1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il>
7 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
9 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
10 ;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
11 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
12 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
13 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
14 ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com>
16 ;;; This file is part of GNU Guix.
18 ;;; GNU Guix is free software; you can redistribute it and/or modify it
19 ;;; under the terms of the GNU General Public License as published by
20 ;;; the Free Software Foundation; either version 3 of the License, or (at
21 ;;; your option) any later version.
23 ;;; GNU Guix is distributed in the hope that it will be useful, but
24 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
25 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
26 ;;; GNU General Public License for more details.
28 ;;; You should have received a copy of the GNU General Public License
29 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
31 (define-module (gnu packages bioconductor)
32 #:use-module ((guix licenses) #:prefix license:)
33 #:use-module (guix packages)
34 #:use-module (guix download)
35 #:use-module (guix git-download)
36 #:use-module (guix build-system r)
37 #:use-module (gnu packages)
38 #:use-module (gnu packages autotools)
39 #:use-module (gnu packages base)
40 #:use-module (gnu packages bioinformatics)
41 #:use-module (gnu packages boost)
42 #:use-module (gnu packages cran)
43 #:use-module (gnu packages compression)
44 #:use-module (gnu packages curl)
45 #:use-module (gnu packages docker)
46 #:use-module (gnu packages gcc)
47 #:use-module (gnu packages graph)
48 #:use-module (gnu packages graphviz)
49 #:use-module (gnu packages haskell-xyz)
50 #:use-module (gnu packages image)
51 #:use-module (gnu packages java)
52 #:use-module (gnu packages maths)
53 #:use-module (gnu packages netpbm)
54 #:use-module (gnu packages python)
55 #:use-module (gnu packages perl)
56 #:use-module (gnu packages pkg-config)
57 #:use-module (gnu packages statistics)
58 #:use-module (gnu packages web)
59 #:use-module (gnu packages xml)
60 #:use-module (srfi srfi-1))
65 (define-public r-org-eck12-eg-db
67 (name "r-org-eck12-eg-db")
72 (uri (bioconductor-uri "org.EcK12.eg.db" version 'annotation))
74 (base32 "0c4p6jr83k0gm6pvn760yr8xf33wggrfcr6fg7a42a96bcf817gs"))))
76 `((upstream-name . "org.EcK12.eg.db")))
77 (build-system r-build-system)
79 (list r-annotationdbi))
80 (home-page "https://bioconductor.org/packages/org.EcK12.eg.db")
81 (synopsis "Genome wide annotation for E coli strain K12")
83 "This package provides genome wide annotation for E coli strain K12,
84 primarily based on mapping using Entrez Gene identifiers. Entrez Gene is
85 National Center for Biotechnology Information (NCBI)’s database for
86 gene-specific information. Entrez Gene maintains records from genomes which
87 have been completely sequenced, which have an active research community to
88 submit gene-specific information, or which are scheduled for intense sequence
90 (license license:artistic2.0)))
92 (define-public r-org-bt-eg-db
94 (name "r-org-bt-eg-db")
99 (uri (bioconductor-uri
105 "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi"))))
106 (properties `((upstream-name . "org.Bt.eg.db")))
107 (build-system r-build-system)
109 (list r-annotationdbi))
110 (home-page "https://bioconductor.org/packages/org.Bt.eg.db")
111 (synopsis "Genome wide annotation for Bovine")
113 "This package provides genome wide annotations for Bovine, primarily
114 based on mapping using Entrez Gene identifiers.")
115 (license license:artistic2.0)))
117 (define-public r-reactome-db
119 (name "r-reactome-db")
124 (uri (bioconductor-uri "reactome.db" version 'annotation))
127 "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg"))))
128 (properties `((upstream-name . "reactome.db")))
129 (build-system r-build-system)
131 (list r-annotationdbi))
132 (home-page "https://bioconductor.org/packages/reactome.db/")
133 (synopsis "Annotation maps for reactome")
135 "This package provides a set of annotation maps for the REACTOME
136 database, assembled using data from REACTOME.")
137 (license license:cc-by4.0)))
139 (define-public r-bsgenome-btaurus-ucsc-bostau8
141 (name "r-bsgenome-btaurus-ucsc-bostau8")
145 (uri (bioconductor-uri "BSgenome.Btaurus.UCSC.bosTau8"
146 version 'annotation))
149 "16wjy1aw9nvx03r7w8yh5w7sw3pn8i9nczd0n0728l6nnyqxlsz6"))))
151 `((upstream-name . "BSgenome.Btaurus.UCSC.bosTau8")))
152 (build-system r-build-system)
156 "https://www.bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau8/")
157 (synopsis "Full genome sequences for Bos taurus (UCSC version bosTau8)")
158 (description "This package provides the full genome sequences for Bos
159 taurus (UCSC version bosTau8).")
160 (license license:artistic2.0)))
162 (define-public r-bsgenome-celegans-ucsc-ce6
164 (name "r-bsgenome-celegans-ucsc-ce6")
168 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6"
169 version 'annotation))
172 "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9"))))
174 `((upstream-name . "BSgenome.Celegans.UCSC.ce6")))
175 (build-system r-build-system)
179 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/")
180 (synopsis "Full genome sequences for Worm")
182 "This package provides full genome sequences for Caenorhabditis
183 elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings
185 (license license:artistic2.0)))
187 (define-public r-bsgenome-celegans-ucsc-ce10
189 (name "r-bsgenome-celegans-ucsc-ce10")
193 (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10"
194 version 'annotation))
197 "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk"))))
199 `((upstream-name . "BSgenome.Celegans.UCSC.ce10")))
200 (build-system r-build-system)
204 "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/")
205 (synopsis "Full genome sequences for Worm")
207 "This package provides full genome sequences for Caenorhabditis
208 elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings
210 (license license:artistic2.0)))
212 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
214 (name "r-bsgenome-dmelanogaster-ucsc-dm6")
218 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6"
219 version 'annotation))
222 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
224 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
225 (build-system r-build-system)
229 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
230 (synopsis "Full genome sequences for Fly")
232 "This package provides full genome sequences for Drosophila
233 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
235 (license license:artistic2.0)))
237 (define-public r-bsgenome-dmelanogaster-ucsc-dm3
239 (name "r-bsgenome-dmelanogaster-ucsc-dm3")
243 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3"
244 version 'annotation))
247 "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8"))))
249 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3")))
250 (build-system r-build-system)
254 "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/")
255 (synopsis "Full genome sequences for Fly")
257 "This package provides full genome sequences for Drosophila
258 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
259 Biostrings objects.")
260 (license license:artistic2.0)))
262 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
264 (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
268 (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked"
269 version 'annotation))
272 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
274 `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
275 (build-system r-build-system)
277 (list r-bsgenome r-bsgenome-dmelanogaster-ucsc-dm3))
278 (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
279 (synopsis "Full masked genome sequences for Fly")
281 "This package provides full masked genome sequences for Drosophila
282 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
283 Biostrings objects. The sequences are the same as in
284 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
285 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
286 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
287 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
288 Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.")
289 (license license:artistic2.0)))
291 (define-public r-bsgenome-drerio-ucsc-danrer11
293 (name "r-bsgenome-drerio-ucsc-danrer11")
298 (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11"
299 version 'annotation))
301 (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v"))))
302 (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11")))
303 (build-system r-build-system)
306 (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11")
307 (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)")
309 "This package provides full genome sequences for Danio rerio (Zebrafish)
310 as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.")
311 (license license:artistic2.0)))
313 (define-public r-bsgenome-hsapiens-1000genomes-hs37d5
315 (name "r-bsgenome-hsapiens-1000genomes-hs37d5")
319 (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5"
320 version 'annotation))
323 "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr"))))
325 `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5")))
326 (build-system r-build-system)
330 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/")
331 (synopsis "Full genome sequences for Homo sapiens")
333 "This package provides full genome sequences for Homo sapiens from
334 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.")
335 (license license:artistic2.0)))
337 (define-public r-bsgenome-hsapiens-ncbi-grch38
339 (name "r-bsgenome-hsapiens-ncbi-grch38")
344 (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38"
345 version 'annotation))
348 "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1"))))
349 (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38")))
350 (build-system r-build-system)
351 (propagated-inputs (list r-bsgenome))
353 "https://bioconductor.org/packages/release/data/annotation/html/\
354 BSgenome.Hsapiens.NCBI.GRCh38.html")
355 (synopsis "Full genome sequences for Homo sapiens (GRCh38)")
357 "This package provides full genome sequences for Homo sapiens (Human) as
358 provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.")
359 (license license:artistic2.0)))
361 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
363 (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
368 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked"
369 version 'annotation))
371 (base32 "19533ihgad67bzhavycv6z708012ylz9cw1qdfmk2b7ikf3kiaz9"))))
373 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
374 (build-system r-build-system)
376 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19))
377 (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
378 (synopsis "Full masked genome sequences for Homo sapiens")
380 "This package provides full genome sequences for Homo sapiens (Human) as
381 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The
382 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
383 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
384 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
385 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
386 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
388 (license license:artistic2.0)))
390 (define-public r-bsgenome-mmusculus-ucsc-mm9
392 (name "r-bsgenome-mmusculus-ucsc-mm9")
396 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9"
397 version 'annotation))
400 "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i"))))
402 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9")))
403 (build-system r-build-system)
407 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/")
408 (synopsis "Full genome sequences for Mouse")
410 "This package provides full genome sequences for Mus musculus (Mouse) as
411 provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
412 (license license:artistic2.0)))
414 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
416 (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
420 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked"
421 version 'annotation))
424 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
426 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
427 (build-system r-build-system)
429 (list r-bsgenome r-bsgenome-mmusculus-ucsc-mm9))
430 (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
431 (synopsis "Full masked genome sequences for Mouse")
433 "This package provides full genome sequences for Mus musculus (Mouse) as
434 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The
435 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
436 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
437 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
438 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
439 Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by
441 (license license:artistic2.0)))
443 (define-public r-bsgenome-mmusculus-ucsc-mm10
445 (name "r-bsgenome-mmusculus-ucsc-mm10")
449 (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10"
450 version 'annotation))
453 "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf"))))
455 `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10")))
456 (build-system r-build-system)
460 "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/")
461 (synopsis "Full genome sequences for Mouse")
463 "This package provides full genome sequences for Mus
464 musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored
465 in Biostrings objects.")
466 (license license:artistic2.0)))
468 (define-public r-genomeinfodbdata
470 (name "r-genomeinfodbdata")
474 (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation))
477 "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c"))))
479 `((upstream-name . "GenomeInfoDbData")))
480 (build-system r-build-system)
481 (home-page "https://bioconductor.org/packages/GenomeInfoDbData")
482 (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb")
483 (description "This package contains data for mapping between NCBI taxonomy
484 ID and species. It is used by functions in the GenomeInfoDb package.")
485 (license license:artistic2.0)))
487 (define-public r-go-db
493 (uri (bioconductor-uri "GO.db" version 'annotation))
496 "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
498 `((upstream-name . "GO.db")))
499 (build-system r-build-system)
501 (list r-annotationdbi))
502 (home-page "https://bioconductor.org/packages/GO.db")
503 (synopsis "Annotation maps describing the entire Gene Ontology")
505 "The purpose of this GO.db annotation package is to provide detailed
506 information about the latest version of the Gene Ontologies.")
507 (license license:artistic2.0)))
509 (define-public r-homo-sapiens
511 (name "r-homo-sapiens")
515 (uri (bioconductor-uri "Homo.sapiens" version 'annotation))
518 "151vj7h5p1c8yd5swrchk46z469p135wk50hvkl0nhgndvy0jj01"))))
520 `((upstream-name . "Homo.sapiens")))
521 (build-system r-build-system)
523 (list r-genomicfeatures
526 r-txdb-hsapiens-ucsc-hg19-knowngene
529 (home-page "https://bioconductor.org/packages/Homo.sapiens/")
530 (synopsis "Annotation package for the Homo.sapiens object")
532 "This package contains the Homo.sapiens object to access data from
533 several related annotation packages.")
534 (license license:artistic2.0)))
536 (define-public r-mus-musculus
538 (name "r-mus-musculus")
543 (uri (bioconductor-uri "Mus.musculus" version 'annotation))
546 "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y"))))
547 (properties `((upstream-name . "Mus.musculus")))
548 (build-system r-build-system)
550 (list r-annotationdbi
555 r-txdb-mmusculus-ucsc-mm10-knowngene))
556 (home-page "https://bioconductor.org/packages/Mus.musculus")
557 (synopsis "Annotation package for the Mus.musculus object")
559 "This package contains the @code{Mus.musculus} object to access data
560 from several related annotation packages.")
561 (license license:artistic2.0)))
563 (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19
565 (name "r-illuminahumanmethylation450kanno-ilmn12-hg19")
570 (uri (bioconductor-uri
571 "IlluminaHumanMethylation450kanno.ilmn12.hg19"
572 version 'annotation))
575 "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4"))))
578 . "IlluminaHumanMethylation450kanno.ilmn12.hg19")))
579 (build-system r-build-system)
580 (propagated-inputs (list r-minfi))
582 "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/")
583 (synopsis "Annotation for Illumina's 450k methylation arrays")
585 "This package provides manifests and annotation for Illumina's 450k array
587 (license license:artistic2.0)))
589 (define-public r-org-ce-eg-db
591 (name "r-org-ce-eg-db")
595 (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation))
598 "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz"))))
600 `((upstream-name . "org.Ce.eg.db")))
601 (build-system r-build-system)
603 (list r-annotationdbi))
604 (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/")
605 (synopsis "Genome wide annotation for Worm")
607 "This package provides mappings from Entrez gene identifiers to various
608 annotations for the genome of the model worm Caenorhabditis elegans.")
609 (license license:artistic2.0)))
611 (define-public r-org-dm-eg-db
613 (name "r-org-dm-eg-db")
617 (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation))
620 "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3"))))
622 `((upstream-name . "org.Dm.eg.db")))
623 (build-system r-build-system)
625 (list r-annotationdbi))
626 (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/")
627 (synopsis "Genome wide annotation for Fly")
629 "This package provides mappings from Entrez gene identifiers to various
630 annotations for the genome of the model fruit fly Drosophila melanogaster.")
631 (license license:artistic2.0)))
633 (define-public r-org-dr-eg-db
635 (name "r-org-dr-eg-db")
639 (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation))
642 "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx"))))
644 `((upstream-name . "org.Dr.eg.db")))
645 (build-system r-build-system)
647 (list r-annotationdbi))
648 (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/")
649 (synopsis "Annotation for Zebrafish")
651 "This package provides genome wide annotations for Zebrafish, primarily
652 based on mapping using Entrez Gene identifiers.")
653 (license license:artistic2.0)))
655 (define-public r-org-hs-eg-db
657 (name "r-org-hs-eg-db")
661 (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
664 "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
666 `((upstream-name . "org.Hs.eg.db")))
667 (build-system r-build-system)
669 (list r-annotationdbi))
670 (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/")
671 (synopsis "Genome wide annotation for Human")
673 "This package contains genome-wide annotations for Human, primarily based
674 on mapping using Entrez Gene identifiers.")
675 (license license:artistic2.0)))
677 (define-public r-org-mm-eg-db
679 (name "r-org-mm-eg-db")
683 (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation))
686 "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx"))))
688 `((upstream-name . "org.Mm.eg.db")))
689 (build-system r-build-system)
691 (list r-annotationdbi))
692 (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/")
693 (synopsis "Genome wide annotation for Mouse")
695 "This package provides mappings from Entrez gene identifiers to various
696 annotations for the genome of the model mouse Mus musculus.")
697 (license license:artistic2.0)))
699 (define-public r-bsgenome-hsapiens-ucsc-hg19
701 (name "r-bsgenome-hsapiens-ucsc-hg19")
705 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19"
706 version 'annotation))
709 "06lx7q7i52lg3vkjkqy492z9ianzgi4nhs9m1jrxjjb4hgbnbyjv"))))
711 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19")))
712 (build-system r-build-system)
716 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/")
717 (synopsis "Full genome sequences for Homo sapiens")
719 "This package provides full genome sequences for Homo sapiens as provided
720 by UCSC (hg19, February 2009) and stored in Biostrings objects.")
721 (license license:artistic2.0)))
723 (define-public r-bsgenome-hsapiens-ucsc-hg38
725 (name "r-bsgenome-hsapiens-ucsc-hg38")
729 (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38"
730 version 'annotation))
732 (base32 "03xmh6q99nqjxz29m6j0ymxlk22jq0nlvpf4a2yhg3hgnxqkakh2"))))
734 `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38")))
735 (build-system r-build-system)
739 "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/")
740 (synopsis "Full genome sequences for Homo sapiens")
742 "This package provides full genome sequences for Homo sapiens (Human)
743 as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.")
744 (license license:artistic2.0)))
746 (define-public r-ensdb-hsapiens-v75
748 (name "r-ensdb-hsapiens-v75")
753 (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation))
756 "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c"))))
758 `((upstream-name . "EnsDb.Hsapiens.v75")))
759 (build-system r-build-system)
762 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75")
763 (synopsis "Ensembl based annotation package")
765 "This package exposes an annotation database generated from Ensembl.")
766 (license license:artistic2.0)))
768 (define-public r-ensdb-hsapiens-v86
770 (name "r-ensdb-hsapiens-v86")
775 (uri (bioconductor-uri "EnsDb.Hsapiens.v86" version 'annotation))
777 (base32 "1gp7xrzddpvmh2vrcp571wyy00skxgxfl39ksj4h0hm1qay0fb2m"))))
778 (properties `((upstream-name . "EnsDb.Hsapiens.v86")))
779 (build-system r-build-system)
780 (propagated-inputs (list r-ensembldb))
781 (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v86")
782 (synopsis "Ensembl based annotation package")
783 (description "This package exposes an annotation database generated from
785 (license license:artistic2.0)))
787 (define-public r-ensdb-mmusculus-v79
789 (name "r-ensdb-mmusculus-v79")
794 (uri (bioconductor-uri "EnsDb.Mmusculus.v79" version 'annotation))
796 (base32 "1zpmq7v55if6q9r0h883q9k8l70ym20b01m9hxf121wb256rl9f7"))))
797 (properties `((upstream-name . "EnsDb.Mmusculus.v79")))
798 (build-system r-build-system)
799 (propagated-inputs (list r-ensembldb))
800 (home-page "https://bioconductor.org/packages/EnsDb.Mmusculus.v79")
801 (synopsis "Ensembl based annotation package")
802 (description "This package exposes an annotation database generated from
804 (license license:artistic2.0)))
806 (define-public r-snplocs-hsapiens-dbsnp144-grch37
808 (name "r-snplocs-hsapiens-dbsnp144-grch37")
812 (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37"
813 version 'annotation))
816 "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz"))))
817 (build-system r-build-system)
818 ;; As this package provides little more than a very large data file it
819 ;; doesn't make sense to build substitutes.
820 (arguments `(#:substitutable? #f))
830 "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/")
831 (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)")
832 (description "This package provides SNP locations and alleles for Homo
833 sapiens extracted from NCBI dbSNP Build 144. The source data files used for
834 this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped
835 to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a
836 patched version of GRCh37. However the patch doesn't alter chromosomes 1-22,
837 X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for
838 the mitochondrion chromosome. Therefore, the SNPs in this package can be
839 injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the
840 correct position but this injection will exclude chrM (i.e. nothing will be
841 injected in that sequence).")
842 (license license:artistic2.0)))
844 (define-public r-txdb-dmelanogaster-ucsc-dm6-ensgene
846 (name "r-txdb-dmelanogaster-ucsc-dm6-ensgene")
851 (uri (bioconductor-uri "TxDb.Dmelanogaster.UCSC.dm6.ensGene"
852 version 'annotation))
855 "0yij7zyqkmmr13389rs2gfa5anvvw648nnl1kjbsgvyxkggif8q4"))))
857 `((upstream-name . "TxDb.Dmelanogaster.UCSC.dm6.ensGene")))
858 (build-system r-build-system)
860 (list r-annotationdbi r-genomicfeatures))
862 "https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene")
863 (synopsis "Annotation package for TxDb object(s)")
865 "This package exposes an annotation databases generated from UCSC by
866 exposing these as TxDb objects.")
867 (license license:artistic2.0)))
869 (define-public r-txdb-hsapiens-ucsc-hg19-knowngene
871 (name "r-txdb-hsapiens-ucsc-hg19-knowngene")
875 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene"
876 version 'annotation))
879 "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86"))))
881 `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene")))
882 (build-system r-build-system)
884 (list r-genomicfeatures))
886 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/")
887 (synopsis "Annotation package for human genome in TxDb format")
889 "This package provides an annotation database of Homo sapiens genome
890 data. It is derived from the UCSC hg19 genome and based on the \"knownGene\"
891 track. The database is exposed as a @code{TxDb} object.")
892 (license license:artistic2.0)))
894 (define-public r-txdb-hsapiens-ucsc-hg38-knowngene
896 (name "r-txdb-hsapiens-ucsc-hg38-knowngene")
900 (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene"
901 version 'annotation))
903 (base32 "1y9fqhkk5wgny43bxc0j82afy49vz34rblcmcfmwavngdkpnj879"))))
905 `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene")))
906 (build-system r-build-system)
908 (list r-annotationdbi r-genomicfeatures))
910 "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/")
911 (synopsis "Annotation package for human genome in TxDb format")
913 "This package provides an annotation database of Homo sapiens genome
914 data. It is derived from the UCSC hg38 genome and based on the \"knownGene\"
915 track. The database is exposed as a @code{TxDb} object.")
916 (license license:artistic2.0)))
918 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
920 (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
924 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene"
925 version 'annotation))
928 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
930 `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
931 (build-system r-build-system)
933 (list r-genomicfeatures r-annotationdbi))
935 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
936 (synopsis "Annotation package for mouse genome in TxDb format")
938 "This package provides an annotation database of Mouse genome data. It
939 is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The
940 database is exposed as a @code{TxDb} object.")
941 (license license:artistic2.0)))
943 (define-public r-txdb-mmusculus-ucsc-mm10-knowngene
945 (name "r-txdb-mmusculus-ucsc-mm10-knowngene")
949 (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene"
950 version 'annotation))
953 "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9"))))
955 `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene")))
956 (build-system r-build-system)
958 (list r-bsgenome r-genomicfeatures r-annotationdbi))
960 "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/")
961 (synopsis "Annotation package for TxDb knownGene object(s) for Mouse")
963 "This package loads a TxDb object, which is an R interface to
964 prefabricated databases contained in this package. This package provides
965 the TxDb object of Mouse data as provided by UCSC (mm10, December 2011)
966 based on the knownGene track.")
967 (license license:artistic2.0)))
969 (define-public r-txdb-celegans-ucsc-ce6-ensgene
971 (name "r-txdb-celegans-ucsc-ce6-ensgene")
976 (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene"
977 version 'annotation))
980 "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90"))))
982 `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene")))
983 (build-system r-build-system)
985 (list r-annotationdbi r-genomicfeatures))
986 (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/")
987 (synopsis "Annotation package for C elegans TxDb objects")
989 "This package exposes a C elegans annotation database generated from UCSC
990 by exposing these as TxDb objects.")
991 (license license:artistic2.0)))
993 (define-public r-fdb-infiniummethylation-hg19
995 (name "r-fdb-infiniummethylation-hg19")
999 (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19"
1000 version 'annotation))
1003 "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0"))))
1005 `((upstream-name . "FDb.InfiniumMethylation.hg19")))
1006 (build-system r-build-system)
1008 (list r-biostrings r-genomicfeatures r-annotationdbi r-org-hs-eg-db
1009 r-txdb-hsapiens-ucsc-hg19-knowngene))
1010 (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/")
1011 (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations")
1013 "This is an annotation package for Illumina Infinium DNA methylation
1014 probes. It contains the compiled HumanMethylation27 and HumanMethylation450
1016 (license license:artistic2.0)))
1018 (define-public r-illuminahumanmethylationepicmanifest
1020 (name "r-illuminahumanmethylationepicmanifest")
1024 (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest"
1025 version 'annotation))
1028 "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3"))))
1030 `((upstream-name . "IlluminaHumanMethylationEPICmanifest")))
1031 (build-system r-build-system)
1034 (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/")
1035 (synopsis "Manifest for Illumina's EPIC methylation arrays")
1037 "This is a manifest package for Illumina's EPIC methylation arrays.")
1038 (license license:artistic2.0)))
1040 (define-public r-do-db
1046 (uri (bioconductor-uri "DO.db" version 'annotation))
1049 "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn"))))
1051 `((upstream-name . "DO.db")))
1052 (build-system r-build-system)
1054 (list r-annotationdbi))
1055 (home-page "https://www.bioconductor.org/packages/DO.db/")
1056 (synopsis "Annotation maps describing the entire Disease Ontology")
1058 "This package provides a set of annotation maps describing the entire
1060 (license license:artistic2.0)))
1062 (define-public r-hgu133plus2-db
1064 (name "r-hgu133plus2-db")
1069 (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
1071 (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
1072 (properties `((upstream-name . "hgu133plus2.db")))
1073 (build-system r-build-system)
1074 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
1075 (home-page "https://bioconductor.org/packages/hgu133plus2.db")
1076 (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
1078 "This package provides Affymetrix HG-U133_Plus_2 array annotation
1079 data (chip hgu133plus2) assembled using data from public repositories.")
1080 (license license:artistic2.0)))
1082 (define-public r-pfam-db
1089 (uri (bioconductor-uri "PFAM.db" version 'annotation))
1091 (base32 "03vjfb9vx1gxrw1jkq6y4i46qhjj9z2mkdiflglbd6kpfrgnl0z7"))))
1092 (properties `((upstream-name . "PFAM.db")))
1093 (build-system r-build-system)
1095 (list r-annotationdbi))
1096 (home-page "https://bioconductor.org/packages/PFAM.db")
1097 (synopsis "Set of protein ID mappings for PFAM")
1099 "This package provides a set of protein ID mappings for PFAM, assembled
1100 using data from public repositories.")
1101 (license license:artistic2.0)))
1103 (define-public r-phastcons100way-ucsc-hg19
1105 (name "r-phastcons100way-ucsc-hg19")
1110 (uri (bioconductor-uri "phastCons100way.UCSC.hg19"
1111 version 'annotation))
1114 "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa"))))
1116 `((upstream-name . "phastCons100way.UCSC.hg19")))
1117 (build-system r-build-system)
1125 (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19")
1126 (synopsis "UCSC phastCons conservation scores for hg19")
1128 "This package provides UCSC phastCons conservation scores for the human
1129 genome (hg19) calculated from multiple alignments with other 99 vertebrate
1131 (license license:artistic2.0)))
1136 (define-public r-abadata
1142 (uri (bioconductor-uri "ABAData" version 'experiment))
1145 "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z"))))
1147 `((upstream-name . "ABAData")))
1148 (build-system r-build-system)
1150 (list r-annotationdbi))
1151 (home-page "https://www.bioconductor.org/packages/ABAData/")
1152 (synopsis "Gene expression in human brain regions from Allen Brain Atlas")
1154 "This package provides the data for the gene expression enrichment
1155 analysis conducted in the package ABAEnrichment. The package includes three
1156 datasets which are derived from the Allen Brain Atlas:
1159 @item Gene expression data from Human Brain (adults) averaged across donors,
1160 @item Gene expression data from the Developing Human Brain pooled into five
1161 age categories and averaged across donors, and
1162 @item a developmental effect score based on the Developing Human Brain
1166 All datasets are restricted to protein coding genes.")
1167 (license license:gpl2+)))
1169 (define-public r-adductdata
1171 (name "r-adductdata")
1175 (uri (bioconductor-uri "adductData" version 'experiment))
1177 (base32 "02r7p1645vhhf7wn5x0aklmf7l97h6fjb8v9mldim4waccmpyg48"))))
1178 (properties `((upstream-name . "adductData")))
1179 (build-system r-build-system)
1180 (propagated-inputs (list r-annotationhub r-experimenthub))
1181 (native-inputs (list r-knitr))
1182 (home-page "https://bioconductor.org/packages/adductData")
1183 (synopsis "Data from untargeted mass spectrometry of modifications to Cys34")
1185 "This package contains data from untargeted @dfn{mass spectrometry} (MS)
1186 of modifications to @dfn{oxidized cysteine} (Cys) 34 in @dfn{human serum
1188 (license license:artistic2.0)))
1190 (define-public r-aneufinderdata
1192 (name "r-aneufinderdata")
1196 (uri (bioconductor-uri "AneuFinderData" version 'experiment))
1198 (base32 "0cncb8km0sc2xh95rgnnm38kys5ml0n8gh8cl6x7ls1xh9sm83f7"))))
1199 (build-system r-build-system)
1200 (home-page "https://bioconductor.org/packages/AneuFinderData/")
1201 (synopsis "Data package for @code{AneuFinder}")
1202 (description "This package contains whole-genome single cell sequencing data for
1203 demonstration purposes in the @code{AneuFinder} package.")
1204 (license license:artistic2.0)))
1206 (define-public r-arrmdata
1212 (uri (bioconductor-uri "ARRmData" version 'experiment))
1214 (base32 "1cjzr58426s9z2bwjz3wzlkh52fv0q85cw4gbjnhwakh9sr3dd5p"))))
1216 `((upstream-name . "ARRmData")))
1217 (build-system r-build-system)
1218 (home-page "https://www.bioconductor.org/packages/ARRmData/")
1219 (synopsis "Example dataset for normalization of Illumina 450k methylation data")
1221 "This package provides raw beta values from 36 samples across 3 groups
1222 from Illumina 450k methylation arrays.")
1223 (license license:artistic2.0)))
1225 (define-public r-bladderbatch
1227 (name "r-bladderbatch")
1231 (uri (bioconductor-uri "bladderbatch" version
1235 "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k"))))
1236 (properties `((upstream-name . "bladderbatch")))
1237 (build-system r-build-system)
1238 (propagated-inputs (list r-biobase))
1239 (home-page "https://bioconductor.org/packages/bladderbatch")
1240 (synopsis "Bladder gene expression data illustrating batch effects")
1242 "This package contains microarray gene expression data on 57 bladder samples from
1243 5 batches. The data are used as an illustrative example for the sva package.")
1244 (license license:artistic2.0)))
1246 (define-public r-biscuiteerdata
1248 (name "r-biscuiteerdata")
1253 (uri (bioconductor-uri "biscuiteerData" version 'experiment))
1255 (base32 "0nda6b8mkv93s513y0xfgxvi7zn8v07jx323ii709rknlncm6qqw"))))
1257 `((upstream-name . "biscuiteerData")))
1258 (build-system r-build-system)
1260 (list r-annotationhub r-curl r-experimenthub))
1261 (native-inputs (list r-knitr))
1262 (home-page "https://bioconductor.org/packages/biscuiteerData")
1263 (synopsis "Data package for Biscuiteer")
1265 "This package contains default datasets used by the Bioconductor package
1267 (license license:gpl3)))
1269 (define-public r-celldex
1276 (uri (bioconductor-uri "celldex" version 'experiment))
1278 (base32 "1fjldmhb9yg6yr3aq5ldvc8xwqw71ix4cdlr53xxckgwljjq7x10"))))
1279 (properties `((upstream-name . "celldex")))
1280 (build-system r-build-system)
1282 (list r-annotationdbi
1285 r-delayedmatrixstats
1288 r-summarizedexperiment))
1289 (native-inputs (list r-knitr))
1290 (home-page "https://github.com/LTLA/celldex")
1291 (synopsis "Reference index for cell types")
1293 "This package provides a collection of reference expression datasets with
1294 curated cell type labels, for use in procedures like automated annotation of
1295 single-cell data or deconvolution of bulk RNA-seq.")
1296 (license license:gpl3)))
1298 (define-public r-chromstardata
1300 (name "r-chromstardata")
1305 (uri (bioconductor-uri "chromstaRData" version 'experiment))
1307 (base32 "1ajwnkibpi01c93nrplxhy6grw8jj5219g4pii4rkan4k5815kv1"))))
1308 (properties `((upstream-name . "chromstaRData")))
1309 (build-system r-build-system)
1310 (home-page "https://bioconductor.org/packages/chromstaRData/")
1311 (synopsis "ChIP-seq data for demonstration purposes")
1313 "This package provides ChIP-seq data for demonstration purposes in the
1314 chromstaR package.")
1315 (license license:gpl3)))
1317 (define-public r-copyhelper
1319 (name "r-copyhelper")
1324 (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
1326 (base32 "0klrnxck0q14birnpwzkiwmj77hwdn6gazvdg0lqn9y6j5mbkyx1"))))
1327 (properties `((upstream-name . "CopyhelpeR")))
1328 (build-system r-build-system)
1329 (home-page "https://bioconductor.org/packages/CopyhelpeR/")
1330 (synopsis "Helper files for CopywriteR")
1332 "This package contains the helper files that are required to run the
1333 Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
1334 and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
1335 mm10. In addition, it contains a blacklist filter to remove regions that
1336 display copy number variation. Files are stored as GRanges objects from the
1337 GenomicRanges Bioconductor package.")
1338 (license license:gpl2)))
1340 (define-public r-genelendatabase
1342 (name "r-genelendatabase")
1347 (uri (bioconductor-uri "geneLenDataBase" version 'experiment))
1349 (base32 "0p4rmd3qszsnyn47mfbk96zfa0bhpyyvsh4ma1ligjrsnmkicsaz"))))
1351 `((upstream-name . "geneLenDataBase")))
1352 (build-system r-build-system)
1354 (list r-rtracklayer r-genomicfeatures))
1355 (home-page "https://bioconductor.org/packages/geneLenDataBase/")
1356 (synopsis "Lengths of mRNA transcripts for a number of genomes")
1358 "This package provides the lengths of mRNA transcripts for a number of
1359 genomes and gene ID formats, largely based on the UCSC table browser.")
1360 (license license:lgpl2.0+)))
1362 (define-public r-genomationdata
1364 (name "r-genomationdata")
1369 (uri (bioconductor-uri "genomationData" version 'experiment))
1371 (base32 "0ckdgmarndpz6r0y9sd4nmypzjgivj32w2890yl15xmxkx4397fh"))))
1373 `((upstream-name . "genomationData")))
1374 (build-system r-build-system)
1375 ;; As this package provides little more than large data files, it doesn't
1376 ;; make sense to build substitutes.
1377 (arguments `(#:substitutable? #f))
1380 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
1381 (synopsis "Experimental data for use with the genomation package")
1383 "This package contains experimental genetic data for use with the
1384 genomation package. Included are Chip Seq, Methylation and Cage data,
1385 downloaded from Encode.")
1386 (license license:gpl3+)))
1388 (define-public r-macrophage
1390 (name "r-macrophage")
1394 (uri (bioconductor-uri "macrophage" version
1398 "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms"))))
1399 (properties `((upstream-name . "macrophage")))
1400 (build-system r-build-system)
1401 (native-inputs (list r-knitr))
1402 (home-page "https://bioconductor.org/packages/macrophage")
1403 (synopsis "Human macrophage immune response data")
1405 "This package provides the output of running @code{Salmon} on a set of 24
1406 RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and
1407 gene expression indicate a role for enhancer priming in immune response\", published
1408 in Nature Genetics, January 2018.")
1409 (license license:gpl2+)))
1411 (define-public r-msdata
1418 (uri (bioconductor-uri "msdata" version 'experiment))
1420 (base32 "0nqb7d7fa9l15bxy3s9wmy2h79jb6ldwww0hzk5mifabacmzx691"))))
1421 (properties `((upstream-name . "msdata")))
1422 (build-system r-build-system)
1423 (home-page "https://bioconductor.org/packages/msdata")
1424 (synopsis "Various Mass Spectrometry raw data example files")
1426 "This package provides Ion Trap positive ionization mode data in mzML file
1427 format. It includes a subset from 500-850 m/z and 1190-1310 seconds,
1428 including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex
1429 III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5;
1430 LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example
1431 files for various search engines.")
1432 (license license:gpl2+)))
1434 (define-public r-pasilla
1441 (uri (bioconductor-uri "pasilla" version 'experiment))
1443 (base32 "1vsxh7mv2krkbdqs5gsgjsxarjbll0bpyk94syrwh56z67n7jyib"))))
1444 (build-system r-build-system)
1445 (propagated-inputs (list r-dexseq))
1446 (native-inputs (list r-knitr))
1447 (home-page "https://www.bioconductor.org/packages/pasilla/")
1448 (synopsis "Data package with per-exon and per-gene read counts")
1449 (description "This package provides per-exon and per-gene read counts
1450 computed for selected genes from RNA-seq data that were presented in the
1451 article 'Conservation of an RNA regulatory map between Drosophila and mammals'
1452 by Brooks et al., Genome Research 2011.")
1453 (license license:lgpl2.1+)))
1455 (define-public r-hsmmsinglecell
1457 (name "r-hsmmsinglecell")
1462 (uri (bioconductor-uri "HSMMSingleCell" version 'experiment))
1464 (base32 "12whx0pl9461xbak5r9zi6ggx5is8sk6mgrbjwlmx3mbr9am116v"))))
1466 `((upstream-name . "HSMMSingleCell")))
1467 (build-system r-build-system)
1468 (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/")
1469 (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)")
1471 "Skeletal myoblasts undergo a well-characterized sequence of
1472 morphological and transcriptional changes during differentiation. In this
1473 experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded
1474 under high mitogen conditions (GM) and then differentiated by switching to
1475 low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several
1476 hundred cells taken over a time-course of serum-induced differentiation.
1477 Between 49 and 77 cells were captured at each of four time points (0, 24, 48,
1478 72 hours) following serum switch using the Fluidigm C1 microfluidic system.
1479 RNA from each cell was isolated and used to construct mRNA-Seq libraries,
1480 which were then sequenced to a depth of ~4 million reads per library,
1481 resulting in a complete gene expression profile for each cell.")
1482 (license license:artistic2.0)))
1484 (define-public r-all
1491 (uri (bioconductor-uri "ALL" version 'experiment))
1493 (base32 "0410045x327wmfkksshd8yishw4yxij08vn8p65cdj7hb3qy3p0z"))))
1494 (properties `((upstream-name . "ALL")))
1495 (build-system r-build-system)
1498 (home-page "https://bioconductor.org/packages/ALL")
1499 (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory")
1501 "The data consist of microarrays from 128 different individuals with
1502 @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates
1503 are available. The data have been normalized (using rma) and it is the
1504 jointly normalized data that are available here. The data are presented in
1505 the form of an @code{exprSet} object.")
1506 (license license:artistic2.0)))
1508 (define-public r-affydata
1515 (uri (bioconductor-uri "affydata" version 'experiment))
1517 (base32 "1d8ims7hks536v739r5hhfkkzyzqrf398aqal3hzyfm0psv15jbp"))))
1518 (properties `((upstream-name . "affydata")))
1519 (build-system r-build-system)
1522 (home-page "https://bioconductor.org/packages/affydata/")
1523 (synopsis "Affymetrix data for demonstration purposes")
1525 "This package provides example datasets that represent 'real world
1526 examples' of Affymetrix data, unlike the artificial examples included in the
1527 package @code{affy}.")
1528 (license license:gpl2+)))
1530 (define-public r-gagedata
1537 (uri (bioconductor-uri "gageData" version 'experiment))
1539 (base32 "00s2aig9r0bvk45brc0shildrgl2z0i0k8xlvqc9h1s274nnslk9"))))
1540 (properties `((upstream-name . "gageData")))
1541 (build-system r-build-system)
1542 (home-page "https://bioconductor.org/packages/gageData")
1543 (synopsis "Auxiliary data for the gage package")
1545 "This is a supportive data package for the software package @code{gage}.
1546 However, the data supplied here are also useful for gene set or pathway
1547 analysis or microarray data analysis in general. In this package, we provide
1548 two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and
1549 BMP6 (originally published as an demo dataset for GAGE, also registered as
1550 GSE13604 in GEO). This package also includes commonly used gene set data based
1551 on KEGG pathways and GO terms for major research species, including human,
1552 mouse, rat and budding yeast. Mapping data between common gene IDs for budding
1553 yeast are also included.")
1554 (license license:gpl2+)))
1556 (define-public r-curatedtcgadata
1558 (name "r-curatedtcgadata")
1563 (uri (bioconductor-uri "curatedTCGAData" version 'experiment))
1565 (base32 "0h3mpwy6lhyn8hfry13sdjgb35gqyi3g26igfjqzshc5wvsniwpr"))))
1567 `((upstream-name . "curatedTCGAData")))
1568 (build-system r-build-system)
1570 (list r-annotationhub
1573 r-multiassayexperiment
1575 r-summarizedexperiment))
1576 (native-inputs (list r-knitr))
1577 (home-page "https://bioconductor.org/packages/curatedTCGAData/")
1578 (synopsis "Curated data from The Cancer Genome Atlas")
1580 "This package provides publicly available data from The Cancer Genome
1581 Atlas (TCGA) as @code{MultiAssayExperiment} objects.
1582 @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy
1583 number, mutation, microRNA, protein, and others) with clinical / pathological
1584 data. It also links assay barcodes with patient identifiers, enabling
1585 harmonized subsetting of rows (features) and columns (patients / samples)
1586 across the entire multi-'omics experiment.")
1587 (license license:artistic2.0)))
1589 (define-public r-parathyroidse
1591 (name "r-parathyroidse")
1595 (uri (bioconductor-uri "parathyroidSE" version
1599 "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16"))))
1600 (properties `((upstream-name . "parathyroidSE")))
1601 (build-system r-build-system)
1602 (propagated-inputs (list r-summarizedexperiment))
1603 (home-page "https://bioconductor.org/packages/parathyroidSE")
1604 (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors")
1606 "This package provides @code{RangedSummarizedExperiment} objects of read
1607 counts in genes and exonic parts for paired-end RNA-Seq data from experiments on
1608 primary cultures of parathyroid tumors. The sequencing was performed on tumor
1609 cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).")
1610 ;; The author(s) mentions only LGPL without any specific version.
1611 (license license:lgpl2.1+)))
1613 (define-public r-tcgabiolinksgui-data
1615 (name "r-tcgabiolinksgui-data")
1620 (uri (bioconductor-uri "TCGAbiolinksGUI.data" version 'experiment))
1622 (base32 "1mb2z59acs1pi1gqvgjyh62wnmbxskc5l0p42gpjajsjip5x1x7g"))))
1623 (properties `((upstream-name . "TCGAbiolinksGUI.data")))
1624 (build-system r-build-system)
1625 (native-inputs (list r-knitr))
1626 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data")
1627 (synopsis "Data for the TCGAbiolinksGUI package")
1628 (description "This package provides supporting data for the
1629 TCGAbiolinksGUI package.")
1630 (license license:gpl3)))
1632 (define-public r-tximportdata
1634 (name "r-tximportdata")
1638 (uri (bioconductor-uri "tximportData" version
1642 "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy"))))
1643 (properties `((upstream-name . "tximportData")))
1644 (build-system r-build-system)
1645 (native-inputs (list r-knitr))
1646 (home-page "https://bioconductor.org/packages/tximportData")
1647 (synopsis "Data for the tximport package")
1649 "This package provides the output of running various transcript abundance
1650 quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The
1651 quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon}
1652 and @code{Sailfish}. Alevin example output is also included.")
1653 (license license:gpl2+)))
1659 (define-public r-abarray
1665 (uri (bioconductor-uri "ABarray" version))
1668 "0kjq00i2mb21xyjjs3jy09ps80f11cy37wywzjvmxyjxzbsk4d7r"))))
1669 (properties `((upstream-name . "ABarray")))
1670 (build-system r-build-system)
1671 (propagated-inputs (list r-biobase r-multtest))
1672 (home-page "https://bioconductor.org/packages/ABarray")
1674 "Gene expression analysis for Applied Biosystems Genome Survey Microarray")
1676 "The package @code{ABarray} is designed to work with Applied Biosystems
1677 whole genome microarray platform, as well as any other platform whose data can
1678 be transformed into expression data matrix. Functions include data
1679 preprocessing, filtering, control probe analysis, statistical analysis in one
1680 single function. A @dfn{graphical user interface} (GUI) is also provided. The
1681 raw data, processed data, graphics output and statistical results are organized
1682 into folders according to the analysis settings used.")
1683 (license license:gpl2+)))
1685 (define-public r-absseq
1691 (uri (bioconductor-uri "ABSSeq" version))
1694 "1kwl0gcqwbgblwvpbvqlgnsi91km77j11f0q1f0gd6hhnv38mmlv"))))
1695 (properties `((upstream-name . "ABSSeq")))
1696 (build-system r-build-system)
1697 (propagated-inputs (list r-limma r-locfit))
1698 (home-page "https://bioconductor.org/packages/ABSSeq")
1700 "RNA-Seq analysis based on modelling absolute expression differences")
1702 "This package implements a new RNA-Seq analysis method and integrates two
1703 modules: a basic model for pairwise comparison and a linear model for complex
1704 design. RNA-Seq quantifies gene expression with reads count, which usually
1705 consists of conditions (or treatments) and several replicates for each
1706 condition. This software infers differential expression directly by the
1707 counts difference between conditions. It assumes that the sum counts
1708 difference between conditions follow a negative binomial distribution. In
1709 addition, @code{ABSSeq} moderates the fold-changes by two steps: the
1710 expression level and gene-specific dispersion, that might facilitate the gene
1711 ranking by fold-change and visualization.")
1712 (license license:gpl3+)))
1714 (define-public r-adam
1720 (uri (bioconductor-uri "ADAM" version))
1723 "1cgcjykik9hjrwlvvgaccprcrimgq5kwh9cj6367yk9m574a4gmn"))))
1724 (properties `((upstream-name . "ADAM")))
1725 (build-system r-build-system)
1726 (propagated-inputs (list r-dplyr
1734 r-summarizedexperiment))
1735 (native-inputs (list r-knitr))
1736 (home-page "https://bioconductor.org/packages/ADAM")
1737 (synopsis "Gene activity and diversity analysis module")
1739 "This software @code{ADAM} is a @dfn{Gene set enrichment analysis} (GSEA)
1740 package created to group a set of genes from comparative samples (control
1741 versus experiment) belonging to different species according to their respective
1742 functions. The corresponding roles are extracted from the default collections
1743 like Gene ontology and @dfn{Kyoto encyclopedia of genes and genomes} (KEGG).
1744 @code{ADAM} show their significance by calculating the p-values referring to
1745 gene diversity and activity. Each group of genes is called @dfn{Group of
1746 functionally associated genes} (GFAG).")
1747 (license license:gpl2+)))
1749 (define-public r-adamgui
1755 (uri (bioconductor-uri "ADAMgui" version))
1758 "0vvd5qdwkfcr7zg7z63x3vvrcg63r6c9p383yvcg2lp8zmx8hsbs"))))
1759 (properties `((upstream-name . "ADAMgui")))
1760 (build-system r-build-system)
1782 (native-inputs (list r-knitr))
1783 (home-page "https://bioconductor.org/packages/ADAMgui/")
1784 (synopsis "GUI for gene activity and diversity analysis")
1786 "This package @code{ADAMgui} is a @dfn{graphical user interface} (GUI)
1787 for the @code{ADAM} package. The @code{ADAMgui} package provides two
1788 shiny-based applications that allows the user to study the output of the
1789 @code{ADAM} package files through different plots. It's possible, for
1790 example, to choose a specific @dfn{group of functionally associated
1791 genes} (GFAG) and observe the gene expression behavior with the plots created
1792 with the @code{GFAGtargetUi} function. Features such as differential
1793 expression and fold change can be easily seen with aid of the plots made with
1794 the @code{GFAGpathUi} function.")
1795 (license license:gpl2+)))
1797 (define-public r-adimpute
1803 (uri (bioconductor-uri "ADImpute" version))
1806 "0885kd8mpmwjpzpx14pi6l3mqcvsixk10vkf5h4sqb7di0nnna4w"))))
1807 (properties `((upstream-name . "ADImpute")))
1808 (build-system r-build-system)
1810 (list r-biocparallel
1820 r-singlecellexperiment
1821 r-summarizedexperiment))
1822 (native-inputs (list r-knitr))
1823 (home-page "https://bioconductor.org/packages/ADImpute")
1824 (synopsis "Adaptive computational prediction for dropout imputations")
1826 "@dfn{Single-cell RNA sequencing} (scRNA-seq) methods are typically
1827 unable to quantify the expression levels of all genes in a cell, creating a
1828 need for the computational prediction of missing values (dropout imputation).
1829 Most existing dropout imputation methods are limited in the sense that they
1830 exclusively use the scRNA-seq dataset at hand and do not exploit external
1831 gene-gene relationship information. The @code{ADImpute} package proposes two
1832 methods to address this issue:
1835 @item a gene regulatory network-based approach using gene-gene relationships
1836 learnt from external data;
1837 @item a baseline approach corresponding to a sample-wide average.
1840 @code{ADImpute} implements these novel methods and also combines them with
1841 existing imputation methods like @code{DrImpute} and @code{SAVER}.
1842 @code{ADImpute} can learn the best performing method per gene and combine the
1843 results from different methods into an ensemble.")
1844 (license license:gpl3+)))
1846 (define-public r-adsplit
1852 (uri (bioconductor-uri "adSplit" version))
1855 "1wl2gd0b7krf485clw67cxayp0g9argklkzn8nw1vrkil0vvr4jm"))))
1856 (properties `((upstream-name . "adSplit")))
1857 (build-system r-build-system)
1859 (list r-annotationdbi
1865 (home-page "https://compdiag.molgen.mpg.de/software/adSplit.shtml")
1866 (synopsis "Annotation-driven splits in microarray data")
1868 "This package implements clustering of microarray gene expression
1869 profiles according to functional annotations. For each term genes are
1870 annotated to, splits into two subclasses are computed and a significance of
1871 the supporting gene set is determined.")
1872 (license license:gpl2+)))
1874 (define-public r-affixcan
1880 (uri (bioconductor-uri "AffiXcan" version))
1883 "0wj9shzmlxpksbxny571xzfcmmqqzjlk1vq4mx1is2r6ma7jkblq"))))
1884 (properties `((upstream-name . "AffiXcan")))
1885 (build-system r-build-system)
1887 (list r-biocparallel
1889 r-multiassayexperiment
1890 r-summarizedexperiment))
1891 (native-inputs (list r-knitr))
1892 (home-page "https://bioconductor.org/packages/AffiXcan")
1893 (synopsis "Functional approach to impute genetically regulated expression")
1895 "The @code{AffiXcan} package imputes a @dfn{genetically regulated
1896 expression} (GReX) for a set of genes in a sample of individuals, using a
1897 method based on the @dfn{total binding affinity} (TBA). Statistical models to
1898 impute GReX can be trained with a training dataset where the real total
1899 expression values are known.")
1900 (license license:gpl3)))
1902 (define-public r-affyrnadegradation
1904 (name "r-affyrnadegradation")
1908 (uri (bioconductor-uri "AffyRNADegradation" version))
1911 "16akwmpzwxai7ks5bvc1yyb9sx2scv9b9gas5avb0sk5fk0h3nsf"))))
1912 (properties `((upstream-name . "AffyRNADegradation")))
1913 (build-system r-build-system)
1914 (propagated-inputs (list r-affy))
1915 (home-page "https://bioconductor.org/packages/AffyRNADegradation")
1917 "Analyze and correct probe positional bias in data due to RNA degradation")
1919 "The @code{AffyRNADegradation} package helps with the assessment and
1920 correction of RNA degradation effects in Affymetrix 3 expression arrays. The
1921 parameter @code{d} gives a robust and accurate measure of RNA integrity. The
1922 correction removes the probe positional bias, and thus improves comparability
1923 of samples that are affected by RNA degradation.")
1924 ;; the R file header specifies GPL2 or later
1925 (license license:gpl2+)))
1927 (define-public r-agdex
1933 (uri (bioconductor-uri "AGDEX" version))
1936 "0c44fw5ajdjc13409rn3lsv0jhlqa2qcak9b1k8hpig486xxzsr9"))))
1937 (properties `((upstream-name . "AGDEX")))
1938 (build-system r-build-system)
1939 (propagated-inputs (list r-biobase r-gseabase))
1940 (home-page "https://bioconductor.org/packages/AGDEX")
1942 "Evaluate agreement of differential expression for cross-species genomics")
1944 "The objective of @code{AGDEX} is to evaluate whether the results of a
1945 pair of two-group differential expression analysis comparisons show a level of
1946 agreement that is greater than expected if the group labels for each two-group
1947 comparison are randomly assigned. The agreement is evaluated for the entire
1948 transcriptome and (optionally) for a collection of pre-defined gene-sets.
1949 Additionally, the procedure performs permutation-based differential expression
1950 and meta analysis at both gene and gene-set levels of the data from each
1952 (license license:gpl2+)))
1954 (define-public r-aggregatebiovar
1956 (name "r-aggregatebiovar")
1960 (uri (bioconductor-uri "aggregateBioVar" version))
1963 "0ngg12bgr95m4wm12scmrb55dgy4909c6qrg169l6dkng99v4nx1"))))
1964 (properties `((upstream-name . "aggregateBioVar")))
1965 (build-system r-build-system)
1970 r-singlecellexperiment
1971 r-summarizedexperiment
1973 (native-inputs (list r-knitr))
1974 (home-page "https://github.com/jasonratcliff/aggregateBioVar")
1975 (synopsis "Differential gene expression analysis for multi-subject scRNA-seq")
1977 "This package @code{aggregateBioVar} contains tools to summarize single
1978 cell gene expression profiles at the level of subject for single cell RNA-seq
1979 data collected from more than one subject (e.g. biological sample or technical
1980 replicates). A @code{SingleCellExperiment} object is taken as input and
1981 converted to a list of @code{SummarizedExperiment} objects, where each list
1982 element corresponds to an assigned cell type. The @code{SummarizedExperiment}
1983 objects contain aggregate gene-by-subject count matrices and inter-subject
1984 column metadata for individual subjects that can be processed using downstream
1985 bulk RNA-seq tools.")
1986 (license license:gpl3)))
1988 (define-public r-agilp
1994 (uri (bioconductor-uri "agilp" version))
1997 "1pm329y2nfcnx98ggxq0prdd5pxfcl5iylvsjjnhw5lyz1awg1yf"))))
1998 (properties `((upstream-name . "agilp")))
1999 (build-system r-build-system)
2000 (home-page "https://bioconductor.org/packages/agilp")
2001 (synopsis "Processing of Agilent expression array")
2003 "This package aims to provide a pipeline for the low-level analysis of
2004 gene expression microarray data, primarily focused on the Agilent platform,
2005 but which also provides utilities which may be useful for other platforms.")
2006 ;; Some files are under GPLv2+ but the combined work is released under the
2008 (license license:gpl3)))
2010 (define-public r-adductomicsr
2012 (name "r-adductomicsr")
2016 (uri (bioconductor-uri "adductomicsR" version))
2019 "0623qf06xgdsyz0in2wnxwvpdw8kj6cnwf8vlqmgp7g0n3w701ys"))))
2020 (properties `((upstream-name . "adductomicsR")))
2021 (build-system r-build-system)
2044 (native-inputs (list r-knitr))
2045 (home-page "https://bioconductor.org/packages/adductomicsR")
2046 (synopsis "Processing of adductomic mass spectral datasets")
2048 "This package @code{adductomicsR} processes data generated by the
2049 @dfn{second stage of mass spectrometry} (MS2) to identify potentially adducted
2050 peptides from spectra that has been corrected for mass drift and retention
2051 time drift and quantifies level mass spectral peaks from @dfn{first stage of
2052 mass spectrometry} (MS1) data.")
2053 (license license:artistic2.0)))
2055 (define-public r-agimicrorna
2057 (name "r-agimicrorna")
2061 (uri (bioconductor-uri "AgiMicroRna" version))
2064 "0jic89gyphbv7jzlfgm9bh1aq48lp86rq6hr34gsg9z0pa1192xa"))))
2065 (properties `((upstream-name . "AgiMicroRna")))
2066 (build-system r-build-system)
2073 (home-page "https://git.bioconductor.org/packages/AgiMicroRna")
2075 "Processing and differential expression analysis of Agilent microRNA chips")
2077 "@code{AgiMicroRna} provides useful functionality for the processing,
2078 quality assessment and differential expression analysis of Agilent microRNA
2079 array data. The package uses a limma-like structure to generate the processed
2080 data in order to make statistical inferences about differential expression
2081 using the linear model features implemented in limma. Standard Bioconductor
2082 objects are used so that other packages could be used as well.")
2083 (license license:gpl3)))
2085 (define-public r-airpart
2091 (uri (bioconductor-uri "airpart" version))
2094 "0ljankgvgf8rby4z340wxx8v7acs9yz955p3a40jl6y8rz1svc06"))))
2095 (properties `((upstream-name . "airpart")))
2096 (build-system r-build-system)
2115 r-singlecellexperiment
2117 r-summarizedexperiment))
2118 (native-inputs (list r-knitr))
2119 (home-page "https://bioconductor.org/packages/airpart")
2120 (synopsis "Differential cell-type-specific allelic imbalance")
2122 "The airpart package identifies sets of genes displaying differential
2123 cell-type-specific allelic imbalance across cell types or states, utilizing
2124 single-cell allelic counts. It makes use of a generalized fused lasso with
2125 binomial observations of allelic counts to partition cell types by their
2126 allelic imbalance. Alternatively, a nonparametric method for partitioning
2127 cell types is offered. The package includes a number of visualizations and
2128 quality control functions for examining single cell allelic imbalance
2130 (license license:gpl2)))
2132 (define-public r-amountain
2134 (name "r-amountain")
2138 (uri (bioconductor-uri "AMOUNTAIN" version))
2141 "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54"))))
2142 (properties `((upstream-name . "AMOUNTAIN")))
2143 (build-system r-build-system)
2145 (native-inputs (list r-knitr))
2146 (home-page "https://bioconductor.org/packages/AMOUNTAIN")
2147 (synopsis "Modules for multilayer weighted gene co-expression networks")
2149 "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted
2150 gene co-expression network) could be constructed only from expression profile.
2151 Different layers in such networks may represent different time points, multiple
2152 conditions or various species. @code{AMOUNTAIN} aims to search active modules
2153 in multi-layer WGCN using a continuous optimization approach.")
2154 (license license:gpl2+)))
2156 (define-public r-amaretto
2162 (uri (bioconductor-uri "AMARETTO" version))
2165 "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx"))))
2166 (properties `((upstream-name . "AMARETTO")))
2167 (build-system r-build-system)
2169 (list r-biocfilecache
2187 r-multiassayexperiment
2193 (native-inputs (list r-knitr))
2194 (home-page "https://bioconductor.org/packages/AMARETTO")
2195 (synopsis "Regulatory network inference and driver gene evaluation")
2197 "This package @code{AMARETTO} represents an algorithm that integrates copy
2198 number, DNA methylation and gene expression data to identify a set of driver
2199 genes by analyzing cancer samples and connects them to clusters of co-expressed
2200 genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer
2201 setting to identify cancer driver genes and their modules on multiple cancer
2202 sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle
2203 and EMT, and modules that accurately predict survival and molecular subtypes.
2204 This allows @code{AMARETTO} to identify novel cancer driver genes directing
2205 canonical cancer pathways.")
2206 (license license:asl2.0)))
2208 (define-public r-anaquin
2214 (uri (bioconductor-uri "Anaquin" version))
2217 "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd"))))
2218 (properties `((upstream-name . "Anaquin")))
2219 (build-system r-build-system)
2228 (native-inputs (list r-knitr))
2229 (home-page "https://www.sequinstandards.com/")
2230 (synopsis "Statistical analysis of sequins")
2232 "The project is intended to support the use of @dfn{sequins}(synthetic
2233 sequencing spike-in controls) owned and made available by the Garvan Institute
2234 of Medical Research. The goal is to provide a standard library for quantitative
2235 analysis, modelling, and visualization of spike-in controls.")
2236 (license license:bsd-3)))
2238 (define-public r-aldex2
2244 (uri (bioconductor-uri "ALDEx2" version))
2247 "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9"))))
2248 (properties `((upstream-name . "ALDEx2")))
2249 (build-system r-build-system)
2251 (list r-biocparallel
2257 r-summarizedexperiment
2259 (native-inputs (list r-knitr))
2260 (home-page "https://github.com/ggloor/ALDEx_bioc")
2261 (synopsis "Analysis of differential abundance taking sample variation into account")
2263 "This package provides a differential abundance analysis for the
2264 comparison of two or more conditions. Useful for analyzing data from standard
2265 RNA-seq or meta-RNA-seq assays as well as selected and unselected values from
2266 in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer
2267 abundance from counts, optimized for three or more experimental replicates.
2268 The method infers biological and sampling variation to calculate the expected
2269 false discovery rate, given the variation, based on a Wilcoxon Rank Sum test
2270 and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a
2271 correlation test. All tests report p-values and Benjamini-Hochberg corrected
2272 p-values. ALDEx2 also calculates expected standardized effect sizes for
2273 paired or unpaired study designs.")
2274 ;; The code for the function "rdirichlet" is from the R package
2275 ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the
2276 ;; package's LICENSE is specified as GPL-3.
2277 (license (list license:agpl3+ license:gpl2+ license:gpl3))))
2279 (define-public r-alpine
2285 (uri (bioconductor-uri "alpine" version))
2288 "1nl1hxwakh5m9rqm3ksn2jzknsj9xnwl51bmc30knknm4q35wdv9"))))
2289 (properties `((upstream-name . "alpine")))
2290 (build-system r-build-system)
2304 r-summarizedexperiment))
2305 (native-inputs (list r-knitr))
2306 (home-page "https://bioconductor.org/packages/alpine")
2307 (synopsis "Modeling and correcting fragment sequence bias")
2309 "The package @code{alpine} helps to model bias parameters and then using
2310 those parameters to estimate RNA-seq transcript abundance. @code{Alpine} is a
2311 package for estimating and visualizing many forms of sample-specific biases that
2312 can arise in RNA-seq, including fragment length distribution, positional bias on
2313 the transcript, read start bias (random hexamer priming), and fragment GC-content
2314 (amplification). It also offers bias-corrected estimates of transcript
2315 abundance in @dfn{FPKM}(Fragments Per Kilobase of transcript per Million
2316 mapped reads). It is currently designed for un-stranded paired-end RNA-seq
2318 (license license:gpl2+)))
2320 (define-public r-aneufinder
2322 (name "r-aneufinder")
2326 (uri (bioconductor-uri "AneuFinder" version))
2329 "1acsp987jv2x4qwbgy3y7ff4r2qz7680b0nbr37m4lmncqfgh8yl"))))
2330 (build-system r-build-system)
2334 (list r-genomicranges
2355 (home-page "https://bioconductor.org/packages/AneuFinder/")
2356 (synopsis "Copy number variation analysis in single-cell-sequencing data")
2357 (description "This package implements functions for copy number variant
2358 calling, plotting, export and analysis from whole-genome single cell
2360 (license license:artistic2.0)))
2362 (define-public r-anf
2368 (uri (bioconductor-uri "ANF" version))
2371 "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj"))))
2372 (properties `((upstream-name . "ANF")))
2373 (build-system r-build-system)
2380 (native-inputs (list r-knitr))
2381 (home-page "https://bioconductor.org/packages/ANF")
2382 (synopsis "Affinity network fusion for complex patient clustering")
2384 "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity
2385 matrix construction and fusion as well as spectral clustering. This package is
2386 used for complex patient clustering by integrating multi-omic data through affinity
2388 (license license:gpl3)))
2390 (define-public r-annmap
2396 (uri (bioconductor-uri "annmap" version))
2399 "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv"))))
2400 (properties `((upstream-name . "annmap")))
2401 (build-system r-build-system)
2413 (home-page "https://github.com/cruk-mi/annmap")
2415 "Genome annotation and visualisation for Affymetrix arrays and NGS analysis")
2417 "This package @code{annmap} provides annotation mappings for Affymetrix exon
2418 arrays and coordinate based queries to support deep sequencing data analysis.
2419 Database access is hidden behind the API which provides a set of functions such
2420 as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc.
2421 Functions to plot gene architecture and BAM file data are also provided.")
2422 (license license:gpl2)))
2424 (define-public r-antiprofiles
2426 (name "r-antiprofiles")
2430 (uri (bioconductor-uri "antiProfiles" version))
2433 "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40"))))
2434 (properties `((upstream-name . "antiProfiles")))
2435 (build-system r-build-system)
2439 (home-page "https://github.com/HCBravoLab/antiProfiles")
2440 (synopsis "Implementation of gene expression anti-profiles")
2442 "This package implements the gene expression anti-profiles method.
2443 Anti-profiles are a new approach for developing cancer genomic signatures that
2444 specifically take advantage of gene expression heterogeneity. They explicitly
2445 model increased gene expression variability in cancer to define robust and
2446 reproducible gene expression signatures capable of accurately distinguishing
2447 tumor samples from healthy controls.")
2448 (license license:artistic2.0)))
2450 (define-public r-aseb
2456 (uri (bioconductor-uri "ASEB" version))
2459 "1i0r4vimk6is4j4rr14ajp8papznpmmr0bhwd96s8w53cqdqph7p"))))
2460 (properties `((upstream-name . "ASEB")))
2461 (build-system r-build-system)
2462 (home-page "https://bioconductor.org/packages/ASEB")
2463 (synopsis "Predict acetylated lysine sites")
2465 "ASEB is an R package to predict lysine sites that can be acetylated by a
2466 specific @dfn{KAT} (K-acetyl-transferases) family. Lysine acetylation is a
2467 well-studied posttranslational modification on kinds of proteins. About four
2468 thousand lysine acetylation sites and over 20 lysine KATs have been
2469 identified. However, which KAT is responsible for a given protein or lysine
2470 site acetylation is mostly unknown. In this package, we use a
2471 @dfn{GSEA}-like (Gene Set Enrichment Analysis) method to make predictions.
2472 GSEA method was developed and successfully used to detect coordinated
2473 expression changes and find the putative functions of the long non-coding
2475 (license license:gpl3+)))
2477 (define-public r-asgsca
2483 (uri (bioconductor-uri "ASGSCA" version))
2486 "0mxrrkm2lg7gxjh8ynn6qmryn8wqda7b83sr51dpgblay83jcbaq"))))
2487 (properties `((upstream-name . "ASGSCA")))
2488 (build-system r-build-system)
2489 (propagated-inputs (list r-mass r-matrix))
2490 (home-page "https://bioconductor.org/packages/ASGSCA")
2491 (synopsis "Analysis of associations between multiple genotypes and traits")
2493 "The package @dfn{ASGSCA} (Association Study using Generalized Structured
2494 Component Analysis) provides tools to model and test the association between
2495 multiple genotypes and multiple traits, taking into account the prior
2496 biological knowledge. Genes, and clinical pathways are incorporated in the
2497 model as latent variables.")
2498 (license license:gpl3)))
2500 (define-public r-aspli
2506 (uri (bioconductor-uri "ASpli" version))
2509 "1frlcwa8m4imfx6ncav8r8yskyaf4ibha177mfnp9y84w6mphynz"))))
2510 (properties `((upstream-name . "ASpli")))
2511 (build-system r-build-system)
2513 (list r-annotationdbi
2533 (home-page "https://bioconductor.org/packages/ASpli")
2534 (synopsis "Analysis of alternative splicing using RNA-Seq")
2536 "@dfn{AS} (alternative splicing) is a common mechanism of
2537 post-transcriptional gene regulation in eukaryotic organisms that expands the
2538 functional and regulatory diversity of a single gene by generating multiple
2539 mRNA isoforms that encode structurally and functionally distinct proteins.
2540 ASpli is an integrative pipeline and user-friendly R package that facilitates
2541 the analysis of changes in both annotated and novel AS events. ASpli
2542 integrates several independent signals in order to deal with the complexity
2543 that might arise in splicing patterns.")
2544 ;; The authors didn't specify any GPL version in description or in the
2546 (license (list license:gpl2+ license:gpl3+))))
2548 (define-public r-assessorf
2550 (name "r-assessorf")
2554 (uri (bioconductor-uri "AssessORF" version))
2557 "1l87bpny9k3jbzbzmb9h2ijvblrj471gqv26fyzbvb3vr6y406z7"))))
2558 (properties `((upstream-name . "AssessORF")))
2559 (build-system r-build-system)
2565 (native-inputs (list r-knitr))
2566 (home-page "https://bioconductor.org/packages/AssessORF")
2567 (synopsis "Assess gene predictions using proteomics and evolutionary conservation")
2569 "In order to assess the quality of a set of predicted genes for a genome,
2570 evidence must first be mapped to that genome. Next, each gene must be
2571 categorized based on how strong the evidence is for or against that gene. The
2572 AssessORF package provides the functions and class structures necessary for
2573 accomplishing those tasks, using proteomics hits and evolutionarily conserved
2574 start codons as the forms of evidence.")
2575 (license license:gpl3)))
2577 (define-public r-asset
2583 (uri (bioconductor-uri "ASSET" version))
2586 "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg"))))
2587 (properties `((upstream-name . "ASSET")))
2588 (build-system r-build-system)
2589 (propagated-inputs (list r-mass r-msm r-rmeta))
2590 (native-inputs (list r-knitr))
2591 (home-page "https://bioconductor.org/packages/ASSET")
2593 "Subset-based association analysis of heterogeneous traits and subtypes")
2595 "This package is an R program for the subset-based analysis of
2596 heterogeneous traits and disease subtypes. ASSET allows the user to search
2597 through all possible subsets of z-scores to identify the subset of traits
2598 giving the best meta-analyzed z-score. Further, it returns a p-value
2599 adjusting for the multiple-testing involved in the search. It also allows for
2600 searching for the best combination of disease subtypes associated with each
2602 (license license:gpl2)))
2604 (define-public r-atena
2610 (uri (bioconductor-uri "atena" version))
2613 "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp"))))
2614 (properties `((upstream-name . "atena")))
2615 (build-system r-build-system)
2617 (list r-annotationhub
2630 r-summarizedexperiment))
2631 (native-inputs (list r-knitr))
2632 (home-page "https://github.com/functionalgenomics/atena")
2633 (synopsis "Analysis of transposable elements")
2635 "The atena package quantifies expression of @dfn{TEs} (transposable
2636 elements) from RNA-seq data through different methods, including ERVmap,
2637 TEtranscripts and Telescope. A common interface is provided to use each of
2638 these methods, which consists of building a parameter object, calling the
2639 quantification function with this object and getting a
2640 @code{SummarizedExperiment} object as an output container of the quantified
2641 expression profiles. The implementation allows quantifing TEs and gene
2642 transcripts in an integrated manner.")
2643 (license license:artistic2.0)))
2645 (define-public r-atsnp
2651 (uri (bioconductor-uri "atSNP" version))
2654 "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz"))))
2655 (properties `((upstream-name . "atSNP")))
2656 (build-system r-build-system)
2658 (list r-biocfilecache
2668 (native-inputs (list r-knitr))
2669 (home-page "https://github.com/sunyoungshin/atSNP")
2671 "Affinity test for identifying regulatory single nucleotide polymorphisms")
2673 "The atSNP package performs affinity tests of motif matches with the
2674 @dfn{SNP} (single nucleotide polymorphism) or the reference genomes and
2675 SNP-led changes in motif matches.")
2676 (license license:gpl2)))
2678 (define-public r-attract
2684 (uri (bioconductor-uri "attract" version))
2687 "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82"))))
2688 (properties `((upstream-name . "attract")))
2689 (build-system r-build-system)
2691 (list r-annotationdbi
2699 (home-page "https://bioconductor.org/packages/attract")
2700 (synopsis "Finding drivers of Kauffman's attractor landscape")
2702 "This package contains the functions to find the gene expression modules
2703 that represent the drivers of Kauffman's attractor landscape. The modules are
2704 the core attractor pathways that discriminate between different cell types of
2705 groups of interest. Each pathway has a set of synexpression groups, which show
2706 transcriptionally-coordinated changes in gene expression.")
2707 (license license:lgpl2.0+)))
2709 (define-public r-awfisher
2715 (uri (bioconductor-uri "AWFisher" version))
2718 "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1"))))
2719 (properties `((upstream-name . "AWFisher")))
2720 (build-system r-build-system)
2724 (native-inputs (list r-knitr))
2725 (home-page "https://bioconductor.org/packages/AWFisher")
2726 (synopsis "Fast computing for adaptively weighted fisher's method")
2728 "This package is an implementation of the Adaptively Weighted Fisher's
2729 method, including fast p-value computing, variability index, and
2731 (license license:gpl3)))
2733 (define-public r-awst
2739 (uri (bioconductor-uri "awst" version))
2742 "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav"))))
2743 (properties `((upstream-name . "awst")))
2744 (build-system r-build-system)
2745 (propagated-inputs (list r-summarizedexperiment))
2746 (native-inputs (list r-knitr))
2747 (home-page "https://github.com/drisso/awst")
2748 (synopsis "Asymmetric within-sample transformation")
2750 "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that
2751 regularizes RNA-seq read counts and reduces the effect of noise on the
2752 classification of samples. AWST comprises two main steps: standardization and
2753 smoothing. These steps transform gene expression data to reduce the noise of
2754 the lowly expressed features, which suffer from background effects and low
2755 signal-to-noise ratio, and the influence of the highly expressed features,
2756 which may be the result of amplification bias and other experimental
2758 (license license:expat)))
2760 (define-public r-baalchip
2766 (uri (bioconductor-uri "BaalChIP" version))
2769 "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
2770 (properties `((upstream-name . "BaalChIP")))
2771 (build-system r-build-system)
2772 (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
2786 (native-inputs (list r-knitr))
2787 (home-page "https://bioconductor.org/packages/BaalChIP")
2789 "Analysis of allele-specific transcription factor binding in cancer genomes")
2791 "This package offers functions to process multiple @code{ChIP-seq BAM}
2792 files and detect allele-specific events. It computes allele counts at
2793 individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
2794 control) steps to remove problematic variants, and utilizes a Bayesian
2795 framework to identify statistically significant allele-specific events.
2796 BaalChIP is able to account for copy number differences between the two
2797 alleles, a known phenotypical feature of cancer samples.")
2798 (license license:artistic2.0)))
2800 (define-public r-basespacer
2802 (name "r-basespacer")
2806 (uri (bioconductor-uri "BaseSpaceR" version))
2809 "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj"))))
2810 (properties `((upstream-name . "BaseSpaceR")))
2811 (build-system r-build-system)
2812 (propagated-inputs (list r-rcurl r-rjsonio))
2813 (home-page "https://bioconductor.org/packages/BaseSpaceR")
2814 (synopsis "R SDK for BaseSpace RESTful API")
2816 "This package provides an R interface to Illumina's BaseSpace cloud
2817 computing environment, enabling the fast development of data analysis and
2818 visualization tools. Besides providing an easy to use set of tools for
2819 manipulating the data from BaseSpace, it also facilitates the access to R's
2820 rich environment of statistical and data analysis tools.")
2821 (license license:asl2.0)))
2823 (define-public r-bac
2829 (uri (bioconductor-uri "BAC" version))
2832 "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2"))))
2833 (properties `((upstream-name . "BAC")))
2834 (build-system r-build-system)
2835 (home-page "https://bioconductor.org/packages/BAC")
2836 (synopsis "Bayesian analysis of Chip-chip experiment")
2838 "This package uses a Bayesian hierarchical model to detect enriched
2839 regions from ChIP-chip experiments. The common goal in analyzing this
2840 ChIP-chip data is to detect DNA-protein interactions from ChIP-chip
2841 experiments. The BAC package has mainly been tested with Affymetrix tiling
2842 array data. However, we expect it to work with other platforms (e.g. Agilent,
2843 Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so
2844 you will have to normalize your data beforehand.")
2845 (license license:artistic2.0)))
2847 (define-public r-bader
2853 (uri (bioconductor-uri "BADER" version))
2856 "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm"))))
2857 (properties `((upstream-name . "BADER")))
2858 (build-system r-build-system)
2859 (home-page "https://bioconductor.org/packages/BADER")
2861 "Bayesian analysis of differential expression in RNA sequencing data")
2863 "The BADER package is intended for the analysis of RNA sequencing data.
2864 The algorithm fits a Bayesian hierarchical model for RNA sequencing count
2865 data. BADER returns the posterior probability of differential expression for
2866 each gene between two groups A and B. The joint posterior distribution of the
2867 variables in the model can be returned in the form of posterior samples, which
2868 can be used for further down-stream analyses such as gene set enrichment.")
2869 (license license:gpl2)))
2871 (define-public r-badregionfinder
2873 (name "r-badregionfinder")
2877 (uri (bioconductor-uri "BadRegionFinder" version))
2880 "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9"))))
2881 (properties `((upstream-name . "BadRegionFinder")))
2882 (build-system r-build-system)
2888 r-variantannotation))
2889 (home-page "https://bioconductor.org/packages/BadRegionFinder")
2890 (synopsis "Identifying regions with bad coverage in sequence alignment data")
2892 "BadRegionFinder is a package for identifying regions with a bad,
2893 acceptable and good coverage in sequence alignment data available as bam
2894 files. The whole genome may be considered as well as a set of target regions.
2895 Various visual and textual types of output are available.")
2896 (license license:lgpl3)))
2898 (define-public r-bambu
2904 (uri (bioconductor-uri "bambu" version))
2907 "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w"))))
2908 (properties `((upstream-name . "bambu")))
2909 (build-system r-build-system)
2911 (list r-biocgenerics
2925 r-summarizedexperiment
2928 (native-inputs (list r-knitr))
2929 (home-page "https://github.com/GoekeLab/bambu")
2931 "Isoform reconstruction and quantification for long read RNA-Seq data")
2933 "This R package is for multi-sample transcript discovery and
2934 quantification using long read RNA-Seq data. You can use bambu after read
2935 alignment to obtain expression estimates for known and novel transcripts and
2936 genes. The output from bambu can directly be used for visualisation and
2937 downstream analysis, such as differential gene expression or transcript
2939 (license license:gpl3)))
2941 (define-public r-bandits
2947 (uri (bioconductor-uri "BANDITS" version))
2950 "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9"))))
2951 (properties `((upstream-name . "BANDITS")))
2952 (build-system r-build-system)
2954 (list r-biocparallel
2965 (native-inputs (list r-knitr))
2966 (home-page "https://github.com/SimoneTiberi/BANDITS")
2967 (synopsis "Bayesian analysis of differential splicing")
2969 "BANDITS is a Bayesian hierarchical model for detecting differential
2970 splicing of genes and transcripts, via @dfn{DTU} (differential transcript
2971 usage), between two or more conditions. The method uses a Bayesian
2972 hierarchical framework, which allows for sample specific proportions in a
2973 Dirichlet-Multinomial model, and samples the allocation of fragments to the
2974 transcripts. Parameters are inferred via @dfn{MCMC} (Markov chain Monte
2975 Carlo) techniques and a DTU test is performed via a multivariate Wald test on
2976 the posterior densities for the average relative abundance of transcripts.")
2977 (license license:gpl3+)))
2979 (define-public r-banocc
2985 (uri (bioconductor-uri "banocc" version))
2988 "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx"))))
2989 (properties `((upstream-name . "banocc")))
2990 (build-system r-build-system)
2996 (native-inputs (list r-knitr))
2997 (home-page "https://bioconductor.org/packages/banocc")
2998 (synopsis "Bayesian analysis of compositional covariance")
3000 "BAnOCC is a package designed for compositional data, where each sample
3001 sums to one. It infers the approximate covariance of the unconstrained data
3002 using a Bayesian model coded with @code{rstan}. It provides as output the
3003 @code{stanfit} object as well as posterior median and credible interval
3004 estimates for each correlation element.")
3005 (license license:expat)))
3007 (define-public r-barcodetrackr
3009 (name "r-barcodetrackr")
3013 (uri (bioconductor-uri "barcodetrackR" version))
3016 "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3"))))
3017 (properties `((upstream-name . "barcodetrackR")))
3018 (build-system r-build-system)
3034 r-summarizedexperiment
3039 (native-inputs (list r-knitr))
3040 (home-page "https://github.com/dunbarlabNIH/barcodetrackR")
3041 (synopsis "Functions for analyzing cellular barcoding data")
3043 "This package is developed for the analysis and visualization of clonal
3044 tracking data. The required data is formed by samples and tag abundances in
3045 matrix form, usually from cellular barcoding experiments, integration site
3046 retrieval analyses, or similar technologies.")
3047 (license license:cc0)))
3049 (define-public r-biocversion
3051 (name "r-biocversion")
3056 (uri (bioconductor-uri "BiocVersion" version))
3059 "0rs4nyza4hqqk204d037gi013135wgfhx5asq2dsdjc9vk5nwzfn"))))
3060 (properties `((upstream-name . "BiocVersion")))
3061 (build-system r-build-system)
3062 (home-page "https://bioconductor.org/packages/BiocVersion/")
3063 (synopsis "Set the appropriate version of Bioconductor packages")
3065 "This package provides repository information for the appropriate version
3067 (license license:artistic2.0)))
3069 (define-public r-biocgenerics
3071 (name "r-biocgenerics")
3075 (uri (bioconductor-uri "BiocGenerics" version))
3078 "0iv9bnpw2hycndwbmjsszqfwrksz6dfr6qcz78jkssc9ldsgmdhc"))))
3080 `((upstream-name . "BiocGenerics")))
3081 (build-system r-build-system)
3082 (home-page "https://bioconductor.org/packages/BiocGenerics")
3083 (synopsis "S4 generic functions for Bioconductor")
3085 "This package provides S4 generic functions needed by many Bioconductor
3087 (license license:artistic2.0)))
3089 (define-public r-coverageview
3091 (name "r-coverageview")
3095 (uri (bioconductor-uri "CoverageView" version))
3098 "0mh66l4yh6rpd1r7qbqwh5jkklqyvpfiap0zcqhz9kimssm2pbbp"))))
3099 (build-system r-build-system)
3107 (home-page "https://bioconductor.org/packages/CoverageView/")
3108 (synopsis "Coverage visualization package for R")
3109 (description "This package provides a framework for the visualization of
3110 genome coverage profiles. It can be used for ChIP-seq experiments, but it can
3111 be also used for genome-wide nucleosome positioning experiments or other
3112 experiment types where it is important to have a framework in order to inspect
3113 how the coverage distributed across the genome.")
3114 (license license:artistic2.0)))
3116 (define-public r-cummerbund
3118 (name "r-cummerbund")
3122 (uri (bioconductor-uri "cummeRbund" version))
3125 "1p4anmi436zykp0ir307g75g23kj8b7shxg4r65qq6zdwflphm0q"))))
3126 (build-system r-build-system)
3138 (home-page "https://bioconductor.org/packages/cummeRbund/")
3139 (synopsis "Analyze Cufflinks high-throughput sequencing data")
3140 (description "This package allows for persistent storage, access,
3141 exploration, and manipulation of Cufflinks high-throughput sequencing
3142 data. In addition, provides numerous plotting functions for commonly
3143 used visualizations.")
3144 (license license:artistic2.0)))
3146 (define-public r-dama
3152 (uri (bioconductor-uri "daMA" version))
3155 "1mpjvl24wsdmpgra3iasgfvy29m71318gj6j1gg6081w0n4cq72m"))))
3156 (properties `((upstream-name . "daMA")))
3157 (build-system r-build-system)
3158 (propagated-inputs (list r-mass))
3159 (home-page "https://bioconductor.org/packages/release/bioc/html/daMA.html")
3161 "Efficient design and analysis of factorial two-colour microarray data")
3163 "This package contains functions for the efficient design of factorial
3164 two-colour microarray experiments and for the statistical analysis of
3165 factorial microarray data.")
3166 (license license:gpl2+)))
3168 (define-public r-damefinder
3170 (name "r-damefinder")
3174 (uri (bioconductor-uri "DAMEfinder" version))
3177 "123ra94bij0m45j2fzqr7fjipj4ld9kgk0kir1zfdbbd5h8h4mdf"))))
3178 (properties `((upstream-name . "DAMEfinder")))
3179 (build-system r-build-system)
3181 (list r-biocgenerics
3197 r-summarizedexperiment
3198 r-variantannotation))
3199 (native-inputs (list r-knitr))
3200 (home-page "https://bioconductor.org/packages/DAMEfinder")
3201 (synopsis "Differential allelicly methylated regions")
3203 "This package offers functionality for taking methtuple or Bismark
3204 outputs to calculate @acronym{ASM, Allele-Specific Methylation} scores and
3205 compute @acronym{DAMEs, Differential Allelicly MEthylated} regions. It also
3206 offers nice visualization of methyl-circle plots.")
3207 (license license:expat)))
3209 (define-public r-dearseq
3216 (uri (bioconductor-uri "dearseq" version))
3219 "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl"))))
3220 (build-system r-build-system)
3222 (list r-compquadform
3238 (home-page "https://github.com/borishejblum/dearseq")
3239 (synopsis "DEA for RNA-seq data through a robust variance component test")
3241 "This is a package for Differential Expression Analysis of RNA-seq data.
3242 It features a variance component score test accounting for data
3243 heteroscedasticity through precision weights. Perform both gene-wise and gene
3244 set analyses, and can deal with repeated or longitudinal data.")
3245 (license license:gpl2)))
3247 (define-public r-debcam
3253 (uri (bioconductor-uri "debCAM" version))
3256 "1ynz57kkxl8nx80zhh1vhhydqb5n6r9d7p69f0k9nj8rp4hdgng7"))))
3257 (properties `((upstream-name . "debCAM")))
3258 (build-system r-build-system)
3259 (inputs (list openjdk))
3271 r-summarizedexperiment))
3272 (native-inputs (list r-knitr))
3273 (home-page "https://bioconductor.org/packages/debCAM")
3274 (synopsis "Deconvolution by convex analysis of mixtures")
3276 "This package is an R implementation for fully unsupervised deconvolution
3277 of complex tissues. DebCAM provides basic functions to perform unsupervised
3278 deconvolution on mixture expression profiles by @acronym{CAM, Convex Analysis
3279 of Mixtures} and some auxiliary functions to help understand the
3280 subpopulation- specific results. It also implements functions to perform
3281 supervised deconvolution based on prior knowledge of molecular markers, S
3282 matrix or A matrix. Combining molecular markers from CAM and from prior
3283 knowledge can achieve semi-supervised deconvolution of mixtures.")
3284 (license license:gpl2)))
3286 (define-public r-decipher
3292 (uri (bioconductor-uri "DECIPHER" version))
3295 "045q2bfzgq1yzhyrzvrhrnmlpka4gikrajxxwv05szksy5nvp7q5"))))
3296 (build-system r-build-system)
3304 (home-page "https://www.bioconductor.org/packages/DECIPHER/")
3305 (synopsis "Tools for deciphering and managing biological sequences")
3306 (description "This package provides a toolset for deciphering and managing
3307 biological sequences.")
3308 (license license:gpl3)))
3310 (define-public r-deco
3316 (uri (bioconductor-uri "deco" version))
3319 "18n5zgln33c79jbjzjlivs8ihyg8zci6minfqlvagxgzcpa67k0m"))))
3320 (properties `((upstream-name . "deco")))
3321 (build-system r-build-system)
3341 r-summarizedexperiment))
3342 (native-inputs (list r-knitr))
3343 (home-page "https://github.com/fjcamlab/deco")
3344 (synopsis "Decomposing heterogeneous cohorts using omic data profiling")
3346 "This package discovers differential features in hetero- and homogeneous
3347 omic data by a two-step method including subsampling LIMMA and NSCA. DECO
3348 reveals feature associations to hidden subclasses not exclusively related to
3349 higher deregulation levels.")
3350 (license license:gpl3+)))
3352 (define-public r-decomplexdisease
3354 (name "r-decomplexdisease")
3358 (uri (bioconductor-uri "DEComplexDisease" version))
3361 "09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d"))))
3362 (properties `((upstream-name . "DEComplexDisease")))
3363 (build-system r-build-system)
3365 (list r-biocparallel
3370 r-summarizedexperiment))
3371 (native-inputs (list r-knitr))
3372 (home-page "https://bioconductor.org/packages/DEComplexDisease")
3373 (synopsis "Investigations of complex diseases by bi-clustering analysis")
3375 "DEComplexDisease is designed to find the @acronym{DEGs, Differential
3376 Expressed Genes} for complex disease, which is characterized by the
3377 heterogeneous genomic expression profiles. Different from the established DEG
3378 analysis tools, it does not assume the patients of complex diseases to share
3379 the common DEGs. By applying a bi-clustering algorithm, DEComplexDisease
3380 finds the DEGs shared by as many patients. Applying the DEComplexDisease
3381 analysis results, users are possible to find the patients affected by the same
3382 mechanism based on the shared signatures.")
3383 (license license:gpl3)))
3385 (define-public r-decomptumor2sig
3387 (name "r-decomptumor2sig")
3391 (uri (bioconductor-uri "decompTumor2Sig" version))
3394 "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6"))))
3395 (properties `((upstream-name . "decompTumor2Sig")))
3396 (build-system r-build-system)
3397 (inputs (list perl)) ;script/extractSpecColumns.pl
3399 (list r-biocgenerics
3401 r-bsgenome-hsapiens-ucsc-hg19
3414 r-summarizedexperiment
3415 r-txdb-hsapiens-ucsc-hg19-knowngene
3416 r-variantannotation))
3417 (native-inputs (list r-knitr))
3418 (home-page "https://rmpiro.net/decompTumor2Sig/")
3419 (synopsis "Decomposition of individual tumors into mutational signatures")
3421 "The package uses quadratic programming for signature refitting, i.e., to
3422 decompose the mutation catalog from an individual tumor sample into a set of
3423 given mutational signatures (either Alexandrov-model signatures or
3424 Shiraishi-model signatures), computing weights that reflect the contributions
3425 of the signatures to the mutation load of the tumor.")
3426 (license license:gpl2)))
3428 (define-public r-deconrnaseq
3430 (name "r-deconrnaseq")
3434 (uri (bioconductor-uri "DeconRNASeq" version))
3437 "10smk88srxm58hli0fhkdfd6l5z02q58xc9mww39gkn71y0127k6"))))
3438 (properties `((upstream-name . "DeconRNASeq")))
3439 (build-system r-build-system)
3444 (home-page "https://bioconductor.org/packages/DeconRNASeq")
3446 "Deconvolution of heterogeneous tissue samples for mRNA-Seq data")
3448 "DeconSeq is an R package for deconvolution of heterogeneous tissues
3449 based on mRNA-Seq data. It models the expression levels from heterogeneous
3450 cell populations in mRNA-Seq as the weighted average of expression from
3451 different constituting cell types and predicted cell type proportions of
3452 single expression profiles.")
3453 (license license:gpl2)))
3455 (define-public r-decontam
3461 (uri (bioconductor-uri "decontam" version))
3464 "1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9"))))
3465 (properties `((upstream-name . "decontam")))
3466 (build-system r-build-system)
3468 (list r-ggplot2 r-reshape2))
3469 (native-inputs (list r-knitr))
3470 (home-page "https://github.com/benjjneb/decontam")
3472 "Identification of contaminants in marker-gene and metagenomics data")
3474 "This package offers simple statistical identification of contaminating
3475 sequence features in marker-gene or metagenomics data. It works on any kind
3476 of feature derived from environmental sequencing data (e.g. ASVs, OTUs,
3477 taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced
3478 negative control samples.")
3479 (license license:artistic2.0)))
3481 (define-public r-deconvr
3487 (uri (bioconductor-uri "deconvR" version))
3490 "091z3lncamscsvzj63zzbw7dr7vnkn0jwfkm5ljq4112w4rxgrm3"))))
3491 (properties `((upstream-name . "deconvR")))
3492 (build-system r-build-system)
3511 (native-inputs (list r-knitr))
3512 (home-page "https://github.com/BIMSBbioinfo/deconvR")
3513 (synopsis "Simulation and deconvolution of omic profiles")
3515 "This package provides a collection of functions designed for analyzing
3516 deconvolution of the bulk sample(s) using an atlas of reference omic signature
3517 profiles and a user-selected model. Users are given the option to create or
3518 extend a reference atlas and,also simulate the desired size of the bulk
3519 signature profile of the reference cell types. The package includes the
3520 cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can
3521 be used in deconvolution. Additionally, we included @code{BSmeth2Probe}, to
3522 make mapping WGBS data to their probe IDs easier.")
3523 (license license:artistic2.0)))
3525 (define-public r-decoupler
3527 (name "r-decoupler")
3532 (uri (bioconductor-uri "decoupleR" version))
3534 (base32 "0q1w8yw3bwx8ai5z8rw8lz97w4cplxijq93634hza2vgkig1ck9m"))))
3535 (properties `((upstream-name . "decoupleR")))
3536 (build-system r-build-system)
3549 (native-inputs (list r-knitr))
3550 (home-page "https://saezlab.github.io/decoupleR/")
3551 (synopsis "Computational methods to infer biological activities from omics data")
3553 "Many methods allow us to extract biological activities from omics data using
3554 information from prior knowledge resources, reducing the dimensionality for
3555 increased statistical power and better interpretability. decoupleR is a
3556 Bioconductor package containing different statistical methods to extract these
3557 signatures within a unified framework. decoupleR allows the user to flexibly
3558 test any method with any resource. It incorporates methods that take into
3559 account the sign and weight of network interactions. decoupleR can be used
3560 with any omic, as long as its features can be linked to a biological process
3561 based on prior knowledge. For example, in transcriptomics gene sets regulated
3562 by a transcription factor, or in phospho-proteomics phosphosites that are
3563 targeted by a kinase.")
3564 (license license:gpl3)))
3566 (define-public r-deepsnv
3572 (uri (bioconductor-uri "deepSNV" version))
3575 "0bgj1grv3a5bqhcdsw445x49kl3pz367svy6fnrzfsk9bmj46kgn"))))
3576 (properties `((upstream-name . "deepSNV")))
3577 (build-system r-build-system)
3583 r-summarizedexperiment
3588 (home-page "https://github.com/gerstung-lab/deepSNV/")
3589 (synopsis "Detection of subclonal SNVs in deep sequencing data")
3591 "This package provides quantitative variant callers for detecting
3592 subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments.
3593 The deepSNV algorithm is used for a comparative setup with a control experiment
3594 of the same loci and uses a beta-binomial model and a likelihood ratio test to
3595 discriminate sequencing errors and subclonal SNVs. The shearwater algorithm
3596 computes a Bayes classifier based on a beta-binomial model for variant calling
3597 with multiple samples for precisely estimating model parameters - such as local
3598 error rates and dispersion - and prior knowledge, e.g. from variation data
3599 bases such as COSMIC.")
3600 (license license:gpl3)))
3602 (define-public r-delayedarray
3604 (name "r-delayedarray")
3608 (uri (bioconductor-uri "DelayedArray" version))
3611 "11id63qza9dxl1364gllqafxmx25a0q22jv5q8h709bgc3f0grqy"))))
3613 `((upstream-name . "DelayedArray")))
3614 (build-system r-build-system)
3616 (list r-biocgenerics r-s4vectors r-iranges r-matrix
3620 (home-page "https://bioconductor.org/packages/DelayedArray")
3621 (synopsis "Delayed operations on array-like objects")
3623 "Wrapping an array-like object (typically an on-disk object) in a
3624 @code{DelayedArray} object allows one to perform common array operations on it
3625 without loading the object in memory. In order to reduce memory usage and
3626 optimize performance, operations on the object are either delayed or executed
3627 using a block processing mechanism. Note that this also works on in-memory
3628 array-like objects like @code{DataFrame} objects (typically with Rle columns),
3629 @code{Matrix} objects, and ordinary arrays and data frames.")
3630 (license license:artistic2.0)))
3632 (define-public r-derfinderhelper
3634 (name "r-derfinderhelper")
3639 (uri (bioconductor-uri "derfinderHelper" version))
3641 (base32 "0r7zbx5bfmh5cjs12y8d9qwz53nz340gdy3sx7zcn4rzn7rpslp5"))))
3642 (properties `((upstream-name . "derfinderHelper")))
3643 (build-system r-build-system)
3645 (list r-iranges r-matrix r-s4vectors))
3648 (home-page "https://github.com/leekgroup/derfinderHelper")
3649 (synopsis "Helper for derfinder")
3651 "This package speeds up the derfinder package when using multiple cores.
3652 It is particularly useful when using BiocParallel and it helps reduce the time
3653 spent loading the full derfinder package when running the F-statistics
3654 calculation in parallel.")
3655 (license license:artistic2.0)))
3657 (define-public r-drimseq
3664 (uri (bioconductor-uri "DRIMSeq" version))
3666 (base32 "1dph483ij43ayw0z5dbnp6gwp53ka7k5si1hp3miac7z8dqzv94l"))))
3667 (properties `((upstream-name . "DRIMSeq")))
3668 (build-system r-build-system)
3670 (list r-biocgenerics
3680 (native-inputs (list r-knitr))
3681 (home-page "https://bioconductor.org/packages/DRIMSeq")
3682 (synopsis "Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq")
3684 "The package provides two frameworks. One for the differential
3685 transcript usage analysis between different conditions and one for the tuQTL
3686 analysis. Both are based on modeling the counts of genomic features (i.e.,
3687 transcripts) with the Dirichlet-multinomial distribution. The package also
3688 makes available functions for visualization and exploration of the data and
3690 (license license:gpl3+)))
3692 (define-public r-bluster
3698 (uri (bioconductor-uri "bluster" version))
3701 "1g496yc7mdhshf6r0n8xhj7ax936ia5z2cx72lqyk2vzzzl5c4v8"))))
3702 (properties `((upstream-name . "bluster")))
3703 (build-system r-build-system)
3705 (list r-biocneighbors
3714 (home-page "https://bioconductor.org/packages/bluster")
3715 (synopsis "Clustering algorithms for Bioconductor")
3716 (description"This package wraps common clustering algorithms in an easily
3717 extended S4 framework. Backends are implemented for hierarchical, k-means
3718 and graph-based clustering. Several utilities are also provided to compare
3719 and evaluate clustering results.")
3720 (license license:gpl3)))
3722 (define-public r-ideoviz
3728 (uri (bioconductor-uri "IdeoViz" version))
3731 "1wwh3ifdijhpm58lw7cmnx084xwfxnc7i0206w8rhrjnvnq6ljh3"))))
3732 (build-system r-build-system)
3740 (home-page "https://bioconductor.org/packages/IdeoViz/")
3741 (synopsis "Plots data along a chromosomal ideogram")
3742 (description "This package provides functions to plot data associated with
3743 arbitrary genomic intervals along chromosomal ideogram.")
3744 (license license:gpl2)))
3746 (define-public r-infercnv
3753 (uri (bioconductor-uri "infercnv" version))
3756 "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
3757 (properties `((upstream-name . "infercnv")))
3758 (build-system r-build-system)
3759 (inputs (list python))
3788 r-singlecellexperiment
3789 r-summarizedexperiment
3791 (native-inputs (list r-knitr))
3792 (home-page "https://github.com/broadinstitute/inferCNV/wiki")
3793 (synopsis "Infer copy number variation from single-cell RNA-Seq data")
3795 "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
3796 evidence for somatic large-scale chromosomal copy number alterations, such as gains
3797 or deletions of entire chromosomes or large segments of chromosomes. This is done
3798 by exploring expression intensity of genes across positions of a tumor genome in
3799 comparison to a set of reference \"normal\" cells. A heatmap is generated
3800 illustrating the relative expression intensities across each chromosome, and it
3801 often becomes readily apparent as to which regions of the tumor genome are
3802 over-abundant or less-abundant as compared to that of normal cells.")
3803 (license license:bsd-3)))
3805 (define-public r-iranges
3811 (uri (bioconductor-uri "IRanges" version))
3814 "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
3816 `((upstream-name . "IRanges")))
3817 (build-system r-build-system)
3819 (list r-biocgenerics r-s4vectors))
3820 (home-page "https://bioconductor.org/packages/IRanges")
3821 (synopsis "Infrastructure for manipulating intervals on sequences")
3823 "This package provides efficient low-level and highly reusable S4 classes
3824 for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more
3825 generally, data that can be organized sequentially (formally defined as
3826 @code{Vector} objects), as well as views on these @code{Vector} objects.
3827 Efficient list-like classes are also provided for storing big collections of
3828 instances of the basic classes. All classes in the package use consistent
3829 naming and share the same rich and consistent \"Vector API\" as much as
3831 (license license:artistic2.0)))
3833 (define-public r-isoformswitchanalyzer
3835 (name "r-isoformswitchanalyzer")
3840 (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version))
3842 (base32 "0n1gb9azxa1mxpsqvw3i3kf72f45nyjj1kgwwrzhd88n3g63lvkd"))))
3843 (properties `((upstream-name . "IsoformSwitchAnalyzeR")))
3844 (build-system r-build-system)
3877 (home-page "https://bioconductor.org/packages/IsoformSwitchAnalyzeR/")
3878 (synopsis "Analyze alternative splicing in RNA-seq data")
3880 "This is a package for the analysis of alternative splicing and isoform
3881 switches with predicted functional consequences (e.g. gain/loss of protein
3882 domains etc.) from quantification of all types of RNASeq by tools such as
3883 Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
3884 (license license:gpl2+)))
3886 ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor.
3887 (define-public r-absfiltergsea
3889 (name "r-absfiltergsea")
3894 (uri (cran-uri "AbsFilterGSEA" version))
3896 (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
3897 (properties `((upstream-name . "AbsFilterGSEA")))
3898 (build-system r-build-system)
3900 (list r-biobase r-deseq r-limma r-rcpp r-rcpparmadillo))
3901 (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
3902 (synopsis "Improved false positive control of gene-permuting with absolute filtering")
3904 "This package provides a function that performs gene-permuting of a gene-set
3905 enrichment analysis (GSEA) calculation with or without the absolute filtering.
3906 Without filtering, users can perform (original) two-tailed or one-tailed
3908 (license license:gpl2)))
3910 ;; This is a CRAN package, but it depends on r-biobase from Bioconductor.
3911 (define-public r-bisquerna
3913 (name "r-bisquerna")
3917 (uri (cran-uri "BisqueRNA" version))
3920 "0p3p5lp69gri7vs6qfpm7br4ksbs4l7clm4nj8ki99wpqiqni23n"))))
3921 (properties `((upstream-name . "BisqueRNA")))
3922 (build-system r-build-system)
3924 (list r-biobase r-limsolve))
3927 (home-page "https://www.biorxiv.org/content/10.1101/669911v1")
3928 (synopsis "Decomposition of bulk expression with single-cell sequencing")
3929 (description "This package provides tools to accurately estimate cell type
3930 abundances from heterogeneous bulk expression. A reference-based method
3931 utilizes single-cell information to generate a signature matrix and
3932 transformation of bulk expression for accurate regression based estimates.
3933 A marker-based method utilizes known cell-specific marker genes to measure
3934 relative abundances across samples.")
3935 (license license:gpl3)))
3937 ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19
3938 ;; from Bioconductor.
3939 (define-public r-deconstructsigs
3941 (name "r-deconstructsigs")
3945 (uri (cran-uri "deconstructSigs" version))
3948 "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a"))))
3950 `((upstream-name . "deconstructSigs")))
3951 (build-system r-build-system)
3953 (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg19 r-genomeinfodb
3955 (home-page "https://github.com/raerose01/deconstructSigs")
3956 (synopsis "Identifies signatures present in a tumor sample")
3957 (description "This package takes sample information in the form of the
3958 fraction of mutations in each of 96 trinucleotide contexts and identifies
3959 the weighted combination of published signatures that, when summed, most
3960 closely reconstructs the mutational profile.")
3961 (license license:gpl2+)))
3963 ;; This is a CRAN package, but it depends on Bioconductor packages.
3964 (define-public r-jetset
3971 (uri (cran-uri "jetset" version))
3973 (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
3974 (properties `((upstream-name . "jetset")))
3975 (build-system r-build-system)
3976 (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
3977 (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
3978 (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
3980 "This package provides a one-to-one mapping from gene to \"best\" probe
3981 set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
3982 hgu133plus2, and u133x3p. On Affymetrix gene expression microarrays, a single
3983 gene may be measured by multiple probe sets. This can present a mild
3984 conundrum when attempting to evaluate a gene \"signature\" that is defined by
3985 gene names rather than by specific probe sets. This package also includes the
3986 pre-calculated probe set quality scores that were used to define the
3988 (license license:artistic2.0)))
3990 ;; This is a CRAN package, but it depends on Bioconductor packages.
3991 (define-public r-nmf
3998 (uri (cran-uri "NMF" version))
4001 "14yxra6in5c1md5nr75y8cdmh9pg0lxqabqflvlhgg1vbg9i2628"))))
4002 (properties `((upstream-name . "NMF")))
4003 (build-system r-build-system)
4008 r-bigmemory ; suggested
4009 r-synchronicity ; suggested
4024 (home-page "http://renozao.github.io/NMF")
4025 (synopsis "Algorithms and framework for nonnegative matrix factorization")
4027 "This package provides a framework to perform Non-negative Matrix
4028 Factorization (NMF). The package implements a set of already published
4029 algorithms and seeding methods, and provides a framework to test, develop and
4030 plug new or custom algorithms. Most of the built-in algorithms have been
4031 optimized in C++, and the main interface function provides an easy way of
4032 performing parallel computations on multicore machines.")
4033 (license license:gpl2+)))
4035 (define-public r-affy
4042 (uri (bioconductor-uri "affy" version))
4045 "02l77y4d4m4jwgkb3jdaskv6shmba5292whp0i29mg9asxv4rdc7"))))
4046 (build-system r-build-system)
4056 (home-page "https://bioconductor.org/packages/affy")
4057 (synopsis "Methods for affymetrix oligonucleotide arrays")
4059 "This package contains functions for exploratory oligonucleotide array
4061 (license license:lgpl2.0+)))
4063 (define-public r-affycomp
4070 (uri (bioconductor-uri "affycomp" version))
4073 "0aq5p56sqpvba0yhgd75302s9bazchh1izgymng6cpb78y5wfpj0"))))
4074 (properties `((upstream-name . "affycomp")))
4075 (build-system r-build-system)
4076 (propagated-inputs (list r-biobase))
4077 (home-page "https://bioconductor.org/packages/affycomp/")
4078 (synopsis "Graphics toolbox for assessment of Affymetrix expression measures")
4080 "The package contains functions that can be used to compare expression
4081 measures for Affymetrix Oligonucleotide Arrays.")
4082 (license license:gpl2+)))
4084 (define-public r-affycompatible
4086 (name "r-affycompatible")
4091 (uri (bioconductor-uri "AffyCompatible" version))
4094 "0x3lj1jgqq67389rzfklah5p878ns9b4fpdpz455m2gq9sk7qsda"))))
4096 `((upstream-name . "AffyCompatible")))
4097 (build-system r-build-system)
4101 `(modify-phases %standard-phases
4102 (add-after 'unpack 'make-reproducible
4104 ;; Order DTD elements before generating R code from them.
4105 (substitute* "R/methods-AffyCompatible.R"
4108 elements <- dtd$elements
4109 ordered <- elements[order(names(elements))]\n"))
4110 (("elt in dtd\\$elements")
4112 ;; Use a predictable directory name for code generation.
4113 (mkdir-p "/tmp/NetAffxResourcePrototype")
4114 (substitute* "R/DataClasses.R"
4115 (("directory=tempdir\\(\\)")
4116 "directory=\"/tmp/NetAffxResourcePrototype\"")))))))
4118 (list r-biostrings r-rcurl r-xml))
4119 (home-page "https://bioconductor.org/packages/AffyCompatible/")
4120 (synopsis "Work with Affymetrix GeneChip files")
4122 "This package provides an interface to Affymetrix chip annotation and
4123 sample attribute files. The package allows an easy way for users to download
4124 and manage local data bases of Affynmetrix NetAffx annotation files. It also
4125 provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip
4126 Command Console} (AGCC)-compatible sample annotation files.")
4127 (license license:artistic2.0)))
4129 (define-public r-affycontam
4131 (name "r-affycontam")
4136 (uri (bioconductor-uri "affyContam" version))
4139 "1pyd4rj6pp139kvhh97whi4afvx029w5lglr4mnscw7m3f618v0p"))))
4140 (properties `((upstream-name . "affyContam")))
4141 (build-system r-build-system)
4143 (list r-affy r-affydata r-biobase))
4144 (home-page "https://bioconductor.org/packages/affyContam/")
4145 (synopsis "Structured corruption of Affymetrix CEL file data")
4147 "Microarray quality assessment is a major concern of microarray analysts.
4148 This package provides some simple approaches to in silico creation of quality
4149 problems in CEL-level data to help evaluate performance of quality metrics.")
4150 (license license:artistic2.0)))
4152 (define-public r-affycoretools
4154 (name "r-affycoretools")
4159 (uri (bioconductor-uri "affycoretools" version))
4162 "05x64hy5jpmg973biwq4q9gzy1n0iqc0pxrix1f6bri1w6vil3ww"))))
4163 (properties `((upstream-name . "affycoretools")))
4164 (build-system r-build-system)
4187 (home-page "https://bioconductor.org/packages/affycoretools/")
4188 (synopsis "Functions for analyses with Affymetrix GeneChips")
4190 "This package provides various wrapper functions that have been written
4191 to streamline the more common analyses that a Biostatistician might see.")
4192 (license license:artistic2.0)))
4194 (define-public r-affyio
4201 (uri (bioconductor-uri "affyio" version))
4204 "19cw82qvzkz6vh2gm302y7digsf6xif7c9l2q9s6lkx2yflqpgfp"))))
4205 (build-system r-build-system)
4210 (home-page "https://github.com/bmbolstad/affyio")
4211 (synopsis "Tools for parsing Affymetrix data files")
4213 "This package provides routines for parsing Affymetrix data files based
4214 upon file format information. The primary focus is on accessing the CEL and
4216 (license license:lgpl2.0+)))
4218 (define-public r-affxparser
4220 (name "r-affxparser")
4225 (uri (bioconductor-uri "affxparser" version))
4228 "16x92gwsy7zdyz4md4cw847xn2ymqd6gqsn0rlr2nnf3qmnjnils"))))
4229 (properties `((upstream-name . "affxparser")))
4230 (build-system r-build-system)
4231 (home-page "https://github.com/HenrikBengtsson/affxparser")
4232 (synopsis "Affymetrix File Parsing SDK")
4234 "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP,
4235 BAR). It provides methods for fast and memory efficient parsing of Affymetrix
4236 files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files
4237 are supported. Currently, there are methods for reading @dfn{chip definition
4238 file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read
4239 either in full or in part. For example, probe signals from a few probesets
4240 can be extracted very quickly from a set of CEL files into a convenient list
4242 ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is
4244 (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2))))
4246 (define-public r-annotate
4253 (uri (bioconductor-uri "annotate" version))
4256 "0x6vddpiw2g713vicf70198x8dlrwf36p8jjygdsfnl56ls5bh2g"))))
4257 (build-system r-build-system)
4259 (list r-annotationdbi
4267 "https://bioconductor.org/packages/annotate")
4268 (synopsis "Annotation for microarrays")
4269 (description "This package provides R environments for the annotation of
4271 (license license:artistic2.0)))
4273 (define-public r-annotationdbi
4275 (name "r-annotationdbi")
4279 (uri (bioconductor-uri "AnnotationDbi" version))
4282 "15cwy7lic89jwl3dr7j4pb5bx457jdpvzvylr71624s0p0j9rgwn"))))
4284 `((upstream-name . "AnnotationDbi")))
4285 (build-system r-build-system)
4296 (home-page "https://bioconductor.org/packages/AnnotationDbi")
4297 (synopsis "Annotation database interface")
4299 "This package provides user interface and database connection code for
4300 annotation data packages using SQLite data storage.")
4301 (license license:artistic2.0)))
4303 (define-public r-annotationfilter
4305 (name "r-annotationfilter")
4309 (uri (bioconductor-uri "AnnotationFilter" version))
4312 "082lpcd6yr2nkxndlck2wqqd3nfdx7lnpw8barxgv41q4l7v4ald"))))
4314 `((upstream-name . "AnnotationFilter")))
4315 (build-system r-build-system)
4317 (list r-genomicranges r-lazyeval))
4320 (home-page "https://github.com/Bioconductor/AnnotationFilter")
4321 (synopsis "Facilities for filtering Bioconductor annotation resources")
4323 "This package provides classes and other infrastructure to implement
4324 filters for manipulating Bioconductor annotation resources. The filters are
4325 used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
4326 (license license:artistic2.0)))
4328 (define-public r-annotationforge
4330 (name "r-annotationforge")
4335 (uri (bioconductor-uri "AnnotationForge" version))
4338 "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v"))))
4340 `((upstream-name . "AnnotationForge")))
4341 (build-system r-build-system)
4343 (list r-annotationdbi
4353 (home-page "https://bioconductor.org/packages/AnnotationForge")
4354 (synopsis "Code for building annotation database packages")
4356 "This package provides code for generating Annotation packages and their
4357 databases. Packages produced are intended to be used with AnnotationDbi.")
4358 (license license:artistic2.0)))
4360 (define-public r-annotationhub
4362 (name "r-annotationhub")
4367 (uri (bioconductor-uri "AnnotationHub" version))
4370 "03dmbx43rsv9xv94lk12gpraq47ryc13jijwma3q05hl9wn8xjxs"))))
4371 (properties `((upstream-name . "AnnotationHub")))
4372 (build-system r-build-system)
4374 (list r-annotationdbi
4382 r-interactivedisplaybase
4389 (home-page "https://bioconductor.org/packages/AnnotationHub")
4390 (synopsis "Client to access AnnotationHub resources")
4392 "This package provides a client for the Bioconductor AnnotationHub web
4393 resource. The AnnotationHub web resource provides a central location where
4394 genomic files (e.g. VCF, bed, wig) and other resources from standard
4395 locations (e.g. UCSC, Ensembl) can be discovered. The resource includes
4396 metadata about each resource, e.g., a textual description, tags, and date of
4397 modification. The client creates and manages a local cache of files retrieved
4398 by the user, helping with quick and reproducible access.")
4399 (license license:artistic2.0)))
4401 (define-public r-aroma-light
4403 (name "r-aroma-light")
4408 (uri (bioconductor-uri "aroma.light" version))
4411 "1240v9wvsf205g998ms19hncki8g6shidg09dy5np9pqpiix4vys"))))
4412 (properties `((upstream-name . "aroma.light")))
4413 (build-system r-build-system)
4415 (list r-matrixstats r-r-methodss3 r-r-oo r-r-utils))
4416 (home-page "https://github.com/HenrikBengtsson/aroma.light")
4417 (synopsis "Methods for normalization and visualization of microarray data")
4419 "This package provides methods for microarray analysis that take basic
4420 data types such as matrices and lists of vectors. These methods can be used
4421 standalone, be utilized in other packages, or be wrapped up in higher-level
4423 (license license:gpl2+)))
4425 (define-public r-bamsignals
4427 (name "r-bamsignals")
4432 (uri (bioconductor-uri "bamsignals" version))
4435 "0ywbxq829hclhr5bb6p77rspxvfs580zlwd2f5kr3an6rdgyx9ky"))))
4436 (build-system r-build-system)
4438 (list r-biocgenerics
4446 (home-page "https://bioconductor.org/packages/bamsignals")
4447 (synopsis "Extract read count signals from bam files")
4449 "This package efficiently obtains count vectors from indexed bam
4450 files. It counts the number of nucleotide sequence reads in given genomic
4451 ranges and it computes reads profiles and coverage profiles. It also handles
4453 (license license:gpl2+)))
4455 (define-public r-biobase
4461 (uri (bioconductor-uri "Biobase" version))
4464 "1mnxky78an079p60427cjvk4fzilp0xzy6b85fq274qvdcrz8jbv"))))
4466 `((upstream-name . "Biobase")))
4467 (build-system r-build-system)
4469 (list r-biocgenerics))
4470 (home-page "https://bioconductor.org/packages/Biobase")
4471 (synopsis "Base functions for Bioconductor")
4473 "This package provides functions that are needed by many other packages
4474 on Bioconductor or which replace R functions.")
4475 (license license:artistic2.0)))
4477 (define-public r-biomart
4483 (uri (bioconductor-uri "biomaRt" version))
4486 "0yn3kanyrplc89a900xiz33nw1v23mkljvd5isizgs8gzvwzf8xg"))))
4488 `((upstream-name . "biomaRt")))
4489 (build-system r-build-system)
4491 (list r-annotationdbi
4502 (home-page "https://bioconductor.org/packages/biomaRt")
4503 (synopsis "Interface to BioMart databases")
4505 "biomaRt provides an interface to a growing collection of databases
4506 implementing the @url{BioMart software suite, http://www.biomart.org}. The
4507 package enables retrieval of large amounts of data in a uniform way without
4508 the need to know the underlying database schemas or write complex SQL queries.
4509 Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene,
4510 Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt
4511 users direct access to a diverse set of data and enable a wide range of
4512 powerful online queries from gene annotation to database mining.")
4513 (license license:artistic2.0)))
4515 ;; This is a CRAN package, but it depends on a Bioconductor package:
4517 (define-public r-biomartr
4523 (uri (cran-uri "biomartr" version))
4526 "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz"))))
4527 (properties `((upstream-name . "biomartr")))
4528 (build-system r-build-system)
4548 (native-inputs (list r-knitr))
4549 (home-page "https://docs.ropensci.org/biomartr/")
4550 (synopsis "Genomic data retrieval")
4552 "Perform large scale genomic data retrieval and functional annotation
4553 retrieval. This package aims to provide users with a standardized way to
4554 automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome
4555 retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases.
4556 Furthermore, an interface to the BioMart database allows users to retrieve
4557 functional annotation for genomic loci. In addition, users can download
4558 entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with
4560 (license license:gpl2)))
4562 (define-public r-biocparallel
4564 (name "r-biocparallel")
4568 (uri (bioconductor-uri "BiocParallel" version))
4571 "1rs3wmasl9mx7f399iclvm0bnvggvjj2a88zbi294r5m8wxqlc92"))))
4573 `((upstream-name . "BiocParallel")))
4574 (build-system r-build-system)
4577 (modify-phases %standard-phases
4578 (add-after 'unpack 'make-reproducible
4580 ;; Remove generated documentation.
4581 (for-each delete-file
4582 '("inst/doc/BiocParallel_BatchtoolsParam.pdf"
4583 "inst/doc/Introduction_To_BiocParallel.pdf"
4584 "inst/doc/Errors_Logs_And_Debugging.pdf"
4585 "inst/doc/BiocParallel_BatchtoolsParam.R"
4586 "inst/doc/Introduction_To_BiocParallel.R"
4587 "inst/doc/Errors_Logs_And_Debugging.R"))
4589 ;; Remove time-dependent macro
4590 (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw"
4591 "inst/doc/Introduction_To_BiocParallel.Rnw"
4592 "inst/doc/Errors_Logs_And_Debugging.Rnw"
4593 "vignettes/BiocParallel_BatchtoolsParam.Rnw"
4594 "vignettes/Introduction_To_BiocParallel.Rnw"
4595 "vignettes/Errors_Logs_And_Debugging.Rnw")
4596 (("\\today") "later"))
4598 ;; Initialize the random number generator seed when building.
4599 (substitute* "R/rng.R"
4600 (("\"L'Ecuyer-CMRG\"\\)" m)
4602 m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n"))))))))
4604 (list r-bh r-codetools r-futile-logger r-snow))
4607 (home-page "https://bioconductor.org/packages/BiocParallel")
4608 (synopsis "Bioconductor facilities for parallel evaluation")
4610 "This package provides modified versions and novel implementation of
4611 functions for parallel evaluation, tailored to use with Bioconductor
4613 (license (list license:gpl2+ license:gpl3+))))
4615 (define-public r-biostrings
4617 (name "r-biostrings")
4621 (uri (bioconductor-uri "Biostrings" version))
4624 "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"))))
4626 `((upstream-name . "Biostrings")))
4627 (build-system r-build-system)
4629 (list r-biocgenerics
4635 (home-page "https://bioconductor.org/packages/Biostrings")
4636 (synopsis "String objects and algorithms for biological sequences")
4638 "This package provides memory efficient string containers, string
4639 matching algorithms, and other utilities, for fast manipulation of large
4640 biological sequences or sets of sequences.")
4641 (license license:artistic2.0)))
4643 (define-public r-biovizbase
4645 (name "r-biovizbase")
4650 (uri (bioconductor-uri "biovizBase" version))
4653 "1ffzf7yvl47l8v8a50m8g9q33hgwvxg4fcm8ld2yy8hd2zl86zyd"))))
4654 (properties `((upstream-name . "biovizBase")))
4655 (build-system r-build-system)
4657 (list r-annotationdbi
4674 r-summarizedexperiment
4675 r-variantannotation))
4676 (home-page "https://bioconductor.org/packages/biovizBase")
4677 (synopsis "Basic graphic utilities for visualization of genomic data")
4679 "The biovizBase package is designed to provide a set of utilities, color
4680 schemes and conventions for genomic data. It serves as the base for various
4681 high-level packages for biological data visualization. This saves development
4682 effort and encourages consistency.")
4683 (license license:artistic2.0)))
4685 (define-public r-bsgenome
4691 (uri (bioconductor-uri "BSgenome" version))
4694 "17gqrmaf6xxghgrzcansl9gfw3ghkrqp87swlnwgyghqvflr5qxc"))))
4696 `((upstream-name . "BSgenome")))
4697 (build-system r-build-system)
4699 (list r-biocgenerics
4709 (home-page "https://bioconductor.org/packages/BSgenome")
4710 (synopsis "Infrastructure for Biostrings-based genome data packages")
4712 "This package provides infrastructure shared by all Biostrings-based
4713 genome data packages and support for efficient SNP representation.")
4714 (license license:artistic2.0)))
4716 (define-public r-category
4723 (uri (bioconductor-uri "Category" version))
4726 "07js03cfdd6gzbzw14iavlqxynfcqszh988v6k1a3h074wxiivqd"))))
4727 (properties `((upstream-name . "Category")))
4728 (build-system r-build-system)
4740 (home-page "https://bioconductor.org/packages/Category")
4741 (synopsis "Category analysis")
4743 "This package provides a collection of tools for performing category
4745 (license license:artistic2.0)))
4747 (define-public r-chipseeker
4749 (name "r-chipseeker")
4753 (uri (bioconductor-uri "ChIPseeker" version))
4756 "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"))))
4757 (build-system r-build-system)
4761 (list r-annotationdbi
4780 r-txdb-hsapiens-ucsc-hg19-knowngene))
4781 (home-page "https://www.bioconductor.org/packages/ChIPseeker/")
4782 (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization")
4783 (description "This package implements functions to retrieve the nearest
4784 genes around the peak, annotate genomic region of the peak, statstical methods
4785 for estimate the significance of overlap among ChIP peak data sets, and
4786 incorporate GEO database for user to compare the own dataset with those
4787 deposited in database. The comparison can be used to infer cooperative
4788 regulation and thus can be used to generate hypotheses. Several visualization
4789 functions are implemented to summarize the coverage of the peak experiment,
4790 average profile and heatmap of peaks binding to TSS regions, genomic
4791 annotation, distance to TSS, and overlap of peaks or genes.")
4792 (license license:artistic2.0)))
4794 (define-public r-chipseq
4801 (uri (bioconductor-uri "chipseq" version))
4804 "1vh0hvgnw7ykj401v1q807sl14s4nixp1d8xbm41n01q6w8x834i"))))
4805 (build-system r-build-system)
4807 (list r-biocgenerics
4813 (home-page "https://bioconductor.org/packages/chipseq")
4814 (synopsis "Package for analyzing ChIPseq data")
4816 "This package provides tools for processing short read data from ChIPseq
4818 (license license:artistic2.0)))
4820 (define-public r-complexheatmap
4822 (name "r-complexheatmap")
4827 (uri (bioconductor-uri "ComplexHeatmap" version))
4830 "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"))))
4832 `((upstream-name . "ComplexHeatmap")))
4833 (build-system r-build-system)
4851 "https://github.com/jokergoo/ComplexHeatmap")
4852 (synopsis "Making Complex Heatmaps")
4854 "Complex heatmaps are efficient to visualize associations between
4855 different sources of data sets and reveal potential structures. This package
4856 provides a highly flexible way to arrange multiple heatmaps and supports
4857 self-defined annotation graphics.")
4858 (license license:gpl2+)))
4860 (define-public r-copywriter
4862 (name "r-copywriter")
4867 (uri (bioconductor-uri "CopywriteR" version))
4870 "1k11kvam96hpg71hz2n9cfzizmb7d1bmq5zfvm34s7fn09is60xb"))))
4871 (properties `((upstream-name . "CopywriteR")))
4872 (build-system r-build-system)
4874 (list r-biocparallel
4888 (home-page "https://github.com/PeeperLab/CopywriteR")
4889 (synopsis "Copy number information from targeted sequencing")
4891 "CopywriteR extracts DNA copy number information from targeted sequencing
4892 by utilizing off-target reads. It allows for extracting uniformly distributed
4893 copy number information, can be used without reference, and can be applied to
4894 sequencing data obtained from various techniques including chromatin
4895 immunoprecipitation and target enrichment on small gene panels. Thereby,
4896 CopywriteR constitutes a widely applicable alternative to available copy
4897 number detection tools.")
4898 (license license:gpl2)))
4900 (define-public r-deseq
4907 (uri (bioconductor-uri "DESeq" version))
4910 "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
4911 (properties `((upstream-name . "DESeq")))
4912 (build-system r-build-system)
4922 (home-page "https://www-huber.embl.de/users/anders/DESeq/")
4923 (synopsis "Differential gene expression analysis")
4925 "This package provides tools for estimating variance-mean dependence in
4926 count data from high-throughput genetic sequencing assays and for testing for
4927 differential expression based on a model using the negative binomial
4929 (license license:gpl3+)))
4931 (define-public r-deseq2
4938 (uri (bioconductor-uri "DESeq2" version))
4941 "06mvb0jqn2fg96wfwspv0kzpa8xpimzaldrcy8m2d4yk76xwsdr7"))))
4942 (properties `((upstream-name . "DESeq2")))
4943 (build-system r-build-system)
4957 r-summarizedexperiment))
4960 (home-page "https://bioconductor.org/packages/DESeq2")
4961 (synopsis "Differential gene expression analysis")
4963 "This package provides functions to estimate variance-mean dependence in
4964 count data from high-throughput nucleotide sequencing assays and test for
4965 differential expression based on a model using the negative binomial
4967 (license license:lgpl3+)))
4969 (define-public r-dexseq
4976 (uri (bioconductor-uri "DEXSeq" version))
4979 "1dzx9mvm8pvcrwr88rin3flnpmzp3vq8mvspx9s8virqhv1102am"))))
4980 (properties `((upstream-name . "DEXSeq")))
4981 (build-system r-build-system)
4983 (list r-annotationdbi
4999 r-summarizedexperiment))
5002 (home-page "https://bioconductor.org/packages/DEXSeq")
5003 (synopsis "Inference of differential exon usage in RNA-Seq")
5005 "This package is focused on finding differential exon usage using RNA-seq
5006 exon counts between samples with different experimental designs. It provides
5007 functions that allows the user to make the necessary statistical tests based
5008 on a model that uses the negative binomial distribution to estimate the
5009 variance between biological replicates and generalized linear models for
5010 testing. The package also provides functions for the visualization and
5011 exploration of the results.")
5012 (license license:gpl3+)))
5014 (define-public r-diffcyt
5021 (uri (bioconductor-uri "diffcyt" version))
5023 (base32 "0mysylzmg24g7lm1xan4yklzqmskfgh53j6vjcz2gzakz5rq3rdb"))))
5024 (properties `((upstream-name . "diffcyt")))
5025 (build-system r-build-system)
5039 r-summarizedexperiment
5041 (native-inputs (list r-knitr))
5042 (home-page "https://github.com/lmweber/diffcyt")
5043 (synopsis "Differential discovery in high-dimensional cytometry")
5045 "This package provides statistical methods for differential discovery
5046 analyses in high-dimensional cytometry data (including flow cytometry, mass
5047 cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a
5048 combination of high-resolution clustering and empirical Bayes moderated tests
5049 adapted from transcriptomics.")
5050 (license license:expat)))
5052 (define-public r-dirichletmultinomial
5054 (name "r-dirichletmultinomial")
5059 (uri (bioconductor-uri "DirichletMultinomial" version))
5062 "15l0h2qz80lmrm5rva3v7lkgddn42igyxxwims57zwpwyhrk9bmx"))))
5064 `((upstream-name . "DirichletMultinomial")))
5065 (build-system r-build-system)
5069 (list r-biocgenerics r-iranges r-s4vectors))
5070 (home-page "https://bioconductor.org/packages/DirichletMultinomial")
5071 (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
5073 "Dirichlet-multinomial mixture models can be used to describe variability
5074 in microbial metagenomic data. This package is an interface to code
5075 originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
5077 (license license:lgpl3)))
5079 (define-public r-dittoseq
5085 (uri (bioconductor-uri "dittoSeq" version))
5088 "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4"))))
5089 (properties `((upstream-name . "dittoSeq")))
5090 (build-system r-build-system)
5101 r-singlecellexperiment
5102 r-summarizedexperiment))
5103 (native-inputs (list r-knitr))
5104 (home-page "https://bioconductor.org/packages/dittoSeq")
5105 (synopsis "Single-cell and bulk RNA sequencing visualization")
5107 "This package provides a universal, user friendly, single-cell and bulk RNA
5108 sequencing visualization toolkit that allows highly customizable creation of
5109 color blindness friendly, publication-quality figures. dittoSeq accepts both
5110 SingleCellExperiment (SCE) and Seurat objects, as well as the import and
5111 usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data.
5112 Visualizations include dimensionality reduction plots, heatmaps, scatterplots,
5113 percent composition or expression across groups, and more. Customizations
5114 range from size and title adjustments to automatic generation of annotations
5115 for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton
5116 plot, hidden data overlay upon cursor hovering via ggplotly conversion, and
5117 many more. All with simple, discrete inputs. Color blindness friendliness is
5118 powered by legend adjustments (enlarged keys), and by allowing the use of
5119 shapes or letter-overlay in addition to the carefully selected
5120 code{dittoColors()}.")
5121 (license license:expat)))
5123 (define-public r-edaseq
5130 (uri (bioconductor-uri "EDASeq" version))
5133 "1qnpbmhxvqsma7ihi6yp3ad962xcanlxald84k2szh011ipxj7ws"))))
5134 (properties `((upstream-name . "EDASeq")))
5135 (build-system r-build-system)
5137 (list r-annotationdbi
5151 (home-page "https://github.com/drisso/EDASeq")
5152 (synopsis "Exploratory data analysis and normalization for RNA-Seq")
5154 "This package provides support for numerical and graphical summaries of
5155 RNA-Seq genomic read data. Provided within-lane normalization procedures to
5156 adjust for GC-content effect (or other gene-level effects) on read counts:
5157 loess robust local regression, global-scaling, and full-quantile
5158 normalization. Between-lane normalization procedures to adjust for
5159 distributional differences between lanes (e.g., sequencing depth):
5160 global-scaling and full-quantile normalization.")
5161 (license license:artistic2.0)))
5163 (define-public r-edger
5169 (uri (bioconductor-uri "edgeR" version))
5172 "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
5173 (properties `((upstream-name . "edgeR")))
5174 (build-system r-build-system)
5176 (list r-limma r-locfit r-rcpp))
5177 (home-page "http://bioinf.wehi.edu.au/edgeR")
5178 (synopsis "EdgeR does empirical analysis of digital gene expression data")
5179 (description "This package can do differential expression analysis of
5180 RNA-seq expression profiles with biological replication. It implements a range
5181 of statistical methodology based on the negative binomial distributions,
5182 including empirical Bayes estimation, exact tests, generalized linear models
5183 and quasi-likelihood tests. It be applied to differential signal analysis of
5184 other types of genomic data that produce counts, including ChIP-seq, SAGE and
5186 (license license:gpl2+)))
5188 (define-public r-ensembldb
5190 (name "r-ensembldb")
5195 (uri (bioconductor-uri "ensembldb" version))
5198 "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc"))))
5199 (build-system r-build-system)
5201 (list r-annotationdbi
5219 (home-page "https://github.com/jotsetung/ensembldb")
5220 (synopsis "Utilities to create and use Ensembl-based annotation databases")
5222 "The package provides functions to create and use transcript-centric
5223 annotation databases/packages. The annotation for the databases are directly
5224 fetched from Ensembl using their Perl API. The functionality and data is
5225 similar to that of the TxDb packages from the @code{GenomicFeatures} package,
5226 but, in addition to retrieve all gene/transcript models and annotations from
5227 the database, the @code{ensembldb} package also provides a filter framework
5228 allowing to retrieve annotations for specific entries like genes encoded on a
5229 chromosome region or transcript models of lincRNA genes.")
5230 ;; No version specified
5231 (license license:lgpl3+)))
5233 (define-public r-fastseg
5240 (uri (bioconductor-uri "fastseg" version))
5243 "1cr1b1jbgp1z1zpf71kl7mljbm2jpi6b97bf3bll3gnagfm489hy"))))
5244 (build-system r-build-system)
5246 (list r-biobase r-biocgenerics r-genomicranges r-iranges
5248 (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
5249 (synopsis "Fast segmentation algorithm for genetic sequencing data")
5251 "Fastseg implements a very fast and efficient segmentation algorithm.
5252 It can segment data from DNA microarrays and data from next generation
5253 sequencing for example to detect copy number segments. Further it can segment
5254 data from RNA microarrays like tiling arrays to identify transcripts. Most
5255 generally, it can segment data given as a matrix or as a vector. Various data
5256 formats can be used as input to fastseg like expression set objects for
5257 microarrays or GRanges for sequencing data.")
5258 (license license:lgpl2.0+)))
5260 (define-public r-gage
5267 (uri (bioconductor-uri "gage" version))
5270 "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"))))
5271 (build-system r-build-system)
5273 (list r-annotationdbi r-go-db r-graph r-keggrest))
5274 (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
5275 "articles/10.1186/1471-2105-10-161"))
5276 (synopsis "Generally applicable gene-set enrichment for pathway analysis")
5278 "GAGE is a published method for gene set (enrichment or GSEA) or pathway
5279 analysis. GAGE is generally applicable independent of microarray or RNA-Seq
5280 data attributes including sample sizes, experimental designs, assay platforms,
5281 and other types of heterogeneity. The gage package provides functions for
5282 basic GAGE analysis, result processing and presentation. In addition, it
5283 provides demo microarray data and commonly used gene set data based on KEGG
5284 pathways and GO terms. These functions and data are also useful for gene set
5285 analysis using other methods.")
5286 (license license:gpl2+)))
5288 (define-public r-genefilter
5290 (name "r-genefilter")
5295 (uri (bioconductor-uri "genefilter" version))
5298 "1lp3alnljhsil8zylf8rvf8ik4wmsyciy3ij4rr9l4191dkkp4aq"))))
5299 (build-system r-build-system)
5301 (list gfortran r-knitr))
5303 (list r-annotate r-annotationdbi r-biobase r-biocgenerics
5305 (home-page "https://bioconductor.org/packages/genefilter")
5306 (synopsis "Filter genes from high-throughput experiments")
5308 "This package provides basic functions for filtering genes from
5309 high-throughput sequencing experiments.")
5310 (license license:artistic2.0)))
5312 (define-public r-geneoverlap
5314 (name "r-geneoverlap")
5318 (uri (bioconductor-uri "GeneOverlap" version))
5321 "0nqwa3x9q1hl9nm06hqzzrn00rirc9kj6s320csjlf7x6rcidr93"))))
5322 (build-system r-build-system)
5324 (list r-rcolorbrewer r-gplots))
5325 (home-page "https://www.bioconductor.org/packages/GeneOverlap/")
5326 (synopsis "Test and visualize gene overlaps")
5327 (description "This package can be used to test two sets of gene lists
5328 and visualize the results.")
5329 (license license:gpl3)))
5331 (define-public r-genomation
5333 (name "r-genomation")
5337 (uri (bioconductor-uri "genomation" version))
5340 "0rvay7gs4g2wi6h42kln8xwy9b05axj1x8mkfayl6pnnlva6xj79"))))
5341 (build-system r-build-system)
5365 (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
5366 (synopsis "Summary, annotation and visualization of genomic data")
5368 "This package provides a package for summary and annotation of genomic
5369 intervals. Users can visualize and quantify genomic intervals over
5370 pre-defined functional regions, such as promoters, exons, introns, etc. The
5371 genomic intervals represent regions with a defined chromosome position, which
5372 may be associated with a score, such as aligned reads from HT-seq experiments,
5373 TF binding sites, methylation scores, etc. The package can use any tabular
5374 genomic feature data as long as it has minimal information on the locations of
5375 genomic intervals. In addition, it can use BAM or BigWig files as input.")
5376 (license license:artistic2.0)))
5378 (define-public r-genomeinfodb
5380 (name "r-genomeinfodb")
5384 (uri (bioconductor-uri "GenomeInfoDb" version))
5387 "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"))))
5389 `((upstream-name . "GenomeInfoDb")))
5390 (build-system r-build-system)
5392 (list r-biocgenerics r-genomeinfodbdata r-iranges r-rcurl
5396 (home-page "https://bioconductor.org/packages/GenomeInfoDb")
5397 (synopsis "Utilities for manipulating chromosome identifiers")
5399 "This package contains data and functions that define and allow
5400 translation between different chromosome sequence naming conventions (e.g.,
5401 \"chr1\" versus \"1\"), including a function that attempts to place sequence
5402 names in their natural, rather than lexicographic, order.")
5403 (license license:artistic2.0)))
5405 (define-public r-genomicalignments
5407 (name "r-genomicalignments")
5411 (uri (bioconductor-uri "GenomicAlignments" version))
5414 "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
5416 `((upstream-name . "GenomicAlignments")))
5417 (build-system r-build-system)
5419 (list r-biocgenerics
5427 r-summarizedexperiment))
5428 (home-page "https://bioconductor.org/packages/GenomicAlignments")
5429 (synopsis "Representation and manipulation of short genomic alignments")
5431 "This package provides efficient containers for storing and manipulating
5432 short genomic alignments (typically obtained by aligning short reads to a
5433 reference genome). This includes read counting, computing the coverage,
5434 junction detection, and working with the nucleotide content of the
5436 (license license:artistic2.0)))
5438 (define-public r-genomicfeatures
5440 (name "r-genomicfeatures")
5444 (uri (bioconductor-uri "GenomicFeatures" version))
5447 "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"))))
5449 `((upstream-name . "GenomicFeatures")))
5450 (build-system r-build-system)
5452 (list r-annotationdbi
5469 (home-page "https://bioconductor.org/packages/GenomicFeatures")
5470 (synopsis "Tools for working with transcript centric annotations")
5472 "This package provides a set of tools and methods for making and
5473 manipulating transcript centric annotations. With these tools the user can
5474 easily download the genomic locations of the transcripts, exons and cds of a
5475 given organism, from either the UCSC Genome Browser or a BioMart
5476 database (more sources will be supported in the future). This information is
5477 then stored in a local database that keeps track of the relationship between
5478 transcripts, exons, cds and genes. Flexible methods are provided for
5479 extracting the desired features in a convenient format.")
5480 (license license:artistic2.0)))
5482 (define-public r-genomicfiles
5484 (name "r-genomicfiles")
5489 (uri (bioconductor-uri "GenomicFiles" version))
5492 "06ycfna26klx27vvsnlpgv46bymfrc8z0zkpag7nm4m23153ivkz"))))
5493 (properties `((upstream-name . "GenomicFiles")))
5494 (build-system r-build-system)
5496 (list r-biocgenerics
5506 r-summarizedexperiment
5507 r-variantannotation))
5508 (home-page "https://bioconductor.org/packages/GenomicFiles")
5509 (synopsis "Distributed computing by file or by range")
5511 "This package provides infrastructure for parallel computations
5512 distributed by file or by range. User defined mapper and reducer functions
5513 provide added flexibility for data combination and manipulation.")
5514 (license license:artistic2.0)))
5516 (define-public r-genomicranges
5518 (name "r-genomicranges")
5522 (uri (bioconductor-uri "GenomicRanges" version))
5525 "088rv1aclwq265pdg4hmks73nl0125vk0vigyi44n3djkrdx48yn"))))
5527 `((upstream-name . "GenomicRanges")))
5528 (build-system r-build-system)
5530 (list r-biocgenerics r-genomeinfodb r-iranges r-s4vectors r-xvector))
5533 (home-page "https://bioconductor.org/packages/GenomicRanges")
5534 (synopsis "Representation and manipulation of genomic intervals")
5536 "This package provides tools to efficiently represent and manipulate
5537 genomic annotations and alignments is playing a central role when it comes to
5538 analyzing high-throughput sequencing data (a.k.a. NGS data). The
5539 GenomicRanges package defines general purpose containers for storing and
5540 manipulating genomic intervals and variables defined along a genome.")
5541 (license license:artistic2.0)))
5543 (define-public r-gostats
5550 (uri (bioconductor-uri "GOstats" version))
5553 "121ly9vifarg8y7mc468571bbs0xv4sx6sflm5zcdqf0p83yvjrm"))))
5554 (properties `((upstream-name . "GOstats")))
5555 (build-system r-build-system)
5566 (home-page "https://bioconductor.org/packages/GOstats")
5567 (synopsis "Tools for manipulating GO and microarrays")
5569 "This package provides a set of tools for interacting with GO and
5570 microarray data. A variety of basic manipulation tools for graphs, hypothesis
5571 testing and other simple calculations.")
5572 (license license:artistic2.0)))
5574 (define-public r-gseabase
5581 (uri (bioconductor-uri "GSEABase" version))
5584 "1qhvgyg392fd98h2qnmfmhg7mil5hp9cy3qmkqs4x1bhpv1m978g"))))
5585 (properties `((upstream-name . "GSEABase")))
5586 (build-system r-build-system)
5596 (home-page "https://bioconductor.org/packages/GSEABase")
5597 (synopsis "Gene set enrichment data structures and methods")
5599 "This package provides classes and methods to support @dfn{Gene Set
5600 Enrichment Analysis} (GSEA).")
5601 (license license:artistic2.0)))
5603 (define-public r-hpar
5610 (uri (bioconductor-uri "hpar" version))
5613 "07c6r703d5xp7y9bqmqalxgna2qrbk1h5s0d992m7360k259mgrj"))))
5614 (build-system r-build-system)
5617 (home-page "https://bioconductor.org/packages/hpar/")
5618 (synopsis "Human Protein Atlas in R")
5619 (description "This package provides a simple interface to and data from
5620 the Human Protein Atlas project.")
5621 (license license:artistic2.0)))
5623 (define-public r-rhtslib
5630 (uri (bioconductor-uri "Rhtslib" version))
5633 "07kws6afkxbmxq4w357mwwl712pdd16alvz7iqijjd2x7rjchj2f"))))
5634 (properties `((upstream-name . "Rhtslib")))
5635 (build-system r-build-system)
5636 ;; Without this a temporary directory ends up in the Rhtslib.so binary,
5637 ;; which makes R abort the build.
5638 (arguments '(#:configure-flags '("--no-staged-install")))
5640 (list curl zlib ; packages using rhtslib need to link with zlib
5643 (list pkg-config r-knitr))
5644 (home-page "https://github.com/nhayden/Rhtslib")
5645 (synopsis "High-throughput sequencing library as an R package")
5647 "This package provides the HTSlib C library for high-throughput
5648 nucleotide sequence analysis. The package is primarily useful to developers
5649 of other R packages who wish to make use of HTSlib.")
5650 (license license:lgpl2.0+)))
5652 (define-public r-impute
5658 (uri (bioconductor-uri "impute" version))
5661 "11b0z7py0im6y43k55xpzz5jnvc0ram9rk3n1n4mwhvs0vhy39r2"))))
5664 (build-system r-build-system)
5665 (home-page "https://bioconductor.org/packages/impute")
5666 (synopsis "Imputation for microarray data")
5668 "This package provides a function to impute missing gene expression
5669 microarray data, using nearest neighbor averaging.")
5670 (license license:gpl2+)))
5672 (define-public r-interactivedisplaybase
5674 (name "r-interactivedisplaybase")
5679 (uri (bioconductor-uri "interactiveDisplayBase" version))
5682 "0fdwx5ch0ch8axdkfiq7zzhhq5hwcvd6kf8fggw9nd3ah1yjwbdg"))))
5684 `((upstream-name . "interactiveDisplayBase")))
5685 (build-system r-build-system)
5687 (list r-biocgenerics r-dt r-shiny))
5690 (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
5691 (synopsis "Base package for web displays of Bioconductor objects")
5693 "This package contains the basic methods needed to generate interactive
5694 Shiny-based display methods for Bioconductor objects.")
5695 (license license:artistic2.0)))
5697 (define-public r-keggrest
5704 (uri (bioconductor-uri "KEGGREST" version))
5707 "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
5708 (properties `((upstream-name . "KEGGREST")))
5709 (build-system r-build-system)
5711 (list r-biostrings r-httr r-png))
5714 (home-page "https://bioconductor.org/packages/KEGGREST")
5715 (synopsis "Client-side REST access to KEGG")
5717 "This package provides a package that provides a client interface to the
5718 @dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
5719 (license license:artistic2.0)))
5721 (define-public r-lfa
5728 (uri (bioconductor-uri "lfa" version))
5730 (base32 "044866h4fnxmzb3sh9vmrd2smgsbcqgvd19dgwxisi418cad577l"))))
5731 (properties `((upstream-name . "lfa")))
5732 (build-system r-build-system)
5733 (propagated-inputs (list r-corpcor))
5734 (native-inputs (list r-knitr))
5735 (home-page "https://github.com/StoreyLab/lfa")
5736 (synopsis "Logistic Factor Analysis for categorical data")
5738 "@dfn{Logistic Factor Analysis} (LFA) is a method for a PCA analogue on
5739 Binomial data via estimation of latent structure in the natural parameter.")
5740 (license license:gpl3)))
5742 (define-public r-limma
5748 (uri (bioconductor-uri "limma" version))
5751 "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"))))
5752 (build-system r-build-system)
5753 (home-page "http://bioinf.wehi.edu.au/limma")
5754 (synopsis "Package for linear models for microarray and RNA-seq data")
5755 (description "This package can be used for the analysis of gene expression
5756 studies, especially the use of linear models for analysing designed experiments
5757 and the assessment of differential expression. The analysis methods apply to
5758 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
5759 (license license:gpl2+)))
5761 (define-public r-made4
5767 (uri (bioconductor-uri "made4" version))
5770 "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
5771 (properties `((upstream-name . "made4")))
5772 (build-system r-build-system)
5779 r-summarizedexperiment))
5780 (native-inputs (list r-knitr))
5781 (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
5782 (synopsis "Multivariate analysis of microarray data using ADE4")
5784 "This is a package for multivariate data analysis and graphical display
5785 of microarray data. Functions are included for supervised dimension
5786 reduction (between group analysis) and joint dimension reduction of two
5787 datasets (coinertia analysis).")
5788 (license license:artistic2.0)))
5790 (define-public r-methylkit
5792 (name "r-methylkit")
5796 (uri (bioconductor-uri "methylKit" version))
5799 "00asjzv05avfg0rrkmfbdqd6xx8d18zi72n3b1kf9wj81z2d2a35"))))
5800 (properties `((upstream-name . "methylKit")))
5801 (build-system r-build-system)
5823 (list r-knitr)) ; for vignettes
5824 (home-page "https://github.com/al2na/methylKit")
5826 "DNA methylation analysis from high-throughput bisulfite sequencing results")
5828 "MethylKit is an R package for DNA methylation analysis and annotation
5829 from high-throughput bisulfite sequencing. The package is designed to deal
5830 with sequencing data from @dfn{Reduced representation bisulfite
5831 sequencing} (RRBS) and its variants, but also target-capture methods and whole
5832 genome bisulfite sequencing. It also has functions to analyze base-pair
5833 resolution 5hmC data from experimental protocols such as oxBS-Seq and
5835 (license license:artistic2.0)))
5837 (define-public r-motifrg
5844 (uri (bioconductor-uri "motifRG" version))
5847 "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
5848 (properties `((upstream-name . "motifRG")))
5849 (build-system r-build-system)
5853 r-bsgenome-hsapiens-ucsc-hg19
5857 (home-page "https://bioconductor.org/packages/motifRG")
5858 (synopsis "Discover motifs in high throughput sequencing data")
5860 "This package provides tools for discriminative motif discovery in high
5861 throughput genetic sequencing data sets using regression methods.")
5862 (license license:artistic2.0)))
5864 (define-public r-muscat
5871 (uri (bioconductor-uri "muscat" version))
5874 "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
5875 (properties `((upstream-name . "muscat")))
5876 (build-system r-build-system)
5878 (list r-biocparallel
5899 r-singlecellexperiment
5900 r-summarizedexperiment
5903 (native-inputs (list r-knitr))
5904 (home-page "https://github.com/HelenaLC/muscat")
5905 (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
5907 "This package @code{muscat} provides various methods and visualization tools
5908 for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
5909 multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
5910 methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
5911 platform that mimics both single and multi-sample scRNA-seq data.")
5912 (license license:gpl3)))
5914 (define-public r-mutationalpatterns
5916 (name "r-mutationalpatterns")
5921 (uri (bioconductor-uri "MutationalPatterns" version))
5924 "113b2hrc0n47qz144xhky93jcm6qh6flzadq5y0plga5jrz0rnwg"))))
5925 (build-system r-build-system)
5929 (list r-biocgenerics
5932 ;; These two packages are suggested packages
5933 r-bsgenome-hsapiens-1000genomes-hs37d5
5934 r-bsgenome-hsapiens-ucsc-hg19
5952 r-variantannotation))
5953 (home-page "https://bioconductor.org/packages/MutationalPatterns/")
5954 (synopsis "Extract and visualize mutational patterns in genomic data")
5955 (description "This package provides an extensive toolset for the
5956 characterization and visualization of a wide range of mutational patterns
5957 in SNV base substitution data.")
5958 (license license:expat)))
5960 (define-public r-msnbase
5967 (uri (bioconductor-uri "MSnbase" version))
5970 "1xzn0k3c2wn6c6gv90hddy3c201sg927342zrw9ig2xap0r053x3"))))
5971 (properties `((upstream-name . "MSnbase")))
5972 (build-system r-build-system)
5998 (home-page "https://github.com/lgatto/MSnbase")
5999 (synopsis "Base functions and classes for MS-based proteomics")
6001 "This package provides basic plotting, data manipulation and processing
6002 of mass spectrometry based proteomics data.")
6003 (license license:artistic2.0)))
6005 (define-public r-msnid
6012 (uri (bioconductor-uri "MSnID" version))
6015 "1yiw95p40nz0pvq7s4i0xg02r9yqmnknak00z4lkw8jij3w3rkkq"))))
6016 (properties `((upstream-name . "MSnID")))
6017 (build-system r-build-system)
6020 (modify-phases %standard-phases
6021 (add-after 'unpack 'set-HOME
6022 (lambda _ (setenv "HOME" "/tmp"))))))
6024 (list r-annotationdbi
6050 (home-page "https://bioconductor.org/packages/MSnID")
6051 (synopsis "Utilities for LC-MSn proteomics identifications")
6053 "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
6054 from mzIdentML (leveraging the mzID package) or text files. After collating
6055 the search results from multiple datasets it assesses their identification
6056 quality and optimize filtering criteria to achieve the maximum number of
6057 identifications while not exceeding a specified false discovery rate. It also
6058 contains a number of utilities to explore the MS/MS results and assess missed
6059 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
6060 (license license:artistic2.0)))
6062 (define-public r-mzid
6069 (uri (bioconductor-uri "mzID" version))
6072 "1q1aqyya9nd494s7m3rdaf3kixipdrwbj825g40kdljwrg85y961"))))
6073 (properties `((upstream-name . "mzID")))
6074 (build-system r-build-system)
6084 (home-page "https://bioconductor.org/packages/mzID")
6085 (synopsis "Parser for mzIdentML files")
6087 "This package provides a parser for mzIdentML files implemented using the
6088 XML package. The parser tries to be general and able to handle all types of
6089 mzIdentML files with the drawback of having less pretty output than a vendor
6091 (license license:gpl2+)))
6093 (define-public r-mzr
6100 (uri (bioconductor-uri "mzR" version))
6103 "1dqa03hb42kbqfg15ksijdkyf9pr54gcl3in4mzjkld5sdi8ncds"))
6104 (modules '((guix build utils)))
6106 '(delete-file-recursively "src/boost"))))
6107 (properties `((upstream-name . "mzR")))
6108 (build-system r-build-system)
6111 (modify-phases %standard-phases
6112 (add-after 'unpack 'use-system-boost
6114 (substitute* "src/Makevars"
6115 (("\\./boost/libs.*") "")
6116 (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
6117 (("\\ARCH_OBJS=" line)
6119 "\nBOOST_LIBS=-lboost_system -lboost_regex \
6120 -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))))))))
6122 (list boost ; use this instead of the bundled boost sources
6133 (home-page "https://github.com/sneumann/mzR/")
6134 (synopsis "Parser for mass spectrometry data files")
6136 "The mzR package provides a unified API to the common file formats and
6137 parsers available for mass spectrometry data. It comes with a wrapper for the
6138 ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
6139 The package contains the original code written by the ISB, and a subset of the
6140 proteowizard library for mzML and mzIdentML. The netCDF reading code has
6141 previously been used in XCMS.")
6142 (license license:artistic2.0)))
6144 (define-public r-organism-dplyr
6146 (name "r-organism-dplyr")
6151 (uri (bioconductor-uri "Organism.dplyr" version))
6154 "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
6155 (properties `((upstream-name . "Organism.dplyr")))
6156 (build-system r-build-system)
6158 (list r-annotationdbi
6172 (native-inputs (list r-knitr))
6173 (home-page "https://bioconductor.org/packages/Organism.dplyr")
6174 (synopsis "Dplyr-based access to Bioconductor annotation resources")
6176 "This package provides an alternative interface to Bioconductor @code{
6177 annotation} resources, in particular the gene identifier mapping functionality
6178 of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
6179 functionality of the @code{TxDb} packages (e.g.,
6180 @code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
6181 (license license:artistic2.0)))
6183 (define-public r-organismdbi
6185 (name "r-organismdbi")
6190 (uri (bioconductor-uri "OrganismDbi" version))
6193 "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619"))))
6194 (properties `((upstream-name . "OrganismDbi")))
6195 (build-system r-build-system)
6197 (list r-annotationdbi
6208 (home-page "https://bioconductor.org/packages/OrganismDbi")
6209 (synopsis "Software to enable the smooth interfacing of database packages")
6210 (description "The package enables a simple unified interface to several
6211 annotation packages each of which has its own schema by taking advantage of
6212 the fact that each of these packages implements a select methods.")
6213 (license license:artistic2.0)))
6215 (define-public r-pcaexplorer
6217 (name "r-pcaexplorer")
6222 (uri (bioconductor-uri "pcaExplorer" version))
6225 "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
6226 (properties `((upstream-name . "pcaExplorer")))
6227 (build-system r-build-system)
6229 (list r-annotationdbi
6255 r-summarizedexperiment
6259 (native-inputs (list r-knitr))
6260 (home-page "https://github.com/federicomarini/pcaExplorer")
6262 "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
6264 "This package provides functionality for interactive visualization of RNA-seq
6265 datasets based on Principal Components Analysis. The methods provided allow for
6266 quick information extraction and effective data exploration. A Shiny
6267 application encapsulates the whole analysis.")
6268 (license license:expat)))
6270 (define-public r-pcamethods
6272 (name "r-pcamethods")
6277 (uri (bioconductor-uri "pcaMethods" version))
6280 "1087sl7y707zld7zpf3ly51gnmdp93vn90dwa5440v7qawvg2h9b"))))
6281 (properties `((upstream-name . "pcaMethods")))
6282 (build-system r-build-system)
6284 (list r-biobase r-biocgenerics r-mass r-rcpp))
6285 (home-page "https://github.com/hredestig/pcamethods")
6286 (synopsis "Collection of PCA methods")
6288 "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
6289 Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method
6290 for missing value estimation is included for comparison. BPCA, PPCA and
6291 NipalsPCA may be used to perform PCA on incomplete data as well as for
6292 accurate missing value estimation. A set of methods for printing and plotting
6293 the results is also provided. All PCA methods make use of the same data
6294 structure (pcaRes) to provide a common interface to the PCA results.")
6295 (license license:gpl3+)))
6297 ;; This is a CRAN package, but it depends on a Bioconductor package:
6298 ;; r-aroma-light, r-dnacopy..
6299 (define-public r-pscbs
6306 (uri (cran-uri "PSCBS" version))
6308 (base32 "14rs2wywipbkia3dbzfhpnkmfgdvm2bf586lggsx63sywlv5d02q"))))
6309 (properties `((upstream-name . "PSCBS")))
6310 (build-system r-build-system)
6313 (modify-phases %standard-phases
6314 (add-before 'install 'change-home-dir
6316 ;; Change from /homeless-shelter to /tmp for write permission.
6317 (setenv "HOME" "/tmp"))))))
6329 (list r-r-rsp ;used to build vignettes
6331 (home-page "https://github.com/HenrikBengtsson/PSCBS")
6332 (synopsis "Analysis of parent-specific DNA copy numbers")
6334 "This is a package for segmentation of allele-specific DNA copy number
6335 data and detection of regions with abnormal copy number within each parental
6336 chromosome. Both tumor-normal paired and tumor-only analyses are supported.")
6337 (license license:gpl2+)))
6339 (define-public r-protgenerics
6341 (name "r-protgenerics")
6346 (uri (bioconductor-uri "ProtGenerics" version))
6349 "04hcgj4q8dbzp1a29rbww2bxxrg679pgys3m09p0ydkpsx76rq05"))))
6350 (properties `((upstream-name . "ProtGenerics")))
6351 (build-system r-build-system)
6352 (home-page "https://github.com/lgatto/ProtGenerics")
6353 (synopsis "S4 generic functions for proteomics infrastructure")
6355 "This package provides S4 generic functions needed by Bioconductor
6356 proteomics packages.")
6357 (license license:artistic2.0)))
6359 (define-public r-rbgl
6366 (uri (bioconductor-uri "RBGL" version))
6369 "0ph089vxla49sng0pdwiyh9rpk9i96cbsx5q2jn46jj4x51ijc7y"))))
6370 (properties `((upstream-name . "RBGL")))
6371 (build-system r-build-system)
6373 (list r-bh r-graph))
6374 (home-page "https://www.bioconductor.org/packages/RBGL")
6375 (synopsis "Interface to the Boost graph library")
6377 "This package provides a fairly extensive and comprehensive interface to
6378 the graph algorithms contained in the Boost library.")
6379 (license license:artistic2.0)))
6381 (define-public r-rcas
6387 (uri (bioconductor-uri "RCAS" version))
6390 "05sj2ab7bxgf41gkmjaskhqm0198xlir1sw3f73x8rjg14rssmqf"))))
6391 (properties `((upstream-name . "RCAS")))
6392 (build-system r-build-system)
6394 (list r-biocgenerics
6397 r-bsgenome-hsapiens-ucsc-hg19
6423 (synopsis "RNA-centric annotation system")
6425 "RCAS aims to be a standalone RNA-centric annotation system that provides
6426 intuitive reports and publication-ready graphics. This package provides the R
6427 library implementing most of the pipeline's features.")
6428 (home-page "https://github.com/BIMSBbioinfo/RCAS")
6429 (license license:artistic2.0)))
6431 (define-public r-regioner
6438 (uri (bioconductor-uri "regioneR" version))
6441 "11whi2v211xiz9s7cjl14d8vavlry2fmhvx12rma25wkjmhrpa3f"))))
6442 (properties `((upstream-name . "regioneR")))
6443 (build-system r-build-system)
6455 (home-page "https://bioconductor.org/packages/regioneR/")
6456 (synopsis "Association analysis of genomic regions")
6457 (description "This package offers a statistical framework based on
6458 customizable permutation tests to assess the association between genomic
6459 region sets and other genomic features.")
6460 (license license:artistic2.0)))
6462 (define-public r-reportingtools
6464 (name "r-reportingtools")
6469 (uri (bioconductor-uri "ReportingTools" version))
6472 "0r8cdqzfh1jxkghhk3j8x3y9kkmdyg9ibfhsic15jqkmp1im6khh"))))
6474 `((upstream-name . "ReportingTools")))
6475 (build-system r-build-system)
6498 (home-page "https://bioconductor.org/packages/ReportingTools/")
6499 (synopsis "Tools for making reports in various formats")
6501 "The ReportingTools package enables users to easily display reports of
6502 analysis results generated from sources such as microarray and sequencing
6503 data. The package allows users to create HTML pages that may be viewed on a
6504 web browser, or in other formats. Users can generate tables with sortable and
6505 filterable columns, make and display plots, and link table entries to other
6506 data sources such as NCBI or larger plots within the HTML page. Using the
6507 package, users can also produce a table of contents page to link various
6508 reports together for a particular project that can be viewed in a web
6510 (license license:artistic2.0)))
6512 (define-public r-rhdf5
6518 (uri (bioconductor-uri "rhdf5" version))
6521 "00cp90mnb8p83jiflm6x4x0qf4p7gvgh47jk9jry6j3qyvfqaiff"))))
6522 (build-system r-build-system)
6524 (list r-rhdf5filters r-rhdf5lib))
6527 (home-page "https://bioconductor.org/packages/rhdf5")
6528 (synopsis "HDF5 interface to R")
6530 "This R/Bioconductor package provides an interface between HDF5 and R.
6531 HDF5's main features are the ability to store and access very large and/or
6532 complex datasets and a wide variety of metadata on mass storage (disk) through
6533 a completely portable file format. The rhdf5 package is thus suited for the
6534 exchange of large and/or complex datasets between R and other software
6535 package, and for letting R applications work on datasets that are larger than
6536 the available RAM.")
6537 (license license:artistic2.0)))
6539 (define-public r-rhdf5filters
6541 (name "r-rhdf5filters")
6546 (uri (bioconductor-uri "rhdf5filters" version))
6549 "1ipg0v8nqz1imj63scqmpiswcxbl4ankg3knfq4p06ic6ypbbmvs"))))
6550 (properties `((upstream-name . "rhdf5filters")))
6551 (build-system r-build-system)
6558 (home-page "https://github.com/grimbough/rhdf5filters")
6559 (synopsis "HDF5 compression filters")
6561 "This package provides a collection of compression filters for use with
6563 (license license:bsd-2)))
6565 (define-public r-rsamtools
6567 (name "r-rsamtools")
6571 (uri (bioconductor-uri "Rsamtools" version))
6574 "1wll703if12qrn0d11ljwf7rqhs4lb27fzyyz1hqwvzn3v361s10"))))
6576 `((upstream-name . "Rsamtools")))
6577 (build-system r-build-system)
6580 (modify-phases %standard-phases
6581 (add-after 'unpack 'use-system-zlib
6583 (substitute* "DESCRIPTION"
6584 (("zlibbioc, ") ""))
6585 (substitute* "NAMESPACE"
6586 (("import\\(zlibbioc\\)") "")))))))
6588 (list r-biocgenerics
6598 (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html")
6599 (synopsis "Interface to samtools, bcftools, and tabix")
6601 "This package provides an interface to the @code{samtools},
6602 @code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence
6603 Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
6604 tab-delimited (tabix) files.")
6605 (license license:expat)))
6607 ;; This is a CRAN package, but it depends on a Bioconductor package:
6609 (define-public r-restfulr
6616 (uri (cran-uri "restfulr" version))
6619 "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0"))))
6620 (properties `((upstream-name . "restfulr")))
6621 (build-system r-build-system)
6623 (list r-rcurl r-rjson r-s4vectors r-xml r-yaml))
6624 (home-page "https://cran.r-project.org/package=restfulr")
6625 (synopsis "R interface to RESTful web services")
6627 "This package models a RESTful service as if it were a nested R list.")
6628 (license license:artistic2.0)))
6630 (define-public r-rtracklayer
6632 (name "r-rtracklayer")
6636 (uri (bioconductor-uri "rtracklayer" version))
6639 "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls"))))
6640 (build-system r-build-system)
6643 (modify-phases %standard-phases
6644 (add-after 'unpack 'use-system-zlib
6646 (substitute* "DESCRIPTION"
6647 ((" zlibbioc,") ""))
6648 (substitute* "NAMESPACE"
6649 (("import\\(zlibbioc\\)") "")))))))
6655 (list r-biocgenerics
6669 (home-page "https://bioconductor.org/packages/rtracklayer")
6670 (synopsis "R interface to genome browsers and their annotation tracks")
6672 "rtracklayer is an extensible framework for interacting with multiple
6673 genome browsers (currently UCSC built-in) and manipulating annotation tracks
6674 in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
6675 built-in). The user may export/import tracks to/from the supported browsers,
6676 as well as query and modify the browser state, such as the current viewport.")
6677 (license license:artistic2.0)))
6679 ;; This is a CRAN package, but it depends on a Bioconductor package.
6680 (define-public r-samr
6687 (uri (cran-uri "samr" version))
6690 "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
6691 (properties `((upstream-name . "samr")))
6692 (build-system r-build-system)
6700 (native-inputs (list gfortran))
6701 (home-page "https://statweb.stanford.edu/~tibs/SAM/")
6702 (synopsis "Significance analysis of Microarrays")
6704 "This is a package for significance analysis of Microarrays for
6705 differential expression analysis, RNAseq data and related problems.")
6706 ;; Any version of the LGPL
6707 (license license:lgpl3+)))
6709 (define-public r-scannotatr
6711 (name "r-scannotatr")
6716 (uri (bioconductor-uri "scAnnotatR" version))
6718 (base32 "067q57kabhqd1z8l3d91fw74aaw89nb48gm6fll4hv00nqza3n5b"))))
6719 (properties `((upstream-name . "scAnnotatR")))
6720 (build-system r-build-system)
6722 (list r-annotationhub
6733 r-singlecellexperiment
6734 r-summarizedexperiment))
6735 (native-inputs (list r-knitr))
6736 (home-page "https://github.com/grisslab/scAnnotatR")
6737 (synopsis "Pretrained models for prediction on single cell RNA-sequencing data")
6739 "This package comprises a set of pretrained machine learning models to
6740 predict basic immune cell types. This enables to quickly get a first
6741 annotation of the cell types present in the dataset without requiring prior
6742 knowledge. The package also lets you train using own models to predict new
6743 cell types based on specific research needs.")
6744 (license license:expat)))
6746 (define-public r-scdblfinder
6748 (name "r-scdblfinder")
6753 (uri (bioconductor-uri "scDblFinder" version))
6755 (base32 "0y14dvdm16b3bvlrnz03adfylm1kj6jrp2fwciyldij2lfal90y0"))))
6756 (properties `((upstream-name . "scDblFinder")))
6757 (build-system r-build-system)
6759 (list r-biocgenerics
6777 r-singlecellexperiment
6778 r-summarizedexperiment
6780 (native-inputs (list r-knitr))
6781 (home-page "https://github.com/plger/scDblFinder")
6782 (synopsis "Detect multiplets in single-cell RNA sequencing data")
6784 "The scDblFinder package gathers various methods for the detection and
6785 handling of doublets/multiplets in single-cell RNA sequencing data (i.e.
6786 multiple cells captured within the same droplet or reaction volume). It
6787 includes methods formerly found in the scran package, and the new fast and
6788 comprehensive scDblFinder method.")
6789 (license license:gpl3)))
6791 (define-public r-scmap
6798 (uri (bioconductor-uri "scmap" version))
6800 (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
6801 (properties `((upstream-name . "scmap")))
6802 (build-system r-build-system)
6817 r-singlecellexperiment
6818 r-summarizedexperiment))
6819 (native-inputs (list r-knitr))
6820 (home-page "https://github.com/hemberg-lab/scmap")
6821 (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
6823 "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
6824 composition of complex tissues since the technology allows researchers to
6825 define cell-types using unsupervised clustering of the transcriptome.
6826 However, due to differences in experimental methods and computational
6827 analyses, it is often challenging to directly compare the cells identified in
6828 two different experiments. @code{scmap} is a method for projecting cells from
6829 a scRNA-seq experiment onto the cell-types or individual cells identified in a
6830 different experiment.")
6831 (license license:gpl3)))
6833 (define-public r-scry
6839 (uri (bioconductor-uri "scry" version))
6842 "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
6843 (properties `((upstream-name . "scry")))
6844 (build-system r-build-system)
6846 (list r-biocsingular
6851 r-singlecellexperiment
6852 r-summarizedexperiment))
6853 (native-inputs (list r-knitr))
6854 (home-page "https://bioconductor.org/packages/scry.html")
6855 (synopsis "Small-count analysis methods for high-dimensional data")
6857 "Many modern biological datasets consist of small counts that are not
6858 well fit by standard linear-Gaussian methods such as principal component
6859 analysis. This package provides implementations of count-based feature
6860 selection and dimension reduction algorithms. These methods can be used to
6861 facilitate unsupervised analysis of any high-dimensional data such as
6862 single-cell RNA-seq.")
6863 (license license:artistic2.0)))
6865 (define-public r-seqlogo
6872 (uri (bioconductor-uri "seqLogo" version))
6875 "1lk3238m17acmd6lgjjbpscyxw8fm63wv34kbbr478wcih1wbwxr"))))
6876 (properties `((upstream-name . "seqLogo")))
6877 (build-system r-build-system)
6880 (home-page "https://bioconductor.org/packages/seqLogo")
6881 (synopsis "Sequence logos for DNA sequence alignments")
6883 "seqLogo takes the position weight matrix of a DNA sequence motif and
6884 plots the corresponding sequence logo as introduced by Schneider and
6886 (license license:lgpl2.0+)))
6888 (define-public r-seqpattern
6890 (name "r-seqpattern")
6894 (uri (bioconductor-uri "seqPattern" version))
6897 "0nrrlr1nl9zxmp88qq8jn7wgmda6jh0xvp4nph94w4nwjsyb7xqn"))))
6899 `((upstream-name . "seqPattern")))
6900 (build-system r-build-system)
6902 (list r-biostrings r-genomicranges r-iranges r-kernsmooth r-plotrix))
6903 (home-page "https://bioconductor.org/packages/seqPattern")
6904 (synopsis "Visualising oligonucleotide patterns and motif occurrences")
6906 "This package provides tools to visualize oligonucleotide patterns and
6907 sequence motif occurrences across a large set of sequences centred at a common
6908 reference point and sorted by a user defined feature.")
6909 (license license:gpl3+)))
6911 (define-public r-shortread
6913 (name "r-shortread")
6918 (uri (bioconductor-uri "ShortRead" version))
6921 "0303198b4v2wjah9kc829kn01030996l6di4jpf8q5ccd212rjhq"))))
6922 (properties `((upstream-name . "ShortRead")))
6923 (build-system r-build-system)
6943 (home-page "https://bioconductor.org/packages/ShortRead")
6944 (synopsis "FASTQ input and manipulation tools")
6946 "This package implements sampling, iteration, and input of FASTQ files.
6947 It includes functions for filtering and trimming reads, and for generating a
6948 quality assessment report. Data are represented as
6949 @code{DNAStringSet}-derived objects, and easily manipulated for a diversity of
6950 purposes. The package also contains legacy support for early single-end,
6951 ungapped alignment formats.")
6952 (license license:artistic2.0)))
6954 (define-public r-simplifyenrichment
6956 (name "r-simplifyenrichment")
6961 (uri (bioconductor-uri "simplifyEnrichment" version))
6964 "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6"))))
6966 `((upstream-name . "simplifyEnrichment")))
6967 (build-system r-build-system)
6969 (list r-annotationdbi
6986 (native-inputs (list r-knitr))
6987 (home-page "https://github.com/jokergoo/simplifyEnrichment")
6988 (synopsis "Simplify functional enrichment results")
6989 (description "This package provides a new clustering algorithm, binary
6990 cut, for clustering similarity matrices of functional terms is implemented in
6991 this package. It also provides functionalities for visualizing, summarizing
6992 and comparing the clusterings.")
6993 (license license:expat)))
6995 (define-public r-transcriptr
6997 (name "r-transcriptr")
7002 (uri (bioconductor-uri "transcriptR" version))
7004 (base32 "1zc6aasd5nzwl9jxr0rdriiq85adqdbfi5b9m3jyf69pa71sgy03"))))
7005 (properties `((upstream-name . "transcriptR")))
7006 (build-system r-build-system)
7008 (list r-biocgenerics
7023 (native-inputs (list r-knitr))
7024 (home-page "https://bioconductor.org/packages/transcriptR")
7025 (synopsis "Primary transcripts detection and quantification")
7027 "The differences in the RNA types being sequenced have an impact on the
7028 resulting sequencing profiles. mRNA-seq data is enriched with reads derived
7029 from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial
7030 broader coverage of both exonic and intronic regions. The presence of
7031 intronic reads in GRO-seq type of data makes it possible to use it to
7032 computationally identify and quantify all de novo continuous regions of
7033 transcription distributed across the genome. This type of data, however, is
7034 more challenging to interpret and less common practice compared to mRNA-seq.
7035 One of the challenges for primary transcript detection concerns the
7036 simultaneous transcription of closely spaced genes, which needs to be properly
7037 divided into individually transcribed units. The R package transcriptR
7038 combines RNA-seq data with ChIP-seq data of histone modifications that mark
7039 active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to
7040 overcome this challenge. The advantage of this approach over the use of, for
7041 example, gene annotations is that this approach is data driven and therefore
7042 able to deal also with novel and case specific events.")
7043 (license license:gpl3)))
7045 (define-public r-trajectoryutils
7047 (name "r-trajectoryutils")
7052 (uri (bioconductor-uri "TrajectoryUtils" version))
7055 "07hcr3zplxlzlwc13wh9006m5kaqm57cm1b2x74bpp857f2q93dj"))))
7057 `((upstream-name . "TrajectoryUtils")))
7058 (build-system r-build-system)
7060 (list r-igraph r-matrix r-s4vectors r-singlecellexperiment
7061 r-summarizedexperiment))
7062 (native-inputs (list r-knitr))
7063 (home-page "https://bioconductor.org/packages/TrajectoryUtils")
7064 (synopsis "Single-cell trajectory analysis utilities")
7066 "This package implements low-level utilities for single-cell trajectory
7067 analysis, primarily intended for re-use inside higher-level packages. It
7068 includes a function to create a cluster-level minimum spanning tree and data
7069 structures to hold pseudotime inference results.")
7070 (license license:gpl3)))
7072 (define-public r-slingshot
7074 (name "r-slingshot")
7078 (uri (bioconductor-uri "slingshot" version))
7081 "0xapi66l5z2qdqns3fcjqcjal6npqj7rxra60lwjvbrq49pq69p2"))))
7082 (build-system r-build-system)
7088 r-singlecellexperiment
7089 r-summarizedexperiment
7093 (home-page "https://bioconductor.org/packages/slingshot")
7094 (synopsis "Tools for ordering single-cell sequencing")
7095 (description "This package provides functions for inferring continuous,
7096 branching lineage structures in low-dimensional data. Slingshot was designed
7097 to model developmental trajectories in single-cell RNA sequencing data and
7098 serve as a component in an analysis pipeline after dimensionality reduction
7099 and clustering. It is flexible enough to handle arbitrarily many branching
7100 events and allows for the incorporation of prior knowledge through supervised
7101 graph construction.")
7102 (license license:artistic2.0)))
7104 (define-public r-stager
7111 (uri (bioconductor-uri "stageR" version))
7113 (base32 "0ns3ih6l4na6irshrc5iy4d9qf7hrnqq3ndnlcjb2i1cn38l2w9y"))))
7114 (properties `((upstream-name . "stageR")))
7115 (build-system r-build-system)
7116 (propagated-inputs (list r-summarizedexperiment))
7117 (native-inputs (list r-knitr))
7118 (home-page "https://bioconductor.org/packages/stageR")
7119 (synopsis "Stage-wise analysis of high throughput gene expression data")
7121 "The stageR package allows automated stage-wise analysis of
7122 high-throughput gene expression data. The method is published in Genome
7124 @url{https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0}.")
7125 (license license:gpl3)))
7127 (define-public r-stringdb
7134 (uri (bioconductor-uri "STRINGdb" version))
7136 (base32 "1jn6080v6097zpqsr4gfbx31gqqdhpzjrk63avk3v3xwawmf2379"))))
7137 (properties `((upstream-name . "STRINGdb")))
7138 (build-system r-build-system)
7149 (home-page "https://git.bioconductor.org/packages/STRINGdb")
7150 (synopsis "Search tool for the retrieval of interacting proteins database")
7152 "The @code{STRINGdb} package provides an R interface to the STRING
7153 protein-protein interactions database. @url{https://www.string-db.org,
7154 STRING} is a database of known and predicted protein-protein interactions.
7155 The interactions include direct (physical) and indirect (functional)
7156 associations. Each interaction is associated with a combined confidence score
7157 that integrates the various evidences.")
7158 (license license:gpl2)))
7160 (define-public r-structuralvariantannotation
7162 (name "r-structuralvariantannotation")
7167 (uri (bioconductor-uri "StructuralVariantAnnotation" version))
7169 (base32 "0f3x74ic3blg8nm5xlv79k0n8j3fpl98mmhfanqfzmdl0g3j6wx6"))))
7170 (build-system r-build-system)
7184 r-summarizedexperiment
7185 r-variantannotation))
7188 (home-page "https://bioconductor.org/packages/StructuralVariantAnnotation/")
7189 (synopsis "R package designed to simplify structural variant analysis")
7191 "This package contains useful helper functions for dealing with structural
7192 variants in VCF format. The packages contains functions for parsing VCFs from
7193 a number of popular callers as well as functions for dealing with breakpoints
7194 involving two separate genomic loci encoded as GRanges objects.")
7195 (license license:gpl3)))
7197 (define-public r-summarizedexperiment
7199 (name "r-summarizedexperiment")
7203 (uri (bioconductor-uri "SummarizedExperiment" version))
7206 "02vlqzmslyijs09jl0gdjxqjjnnl4yqbqqqlb4vb7nr0fspmyz39"))))
7208 `((upstream-name . "SummarizedExperiment")))
7209 (build-system r-build-system)
7222 (home-page "https://bioconductor.org/packages/SummarizedExperiment")
7223 (synopsis "Container for representing genomic ranges by sample")
7225 "The SummarizedExperiment container contains one or more assays, each
7226 represented by a matrix-like object of numeric or other mode. The rows
7227 typically represent genomic ranges of interest and the columns represent
7229 (license license:artistic2.0)))
7231 (define-public r-sva
7238 (uri (bioconductor-uri "sva" version))
7241 "0ka259rn0la0hjslj7w24q1dyyh79h84nw6mxp7armqbfjb207a4"))))
7242 (build-system r-build-system)
7250 (home-page "https://bioconductor.org/packages/sva")
7251 (synopsis "Surrogate variable analysis")
7253 "This package contains functions for removing batch effects and other
7254 unwanted variation in high-throughput experiment. It also contains functions
7255 for identifying and building surrogate variables for high-dimensional data
7256 sets. Surrogate variables are covariates constructed directly from
7257 high-dimensional data like gene expression/RNA sequencing/methylation/brain
7258 imaging data that can be used in subsequent analyses to adjust for unknown,
7259 unmodeled, or latent sources of noise.")
7260 (license license:artistic2.0)))
7262 (define-public r-systempiper
7264 (name "r-systempiper")
7269 (uri (bioconductor-uri "systemPipeR" version))
7272 "1yybbff29gwv6rm0nw4yjw73bbl5prfj8gj4zky917smjfd459im"))))
7273 (properties `((upstream-name . "systemPipeR")))
7274 (build-system r-build-system)
7276 (list r-biocgenerics
7287 r-summarizedexperiment
7291 (home-page "https://github.com/tgirke/systemPipeR")
7292 (synopsis "Next generation sequencing workflow and reporting environment")
7294 "This R package provides tools for building and running automated
7295 end-to-end analysis workflows for a wide range of @dfn{next generation
7296 sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq.
7297 Important features include a uniform workflow interface across different NGS
7298 applications, automated report generation, and support for running both R and
7299 command-line software, such as NGS aligners or peak/variant callers, on local
7300 computers or compute clusters. Efficient handling of complex sample sets and
7301 experimental designs is facilitated by a consistently implemented sample
7302 annotation infrastructure.")
7303 (license license:artistic2.0)))
7305 (define-public r-topgo
7311 (uri (bioconductor-uri "topGO" version))
7314 "125r42ymk1irjmwk4sywjkcshs71s26p3zsvryfdvf56k5w162v6"))))
7316 `((upstream-name . "topGO")))
7317 (build-system r-build-system)
7319 (list r-annotationdbi
7328 (home-page "https://bioconductor.org/packages/topGO")
7329 (synopsis "Enrichment analysis for gene ontology")
7331 "The topGO package provides tools for testing @dfn{gene ontology} (GO)
7332 terms while accounting for the topology of the GO graph. Different test
7333 statistics and different methods for eliminating local similarities and
7334 dependencies between GO terms can be implemented and applied.")
7335 ;; Any version of the LGPL applies.
7336 (license license:lgpl2.1+)))
7338 (define-public r-tximport
7344 (uri (bioconductor-uri "tximport" version))
7347 "1cnra82pvwz79a1hkw0phc6aa3v43r5p4nx8xyx5wzmkd7rjkc8x"))))
7348 (build-system r-build-system)
7351 (home-page "https://bioconductor.org/packages/tximport")
7352 (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
7354 "This package provides tools to import transcript-level abundance,
7355 estimated counts and transcript lengths, and to summarize them into matrices
7356 for use with downstream gene-level analysis packages. Average transcript
7357 length, weighted by sample-specific transcript abundance estimates, is
7358 provided as a matrix which can be used as an offset for different expression
7359 of gene-level counts.")
7360 (license license:gpl2+)))
7362 ;; This is a CRAN package, but it depends on a Bioconductor package.
7363 (define-public r-valr
7370 (uri (cran-uri "valr" version))
7373 "0w3j8fkssp9s4ybaw8hvqbmsh5m991xkgr4nji3zar2pgmgk3qph"))))
7374 (build-system r-build-system)
7383 r-rtracklayer ;bioconductor package
7388 (home-page "https://github.com/rnabioco/valr")
7389 (synopsis "Genome interval arithmetic in R")
7391 "This package enables you to read and manipulate genome intervals and
7392 signals. It provides functionality similar to command-line tool suites within
7393 R, enabling interactive analysis and visualization of genome-scale data.")
7394 (license license:expat)))
7396 (define-public r-variantannotation
7398 (name "r-variantannotation")
7402 (uri (bioconductor-uri "VariantAnnotation" version))
7405 "12d5hkx6pby6l2asyg4jp4jb2x17ybwhqd55rl64h37mwcndbdg1"))))
7407 `((upstream-name . "VariantAnnotation")))
7409 (list r-annotationdbi
7420 r-summarizedexperiment
7427 (build-system r-build-system)
7428 (home-page "https://bioconductor.org/packages/VariantAnnotation")
7429 (synopsis "Package for annotation of genetic variants")
7430 (description "This R package can annotate variants, compute amino acid
7431 coding changes and predict coding outcomes.")
7432 (license license:artistic2.0)))
7434 (define-public r-vsn
7441 (uri (bioconductor-uri "vsn" version))
7444 "1ja7vdjvgx671l57f9fzfn4vc6q7xzfmqs4krg2rdyfaaf531gqf"))))
7445 (build-system r-build-system)
7447 (list r-affy r-biobase r-ggplot2 r-lattice r-limma))
7449 (list r-knitr)) ; for vignettes
7450 (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
7451 (synopsis "Variance stabilization and calibration for microarray data")
7453 "The package implements a method for normalising microarray intensities,
7454 and works for single- and multiple-color arrays. It can also be used for data
7455 from other technologies, as long as they have similar format. The method uses
7456 a robust variant of the maximum-likelihood estimator for an
7457 additive-multiplicative error model and affine calibration. The model
7458 incorporates data calibration step (a.k.a. normalization), a model for the
7459 dependence of the variance on the mean intensity and a variance stabilizing
7460 data transformation. Differences between transformed intensities are
7461 analogous to \"normalized log-ratios\". However, in contrast to the latter,
7462 their variance is independent of the mean, and they are usually more sensitive
7463 and specific in detecting differential transcription.")
7464 (license license:artistic2.0)))
7466 ;; There is no source tarball, so we fetch the code from the Bioconductor git
7468 (define-public r-xcir
7469 (let ((commit "3b59d456f2ad7f70285915b036b1dc4279687277")
7473 (version (git-version "1.8.0" revision commit))
7477 (url "https://git.bioconductor.org/packages/XCIR")
7479 (file-name (git-file-name name version))
7482 "1xxw5ady5j2p7z7zjxgx7lhm85x7fxbljiv49lc2ghsvh9wm937p"))))
7483 (properties `((upstream-name . "XCIR")))
7484 (build-system r-build-system)
7485 (propagated-inputs (list r-biomart
7493 r-variantannotation))
7494 (native-inputs (list r-knitr))
7495 (home-page "https://github.com/SRenan/XCIR")
7496 (synopsis "Analysis of X chromosome inactivation")
7498 "This package is an R package that offers models and tools for subject
7499 level analysis of @dfn{X chromosome inactivation} (XCI) and XCI-escape
7501 (license license:gpl2))))
7503 (define-public r-xina
7510 (uri (bioconductor-uri "XINA" version))
7512 (base32 "03gf7mqpnwx12kny9fsaskgrw83b0wi2cf1j4dbq46pfxjx34v1g"))))
7513 (properties `((upstream-name . "XINA")))
7514 (build-system r-build-system)
7523 (native-inputs (list r-knitr))
7524 (home-page "https://git.bioconductor.org/packages/XINA")
7525 (synopsis "Identifying proteins that exhibit similar patterns")
7527 "The aim of @code{XINA} is to determine which proteins exhibit similar
7528 patterns within and across experimental conditions, since proteins with
7529 co-abundance patterns may have common molecular functions. @code{XINA} imports
7530 multiple datasets, tags dataset in silico, and combines the data for subsequent
7531 subgrouping into multiple clusters. The result is a single output depicting
7532 the variation across all conditions. @code{XINA} not only extracts
7533 coabundance profiles within and across experiments, but also incorporates
7534 protein-protein interaction databases and integrative resources such as
7535 @dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and
7536 molecular functions, respectively, and produces intuitive graphical outputs.")
7537 (license license:gpl3)))
7539 (define-public r-xmapbridge
7541 (name "r-xmapbridge")
7546 (uri (bioconductor-uri "xmapbridge" version))
7548 (base32 "1n3nxc4jwxf5z32i70sza52nyk29adhp8vc3hac7r5b8mbi6gg10"))))
7549 (properties `((upstream-name . "xmapbridge")))
7550 (build-system r-build-system)
7551 (home-page "https://git.bioconductor.org/packages/xmapbridge")
7552 (synopsis "Display numeric data in the web based genome browser X:MAP")
7554 "The package @code{xmapbridge} can plot graphs in the X:Map genome
7555 browser. X:Map uses the Google Maps API to provide a scrollable view of the
7556 genome. It supports a number of species, and can be accessed at
7557 @url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a
7558 suitable format. Graph plotting in R is done using calls to the functions
7559 @code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be
7560 similar to those used by the standard plot methods in R. These result in data
7561 being written to a set of files (in a specific directory structure) that
7562 contain the data to be displayed, as well as some additional meta-data
7563 describing each of the graphs.")
7564 (license license:lgpl3)))
7566 (define-public r-xvector
7572 (uri (bioconductor-uri "XVector" version))
7575 "1f3sbqy279gb9k13l73j00ixywa1havlqy81zx766r1xkz15nvhk"))))
7577 `((upstream-name . "XVector")))
7578 (build-system r-build-system)
7581 (modify-phases %standard-phases
7582 (add-after 'unpack 'use-system-zlib
7584 (substitute* "DESCRIPTION"
7585 (("zlibbioc, ") ""))
7586 (substitute* "NAMESPACE"
7587 (("import\\(zlibbioc\\)") ""))
7592 (list r-biocgenerics r-iranges r-s4vectors))
7593 (home-page "https://bioconductor.org/packages/XVector")
7594 (synopsis "Representation and manpulation of external sequences")
7596 "This package provides memory efficient S4 classes for storing sequences
7597 \"externally\" (behind an R external pointer, or on disk).")
7598 (license license:artistic2.0)))
7600 (define-public r-zlibbioc
7606 (uri (bioconductor-uri "zlibbioc" version))
7609 "0w0y9jixdk6akmasn55g9g0nhlh93hbca5bwx5w1fypnvqrqpxzv"))))
7611 `((upstream-name . "zlibbioc")))
7612 (build-system r-build-system)
7613 (home-page "https://bioconductor.org/packages/zlibbioc")
7614 (synopsis "Provider for zlib-1.2.5 to R packages")
7615 (description "This package uses the source code of zlib-1.2.5 to create
7616 libraries for systems that do not have these available via other means.")
7617 (license license:artistic2.0)))
7619 (define-public r-zellkonverter
7621 (name "r-zellkonverter")
7626 (uri (bioconductor-uri "zellkonverter" version))
7628 (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"))))
7629 (properties `((upstream-name . "zellkonverter")))
7630 (build-system r-build-system)
7638 r-singlecellexperiment
7639 r-summarizedexperiment))
7640 (native-inputs (list r-knitr))
7641 (home-page "https://github.com/theislab/zellkonverter")
7642 (synopsis "Conversion between AnnData and single-cell experiments objects")
7644 "This package provides methods to convert between Python AnnData objects
7645 and SingleCellExperiment objects. These are primarily intended for use by
7646 downstream Bioconductor packages that wrap Python methods for single-cell data
7647 analysis. It also includes functions to read and write H5AD files used for
7648 saving AnnData objects to disk.")
7649 (license license:expat)))
7651 (define-public r-geneplotter
7653 (name "r-geneplotter")
7658 (uri (bioconductor-uri "geneplotter" version))
7661 "13230mzrdralnvf9jp032s16a8mk3kx5476nnvpa4pvcgp1i1ijc"))))
7662 (build-system r-build-system)
7670 (home-page "https://bioconductor.org/packages/geneplotter")
7671 (synopsis "Graphics functions for genomic data")
7673 "This package provides functions for plotting genomic data.")
7674 (license license:artistic2.0)))
7676 (define-public r-oligoclasses
7678 (name "r-oligoclasses")
7683 (uri (bioconductor-uri "oligoClasses" version))
7686 "1m4x50gl1fm5waa531v7ml0q229q65qn9cgiwnvjg721fvra7mdk"))))
7687 (properties `((upstream-name . "oligoClasses")))
7688 (build-system r-build-system)
7702 r-summarizedexperiment))
7703 (home-page "https://bioconductor.org/packages/oligoClasses/")
7704 (synopsis "Classes for high-throughput arrays")
7706 "This package contains class definitions, validity checks, and
7707 initialization methods for classes used by the @code{oligo} and @code{crlmm}
7709 (license license:gpl2+)))
7711 (define-public r-oligo
7718 (uri (bioconductor-uri "oligo" version))
7721 "0y7j96rafm9b85sxq2483i73685i3j67lk33fn8nfcav6lmsv5vy"))))
7722 (properties `((upstream-name . "oligo")))
7723 (build-system r-build-system)
7724 (inputs (list zlib))
7739 (home-page "https://bioconductor.org/packages/oligo/")
7740 (synopsis "Preprocessing tools for oligonucleotide arrays")
7742 "This package provides a package to analyze oligonucleotide
7743 arrays (expression/SNP/tiling/exon) at probe-level. It currently supports
7744 Affymetrix (CEL files) and NimbleGen arrays (XYS files).")
7745 (license license:lgpl2.0+)))
7747 (define-public r-qvalue
7754 (uri (bioconductor-uri "qvalue" version))
7757 "0cvhm5cldcnnxwa293dig1pj9lvj2hnz9zh4gfr25sw0xlcjzmyw"))))
7758 (build-system r-build-system)
7760 (list r-ggplot2 r-reshape2))
7763 (home-page "https://github.com/StoreyLab/qvalue")
7764 (synopsis "Q-value estimation for false discovery rate control")
7766 "This package takes a list of p-values resulting from the simultaneous
7767 testing of many hypotheses and estimates their q-values and local @dfn{false
7768 discovery rate} (FDR) values. The q-value of a test measures the proportion
7769 of false positives incurred when that particular test is called significant.
7770 The local FDR measures the posterior probability the null hypothesis is true
7771 given the test's p-value. Various plots are automatically generated, allowing
7772 one to make sensible significance cut-offs. The software can be applied to
7773 problems in genomics, brain imaging, astrophysics, and data mining.")
7774 ;; Any version of the LGPL.
7775 (license license:lgpl3+)))
7777 (define r-rcppnumerical
7779 (name "r-rcppnumerical")
7783 (uri (cran-uri "RcppNumerical" version))
7786 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
7787 (properties `((upstream-name . "RcppNumerical")))
7788 (build-system r-build-system)
7790 `(("r-rcpp" ,r-rcpp)
7791 ("r-rcppeigen" ,r-rcppeigen)))
7793 `(("r-knitr" ,r-knitr)))
7794 (home-page "https://github.com/yixuan/RcppNumerical")
7795 (synopsis "Rcpp integration for numerical computing libraries")
7797 "This package provides a collection of libraries for numerical computing
7798 (numerical integration, optimization, etc.) and their integration with
7800 (license license:gpl2+)))
7802 (define-public r-apeglm
7808 (uri (bioconductor-uri "apeglm" version))
7811 "1ppwk4g66x46hpqsfsvhl12398d1srqr47nmp0y2gz212kff0rby"))))
7812 (properties `((upstream-name . "apeglm")))
7813 (build-system r-build-system)
7820 r-summarizedexperiment))
7821 (native-inputs (list r-knitr))
7822 (home-page "https://bioconductor.org/packages/apeglm")
7823 (synopsis "Approximate posterior estimation for GLM coefficients")
7824 (description "This package provides Bayesian shrinkage estimators for
7825 effect sizes for a variety of GLM models, using approximation of the
7826 posterior for individual coefficients.")
7827 (license license:gpl2)))
7829 (define-public r-greylistchip
7831 (name "r-greylistchip")
7835 (uri (bioconductor-uri "GreyListChIP" version))
7838 "0w52vwvjarql19bsv40b80yn701qx8c9d0clsjhj85wmzj2p6dhg"))))
7839 (properties `((upstream-name . "GreyListChIP")))
7840 (build-system r-build-system)
7849 r-summarizedexperiment))
7850 (home-page "https://bioconductor.org/packages/GreyListChIP")
7851 (synopsis "Greylist artefact regions based on ChIP inputs")
7852 (description "This package identifies regions of ChIP experiments with high
7853 signal in the input, that lead to spurious peaks during peak calling.")
7854 (license license:artistic2.0)))
7856 (define-public r-diffbind
7863 (uri (bioconductor-uri "DiffBind" version))
7866 "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr"))))
7867 (properties `((upstream-name . "DiffBind")))
7868 (build-system r-build-system)
7891 r-summarizedexperiment
7893 (home-page "https://bioconductor.org/packages/DiffBind")
7894 (synopsis "Differential binding analysis of ChIP-Seq peak data")
7896 "This package computes differentially bound sites from multiple
7897 ChIP-seq experiments using affinity (quantitative) data. Also enables
7898 occupancy (overlap) analysis and plotting functions.")
7899 (license license:artistic2.0)))
7901 (define-public r-ripseeker
7903 (name "r-ripseeker")
7908 (uri (bioconductor-uri "RIPSeeker" version))
7911 "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs"))))
7912 (properties `((upstream-name . "RIPSeeker")))
7913 (build-system r-build-system)
7918 r-summarizedexperiment
7922 (home-page "https://bioconductor.org/packages/RIPSeeker")
7924 "Identifying protein-associated transcripts from RIP-seq experiments")
7926 "This package infers and discriminates RIP peaks from RIP-seq alignments
7927 using two-state HMM with negative binomial emission probability. While
7928 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
7929 a suite of bioinformatics tools integrated within this self-contained software
7930 package comprehensively addressing issues ranging from post-alignments
7931 processing to visualization and annotation.")
7932 (license license:gpl2)))
7934 (define-public r-mbkmeans
7940 (uri (bioconductor-uri "mbkmeans" version))
7943 "1f5krzlyqljz763vkp1a50danjn78xhn35s8qqdvzrmwyx0fzphg"))))
7944 (build-system r-build-system)
7958 r-singlecellexperiment
7959 r-summarizedexperiment))
7960 (home-page "https://bioconductor.org/packages/mbkmeans")
7961 (synopsis "Mini-batch k-means clustering for single-cell RNA-seq")
7962 (description "This package implements the mini-batch k-means algorithm for
7963 large datasets, including support for on-disk data representation.")
7964 (license license:expat)))
7966 (define-public r-multtest
7973 (uri (bioconductor-uri "multtest" version))
7976 "037wcmwk1wvhjxgmlvnk289pkwishi1753ajkmy9x14xlmldix82"))))
7977 (build-system r-build-system)
7979 (list r-survival r-biocgenerics r-biobase r-mass))
7980 (home-page "https://bioconductor.org/packages/multtest")
7981 (synopsis "Resampling-based multiple hypothesis testing")
7983 "This package can do non-parametric bootstrap and permutation
7984 resampling-based multiple testing procedures (including empirical Bayes
7985 methods) for controlling the family-wise error rate (FWER), generalized
7986 family-wise error rate (gFWER), tail probability of the proportion of
7987 false positives (TPPFP), and false discovery rate (FDR). Several choices
7988 of bootstrap-based null distribution are implemented (centered, centered
7989 and scaled, quantile-transformed). Single-step and step-wise methods are
7990 available. Tests based on a variety of T- and F-statistics (including
7991 T-statistics based on regression parameters from linear and survival models
7992 as well as those based on correlation parameters) are included. When probing
7993 hypotheses with T-statistics, users may also select a potentially faster null
7994 distribution which is multivariate normal with mean zero and variance
7995 covariance matrix derived from the vector influence function. Results are
7996 reported in terms of adjusted P-values, confidence regions and test statistic
7997 cutoffs. The procedures are directly applicable to identifying differentially
7998 expressed genes in DNA microarray experiments.")
7999 (license license:lgpl3)))
8001 (define-public r-graph
8007 (uri (bioconductor-uri "graph" version))
8010 "1b8hrjwjg82kicls1496fxfzv75xjvq2k6r9apzsd3qlbyg3ilg4"))))
8011 (build-system r-build-system)
8013 (list r-biocgenerics))
8014 (home-page "https://bioconductor.org/packages/graph")
8015 (synopsis "Handle graph data structures in R")
8017 "This package implements some simple graph handling capabilities for R.")
8018 (license license:artistic2.0)))
8020 ;; This is a CRAN package, but it depends on a Bioconductor package.
8021 (define-public r-ggm
8028 (uri (cran-uri "ggm" version))
8031 "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di"))))
8032 (properties `((upstream-name . "ggm")))
8033 (build-system r-build-system)
8035 (list r-graph r-igraph))
8036 (home-page "https://cran.r-project.org/package=ggm")
8037 (synopsis "Functions for graphical Markov models")
8039 "This package provides functions and datasets for maximum likelihood
8040 fitting of some classes of graphical Markov models.")
8041 (license license:gpl2+)))
8043 ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph.
8044 (define-public r-perfmeas
8051 (uri (cran-uri "PerfMeas" version))
8054 "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
8055 (properties `((upstream-name . "PerfMeas")))
8056 (build-system r-build-system)
8058 (list r-graph r-limma r-rbgl))
8059 (home-page "https://cran.r-project.org/web/packages/PerfMeas/")
8060 (synopsis "Performance measures for ranking and classification tasks")
8062 "This package implements different performance measures for
8063 classification and ranking tasks. @dfn{Area under curve} (AUC), precision at
8064 a given recall, F-score for single and multiple classes are available.")
8065 (license license:gpl2+)))
8067 ;; This is a CRAN package, but it depends on a Bioconductor package.
8068 (define-public r-codedepends
8070 (name "r-codedepends")
8075 (uri (cran-uri "CodeDepends" version))
8078 "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
8079 (properties `((upstream-name . "CodeDepends")))
8080 (build-system r-build-system)
8082 (list r-codetools r-graph r-xml))
8083 (home-page "https://cran.r-project.org/web/packages/CodeDepends")
8084 (synopsis "Analysis of R code for reproducible research and code comprehension")
8086 "This package provides tools for analyzing R expressions or blocks of
8087 code and determining the dependencies between them. It focuses on R scripts,
8088 but can be used on the bodies of functions. There are many facilities
8089 including the ability to summarize or get a high-level view of code,
8090 determining dependencies between variables, code improvement suggestions.")
8091 ;; Any version of the GPL
8092 (license (list license:gpl2+ license:gpl3+))))
8094 (define-public r-chippeakanno
8096 (name "r-chippeakanno")
8101 (uri (bioconductor-uri "ChIPpeakAnno" version))
8104 "0a26glldxczcfymjvd45gv5m4hympziivm6wwx4ab9wld7n43l8y"))))
8105 (properties `((upstream-name . "ChIPpeakAnno")))
8106 (build-system r-build-system)
8108 (list r-annotationdbi
8131 r-summarizedexperiment
8135 (home-page "https://bioconductor.org/packages/ChIPpeakAnno")
8136 (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
8138 "The package includes functions to retrieve the sequences around the peak,
8139 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
8140 custom features such as most conserved elements and other transcription factor
8141 binding sites supplied by users. Starting 2.0.5, new functions have been added
8142 for finding the peaks with bi-directional promoters with summary statistics
8143 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
8144 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
8145 enrichedGO (addGeneIDs).")
8146 (license license:gpl2+)))
8148 (define-public r-matrixgenerics
8150 (name "r-matrixgenerics")
8154 (uri (bioconductor-uri "MatrixGenerics" version))
8157 "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f"))))
8159 `((upstream-name . "MatrixGenerics")))
8160 (build-system r-build-system)
8162 (list r-matrixstats))
8163 (home-page "https://bioconductor.org/packages/MatrixGenerics")
8164 (synopsis "S4 generic summary statistic functions for matrix-like objects")
8166 "This package provides S4 generic functions modeled after the
8167 @code{matrixStats} API for alternative matrix implementations. Packages with
8168 alternative matrix implementation can depend on this package and implement the
8169 generic functions that are defined here for a useful set of row and column
8170 summary statistics. Other package developers can import this package and
8171 handle a different matrix implementations without worrying about
8172 incompatibilities.")
8173 (license license:artistic2.0)))
8175 (define-public r-marray
8181 (uri (bioconductor-uri "marray" version))
8183 (base32 "0awfz0akz3sylyw1jxhxgadv1rqdzvy9v11933yxkl9a8m9ngm8i"))))
8184 (build-system r-build-system)
8187 (home-page "https://bioconductor.org/packages/marray")
8188 (synopsis "Exploratory analysis for two-color spotted microarray data")
8189 (description "This package contains class definitions for two-color spotted
8190 microarray data. It also includes functions for data input, diagnostic plots,
8191 normalization and quality checking.")
8192 (license license:lgpl2.0+)))
8194 (define-public r-cghbase
8200 (uri (bioconductor-uri "CGHbase" version))
8202 (base32 "1q8yy60r4g5nyv2gbfdgk192xd73c0rrjr668d5616ddb7sx8wcr"))))
8203 (properties `((upstream-name . "CGHbase")))
8204 (build-system r-build-system)
8206 (list r-biobase r-marray))
8207 (home-page "https://bioconductor.org/packages/CGHbase")
8208 (synopsis "Base functions and classes for arrayCGH data analysis")
8209 (description "This package contains functions and classes that are needed by
8210 the @code{arrayCGH} packages.")
8211 (license license:gpl2+)))
8213 (define-public r-cghcall
8219 (uri (bioconductor-uri "CGHcall" version))
8221 (base32 "1qpsibp4gb09sn6fkwwrdjkh3a28lqfbk18c6fvn4m386j96ps65"))))
8222 (properties `((upstream-name . "CGHcall")))
8223 (build-system r-build-system)
8225 (list r-biobase r-cghbase r-impute r-dnacopy r-snowfall))
8226 (home-page "https://bioconductor.org/packages/CGHcall")
8227 (synopsis "Base functions and classes for arrayCGH data analysis")
8228 (description "This package contains functions and classes that are needed by
8229 @code{arrayCGH} packages.")
8230 (license license:gpl2+)))
8232 (define-public r-qdnaseq
8238 (uri (bioconductor-uri "QDNAseq" version))
8240 (base32 "0s360s72lfn9vjml88gg1m40n61s0dc66ilzgfjdcp65djdxxfvm"))))
8241 (properties `((upstream-name . "QDNAseq")))
8242 (build-system r-build-system)
8254 (home-page "https://bioconductor.org/packages/QDNAseq")
8255 (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
8256 (description "The genome is divided into non-overlapping fixed-sized bins,
8257 number of sequence reads in each counted, adjusted with a simultaneous
8258 two-dimensional loess correction for sequence mappability and GC content, and
8259 filtered to remove spurious regions in the genome. Downstream steps of
8260 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
8262 (license license:gpl2+)))
8264 (define-public r-bayseq
8271 (uri (bioconductor-uri "baySeq" version))
8274 "1yqykndyv32s2rk7x86qf410qr0pigc8z4gdkl8vhj4dgyr47n2j"))))
8275 (properties `((upstream-name . "baySeq")))
8276 (build-system r-build-system)
8278 (list r-abind r-edger r-genomicranges))
8279 (home-page "https://bioconductor.org/packages/baySeq/")
8280 (synopsis "Bayesian analysis of differential expression patterns in count data")
8282 "This package identifies differential expression in high-throughput count
8283 data, such as that derived from next-generation sequencing machines,
8284 calculating estimated posterior likelihoods of differential expression (or
8285 more complex hypotheses) via empirical Bayesian methods.")
8286 (license license:gpl3)))
8288 (define-public r-chipcomp
8295 (uri (bioconductor-uri "ChIPComp" version))
8298 "06q34y59gf1iz0rs7y5x8ndy1wa95j65rfmz37aym5c46ijqsnq0"))))
8299 (properties `((upstream-name . "ChIPComp")))
8300 (build-system r-build-system)
8302 (list r-biocgenerics
8303 r-bsgenome-hsapiens-ucsc-hg19
8304 r-bsgenome-mmusculus-ucsc-mm9
8312 (home-page "https://bioconductor.org/packages/ChIPComp")
8313 (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
8315 "ChIPComp implements a statistical method for quantitative comparison of
8316 multiple ChIP-seq datasets. It detects differentially bound sharp binding
8317 sites across multiple conditions considering matching control in ChIP-seq
8319 ;; Any version of the GPL.
8320 (license license:gpl3+)))
8322 (define-public r-riboprofiling
8324 (name "r-riboprofiling")
8329 (uri (bioconductor-uri "RiboProfiling" version))
8332 "08m4rc530bkzcc43iwzg2fw9cjlf4wc2d8akv5vblsb42xdn8sqp"))))
8333 (properties `((upstream-name . "RiboProfiling")))
8334 (build-system r-build-system)
8336 (list r-biocgenerics
8354 (home-page "https://bioconductor.org/packages/RiboProfiling/")
8355 (synopsis "Ribosome profiling data analysis")
8356 (description "Starting with a BAM file, this package provides the
8357 necessary functions for quality assessment, read start position recalibration,
8358 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
8359 of count data: pairs, log fold-change, codon frequency and coverage
8360 assessment, principal component analysis on codon coverage.")
8361 (license license:gpl3)))
8363 (define-public r-riboseqr
8370 (uri (bioconductor-uri "riboSeqR" version))
8373 "1zs3y0icsqrndjp9wwqz3jxysvyc9pch45y49j6g9b5b2l44ma26"))))
8374 (properties `((upstream-name . "riboSeqR")))
8375 (build-system r-build-system)
8384 (home-page "https://bioconductor.org/packages/riboSeqR/")
8385 (synopsis "Analysis of sequencing data from ribosome profiling experiments")
8387 "This package provides plotting functions, frameshift detection and
8388 parsing of genetic sequencing data from ribosome profiling experiments.")
8389 (license license:gpl3)))
8391 (define-public r-interactionset
8393 (name "r-interactionset")
8398 (uri (bioconductor-uri "InteractionSet" version))
8401 "0qjimx25jvm8siq8hmlbf2z6mknzpbq945p06fsj826k57bpcsm5"))))
8403 `((upstream-name . "InteractionSet")))
8404 (build-system r-build-system)
8406 (list r-biocgenerics
8413 r-summarizedexperiment))
8416 (home-page "https://bioconductor.org/packages/InteractionSet")
8417 (synopsis "Base classes for storing genomic interaction data")
8419 "This package provides the @code{GInteractions},
8420 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
8421 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
8423 (license license:gpl3)))
8425 (define-public r-genomicinteractions
8427 (name "r-genomicinteractions")
8432 (uri (bioconductor-uri "GenomicInteractions" version))
8435 "0aph1hja5vfprxs3jl4zd1inhvih6m3v1p3jkm6w7xpj3jzvmgbx"))))
8437 `((upstream-name . "GenomicInteractions")))
8438 (build-system r-build-system)
8458 (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
8459 (synopsis "R package for handling genomic interaction data")
8461 "This R package provides tools for handling genomic interaction data,
8462 such as ChIA-PET/Hi-C, annotating genomic features with interaction
8463 information and producing various plots and statistics.")
8464 (license license:gpl3)))
8466 (define-public r-ctc
8473 (uri (bioconductor-uri "ctc" version))
8476 "0c9pgp25dqx12fmi4cqm7xyxjmy6g7wv9vbljgdjghaij2lrc4pb"))))
8477 (build-system r-build-system)
8478 (propagated-inputs (list r-amap))
8479 (home-page "https://bioconductor.org/packages/ctc/")
8480 (synopsis "Cluster and tree conversion")
8482 "This package provides tools for exporting and importing classification
8483 trees and clusters to other programs.")
8484 (license license:gpl2)))
8486 (define-public r-goseq
8493 (uri (bioconductor-uri "goseq" version))
8496 "1w0rwzhqkvp2x7y5v0qcyjbss0p95gb1jrnx5sdkqginbvrmrd48"))))
8497 (build-system r-build-system)
8499 (list r-annotationdbi
8505 (home-page "https://bioconductor.org/packages/goseq/")
8506 (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
8508 "This package provides tools to detect Gene Ontology and/or other user
8509 defined categories which are over/under represented in RNA-seq data.")
8510 (license license:lgpl2.0+)))
8512 (define-public r-glimma
8519 (uri (bioconductor-uri "Glimma" version))
8522 "1k17ay09vhb2hakg1vrgvpp1zliavlj7cdkxaal162bc3v8pyvyz"))))
8523 (properties `((upstream-name . "Glimma")))
8524 (build-system r-build-system)
8532 r-summarizedexperiment))
8535 (home-page "https://github.com/Shians/Glimma")
8536 (synopsis "Interactive HTML graphics")
8538 "This package generates interactive visualisations for analysis of
8539 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
8540 HTML page. The interactions are built on top of the popular static
8541 representations of analysis results in order to provide additional
8543 (license license:lgpl3)))
8545 (define-public r-rots
8552 (uri (bioconductor-uri "ROTS" version))
8555 "021a578p8kcl5yd9myiy0h2qp10r30ggnip2kp6xs7dx8nzic96r"))))
8556 (properties `((upstream-name . "ROTS")))
8557 (build-system r-build-system)
8559 (list r-biobase r-rcpp))
8560 (home-page "https://bioconductor.org/packages/ROTS/")
8561 (synopsis "Reproducibility-Optimized Test Statistic")
8563 "This package provides tools for calculating the
8564 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
8566 (license license:gpl2+)))
8568 (define-public r-plgem
8575 (uri (bioconductor-uri "plgem" version))
8578 "07zxflxcay17hxjw3wh5kfdwl2x8537csb18p1qzmyrkvscnja77"))))
8579 (build-system r-build-system)
8581 (list r-biobase r-mass))
8582 (home-page "http://www.genopolis.it")
8583 (synopsis "Detect differential expression in microarray and proteomics datasets")
8585 "The Power Law Global Error Model (PLGEM) has been shown to faithfully
8586 model the variance-versus-mean dependence that exists in a variety of
8587 genome-wide datasets, including microarray and proteomics data. The use of
8588 PLGEM has been shown to improve the detection of differentially expressed
8589 genes or proteins in these datasets.")
8590 (license license:gpl2)))
8592 (define-public r-inspect
8599 (uri (bioconductor-uri "INSPEcT" version))
8602 "0jx887vhxwd8zlqajr9czvn9nx88ryyxlnl58hxrlajjpcjkz9ax"))))
8603 (properties `((upstream-name . "INSPEcT")))
8604 (build-system r-build-system)
8625 r-summarizedexperiment
8626 r-txdb-mmusculus-ucsc-mm9-knowngene))
8629 (home-page "https://bioconductor.org/packages/INSPEcT")
8630 (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
8632 "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
8633 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
8634 order to evaluate synthesis, processing and degradation rates and assess via
8635 modeling the rates that determines changes in mature mRNA levels.")
8636 (license license:gpl2)))
8638 (define-public r-dnabarcodes
8640 (name "r-dnabarcodes")
8645 (uri (bioconductor-uri "DNABarcodes" version))
8648 "0n2qlvpcjhrxr3br27gz9vhwcpf7sn6g4xdjazvvi3gqcgk90xc6"))))
8649 (properties `((upstream-name . "DNABarcodes")))
8650 (build-system r-build-system)
8652 (list r-bh r-matrix r-rcpp))
8655 (home-page "https://bioconductor.org/packages/DNABarcodes")
8656 (synopsis "Create and analyze DNA barcodes")
8658 "This package offers tools to create DNA barcode sets capable of
8659 correcting insertion, deletion, and substitution errors. Existing barcodes
8660 can be analyzed regarding their minimal, maximal and average distances between
8661 barcodes. Finally, reads that start with a (possibly mutated) barcode can be
8662 demultiplexed, i.e. assigned to their original reference barcode.")
8663 (license license:gpl2)))
8665 (define-public r-ruvseq
8672 (uri (bioconductor-uri "RUVSeq" version))
8675 "001h07b074hvj16bjdp9llb9psphw7r6kpwhq61bj4519y6lpg7x"))))
8676 (properties `((upstream-name . "RUVSeq")))
8677 (build-system r-build-system)
8679 (list r-biobase r-edaseq r-edger r-mass))
8682 (home-page "https://github.com/drisso/RUVSeq")
8683 (synopsis "Remove unwanted variation from RNA-Seq data")
8685 "This package implements methods to @dfn{remove unwanted variation} (RUV)
8686 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
8688 (license license:artistic2.0)))
8690 (define-public r-biocneighbors
8692 (name "r-biocneighbors")
8697 (uri (bioconductor-uri "BiocNeighbors" version))
8700 "1a43hzmcpxviqa9723hkafr6gm358amfpqj9d56imclkkfkdz95x"))))
8701 (properties `((upstream-name . "BiocNeighbors")))
8702 (build-system r-build-system)
8704 (list r-biocparallel r-matrix r-rcpp r-rcpphnsw r-s4vectors))
8707 (home-page "https://bioconductor.org/packages/BiocNeighbors")
8708 (synopsis "Nearest Neighbor Detection for Bioconductor packages")
8710 "This package implements exact and approximate methods for nearest
8711 neighbor detection, in a framework that allows them to be easily switched
8712 within Bioconductor packages or workflows. The exact algorithm is implemented
8713 using pre-clustering with the k-means algorithm. Functions are also provided
8714 to search for all neighbors within a given distance. Parallelization is
8715 achieved for all methods using the BiocParallel framework.")
8716 (license license:gpl3)))
8718 (define-public r-scaledmatrix
8720 (name "r-scaledmatrix")
8725 (uri (bioconductor-uri "ScaledMatrix" version))
8728 "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"))))
8729 (properties `((upstream-name . "ScaledMatrix")))
8730 (build-system r-build-system)
8732 (list r-delayedarray r-matrix r-s4vectors))
8733 (native-inputs (list r-knitr))
8734 (home-page "https://github.com/LTLA/ScaledMatrix")
8735 (synopsis "Create a DelayedMatrix of scaled and centered values")
8737 "This package provides delayed computation of a matrix of scaled and
8738 centered values. The result is equivalent to using the @code{scale} function
8739 but avoids explicit realization of a dense matrix during block processing.
8740 This permits greater efficiency in common operations, most notably matrix
8742 (license license:gpl3)))
8744 (define-public r-treeio
8751 (uri (bioconductor-uri "treeio" version))
8754 "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"))))
8755 (properties `((upstream-name . "treeio")))
8756 (build-system r-build-system)
8765 (native-inputs (list r-knitr))
8766 (home-page "https://github.com/YuLab-SMU/treeio")
8767 (synopsis "Base classes and functions for Phylogenetic tree input and output")
8769 "This is an R package to make it easier to import and store phylogenetic
8770 trees with associated data; and to link external data from different sources
8771 to phylogeny. It also supports exporting phylogenetic trees with
8772 heterogeneous associated data to a single tree file and can be served as a
8773 platform for merging tree with associated data and converting file formats.")
8774 (license license:artistic2.0)))
8776 (define-public r-ggtree
8783 (uri (bioconductor-uri "ggtree" version))
8786 "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"))))
8787 (properties `((upstream-name . "ggtree")))
8788 (build-system r-build-system)
8803 (native-inputs (list r-knitr))
8804 (home-page "https://yulab-smu.top/treedata-book/")
8805 (synopsis "R package for visualization of trees and annotation data")
8807 "This package extends the ggplot2 plotting system which implements a
8808 grammar of graphics. ggtree is designed for visualization and annotation of
8809 phylogenetic trees and other tree-like structures with their annotation
8811 (license license:artistic2.0)))
8813 (define-public r-metapod
8820 (uri (bioconductor-uri "metapod" version))
8823 "19g9c08alg4qqr710si465wlb5dy759m5d8wn91zwj24077dds7b"))))
8824 (properties `((upstream-name . "metapod")))
8825 (build-system r-build-system)
8830 (home-page "https://bioconductor.org/packages/metapod")
8831 (synopsis "Meta-analyses on p-values of differential analyses")
8833 "This package implements a variety of methods for combining p-values in
8834 differential analyses of genome-scale datasets. Functions can combine
8835 p-values across different tests in the same analysis (e.g., genomic windows in
8836 ChIP-seq, exons in RNA-seq) or for corresponding tests across separate
8837 analyses (e.g., replicated comparisons, effect of different treatment
8838 conditions). Support is provided for handling log-transformed input p-values,
8839 missing values and weighting where appropriate.")
8840 (license license:gpl3)))
8842 (define-public r-biocsingular
8844 (name "r-biocsingular")
8849 (uri (bioconductor-uri "BiocSingular" version))
8852 "1sraycnn0jahpi8kni1y8ik00ga89fvwqjmbr8388968q22mvm3x"))))
8853 (properties `((upstream-name . "BiocSingular")))
8854 (build-system r-build-system)
8868 (home-page "https://github.com/LTLA/BiocSingular")
8869 (synopsis "Singular value decomposition for Bioconductor packages")
8871 "This package implements exact and approximate methods for singular value
8872 decomposition and principal components analysis, in a framework that allows
8873 them to be easily switched within Bioconductor packages or workflows. Where
8874 possible, parallelization is achieved using the BiocParallel framework.")
8875 (license license:gpl3)))
8877 (define-public r-destiny
8884 (uri (bioconductor-uri "destiny" version))
8887 "1c85ky5ggdsi0ab1l4ipl85gc1kj1zv3wp08qrvslax3z0yw0ljy"))))
8888 (build-system r-build-system)
8906 r-singlecellexperiment
8908 r-summarizedexperiment
8913 (list r-knitr r-nbconvertr)) ; for vignettes
8914 (home-page "https://bioconductor.org/packages/destiny/")
8915 (synopsis "Create and plot diffusion maps")
8916 (description "This package provides tools to create and plot diffusion
8918 ;; Any version of the GPL
8919 (license license:gpl3+)))
8921 (define-public r-savr
8928 (uri (bioconductor-uri "savR" version))
8931 "04zlf3lyr6vnpj80m6fd2is2f7302sxwih8nzzjnc4ss972jid2k"))))
8932 (properties `((upstream-name . "savR")))
8933 (build-system r-build-system)
8935 (list r-ggplot2 r-gridextra r-reshape2 r-scales r-xml))
8936 (home-page "https://github.com/bcalder/savR")
8937 (synopsis "Parse and analyze Illumina SAV files")
8939 "This package provides tools to parse Illumina Sequence Analysis
8940 Viewer (SAV) files, access data, and generate QC plots.")
8941 (license license:agpl3+)))
8943 (define-public r-chipexoqual
8945 (name "r-chipexoqual")
8950 (uri (bioconductor-uri "ChIPexoQual" version))
8953 "1r4s8awvwwj1g33jpnzfxji23mfy0chkhi14i0ml5sh090xijpaz"))))
8954 (properties `((upstream-name . "ChIPexoQual")))
8955 (build-system r-build-system)
8957 (list r-biocparallel
8976 (home-page "https://github.com/keleslab/ChIPexoQual")
8977 (synopsis "Quality control pipeline for ChIP-exo/nexus data")
8979 "This package provides a quality control pipeline for ChIP-exo/nexus
8981 (license license:gpl2+)))
8983 (define-public r-copynumber
8985 (name "r-copynumber")
8989 (uri (bioconductor-uri "copynumber" version))
8992 "1gr8q9ri49x8qlmbsi6k6wcak1w9v48wr1qy7axc86brzx6z6mhd"))))
8993 (build-system r-build-system)
8995 (list r-s4vectors r-iranges r-genomicranges r-biocgenerics))
8996 (home-page "https://bioconductor.org/packages/copynumber")
8997 (synopsis "Segmentation of single- and multi-track copy number data")
8999 "This package segments single- and multi-track copy number data by a
9000 penalized least squares regression method.")
9001 (license license:artistic2.0)))
9003 (define-public r-dnacopy
9010 (uri (bioconductor-uri "DNAcopy" version))
9013 "10bh4p8nbl84rfngsm3bi9w542m159kff95f8c2hvjcxv5yw7iwc"))))
9014 (properties `((upstream-name . "DNAcopy")))
9015 (build-system r-build-system)
9016 (native-inputs (list gfortran))
9017 (home-page "https://bioconductor.org/packages/DNAcopy")
9018 (synopsis "DNA copy number data analysis")
9020 "This package implements the @dfn{circular binary segmentation} (CBS)
9021 algorithm to segment DNA copy number data and identify genomic regions with
9022 abnormal copy number.")
9023 (license license:gpl2+)))
9025 ;; This is a CRAN package, but it uncharacteristically depends on a
9026 ;; Bioconductor package.
9027 (define-public r-htscluster
9029 (name "r-htscluster")
9034 (uri (cran-uri "HTSCluster" version))
9037 "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
9038 (properties `((upstream-name . "HTSCluster")))
9039 (build-system r-build-system)
9041 (list r-capushe r-edger r-plotrix))
9042 (home-page "https://cran.r-project.org/web/packages/HTSCluster")
9043 (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
9045 "This package provides a Poisson mixture model is implemented to cluster
9046 genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter
9047 estimation is performed using either the EM or CEM algorithm, and the slope
9048 heuristics are used for model selection (i.e., to choose the number of
9050 (license license:gpl3+)))
9052 (define-public r-deds
9059 (uri (bioconductor-uri "DEDS" version))
9062 "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8"))))
9063 (properties `((upstream-name . "DEDS")))
9064 (build-system r-build-system)
9065 (home-page "https://bioconductor.org/packages/DEDS/")
9066 (synopsis "Differential expression via distance summary for microarray data")
9068 "This library contains functions that calculate various statistics of
9069 differential expression for microarray data, including t statistics, fold
9070 change, F statistics, SAM, moderated t and F statistics and B statistics. It
9071 also implements a new methodology called DEDS (Differential Expression via
9072 Distance Summary), which selects differentially expressed genes by integrating
9073 and summarizing a set of statistics using a weighted distance approach.")
9074 ;; Any version of the LGPL.
9075 (license license:lgpl3+)))
9077 ;; This is a CRAN package, but since it depends on a Bioconductor package we
9079 (define-public r-nbpseq
9086 (uri (cran-uri "NBPSeq" version))
9089 "07mnnk4n0cyksp1mw36y6369is62kxsfg3wb8d3dwswycdmj8m14"))))
9090 (properties `((upstream-name . "NBPSeq")))
9091 (build-system r-build-system)
9094 (home-page "https://cran.r-project.org/web/packages/NBPSeq")
9095 (synopsis "Negative binomial models for RNA-Seq data")
9097 "This package provides negative binomial models for two-group comparisons
9098 and regression inferences from RNA-sequencing data.")
9099 (license license:gpl2)))
9101 (define-public r-ebseq
9108 (uri (bioconductor-uri "EBSeq" version))
9111 "192xl9fwsh04w563yk33mfl303d1kqby2ssbqkckqsdr4jb7d57y"))))
9112 (properties `((upstream-name . "EBSeq")))
9113 (build-system r-build-system)
9115 (list r-blockmodeling r-gplots r-testthat))
9116 (home-page "https://bioconductor.org/packages/EBSeq")
9117 (synopsis "Differential expression analysis of RNA-seq data")
9119 "This package provides tools for differential expression analysis at both
9120 gene and isoform level using RNA-seq data")
9121 (license license:artistic2.0)))
9123 (define-public r-karyoploter
9125 (name "r-karyoploter")
9129 (uri (bioconductor-uri "karyoploteR" version))
9132 "0hawq9wi3ikvlcdgnjfy5fiiwfq22zwx1p8xf5h4bpypp96pknsk"))))
9133 (build-system r-build-system)
9135 (list r-annotationdbi
9149 r-variantannotation))
9152 (home-page "https://bioconductor.org/packages/karyoploteR/")
9153 (synopsis "Plot customizable linear genomes displaying arbitrary data")
9154 (description "This package creates karyotype plots of arbitrary genomes and
9155 offers a complete set of functions to plot arbitrary data on them. It mimics
9156 many R base graphics functions coupling them with a coordinate change function
9157 automatically mapping the chromosome and data coordinates into the plot
9159 (license license:artistic2.0)))
9161 (define-public r-lpsymphony
9163 (name "r-lpsymphony")
9168 (uri (bioconductor-uri "lpsymphony" version))
9171 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
9172 (build-system r-build-system)
9176 '(modify-phases %standard-phases
9177 (add-after 'unpack 'make-build-order-reproducible
9179 (substitute* '("src/SYMPHONY/Cgl/configure.ac"
9180 "src/SYMPHONY/Cgl/configure")
9181 (("for file in `ls \\*/Makefile.in`")
9182 "for file in `ls */Makefile.in | sort`")))))))
9186 (list pkg-config r-knitr))
9187 (home-page "https://r-forge.r-project.org/projects/rsymphony")
9188 (synopsis "Symphony integer linear programming solver in R")
9190 "This package was derived from Rsymphony. The package provides an R
9191 interface to SYMPHONY, a linear programming solver written in C++. The main
9192 difference between this package and Rsymphony is that it includes the solver
9193 source code, while Rsymphony expects to find header and library files on the
9194 users' system. Thus the intention of @code{lpsymphony} is to provide an easy
9195 to install interface to SYMPHONY.")
9196 ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0.
9197 ;; lpsimphony is released under the same terms.
9198 (license license:epl1.0)))
9200 (define-public r-ihw
9207 (uri (bioconductor-uri "IHW" version))
9210 "1gsfy75dz7xh16z844llcmjnp0a0ridszmrbbv2bdaa43na5msmf"))))
9211 (properties `((upstream-name . "IHW")))
9212 (build-system r-build-system)
9214 (list r-biocgenerics r-fdrtool r-lpsymphony r-slam))
9217 (home-page "https://bioconductor.org/packages/IHW")
9218 (synopsis "Independent hypothesis weighting")
9220 "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing
9221 procedure that increases power compared to the method of Benjamini and
9222 Hochberg by assigning data-driven weights to each hypothesis. The input to
9223 IHW is a two-column table of p-values and covariates. The covariate can be
9224 any continuous-valued or categorical variable that is thought to be
9225 informative on the statistical properties of each hypothesis test, while it is
9226 independent of the p-value under the null hypothesis.")
9227 (license license:artistic2.0)))
9229 (define-public r-icobra
9236 (uri (bioconductor-uri "iCOBRA" version))
9239 "1gvra5bgsf6lvs4f2md3xx7xxsx4j8079c2nr8vz9lvy2sfyl6s9"))))
9240 (properties `((upstream-name . "iCOBRA")))
9241 (build-system r-build-system)
9257 (home-page "https://bioconductor.org/packages/iCOBRA")
9258 (synopsis "Comparison and visualization of ranking and assignment methods")
9260 "This package provides functions for calculation and visualization of
9261 performance metrics for evaluation of ranking and binary
9262 classification (assignment) methods. It also contains a Shiny application for
9263 interactive exploration of results.")
9264 (license license:gpl2+)))
9266 (define-public r-residualmatrix
9268 (name "r-residualmatrix")
9273 (uri (bioconductor-uri "ResidualMatrix" version))
9276 "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"))))
9278 `((upstream-name . "ResidualMatrix")))
9279 (build-system r-build-system)
9281 (list r-delayedarray r-matrix r-s4vectors))
9284 (home-page "https://github.com/LTLA/ResidualMatrix")
9285 (synopsis "Create a DelayedMatrix of regression residuals")
9287 "This package implements tools for delayed computation of a matrix of
9288 residuals after fitting a linear model to each column of an input matrix. It
9289 also supports partial computation of residuals where selected factors are to
9290 be preserved in the output matrix. It implements a number of efficient
9291 methods for operating on the delayed matrix of residuals, most notably matrix
9292 multiplication and calculation of row/column sums or means.")
9293 (license license:gpl3)))
9295 (define-public r-batchelor
9297 (name "r-batchelor")
9302 (uri (bioconductor-uri "batchelor" version))
9305 "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc"))))
9306 (properties `((upstream-name . "batchelor")))
9307 (build-system r-build-system)
9315 r-delayedmatrixstats
9323 r-singlecellexperiment
9324 r-summarizedexperiment))
9325 (native-inputs (list r-knitr))
9326 (home-page "https://bioconductor.org/packages/batchelor")
9327 (synopsis "Single-Cell Batch Correction Methods")
9329 "This package implements a variety of methods for batch correction of
9330 single-cell (RNA sequencing) data. This includes methods based on detecting
9331 mutually nearest neighbors, as well as several efficient variants of linear
9332 regression of the log-expression values. Functions are also provided to
9333 perform global rescaling to remove differences in depth between batches, and
9334 to perform a principal components analysis that is robust to differences in
9335 the numbers of cells across batches.")
9336 (license license:gpl3)))
9338 (define-public r-mast
9345 (uri (bioconductor-uri "MAST" version))
9348 "1kmrqxcfzzcs8l33n9qn0vahc6wxq6ks3cjx95vg96maf2qzhzzi"))))
9349 (properties `((upstream-name . "MAST")))
9350 (build-system r-build-system)
9361 r-singlecellexperiment
9363 r-summarizedexperiment))
9366 (home-page "https://github.com/RGLab/MAST/")
9367 (synopsis "Model-based analysis of single cell transcriptomics")
9369 "This package provides methods and models for handling zero-inflated
9370 single cell assay data.")
9371 (license license:gpl2+)))
9373 (define-public r-monocle
9380 (uri (bioconductor-uri "monocle" version))
9383 "11g1wx0f1yzhg3x1aa3d5l7pqlzxj16s0gha21skxkgld8k2x8xn"))))
9384 (build-system r-build-system)
9418 (home-page "https://bioconductor.org/packages/monocle")
9419 (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq")
9421 "Monocle performs differential expression and time-series analysis for
9422 single-cell expression experiments. It orders individual cells according to
9423 progress through a biological process, without knowing ahead of time which
9424 genes define progress through that process. Monocle also performs
9425 differential expression analysis, clustering, visualization, and other useful
9426 tasks on single cell expression data. It is designed to work with RNA-Seq and
9427 qPCR data, but could be used with other types as well.")
9428 (license license:artistic2.0)))
9430 (define-public r-leidenbase
9431 (let ((commit "a11b8455fa3307d9e3ac4e3a5accddf3c83b9a96")
9434 (name "r-leidenbase")
9435 (version (git-version "0.1.9" revision commit))
9440 (url "https://github.com/cole-trapnell-lab/leidenbase")
9442 (file-name (git-file-name name version))
9445 "1f54mycsffvzmblz5pzgs3v4jygnbvz0c9d3x710gw5mxkq2p84f"))))
9446 (properties `((upstream-name . "leidenbase")))
9447 (build-system r-build-system)
9454 (home-page "https://github.com/cole-trapnell-lab/leidenbase")
9455 (synopsis "R and C wrappers to run the Leiden find_partition function")
9457 "This package provides an R to C interface that runs the Leiden
9458 community detection algorithm to find a basic partition. It runs the
9459 equivalent of the @code{find_partition} function. This package includes the
9460 required source code files from the official Leidenalg distribution and
9461 several functions from the R igraph package.")
9462 (license license:gpl3+))))
9464 (define-public r-sanssouci
9465 ;; sansscouci doesn't have a (versioned) release yet.
9466 ;; This is the latest commit as of packaging for Guix.
9467 (let ((commit "5fe20a9aaf4ac637fa83d9cc73ff1c22de97ca6f")
9470 (name "r-sanssouci")
9471 (version (git-version "0" revision commit))
9475 (url "https://github.com/pneuvial/sanssouci.git")
9477 (file-name (git-file-name name version))
9480 "13ycdd790qw64qy2zdvcrpj3fc8as628rsly32438d3rifnlc5sk"))))
9481 (build-system r-build-system)
9483 (list r-generics r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
9484 (home-page "https://pneuvial.github.io/sanssouci")
9485 (synopsis "Post Hoc multiple testing inference")
9487 "The goal of sansSouci is to perform post hoc inference: in a multiple
9488 testing context, sansSouci provides statistical guarantees on possibly
9489 user-defined and/or data-driven sets of hypotheses.")
9490 (license license:gpl3))))
9492 (define-public r-monocle3
9500 (url "https://github.com/cole-trapnell-lab/monocle3")
9502 (file-name (git-file-name name version))
9505 "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4"))))
9506 (build-system r-build-system)
9512 r-delayedmatrixstats
9547 r-singlecellexperiment
9552 (home-page "https://github.com/cole-trapnell-lab/monocle3")
9553 (synopsis "Analysis toolkit for single-cell RNA-Seq data")
9555 "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.")
9556 (license license:expat)))
9558 (define-public r-noiseq
9565 (uri (bioconductor-uri "NOISeq" version))
9568 "0ah6adlhv4254jkssinn2ik8n811hd1nw85bnzqk2kwhl49nrk27"))))
9569 (properties `((upstream-name . "NOISeq")))
9570 (build-system r-build-system)
9572 (list r-biobase r-matrix))
9573 (home-page "https://bioconductor.org/packages/NOISeq")
9574 (synopsis "Exploratory analysis and differential expression for RNA-seq data")
9576 "This package provides tools to support the analysis of RNA-seq
9577 expression data or other similar kind of data. It provides exploratory plots
9578 to evaluate saturation, count distribution, expression per chromosome, type of
9579 detected features, features length, etc. It also supports the analysis of
9580 differential expression between two experimental conditions with no parametric
9582 (license license:artistic2.0)))
9584 (define-public r-scdd
9591 (uri (bioconductor-uri "scDD" version))
9594 "0bjww338z5qf2g97kbh85h9kpagjr59ff9f4alm33h16xz5mb7k0"))))
9595 (properties `((upstream-name . "scDD")))
9596 (build-system r-build-system)
9607 r-singlecellexperiment
9608 r-summarizedexperiment))
9611 (home-page "https://github.com/kdkorthauer/scDD")
9612 (synopsis "Mixture modeling of single-cell RNA-seq data")
9614 "This package implements a method to analyze single-cell RNA-seq data
9615 utilizing flexible Dirichlet Process mixture models. Genes with differential
9616 distributions of expression are classified into several interesting patterns
9617 of differences between two conditions. The package also includes functions
9618 for simulating data with these patterns from negative binomial
9620 (license license:gpl2)))
9622 (define-public r-scone
9629 (uri (bioconductor-uri "scone" version))
9632 "05id34n6min03ha1chg5mrvx399qm2mby9kxkaz5w8fbidp97851"))))
9633 (build-system r-build-system)
9654 r-singlecellexperiment
9655 r-summarizedexperiment))
9658 (home-page "https://bioconductor.org/packages/scone")
9659 (synopsis "Single cell overview of normalized expression data")
9661 "SCONE is an R package for comparing and ranking the performance of
9662 different normalization schemes for single-cell RNA-seq and other
9663 high-throughput analyses.")
9664 (license license:artistic2.0)))
9666 (define-public r-geoquery
9673 (uri (bioconductor-uri "GEOquery" version))
9676 "1cvkvq2haz831qi8w0gd3ayvxfxsl0z5klhki4gkfi9xqdv1gi9x"))))
9677 (properties `((upstream-name . "GEOquery")))
9678 (build-system r-build-system)
9692 (home-page "https://github.com/seandavi/GEOquery/")
9693 (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)")
9695 "The NCBI Gene Expression Omnibus (GEO) is a public repository of
9696 microarray data. Given the rich and varied nature of this resource, it is
9697 only natural to want to apply BioConductor tools to these data. GEOquery is
9698 the bridge between GEO and BioConductor.")
9699 (license license:gpl2)))
9701 (define-public r-illuminaio
9703 (name "r-illuminaio")
9708 (uri (bioconductor-uri "illuminaio" version))
9711 "1xk057a9w4ps8xi8jyw8imkjcicfmzns8g92grn4af7yiip68h62"))))
9712 (build-system r-build-system)
9715 (home-page "https://github.com/HenrikBengtsson/illuminaio/")
9716 (synopsis "Parse Illumina microarray output files")
9718 "This package provides tools for parsing Illumina's microarray output
9719 files, including IDAT.")
9720 (license license:gpl2)))
9722 (define-public r-siggenes
9729 (uri (bioconductor-uri "siggenes" version))
9732 "0amjqm2c8p1vjzx109p7n81wbsbx8rljwn6mbkl7dpi834im9d7l"))))
9733 (build-system r-build-system)
9735 (list r-biobase r-multtest r-scrime))
9736 (home-page "https://bioconductor.org/packages/siggenes/")
9738 "Multiple testing using SAM and Efron's empirical Bayes approaches")
9740 "This package provides tools for the identification of differentially
9741 expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using
9742 both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical
9743 Bayes Analyses of Microarrays} (EBAM).")
9744 (license license:lgpl2.0+)))
9746 (define-public r-bumphunter
9748 (name "r-bumphunter")
9753 (uri (bioconductor-uri "bumphunter" version))
9756 "0k92ps9chqsimbc7vsr8swg679zfv8nfn5zahbqq4nknhhy7hwxw"))))
9757 (build-system r-build-system)
9759 (list r-annotationdbi
9772 (home-page "https://github.com/ririzarr/bumphunter")
9773 (synopsis "Find bumps in genomic data")
9775 "This package provides tools for finding bumps in genomic data in order
9776 to identify differentially methylated regions in epigenetic epidemiology
9778 (license license:artistic2.0)))
9780 (define-public r-microbiome
9782 (name "r-microbiome")
9786 (uri (bioconductor-uri "microbiome" version))
9789 "1z9arkjp5xszlg07mzb4p163i74jfbd9p4gbwv5syivnpl040k12"))))
9790 (properties `((upstream-name . "microbiome")))
9791 (build-system r-build-system)
9804 (native-inputs (list r-knitr))
9805 (home-page "https://microbiome.github.io/microbiome/")
9806 (synopsis "Tools for microbiome analysis")
9808 "This package facilitates phyloseq exploration and analysis of taxonomic
9809 profiling data. This package provides tools for the manipulation, statistical
9810 analysis, and visualization of taxonomic profiling data. In addition to
9811 targeted case-control studies, microbiome facilitates scalable exploration of
9812 population cohorts. This package supports the independent phyloseq data
9813 format and expands the available toolkit in order to facilitate the
9814 standardization of the analyses and the development of best practices.")
9815 (license license:bsd-2)))
9817 (define-public r-milor
9823 (uri (bioconductor-uri "miloR" version))
9826 "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
9827 (properties `((upstream-name . "miloR")))
9828 (build-system r-build-system)
9830 (list r-biocgenerics
9850 r-singlecellexperiment
9852 r-summarizedexperiment
9855 (native-inputs (list r-knitr))
9856 (home-page "https://marionilab.github.io/miloR")
9857 (synopsis "Differential neighbourhood abundance testing on a graph")
9859 "Milo performs single-cell differential abundance testing. Cell states
9860 are modelled as representative neighbourhoods on a nearest neighbour graph.
9861 Hypothesis testing is performed using a negative bionomial generalized linear
9863 (license license:gpl3)))
9865 (define-public r-minfi
9872 (uri (bioconductor-uri "minfi" version))
9875 "0255z7w5i5k01w8wn7jkb37h3q7m7vg0szqgk76h330yydnmkrq6"))))
9876 (build-system r-build-system)
9886 r-delayedmatrixstats
9906 r-summarizedexperiment))
9909 (home-page "https://github.com/hansenlab/minfi")
9910 (synopsis "Analyze Illumina Infinium DNA methylation arrays")
9912 "This package provides tools to analyze and visualize Illumina Infinium
9913 methylation arrays.")
9914 (license license:artistic2.0)))
9916 (define-public r-methylumi
9918 (name "r-methylumi")
9923 (uri (bioconductor-uri "methylumi" version))
9926 "0klkinq55lfj1d4z8gkrv98849079x1l5gd15habw7jq9xxvhjww"))))
9927 (build-system r-build-system)
9933 r-fdb-infiniummethylation-hg19
9947 r-summarizedexperiment))
9950 (home-page "https://bioconductor.org/packages/methylumi")
9951 (synopsis "Handle Illumina methylation data")
9953 "This package provides classes for holding and manipulating Illumina
9954 methylation data. Based on eSet, it can contain MIAME information, sample
9955 information, feature information, and multiple matrices of data. An
9956 \"intelligent\" import function, methylumiR can read the Illumina text files
9957 and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from
9958 HumanMethylation27 and HumanMethylation450 microarrays. Normalization,
9959 background correction, and quality control features for GoldenGate, Infinium,
9960 and Infinium HD arrays are also included.")
9961 (license license:gpl2)))
9963 (define-public r-lumi
9970 (uri (bioconductor-uri "lumi" version))
9973 "06zmll5j1yymsm3byarhllrz4q1w5mzv267a9g6visn73wan8y9d"))))
9974 (build-system r-build-system)
9991 (home-page "https://bioconductor.org/packages/lumi")
9992 (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays")
9994 "The lumi package provides an integrated solution for the Illumina
9995 microarray data analysis. It includes functions of Illumina
9996 BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific
9997 variance stabilization, normalization and gene annotation at the probe level.
9998 It also includes the functions of processing Illumina methylation microarrays,
9999 especially Illumina Infinium methylation microarrays.")
10000 (license license:lgpl2.0+)))
10002 (define-public r-linnorm
10009 (uri (bioconductor-uri "Linnorm" version))
10012 "1002lllgns5klv3q2wsikkbypa2bafpka7a8mri0y5bfxncfr2zb"))))
10013 (properties `((upstream-name . "Linnorm")))
10014 (build-system r-build-system)
10036 (home-page "http://www.jjwanglab.org/Linnorm/")
10037 (synopsis "Linear model and normality based transformation method")
10039 "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq
10040 count data or any large scale count data. It transforms such datasets for
10041 parametric tests. In addition to the transformtion function (@code{Linnorm}),
10042 the following pipelines are implemented:
10045 @item Library size/batch effect normalization (@code{Linnorm.Norm})
10046 @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means
10047 clustering or hierarchical clustering (@code{Linnorm.tSNE},
10048 @code{Linnorm.PCA}, @code{Linnorm.HClust})
10049 @item Differential expression analysis or differential peak detection using
10050 limma (@code{Linnorm.limma})
10051 @item Highly variable gene discovery and visualization (@code{Linnorm.HVar})
10052 @item Gene correlation network analysis and visualization (@code{Linnorm.Cor})
10053 @item Stable gene selection for scRNA-seq data; for users without or who do
10054 not want to rely on spike-in genes (@code{Linnorm.SGenes})
10055 @item Data imputation (@code{Linnorm.DataImput}).
10058 Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the
10059 @code{RnaXSim} function is included for simulating RNA-seq data for the
10060 evaluation of DEG analysis methods.")
10061 (license license:expat)))
10063 (define-public r-ioniser
10070 (uri (bioconductor-uri "IONiseR" version))
10073 "0cgx1dcfh617l9vr4r3ky8w7f0snl0vpavfd9n1h5n68p0p42dwi"))))
10074 (properties `((upstream-name . "IONiseR")))
10075 (build-system r-build-system)
10077 (list r-biocgenerics
10092 (home-page "https://bioconductor.org/packages/IONiseR/")
10093 (synopsis "Quality assessment tools for Oxford Nanopore MinION data")
10095 "IONiseR provides tools for the quality assessment of Oxford Nanopore
10096 MinION data. It extracts summary statistics from a set of fast5 files and can
10097 be used either before or after base calling. In addition to standard
10098 summaries of the read-types produced, it provides a number of plots for
10099 visualising metrics relative to experiment run time or spatially over the
10100 surface of a flowcell.")
10101 (license license:expat)))
10103 ;; This is a CRAN package, but it depends on multtest from Bioconductor.
10104 (define-public r-mutoss
10111 (uri (cran-uri "mutoss" version))
10114 "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298"))))
10115 (properties `((upstream-name . "mutoss")))
10116 (build-system r-build-system)
10118 (list r-multcomp r-multtest r-mvtnorm r-plotrix))
10119 (home-page "https://github.com/kornl/mutoss/")
10120 (synopsis "Unified multiple testing procedures")
10122 "This package is designed to ease the application and comparison of
10123 multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods
10124 are standardized and usable by the accompanying mutossGUI package.")
10125 ;; Any version of the GPL.
10126 (license (list license:gpl2+ license:gpl3+))))
10128 ;; This is a CRAN package, but it depends on mutoss, which depends on multtest
10129 ;; from Bioconductor, so we put it here.
10130 (define-public r-metap
10137 (uri (cran-uri "metap" version))
10140 "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf"))))
10141 (build-system r-build-system)
10149 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
10150 (synopsis "Meta-analysis of significance values")
10152 "The canonical way to perform meta-analysis involves using effect sizes.
10153 When they are not available this package provides a number of methods for
10154 meta-analysis of significance values including the methods of Edgington,
10155 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
10156 published results; and a routine for graphical display.")
10157 (license license:gpl2)))
10159 (define-public r-tradeseq
10161 (name "r-tradeseq")
10165 (uri (bioconductor-uri "tradeSeq" version))
10168 "0v9nqxrwa69qhmyaicn2vvs8haha4kzs93iqim306331vadp9qm0"))))
10169 (build-system r-build-system)
10185 r-singlecellexperiment
10187 r-summarizedexperiment
10193 (home-page "https://statomics.github.io/tradeSeq/index.html")
10194 (synopsis "Trajectory-based differential expression analysis")
10196 "This package provides a flexible method for fitting regression models that
10197 can be used to find genes that are differentially expressed along one or
10198 multiple lineages in a trajectory. Based on the fitted models, it uses a
10199 variety of tests suited to answer different questions of interest, e.g. the
10200 discovery of genes for which expression is associated with pseudotime, or which
10201 are differentially expressed (in a specific region) along the trajectory. It
10202 fits a negative binomial generalized additive model (GAM) for each gene, and
10203 performs inference on the parameters of the GAM.")
10204 (license license:expat)))
10206 (define-public r-triform
10213 (uri (bioconductor-uri "triform" version))
10216 "089b7f6dwpi9abj0ncswbi4s30k45996zb99sh43avw6jcb6qj60"))))
10217 (build-system r-build-system)
10219 (list r-biocgenerics r-iranges r-yaml))
10220 (home-page "https://bioconductor.org/packages/triform/")
10221 (synopsis "Find enriched regions in transcription factor ChIP-sequencing data")
10223 "The Triform algorithm uses model-free statistics to identify peak-like
10224 distributions of TF ChIP sequencing reads, taking advantage of an improved
10225 peak definition in combination with known profile characteristics.")
10226 (license license:gpl2)))
10228 (define-public r-varianttools
10230 (name "r-varianttools")
10235 (uri (bioconductor-uri "VariantTools" version))
10238 "18nxcamfgnw4n2ab0czxglw0sqc9wzdqzpjv43lcyyal23lzzsix"))))
10239 (properties `((upstream-name . "VariantTools")))
10240 (build-system r-build-system)
10255 r-variantannotation))
10256 (home-page "https://bioconductor.org/packages/VariantTools/")
10257 (synopsis "Tools for exploratory analysis of variant calls")
10259 "Explore, diagnose, and compare variant calls using filters. The
10260 VariantTools package supports a workflow for loading data, calling single
10261 sample variants and tumor-specific somatic mutations or other sample-specific
10262 variant types (e.g., RNA editing). Most of the functions operate on
10263 alignments (BAM files) or datasets of called variants. The user is expected
10264 to have already aligned the reads with a separate tool, e.g., GSNAP via
10266 (license license:artistic2.0)))
10268 (define-public r-heatplus
10270 (name "r-heatplus")
10275 (uri (bioconductor-uri "Heatplus" version))
10278 "0b1mzxysmrqinp93p587apna8p0llmawblwj93icydqxxm2jkhb1"))))
10279 (properties `((upstream-name . "Heatplus")))
10280 (build-system r-build-system)
10282 (list r-rcolorbrewer))
10283 (home-page "https://github.com/alexploner/Heatplus")
10284 (synopsis "Heatmaps with row and/or column covariates and colored clusters")
10286 "This package provides tools to display a rectangular heatmap (intensity
10287 plot) of a data matrix. By default, both samples (columns) and features (row)
10288 of the matrix are sorted according to a hierarchical clustering, and the
10289 corresponding dendrogram is plotted. Optionally, panels with additional
10290 information about samples and features can be added to the plot.")
10291 (license license:gpl2+)))
10293 (define-public r-gosemsim
10295 (name "r-gosemsim")
10300 (uri (bioconductor-uri "GOSemSim" version))
10303 "1hp15pzd0m0g9f8kglyfsgjqxnvxcmm9022xnsrkzfvmj2yw14vd"))))
10304 (properties `((upstream-name . "GOSemSim")))
10305 (build-system r-build-system)
10307 (list r-annotationdbi r-go-db r-rcpp))
10310 (home-page "https://guangchuangyu.github.io/software/GOSemSim")
10311 (synopsis "GO-terms semantic similarity measures")
10313 "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide
10314 quantitative ways to compute similarities between genes and gene groups, and
10315 have became important basis for many bioinformatics analysis approaches.
10316 GOSemSim is an R package for semantic similarity computation among GO terms,
10317 sets of GO terms, gene products and gene clusters.")
10318 (license license:artistic2.0)))
10320 (define-public r-anota
10327 (uri (bioconductor-uri "anota" version))
10330 "1x75r5znl8jllqsgzpxsqj62ch11bpwhmyzmbjmb8sz8f8ww923c"))))
10331 (build-system r-build-system)
10333 (list r-multtest r-qvalue))
10334 (home-page "https://bioconductor.org/packages/anota/")
10335 (synopsis "Analysis of translational activity")
10337 "Genome wide studies of translational control is emerging as a tool to
10338 study various biological conditions. The output from such analysis is both
10339 the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
10340 involved in translation (the actively translating mRNA level) for each mRNA.
10341 The standard analysis of such data strives towards identifying differential
10342 translational between two or more sample classes - i.e., differences in
10343 actively translated mRNA levels that are independent of underlying differences
10344 in cytosolic mRNA levels. This package allows for such analysis using partial
10345 variances and the random variance model. As 10s of thousands of mRNAs are
10346 analyzed in parallel the library performs a number of tests to assure that
10347 the data set is suitable for such analysis.")
10348 (license license:gpl3)))
10350 (define-public r-sigpathway
10352 (name "r-sigpathway")
10357 (uri (bioconductor-uri "sigPathway" version))
10360 "1c2kwhbxgf66az7ssm2mab9n5x59zy4kxq8vblz5r9636xqaysif"))))
10361 (properties `((upstream-name . "sigPathway")))
10362 (build-system r-build-system)
10363 (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102")
10364 (synopsis "Pathway analysis")
10366 "This package is used to conduct pathway analysis by calculating the NT_k
10367 and NE_k statistics in a statistical framework for determining whether a
10368 specified group of genes for a pathway has a coordinated association with a
10369 phenotype of interest.")
10370 (license license:gpl2)))
10372 (define-public r-fcscan
10379 (uri (bioconductor-uri "fcScan" version))
10381 (base32 "0yv7ifw0xxx1v9z8dxszv0cb72q3frd74dyxfbvrcs6x9y9v3jzp"))))
10382 (properties `((upstream-name . "fcScan")))
10383 (build-system r-build-system)
10391 r-summarizedexperiment
10392 r-variantannotation))
10393 (native-inputs (list r-knitr))
10394 (home-page "https://bioconductor.org/packages/fcScan")
10395 (synopsis "Detect clusters of coordinates with user defined options")
10397 "This package is used to detect combination of genomic coordinates
10398 falling within a user defined window size along with user defined overlap
10399 between identified neighboring clusters. It can be used for genomic data
10400 where the clusters are built on a specific chromosome or specific strand.
10401 Clustering can be performed with a \"greedy\" option allowing thus the
10402 presence of additional sites within the allowed window size.")
10403 (license license:artistic2.0)))
10405 (define-public r-fgsea
10412 (uri (bioconductor-uri "fgsea" version))
10415 "0innyggai6l4fpl4qrblzdc52vqw9jaszmip0yr1lv7rzwyl6mpg"))))
10416 (build-system r-build-system)
10428 (home-page "https://github.com/ctlab/fgsea/")
10429 (synopsis "Fast gene set enrichment analysis")
10431 "The package implements an algorithm for fast gene set enrichment
10432 analysis. Using the fast algorithm makes more permutations and gets
10433 more fine grained p-values, which allows using accurate standard approaches
10434 to multiple hypothesis correction.")
10435 (license license:expat)))
10437 (define-public r-dose
10444 (uri (bioconductor-uri "DOSE" version))
10447 "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"))))
10448 (properties `((upstream-name . "DOSE")))
10449 (build-system r-build-system)
10451 (list r-annotationdbi
10461 (home-page "https://guangchuangyu.github.io/software/DOSE/")
10462 (synopsis "Disease ontology semantic and enrichment analysis")
10464 "This package implements five methods proposed by Resnik, Schlicker,
10465 Jiang, Lin and Wang, respectively, for measuring semantic similarities among
10466 @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses
10467 including hypergeometric model and gene set enrichment analysis are also
10468 implemented for discovering disease associations of high-throughput biological
10470 (license license:artistic2.0)))
10472 (define-public r-enrichplot
10474 (name "r-enrichplot")
10479 (uri (bioconductor-uri "enrichplot" version))
10482 "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"))))
10483 (build-system r-build-system)
10502 (home-page "https://github.com/GuangchuangYu/enrichplot")
10503 (synopsis "Visualization of functional enrichment result")
10505 "The enrichplot package implements several visualization methods for
10506 interpreting functional enrichment results obtained from ORA or GSEA analyses.
10507 All the visualization methods are developed based on ggplot2 graphics.")
10508 (license license:artistic2.0)))
10510 (define-public r-clusterprofiler
10512 (name "r-clusterprofiler")
10517 (uri (bioconductor-uri "clusterProfiler" version))
10520 "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5"))))
10522 `((upstream-name . "clusterProfiler")))
10523 (build-system r-build-system)
10525 (list r-annotationdbi
10540 (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
10541 (synopsis "Analysis and visualization of functional profiles for gene clusters")
10543 "This package implements methods to analyze and visualize functional
10544 profiles (GO and KEGG) of gene and gene clusters.")
10545 (license license:artistic2.0)))
10547 (define-public r-clusterexperiment
10549 (name "r-clusterexperiment")
10553 (uri (bioconductor-uri "clusterExperiment" version))
10556 "1xd2kxmdg51hhj0zvz7pxmpdvb1sya7prsf9ny2wj2y8ivrqgn4f"))))
10557 (build-system r-build-system)
10582 r-singlecellexperiment
10584 r-summarizedexperiment
10586 (home-page "https://bioconductor.org/packages/clusterExperiment/")
10587 (synopsis "Compare clusterings for single-cell sequencing")
10588 (description "This package provides functionality for running and comparing
10589 many different clusterings of single-cell sequencing data or other large mRNA
10590 expression data sets.")
10591 (license license:artistic2.0)))
10593 (define-public r-mlinterfaces
10595 (name "r-mlinterfaces")
10600 (uri (bioconductor-uri "MLInterfaces" version))
10603 "179d19kxjipfkc40z15337x1vzqd7vz3gbmr2lw5w7x9l857ngs5"))))
10604 (properties `((upstream-name . "MLInterfaces")))
10605 (build-system r-build-system)
10627 (home-page "https://bioconductor.org/packages/MLInterfaces/")
10628 (synopsis "Interfaces to R machine learning procedures")
10630 "This package provides uniform interfaces to machine learning code for
10631 data in R and Bioconductor containers.")
10632 ;; Any version of the LGPL.
10633 (license license:lgpl2.1+)))
10635 (define-public r-annaffy
10642 (uri (bioconductor-uri "annaffy" version))
10645 "1fbqknwbl4534h66xrhcryg9pavm9fkja47gqbsxf8bd5yhk5mgq"))))
10646 (build-system r-build-system)
10649 (modify-phases %standard-phases
10650 (add-after 'unpack 'remove-reference-to-non-free-data
10652 (substitute* "DESCRIPTION"
10653 ((", KEGG.db") "")))))))
10655 (list r-annotationdbi r-biobase r-biocmanager r-dbi r-go-db))
10656 (home-page "https://bioconductor.org/packages/annaffy/")
10657 (synopsis "Annotation tools for Affymetrix biological metadata")
10659 "This package provides functions for handling data from Bioconductor
10660 Affymetrix annotation data packages. It produces compact HTML and text
10661 reports including experimental data and URL links to many online databases.
10662 It allows searching of biological metadata using various criteria.")
10663 ;; Any version of the LGPL according to the DESCRIPTION file. A copy of
10664 ;; the LGPL 2.1 is included.
10665 (license license:lgpl2.1+)))
10667 (define-public r-a4core
10674 (uri (bioconductor-uri "a4Core" version))
10677 "1ky1lphq6bqxj6h12pg06cvs451fziqam8gd56wmpk6r5pbg4390"))))
10678 (properties `((upstream-name . "a4Core")))
10679 (build-system r-build-system)
10681 (list r-biobase r-glmnet))
10684 (home-page "https://bioconductor.org/packages/a4Core")
10685 (synopsis "Automated Affymetrix array analysis core package")
10687 "This is the core package for the automated analysis of Affymetrix
10689 (license license:gpl3)))
10691 (define-public r-a4classif
10693 (name "r-a4classif")
10698 (uri (bioconductor-uri "a4Classif" version))
10701 "1v61vgpqrf7bhk44n2gkxb8dm5d0rr8c9rd6fdcjs50nhij0lbiw"))))
10702 (properties `((upstream-name . "a4Classif")))
10703 (build-system r-build-system)
10714 (home-page "https://bioconductor.org/packages/a4Classif/")
10715 (synopsis "Automated Affymetrix array analysis classification package")
10717 "This is the classification package for the automated analysis of
10718 Affymetrix arrays.")
10719 (license license:gpl3)))
10721 (define-public r-a4preproc
10723 (name "r-a4preproc")
10728 (uri (bioconductor-uri "a4Preproc" version))
10731 "098yzy7x5536bj76iavismdsdn7x6x07aw0j3knj6i9www9y8yz9"))))
10732 (properties `((upstream-name . "a4Preproc")))
10733 (build-system r-build-system)
10735 (list r-biobase r-biocgenerics))
10738 (home-page "https://bioconductor.org/packages/a4Preproc/")
10739 (synopsis "Automated Affymetrix array analysis preprocessing package")
10741 "This is a package for the automated analysis of Affymetrix arrays. It
10742 is used for preprocessing the arrays.")
10743 (license license:gpl3)))
10745 (define-public r-a4reporting
10747 (name "r-a4reporting")
10752 (uri (bioconductor-uri "a4Reporting" version))
10755 "03sypayh187gqc6hykkqr1g0vb3zxc2c3xyp00jfbn12b35acnb0"))))
10756 (properties `((upstream-name . "a4Reporting")))
10757 (build-system r-build-system)
10762 (home-page "https://bioconductor.org/packages/a4Reporting/")
10763 (synopsis "Automated Affymetrix array analysis reporting package")
10765 "This is a package for the automated analysis of Affymetrix arrays. It
10766 provides reporting features.")
10767 (license license:gpl3)))
10769 (define-public r-a4base
10776 (uri (bioconductor-uri "a4Base" version))
10779 "15zqirz16gpks9f5d3d76h85b936za2jih74vfr55l5arqrrvvsn"))))
10780 (properties `((upstream-name . "a4Base")))
10781 (build-system r-build-system)
10793 (home-page "https://bioconductor.org/packages/a4Base/")
10794 (synopsis "Automated Affymetrix array analysis base package")
10796 "This package provides basic features for the automated analysis of
10797 Affymetrix arrays.")
10798 (license license:gpl3)))
10800 (define-public r-a4
10807 (uri (bioconductor-uri "a4" version))
10810 "1zs8fs6mdd7fhsmx4k824mid0jk400cm6dwfhl8z5lg85y8y2n0r"))))
10811 (build-system r-build-system)
10813 (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting))
10814 (home-page "https://bioconductor.org/packages/a4/")
10815 (synopsis "Automated Affymetrix array analysis umbrella package")
10817 "This package provides a software suite for the automated analysis of
10818 Affymetrix arrays.")
10819 (license license:gpl3)))
10821 (define-public r-abseqr
10828 (uri (bioconductor-uri "abseqR" version))
10831 "0jh3rj6ag07vpw6fymqm6m4jkrm9mgf50zkjncahxdf52mna8a9b"))))
10832 (properties `((upstream-name . "abseqR")))
10833 (build-system r-build-system)
10837 (list r-biocparallel
10857 (home-page "https://github.com/malhamdoosh/abseqR")
10858 (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries")
10860 "AbSeq is a comprehensive bioinformatic pipeline for the analysis of
10861 sequencing datasets generated from antibody libraries and abseqR is one of its
10862 packages. AbseqR empowers the users of abseqPy with plotting and reporting
10863 capabilities and allows them to generate interactive HTML reports for the
10864 convenience of viewing and sharing with other researchers. Additionally,
10865 abseqR extends abseqPy to compare multiple repertoire analyses and perform
10866 further downstream analysis on its output.")
10867 (license license:gpl3)))
10869 (define-public r-bacon
10876 (uri (bioconductor-uri "bacon" version))
10879 "1zvcxdj3r892898ik5gq3jdbfig1438qws4bwd465ik8vi7g39v8"))))
10880 (build-system r-build-system)
10882 (list r-biocparallel r-ellipse r-ggplot2))
10885 (home-page "https://bioconductor.org/packages/bacon/")
10886 (synopsis "Controlling bias and inflation in association studies")
10888 "Bacon can be used to remove inflation and bias often observed in
10889 epigenome- and transcriptome-wide association studies. To this end bacon
10890 constructs an empirical null distribution using a Gibbs Sampling algorithm by
10891 fitting a three-component normal mixture on z-scores.")
10892 (license license:gpl2+)))
10894 (define-public r-rgadem
10901 (uri (bioconductor-uri "rGADEM" version))
10904 "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"))))
10905 (properties `((upstream-name . "rGADEM")))
10906 (build-system r-build-system)
10908 (list r-biostrings r-bsgenome r-genomicranges r-iranges r-seqlogo))
10909 (home-page "https://bioconductor.org/packages/rGADEM/")
10910 (synopsis "De novo sequence motif discovery")
10912 "rGADEM is an efficient de novo motif discovery tool for large-scale
10913 genomic sequence data.")
10914 (license license:artistic2.0)))
10916 (define-public r-motiv
10923 (uri (bioconductor-uri "MotIV" version))
10926 "1yqqymcrnwlpv6h3w80yliv19922g32xqlqszaqjk6zp853qilh6"))))
10927 (properties `((upstream-name . "MotIV")))
10928 (build-system r-build-system)
10932 (list r-biocgenerics
10939 (home-page "https://bioconductor.org/packages/MotIV/")
10940 (synopsis "Motif identification and validation")
10942 "This package is used for the identification and validation of sequence
10943 motifs. It makes use of STAMP for comparing a set of motifs to a given
10944 database (e.g. JASPAR). It can also be used to visualize motifs, motif
10945 distributions, modules and filter motifs.")
10946 (license license:gpl2)))
10948 (define-public r-motifdb
10954 (uri (bioconductor-uri "MotifDb" version))
10956 (base32 "1cyfz0l0yvdii3idaiq5w39yzxlzfpifa4v5pv7hdjfjj83a8rbi"))))
10957 (properties `((upstream-name . "MotifDb")))
10958 (build-system r-build-system)
10960 (list r-biocgenerics
10966 r-splitstackshape))
10969 (home-page "https://www.bioconductor.org/packages/MotifDb/")
10970 (synopsis "Annotated collection of protein-DNA binding sequence motifs")
10971 (description "This package provides more than 2000 annotated position
10972 frequency matrices from nine public sources, for multiple organisms.")
10973 (license license:artistic2.0)))
10975 (define-public r-motifbreakr
10977 (name "r-motifbreakr")
10981 (uri (bioconductor-uri "motifbreakR" version))
10983 (base32 "0sad73jjx52qzp1fmygp6xqvaxwl5szi69f00f94i1pdyq70qhlg"))))
10984 (properties `((upstream-name . "motifbreakR")))
10985 (build-system r-build-system)
10987 (list r-biocgenerics
11001 r-summarizedexperiment
11003 r-variantannotation))
11006 (home-page "https://www.bioconductor.org/packages/motifbreakR/")
11007 (synopsis "Predicting disruptiveness of single nucleotide polymorphisms")
11008 (description "This package allows biologists to judge in the first place
11009 whether the sequence surrounding the polymorphism is a good match, and in
11010 the second place how much information is gained or lost in one allele of
11011 the polymorphism relative to another. This package gives a choice of
11012 algorithms for interrogation of genomes with motifs from public sources:
11014 @item a weighted-sum probability matrix;
11015 @item log-probabilities;
11016 @item weighted by relative entropy.
11019 This package can predict effects for novel or previously described variants in
11020 public databases, making it suitable for tasks beyond the scope of its original
11021 design. Lastly, it can be used to interrogate any genome curated within
11023 (license license:gpl2+)))
11025 (define-public r-motifstack
11027 (name "r-motifstack")
11032 (uri (bioconductor-uri "motifStack" version))
11035 "0d2ihx73chczbv6f91n04qb372plrdv7k4qws8shyw1fmvb1rq0z"))))
11036 (properties `((upstream-name . "motifStack")))
11037 (build-system r-build-system)
11047 (home-page "https://bioconductor.org/packages/motifStack/")
11048 (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences")
11050 "The motifStack package is designed for graphic representation of
11051 multiple motifs with different similarity scores. It works with both DNA/RNA
11052 sequence motifs and amino acid sequence motifs. In addition, it provides the
11053 flexibility for users to customize the graphic parameters such as the font
11054 type and symbol colors.")
11055 (license license:gpl2+)))
11057 (define-public r-genomicscores
11059 (name "r-genomicscores")
11064 (uri (bioconductor-uri "GenomicScores" version))
11067 "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j"))))
11068 (properties `((upstream-name . "GenomicScores")))
11069 (build-system r-build-system)
11071 (list r-annotationhub
11088 (home-page "https://github.com/rcastelo/GenomicScores/")
11089 (synopsis "Work with genome-wide position-specific scores")
11091 "This package provides infrastructure to store and access genome-wide
11092 position-specific scores within R and Bioconductor.")
11093 (license license:artistic2.0)))
11095 (define-public r-atacseqqc
11097 (name "r-atacseqqc")
11102 (uri (bioconductor-uri "ATACseqQC" version))
11105 "0jj7n0mcj0gciw0ksazlksgmwzp51a40pwqhf0c7la0cc4bnrkqp"))))
11106 (properties `((upstream-name . "ATACseqQC")))
11107 (build-system r-build-system)
11109 (list r-biocgenerics
11115 r-genomicalignments
11129 (home-page "https://bioconductor.org/packages/ATACseqQC/")
11130 (synopsis "ATAC-seq quality control")
11132 "ATAC-seq, an assay for Transposase-Accessible Chromatin using
11133 sequencing, is a rapid and sensitive method for chromatin accessibility
11134 analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq
11135 and DNAse-seq. The ATACseqQC package was developed to help users to quickly
11136 assess whether their ATAC-seq experiment is successful. It includes
11137 diagnostic plots of fragment size distribution, proportion of mitochondria
11138 reads, nucleosome positioning pattern, and CTCF or other Transcript Factor
11140 (license license:gpl2+)))
11142 (define-public r-gofuncr
11149 (uri (bioconductor-uri "GOfuncR" version))
11152 "02vdfsjrqp0m06mfbspwkxjyqxfca0w1idgygpi1a9i5m4fqhwpk"))))
11153 (properties `((upstream-name . "GOfuncR")))
11154 (build-system r-build-system)
11156 (list r-annotationdbi
11165 (home-page "https://bioconductor.org/packages/GOfuncR/")
11166 (synopsis "Gene ontology enrichment using FUNC")
11168 "GOfuncR performs a gene ontology enrichment analysis based on the
11169 ontology enrichment software FUNC. GO-annotations are obtained from
11170 OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is
11171 included in the package and updated regularly. GOfuncR provides the standard
11172 candidate vs background enrichment analysis using the hypergeometric test, as
11173 well as three additional tests:
11176 @item the Wilcoxon rank-sum test that is used when genes are ranked,
11177 @item a binomial test that is used when genes are associated with two counts,
11179 @item a Chi-square or Fisher's exact test that is used in cases when genes are
11180 associated with four counts.
11183 To correct for multiple testing and interdependency of the tests, family-wise
11184 error rates are computed based on random permutations of the gene-associated
11185 variables. GOfuncR also provides tools for exploring the ontology graph and
11186 the annotations, and options to take gene-length or spatial clustering of
11187 genes into account. It is also possible to provide custom gene coordinates,
11188 annotations and ontologies.")
11189 (license license:gpl2+)))
11191 (define-public r-abaenrichment
11193 (name "r-abaenrichment")
11198 (uri (bioconductor-uri "ABAEnrichment" version))
11201 "1sp3f72rzlr822dxx42bswynrwwfx6f520hdhfdikqp13p2y4044"))))
11202 (properties `((upstream-name . "ABAEnrichment")))
11203 (build-system r-build-system)
11213 (home-page "https://bioconductor.org/packages/ABAEnrichment/")
11214 (synopsis "Gene expression enrichment in human brain regions")
11216 "The package ABAEnrichment is designed to test for enrichment of user
11217 defined candidate genes in the set of expressed genes in different human brain
11218 regions. The core function @code{aba_enrich} integrates the expression of the
11219 candidate gene set (averaged across donors) and the structural information of
11220 the brain using an ontology, both provided by the Allen Brain Atlas project.")
11221 (license license:gpl2+)))
11223 (define-public r-annotationfuncs
11225 (name "r-annotationfuncs")
11230 (uri (bioconductor-uri "AnnotationFuncs" version))
11233 "0xsm7741zm81bi4c9hy0zaacnk8a6bahdpc6srqzrbsz0pfzdyhr"))))
11235 `((upstream-name . "AnnotationFuncs")))
11236 (build-system r-build-system)
11238 (list r-annotationdbi r-dbi))
11239 (home-page "https://www.iysik.com/r/annotationfuncs")
11240 (synopsis "Annotation translation functions")
11242 "This package provides functions for handling translating between
11243 different identifieres using the Biocore Data Team data-packages (e.g.
11244 @code{org.Bt.eg.db}).")
11245 (license license:gpl2)))
11247 (define-public r-annotationtools
11249 (name "r-annotationtools")
11254 (uri (bioconductor-uri "annotationTools" version))
11257 "122b424zida3j0vqkn8d06sg3jpc3ngsgidr8kgg00n4cjngkc51"))))
11259 `((upstream-name . "annotationTools")))
11260 (build-system r-build-system)
11261 (propagated-inputs (list r-biobase))
11262 (home-page "https://bioconductor.org/packages/annotationTools/")
11263 (synopsis "Annotate microarrays and perform gene expression analyses")
11265 "This package provides functions to annotate microarrays, find orthologs,
11266 and integrate heterogeneous gene expression profiles using annotation and
11267 other molecular biology information available as flat file database (plain
11269 ;; Any version of the GPL.
11270 (license (list license:gpl2+))))
11272 (define-public r-allelicimbalance
11274 (name "r-allelicimbalance")
11279 (uri (bioconductor-uri "AllelicImbalance" version))
11282 "0w4xd0xzkwx7bbhrgqligpahlhg85rginknx520z891r8v0bim2z"))))
11284 `((upstream-name . "AllelicImbalance")))
11285 (build-system r-build-system)
11287 (list r-annotationdbi
11292 r-genomicalignments
11304 r-summarizedexperiment
11305 r-variantannotation))
11308 (home-page "https://github.com/pappewaio/AllelicImbalance")
11309 (synopsis "Investigate allele-specific expression")
11311 "This package provides a framework for allele-specific expression
11312 investigation using RNA-seq data.")
11313 (license license:gpl3)))
11315 (define-public r-aucell
11322 (uri (bioconductor-uri "AUCell" version))
11325 "17wr7dycll0l1gax4w268qw7is163bs51rj6p1qnx1dgc9ibnsgr"))))
11326 (properties `((upstream-name . "AUCell")))
11327 (build-system r-build-system)
11329 (list r-biocgenerics
11332 r-delayedmatrixstats
11337 r-summarizedexperiment))
11340 (home-page "https://bioconductor.org/packages/AUCell/")
11341 (synopsis "Analysis of gene set activity in single-cell RNA-seq data")
11343 "AUCell identifies cells with active gene sets (e.g. signatures,
11344 gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area
11345 Under the Curve} (AUC) to calculate whether a critical subset of the input
11346 gene set is enriched within the expressed genes for each cell. The
11347 distribution of AUC scores across all the cells allows exploring the relative
11348 expression of the signature. Since the scoring method is ranking-based,
11349 AUCell is independent of the gene expression units and the normalization
11350 procedure. In addition, since the cells are evaluated individually, it can
11351 easily be applied to bigger datasets, subsetting the expression matrix if
11353 (license license:gpl3)))
11355 (define-public r-ebimage
11362 (uri (bioconductor-uri "EBImage" version))
11365 "1vcx45bw36k9daw9dywj5bz77jmqk4gjfwsym8ajjnc1jmlq20si"))))
11366 (properties `((upstream-name . "EBImage")))
11367 (build-system r-build-system)
11380 (list r-knitr)) ; for vignettes
11381 (home-page "https://github.com/aoles/EBImage")
11382 (synopsis "Image processing and analysis toolbox for R")
11384 "EBImage provides general purpose functionality for image processing and
11385 analysis. In the context of (high-throughput) microscopy-based cellular
11386 assays, EBImage offers tools to segment cells and extract quantitative
11387 cellular descriptors. This allows the automation of such tasks using the R
11388 programming language and facilitates the use of other tools in the R
11389 environment for signal processing, statistical modeling, machine learning and
11390 visualization with image data.")
11391 ;; Any version of the LGPL.
11392 (license license:lgpl2.1+)))
11394 (define-public r-yamss
11401 (uri (bioconductor-uri "yamss" version))
11404 "1lcfxw73cxvpy3bnq28pxdy5128mpq5xklsa0mzxdjyqc4g55hy8"))))
11405 (build-system r-build-system)
11407 (list r-biocgenerics
11415 r-summarizedexperiment))
11418 (home-page "https://github.com/hansenlab/yamss")
11419 (synopsis "Tools for high-throughput metabolomics")
11421 "This package provides tools to analyze and visualize high-throughput
11422 metabolomics data acquired using chromatography-mass spectrometry. These tools
11423 preprocess data in a way that enables reliable and powerful differential
11425 (license license:artistic2.0)))
11427 (define-public r-gtrellis
11429 (name "r-gtrellis")
11434 (uri (bioconductor-uri "gtrellis" version))
11437 "1s4xczzv6hz2kyv32xgcq84540w75qr3f644w1s4c3kwxgyq2gff"))))
11438 (build-system r-build-system)
11440 (list r-circlize r-genomicranges r-getoptlong r-iranges))
11443 (home-page "https://github.com/jokergoo/gtrellis")
11444 (synopsis "Genome level Trellis layout")
11446 "Genome level Trellis graph visualizes genomic data conditioned by
11447 genomic categories (e.g. chromosomes). For each genomic category, multiple
11448 dimensional data which are represented as tracks describe different features
11449 from different aspects. This package provides high flexibility to arrange
11450 genomic categories and to add self-defined graphics in the plot.")
11451 (license license:expat)))
11453 (define-public r-somaticsignatures
11455 (name "r-somaticsignatures")
11460 (uri (bioconductor-uri "SomaticSignatures" version))
11463 "1ydnp54laznzpi08s403kxhnr5nqhvm3iilaxlcdlz0ngxhm6vx6"))))
11465 `((upstream-name . "SomaticSignatures")))
11466 (build-system r-build-system)
11480 r-variantannotation))
11483 (home-page "https://github.com/juliangehring/SomaticSignatures")
11484 (synopsis "Somatic signatures")
11486 "This package identifies mutational signatures of @dfn{single nucleotide
11487 variants} (SNVs). It provides a infrastructure related to the methodology
11488 described in Nik-Zainal (2012, Cell), with flexibility in the matrix
11489 decomposition algorithms.")
11490 (license license:expat)))
11492 (define-public r-yapsa
11499 (uri (bioconductor-uri "YAPSA" version))
11502 "1klqfif4sadkxw7agywk2ncvcdqsnfb1d6adnacdfdasr8abvhid"))))
11503 (properties `((upstream-name . "YAPSA")))
11504 (build-system r-build-system)
11507 r-bsgenome-hsapiens-ucsc-hg19
11527 r-somaticsignatures
11528 r-variantannotation))
11531 (home-page "https://bioconductor.org/packages/YAPSA/")
11532 (synopsis "Yet another package for signature analysis")
11534 "This package provides functions and routines useful in the analysis of
11535 somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular,
11536 functions to perform a signature analysis with known signatures and a
11537 signature analysis on @dfn{stratified mutational catalogue} (SMC) are
11539 (license license:gpl3)))
11541 (define-public r-gcrma
11548 (uri (bioconductor-uri "gcrma" version))
11551 "13a8igr2b02gsa6n3437kb33wg6h7si82fmqi35dzpfzhvx0qf6d"))))
11552 (build-system r-build-system)
11560 (home-page "https://bioconductor.org/packages/gcrma/")
11561 (synopsis "Background adjustment using sequence information")
11563 "Gcrma adjusts for background intensities in Affymetrix array data which
11564 include optical noise and @dfn{non-specific binding} (NSB). The main function
11565 @code{gcrma} converts background adjusted probe intensities to expression
11566 measures using the same normalization and summarization methods as a
11567 @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information
11568 to estimate probe affinity to NSB. The sequence information is summarized in
11569 a more complex way than the simple GC content. Instead, the base types (A, T,
11570 G or C) at each position along the probe determine the affinity of each probe.
11571 The parameters of the position-specific base contributions to the probe
11572 affinity is estimated in an NSB experiment in which only NSB but no
11573 gene-specific binding is expected.")
11574 ;; Any version of the LGPL
11575 (license license:lgpl2.1+)))
11577 (define-public r-simpleaffy
11579 (name "r-simpleaffy")
11584 (uri (bioconductor-uri "simpleaffy" version))
11587 "04a11dsqd5y4b39nny94acnh0qhdazjc6d1803izza4vrgmw2csb"))))
11588 (build-system r-build-system)
11590 (list r-affy r-biobase r-biocgenerics r-gcrma r-genefilter))
11591 (home-page "https://bioconductor.org/packages/simpleaffy/")
11592 (synopsis "Very simple high level analysis of Affymetrix data")
11594 "This package provides high level functions for reading Affy @file{.CEL}
11595 files, phenotypic data, and then computing simple things with it, such as
11596 t-tests, fold changes and the like. It makes heavy use of the @code{affy}
11597 library. It also has some basic scatter plot functions and mechanisms for
11598 generating high resolution journal figures.")
11599 (license license:gpl2+)))
11601 (define-public r-yaqcaffy
11603 (name "r-yaqcaffy")
11608 (uri (bioconductor-uri "yaqcaffy" version))
11611 "18gphcjj15iivrahp52186bvdg07yd2dvrykfjdd4r1vyf33im96"))))
11612 (build-system r-build-system)
11614 (list r-simpleaffy))
11615 (home-page "https://bioconductor.org/packages/yaqcaffy/")
11616 (synopsis "Affymetrix quality control and reproducibility analysis")
11618 "This is a package that can be used for quality control of Affymetrix
11619 GeneChip expression data and reproducibility analysis of human whole genome
11620 chips with the MAQC reference datasets.")
11621 (license license:artistic2.0)))
11623 (define-public r-quantro
11630 (uri (bioconductor-uri "quantro" version))
11633 "1zfrz7lxyrbf0c8d277npzj1h4six9whkqplvcjmn3li0xj5qng3"))))
11634 (build-system r-build-system)
11645 (home-page "https://bioconductor.org/packages/quantro/")
11646 (synopsis "Test for when to use quantile normalization")
11648 "This package provides a data-driven test for the assumptions of quantile
11649 normalization using raw data such as objects that inherit eSets (e.g.
11650 ExpressionSet, MethylSet). Group level information about each sample (such as
11651 Tumor / Normal status) must also be provided because the test assesses if
11652 there are global differences in the distributions between the user-defined
11654 (license license:gpl3+)))
11656 (define-public r-yarn
11663 (uri (bioconductor-uri "yarn" version))
11666 "0z5202pqq02fwm8qf1g36004k7sv668s1xacbpr1cvw5sl452lbg"))))
11667 (build-system r-build-system)
11682 (home-page "https://bioconductor.org/packages/yarn/")
11683 (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization")
11685 "Expedite large RNA-Seq analyses using a combination of previously
11686 developed tools. YARN is meant to make it easier for the user in performing
11687 basic mis-annotation quality control, filtering, and condition-aware
11688 normalization. YARN leverages many Bioconductor tools and statistical
11689 techniques to account for the large heterogeneity and sparsity found in very
11690 large RNA-seq experiments.")
11691 (license license:artistic2.0)))
11693 (define-public r-roar
11700 (uri (bioconductor-uri "roar" version))
11703 "0zq1praf5h9294cvmrb06l3chx8v40xw2sfvhlnh1516x9sjkwfc"))))
11704 (build-system r-build-system)
11706 (list r-biocgenerics
11708 r-genomicalignments
11713 r-summarizedexperiment))
11714 (home-page "https://github.com/vodkatad/roar/")
11715 (synopsis "Identify differential APA usage from RNA-seq alignments")
11717 "This package provides tools for identifying preferential usage of APA
11718 sites, comparing two biological conditions, starting from known alternative
11719 sites and alignments obtained from standard RNA-seq experiments.")
11720 (license license:gpl3)))
11722 (define-public r-xbseq
11729 (uri (bioconductor-uri "XBSeq" version))
11732 "1dvk2jpsdynqw5071z54yd5j0ddprhc1ppk834cz9liibd72d7vz"))))
11733 (properties `((upstream-name . "XBSeq")))
11734 (build-system r-build-system)
11747 (home-page "https://github.com/Liuy12/XBSeq")
11748 (synopsis "Test for differential expression for RNA-seq data")
11750 "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential
11751 expression} (DE), where a statistical model was established based on the
11752 assumption that observed signals are the convolution of true expression
11753 signals and sequencing noises. The mapped reads in non-exonic regions are
11754 considered as sequencing noises, which follows a Poisson distribution. Given
11755 measurable observed signal and background noise from RNA-seq data, true
11756 expression signals, assuming governed by the negative binomial distribution,
11757 can be delineated and thus the accurate detection of differential expressed
11759 (license license:gpl3+)))
11761 (define-public r-massspecwavelet
11763 (name "r-massspecwavelet")
11768 (uri (bioconductor-uri "MassSpecWavelet" version))
11771 "0g9izdy3f7h1zmsfbq45ahdz0ak5013rp3vxc4ijb1mpqx8ldd39"))))
11773 `((upstream-name . "MassSpecWavelet")))
11774 (build-system r-build-system)
11777 (home-page "https://bioconductor.org/packages/MassSpecWavelet/")
11778 (synopsis "Mass spectrum processing by wavelet-based algorithms")
11780 "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS)
11781 data mainly through the use of wavelet transforms. It supports peak detection
11782 based on @dfn{Continuous Wavelet Transform} (CWT).")
11783 (license license:lgpl2.0+)))
11785 (define-public r-xcms
11792 (uri (bioconductor-uri "xcms" version))
11795 "0p2zd2728lj5q8y24gdfvsjijd6zl2i73hrcf017n32jq7vn71xm"))))
11796 (build-system r-build-system)
11814 r-summarizedexperiment))
11817 (home-page "https://bioconductor.org/packages/xcms/")
11818 (synopsis "LC/MS and GC/MS mass spectrometry data analysis")
11820 "This package provides a framework for processing and visualization of
11821 chromatographically separated and single-spectra mass spectral data. It
11822 imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses
11823 data for high-throughput, untargeted analyte profiling.")
11824 (license license:gpl2+)))
11826 (define-public r-wppi
11832 (uri (bioconductor-uri "wppi" version))
11835 "1008s39bb7sd261cy1vfgdah7bmhfw9qq322fh7g4wvpfw63ii9f"))))
11836 (properties `((upstream-name . "wppi")))
11837 (build-system r-build-system)
11838 ;; This is necessary because omnipathr attempts to write a configuration
11842 (modify-phases %standard-phases
11843 (add-after 'unpack 'set-HOME
11844 (lambda _ (setenv "HOME" "/tmp"))))))
11845 (propagated-inputs (list r-dplyr
11857 (native-inputs (list r-knitr))
11858 (home-page "https://github.com/AnaGalhoz37/wppi")
11859 (synopsis "Weighting protein-protein interactions")
11861 "This package predicts functional relevance of protein-protein
11862 interactions based on functional annotations such as Human Protein Ontology
11863 and Gene Ontology, and prioritizes genes based on network topology, functional
11864 scores and a path search algorithm.")
11865 (license license:expat)))
11867 (define-public r-wrench
11874 (uri (bioconductor-uri "Wrench" version))
11877 "1zx65s4m71wj85s2sq8ip54pq12r4sxfv8b2rxc41gfc5aj0zzca"))))
11878 (properties `((upstream-name . "Wrench")))
11879 (build-system r-build-system)
11881 (list r-limma r-locfit r-matrixstats))
11884 (home-page "https://github.com/HCBravoLab/Wrench")
11885 (synopsis "Wrench normalization for sparse count data")
11887 "Wrench is a package for normalization sparse genomic count data, like
11888 that arising from 16s metagenomic surveys.")
11889 (license license:artistic2.0)))
11891 (define-public r-wiggleplotr
11893 (name "r-wiggleplotr")
11898 (uri (bioconductor-uri "wiggleplotr" version))
11901 "0s128mm5w8n072k6j0fv1mxnxjpwisjp5lpz8a9z96cnn69bnr0i"))))
11902 (build-system r-build-system)
11916 (home-page "https://bioconductor.org/packages/wiggleplotr/")
11917 (synopsis "Make read coverage plots from BigWig files")
11919 "This package provides tools to visualize read coverage from sequencing
11920 experiments together with genomic annotations (genes, transcripts, peaks).
11921 Introns of long transcripts can be rescaled to a fixed length for better
11922 visualization of exonic read coverage.")
11923 (license license:asl2.0)))
11925 (define-public r-widgettools
11927 (name "r-widgettools")
11932 (uri (bioconductor-uri "widgetTools" version))
11935 "10w1s5h4za6ibmphvj145ir3lp22qgah2z8fvmipmf8ciq1jf86d"))))
11936 (properties `((upstream-name . "widgetTools")))
11937 (build-system r-build-system)
11938 (home-page "https://bioconductor.org/packages/widgetTools/")
11939 (synopsis "Tools for creating interactive tcltk widgets")
11941 "This package contains tools to support the construction of tcltk
11943 ;; Any version of the LGPL.
11944 (license license:lgpl3+)))
11946 (define-public r-webbioc
11953 (uri (bioconductor-uri "webbioc" version))
11956 "1g3srxsa2fqcn3r4wz4y19fwjmw3vawlcvdw6lbjdnvbgcafq1ah"))))
11957 (build-system r-build-system)
11959 (list netpbm perl))
11969 (home-page "https://www.bioconductor.org/")
11970 (synopsis "Bioconductor web interface")
11972 "This package provides an integrated web interface for doing microarray
11973 analysis using several of the Bioconductor packages. It is intended to be
11974 deployed as a centralized bioinformatics resource for use by many users.
11975 Currently only Affymetrix oligonucleotide analysis is supported.")
11976 (license license:gpl2+)))
11978 (define-public r-zinbwave
11980 (name "r-zinbwave")
11985 (uri (bioconductor-uri "zinbwave" version))
11988 "0vpz721sciw5b4ypxj5lj8p53gwkpfwlwkn6k3y8i65zg80p1g6i"))))
11989 (build-system r-build-system)
11991 (list r-biocparallel
11995 r-singlecellexperiment
11997 r-summarizedexperiment))
12000 (home-page "https://bioconductor.org/packages/zinbwave")
12001 (synopsis "Zero-inflated negative binomial model for RNA-seq data")
12002 (description "This package implements a general and flexible zero-inflated
12003 negative binomial model that can be used to provide a low-dimensional
12004 representations of single-cell RNA-seq data. The model accounts for zero
12005 inflation (dropouts), over-dispersion, and the count nature of the data.
12006 The model also accounts for the difference in library sizes and optionally
12007 for batch effects and/or other covariates, avoiding the need for pre-normalize
12009 (license license:artistic2.0)))
12011 (define-public r-zfpkm
12018 (uri (bioconductor-uri "zFPKM" version))
12021 "1h7g553rgb5mkmmsp8dyqqs9n9x17xmmcg3iijhb54nyrr2j1mji"))))
12022 (properties `((upstream-name . "zFPKM")))
12023 (build-system r-build-system)
12025 (list r-checkmate r-dplyr r-ggplot2 r-summarizedexperiment r-tidyr))
12028 (home-page "https://github.com/ronammar/zFPKM/")
12029 (synopsis "Functions to facilitate zFPKM transformations")
12031 "This is a package to perform the zFPKM transform on RNA-seq FPKM data.
12032 This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
12034 (license license:gpl3)))
12036 (define-public r-rbowtie2
12038 (name "r-rbowtie2")
12043 (uri (bioconductor-uri "Rbowtie2" version))
12046 "0dhdx27vrkhd4fak0qb5q9amlcpi97xhf3ry39zk0ifx5zpjynkg"))))
12047 (properties `((upstream-name . "Rbowtie2")))
12048 (build-system r-build-system)
12050 (list r-magrittr r-rsamtools))
12052 (list samtools zlib))
12055 (home-page "https://bioconductor.org/packages/Rbowtie2/")
12056 (synopsis "R wrapper for Bowtie2 and AdapterRemoval")
12058 "This package provides an R wrapper of the popular @code{bowtie2}
12059 sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for
12060 rapid adapter trimming, identification, and read merging.")
12061 (license license:gpl3+)))
12063 (define-public r-progeny
12070 (uri (bioconductor-uri "progeny" version))
12073 "1rhy2l2yf9ndxlvff8756s6n8qyi42nz7a75lgygj5aqqckkj21b"))))
12074 (build-system r-build-system)
12086 (home-page "https://github.com/saezlab/progeny")
12087 (synopsis "Pathway responsive gene activity inference")
12089 "This package provides a function to infer pathway activity from gene
12090 expression. It contains the linear model inferred in the publication
12091 \"Perturbation-response genes reveal signaling footprints in cancer gene
12093 (license license:asl2.0)))
12095 (define-public r-arrmnormalization
12097 (name "r-arrmnormalization")
12102 (uri (bioconductor-uri "ARRmNormalization" version))
12105 "1pnvw8psbql787m8lrmhd9xbmgkc3dbc70yfds1aggv50dk3yjk1"))))
12107 `((upstream-name . "ARRmNormalization")))
12108 (build-system r-build-system)
12109 (propagated-inputs (list r-arrmdata))
12110 (home-page "https://bioconductor.org/packages/ARRmNormalization/")
12111 (synopsis "Adaptive robust regression normalization for methylation data")
12113 "This is a package to perform the @dfn{Adaptive Robust Regression
12114 method} (ARRm) for the normalization of methylation data from the Illumina
12115 Infinium HumanMethylation 450k assay.")
12116 (license license:artistic2.0)))
12118 (define-public r-biocfilecache
12120 (name "r-biocfilecache")
12125 (uri (bioconductor-uri "BiocFileCache" version))
12128 "1bdbmlixrd8wvs25nmzdksq5hwnsxf8b6ds9qwx01h284vky5vsw"))))
12129 (properties `((upstream-name . "BiocFileCache")))
12130 (build-system r-build-system)
12142 (home-page "https://bioconductor.org/packages/BiocFileCache/")
12143 (synopsis "Manage files across sessions")
12145 "This package creates a persistent on-disk cache of files that the user
12146 can add, update, and retrieve. It is useful for managing resources (such as
12147 custom Txdb objects) that are costly or difficult to create, web resources,
12148 and data files used across sessions.")
12149 (license license:artistic2.0)))
12151 (define-public r-iclusterplus
12153 (name "r-iclusterplus")
12158 (uri (bioconductor-uri "iClusterPlus" version))
12161 "0xzx3vly3p99zc5a69pra4jjp8d3bdhx7dl1l76w459cs58zy0sm"))))
12162 (properties `((upstream-name . "iClusterPlus")))
12163 (build-system r-build-system)
12164 (native-inputs (list gfortran))
12165 (home-page "https://bioconductor.org/packages/iClusterPlus/")
12166 (synopsis "Integrative clustering of multi-type genomic data")
12168 "iClusterPlus is developed for integrative clustering analysis of
12169 multi-type genomic data and is an enhanced version of iCluster proposed and
12170 developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise
12171 from the experiments where biological samples (e.g. tumor samples) are
12172 analyzed by multiple techniques, for instance, @dfn{array comparative genomic
12173 hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so
12174 on. In the iClusterPlus model, binary observations such as somatic mutation
12175 are modeled as Binomial processes; categorical observations such as copy
12176 number states are realizations of Multinomial random variables; counts are
12177 modeled as Poisson random processes; and continuous measures are modeled by
12178 Gaussian distributions.")
12179 (license license:gpl2+)))
12181 (define-public r-rbowtie
12188 (uri (bioconductor-uri "Rbowtie" version))
12191 "1ya1irwshsyy9l1fj51b04nv1ahq7a47ck7q19h2cly6yskc4x1q"))))
12192 (properties `((upstream-name . "Rbowtie")))
12193 (build-system r-build-system)
12196 ;; Disable unsupported `popcnt' instructions on
12197 ;; architectures other than x86_64
12198 ,(if (string-prefix? "x86_64"
12199 (or (%current-target-system)
12200 (%current-system)))
12202 '(modify-phases %standard-phases
12203 (add-after 'unpack 'patch-sources
12205 (setenv "POPCNT_CAPABILITY" "0")))))))
12206 (inputs (list zlib))
12209 (home-page "https://bioconductor.org/packages/Rbowtie/")
12210 (synopsis "R bowtie wrapper")
12212 "This package provides an R wrapper around the popular bowtie short read
12213 aligner and around SpliceMap, a de novo splice junction discovery and
12215 (license license:artistic2.0)))
12217 (define-public r-sgseq
12224 (uri (bioconductor-uri "SGSeq" version))
12227 "0hz45367i70wl97silnimicdvs3g41zyf8syc6igz6471wbwkxwp"))))
12228 (properties `((upstream-name . "SGSeq")))
12229 (build-system r-build-system)
12231 (list r-annotationdbi
12235 r-genomicalignments
12244 r-summarizedexperiment))
12247 (home-page "https://bioconductor.org/packages/SGSeq/")
12248 (synopsis "Splice event prediction and quantification from RNA-seq data")
12250 "SGSeq is a package for analyzing splice events from RNA-seq data. Input
12251 data are RNA-seq reads mapped to a reference genome in BAM format. Genes are
12252 represented as a splice graph, which can be obtained from existing annotation
12253 or predicted from the mapped sequence reads. Splice events are identified
12254 from the graph and are quantified locally using structurally compatible reads
12255 at the start or end of each splice variant. The software includes functions
12256 for splice event prediction, quantification, visualization and
12258 (license license:artistic2.0)))
12260 (define-public r-rhisat2
12267 (uri (bioconductor-uri "Rhisat2" version))
12270 "0hzair41l47kzykymd169a34pfhb98vrjgkgdf15m17csyz7pnv7"))))
12271 (properties `((upstream-name . "Rhisat2")))
12272 (build-system r-build-system)
12275 (modify-phases %standard-phases
12276 (add-after 'unpack 'make-reproducible
12278 (substitute* "src/Makefile"
12279 (("`hostname`") "guix")
12281 ;; Avoid shelling out to "which".
12282 (("^CC =.*") (which "gcc"))
12283 (("^CPP =.*") (which "g++")))
12286 (list r-genomicfeatures r-genomicranges r-sgseq))
12289 (home-page "https://github.com/fmicompbio/Rhisat2")
12290 (synopsis "R Wrapper for HISAT2 sequence aligner")
12292 "This package provides an R interface to the HISAT2 spliced short-read
12293 aligner by Kim et al. (2015). The package contains wrapper functions to
12294 create a genome index and to perform the read alignment to the generated
12296 (license license:gpl3)))
12298 (define-public r-quasr
12305 (uri (bioconductor-uri "QuasR" version))
12308 "1m0c0rdakkdn4rr6dh51c6rs40cbxkvz93n6s0m2kc6fqjv9zplf"))))
12309 (properties `((upstream-name . "QuasR")))
12310 (build-system r-build-system)
12312 (list r-annotationdbi
12331 (home-page "https://bioconductor.org/packages/QuasR/")
12332 (synopsis "Quantify and annotate short reads in R")
12334 "This package provides a framework for the quantification and analysis of
12335 short genomic reads. It covers a complete workflow starting from raw sequence
12336 reads, over creation of alignments and quality control plots, to the
12337 quantification of genomic regions of interest.")
12338 (license license:gpl2)))
12340 (define-public r-rqc
12347 (uri (bioconductor-uri "Rqc" version))
12350 "11j8m69zdcmpjb3xzr4s8sqmv8aqgl8q7k81gnd09l3nyjzy0h1k"))))
12351 (properties `((upstream-name . "Rqc")))
12352 (build-system r-build-system)
12354 (list r-biocgenerics
12359 r-genomicalignments
12374 (home-page "https://github.com/labbcb/Rqc")
12375 (synopsis "Quality control tool for high-throughput sequencing data")
12377 "Rqc is an optimized tool designed for quality control and assessment of
12378 high-throughput sequencing data. It performs parallel processing of entire
12379 files and produces a report which contains a set of high-resolution
12381 (license license:gpl2+)))
12383 (define-public r-birewire
12385 (name "r-birewire")
12390 (uri (bioconductor-uri "BiRewire" version))
12393 "0r3i7n45qgj8wzdsx8wmfk0lc4xbcvxvmfziiqzig7r706q2c2hm"))))
12394 (properties `((upstream-name . "BiRewire")))
12395 (build-system r-build-system)
12397 (list r-igraph r-matrix r-rtsne r-slam))
12398 (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html")
12399 (synopsis "Tools for randomization of bipartite graphs")
12401 "This package provides functions for bipartite network rewiring through N
12402 consecutive switching steps and for the computation of the minimal number of
12403 switching steps to be performed in order to maximise the dissimilarity with
12404 respect to the original network. It includes functions for the analysis of
12405 the introduced randomness across the switching steps and several other
12406 routines to analyse the resulting networks and their natural projections.")
12407 (license license:gpl3)))
12409 (define-public r-birta
12416 (uri (bioconductor-uri "birta" version))
12419 "00a1kcfmcgdbx6wpnhk45wm45bynhry5m93l9hm75j2rwyc4lnca"))))
12420 (build-system r-build-system)
12422 (list r-biobase r-limma r-mass))
12423 (home-page "https://bioconductor.org/packages/birta")
12424 (synopsis "Bayesian inference of regulation of transcriptional activity")
12426 "Expression levels of mRNA molecules are regulated by different
12427 processes, comprising inhibition or activation by transcription factors and
12428 post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian
12429 Inference of Regulation of Transcriptional Activity) uses the regulatory
12430 networks of transcription factors and miRNAs together with mRNA and miRNA
12431 expression data to predict switches in regulatory activity between two
12432 conditions. A Bayesian network is used to model the regulatory structure and
12433 Markov-Chain-Monte-Carlo is applied to sample the activity states.")
12434 (license license:gpl2+)))
12436 (define-public r-multidataset
12438 (name "r-multidataset")
12443 (uri (bioconductor-uri "MultiDataSet" version))
12446 "0rfs6jkzh1i4mj1pgfk4lwzmcl8pcwizra3q3282x3d8h2g98qnf"))))
12447 (properties `((upstream-name . "MultiDataSet")))
12448 (build-system r-build-system)
12459 r-summarizedexperiment))
12462 (home-page "https://bioconductor.org/packages/MultiDataSet/")
12463 (synopsis "Implementation of MultiDataSet and ResultSet")
12465 "This package provides an implementation of the BRGE's (Bioinformatic
12466 Research Group in Epidemiology from Center for Research in Environmental
12467 Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for
12468 integrating multi omics data sets and ResultSet is a container for omics
12469 results. This package contains base classes for MEAL and rexposome
12471 (license license:expat)))
12473 (define-public r-ropls
12480 (uri (bioconductor-uri "ropls" version))
12483 "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c"))))
12484 (build-system r-build-system)
12487 r-multiassayexperiment
12489 r-summarizedexperiment))
12491 (list r-knitr)) ; for vignettes
12492 (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354")
12493 (synopsis "Multivariate analysis and feature selection of omics data")
12495 "Latent variable modeling with @dfn{Principal Component Analysis} (PCA)
12496 and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization,
12497 regression, classification, and feature selection of omics data where the
12498 number of variables exceeds the number of samples and with multicollinearity
12499 among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to
12500 separately model the variation correlated (predictive) to the factor of
12501 interest and the uncorrelated (orthogonal) variation. While performing
12502 similarly to PLS, OPLS facilitates interpretation.
12504 This package provides imlementations of PCA, PLS, and OPLS for multivariate
12505 analysis and feature selection of omics data. In addition to scores, loadings
12506 and weights plots, the package provides metrics and graphics to determine the
12507 optimal number of components (e.g. with the R2 and Q2 coefficients), check the
12508 validity of the model by permutation testing, detect outliers, and perform
12509 feature selection (e.g. with Variable Importance in Projection or regression
12511 (license license:cecill)))
12513 (define-public r-biosigner
12515 (name "r-biosigner")
12520 (uri (bioconductor-uri "biosigner" version))
12523 "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m"))))
12524 (build-system r-build-system)
12528 r-multiassayexperiment
12532 r-summarizedexperiment))
12535 (home-page "https://bioconductor.org/packages/biosigner/")
12536 (synopsis "Signature discovery from omics data")
12538 "Feature selection is critical in omics data analysis to extract
12539 restricted and meaningful molecular signatures from complex and high-dimension
12540 data, and to build robust classifiers. This package implements a method to
12541 assess the relevance of the variables for the prediction performances of the
12542 classifier. The approach can be run in parallel with the PLS-DA, Random
12543 Forest, and SVM binary classifiers. The signatures and the corresponding
12544 'restricted' models are returned, enabling future predictions on new
12546 (license license:cecill)))
12548 (define-public r-annotatr
12550 (name "r-annotatr")
12555 (uri (bioconductor-uri "annotatr" version))
12558 "1fbax9v3d486c8lwf3yfjbf4w7zf53wmdpxk2clwm8ngm7w0pqm0"))))
12559 (build-system r-build-system)
12561 (list r-annotationdbi
12576 (home-page "https://bioconductor.org/packages/annotatr/")
12577 (synopsis "Annotation of genomic regions to genomic annotations")
12579 "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs,
12580 differentially methylated CpGs or regions, SNPs, etc.) it is often of interest
12581 to investigate the intersecting genomic annotations. Such annotations include
12582 those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs),
12583 CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as
12584 enhancers. The annotatr package provides an easy way to summarize and
12585 visualize the intersection of genomic sites/regions with genomic
12587 (license license:gpl3)))
12589 (define-public r-rsubread
12591 (name "r-rsubread")
12596 (uri (bioconductor-uri "Rsubread" version))
12599 "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2"))))
12600 (properties `((upstream-name . "Rsubread")))
12601 (build-system r-build-system)
12602 (inputs (list zlib))
12605 (home-page "https://bioconductor.org/packages/Rsubread/")
12606 (synopsis "Subread sequence alignment and counting for R")
12608 "This package provides tools for alignment, quantification and analysis
12609 of second and third generation sequencing data. It includes functionality for
12610 read mapping, read counting, SNP calling, structural variant detection and
12611 gene fusion discovery. It can be applied to all major sequencing techologies
12612 and to both short and long sequence reads.")
12613 (license license:gpl3)))
12615 (define-public r-flowutils
12617 (name "r-flowutils")
12622 (uri (bioconductor-uri "flowUtils" version))
12625 "11x362dqb9mjlsbq6g1qkb8hhnkvm22z5s3wkgmpyy9kyifjkm26"))))
12626 (properties `((upstream-name . "flowUtils")))
12627 (build-system r-build-system)
12635 (home-page "https://github.com/jspidlen/flowUtils")
12636 (synopsis "Utilities for flow cytometry")
12638 "This package provides utilities for flow cytometry data.")
12639 (license license:artistic2.0)))
12641 (define-public r-consensusclusterplus
12643 (name "r-consensusclusterplus")
12648 (uri (bioconductor-uri "ConsensusClusterPlus" version))
12651 "1021cix4mr9qsafskw4kk1l3wdzx9pk2gcwjifz6f4zqxss9v07p"))))
12653 `((upstream-name . "ConsensusClusterPlus")))
12654 (build-system r-build-system)
12656 (list r-all r-biobase r-cluster))
12657 (home-page "https://bioconductor.org/packages/ConsensusClusterPlus")
12658 (synopsis "Clustering algorithm")
12660 "This package provides an implementation of an algorithm for determining
12661 cluster count and membership by stability evidence in unsupervised analysis.")
12662 (license license:gpl2)))
12664 ;; This is the latest commit and it solves a bug from the latest release.
12665 (define-public r-cycombine
12666 (let ((commit "f18504bc83ff5daee2b5eb4b28f09abdaaa66698") (revision "1"))
12668 (name "r-cycombine")
12669 (version (git-version "0.2.6" revision commit))
12672 (uri (git-reference
12673 (url "https://github.com/biosurf/cyCombine")
12675 (file-name (git-file-name name version))
12678 "1fiwnik8iahg01732fik85xhz359x32f1xc59h443pdf7jancskm"))))
12679 (properties `((upstream-name . "cyCombine")))
12680 (build-system r-build-system)
12698 (native-inputs (list r-knitr))
12699 (home-page "https://github.com/biosurf/cyCombine")
12700 (synopsis "Integration of single-cell cytometry datasets")
12702 "This package provides a method for combining single-cell cytometry
12703 datasets, which increases the analytical flexibility and the statistical power
12704 of the analyses while minimizing technical noise.")
12705 (license license:expat))))
12707 (define-public r-cytolib
12714 (uri (bioconductor-uri "cytolib" version))
12717 "18b532sicca5l8sn334prrm7g1z1cakiwydccz4i833168pnsjyg"))))
12718 (properties `((upstream-name . "cytolib")))
12719 (build-system r-build-system)
12729 (home-page "https://bioconductor.org/packages/cytolib/")
12730 (synopsis "C++ infrastructure for working with gated cytometry")
12732 "This package provides the core data structure and API to represent and
12733 interact with gated cytometry data.")
12734 (license license:artistic2.0)))
12736 (define-public r-flowcore
12738 (name "r-flowcore")
12743 (uri (bioconductor-uri "flowCore" version))
12746 "17nci6rc4i0vs0ibw5q8zy30ap7q4550qpq4ifkbblqbyzxlzkhr"))))
12747 (properties `((upstream-name . "flowCore")))
12748 (build-system r-build-system)
12761 (home-page "https://bioconductor.org/packages/flowCore")
12762 (synopsis "Basic structures for flow cytometry data")
12764 "This package provides S4 data structures and basic functions to deal
12765 with flow cytometry data.")
12766 (license license:artistic2.0)))
12768 (define-public r-flowmeans
12770 (name "r-flowmeans")
12775 (uri (bioconductor-uri "flowMeans" version))
12778 "1n4li43ydwwf5gvgmdml4ba28cxymybg5wnz6jvp35n959fwxv6y"))))
12779 (properties `((upstream-name . "flowMeans")))
12780 (build-system r-build-system)
12782 (list r-biobase r-feature r-flowcore r-rrcov))
12783 (home-page "https://bioconductor.org/packages/flowMeans")
12784 (synopsis "Non-parametric flow cytometry data gating")
12786 "This package provides tools to identify cell populations in Flow
12787 Cytometry data using non-parametric clustering and segmented-regression-based
12788 change point detection.")
12789 (license license:artistic2.0)))
12791 (define-public r-ncdfflow
12793 (name "r-ncdfflow")
12798 (uri (bioconductor-uri "ncdfFlow" version))
12801 "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7"))))
12802 (properties `((upstream-name . "ncdfFlow")))
12803 (build-system r-build-system)
12815 (home-page "https://bioconductor.org/packages/ncdfFlow/")
12816 (synopsis "HDF5 based storage for flow cytometry data")
12818 "This package provides HDF5 storage based methods and functions for
12819 manipulation of flow cytometry data.")
12820 (license license:artistic2.0)))
12822 (define-public r-ggcyto
12829 (uri (bioconductor-uri "ggcyto" version))
12832 "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325"))))
12833 (properties `((upstream-name . "ggcyto")))
12834 (build-system r-build-system)
12849 (home-page "https://github.com/RGLab/ggcyto/issues")
12850 (synopsis "Visualize Cytometry data with ggplot")
12852 "With the dedicated fortify method implemented for @code{flowSet},
12853 @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow
12854 cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper
12855 and some custom layers also make it easy to add gates and population
12856 statistics to the plot.")
12857 (license license:artistic2.0)))
12859 (define-public r-flowviz
12866 (uri (bioconductor-uri "flowViz" version))
12869 "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95"))))
12870 (properties `((upstream-name . "flowViz")))
12871 (build-system r-build-system)
12884 (home-page "https://bioconductor.org/packages/flowViz/")
12885 (synopsis "Visualization for flow cytometry")
12887 "This package provides visualization tools for flow cytometry data.")
12888 (license license:artistic2.0)))
12890 (define-public r-flowclust
12892 (name "r-flowclust")
12897 (uri (bioconductor-uri "flowClust" version))
12900 "055vm9s8aha92znhpjqkipzprw8bkrinwjaik4ygmhym7w6vbblk"))))
12901 (properties `((upstream-name . "flowClust")))
12902 (build-system r-build-system)
12904 `(#:configure-flags
12905 (list "--configure-args=--enable-bundled-gsl=no")))
12914 (list pkg-config r-knitr))
12915 (home-page "https://bioconductor.org/packages/flowClust")
12916 (synopsis "Clustering for flow cytometry")
12918 "This package provides robust model-based clustering using a t-mixture
12919 model with Box-Cox transformation.")
12920 (license license:artistic2.0)))
12922 ;; TODO: this package bundles an old version of protobuf. It's not easy to
12923 ;; make it use our protobuf package instead.
12924 (define-public r-rprotobuflib
12926 (name "r-rprotobuflib")
12931 (uri (bioconductor-uri "RProtoBufLib" version))
12934 "1mvqwrm1y0vij66gdwgpf5l1h660wsi9jzjfs4ihw3zm4cb0q5pp"))))
12935 (properties `((upstream-name . "RProtoBufLib")))
12936 (build-system r-build-system)
12939 (modify-phases %standard-phases
12940 (add-after 'unpack 'unpack-bundled-sources
12942 (with-directory-excursion "src"
12943 (invoke "tar" "xf" "protobuf-3.8.0.tar.gz")))))))
12946 (home-page "https://bioconductor.org/packages/RProtoBufLib/")
12947 (synopsis "C++ headers and static libraries of Protocol buffers")
12949 "This package provides the headers and static library of Protocol buffers
12950 for other R packages to compile and link against.")
12951 (license license:bsd-3)))
12953 (define-public r-flowworkspace
12955 (name "r-flowworkspace")
12960 (uri (bioconductor-uri "flowWorkspace" version))
12963 "0riyi9628cx1j5x6hmdd28yq75xh25j8ckcdz8dnb94dpvnhaqss"))))
12964 (properties `((upstream-name . "flowWorkspace")))
12965 (build-system r-build-system)
12996 (home-page "https://bioconductor.org/packages/flowWorkspace/")
12997 (synopsis "Infrastructure for working with cytometry data")
12999 "This package is designed to facilitate comparison of automated gating
13000 methods against manual gating done in flowJo. This package allows you to
13001 import basic flowJo workspaces into BioConductor and replicate the gating from
13002 flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of
13003 samples, compensation, and transformation are performed so that the output
13004 matches the flowJo analysis.")
13005 (license license:artistic2.0)))
13007 (define-public r-flowstats
13009 (name "r-flowstats")
13014 (uri (bioconductor-uri "flowStats" version))
13017 "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc"))))
13018 (properties `((upstream-name . "flowStats")))
13019 (build-system r-build-system)
13037 (home-page "http://www.github.com/RGLab/flowStats")
13038 (synopsis "Statistical methods for the analysis of flow cytometry data")
13040 "This package provides methods and functionality to analyze flow data
13041 that is beyond the basic infrastructure provided by the @code{flowCore}
13043 (license license:artistic2.0)))
13045 (define-public r-opencyto
13047 (name "r-opencyto")
13052 (uri (bioconductor-uri "openCyto" version))
13055 "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0"))))
13056 (properties `((upstream-name . "openCyto")))
13057 (build-system r-build-system)
13082 (home-page "https://bioconductor.org/packages/openCyto")
13083 (synopsis "Hierarchical gating pipeline for flow cytometry data")
13085 "This package is designed to facilitate the automated gating methods in a
13086 sequential way to mimic the manual gating strategy.")
13087 (license license:artistic2.0)))
13089 (define-public r-cytoml
13096 (uri (bioconductor-uri "CytoML" version))
13099 "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw"))))
13100 (properties `((upstream-name . "CytoML")))
13101 (build-system r-build-system)
13103 (list libxml2 zlib))
13134 (home-page "https://github.com/RGLab/CytoML")
13135 (synopsis "GatingML interface for cross platform cytometry data sharing")
13137 "This package provides an interface to implementations of the GatingML2.0
13138 standard to exchange gated cytometry data with other software platforms.")
13139 (license license:artistic2.0)))
13141 (define-public r-flowsom
13148 (uri (bioconductor-uri "FlowSOM" version))
13151 "0balsds5mm981cqamdjv3ndq1y9arharisd6f2lrpkzgvwawa645"))))
13152 (properties `((upstream-name . "FlowSOM")))
13153 (build-system r-build-system)
13155 (list r-biocgenerics
13157 r-consensusclusterplus
13177 (home-page "https://bioconductor.org/packages/FlowSOM/")
13178 (synopsis "Visualize and interpret cytometry data")
13180 "FlowSOM offers visualization options for cytometry data, by using
13181 self-organizing map clustering and minimal spanning trees.")
13182 (license license:gpl2+)))
13184 (define-public r-mixomics
13186 (name "r-mixomics")
13191 (uri (bioconductor-uri "mixOmics" version))
13194 "0fwc2w7frj0bjijzfckkxf7ipx1z13gw7907q4zr5qfl9mh127w7"))))
13195 (properties `((upstream-name . "mixOmics")))
13196 (build-system r-build-system)
13198 (list r-biocparallel
13215 (home-page "http://www.mixOmics.org")
13216 (synopsis "Multivariate methods for exploration of biological datasets")
13218 "mixOmics offers a wide range of multivariate methods for the exploration
13219 and integration of biological datasets with a particular focus on variable
13220 selection. The package proposes several sparse multivariate models we have
13221 developed to identify the key variables that are highly correlated, and/or
13222 explain the biological outcome of interest. The data that can be analysed
13223 with mixOmics may come from high throughput sequencing technologies, such as
13224 omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but
13225 also beyond the realm of omics (e.g. spectral imaging). The methods
13226 implemented in mixOmics can also handle missing values without having to
13227 delete entire rows with missing data.")
13228 (license license:gpl2+)))
13230 (define-public r-depecher
13231 (package ;Source/Weave error
13232 (name "r-depecher")
13237 (uri (bioconductor-uri "DepecheR" version))
13240 "0rixczdds5gpac50wap6s68kmpdj4208l38gcihkrysz5frbvqjp"))))
13241 (properties `((upstream-name . "DepecheR")))
13242 (build-system r-build-system)
13263 (home-page "https://bioconductor.org/packages/DepecheR/")
13264 (synopsis "Identify traits of clusters in high-dimensional entities")
13266 "The purpose of this package is to identify traits in a dataset that can
13267 separate groups. This is done on two levels. First, clustering is performed,
13268 using an implementation of sparse K-means. Secondly, the generated clusters
13269 are used to predict outcomes of groups of individuals based on their
13270 distribution of observations in the different clusters. As certain clusters
13271 with separating information will be identified, and these clusters are defined
13272 by a sparse number of variables, this method can reduce the complexity of
13273 data, to only emphasize the data that actually matters.")
13274 (license license:expat)))
13276 (define-public r-rcistarget
13278 (name "r-rcistarget")
13283 (uri (bioconductor-uri "RcisTarget" version))
13286 "17fnjkg6rjqj33v7slg81skqag10y6dc14g5iv69gqshjal4w4im"))))
13287 (properties `((upstream-name . "RcisTarget")))
13288 (build-system r-build-system)
13300 r-summarizedexperiment
13304 (home-page "https://aertslab.org/#scenic")
13305 (synopsis "Identify transcription factor binding motifs enriched on a gene list")
13307 "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS)
13308 over-represented on a gene list. In a first step, RcisTarget selects DNA
13309 motifs that are significantly over-represented in the surroundings of the
13310 @dfn{transcription start site} (TSS) of the genes in the gene-set. This is
13311 achieved by using a database that contains genome-wide cross-species rankings
13312 for each motif. The motifs that are then annotated to TFs and those that have
13313 a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for
13314 each motif and gene-set, RcisTarget predicts the candidate target genes (i.e.
13315 genes in the gene-set that are ranked above the leading edge).")
13316 (license license:gpl3)))
13318 (define-public r-chicago
13325 (uri (bioconductor-uri "Chicago" version))
13328 "13vzxmvxpc3r9gii37zvhhr5nbnaggrva97g6m2n02qn9daf6vmm"))))
13329 (properties `((upstream-name . "Chicago")))
13330 (build-system r-build-system)
13332 (list r-data-table r-delaporte r-hmisc r-mass r-matrixstats))
13333 (native-inputs (list r-knitr))
13334 (home-page "https://bioconductor.org/packages/Chicago")
13335 (synopsis "Capture Hi-C analysis of genomic organization")
13337 "This package provides a pipeline for analysing Capture Hi-C data.")
13338 (license license:artistic2.0)))
13340 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
13342 (define-public r-ciara
13348 (uri (cran-uri "CIARA" version))
13351 "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
13352 (properties `((upstream-name . "CIARA")))
13353 (build-system r-build-system)
13354 (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
13355 (native-inputs (list r-knitr))
13356 (home-page "https://cran.r-project.org/package=CIARA")
13357 (synopsis "Cluster-independent algorithm for rare cell types identification")
13359 "This is a package to support identification of markers of rare cell
13360 types by looking at genes whose expression is confined in small regions of the
13361 expression space.")
13362 (license license:artistic2.0)))
13364 (define-public r-cicero
13371 (uri (bioconductor-uri "cicero" version))
13374 "1ip12ijazlmcfbym078slxykpkz7d1zwvs8l8aqdnqpxjfk1ipx5"))))
13375 (build-system r-build-system)
13401 (home-page "https://bioconductor.org/packages/cicero/")
13402 (synopsis "Predict cis-co-accessibility from single-cell data")
13404 "Cicero computes putative cis-regulatory maps from single-cell chromatin
13405 accessibility data. It also extends the monocle package for use in chromatin
13406 accessibility data.")
13407 (license license:expat)))
13409 ;; This is the latest commit on the "monocle3" branch.
13410 (define-public r-cicero-monocle3
13411 (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b")
13413 (package (inherit r-cicero)
13414 (name "r-cicero-monocle3")
13415 (version (git-version "1.3.2" revision commit))
13419 (uri (git-reference
13420 (url "https://github.com/cole-trapnell-lab/cicero-release")
13422 (file-name (git-file-name name version))
13425 "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c"))))
13427 (modify-inputs (package-propagated-inputs r-cicero)
13428 (delete "r-monocle")
13429 (prepend r-monocle3))))))
13431 (define-public r-circrnaprofiler
13433 (name "r-circrnaprofiler")
13438 (uri (bioconductor-uri "circRNAprofiler" version))
13441 "1gwm416shhv2p3gh1n6kv1rvx0n0imy25b7z62z4s8b3gs3nfp5j"))))
13443 `((upstream-name . "circRNAprofiler")))
13444 (build-system r-build-system)
13446 (list r-annotationhub
13449 r-bsgenome-hsapiens-ucsc-hg19
13472 "https://github.com/Aufiero/circRNAprofiler")
13474 "Computational framework for the downstream analysis of circular RNA's")
13476 "@code{r-circrnaprofiler} is a computational framework for a comprehensive
13477 in silico analysis of @dfn{circular RNA} (circRNAs). This computational
13478 framework allows combining and analyzing circRNAs previously detected by
13479 multiple publicly available annotation-based circRNA detection tools. It
13480 covers different aspects of circRNAs analysis from differential expression
13481 analysis, evolutionary conservation, biogenesis to functional analysis.")
13482 (license license:gpl3)))
13484 (define-public r-cistopic
13486 (name "r-cistopic")
13491 (uri (git-reference
13492 (url "https://github.com/aertslab/cisTopic")
13493 (commit (string-append "v" version))))
13494 (file-name (git-file-name name version))
13497 "0c4553rnxq7b1w451kcc3iwvak4qa5h2b43xmfw6ii8096zd1gbf"))))
13498 (build-system r-build-system)
13515 (home-page "https://github.com/aertslab/cisTopic")
13516 (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
13518 "The sparse nature of single cell epigenomics data can be overruled using
13519 probabilistic modelling methods such as @dfn{Latent Dirichlet
13520 Allocation} (LDA). This package allows the probabilistic modelling of
13521 cis-regulatory topics (cisTopics) from single cell epigenomics data, and
13522 includes functionalities to identify cell states based on the contribution of
13523 cisTopics and explore the nature and regulatory proteins driving them.")
13524 (license license:gpl3)))
13526 (define-public r-cistopic-next
13527 (let ((commit "04cecbb9d1112fcc1a6edc28b5a506bcb49f2803")
13530 (inherit r-cistopic)
13531 (name "r-cistopic-next")
13532 ;; The DESCRIPTION file says this is version 0.3.0, which is a bit odd
13533 ;; since the previous release is 2.1.0. Oh well.
13534 (version (git-version "0.3.0" revision commit))
13538 (uri (git-reference
13539 (url "https://github.com/aertslab/cisTopic")
13541 (file-name (git-file-name name version))
13544 "11cg9szlysnsjiaahda4k5v2vh4rxx27zhz53hafgaq9mdz0kgi2"))))
13545 (properties `((upstream-name . "cisTopic")))
13566 (define-public r-genie3
13573 (uri (bioconductor-uri "GENIE3" version))
13576 "0h3vnpnznb9rda8gfwp4cnd2mqsvs1vzmfx90dchn5pqaphz1k2l"))))
13577 (properties `((upstream-name . "GENIE3")))
13578 (build-system r-build-system)
13580 (list r-dplyr r-reshape2))
13583 (home-page "https://bioconductor.org/packages/GENIE3")
13584 (synopsis "Gene network inference with ensemble of trees")
13586 "This package implements the GENIE3 algorithm for inferring gene
13587 regulatory networks from expression data.")
13588 (license license:gpl2+)))
13590 (define-public r-roc
13597 (uri (bioconductor-uri "ROC" version))
13600 "0yfq0d0j2bzqdnjs6l2h6p48kmv9wfphlqym3brgndlnadipq1v2"))))
13601 (properties `((upstream-name . "ROC")))
13602 (build-system r-build-system)
13605 (home-page "https://www.bioconductor.org/packages/ROC/")
13606 (synopsis "Utilities for ROC curves")
13608 "This package provides utilities for @dfn{Receiver Operating
13609 Characteristic} (ROC) curves, with a focus on micro arrays.")
13610 (license license:artistic2.0)))
13612 (define-public r-watermelon
13614 (name "r-watermelon")
13619 (uri (bioconductor-uri "wateRmelon" version))
13622 "0adqyfabrvfcaj3mwp0rbqlcgpj92yb205cyhibbrs5gdr5ri4pv"))))
13623 (properties `((upstream-name . "wateRmelon")))
13624 (build-system r-build-system)
13627 r-illuminahumanmethylation450kanno-ilmn12-hg19
13636 (home-page "https://bioconductor.org/packages/wateRmelon/")
13637 (synopsis "Illumina 450 methylation array normalization and metrics")
13639 "The standard index of DNA methylation (beta) is computed from methylated
13640 and unmethylated signal intensities. Betas calculated from raw signal
13641 intensities perform well, but using 11 methylomic datasets we demonstrate that
13642 quantile normalization methods produce marked improvement. The commonly used
13643 procedure of normalizing betas is inferior to the separate normalization of M
13644 and U, and it is also advantageous to normalize Type I and Type II assays
13645 separately. This package provides 15 flavours of betas and three performance
13646 metrics, with methods for objects produced by the @code{methylumi} and
13647 @code{minfi} packages.")
13648 (license license:gpl3)))
13650 (define-public r-gdsfmt
13657 (uri (bioconductor-uri "gdsfmt" version))
13660 "1cdwyivgfc6yw5hj9b3j57wx55gckwhx6fwx2lvqynrjzjyzf3q0"))
13661 (modules '((guix build utils)))
13662 ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build
13663 ;; them and link with system libraries instead.
13666 (for-each delete-file-recursively
13670 (substitute* "src/Makevars"
13671 (("all: \\$\\(SHLIB\\)") "all:")
13672 (("\\$\\(SHLIB\\): liblzma.a") "")
13673 (("^ (ZLIB|LZ4)/.*") "")
13674 (("CoreArray/dVLIntGDS.cpp.*")
13675 "CoreArray/dVLIntGDS.cpp")
13676 (("CoreArray/dVLIntGDS.o.*")
13677 "CoreArray/dVLIntGDS.o")
13678 (("PKG_LIBS = ./liblzma.a")
13679 "PKG_LIBS = -llz4"))
13680 (substitute* "src/CoreArray/dStream.h"
13681 (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
13682 (string-append "include <" header ">")))))))
13683 (properties `((upstream-name . "gdsfmt")))
13684 (build-system r-build-system)
13686 (list lz4 xz zlib))
13689 (home-page "http://corearray.sourceforge.net/")
13691 "R Interface to CoreArray Genomic Data Structure (GDS) Files")
13693 "This package provides a high-level R interface to CoreArray @dfn{Genomic
13694 Data Structure} (GDS) data files, which are portable across platforms with
13695 hierarchical structure to store multiple scalable array-oriented data sets
13696 with metadata information. It is suited for large-scale datasets, especially
13697 for data which are much larger than the available random-access memory. The
13698 @code{gdsfmt} package offers efficient operations specifically designed for
13699 integers of less than 8 bits, since a diploid genotype, like
13700 @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a
13701 byte. Data compression and decompression are available with relatively
13702 efficient random access. It is also allowed to read a GDS file in parallel
13703 with multiple R processes supported by the package @code{parallel}.")
13704 (license license:lgpl3)))
13706 (define-public r-bigmelon
13708 (name "r-bigmelon")
13713 (uri (bioconductor-uri "bigmelon" version))
13716 "1msch4qbifkdqv0bbw03xj6d9w28z91mf4ki41rqg6048cq17h2k"))))
13717 (properties `((upstream-name . "bigmelon")))
13718 (build-system r-build-system)
13730 (home-page "https://bioconductor.org/packages/bigmelon/")
13731 (synopsis "Illumina methylation array analysis for large experiments")
13733 "This package provides methods for working with Illumina arrays using the
13734 @code{gdsfmt} package.")
13735 (license license:gpl3)))
13737 (define-public r-seqbias
13744 (uri (bioconductor-uri "seqbias" version))
13747 "085nq6pf0bdn17wsbr5jnyy512v7rf67xff9rp5wz47mcifbv6rg"))))
13748 (properties `((upstream-name . "seqbias")))
13749 (build-system r-build-system)
13751 (list r-biostrings r-genomicranges r-rhtslib))
13752 (home-page "https://bioconductor.org/packages/seqbias/")
13753 (synopsis "Estimation of per-position bias in high-throughput sequencing data")
13755 "This package implements a model of per-position sequencing bias in
13756 high-throughput sequencing data using a simple Bayesian network, the structure
13757 and parameters of which are trained on a set of aligned reads and a reference
13759 (license license:lgpl3)))
13761 (define-public r-reqon
13768 (uri (bioconductor-uri "ReQON" version))
13771 "1f5pplm8fy3wvl0b6n18gph4dq9i9x5qiyjrj0bk0kwlkbpba74r"))))
13772 (properties `((upstream-name . "ReQON")))
13773 (build-system r-build-system)
13775 (list r-rjava r-rsamtools r-seqbias))
13776 (home-page "https://bioconductor.org/packages/ReQON/")
13777 (synopsis "Recalibrating quality of nucleotides")
13779 "This package provides an implementation of an algorithm for
13780 recalibrating the base quality scores for aligned sequencing data in BAM
13782 (license license:gpl2)))
13784 (define-public r-wavcluster
13786 (name "r-wavcluster")
13791 (uri (bioconductor-uri "wavClusteR" version))
13794 "04di095i9i19j9ppx8gdsk7n18vd02d4rjdi9d4a3p0xv05ihnb6"))))
13795 (properties `((upstream-name . "wavClusteR")))
13796 (build-system r-build-system)
13798 (list r-biocgenerics
13814 (home-page "https://bioconductor.org/packages/wavClusteR/")
13815 (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data")
13817 "This package provides an integrated pipeline for the analysis of
13818 PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from
13819 sequencing errors, SNPs and additional non-experimental sources by a non-
13820 parametric mixture model. The protein binding sites (clusters) are then
13821 resolved at high resolution and cluster statistics are estimated using a
13822 rigorous Bayesian framework. Post-processing of the results, data export for
13823 UCSC genome browser visualization and motif search analysis are provided. In
13824 addition, the package integrates RNA-Seq data to estimate the False
13825 Discovery Rate of cluster detection. Key functions support parallel multicore
13826 computing. While wavClusteR was designed for PAR-CLIP data analysis, it can
13827 be applied to the analysis of other NGS data obtained from experimental
13828 procedures that induce nucleotide substitutions (e.g. BisSeq).")
13829 (license license:gpl2)))
13831 (define-public r-timeseriesexperiment
13833 (name "r-timeseriesexperiment")
13838 (uri (bioconductor-uri "TimeSeriesExperiment" version))
13841 "0bdpxxr739qdg92qabfx122k9f43vw2hyxp4yxqlbp37vzgcdf2c"))))
13843 `((upstream-name . "TimeSeriesExperiment")))
13844 (build-system r-build-system)
13856 r-summarizedexperiment
13863 (home-page "https://github.com/nlhuong/TimeSeriesExperiment/")
13864 (synopsis "Analysis for short time-series data")
13866 "This package is a visualization and analysis toolbox for short time
13867 course data which includes dimensionality reduction, clustering, two-sample
13868 differential expression testing and gene ranking techniques. The package also
13869 provides methods for retrieving enriched pathways.")
13870 (license license:lgpl3+)))
13872 (define-public r-variantfiltering
13874 (name "r-variantfiltering")
13879 (uri (bioconductor-uri "VariantFiltering" version))
13882 "1bjqn8qik221x0bqvgd99p87v45iihwp6cxckh4ks964pd0c1xk8"))))
13884 `((upstream-name . "VariantFiltering")))
13885 (build-system r-build-system)
13887 (list r-annotationdbi
13908 r-summarizedexperiment
13909 r-variantannotation
13911 (home-page "https://github.com/rcastelo/VariantFiltering")
13912 (synopsis "Filtering of coding and non-coding genetic variants")
13914 "Filter genetic variants using different criteria such as inheritance
13915 model, amino acid change consequence, minor allele frequencies across human
13916 populations, splice site strength, conservation, etc.")
13917 (license license:artistic2.0)))
13919 (define-public r-genomegraphs
13921 (name "r-genomegraphs")
13926 (uri (bioconductor-uri "GenomeGraphs" version))
13929 "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags"))))
13930 (properties `((upstream-name . "GenomeGraphs")))
13931 (build-system r-build-system)
13934 (home-page "https://bioconductor.org/packages/GenomeGraphs/")
13935 (synopsis "Plotting genomic information from Ensembl")
13937 "Genomic data analyses requires integrated visualization of known genomic
13938 information and new experimental data. GenomeGraphs uses the biomaRt package
13939 to perform live annotation queries to Ensembl and translates this to e.g.
13940 gene/transcript structures in viewports of the grid graphics package. This
13941 results in genomic information plotted together with your data. Another
13942 strength of GenomeGraphs is to plot different data types such as array CGH,
13943 gene expression, sequencing and other data, together in one plot using the
13944 same genome coordinate system.")
13945 (license license:artistic2.0)))
13947 (define-public r-wavetiling
13949 (name "r-wavetiling")
13954 (uri (bioconductor-uri "waveTiling" version))
13957 "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf"))))
13958 (properties `((upstream-name . "waveTiling")))
13959 (build-system r-build-system)
13971 (home-page "https://r-forge.r-project.org/projects/wavetiling/")
13972 (synopsis "Wavelet-based models for tiling array transcriptome analysis")
13974 "This package is designed to conduct transcriptome analysis for tiling
13975 arrays based on fast wavelet-based functional models.")
13976 (license license:gpl2+)))
13978 (define-public r-variancepartition
13980 (name "r-variancepartition")
13985 (uri (bioconductor-uri "variancePartition" version))
13988 "0wk1xql8b0gxyrqz9hs54xvmp7qdw9b8jnv88p4vgv061iwyk7wv"))))
13990 `((upstream-name . "variancePartition")))
13991 (build-system r-build-system)
14015 (home-page "https://bioconductor.org/packages/variancePartition/")
14016 (synopsis "Analyze variation in gene expression experiments")
14018 "This is a package providing tools to quantify and interpret multiple
14019 sources of biological and technical variation in gene expression experiments.
14020 It uses a linear mixed model to quantify variation in gene expression
14021 attributable to individual, tissue, time point, or technical variables. The
14022 package includes dream differential expression analysis for repeated
14024 (license license:gpl2+)))
14026 (define-public r-htqpcr
14033 (uri (bioconductor-uri "HTqPCR" version))
14036 "0am98rzwpi3kybq1l27c5qn3n1pg5aqwmh6jq9q0lzbjjin3haqc"))))
14037 (properties `((upstream-name . "HTqPCR")))
14038 (build-system r-build-system)
14040 (list r-affy r-biobase r-gplots r-limma r-rcolorbrewer))
14041 (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/"
14042 "groups/bertone/software/HTqPCR.pdf"))
14043 (synopsis "Automated analysis of high-throughput qPCR data")
14045 "Analysis of Ct values from high throughput quantitative real-time
14046 PCR (qPCR) assays across multiple conditions or replicates. The input data
14047 can be from spatially-defined formats such ABI TaqMan Low Density Arrays or
14048 OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad
14049 Laboratories; conventional 96- or 384-well plates; or microfluidic devices
14050 such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data
14051 loading, quality assessment, normalization, visualization and parametric or
14052 non-parametric testing for statistical significance in Ct values between
14053 features (e.g. genes, microRNAs).")
14054 (license license:artistic2.0)))
14056 (define-public r-unifiedwmwqpcr
14058 (name "r-unifiedwmwqpcr")
14063 (uri (bioconductor-uri "unifiedWMWqPCR" version))
14066 "1skfs94a6bv05c844zf5vfqw1fbgxyppgdnckdbhxg2a2470a4wh"))))
14068 `((upstream-name . "unifiedWMWqPCR")))
14069 (build-system r-build-system)
14071 (list r-biocgenerics r-htqpcr))
14072 (home-page "https://bioconductor.org/packages/unifiedWMWqPCR")
14073 (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data")
14075 "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR
14076 data. This modified test allows for testing differential expression in qPCR
14078 (license license:gpl2+)))
14080 (define-public r-universalmotif
14082 (name "r-universalmotif")
14087 (uri (bioconductor-uri "universalmotif" version))
14090 "1sm54z8aq3534qjsa19wychhwcvwnjlkydmiqqvidiiwcxwqpjsr"))))
14092 `((upstream-name . "universalmotif")))
14093 (build-system r-build-system)
14096 (modify-phases %standard-phases
14097 (add-after 'unpack 'fix-reference-to-strip
14099 (substitute* "src/Makevars"
14100 (("/usr/bin/strip") (which "strip"))))))))
14102 (list r-biocgenerics
14115 "https://bioconductor.org/packages/universalmotif/")
14117 "Specific structures importer, modifier, and exporter for R")
14119 "This package allows importing most common @dfn{specific structure}
14120 (motif) types into R for use by functions provided by other Bioconductor
14121 motif-related packages. Motifs can be exported into most major motif formats
14122 from various classes as defined by other Bioconductor packages. A suite of
14123 motif and sequence manipulation and analysis functions are included, including
14124 enrichment, comparison, P-value calculation, shuffling, trimming, higher-order
14125 motifs, and others.")
14126 (license license:gpl3)))
14128 (define-public r-ace
14134 (uri (bioconductor-uri "ACE" version))
14137 "1xnw288vz810vjkidar5h218wyc0q2hx0k4zi3r88vaz5rfhc05m"))))
14138 (properties `((upstream-name . "ACE")))
14139 (build-system r-build-system)
14140 (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq))
14141 (native-inputs (list r-knitr))
14142 (home-page "https://github.com/tgac-vumc/ACE")
14144 "Absolute copy number estimation from low-coverage whole genome sequencing")
14146 "This package uses segmented copy number data to estimate tumor cell
14147 percentage and produce copy number plots displaying absolute copy numbers. For
14148 this it uses segmented data from the @code{QDNAseq} package, which in turn uses
14149 a number of dependencies to turn mapped reads into segmented data. @code{ACE}
14150 will run @code{QDNAseq} or use its output rds-file of segmented data. It will
14151 subsequently run through all samples in the object(s), for which it will create
14152 individual subdirectories. For each sample, it will calculate how well the
14153 segments fit (the relative error) to integer copy numbers for each percentage
14154 of @dfn{tumor cells} (cells with divergent segments).")
14155 (license license:gpl2)))
14157 (define-public r-acgh
14163 (uri (bioconductor-uri "aCGH" version))
14166 "00ni0kwy68v33ggfi8g5vffirhmbhaxg4l54hcqhx75m535z1x7d"))))
14167 (properties `((upstream-name . "aCGH")))
14168 (build-system r-build-system)
14169 (propagated-inputs (list r-biobase r-cluster r-multtest r-survival))
14170 (home-page "https://bioconductor.org/packages/aCGH")
14172 "Classes and functions for array comparative genomic hybridization data")
14174 "This package provides functions for reading
14175 @dfn{array comparative genomic hybridization} (aCGH) data from image analysis
14176 output files and clone information files, creation of @code{aCGH} objects for
14177 storing these data. Basic methods are accessing/replacing, subsetting,
14178 printing and plotting @code{aCGH} objects.")
14179 (license license:gpl2)))
14181 (define-public r-acme
14187 (uri (bioconductor-uri "ACME" version))
14190 "0ilcsgpc4m47gifxc0yzx2xi3g4day515mncnnjvfdj3iq8xwk25"))))
14191 (properties `((upstream-name . "ACME")))
14192 (build-system r-build-system)
14193 (propagated-inputs (list r-biobase r-biocgenerics))
14194 (home-page "https://bioconductor.org/packages/aCGH/")
14195 (synopsis "Calculating microarray enrichment")
14197 "This package implements @dfn{algorithms for calculating microarray
14198 enrichment} (ACME), and it is a set of tools for analysing tiling array of
14199 @dfn{combined chromatin immunoprecipitation with DNA microarray} (ChIP/chip),
14200 DNAse hypersensitivity, or other experiments that result in regions of the
14201 genome showing enrichment. It does not rely on a specific array technology
14202 (although the array should be a tiling array), is very general (can be applied
14203 in experiments resulting in regions of enrichment), and is very insensitive to
14204 array noise or normalization methods. It is also very fast and can be applied
14205 on whole-genome tiling array experiments quite easily with enough memory.")
14206 (license license:gpl2+)))
14208 (define-public r-acde
14214 (uri (bioconductor-uri "acde" version))
14217 "0lgq546y4qklfzbc6fjr3d656hn76p6dn4694qfiafql2nlsjbj2"))))
14218 (properties `((upstream-name . "acde")))
14219 (build-system r-build-system)
14220 (propagated-inputs (list r-boot))
14221 (home-page "https://bioconductor.org/packages/acde")
14223 "Identification of differentially expressed genes with artificial components")
14225 "This package provides a multivariate inferential analysis method for
14226 detecting differentially expressed genes in gene expression data. It uses
14227 artificial components, close to the data's principal components but with an
14228 exact interpretation in terms of differential genetic expression, to identify
14229 differentially expressed genes while controlling the @dfn{false discovery
14231 (license license:gpl3)))
14233 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
14235 (define-public r-activedriverwgs
14237 (name "r-activedriverwgs")
14242 (uri (cran-uri "ActiveDriverWGS" version))
14245 "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
14247 `((upstream-name . "ActiveDriverWGS")))
14248 (build-system r-build-system)
14252 r-bsgenome-hsapiens-ucsc-hg19
14253 r-bsgenome-hsapiens-ucsc-hg38
14254 r-bsgenome-mmusculus-ucsc-mm9
14255 r-bsgenome-mmusculus-ucsc-mm10
14262 (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
14263 (synopsis "Driver discovery tool for cancer whole genomes")
14265 "This package provides a method for finding an enrichment of cancer
14266 simple somatic mutations (SNVs and Indels) in functional elements across the
14267 human genome. ActiveDriverWGS detects coding and noncoding driver elements
14268 using whole genome sequencing data.")
14269 (license license:gpl3)))
14271 ;; This is a CRAN package, but it depends on Bioconductor packages, so we put
14273 (define-public r-activepathways
14275 (name "r-activepathways")
14280 (uri (cran-uri "ActivePathways" version))
14283 "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
14285 `((upstream-name . "ActivePathways")))
14286 (build-system r-build-system)
14288 (list r-data-table r-ggplot2))
14291 (home-page "https://cran.r-project.org/web/packages/ActivePathways/")
14292 (synopsis "Multivariate pathway enrichment analysis")
14294 "This package represents an integrative method of analyzing multi omics
14295 data that conducts enrichment analysis of annotated gene sets. ActivePathways
14296 uses a statistical data fusion approach, rationalizes contributing evidence
14297 and highlights associated genes, improving systems-level understanding of
14298 cellular organization in health and disease.")
14299 (license license:gpl3)))
14301 (define-public r-bgmix
14308 (uri (bioconductor-uri "BGmix" version))
14311 "03f6nknp3n49yvg2d9qsmds676rva70pr4wjz0md228jczgjk0vj"))))
14312 (properties `((upstream-name . "BGmix")))
14313 (build-system r-build-system)
14315 (list r-kernsmooth))
14316 (home-page "https://bioconductor.org/packages/BGmix/")
14317 (synopsis "Bayesian models for differential gene expression")
14319 "This package provides fully Bayesian mixture models for differential
14321 (license license:gpl2)))
14323 (define-public r-bgx
14330 (uri (bioconductor-uri "bgx" version))
14333 "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
14334 (properties `((upstream-name . "bgx")))
14335 (build-system r-build-system)
14339 '(modify-phases %standard-phases
14340 (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
14342 (substitute* "configure.ac"
14343 (("AX_GCC_ARCHFLAG.*") ""))
14344 (delete-file "configure")
14345 (invoke "autoreconf" "-vif"))))))
14349 (list r-affy r-biobase r-gcrma r-rcpp))
14351 (list autoconf automake))
14352 (home-page "https://bioconductor.org/packages/bgx/")
14353 (synopsis "Bayesian gene expression")
14355 "This package provides tools for Bayesian integrated analysis of
14356 Affymetrix GeneChips.")
14357 (license license:gpl2)))
14359 (define-public r-bhc
14366 (uri (bioconductor-uri "BHC" version))
14369 "1kqajd16981y5yaak2imaq1i7pilgqdr3nbhggsakh787j1d9rc5"))))
14370 (properties `((upstream-name . "BHC")))
14371 (build-system r-build-system)
14372 (home-page "https://bioconductor.org/packages/BHC/")
14373 (synopsis "Bayesian hierarchical clustering")
14375 "The method implemented in this package performs bottom-up hierarchical
14376 clustering, using a Dirichlet Process (infinite mixture) to model uncertainty
14377 in the data and Bayesian model selection to decide at each step which clusters
14378 to merge. This avoids several limitations of traditional methods, for example
14379 how many clusters there should be and how to choose a principled distance
14380 metric. This implementation accepts multinomial (i.e. discrete, with 2+
14381 categories) or time-series data. This version also includes a randomised
14382 algorithm which is more efficient for larger data sets.")
14383 (license license:gpl3)))
14385 (define-public r-bicare
14392 (uri (bioconductor-uri "BicARE" version))
14395 "0qjh5bsjcjry6k1vzdaascwy2shjrkc2bw0w57w0qa458cbi89z2"))))
14396 (properties `((upstream-name . "BicARE")))
14397 (build-system r-build-system)
14399 (list r-biobase r-gseabase r-multtest))
14400 (home-page "http://bioinfo.curie.fr")
14401 (synopsis "Biclustering analysis and results exploration")
14403 "This is a package for biclustering analysis and exploration of
14405 (license license:gpl2)))
14407 (define-public r-bifet
14414 (uri (bioconductor-uri "BiFET" version))
14417 "03ypbbn8i0f4bl4m6wfdcv702jydniak56wqjb1vlrckd9aphwzq"))))
14418 (properties `((upstream-name . "BiFET")))
14419 (build-system r-build-system)
14421 (list r-genomicranges r-poibin))
14424 (home-page "https://bioconductor.org/packages/BiFET")
14425 (synopsis "Bias-free footprint enrichment test")
14427 "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are
14428 over-represented in target regions compared to background regions after
14429 correcting for the bias arising from the imbalance in read counts and GC
14430 contents between the target and background regions. For a given TF k, BiFET
14431 tests the null hypothesis that the target regions have the same probability of
14432 having footprints for the TF k as the background regions while correcting for
14433 the read count and GC content bias.")
14434 (license license:gpl3)))
14436 (define-public r-rsbml
14443 (uri (bioconductor-uri "rsbml" version))
14446 "1v11pspkml6xdsacgwxw8r4qdhbnn2h2sqgpm9aidaq9p2085b0v"))))
14447 (properties `((upstream-name . "rsbml")))
14448 (build-system r-build-system)
14452 (list r-biocgenerics r-graph))
14455 (home-page "http://www.sbml.org")
14456 (synopsis "R support for SBML")
14458 "This package provides an R interface to libsbml for SBML parsing,
14459 validating output, provides an S4 SBML DOM, converts SBML to R graph objects.")
14460 (license license:artistic2.0)))
14462 (define-public r-hypergraph
14464 (name "r-hypergraph")
14469 (uri (bioconductor-uri "hypergraph" version))
14472 "0xmryqj5yw1ns6wbhjqbb6h14jlj89zrznzvqnvd4n03ci20kzzp"))))
14473 (properties `((upstream-name . "hypergraph")))
14474 (build-system r-build-system)
14477 (home-page "https://bioconductor.org/packages/hypergraph")
14478 (synopsis "Hypergraph data structures")
14480 "This package implements some simple capabilities for representing and
14481 manipulating hypergraphs.")
14482 (license license:artistic2.0)))
14484 (define-public r-hyperdraw
14486 (name "r-hyperdraw")
14491 (uri (bioconductor-uri "hyperdraw" version))
14494 "0ndw4y6b15jy4w86vfkahmdc81d3ycjsvqy1mxi55dwvd8xq0ap6"))))
14495 (properties `((upstream-name . "hyperdraw")))
14496 (build-system r-build-system)
14497 (inputs (list graphviz))
14499 (list r-graph r-hypergraph r-rgraphviz))
14500 (home-page "https://bioconductor.org/packages/hyperdraw")
14501 (synopsis "Visualizing hypergraphs")
14503 "This package provides functions for visualizing hypergraphs.")
14504 (license license:gpl2+)))
14506 (define-public r-biggr
14513 (uri (bioconductor-uri "BiGGR" version))
14516 "0n57bgl6xz5b1gpw4isimq2pqxmlabn7jzhbjg2fbxcklabdvrcw"))))
14517 (properties `((upstream-name . "BiGGR")))
14518 (build-system r-build-system)
14526 (home-page "https://bioconductor.org/packages/BiGGR/")
14527 (synopsis "Constraint based modeling using metabolic reconstruction databases")
14529 "This package provides an interface to simulate metabolic reconstruction
14530 from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic
14531 reconstruction databases. The package facilitates @dfn{flux balance
14532 analysis} (FBA) and the sampling of feasible flux distributions. Metabolic
14533 networks and estimated fluxes can be visualized with hypergraphs.")
14534 (license license:gpl3+)))
14536 (define-public r-bigmemoryextras
14538 (name "r-bigmemoryextras")
14543 (uri (bioconductor-uri "bigmemoryExtras" version))
14546 "1k31h746j8r3f92vj62s38fw12qjkv5814ipcqfbswnxgaan17zj"))))
14548 `((upstream-name . "bigmemoryExtras")))
14549 (build-system r-build-system)
14551 (list r-bigmemory))
14554 (home-page "https://github.com/phaverty/bigmemoryExtras")
14555 (synopsis "Extension of the bigmemory package")
14557 "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds
14558 safety and convenience features to the @code{filebacked.big.matrix} class from
14559 the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by
14560 monitoring and gracefully restoring the connection to on-disk data and it also
14561 protects against accidental data modification with a file-system-based
14562 permissions system. Utilities are provided for using @code{BigMatrix}-derived
14563 classes as @code{assayData} matrices within the @code{Biobase} package's
14564 @code{eSet} family of classes. @code{BigMatrix} provides some optimizations
14565 related to attaching to, and indexing into, file-backed matrices with
14566 dimnames. Additionally, the package provides a @code{BigMatrixFactor} class,
14567 a file-backed matrix with factor properties.")
14568 (license license:artistic2.0)))
14570 (define-public r-bigpint
14577 (uri (bioconductor-uri "bigPint" version))
14580 "1hp69j2qcidrxqs3dxjjngb09nbzp5x2yy4jz1rjmv6ghif9ccfj"))))
14581 (properties `((upstream-name . "bigPint")))
14582 (build-system r-build-system)
14584 (list r-delayedarray
14600 r-summarizedexperiment
14604 (home-page "https://github.com/lindsayrutter/bigPint")
14605 (synopsis "Big multivariate data plotted interactively")
14607 "This package provides methods for visualizing large multivariate
14608 datasets using static and interactive scatterplot matrices, parallel
14609 coordinate plots, volcano plots, and litre plots. It includes examples for
14610 visualizing RNA-sequencing datasets and differentially expressed genes.")
14611 (license license:gpl3)))
14613 (define-public r-chemminer
14615 (name "r-chemminer")
14620 (uri (bioconductor-uri "ChemmineR" version))
14623 "1nri4zkc9lp1mqgsi0h58486vixwiv2989b6pmx2aj5c3575i0ma"))))
14624 (properties `((upstream-name . "ChemmineR")))
14625 (build-system r-build-system)
14644 (home-page "https://github.com/girke-lab/ChemmineR")
14645 (synopsis "Cheminformatics toolkit for R")
14647 "ChemmineR is a cheminformatics package for analyzing drug-like small
14648 molecule data in R. It contains functions for efficient processing of large
14649 numbers of molecules, physicochemical/structural property predictions,
14650 structural similarity searching, classification and clustering of compound
14651 libraries with a wide spectrum of algorithms. In addition, it offers
14652 visualization functions for compound clustering results and chemical
14654 (license license:artistic2.0)))
14656 (define-public r-fmcsr
14663 (uri (bioconductor-uri "fmcsR" version))
14665 (base32 "1mblmk21dxc9v2fikhvfg2njwgl190gkysppl6msxizwcmxsmh30"))))
14666 (properties `((upstream-name . "fmcsR")))
14667 (build-system r-build-system)
14669 (list r-biocgenerics r-chemminer r-runit))
14670 (native-inputs (list r-knitr))
14671 (home-page "https://github.com/girke-lab/fmcsR")
14672 (synopsis "Mismatch tolerant maximum common substructure searching")
14674 "The fmcsR package introduces an efficient @dfn{maximum common
14675 substructure} (MCS) algorithms combined with a novel matching strategy that
14676 allows for atom and/or bond mismatches in the substructures shared among two
14677 small molecules. The resulting flexible MCSs (FMCSs) are often larger than
14678 strict MCSs, resulting in the identification of more common features in their
14679 source structures, as well as a higher sensitivity in finding compounds with
14680 weak structural similarities. The fmcsR package provides several utilities to
14681 use the FMCS algorithm for pairwise compound comparisons, structure similarity
14682 searching and clustering.")
14683 (license license:artistic2.0)))
14685 (define-public r-bioassayr
14687 (name "r-bioassayr")
14692 (uri (bioconductor-uri "bioassayR" version))
14695 "0zbrci0vgk4qca28i0qb2izhyrz3r95l1w54h9h3zj9f3vd61wrz"))))
14696 (properties `((upstream-name . "bioassayR")))
14697 (build-system r-build-system)
14699 (list r-biocgenerics
14708 (home-page "https://github.com/girke-lab/bioassayR")
14709 (synopsis "Cross-target analysis of small molecule bioactivity")
14711 "bioassayR is a computational tool that enables simultaneous analysis of
14712 thousands of bioassay experiments performed over a diverse set of compounds
14713 and biological targets. Unique features include support for large-scale
14714 cross-target analyses of both public and custom bioassays, generation of
14715 @dfn{high throughput screening fingerprints} (HTSFPs), and an optional
14716 preloaded database that provides access to a substantial portion of publicly
14717 available bioactivity data.")
14718 (license license:artistic2.0)))
14720 (define-public r-biobroom
14722 (name "r-biobroom")
14727 (uri (bioconductor-uri "biobroom" version))
14730 "04x1z9nchm4mbhqr31011zdprc4md156j4zf003s7xx0n278xsgh"))))
14731 (properties `((upstream-name . "biobroom")))
14732 (build-system r-build-system)
14734 (list r-biobase r-broom r-dplyr r-tidyr))
14737 (home-page "https://github.com/StoreyLab/biobroom")
14738 (synopsis "Turn Bioconductor objects into tidy data frames")
14740 "This package contains methods for converting standard objects
14741 constructed by bioinformatics packages, especially those in Bioconductor, and
14742 converting them to @code{tidy} data. It thus serves as a complement to the
14743 @code{broom} package, and follows the same tidy, augment, glance division of
14744 tidying methods. Tidying data makes it easy to recombine, reshape and
14745 visualize bioinformatics analyses.")
14746 ;; Any version of the LGPL.
14747 (license license:lgpl3+)))
14749 (define-public r-graphite
14751 (name "r-graphite")
14756 (uri (bioconductor-uri "graphite" version))
14759 "0nl5mkgrvf7vsqjy48ij9b1dmxfvp9lf8cpay55h93c4qz4x606g"))))
14760 (properties `((upstream-name . "graphite")))
14761 (build-system r-build-system)
14763 (list r-annotationdbi r-graph r-httr r-rappdirs r-rlang))
14764 (home-page "https://bioconductor.org/packages/graphite/")
14765 (synopsis "Networks from pathway databases")
14767 "Graphite provides networks derived from eight public pathway databases,
14768 and automates the conversion of node identifiers (e.g. from Entrez IDs to gene
14770 (license license:agpl3+)))
14772 (define-public r-reactomepa
14774 (name "r-reactomepa")
14779 (uri (bioconductor-uri "ReactomePA" version))
14782 "1fd72m2afxbbvbgwy8knp6fiq1h561plmsh4r8a08w21ngmkz2s5"))))
14783 (properties `((upstream-name . "ReactomePA")))
14784 (build-system r-build-system)
14786 (list r-annotationdbi
14796 (home-page "https://guangchuangyu.github.io/software/ReactomePA")
14797 (synopsis "Reactome pathway analysis")
14799 "This package provides functions for pathway analysis based on the
14800 REACTOME pathway database. It implements enrichment analysis, gene set
14801 enrichment analysis and several functions for visualization.")
14802 (license license:gpl2)))
14804 (define-public r-ebarrays
14806 (name "r-ebarrays")
14811 (uri (bioconductor-uri "EBarrays" version))
14814 "027zarnpxpdnyl877swp5ypxj7zvq0cjp2q2xs6g6yn5dpqjvxxk"))))
14815 (properties `((upstream-name . "EBarrays")))
14816 (build-system r-build-system)
14818 (list r-biobase r-cluster r-lattice))
14819 (home-page "https://bioconductor.org/packages/EBarrays/")
14820 (synopsis "Gene clustering and differential expression identification")
14822 "EBarrays provides tools for the analysis of replicated/unreplicated
14824 (license license:gpl2+)))
14826 (define-public r-bioccasestudies
14828 (name "r-bioccasestudies")
14833 (uri (bioconductor-uri "BiocCaseStudies" version))
14836 "03n49b6fvyyzmvdy4yif3cl7yv21c09c8xdx4cvvax5zz4v4sab1"))))
14838 `((upstream-name . "BiocCaseStudies")))
14839 (build-system r-build-system)
14840 (propagated-inputs (list r-biobase))
14841 (home-page "https://bioconductor.org/packages/BiocCaseStudies")
14842 (synopsis "Support for the case studies monograph")
14844 "This package provides software and data to support the case studies
14846 (license license:artistic2.0)))
14848 (define-public r-bioccheck
14850 (name "r-bioccheck")
14854 (uri (bioconductor-uri "BiocCheck" version))
14857 "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw"))))
14859 `((upstream-name . "BiocCheck")))
14860 (build-system r-build-system)
14871 (home-page "https://bioconductor.org/packages/BiocCheck")
14872 (synopsis "Executes Bioconductor-specific package checks")
14873 (description "This package contains tools to perform additional quality
14874 checks on R packages that are to be submitted to the Bioconductor repository.")
14875 (license license:artistic2.0)))
14877 (define-public r-biocgraph
14879 (name "r-biocgraph")
14884 (uri (bioconductor-uri "biocGraph" version))
14887 "1y59a7c4ahhn1g2wz2hkx83izfn8i85mmxxp63jdd0rg7zwhr6nn"))))
14888 (properties `((upstream-name . "biocGraph")))
14889 (build-system r-build-system)
14891 (list r-biocgenerics r-geneplotter r-graph r-rgraphviz))
14892 (home-page "https://bioconductor.org/packages/biocGraph/")
14893 (synopsis "Graph examples and use cases in Bioinformatics")
14895 "This package provides examples and code that make use of the
14896 different graph related packages produced by Bioconductor.")
14897 (license license:artistic2.0)))
14899 (define-public r-biocstyle
14901 (name "r-biocstyle")
14905 (uri (bioconductor-uri "BiocStyle" version))
14908 "1nwiib201b9q1x19ihqjqr5jl0vnid8wfgpi8sa3y02bn722g5a5"))))
14910 `((upstream-name . "BiocStyle")))
14911 (build-system r-build-system)
14913 (list r-biocmanager r-bookdown r-knitr r-rmarkdown r-yaml))
14916 (home-page "https://bioconductor.org/packages/BiocStyle")
14917 (synopsis "Bioconductor formatting styles")
14918 (description "This package provides standard formatting styles for
14919 Bioconductor PDF and HTML documents. Package vignettes illustrate use and
14921 (license license:artistic2.0)))
14923 (define-public r-biocviews
14925 (name "r-biocviews")
14929 (uri (bioconductor-uri "biocViews" version))
14932 "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38"))))
14934 `((upstream-name . "biocViews")))
14935 (build-system r-build-system)
14944 (home-page "https://bioconductor.org/packages/biocViews")
14945 (synopsis "Bioconductor package categorization helper")
14946 (description "The purpose of biocViews is to create HTML pages that
14947 categorize packages in a Bioconductor package repository according to keywords,
14948 also known as views, in a controlled vocabulary.")
14949 (license license:artistic2.0)))
14951 (define-public r-experimenthub
14953 (name "r-experimenthub")
14958 (uri (bioconductor-uri "ExperimentHub" version))
14961 "11hna8vrm1az1zk7pw2dv0wh84sd0hw2bi55w40hqvs36csb7lkl"))))
14962 (properties `((upstream-name . "ExperimentHub")))
14963 (build-system r-build-system)
14965 (list r-annotationhub
14974 (home-page "https://bioconductor.org/packages/ExperimentHub/")
14975 (synopsis "Client to access ExperimentHub resources")
14977 "This package provides a client for the Bioconductor ExperimentHub web
14978 resource. ExperimentHub provides a central location where curated data from
14979 experiments, publications or training courses can be accessed. Each resource
14980 has associated metadata, tags and date of modification. The client creates
14981 and manages a local cache of files retrieved enabling quick and reproducible
14983 (license license:artistic2.0)))
14985 (define-public r-grohmm
14992 (uri (bioconductor-uri "groHMM" version))
14995 "0v2mk7xcy483w2nygpmyjp73kj3v5pkk1kf1wr41n33dxqlddqai"))))
14996 (properties `((upstream-name . "groHMM")))
14997 (build-system r-build-system)
14999 (list r-genomeinfodb
15000 r-genomicalignments
15006 (home-page "https://github.com/Kraus-Lab/groHMM")
15007 (synopsis "GRO-seq analysis pipeline")
15009 "This package provides a pipeline for the analysis of GRO-seq data.")
15010 (license license:gpl3+)))
15012 (define-public r-multiassayexperiment
15014 (name "r-multiassayexperiment")
15019 (uri (bioconductor-uri "MultiAssayExperiment" version))
15022 "1wnp52l9vifxn1wzqgndzp9b6ih0s1cflxx1fhw32k32d05cw9q1"))))
15024 `((upstream-name . "MultiAssayExperiment")))
15025 (build-system r-build-system)
15032 r-summarizedexperiment
15036 (home-page "https://waldronlab.io/MultiAssayExperiment/")
15037 (synopsis "Integration of multi-omics experiments in Bioconductor")
15039 "MultiAssayExperiment harmonizes data management of multiple assays
15040 performed on an overlapping set of specimens. It provides a familiar
15041 Bioconductor user experience by extending concepts from
15042 @code{SummarizedExperiment}, supporting an open-ended mix of standard data
15043 classes for individual assays, and allowing subsetting by genomic ranges or
15045 (license license:artistic2.0)))
15047 (define-public r-bioconcotk
15049 (name "r-bioconcotk")
15054 (uri (bioconductor-uri "BiocOncoTK" version))
15057 "1alplszw84vqa1mvzp996f94s40scmh4qwbrqhg43hrnyvbnq7pi"))))
15058 (properties `((upstream-name . "BiocOncoTK")))
15059 (build-system r-build-system)
15082 r-summarizedexperiment))
15085 (home-page "https://bioconductor.org/packages/BiocOncoTK")
15086 (synopsis "Bioconductor components for general cancer genomics")
15088 "The purpose of this package is to provide a central interface to various
15089 tools for genome-scale analysis of cancer studies.")
15090 (license license:artistic2.0)))
15092 (define-public r-biocor
15099 (uri (bioconductor-uri "BioCor" version))
15102 "004mksswampwisljcdz6fswwbgdjdii3y86gjzib0gf8v4w7w4q3"))))
15103 (properties `((upstream-name . "BioCor")))
15104 (build-system r-build-system)
15106 (list r-biocparallel r-gseabase r-matrix))
15109 (home-page "https://llrs.github.io/BioCor/")
15110 (synopsis "Functional similarities")
15112 "This package provides tools to calculate functional similarities based
15113 on the pathways described on KEGG and REACTOME or in gene sets. These
15114 similarities can be calculated for pathways or gene sets, genes, or clusters
15115 and combined with other similarities. They can be used to improve networks,
15116 gene selection, testing relationships, and so on.")
15117 (license license:expat)))
15119 (define-public r-biocpkgtools
15121 (name "r-biocpkgtools")
15126 (uri (bioconductor-uri "BiocPkgTools" version))
15129 "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd"))))
15130 (properties `((upstream-name . "BiocPkgTools")))
15131 (build-system r-build-system)
15133 (list r-biocfilecache
15157 (home-page "https://github.com/seandavi/BiocPkgTools")
15158 (synopsis "Collection of tools for learning about Bioconductor packages")
15160 "Bioconductor has a rich ecosystem of metadata around packages, usage,
15161 and build status. This package is a simple collection of functions to access
15162 that metadata from R. The goal is to expose metadata for data mining and
15163 value-added functionality such as package searching, text mining, and
15164 analytics on packages.")
15165 (license license:expat)))
15167 (define-public r-biocset
15174 (uri (bioconductor-uri "BiocSet" version))
15177 "1ghba7020inrdxlbrrgds9gjymjxjma2p89b9lgkjin89zalqglh"))))
15178 (properties `((upstream-name . "BiocSet")))
15179 (build-system r-build-system)
15181 (list r-annotationdbi
15194 "https://bioconductor.org/packages/BiocSet")
15196 "Representing Different Biological Sets")
15198 "BiocSet displays different biological sets in a triple tibble format.
15199 These three tibbles are @code{element}, @code{set}, and @code{elementset}.
15200 The user has the ability to activate one of these three tibbles to perform
15201 common functions from the @code{dplyr} package. Mapping functionality and
15202 accessing web references for elements/sets are also available in BiocSet.")
15203 (license license:artistic2.0)))
15205 (define-public r-biocworkflowtools
15207 (name "r-biocworkflowtools")
15212 (uri (bioconductor-uri "BiocWorkflowTools" version))
15215 "1jj4icpkhrv9f6yx3vghkpdil1pfghf3yvc9756wmndvhs100r5l"))))
15217 `((upstream-name . "BiocWorkflowTools")))
15218 (build-system r-build-system)
15231 (home-page "https://bioconductor.org/packages/BiocWorkflowTools/")
15232 (synopsis "Tools to aid the development of Bioconductor Workflow packages")
15234 "This package provides functions to ease the transition between
15235 Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.")
15236 (license license:expat)))
15238 (define-public r-biodist
15245 (uri (bioconductor-uri "bioDist" version))
15248 "04nrvrcvpj0sn8p2i8n3ggsl2s7r4na576174i7bn1sj21vr0yb0"))))
15249 (properties `((upstream-name . "bioDist")))
15250 (build-system r-build-system)
15252 (list r-biobase r-kernsmooth))
15253 (home-page "https://bioconductor.org/packages/bioDist/")
15254 (synopsis "Different distance measures")
15256 "This package provides a collection of software tools for calculating
15257 distance measures.")
15258 (license license:artistic2.0)))
15260 (define-public r-pcatools
15262 (name "r-pcatools")
15267 (uri (bioconductor-uri "PCAtools" version))
15270 "03s4dh008fys2rrcpzanc0892p63f6jyyvzc9m42jbi1dlkyx26v"))))
15271 (properties `((upstream-name . "PCAtools")))
15272 (build-system r-build-system)
15280 r-delayedmatrixstats
15288 (native-inputs (list r-knitr))
15289 (home-page "https://github.com/kevinblighe/PCAtools")
15290 (synopsis "PCAtools: everything Principal Components Analysis")
15292 "@dfn{Principal Component Analysis} (PCA) extracts the fundamental
15293 structure of the data without the need to build any model to represent it.
15294 This \"summary\" of the data is arrived at through a process of reduction that
15295 can transform the large number of variables into a lesser number that are
15296 uncorrelated (i.e. the 'principal components'), while at the same time being
15297 capable of easy interpretation on the original data. PCAtools provides
15298 functions for data exploration via PCA, and allows the user to generate
15299 publication-ready figures. PCA is performed via @code{BiocSingular}; users
15300 can also identify an optimal number of principal components via different
15301 metrics, such as the elbow method and Horn's parallel analysis, which has
15302 relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high
15303 dimensional mass cytometry data.")
15304 (license license:gpl3)))
15306 (define-public r-rgreat
15313 (uri (bioconductor-uri "rGREAT" version))
15316 "0px72r8mjimf5mxfwb9qz46kqpgjw5gaqq41hy0212ymjd8whaky"))))
15317 (properties `((upstream-name . "rGREAT")))
15318 (build-system r-build-system)
15320 (list r-genomicranges r-getoptlong r-iranges r-rcurl r-rjson))
15321 (native-inputs (list r-knitr))
15322 (home-page "https://github.com/jokergoo/rGREAT")
15323 (synopsis "Client for GREAT analysis")
15325 "This package makes GREAT (Genomic Regions Enrichment of Annotations
15326 Tool) analysis automatic by constructing a HTTP POST request according to
15327 user's input and automatically retrieving results from GREAT web server.")
15328 (license license:expat)))
15330 (define-public r-m3c
15337 (uri (bioconductor-uri "M3C" version))
15340 "120gd7gkgc98d1l6hl2ij799b3jksdnga5iyb44ps9mbc79hl012"))))
15341 (properties `((upstream-name . "M3C")))
15342 (build-system r-build-system)
15354 (native-inputs (list r-knitr))
15355 (home-page "https://bioconductor.org/packages/M3C")
15356 (synopsis "Monte Carlo reference-based consensus clustering")
15358 "M3C is a consensus clustering algorithm that uses a Monte Carlo
15359 simulation to eliminate overestimation of @code{K} and can reject the null
15360 hypothesis @code{K=1}.")
15361 (license license:agpl3+)))
15363 (define-public r-icens
15370 (uri (bioconductor-uri "Icens" version))
15373 "0jnbfv7js8bw0ginql90krrpk0p54whj9igw0zk3jc45jqvj2vyc"))))
15374 (properties `((upstream-name . "Icens")))
15375 (build-system r-build-system)
15378 (home-page "https://bioconductor.org/packages/Icens")
15379 (synopsis "NPMLE for censored and truncated data")
15381 "This package provides many functions for computing the
15382 @dfn{nonparametric maximum likelihood estimator} (NPMLE) for censored and
15384 (license license:artistic2.0)))
15386 ;; This is a CRAN package but it depends on r-icens, which is published on
15388 (define-public r-interval
15390 (name "r-interval")
15391 (version "1.1-0.8")
15395 (uri (cran-uri "interval" version))
15398 "0g0k9nri19p3y3s70ic1w3i3sxq8fbsxaikd7c4d6afqzr8hk2nl"))))
15399 (properties `((upstream-name . "interval")))
15400 (build-system r-build-system)
15402 (list r-icens r-mlecens r-perm r-survival))
15403 (home-page "https://cran.r-project.org/web/packages/interval/")
15404 (synopsis "Weighted Logrank tests and NPMLE for interval censored data")
15406 "This package provides functions to fit nonparametric survival curves,
15407 plot them, and perform logrank or Wilcoxon type tests.")
15408 (license license:gpl2+)))
15410 ;; This is a CRAN package, but it depends on r-interval, which depends on a
15411 ;; Bioconductor package.
15412 (define-public r-fhtest
15419 (uri (cran-uri "FHtest" version))
15422 "00mql2r4f5hxhdqf27q3x9s5rz2zzakx2myym97b1w1s7c5znl4q"))))
15423 (properties `((upstream-name . "FHtest")))
15424 (build-system r-build-system)
15426 (list r-interval r-kmsurv r-mass r-perm r-survival))
15427 (home-page "https://cran.r-project.org/web/packages/FHtest/")
15428 (synopsis "Tests for survival data based on the Fleming-Harrington class")
15430 "This package provides functions to compare two or more survival curves
15434 @item The Fleming-Harrington test for right-censored data based on
15435 permutations and on counting processes.
15436 @item An extension of the Fleming-Harrington test for interval-censored data
15437 based on a permutation distribution and on a score vector distribution.
15440 (license license:gpl2+)))
15442 (define-public r-fourcseq
15444 (name "r-fourcseq")
15449 (uri (bioconductor-uri "FourCSeq" version))
15451 (base32 "1rwdphcj26xis47n8j1fiyc3k3qbsgn0bhf5bhgy5vm11yqyvicb"))))
15452 (properties `((upstream-name . "FourCSeq")))
15453 (build-system r-build-system)
15459 r-genomicalignments
15469 r-summarizedexperiment))
15473 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
15474 (synopsis "Analysis of multiplexed 4C sequencing data")
15476 "This package is an R package dedicated to the analysis of (multiplexed)
15477 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
15478 interactions between DNA elements and identify differential interactions
15479 between conditions. The statistical analysis in R starts with individual bam
15480 files for each sample as inputs. To obtain these files, the package contains
15481 a Python script to demultiplex libraries and trim off primer sequences. With
15482 a standard alignment software the required bam files can be then be
15484 (license license:gpl3+)))
15486 (define-public r-preprocesscore
15488 (name "r-preprocesscore")
15493 (uri (bioconductor-uri "preprocessCore" version))
15496 "1sqpp00hhv6gypflrjw8qpqyqgdcp29m86gmi1di1574x8casdkf"))))
15498 `((upstream-name . "preprocessCore")))
15499 (build-system r-build-system)
15500 (home-page "https://github.com/bmbolstad/preprocessCore")
15501 (synopsis "Collection of pre-processing functions")
15503 "This package provides a library of core pre-processing and normalization
15505 (license license:lgpl2.0+)))
15507 (define-public r-s4vectors
15509 (name "r-s4vectors")
15513 (uri (bioconductor-uri "S4Vectors" version))
15516 "0j3ybhzdhlhw8527nks3mjja28asjya2n0m0rjkh4bw66rkfys4k"))))
15518 `((upstream-name . "S4Vectors")))
15519 (build-system r-build-system)
15521 (list r-biocgenerics))
15522 (home-page "https://bioconductor.org/packages/S4Vectors")
15523 (synopsis "S4 implementation of vectors and lists")
15525 "The S4Vectors package defines the @code{Vector} and @code{List} virtual
15526 classes and a set of generic functions that extend the semantic of ordinary
15527 vectors and lists in R. Package developers can easily implement vector-like
15528 or list-like objects as concrete subclasses of @code{Vector} or @code{List}.
15529 In addition, a few low-level concrete subclasses of general interest (e.g.
15530 @code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the
15531 S4Vectors package itself.")
15532 (license license:artistic2.0)))
15534 ;; This is a CRAN package, but it depends on preprocessorcore, which is a
15535 ;; Bioconductor package.
15536 (define-public r-wgcna
15543 (uri (cran-uri "WGCNA" version))
15546 "027pkc4pyn9bifqbjs05318gvlm06mffw016j50n59wfi2g39x91"))))
15547 (properties `((upstream-name . "WGCNA")))
15548 (build-system r-build-system)
15550 (list r-annotationdbi
15563 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
15564 (synopsis "Weighted correlation network analysis")
15566 "This package provides functions necessary to perform Weighted
15567 Correlation Network Analysis on high-dimensional data. It includes functions
15568 for rudimentary data cleaning, construction and summarization of correlation
15569 networks, module identification and functions for relating both variables and
15570 modules to sample traits. It also includes a number of utility functions for
15571 data manipulation and visualization.")
15572 (license license:gpl2+)))
15574 (define-public r-rgraphviz
15576 (name "r-rgraphviz")
15581 (uri (bioconductor-uri "Rgraphviz" version))
15584 "1r6ff7w2bmyfl1vzjvpgnhb8f5arwjlpab8fw5ph8fgyiqbcx94l"))))
15585 (properties `((upstream-name . "Rgraphviz")))
15586 (build-system r-build-system)
15589 (modify-phases %standard-phases
15590 (add-after 'unpack 'make-reproducible
15592 ;; The replacement value is taken from src/graphviz/builddate.h
15593 (substitute* "src/graphviz/configure"
15594 (("VERSION_DATE=.*")
15595 "VERSION_DATE=20200427.2341\n"))
15597 ;; FIXME: Rgraphviz bundles the sources of an older variant of
15598 ;; graphviz. It does not build with the latest version of graphviz, so
15599 ;; we do not add graphviz to the inputs.
15600 (inputs (list zlib))
15605 (home-page "https://bioconductor.org/packages/Rgraphviz")
15606 (synopsis "Plotting capabilities for R graph objects")
15608 "This package interfaces R with the graphviz library for plotting R graph
15609 objects from the @code{graph} package.")
15610 (license license:epl1.0)))
15612 (define-public r-fishpond
15614 (name "r-fishpond")
15618 (uri (bioconductor-uri "fishpond" version))
15621 "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym"))))
15622 (properties `((upstream-name . "fishpond")))
15623 (build-system r-build-system)
15624 (inputs (list zlib))
15636 r-singlecellexperiment
15637 r-summarizedexperiment
15639 (native-inputs (list r-knitr))
15640 (home-page "https://github.com/mikelove/fishpond")
15641 (synopsis "Downstream methods and tools for expression data")
15643 "The @code{fishpond} package contains methods for differential transcript
15644 and gene expression analysis of RNA-seq data using inferential replicates for
15645 uncertainty of abundance quantification, as generated by Gibbs sampling or
15646 bootstrap sampling. Also the package contains a number of utilities for
15647 working with Salmon and Alevin quantification files.")
15648 (license license:gpl2)))
15650 (define-public r-fithic
15656 (uri (bioconductor-uri "FitHiC" version))
15659 "0iv14yx3g7shzl8qrjknyxbmiylj51sbd1wzr1ff9lc5shgl55kq"))))
15660 (properties `((upstream-name . "FitHiC")))
15661 (build-system r-build-system)
15663 (list r-data-table r-fdrtool r-rcpp))
15666 (home-page "https://bioconductor.org/packages/FitHiC")
15667 (synopsis "Confidence estimation for intra-chromosomal contact maps")
15669 "Fit-Hi-C is a tool for assigning statistical confidence estimates to
15670 intra-chromosomal contact maps produced by genome-wide genome architecture
15671 assays such as Hi-C.")
15672 (license license:gpl2+)))
15674 (define-public r-hitc
15680 (uri (bioconductor-uri "HiTC" version))
15683 "1pkshlrra26cad0hf8a54brlkazni6rsvrplh36azxapx5rpps4s"))))
15684 (properties `((upstream-name . "HiTC")))
15685 (build-system r-build-system)
15694 (home-page "https://bioconductor.org/packages/HiTC")
15695 (synopsis "High throughput chromosome conformation capture analysis")
15697 "The HiTC package was developed to explore high-throughput \"C\" data
15698 such as 5C or Hi-C. Dedicated R classes as well as standard methods for
15699 quality controls, normalization, visualization, and further analysis are also
15701 (license license:artistic2.0)))
15703 (define-public r-hdf5array
15705 (name "r-hdf5array")
15710 (uri (bioconductor-uri "HDF5Array" version))
15713 "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9"))))
15714 (properties `((upstream-name . "HDF5Array")))
15715 (build-system r-build-system)
15719 (list r-biocgenerics
15727 (home-page "https://bioconductor.org/packages/HDF5Array")
15728 (synopsis "HDF5 back end for DelayedArray objects")
15729 (description "This package provides an array-like container for convenient
15730 access and manipulation of HDF5 datasets. It supports delayed operations and
15731 block processing.")
15732 (license license:artistic2.0)))
15734 (define-public r-rhdf5lib
15736 (name "r-rhdf5lib")
15741 (uri (bioconductor-uri "Rhdf5lib" version))
15744 "1jpb8h7c724yz51zjfqs90bsqxgmy1rry2ra9qamsgqpr2j9764g"))
15745 (modules '((guix build utils)))
15748 ;; Delete bundled binaries
15749 (delete-file-recursively "src/wininclude/")
15750 (delete-file-recursively "src/winlib/")
15751 (delete-file "src/hdf5small_cxx_hl_1.10.7.tar.gz")))))
15752 (properties `((upstream-name . "Rhdf5lib")))
15753 (build-system r-build-system)
15756 (modify-phases %standard-phases
15757 (add-after 'unpack 'do-not-use-bundled-hdf5
15758 (lambda* (#:key inputs #:allow-other-keys)
15759 (for-each delete-file '("configure" "configure.ac"))
15760 (substitute* "R/zzz.R"
15761 (("return\\(links\\)") "return(\" -lz\")"))
15762 (with-directory-excursion "src"
15763 (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
15764 (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
15766 ;; Remove timestamp and host system information to make
15767 ;; the build reproducible.
15768 (substitute* "hdf5/src/libhdf5.settings.in"
15769 (("Configured on: @CONFIG_DATE@")
15770 "Configured on: Guix")
15771 (("Uname information:.*")
15772 "Uname information: Linux\n")
15773 ;; Remove unnecessary store reference.
15775 "C Compiler: GCC\n"))
15776 (rename-file "hdf5/src/libhdf5.settings.in"
15777 "hdf5/src/libhdf5.settings")
15778 (rename-file "Makevars.in" "Makevars")
15779 (substitute* "Makevars"
15780 (("@BUILD_HDF5@") "")
15781 (("@COPY_SZIP@") "")
15782 (("@ZLIB_LIB@") "-lz")
15783 (("@ZLIB_INCLUDE@") "")
15784 (("HDF5_CXX_LIB=.*")
15785 (string-append "HDF5_CXX_LIB="
15786 (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
15788 (string-append "HDF5_LIB="
15789 (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n"))
15790 (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n")
15791 (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n")
15792 (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n")
15793 (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n")
15794 (("HDF5_HL_LIB=.*")
15795 (string-append "HDF5_HL_LIB="
15796 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n"))
15797 (("HDF5_HL_CXX_LIB=.*")
15798 (string-append "HDF5_HL_CXX_LIB="
15799 (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n"))
15800 ;; szip is non-free software
15801 (("cp \"\\$\\{SZIP_LIB\\}.*") "")
15802 (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))))))))
15804 (list hdf5-1.10 zlib))
15806 `(("hdf5-source" ,(package-source hdf5-1.10))
15807 ("r-knitr" ,r-knitr)))
15808 (home-page "https://bioconductor.org/packages/Rhdf5lib")
15809 (synopsis "HDF5 library as an R package")
15810 (description "This package provides C and C++ HDF5 libraries for use in R
15812 (license license:artistic2.0)))
15814 (define-public r-beachmat
15816 (name "r-beachmat")
15821 (uri (bioconductor-uri "beachmat" version))
15824 "0fc6vvjjq1mfjfj2zqkap3rwvinnfqjs0cpk1447sspvd1rjya8c"))))
15825 (build-system r-build-system)
15827 (list r-biocgenerics r-delayedarray r-matrix r-rcpp))
15830 (home-page "https://bioconductor.org/packages/beachmat")
15831 (synopsis "Compiling Bioconductor to handle each matrix type")
15832 (description "This package provides a consistent C++ class interface for a
15833 variety of commonly used matrix types, including sparse and HDF5-backed
15835 (license license:gpl3)))
15837 ;; This package includes files that have been taken from kentutils. Some
15838 ;; parts of kentutils are not released under a free license, but this package
15839 ;; only uses files that are also found in the free parts of kentutils.
15840 (define-public r-cner
15847 (uri (bioconductor-uri "CNEr" version))
15849 (base32 "05zvr5fv8nprxqh2wvvrlf737dq242i20p1rpyqjaxihl6xl62kq"))))
15850 (properties `((upstream-name . "CNEr")))
15851 (build-system r-build-system)
15852 (inputs (list zlib))
15859 r-genomicalignments
15875 (home-page "https://github.com/ge11232002/CNEr")
15876 (synopsis "CNE Detection and Visualization")
15878 "This package provides tools for large-scale identification and
15879 advanced visualization of sets of conserved noncoding elements.")
15880 ;; For all files in src/ucsc "license is hereby granted for all use -
15881 ;; public, private or commercial"; this includes those files that don't
15882 ;; have a license header, because they are included in the free parts of
15883 ;; the kentutils package.
15884 (license (list license:gpl2
15885 (license:non-copyleft
15886 "https://raw.githubusercontent.com/ucscGenomeBrowser/kent/v410_base/src/lib/LICENSE")))))
15888 (define-public r-tfbstools
15890 (name "r-tfbstools")
15895 (uri (bioconductor-uri "TFBSTools" version))
15898 "0l6j1r2cx7jfd39qzbyynk4jvzd81ys6yypzxjc97js4kkyrx29w"))))
15899 (properties `((upstream-name . "TFBSTools")))
15900 (build-system r-build-system)
15910 r-dirichletmultinomial
15922 (native-inputs (list r-knitr))
15923 (home-page "https://github.com/ge11232002/TFBSTools")
15924 (synopsis "Transcription factor binding site (TFBS) analysis")
15926 "TFBSTools is a package for the analysis and manipulation of
15927 transcription factor binding sites. It includes matrices conversion
15928 between @dfn{Position Frequency Matrix} (PFM), @dfn{Position Weight
15929 Matrix} (PWM) and @dfn{Information Content Matrix} (ICM). It can also
15930 scan putative TFBS from sequence/alignment, query JASPAR database and
15931 provides a wrapper of de novo motif discovery software.")
15932 (license license:gpl2)))
15934 (define-public r-maftools
15936 (name "r-maftools")
15941 (uri (bioconductor-uri "maftools" version))
15943 (base32 "1gqfi95v4fs64n4walij0g2kds3fbbwp6lih5yakmgf6kj8fpkk6"))))
15944 (properties `((upstream-name . "maftools")))
15945 (build-system r-build-system)
15953 (native-inputs (list r-knitr))
15954 (home-page "https://github.com/PoisonAlien/maftools")
15955 (synopsis "Summarize, analyze and visualize MAF files")
15957 "Analyze and visualize Mutation Annotation Format (MAF) files from large
15958 scale sequencing studies. This package provides various functions to perform
15959 most commonly used analyses in cancer genomics and to create feature rich
15960 customizable visualzations with minimal effort.")
15961 (license license:expat)))
15963 (define-public r-motifmatchr
15965 (name "r-motifmatchr")
15970 (uri (bioconductor-uri "motifmatchr" version))
15973 "1ssn00mxwk23zr5na0vcmxvm69i68f0ga0wqlv1nk2isg0wpv878"))))
15974 (properties `((upstream-name . "motifmatchr")))
15975 (build-system r-build-system)
15987 r-summarizedexperiment
15989 (native-inputs (list r-knitr))
15990 (home-page "https://bioconductor.org/packages/motifmatchr")
15991 (synopsis "Fast motif matching in R")
15993 "Quickly find motif matches for many motifs and many sequences.
15994 This package wraps C++ code from the MOODS motif calling library.")
15995 (license license:gpl3)))
15997 (define-public r-chromvar
15999 (name "r-chromvar")
16004 (uri (bioconductor-uri "chromVAR" version))
16006 (base32 "0vhsvkm4kvln0002f13ayk57f9fmiz1kw9vwpsm1vds1vahd656m"))))
16007 (properties `((upstream-name . "chromVAR")))
16008 (build-system r-build-system)
16010 (list r-biocgenerics
16030 r-summarizedexperiment
16032 (native-inputs (list r-knitr))
16033 (home-page "https://bioconductor.org/packages/release/bioc/html/chromVAR.html")
16034 (synopsis "Determine chromatin variation across regions")
16036 "This package @code{r-chromvar} determines variation in chromatin
16037 accessibility across sets of annotations or peaks. @code{r-chromvar} is
16038 designed primarily for single-cell or sparse chromatin accessibility data like
16039 single cell assay for transposase-accessible chromatin using
16040 sequencing (@code{scATAC-seq} or sparse bulk ATAC or deoxyribonuclease
16041 sequence (@code{DNAse-seq}) experiments.")
16042 (license license:expat)))
16044 (define-public r-singlecellexperiment
16046 (name "r-singlecellexperiment")
16051 (uri (bioconductor-uri "SingleCellExperiment" version))
16054 "0s1aqbvlfnzijzfywjfpinqmxqj269dq2d3zlgf4xw9c1nwwnv7p"))))
16056 `((upstream-name . "SingleCellExperiment")))
16057 (build-system r-build-system)
16059 (list r-biocgenerics r-delayedarray r-genomicranges r-s4vectors
16060 r-summarizedexperiment))
16063 (home-page "https://bioconductor.org/packages/SingleCellExperiment")
16064 (synopsis "S4 classes for single cell data")
16065 (description "This package defines an S4 class for storing data from
16066 single-cell experiments. This includes specialized methods to store and
16067 retrieve spike-in information, dimensionality reduction coordinates and size
16068 factors for each cell, along with the usual metadata for genes and
16070 (license license:gpl3)))
16072 (define-public r-singler
16079 (uri (bioconductor-uri "SingleR" version))
16081 (base32 "0qbyc6ygw2xv3li9187i3axsw6ihwpa7pkvxvy9cagv7xck45c5y"))))
16082 (properties `((upstream-name . "SingleR")))
16083 (build-system r-build-system)
16090 r-delayedmatrixstats
16094 r-summarizedexperiment))
16095 (native-inputs (list r-knitr))
16096 (home-page "https://github.com/LTLA/SingleR")
16097 (synopsis "Reference-based single-cell RNA-seq annotation")
16099 "This package performs unbiased cell type recognition from single-cell
16100 RNA sequencing data, by leveraging reference transcriptomic datasets of pure
16101 cell types to infer the cell of origin of each single cell independently.")
16102 (license license:gpl3)))
16104 (define-public r-scuttle
16111 (uri (bioconductor-uri "scuttle" version))
16114 "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671"))))
16115 (properties `((upstream-name . "scuttle")))
16116 (build-system r-build-system)
16122 r-delayedmatrixstats
16127 r-singlecellexperiment
16128 r-summarizedexperiment))
16129 (native-inputs (list r-knitr))
16130 (home-page "https://bioconductor.org/packages/scuttle")
16131 (synopsis "Single-cell RNA-Seq analysis utilities")
16133 "This package provides basic utility functions for performing single-cell
16134 analyses, focusing on simple normalization, quality control and data
16135 transformations. It also provides some helper functions to assist development
16136 of other packages.")
16137 (license license:gpl3)))
16139 (define-public r-scater
16145 (uri (bioconductor-uri "scater" version))
16148 "0dqirggw7my5nq4ln9q0ya18ciqplkz9gx318ffias9ag3yii5rw"))))
16149 (build-system r-build-system)
16157 r-delayedmatrixstats
16169 r-singlecellexperiment
16170 r-summarizedexperiment
16174 (home-page "https://github.com/davismcc/scater")
16175 (synopsis "Single-cell analysis toolkit for gene expression data in R")
16176 (description "This package provides a collection of tools for doing
16177 various analyses of single-cell RNA-seq gene expression data, with a focus on
16179 (license license:gpl2+)))
16181 (define-public r-scran
16188 (uri (bioconductor-uri "scran" version))
16191 "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni"))))
16192 (build-system r-build-system)
16201 r-delayedmatrixstats
16211 r-singlecellexperiment
16213 r-summarizedexperiment))
16216 (home-page "https://bioconductor.org/packages/scran")
16217 (synopsis "Methods for single-cell RNA-Seq data analysis")
16218 (description "This package implements a variety of low-level analyses of
16219 single-cell RNA-seq data. Methods are provided for normalization of
16220 cell-specific biases, assignment of cell cycle phase, and detection of highly
16221 variable and significantly correlated genes.")
16222 (license license:gpl3)))
16224 (define-public r-sparsematrixstats
16226 (name "r-sparsematrixstats")
16231 (uri (bioconductor-uri "sparseMatrixStats" version))
16234 "0p12kay7p5zbfm2589wdx0n9jhgpf5fb2fsmkhn3p4ck4xcy13x2"))))
16236 `((upstream-name . "sparseMatrixStats")))
16237 (build-system r-build-system)
16239 (list r-matrix r-matrixgenerics r-matrixstats r-rcpp))
16240 (native-inputs (list r-knitr))
16241 (home-page "https://bioconductor.org/packages/sparseMatrixStats/")
16242 (synopsis "Summary statistics for rows and columns of sparse matrices")
16244 "This package provides high performance functions for row and column
16245 operations on sparse matrices. Currently, the optimizations are limited to
16246 data in the column sparse format.")
16247 (license license:expat)))
16249 (define-public r-delayedmatrixstats
16251 (name "r-delayedmatrixstats")
16256 (uri (bioconductor-uri "DelayedMatrixStats" version))
16259 "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv"))))
16261 `((upstream-name . "DelayedMatrixStats")))
16262 (build-system r-build-system)
16264 (list r-delayedarray
16270 r-sparsematrixstats))
16273 (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
16274 (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
16276 "This package provides a port of the @code{matrixStats} API for use with
16277 @code{DelayedMatrix} objects from the @code{DelayedArray} package. It
16278 contains high-performing functions operating on rows and columns of
16279 @code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
16280 @code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
16281 are optimized per data type and for subsetted calculations such that both
16282 memory usage and processing time is minimized.")
16283 (license license:expat)))
16285 (define-public r-mscoreutils
16287 (name "r-mscoreutils")
16292 (uri (bioconductor-uri "MsCoreUtils" version))
16295 "077x1zcy27x8akmagjn75j97082cgnahrbfw0qx08q455m5x3xzh"))))
16296 (properties `((upstream-name . "MsCoreUtils")))
16297 (build-system r-build-system)
16299 (list r-clue r-mass r-rcpp r-s4vectors))
16302 (home-page "https://github.com/RforMassSpectrometry/MsCoreUtils")
16303 (synopsis "Core utils for mass spectrometry data")
16305 "This package defines low-level functions for mass spectrometry data and
16306 is independent of any high-level data structures. These functions include
16307 mass spectra processing functions (noise estimation, smoothing, binning),
16308 quantitative aggregation functions (median polish, robust summarisation,
16309 etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as
16310 well as misc helper functions, that are used across high-level data structure
16311 within the R for Mass Spectrometry packages.")
16312 (license license:artistic2.0)))
16314 (define-public r-msfeatures
16316 (name "r-msfeatures")
16321 (uri (bioconductor-uri "MsFeatures" version))
16323 (base32 "111iqcq4q315pb4j8z427shin9b00p179m2s9h6dd7imvbd68yq3"))))
16324 (properties `((upstream-name . "MsFeatures")))
16325 (build-system r-build-system)
16327 (list r-mscoreutils r-protgenerics r-summarizedexperiment))
16330 (home-page "https://github.com/RforMassSpectrometry/MsFeatures")
16331 (synopsis "Functionality for mass spectrometry features")
16333 "The MsFeature package defines functionality for Mass Spectrometry
16334 features. This includes functions to group (LC-MS) features based on some of
16335 their properties, such as retention time (coeluting features), or correlation
16336 of signals across samples. This package hence can be used to group features, and
16337 its results can be used as an input for the @code{QFeatures} package which
16338 allows aggregating abundance levels of features within each group. This
16339 package defines concepts and functions for base and common data types,
16340 implementations for more specific data types are expected to be implemented in
16341 the respective packages (such as e.g. @code{xcms}).")
16342 (license license:artistic2.0)))
16344 (define-public r-biocio
16351 (uri (bioconductor-uri "BiocIO" version))
16354 "16j826w4zrmbgpmq6nyglcrjailsfv48ih1rz1qn383g7v503ydp"))))
16355 (properties `((upstream-name . "BiocIO")))
16356 (build-system r-build-system)
16358 (list r-biocgenerics r-s4vectors))
16361 (home-page "https://bioconductor.org/packages/BiocIO")
16362 (synopsis "Standard input and output for Bioconductor packages")
16364 "This package implements `import()` and `export()` standard generics for
16365 importing and exporting biological data formats. `import()` supports
16366 whole-file as well as chunk-wise iterative import. The `import()` interface
16367 optionally provides a standard mechanism for 'lazy' access via `filter()` (on
16368 row or element-like components of the file resource), `select()` (on
16369 column-like components of the file resource) and `collect()`. The `import()`
16370 interface optionally provides transparent access to remote (e.g. via https)
16371 as well as local access. Developers can register a file extension, e.g.,
16372 `.loom` for dispatch from character-based URIs to specific `import()` /
16373 `export()` methods based on classes representing file types, e.g.,
16375 (license license:artistic2.0)))
16377 (define-public r-msmseda
16384 (uri (bioconductor-uri "msmsEDA" version))
16387 "0jnaq9ar4mnf3pfhka9hvk61p51ny9jws49xi8z29dq288b42b42"))))
16388 (properties `((upstream-name . "msmsEDA")))
16389 (build-system r-build-system)
16391 (list r-gplots r-mass r-msnbase r-rcolorbrewer))
16393 "https://bioconductor.org/packages/msmsEDA")
16394 (synopsis "Exploratory data analysis of LC-MS/MS data by spectral counts")
16396 "Exploratory data analysis to assess the quality of a set of LC-MS/MS
16397 experiments, and visualize de influence of the involved factors.")
16398 (license license:gpl2)))
16400 (define-public r-msmstests
16402 (name "r-msmstests")
16407 (uri (bioconductor-uri "msmsTests" version))
16410 "1wzdz0p9wmr243xkmymx9fwskafkyxgmlip4sd1fy2s06px7r0xi"))))
16411 (properties `((upstream-name . "msmsTests")))
16412 (build-system r-build-system)
16414 (list r-edger r-msmseda r-msnbase r-qvalue))
16416 "https://bioconductor.org/packages/msmsTests")
16417 (synopsis "Differential LC-MS/MS expression tests")
16419 "This package provides statistical tests for label-free LC-MS/MS data
16420 by spectral counts, to discover differentially expressed proteins between two
16421 biological conditions. Three tests are available: Poisson GLM regression,
16422 quasi-likelihood GLM regression, and the negative binomial of the edgeR
16423 package. The three models admit blocking factors to control for nuisance
16424 variables. To assure a good level of reproducibility a post-test filter is
16425 available, where we may set the minimum effect size considered biologicaly
16426 relevant, and the minimum expression of the most abundant condition.")
16427 (license license:gpl2)))
16429 (define-public r-catalyst
16431 (name "r-catalyst")
16436 (uri (bioconductor-uri "CATALYST" version))
16439 "05vfqwa9qsm16px77s9bzygs6zymcxshymmpvz86a9l1cy1yxbza"))))
16440 (properties `((upstream-name . "CATALYST")))
16441 (build-system r-build-system)
16445 r-consensusclusterplus
16467 r-singlecellexperiment
16468 r-summarizedexperiment))
16471 (home-page "https://github.com/HelenaLC/CATALYST")
16472 (synopsis "Cytometry data analysis tools")
16474 "This package is @dfn{Cytometry dATa anALYSis Tools} (CATALYST). Mass
16475 cytometry like @dfn{Cytometry by time of flight} (CyTOF) uses heavy metal
16476 isotopes rather than fluorescent tags as reporters to label antibodies,
16477 thereby substantially decreasing spectral overlap and allowing for examination
16478 of over 50 parameters at the single cell level. While spectral overlap is
16479 significantly less pronounced in CyTOF than flow cytometry, spillover due to
16480 detection sensitivity, isotopic impurities, and oxide formation can impede
16481 data interpretability. @code{CATALYST} was designed to provide a pipeline for
16482 preprocessing of cytometry data, including:
16485 @item normalization using bead standards;
16486 @item single-cell deconvolution;
16487 @item bead-based compensation.
16490 (license license:gpl2+)))
16492 (define-public r-erma
16499 (uri (bioconductor-uri "erma" version))
16502 "1ilq01cr2ipxpmp422fikiz6nj4nasjhj0ikcagjn2zmmarpgi1b"))))
16503 (build-system r-build-system)
16505 (list r-annotationdbi
16518 r-summarizedexperiment))
16521 (home-page "https://bioconductor.org/packages/erma")
16522 (synopsis "Epigenomic road map adventures")
16524 "The epigenomics road map describes locations of epigenetic marks in DNA
16525 from a variety of cell types. Of interest are locations of histone
16526 modifications, sites of DNA methylation, and regions of accessible chromatin.
16527 This package presents a selection of elements of the road map including
16528 metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines
16529 by Ernst and Kellis.")
16530 (license license:artistic2.0)))
16532 (define-public r-ggbio
16539 (uri (bioconductor-uri "ggbio" version))
16542 "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg"))))
16543 (build-system r-build-system)
16546 (modify-phases %standard-phases
16547 ;; See https://github.com/tengfei/ggbio/issues/117
16548 ;; This fix will be included in the next release.
16549 (add-after 'unpack 'fix-typo
16551 (substitute* "R/GGbio-class.R"
16552 (("fechable") "fetchable"))
16555 (list r-annotationdbi
16564 r-genomicalignments
16580 r-summarizedexperiment
16581 r-variantannotation))
16584 (home-page "http://www.tengfei.name/ggbio/")
16585 (synopsis "Visualization tools for genomic data")
16587 "The ggbio package extends and specializes the grammar of graphics for
16588 biological data. The graphics are designed to answer common scientific
16589 questions, in particular those often asked of high throughput genomics data.
16590 All core Bioconductor data structures are supported, where appropriate. The
16591 package supports detailed views of particular genomic regions, as well as
16592 genome-wide overviews. Supported overviews include ideograms and grand linear
16593 views. High-level plots include sequence fragment length, edge-linked
16594 interval to data view, mismatch pileup, and several splicing summaries.")
16595 (license license:artistic2.0)))
16597 (define-public r-gqtlbase
16599 (name "r-gqtlbase")
16604 (uri (bioconductor-uri "gQTLBase" version))
16607 "0nipibm1bk9k70ajbw1f6vjmz0dh7gk21l17q3m54bnawxsggrfh"))))
16608 (properties `((upstream-name . "gQTLBase")))
16609 (build-system r-build-system)
16612 (modify-phases %standard-phases
16613 ;; This is an upstream bug.
16614 (add-after 'unpack 'fix-imports
16616 (substitute* "NAMESPACE"
16617 ((".*maxffmode.*") "")
16618 (("importFrom\\(ff,.*") "import(ff)\n"))
16633 r-summarizedexperiment))
16636 (home-page "https://bioconductor.org/packages/gQTLBase")
16637 (synopsis "Infrastructure for eQTL, mQTL and similar studies")
16639 "The purpose of this package is to simplify the storage and interrogation
16640 of @dfn{quantitative trait loci} (QTL) archives, such as eQTL, mQTL, dsQTL,
16642 (license license:artistic2.0)))
16644 (define-public r-gqtlstats
16646 (name "r-gqtlstats")
16651 (uri (bioconductor-uri "gQTLstats" version))
16654 "1h78l23idf867djmdk97b02jxgmz4vfr2dai01fp648d0lsx5mkl"))))
16655 (properties `((upstream-name . "gQTLstats")))
16656 (build-system r-build-system)
16658 (list r-annotationdbi
16686 r-summarizedexperiment
16687 r-variantannotation))
16690 (home-page "https://bioconductor.org/packages/gQTLstats")
16691 (synopsis "Computationally efficient analysis for eQTL and allied studies")
16693 "This package provides tools for the computationally efficient analysis
16694 of @dfn{quantitative trait loci} (QTL) data, including eQTL, mQTL, dsQTL, etc.
16695 The software in this package aims to support refinements and functional
16696 interpretation of members of a collection of association statistics on a
16697 family of feature/genome hypotheses.")
16698 (license license:artistic2.0)))
16700 (define-public r-gviz
16707 (uri (bioconductor-uri "Gviz" version))
16710 "0as3sxhv21bqqrpvafcqim7798hhkzj3q40hy1rqyhv2lhj4rbvi"))))
16711 (properties `((upstream-name . "Gviz")))
16712 (build-system r-build-system)
16714 (list r-annotationdbi
16724 r-genomicalignments
16738 (home-page "https://bioconductor.org/packages/Gviz")
16739 (synopsis "Plotting data and annotation information along genomic coordinates")
16741 "Genomic data analyses requires integrated visualization of known genomic
16742 information and new experimental data. Gviz uses the biomaRt and the
16743 rtracklayer packages to perform live annotation queries to Ensembl and UCSC
16744 and translates this to e.g. gene/transcript structures in viewports of the
16745 grid graphics package. This results in genomic information plotted together
16747 (license license:artistic2.0)))
16749 (define-public r-gwascat
16756 (uri (bioconductor-uri "gwascat" version))
16759 "19ymdxj8966i4yk0zalfw23938cpv4q7pywg4qb242p44na5y9sl"))))
16760 (build-system r-build-system)
16762 (list r-annotationdbi
16773 r-variantannotation))
16776 (home-page "https://bioconductor.org/packages/gwascat")
16777 (synopsis "Tools for data in the EMBL-EBI GWAS catalog")
16779 "This package provides tools for representing and modeling data in the
16780 EMBL-EBI GWAS catalog.")
16781 (license license:artistic2.0)))
16783 (define-public r-kegggraph
16785 (name "r-kegggraph")
16790 (uri (bioconductor-uri "KEGGgraph" version))
16792 (base32 "15pq040pcg8hr18xixmjp59xb7mgvygjv6kisqk8yv99l1611ndx"))))
16793 (properties `((upstream-name . "KEGGgraph")))
16794 (build-system r-build-system)
16796 (list r-graph r-rcurl r-rgraphviz r-xml))
16797 (home-page "https://bioconductor.org/packages/KEGGgraph")
16798 (synopsis "Graph approach to Kegg Pathway database in R and Bioconductor")
16800 "@code{r-kegggraph} is an interface between Kegg Pathway database and graph
16801 object as well as a collection of tools to analyze, dissect and visualize these
16802 graphs. It parses the regularly updated kgml (Kegg XML) files into graph models
16803 maintaining all essential pathway attributes. The package offers
16804 functionalities including parsing, graph operation, visualization and etc.")
16805 (license license:gpl2+)))
16807 (define-public r-ldblock
16814 (uri (bioconductor-uri "ldblock" version))
16817 "08ss03b93czwb4x60hsi30ad4lmamvq5mxa8nj0g18z68qcraijm"))))
16818 (build-system r-build-system)
16820 (list r-biocgenerics
16821 r-ensdb-hsapiens-v75
16829 r-variantannotation))
16832 (home-page "https://bioconductor.org/packages/ldblock")
16833 (synopsis "Data structures for linkage disequilibrium measures in populations")
16835 "This package defines data structures for @dfn{linkage
16836 disequilibrium} (LD) measures in populations. Its purpose is to simplify
16837 handling of existing population-level data for the purpose of flexibly
16838 defining LD blocks.")
16839 (license license:artistic2.0)))
16841 ;; This is a CRAN package, but it depends on r-snpstats, which is a
16842 ;; Bioconductor package.
16843 (define-public r-ldheatmap
16845 (name "r-ldheatmap")
16850 (uri (cran-uri "LDheatmap" version))
16853 "0gr99kys1ahyl8s6cbj6rmh4vwid8kn92lcbjnwh0ahb73m2xjjc"))))
16854 (properties `((upstream-name . "LDheatmap")))
16855 (build-system r-build-system)
16857 (list r-genetics r-rcpp r-snpstats))
16858 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
16859 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
16861 "This package provides tools to produce a graphical display, as a heat
16862 map, of measures of pairwise linkage disequilibria between SNPs. Users may
16863 optionally include the physical locations or genetic map distances of each SNP
16865 (license license:gpl3)))
16867 ;; This is a CRAN package, but it depends on r-rgraphviz, which is a
16868 ;; Bioconductor package.
16869 (define-public r-abn
16876 (uri (cran-uri "abn" version))
16879 "1w3jns96m8b9scvaa4hcla3i88a0cfh9qis2l04yixvda5q91gpr"))))
16880 (build-system r-build-system)
16893 (home-page "https://r-bayesian-networks.org/")
16894 (synopsis "Modelling multivariate data with additive bayesian networks")
16896 "Bayesian network analysis is a form of probabilistic graphical models
16897 which derives from empirical data a directed acyclic graph, DAG, describing
16898 the dependency structure between random variables. An additive Bayesian
16899 network model consists of a form of a DAG where each node comprises a
16900 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
16901 equivalent to Bayesian multivariate regression using graphical modelling, they
16902 generalises the usual multivariable regression, GLM, to multiple dependent
16903 variables. This package provides routines to help determine optimal Bayesian
16904 network models for a given data set, where these models are used to identify
16905 statistical dependencies in messy, complex data.")
16906 (license license:gpl2+)))
16908 ;; This is a CRAN package, but it depends on r-rsamtools, which is a
16909 ;; Bioconductor package.
16910 (define-public r-spp
16916 (uri (cran-uri "spp" version))
16919 "08zxxgyp0h6733b08jmml7k4rhfd3mi5dda3jrzid0s184y0z29w"))))
16920 (build-system r-build-system)
16924 (list r-bh r-catools r-rcpp r-rsamtools))
16925 (home-page "https://cran.r-project.org/web/packages/spp/")
16926 (synopsis "ChIP-Seq processing pipeline")
16927 (description "This package provides tools for analysis of ChIP-seq and
16928 other functional sequencing data.")
16929 (license license:gpl2)))
16931 (define-public r-pathview
16933 (name "r-pathview")
16938 (uri (bioconductor-uri "pathview" version))
16940 (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71"))))
16941 (properties `((upstream-name . "pathview")))
16942 (build-system r-build-system)
16944 (list r-annotationdbi
16952 (home-page "https://pathview.uncc.edu/")
16953 (synopsis "Tool set for pathway based data integration and visualization")
16955 "@code{r-pathview} is a tool set for pathway based data integration and
16956 visualization. It maps and renders a wide variety of biological data on
16957 relevant pathway graphs. All users need is to supply their data and specify
16958 the target pathway. This package automatically downloads the pathway graph
16959 data, parses the data file, maps user data to the pathway, and render pathway
16960 graph with the mapped data. In addition, @code{r-pathview} also seamlessly
16961 integrates with pathway and gene set (enrichment) analysis tools for
16962 large-scale and fully automated analysis.")
16963 (license license:gpl3+)))
16965 (define-public r-snpstats
16967 (name "r-snpstats")
16972 (uri (bioconductor-uri "snpStats" version))
16975 "0a5b5nqc7n965jk45ijwkzbn416ib4gfhp8xl39z8f2bdskip4a2"))))
16976 (properties `((upstream-name . "snpStats")))
16977 (build-system r-build-system)
16978 (inputs (list zlib))
16980 (list r-biocgenerics r-matrix r-survival r-zlibbioc))
16981 (home-page "https://bioconductor.org/packages/snpStats")
16982 (synopsis "Methods for SNP association studies")
16984 "This package provides classes and statistical methods for large
16985 @dfn{single-nucleotide polymorphism} (SNP) association studies. This extends
16986 the earlier snpMatrix package, allowing for uncertainty in genotypes.")
16987 (license license:gpl3)))
16989 (define-public r-chromstar
16991 (name "r-chromstar")
16996 (uri (bioconductor-uri "chromstaR" version))
16999 "1xjwmnr4hk8v3nwvhqd6ixk5qr2dv0n4mb9wd6nl7cgjfhjsdgj7"))))
17000 (properties `((upstream-name . "chromstaR")))
17001 (build-system r-build-system)
17009 r-genomicalignments
17017 (native-inputs (list r-knitr))
17018 (home-page "https://github.com/ataudt/chromstaR")
17019 (synopsis "Chromatin state analysis for ChIP-Seq data")
17021 "This package implements functions for combinatorial and differential
17022 analysis of ChIP-seq data. It includes uni- and multivariate peak-calling,
17023 export to genome browser viewable files, and functions for enrichment
17025 (license license:artistic2.0)))
17027 (define-public r-guitar
17034 (uri (bioconductor-uri "Guitar" version))
17037 "09grsasnnk7rmlzjh4lhas9r5spzcsrvmdqj6fx1dk22sckcqahh"))))
17038 (properties `((upstream-name . "Guitar")))
17039 (build-system r-build-system)
17041 (list r-annotationdbi
17051 (home-page "https://bioconductor.org/packages/Guitar")
17052 (synopsis "Visualize genomic features")
17054 "This package is designed for visualization of RNA-related genomic
17055 features with respect to the landmarks of RNA transcripts, i.e., transcription
17056 starting site, start codon, stop codon and transcription ending site.")
17057 (license license:gpl2)))
17059 (define-public r-sushi
17065 (uri (bioconductor-uri "Sushi" version))
17068 "0adswrbzd93rhy3q56ypwkrk6155vd4zxapvznswyjlxp8ha813q"))))
17069 (properties `((upstream-name . "Sushi")))
17070 (build-system r-build-system)
17072 (list r-biomart r-zoo))
17073 (home-page "https://bioconductor.org/packages/Sushi")
17074 (synopsis "Tools for visualizing genomics data")
17076 "This package provides flexible, quantitative, and integrative genomic
17077 visualizations for publication-quality multi-panel figures.")
17078 (license license:gpl2+)))
17080 (define-public r-ballgown
17082 (name "r-ballgown")
17087 (uri (bioconductor-uri "ballgown" version))
17090 "0l8q3fymskxmsi5jcikzjz5xi66lpzgv7bjymir4izah2v68z708"))))
17091 (properties `((upstream-name . "ballgown")))
17092 (build-system r-build-system)
17105 (home-page "https://bioconductor.org/packages/ballgown")
17106 (synopsis "Flexible, isoform-level differential expression analysis")
17108 "This package provides tools for statistical analysis of assembled
17109 transcriptomes, including flexible differential expression analysis,
17110 visualization of transcript structures, and matching of assembled transcripts
17112 (license license:artistic2.0)))
17114 (define-public r-megadepth
17116 (name "r-megadepth")
17121 (uri (bioconductor-uri "megadepth" version))
17124 "0qq82dmd3drr2bhn51bgbc6ml40klfmmhj6wdj72n9ya6n60lwy8"))))
17125 (properties `((upstream-name . "megadepth")))
17126 (build-system r-build-system)
17127 (inputs (list megadepth))
17138 (home-page "https://github.com/LieberInstitute/megadepth")
17139 (synopsis "BigWig and BAM related utilities")
17141 "This package provides an R interface to Megadepth. It is particularly
17142 useful for computing the coverage of a set of genomic regions across bigWig or
17143 BAM files. With this package, you can build base-pair coverage matrices for
17144 regions or annotations of your choice from BigWig files.")
17145 (license license:artistic2.0)))
17147 (define-public r-beclear
17154 (uri (bioconductor-uri "BEclear" version))
17157 "0x43yfnmb2d782g3g52nqdfs90i3zrrlqz8qy3ybmgv5f8n92p15"))))
17158 (properties `((upstream-name . "BEclear")))
17159 (build-system r-build-system)
17171 (home-page "https://github.com/uds-helms/BEclear")
17172 (synopsis "Correction of batch effects in DNA methylation data")
17174 "This package provides functions to detect and correct for batch effects
17175 in DNA methylation data. The core function is based on latent factor models
17176 and can also be used to predict missing values in any other matrix containing
17178 (license license:gpl3)))
17180 (define-public r-bgeecall
17182 (name "r-bgeecall")
17187 (uri (bioconductor-uri "BgeeCall" version))
17190 "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil"))))
17191 (properties `((upstream-name . "BgeeCall")))
17192 (build-system r-build-system)
17206 (native-inputs (list r-knitr))
17207 (home-page "https://github.com/BgeeDB/BgeeCall")
17208 (synopsis "RNA-Seq present/absent gene expression calls generation")
17210 "BgeeCall allows generating present/absent gene expression calls without
17211 using an arbitrary cutoff like TPM<1. Calls are generated based on reference
17212 intergenic sequences. These sequences are generated based on expression of
17213 all RNA-Seq libraries of each species integrated in Bgee.")
17214 (license license:gpl3)))
17216 (define-public r-bgeedb
17223 (uri (bioconductor-uri "BgeeDB" version))
17226 "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k"))))
17227 (properties `((upstream-name . "BgeeDB")))
17228 (build-system r-build-system)
17241 (native-inputs (list r-knitr))
17242 (home-page "https://github.com/BgeeDB/BgeeDB_R")
17243 (synopsis "Annotation and gene expression data retrieval from Bgee database")
17245 "This package provides a package for the annotation and gene expression
17246 data download from Bgee database, and TopAnat analysis: GO-like enrichment of
17247 anatomical terms, mapped to genes by expression patterns.")
17248 (license license:gpl3)))
17250 (define-public r-biobtreer
17252 (name "r-biobtreer")
17257 (uri (bioconductor-uri "biobtreeR" version))
17260 "0cx46hdqqm6mbj0vp4y86axv0qccd4sgk2jwwjvnqp5pynq9bbqa"))))
17261 (properties `((upstream-name . "biobtreeR")))
17262 (build-system r-build-system)
17264 (list r-httpuv r-httr r-jsonlite r-stringi))
17265 (native-inputs (list r-knitr))
17266 (home-page "https://github.com/tamerh/biobtreeR")
17267 (synopsis "Use biobtree tool from R")
17269 "The biobtreeR package provides an interface to biobtree, a tool which
17270 covers large sets of bioinformatics datasets and allows search and chain
17271 mappings functionalities.")
17272 (license license:expat)))
17274 (define-public r-minet
17281 (uri (bioconductor-uri "minet" version))
17284 "0q6jw2jqkl9qynjpzaygz45c7dmx1l5y2d8s1illpcf87siawcam"))))
17285 (properties `((upstream-name . "minet")))
17286 (build-system r-build-system)
17289 (home-page "http://minet.meyerp.com")
17290 (synopsis "Mutual information networks")
17292 "This package implements various algorithms for inferring mutual
17293 information networks from data.")
17294 (license license:artistic2.0)))
17296 (define-public r-genetclassifier
17298 (name "r-genetclassifier")
17303 (uri (bioconductor-uri "geNetClassifier" version))
17306 "1kh7mp5h0n7yd1klcd7w4v7i3fh9pkmvgf7189wangfzbcsr4f70"))))
17308 `((upstream-name . "geNetClassifier")))
17309 (build-system r-build-system)
17311 (list r-biobase r-e1071 r-ebarrays r-minet))
17312 (home-page "https://www.cicancer.org")
17313 (synopsis "Classify diseases and build gene networks using expression profiles")
17315 "This is a comprehensive package to automatically train and validate a
17316 multi-class SVM classifier based on gene expression data. It provides
17317 transparent selection of gene markers, their coexpression networks, and an
17318 interface to query the classifier.")
17319 (license license:gpl2+)))
17321 (define-public r-dir-expiry
17323 (name "r-dir-expiry")
17328 (uri (bioconductor-uri "dir.expiry" version))
17331 "098wzm8hlpy70c99k2sl4k8z2dllhw7rwdj8dhcskr7kaw71k3sq"))))
17332 (properties `((upstream-name . "dir.expiry")))
17333 (build-system r-build-system)
17334 (propagated-inputs (list r-filelock))
17335 (native-inputs (list r-knitr))
17336 (home-page "https://bioconductor.org/packages/dir.expiry")
17337 (synopsis "Managing expiration for cache directories")
17339 "This package implements an expiration system for access to versioned
17340 directories. Directories that have not been accessed by a registered function
17341 within a certain time frame are deleted. This aims to reduce disk usage by
17342 eliminating obsolete caches generated by old versions of packages.")
17343 (license license:gpl3)))
17345 (define-public r-basilisk-utils
17347 (name "r-basilisk-utils")
17352 (uri (bioconductor-uri "basilisk.utils" version))
17355 "1jnqv0rlljkq27rd4ixl763v335f2aanm4fzr386yc81fj4vnmhk"))))
17357 `((upstream-name . "basilisk.utils")))
17358 (build-system r-build-system)
17360 (list r-dir-expiry))
17361 (native-inputs (list r-knitr))
17362 (home-page "https://bioconductor.org/packages/basilisk.utils")
17363 (synopsis "Basilisk installation utilities")
17365 "This package implements utilities for installation of the basilisk
17366 package, primarily for creation of the underlying Conda instance.")
17367 (license license:gpl3)))
17369 (define-public r-basilisk
17371 (name "r-basilisk")
17376 (uri (bioconductor-uri "basilisk" version))
17379 "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk"))))
17380 (properties `((upstream-name . "basilisk")))
17381 (build-system r-build-system)
17383 (list r-basilisk-utils r-dir-expiry r-reticulate))
17384 (native-inputs (list r-knitr))
17385 (home-page "https://bioconductor.org/packages/basilisk")
17386 (synopsis "Freeze Python dependencies inside Bioconductor packages")
17388 "This package installs a self-contained Conda instance that is managed by
17389 the R/Bioconductor installation machinery. This aims to provide a consistent
17390 Python environment that can be used reliably by Bioconductor packages.
17391 Functions are also provided to enable smooth interoperability of multiple
17392 Python environments in a single R session.")
17393 (license license:gpl3)))
17395 (define-public r-biocthis
17397 (name "r-biocthis")
17402 (uri (bioconductor-uri "biocthis" version))
17405 "1hdgjp00d2si3mr7m1d289i9wn7g927z6n8n27d5sm94lb91qln0"))))
17406 (properties `((upstream-name . "biocthis")))
17407 (build-system r-build-system)
17410 (modify-phases %standard-phases
17411 (add-after 'unpack 'set-HOME
17412 (lambda _ (setenv "HOME" "/tmp"))))))
17414 (list r-biocmanager
17420 (native-inputs (list r-knitr))
17421 (home-page "https://github.com/lcolladotor/biocthis")
17422 (synopsis "Automate package and project setup for Bioconductor packages")
17424 "This package expands the @code{usethis} package with the goal of helping
17425 automate the process of creating R packages for Bioconductor or making them
17426 Bioconductor-friendly.")
17427 (license license:artistic2.0)))
17429 (define-public r-biocdockermanager
17431 (name "r-biocdockermanager")
17436 (uri (bioconductor-uri "BiocDockerManager" version))
17439 "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d"))))
17441 `((upstream-name . "BiocDockerManager")))
17442 (build-system r-build-system)
17450 (native-inputs (list r-knitr))
17451 (home-page "https://bioconductor.org/packages/BiocDockerManager")
17452 (synopsis "Access and manage Bioconductor Docker images")
17454 "This package works analogous to BiocManager but for Docker images. Use
17455 the BiocDockerManager package to install and manage Docker images provided by
17456 the Bioconductor project.")
17457 (license license:artistic2.0)))
17459 (define-public r-biodb
17466 (uri (bioconductor-uri "biodb" version))
17469 "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1"))))
17470 (properties `((upstream-name . "biodb")))
17471 (build-system r-build-system)
17473 (list r-biocfilecache
17491 (native-inputs (list r-knitr))
17492 (home-page "https://bioconductor.org/packages/biodb")
17493 (synopsis "Library for connecting to chemical and biological databases")
17495 "The biodb package provides access to standard remote chemical and
17496 biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local
17497 database files (CSV, SQLite), with easy retrieval of entries, access to web
17498 services, search of compounds by mass and/or name, and mass spectra matching
17499 for LCMS and MSMS. Its architecture as a development framework facilitates
17500 the development of new database connectors for local projects or inside
17501 separate published packages.")
17502 (license license:agpl3+)))
17504 (define-public r-biomformat
17506 (name "r-biomformat")
17511 (uri (bioconductor-uri "biomformat" version))
17514 "12wqjipxhngmlnrdmx329dqmkmy2wa4nkkrhwaqv2nwy90dncs9n"))))
17515 (properties `((upstream-name . "biomformat")))
17516 (build-system r-build-system)
17518 (list r-jsonlite r-matrix r-plyr r-rhdf5))
17519 (native-inputs (list r-knitr))
17520 (home-page "https://github.com/joey711/biomformat/")
17521 (synopsis "Interface package for the BIOM file format")
17523 "This is an R package for interfacing with the BIOM format. This package
17524 includes basic tools for reading biom-format files, accessing and subsetting
17525 data tables from a biom object (which is more complex than a single table), as
17526 well as limited support for writing a biom-object back to a biom-format file.
17527 The design of this API is intended to match the Python API and other tools
17528 included with the biom-format project, but with a decidedly \"R flavor\" that
17529 should be familiar to R users. This includes S4 classes and methods, as well
17530 as extensions of common core functions/methods.")
17531 (license license:gpl2)))
17533 (define-public r-mvcclass
17535 (name "r-mvcclass")
17540 (uri (bioconductor-uri "MVCClass" version))
17543 "0apcjlq4i2mg8mlfqgvlcsqkiy51whzid3nd0m830jff0ywgh47g"))))
17544 (properties `((upstream-name . "MVCClass")))
17545 (build-system r-build-system)
17546 (home-page "https://bioconductor.org/packages/MVCClass")
17547 (synopsis "Model-View-Controller (MVC) classes")
17549 "This package contains classes used in model-view-controller (MVC)
17551 (license license:lgpl2.1+)))
17553 (define-public r-biomvcclass
17555 (name "r-biomvcclass")
17560 (uri (bioconductor-uri "BioMVCClass" version))
17563 "078pnyygbvbfxziqspfr1nn78w67xyb4qmiwc34czga5psblvfwz"))))
17564 (properties `((upstream-name . "BioMVCClass")))
17565 (build-system r-build-system)
17567 (list r-biobase r-graph r-mvcclass r-rgraphviz))
17568 (home-page "https://bioconductor.org/packages/BioMVCClass")
17569 (synopsis "Model-View-Controller (MVC) classes that use Biobase")
17571 "This package contains classes used in model-view-controller (MVC)
17573 (license license:lgpl2.1+)))
17575 (define-public r-biomvrcns
17577 (name "r-biomvrcns")
17582 (uri (bioconductor-uri "biomvRCNS" version))
17585 "0i576g7pkivqaxff1pkb760mdpx8v9fh071aic1mwfnlfa7k87ln"))))
17586 (properties `((upstream-name . "biomvRCNS")))
17587 (build-system r-build-system)
17589 (list r-genomicranges r-gviz r-iranges r-mvtnorm))
17590 (home-page "https://bioconductor.org/packages/biomvRCNS")
17591 (synopsis "Copy number study and segmentation for multivariate biological data")
17593 "In this package, a @dfn{Hidden Semi Markov Model} (HSMM) and one
17594 homogeneous segmentation model are designed and implemented for segmentation
17595 genomic data, with the aim of assisting in transcripts detection using high
17596 throughput technology like RNA-seq or tiling array, and copy number analysis
17597 using aCGH or sequencing.")
17598 (license license:gpl2+)))
17600 (define-public r-bionero
17607 (uri (bioconductor-uri "BioNERO" version))
17610 "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp"))))
17611 (properties `((upstream-name . "BioNERO")))
17612 (build-system r-build-system)
17614 (list r-biocparallel
17631 r-summarizedexperiment
17636 (home-page "https://github.com/almeidasilvaf/BioNERO")
17637 (synopsis "Biological network reconstruction omnibus")
17639 "BioNERO aims to integrate all aspects of biological network inference in
17640 a single package, including data preprocessing, exploratory analyses, network
17641 inference, and analyses for biological interpretations. BioNERO can be used
17642 to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs)
17643 from gene expression data. Additionally, it can be used to explore
17644 topological properties of protein-protein interaction (PPI) networks. GCN
17645 inference relies on the popular WGCNA algorithm. GRN inference is based on
17646 the \"wisdom of the crowds\" principle, which consists in inferring GRNs with
17647 multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average
17648 rank for each interaction pair. As all steps of network analyses are included
17649 in this package, BioNERO makes users avoid having to learn the syntaxes of
17650 several packages and how to communicate between them. Finally, users can also
17651 identify consensus modules across independent expression sets and calculate
17652 intra and interspecies module preservation statistics between different
17654 (license license:gpl3)))
17656 (define-public r-bionet
17663 (uri (bioconductor-uri "BioNet" version))
17666 "0kcw71j4nmdkn373wk21ak6h0v4gycivnfrklb72kk1qcmsy1wrm"))))
17667 (properties `((upstream-name . "BioNet")))
17668 (build-system r-build-system)
17670 (list r-annotationdbi r-biobase r-graph r-igraph r-rbgl))
17671 (home-page "http://bioconductor.org/packages/release/bioc/html/BioNet.html")
17672 (synopsis "Functional analysis of biological networks")
17674 "This package provides functions for the integrated analysis of
17675 protein-protein interaction networks and the detection of functional modules.
17676 Different datasets can be integrated into the network by assigning p-values of
17677 statistical tests to the nodes of the network. E.g. p-values obtained from
17678 the differential expression of the genes from an Affymetrix array are assigned
17679 to the nodes of the network. By fitting a beta-uniform mixture model and
17680 calculating scores from the p-values, overall scores of network regions can be
17681 calculated and an integer linear programming algorithm identifies the maximum
17682 scoring subnetwork.")
17683 (license license:gpl2+)))
17685 (define-public r-bionetstat
17687 (name "r-bionetstat")
17692 (uri (bioconductor-uri "BioNetStat" version))
17695 "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2"))))
17696 (properties `((upstream-name . "BioNetStat")))
17697 (build-system r-build-system)
17699 (list r-biocparallel
17719 (home-page "https://github.com/jardimViniciusC/BioNetStat")
17720 (synopsis "Biological network analysis")
17722 "This package provides a package to perform differential network
17723 analysis, differential node analysis (differential coexpression analysis),
17724 network and metabolic pathways view.")
17725 (license license:gpl3+)))
17727 (define-public r-bioqc
17734 (uri (bioconductor-uri "BioQC" version))
17737 "0vb2nnzqvyv25pw8qshcmijravswafg0858pkgqjgiv7wsr2mn3m"))))
17738 (properties `((upstream-name . "BioQC")))
17739 (build-system r-build-system)
17741 (list r-biobase r-edger r-rcpp))
17744 (home-page "https://accio.github.io/BioQC/")
17745 (synopsis "Detect tissue heterogeneity in expression profiles with gene sets")
17747 "BioQC performs quality control of high-throughput expression data based
17748 on tissue gene signatures. It can detect tissue heterogeneity in gene
17749 expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is
17750 optimised for high performance.")
17751 (license license:gpl3+)))
17753 (define-public r-biotip
17760 (uri (bioconductor-uri "BioTIP" version))
17763 "1sihi5zy7mlabh3ix1wvdqz8ibfq1avl8bnxjhvxyzq40zbcklh6"))))
17764 (properties `((upstream-name . "BioTIP")))
17765 (build-system r-build-system)
17776 (home-page "https://github.com/xyang2uchicago/BioTIP")
17777 (synopsis "R package for characterization of biological tipping-point")
17779 "This package adopts tipping-point theory to transcriptome profiles to
17780 help unravel disease regulatory trajectory.")
17781 (license license:gpl2)))
17783 (define-public r-biotmle
17790 (uri (bioconductor-uri "biotmle" version))
17793 "1frig90krvfdk6nwpmslpj0pvligyzwzfwwci7hzwcmbglk5jj22"))))
17794 (properties `((upstream-name . "biotmle")))
17795 (build-system r-build-system)
17806 r-summarizedexperiment
17811 (home-page "https://code.nimahejazi.org/biotmle/")
17812 (synopsis "Targeted learning with moderated statistics for biomarker discovery")
17814 "This package provides tools for differential expression biomarker
17815 discovery based on microarray and next-generation sequencing data that
17816 leverage efficient semiparametric estimators of the average treatment effect
17817 for variable importance analysis. Estimation and inference of the (marginal)
17818 average treatment effects of potential biomarkers are computed by targeted
17819 minimum loss-based estimation, with joint, stable inference constructed across
17820 all biomarkers using a generalization of moderated statistics for use with the
17821 estimated efficient influence function. The procedure accommodates the use of
17822 ensemble machine learning for the estimation of nuisance functions.")
17823 (license license:expat)))
17825 (define-public r-bsseq
17832 (uri (bioconductor-uri "bsseq" version))
17835 "1jpfib2vb6hd7pgh3d33jgch24lba175zmbalwsbgvlmmyyf1ki5"))))
17836 (properties `((upstream-name . "bsseq")))
17837 (build-system r-build-system)
17847 r-delayedmatrixstats
17861 r-summarizedexperiment))
17864 (home-page "https://github.com/hansenlab/bsseq")
17865 (synopsis "Analyze, manage and store bisulfite sequencing data")
17867 "This package provides a collection of tools for analyzing and
17868 visualizing bisulfite sequencing data.")
17869 (license license:artistic2.0)))
17871 (define-public r-dada2
17877 (uri (bioconductor-uri "dada2" version))
17880 "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x"))))
17881 (properties `((upstream-name . "dada2")))
17882 (build-system r-build-system)
17884 (list r-biocgenerics
17893 (native-inputs (list r-knitr))
17894 (home-page "https://benjjneb.github.io/dada2/")
17896 "Accurate, high-resolution sample inference from amplicon sequencing data")
17898 "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
17899 from high-throughput amplicon sequencing data, replacing the coarser and less
17900 accurate OTU clustering approach. The dada2 pipeline takes as input
17901 demultiplexed fastq files, and outputs the sequence variants and their
17902 sample-wise abundances after removing substitution and chimera errors.
17903 Taxonomic classification is available via a native implementation of the RDP
17904 naive Bayesian classifier, and species-level assignment to 16S rRNA gene
17905 fragments by exact matching.")
17906 (license license:lgpl2.0)))
17908 (define-public r-dmrseq
17915 (uri (bioconductor-uri "dmrseq" version))
17918 "1c99l62fi26bnbvpzrlsvvs722za0l5vfhddcrhzzzasabhccb4n"))))
17919 (properties `((upstream-name . "dmrseq")))
17920 (build-system r-build-system)
17922 (list r-annotationhub
17927 r-delayedmatrixstats
17941 (home-page "https://bioconductor.org/packages/dmrseq")
17942 (synopsis "Detection and inference of differentially methylated regions")
17944 "This package implements an approach for scanning the genome to detect
17945 and perform accurate inference on differentially methylated regions from Whole
17946 Genome Bisulfite Sequencing data. The method is based on comparing detected
17947 regions to a pooled null distribution, that can be implemented even when as
17948 few as two samples per population are available. Region-level statistics are
17949 obtained by fitting a @dfn{generalized least squares} (GLS) regression model
17950 with a nested autoregressive correlated error structure for the effect of
17951 interest on transformed methylation proportions.")
17952 (license license:expat)))
17954 (define-public r-omicade4
17956 (name "r-omicade4")
17960 (uri (bioconductor-uri "omicade4" version))
17963 "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
17964 (properties `((upstream-name . "omicade4")))
17965 (build-system r-build-system)
17966 (propagated-inputs (list r-ade4 r-biobase r-made4))
17967 (home-page "https://bioconductor.org/packages/omicade4")
17968 (synopsis "Multiple co-inertia analysis of omics datasets")
17970 "This package performes multiple co-inertia analysis of omics datasets.")
17971 (license license:gpl2)))
17973 (define-public r-omnipathr
17975 (name "r-omnipathr")
17980 (uri (bioconductor-uri "OmnipathR" version))
17982 (base32 "0vk0fv09j3ql78mzzhdxwxb2b83qqdz2qfd8wpp1vydmcx2vvgni"))))
17983 (properties `((upstream-name . "OmnipathR")))
17984 (build-system r-build-system)
17987 (modify-phases %standard-phases
17988 (add-after 'unpack 'set-HOME
17989 (lambda _ (setenv "HOME" "/tmp"))))))
18015 (native-inputs (list r-knitr))
18016 (home-page "https://saezlab.github.io/OmnipathR/")
18017 (synopsis "OmniPath web service client and more")
18019 "This package provides a client for the OmniPath web service and many
18020 other resources. It also includes functions to transform and pretty print
18021 some of the downloaded data, functions to access a number of other resources.
18022 Furthermore, OmnipathR features a close integration with the NicheNet method
18023 for ligand activity prediction from transcriptomics data.")
18024 (license license:expat)))
18026 (define-public r-biscuiteer
18028 (name "r-biscuiteer")
18033 (uri (bioconductor-uri "biscuiteer" version))
18036 "0y7vbdaafiga16yr0d22w1v4p0jmczndcar0r0km06f5y1b74amr"))))
18037 (properties `((upstream-name . "biscuiteer")))
18038 (build-system r-build-system)
18046 r-delayedmatrixstats
18065 r-summarizedexperiment
18066 r-variantannotation))
18069 (home-page "https://github.com/trichelab/biscuiteer")
18070 (synopsis "Convenience functions for the Biscuit package")
18072 "This package provides a test harness for bsseq loading of Biscuit
18073 output, summarization of WGBS data over defined regions and in mappable
18074 samples, with or without imputation, dropping of mostly-NA rows, age
18076 (license license:gpl3)))
18078 (define-public r-tcgabiolinks
18080 (name "r-tcgabiolinks")
18085 (uri (bioconductor-uri "TCGAbiolinks" version))
18087 (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms"))))
18088 (properties `((upstream-name . "TCGAbiolinks")))
18089 (build-system r-build-system)
18108 r-summarizedexperiment
18109 r-tcgabiolinksgui-data
18114 (native-inputs (list r-knitr))
18115 (home-page "https://github.com/BioinformaticsFMRP/TCGAbiolinks")
18116 (synopsis "Integrative analysis with GDC data")
18118 "The aim of TCGAbiolinks is:
18121 @item facilitate GDC open-access data retrieval;
18122 @item prepare the data using the appropriate pre-processing strategies;
18123 @item provide the means to carry out different standard analyses, and;
18124 @item to easily reproduce earlier research results.
18127 In more detail, the package provides multiple methods for analysis (e.g.,
18128 differential expression analysis, identifying differentially methylated
18129 regions) and methods for visualization (e.g., survival plots, volcano plots,
18130 starburst plots) in order to easily develop complete analysis pipelines.")
18131 (license license:gpl3+)))
18133 (define-public r-tricycle
18135 (name "r-tricycle")
18139 (uri (bioconductor-uri "tricycle" version))
18142 "0bjkajcz6xcfak6071d0ihakrvgf7s0pmkn6vqkjd6yxbfld7zln"))))
18143 (properties `((upstream-name . "tricycle")))
18144 (build-system r-build-system)
18146 (list r-annotationdbi
18157 r-singlecellexperiment
18158 r-summarizedexperiment))
18159 (native-inputs (list r-knitr))
18160 (home-page "https://github.com/hansenlab/tricycle")
18161 (synopsis "Transferable representation and inference of cell cycle")
18163 "The package contains functions to infer and visualize cell cycle process
18164 using Single-cell RNA-Seq data. It exploits the idea of transfer learning,
18165 projecting new data to the previous learned biologically interpretable space.
18166 The @code{tricycle} provides a pre-learned cell cycle space, which could be
18167 used to infer cell cycle time of human and mouse single cell samples. In
18168 addition, it also offer functions to visualize cell cycle time on different
18169 embeddings and functions to build new reference.")
18170 (license license:gpl3)))
18172 (define-public r-tximeta
18179 (uri (bioconductor-uri "tximeta" version))
18182 "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8"))))
18183 (properties `((upstream-name . "tximeta")))
18184 (build-system r-build-system)
18186 (list r-annotationdbi
18198 r-summarizedexperiment
18203 (home-page "https://github.com/mikelove/tximeta")
18204 (synopsis "Transcript quantification import with automatic metadata")
18206 "This package implements transcript quantification import from Salmon and
18207 alevin with automatic attachment of transcript ranges and release information,
18208 and other associated metadata. De novo transcriptomes can be linked to the
18209 appropriate sources with linkedTxomes and shared for computational
18211 (license license:gpl2)))
18213 (define-public r-phyloseq
18215 (name "r-phyloseq")
18220 (uri (bioconductor-uri "phyloseq" version))
18222 (base32 "0hcyv4ziyaw74mc9vf7bad3q9izi9p0whg3hspbs6w8b3hp34y2k"))))
18223 (properties `((upstream-name . "phyloseq")))
18224 (build-system r-build-system)
18244 (home-page "https://github.com/joey711/phyloseq")
18245 (synopsis "Handling and analysis of high-throughput microbiome census data")
18247 "Phyloseq provides a set of classes and tools to facilitate the import,
18248 storage, analysis, and graphical display of microbiome census data.")
18249 (license license:agpl3)))
18252 ;;; Avoid adding new packages to the end of this file. To reduce the chances
18253 ;;; of a merge conflict, place them above by existing packages with similar
18254 ;;; functionality or similar names.
HCoop / jackhill / guix / guix.git / blob