington test for interval-censored data
14051 based on a permutation distribution and on a score vector distribution.
14054 (license license:gpl2+)))
14056 (define-public r-fourcseq
14058 (name "r-fourcseq")
14063 (uri (bioconductor-uri "FourCSeq" version))
14065 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
14066 (properties `((upstream-name . "FourCSeq")))
14067 (build-system r-build-system)
14073 r-genomicalignments
14083 r-summarizedexperiment))
14087 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
14088 (synopsis "Analysis of multiplexed 4C sequencing data")
14090 "This package is an R package dedicated to the analysis of (multiplexed)
14091 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
14092 interactions between DNA elements and identify differential interactions
14093 between conditions. The statistical analysis in R starts with individual bam
14094 files for each sample as inputs. To obtain these files, the package contains
14095 a Python script to demultiplex libraries and trim off primer sequences. With
14096 a standard alignment software the required bam files can be then be
14098 (license license:gpl3+)))
14100 (define-public r-preprocesscore
14102 (name "r-preprocesscore")
14107 (uri (bioconductor-uri "preprocessCore" version))
14110 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
14112 `((upstream-name . "preprocessCore")))
14113 (build-system r-build-system)
14114 (home-page "https://github.com/bmbolstad/preprocessCore")
14115 (synopsis "Collection of pre-processing functions")
14117 "This package provides a library of core pre-processing and normalization
14119 (license license:lgpl2.0+)))
14121 (define-public r-s4vectors
14123 (name "r-s4vectors")
14127 (uri (bioconductor-uri "S4Vectors" version))
14130 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
14132 `((upstream-name . "S4Vectors")))
14133 (build-system r-build-system)
14135 (list r-biocgenerics))
14136 (home-page "https://bioconductor.org/packages/S4Vectors")
14137 (synopsis "S4 implementation of vectors and lists")
14139 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
14140 classes and a set of generic functions that extend the semantic of ordinary
14141 vectors and lists in R. Package developers can easily implement vector-like
14142 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
14143 In addition, a few low-level concrete subclasses of general interest (e.g.
14144 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
14145 S4Vectors package itself.")
14146 (license license:artistic2.0)))
14148 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
14149 ;; Bioconductor package.
14150 (define-public r-wgcna
14157 (uri (cran-uri "WGCNA" version))
14160 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
14161 (properties `((upstream-name . "WGCNA")))
14162 (build-system r-build-system)
14164 (list r-annotationdbi
14177 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14178 (synopsis "Weighted correlation network analysis")
14180 "This package provides functions necessary to perform Weighted
14181 Correlation Network Analysis on high-dimensional data. It includes functions
14182 for rudimentary data cleaning, construction and summarization of correlation
14183 networks, module identification and functions for relating both variables and
14184 modules to sample traits. It also includes a number of utility functions for
14185 data manipulation and visualization.")
14186 (license license:gpl2+)))
14188 (define-public r-rgraphviz
14190 (name "r-rgraphviz")
14195 (uri (bioconductor-uri "Rgraphviz" version))
14198 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
14199 (properties `((upstream-name . "Rgraphviz")))
14200 (build-system r-build-system)
14203 (modify-phases %standard-phases
14204 (add-after 'unpack 'make-reproducible
14206 ;; The replacement value is taken from src/graphviz/builddate.h
14207 (substitute* "src/graphviz/configure"
14208 (("VERSION_DATE=.*")
14209 "VERSION_DATE=20200427.2341\n"))
14211 ;; FIXME: Rgraphviz bundles the sources of an older variant of
14212 ;; graphviz. It does not build with the latest version of graphviz, so
14213 ;; we do not add graphviz to the inputs.
14214 (inputs (list zlib))
14219 (home-page "https://bioconductor.org/packages/Rgraphviz")
14220 (synopsis "Plotting capabilities for R graph objects")
14222 "This package interfaces R with the graphviz library for plotting R graph
14223 objects from the @code{graph} package.")
14224 (license license:epl1.0)))
14226 (define-public r-fithic
14232 (uri (bioconductor-uri "FitHiC" version))
14235 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
14236 (properties `((upstream-name . "FitHiC")))
14237 (build-system r-build-system)
14239 (list r-data-table r-fdrtool r-rcpp))
14242 (home-page "https://bioconductor.org/packages/FitHiC")
14243 (synopsis "Confidence estimation for intra-chromosomal contact maps")
14245 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
14246 intra-chromosomal contact maps produced by genome-wide genome architecture
14247 assays such as Hi-C.")
14248 (license license:gpl2+)))
14250 (define-public r-hitc
14256 (uri (bioconductor-uri "HiTC" version))
14259 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
14260 (properties `((upstream-name . "HiTC")))
14261 (build-system r-build-system)
14270 (home-page "https://bioconductor.org/packages/HiTC")
14271 (synopsis "High throughput chromosome conformation capture analysis")
14273 "The HiTC package was developed to explore high-throughput \"C\" data
14274 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
14275 quality controls, normalization, visualization, and further analysis are also
14277 (license license:artistic2.0)))
14279 (define-public r-hdf5array
14281 (name "r-hdf5array")
14286 (uri (bioconductor-uri "HDF5Array" version))
14289 "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday"))))
14290 (properties `((upstream-name . "HDF5Array")))
14291 (build-system r-build-system)
14295 (list r-biocgenerics
14303 (home-page "https://bioconductor.org/packages/HDF5Array")
14304 (synopsis "HDF5 back end for DelayedArray objects")
14305 (description "This package provides an array-like container for convenient
14306 access and manipulation of HDF5 datasets. It supports delayed operations and
14307 block processing.")
14308 (license license:artistic2.0)))
14310 (define-public r-rhdf5lib
14312 (name "r-rhdf5lib")
14317 (uri (bioconductor-uri "Rhdf5lib" version))
14320 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
14321 (modules '((guix build utils)))
14324 ;; Delete bundled binaries
14325 (delete-file-recursively "src/wininclude/")
14326 (delete-file-recursively "src/winlib/")
14327 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
14328 (properties `((upstream-name . "Rhdf5lib")))
14329 (build-system r-build-system)
14332 (modify-phases %standard-phases
14333 (add-after 'unpack 'do-not-use-bundled-hdf5
14334 (lambda* (#:key inputs #:allow-other-keys)
14335 (for-each delete-file '("configure" "configure.ac"))
14336 (substitute* "R/zzz.R"
14337 (("return\\(links\\)") "return(\" -lz\")"))
14338 (with-directory-excursion "src"
14339 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
14340 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
14342 ;; Remove timestamp and host system information to make
14343 ;; the build reproducible.
14344 (substitute* "hdf5/src/libhdf5.settings.in"
14345 (("Configured on: @CONFIG_DATE@")
14346 "Configured on: Guix")
14347 (("Uname information:.*")
14348 "Uname information: Linux\n")
14349 ;; Remove unnecessary store reference.
14351 "C Compiler: GCC\n"))
14352 (rename-file "hdf5/src/libhdf5.settings.in"
14353 "hdf5/src/libhdf5.settings")
14354 (rename-file "Makevars.in" "Makevars")
14355 (substitute* "Makevars"
14356 (("@BUILD_HDF5@") "")
14357 (("@COPY_SZIP@") "")
14358 (("@ZLIB_LIB@") "-lz")
14359 (("@ZLIB_INCLUDE@") "")
14360 (("HDF5_CXX_LIB=.*")
14361 (string-append "HDF5_CXX_LIB="
14362 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
14364 (string-append "HDF5_LIB="
14365 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
14366 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
14367 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
14368 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
14369 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
14370 (("HDF5_HL_LIB=.*")
14371 (string-append "HDF5_HL_LIB="
14372 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
14373 (("HDF5_HL_CXX_LIB=.*")
14374 (string-append "HDF5_HL_CXX_LIB="
14375 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
14376 ;; szip is non-free software
14377 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
14378 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
14380 (list hdf5-1.10 zlib))
14382 `(("hdf5-source" ,(package-source hdf5-1.10))
14383 ("r-knitr" ,r-knitr)))
14384 (home-page "https://bioconductor.org/packages/Rhdf5lib")
14385 (synopsis "HDF5 library as an R package")
14386 (description "This package provides C and C++ HDF5 libraries for use in R
14388 (license license:artistic2.0)))
14390 (define-public r-beachmat
14392 (name "r-beachmat")
14397 (uri (bioconductor-uri "beachmat" version))
14400 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
14401 (build-system r-build-system)
14403 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
14406 (home-page "https://bioconductor.org/packages/beachmat")
14407 (synopsis "Compiling Bioconductor to handle each matrix type")
14408 (description "This package provides a consistent C++ class interface for a
14409 variety of commonly used matrix types, including sparse and HDF5-backed
14411 (license license:gpl3)))
14413 ;; This package includes files that have been taken from kentutils. Some
14414 ;; parts of kentutils are not released under a free license, but this package
14415 ;; only uses files that are also found in the free parts of kentutils.
14416 (define-public r-cner
14423 (uri (bioconductor-uri "CNEr" version))
14425 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
14426 (properties `((upstream-name . "CNEr")))
14427 (build-system r-build-system)
14428 (inputs (list zlib))
14435 r-genomicalignments
14451 (home-page "https://github.com/ge11232002/CNEr")
14452 (synopsis "CNE Detection and Visualization")
14454 "This package provides tools for large-scale identification and
14455 advanced visualization of sets of conserved noncoding elements.")
14456 ;; For all files in src/ucsc "license is hereby granted for all use -
14457 ;; public, private or commercial"; this includes those files that don't
14458 ;; have a license header, because they are included in the free parts of
14459 ;; the kentutils package.
14460 (license (list license:gpl2
14461 (license:non-copyleft
14462 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
14464 (define-public r-tfbstools
14466 (name "r-tfbstools")
14471 (uri (bioconductor-uri "TFBSTools" version))
14474 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
14475 (properties `((upstream-name . "TFBSTools")))
14476 (build-system r-build-system)
14486 r-dirichletmultinomial
14498 (native-inputs (list r-knitr))
14499 (home-page "https://github.com/ge11232002/TFBSTools")
14500 (synopsis "Transcription factor binding site (TFBS) analysis")
14502 "TFBSTools is a package for the analysis and manipulation of
14503 transcription factor binding sites. It includes matrices conversion
14504 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
14505 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
14506 scan putative TFBS from sequence/alignment, query JASPAR database and
14507 provides a wrapper of de novo motif discovery software.")
14508 (license license:gpl2)))
14510 (define-public r-maftools
14512 (name "r-maftools")
14517 (uri (bioconductor-uri "maftools" version))
14519 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
14520 (properties `((upstream-name . "maftools")))
14521 (build-system r-build-system)
14529 (native-inputs (list r-knitr))
14530 (home-page "https://github.com/PoisonAlien/maftools")
14531 (synopsis "Summarize, analyze and visualize MAF files")
14533 "Analyze and visualize Mutation Annotation Format (MAF) files from large
14534 scale sequencing studies. This package provides various functions to perform
14535 most commonly used analyses in cancer genomics and to create feature rich
14536 customizable visualzations with minimal effort.")
14537 (license license:expat)))
14539 (define-public r-motifmatchr
14541 (name "r-motifmatchr")
14546 (uri (bioconductor-uri "motifmatchr" version))
14549 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
14550 (properties `((upstream-name . "motifmatchr")))
14551 (build-system r-build-system)
14563 r-summarizedexperiment
14565 (native-inputs (list r-knitr))
14566 (home-page "https://bioconductor.org/packages/motifmatchr")
14567 (synopsis "Fast motif matching in R")
14569 "Quickly find motif matches for many motifs and many sequences.
14570 This package wraps C++ code from the MOODS motif calling library.")
14571 (license license:gpl3)))
14573 (define-public r-chromvar
14575 (name "r-chromvar")
14580 (uri (bioconductor-uri "chromVAR" version))
14582 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
14583 (properties `((upstream-name . "chromVAR")))
14584 (build-system r-build-system)
14586 (list r-biocgenerics
14606 r-summarizedexperiment
14608 (native-inputs (list r-knitr))
14609 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
14610 (synopsis "Determine chromatin variation across regions")
14612 "This package @code{r-chromvar} determines variation in chromatin
14613 accessibility across sets of annotations or peaks. @code{r-chromvar} is
14614 designed primarily for single-cell or sparse chromatin accessibility data like
14615 single cell assay for transposase-accessible chromatin using
14616 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
14617 sequence (@code{DNAse-seq}) experiments.")
14618 (license license:expat)))
14620 (define-public r-singlecellexperiment
14622 (name "r-singlecellexperiment")
14627 (uri (bioconductor-uri "SingleCellExperiment" version))
14630 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
14632 `((upstream-name . "SingleCellExperiment")))
14633 (build-system r-build-system)
14635 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
14636 r-summarizedexperiment))
14639 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
14640 (synopsis "S4 classes for single cell data")
14641 (description "This package defines an S4 class for storing data from
14642 single-cell experiments. This includes specialized methods to store and
14643 retrieve spike-in information, dimensionality reduction coordinates and size
14644 factors for each cell, along with the usual metadata for genes and
14646 (license license:gpl3)))
14648 (define-public r-singler
14655 (uri (bioconductor-uri "SingleR" version))
14657 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
14658 (properties `((upstream-name . "SingleR")))
14659 (build-system r-build-system)
14666 r-delayedmatrixstats
14670 r-summarizedexperiment))
14671 (native-inputs (list r-knitr))
14672 (home-page "https://github.com/LTLA/SingleR")
14673 (synopsis "Reference-based single-cell RNA-seq annotation")
14675 "This package performs unbiased cell type recognition from single-cell
14676 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
14677 cell types to infer the cell of origin of each single cell independently.")
14678 (license license:gpl3)))
14680 (define-public r-scuttle
14687 (uri (bioconductor-uri "scuttle" version))
14690 "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"))))
14691 (properties `((upstream-name . "scuttle")))
14692 (build-system r-build-system)
14698 r-delayedmatrixstats
14703 r-singlecellexperiment
14704 r-summarizedexperiment))
14705 (native-inputs (list r-knitr))
14706 (home-page "https://bioconductor.org/packages/scuttle")
14707 (synopsis "Single-cell RNA-Seq analysis utilities")
14709 "This package provides basic utility functions for performing single-cell
14710 analyses, focusing on simple normalization, quality control and data
14711 transformations. It also provides some helper functions to assist development
14712 of other packages.")
14713 (license license:gpl3)))
14715 (define-public r-scater
14721 (uri (bioconductor-uri "scater" version))
14724 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
14725 (build-system r-build-system)
14733 r-delayedmatrixstats
14745 r-singlecellexperiment
14746 r-summarizedexperiment
14750 (home-page "https://github.com/davismcc/scater")
14751 (synopsis "Single-cell analysis toolkit for gene expression data in R")
14752 (description "This package provides a collection of tools for doing
14753 various analyses of single-cell RNA-seq gene expression data, with a focus on
14755 (license license:gpl2+)))
14757 (define-public r-scran
14764 (uri (bioconductor-uri "scran" version))
14767 "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"))))
14768 (build-system r-build-system)
14777 r-delayedmatrixstats
14787 r-singlecellexperiment
14789 r-summarizedexperiment))
14792 (home-page "https://bioconductor.org/packages/scran")
14793 (synopsis "Methods for single-cell RNA-Seq data analysis")
14794 (description "This package implements a variety of low-level analyses of
14795 single-cell RNA-seq data. Methods are provided for normalization of
14796 cell-specific biases, assignment of cell cycle phase, and detection of highly
14797 variable and significantly correlated genes.")
14798 (license license:gpl3)))
14800 (define-public r-sparsematrixstats
14802 (name "r-sparsematrixstats")
14807 (uri (bioconductor-uri "sparseMatrixStats" version))
14810 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
14812 `((upstream-name . "sparseMatrixStats")))
14813 (build-system r-build-system)
14815 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
14816 (native-inputs (list r-knitr))
14817 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
14818 (synopsis "Summary statistics for rows and columns of sparse matrices")
14820 "This package provides high performance functions for row and column
14821 operations on sparse matrices. Currently, the optimizations are limited to
14822 data in the column sparse format.")
14823 (license license:expat)))
14825 (define-public r-delayedmatrixstats
14827 (name "r-delayedmatrixstats")
14832 (uri (bioconductor-uri "DelayedMatrixStats" version))
14835 "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"))))
14837 `((upstream-name . "DelayedMatrixStats")))
14838 (build-system r-build-system)
14840 (list r-delayedarray
14846 r-sparsematrixstats))
14849 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
14850 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
14852 "This package provides a port of the @code{matrixStats} API for use with
14853 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
14854 contains high-performing functions operating on rows and columns of
14855 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
14856 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
14857 are optimized per data type and for subsetted calculations such that both
14858 memory usage and processing time is minimized.")
14859 (license license:expat)))
14861 (define-public r-mscoreutils
14863 (name "r-mscoreutils")
14868 (uri (bioconductor-uri "MsCoreUtils" version))
14871 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
14872 (properties `((upstream-name . "MsCoreUtils")))
14873 (build-system r-build-system)
14875 (list r-clue r-mass r-rcpp r-s4vectors))
14878 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
14879 (synopsis "Core utils for mass spectrometry data")
14881 "This package defines low-level functions for mass spectrometry data and
14882 is independent of any high-level data structures. These functions include
14883 mass spectra processing functions (noise estimation, smoothing, binning),
14884 quantitative aggregation functions (median polish, robust summarisation,
14885 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
14886 well as misc helper functions, that are used across high-level data structure
14887 within the R for Mass Spectrometry packages.")
14888 (license license:artistic2.0)))
14890 (define-public r-msfeatures
14892 (name "r-msfeatures")
14897 (uri (bioconductor-uri "MsFeatures" version))
14899 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
14900 (properties `((upstream-name . "MsFeatures")))
14901 (build-system r-build-system)
14903 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
14906 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
14907 (synopsis "Functionality for mass spectrometry features")
14909 "The MsFeature package defines functionality for Mass Spectrometry
14910 features. This includes functions to group (LC-MS) features based on some of
14911 their properties, such as retention time (coeluting features), or correlation
14912 of signals across samples. This package hence can be used to group features, and
14913 its results can be used as an input for the @code{QFeatures} package which
14914 allows aggregating abundance levels of features within each group. This
14915 package defines concepts and functions for base and common data types,
14916 implementations for more specific data types are expected to be implemented in
14917 the respective packages (such as e.g. @code{xcms}).")
14918 (license license:artistic2.0)))
14920 (define-public r-biocio
14927 (uri (bioconductor-uri "BiocIO" version))
14930 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
14931 (properties `((upstream-name . "BiocIO")))
14932 (build-system r-build-system)
14934 (list r-biocgenerics r-s4vectors))
14937 (home-page "https://bioconductor.org/packages/BiocIO")
14938 (synopsis "Standard input and output for Bioconductor packages")
14940 "This package implements `import()` and `export()` standard generics for
14941 importing and exporting biological data formats. `import()` supports
14942 whole-file as well as chunk-wise iterative import. The `import()` interface
14943 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
14944 row or element-like components of the file resource), `select()` (on
14945 column-like components of the file resource) and `collect()`. The `import()`
14946 interface optionally provides transparent access to remote (e.g. via https)
14947 as well as local access. Developers can register a file extension, e.g.,
14948 `.loom` for dispatch from character-based URIs to specific `import()` /
14949 `export()` methods based on classes representing file types, e.g.,
14951 (license license:artistic2.0)))
14953 (define-public r-msmseda
14960 (uri (bioconductor-uri "msmsEDA" version))
14963 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
14964 (properties `((upstream-name . "msmsEDA")))
14965 (build-system r-build-system)
14967 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
14969 "https://bioconductor.org/packages/msmsEDA")
14970 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
14972 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
14973 experiments, and visualize de influence of the involved factors.")
14974 (license license:gpl2)))
14976 (define-public r-msmstests
14978 (name "r-msmstests")
14983 (uri (bioconductor-uri "msmsTests" version))
14986 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
14987 (properties `((upstream-name . "msmsTests")))
14988 (build-system r-build-system)
14990 (list r-edger r-msmseda r-msnbase r-qvalue))
14992 "https://bioconductor.org/packages/msmsTests")
14993 (synopsis "Differential LC-MS/MS expression tests")
14995 "This package provides statistical tests for label-free LC-MS/MS data
14996 by spectral counts, to discover differentially expressed proteins between two
14997 biological conditions. Three tests are available: Poisson GLM regression,
14998 quasi-likelihood GLM regression, and the negative binomial of the edgeR
14999 package. The three models admit blocking factors to control for nuisance
15000 variables. To assure a good level of reproducibility a post-test filter is
15001 available, where we may set the minimum effect size considered biologicaly
15002 relevant, and the minimum expression of the most abundant condition.")
15003 (license license:gpl2)))
15005 (define-public r-catalyst
15007 (name "r-catalyst")
15012 (uri (bioconductor-uri "CATALYST" version))
15015 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
15016 (properties `((upstream-name . "CATALYST")))
15017 (build-system r-build-system)
15021 r-consensusclusterplus
15043 r-singlecellexperiment
15044 r-summarizedexperiment))
15047 (home-page "https://github.com/HelenaLC/CATALYST")
15048 (synopsis "Cytometry data analysis tools")
15050 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
15051 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
15052 isotopes rather than fluorescent tags as reporters to label antibodies,
15053 thereby substantially decreasing spectral overlap and allowing for examination
15054 of over 50 parameters at the single cell level. While spectral overlap is
15055 significantly less pronounced in CyTOF than flow cytometry, spillover due to
15056 detection sensitivity, isotopic impurities, and oxide formation can impede
15057 data interpretability. @code{CATALYST} was designed to provide a pipeline for
15058 preprocessing of cytometry data, including:
15061 @item normalization using bead standards;
15062 @item single-cell deconvolution;
15063 @item bead-based compensation.
15066 (license license:gpl2+)))
15068 (define-public r-erma
15075 (uri (bioconductor-uri "erma" version))
15078 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
15079 (build-system r-build-system)
15081 (list r-annotationdbi
15094 r-summarizedexperiment))
15097 (home-page "https://bioconductor.org/packages/erma")
15098 (synopsis "Epigenomic road map adventures")
15100 "The epigenomics road map describes locations of epigenetic marks in DNA
15101 from a variety of cell types. Of interest are locations of histone
15102 modifications, sites of DNA methylation, and regions of accessible chromatin.
15103 This package presents a selection of elements of the road map including
15104 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
15105 by Ernst and Kellis.")
15106 (license license:artistic2.0)))
15108 (define-public r-ggbio
15115 (uri (bioconductor-uri "ggbio" version))
15118 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
15119 (build-system r-build-system)
15122 (modify-phases %standard-phases
15123 ;; See https://github.com/tengfei/ggbio/issues/117
15124 ;; This fix will be included in the next release.
15125 (add-after 'unpack 'fix-typo
15127 (substitute* "R/GGbio-class.R"
15128 (("fechable") "fetchable"))
15131 (list r-annotationdbi
15140 r-genomicalignments
15156 r-summarizedexperiment
15157 r-variantannotation))
15160 (home-page "http://www.tengfei.name/ggbio/")
15161 (synopsis "Visualization tools for genomic data")
15163 "The ggbio package extends and specializes the grammar of graphics for
15164 biological data. The graphics are designed to answer common scientific
15165 questions, in particular those often asked of high throughput genomics data.
15166 All core Bioconductor data structures are supported, where appropriate. The
15167 package supports detailed views of particular genomic regions, as well as
15168 genome-wide overviews. Supported overviews include ideograms and grand linear
15169 views. High-level plots include sequence fragment length, edge-linked
15170 interval to data view, mismatch pileup, and several splicing summaries.")
15171 (license license:artistic2.0)))
15173 (define-public r-gqtlbase
15175 (name "r-gqtlbase")
15180 (uri (bioconductor-uri "gQTLBase" version))
15183 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
15184 (properties `((upstream-name . "gQTLBase")))
15185 (build-system r-build-system)
15188 (modify-phases %standard-phases
15189 ;; This is an upstream bug.
15190 (add-after 'unpack 'fix-imports
15192 (substitute* "NAMESPACE"
15193 ((".*maxffmode.*") "")
15194 (("importFrom\\(ff,.*") "import(ff)\n"))
15209 r-summarizedexperiment))
15212 (home-page "https://bioconductor.org/packages/gQTLBase")
15213 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
15215 "The purpose of this package is to simplify the storage and interrogation
15216 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
15218 (license license:artistic2.0)))
15220 (define-public r-gqtlstats
15222 (name "r-gqtlstats")
15227 (uri (bioconductor-uri "gQTLstats" version))
15230 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
15231 (properties `((upstream-name . "gQTLstats")))
15232 (build-system r-build-system)
15234 (list r-annotationdbi
15262 r-summarizedexperiment
15263 r-variantannotation))
15266 (home-page "https://bioconductor.org/packages/gQTLstats")
15267 (synopsis "Computationally efficient analysis for eQTL and allied studies")
15269 "This package provides tools for the computationally efficient analysis
15270 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
15271 The software in this package aims to support refinements and functional
15272 interpretation of members of a collection of association statistics on a
15273 family of feature/genome hypotheses.")
15274 (license license:artistic2.0)))
15276 (define-public r-gviz
15283 (uri (bioconductor-uri "Gviz" version))
15286 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
15287 (properties `((upstream-name . "Gviz")))
15288 (build-system r-build-system)
15290 (list r-annotationdbi
15300 r-genomicalignments
15314 (home-page "https://bioconductor.org/packages/Gviz")
15315 (synopsis "Plotting data and annotation information along genomic coordinates")
15317 "Genomic data analyses requires integrated visualization of known genomic
15318 information and new experimental data. Gviz uses the biomaRt and the
15319 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
15320 and translates this to e.g. gene/transcript structures in viewports of the
15321 grid graphics package. This results in genomic information plotted together
15323 (license license:artistic2.0)))
15325 (define-public r-gwascat
15332 (uri (bioconductor-uri "gwascat" version))
15335 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
15336 (build-system r-build-system)
15338 (list r-annotationdbi
15349 r-variantannotation))
15352 (home-page "https://bioconductor.org/packages/gwascat")
15353 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
15355 "This package provides tools for representing and modeling data in the
15356 EMBL-EBI GWAS catalog.")
15357 (license license:artistic2.0)))
15359 (define-public r-kegggraph
15361 (name "r-kegggraph")
15366 (uri (bioconductor-uri "KEGGgraph" version))
15368 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
15369 (properties `((upstream-name . "KEGGgraph")))
15370 (build-system r-build-system)
15372 (list r-graph r-rcurl r-rgraphviz r-xml))
15373 (home-page "https://bioconductor.org/packages/KEGGgraph")
15374 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
15376 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
15377 object as well as a collection of tools to analyze, dissect and visualize these
15378 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
15379 maintaining all essential pathway attributes. The package offers
15380 functionalities including parsing, graph operation, visualization and etc.")
15381 (license license:gpl2+)))
15383 (define-public r-ldblock
15390 (uri (bioconductor-uri "ldblock" version))
15393 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
15394 (build-system r-build-system)
15396 (list r-biocgenerics
15397 r-ensdb-hsapiens-v75
15405 r-variantannotation))
15408 (home-page "https://bioconductor.org/packages/ldblock")
15409 (synopsis "Data structures for linkage disequilibrium measures in populations")
15411 "This package defines data structures for @dfn{linkage
15412 disequilibrium} (LD) measures in populations. Its purpose is to simplify
15413 handling of existing population-level data for the purpose of flexibly
15414 defining LD blocks.")
15415 (license license:artistic2.0)))
15417 ;; This is a CRAN package, but it depends on r-snpstats, which is a
15418 ;; Bioconductor package.
15419 (define-public r-ldheatmap
15421 (name "r-ldheatmap")
15426 (uri (cran-uri "LDheatmap" version))
15429 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
15430 (properties `((upstream-name . "LDheatmap")))
15431 (build-system r-build-system)
15433 (list r-genetics r-rcpp r-snpstats))
15434 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
15435 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
15437 "This package provides tools to produce a graphical display, as a heat
15438 map, of measures of pairwise linkage disequilibria between SNPs. Users may
15439 optionally include the physical locations or genetic map distances of each SNP
15441 (license license:gpl3)))
15443 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
15444 ;; Bioconductor package.
15445 (define-public r-abn
15452 (uri (cran-uri "abn" version))
15455 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
15456 (build-system r-build-system)
15469 (home-page "https://r-bayesian-networks.org/")
15470 (synopsis "Modelling multivariate data with additive bayesian networks")
15472 "Bayesian network analysis is a form of probabilistic graphical models
15473 which derives from empirical data a directed acyclic graph, DAG, describing
15474 the dependency structure between random variables. An additive Bayesian
15475 network model consists of a form of a DAG where each node comprises a
15476 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
15477 equivalent to Bayesian multivariate regression using graphical modelling, they
15478 generalises the usual multivariable regression, GLM, to multiple dependent
15479 variables. This package provides routines to help determine optimal Bayesian
15480 network models for a given data set, where these models are used to identify
15481 statistical dependencies in messy, complex data.")
15482 (license license:gpl2+)))
15484 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
15485 ;; Bioconductor package.
15486 (define-public r-spp
15492 (uri (cran-uri "spp" version))
15495 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
15496 (build-system r-build-system)
15500 (list r-bh r-catools r-rcpp r-rsamtools))
15501 (home-page "https://cran.r-project.org/web/packages/spp/")
15502 (synopsis "ChIP-Seq processing pipeline")
15503 (description "This package provides tools for analysis of ChIP-seq and
15504 other functional sequencing data.")
15505 (license license:gpl2)))
15507 (define-public r-pathview
15509 (name "r-pathview")
15514 (uri (bioconductor-uri "pathview" version))
15516 (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"))))
15517 (properties `((upstream-name . "pathview")))
15518 (build-system r-build-system)
15520 (list r-annotationdbi
15528 (home-page "https://pathview.uncc.edu/")
15529 (synopsis "Tool set for pathway based data integration and visualization")
15531 "@code{r-pathview} is a tool set for pathway based data integration and
15532 visualization. It maps and renders a wide variety of biological data on
15533 relevant pathway graphs. All users need is to supply their data and specify
15534 the target pathway. This package automatically downloads the pathway graph
15535 data, parses the data file, maps user data to the pathway, and render pathway
15536 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
15537 integrates with pathway and gene set (enrichment) analysis tools for
15538 large-scale and fully automated analysis.")
15539 (license license:gpl3+)))
15541 (define-public r-snpstats
15543 (name "r-snpstats")
15548 (uri (bioconductor-uri "snpStats" version))
15551 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
15552 (properties `((upstream-name . "snpStats")))
15553 (build-system r-build-system)
15554 (inputs (list zlib))
15556 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
15557 (home-page "https://bioconductor.org/packages/snpStats")
15558 (synopsis "Methods for SNP association studies")
15560 "This package provides classes and statistical methods for large
15561 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
15562 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
15563 (license license:gpl3)))
15565 (define-public r-chromstar
15567 (name "r-chromstar")
15572 (uri (bioconductor-uri "chromstaR" version))
15575 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
15576 (properties `((upstream-name . "chromstaR")))
15577 (build-system r-build-system)
15585 r-genomicalignments
15593 (native-inputs (list r-knitr))
15594 (home-page "https://github.com/ataudt/chromstaR")
15595 (synopsis "Chromatin state analysis for ChIP-Seq data")
15597 "This package implements functions for combinatorial and differential
15598 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
15599 export to genome browser viewable files, and functions for enrichment
15601 (license license:artistic2.0)))
15603 (define-public r-guitar
15610 (uri (bioconductor-uri "Guitar" version))
15613 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
15614 (properties `((upstream-name . "Guitar")))
15615 (build-system r-build-system)
15617 (list r-annotationdbi
15627 (home-page "https://bioconductor.org/packages/Guitar")
15628 (synopsis "Visualize genomic features")
15630 "This package is designed for visualization of RNA-related genomic
15631 features with respect to the landmarks of RNA transcripts, i.e., transcription
15632 starting site, start codon, stop codon and transcription ending site.")
15633 (license license:gpl2)))
15635 (define-public r-sushi
15641 (uri (bioconductor-uri "Sushi" version))
15644 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
15645 (properties `((upstream-name . "Sushi")))
15646 (build-system r-build-system)
15648 (list r-biomart r-zoo))
15649 (home-page "https://bioconductor.org/packages/Sushi")
15650 (synopsis "Tools for visualizing genomics data")
15652 "This package provides flexible, quantitative, and integrative genomic
15653 visualizations for publication-quality multi-panel figures.")
15654 (license license:gpl2+)))
15656 (define-public r-ballgown
15658 (name "r-ballgown")
15663 (uri (bioconductor-uri "ballgown" version))
15666 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
15667 (properties `((upstream-name . "ballgown")))
15668 (build-system r-build-system)
15681 (home-page "https://bioconductor.org/packages/ballgown")
15682 (synopsis "Flexible, isoform-level differential expression analysis")
15684 "This package provides tools for statistical analysis of assembled
15685 transcriptomes, including flexible differential expression analysis,
15686 visualization of transcript structures, and matching of assembled transcripts
15688 (license license:artistic2.0)))
15690 (define-public r-megadepth
15692 (name "r-megadepth")
15697 (uri (bioconductor-uri "megadepth" version))
15700 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
15701 (properties `((upstream-name . "megadepth")))
15702 (build-system r-build-system)
15703 (inputs (list megadepth))
15714 (home-page "https://github.com/LieberInstitute/megadepth")
15715 (synopsis "BigWig and BAM related utilities")
15717 "This package provides an R interface to Megadepth. It is particularly
15718 useful for computing the coverage of a set of genomic regions across bigWig or
15719 BAM files. With this package, you can build base-pair coverage matrices for
15720 regions or annotations of your choice from BigWig files.")
15721 (license license:artistic2.0)))
15723 (define-public r-beclear
15730 (uri (bioconductor-uri "BEclear" version))
15733 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
15734 (properties `((upstream-name . "BEclear")))
15735 (build-system r-build-system)
15747 (home-page "https://github.com/uds-helms/BEclear")
15748 (synopsis "Correction of batch effects in DNA methylation data")
15750 "This package provides functions to detect and correct for batch effects
15751 in DNA methylation data. The core function is based on latent factor models
15752 and can also be used to predict missing values in any other matrix containing
15754 (license license:gpl3)))
15756 (define-public r-bgeecall
15758 (name "r-bgeecall")
15763 (uri (bioconductor-uri "BgeeCall" version))
15766 "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"))))
15767 (properties `((upstream-name . "BgeeCall")))
15768 (build-system r-build-system)
15782 (native-inputs (list r-knitr))
15783 (home-page "https://github.com/BgeeDB/BgeeCall")
15784 (synopsis "RNA-Seq present/absent gene expression calls generation")
15786 "BgeeCall allows generating present/absent gene expression calls without
15787 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
15788 intergenic sequences. These sequences are generated based on expression of
15789 all RNA-Seq libraries of each species integrated in Bgee.")
15790 (license license:gpl3)))
15792 (define-public r-bgeedb
15799 (uri (bioconductor-uri "BgeeDB" version))
15802 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
15803 (properties `((upstream-name . "BgeeDB")))
15804 (build-system r-build-system)
15817 (native-inputs (list r-knitr))
15818 (home-page "https://github.com/BgeeDB/BgeeDB_R")
15819 (synopsis "Annotation and gene expression data retrieval from Bgee database")
15821 "This package provides a package for the annotation and gene expression
15822 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
15823 anatomical terms, mapped to genes by expression patterns.")
15824 (license license:gpl3)))
15826 (define-public r-biobtreer
15828 (name "r-biobtreer")
15833 (uri (bioconductor-uri "biobtreeR" version))
15836 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
15837 (properties `((upstream-name . "biobtreeR")))
15838 (build-system r-build-system)
15840 (list r-httpuv r-httr r-jsonlite r-stringi))
15841 (native-inputs (list r-knitr))
15842 (home-page "https://github.com/tamerh/biobtreeR")
15843 (synopsis "Use biobtree tool from R")
15845 "The biobtreeR package provides an interface to biobtree, a tool which
15846 covers large sets of bioinformatics datasets and allows search and chain
15847 mappings functionalities.")
15848 (license license:expat)))
15850 (define-public r-minet
15857 (uri (bioconductor-uri "minet" version))
15860 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
15861 (properties `((upstream-name . "minet")))
15862 (build-system r-build-system)
15865 (home-page "http://minet.meyerp.com")
15866 (synopsis "Mutual information networks")
15868 "This package implements various algorithms for inferring mutual
15869 information networks from data.")
15870 (license license:artistic2.0)))
15872 (define-public r-genetclassifier
15874 (name "r-genetclassifier")
15879 (uri (bioconductor-uri "geNetClassifier" version))
15882 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
15884 `((upstream-name . "geNetClassifier")))
15885 (build-system r-build-system)
15887 (list r-biobase r-e1071 r-ebarrays r-minet))
15888 (home-page "https://www.cicancer.org")
15889 (synopsis "Classify diseases and build gene networks using expression profiles")
15891 "This is a comprehensive package to automatically train and validate a
15892 multi-class SVM classifier based on gene expression data. It provides
15893 transparent selection of gene markers, their coexpression networks, and an
15894 interface to query the classifier.")
15895 (license license:gpl2+)))
15897 (define-public r-dir-expiry
15899 (name "r-dir-expiry")
15904 (uri (bioconductor-uri "dir.expiry" version))
15907 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
15908 (properties `((upstream-name . "dir.expiry")))
15909 (build-system r-build-system)
15910 (propagated-inputs (list r-filelock))
15911 (native-inputs (list r-knitr))
15912 (home-page "https://bioconductor.org/packages/dir.expiry")
15913 (synopsis "Managing expiration for cache directories")
15915 "This package implements an expiration system for access to versioned
15916 directories. Directories that have not been accessed by a registered function
15917 within a certain time frame are deleted. This aims to reduce disk usage by
15918 eliminating obsolete caches generated by old versions of packages.")
15919 (license license:gpl3)))
15921 (define-public r-basilisk-utils
15923 (name "r-basilisk-utils")
15928 (uri (bioconductor-uri "basilisk.utils" version))
15931 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
15933 `((upstream-name . "basilisk.utils")))
15934 (build-system r-build-system)
15936 (list r-dir-expiry))
15937 (native-inputs (list r-knitr))
15938 (home-page "https://bioconductor.org/packages/basilisk.utils")
15939 (synopsis "Basilisk installation utilities")
15941 "This package implements utilities for installation of the basilisk
15942 package, primarily for creation of the underlying Conda instance.")
15943 (license license:gpl3)))
15945 (define-public r-basilisk
15947 (name "r-basilisk")
15952 (uri (bioconductor-uri "basilisk" version))
15955 "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"))))
15956 (properties `((upstream-name . "basilisk")))
15957 (build-system r-build-system)
15959 (list r-basilisk-utils r-dir-expiry r-reticulate))
15960 (native-inputs (list r-knitr))
15961 (home-page "https://bioconductor.org/packages/basilisk")
15962 (synopsis "Freeze Python dependencies inside Bioconductor packages")
15964 "This package installs a self-contained Conda instance that is managed by
15965 the R/Bioconductor installation machinery. This aims to provide a consistent
15966 Python environment that can be used reliably by Bioconductor packages.
15967 Functions are also provided to enable smooth interoperability of multiple
15968 Python environments in a single R session.")
15969 (license license:gpl3)))
15971 (define-public r-biocthis
15973 (name "r-biocthis")
15978 (uri (bioconductor-uri "biocthis" version))
15981 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
15982 (properties `((upstream-name . "biocthis")))
15983 (build-system r-build-system)
15986 (modify-phases %standard-phases
15987 (add-after 'unpack 'set-HOME
15988 (lambda _ (setenv "HOME" "/tmp"))))))
15990 (list r-biocmanager
15996 (native-inputs (list r-knitr))
15997 (home-page "https://github.com/lcolladotor/biocthis")
15998 (synopsis "Automate package and project setup for Bioconductor packages")
16000 "This package expands the @code{usethis} package with the goal of helping
16001 automate the process of creating R packages for Bioconductor or making them
16002 Bioconductor-friendly.")
16003 (license license:artistic2.0)))
16005 (define-public r-biocdockermanager
16007 (name "r-biocdockermanager")
16012 (uri (bioconductor-uri "BiocDockerManager" version))
16015 "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"))))
16017 `((upstream-name . "BiocDockerManager")))
16018 (build-system r-build-system)
16026 (native-inputs (list r-knitr))
16027 (home-page "https://bioconductor.org/packages/BiocDockerManager")
16028 (synopsis "Access and manage Bioconductor Docker images")
16030 "This package works analogous to BiocManager but for Docker images. Use
16031 the BiocDockerManager package to install and manage Docker images provided by
16032 the Bioconductor project.")
16033 (license license:artistic2.0)))
16035 (define-public r-biodb
16042 (uri (bioconductor-uri "biodb" version))
16045 "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"))))
16046 (properties `((upstream-name . "biodb")))
16047 (build-system r-build-system)
16049 (list r-biocfilecache
16067 (native-inputs (list r-knitr))
16068 (home-page "https://bioconductor.org/packages/biodb")
16069 (synopsis "Library for connecting to chemical and biological databases")
16071 "The biodb package provides access to standard remote chemical and
16072 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
16073 database files (CSV, SQLite), with easy retrieval of entries, access to web
16074 services, search of compounds by mass and/or name, and mass spectra matching
16075 for LCMS and MSMS. Its architecture as a development framework facilitates
16076 the development of new database connectors for local projects or inside
16077 separate published packages.")
16078 (license license:agpl3+)))
16080 (define-public r-biomformat
16082 (name "r-biomformat")
16087 (uri (bioconductor-uri "biomformat" version))
16090 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
16091 (properties `((upstream-name . "biomformat")))
16092 (build-system r-build-system)
16094 (list r-jsonlite r-matrix r-plyr r-rhdf5))
16095 (native-inputs (list r-knitr))
16096 (home-page "https://github.com/joey711/biomformat/")
16097 (synopsis "Interface package for the BIOM file format")
16099 "This is an R package for interfacing with the BIOM format. This package
16100 includes basic tools for reading biom-format files, accessing and subsetting
16101 data tables from a biom object (which is more complex than a single table), as
16102 well as limited support for writing a biom-object back to a biom-format file.
16103 The design of this API is intended to match the Python API and other tools
16104 included with the biom-format project, but with a decidedly \"R flavor\" that
16105 should be familiar to R users. This includes S4 classes and methods, as well
16106 as extensions of common core functions/methods.")
16107 (license license:gpl2)))
16109 (define-public r-mvcclass
16111 (name "r-mvcclass")
16116 (uri (bioconductor-uri "MVCClass" version))
16119 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
16120 (properties `((upstream-name . "MVCClass")))
16121 (build-system r-build-system)
16122 (home-page "https://bioconductor.org/packages/MVCClass")
16123 (synopsis "Model-View-Controller (MVC) classes")
16125 "This package contains classes used in model-view-controller (MVC)
16127 (license license:lgpl2.1+)))
16129 (define-public r-biomvcclass
16131 (name "r-biomvcclass")
16136 (uri (bioconductor-uri "BioMVCClass" version))
16139 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
16140 (properties `((upstream-name . "BioMVCClass")))
16141 (build-system r-build-system)
16143 (list r-biobase r-graph r-mvcclass r-rgraphviz))
16144 (home-page "https://bioconductor.org/packages/BioMVCClass")
16145 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
16147 "This package contains classes used in model-view-controller (MVC)
16149 (license license:lgpl2.1+)))
16151 (define-public r-biomvrcns
16153 (name "r-biomvrcns")
16158 (uri (bioconductor-uri "biomvRCNS" version))
16161 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
16162 (properties `((upstream-name . "biomvRCNS")))
16163 (build-system r-build-system)
16165 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
16166 (home-page "https://bioconductor.org/packages/biomvRCNS")
16167 (synopsis "Copy number study and segmentation for multivariate biological data")
16169 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
16170 homogeneous segmentation model are designed and implemented for segmentation
16171 genomic data, with the aim of assisting in transcripts detection using high
16172 throughput technology like RNA-seq or tiling array, and copy number analysis
16173 using aCGH or sequencing.")
16174 (license license:gpl2+)))
16176 (define-public r-bionero
16183 (uri (bioconductor-uri "BioNERO" version))
16186 "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"))))
16187 (properties `((upstream-name . "BioNERO")))
16188 (build-system r-build-system)
16190 (list r-biocparallel
16207 r-summarizedexperiment
16212 (home-page "https://github.com/almeidasilvaf/BioNERO")
16213 (synopsis "Biological network reconstruction omnibus")
16215 "BioNERO aims to integrate all aspects of biological network inference in
16216 a single package, including data preprocessing, exploratory analyses, network
16217 inference, and analyses for biological interpretations. BioNERO can be used
16218 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
16219 from gene expression data. Additionally, it can be used to explore
16220 topological properties of protein-protein interaction (PPI) networks. GCN
16221 inference relies on the popular WGCNA algorithm. GRN inference is based on
16222 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
16223 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
16224 rank for each interaction pair. As all steps of network analyses are included
16225 in this package, BioNERO makes users avoid having to learn the syntaxes of
16226 several packages and how to communicate between them. Finally, users can also
16227 identify consensus modules across independent expression sets and calculate
16228 intra and interspecies module preservation statistics between different
16230 (license license:gpl3)))
16232 (define-public r-bionet
16239 (uri (bioconductor-uri "BioNet" version))
16242 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
16243 (properties `((upstream-name . "BioNet")))
16244 (build-system r-build-system)
16246 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
16247 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
16248 (synopsis "Functional analysis of biological networks")
16250 "This package provides functions for the integrated analysis of
16251 protein-protein interaction networks and the detection of functional modules.
16252 Different datasets can be integrated into the network by assigning p-values of
16253 statistical tests to the nodes of the network. E.g. p-values obtained from
16254 the differential expression of the genes from an Affymetrix array are assigned
16255 to the nodes of the network. By fitting a beta-uniform mixture model and
16256 calculating scores from the p-values, overall scores of network regions can be
16257 calculated and an integer linear programming algorithm identifies the maximum
16258 scoring subnetwork.")
16259 (license license:gpl2+)))
16261 (define-public r-bionetstat
16263 (name "r-bionetstat")
16268 (uri (bioconductor-uri "BioNetStat" version))
16271 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
16272 (properties `((upstream-name . "BioNetStat")))
16273 (build-system r-build-system)
16275 (list r-biocparallel
16295 (home-page "https://github.com/jardimViniciusC/BioNetStat")
16296 (synopsis "Biological network analysis")
16298 "This package provides a package to perform differential network
16299 analysis, differential node analysis (differential coexpression analysis),
16300 network and metabolic pathways view.")
16301 (license license:gpl3+)))
16303 (define-public r-bioqc
16310 (uri (bioconductor-uri "BioQC" version))
16313 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
16314 (properties `((upstream-name . "BioQC")))
16315 (build-system r-build-system)
16317 (list r-biobase r-edger r-rcpp))
16320 (home-page "https://accio.github.io/BioQC/")
16321 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
16323 "BioQC performs quality control of high-throughput expression data based
16324 on tissue gene signatures. It can detect tissue heterogeneity in gene
16325 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
16326 optimised for high performance.")
16327 (license license:gpl3+)))
16329 (define-public r-biotip
16336 (uri (bioconductor-uri "BioTIP" version))
16339 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
16340 (properties `((upstream-name . "BioTIP")))
16341 (build-system r-build-system)
16352 (home-page "https://github.com/xyang2uchicago/BioTIP")
16353 (synopsis "R package for characterization of biological tipping-point")
16355 "This package adopts tipping-point theory to transcriptome profiles to
16356 help unravel disease regulatory trajectory.")
16357 (license license:gpl2)))
16359 (define-public r-biotmle
16366 (uri (bioconductor-uri "biotmle" version))
16369 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
16370 (properties `((upstream-name . "biotmle")))
16371 (build-system r-build-system)
16382 r-summarizedexperiment
16387 (home-page "https://code.nimahejazi.org/biotmle/")
16388 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
16390 "This package provides tools for differential expression biomarker
16391 discovery based on microarray and next-generation sequencing data that
16392 leverage efficient semiparametric estimators of the average treatment effect
16393 for variable importance analysis. Estimation and inference of the (marginal)
16394 average treatment effects of potential biomarkers are computed by targeted
16395 minimum loss-based estimation, with joint, stable inference constructed across
16396 all biomarkers using a generalization of moderated statistics for use with the
16397 estimated efficient influence function. The procedure accommodates the use of
16398 ensemble machine learning for the estimation of nuisance functions.")
16399 (license license:expat)))
16401 (define-public r-bsseq
16408 (uri (bioconductor-uri "bsseq" version))
16411 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
16412 (properties `((upstream-name . "bsseq")))
16413 (build-system r-build-system)
16423 r-delayedmatrixstats
16437 r-summarizedexperiment))
16440 (home-page "https://github.com/hansenlab/bsseq")
16441 (synopsis "Analyze, manage and store bisulfite sequencing data")
16443 "This package provides a collection of tools for analyzing and
16444 visualizing bisulfite sequencing data.")
16445 (license license:artistic2.0)))
16447 (define-public r-dmrseq
16454 (uri (bioconductor-uri "dmrseq" version))
16457 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
16458 (properties `((upstream-name . "dmrseq")))
16459 (build-system r-build-system)
16461 (list r-annotationhub
16466 r-delayedmatrixstats
16480 (home-page "https://bioconductor.org/packages/dmrseq")
16481 (synopsis "Detection and inference of differentially methylated regions")
16483 "This package implements an approach for scanning the genome to detect
16484 and perform accurate inference on differentially methylated regions from Whole
16485 Genome Bisulfite Sequencing data. The method is based on comparing detected
16486 regions to a pooled null distribution, that can be implemented even when as
16487 few as two samples per population are available. Region-level statistics are
16488 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
16489 with a nested autoregressive correlated error structure for the effect of
16490 interest on transformed methylation proportions.")
16491 (license license:expat)))
16493 (define-public r-omnipathr
16495 (name "r-omnipathr")
16500 (uri (bioconductor-uri "OmnipathR" version))
16502 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
16503 (properties `((upstream-name . "OmnipathR")))
16504 (build-system r-build-system)
16507 (modify-phases %standard-phases
16508 (add-after 'unpack 'set-HOME
16509 (lambda _ (setenv "HOME" "/tmp"))))))
16535 (native-inputs (list r-knitr))
16536 (home-page "https://saezlab.github.io/OmnipathR/")
16537 (synopsis "OmniPath web service client and more")
16539 "This package provides a client for the OmniPath web service and many
16540 other resources. It also includes functions to transform and pretty print
16541 some of the downloaded data, functions to access a number of other resources.
16542 Furthermore, OmnipathR features a close integration with the NicheNet method
16543 for ligand activity prediction from transcriptomics data.")
16544 (license license:expat)))
16546 (define-public r-biscuiteer
16548 (name "r-biscuiteer")
16553 (uri (bioconductor-uri "biscuiteer" version))
16556 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
16557 (properties `((upstream-name . "biscuiteer")))
16558 (build-system r-build-system)
16566 r-delayedmatrixstats
16585 r-summarizedexperiment
16586 r-variantannotation))
16589 (home-page "https://github.com/trichelab/biscuiteer")
16590 (synopsis "Convenience functions for the Biscuit package")
16592 "This package provides a test harness for bsseq loading of Biscuit
16593 output, summarization of WGBS data over defined regions and in mappable
16594 samples, with or without imputation, dropping of mostly-NA rows, age
16596 (license license:gpl3)))
16598 (define-public r-tcgabiolinks
16600 (name "r-tcgabiolinks")
16605 (uri (bioconductor-uri "TCGAbiolinks" version))
16607 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
16608 (properties `((upstream-name . "TCGAbiolinks")))
16609 (build-system r-build-system)
16628 r-summarizedexperiment
16629 r-tcgabiolinksgui-data
16634 (native-inputs (list r-knitr))
16635 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
16636 (synopsis "Integrative analysis with GDC data")
16638 "The aim of TCGAbiolinks is:
16641 @item facilitate GDC open-access data retrieval;
16642 @item prepare the data using the appropriate pre-processing strategies;
16643 @item provide the means to carry out different standard analyses, and;
16644 @item to easily reproduce earlier research results.
16647 In more detail, the package provides multiple methods for analysis (e.g.,
16648 differential expression analysis, identifying differentially methylated
16649 regions) and methods for visualization (e.g., survival plots, volcano plots,
16650 starburst plots) in order to easily develop complete analysis pipelines.")
16651 (license license:gpl3+)))
16653 (define-public r-tricycle
16655 (name "r-tricycle")
16659 (uri (bioconductor-uri "tricycle" version))
16662 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
16663 (properties `((upstream-name . "tricycle")))
16664 (build-system r-build-system)
16666 (list r-annotationdbi
16677 r-singlecellexperiment
16678 r-summarizedexperiment))
16679 (native-inputs (list r-knitr))
16680 (home-page "https://github.com/hansenlab/tricycle")
16681 (synopsis "Transferable representation and inference of cell cycle")
16683 "The package contains functions to infer and visualize cell cycle process
16684 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
16685 projecting new data to the previous learned biologically interpretable space.
16686 The @code{tricycle} provides a pre-learned cell cycle space, which could be
16687 used to infer cell cycle time of human and mouse single cell samples. In
16688 addition, it also offer functions to visualize cell cycle time on different
16689 embeddings and functions to build new reference.")
16690 (license license:gpl3)))
16692 (define-public r-tximeta
16699 (uri (bioconductor-uri "tximeta" version))
16702 "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl"))))
16703 (properties `((upstream-name . "tximeta")))
16704 (build-system r-build-system)
16706 (list r-annotationdbi
16718 r-summarizedexperiment
16723 (home-page "https://github.com/mikelove/tximeta")
16724 (synopsis "Transcript quantification import with automatic metadata")
16726 "This package implements transcript quantification import from Salmon and
16727 alevin with automatic attachment of transcript ranges and release information,
16728 and other associated metadata. De novo transcriptomes can be linked to the
16729 appropriate sources with linkedTxomes and shared for computational
16731 (license license:gpl2)))
16733 (define-public r-phyloseq
16735 (name "r-phyloseq")
16740 (uri (bioconductor-uri "phyloseq" version))
16742 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
16743 (properties `((upstream-name . "phyloseq")))
16744 (build-system r-build-system)
16764 (home-page "https://github.com/joey711/phyloseq")
16765 (synopsis "Handling and analysis of high-throughput microbiome census data")
16767 "Phyloseq provides a set of classes and tools to facilitate the import,
16768 storage, analysis, and graphical display of microbiome census data.")
16769 (license license:agpl3)))
HCoop / jackhill / guix / guix.git / blob